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Sample records for scan detects quantitative

  1. Using rapid-scan EPR to improve the detection limit of quantitative EPR by more than one order of magnitude.

    PubMed

    Möser, J; Lips, K; Tseytlin, M; Eaton, G R; Eaton, S S; Schnegg, A

    2017-08-01

    X-band rapid-scan EPR was implemented on a commercially available Bruker ELEXSYS E580 spectrometer. Room temperature rapid-scan and continuous-wave EPR spectra were recorded for amorphous silicon powder samples. By comparing the resulting signal intensities the feasibility of performing quantitative rapid-scan EPR is demonstrated. For different hydrogenated amorphous silicon samples, rapid-scan EPR results in signal-to-noise improvements by factors between 10 and 50. Rapid-scan EPR is thus capable of improving the detection limit of quantitative EPR by at least one order of magnitude. In addition, we provide a recipe for setting up and calibrating a conventional pulsed and continuous-wave EPR spectrometer for rapid-scan EPR. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Using rapid-scan EPR to improve the detection limit of quantitative EPR by more than one order of magnitude

    NASA Astrophysics Data System (ADS)

    Möser, J.; Lips, K.; Tseytlin, M.; Eaton, G. R.; Eaton, S. S.; Schnegg, A.

    2017-08-01

    X-band rapid-scan EPR was implemented on a commercially available Bruker ELEXSYS E580 spectrometer. Room temperature rapid-scan and continuous-wave EPR spectra were recorded for amorphous silicon powder samples. By comparing the resulting signal intensities the feasibility of performing quantitative rapid-scan EPR is demonstrated. For different hydrogenated amorphous silicon samples, rapid-scan EPR results in signal-to-noise improvements by factors between 10 and 50. Rapid-scan EPR is thus capable of improving the detection limit of quantitative EPR by at least one order of magnitude. In addition, we provide a recipe for setting up and calibrating a conventional pulsed and continuous-wave EPR spectrometer for rapid-scan EPR.

  3. Qualitative and quantitative detection of DNA amplified with HRP-modified SiO2 nanoparticles using scanning electrochemical microscopy.

    PubMed

    Fan, Huajun; Jiao, Fang; Chen, Hong; Zhang, Fan; Wang, Qingjiang; He, Pingang; Fang, Yuzhi

    2013-09-15

    Qualitative and quantitative detection of DNA was achieved by a "sandwich" DNA sensor through SG/TC (substrate generation and tip collection) mode of scanning electrochemical microscopy (SECM). The "sandwich" DNA structure was formed by the hybridization of thiol-tethered oligodeoxynucleotide probes (capture probe), assembled on the gold substrate surface, with target DNA and biotinylated indicator probe. HRP (horseradish peroxidase)-wrapped SiO2 nanoparticles were linked to the sandwich structure through biotin-streptavidin interaction. Hydroquinone (H2Q) was oxidized to benzoquinone (BQ) at the modified substrate surface where sequence-specific hybridization had occurred through the HRP-catalyzed reaction in the presence of H2O2. The detection was based on the reduction of BQ generated on the modified substrate by SECM tip. For SECM imaging experiment, we structured the microsensor platform through localized desorption of 1-dodecanethiol monolayer. Approach curves were employed for quantitative detection of DNA concentration. The detection limit of complementary DNA was as low as 0.8pM. This technique is promising for the application on electrochemical DNA chip.

  4. An exploratory method to detect tephras from quantitative XRD scans: Examples from Iceland and east Greenland marine sediments

    USGS Publications Warehouse

    Andrews, John T.; Eberl, D.D.; Kristjansdottir, G.B.

    2006-01-01

    Tephras, mainly from Iceland, are becoming increasingly important in interpreting leads and lags in the Holocene climate system across NW Europe. Here we demonstrate that Quantitative Phase Analysis of x-ray diffractograms of the 150 um fraction and identify these same peaks in XRD scans - two of these correlate geochemically and chronologically with Hekla 1104 and 3. At a distal site to the WNW of Iceland, on the East Greenland margin (core MD99-2317), the weight% of volcanic glass reaches values of 11% at about the time of the Saksunarvatn tephra. The XRD method identifies the presence of volcanic glass but not its elemental composition; hence it will assist in focusing attention on specific sections of sediment cores for subsequent geochemical fingerprinting of tephras. ?? 2006 SAGE Publications.

  5. Non-amplified Quantitative Detection of Nucleic Acid Sequences Using a Gold Nanoparticle Probe Set and Field-Emission Scanning Electron Microscopy

    NASA Astrophysics Data System (ADS)

    Hyonchol Kim,; Atsushi Kira,; Kenji Yasuda,

    2010-06-01

    For the precise detection of the number of expressed biomarkers at the single-cell level, we have developed a method of quantifying and specifying target DNA fragments by using a set of gold nanoparticles as labels and field-emission scanning electron microscopy (FE-SEM) to measure the number and sizes of gold nanoparticles attached to target samples. One or more target DNAs on a substrate were labeled with a set of different-sized gold nanoparticle probes having complementary sequences to different target candidates. The type and number of the target DNAs having a specific sequence were identified by counting the attached nanoparticles of a specific size in FE-SEM images. The results evaluated using a DNA microarray showed high specificity and sensitivity, and a linear correlation between the number of attached particles and the target DNA concentration, indicating the feasibility of quantitative detection in the femtomolar to nanomolar concentration range.

  6. Laser scanning confocal microscopy and quantitative microscopy with a charge coupled device camera improve detection of human papillomavirus DNA revealed by fluorescence in situ hybridization.

    PubMed

    Lizard, G; Chignol, M C; Souchier, C; Schmitt, D; Chardonnet, Y

    1994-04-01

    Epithelial cervical CaSki, SiHa and HeLa cells containing respectively 600 copies of human papillomavirus (HPV) DNA type 16, 1-2 copies of HPV DNA type 16 and 10-50 copies of HPV DNA type 18 were used as model to detect different quantities of integrated HPV genome. The HPV DNA was identified on cell deposits with specific biotinylated DNA probes either by enzymatic in situ hybridization (EISH) or fluorescence in situ hybridization (FISH) involving successively a rabbit anti-biotin antibody, a biotinylated goat anti-rabbit antibody and streptavidin-alkaline phosphatase complex or streptavidin-fluorescein isothiocyanate complex. With brightfield microscopy and EISH, hybridization spots were observed in CaSki and HeLa cells but hardly any in SiHa cells. With fluorescence microscopy and FISH, hybridization spots were clearly seen only on CaSki cell nuclei. In an attempt to improve the detection of low quantities of HPV DNA signals revealed by FISH, laser scanning confocal microscopy (LSCM) and quantitative microscopy with an intensified charge coupled device (CCD) camera were used. With both LSCM and quantitative microscopy, as few as 1-2 copies of HPV DNA were detected and found to be confined to cell nuclei counterstained with propidium iodide. Under Nomarski phase contrast, a good preservation of the cell structure was observed. With quantitative microscopy, differences in the number, size, total area and integrated fluorescence intensity of hybridization spots per nucleus were revealed between CaSki, SiHa and HeLa cells.(ABSTRACT TRUNCATED AT 250 WORDS)

  7. A whole genome scan to detect quantitative trait loci for gestation length and sow maternal ability related traits in a White Duroc × Erhualian F2 resource population.

    PubMed

    Chen, C Y; Guo, Y M; Zhang, Z Y; Ren, J; Huang, L S

    2010-06-01

    Gestation length and maternal ability are important to improve the sow reproduction efficiency and their offspring survival. To map quantitative trait loci (QTL) for gestation length and maternal ability related traits including piglet survival rate and average body weight of piglets at weaning, more than 200 F2 sows from a White Duroc × Erhualian resource population were phenotyped. A genome-wide scan was performed with 194 microsatellite markers covering the whole pig genome. QTL analysis was carried out using a composite regression interval mapping method via QTL express. The results showed that total number of born piglets was significantly correlated with gestation length (r = -0.13, P < 0.05). Three QTL were detected on pig chromosome (SSC)2, 8 and 12 for gestation length. The QTL on SSC2 achieved the 5% genome-wide significant level and the QTL on SSC8 was consistent with previous reports. Four suggestive QTL were identified for maternal ability related traits including 1 QTL for survival rate of piglets at weaning on SSC8, 3 QTL for average body weight of piglet at weaning on SSC3, 11 and 13.

  8. Immunofluorescent detection and quantitation of hepatitis A virus in sewage treatment effluent and on agri-food surfaces using scanning confocal microscopy.

    PubMed

    Kukavica-Ibrulj, Irena; Darveau, André; Fliss, Ismaïl

    2003-03-01

    An immunofluorescent (IF) assay was developed for specific detection and quantitation of hepatitis A virus (HAV) in sewage treatment effluent or attached to stainless steel, copper, high density polyethylene and polyvinyl chloride surfaces. Polyclonal antibodies were produced in rabbits and characterized for specificity to HAV. Purified anti-HAV antibodies were used in combination with ALEXA-anti-rabbit conjugate and confocal microscopy for detection and quantitation of HAV in effluent samples. Using this immunological approach, as little as 2 x 10(5) PFU/ml were detected and the signal generated was proportional to the concentration of HAV up to 2 x 10(8) PFU/ml. Counts obtained by IF assay were highly correlated with those of the SYBR Green II nucleic acid labelling method (r(2)=0.995) and conventional plaque assay (r(2)=0.988). The IF assay described is rapid (3 h), sensitive, specific to HAV and suitable for qualitative as well as quantitative studies.

  9. The determination of firing distance applying a microscopic quantitative method and confocal laser scanning microscopy for detection of gunshot residue particles.

    PubMed

    Neri, Margherita; Turillazzi, Emanuela; Riezzo, Irene; Fineschi, Vittorio

    2007-07-01

    In this study, we applied a microscopic quantitative method based on the use of sodium rhodizonate to verify the presence of residues and their distribution on the cutis of gunshot wounds. A total of 250 skin samples were selected from cases in which the manner of death (accidental, suicide, and homicide) and the shooting distance could be reliably determined. The samples were examined under a light microscope, in transmitted bright field illumination and phase contrast mode, and with confocal laser scanning microscopy. In all skin specimens the area of each histological section was directly measured by an image analysis system. Both the number and the size of powder particles were measured. The distribution of gunshot residues (GSR) in the epidermal and subepidermal layers was also analyzed. The evaluation of the microscopic entrance wounds demonstrated different findings related to the range of fire. The data derived from the evaluation of both macroscopic and microscopic features demonstrated that the amount and the spatial distribution of GSR deposits in the skin surrounding entrance wounds strictly correlate with shooting distance.

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

    PubMed

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

    2017-10-01

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

  11. Quantitation of dopamine, serotonin and adenosine content in a tissue punch from a brain slice using capillary electrophoresis with fast-scan cyclic voltammetry detection.

    PubMed

    Fang, Huaifang; Pajski, Megan L; Ross, Ashley E; Venton, B Jill

    2013-01-01

    Methods to determine neurochemical concentrations in small samples of tissue are needed to map interactions among neurotransmitters. In particular, correlating physiological measurements of neurotransmitter release and the tissue content in a small region would be valuable. HPLC is the standard method for tissue content analysis but it requires microliter samples and the detector often varies by the class of compound being quantified; thus detecting molecules from different classes can be difficult. In this paper, we develop capillary electrophoresis with fast-scan cyclic voltammetry detection (CE-FSCV) for analysis of dopamine, serotonin, and adenosine content in tissue punches from rat brain slices. Using field-amplified sample stacking, the limit of detection was 5 nM for dopamine, 10 nM for serotonin, and 50 nM for adenosine. Neurotransmitters could be measured from a tissue punch as small as 7 µg (7 nL) of tissue, three orders of magnitude smaller than a typical HPLC sample. Tissue content analysis of punches in successive slices through the striatum revealed higher dopamine but lower adenosine content in the anterior striatum. Stimulated dopamine release was measured in a brain slice, then a tissue punch collected from the recording region. Dopamine content and release had a correlation coefficient of 0.71, which indicates much of the variance in stimulated release is due to variance in tissue content. CE-FSCV should facilitate measurements of tissue content in nanoliter samples, leading to a better understanding of how diseases or drugs affect dopamine, serotonin, and adenosine content.

  12. Improved method for quantitative bone scanning.

    PubMed

    Lurye, D R; Castronovo, F P; Potsaid, M S

    1977-11-01

    A quantitative gamma-camera technique is used to calculate the percentage of administered activity taken up by various areas of the skeleton. The method uses an external standard source of activity as a reference, and in addition presents the information in a new format, the Organ Uptake Image (OUI). Two cases of Paget's disease serve to illustrate the usefulness of this approach to quantitative bone imaging.

  13. Quantitative optical scanning tests of complex microcircuits

    NASA Technical Reports Server (NTRS)

    Erickson, J. J.

    1980-01-01

    An approach for the development of the optical scanner as a screening inspection instrument for microcircuits involves comparing the quantitative differences in photoresponse images and then correlating them with electrical parameter differences in test devices. The existing optical scanner was modified so that the photoresponse data could be recorded and subsequently digitized. A method was devised for applying digital image processing techniques to the digitized photoresponse data in order to quantitatively compare the data. Electrical tests were performed and photoresponse images were recorded before and following life test intervals on two groups of test devices. Correlations were made between differences or changes in the electrical parameters of the test devices.

  14. Lumber Scanning System for Surface Defect Detection

    Treesearch

    D. Earl Kline; Y. Jason Hou; Richard W. Conners; Daniel L. Schmoldt; Philip A. Araman

    1992-01-01

    This paper describes research aimed at developing a machine vision technology to drive automated processes in the hardwood forest products manufacturing industry. An industrial-scale machine vision system has been designed to scan variable-size hardwood lumber for detecting important features that influence the grade and value of lumber such as knots, holes, wane,...

  15. Quantitative single-molecule imaging by confocal laser scanning microscopy.

    PubMed

    Vukojevic, Vladana; Heidkamp, Marcus; Ming, Yu; Johansson, Björn; Terenius, Lars; Rigler, Rudolf

    2008-11-25

    A new approach to quantitative single-molecule imaging by confocal laser scanning microscopy (CLSM) is presented. It relies on fluorescence intensity distribution to analyze the molecular occurrence statistics captured by digital imaging and enables direct determination of the number of fluorescent molecules and their diffusion rates without resorting to temporal or spatial autocorrelation analyses. Digital images of fluorescent molecules were recorded by using fast scanning and avalanche photodiode detectors. In this way the signal-to-background ratio was significantly improved, enabling direct quantitative imaging by CLSM. The potential of the proposed approach is demonstrated by using standard solutions of fluorescent dyes, fluorescently labeled DNA molecules, quantum dots, and the Enhanced Green Fluorescent Protein in solution and in live cells. The method was verified by using fluorescence correlation spectroscopy. The relevance for biological applications, in particular, for live cell imaging, is discussed.

  16. Damage detection using scanning laser vibrometer

    NASA Astrophysics Data System (ADS)

    Chen, Shen-En; Venkatappa, Suhas; Petro, Samer H.; Gangarao, Hota V.

    1998-06-01

    A damage detection algorithm based on the principle of curvature changes has been developed at CFC-WVU. However, the algorithm requires accurate mode shapes with adequate spatial density. Existing contact sensors can not provide adequate spatial density without adding excessive mass. Hence, non-contact scanning techniques, such as scanning laser vibrometer (SLV) has adequate sensitivity and accuracy is yet to be proven. The applicability of SLV on large structures is also questionable. To assess the suitability of using SLV for damage detection, a beam specimen has been tested using an existing system. The results confirm that damage detection using vibration measurements from SLV is successful. Due to more spatial density, the SLV data is shown to be more sensitive than the contact sensor test.

  17. Quantitative techniques in 18FDG PET scanning in oncology.

    PubMed

    Castell, F; Cook, G J R

    2008-05-20

    The clinical applications of (18)F-fluoro-2-deoxyglucose ((18)FDG) positron emission tomography (PET) in oncology are becoming established. While simple static scanning techniques are used for the majority of routine clinical examinations, increasing use of PET in clinical trials to monitor treatment response with (18)FDG and novel tracers reflecting different pharmacodynamic end points, often necessitates a more complex and quantitative analysis of radiopharmaceutical kinetics. A wide range of PET analysis techniques exist, ranging from simple visual analysis and semiquantitative methods to full dynamic studies with kinetic analysis. These methods are discussed, focusing particularly on the available methodologies that can be utilised in clinical trials.

  18. Automated Quantitative Rare Earth Elements Mineralogy by Scanning Electron Microscopy

    NASA Astrophysics Data System (ADS)

    Sindern, Sven; Meyer, F. Michael

    2016-09-01

    Increasing industrial demand of rare earth elements (REEs) stems from the central role they play for advanced technologies and the accelerating move away from carbon-based fuels. However, REE production is often hampered by the chemical, mineralogical as well as textural complexity of the ores with a need for better understanding of their salient properties. This is not only essential for in-depth genetic interpretations but also for a robust assessment of ore quality and economic viability. The design of energy and cost-efficient processing of REE ores depends heavily on information about REE element deportment that can be made available employing automated quantitative process mineralogy. Quantitative mineralogy assigns numeric values to compositional and textural properties of mineral matter. Scanning electron microscopy (SEM) combined with a suitable software package for acquisition of backscatter electron and X-ray signals, phase assignment and image analysis is one of the most efficient tools for quantitative mineralogy. The four different SEM-based automated quantitative mineralogy systems, i.e. FEI QEMSCAN and MLA, Tescan TIMA and Zeiss Mineralogic Mining, which are commercially available, are briefly characterized. Using examples of quantitative REE mineralogy, this chapter illustrates capabilities and limitations of automated SEM-based systems. Chemical variability of REE minerals and analytical uncertainty can reduce performance of phase assignment. This is shown for the REE phases parisite and synchysite. In another example from a monazite REE deposit, the quantitative mineralogical parameters surface roughness and mineral association derived from image analysis are applied for automated discrimination of apatite formed in a breakdown reaction of monazite and apatite formed by metamorphism prior to monazite breakdown. SEM-based automated mineralogy fulfils all requirements for characterization of complex unconventional REE ores that will become

  19. Prediction of trabecular bone qualitative properties using scanning quantitative ultrasound

    PubMed Central

    Qin, Yi-Xian; Lin, Wei; Mittra, Erik; Xia, Yi; Cheng, Jiqi; Judex, Stefan; Rubin, Clint; Müller, Ralph

    2012-01-01

    Microgravity induced bone loss represents a critical health problem in astronauts, particularly occurred in weight-supporting skeleton, which leads to osteopenia and increase of fracture risk. Lack of suitable evaluation modality makes it difficult for monitoring skeletal status in long term space mission and increases potential risk of complication. Such disuse osteopenia and osteoporosis compromise trabecular bone density, and architectural and mechanical properties. While X-ray based imaging would not be practical in space, quantitative ultrasound may provide advantages to characterize bone density and strength through wave propagation in complex trabecular structure. This study used a scanning confocal acoustic diagnostic and navigation system (SCAN) to evaluate trabecular bone quality in 60 cubic trabecular samples harvested from adult sheep. Ultrasound image based SCAN measurements in structural and strength properties were validated by μCT and compressive mechanical testing. This result indicated a moderately strong negative correlations observed between broadband ultrasonic attenuation (BUA) and μCT-determined bone volume fraction (BV/TV, R2=0.53). Strong correlations were observed between ultrasound velocity (UV) and bone’s mechanical strength and structural parameters, i.e., bulk Young’s modulus (R2=0.67) and BV/TV (R2=0.85). The predictions for bone density and mechanical strength were significantly improved by using a linear combination of both BUA and UV, yielding R2=0.92 for BV/TV and R2=0.71 for bulk Young’s modulus. These results imply that quantitative ultrasound can characterize trabecular structural and mechanical properties through measurements of particular ultrasound parameters, and potentially provide an excellent estimation for bone’s structural integrity. PMID:23976803

  20. Prediction of trabecular bone qualitative properties using scanning quantitative ultrasound.

    PubMed

    Qin, Yi-Xian; Lin, Wei; Mittra, Erik; Xia, Yi; Cheng, Jiqi; Judex, Stefan; Rubin, Clint; Müller, Ralph

    2013-11-01

    Microgravity induced bone loss represents a critical health problem in astronauts, particularly occurred in weight-supporting skeleton, which leads to osteopenia and increase of fracture risk. Lack of suitable evaluation modality makes it difficult for monitoring skeletal status in long term space mission and increases potential risk of complication. Such disuse osteopenia and osteoporosis compromise trabecular bone density, and architectural and mechanical properties. While X-ray based imaging would not be practical in space, quantitative ultrasound may provide advantages to characterize bone density and strength through wave propagation in complex trabecular structure. This study used a scanning confocal acoustic diagnostic and navigation system (SCAN) to evaluate trabecular bone quality in 60 cubic trabecular samples harvested from adult sheep. Ultrasound image based SCAN measurements in structural and strength properties were validated by μCT and compressive mechanical testing. This result indicated a moderately strong negative correlations observed between broadband ultrasonic attenuation (BUA) and μCT-determined bone volume fraction (BV/TV, R(2)=0.53). Strong correlations were observed between ultrasound velocity (UV) and bone's mechanical strength and structural parameters, i.e., bulk Young's modulus (R(2)=0.67) and BV/TV (R(2)=0.85). The predictions for bone density and mechanical strength were significantly improved by using a linear combination of both BUA and UV, yielding R(2)=0.92 for BV/TV and R(2)=0.71 for bulk Young's modulus. These results imply that quantitative ultrasound can characterize trabecular structural and mechanical properties through measurements of particular ultrasound parameters, and potentially provide an excellent estimation for bone's structural integrity.

  1. Prediction of trabecular bone qualitative properties using scanning quantitative ultrasound

    NASA Astrophysics Data System (ADS)

    Qin, Yi-Xian; Lin, Wei; Mittra, Erik; Xia, Yi; Cheng, Jiqi; Judex, Stefan; Rubin, Clint; Müller, Ralph

    2013-11-01

    Microgravity induced bone loss represents a critical health problem in astronauts, particularly occurred in weight-supporting skeleton, which leads to osteopenia and increase of fracture risk. Lack of suitable evaluation modality makes it difficult for monitoring skeletal status in long term space mission and increases potential risk of complication. Such disuse osteopenia and osteoporosis compromise trabecular bone density, and architectural and mechanical properties. While X-ray based imaging would not be practical in space, quantitative ultrasound may provide advantages to characterize bone density and strength through wave propagation in complex trabecular structure. This study used a scanning confocal acoustic diagnostic and navigation system (SCAN) to evaluate trabecular bone quality in 60 cubic trabecular samples harvested from adult sheep. Ultrasound image based SCAN measurements in structural and strength properties were validated by μCT and compressive mechanical testing. This result indicated a moderately strong negative correlations observed between broadband ultrasonic attenuation (BUA) and μCT-determined bone volume fraction (BV/TV, R2=0.53). Strong correlations were observed between ultrasound velocity (UV) and bone's mechanical strength and structural parameters, i.e., bulk Young's modulus (R2=0.67) and BV/TV (R2=0.85). The predictions for bone density and mechanical strength were significantly improved by using a linear combination of both BUA and UV, yielding R2=0.92 for BV/TV and R2=0.71 for bulk Young's modulus. These results imply that quantitative ultrasound can characterize trabecular structural and mechanical properties through measurements of particular ultrasound parameters, and potentially provide an excellent estimation for bone's structural integrity.

  2. Effects of instrument imperfections on quantitative scanning transmission electron microscopy.

    PubMed

    Krause, Florian F; Schowalter, Marco; Grieb, Tim; Müller-Caspary, Knut; Mehrtens, Thorsten; Rosenauer, Andreas

    2016-02-01

    Several instrumental imperfections of transmission electron microscopes are characterized and their effects on the results of quantitative scanning electron microscopy (STEM) are investigated and quantified using simulations. Methods to either avoid influences of these imperfections during acquisition or to include them in reference calculations are proposed. Particularly, distortions inflicted on the diffraction pattern by an image-aberration corrector can cause severe errors of more than 20% if not accounted for. A procedure for their measurement is proposed here. Furthermore, afterglow phenomena and nonlinear behavior of the detector itself can lead to incorrect normalization of measured intensities. Single electrons accidentally impinging on the detector are another source of error but can also be exploited for threshold-less calibration of STEM images to absolute dose, incident beam current determination and measurement of the detector sensitivity. Copyright © 2015 Elsevier B.V. All rights reserved.

  3. Automatic change detection using mobile laser scanning

    NASA Astrophysics Data System (ADS)

    Hebel, M.; Hammer, M.; Gordon, M.; Arens, M.

    2014-10-01

    Automatic change detection in 3D environments requires the comparison of multi-temporal data. By comparing current data with past data of the same area, changes can be automatically detected and identified. Volumetric changes in the scene hint at suspicious activities like the movement of military vehicles, the application of camouflage nets, or the placement of IEDs, etc. In contrast to broad research activities in remote sensing with optical cameras, this paper addresses the topic using 3D data acquired by mobile laser scanning (MLS). We present a framework for immediate comparison of current MLS data to given 3D reference data. Our method extends the concept of occupancy grids known from robot mapping, which incorporates the sensor positions in the processing of the 3D point clouds. This allows extracting the information that is included in the data acquisition geometry. For each single range measurement, it becomes apparent that an object reflects laser pulses in the measured range distance, i.e., space is occupied at that 3D position. In addition, it is obvious that space is empty along the line of sight between sensor and the reflecting object. Everywhere else, the occupancy of space remains unknown. This approach handles occlusions and changes implicitly, such that the latter are identifiable by conflicts of empty space and occupied space. The presented concept of change detection has been successfully validated in experiments with recorded MLS data streams. Results are shown for test sites at which MLS data were acquired at different time intervals.

  4. Qualitative and quantitative processing of side-scan sonar data

    SciTech Connect

    Dwan, F.S.; Anderson, A.L.; Hilde, T.W.C. )

    1990-06-01

    Modern side-scan sonar systems allow vast areas of seafloor to be rapidly imaged and quantitatively mapped in detail. The application of remote sensing image processing techniques can be used to correct for various distortions inherent in raw sonography. Corrections are possible for water column, slant-range, aspect ratio, speckle and striping noise, multiple returns, power drop-off, and for georeferencing. The final products reveal seafloor features and patterns that are geometrically correct, georeferenced, and have improved signal/noise ratio. These products can be merged with other georeferenced data bases for further database management and information extraction. In order to compare data collected by different systems from a common area and to ground truth measurements and geoacoustic models, quantitative correction must be made for calibrated sonar system and bathymetry effects. Such data inversion must account for system source level, beam pattern, time-varying gain, processing gain, transmission loss, absorption, insonified area, and grazing angle effects. Seafloor classification can then be performed on the calculated back-scattering strength using Lambert's Law and regression analysis. Examples are given using both approaches: image analysis and inversion of data based on the sonar equation.

  5. Factors influencing quantitative liquid (scanning) transmission electron microscopy

    SciTech Connect

    Abellan Baeza, Patricia; Woehl, Taylor J.; Parent, Lucas R.; Browning, Nigel D.; Evans, James E.; Arslan, Ilke

    2014-04-15

    One of the experimental challenges in the study of nanomaterials in liquids in the (scanning) transmission electron microscope ((S)TEM) is gaining quantitative information. A successful experiment in the fluid stage will depend upon the ability to plan for sensitive factors such as the electron dose applied, imaging mode, acceleration voltage, beam-induced solution chemistry changes, and the specifics of solution reactivity. In this paper, we make use of a visual approach to show the extent of damage of different instrumental and experimental factors in liquid samples imaged in the (S)TEM. Previous results as well as new insights are presented to create an overview of beam-sample interactions identified for changing imaging and experimental conditions. This work establishes procedures to understand the effect of the electron beam on a solution, provides information to allow for a deliberate choice of the optimal experimental conditions to enable quantification, and identifies the experimental factors that require further analysis for achieving fully quantitative results in the liquid (S)TEM.

  6. Quantitative analysis of multiple components based on liquid chromatography with mass spectrometry in full scan mode.

    PubMed

    Xu, Min Li; Li, Bao Qiong; Wang, Xue; Chen, Jing; Zhai, Hong Lin

    2016-08-01

    Although liquid chromatography with mass spectrometry in full scan mode can obtain all the signals simultaneously in a large range and low cost, it is rarely used in quantitative analysis due to several problems such as chromatographic drifts and peak overlap. In this paper, we propose a Tchebichef moment method for the simultaneous quantitative analysis of three active compounds in Qingrejiedu oral liquid based on three-dimensional spectra in full scan mode of liquid chromatography with mass spectrometry. After the Tchebichef moments were calculated directly from the spectra, the quantitative linear models for three active compounds were established by stepwise regression. All the correlation coefficients were more than 0.9978. The limits of detection and limits of quantitation were less than 0.11 and 0.49 μg/mL, respectively. The intra- and interday precisions were less than 6.54 and 9.47%, while the recovery ranged from 102.56 to 112.15%. Owing to the advantages of multi-resolution and inherent invariance properties, Tchebichef moments could provide favorable results even in the situation of peaks shifting and overlapping, unknown interferences and noise signals, so it could be applied to the analysis of three-dimensional spectra in full scan mode of liquid chromatography with mass spectrometry.

  7. Optimal handling of dimercaptosuccinic acid for quantitative renal scanning

    SciTech Connect

    Taylor, A. Jr.; Lallone, R.L.; Hagan, P.L.

    1980-12-01

    Methods of optimizing quantitative renal imaging with Tc-99m dimercaptosuccinic acid (DMSA) were investigated. Rats were injected with DMSA (one kit per rat) and sacrificed at 0.5, 2.0, and 24 hr after injection. Fifty percent of the injected dose localized in the kidneys at 0.5, 2, and 24 hr after injection while background activity peaked at 0.5 hr and then declined to give substantially higher kidney-to-background ratios at 24 hr. Delayed scanning should increase the accuracy of clinical studies in patients with low kidney-to-background ratios at 1 to 2 hr. After injection of DMSA, 1 ml of air was introduced into the reaction vials and incubated 20 min. Kidney uptake decreased from 50 to 40% and liver uptake increased from 7.5 to 17%. If multiple doses must be drawn from a single vial, air should not be introduced, and the doses should be drawn together and administered immediately to minimize radiopharmaceutical deterioration.

  8. Detection of quantitative trait loci affecting caffeine metabolism by interval mapping in a genome-wide scan of C3H/HeJ x APN F(2) mice.

    PubMed

    Casley, W L; Menzies, J A; Whitehouse, L W; Moon, T W

    1999-12-01

    Caffeine metabolite ratios have been widely used to measure cytochrome P-450 1A2 activity in humans. Serum paraxanthine/caffeine ratio is one such index of this activity. We had previously demonstrated genetic variation of this trait among inbred mouse strains. In the present study, we have undertaken a genome-wide scan for quantitative trait loci affecting this trait with an interval mapping approach on an F(2) intercross population of acetaminophen nonsusceptible and C3H/HeJ inbred mice. A statistically significant association (log-likelihood ratio = 25.0) between a locus on chromosome 9, which colocalized with the murine Cyp1a2 locus, and the plasma paraxanthine/caffeine ratio was identified. This result suggested the presence of an expression polymorphism affecting this gene. A second locus was identified on chromosome 1 (log-likelihood ratio = 9.7) for which no obvious candidate gene has been identified. The influence of this locus on the paraxanthine/caffeine index was more significant among males (log-likelihood ratio = 6.3) than females (log-likelihood ratio = 3.6). A third locus was identified on chromosome 4 with a less statistically robust association (log-likelihood ratio = 3.4) to the paraxanthine/caffeine phenotype. Collectively, these three loci accounted for 63.2% of the variation observed in the F(2) population for this phenotype. These results demonstrate the potential for genetic variation arising from factors other than CYP1A2 activity to influence the plasma paraxanthine/caffeine ratio in mice. This study demonstrates the utility of quantitative genetics in the analysis of polygenic drug metabolism.

  9. Role of Quantitative Bone Scanning in the Assessment of Bone Turnover in Patients With Charcot Foot

    PubMed Central

    Bem, Robert; Jirkovská, Alexandra; Dubský, Michal; Fejfarová, Vladimira; Buncová, Marie; Skibová, Jelena; Jude, Edward B.

    2010-01-01

    OBJECTIVE To assess the new quantitative bone scan parameters as markers of Charcot neuroosteoarthropathy (CNO) activity. RESEARCH DESIGN AND METHODS Forty-two patients with acute (n = 21) and nonacute (n = 21) CNO underwent quantitative bone scanning. Patients with acute CNO were followed for 3–12 months and bone scans were repeated after treatment. New quantitative parameters were assessed and compared with markers of bone turnover and with skin temperature difference (STD). RESULTS Significant correlations between quantitative bone scan parameters and bone turnover markers were observed (all P < 0.05). These parameters decreased after treatment of CNO, and its reduction to the baseline value correlated with differences of bone turnover markers and STD (all P < 0.05). CONCLUSIONS Our study suggests that bone scanning can be used not only for diagnosis of CNO but also for monitoring disease activity by quantitative bone scan parameters. PMID:19933988

  10. Role of quantitative bone scanning in the assessment of bone turnover in patients with Charcot foot.

    PubMed

    Bem, Robert; Jirkovská, Alexandra; Dubsky, Michal; Fejfarová, Vladimira; Buncová, Marie; Skibová, Jelena; Jude, Edward B

    2010-02-01

    To assess the new quantitative bone scan parameters as markers of Charcot neuroosteoarthropathy (CNO) activity. Forty-two patients with acute (n = 21) and nonacute (n = 21) CNO underwent quantitative bone scanning. Patients with acute CNO were followed for 3-12 months and bone scans were repeated after treatment. New quantitative parameters were assessed and compared with markers of bone turnover and with skin temperature difference (STD). Significant correlations between quantitative bone scan parameters and bone turnover markers were observed (all P < 0.05). These parameters decreased after treatment of CNO, and its reduction to the baseline value correlated with differences of bone turnover markers and STD (all P < 0.05). Our study suggests that bone scanning can be used not only for diagnosis of CNO but also for monitoring disease activity by quantitative bone scan parameters.

  11. Parabola detection using matched filtering for ultrasound B-scans.

    PubMed

    Petcher, P A; Dixon, S

    2012-01-01

    Time of flight diffraction (ToFD) outputs B-scans using an ultrasound emitter and receiver at a constant separation, scanned over a sample surface parallel to the line between the transducers. The B-scan, with time and scan position axes, contains parabolic features characteristic of a point-like scatterer. Human vision effectively detects these shapes, but this is time consuming and requires training. A parabola matched filter has been developed that is simple to implement and transforms parabolic shapes to peaks whilst reducing noise in the scan. The scan can then be displayed as depth versus lateral position. Copyright © 2011 Elsevier B.V. All rights reserved.

  12. Computing quantitative indicators of structural renal damage in pediatric DMSA scans.

    PubMed

    Sampedro, F; Domenech, A; Escalera, S; Carrio, I

    The proposal and implementation of a computational framework for the quantification of structural renal damage from (99m)Tc-dimercaptosuccinic acid (DMSA) scans. The aim of this work is to propose, implement, and validate a computational framework for the quantification of structural renal damage from DMSA scans and in an observer-independent manner. From a set of 16 pediatric DMSA-positive scans and 16 matched controls and using both expert-guided and automatic approaches, a set of image-derived quantitative indicators was computed based on the relative size, intensity and histogram distribution of the lesion. A correlation analysis was conducted in order to investigate the association of these indicators with other clinical data of interest in this scenario, including C-reactive protein (CRP), white cell count, vesicoureteral reflux, fever, relative perfusion, and the presence of renal sequelae in a 6-month follow-up DMSA scan. A fully automatic lesion detection and segmentation system was able to successfully classify DMSA-positive from negative scans (AUC=0.92, sensitivity=81% and specificity=94%). The image-computed relative size of the lesion correlated with the presence of fever and CRP levels (p<0.05), and a measurement derived from the distribution histogram of the lesion obtained significant performance results in the detection of permanent renal damage (AUC=0.86, sensitivity=100% and specificity=75%). The proposal and implementation of a computational framework for the quantification of structural renal damage from DMSA scans showed a promising potential to complement visual diagnosis and non-imaging indicators. Copyright © 2016 Elsevier España, S.L.U. y SEMNIM. All rights reserved.

  13. High-speed line-scanning confocal holographic microscopy for quantitative phase imaging (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Liu, Changgeng; Knitter, Sebastian; Cong, Zhilong; Sencan, Ikbal; Cao, Hui; Choma, Michael A.

    2016-03-01

    We present a high speed, phase-sensitive, line-scanning reflectance confocal interference microscope. We achieved rapid confocal imaging using a fast line-scan camera and quantitative phase imaging using off-axis digital holography on a 1D, line-by-line basis. In our prototype system, a He-Ne laser (~1.2 mW) was used to demonstrate the principle of operation. Using a 20 kHz line scan rate (1024 pixels per line scan), we achieved a video-rate frame rate of 20 Hz for 1024x500 pixel en-face confocal images (20 MHz total pixel rate). By using an objective lens of a NA 0.65, we achieved an axial and lateral resolution of ~3.5 micrometers and ~0.8 micrometers, respectively. By z-stack imaging of a custom silicon target with a stepped structure, we confirmed that the axial sectioning of the interference microscope is similar to that of a traditional line-scan confocal microscope (our microscope with the reference arm blocked). The utility of phase-sensitive holographic detection in line-scan confocal was demonstrated in two ways. First, using a custom axial height phantom fabricated using chrome deposition, we demonstrated variations in phase corresponding to heights in the 100 nm range with a contrast-to-noise ratio of ~31 dB. Second, we demonstrate digital refocusing of an out-of-focus holographic image. The mechanism of confocality in our line-scan system is 1D physical pinholing. Our ongoing work aims to add an additional mechanism of confocality by using low spatial coherence sources to impose interferometric pinholing.

  14. Scanning Quadrupole Data Independent Acquisition - Part A. Qualitative and Quantitative Characterization.

    PubMed

    Moseley, M Arthur; Hughes, Christopher J; Juvvadi, Praveen R; Soderblom, Erik J; Lennon, Sarah; Perkins, Simon R; Thompson, J Will; Steinbach, William J; Geromanos, Scott J; Wildgoose, Jason; Langridge, James I; Richardson, Keith; Vissers, Johannes P C

    2017-09-13

    A novel data independent acquisition (DIA) method incorporating a scanning quadrupole in front of a collision cell and orthogonal acceleration time-of-flight mass analyzer is described. The method has been characterized for the qualitative and quantitative label-free proteomic analysis of typical complex biological samples. The principle of the scanning quadrupole DIA method is discussed and analytical instrument characteristics, such as the quadrupole transmission width, scan/integration time, and chromatographic separation, have been optimized in relation to sample complexity for a number of different model proteomes of varying complexity and dynamic range including human plasma, cell lines, and bacteria. In addition, the technological merits over existing DIA approaches are described and contrasted. The qualitative and semi-quantitative performance of the method is illustrated for the analysis of relatively simple protein digest mixtures and a well-characterised human cell line sample using untargeted and targeted search strategies. Finally, the results from a human cell line were compared against publically available data that used similar chromatographic conditions, but were acquired with DDA technology and alternative mass analyzer systems. Qualitative comparison showed excellent concordance of results with over 90% overlap of the detected proteins.

  15. Variation of quantitative emphysema measurements from CT scans

    NASA Astrophysics Data System (ADS)

    Keller, Brad M.; Reeves, Anthony P.; Henschke, Claudia I.; Barr, R. Graham; Yankelevitz, David F.

    2008-03-01

    Emphysema is a lung disease characterized by destruction of the alveolar air sacs and is associated with long-term respiratory dysfunction. CT scans allow for imaging of the anatomical basis of emphysema, and several measures have been introduced for the quantification of the extent of disease. In this paper we compare these measures for repeatability over time. The measures of interest in this study are emphysema index, mean lung density, histogram percentile, and the fractal dimension. To allow for direct comparisons, the measures were normalized to a 0-100 scale. These measures have been computed for a set of 2,027 scan pairs in which the mean interval between scans was 1.15 years (σ: 93 days). These independent pairs were considered with respect to three different scanning conditions (a) 223 pairs where both were scanned with a 5 mm slice thickness protocol, (b) 695 with the first scanned with the 5 mm protocol and the second with a 1.25 mm protocol, and (c) 1109 pairs scanned both times using a 1.25 mm protocol. We found that average normalized emphysema index and histogram percentiles scores increased by 5.9 and 11 points respectively, while the fractal dimension showed stability with a mean difference of 1.2. We also found, a 7 point bias introduced for emphysema index under condition (b), and that the fractal dimension measure is least affected by scanner parameter changes.

  16. Quantitative multiplex detection of pathogen biomarkers

    DOEpatents

    Mukundan, Harshini; Xie, Hongzhi; Swanson, Basil I.; Martinez, Jennifer; Grace, Wynne K.

    2016-02-09

    The present invention addresses the simultaneous detection and quantitative measurement of multiple biomolecules, e.g., pathogen biomarkers through either a sandwich assay approach or a lipid insertion approach. The invention can further employ a multichannel, structure with multi-sensor elements per channel.

  17. Quantitative multiplex detection of pathogen biomarkers

    DOEpatents

    Mukundan, Harshini; Xie, Hongzhi; Swanson, Basil I; Martinez, Jennifer; Grace, Wynne K

    2014-10-14

    The present invention addresses the simultaneous detection and quantitative measurement of multiple biomolecules, e.g., pathogen biomarkers through either a sandwich assay approach or a lipid insertion approach. The invention can further employ a multichannel, structure with multi-sensor elements per channel.

  18. Detection of ureteral obstruction on radionuclide bone scans

    SciTech Connect

    Pollen, J.J.; Gerber, K.; Heil, B.J.; Talner, L.B.

    1983-09-01

    The kidneys are nearly always visible on a routine radionuclide bone scan. To assess the reliability of the bone scan in detecting ureteral obstruction, 220 bone scans and excretory urograms were compared in 53 patients followed serially for prostatic cancer. There were 15 kidneys obstructed on excretory urograms. Only nine were diagnosed as obstructed on the bone scans. Seven of the nine cases of unilaterally obstructed kidneys were detected, whereas only two of the six kidneys in three patients with bilateral obstruction were correctly diagnosed. The results indicate that unilateral obstruction is more likely to be detected, whereas bilateral obstruction is more likely to be missed, on bone scans. Therefore, the routine radionuclide bone scan is an unreliable test for ureteral obstruction.

  19. Detecting Scans at the ISP Level

    DTIC Science & Technology

    2006-04-01

    Paxson, Vern; Berger, Arthur W.; & Balakrishnan, Hari. “Fast Portscan Detection Using Sequential Hypothesis Testing.” In IEEE Symposium on Security...P53-13.gz. [Staniford 00] Staniford, Stuart; Hoagland, James A.; & McAlerney, Joseph M. “Practical Automated Detection of Stealthy Portscans ...Staniford 02] Staniford, Stuart; Hoagland, James; & McAlerney, Joseph. “Practical Automated Detection of Stealthy Portscans .” Journal of

  20. A microarray scanner for the real-time quantitative detection

    NASA Astrophysics Data System (ADS)

    Liu, Quanjun; Zhuang, Ying; Wu, Lingwei; Wu, Zhongwei; Hu, Song; Lu, Zuhong

    2007-05-01

    The real-time and quantitative detection assay is important for the gene detection. With the TaqMan probes for the detection based polymerase chain reaction (PCR), four targets could be checked in a single process in solution assay. A new method is developed to immobilize the TaqMan probes on a microarray, which could be used to the multi-target gene fragment quantitative detection with PCR. A new type microarray scanner is designed for the assay. A thermocycler system was built into the scanner platform. A new type of the vessel sealed with the gene amplification solution which could perform the thermo-cycling and scanning. To decrease the background intensity a confocal system was used as the fluorescent intensity detection in the scanner. To calculate the gene quantity, a standard liner graph was draw with the fluorescent intensity versus the cycles. From the standard liner, the quantity of the original gene fragment could be calculated in time with the cycles. This scanner offers the great advantage of real-time quantitative detection of DNA targets in a microarray.

  1. Aptasensors for quantitative detection of kanamycin.

    PubMed

    Robati, Rezvan Yazdian; Arab, Atefeh; Ramezani, Mohammad; Langroodi, Fatemeh Alebooye; Abnous, Khalil; Taghdisi, Seyed Mohammad

    2016-08-15

    Up till now, various techniques have been developed to detect kanamycin in biological samples. However, due to some problems involved in these methods including time-consuming, expensive equipment and high consumption of reagents, new strategies for detection and quantitative determination of kanamycin are needed. Aptamer-based biosensors with unique recognition capability have attracted more attention of scientists because of its rapid response, high sensitivity and simple fabrication. Hence, we summarized optical and electrochemical kanamycin aptasensors and focuses on recent advances and modern techniques in aptasensor-based kanamycin detection techniques in order to provide readers with an inclusive understanding of its improvement and progress.

  2. Bone scanning in the detection of occult fractures

    SciTech Connect

    Batillas, J.; Vasilas, A.; Pizzi, W.F.; Gokcebay, T.

    1981-07-01

    The potential role of bone scanning in the early detection of occult fractures following acute trauma was investigated. Technetium 99m pyrophosphate bone scans were obtained in patients with major clinical findings and negative or equivocal roentgenograms following trauma. Bone scanning facilitated the prompt diagnosis of occult fractures in the hip, knee, wrist, ribs and costochondral junctions, sternum, vertebrae, sacrum, and coccyx. Several illustrative cases are presented. Roentgenographic confirmation occurred following a delay of days to weeks and, in some instances, the roentgenographic findings were subtle and could be easily overlooked. This study demonstrates bone scanning to be invaluable and definitive in the prompt detection of occult fractures.

  3. Defect Detection Using a Scanning Laser Source

    NASA Astrophysics Data System (ADS)

    Burrows, S. E.; Dixon, S.

    2011-06-01

    Surface breaking defects are identified using a scanning laser source. A Q-switched Nd-YAG laser is used as a non-contact source of ultrasound and an electromagnetic acoustic transducer (EMAT) employed as detector. For a thin plate, an increase in frequency content of the received wave is observed when the laser spot is situated directly over the defect. Time-frequency analysis using a Wigner transform has enabled individual Lamb wave modes to be identified, while propagation of Lamb waves through aluminium sheet is studied by finite element analysis.

  4. Electron beam detection of a Nanotube Scanning Force Microscope.

    PubMed

    Siria, Alessandro; Niguès, Antoine

    2017-09-14

    Atomic Force Microscopy (AFM) allows to probe matter at atomic scale by measuring the perturbation of a nanomechanical oscillator induced by near-field interaction forces. The quest to improve sensitivity and resolution of AFM forced the introduction of a new class of resonators with dimensions at the nanometer scale. In this context, nanotubes are the ultimate mechanical oscillators because of their one dimensional nature, small mass and almost perfect crystallinity. Coupled to the possibility of functionalisation, these properties make them the perfect candidates as ultra sensitive, on-demand force sensors. However their dimensions make the measurement of the mechanical properties a challenging task in particular when working in cavity free geometry at ambient temperature. By using a focused electron beam, we show that the mechanical response of nanotubes can be quantitatively measured while approaching to a surface sample. By coupling electron beam detection of individual nanotubes with a custom AFM we image the surface topography of a sample by continuously measuring the mechanical properties of the nanoresonators. The combination of very small size and mass together with the high resolution of the electron beam detection method offers unprecedented opportunities for the development of a new class of nanotube-based scanning force microscopy.

  5. Quantitative rapid scan EPR spectroscopy at 258 MHz.

    PubMed

    Quine, Richard W; Rinard, George A; Eaton, Sandra S; Eaton, Gareth R

    2010-07-01

    Experimental data obtained with an electron paramagnetic resonance (EPR) rapid scan spectrometer were translated through the reverse transfer functions of the spectrometer hardware to the sample position. Separately, theoretical calculations were performed to predict signal and noise amplitudes at the sample position for specified experimental conditions. A comparison was then made between the translated experimental values and the calculated values. Excellent agreement was obtained.

  6. Anatrophic nephrolithotomy: preservation of renal function demonstrated by differential quantitative radionuclide renal scans

    SciTech Connect

    Belis, J.A.; Morabito, R.A.; Kandzari, S.J.; Lai, J.C.; Gabriele, O.F.

    1981-06-01

    Differential quantitative radionuclide renal scans have been used to confirm that early removal of staghorn calculi by anatrophic nephrolithotomy preserves renal parenchyma without significant renal damage by the surgical procedure. The /sup 99m/technetium diethylenetriaminepentaacetic acid scan was useful in predicting recovery of function in the involved kidney, while the /sup 131/iodine orthoiodohippurate scan provided a quantitative evaluation of the effect of the surgical procedure on individual kidney function. All of 13 consecutive patients evaluated by /sup 131/iodine orthoiodohippurate renal scans had stable or improved effective renal plasma flow to the involved kidney and an unchanged or improved total excretory index 6 months after nephrolithotomy.

  7. Anatrophic nephrolithotomy: preservation of renal function demonstrated by differential quantitative radionuclide renal scans.

    PubMed

    Belis, J A; Morabito, R A; Kandzari, S J; Lai, J C; Gabriele, O F

    1981-06-01

    Differential quantitative radionuclide renal scans have been used to confirm that early removal of staghorn calculi by anatrophic nephrolithotomy preserves renal parenchyma without significant renal damage by the surgical procedure. The 99mtechnetium diethylenetriaminepentaacetic acid scan was useful in predicting recovery of function in the involved kidney, while the 131iodine orthoiodohippurate scan provided a quantitative evaluation of the effect of the surgical procedure on individual kidney function. All of 13 consecutive patients evaluated by 131iodine orthoiodohippurate renal scans had stable or improved effective renal plasma flow to the involved kidney and an unchanged or improved total excretory index 6 months after nephrolithotomy.

  8. Detection of defects in red oak deckboards by ultrasonic scanning

    Treesearch

    Mohammed F. Kabir; Daniel L. Schmoldt; Mark E. Schafer

    2000-01-01

    Experiments were conducted to detect defects in red oak (Quercus rubra, L.) deckboards by ultrasonic scanning. Scanning of the deckboards was carried out with two rolling transducers in a pitch-catch arrangement with pallet parts moving between the transducers at 70 ft/m and 220 ft/m. Data were collected, stored and processed using LabViewTM software. The defects...

  9. Detection of unsuspected malignant pleural effusion by bone scan

    SciTech Connect

    Goldstein, H.A.; Gefter, W.B.

    1984-10-01

    Technetium-99m phosphate compounds may occasionally accumulate in malignant pleural effusions. A case of metastatic pleural effusion first diagnosed by bone scan, prior to its clinical or roentgenographic detection, is reported.

  10. Nonlinear ultrasonic scanning to detect material defects

    NASA Technical Reports Server (NTRS)

    Yost, William T. (Inventor); Cantrell, John H. (Inventor)

    1998-01-01

    A method and system are provided to detect defects in a material. Waves of known frequency(ies) are mixed at an interaction zone in the material. As a result, at least one of a difference wave and a sum wave are generated in the interaction zone. The difference wave occurs at a difference frequency and the sum wave occurs at a sum frequency. The amplitude of at least one nonlinear signal based on the sum and/or difference waves is then measured. The nonlinear signal is defined as the amplitude of one of the difference wave and sum wave relative to the product of the amplitude of the surface waves. The amplitude of the nonlinear signal is an indication of defects (e.g., dislocation dipole density) in the interaction zone.

  11. Simultaneous measurement and quantitation of 4-hydroxyphenylacetic acid and dopamine with fast-scan cyclic voltammetry.

    PubMed

    Shin, Mimi; Kaplan, Sam V; Raider, Kayla D; Johnson, Michael A

    2015-05-07

    Caged compounds have been used extensively to investigate neuronal function in a variety of preparations, including cell culture, ex vivo tissue samples, and in vivo. As a first step toward electrochemically measuring the extent of caged compound photoactivation while also measuring the release of the catecholamine neurotransmitter, dopamine, fast-scan cyclic voltammetry at carbon-fiber microelectrodes (FSCV) was used to electrochemically characterize 4-hydroxyphenylacetic acid (4HPAA) in the absence and presence of dopamine. 4HPAA is a by-product formed during the process of photoactivation of p-hydroxyphenacyl-based caged compounds, such as p-hydroxyphenylglutamate (pHP-Glu). Our data suggest that the oxidation of 4HPAA occurs through the formation of a conjugated species. Moreover, we found that a triangular waveform of -0.4 V to +1.3 V to -0.4 V at 600 V s(-1), repeated every 100 ms, provided an oxidation current of 4HPAA that was enhanced with a limit of detection of 100 nM, while also allowing the detection and quantitation of dopamine within the same scan. Along with quantifying 4HPAA in biological preparations, the results from this work will allow the electrochemical measurement of photoactivation reactions that generate 4HPAA as a by-product as well as provide a framework for measuring the photorelease of electroactive by-products from caged compounds that incorporate other chromophores.

  12. Simultaneous Measurement and Quantitation of 4-Hydroxyphenylacetic acid and Dopamine with Fast-Scan Cyclic Voltammetry

    PubMed Central

    Shin, Mimi; Kaplan, Sam V.; Raider, Kayla D.; Johnson, Michael A.

    2015-01-01

    Caged compounds have been used extensively to investigate neuronal function in a variety of preparations, including cell culture, ex vivo tissue samples, and in vivo. As a first step toward electrochemically measuring the extent of caged compound photoactivation while also measuring the release of the catecholamine neurotransmitter, dopamine, fast-scan cyclic voltammetry at carbon-fiber microelectrodes (FSCV) was used to electrochemically characterize 4-hydroxyphenylacetic acid (4HPAA) in the absence and presence of dopamine. 4HPAA is a by-product formed during the process of photoactivation of p-hydroxyphenylacyl-based caged compounds, such as p-hydroxyphenylglutamate (pHP-Glu). Our data suggest that the oxidation of 4HPAA occurs through the formation of a conjugated species. Moreover, we found that a triangular waveform of −0.4 V to +1.3 V to −0.4 V at 600 V/s, repeated every 100 ms, provided an oxidation current of 4HPAA that was enhanced with a limit of detection of 100 nM, while also allowing the detection and quantitation of dopamine within the same scan. Along with quantifying 4HPAA in biological preparations, the results from this work will allow the electrochemical measurement of photoactivation reactions that generate 4HPAA as a by-product as well as provide a framework for measuring the photorelease of electroactive by-products from caged compounds that incorporate other chromophores. PMID:25785694

  13. Quantitative flaw characterization with scanning laser acoustic microscopy

    SciTech Connect

    Generazio, E.R.; Roth, D.J.

    1986-06-01

    Surface roughness and diffraction are two factors that have been observed to affect the accuracy of flaw characterization with scanning laser acoustic microscopy. Inaccuracies can arise when the surface of the test sample is acoustically rough. It is shown that, in this case, Snell's law is no longer valid for determining the direction of sound propagation within the sample. The relationship between the direction of sound propagation within the sample, the apparent flaw depth, and the sample's surface roughness is investigated. Diffraction effects can mask the acoustic images of minute flaws and make it difficult to establish their size, depth, and other characteristics. It is shown that for Fraunhofer diffraction conditions the acoustic image of a subsurface defect corresponds to a two-dimensional Fourier transform. Transforms based on simulated flaws are used to infer the size and shape of the actual flaw. 15 references.

  14. Quantitative flaw characterization with scanning laser acoustic microscopy

    NASA Technical Reports Server (NTRS)

    Generazio, E. R.; Roth, D. J.

    1986-01-01

    Surface roughness and diffraction are two factors that have been observed to affect the accuracy of flaw characterization with scanning laser acoustic microscopy. Inaccuracies can arise when the surface of the test sample is acoustically rough. It is shown that, in this case, Snell's law is no longer valid for determining the direction of sound propagation within the sample. The relationship between the direction of sound propagation within the sample, the apparent flaw depth, and the sample's surface roughness is investigated. Diffraction effects can mask the acoustic images of minute flaws and make it difficult to establish their size, depth, and other characteristics. It is shown that for Fraunhofer diffraction conditions the acoustic image of a subsurface defect corresponds to a two-dimensional Fourier transform. Transforms based on simulated flaws are used to infer the size and shape of the actual flaw.

  15. Quantitative flaw characterization with scanning laser acoustic microscopy

    NASA Technical Reports Server (NTRS)

    Generazio, E. R.; Roth, D. J.

    1986-01-01

    Surface roughness and diffraction are two factors that have been observed to affect the accuracy of flaw characterization with scanning laser acoustic microscopy. In accuracies can arise when the surface of the test sample is acoustically rough. It is shown that, in this case, Snell's law is no longer valid for determining the direction of sound propagation within the sample. The relationship between the direction of sound propagation within the sample, the apparent flaw depth, and the sample's surface roughness is investigated. Diffraction effects can mask the acoustic images of minute flaws and make it difficult to establish their size, depth, and other characteristics. It is shown that for Fraunhofer diffraction conditions the acoustic image of a subsurface defect corresponds to a two-dimensional Fourier transform. Transforms based on simulated flaws are used to infer the size and shape of the actual flaw.

  16. High Resolution Quantitative Angle-Scanning Widefield Surface Plasmon Microscopy

    PubMed Central

    Tan, Han-Min; Pechprasarn, Suejit; Zhang, Jing; Pitter, Mark C.; Somekh, Michael G.

    2016-01-01

    We describe the construction of a prismless widefield surface plasmon microscope; this has been applied to imaging of the interactions of protein and antibodies in aqueous media. The illumination angle of spatially incoherent diffuse laser illumination was controlled with an amplitude spatial light modulator placed in a conjugate back focal plane to allow dynamic control of the illumination angle. Quantitative surface plasmon microscopy images with high spatial resolution were acquired by post-processing a series of images obtained as a function of illumination angle. Experimental results are presented showing spatially and temporally resolved binding of a protein to a ligand. We also show theoretical results calculated by vector diffraction theory that accurately predict the response of the microscope on a spatially varying sample thus allowing proper quantification and interpretation of the experimental results. PMID:26830146

  17. Photoelectric AFP quantitative detection of immunochromatographic assay strip

    NASA Astrophysics Data System (ADS)

    Du, Min; Jiang, Hai-yan

    2006-09-01

    An immunochromatographic assay (ICA) system for quantitative determination of analyte in sample is described in this paper. The designed system not only quantitatively detect target analytes in sample but also enhance detection precision in immunochromatographic assay technique.

  18. Influence analysis in quantitative trait loci detection

    PubMed Central

    Dou, Xiaoling; Kuriki, Satoshi; Maeno, Akiteru; Takada, Toyoyuki; Shiroishi, Toshihiko

    2014-01-01

    This paper presents systematic methods for the detection of influential individuals that affect the log odds (LOD) score curve. We derive general formulas of influence functions for profile likelihoods and introduce them into two standard quantitative trait locus detection methods—the interval mapping method and single marker analysis. Besides influence analysis on specific LOD scores, we also develop influence analysis methods on the shape of the LOD score curves. A simulation-based method is proposed to assess the significance of the influence of the individuals. These methods are shown useful in the influence analysis of a real dataset of an experimental population from an F2 mouse cross. By receiver operating characteristic analysis, we confirm that the proposed methods show better performance than existing diagnostics. PMID:24740424

  19. Influence analysis in quantitative trait loci detection.

    PubMed

    Dou, Xiaoling; Kuriki, Satoshi; Maeno, Akiteru; Takada, Toyoyuki; Shiroishi, Toshihiko

    2014-07-01

    This paper presents systematic methods for the detection of influential individuals that affect the log odds (LOD) score curve. We derive general formulas of influence functions for profile likelihoods and introduce them into two standard quantitative trait locus detection methods-the interval mapping method and single marker analysis. Besides influence analysis on specific LOD scores, we also develop influence analysis methods on the shape of the LOD score curves. A simulation-based method is proposed to assess the significance of the influence of the individuals. These methods are shown useful in the influence analysis of a real dataset of an experimental population from an F2 mouse cross. By receiver operating characteristic analysis, we confirm that the proposed methods show better performance than existing diagnostics. © 2014 The Author. Biometrical Journal published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Improvement in Radar Detection Under Scan to Scan Processing and Scan Rate Reduction

    DTIC Science & Technology

    1991-06-01

    Swerling Case 4 Target Model ........................... .122 3.3-7. Detection Performance of the Baseline, Non - Fluctuating (Marcum) Target Model ...earlier using the Mallett and Brennan approach. Both the Mallett and Brennan and DiFranco and Rubin teams assume that there is no radar line of sight ...false alarm probability and complicates determination of the optimum frame time. Imposing a line of sight limitation or time constraint in achieving the

  1. Quantitative impedance characterization of sub-10 nm scale capacitors and tunnel junctions with an interferometric scanning microwave microscope.

    PubMed

    Wang, Fei; Clément, Nicolas; Ducatteau, Damien; Troadec, David; Tanbakuchi, Hassan; Legrand, Bernard; Dambrine, Gilles; Théron, Didier

    2014-10-10

    We present a method to characterize sub-10 nm capacitors and tunnel junctions by interferometric scanning microwave microscopy (iSMM) at 7.8 GHz. At such device scaling, the small water meniscus surrounding the iSMM tip should be reduced by proper tip tuning. Quantitative impedance characterization of attofarad range capacitors is achieved using an 'on-chip' calibration kit facing thousands of nanodevices. Nanoscale capacitors and tunnel barriers were detected through variations in the amplitude and phase of the reflected microwave signal, respectively. This study promises quantitative impedance characterization of a wide range of emerging functional nanoscale devices.

  2. Quantitative Scanning Transmission Electron Microscopy of Electronic and Nanostructured Materials

    NASA Astrophysics Data System (ADS)

    Yankovich, Andrew B.

    Electronic and nanostructured materials have been investigated using advanced scanning transmission electron microscopy (STEM) techniques. The first topic is the microstructure of Ga and Sb-doped ZnO. Ga-doped ZnO is a candidate transparent conducting oxide material. The microstructure of GZO thin films grown by MBE under different growth conditions and different substrates were examined using various electron microscopy (EM) techniques. The microstructure, prevalent defects, and polarity in these films strongly depend on the growth conditions and substrate. Sb-doped ZnO nanowires have been shown to be the first route to stable p-type ZnO. Using Z-contrast STEM, I have showed that an unusual microstructure of Sb-decorated head-to-head inversion domain boundaries and internal voids contain all the Sb in the nanowires and cause the p-type conduction. InGaN thin films and InGaN / GaN quantum wells (QW) for light emitting diodes are the second topic. Low-dose Z-contrast STEM, PACBED, and EDS on InGaN QW LED structures grown by MOCVD show no evidence for nanoscale composition variations, contradicting previous reports. In addition, a new extended defect in GaN and InGaN was discovered. The defect consists of a faceted pyramid-shaped void that produces a threading dislocation along the [0001] growth direction, and is likely caused by carbon contamination during growth. Non-rigid registration (NRR) and high-precision STEM of nanoparticles is the final topic. NRR is a new image processing technique that corrects distortions arising from the serial nature of STEM acquisition that previously limited the precision of locating atomic columns and counting the number of atoms in images. NRR was used to demonstrate sub-picometer precision in STEM images of single crystal Si and GaN, the best achieved in EM. NRR was used to measure the atomic surface structure of Pt nanoacatalysts and Au nanoparticles, which revealed new bond length variation phenomenon of surface atoms. In

  3. Fluorescence detection in capillary arrays based on galvanometer step scanning.

    PubMed

    Xue, G; Yeung, E S

    2001-10-01

    A computer-controlled galvanometer scanner is adapted for scanning a focused laser beam across a 96-capillary array for laser-induced fluorescence detection. The signal at a single photomultiplier tube is temporally sorted to distinguish among the capillaries. The limit of detection for fluoresceins is 3 x 10(-11) M (S/N = 3) for 5 mW of total laser power scanned at 4 Hz. The observed cross-talk among capillaries is 0.2%. Advantages include the efficient utilization of light due to the high duty-cycle of step scan, good detection performance due to the reduction of stray light, ruggedness due to the small mass of the galvanometer mirror, low cost due to the simplicity of components, and flexibility due to the independent paths for excitation and emission.

  4. Hybrid detection of lung nodules on CT scan images

    SciTech Connect

    Lu, Lin; Tan, Yongqiang; Schwartz, Lawrence H.; Zhao, Binsheng

    2015-09-15

    Purpose: The diversity of lung nodules poses difficulty for the current computer-aided diagnostic (CAD) schemes for lung nodule detection on computed tomography (CT) scan images, especially in large-scale CT screening studies. We proposed a novel CAD scheme based on a hybrid method to address the challenges of detection in diverse lung nodules. Methods: The hybrid method proposed in this paper integrates several existing and widely used algorithms in the field of nodule detection, including morphological operation, dot-enhancement based on Hessian matrix, fuzzy connectedness segmentation, local density maximum algorithm, geodesic distance map, and regression tree classification. All of the adopted algorithms were organized into tree structures with multi-nodes. Each node in the tree structure aimed to deal with one type of lung nodule. Results: The method has been evaluated on 294 CT scans from the Lung Image Database Consortium (LIDC) dataset. The CT scans were randomly divided into two independent subsets: a training set (196 scans) and a test set (98 scans). In total, the 294 CT scans contained 631 lung nodules, which were annotated by at least two radiologists participating in the LIDC project. The sensitivity and false positive per scan for the training set were 87% and 2.61%. The sensitivity and false positive per scan for the testing set were 85.2% and 3.13%. Conclusions: The proposed hybrid method yielded high performance on the evaluation dataset and exhibits advantages over existing CAD schemes. We believe that the present method would be useful for a wide variety of CT imaging protocols used in both routine diagnosis and screening studies.

  5. Application of Scan Statistics to Detect Suicide Clusters in Australia

    PubMed Central

    Cheung, Yee Tak Derek; Spittal, Matthew J.; Williamson, Michelle Kate; Tung, Sui Jay; Pirkis, Jane

    2013-01-01

    Background Suicide clustering occurs when multiple suicide incidents take place in a small area or/and within a short period of time. In spite of the multi-national research attention and particular efforts in preparing guidelines for tackling suicide clusters, the broader picture of epidemiology of suicide clustering remains unclear. This study aimed to develop techniques in using scan statistics to detect clusters, with the detection of suicide clusters in Australia as example. Methods and Findings Scan statistics was applied to detect clusters among suicides occurring between 2004 and 2008. Manipulation of parameter settings and change of area for scan statistics were performed to remedy shortcomings in existing methods. In total, 243 suicides out of 10,176 (2.4%) were identified as belonging to 15 suicide clusters. These clusters were mainly located in the Northern Territory, the northern part of Western Australia, and the northern part of Queensland. Among the 15 clusters, 4 (26.7%) were detected by both national and state cluster detections, 8 (53.3%) were only detected by the state cluster detection, and 3 (20%) were only detected by the national cluster detection. Conclusions These findings illustrate that the majority of spatial-temporal clusters of suicide were located in the inland northern areas, with socio-economic deprivation and higher proportions of indigenous people. Discrepancies between national and state/territory cluster detection by scan statistics were due to the contrast of the underlying suicide rates across states/territories. Performing both small-area and large-area analyses, and applying multiple parameter settings may yield the maximum benefits for exploring clusters. PMID:23342098

  6. A gold nanoparticle-based semi-quantitative and quantitative ultrasensitive paper sensor for the detection of twenty mycotoxins.

    PubMed

    Kong, Dezhao; Liu, Liqiang; Song, Shanshan; Suryoprabowo, Steven; Li, Aike; Kuang, Hua; Wang, Libing; Xu, Chuanlai

    2016-03-07

    A semi-quantitative and quantitative multi-immunochromatographic (ICA) strip detection assay was developed for the simultaneous detection of twenty types of mycotoxins from five classes, including zearalenones (ZEAs), deoxynivalenols (DONs), T-2 toxins (T-2s), aflatoxins (AFs), and fumonisins (FBs), in cereal food samples. Sensitive and specific monoclonal antibodies were selected for this assay. The semi-quantitative results were obtained within 20 min by the naked eye, with visual limits of detection for ZEAs, DONs, T-2s, AFs and FBs of 0.1-0.5, 2.5-250, 0.5-1, 0.25-1 and 2.5-10 μg kg(-1), and cut-off values of 0.25-1, 5-500, 1-10, 0.5-2.5 and 5-25 μg kg(-1), respectively. The quantitative results were obtained using a hand-held strip scan reader, with the calculated limits of detection for ZEAs, DONs, T-2s, AFs and FBs of 0.04-0.17, 0.06-49, 0.15-0.22, 0.056-0.49 and 0.53-1.05 μg kg(-1), respectively. The analytical results of spiked samples were in accordance with the accurate content in the simultaneous detection analysis. This newly developed ICA strip assay is suitable for the on-site detection and rapid initial screening of mycotoxins in cereal samples, facilitating both semi-quantitative and quantitative determination.

  7. Quantitative crystallinity determination for E1010, a novel carbapenem antibiotic, using differential scanning calorimetry.

    PubMed

    Kushida, Ikuo

    2012-03-01

    The objective of this study was to develop a quantitative crystallinity analysis method for the bulk drug of E1010 ((+)-(4R,5S,6S)-6-[(R)-1-hydroxyethyl]-3-[(2S,4S)-2-[(R)-1-hydroxy-1-[(R)-pyrrolidin-3 -yl]methyl]pyrrolidin-4-yl]thio-4-methyl-7-oxo-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid monohydrochloride), a novel carbapenem antibiotic. X-ray analyses, thermal analyses and hygroscopicity measurements were used to elucidate the crystal structure and the solid state properties. To develop a quantitative method for the crystallinity of E1010 bulk drug, the relationship between enthalpy change obtained by differential scanning calorimetry (DSC) and crystalline form ratio was investigated. E1010 bulk drug was found to exist in a crystalline trihydrate formed in two layers, i.e. a layer of E1010 free form, and a layer consisting of chloride ions and water molecules. The thermal analysis showed an endothermic peak derived from dehydration with the loss of crystal lattices at around 100°C as an onset. The enthalpy change value for the endothermic peak correlated well with crystalline content in binary physical mixtures of the crystalline trihydrate and the amorphous form. In addition, for nine lots of the bulk drug, a positive correlation between the enthalpy change and chemical stability in the solid state was observed. This quantitative analysis of crystallinity using DSC could be applicable for the quality control of the bulk drug to detect variability among manufacturing batches and to estimate the chemical stability of partially amorphous samples. © 2011 The Author. JPP © 2011 Royal Pharmaceutical Society.

  8. Quantitative profiling of phospholipids by multiple precursor ion scanning on a hybrid quadrupole time-of-flight mass spectrometer.

    PubMed

    Ekroos, Kim; Chernushevich, Igor V; Simons, Kai; Shevchenko, Andrej

    2002-03-01

    A hybrid quadrupole time-of-flight mass spectrometer featured with ion trapping capabilities was employed for quantitative profiling of total extracts of endogenous phospholipids. Simultaneous acquisition of precursor ion spectra of multiple fragment ions allowed detection of major classes of phospholipids in a single experiment. Relative changes in their concentration were monitored using a mixture of isotopically labeled endogenous lipids as a comprehensive internal standard. Precursor ion scanning spectra were acquired simultaneously for acyl anions of major fatty acids in negative ion mode and identified the fatty acid moieties and their relative position at the glycerol backbone in individual lipid species. Taken together, a combination of multiple precursor ion scans allowed quantitative monitoring of major perturbation in phospholipid composition and elucidating of molecular heterogeneity of individual lipid species.

  9. Pre- and postoperative evaluation of renal function in patients with staghorn calculi utilizing quantitative renal scanning.

    PubMed

    Stage, K H; Lewis, S

    1981-01-01

    Differential quantitative renal scans using 99-technetium diethylene triaminepentaacetic acid (DTPA) or 131I Hippuran were obtained properatively on 12 patients with unilateral or bilateral staghorn calculi. Of the 14 renal units studied, 12 kidneys underwent anatrophic nephrolithotomy, pyelolithotomy, or a combination of both techniques; 2 patients underwent nephrectomy based on poor function of the affected side preoperatively. Postoperative follow-up scans were obtained on the 12 kidneys undergoing stone cleanout. Seven of 12 kidneys (58 per cent) studied pre- and postoperatively showed moderate to significant improvement in per cent contribution to total renal function. Seven of 10 kidneys (70 per cent) studied pre- and postoperatively showed improvement in glomerular filtration rate or effective renal plasma flow. The scans revelaed no dramatic difference in postoperative functional loss between pyelolithotomy and anatrophic nephrolithotomy. The computerizewd quantitative renal scan helps in selection of surgical technique and objective postoperative assessment of surgical results.

  10. Asteroid detection using a single multi-wavelength CCD scan

    NASA Astrophysics Data System (ADS)

    Melton, Jonathan

    2016-09-01

    Asteroid detection is a topic of great interest due to the possibility of diverting possibly dangerous asteroids or mining potentially lucrative ones. Currently, asteroid detection is generally performed by taking multiple images of the same patch of sky separated by 10-15 minutes, then subtracting the images to find movement. However, this is time consuming because of the need to revisit the same area multiple times per night. This paper describes an algorithm that can detect asteroids using a single CCD camera scan, thus cutting down on the time and cost of an asteroid survey. The algorithm is based on the fact that some telescopes scan the sky at multiple wavelengths with a small time separation between the wavelength components. As a result, an object moving with sufficient speed will appear in different places in different wavelength components of the same image. Using image processing techniques we detect the centroids of points of light in the first component and compare these positions to the centroids in the other components using a nearest neighbor algorithm. The algorithm was used on a test set of 49 images obtained from the Sloan telescope in New Mexico and found 100% of known asteroids with only 3 false positives. This algorithm has the advantage of decreasing the amount of time required to perform an asteroid scan, thus allowing more sky to be scanned in the same amount of time or freeing a telescope for other pursuits.

  11. Primary detection of hardwood log defects using laser surface scanning

    Treesearch

    Ed Thomas; Liya Thomas; Lamine Mili; Roger Ehrich; A. Lynn Abbott; Clifford Shaffer; Clifford Shaffer

    2003-01-01

    The use of laser technology to scan hardwood log surfaces for defects holds great promise for improving processing efficiency and the value and volume of lumber produced. External and internal defect detection to optimize hardwood log and lumber processing is one of the top four technological needs in the nation's hardwood industry. The location, type, and...

  12. PE-CMOS based C-scan ultrasound for foreign object detection in soft tissue.

    PubMed

    Liu, Chu-Chuan; Lo, Shih-Chung Ben; Freedman, Matthew T; Lasser, Marvin E; Kula, John; Sarcone, Anita; Wang, Yue

    2010-01-01

    In this paper, we introduce a C-scan ultrasound prototype and three imaging modalities for the detection of foreign objects inserted in porcine soft tissue. The object materials include bamboo, plastics, glass and aluminum alloys. The images of foreign objects were acquired using the C-scan ultrasound, a portable B-scan ultrasound, film-based radiography, and computerized radiography. The C-scan ultrasound consists of a plane wave transducer, a compound acoustic lens system, and a newly developed ultrasound sensor array based on the complementary metal-oxide semiconductor coated with piezoelectric material (PE-CMOS). The contrast-to-noise ratio (CNR) of the images were analyzed to quantitatively evaluate the detectability using different imaging modalities. The experimental results indicate that the C-scan prototype has better CNR values in 4 out of 7 objects than other modalities. Specifically, the C-scan prototype provides more detail information of the soft tissues without the speckle artifacts that are commonly seen with conventional B-scan ultrasound, and has the same orientation as the standard radiographs but without ionizing radiation.

  13. Line-scanning Raman imaging spectroscopy for detection of fingerprints.

    PubMed

    Deng, Sunan; Liu, Le; Liu, Zhiyi; Shen, Zhiyuan; Li, Guohua; He, Yonghong

    2012-06-10

    Fingerprints are the best form of personal identification for criminal investigation purposes. We present a line-scanning Raman imaging system and use it to detect fingerprints composed of β-carotene and fish oil on different substrates. Although the line-scanning Raman system has been used to map the distribution of materials such as polystyrene spheres and minerals within geological samples, this is the first time to our knowledge that the method is used in imaging fingerprints. Two Raman peaks of β-carotene (501.2, 510.3 nm) are detected and the results demonstrate that both peaks can generate excellent images with little difference between them. The system operates at a spectra resolution of about 0.4 nm and can detect β-carotene signals in petroleum ether solution with the limit of detection of 3.4×10(-9) mol/L. The results show that the line-scanning Raman imaging spectroscopy we have built has a high accuracy and can be used in the detection of latent fingerprints in the future.

  14. Detection of defects in optics based on scanning

    NASA Astrophysics Data System (ADS)

    Zhou, Bin; Bai, Jian; Liang, Yiyong; Wang, Kaiwei; Lu, Qianbo; Zhang, Sai

    2015-08-01

    In this paper, a method to detect internal pocks and bubbles of optical elements based on laser line source scanning is proposed. In dark field environment, a laser line source is used to illuminate from one side of the glass under test, a high-resolution CCD camera is used to take pictures in front of the glass sample. Images which contain information of defects are acquired through rough scanning and accurate scanning. Accurate three-dimensional coordinates of the internal defects are acquired after image processing, which descript the characteristic information of internal defects quantificationally. Compared with the microscope imaging measurement, this proposed detection of defects in optics based on laser line source scanning has a relative aberration smaller than 2%. In addition, the detection time is approximately reduced to 20 minutes from 1 hour dramatically. The analysis indicates that the error of the position of defects is much smaller than the size of them, which means the position of the defects can be acquired accurately by this approach.

  15. Depth resolution enhancement in double-detection optical scanning holography.

    PubMed

    Ou, Haiyan; Poon, Ting-Chung; Wong, Kenneth K Y; Lam, Edmund Y

    2013-05-01

    We propose an optical scanning holography system with enhanced axial resolution using two detections at different depths. By scanning the object twice, we can obtain two different sets of Fresnel zone plates to sample the same object, which in turn provides more information for the sectional image reconstruction process. We develop the computation algorithm that makes use of such information, solving a constrained optimization problem using the conjugate gradient method. Simulation results show that this method can achieve a depth resolution up to 1 μm.

  16. [Using of scanning electron microscopy for detection of gunshot residue].

    PubMed

    Havel, J; Vajtr, D; Starý, V; Vrána, J; Zelenka, K; Adámek, T

    2006-07-01

    Scanning electron microscope improves the possibility of investigation of surroundings near of gunshot wounds in forensic medicine, it is the next subsequent method for differentiating of area of entrance and exit wound, supplemental method for determination of firing distance, permit of detection (GSR) on the hand of shooter and ensured describing of samples and their stored. Detection of GSR provides many information about composition of bullet and primer. Authors are demonstrating the possibility of detection of GSR on experimental shooting to the krupon (pigs' skin) in different situation (such as in a room and in outside area) and using of different weapon (hand gun CZ No.75 and machine gun No.58).

  17. Super-resolution scanning laser microscopy through virtually structured detection

    PubMed Central

    Lu, Rong-Wen; Wang, Ben-Quan; Zhang, Qiu-Xiang; Yao, Xin-Cheng

    2013-01-01

    High resolution microscopy is essential for advanced study of biological structures and accurate diagnosis of medical diseases. The spatial resolution of conventional microscopes is light diffraction limited. Structured illumination has been extensively explored to break the diffraction limit in wide field light microscopy. However, deployable application of the structured illumination in scanning laser microscopy is challenging due to the complexity of the illumination system and possible phase errors in sequential illumination patterns required for super-resolution reconstruction. We report here a super-resolution scanning laser imaging system which employs virtually structured detection (VSD) to break the diffraction limit. Without the complexity of structured illumination, VSD provides an easy, low-cost and phase-artifact free strategy to achieve super-resolution in scanning laser microscopy. PMID:24049688

  18. Colitis detection on abdominal CT scans by rich feature hierarchies

    NASA Astrophysics Data System (ADS)

    Liu, Jiamin; Lay, Nathan; Wei, Zhuoshi; Lu, Le; Kim, Lauren; Turkbey, Evrim; Summers, Ronald M.

    2016-03-01

    Colitis is inflammation of the colon due to neutropenia, inflammatory bowel disease (such as Crohn disease), infection and immune compromise. Colitis is often associated with thickening of the colon wall. The wall of a colon afflicted with colitis is much thicker than normal. For example, the mean wall thickness in Crohn disease is 11-13 mm compared to the wall of the normal colon that should measure less than 3 mm. Colitis can be debilitating or life threatening, and early detection is essential to initiate proper treatment. In this work, we apply high-capacity convolutional neural networks (CNNs) to bottom-up region proposals to detect potential colitis on CT scans. Our method first generates around 3000 category-independent region proposals for each slice of the input CT scan using selective search. Then, a fixed-length feature vector is extracted from each region proposal using a CNN. Finally, each region proposal is classified and assigned a confidence score with linear SVMs. We applied the detection method to 260 images from 26 CT scans of patients with colitis for evaluation. The detection system can achieve 0.85 sensitivity at 1 false positive per image.

  19. Quantitative phase tomography by using x-ray microscope with Foucault knife-edge scanning filter

    SciTech Connect

    Watanabe, Norio; Tsuburaya, Yuji; Shimada, Akihiro; Aoki, Sadao

    2016-01-28

    Quantitative phase tomography was evaluated by using a differential phase microscope with a Foucault knife-edge scanning filter. A 3D x-ray phase image of polystyrene beads was obtained at 5.4 keV. The reconstructed refractive index was fairly good agreement with the Henke’s tabulated data.

  20. Quantitative phase tomography by using x-ray microscope with Foucault knife-edge scanning filter

    NASA Astrophysics Data System (ADS)

    Watanabe, Norio; Tsuburaya, Yuji; Shimada, Akihiro; Aoki, Sadao

    2016-01-01

    Quantitative phase tomography was evaluated by using a differential phase microscope with a Foucault knife-edge scanning filter. A 3D x-ray phase image of polystyrene beads was obtained at 5.4 keV. The reconstructed refractive index was fairly good agreement with the Henke's tabulated data.

  1. Quantitative Phase Imaging with a Scanning Transmission X-Ray Microscope

    PubMed Central

    de Jonge, M. D.; Hornberger, B.; Holzner, C.; Legnini, D.; Paterson, D.; McNulty, I.; Jacobsen, C.; Vogt, S.

    2010-01-01

    We obtain quantitative phase reconstructions from differential phase contrast images obtained with a scanning transmission x-ray microscope and 2.5 keV x rays. The theoretical basis of the technique is presented along with measurements and their interpretation. PMID:18518198

  2. Hyperspectral imaging fluorescence excitation scanning for colon cancer detection

    NASA Astrophysics Data System (ADS)

    Leavesley, Silas J.; Walters, Mikayla; Lopez, Carmen; Baker, Thomas; Favreau, Peter F.; Rich, Thomas C.; Rider, Paul F.; Boudreaux, Carole W.

    2016-10-01

    Optical spectroscopy and hyperspectral imaging have shown the potential to discriminate between cancerous and noncancerous tissue with high sensitivity and specificity. However, to date, these techniques have not been effectively translated to real-time endoscope platforms. Hyperspectral imaging of the fluorescence excitation spectrum represents new technology that may be well suited for endoscopic implementation. However, the feasibility of detecting differences between normal and cancerous mucosa using fluorescence excitation-scanning hyperspectral imaging has not been evaluated. The goal of this study was to evaluate the initial feasibility of using fluorescence excitation-scanning hyperspectral imaging for measuring changes in fluorescence excitation spectrum concurrent with colonic adenocarcinoma using a small pre-pilot-scale sample size. Ex vivo analysis was performed using resected pairs of colorectal adenocarcinoma and normal mucosa. Adenocarcinoma was confirmed by histologic evaluation of hematoxylin and eosin (H&E) permanent sections. Specimens were imaged using a custom hyperspectral imaging fluorescence excitation-scanning microscope system. Results demonstrated consistent spectral differences between normal and cancerous tissues over the fluorescence excitation range of 390 to 450 nm that could be the basis for wavelength-dependent detection of colorectal cancers. Hence, excitation-scanning hyperspectral imaging may offer an alternative approach for discriminating adenocarcinoma from surrounding normal colonic mucosa, but further studies will be required to evaluate the accuracy of this approach using a larger patient cohort.

  3. Improved detection of differentially expressed genes in microarray experiments through multiple scanning and image integration

    PubMed Central

    Romualdi, Chiara; Trevisan, Silvia; Celegato, Barbara; Costa, Germano; Lanfranchi, Gerolamo

    2003-01-01

    The variability of results in microarray technology is in part due to the fact that independent scans of a single hybridised microarray give spot images that are not quite the same. To solve this problem and turn it to our advantage, we introduced the approach of multiple scanning and of image integration of microarrays. To this end, we have developed specific software that creates a virtual image that statistically summarises a series of consecutive scans of a microarray. We provide evidence that the use of multiple imaging (i) enhances the detection of differentially expressed genes; (ii) increases the image homogeneity; and (iii) reveals false-positive results such as differentially expressed genes that are detected by a single scan but not confirmed by successive scanning replicates. The increase in the final number of differentially expressed genes detected in a microarray experiment with this approach is remarkable; 50% more for microarrays hybridised with targets labelled by reverse transcriptase, and 200% more for microarrays developed with the tyramide signal amplification (TSA) technique. The results have been confirmed by semi-quantitative RT–PCR tests. PMID:14627839

  4. CT scan range estimation using multiple body parts detection: let PACS learn the CT image content.

    PubMed

    Wang, Chunliang; Lundström, Claes

    2016-02-01

    The aim of this study was to develop an efficient CT scan range estimation method that is based on the analysis of image data itself instead of metadata analysis. This makes it possible to quantitatively compare the scan range of two studies. In our study, 3D stacks are first projected to 2D coronal images via a ray casting-like process. Trained 2D body part classifiers are then used to recognize different body parts in the projected image. The detected candidate regions go into a structure grouping process to eliminate false-positive detections. Finally, the scale and position of the patient relative to the projected figure are estimated based on the detected body parts via a structural voting. The start and end lines of the CT scan are projected to a standard human figure. The position readout is normalized so that the bottom of the feet represents 0.0, and the top of the head is 1.0. Classifiers for 18 body parts were trained using 184 CT scans. The final application was tested on 136 randomly selected heterogeneous CT scans. Ground truth was generated by asking two human observers to mark the start and end positions of each scan on the standard human figure. When compared with the human observers, the mean absolute error of the proposed method is 1.2% (max: 3.5%) and 1.6% (max: 5.4%) for the start and end positions, respectively. We proposed a scan range estimation method using multiple body parts detection and relative structure position analysis. In our preliminary tests, the proposed method delivered promising results.

  5. Detecting damage in steel with scanning SQUID microscopy

    SciTech Connect

    Lee, Tae-Kyu; Clatterbuck, David; Morris Jr., J.W.; Shaw, T.J.; McDermott R.; Clarke, John

    2001-09-04

    A ''Holy Grail'' of NDE research is a non-destructive method for measuring fatigue damage prior to crack initiation. High-Tc scanning SQUID microscopy may be a useful tool. Because of the exceptional magnetic sensitivity of this technique, fatigue damage can be detected well before microcrack initiation, and in the absence of other obvious microstructure or property changes. Given the spatial resolution of the technique, undamaged material can be located and used to set internal standards.

  6. Toward quantitative electrochemical measurements on the nanoscale by scanning probe microscopy: environmental and current spreading effects.

    PubMed

    Arruda, Thomas M; Kumar, Amit; Jesse, Stephen; Veith, Gabriel M; Tselev, Alexander; Baddorf, Arthur P; Balke, Nina; Kalinin, Sergei V

    2013-09-24

    The application of electric bias across tip-surface junctions in scanning probe microscopy can readily induce surface and bulk electrochemical processes that can be further detected though changes in surface topography, Faradaic or conductive currents, or electromechanical strain responses. However, the basic factors controlling tip-induced electrochemical processes, including the relationship between applied tip bias and the thermodynamics of local processes, remains largely unexplored. Using the model Li-ion reduction reaction on the surface in Li-ion conducting glass ceramic, we explore the factors controlling Li-metal formation and find surprisingly strong effects of atmosphere and back electrode composition on the process. We find that reaction processes are highly dependent on the nature of the counter electrode and environmental conditions. Using a nondepleting Li counter electrode, Li particles could grow significantly larger and faster than a depleting counter electrode. Significant Li ion depletion leads to the inability for further Li reduction. Time studies suggest that Li diffusion replenishes the vacant sites after ∼12 h. These studies suggest the feasibility of SPM-based quantitative electrochemical studies under proper environmental controls, extending the concepts of ultramicroelectrodes to the single-digit nanometer scale.

  7. Primary detection of hardwood log defects using laser surface scanning

    NASA Astrophysics Data System (ADS)

    Thomas, Edward; Thomas, Liya; Mili, Lamine; Ehrich, Roger W.; Abbott, A. Lynn; Shaffer, Clifford

    2003-05-01

    The use of laser technology to scan hardwood log surfaces for defects holds great promise for improving processing efficiency and the value and volume of lumber produced. External and internal defect detection to optimize hardwood log and lumber processing is one of the top four technological needs in the nation"s hardwood industry. The location, type, and severity of defects on hardwood logs are the key indicators of log quality and value. These visual cues provide information about internal log characteristics and products for which the log is suitable. We scanned 162 logs with a high-resolution industrial four-head laser surface scanner. The resulting data sets contain hundreds of thousands of three-dimensional coordinate points. The size of the data and noise presented special problems during processing. Robust regression models were used to fit geometric shapes to the data. The estimated orthogonal distances between the fitted model and the log surface are converted to a two-dimensional image to facilitate defect detection. Using robust regression methods and standard image processing tools we have demonstrated that severe surface defects on hardwood logs can be detected using height and contour analyses of three-dimensional laser scan data.

  8. Street environment change detection from mobile laser scanning point clouds

    NASA Astrophysics Data System (ADS)

    Xiao, Wen; Vallet, Bruno; Brédif, Mathieu; Paparoditis, Nicolas

    2015-09-01

    Mobile laser scanning (MLS) has become a popular technique for road inventory, building modelling, infrastructure management, mobility assessment, etc. Meanwhile, due to the high mobility of MLS systems, it is easy to revisit interested areas. However, change detection using MLS data of street environment has seldom been studied. In this paper, an approach that combines occupancy grids and a distance-based method for change detection from MLS point clouds is proposed. Unlike conventional occupancy grids, our occupancy-based method models space based on scanning rays and local point distributions in 3D without voxelization. A local cylindrical reference frame is presented for the interpolation of occupancy between rays according to the scanning geometry. The Dempster-Shafer theory (DST) is utilized for both intra-data evidence fusion and inter-data consistency assessment. Occupancy of reference point cloud is fused at the location of target points and then the consistency is evaluated directly on the points. A point-to-triangle (PTT) distance-based method is combined to improve the occupancy-based method. Because it is robust to penetrable objects, e.g. vegetation, which cause self-conflicts when modelling occupancy. The combined method tackles irregular point density and occlusion problems, also eliminates false detections on penetrable objects.

  9. Surface flaw detection in structural ceramics by scanning photoacoustic spectroscopy

    NASA Technical Reports Server (NTRS)

    Khandelwal, P. K.; Heitman, P. W.; Wakefield, T. D.; Silversmith, A. J.

    1980-01-01

    Laser-scanned photoacoustic spectroscopy has been used to detect tightly closed surface cracks in three structural ceramic materials: sintered silicon nitride, reaction-bonded silicon nitride, and sintered silicon carbide. It is found that the amplitude of the photoacoustic signal from the flaws is greater for the silicon nitrides than for silicon carbide, which is attributed to the lower thermal diffusivity of silicon nitride as well as differences in the grain size distribution and chemical composition. Signal amplitude, reproducibility, and signal-to-noise ratio are acceptable for effective flaw detection

  10. Automated Detection of Ocular Alignment with Binocular Retinal Birefringence Scanning

    NASA Astrophysics Data System (ADS)

    Hunter, David G.; Shah, Ankoor S.; Sau, Soma; Nassif, Deborah; Guyton, David L.

    2003-06-01

    We previously developed a retinal birefringence scanning (RBS) device to detect eye fixation. The purpose of this study was to determine whether a new binocular RBS (BRBS) instrument can detect simultaneous fixation of both eyes. Control (nonmyopic and myopic) and strabismic subjects were studied by use of BRBS at a fixation distance of 45 cm. Binocularity (the percentage of measurements with bilateral fixation) was determined from the BRBS output. All nonstrabismic subjects with good quality signals had binocularity >75%. Binocularity averaged 5% in four subjects with strabismus (range of 0 -20%). BRBS may potentially be used to screen individuals for abnormal eye alignment.

  11. Automatic lung segmentation from thoracic computed tomography scans using a hybrid approach with error detection

    SciTech Connect

    Rikxoort, Eva M. van; Hoop, Bartjan de; Viergever, Max A.; Prokop, Mathias; Ginneken, Bram van

    2009-07-15

    Lung segmentation is a prerequisite for automated analysis of chest CT scans. Conventional lung segmentation methods rely on large attenuation differences between lung parenchyma and surrounding tissue. These methods fail in scans where dense abnormalities are present, which often occurs in clinical data. Some methods to handle these situations have been proposed, but they are too time consuming or too specialized to be used in clinical practice. In this article, a new hybrid lung segmentation method is presented that automatically detects failures of a conventional algorithm and, when needed, resorts to a more complex algorithm, which is expected to produce better results in abnormal cases. In a large quantitative evaluation on a database of 150 scans from different sources, the hybrid method is shown to perform substantially better than a conventional approach at a relatively low increase in computational cost.

  12. Detection Mechanism of Parallel Defect using Scanning Inductive Thermography

    NASA Astrophysics Data System (ADS)

    Zuo, Xianzhang; Song, Benchu; Hu, Yongjiang; He, Yunze

    2017-06-01

    Aiming at the requirement of workpiece integrity for parts processing line, on-line detection using inductive heating thermography for the moving workpieces on the assembly line is studied. In this paper, the detection mechanism of pulsed eddy current thermography for moving workpieces defects is analysed. A two-dimensional model of a magnetic material (45 steel), on which there is a crack parallel to the coil is established by the finite element software named COMSOL 5.2. By analysing the changes of the temperature curves, normalized curves and the temperature difference curves, the optimal detection area for parallel cracks is proposed. The consistency of the conclusions is verified by the experimental platform. The paper can provide a theoretical guidance for quantitative detection using eddy current thermography.

  13. Detection and characterisation of surface cracking using scanning laser techniques

    NASA Astrophysics Data System (ADS)

    Edwards, R. S.; Clough, A. R.; Rosli, M. H.; Hernandez-Valle, J. F.; Dutton, B.

    2012-05-01

    The use of lasers for generating and detecting ultrasound is becoming more established in non-destructive testing. However, there is still scope in developing the techniques to fully realise the benefits of non-contact measurements. One application is the detection of surface defects in metals; for example, rolling contact fatigue in rails, and surface cracking on billets or plates. We present measurements using a pulsed Nd:YAG laser to generate surface ultrasonic waves and an interferometer to detect the surface displacement on the sample, and investigate the interaction of Rayleigh or Lamb waves with surface defects. Signal enhancement in the near-field is observed for Rayleigh waves when either the generator or detector is close to a defect. For a scanned detector measurement, enhancement is observed due to constructive interference of the incident and reflected waves. For a scanned generator measurement, the change in generation conditions when the laser is over the defect also lead to an enhancement. In measurements of plate samples we observe similar enhancement effects whereby higher order modes are observed when the laser is above a defect. We discuss the implications of signal enhancements for detecting and characterising surface cracking.

  14. X-Ray Scan Detection for Cargo Integrity

    SciTech Connect

    Valencia, Juan D.; Miller, Steven D.

    2011-04-18

    ABSTRACT The increase of terrorism and its global impact has made the determination of the contents of cargo containers a necessity. Existing technology allows non-intrusive inspections to determine the contents of a container rapidly and accurately. However, some cargo shipments are exempt from such inspections. Hence, there is a need for a technology that enables rapid and accurate means of detecting whether such containers were non-intrusively inspected. Non-intrusive inspections are most commonly performed utilizing high powered X-ray equipment. The challenge is creating a device that can detect short duration X-ray scans while maintaining a portable, battery powered, low cost, and easy to use platform. The Pacific Northwest National Laboratory (PNNL) has developed a methodology and prototype device focused on this challenge. The prototype, developed by PNNL, is a battery powered electronic device that continuously measures its X-ray and Gamma exposure, calculates the dose equivalent rate, and makes a determination of whether the device has been exposed to the amount of radiation experienced during an X-ray inspection. Once an inspection is detected, the device will record a timestamp of the event and relay the information to authorized personnel via a visual alert, USB connection, and/or wireless communication. The results of this research demonstrate that PNNL’s prototype device can be effective at determining whether a container was scanned by X-ray equipment typically used for cargo container inspections. This paper focuses on laboratory measurements and test results acquired with the PNNL prototype device using several X-ray radiation levels. Keywords: Radiation, Scan, X-ray, Gamma, Detection, Cargo, Container, Wireless, RF

  15. Detection of windthrown trees using airborne laser scanning

    NASA Astrophysics Data System (ADS)

    Nyström, Mattias; Holmgren, Johan; Fransson, Johan E. S.; Olsson, Håkan

    2014-08-01

    In this study, a method has been developed for the detection of windthrown trees under a forest canopy, using the difference between two elevation models created from the same high density (65 points/m2) airborne laser scanning data. The difference image showing objects near the ground was created by subtracting a standard digital elevation model (DEM) from a more detailed DEM created using an active surface algorithm. Template matching was used to automatically detect windthrown trees in the difference image. The 54 ha study area is located in hemi-boreal forest in southern Sweden (Lat. 58°29‧ N, Long. 13°38‧ E) and is dominated by Norway spruce (Picea abies) with 3.5% deciduous species (mostly birch) and 1.7% Scots pine (Pinus sylvestris). The result was evaluated using 651 field measured windthrown trees. At individual tree level, the detection rate was 38% with a commission error of 36%. Much higher detection rates were obtained for taller trees; 89% of the trees taller than 27 m were detected. For pine the individual tree detection rate was 82%, most likely due to the more easily visible stem and lack of branches. When aggregating the results to 40 m square grid cells, at least one tree was detected in 77% of the grid cells which according to the field measurements contained one or more windthrown trees.

  16. A gold nanoparticle-based semi-quantitative and quantitative ultrasensitive paper sensor for the detection of twenty mycotoxins

    NASA Astrophysics Data System (ADS)

    Kong, Dezhao; Liu, Liqiang; Song, Shanshan; Suryoprabowo, Steven; Li, Aike; Kuang, Hua; Wang, Libing; Xu, Chuanlai

    2016-02-01

    A semi-quantitative and quantitative multi-immunochromatographic (ICA) strip detection assay was developed for the simultaneous detection of twenty types of mycotoxins from five classes, including zearalenones (ZEAs), deoxynivalenols (DONs), T-2 toxins (T-2s), aflatoxins (AFs), and fumonisins (FBs), in cereal food samples. Sensitive and specific monoclonal antibodies were selected for this assay. The semi-quantitative results were obtained within 20 min by the naked eye, with visual limits of detection for ZEAs, DONs, T-2s, AFs and FBs of 0.1-0.5, 2.5-250, 0.5-1, 0.25-1 and 2.5-10 μg kg-1, and cut-off values of 0.25-1, 5-500, 1-10, 0.5-2.5 and 5-25 μg kg-1, respectively. The quantitative results were obtained using a hand-held strip scan reader, with the calculated limits of detection for ZEAs, DONs, T-2s, AFs and FBs of 0.04-0.17, 0.06-49, 0.15-0.22, 0.056-0.49 and 0.53-1.05 μg kg-1, respectively. The analytical results of spiked samples were in accordance with the accurate content in the simultaneous detection analysis. This newly developed ICA strip assay is suitable for the on-site detection and rapid initial screening of mycotoxins in cereal samples, facilitating both semi-quantitative and quantitative determination.A semi-quantitative and quantitative multi-immunochromatographic (ICA) strip detection assay was developed for the simultaneous detection of twenty types of mycotoxins from five classes, including zearalenones (ZEAs), deoxynivalenols (DONs), T-2 toxins (T-2s), aflatoxins (AFs), and fumonisins (FBs), in cereal food samples. Sensitive and specific monoclonal antibodies were selected for this assay. The semi-quantitative results were obtained within 20 min by the naked eye, with visual limits of detection for ZEAs, DONs, T-2s, AFs and FBs of 0.1-0.5, 2.5-250, 0.5-1, 0.25-1 and 2.5-10 μg kg-1, and cut-off values of 0.25-1, 5-500, 1-10, 0.5-2.5 and 5-25 μg kg-1, respectively. The quantitative results were obtained using a hand-held strip scan

  17. Passive cylindrical scan by unphased diffraction-limited antennas for low-cost concealed weapon detection

    NASA Astrophysics Data System (ADS)

    Serenelli, Roberto

    2005-05-01

    This paper analyzes a simple low-cost scan system for concealed weapon detection (CWD) on a cooperative subject. The passive imaging system is based on a cylindrical sensing geometry, realized by mechanical vertical scan of a horizontal circle, filled with many diffraction-limited antennas surrounding the subject, over the whole body height. This system is dimensioned to scan an ideally coaxial cylindrical subject of known radius with a fixed spatial resolution. Several system parameters influence the capability of anomaly detection: horizontal spatial resolution (constrained by diffraction limitations on the sensing circle), vertical spatial resolution and radiometric sensitivity (both related to vertical scan settings). Spatial resolution calculations are carried out in function of the working frequency, and achievable resolutions according to diffraction limitations are discussed. A qualitative and quantitative study is done to determine how high radiometric sensitivity (achievable with well-established commercial components) could overcome the poor spatial resolution related to low working frequencies, in view of dielectric anomaly detection; the optimal dwell time (giving a good radiometric/spatial resolution trade-off) is evaluated. Sub-pixel resolution capabilities are briefly considered, together with a least square matching criterium. Performance of an alternative configuration, consisting of a rotating vertical array, is derived from the circular system. Finally, the data fusion from both configurations is suggested.

  18. Confocal scanning laser microscopy and quantitative image analysis: application to cream cheese microstructure investigation.

    PubMed

    Fenoul, F; Le Denmat, M; Hamdi, F; Cuvelier, G; Michon, C

    2008-04-01

    The naked eye observation of cream cheese confocal scanning laser microscopy images only provides qualitative information about its microstructure. Because those products are dense dairy gels, confocal scanning laser microscopy images of 2 different cream cheeses may appear close. Quantitative image analysis is then necessary to compensate for human eye deficiency (e.g., lack of precision, subjectivity). Two kinds of quantitative image analysis were performed in this study: high-order statistical methods and grayscale mathematical morphology. They were applied to study the microstructure of 3 different cream cheeses (same manufacturing process, same dry matter content, but different fat and protein contents). Advantages and drawbacks of both methods are reviewed. The way they may be used to describe cream cheese microstructure is also presented.

  19. Augmenting Amyloid PET Interpretations With Quantitative Information Improves Consistency of Early Amyloid Detection.

    PubMed

    Harn, Nicholas R; Hunt, Suzanne L; Hill, Jacqueline; Vidoni, Eric; Perry, Mark; Burns, Jeffrey M

    2017-08-01

    Establishing reliable methods for interpreting elevated cerebral amyloid-β plaque on PET scans is increasingly important for radiologists, as availability of PET imaging in clinical practice increases. We examined a 3-step method to detect plaque in cognitively normal older adults, focusing on the additive value of quantitative information during the PET scan interpretation process. Fifty-five F-florbetapir PET scans were evaluated by 3 experienced raters. Scans were first visually interpreted as having "elevated" or "nonelevated" plaque burden ("Visual Read"). Images were then processed using a standardized quantitative analysis software (MIMneuro) to generate whole brain and region of interest SUV ratios. This "Quantitative Read" was considered elevated if at least 2 of 6 regions of interest had an SUV ratio of more than 1.1. The final interpretation combined both visual and quantitative data together ("VisQ Read"). Cohen kappa values were assessed as a measure of interpretation agreement. Plaque was elevated in 25.5% to 29.1% of the 165 total Visual Reads. Interrater agreement was strong (kappa = 0.73-0.82) and consistent with reported values. Quantitative Reads were elevated in 45.5% of participants. Final VisQ Reads changed from initial Visual Reads in 16 interpretations (9.7%), with most changing from "nonelevated" Visual Reads to "elevated." These changed interpretations demonstrated lower plaque quantification than those initially read as "elevated" that remained unchanged. Interrater variability improved for VisQ Reads with the addition of quantitative information (kappa = 0.88-0.96). Inclusion of quantitative information increases consistency of PET scan interpretations for early detection of cerebral amyloid-β plaque accumulation.

  20. Minimum Detectable Activity for Tomographic Gamma Scanning System

    SciTech Connect

    Venkataraman, Ram; Smith, Susan; Kirkpatrick, J. M.; Croft, Stephen

    2015-01-01

    For any radiation measurement system, it is useful to explore and establish the detection limits and a minimum detectable activity (MDA) for the radionuclides of interest, even if the system is to be used at far higher values. The MDA serves as an important figure of merit, and often a system is optimized and configured so that it can meet the MDA requirements of a measurement campaign. The non-destructive assay (NDA) systems based on gamma ray analysis are no exception and well established conventions, such the Currie method, exist for estimating the detection limits and the MDA. However, the Tomographic Gamma Scanning (TGS) technique poses some challenges for the estimation of detection limits and MDAs. The TGS combines high resolution gamma ray spectrometry (HRGS) with low spatial resolution image reconstruction techniques. In non-imaging gamma ray based NDA techniques measured counts in a full energy peak can be used to estimate the activity of a radionuclide, independently of other counting trials. However, in the case of the TGS each “view” is a full spectral grab (each a counting trial), and each scan consists of 150 spectral grabs in the transmission and emission scans per vertical layer of the item. The set of views in a complete scan are then used to solve for the radionuclide activities on a voxel by voxel basis, over 16 layers of a 10x10 voxel grid. Thus, the raw count data are not independent trials any more, but rather constitute input to a matrix solution for the emission image values at the various locations inside the item volume used in the reconstruction. So, the validity of the methods used to estimate MDA for an imaging technique such as TGS warrant a close scrutiny, because the pair-counting concept of Currie is not directly applicable. One can also raise questions as to whether the TGS, along with other image reconstruction techniques which heavily intertwine data, is a suitable method if one expects to measure samples whose activities

  1. Automatic road edge detection from Mobile Laser Scanning (MLS)

    NASA Astrophysics Data System (ADS)

    Cabo, Carlos; García-Cortés, Silverio; Menéndez-Díaz, Agustín.; Ordoñez, Celestino

    2016-11-01

    In this article we present an algorithm for automatic road edge detection from MLS (Mobile Laser Scanning) data. The method takes advantage of linear structures derived from MLS point clouds. These lines are extracted from the point cloud and grouped following geometric restrictions. Then, the outlines of the groups are extracted as road edges. Finally, a moving window filter is applied to those points in order to remove outliers and delineate the road edge. The method was tested on an 800m stretch of road, and the results were checked through visual inspection. Correctness and completeness were 99.1% and 97.5%, respectively.

  2. Quantitative imaging of tissue sections using infrared scanning technology.

    PubMed

    Eaton, Samantha L; Cumyn, Elizabeth; King, Declan; Kline, Rachel A; Carpanini, Sarah M; Del-Pozo, Jorge; Barron, Rona; Wishart, Thomas M

    2016-01-01

    Quantification of immunohistochemically (IHC) labelled tissue sections typically yields semi-quantitative results. Visualising infrared (IR) 'tags', with an appropriate scanner, provides an alternative system where the linear nature of the IR fluorophore emittance enables realistic quantitative fluorescence IHC (QFIHC). Importantly, this new technology enables entire tissue sections to be scanned, allowing accurate area and protein abundance measurements to be calculated from rapidly acquired images. Here, some of the potential benefits of using IR-based tissue imaging are examined, and the following are demonstrated. Firstly, image capture and analysis using IR-based scanning technology yields comparable area-based quantification to those obtained from a modern high-resolution digital slide scanner. Secondly, IR-based dual target visualisation and expression-based quantification is rapid and simple. Thirdly, IR-based relative protein abundance QIHC measurements are an accurate reflection of tissue sample protein abundance, as demonstrated by comparison with quantitative fluorescent Western blotting data. In summary, it is proposed that IR-based QFIHC provides an alternative method of rapid whole-tissue section low-resolution imaging for the production of reliable and accurate quantitative data. © 2015 The Authors. Journal of Anatomy published by John Wiley & Sons Ltd on behalf of Anatomical Society.

  3. Defect detection in thin plates using So Lamb wave scanning

    NASA Astrophysics Data System (ADS)

    De Villa, Francisco; Roldan, Enrique; Tirado, Cesar; Mares, Rodrigo; Nazarian, Soheil; Osegueda, Roberto A.

    2001-07-01

    This paper describes work towards the development of a Lamb wave scanning method for the detection of defects in thin plates. The approach requires the generation of an ultrasonic S0-Mode Lamb wave using an incident transmitter excited with a tone burst centered at a near non-dispersive frequency. A pair of receiving transducers, with a fixed relative separation, remotely scans line sections of the thin plate. The global position of the receiver pair is moved to cover a large plate area. The arrival time information coming from incident and reflected waves contain information associated with the location of reflection surfaces or potential flaws. The cross-correlation between the excitation signal and the receivers' waveforms is obtained and subsequently demodulated using a quadrature amplitude method in order to facilitate the determination of arrival times. Distances from the source, to the reflection surface and to the receivers are found from the arrival times of the reflected waves and the Lamb wave phase velocity. The distances and the source and receiver locations are incorporated in an elliptical solution to find coordinates of the reflection points. In a line scanning the set of predicted reflection points define the extent of the defect. The Lamb wave scanning approach is tested using 1.6 mm-thick Aluminum plates with notches of various lengths and orientations from 0, 22.5 and 45 degrees with respect to the far edge of the plates. The results are summarized with defect maps that compare favorably to the actual notch locations.

  4. Automated detection of bone metastatic changes using serial CT scans.

    PubMed

    Oh, Jihun; Kim, Gyehyun; Lee, Jaesung; Cheon, Minsu; Park, Yongsup; Kim, Sewon; Yi, Jonghyon; Lee, Ho Yun

    2017-06-01

    Bone metastases resulting from a primary tumor invasion to the bone are common and cause significant morbidity in advanced cancer patients. Although the detection of bone metastases is often straightforward, it is difficult to identify their spread and track their changes, particularly in early stages. This paper presents a novel method that automatically finds the changes in appearance and the progress of bone metastases using longitudinal CT images. In contrast to previous methods based on nodule detection within a specific bone site in an individual CT scan, the approach in the present study is based on the subtraction between two registered CT volumes. The volumes registered using the proposed weighted-Demons registration and symmetric warping were subtracted with minimizing noise, and the Jacobian and false positive suppressions were performed to reduce false alarms. The proposed method detects the changes in bone metastases within 3min for entire chest bone structures covering the spine, ribs, and sternum. The method was validated based on 3-fold cross validation using the radiologists' markings of 459 lesions in 24 subjects and was performed with a sensitivity of 92.59%, a false positive volume of 2.58%, and 9.71 false positives per patient. Note that 113 lesions (24%) missed by the radiologists were identified by the present system and confirmed to be true metastases. Indeed, three patients diagnosed initially as normal, having no metastatic difference, by radiologists were found to be abnormal using the proposed system. Automatic detection method of bone metastatic changes in the entire chest bone was developed. Weighted Demons, symmetric warping, following false positive suppressions, and their parallel computing implementation enabled precise and fast computation of delicate changes in serial CT scans. The cross validation proved that this method can be quite useful for assisting radiologists in sensing minute metastatic changes from early stage

  5. SCAN+

    SciTech Connect

    Kenneth Krebs, John Svoboda

    2009-11-01

    SCAN+ is a software application specifically designed to control the positioning of a gamma spectrometer by a two dimensional translation system above spent fuel bundles located in a sealed spent fuel cask. The gamma spectrometer collects gamma spectrum information for the purpose of spent fuel cask fuel loading verification. SCAN+ performs manual and automatic gamma spectrometer positioning functions as-well-as exercising control of the gamma spectrometer data acquisitioning functions. Cask configuration files are used to determine the positions of spent fuel bundles. Cask scanning files are used to determine the desired scan paths for scanning a spent fuel cask allowing for automatic unattended cask scanning that may take several hours.

  6. An Automated Road Roughness Detection from Mobile Laser Scanning Data

    NASA Astrophysics Data System (ADS)

    Kumar, P.; Angelats, E.

    2017-05-01

    Rough roads influence the safety of the road users as accident rate increases with increasing unevenness of the road surface. Road roughness regions are required to be efficiently detected and located in order to ensure their maintenance. Mobile Laser Scanning (MLS) systems provide a rapid and cost-effective alternative by providing accurate and dense point cloud data along route corridor. In this paper, an automated algorithm is presented for detecting road roughness from MLS data. The presented algorithm is based on interpolating smooth intensity raster surface from LiDAR point cloud data using point thinning process. The interpolated surface is further processed using morphological and multi-level Otsu thresholding operations to identify candidate road roughness regions. The candidate regions are finally filtered based on spatial density and standard deviation of elevation criteria to detect the roughness along the road surface. The test results of road roughness detection algorithm on two road sections are presented. The developed approach can be used to provide comprehensive information to road authorities in order to schedule maintenance and ensure maximum safety conditions for road users.

  7. Rapid Detection of Coseismic Displacements with PALSAR ScanSAR-ScanSAR Interferometry

    NASA Astrophysics Data System (ADS)

    Hashimoto, M.; Ozawa, T.; Tobita, M.; Miyawaki, M.; Shimada, M.

    2010-12-01

    On large earthquake disasters, researchers and disaster managers eager to grasp the over-all image of the event immediately with as high resolution as possible. The rapid detection of coseismic deformation enables us to discriminate co- and postseismic deformations and estimate fault parameters, which definitely contributes to the evaluation of stress transfer which leads to aftershock forecast. The ScanSAR-ScanSAR interferometry is one of techniques that can provide information on coseismic displacement field in a wide region. Phased Array-type L-band SAR (PALSAR) onboard Japan’s Advanced Land Observation Satellite (ALOS) is capable to make an observation with ScanSAR mode with as wide swath as 350km. Owing to its long wavelength, coherence is high enough to perform interferometry in vegetated areas and steep mountains. We have applied this technique to images acquired before and after 4 events that occurred this year. We use the full-aperture algorithm to produce single look complex images for each swath and apply usual 2-pass interferometry to SLC’s. It is quite important to synchronize bursts of two ScanSAR images for interferometry, but this could be done only by the Japan Aerospace Exploration Agency (JAXA). Our first trial was the Haiti earthquake of January, 2010. After its occurrence, we requested JAXA to acquire a ScanSAR image of the western Hispaniola Island. On February 11, the acquisition was made. JAXA synchronized its bursts to the image acquired on Sept. 26, 2009. We observed coseismic fringes near the epicenter along the Enriquillo fault similar to those obtained from strip-map mode images. On the other hand, no notable deformation was found near the Septentrional fault, northern Haiti. The second example was the Chile earthquake of February 27, 2010. Post-earthquake observation was made on March 1, 2010. The observed area was as wide as 350km, from the Pacific coast to the eastern frank of the Andes, and as long as 1000km. This image was

  8. X-ray scan detection for cargo integrity

    NASA Astrophysics Data System (ADS)

    Valencia, Juan; Miller, Steve

    2011-04-01

    The increase of terrorism and its global impact has made the determination of the contents of cargo containers a necessity. Existing technology allows non-intrusive inspections to determine the contents of a container rapidly and accurately. However, some cargo shipments are exempt from such inspections. Hence, there is a need for a technology that enables rapid and accurate means of detecting whether such containers were non-intrusively inspected. Non-intrusive inspections are most commonly performed utilizing high powered X-ray equipment. The challenge is creating a device that can detect short duration X-ray scans while maintaining a portable, battery powered, low cost, and easy to use platform. The Pacific Northwest National Laboratory (PNNL) has developed a methodology and prototype device focused on this challenge. The prototype, developed by PNNL, is a battery powered electronic device that continuously measures its X-ray and Gamma exposure, calculates the dose equivalent rate, and makes a determination of whether the device has been exposed to the amount of radiation experienced during an X-ray inspection. Once an inspection is detected, the device will record a timestamp of the event and relay the information to authorized personnel via a visual alert, USB connection, and/or wireless communication. The results of this research demonstrate that PNNL's prototype device can be effective at determining whether a container was scanned by X-ray equipment typically used for cargo container inspections. This paper focuses on laboratory measurements and test results acquired with the PNNL prototype device using several X-ray radiation levels.

  9. Quantitative permeability magnetic resonance imaging in acute ischemic stroke: how long do we need to scan?

    PubMed

    Vidarsson, Logi; Thornhill, Rebecca E; Liu, Fang; Mikulis, David J; Kassner, Andrea

    2009-11-01

    Blood-brain barrier (BBB) permeability estimation with dynamic contrast-enhanced MRI (DCE-MRI) has shown significant potential for predicting hemorrhagic transformation (HT) in patients presenting with acute ischemic stroke (AIS). In this work, the effects of scan duration on quantitative BBB permeability estimates (KPS) were investigated. Data from eight patients (three with HT) aged 37-93 years old were retrospectively studied by directly calculating the standard deviation of KPS as a function of scan time. The uncertainty in KPS was reduced only slightly for a scan time of 3 min and 30 s (4% reduction in P value from .047 to .045). When more than 3 min and 30 s of data were used, quantitative permeability MRI was able to separate those patients who proceeded to HT from those who did not (P value <.05). Our findings indicate that reducing permeability acquisition times is feasible in keeping with the need to maintain time-efficient MR protocols in the setting of AIS.

  10. Quantitative sub-surface and non-contact imaging using scanning microwave microscopy

    NASA Astrophysics Data System (ADS)

    Gramse, Georg; Brinciotti, Enrico; Lucibello, Andrea; Patil, Samadhan B.; Kasper, Manuel; Rankl, Christian; Giridharagopal, Rajiv; Hinterdorfer, Peter; Marcelli, Romolo; Kienberger, Ferry

    2015-03-01

    The capability of scanning microwave microscopy for calibrated sub-surface and non-contact capacitance imaging of silicon (Si) samples is quantitatively studied at broadband frequencies ranging from 1 to 20 GHz. Calibrated capacitance images of flat Si test samples with varying dopant density (1015-1019 atoms cm-3) and covered with dielectric thin films of SiO2 (100-400 nm thickness) are measured to demonstrate the sensitivity of scanning microwave microscopy (SMM) for sub-surface imaging. Using standard SMM imaging conditions the dopant areas could still be sensed under a 400 nm thick oxide layer. Non-contact SMM imaging in lift-mode and constant height mode is quantitatively demonstrated on a 50 nm thick SiO2 test pad. The differences between non-contact and contact mode capacitances are studied with respect to the main parameters influencing the imaging contrast, namely the probe tip diameter and the tip-sample distance. Finite element modelling was used to further analyse the influence of the tip radius and the tip-sample distance on the SMM sensitivity. The understanding of how the two key parameters determine the SMM sensitivity and quantitative capacitances represents an important step towards its routine application for non-contact and sub-surface imaging.

  11. Detecting submerged bodies: controlled research using side-scan sonar to detect submerged proxy cadavers.

    PubMed

    Healy, Carrie A; Schultz, John J; Parker, Kenneth; Lowers, Bim

    2015-05-01

    Forensic investigators routinely deploy side-scan sonar for submerged body searches. This study adds to the limited body of literature by undertaking a controlled project to understand how variables affect detection of submerged bodies using side-scan sonar. Research consisted of two phases using small and medium-sized pig (Sus scrofa) carcasses as proxies for human bodies to investigate the effects of terrain, body size, frequency, swath width, and state of decomposition. Results demonstrated that a clear, flat, sandy pond floor terrain was optimal for detection of the target as irregular terrain and/or vegetation are major limitations that can obscure the target. A higher frequency towfish was preferred for small bodies, and a 20 m swath width allowed greater visibility and easier maneuverability of the boat in this environment. Also, the medium-sized carcasses were discernable throughout the 81-day study period, indicating that it is possible to detect bodies undergoing decomposition with side-scan sonar.

  12. Raman detected differential scanning calorimetry of polymorphic transformations in acetaminophen.

    PubMed

    Kauffman, John F; Batykefer, Linda M; Tuschel, David D

    2008-12-15

    Acetaminophen is known to crystallize in three polymorphic forms. Thermally induced transformations between the crystalline forms and the super-cooled liquid have been observed by differential scanning calorimetry (DSC), but the assignment of calorimetric transitions to specific polymorphic transformations remains challenging, because the transition temperatures for several transformations are close to one another, and the characteristics of the observed transitions depend on experimental variables that are often poorly controlled. This paper demonstrates the simultaneous application of DSC and Raman microscopy for the observation of thermally driven transitions between polymorphs of pharmaceutical materials. Raman detected differential scanning calorimetry (RD-DSC) has been used to monitor the DSC thermograms of super-cooled liquid acetaminophen and confirms the assignment of two exothermic transitions to specific polymorphic transformations. Principal component analysis of the Raman spectra have been used to determine the number of independent components that participate in the phase transformations, and multivariate regression has been used to determine transition temperatures from the spectral data. The influence of the laser excitation source on measured DSC thermograms has also been investigated, and it has been demonstrated that a baseline shift occurs in RD-DSC when a polymorphic transformation occurs between crystalline and amorphous forms. RD-DSC has been used to examine the influence of sample aging and sample pan configuration on the observed polymorphic transformations, and both of these variables were found to influence the thermal behavior of the sample. The results demonstrate the advantage of simultaneous Raman spectroscopy and differential scanning calorimetry for the unambiguous assignment of thermally driven polymorphic transformations.

  13. Detection of diatoms in water and tissues by combination of microwave digestion, vacuum filtration and scanning electron microscopy.

    PubMed

    Hu, Sunlin; Liu, Chao; Wen, Jinfeng; Dai, Weilie; Wang, Songcai; Su, HuiFang; Zhao, Jian

    2013-03-10

    The detection of diatoms has been proposed to be useful in the diagnosis of drowning. In the presented paper, we describe a novel method for qualitative and quantitative analysis of diatoms in water and organs. Samples were treated by microwave digestion. The fluid obtained was vacuum-filtrated; its sediment on the membrane was coated and examined under the scanning electron microscope with the mode of automatic field scanning; and qualitative and quantitative diatom analysis was performed based on the images captured automatically and on manual identification of the suspected diatoms at a required higher magnification. The method is rapid, sensitive, labor-saving, and accurate for qualitative and quantitative diatom analysis. However, further scientific research in the field of automatic diatom identification using SEM images has to be done in order to automate the process of detection and identification of diatoms in water and tissues for the diagnosis of drowning. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  14. Pedestrian Detection by Laser Scanning and Depth Imagery

    NASA Astrophysics Data System (ADS)

    Barsi, A.; Lovas, T.; Molnar, B.; Somogyi, A.; Igazvolgyi, Z.

    2016-06-01

    Pedestrian flow is much less regulated and controlled compared to vehicle traffic. Estimating flow parameters would support many safety, security or commercial applications. Current paper discusses a method that enables acquiring information on pedestrian movements without disturbing and changing their motion. Profile laser scanner and depth camera have been applied to capture the geometry of the moving people as time series. Procedures have been developed to derive complex flow parameters, such as count, volume, walking direction and velocity from laser scanned point clouds. Since no images are captured from the faces of pedestrians, no privacy issues raised. The paper includes accuracy analysis of the estimated parameters based on video footage as reference. Due to the dense point clouds, detailed geometry analysis has been conducted to obtain the height and shoulder width of pedestrians and to detect whether luggage has been carried or not. The derived parameters support safety (e.g. detecting critical pedestrian density in mass events), security (e.g. detecting prohibited baggage in endangered areas) and commercial applications (e.g. counting pedestrians at all entrances/exits of a shopping mall).

  15. Scanning Mode Sensor for Detection of Flow Inhomogeneities

    NASA Technical Reports Server (NTRS)

    Adamovsky, Grigory (Inventor)

    1998-01-01

    A scanning mode sensor and method is provided for detection of flow inhomogeneities such as shock. The field of use of this invention is ground test control and engine control during supersonic flight. Prior art measuring techniques include interferometry. Schlieren, and shadowgraph techniques. These techniques. however, have problems with light dissipation. The present method and sensor utilizes a pencil beam of energy which is passed through a transparent aperture in a flow inlet in a time-sequential manner so as to alter the energy beam. The altered beam or its effects are processed and can be studied to reveal information about flow through the inlet which can in turn be used for engine control.

  16. Refractive index matched scanning and detection of soft particles

    NASA Astrophysics Data System (ADS)

    Dijksman, Joshua A.; Brodu, Nicolas; Behringer, Robert P.

    2017-05-01

    We describe here how to apply the three-dimensional imaging technique of refractive index matched scanning to hydrogel spheres. Hydrogels are water based materials with a low refractive index, which allows for index matching with water-based solvent mixtures. We discuss here various experimental techniques required to handle specifically hydrogel spheres as opposed to other transparent materials. The deformability of hydrogel spheres makes their identification in three-dimensional images non-trivial. We will also discuss numerical techniques that can be used in general to detect contacting, non-spherical particles in a three-dimensional image. The experimental and numerical techniques presented here give experimental access to the stress tensor of a packing of deformed particles.

  17. Scanning Mode Sensor for Detection of Flow Inhomogeneities

    NASA Technical Reports Server (NTRS)

    Adamovsky, Grigory (Inventor)

    1996-01-01

    A scanning mode sensor and method is provided for detection of flow inhomogeneities such as shock. The field of use of this invention is ground test control and engine control during supersonic flight. Prior art measuring techniques include interferometry, Schlieren, and shadowgraph techniques. These techniques, however, have problems with light dissipation. The present method and sensor utilizes a pencil beam of energy which is passed through a transparent aperture in a flow inlet in a time-sequential manner so as to alter the energy beam. The altered beam or its effects are processed and can be studied to reveal information about flow through the inlet which can in turn be used for engine control.

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

    NASA Astrophysics Data System (ADS)

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

    2009-02-01

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

  19. Quantitative study of mammalian cells by scanning transmission soft X-ray microscopy

    NASA Astrophysics Data System (ADS)

    Shinohara, K.; Ohigashi, T.; Toné, S.; Kado, M.; Ito, A.

    2017-06-01

    Molecular distribution in mammalian cells was studied by soft X-ray scanning transmission microscopy with respect to the quantitative aspect of analysis. NEXAFS profiles at the C, N and O K-absorption edges were combined and used for the analysis. For the estimation of quantity for nucleic acids and proteins, NEXAFS profiles of DNA and bovine serum albumin (BSA) at the N K-absorption edge were applied assuming that those were their representatives. The method has a potential to explore the other molecular components than nucleic acids and proteins.

  20. Quantitative thermal imaging of single-walled carbon nanotube devices by scanning Joule expansion microscopy.

    PubMed

    Xie, Xu; Grosse, Kyle L; Song, Jizhou; Lu, Chaofeng; Dunham, Simon; Du, Frank; Islam, Ahmad E; Li, Yuhang; Zhang, Yihui; Pop, Eric; Huang, Yonggang; King, William P; Rogers, John A

    2012-11-27

    Electrical generation of heat in single-walled carbon nanotubes (SWNTs) and subsequent thermal transport into the surroundings can critically affect the design, operation, and reliability of electronic and optoelectronic devices based on these materials. Here we investigate such heat generation and transport characteristics in perfectly aligned, horizontal arrays of SWNTs integrated into transistor structures. We present quantitative assessments of local thermometry at individual SWNTs in these arrays, evaluated using scanning Joule expansion microscopy. Measurements at different applied voltages reveal electronic behaviors, including metallic and semiconducting responses, spatial variations in diameter or chirality, and localized defect sites. Analytical models, validated by measurements performed on different device structures at various conditions, enable accurate, quantitative extraction of temperature distributions at the level of individual SWNTs. Using current equipment, the spatial resolution and temperature precision are as good as ∼100 nm and ∼0.7 K, respectively.

  1. Quantitative Computerized Two-Point Correlation Analysis of Lung CT Scans Correlates With Pulmonary Function in Pulmonary Sarcoidosis

    PubMed Central

    Erdal, Barbaros Selnur; Yildiz, Vedat; King, Mark A.; Patterson, Andrew T.; Knopp, Michael V.; Clymer, Bradley D.

    2012-01-01

    Background: Chest CT scans are commonly used to clinically assess disease severity in patients presenting with pulmonary sarcoidosis. Despite their ability to reliably detect subtle changes in lung disease, the utility of chest CT scans for guiding therapy is limited by the fact that image interpretation by radiologists is qualitative and highly variable. We sought to create a computerized CT image analysis tool that would provide quantitative and clinically relevant information. Methods: We established that a two-point correlation analysis approach reduced the background signal attendant to normal lung structures, such as blood vessels, airways, and lymphatics while highlighting diseased tissue. This approach was applied to multiple lung fields to generate an overall lung texture score (LTS) representing the quantity of diseased lung parenchyma. Using deidentified lung CT scan and pulmonary function test (PFT) data from The Ohio State University Medical Center’s Information Warehouse, we analyzed 71 consecutive CT scans from patients with sarcoidosis for whom simultaneous matching PFTs were available to determine whether the LTS correlated with standard PFT results. Results: We found a high correlation between LTS and FVC, total lung capacity, and diffusing capacity of the lung for carbon monoxide (P < .0001 for all comparisons). Moreover, LTS was equivalent to PFTs for the detection of active lung disease. The image analysis protocol was conducted quickly (< 1 min per study) on a standard laptop computer connected to a publicly available National Institutes of Health ImageJ toolkit. Conclusions: The two-point image analysis tool is highly practical and appears to reliably assess lung disease severity. We predict that this tool will be useful for clinical and research applications. PMID:22628487

  2. Lesion detection and quantitation of positron emission mammography

    SciTech Connect

    Qi, Jinyi; Huesman, Ronald H.

    2001-12-01

    A Positron Emission Mammography (PEM) scanner dedicated to breast imaging is being developed at our laboratory. We have developed a list mode likelihood reconstruction algorithm for this scanner. Here we theoretically study the lesion detection and quantitation. The lesion detectability is studied theoretically using computer observers. We found that for the zero-order quadratic prior, the region of interest observer can achieve the performance of the prewhitening observer with a properly selected smoothing parameter. We also study the lesion quantitation using the test statistic of the region of interest observer. The theoretical expressions for the bias, variance, and ensemble mean squared error of the quantitation are derived. Computer simulations show that the theoretical predictions are in good agreement with the Monte Carlo results for both lesion detection and quantitation.

  3. High-Speed Edge-Detecting Line Scan Smart Camera

    NASA Technical Reports Server (NTRS)

    Prokop, Norman F.

    2012-01-01

    A high-speed edge-detecting line scan smart camera was developed. The camera is designed to operate as a component in a NASA Glenn Research Center developed inlet shock detection system. The inlet shock is detected by projecting a laser sheet through the airflow. The shock within the airflow is the densest part and refracts the laser sheet the most in its vicinity, leaving a dark spot or shadowgraph. These spots show up as a dip or negative peak within the pixel intensity profile of an image of the projected laser sheet. The smart camera acquires and processes in real-time the linear image containing the shock shadowgraph and outputting the shock location. Previously a high-speed camera and personal computer would perform the image capture and processing to determine the shock location. This innovation consists of a linear image sensor, analog signal processing circuit, and a digital circuit that provides a numerical digital output of the shock or negative edge location. The smart camera is capable of capturing and processing linear images at over 1,000 frames per second. The edges are identified as numeric pixel values within the linear array of pixels, and the edge location information can be sent out from the circuit in a variety of ways, such as by using a microcontroller and onboard or external digital interface to include serial data such as RS-232/485, USB, Ethernet, or CAN BUS; parallel digital data; or an analog signal. The smart camera system can be integrated into a small package with a relatively small number of parts, reducing size and increasing reliability over the previous imaging system..

  4. Fast automatic algorithm for bifurcation detection in vascular CTA scans

    NASA Astrophysics Data System (ADS)

    Brozio, Matthias; Gorbunova, Vladlena; Godenschwager, Christian; Beck, Thomas; Bernhardt, Dominik

    2012-02-01

    Endovascular imaging aims at identifying vessels and their branches. Automatic vessel segmentation and bifurcation detection eases both clinical research and routine work. In this article a state of the art bifurcation detection algorithm is developed and applied on vascular computed tomography angiography (CTA) scans to mark the common iliac artery and its branches, the internal and external iliacs. In contrast to other methods our algorithm does not rely on a complete segmentation of a vessel in the 3D volume, but evaluates the cross-sections of the vessel slice by slice. Candidates for vessels are obtained by thresholding, following by 2D connected component labeling and prefiltering by size and position. The remaining candidates are connected in a squared distanced weighted graph. With Dijkstra algorithm the graph is traversed to get candidates for the arteries. We use another set of features considering length and shape of the paths to determine the best candidate and detect the bifurcation. The method was tested on 119 datasets acquired with different CT scanners and varying protocols. Both easy to evaluate datasets with high resolution and no apparent clinical diseases and difficult ones with low resolution, major calcifications, stents or poor contrast between the vessel and surrounding tissue were included. The presented results are promising, in 75.7% of the cases the bifurcation was labeled correctly, and in 82.7% the common artery and one of its branches were assigned correctly. The computation time was on average 0.49 s +/- 0.28 s, close to human interaction time, which makes the algorithm applicable for time-critical applications.

  5. Scoring systems of quantitative bone scanning in prostate cancer: historical overview, current status and future perspectives.

    PubMed

    Zafeirakis, Athanasios

    2014-01-01

    Whole-body bone scintigraphy using technetium-99m-methylene-diphosphonate ((99m)Tc-MDP) is the most widely used radionuclide imaging modality applied in patients with prostate cancer. With this technique, the choice of methods to estimate the extend of the metastatic disease on the skeletal system includes various different approaches, classified in two main categories: First, the quantitative measurements of tracer uptake, defined either as the percentage of the injected dose of tracer, or as the more complicated plasma clearance techniques and second, the various semi-quantitative scoring systems of the bone scan images. These scoring systems can be based either on visual counting of bone lesions, or on the estimation of a numerical index that expresses the fractional involvement of each bone by tumour, called "Bone Scan Index" (BSI); the latter can be produced either visually (manually) or by the more sophisticated techniques of fully- or semi-automated (computerized) forms. In this review, a brief chronological overview of the aforementioned methods is presented, along with the main advantages, drawbacks and the prognostic implications of each method. There remains, however, the challenge of defining, developing and validating the optimal measurement methodology in order these scoring systems to obtain a wider clinical use.

  6. Quantitative assessment of macular thickness in normal subjects and patients with diabetic retinopathy by scanning retinal thickness analyser

    PubMed Central

    Oshima, Y.; Emi, K.; Yamanishi, S.; Motokura, M.

    1999-01-01

    AIMS—To evaluate the scanning retinal thickness analyser (RTA), a novel non-invasive imaging instrument, in diagnosing and quantitatively characterising diabetic macular oedema, and to investigate the relation between central macula thickness measured by RTA and other clinical examinations.
METHODS—Central macular thickness was measured using the RTA in 40 normal subjects and 60 patients with diabetic retinopathy. The reproducibility of the retinal thickness measurements was evaluated by calculating the mean of the inter- and intrasession variations. Central macular thickness was correlated with the results of visual acuity measurements, biomicroscopy, and fluorescein angiography.
RESULTS—Intra- and intersession reproducibility of the RTA in normal subjects was plus or minus 5.2% (16 µm) and plus or minus 6.1% (19 µm), respectively. The mean central macular thickness was 182 (SD 16) µm in normal subjects, 283 (116) µm in diabetic eyes without clinically significant macular oedema (CSMO), and 564 (168) µm in diabetic eyes with CSMO. Central macular thickness was significantly greater (p<0.001) in eyes with diabetic retinopathy than in normal subjects, even when macular thickening did not meet the standard for CSMO (p=0.019) measured by biomicroscopy. Although greater fluorescein leakage at the macula results in greater central macular thickness, only eyes with diffuse leakage had statistically significant macular thickening compared with normal subjects (p=0.022). Central macular thickness measured with the RTA was significantly correlated with the logarithmic converted visual acuity (r2= 0.76) in diabetic eyes.
CONCLUSION—Scanning RTA, which has good reproducibility, might be useful to quantitatively detect and monitor macular thickening in diabetic retinopathy. Central macular thickness was highly correlated with logarithmic converted visual acuity in diabetic macular oedema.

 Keywords: scanning retinal thickness analyser; macular

  7. Detection and validation of quantitative trait loci for soybean isoflavones

    USDA-ARS?s Scientific Manuscript database

    Interest in soybean [Glycine max (L.) Merrill] isoflavones has increased in recent years due to numerous potential health benefits. Consequently, quantitative trait loci (QTL) detection for marker assisted breeding is being examined for potential genetic gains. This study sought to detect QTL for ...

  8. The measurement of liver fat from single-energy quantitative computed tomography scans.

    PubMed

    Cheng, Xiaoguang; Blake, Glen M; Brown, J Keenan; Guo, Zhe; Zhou, Jun; Wang, Fengzhe; Yang, Liqiang; Wang, Xiaohong; Xu, Li

    2017-06-01

    Studies of soft tissue composition using computed tomography (CT) scans are often semi-quantitative and based on Hounsfield units (HU) measurements that have not been calibrated with a quantitative CT (QCT) phantom. We describe a study to establish the water (H2O) and dipotassium hydrogen phosphate (K2HPO4) basis set equivalent densities of fat and fat-free liver tissue. With this information liver fat can be accurately measured from any abdominal CT scan calibrated with a suitable phantom. Liver fat content was measured by comparing single-energy QCT (SEQCT) HU measurements of the liver with predicted HU values for fat and fat-free liver tissue calculated from their H2O and K2HPO4 equivalent densities and calibration data from a QCT phantom. The equivalent densities of fat were derived from a listing of its constituent fatty acids, and those of fat-free liver tissue from a dual-energy QCT (DEQCT) study performed in 14 healthy Chinese subjects. This information was used to calculate liver fat from abdominal SEQCT scans performed in a further 541 healthy Chinese subjects (mean age 62 years; range, 31-95 years) enrolled in the Prospective Urban Rural Epidemiology (PURE) Study. The equivalent densities of fat were 941.75 mg/cm(3) H2O and -43.72 mg/cm(3) K2HPO4, and for fat-free liver tissue 1,040.13 mg/cm(3) H2O and 21.34 mg/cm(3) K2HPO4. Liver fat in the 14 subjects in the DEQCT study varied from 0-17.9% [median: 4.5%; interquartile range (IQR): 3.0-7.9%]. Liver fat in the 541 PURE study subjects varied from -0.3-29.9% (median: 4.9%; IQR: 3.4-6.9%). We have established H2O and K2HPO4 equivalent densities for fat and fat-free liver tissue that allow a measurement of liver fat to be obtained from any abdominal CT scan acquired with a QCT phantom. Although radiation dose considerations preclude the routine use of QCT to measure liver fat, the method described here facilitates its measurement in patients having CT scans performed for other purposes. Further studies

  9. The measurement of liver fat from single-energy quantitative computed tomography scans

    PubMed Central

    Cheng, Xiaoguang; Brown, J. Keenan; Guo, Zhe; Zhou, Jun; Wang, Fengzhe; Yang, Liqiang; Wang, Xiaohong; Xu, Li

    2017-01-01

    Background Studies of soft tissue composition using computed tomography (CT) scans are often semi-quantitative and based on Hounsfield units (HU) measurements that have not been calibrated with a quantitative CT (QCT) phantom. We describe a study to establish the water (H2O) and dipotassium hydrogen phosphate (K2HPO4) basis set equivalent densities of fat and fat-free liver tissue. With this information liver fat can be accurately measured from any abdominal CT scan calibrated with a suitable phantom. Methods Liver fat content was measured by comparing single-energy QCT (SEQCT) HU measurements of the liver with predicted HU values for fat and fat-free liver tissue calculated from their H2O and K2HPO4 equivalent densities and calibration data from a QCT phantom. The equivalent densities of fat were derived from a listing of its constituent fatty acids, and those of fat-free liver tissue from a dual-energy QCT (DEQCT) study performed in 14 healthy Chinese subjects. This information was used to calculate liver fat from abdominal SEQCT scans performed in a further 541 healthy Chinese subjects (mean age 62 years; range, 31–95 years) enrolled in the Prospective Urban Rural Epidemiology (PURE) Study. Results The equivalent densities of fat were 941.75 mg/cm3 H2O and –43.72 mg/cm3 K2HPO4, and for fat-free liver tissue 1,040.13 mg/cm3 H2O and 21.34 mg/cm3 K2HPO4. Liver fat in the 14 subjects in the DEQCT study varied from 0–17.9% [median: 4.5%; interquartile range (IQR): 3.0–7.9%]. Liver fat in the 541 PURE study subjects varied from –0.3–29.9% (median: 4.9%; IQR: 3.4–6.9%). Conclusions We have established H2O and K2HPO4 equivalent densities for fat and fat-free liver tissue that allow a measurement of liver fat to be obtained from any abdominal CT scan acquired with a QCT phantom. Although radiation dose considerations preclude the routine use of QCT to measure liver fat, the method described here facilitates its measurement in patients having CT scans

  10. A Genome-wide Quantitative Linkage Scan of Niacin Skin Flush Response in Families With Schizophrenia

    PubMed Central

    Lien, Yin-Ju; Huang, Sih-Syuan; Liu, Chih-Min; Hwu, Hai-Gwo; Faraone, Stephen V.; Tsuang, Ming T.; Chen, Wei J.

    2013-01-01

    Schizophrenia patients frequently display reduced niacin flush responses, and similar characteristics are also observed in their nonpsychotic relatives. This study aimed to identify loci influencing flush response to niacin in schizophrenia using genome-wide quantitative linkage scan. In a nationwide sample of families with at least 2 siblings affected with schizophrenia in each family, 115 families that had at least 2 affected siblings with information on the niacin skin test were subjected to quantitative trait loci linkage analysis, either involving affected individuals only or the whole family. Nonparametric linkage z (NPL-Z) scores were calculated for each of 386 microsatellite markers spaced at an average of 9-cM intervals. Niacin patches of 3 concentrations (0.001M, 0.01, and 0.1M) were applied to forearm skin, and the flush response was rated at 5, 10, and 15 minutes, respectively, with a 4-point scale. Determination of genome-wide empirical significance was implemented using 1000 simulated genome scans. One linkage peak attaining genome-wide significance was identified at chromosomal region 14q32.12 for 0.01M concentration at 5 minutes (NPL-Z scores = 3.39, genome-wide empirical P = .03) in affected individuals, and the corresponding linkage signal remained strong (NPL-Z scores = 2.87) for the analyses of the whole family. This locus is distinct from the chromosomal region identified in the previous genome-wide scan for the diagnosis of schizophrenia, and the signal was higher than the peak linkage signal in that study. These findings indicate that there might be modifier or susceptibility-modifier genes at 14q32.12 for schizophrenia-related attenuation of flush response to niacin. PMID:21653277

  11. Fast quantitative single-molecule detection at ultralow concentrations.

    PubMed

    Haas, Philippe; Then, Patrick; Wild, Andreas; Grange, Wilfried; Zorman, Sylvain; Hegner, Martin; Calame, Michel; Aebi, Ueli; Flammer, Josef; Hecht, Bert

    2010-07-15

    The applicability of single-molecule fluorescence assays in liquids is limited by diffusion to concentrations in the low picomolar range. Here, we demonstrate quantitative single-molecule detection at attomolar concentrations within 1 min by excitation and detection of fluorescence through a single-mode optical fiber in presence of turbulent flow. The combination of high detectability and short measurement times promises applications in ultrasensitive assays, sensors, and point-of-care medical diagnostics.

  12. Ultra-high vacuum scanning thermal microscopy for nanometer resolution quantitative thermometry.

    PubMed

    Kim, Kyeongtae; Jeong, Wonho; Lee, Woochul; Reddy, Pramod

    2012-05-22

    Understanding energy dissipation at the nanoscale requires the ability to probe temperature fields with nanometer resolution. Here, we describe an ultra-high vacuum (UHV)-based scanning thermal microscope (SThM) technique that is capable of quantitatively mapping temperature fields with ∼15 mK temperature resolution and ∼10 nm spatial resolution. In this technique, a custom fabricated atomic force microscope (AFM) cantilever, with a nanoscale Au-Cr thermocouple integrated into the tip of the probe, is used to measure temperature fields of surfaces. Operation in an UHV environment eliminates parasitic heat transport between the tip and the sample enabling quantitative measurement of temperature fields on metal and dielectric surfaces with nanoscale resolution. We demonstrate the capabilities of this technique by directly imaging thermal fields in the vicinity of a 200 nm wide, self-heated, Pt line. Our measurements are in excellent agreement with computational results-unambiguously demonstrating the quantitative capabilities of the technique. UHV-SThM techniques will play an important role in the study of energy dissipation in nanometer-sized electronic and photonic devices and the study of phonon and electron transport at the nanoscale.

  13. Scanning probe microscopy beyond imaging: a general tool for quantitative analysis.

    PubMed

    Liscio, Andrea

    2013-04-15

    A simple, fast and general approach for quantitative analysis of scanning probe microscopy (SPM) images is reported. As a proof of concept it is used to determine with a high degree of precision the value of observables such as 1) the height, 2) the flowing current and 3) the corresponding surface potential (SP) of flat nanostructures such as gold electrodes, organic semiconductor architectures and graphenic sheets. Despite histogram analysis, or frequency count (Fc), being the most common mathematical tool used to analyse SPM images, the analytical approach is still lacking. By using the mathematical relationship between Fc and the collected data, the proposed method allows quantitative information on observable values close to the noise level to be gained. For instance, the thickness of nanostructures deposited on very rough substrates can be quantified, and this makes it possible to distinguish the contribution of an adsorbed nanostructure from that of the underlying substrate. Being non-numerical, this versatile analytical approach is a useful and general tool for quantitative analysis of the Fc that enables all signals acquired and recorded by an SPM data array to be studied with high precision. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Driving with hemianopia: IV. Head scanning and detection at intersections in a simulator.

    PubMed

    Bowers, Alex R; Ananyev, Egor; Mandel, Aaron J; Goldstein, Robert B; Peli, Eli

    2014-03-13

    Using a driving simulator, we examined the effects of homonymous hemianopia (HH) on head scanning behaviors at intersections and evaluated the role of inadequate head scanning in detection failures. Fourteen people with complete HH and without cognitive decline or visual neglect and 12 normally sighted (NV) current drivers participated. They drove in an urban environment following predetermined routes, which included multiple intersections. Head scanning behaviors were quantified at T-intersections (n = 32) with a stop or yield sign. Participants also performed a pedestrian detection task. The relationship between head scanning and detection was examined at 10 intersections. For HH drivers, the first scan was more likely to be toward the blind than the seeing hemifield. They also made a greater proportion of head scans overall to the blind side than did the NV drivers to the corresponding side (P = 0.003). However, head scan magnitudes of HH drivers were smaller than those of the NV group (P < 0.001). Drivers with HH had impaired detection of blind-side pedestrians due either to not scanning in the direction of the pedestrian or to an insufficient scan magnitude (left HH detected only 46% and right HH 8% at the extreme left and right of the intersection, respectively). Drivers with HH demonstrated compensatory head scan patterns, but not scan magnitudes. Inadequate scanning resulted in blind-side detection failures, which might place HH drivers at increased risk for collisions at intersections. Scanning training tailored to specific problem areas identified in this study might be beneficial.

  15. [Environmental scanning electron microscopy for biofilm detection in tonsils].

    PubMed

    Ramírez-Camacho, Rafael; González-Tallón, Ana Isabel; Gómez, David; Trinidad, Almudena; Ibáñez, Andrés; García-Berrocal, José Ramón; Verdaguer, José María; González-García, José Angel; San Román, Julio

    2008-01-01

    To describe an environmental scanning electron microscopic method for the study of biofilms in clinical samples. A comparison with standard scanning electron microscopy is performed. Nine patients with a past history of recurrent tonsillitis underwent tonsillectomy. Samples from each patient were obtained for both conventional and environmental scanning electron microscopy. The tonsils removed from 2 patients with sleep apnoea syndrome were used as controls. Eight of nine tonsils had biofilms on their surface. Scanning electron microscopy showed accumulations of bacteria covered by fibrillar structures resulting from the sample dehydration process. Environmental scanning electron microscopy provided a view of bacteria embedded in a homogeneous, amorphous substance that was preserved during the examination. Environmental scanning electron microscopy permits the imaging of wet systems at different degrees of dehydration. It therefore allows researchers to observe biofilms in their natural hydrated state.

  16. Computer-aided detection and quantification of cavitary tuberculosis from CT scans

    PubMed Central

    Xu, Ziyue; Bagci, Ulas; Kubler, Andre; Luna, Brian; Jain, Sanjay; Bishai, William R.; Mollura, Daniel J.

    2013-01-01

    Purpose: To present a computer-aided detection tool for identifying, quantifying, and evaluating tuberculosis (TB) cavities in the infected lungs from computed tomography (CT) scans. Methods: The authors’ proposed method is based on a novel shape-based automated detection algorithm on CT scans followed by a fuzzy connectedness (FC) delineation procedure. In order to assess interaction between cavities and airways, the authors first roughly identified air-filled structures (airway, cavities, esophagus, etc.) by thresholding over Hounsfield unit of CT image. Then, airway and cavity structure detection was conducted within the support vector machine classification algorithm. Once airway and cavities were detected automatically, the authors extracted airway tree using a hybrid multiscale approach based on novel affinity relations within the FC framework and segmented cavities using intensity-based FC algorithm. At final step, the authors refined airway structures within the local regions of FC with finer control. Cavity segmentation results were compared to the reference truths provided by expert radiologists and cavity formation was tracked longitudinally from serial CT scans through shape and volume information automatically determined through the authors’ proposed system. Morphological evolution of the cavitary TB were analyzed accordingly with this process. Finally, the authors computed the minimum distance between cavity surface and nearby airway structures by using the linear time distance transform algorithm to explore potential role of airways in cavity formation and morphological evolution. Results: The proposed methodology was qualitatively and quantitatively evaluated on pulmonary CT images of rabbits experimentally infected with TB, and multiple markers such as cavity volume, cavity surface area, minimum distance from cavity surface to the nearest bronchial-tree, and longitudinal change of these markers (namely, morphological evolution of cavities) were

  17. Quantitative Description of Crystal Nucleation and Growth from in Situ Liquid Scanning Transmission Electron Microscopy.

    PubMed

    Ievlev, Anton V; Jesse, Stephen; Cochell, Thomas J; Unocic, Raymond R; Protopopescu, Vladimir A; Kalinin, Sergei V

    2015-12-22

    Recent advances in liquid cell (scanning) transmission electron microscopy (S)TEM has enabled in situ nanoscale investigations of controlled nanocrystal growth mechanisms. Here, we experimentally and quantitatively investigated the nucleation and growth mechanisms of Pt nanostructures from an aqueous solution of K2PtCl6. Averaged statistical, network, and local approaches have been used for the data analysis and the description of both collective particles dynamics and local growth features. In particular, interaction between neighboring particles has been revealed and attributed to reduction of the platinum concentration in the vicinity of the particle boundary. The local approach for solving the inverse problem showed that particles dynamics can be simulated by a stationary diffusional model. The obtained results are important for understanding nanocrystal formation and growth processes and for optimization of synthesis conditions.

  18. Scanning single quantum emitter fluorescence lifetime imaging: quantitative analysis of the local density of photonic states.

    PubMed

    Schell, Andreas W; Engel, Philip; Werra, Julia F M; Wolff, Christian; Busch, Kurt; Benson, Oliver

    2014-05-14

    Their intrinsic properties render single quantum systems as ideal tools for quantum enhanced sensing and microscopy. As an additional benefit, their size is typically on an atomic scale that enables sensing with very high spatial resolution. Here, we report on utilizing a single nitrogen vacancy center in nanodiamond for performing three-dimensional scanning-probe fluorescence lifetime imaging microscopy. By measuring changes of the single emitter's lifetime, information on the local density of optical states is acquired at the nanoscale. Three-dimensional ab initio discontinuous Galerkin time-domain simulations are used in order to verify the results and to obtain additional insights. This combination of experiment and simulations to gather quantitative information on the local density of optical states is of direct relevance for the understanding of fundamental quantum optical processes as well as for the engineering of novel photonic and plasmonic devices.

  19. Quantitative index imaging of coculture cells by scanning focused refractive index microscopy

    NASA Astrophysics Data System (ADS)

    Sun, Teng-Qian; Ye, Qing; Hu, Fen; Liu, Shi-ke; Wang, Xiao-Wan; Wang, Jin; Deng, Zhi-Chao; Mei, Jian-Chun; Zhou, Wen-Yuan; Zhang, Chun-Ping; Wang, Xin-Yu; Pan, Lei-Ting; Tian, Jian-Guo

    2016-08-01

    We report the quantitative refractive index (RI) imaging of cocultured cells in their living environment by scanning focused refractive index microscopy (SFRIM). Mouse microglial cells and synovial cells are cocultured on the top surface of a trapezoid prism. The RI imaging of living cells is obtained in a reflection-type method. The RI information is deduced with the simple derivative total internal reflection method, where a complex retrieval algorithm or reconstruction process is unnecessary. The outline of each cell is determined according to the RI value compared with that of the immersion liquid. The cocultured cells can be discriminated in the RI image. The measurement is nondestructive and label-free. The experimental results prove that SFRIM is a promising tool in the field of biological optics.

  20. Quantitative analysis of Scanning Tunneling Microscopy images for surface structure determination: Sulfur on Re(0001)

    SciTech Connect

    Ogletree, D.F.; Dunphy, J.C.; Salmeron, M.B.; Sautet, P. |

    1993-02-01

    Scanning Tunneling Microscopy (STM) images of adsorbed atoms and molecules on single crystal substrates provide important information on surface structure and order. In many cases images are interpreted qualitatively based on other information on the system. To obtain quantitative information, a theoretical analysis of the STM image is required. A new method of calculating STM images is presented that includes a full description of the STM tip and surface structure. This method is applied to experimental STM images of sulfur adsorbed on Re(0001). Effects of adsorption site, adsorbate geometry, tip composition and tunnel gap resistance on STM image contrast are analyzed. The chemical identity of tip apex atom and substrate subsurface structure are both shown to significantly affect STM image contrast.

  1. Aortic endothelium of alloxan diabetic rabbits: a quantitative study using scanning electron microscopy.

    PubMed

    Dolgov, V V; Zaikina, O E; Bondarenko, M F; Repin, V S

    1982-05-01

    Scanning electron microscope studies of the aorta and other major arteries have been performed in alloxan-induced diabetic rabbits. After 5 weeks, a variety of structural abnormalities of the endothelial lining were detected including a significant increase in the number of argyrophilic cells and an increased number of craters or openings in the endothelial junctional region. Evidence of more extensive micro-damage was present after 5 months duration of diabetes. These zones with structural changes in the endothelial lining of major vessels seem to be areas of high predilection to atherosclerosis in diabetes.

  2. Quantitative analysis of scanning tunneling microscopy images of mixed-ligand-functionalized nanoparticles.

    PubMed

    Biscarini, Fabio; Ong, Quy Khac; Albonetti, Cristiano; Liscio, Fabiola; Longobardi, Maria; Mali, Kunal S; Ciesielski, Artur; Reguera, Javier; Renner, Christoph; De Feyter, Steven; Samorì, Paolo; Stellacci, Francesco

    2013-11-12

    Ligand-protected gold nanoparticles exhibit large local curvatures, features rapidly varying over small scales, and chemical heterogeneity. Their imaging by scanning tunneling microscopy (STM) can, in principle, provide direct information on the architecture of their ligand shell, yet STM images require laborious analysis and are challenging to interpret. Here, we report a straightforward, robust, and rigorous method for the quantitative analysis of the multiscale features contained in STM images of samples consisting of functionalized Au nanoparticles deposited onto Au/mica. The method relies on the analysis of the topographical power spectral density (PSD) and allows us to extract the characteristic length scales of the features exhibited by nanoparticles in STM images. For the mixed-ligand-protected Au nanoparticles analyzed here, the characteristic length scale is 1.2 ± 0.1 nm, whereas for the homoligand Au NPs this scale is 0.75 ± 0.05 nm. These length scales represent spatial correlations independent of scanning parameters, and hence the features in the PSD can be ascribed to a fingerprint of the STM contrast of ligand-protected nanoparticles. PSD spectra from images recorded at different laboratories using different microscopes and operators can be overlapped across most of the frequency range, proving that the features in the STM images of nanoparticles can be compared and reproduced.

  3. Facile and quantitative electrochemical detection of yeast cell apoptosis

    NASA Astrophysics Data System (ADS)

    Yue, Qiulin; Xiong, Shiquan; Cai, Dongqing; Wu, Zhengyan; Zhang, Xin

    2014-03-01

    An electrochemical method based on square wave anodic stripping voltammetry (SWASV) was developed to detect the apoptosis of yeast cells conveniently and quantitatively through the high affinity between Cu2+ and phosphatidylserine (PS) translocated from the inner to the outer plasma membrane of the apoptotic cells. The combination of negatively charged PS and Cu2+ could decrease the electrochemical response of Cu2+ on the electrode. The results showed that the apoptotic rates of cells could be detected quantitatively through the variations of peak currents of Cu2+ by SWASV, and agreed well with those obtained through traditional flow cytometry detection. This work thus may provide a novel, simple, immediate and accurate detection method for cell apoptosis.

  4. A statistical framework for genome-wide scanning and testing of imprinted quantitative trait loci.

    PubMed

    Cui, Yuehua

    2007-01-07

    Non-equivalent expression of alleles at a locus results in genomic imprinting. In this article, a statistical framework for genome-wide scanning and testing of imprinted quantitative trait loci (iQTL) underlying complex traits is developed based on experimental crosses of inbred line species in backcross populations. The joint likelihood function is composed of four component likelihood functions with each of them derived from one of four backcross families. The proposed approach models genomic imprinting effect as a probability measure with which one can test the degree of imprinting. Simulation results show that the model is robust for identifying iQTL with various degree of imprinting ranging from no imprinting, partial imprinting to complete imprinting. Under various simulation scenarios, the proposed model shows consistent parameter estimation with reasonable precision and high power in testing iQTL. When a QTL shows Mendelian effect, the proposed model also outperforms traditional Mendelian model. Extension to incorporate maternal effect is also given. The developed model, built within the maximum likelihood framework and implemented with the EM algorithm, provides a quantitative framework for testing and estimating iQTL involved in the genetic control of complex traits.

  5. Spin-polarized scanning tunneling microscopy with quantitative insights into magnetic probes.

    PubMed

    Phark, Soo-Hyon; Sander, Dirk

    2017-01-01

    Spin-polarized scanning tunneling microscopy and spectroscopy (spin-STM/S) have been successfully applied to magnetic characterizations of individual nanostructures. Spin-STM/S is often performed in magnetic fields of up to some Tesla, which may strongly influence the tip state. In spite of the pivotal role of the tip in spin-STM/S, the contribution of the tip to the differential conductance dI/dV signal in an external field has rarely been investigated in detail. In this review, an advanced analysis of spin-STM/S data measured on magnetic nanoislands, which relies on a quantitative magnetic characterization of tips, is discussed. Taking advantage of the uniaxial out-of-plane magnetic anisotropy of Co bilayer nanoisland on Cu(111), in-field spin-STM on this system has enabled a quantitative determination, and thereby, a categorization of the magnetic states of the tips. The resulting in-depth and conclusive analysis of magnetic characterization of the tip opens new venues for a clear-cut sub-nanometer scale spin ordering and spin-dependent electronic structure of the non-collinear magnetic state in bilayer high Fe nanoislands on Cu(111).

  6. Spin-polarized scanning tunneling microscopy with quantitative insights into magnetic probes

    NASA Astrophysics Data System (ADS)

    Phark, Soo-hyon; Sander, Dirk

    2017-04-01

    Spin-polarized scanning tunneling microscopy and spectroscopy (spin-STM/S) have been successfully applied to magnetic characterizations of individual nanostructures. Spin-STM/S is often performed in magnetic fields of up to some Tesla, which may strongly influence the tip state. In spite of the pivotal role of the tip in spin-STM/S, the contribution of the tip to the differential conductance d I/d V signal in an external field has rarely been investigated in detail. In this review, an advanced analysis of spin-STM/S data measured on magnetic nanoislands, which relies on a quantitative magnetic characterization of tips, is discussed. Taking advantage of the uniaxial out-of-plane magnetic anisotropy of Co bilayer nanoisland on Cu(111), in-field spin-STM on this system has enabled a quantitative determination, and thereby, a categorization of the magnetic states of the tips. The resulting in-depth and conclusive analysis of magnetic characterization of the tip opens new venues for a clear-cut sub-nanometer scale spin ordering and spin-dependent electronic structure of the non-collinear magnetic state in bilayer high Fe nanoislands on Cu(111).

  7. Quantitation and detection of vanadium in biologic and pollution materials

    NASA Technical Reports Server (NTRS)

    Gordon, W. A.

    1974-01-01

    A review is presented of special considerations and methodology for determining vanadium in biological and air pollution materials. In addition to descriptions of specific analysis procedures, general sections are included on quantitation of analysis procedures, sample preparation, blanks, and methods of detection of vanadium. Most of the information presented is applicable to the determination of other trace elements in addition to vanadium.

  8. Competitor internal standards for quantitative detection of mycoplasma DNA.

    PubMed

    Sidhu, M K; Rashidbaigi, A; Testa, D; Liao, M J

    1995-05-01

    Homologous internal controls were used as competitor DNA in the polymerase chain reaction for the quantitative detection of mycoplasma DNA. PCR primer sets were designed on the basis of the most conserved nucleotide sequences of the 16S rRNA gene of mycoplasma species. Amplification of this gene was examined in five different mycoplasma species: Mycoplasma orale, M. hyorhinus, M. synoviae, M. gallisepticum and M. pneumoniae. To evaluate the primers, a number of different cell lines were assayed for the detection of mycoplasma infections. All positive cell lines showed a distinct product on agarose gels while uninfected cells showed no DNA amplification. Neither bacterial nor eukaryotic DNA produced any cross-reaction with the primers used, thus confirming their specificity. Internal control DNA to be used for quantitation was constructed by modifying the sizes of the wild-type amplified products and cloning them in plasmid vectors. These controls used the same primer binding sites as the wild-type and the amplified products were differentiated by a size difference. The detection limits for all the mycoplasma species by competitive quantitative PCR were estimated to range from 4 to 60 genome copies per assay as determined by ethidium bromide-stained agarose gels. These internal standards also serve as positive controls in PCR-based detection of mycoplasma DNA, and therefore accidental contamination of test samples with wild-type positive controls can be eliminated. The quantitative PCR method developed will be useful in monitoring the progression and significance of mycoplasma in the disease process.

  9. Street-side vehicle detection, classification and change detection using mobile laser scanning data

    NASA Astrophysics Data System (ADS)

    Xiao, Wen; Vallet, Bruno; Schindler, Konrad; Paparoditis, Nicolas

    2016-04-01

    Statistics on street-side car parks, e.g. occupancy rates, parked vehicle types, parking durations, are of great importance for urban planning and policy making. Related studies, e.g. vehicle detection and classification, mostly focus on static images or video. Whereas mobile laser scanning (MLS) systems are increasingly utilized for urban street environment perception due to their direct 3D information acquisition, high accuracy and movability. In this paper, we design a complete system for car park monitoring, including vehicle recognition, localization, classification and change detection, from laser scanning point clouds. The experimental data are acquired by an MLS system using high frequency laser scanner which scans the streets vertically along the system's moving trajectory. The point clouds are firstly classified as ground, building façade, and street objects which are then segmented using state-of-the-art methods. Each segment is treated as an object hypothesis, and its geometric features are extracted. Moreover, a deformable vehicle model is fitted to each object. By fitting an explicit model to the vehicle points, detailed information, such as precise position and orientation, can be obtained. The model parameters are also treated as vehicle features. Together with the geometric features, they are applied to a supervised learning procedure for vehicle or non-vehicle recognition. The classes of detected vehicles are also investigated. Whether vehicles have changed across two datasets acquired at different times is detected to estimate the durations. Here, vehicles are trained pair-wisely. Two same or different vehicles are paired up as training samples. As a result, the vehicle recognition, classification and change detection accuracies are 95.9%, 86.0% and 98.7%, respectively. Vehicle modelling improves not only the recognition rate, but also the localization precision compared to bounding boxes.

  10. Automatic detection of cone photoreceptors in split detector adaptive optics scanning light ophthalmoscope images

    PubMed Central

    Cunefare, David; Cooper, Robert F.; Higgins, Brian; Katz, David F.; Dubra, Alfredo; Carroll, Joseph; Farsiu, Sina

    2016-01-01

    Quantitative analysis of the cone photoreceptor mosaic in the living retina is potentially useful for early diagnosis and prognosis of many ocular diseases. Non-confocal split detector based adaptive optics scanning light ophthalmoscope (AOSLO) imaging reveals the cone photoreceptor inner segment mosaics often not visualized on confocal AOSLO imaging. Despite recent advances in automated cone segmentation algorithms for confocal AOSLO imagery, quantitative analysis of split detector AOSLO images is currently a time-consuming manual process. In this paper, we present the fully automatic adaptive filtering and local detection (AFLD) method for detecting cones in split detector AOSLO images. We validated our algorithm on 80 images from 10 subjects, showing an overall mean Dice’s coefficient of 0.95 (standard deviation 0.03), when comparing our AFLD algorithm to an expert grader. This is comparable to the inter-observer Dice’s coefficient of 0.94 (standard deviation 0.04). To the best of our knowledge, this is the first validated, fully-automated segmentation method which has been applied to split detector AOSLO images. PMID:27231641

  11. Automatic detection of cone photoreceptors in split detector adaptive optics scanning light ophthalmoscope images.

    PubMed

    Cunefare, David; Cooper, Robert F; Higgins, Brian; Katz, David F; Dubra, Alfredo; Carroll, Joseph; Farsiu, Sina

    2016-05-01

    Quantitative analysis of the cone photoreceptor mosaic in the living retina is potentially useful for early diagnosis and prognosis of many ocular diseases. Non-confocal split detector based adaptive optics scanning light ophthalmoscope (AOSLO) imaging reveals the cone photoreceptor inner segment mosaics often not visualized on confocal AOSLO imaging. Despite recent advances in automated cone segmentation algorithms for confocal AOSLO imagery, quantitative analysis of split detector AOSLO images is currently a time-consuming manual process. In this paper, we present the fully automatic adaptive filtering and local detection (AFLD) method for detecting cones in split detector AOSLO images. We validated our algorithm on 80 images from 10 subjects, showing an overall mean Dice's coefficient of 0.95 (standard deviation 0.03), when comparing our AFLD algorithm to an expert grader. This is comparable to the inter-observer Dice's coefficient of 0.94 (standard deviation 0.04). To the best of our knowledge, this is the first validated, fully-automated segmentation method which has been applied to split detector AOSLO images.

  12. Accounting for imperfect detection in ecology: a quantitative review.

    PubMed

    Kellner, Kenneth F; Swihart, Robert K

    2014-01-01

    Detection in studies of species abundance and distribution is often imperfect. Assuming perfect detection introduces bias into estimation that can weaken inference upon which understanding and policy are based. Despite availability of numerous methods designed to address this assumption, many refereed papers in ecology fail to account for non-detection error. We conducted a quantitative literature review of 537 ecological articles to measure the degree to which studies of different taxa, at various scales, and over time have accounted for imperfect detection. Overall, just 23% of articles accounted for imperfect detection. The probability that an article incorporated imperfect detection increased with time and varied among taxa studied; studies of vertebrates were more likely to incorporate imperfect detection. Among articles that reported detection probability, 70% contained per-survey estimates of detection that were less than 0.5. For articles in which constancy of detection was tested, 86% reported significant variation. We hope that our findings prompt more ecologists to consider carefully the detection process when designing studies and analyzing results, especially for sub-disciplines where incorporation of imperfect detection in study design and analysis so far has been lacking.

  13. Optical detection of metastatic cancer cells using a scanned laser pico-projection system

    NASA Astrophysics Data System (ADS)

    Huang, Chih-Ling; Chiu, Wen-Tai; Lo, Yu-Lung; Chuang, Chin-Ho; Chen, Yu-Bin; Chang, Shu-Jing; Ke, Tung-Ting; Cheng, Hung-Chi; Wu, Hua-Lin

    2015-03-01

    Metastasis is responsible for 90% of all cancer-related deaths in humans. As a result, reliable techniques for detecting metastatic cells are urgently required. Although various techniques have been proposed for metastasis detection, they are generally capable of detecting metastatic cells only once migration has already occurred. Accordingly, the present study proposes an optical method for physical characterization of metastatic cancer cells using a scanned laser pico-projection system (SLPP). The validity of the proposed method is demonstrated using five pairs of cancer cell lines and two pairs of non-cancer cell lines treated by IPTG induction in order to mimic normal cells with an overexpression of oncogene. The results show that for all of the considered cell lines, the SLPP speckle contrast of the high-metastatic cells is significantly higher than that of the low-metastatic cells. As a result, the speckle contrast measurement provides a reliable means of distinguishing quantitatively between low- and high-metastatic cells of the same origin. Compared to existing metastasis detection methods, the proposed SLPP approach has many advantages, including a higher throughput, a lower cost, a larger sample size and a more reliable diagnostic performance. As a result, it provides a highly promising solution for physical characterization of metastatic cancer cells in vitro.

  14. Evaluating the performance of selection scans to detect selective sweeps in domestic dogs

    PubMed Central

    Schlamp, Florencia; van der Made, Julian; Stambler, Rebecca; Chesebrough, Lewis; Boyko, Adam R.; Messer, Philipp W.

    2015-01-01

    Selective breeding of dogs has resulted in repeated artificial selection on breed-specific morphological phenotypes. A number of quantitative trait loci associated with these phenotypes have been identified in genetic mapping studies. We analyzed the population genomic signatures observed around the causal mutations for 12 of these loci in 25 dog breeds, for which we genotyped 25 individuals in each breed. By measuring the population frequencies of the causal mutations in each breed, we identified those breeds in which specific mutations most likely experienced positive selection. These instances were then used as positive controls for assessing the performance of popular statistics to detect selection from population genomic data. We found that artificial selection during dog domestication has left characteristic signatures in the haplotype and nucleotide polymorphism patterns around selected loci that can be detected in the genotype data from a single population sample. However, the sensitivity and accuracy at which such signatures were detected varied widely between loci, the particular statistic used, and the choice of analysis parameters. We observed examples of both hard and soft selective sweeps and detected strong selective events that removed genetic diversity almost entirely over regions >10 Mbp. Our study demonstrates the power and limitations of selection scans in populations with high levels of linkage disequilibrium due to severe founder effects and recent population bottlenecks. PMID:26589239

  15. Evaluating the performance of selection scans to detect selective sweeps in domestic dogs.

    PubMed

    Schlamp, Florencia; van der Made, Julian; Stambler, Rebecca; Chesebrough, Lewis; Boyko, Adam R; Messer, Philipp W

    2016-01-01

    Selective breeding of dogs has resulted in repeated artificial selection on breed-specific morphological phenotypes. A number of quantitative trait loci associated with these phenotypes have been identified in genetic mapping studies. We analysed the population genomic signatures observed around the causal mutations for 12 of these loci in 25 dog breeds, for which we genotyped 25 individuals in each breed. By measuring the population frequencies of the causal mutations in each breed, we identified those breeds in which specific mutations most likely experienced positive selection. These instances were then used as positive controls for assessing the performance of popular statistics to detect selection from population genomic data. We found that artificial selection during dog domestication has left characteristic signatures in the haplotype and nucleotide polymorphism patterns around selected loci that can be detected in the genotype data from a single population sample. However, the sensitivity and accuracy at which such signatures were detected varied widely between loci, the particular statistic used and the choice of analysis parameters. We observed examples of both hard and soft selective sweeps and detected strong selective events that removed genetic diversity almost entirely over regions >10 Mbp. Our study demonstrates the power and limitations of selection scans in populations with high levels of linkage disequilibrium due to severe founder effects and recent population bottlenecks.

  16. Perfusion lung scan: an aid in detection of lymphangitic carcinomatosis

    SciTech Connect

    Bates, S.E.; Tranum, B.L.

    1982-07-15

    Lymphangitic carcinomatosis is usually a late manifestation of metastatic disease. The patient usually presents with cough or dyspnea, and the chest radiograph is often nondiagnostic. Two patients are presented who developed symptoms while on adjuvant chemotherapy. Both had abnormal perfusion lung scans. One had matching ventilation defects; the other a normal ventilation study. Biopsy revealed metastatic carcinoma; in one case tumor was seen in both the pulmonary lymphatics and arterioles; in the other, tumor was identified but the site could not be specified. The radionuclide lung scan is a technique which can speed diagnosis and institution of therapy in lymphangitic carcinomatosis.

  17. Does the truth come out in the writing? Scan as a lie detection tool.

    PubMed

    Nahari, Galit; Vrij, Aldert; Fisher, Ronald P

    2012-02-01

    We tested the accuracy of Scientific Content Analysis (SCAN), a verbal lie detection tool that is used world-wide by federal law enforcement and military agencies. Sixty-one participants were requested to write down the truth, an outright lie or a concealment lie about activities they had just completed. The statements were coded with SCAN and with another verbal lie detection tool, Reality Monitoring (RM). RM discriminated significantly between truth tellers and outright liars and between truth tellers and concealment liars, whereas SCAN did not discriminate between truth tellers and either kind of liar. Implications of the findings for the suitability of SCAN as a lie detection tool are discussed.

  18. Quantitative imaging of graphene impedance with the near-field scanning microwave microscope.

    SciTech Connect

    Kalugin, Nikolai G.; Gonzales, Edward; Kalichava, Irakli; Gin, Aaron V.; Wickey, Lee; Del Barga, Christopher; Talanov, Vladimir V.; Shaner, Eric Arthur

    2010-07-01

    Graphene has emerged as a promising material for high speed nano-electronics due to the relatively high carrier mobility that can be achieved. To further investigate electronic transport in graphene and reveal its potential for microwave applications, we employed a near-field scanning microwave microscope with the probe formed by an electrically open end of a 4 GHz half-lambda parallel-strip transmission line resonator. Because of the balanced probe geometry, our microscope allows for truly localized quantitative characterization of various bulk and low-dimensional materials, with the response region defined by the one micron spacing between the two metallic strips at the probe tip. The single- and few-layer graphene flakes were fabricated by a mechanical cleavage method on 300-nm-thick silicon dioxide grown on low resistivity Si wafer. The flake thickness was determined using both AFM and Raman microscopies. We observe clear correlation between the near-field microwave and far-field optical images of graphene produced by the probe resonant frequency shift and thickness-defined color gradation, respectively. We show that the microwave response of graphene flakes is determined by the local sheet impedance, which is found to be predominantly active. Furthermore, we apply a quantitative electrodynamic model relating the probe resonant frequency shift to 2D conductivity of single- and few-layer graphene. From fitting a model to the experimental data we evaluate graphene sheet resistance as a function of thickness. Near-field scanning microwave microscopy can simultaneously image location, geometry, thickness, and distribution of electrical properties of graphene without a need for device fabrication. The approach may be useful for design of graphene-based microwave transistors, quality control of large area graphene sheets, or investigation of chemical and electrical doping effects on graphene transport properties. We acknowledge support from the DOE Center for

  19. High-resolution quantitative determination of dielectric function by using scattering scanning near-field optical microscopy.

    PubMed

    Tranca, D E; Stanciu, S G; Hristu, R; Stoichita, C; Tofail, S A M; Stanciu, G A

    2015-07-03

    A new method for high-resolution quantitative measurement of the dielectric function by using scattering scanning near-field optical microscopy (s-SNOM) is presented. The method is based on a calibration procedure that uses the s-SNOM oscillating dipole model of the probe-sample interaction and quantitative s-SNOM measurements. The nanoscale capabilities of the method have the potential to enable novel applications in various fields such as nano-electronics, nano-photonics, biology or medicine.

  20. Approximating the Poisson Scan and (lambda-sigma) Acoustic Detection Model with the Random Search Formula

    DTIC Science & Technology

    2009-12-01

    of area search with acoustic sensors modeled by the Poisson Scan model and the Lambda-Sigma model. Detection time results are compared to those...MATLAB simulation of area search with acoustic sensors modeled by the Poisson Scan model and the Lambda-Sigma  model. Detection time results are...study, the author develops a MATLAB simulation of area search with acoustic sensors modeled by the Poisson Scan and the Lambda-Sigma  models. Both

  1. Benign Brenner tumor of the ovary detected on Tc-99m methylene diphosphonate bone scan

    SciTech Connect

    Renner, J.B.; McCartney, W.H.

    1984-11-01

    Many disease states, including neoplasia, have been detected by bone scanning. Among the neoplastic processes detected by bone imaging agents are ovarian tumors, both benign and malignant. This report is concerned with the visualization of a benign Brenner tumor during routine Tc-99m MDP bone scanning.

  2. Reproducibility and quantitation of amplicon sequencing-based detection

    PubMed Central

    Zhou, Jizhong; Wu, Liyou; Deng, Ye; Zhi, Xiaoyang; Jiang, Yi-Huei; Tu, Qichao; Xie, Jianping; Van Nostrand, Joy D; He, Zhili; Yang, Yunfeng

    2011-01-01

    To determine the reproducibility and quantitation of the amplicon sequencing-based detection approach for analyzing microbial community structure, a total of 24 microbial communities from a long-term global change experimental site were examined. Genomic DNA obtained from each community was used to amplify 16S rRNA genes with two or three barcode tags as technical replicates in the presence of a small quantity (0.1% wt/wt) of genomic DNA from Shewanella oneidensis MR-1 as the control. The technical reproducibility of the amplicon sequencing-based detection approach is quite low, with an average operational taxonomic unit (OTU) overlap of 17.2%±2.3% between two technical replicates, and 8.2%±2.3% among three technical replicates, which is most likely due to problems associated with random sampling processes. Such variations in technical replicates could have substantial effects on estimating β-diversity but less on α-diversity. A high variation was also observed in the control across different samples (for example, 66.7-fold for the forward primer), suggesting that the amplicon sequencing-based detection approach could not be quantitative. In addition, various strategies were examined to improve the comparability of amplicon sequencing data, such as increasing biological replicates, and removing singleton sequences and less-representative OTUs across biological replicates. Finally, as expected, various statistical analyses with preprocessed experimental data revealed clear differences in the composition and structure of microbial communities between warming and non-warming, or between clipping and non-clipping. Taken together, these results suggest that amplicon sequencing-based detection is useful in analyzing microbial community structure even though it is not reproducible and quantitative. However, great caution should be taken in experimental design and data interpretation when the amplicon sequencing-based detection approach is used for quantitative

  3. Three-dimensional visualization and quantitation of fibrin in solid tumors by confocal laser scanning microscopy.

    PubMed

    Biggerstaff, J; Amirkhosravi, A; Francis, J L

    1997-10-01

    Fibrin forms part of the stroma essential for growth of solid tumors. Anticoagulants reduce primary tumor growth and tumor metastasis in murine and some human tumors. These effects may be partly mediated by reduction of intra-tumor fibrin, although there are no quantitative data to support this hypothesis. We therefore evaluated the effect of warfarin on fibrin deposition in a subcutaneously (s.c.) implanted murine tumor using confocal laser scanning microscopy (CLSM). AJ mice received no treatment (n = 6) or sodium warfarin (3.5 mg/L in drinking water, n = 5). All animals received 2 x 10(6) syngeneic Neuro2a neuroblastoma cells s.c. After 14 days, primary tumors were excised and placed in liquid nitrogen. Warfarin treatment resulted in a small, but significant (P < 0.05), decrease in wet tumor weight. Frozen sections (20 microns) were incubated with goat anti-mouse fibrin(ogen) or normal goat serum (isotypic control) and stained with FITC-conjugated rabbit anti-goat antibody. Using a Multiprobe 2001 CLSM (Molecular Dynamics, Sunnyvale, CA), 20 serial optical sections were taken from five, randomly chosen, high power fields (60x objective) for each slide. A threshold excluded all fluorescence except that from structural components within the tumor stroma (fibrin). The volume of fibrin in each section series was determined, and the percentage of tumor volume occupied by fibrin calculated. Intra- and inter-assay variation were assessed on serial frozen tumor sections from an untreated animal. The percentage fibrin volume was not significantly different among or within experiments, indicating that the procedure was reproducible. In controls, the median (range) volume occupied by fibrin was 8.1% (2.4-22.3%), whereas in anticoagulated animals, this was reduced to 3.7% (0.4-14.0%; P < 0.001). This is the first quantitative demonstration that warfarin reduces fibrin deposition in solid tumors. We conclude that three-dimensional CLSM is useful for the quantitation of

  4. Polymorphism in nimodipine raw materials: development and validation of a quantitative method through differential scanning calorimetry.

    PubMed

    Riekes, Manoela Klüppel; Pereira, Rafael Nicolay; Rauber, Gabriela Schneider; Cuffini, Silvia Lucia; de Campos, Carlos Eduardo Maduro; Silva, Marcos Antonio Segatto; Stulzer, Hellen Karine

    2012-11-01

    Due to the physical-chemical and therapeutic impacts of polymorphism, its monitoring in raw materials is necessary. The purpose of this study was to develop and validate a quantitative method to determine the polymorphic content of nimodipine (NMP) raw materials based on differential scanning calorimetry (DSC). The polymorphs required for the development of the method were characterized through DSC, X-ray powder diffraction (XRPD) and Raman spectroscopy and their polymorphic identity was confirmed. The developed method was found to be linear, robust, precise, accurate and specific. Three different samples obtained from distinct suppliers (NMP 1, NMP 2 and NMP 3) were firstly characterized through XRPD and DSC as polymorphic mixtures. The determination of their polymorphic identity revealed that all samples presented the Modification I (Mod I) or metastable form in greatest proportion. Since the commercial polymorph is Mod I, the polymorphic characteristic of the samples analyzed needs to be investigated. Thus, the proposed method provides a useful tool for the monitoring of the polymorphic content of NMP raw materials.

  5. Quantitative atomic resolution mapping using high-angle annular dark field scanning transmission electron microscopy.

    PubMed

    Van Aert, S; Verbeeck, J; Erni, R; Bals, S; Luysberg, M; Van Dyck, D; Van Tendeloo, G

    2009-09-01

    A model-based method is proposed to relatively quantify the chemical composition of atomic columns using high angle annular dark field (HAADF) scanning transmission electron microscopy (STEM) images. The method is based on a quantification of the total intensity of the scattered electrons for the individual atomic columns using statistical parameter estimation theory. In order to apply this theory, a model is required describing the image contrast of the HAADF STEM images. Therefore, a simple, effective incoherent model has been assumed which takes the probe intensity profile into account. The scattered intensities can then be estimated by fitting this model to an experimental HAADF STEM image. These estimates are used as a performance measure to distinguish between different atomic column types and to identify the nature of unknown columns with good accuracy and precision using statistical hypothesis testing. The reliability of the method is supported by means of simulated HAADF STEM images as well as a combination of experimental images and electron energy-loss spectra. It is experimentally shown that statistically meaningful information on the composition of individual columns can be obtained even if the difference in averaged atomic number Z is only 3. Using this method, quantitative mapping at atomic resolution using HAADF STEM images only has become possible without the need of simultaneously recorded electron energy loss spectra.

  6. A new quantitative method to measure activity of ice structuring proteins using differential scanning calorimetry.

    PubMed

    Hassa-Roudsari, Majid; Goff, H Douglas

    2012-01-01

    There are very few quantitative assays to measure the activity of antifreeze proteins (AFPs, or Ice Structuring Proteins, ISPs) and these can be prone to various inaccuracies and inconsistencies. Some methods rely only on unassisted visual assessment. When microscopy is used to measure ice crystal size, it is critical that standardized procedures be adopted, especially when image analysis software is used to quantify sizes. Differential Scanning Calorimetry (DSC) has been used to measure the thermal hysteresis activity (TH) of AFPs. In this study, DSC was used isothermally to measure enthalpic changes associated with structural rearrangements as a function of time. Differences in slopes of isothermal heat flow vs. time between winter wheat ISP or AFP type I containing samples, and those without ISP or AFP type I were demonstrated. ISP or AFP type I containing samples had significantly higher slopes compared to those without ISP or AFP type I. Samples with higher concentration of ISP or AFP type I showed higher slope values during the first hour and took up to 3 hr to attain equilibrium. Differences were attributed to activity of the proteins at the ice interface. Proteinaceous activity of ISPs or AFP type I was confirmed by loss of activity after treatment with protease.

  7. Weak-beam scanning transmission electron microscopy for quantitative dislocation density measurement in steels.

    PubMed

    Yoshida, Kenta; Shimodaira, Masaki; Toyama, Takeshi; Shimizu, Yasuo; Inoue, Koji; Yoshiie, Toshimasa; Milan, Konstantinovic J; Gerard, Robert; Nagai, Yasuyoshi

    2017-04-01

    To evaluate dislocations induced by neutron irradiation, we developed a weak-beam scanning transmission electron microscopy (WB-STEM) system by installing a novel beam selector, an annular detector, a high-speed CCD camera and an imaging filter in the camera chamber of a spherical aberration-corrected transmission electron microscope. The capabilities of the WB-STEM with respect to wide-view imaging, real-time diffraction monitoring and multi-contrast imaging are demonstrated using typical reactor pressure vessel steel that had been used in an European nuclear reactor for 30 years as a surveillance test piece with a fluence of 1.09 × 1020 neutrons cm-2. The quantitatively measured size distribution (average loop size = 3.6 ± 2.1 nm), number density of the dislocation loops (3.6 × 1022 m-3) and dislocation density (7.8 × 1013 m m-3) were carefully compared with the values obtained via conventional weak-beam transmission electron microscopy studies. In addition, cluster analysis using atom probe tomography (APT) further demonstrated the potential of the WB-STEM for correlative electron tomography/APT experiments. © The Author 2017. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  8. Scanning mass spectrometer for quantitative reaction studies on catalytically active microstructures.

    PubMed

    Roos, M; Kielbassa, S; Schirling, C; Häring, T; Bansmann, J; Behm, R J

    2007-08-01

    We describe an apparatus for spatially resolving scanning mass spectrometry which is able to measure the gas composition above catalytically active microstructures or arrays of these microstructures with a lateral resolution of better than 100 mum under reaction conditions and which allows us to quantitatively determine reaction rates on individual microstructures. Measurements of the three-dimensional gas composition at different vertical distances and separations between active structures allow the evaluation of gas phase mass transport effects. The system is based on a piezoelectrically driven positioning substage for controlled lateral and vertical positioning of the sample under a rigidly mounted capillary probe connecting to a mass spectrometer. Measurements can be performed at pressures in the range of <10(-2)-10 mbars and temperatures between room temperature and 450 degrees C. The performance of the setup is demonstrated using the CO oxidation reaction on Pt microstructures on Si with sizes between 100 and 300 mum and distances in the same order of magnitude, evaluating CO(2) formation and CO consumption above the microstructures. The rapidly decaying lateral resolution with increasing distance between sample and probe underlines the effects of (lateral) gas transport in the room between sample and probe. The reaction rates and apparent activation energy obtained from such measurements agree with previous data on extended surfaces, demonstrating the feasibility of determining absolute reaction rates on individual microstructures.

  9. Scanning mass spectrometer for quantitative reaction studies on catalytically active microstructures

    SciTech Connect

    Roos, M.; Kielbassa, S.; Schirling, C.; Haering, T.; Bansmann, J.; Behm, R. J.

    2007-08-15

    We describe an apparatus for spatially resolving scanning mass spectrometry which is able to measure the gas composition above catalytically active microstructures or arrays of these microstructures with a lateral resolution of better than 100 {mu}m under reaction conditions and which allows us to quantitatively determine reaction rates on individual microstructures. Measurements of the three-dimensional gas composition at different vertical distances and separations between active structures allow the evaluation of gas phase mass transport effects. The system is based on a piezoelectrically driven positioning substage for controlled lateral and vertical positioning of the sample under a rigidly mounted capillary probe connecting to a mass spectrometer. Measurements can be performed at pressures in the range of <10{sup -2}-10 mbars and temperatures between room temperature and 450 deg. C. The performance of the setup is demonstrated using the CO oxidation reaction on Pt microstructures on Si with sizes between 100 and 300 {mu}m and distances in the same order of magnitude, evaluating CO{sub 2} formation and CO consumption above the microstructures. The rapidly decaying lateral resolution with increasing distance between sample and probe underlines the effects of (lateral) gas transport in the room between sample and probe. The reaction rates and apparent activation energy obtained from such measurements agree with previous data on extended surfaces, demonstrating the feasibility of determining absolute reaction rates on individual microstructures.

  10. Rapid and quantitative detection of hepatitis B virus.

    PubMed

    Liu, Yue-Ping; Yao, Chun-Yan

    2015-11-14

    Despite availability of a universal vaccine, hepatitis B virus (HBV) infection has a huge impact on public health worldwide. Accurate and timely diagnosis of HBV infection is needed. Rapid developments have been made in the diagnostic and monitoring methods for HBV infection, including serological and molecular assays. In clinical practice, qualitative hepatitis B surface antigen (HBsAg) testing has long served as a diagnostic marker for individuals infected with HBV. More recently, HBsAg level has been used to predict treatment outcome when determined early during treatment or at baseline. However, identification of HBV DNA positive cases that do not have detectable HBsAg has encouraged the application of molecular tests. Hence, combination of quantitative detection of HBV DNA and HBsAg can be used to discriminate patients during the course of HBV infection and to monitor therapy. This article reviews the most commonly used quantitative methods for HBsAg and HBV DNA.

  11. Labeled leukocyte scans for detection of retained polyurethane foam

    SciTech Connect

    Ellenberger, P.; Graham, W.P. 3d.; Manders, E.K.; Basarab, R.M.

    1986-01-01

    Complete removal of an infected polyurethane-covered breast prosthesis is difficult, and retained tissue-embedded foam can form a nidus for persistent infection. Scanning the chest wall after administration of indium-111 oxine-labeled autogenous leukocytes will locate areas of infection around retained fragments of foam, thereby facilitating their removal and allowing eventual successful reconstruction. This technique may deserve wider application for locating infected foreign bodies in a variety of patient problems.

  12. Perfusion lung scan: an aid in detection of lymphangitic carcinomatosis

    SciTech Connect

    Bates, S.E.; Tranum, B.L.

    1982-07-15

    Lymphangitic carcinomatosis is usually a late manifestation of metastatic disease. The patient usually presents with cough or dyspnea, and the chest radiograph is often nondiagnostic. Two patients are presented who developed symptoms while on adjuvant chemotherapy. Both had abnormal perfusion lung scans. One had matching ventilation defects; the other a normal ventilation study. Biopsy revealed metastatic carcinoma; in one case tumor was seen in both the pulmonary lymphatics and arterioles; in technique which can speed diagnosis and institution of therapy in lymphangitic carcinomatosis.

  13. Detection of varicocele by radionuclide blood-pool scanning

    SciTech Connect

    Freund, J.; Handelsman, D.J.; Bautovich, G.J.; Conway, A.J.; Morris, J.G.

    1980-10-01

    Varicocele is a common and treatable cause of male subfertility. The authors describe a new technique for varicocele detection using radionuclide blood-pool imaging of the scrotum. The results indicate that this technique detects unilateral varicoceles with high sensitivity, including some which are subclinical. There may be significant implications for treatment of infertility.

  14. Quantitative scanning thermal microscopy of graphene devices on flexible polyimide substrates

    NASA Astrophysics Data System (ADS)

    Sadeghi, Mir Mohammad; Park, Saungeun; Huang, Yu; Akinwande, Deji; Yao, Zhen; Murthy, Jayathi; Shi, Li

    2016-06-01

    A triple-scan scanning thermal microscopy (SThM) method and a zero-heat flux laser-heated SThM technique are investigated for quantitative thermal imaging of flexible graphene devices. A similar local tip-sample thermal resistance is observed on both the graphene and metal areas of the sample, and is attributed to the presence of a polymer residue layer on the sample surface and a liquid meniscus at the tip-sample junction. In addition, it is found that the tip-sample thermal resistance is insensitive to the temperature until it begins to increase as the temperature increases to 80 °C and exhibits an abrupt increase at 110 °C because of evaporation of the liquid meniscus at the tip-sample junction. Moreover, the variation in the tip-sample thermal resistance due to surface roughness is within the experimental tolerance except at areas with roughness height exceeding tens of nanometers. Because of the low thermal conductivity of the flexible polyimide substrate, the SThM measurements have found that the temperature rise in flexible graphene devices is more than one order of magnitude higher than those reported for graphene devices fabricated on a silicon substrate with comparable dimensions and power density. Unlike a graphene device on a silicon substrate where the majority of the electrical heating in the graphene device is conducted vertically through the thin silicon dioxide dielectric layer to the high-thermal conductivity silicon substrate, lateral heat spreading is important in the flexible graphene devices, as shown by the observed decrease in the average temperature rise normalized by the power density with decreasing graphene channel length from about 30 μm to 10 μm. However, it is shown by numerical heat transfer analysis that this trend is mainly caused by the size scaling of the thermal spreading resistance of the polymer substrate instead of lateral heat spreading by the graphene. In addition, thermoelectric effects are found to be negligible

  15. Quantitative and qualitative image quality analysis of super resolution images from a low cost scanning laser ophthalmoscope

    NASA Astrophysics Data System (ADS)

    Murillo, Sergio; Echegaray, Sebastian; Zamora, Gilberto; Soliz, Peter; Bauman, Wendall

    2011-03-01

    The lurking epidemic of eye diseases caused by diabetes and aging will put more than 130 million Americans at risk of blindness by 2020. Screening has been touted as a means to prevent blindness by identifying those individuals at risk. However, the cost of most of today's commercial retinal imaging devices makes their use economically impractical for mass screening. Thus, low cost devices are needed. With these devices, low cost often comes at the expense of image quality with high levels of noise and distortion hindering the clinical evaluation of those retinas. A software-based super resolution (SR) reconstruction methodology that produces images with improved resolution and quality from multiple low resolution (LR) observations is introduced. The LR images are taken with a low-cost Scanning Laser Ophthalmoscope (SLO). The non-redundant information of these LR images is combined to produce a single image in an implementation that also removes noise and imaging distortions while preserving fine blood vessels and small lesions. The feasibility of using the resulting SR images for screening of eye diseases was tested using quantitative and qualitative assessments. Qualitatively, expert image readers evaluated their ability of detecting clinically significant features on the SR images and compared their findings with those obtained from matching images of the same eyes taken with commercially available high-end cameras. Quantitatively, measures of image quality were calculated from SR images and compared to subject-matched images from a commercial fundus imager. Our results show that the SR images have indeed enough quality and spatial detail for screening purposes.

  16. Modeling of the lung nodules for detection in LDCT scans.

    PubMed

    Farag, Amal; Elhabian, Shireen; Graham, James; Farag, Aly; Elshazly, Salwa; Falk, Robert; Mahdi, Hani; Abdelmunim, Hossam; Al-Ghaafary, Sahar

    2010-01-01

    A novel approach is proposed for generating data driven models of the lung nodules appearing in low dose CT (LDCT) scans of the human chest. Four types of common lung nodules are analyzed using Active Appearance Model methods to create descriptive lung nodule models. The proposed approach is also applicable for automatic classification of nodules into pathologies given a descriptive database. This approach is a major step forward for early diagnosis of lung cancer. We show the performance of the new nodule models on clinical datasets which illustrates significant improvements in both sensitivity and specificity.

  17. Barriers to Quantitative Electron Probe X-Ray Microanalysis for Low Voltage Scanning Electron Microscopy.

    PubMed

    Newbury, Dale E

    2002-01-01

    Low voltage x-ray microanalysis, defined as being performed with an incident beam energy ≤5 keV, can achieve spatial resolution, laterally and in depth, of 100 nm or less, depending on the exact selection of beam energy and the composition of the target. The shallow depth of beam penetration, with the consequent short path length for x-ray absorption, and the low overvoltage, the ratio of beam energy to the critical ionization energy, both contribute to minimizing the matrix effects in quantitative x-ray microanalysis when the unknown is compared to pure element standards. The low beam energy restricts the energy of the atomic shells that can be excited, forcing the analyst to choose unfamiliar shells/characteristic peaks. The low photon energy shells are subject to low fluorescence yield, so that the peak-to-continuum background is reduced, severely limiting detectability. The limited resolution of semiconductor energy dispersive spectrometry results in frequent peak interference situations and further exacerbates detection limits. Future improvements to the x-ray spectrometry limitations are possible with x-ray optics-augmented wavelength dispersive spectrometry and microcalorimeter energy dispersive spectrometry.

  18. Rapid detection and quantitation of ganciclovir resistance in cytomegalovirus quasispecies.

    PubMed

    Ruiz-Carrascoso, Guillermo; Romero-Gómez, María Pilar; Plaza, Diego; Mingorance, Jesús

    2013-07-01

    Human cytomegalovirus (HCMV) may cause severe or fatal disease among immunocompromised patients. The first line prophylaxis and systemic HCMV disease therapy is ganciclovir (GCV). The presence of GCV-resistant virus has been linked to fatal HCMV disease. The implementation of rapid and sensitive techniques for the early detection and monitoring of GCV-resistance may be helpful to support antiviral therapy management. A pyrosequencing assay for the detection and quantitation of the most frequent mutations conferring moderate- and high-grade GCV resistance was implemented. The pyrosequencing achieved an analytical sensitivity for adequate interpretation of ≥10(3)  copies/ml. The assay was validated with 18 whole blood samples taken over a 6-month period from an umbilical cord blood recipient infected persistently with HCMV and allowed the detection and monitoring of the M460I and A594V GCV-resistant mutations. The percentage of resistant quasispecies ranged from 7.9% to 55.2% for the M460I mutation and from 19.8% to 43% for the A594V mutation. Clearance of the M460I mutation occurred in parallel with a decrease in the HCMV viremia, while the A594V mutation persisted. The pyrosequencing method for detection of GCV is sensitive enough to be used directly on clinical samples for the early identification of resistance mutations and allows the quantitation of resistant and wild type virus quasispecies within hours. The quantitation of minor resistant variants is an important issue to understand their relationship with viral load modification, and potentially anticipate treatment adjustment.

  19. Blastomyces dermatitidis Antigen Detection by Quantitative Enzyme Immunoassay

    PubMed Central

    Hage, Chadi A.; Bariola, J. Ryan; Bensadoun, Eric; Rodgers, Mark; Bradsher, Robert W.; Wheat, L. Joseph

    2012-01-01

    The second-generation MVista Blastomyces antigen enzyme immunoassay was not quantitative; therefore, specimens obtained previously were tested in the same assay as new specimens to assess the change in antigen levels. Furthermore, the sensitivity in serum had not been fully evaluated. The purpose of this study was to evaluate a quantitative Blastomyces antigen assay and detection of antigen in serum. Calibrators containing known concentrations of Blastomyces galactomannan were used to quantify antigen in urine and serum from patients with proven blastomycosis and from controls. Paired current and previously obtained urine specimens were tested to determine if quantification eliminated the need for concurrent testing to assess change in antigen. Pretreatment of serum with EDTA at 104°C was evaluated to determine if dissociation of immune complexes improved detection of antigenemia. Antigenuria was detected in 89.9% of patients with culture- or histopathology-proven blastomycosis. Specificity was 99.0% in patients with nonfungal infections and healthy subjects, but cross-reactions occurred in 95.6% of patients with histoplasmosis. Change in antigen level categorized as increase, no change, or decrease based on antigen units determined in the same assay agreed closely with the category of change in ng/ml determined from different assays. Pretreatment increased the sensitivity of detection of antigenemia from 35.7% to 57.1%. Quantification eliminated the need for concurrent testing of current and previously obtained specimens for assessment of changes in antigen concentration. Pretreatment increased the sensitivity for detection of antigenemia. Differentiation of histoplasmosis and blastomycosis is not possible by antigen detection. PMID:22116687

  20. Terrestrial laser scanning used to detect asymmetries in boat hulls

    NASA Astrophysics Data System (ADS)

    Roca-Pardiñas, Javier; López-Alvarez, Francisco; Ordóñez, Celestino; Menéndez, Agustín; Bernardo-Sánchez, Antonio

    2012-01-01

    We describe a methodology for identifying asymmetries in boat hull sections reconstructed from point clouds captured using a terrestrial laser scanner (TLS). A surface was first fit to the point cloud using a nonparametric regression method that permitted the construction of a continuous smooth surface. Asymmetries in cross-sections of the surface were identified using a bootstrap resampling technique that took into account uncertainty in the coordinates of the scanned points. Each reconstructed section was analyzed to check, for a given level of significance, that it was within the confidence interval for the theoretical symmetrical section. The method was applied to the study of asymmetries in a medium-sized yacht. Identified were differences of up to 5 cm between the real and theoretical sections in some parts of the hull.

  1. Quantitative Analysis of Torso FDG-PET Scans by Using Anatomical Standardization of Normal Cases from Thorough Physical Examinations.

    PubMed

    Hara, Takeshi; Kobayashi, Tatsunori; Ito, Satoshi; Zhou, Xiangrong; Katafuchi, Tetsuro; Fujita, Hiroshi

    2015-01-01

    Understanding of standardized uptake value (SUV) of 2-deoxy-2-[18F]fluoro-d-glucose positron emission tomography (FDG-PET) depends on the background accumulations of glucose because the SUV often varies the status of patients. The purpose of this study was to develop a new method for quantitative analysis of SUV of FDG-PET scan images. The method included an anatomical standardization and a statistical comparison with normal cases by using Z-score that are often used in SPM or 3D-SSP approach for brain function analysis. Our scheme consisted of two approaches, which included the construction of a normal model and the determination of the SUV scores as Z-score index for measuring the abnormality of an FDG-PET scan image. To construct the normal torso model, all of the normal images were registered into one shape, which indicated the normal range of SUV at all voxels. The image deformation process consisted of a whole body rigid registration of shoulder to bladder region and liver registration and a non-linear registration of body surface by using the thin-plate spline technique. In order to validate usefulness of our method, we segment suspicious regions on FDG-PET images manually, and obtained the Z-scores of the regions based on the corresponding voxels that stores the mean and the standard deviations from the normal model. We collected 243 (143 males and 100 females) normal cases to construct the normal model. We also extracted 432 abnormal spots from 63 abnormal cases (73 cancer lesions) to validate the Z-scores. The Z-scores of 417 out of 432 abnormal spots were higher than 2.0, which statistically indicated the severity of the spots. In conclusions, the Z-scores obtained by our computerized scheme with anatomical standardization of torso region would be useful for visualization and detection of subtle lesions on FDG-PET scan images even when the SUV may not clearly show an abnormality.

  2. Quantitative linkage: a statistical procedure for its detection and estimation.

    PubMed

    Hill, A P

    1975-05-01

    A new approach for detecting and estimating quantitative linkage which uses sibship data is presented. Using a nested analysis of variance design (with marker genotype nested within sibship), it is shown that under the null hypothesis of no linkage, the expected between marker genotype within sibship mean square (EMSbeta) is equal to the expected within marker genotype within sibship mean square (EMSe), while under the alternative hypothesis of linkage, the first is greater than the second. Thus the regular F-ratio, MSbeta/MSe, can be used to test for quantitative linkage. This is true for both backcross and intercross matings and whether or not there is dominance at the marker locus. A second test involving the comparison of the within marker genotype within sibship variances is available for intercross matings. A maximum likelihood procedure for the estimation for the recombination frequency is also presented.

  3. A flexible spatial scan statistic with a restricted likelihood ratio for detecting disease clusters.

    PubMed

    Tango, Toshiro; Takahashi, Kunihiko

    2012-12-30

    Spatial scan statistics are widely used tools for detection of disease clusters. Especially, the circular spatial scan statistic proposed by Kulldorff (1997) has been utilized in a wide variety of epidemiological studies and disease surveillance. However, as it cannot detect noncircular, irregularly shaped clusters, many authors have proposed different spatial scan statistics, including the elliptic version of Kulldorff's scan statistic. The flexible spatial scan statistic proposed by Tango and Takahashi (2005) has also been used for detecting irregularly shaped clusters. However, this method sets a feasible limitation of a maximum of 30 nearest neighbors for searching candidate clusters because of heavy computational load. In this paper, we show a flexible spatial scan statistic implemented with a restricted likelihood ratio proposed by Tango (2008) to (1) eliminate the limitation of 30 nearest neighbors and (2) to have surprisingly much less computational time than the original flexible spatial scan statistic. As a side effect, it is shown to be able to detect clusters with any shape reasonably well as the relative risk of the cluster becomes large via Monte Carlo simulation. We illustrate the proposed spatial scan statistic with data on mortality from cerebrovascular disease in the Tokyo Metropolitan area, Japan.

  4. Quantitative optical imaging for the detection of early cancer

    NASA Astrophysics Data System (ADS)

    Wu, Tao

    The objectives of this thesis are to provide insight of fundamental mechanisms of acetowhitening effect, upon which the colposcopic diagnosis of human cervical cancer is based and to develop novel quantitative optical imaging technologies supplementing colposcopy to improve its performance in detecting early cancer. Firstly, the temporal characteristics of acetowhitening process are studied on monolayer cell cultures. It is found that the dynamic acetowhitening processes in normal and cancerous cells are significantly different. Secondly, the changes in light scattering induced by acetic acid in intact cells and isolated cellular fractions are investigated by using confocal microscopy and light scattering spectroscopy. The results provide evidence that the small-sized components in the cytoplasm are the major contributors to the acetowhitening effect. Thirdly, a unified Mie and fractal model is proposed to interpret light scattering by biological cells. It is found that light scattering in forward directions is dominated by Mie scattering by bare cells and nuclei, whereas light scattering at large angles is determined by fractal scattering by subcellular structures. Fourthly, an optical imaging system based on active stereo vision and motion tracking is built to measure the 3-D surface topology of cervix and track the motion of patient. The information of motion tracking is used to register the time-sequenced images of cervix recorded during colposcopic examination. The imaging system is evaluated by tracking the movements of cervix models. The results demonstrate that the imaging technique holds the promise to enable the quantitative mapping of the acetowhitening kinetics over cervical surface for more accurate diagnosis of cervical cancer. At last, a calibrated autofluorescence imaging system is instrumented for detecting neoplasia in vivo. It is found that the calibrated autofluorescence signals from neoplasia are generally lower than signals from normal

  5. Universal and specific quantitative detection of botulinum neurotoxin genes

    PubMed Central

    2010-01-01

    Background Clostridium botulinum, an obligate anaerobic spore-forming bacterium, produces seven antigenic variants of botulinum toxin that are distinguished serologically and termed "serotypes". Botulinum toxin blocks the release of acetylcholine at neuromuscular junctions resulting in flaccid paralysis. The potential lethality of the disease warrants a fast and accurate means of diagnosing suspected instances of food contamination or human intoxication. Currently, the Food and Drug Administration (FDA)-accepted assay to detect and type botulinum neurotoxins (BoNTs) is the mouse protection bioassay. While specific and sensitive, this assay requires the use of laboratory animals, may take up to four days to achieve a diagnosis, and is unsuitable for high-throughput analysis. We report here a two-step PCR assay that identifies all toxin types, that achieves the specificity of the mouse bioassay while surpassing it in equivalent sensitivity, that has capability for high-throughput analysis, and that provides quantitative results within hours. The first step of our assay consists of a conventional PCR that detects the presence of C. botulinum regardless of the neurotoxin type. The second step uses quantitative PCR (qPCR) technology to determine the specific serotype of the neurotoxin. Results We assayed purified C. botulinum DNA and crude toxin preparations, as well as food and stool from healthy individuals spiked with purified BoNT DNA, and one stool sample from a case of infant botulism for the presence of the NTNH gene, which is part of the BoNT gene cluster, and for the presence of serotype-specific BoNT genes. The PCR surpassed the mouse bioassay both in specificity and sensitivity, detecting positive signals in BoNT preparations containing well below the 1 LD50 required for detection via the mouse bioassay. These results were type-specific and we were reliably able to quantify as few as 10 genomic copies. Conclusions While other studies have reported

  6. Scanning capacitance detection and charge trapping in NOS

    NASA Astrophysics Data System (ADS)

    Terris, Bruce D.; Barrett, Rick; Mamin, H. Jonathon

    1993-06-01

    Charge trapping in thin films of silicon nitride has long been studied for use as a non-volatile semiconductor memory. Recently, this technology has been combined with scanned probe technologies with the sharp probe tip serving as the upper electrode in a Si3N4- SiO2Si (NOS) structure. By applying a voltage pulse between the tip and silicon substrate, charge carriers can be made to tunnel through the oxide and be trapped in the nitride. This trapped charge causes a shift in the capacitance-voltage curve along the voltage axis; the voltage at which depletion occurs is increased. It has been proposed that such a system could be used as a high density data storage device. We have begun to explore some of the issues related to such an application, including data lifetime and data rates. In thermally accelerated life tests, no sign of charge spreading was seen after 100 days at 150 degree(s)C and from the rate of charge decay we would predict room temperature lifetimes in excess of 1 million years. We have also used an air-bearing spindle to conduct high speed measurements on a spinning NOS sample and obtained data rates as high as 500 kHz with carrier-to-noise ratios of approximately 60 dB in a 3 kHz bandwidth.

  7. Structural damage detection and estimation using a scanning laser vibrometer

    NASA Astrophysics Data System (ADS)

    Pai, Perngjin F.; Lee, Seung-Yoon; Schulz, Mark J.

    2001-07-01

    This paper presents a model-independent boundary effect evaluation (BEE) method for pinpointing crack locations and estimating crack sizes using only operational deflection shapes (ODSs) measured by a scanning laser vibrometer. An ODS consists of central and boundary solutions. Central solutions are periodic functions, and boundary solutions are exponentially decaying functions due to boundary constraints. The BEE method uses a sliding-window curve-fitting technique to extract boundary solutions from an experimental ODS. Because cracks introduce localized small boundaries to a structure, boundary solutions exist around cracks as well as structural boundaries. Since crack-induced boundary solutions show characteristics different from those of actual boundaries, cracks can be easily located. A local strain energy method is derived for estimating crack sizes. In the method, the crack-induced strain energy extracted from an ODS is compared with the one calculated using fracture mechanics to estimate the crack size. To verify the capability and accuracy of this BEE method, experiments are performed on six 22' X 1' X 0.25' 2024-T4 aluminum beams each having a through-the-width Mode I crack at its midpoint. These cracks are slots having a width of 0.039' and depths of 0.0625' (25% of the beam thickness), 0.05' (20%), 0.0375' (15%), 0.025' (10%), 0.0125' (5%), and 0.005' (2%), respectively. Results show that this BEE method is capable of locating and estimating small cracks.

  8. Immunoliposome-PCR: a generic ultrasensitive quantitative antigen detection system

    PubMed Central

    2012-01-01

    Background The accurate quantification of antigens at low concentrations over a wide dynamic range is needed for identifying biomarkers associated with disease and detecting protein interactions in high-throughput microarrays used in proteomics. Here we report the development of an ultrasensitive quantitative assay format called immunoliposome polymerase chain reaction (ILPCR) that fulfills these requirements. This method uses a liposome, with reporter DNA encapsulated inside and biotin-labeled polyethylene glycol (PEG) phospholipid conjugates incorporated into the outer surface of the liposome, as a detection reagent. The antigenic target is immobilized in the well of a microplate by a capture antibody and the liposome detection reagent is then coupled to a biotin-labeled second antibody through a NeutrAvidin bridge. The liposome is ruptured to release the reporter DNA, which serves as a surrogate to quantify the protein target using real-time PCR. Results A liposome detection reagent was prepared, which consisted of a population of liposomes ~120 nm in diameter with each liposome possessing ~800 accessible biotin receptors and ~220 encapsulated reporters. This liposome detection reagent was used in an assay to quantify the concentration of carcinoembryonic antigen (CEA) in human serum. This ILPCR assay exhibited a linear dose–response curve from 10-10 M to 10-16 M CEA. Within this range the assay coefficient of variance was <6 % for repeatability and <2 % for reproducibility. The assay detection limit was 13 fg/mL, which is 1,500-times more sensitive than current clinical assays for CEA. An ILPCR assay to quantify HIV-1 p24 core protein in buffer was also developed. Conclusions The ILPCR assay has several advantages over other immuno-PCR methods. The reporter DNA and biotin-labeled PEG phospholipids spontaneously incorporate into the liposomes as they form, simplifying preparation of the detection reagent. Encapsulation of the reporter inside the

  9. High-resolution quantitative determination of dielectric function by using scattering scanning near-field optical microscopy

    PubMed Central

    Tranca, D. E.; Stanciu, S. G.; Hristu, R.; Stoichita, C.; Tofail, S. A. M.; Stanciu, G. A.

    2015-01-01

    A new method for high-resolution quantitative measurement of the dielectric function by using scattering scanning near-field optical microscopy (s-SNOM) is presented. The method is based on a calibration procedure that uses the s-SNOM oscillating dipole model of the probe-sample interaction and quantitative s-SNOM measurements. The nanoscale capabilities of the method have the potential to enable novel applications in various fields such as nano-electronics, nano-photonics, biology or medicine. PMID:26138665

  10. A genome scan for quantitative trait loci influencing carcass, post-natal growth and reproductive traits in commercial Angus cattle.

    PubMed

    McClure, M C; Morsci, N S; Schnabel, R D; Kim, J W; Yao, P; Rolf, M M; McKay, S D; Gregg, S J; Chapple, R H; Northcutt, S L; Taylor, J F

    2010-12-01

    To gain insight into the number of loci of large effect that underlie variation in cattle, a quantitative trait locus (QTL) scan for 14 economically important traits was performed in two commercial Angus populations using 390 microsatellites, 11 single nucleotide polymorphisms (SNPs) and one duplication loci. The first population comprised 1769 registered Angus bulls born between 1955 and 2003, with Expected Progeny Differences computed by the American Angus Association. The second comprised 38 half-sib families containing 1622 steers with six post-natal growth and carcass phenotypes. Linkage analysis was performed by half-sib least squares regression with gridqtl or Bayesian Markov chain Monte Carlo analysis of complex pedigrees with loki. Of the 673 detected QTL, only 118 have previously been reported, reflecting both the conservative approach to QTL reporting in the literature, and the more liberal approach taken in this study. From 33 to 71% of the genetic variance and 35 to 56% of the phenotypic variance in each trait was explained by the detected QTL. To analyse the effects of 11 SNPs and one duplication locus within candidate genes on each trait, a single marker analysis was performed by fitting an additive allele substitution model in both mapping populations. There were 53 associations detected between the SNP/duplication loci and traits with -log(10) P(nominal) ≥ 4.0, where each association explained 0.92% to 4.4% of the genetic variance and 0.01% to 1.86% of the phenotypic variance. Of these associations, only six SNP/duplication loci were located within 8 cM of a QTL peak for the trait, with two being located at the QTL peak: SST_DG156121:c.362A>G for ribeye muscle area and TG_X05380:c.422C>T for calving ease. Strong associations between several SNP/duplication loci and trait variation were obtained in the absence of any detected linked QTL. However, we reject the causality of several commercialized DNA tests, including an association between TG

  11. Simultaneous detection and fine mapping of quantitative trait loci in mice using heterogeneous stocks.

    PubMed Central

    Mott, Richard; Flint, Jonathan

    2002-01-01

    We describe a method to simultaneously detect and fine map quantitative trait loci (QTL) that is especially suited to the mapping of modifier loci in mouse mutant models. The method exploits the high level of historical recombination present in a heterogeneous stock (HS), an outbred population of mice derived from known founder strains. The experimental design is an F(2) cross between the HS and a genetically distinct line, such as one carrying a knockout or transgene. QTL detection is performed by a standard genome scan with approximately 100 markers and fine mapping by typing the same animals using densely spaced markers over those candidate regions detected by the scan. The analysis uses an extension of the dynamic-programming technique employed previously to fine map QTL in HS mice. We show by simulation that a QTL accounting for 5% of the total variance can be detected and fine mapped with >50% probability to within 3 cM by genotyping approximately 1500 animals. PMID:11973314

  12. Migratory birds use head scans to detect the direction of the earth's magnetic field.

    PubMed

    Mouritsen, Henrik; Feenders, Gesa; Liedvogel, Miriam; Kropp, Wiebke

    2004-11-09

    Night-migratory songbirds are known to use a magnetic compass , but how do they detect the reference direction provided by the geomagnetic field, and where is the sensory organ located? The most prominent characteristic of geomagnetic sensory input, whether based on visual patterns or magnetite-mediated forces , is the predicted symmetry around the north-south or east-west magnetic axis. Here, we show that caged migratory garden warblers perform head-scanning behavior well suited to detect this magnetic symmetry plane. In the natural geomagnetic field, birds move toward their migratory direction after head scanning. In a zero-magnetic field , where no symmetry plane exists, the birds almost triple their head-scanning frequency, and the movement direction after a head scan becomes random. Thus, the magnetic sensory organ is located in the bird's head, and head scans are used to locate the reference direction provided by the geomagnetic field.

  13. Detection of musculoskeletal infection with the indium-III leukocyte scan

    SciTech Connect

    Prchal, C.L.; Kahen, H.L.; Blend, M.J.; Barmada, R.

    1987-09-01

    Indium-111-labeled leukocyte scans were performed on 39 patients with suspected musculoskeletal infections to assess the usefulness of this study in detecting bone and joint infections. Results of these scans, as well as results of technetium-99m bone scans, were correlated with the patients' final diagnoses. The indium scan had an overall sensitivity of 77%, a specificity of 69%, and an accuracy of 72%. In 10 patients with a duration of symptoms of six weeks or less, the sensitivity was 100% and the specificity was 75%. In 29 patients with symptoms of greater than six weeks, the sensitivity and specificity were lower at 50% and 71% respectively. Technetium-99m bone scans were performed on 23 patients; sensitivity for infection was 100% while specificity was 60%. Our results suggest that the indium-111 leukocyte scan is a useful adjunct in the diagnosis of acute musculoskeletal infections, but may be inconclusive in chronic infections.

  14. Quantitative Visualization of Molecular Delivery and Uptake at Living Cells with Self-Referencing Scanning Ion Conductance Microscopy-Scanning Electrochemical Microscopy.

    PubMed

    Page, Ashley; Kang, Minkyung; Armitstead, Alexander; Perry, David; Unwin, Patrick R

    2017-03-07

    A multifunctional dual-channel scanning probe nanopipet that enables simultaneous scanning ion conductance microscopy (SICM) and scanning electrochemical microscopy (SECM) measurements is demonstrated to have powerful new capabilities for spatially mapping the uptake of molecules of interest at living cells. One barrel of the probe is filled with electrolyte and the molecules of interest and is open to the bulk solution for both topographical feedback and local delivery to a target interface, while a solid carbon electrode in the other barrel measures the local concentration and flux of the delivered molecules. This setup allows differentiation in molecular uptake rate across several regions of single cells with individual measurements at nanoscale resolution. Further, operating in a "hopping mode", where the probe is translated toward the interface (cell) at each point allows self-referencing to be employed, in which the carbon electrode response is calibrated at each and every pixel in bulk for comparison to the measurement near the surface. This is particularly important for measurements in living systems where an electrode response may change over time. Finite element method (FEM) modeling places the technique on a quantitative footing to allow the response of the carbon electrode and local delivery rates to be quantified. The technique is extremely versatile, with the local delivery of molecules highly tunable via control of the SICM bias to promote or restrict migration from the pipet orifice. It is expected to have a myriad of applications from drug delivery to screening catalysts.

  15. Acousto-optical deflection-based laser beam scanning for fluorescence detection on multichannel electrophoretic microchips.

    PubMed

    Huang, Z; Munro, N; Hühmer, A F; Landers, J P

    1999-12-01

    Laser beam scanning driven by an acousto-optical deflector (AOD) is presented for multimicrochannel laser-induced fluorescence (LIF) detection during microchip-based electrophoresis. While fast laser beam scanning for LIF detection on capillary or microchannel arrays can been achieved with galvanometric scanning or a translating stage, it can also be accomplished by using acoustic waves to deflect the laser beam in a manner that is dependent on the acoustic frequency. AOD scanning differs from other approaches in that no moving parts are required, and the scan frequency is faster than conventional approaches. Using a digital/analog (D/A) converter to provide addressing voltages to a voltage/frequency converter, rapidly changing the frequency input to the AOD allows the laser beam to be addressed accurately on a microchip. With the ability to change the frequency on the nanosecond time scale, scanning rates as high as 30 Hz for Windows-based LabView programming are possible, with much faster scan rates achievable if a microprocessor-embedded system is utilized. In addition to spatial control, temporal control is easily attainable via raster scanning or random addressing, allowing for the scanning process to be self-aligning. Since the D/A output voltages drive the scanning of the laser beam over all channels, the software can define addressing voltages corresponding to the microchannel centers and, subsequently, fluorescence data can be collected from only those locations. This method allows for flexible, high-speed, self-align scanning for fluorescence detection in capillary or microchip electrophoresis and has the potential to be applied to a number of applications.

  16. Optimal experimental design for the detection of light atoms from high-resolution scanning transmission electron microscopy images

    SciTech Connect

    Gonnissen, J.; De Backer, A.; Martinez, G. T.; Van Aert, S.; Dekker, A. J. den; Rosenauer, A.; Sijbers, J.

    2014-08-11

    We report an innovative method to explore the optimal experimental settings to detect light atoms from scanning transmission electron microscopy (STEM) images. Since light elements play a key role in many technologically important materials, such as lithium-battery devices or hydrogen storage applications, much effort has been made to optimize the STEM technique in order to detect light elements. Therefore, classical performance criteria, such as contrast or signal-to-noise ratio, are often discussed hereby aiming at improvements of the direct visual interpretability. However, when images are interpreted quantitatively, one needs an alternative criterion, which we derive based on statistical detection theory. Using realistic simulations of technologically important materials, we demonstrate the benefits of the proposed method and compare the results with existing approaches.

  17. Sensitivity of Quantitative Signal Detection in Regards to Pharmacological Neuroenhancement

    PubMed Central

    Gahr, Maximilian; Connemann, Bernhard J.; Schönfeldt-Lecuona, Carlos; Zeiss, René

    2017-01-01

    Pharmacological neuroenhancement (PNE) is a form of abuse and has not yet been addressed by methods of pharmacovigilance. In the present study, we tested if quantitative signal detection may be sensitive in regards to PNE. We evaluated the risk of drug abuse and dependence (DAAD) related to substances that are known to be used for PNE and divided this group into agents with (methylphenidate) and without a known abuse potential outside the field of PNE (atomoxetine, modafinil, acetylcholine esterase inhibitors, and memantine). Reporting odds ratios (RORs) were calculated using a case/non-case approach based on global and country-specific drug safety data from the Uppsala Monitoring Centre (UMC). Both control substances (diazepam and lorazepam) and methylphenidate were statistically associated with DAAD in all datasets (except methylphenidate in Italy). Modafinil was associated with DAAD in the total dataset (ROR, 2.7 (95% confidence interval (CI), 2.2–3.3)), Germany (ROR, 4.6 (95% CI, 1.8–11.5)), and the USA (ROR, 2.0 (95% CI, 1.6–2.5)). Atomoxetine was associated with DAAD in the total dataset (ROR, 1.3 (95% CI, 1.2–1.5)) and in the UK (ROR, 3.3 (95% CI, 1.8–6.1)). Apart from memantine, which was associated with DAAD in Germany (ROR, 1.8 (95% CI, 1.0–3.2)), no other antidementia drug was associated with DAAD. Quantitative signal detection is suitable to detect agents with a risk for DAAD. Its sensitivity regarding PNE is limited, although atomoxetine and modafinil, which do not have a known abuse potential outside PNE, and no antidementia drugs, whose use in PNE is presumably low, were associated with DAAD in our analysis. PMID:28067776

  18. Picometer stable scan mechanism for gravitational wave detection in space

    NASA Astrophysics Data System (ADS)

    Rijnveld, N.; Pijnenburg, J. A. C. M.

    2010-07-01

    Detection and observation of gravitational waves requires extremely accurate displacement measurement in the frequency range 0.03 mHz to 1 Hz. The Laser Interferometer Space Antenna (LISA) mission will attain this by creating a giant interferometer in space, based on free floating proof masses in three spacecrafts. Due to orbit evolution and time delay in the interferometer arms, the direction of transmitted light changes. To solve this problem, a picometer stable Point-Ahead Angle Mechanism (PAAM) was designed, realized and successfully tested. The PAAM concept is based on a rotatable mirror. The critical requirements are the contribution to the optical path length (less than 1.4 pm / rt Hz) and the angular jitter (less than 8 nrad / rt Hz). Extreme dimensional stability is achieved by manufacturing a monolithical Haberland hinge mechanism out of Ti6Al4V, through high precision wire erosion. Extreme thermal stability is realized by placing the thermal center on the surface of the mirror. Because of piezo actuator noise and leakage, the PAAM has to be controlled in closed-loop. To meet the requirements in the low frequencies, an active target capacitance-to-digital converter is used. Interferometric measurements with a triangular resonant cavity in vacuum proved that the PAAM meets the requirements.

  19. Use of Rapid-Scan EPR to Improve Detection Sensitivity for Spin-Trapped Radicals

    PubMed Central

    Mitchell, Deborah G.; Rosen, Gerald M.; Tseitlin, Mark; Symmes, Breanna; Eaton, Sandra S.; Eaton, Gareth R.

    2013-01-01

    The short lifetime of superoxide and the low rates of formation expected in vivo make detection by standard continuous wave (CW) electron paramagnetic resonance (EPR) challenging. The new rapid-scan EPR method offers improved sensitivity for these types of samples. In rapid-scan EPR, the magnetic field is scanned through resonance in a time that is short relative to electron spin relaxation times, and data are processed to obtain the absorption spectrum. To validate the application of rapid-scan EPR to spin trapping, superoxide was generated by the reaction of xanthine oxidase and hypoxanthine with rates of 0.1–6.0 μM/min and trapped with 5-tert-butoxycarbonyl-5-methyl-1-pyrroline-N-oxide (BMPO). Spin trapping with BMPO to form the BMPO-OOH adduct converts the very short-lived superoxide radical into a more stable spin adduct. There is good agreement between the hyperfine splitting parameters obtained for BMPO-OOH by CW and rapid-scan EPR. For the same signal acquisition time, the signal/noise ratio is >40 times higher for rapid-scan than for CW EPR. Rapid-scan EPR can detect superoxide produced by Enterococcus faecalis at rates that are too low for detection by CW EPR. PMID:23870255

  20. Pelvic artery calcification detection on CT scans using convolutional neural networks

    NASA Astrophysics Data System (ADS)

    Liu, Jiamin; Lu, Le; Yao, Jianhua; Bagheri, Mohammadhadi; Summers, Ronald M.

    2017-03-01

    Artery calcification is observed commonly in elderly patients, especially in patients with chronic kidney disease, and may affect coronary, carotid and peripheral arteries. Vascular calcification has been associated with many clinical outcomes. Manual identification of calcification in CT scans requires substantial expert interaction, which makes it time-consuming and infeasible for large-scale studies. Many works have been proposed for coronary artery calcification detection in cardiac CT scans. In these works, coronary artery extraction is commonly required for calcification detection. However, there are few works about abdominal or pelvic artery calcification detection. In this work, we present a method for automatic pelvic artery calcification detection on CT scan. This method uses the recent advanced faster region-based convolutional neural network (R-CNN) to directly identify artery calcification without a need for artery extraction since pelvic artery extraction itself is challenging. Our method first generates category-independent region proposals for each slice of the input CT scan using region proposal networks (RPN). Then, each region proposal is jointly classified and refined by softmax classifier and bounding box regressor. We applied the detection method to 500 images from 20 CT scans of patients for evaluation. The detection system achieved a 77.4% average precision and a 85% sensitivity at 1 false positive per image.

  1. Carbon nanofiber electrode array for electrochemical detection of dopamine using fast scan cyclic voltammetry

    PubMed Central

    Koehne, Jessica E.; Marsh, Michael; Boakye, Adwoa; Douglas, Brandon; Kim, In Yong; Chang, Su-Youne; Jang, Dong-Pyo; Bennet, Kevin E.; Kimble, Christopher; Andrews, Russell; Meyyappan, M.; Lee, Kendall H.

    2012-01-01

    A carbon nanofiber (CNF) electrode array was integrated with the Wireless Instantaneous Neurotransmitter Sensor System (WINCS) for detection of dopamine using fast scan cyclic voltammetry (FSCV). Dopamine detection performance by CNF arrays was comparable to that of traditional carbon fiber microelectrodes (CFMs), demonstrating that CNF arrays can be utilized as an alternative carbon electrodes for neurochemical monitoring. PMID:21387028

  2. [The analysis and comparison of different edge detection algorithms in ultrasound B-scan images].

    PubMed

    Zhang, Luo-ping; Yang, Bo-yuan; Wang, Chun-hong

    2006-05-01

    In this paper, some familiar algorithms of edge detection in ultrasound B-scan images are analyzed and studied. The results show that Sobel, Prewitt and Laplacian operators are sensitive to noise, Hough transform adapts to the whole detection, while LoG algorithm's average is zero and it couldn't change the whole dynamic area. Accordingly LoG algorithm is preferable.

  3. Detection of alternative lengthening of telomeres by telomere quantitative PCR

    PubMed Central

    Lau, Loretta M. S.; Dagg, Rebecca A.; Henson, Jeremy D.; Au, Amy Y. M.; Royds, Janice A.; Reddel, Roger R.

    2013-01-01

    Alternative lengthening of telomeres (ALT) is one of the two known telomere length maintenance mechanisms that are essential for the unlimited proliferation potential of cancer cells. Existing methods for detecting ALT in tumors require substantial amounts of tumor material and are labor intensive, making it difficult to study prevalence and prognostic significance of ALT in large tumor cohorts. Here, we present a novel strategy utilizing telomere quantitative PCR to diagnose ALT. The protocol is more rapid than conventional methods and scrutinizes two distinct characteristics of ALT cells concurrently: long telomeres and the presence of C-circles (partially double-stranded circles of telomeric C-strand DNA). Requiring only 30 ng of genomic DNA, this protocol will facilitate large-scale studies of ALT in tumors and can be readily adopted by clinical laboratories. PMID:22923525

  4. A quantitative damage imaging technique based on enhanced CCRTM for composite plates using 2D scan

    NASA Astrophysics Data System (ADS)

    He, Jiaze; Yuan, Fuh-Gwo

    2016-10-01

    A two-dimensional (2D) non-contact areal scan system was developed to image and quantify impact damage in a composite plate using an enhanced zero-lag cross-correlation reverse-time migration (E-CCRTM) technique. The system comprises a single piezoelectric wafer mounted on the composite plate and a laser Doppler vibrometer (LDV) for scanning a region in the vicinity of the PZT to capture the scattered wavefield. The proposed damage imaging technique takes into account the amplitude, phase, geometric spreading, and all of the frequency content of the Lamb waves propagating in the plate; thus, a reflectivity coefficients of the delamination is calculated and potentially related to damage severity. Comparisons are made in terms of damage imaging quality between 2D areal scans and 1D line scans as well as between the proposed and existing imaging conditions. The experimental results show that the 2D E-CCRTM performs robustly when imaging and quantifying impact damage in large-scale composites using a single PZT actuator with a nearby areal scan using LDV.

  5. Accelerated noncontact laser ultrasonic scanning for damage detection using combined binary search and compressed sensing

    NASA Astrophysics Data System (ADS)

    Park, Byeongjin; Sohn, Hoon; Liu, Peipei

    2017-08-01

    Laser ultrasonic scanning is attractive for damage detection due to its noncontact nature, sensitivity to local damage, and high spatial resolution. However, its practicality is limited because scanning at a high spatial resolution demands a prohibitively long scanning time. Inspired by binary search and compressed sensing, an accelerated laser scanning technique is developed to localize and visualize damage with reduced scanning points and scanning time. First, the approximate damage location is identified by examining the interactions between the ultrasonic waves and damage at the sparse scanning points that are selected by the binary search algorithm. Here, a time-domain laser ultrasonic response is transformed into a spatial ultrasonic domain using a basis pursuit approach so that the interactions between the ultrasonic waves and damage, such as reflections and transmissions, can be better identified in the spatial ultrasonic domain. Second, wavefield images around the damage are reconstructed from the previously selected scanning points using compressed sensing. The performance of the proposed accelerated laser scanning technique is validated using a numerical simulation performed on an aluminum plate with a notch and experiments performed on an aluminum plate with a crack and a carbon fiber-reinforced plastic plate with delamination. The number of scanning points that is necessary for damage localization and visualization is dramatically reduced from N · M to 2log2 N ·log2 M . N and M represent the number of equally spaced scanning points in the x and y directions, respectively, which are required to obtain full-field wave propagation images of the target inspection region. For example, the number of scanning points in the composite plate experiment is reduced by 97.1% (from 2601 points to 75 points).

  6. On the detection of early osteoarthritis by quantitative microscopic imaging

    NASA Astrophysics Data System (ADS)

    Mittelstaedt, Daniel John

    Articular cartilage is a thin layer of connective tissue that protects the ends of bones in diarthroidal joints. Cartilage distributes mechanical forces during daily movement throughout its unique depth-dependent structure. The extracellular matrix (ECM) of cartilage primarily contains water, collagen, and glycosaminoglycan (GAG). The collagen fibers are intertwined with negatively charged GAG and surround the cells (i.e. chondrocytes) in cartilage. Degradation to the ECM reduces the load bearing properties of cartilage which can be initiated by injury (e.g. anterior cruciate ligament (ACL) rupture) or disease (e.g. osteoarthritis (OA)). Magnetic resonance imaging (MRI) and x-ray computed tomography (CT) are noninvasive imaging techniques that are increasingly being used in the clinical detection of cartilage degradation. The aim of the first project in this dissertation was to quantify and compare the depth-dependent GAG concentration from healthy and biochemically degraded humeral ex vivo articular cartilage using quantitative contrast enhanced micro-computed tomography (qCECT) at high resolution. The second project in this dissertation was aimed to measure the topographical and depth-dependent GAG concentration using qCECT and delayed gadolinium enhanced magnetic resonance imaging of cartilage (dGEMRIC) from the medial tibia cartilage three weeks after unilateral ACL transection which is an animal model of OA (i.e. modified Pond-Nuki model). These GAG measurements were correlated with a biochemical method, inductively couple plasma optical emission spectrometry, to compare the degradation on the medial tibia between the OA and contralateral cartilage. The third project in this dissertation used the same cartilage specimens as in project two to investigate the change in T2 due to OA and the effect on T2 from a contrast agent. Furthermore, the change in T2 relaxation was investigated from static unconfined compression with correlations by biomechanical

  7. Step-scan IR spectroelectrochemistry with ultramicroelectrodes: nonsurface enhanced detection of near femtomole quantities using synchrotron radiation.

    PubMed

    Rosendahl, Scott M; Borondics, Ferenc; May, Tim E; Burgess, Ian J

    2013-09-17

    The result of interfacing step-scan spectroelectrochemistry with an IR microscope and synchrotron infrared (SIR) radiation is provided here. An external reflectance cell containing a 25 μm gold ultramicroelectrode is employed to achieve an electrochemical time constant less than one microsecond. The use of a prototypical electrochemical system, i.e., the mass-transport controlled reduction of ferricyanide, allows for a proof of principle evaluation of the viability of SIR for step-scan spectroelectrochemistry. An analysis of the importance of accounting for synchrotron source variation over the prolonged duration of a step-scan experiment is provided. Modeling of the material flux in the restricted diffusion space afforded by the external reflectance cell allows the quantitative IR results to be compared to theoretical predictions. The results indicate that only at very short times does linear diffusion within the cavity dominate the electrode response and the majority of the transient signal operates under conditions of quasi-hemispherical diffusion. The analytical information provided by the IR signal is found to be considerably less than that derived from the current response due the latter's pronounced edge effects. The results provide a detection limit of 36 fmol for step-scan SIR measurements of ferrocyanide. Implications for future IR spectroelectrochemical studies in the microsecond domain are discussed.

  8. Enabling low-noise null-point scanning thermal microscopy by the optimization of scanning thermal microscope probe through a rigorous theory of quantitative measurement

    NASA Astrophysics Data System (ADS)

    Hwang, Gwangseok; Chung, Jaehun; Kwon, Ohmyoung

    2014-11-01

    The application of conventional scanning thermal microscopy (SThM) is severely limited by three major problems: (i) distortion of the measured signal due to heat transfer through the air, (ii) the unknown and variable value of the tip-sample thermal contact resistance, and (iii) perturbation of the sample temperature due to the heat flux through the tip-sample thermal contact. Recently, we proposed null-point scanning thermal microscopy (NP SThM) as a way of overcoming these problems in principle by tracking the thermal equilibrium between the end of the SThM tip and the sample surface. However, in order to obtain high spatial resolution, which is the primary motivation for SThM, NP SThM requires an extremely sensitive SThM probe that can trace the vanishingly small heat flux through the tip-sample nano-thermal contact. Herein, we derive a relation between the spatial resolution and the design parameters of a SThM probe, optimize the thermal and electrical design, and develop a batch-fabrication process. We also quantitatively demonstrate significantly improved sensitivity, lower measurement noise, and higher spatial resolution of the fabricated SThM probes. By utilizing the exceptional performance of these fabricated probes, we show that NP SThM can be used to obtain a quantitative temperature profile with nanoscale resolution independent of the changing tip-sample thermal contact resistance and without perturbation of the sample temperature or distortion due to the heat transfer through the air.

  9. An Exploratory Study to Detect Ménière's Disease in Conventional MRI Scans Using Radiomics.

    PubMed

    van den Burg, E L; van Hoof, M; Postma, A A; Janssen, A M L; Stokroos, R J; Kingma, H; van de Berg, R

    2016-01-01

    The purpose of this exploratory study was to investigate whether a quantitative image analysis of the labyrinth in conventional magnetic resonance imaging (MRI) scans using a radiomics approach showed differences between patients with Ménière's disease (MD) and the control group. In this retrospective study, MRI scans of the affected labyrinths of 24 patients with MD were compared to the MRI scans of labyrinths of 29 patients with an idiopathic asymmetrical sensorineural hearing loss. The 1.5- and 3-T MRI scans had been previously made in a clinical setting between 2008 and 2015. 3D Slicer 4.4 was used to extract several substructures of the labyrinth. A quantitative analysis of the normalized radiomic image features was performed in Mathematica 10. The image features of the two groups were statistically compared. For numerous image features, there was a statistically significant difference (p-value <0.05) between the MD group and the control group. The statistically significant differences in image features were localized in all the substructures of the labyrinth: 43 in the anterior semicircular canal, 10 in the vestibule, 22 in the cochlea, 12 in the posterior semicircular canal, 24 in the horizontal semicircular canal, 11 in the common crus, and 44 in the volume containing the reuniting duct. Furthermore, some figures contain vertical or horizontal bands (three or more statistically significant image features in the same image feature). Several bands were seen: 9 bands in the anterior semicircular canal, 1 band in the vestibule, 3 bands in the cochlea, 0 bands in the posterior semicircular canal, 5 bands in the horizontal semicircular canal, 3 bands in the common crus, and 10 bands in the volume containing the reuniting duct. In this exploratory study, several differences were found in image features between the MD group and the control group by using a quantitative radiomics approach on high resolution T2-weighted MRI scans of the labyrinth. Further

  10. Detection of plastic deformation in structural steel using scanning SQUID microscopy

    NASA Astrophysics Data System (ADS)

    Bonavolontà, C.; Valentino, M.; Adamo, M.; Sarnelli, E.

    2007-07-01

    The magneto-mechanical behaviour of structural steel specimens stressed up to a plastic deformation stage using a high-Tc scanning SQUID (superconducting quantum interference device) microscope is investigated. The correlation between the gradient of the normal component of the magnetization and dislocation density, before the crack initiation, is carried out. The capability of scanning SQUID microscopy to detect the residual magnetization, due to the tensile stress, with a non-invasive technique is reported.

  11. Equatorial sandhoppers use body scans to detect the earth's magnetic field.

    PubMed

    Ugolini, A

    2006-01-01

    Adults of Talorchestia martensii were individually released in a confined environment, with and without the natural magnetic field, under the sun and in a dark room. The sandhoppers scanned the horizontal component of the magnetic field by left and right oscillations of the entire major body axis. The frequency of this behaviour increased in a zeroed magnetic field, as did the frequencies of other behavioural indicators that reflect the difficulty in identifying the ecologically efficient orientation direction (sea-land axis). Therefore, like head scans in birds, body scans seem to be used by equatorial sandhoppers to detect the magnetic symmetry plane.

  12. Spatial scan statistics for detection of multiple clusters with arbitrary shapes.

    PubMed

    Lin, Pei-Sheng; Kung, Yi-Hung; Clayton, Murray

    2016-12-01

    In applying scan statistics for public health research, it would be valuable to develop a detection method for multiple clusters that accommodates spatial correlation and covariate effects in an integrated model. In this article, we connect the concepts of the likelihood ratio (LR) scan statistic and the quasi-likelihood (QL) scan statistic to provide a series of detection procedures sufficiently flexible to apply to clusters of arbitrary shape. First, we use an independent scan model for detection of clusters and then a variogram tool to examine the existence of spatial correlation and regional variation based on residuals of the independent scan model. When the estimate of regional variation is significantly different from zero, a mixed QL estimating equation is developed to estimate coefficients of geographic clusters and covariates. We use the Benjamini-Hochberg procedure (1995) to find a threshold for p-values to address the multiple testing problem. A quasi-deviance criterion is used to regroup the estimated clusters to find geographic clusters with arbitrary shapes. We conduct simulations to compare the performance of the proposed method with other scan statistics. For illustration, the method is applied to enterovirus data from Taiwan. © 2016, The International Biometric Society.

  13. MAPS: A Quantitative Radiomics Approach for Prostate Cancer Detection.

    PubMed

    Cameron, Andrew; Khalvati, Farzad; Haider, Masoom A; Wong, Alexander

    2016-06-01

    This paper presents a quantitative radiomics feature model for performing prostate cancer detection using multiparametric MRI (mpMRI). It incorporates a novel tumor candidate identification algorithm to efficiently and thoroughly identify the regions of concern and constructs a comprehensive radiomics feature model to detect tumorous regions. In contrast to conventional automated classification schemes, this radiomics-based feature model aims to ground its decisions in a way that can be interpreted and understood by the diagnostician. This is done by grouping features into high-level feature categories which are already used by radiologists to diagnose prostate cancer: Morphology, Asymmetry, Physiology, and Size (MAPS), using biomarkers inspired by the PI-RADS guidelines for performing structured reporting on prostate MRI. Clinical mpMRI data were collected from 13 men with histology-confirmed prostate cancer and labeled by an experienced radiologist. These annotated data were used to train classifiers using the proposed radiomics-driven feature model in order to evaluate the classification performance. The preliminary experimental results indicated that the proposed model outperformed each of its constituent feature groups as well as a comparable conventional mpMRI feature model. A further validation of the proposed algorithm will be conducted using a larger dataset as future work.

  14. Automatic detection of new tumors and tumor burden evaluation in longitudinal liver CT scan studies.

    PubMed

    Vivanti, R; Szeskin, A; Lev-Cohain, N; Sosna, J; Joskowicz, L

    2017-08-30

    Radiological longitudinal follow-up of liver tumors in CT scans is the standard of care for disease progression assessment and for liver tumor therapy. Finding new tumors in the follow-up scan is essential to determine malignancy, to evaluate the total tumor burden, and to determine treatment efficacy. Since new tumors are typically small, they may be missed by examining radiologists. We describe a new method for the automatic detection and segmentation of new tumors in longitudinal liver CT studies and for liver tumors burden quantification. Its inputs are the baseline and follow-up CT scans, the baseline tumors delineation, and a tumor appearance prior model. Its outputs are the new tumors segmentations in the follow-up scan, the tumor burden quantification in both scans, and the tumor burden change. Our method is the first comprehensive method that is explicitly designed to find new liver tumors. It integrates information from the scans, the baseline known tumors delineations, and a tumor appearance prior model in the form of a global convolutional neural network classifier. Unlike other deep learning-based methods, it does not require large tagged training sets. Our experimental results on 246 tumors, of which 97 were new tumors, from 37 longitudinal liver CT studies with radiologist approved ground-truth segmentations, yields a true positive new tumors detection rate of 86 versus 72% with stand-alone detection, and a tumor burden volume overlap error of 16%. New tumors detection and tumor burden volumetry are important for diagnosis and treatment. Our new method enables a simplified radiologist-friendly workflow that is potentially more accurate and reliable than the existing one by automatically and accurately following known tumors and detecting new tumors in the follow-up scan.

  15. Obtaining quantitative global tumoral state indicators based on whole-body PET/CT scans: a breast cancer case study.

    PubMed

    Sampedro, Frederic; Domenech, Anna; Escalera, Sergio

    2014-04-01

    In this work we address the need for the computation of quantitative global tumoral state indicators from oncological whole-body PET/computed tomography scans. The combination of such indicators with other oncological information such as tumor markers or biopsy results would prove useful in oncological decision-making scenarios. From an ordering of 100 breast cancer patients on the basis of oncological state through visual analysis by a consensus of nuclear medicine specialists, a set of numerical indicators computed from image analysis of the PET/computed tomography scan is presented, which attempts to summarize a patient's oncological state in a quantitative manner taking into consideration the total tumor volume, aggressiveness, and spread. Results obtained by comparative analysis of the proposed indicators with respect to the experts' evaluation show up to 87% Pearson's correlation coefficient when providing expert-guided PET metabolic tumor volume segmentation and 64% correlation when using completely automatic image analysis techniques. Global quantitative tumor information obtained by whole-body PET/CT image analysis can prove useful in clinical nuclear medicine settings and oncological decision-making scenarios. The completely automatic computation of such indicators would improve its impact as time efficiency and specialist independence would be achieved.

  16. Innovative Gamma Ray Spectrometer Detection Systems for Conducting Scanning Surveys on Challenging Terrain - 13583

    SciTech Connect

    Palladino, Carl; Mason, Bryan; Engle, Matt; LeVangie, James; Dempsey, Gregg; Klemovich, Ron

    2013-07-01

    The Santa Susana Field Laboratory located near Simi Valley, California was investigated to determine the nature and extent of gamma radiation anomalies. The primary objective was to conduct gamma scanning surveys over 100 percent of the approximately 1,906,000 square meters (471 acre) project site with the most sensitive detection system possible. The site had challenging topography that was not conducive to traditional gamma scanning detection systems. Terrain slope varied from horizontal to 48 degrees and the ground surface ranged from flat, grassy meadows to steep, rocky hillsides. In addition, the site was home to many protected endangered plant and animal species, and archaeologically significant sites that required minimal to no disturbance of the ground surface. Therefore, four innovative and unique gamma ray spectrometer detection systems were designed and constructed to successfully conduct gamma scanning surveys of approximately 1,076,000 square meters (266 acres) of the site. (authors)

  17. The reality of virtual anthropology: Comparing digitizer and laser scan data collection methods for the quantitative assessment of the cranium.

    PubMed

    Algee-Hewitt, Bridget F B; Wheat, Amber D

    2016-05-01

    The use of geometric morphometry to study cranial variation has steadily grown in appeal over the past decade in biological anthropology. Publication trends suggest that the most popular methods for three-dimensional data acquisition involve landmark-based coordinate data collection using a digitizer. Newer laser scan approaches are seeing increasing use, owing to the benefits that densely sampled data offer. While both of these methods have their utility, research that investigates their compatibility is lacking. The purpose of this project is to compare, quantitatively, craniometrics collected with a digitizer against data extracted from laser scans using the same individuals and laboratory conditions. Three-dimensional (x,y,z) coordinates and traditional inter-landmark distances (ILDs) were obtained with a Microscribe digitizer and 360° color models produced from NextEngine laser scans for 38 adult crania representing five cemeteries from the ADBOU skeletal collection in Denmark. Variance-based tests were performed to evaluate the disagreement between data collected with a digitizer and from laser scan models. Consideration was given to differences among landmarks by type, between ILDs calculated from landmark coordinates, and in morphology for the cemetery populations. Further, the reliability of laser scan data collection was assessed by intra-observer error tests. Researchers should be aware of the potential error associated with the use of Types II and III landmarks and the limitations on reliability imposed by object-to-scanner placement. This project reveals how laser scans can provide a valuable digital archive of cranial material that can be reasonably exploited for the "virtual" collection of coordinates and the calculation of ILDs. © 2015 Wiley Periodicals, Inc.

  18. Effect of patient thickness and scan duration on lesion detectability in PET oncology imaging

    NASA Astrophysics Data System (ADS)

    Cheng, Phillip M.; Kinahan, Paul E.; Comtat, Claude; Lartizien, Carole; Lewellen, Thomas K.

    2005-04-01

    A dominant component of image quality for whole-body positron emission tomography (PET) imaging is attenuation, which is determined by patient thickness. This can be partially compensated for by adjusting scan duration. We evaluate the effect of changes in patient thickness and scan duration on lesion detection with model observers. We simulated 2D PET acquisitions of an anthropomorphic phantom with spherical target lesions. Three different anthropomorphic phantoms were used, with effective abdominal diameters of 20 cm, 27 cm, and 35 cm. The diameters of the lesions were varied from 1.0 to 3.0 cm, and the contrast ratios of the lesions were varied from 1.5 to 4.0. Noise-free scans were simulated with an analytical simulator. Poisson noise was added to simulate scan durations ranging from 1 to 10 minutes per bed position, using noise equivalent count rates previously measured using a modified NEMA NU2 countrate phantom. The average detectability of each target lesion under each condition was calculated using a non-prewhitening matched filter from 25 noisy realizations for each combination of parameters. Our results demonstrate the variation of the minimum scan duration required to detect a target of a given size and contrast ratio, for any fixed threshold of detectability. For image quality to remain constant for patients with larger cross-sectional areas, acquisition times should be increased accordingly, although in some cases this may not be possible due to practical constraints.

  19. High-resolution mass spectrometry method for the detection, characterization and quantitation of pharmaceuticals in water.

    PubMed

    Pinhancos, Rebeca; Maass, Sara; Ramanathan, Dil M

    2011-11-01

    The presence of pharmaceuticals in drinking water is an emerging environmental concern. In most environmental testing laboratories, LC-MS/MS assays based on selected reaction monitoring are used as part of a battery of tests used to assure water quality. Although LC-MS/MS continues to be the best tool for detecting pharmaceuticals in water, the combined use of hybrid high-resolution mass spectrometry (HRMS) and ultrahigh pressure liquid chromatography (UHPLC) is starting to become a practical tool to study emerging environmental contaminants. The hybrid LTQ-orbitrap mass spectrometer is suitable for integrated quantitative and qualitative bioanalysis because of the following reasons: (1) the ability to collect full-scan HRMS spectra with scan speeds suitable for UHPLC separations, (2) routine measurement of mass with less than 5 ppm mass accuracy, (3) high mass resolving power, and (4) ability to perform on-the-fly polarity switching in the linear ion trap (LTQ). In the present work, we provide data demonstrating the application of UHPLC-LTQ-orbitrap for the detection, characterization and quantification of pharmaceuticals and their metabolites in drinking water.

  20. Towards routine, quantitative two-dimensional carrier profiling with scanning spreading resistance microscopy

    NASA Astrophysics Data System (ADS)

    Vandervorst, W.; Eyben, P.; Callewaert, S.; Hantschel, T.; Duhayon, N.; Xu, M.; Trenkler, T.; Clarysse, T.

    2001-01-01

    Recent developments in scanning spreading resistance microscopy have enabled to move the technique from the laboratory phase to a commercially available method for 2D-carrier profiling. In view of the large tip consumption methods and software have been developed to arrive at a rapid collection of calibration curves and the characterization of tips. These calibration curves have been integrated in a software package for quantification such that 2D-images can be completely quantified. Scanning Spreading Resistance Spectroscopy (SSRS) has been developed whereby full I-V curves can be collected at every pixel. These developments contribute to a better understanding of the physics of the point-contact, allow to characterize in more detail the electrical behavior of various tips and provide a unique signature for junction identification.

  1. Direct observation of Sr vacancies in SrTiO3 by quantitative scanning transmission electron microscopy

    DOE PAGES

    Kim, Honggyu; Zhang, Jack Y.; Raghavan, Santosh; ...

    2016-12-22

    Unveiling the identity, spatial configuration, and microscopic structure of point defects is one of the key challenges in materials science. Here, we demonstrate that quantitative scanning transmission electron microscopy (STEM) can be used to directly observe Sr vacancies in SrTiO3 and to determine the atom column relaxations around them. By combining recent advances in quantitative STEM, including variableangle, high-angle annular dark-field imaging and rigid registration methods, with frozen phonon multislice image simulations, we identify which Sr columns contain vacancies and quantify the number of vacancies in them. Here, picometer precision measurements of the surrounding atom column positions show that themore » nearest-neighbor Ti atoms are displaced away from the Sr vacancies. The results open up a new methodology for studying the microscopic mechanisms by which point defects control materials properties.« less

  2. Dose limited reliability of quantitative annular dark field scanning transmission electron microscopy for nano-particle atom-counting.

    PubMed

    De Backer, A; Martinez, G T; MacArthur, K E; Jones, L; Béché, A; Nellist, P D; Van Aert, S

    2015-04-01

    Quantitative annular dark field scanning transmission electron microscopy (ADF STEM) has become a powerful technique to characterise nano-particles on an atomic scale. Because of their limited size and beam sensitivity, the atomic structure of such particles may become extremely challenging to determine. Therefore keeping the incoming electron dose to a minimum is important. However, this may reduce the reliability of quantitative ADF STEM which will here be demonstrated for nano-particle atom-counting. Based on experimental ADF STEM images of a real industrial catalyst, we discuss the limits for counting the number of atoms in a projected atomic column with single atom sensitivity. We diagnose these limits by combining a thorough statistical method and detailed image simulations. Copyright © 2014 Elsevier B.V. All rights reserved.

  3. Quantitative detection of fluid distribution using time-lapse seismic

    NASA Astrophysics Data System (ADS)

    Tsuneyama, Futoshi

    The quantitative evaluation of time-lapse seismic data remains a challenge due to poor match between the model predictions and the actual seismic data. Velocity anisotropy is one important reason for the mismatch. I compile experimental velocity-anisotropy data from cores to explore the empirical relationships between anisotropy parameters and general well-log information. Then, I develop a method to estimate Thomsen's anisotropy parameters ε and gamma using a regression of the data in the crossplot domain between velocity and porosity. I present an application result of the method to demonstrate the significance of the correction. Next, using the corrected velocity, I present a method of impedance decomposition into Vp, Vs, and rho using three elastic impedances derived from the seismic inversion of angle stacks. In general, the maximum stack angle of seismic data is limited to be less than 30°, which is not wide enough to obtain the stable calculation result. I discuss the effect of noise on the analysis as the most important reason that decomposition is difficult. I show an innovative method incorporating rock-physics bounds as constraints for the analysis. I apply it to an actual dataset from an offshore oil field; I demonstrate the result of analysis for sand-body detection. Based on the estimated Vp, V s, rho and shale volume from the elastic impedances, I develop a workflow to determine the saturation of formation-water, oil and gas from seismic data. First, I consider the pressure effect and the saturation scale of fluids for time-lapse seismic analysis. Second, I demonstrate a deterministic approach to computing the fluid saturation to evaluate time-lapse seismic data. In this approach, I derive the physical properties of the water-saturated sandstone reservoir. Then, by comparing the in-situ-fluid-saturated properties with the 100% formation-water-saturated reservoir properties, I determine the bulk modulus and the density of the fluid phase in the

  4. An international collaborative family-based whole genome quantitative trait linkage scan for myopic refractive error

    PubMed Central

    Abbott, Diana; Li, Yi-Ju; Guggenheim, Jeremy A.; Metlapally, Ravikanth; Malecaze, Francois; Calvas, Patrick; Rosenberg, Thomas; Paget, Sandrine; Zayats, Tetyana; Mackey, David A.; Feng, Sheng

    2012-01-01

    Purpose To investigate quantitative trait loci linked to refractive error, we performed a genome-wide quantitative trait linkage analysis using single nucleotide polymorphism markers and family data from five international sites. Methods Genomic DNA samples from 254 families were genotyped by the Center for Inherited Disease Research using the Illumina Linkage Panel IVb. Quantitative trait linkage analysis was performed on 225 Caucasian families and 4,656 markers after accounting for linkage disequilibrium and quality control exclusions. Two refractive quantitative phenotypes, sphere (SPH) and spherical equivalent (SE), were analyzed. The SOLAR program was used to estimate identity by descent probabilities and to conduct two-point and multipoint quantitative trait linkage analyses. Results We found 29 markers and 11 linkage regions reaching peak two-point and multipoint logarithms of the odds (LODs)>1.5. Four linkage regions revealed at least one LOD score greater than 2: chromosome 6q13–6q16.1 (LOD=1.96 for SPH, 2.18 for SE), chromosome 5q35.1–35.2 (LOD=2.05 for SPH, 1.80 for SE), chromosome 7q11.23–7q21.2 (LOD=1.19 for SPH, 2.03 for SE), and chromosome 3q29 (LOD=1.07 for SPH, 2.05 for SE). Among these, the chromosome 6 and chromosome 5 regions showed the most consistent results between SPH and SEM. Four linkage regions with multipoint scores above 1.5 are near or within the known myopia (MYP) loci of MYP3, MYP12, MYP14, and MYP16. Overall, we observed consistent linkage signals across the SPH and SEM phenotypes, although scores were generally higher for the SEM phenotype. Conclusions Our quantitative trait linkage analyses of a large myopia family cohort provided additional evidence for several known MYP loci, and identified two additional potential loci at chromosome 6q13–16.1 and chromosome 5q35.1–35.2 for myopia. These results will benefit the efforts toward determining genes for myopic refractive error. PMID:22509102

  5. Quantitative detection of settled coal dust over green canopy

    NASA Astrophysics Data System (ADS)

    Brook, Anna; Sahar, Nir

    2017-04-01

    The main task of environmental and geoscience applications are efficient and accurate quantitative classification of earth surfaces and spatial phenomena. In the past decade, there has been a significant interest in employing spectral unmixing in order to retrieve accurate quantitative information latent in in situ data. Recently, the ground-truth and laboratory measured spectral signatures promoted by advanced algorithms are proposed as a new path toward solving the unmixing problem in semi-supervised fashion. This study presents a practical implementation of field spectroscopy as a quantitative tool to detect settled coal dust over green canopy in free/open environment. Coal dust is a fine powdered form of coal, which is created by the crushing, grinding, and pulverizing of coal. Since the inelastic nature of coal, coal dust can be created during transportation, or by mechanically handling coal. Coal dust, categorized at silt-clay particle size, of particular concern due to heavy metals (lead, mercury, nickel, tin, cadmium, mercury, antimony, arsenic, isotopes of thorium and strontium) which are toxic also at low concentrations. This hazard exposes risk on both environment and public health. It has been identified by medical scientist around the world as causing a range of diseases and health problems, mainly heart and respiratory diseases like asthma and lung cancer. It is due to the fact that the fine invisible coal dust particles (less than 2.5 microns) long lodge in the lungs and are not naturally expelled, so long-term exposure increases the risk of health problems. Numerus studies reported that data to conduct study of geographic distribution of the very fine coal dust (smaller than PM 2.5) and related health impacts from coal exports, is not being collected. Sediment dust load in an indoor environment can be spectrally assessed using reflectance spectroscopy (Chudnovsky and Ben-Dor, 2009). Small amounts of particulate pollution that may carry a signature

  6. Feasibility for detection of autofluorescent signatures in rat organs using a novel excitation-scanning hyperspectral imaging system

    NASA Astrophysics Data System (ADS)

    Favreau, Peter F.; Deal, Joshua A.; Weber, David S.; Rich, Thomas C.; Leavesley, Silas J.

    2016-04-01

    The natural fluorescence (autofluorescence) of tissues has been noted as a biomarker for cancer for several decades. Autofluorescence contrast between tumors and healthy tissues has been of significant interest in endoscopy, leading to development of autofluorescence endoscopes capable of visualizing 2-3 fluorescence emission wavelengths to achieve maximal contrast. However, tumor detection with autofluorescence endoscopes is hindered by low fluorescence signal and limited quantitative information, resulting in prolonged endoscopic procedures, prohibitive acquisition times, and reduced specificity of detection. Our lab has designed a novel excitation-scanning hyperspectral imaging system with high fluorescence signal detection, low acquisition time, and enhanced spectral discrimination. In this study, we surveyed a comprehensive set of excised tissues to assess the feasibility of detecting tissue-specific pathologies using excitation-scanning. Fresh, untreated tissue specimens were imaged from 360 to 550 nm on an inverted fluorescence microscope equipped with a set of thin-film tunable filters (Semrock, A Unit of IDEX). Images were subdivided into training and test sets. Automated endmember extraction (ENVI 5.1, Exelis) with PCA identified endmembers within training images of autofluorescence. A spectral library was created from 9 endmembers. The library was used for identification of endmembers in test images. Our results suggest (1) spectral differentiation of multiple tissue types is possible using excitation scanning; (2) shared spectra between tissue types; and (3) the ability to identify unique morphological features in disparate tissues from shared autofluorescent components. Future work will focus on isolating specific molecular signatures present in tissue spectra, and elucidating the contribution of these signatures in pathologies.

  7. Quantitative in vivo imaging of entire embryos with Digital Scanned Laser Light Sheet Fluorescence Microscopy.

    PubMed

    Keller, Philipp J; Stelzer, Ernst H K

    2008-12-01

    The observation of biological processes in their natural in vivo context is a key requirement for quantitative experimental studies in the life sciences. In many instances, it will be crucial to achieve high temporal and spatial resolution over long periods of time without compromising the physiological development of the specimen. Here, we discuss the principles underlying light sheet-based fluorescence microscopes. The most recent implementation DSLM is a tool optimized to deliver quantitative data for entire embryos at high spatio-temporal resolution. We compare DSLM to the two established light microscopy techniques: confocal and two-photon fluorescence microscopy. DSLM provides up to 50 times higher imaging speeds and a 10-100 times higher signal-to-noise ratio, while exposing the specimens to at least three orders of magnitude less light energy than confocal and two-photon fluorescence microscopes. We conclude with a perspective for future development.

  8. Quantitative Electron Probe Microanalysis Using a Scanning Electron Microscope and an X-Ray Energy Spectrometer.

    DTIC Science & Technology

    1980-04-01

    necessary to solve the ZAF cor- rections in an iterative manner similar to that used by J . Colby 13in the Magic IV programme . In that programme the...Combined with an Energy Dispersive X-ray Analyzer for Quantitative Analysis", X-ray Spectrometry, 2, 1973. 10. Green, L.: Journ. of Phys. E. Scient ... Instrum ., 2, (3), 1973. 11. Wodke, Norbert F. and Schamber, Frederick, MS 885 Super ML Operation and Programme Description Version 1, Unpublished, Tracor

  9. Evaluation of the Gini Coefficient in Spatial Scan Statistics for Detecting Irregularly Shaped Clusters

    PubMed Central

    Kim, Jiyu; Jung, Inkyung

    2017-01-01

    Spatial scan statistics with circular or elliptic scanning windows are commonly used for cluster detection in various applications, such as the identification of geographical disease clusters from epidemiological data. It has been pointed out that the method may have difficulty in correctly identifying non-compact, arbitrarily shaped clusters. In this paper, we evaluated the Gini coefficient for detecting irregularly shaped clusters through a simulation study. The Gini coefficient, the use of which in spatial scan statistics was recently proposed, is a criterion measure for optimizing the maximum reported cluster size. Our simulation study results showed that using the Gini coefficient works better than the original spatial scan statistic for identifying irregularly shaped clusters, by reporting an optimized and refined collection of clusters rather than a single larger cluster. We have provided a real data example that seems to support the simulation results. We think that using the Gini coefficient in spatial scan statistics can be helpful for the detection of irregularly shaped clusters. PMID:28129368

  10. Evaluation of the Gini Coefficient in Spatial Scan Statistics for Detecting Irregularly Shaped Clusters.

    PubMed

    Kim, Jiyu; Jung, Inkyung

    2017-01-01

    Spatial scan statistics with circular or elliptic scanning windows are commonly used for cluster detection in various applications, such as the identification of geographical disease clusters from epidemiological data. It has been pointed out that the method may have difficulty in correctly identifying non-compact, arbitrarily shaped clusters. In this paper, we evaluated the Gini coefficient for detecting irregularly shaped clusters through a simulation study. The Gini coefficient, the use of which in spatial scan statistics was recently proposed, is a criterion measure for optimizing the maximum reported cluster size. Our simulation study results showed that using the Gini coefficient works better than the original spatial scan statistic for identifying irregularly shaped clusters, by reporting an optimized and refined collection of clusters rather than a single larger cluster. We have provided a real data example that seems to support the simulation results. We think that using the Gini coefficient in spatial scan statistics can be helpful for the detection of irregularly shaped clusters.

  11. Detection of group a streptococcal pharyngitis by quantitative PCR.

    PubMed

    Dunne, Eileen M; Marshall, Julia L; Baker, Ciara A; Manning, Jayne; Gonis, Gena; Danchin, Margaret H; Smeesters, Pierre R; Satzke, Catherine; Steer, Andrew C

    2013-07-11

    Group A streptococcus (GAS) is the most common bacterial cause of sore throat. School-age children bear the highest burden of GAS pharyngitis. Accurate diagnosis is difficult: the majority of sore throats are viral in origin, culture-based identification of GAS requires 24-48 hours, and up to 15% of children are asymptomatic throat carriers of GAS. The aim of this study was to develop a quantitative polymerase chain reaction (qPCR) assay for detecting GAS pharyngitis and assess its suitability for clinical diagnosis. Pharyngeal swabs were collected from children aged 3-18 years (n = 91) and adults (n = 36) located in the Melbourne area who presented with sore throat. Six candidate PCR assays were screened using a panel of reference isolates, and two of these assays, targeting speB and spy1258, were developed into qPCR assays. The qPCR assays were compared to standard culture-based methods for their ability to detect GAS pharyngitis. GAS isolates from culture positive swabs underwent emm-typing. Clinical data were used to calculate McIsaac scores as an indicator of disease severity. Twenty-four of the 127 samples (18.9%) were culture-positive for GAS, and all were in children (26%). The speB qPCR had 100% sensitivity and 100% specificity compared with gold-standard culture, whereas the spy1258 qPCR had 87% sensitivity and 100% specificity. Nine different emm types were found, of which emm 89, 3, and 28 were most common. Bacterial load as measured by qPCR correlated with culture load. There were no associations between symptom severity as indicated by McIsaac scores and GAS bacterial load. The speB qPCR displayed high sensitivity and specificity and may be a useful tool for GAS pharyngitis diagnosis and research.

  12. Graphics processing unit-accelerated quantitative trait Loci detection.

    PubMed

    Chapuis, Guillaume; Filangi, Olivier; Elsen, Jean-Michel; Lavenier, Dominique; Le Roy, Pascale

    2013-09-01

    Mapping quantitative trait loci (QTL) using genetic marker information is a time-consuming analysis that has interested the mapping community in recent decades. The increasing amount of genetic marker data allows one to consider ever more precise QTL analyses while increasing the demand for computation. Part of the difficulty of detecting QTLs resides in finding appropriate critical values or threshold values, above which a QTL effect is considered significant. Different approaches exist to determine these thresholds, using either empirical methods or algebraic approximations. In this article, we present a new implementation of existing software, QTLMap, which takes advantage of the data parallel nature of the problem by offsetting heavy computations to a graphics processing unit (GPU). Developments on the GPU were implemented using Cuda technology. This new implementation performs up to 75 times faster than the previous multicore implementation, while maintaining the same results and level of precision (Double Precision) and computing both QTL values and thresholds. This speedup allows one to perform more complex analyses, such as linkage disequilibrium linkage analyses (LDLA) and multiQTL analyses, in a reasonable time frame.

  13. Human lymphocyte polymorphisms detected by quantitative two-dimensional electrophoresis

    SciTech Connect

    Goldman, D.; Merril, C.R.

    1983-09-01

    A survey of 186 soluble lymphocyte proteins for genetic polymorphism was carried out utilizing two-dimensional electrophoresis of /sup 14/C-labeled phytohemagglutinin (PHA)-stimulated human lymphocyte proteins. Nineteen of these proteins exhibited positional variation consistent with independent genetic polymorphism in a primary sample of 28 individuals. Each of these polymorphisms was characterized by quantitative gene-dosage dependence insofar as the heterozygous phenotype expressed approximately 50% of each allelic gene product as was seen in homozygotes. Patterns observed were also identical in monozygotic twins, replicate samples, and replicate gels. The three expected phenotypes (two homozygotes and a heterozygote) were observed in each of 10 of these polymorphisms while the remaining nine had one of the homozygous classes absent. The presence of the three phenotypes, the demonstration of gene-dosage dependence, and our own and previous pedigree analysis of certain of these polymorphisms supports the genetic basis of these variants. Based on this data, the frequency of polymorphic loci for man is: P . 19/186 . .102, and the average heterozygosity is .024. This estimate is approximately 1/3 to 1/2 the rate of polymorphism previously estimated for man in other studies using one-dimensional electrophoresis of isozyme loci. The newly described polymorphisms and others which should be detectable in larger protein surveys with two-dimensional electrophoresis hold promise as genetic markers of the human genome for use in gene mapping and pedigree analyses.

  14. Quantitative void characterization in structural ceramics using scanning laser acoustic microscopy

    NASA Technical Reports Server (NTRS)

    Roth, D. J.; Generazio, E. R.; Baaklini, G. Y.

    1986-01-01

    The ability of scanning laser acoustic microscopy (SLAM) to characterize artificially seeded voids in sintered silicon nitride structural ceramic specimens was investigated. Using trigonometric relationships and Airy's diffraction theory, predictions of internal void depth and size were obtained from acoustic diffraction patterns produced by the voids. Agreement was observed between actual and predicted void depths. However, predicted void diameters were generally much greater than actual diameters. Precise diameter predictions are difficult to obtain due to measurement uncertainty and the limitations of 100 MHz SLAM applied to typical ceramic specimens.

  15. Scanning electron microscopy of growing dental plaque: a quantitative study with different mouth rinses.

    PubMed

    Jentsch, Holger; Mozaffari, Eshan; Jonas, Ludwig

    2013-08-01

    The aim of this study was to quantify the influence of different mouth rinses on dental plaque. Wearing splints with enamel pieces 24 volunteers rinsed with essential oils, amine/stannous fluoride, or chlorhexidine digluconate (0.12%) mouth rinses. After 24, 48, 72, and 96 h the enamel pieces were analyzed by scanning electron microscopy. The counts of cocci and bacilli in different plaque layers and the plaque thickness were almost similar using essential oils and amine/stannous fluoride. These results differed significantly from those of chlorhexidine digluconate mouth rinses. The results for plaque thickness were without significant differences between the groups at any appointment.

  16. Acquisition of quantitative physiological data and computerized image reconstruction using a single scan TV system

    NASA Technical Reports Server (NTRS)

    Baily, N. A.

    1975-01-01

    Single scan operation of television X-ray fluoroscopic systems allow both analog and digital reconstruction of tomographic sections from single plan images. This type of system combined with a minimum of statistical processing showed excellent capabilities for delineating small changes in differential X-ray attenuation. Patient dose reduction is significant when compared to normal operation or film recording. Flat screen, low light level systems were both rugged and light in weight, making them applicable for a variety of special purposes. Three dimensional information was available from the tomographic methods and the recorded data was sufficient when used with appropriate computer display devices to give representative 3D images.

  17. Acquisition of quantitative physiological data and computerized image reconstruction using a single scan TV system

    NASA Technical Reports Server (NTRS)

    Baily, N. A.

    1975-01-01

    Single scan operation of television X-ray fluoroscopic systems allow both analog and digital reconstruction of tomographic sections from single plan images. This type of system combined with a minimum of statistical processing showed excellent capabilities for delineating small changes in differential X-ray attenuation. Patient dose reduction is significant when compared to normal operation or film recording. Flat screen, low light level systems were both rugged and light in weight, making them applicable for a variety of special purposes. Three dimensional information was available from the tomographic methods and the recorded data was sufficient when used with appropriate computer display devices to give representative 3D images.

  18. Quantitative asymmetric-detection time-stretch optical microscopy (Q-ATOM) for ultrafast quantitative phase imaging flow cytometry (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Lau, Andy K. S.; Tang, Anson H. L.; Chung, Bob M. F.; Tsang, Kwok Yeung; Chan, Antony C. S.; Wei, Xiaoming; Wong, Kenneth K.; Lam, Edmund Y.; Cheah, Kathryn S. E.; Shum, Anderson H. C.; Tsia, Kevin K.

    2016-03-01

    Based on the interferometric or holographic approaches, recent QPM techniques provide quantitative-phase information, e.g cell volume, dry mass and optical scattering properties for label-free cellular physical phenotyping. These approaches generally rely on iterative phase-retrieval algorithms to obtain quantitative-phase information, which are computationally intensive. Moreover, current QPM techniques can only offer limited image acquisition rate by using CMOS/CCD image sensors, these two limitations hinder QPM for high-throughput quantitative image-based single-cell analysis in real-time. To this end, we demonstrate an interferometry-free quantitative phase microscopy developed on a new generation of time-stretch microscopy, asymmetric-detection time-stretch optical microscopy (ATOM), which is coined quantitative ATOM (Q-ATOM) - featuring an unprecedented cell measurement throughput together with the assorted intrinsic optical phenotypes (e.g. angular light scattering profile) and the derived physical properties of the cells (e.g. cell size, dry mass density etc.). Based on a similar concept to Schlieren imaging, Q-ATOM retrieves quantitative-phase information through multiple off-axis light-beam detection at a line-scan rate of <10 MHz - a speed unachievable by any existing QPM techniques. Phase retrieval in Q-ATOM relies on a non-iterative method, significantly reducing the computational complexity of the technique. It is a particularly important feature which facilitates real-time continuous label-free single-cell analysis in Q-ATOM. With the use of a non-interferometric configuration, we demonstrate ultrafast Q-ATOM of mouse chondrocytes and hypertrophic chondrocytes in ultrafast microfluidic flow with sub-cellular resolution at an imaging throughput equivalent to ~100,000 cells/sec without image blur. This technique shows a great potential for ultrahigh throughput label-free image-based single-cell biophysical phentotyping.

  19. Highly sensitive surface-scanning detector for the direct bacterial detection using magnetoelastic (ME) biosensors

    NASA Astrophysics Data System (ADS)

    Liu, Yuzhe; Horikawa, Shin; Chen, I.-Hsuan; Du, Songtao; Wikle, Howard C.; Suh, Sang-Jin; Chin, Bryan A.

    2017-05-01

    This paper demonstrates a highly sensitive surface-scanning detector used for magnetoelastic (ME) biosensors for the detection of Salmonella on the surface of a polyethylene (PE) food preparation surface. The design and fabrication methods of the new planar spiral coil are introduced. Different concentrations of Salmonella were measured on the surface of a PE board. The efficacy of Salmonella capture and detection is discussed.

  20. Semi-empirical inversion technique for retrieval of quantitative attenuation profiles with underwater scanning lidar systems

    NASA Astrophysics Data System (ADS)

    Vuorenkoski, Anni K.; Dalgleish, Fraser R.; Twardowski, Michael S.; Ouyang, Bing; Trees, Charles C.

    2015-05-01

    A fine structure underwater imaging LiDAR (FSUIL) has recently been developed and initial field trials have been conducted. The instrument, which rapidly scans an array of closely spaced, narrow, collimated laser pulses into the water column produces two-dimensional arrays of backscatter profiles, with fine spatial and temporal resolution. In this paper a novel method to derive attenuation profiles is introduced. This approach is particularly attractive in applications where primary on-board processing is required, and other applications where conventional model-based approaches are not feasible due to a limited computational capacity or lack of a priori knowledge of model input parameters. The paper also includes design details regarding the new FSUIL instrument are given, with field results taken in clear to moderately turbid water being presented to illustrate the various effects and considerations in the analysis of the system data. LiDAR waveforms and LiDAR derived attenuation coefficients are analyzed and compared to calibrated beam attenuation, particulate scattering and absorption coefficients. The system was field tested during the NATO Ligurian Sea LIDAR & Optical Measurements Experiment (LLOMEx) cruise in March 2013, during the spring bloom conditions. Throughout a wide range of environmental conditions, the FSUIL was deployed on an in situ profiler obtaining thousands of three-dimensional LiDAR scans from the near surface down to the lower thermocline. Deployed concurrent to the FSUIL was a range of commercially available off-the-shelf instruments providing side-by-side in-situ attenuation measurement.

  1. Time-Gated Orthogonal Scanning Automated Microscopy (OSAM) for High-speed Cell Detection and Analysis

    NASA Astrophysics Data System (ADS)

    Lu, Yiqing; Xi, Peng; Piper, James A.; Huo, Yujing; Jin, Dayong

    2012-11-01

    We report a new development of orthogonal scanning automated microscopy (OSAM) incorporating time-gated detection to locate rare-event organisms regardless of autofluorescent background. The necessity of using long-lifetime (hundreds of microseconds) luminescent biolabels for time-gated detection implies long integration (dwell) time, resulting in slow scan speed. However, here we achieve high scan speed using a new 2-step orthogonal scanning strategy to realise on-the-fly time-gated detection and precise location of 1-μm lanthanide-doped microspheres with signal-to-background ratio of 8.9. This enables analysis of a 15 mm × 15 mm slide area in only 3.3 minutes. We demonstrate that detection of only a few hundred photoelectrons within 100 μs is sufficient to distinguish a target event in a prototype system using ultraviolet LED excitation. Cytometric analysis of lanthanide labelled Giardia cysts achieved a signal-to-background ratio of two orders of magnitude. Results suggest that time-gated OSAM represents a new opportunity for high-throughput background-free biosensing applications.

  2. Influence of Stimulus Symmetry and Complexity upon Haptic Scanning Strategies During Detection, Learning and Recognition Tasks.

    ERIC Educational Resources Information Center

    Locher, Paul J.; Simmons, Roger W.

    Two experiments were conducted to investigate the perceptual processes involved in haptic exploration of randomly generated shapes. Experiment one required subjects to detect symmetrical or asymmetrical characteristics of individually presented plastic shapes, also varying in complexity. Scanning time for both symmetrical and asymmetrical shapes…

  3. Dynamic occlusion detection and inpainting of in situ captured terrestrial laser scanning point clouds sequence

    NASA Astrophysics Data System (ADS)

    Chen, Chi; Yang, Bisheng

    2016-09-01

    Laser point clouds captured using terrestrial laser scanning (TLS) in an uncontrollable urban outdoor or indoor scene suffer from irregular shaped data blanks caused by dynamic occlusion that temporarily exists, i.e., moving objects, such as pedestrians or cars, resulting in integrality and quality losses of the scene data. This paper proposes a novel automatic dynamic occlusion detection and inpainting method for sequential TLS point clouds captured from one scan position. In situ collected laser point clouds sequences are indexed by establishing a novel panoramic space partition that assigns a three dimensional voxel to each laser point according to the scanning setups. Then two stationary background models are constructed at the ray voxel level using the laser reflectance intensity and geometrical attributes of the point set inside each voxel across the TLS sequence. Finally, the background models are combined to detect the points on the dynamic object, and the ray voxels of the detected dynamic points are tracked for further inpainting by replacing the ray voxels with the corresponding background voxels from another scan. The resulting scene is free of dynamic occlusions. Experiments validated the effectiveness of the proposed method for indoor and outdoor TLS point clouds captured by a commercial terrestrial scanner. The proposed method achieves high precision and recall rate for dynamic occlusion detection and produces clean inpainted point clouds for further processing.

  4. Spatially resolved quantitative mapping of thermomechanical properties and phase transition temperatures using scanning probe microscopy

    DOEpatents

    Jesse, Stephen; Kalinin, Sergei V; Nikiforov, Maxim P

    2013-07-09

    An approach for the thermomechanical characterization of phase transitions in polymeric materials (polyethyleneterephthalate) by band excitation acoustic force microscopy is developed. This methodology allows the independent measurement of resonance frequency, Q factor, and oscillation amplitude of a tip-surface contact area as a function of tip temperature, from which the thermal evolution of tip-surface spring constant and mechanical dissipation can be extracted. A heating protocol maintained a constant tip-surface contact area and constant contact force, thereby allowing for reproducible measurements and quantitative extraction of material properties including temperature dependence of indentation-based elastic and loss moduli.

  5. Decision model in the laser scanning system for pavement crack detection

    NASA Astrophysics Data System (ADS)

    Sun, Xiaoming; Huang, Jianping; Liu, Wanyu

    2011-12-01

    Pavement crack detection plays an important role in the pavement maintaining and management. Recently, the laser scanning technique for pavement crack detection becomes more and more popular due to its ability of discriminating dark areas, which are not caused by pavement distress such as tire marks, oil spills, and shadows. However, this technique still bears some errors for pavement crack recognition errors, thus in the present work, the factors contributed to these errors in laser scanning system are first analyzed, and then a decision model for the laser scanning pavement crack detection system based on the hypothesis test is proposed. Experimental analyses and results show that this model not only allows us to build the relationship between the contribution factors and crack detection accuracy and to provide the criteria to compare the detection accuracy for the different roads, but also can be used to judge whether the crack exists with a reasonable number of deformed light stripes. Therefore, the proposed decision model can provide guidance on the pavement crack detection and has a practical value.

  6. A new approach to quantitatively describe permafrost core using multi-energy CT scanning: composition fraction and morphological analysis

    NASA Astrophysics Data System (ADS)

    Chang, C.; McKnight, C.; Kneafsey, T. J.

    2014-12-01

    Composition discernment, fraction calculation and morphological analysis of a shallow core retrieved from Barrow, AK as part of the Next Generation Ecosystem Experiments in the Arctic (NGEE-Arctic) were conducted to give a quantitative description of the core. Imaging of the core was performed using a medical X-ray computed tomography (CT) scanner, which gives a 3D image with a resolution of 0.195×0.195×0.625mm3. The core consists mainly of mineral, ice, organic matter and air and composition discernment and fraction calculation focus on the first three materials. Four scans with different energies were performed because materials with different density show different responses on scans with varying energies. A calibration curve showing the relationship between density and CT value was built by scanning standard materials having a wide range of density. CT value of the three compositions under four energies was determined by the calibration curve and the core scan. Composition fraction was calculated on the assumption that the core CT value is linearly proportional to the composition fraction and by solving linear least-squares problems with bounds. Comparison of the estimated and measured core CT value shows that the correlation coefficient is more than 0.99, indicating the accuracy of the calculation. Two regions with relatively high fraction of organic matter (10%) were distinguished, which are located at the top of the core and ice filled fractures at the bottom of the active layer. Morphological analysis was applied to the mineral and ice because of low fraction of organic matter. Three segmentations corresponding to ice-rich (with a density of 0.86 to 1.24 g/cm3), transition from ice to mineral (1.24 to 1.47 g/cm3) and mineral-rich (1.47 to 2.65 g/cm3) were applied to the core, and two area (area and area standard deviation) and three morphological (circulatory, roundness and rectangularity) parameters were analysed. By conducting Principle Component

  7. Genome-wide linkage scan of quantitative traits representing symptom dimensions in multiplex schizophrenia families.

    PubMed

    Ryu, Seunghyong; Won, Hong-Hee; Oh, Sohee; Kim, Jong-Won; Park, Taesung; Cho, Eun-Young; Cho, Youngah; Park, Dong Yeon; Lee, Yu-Sang; Kwon, Jun Soo; Hong, Kyung Sue

    2013-12-30

    Symptom dimensions of schizophrenia are likely to be the intermediate phenotypes under the control of disease-susceptibility genes, or separate traits related to disease-modifier genes. This study aimed to identify chromosomal loci linked to symptom dimensions of schizophrenia through genome-wide quantitative trait locus (QTL) linkage analysis. The study subjects consisted of 56 families with 183 members including 123 affected individuals. Symptom evaluations were performed on lifetime basis. Through principal component factor analysis, eight quantitative phenotypes representing symptom dimensions were identified. Genotyping was done for 6008 SNP markers, and genome-wide QTL linkage analysis was performed. No symptom dimension showed a significant linkage attaining genome-wide empirical thresholds. We observed seven regions yielding linkage signals attaining genome-wide empirical thresholds for suggestive linkage (NPL Z score = 2.78-3.49); chromosome 15q26.1 for 'non-paranoid delusion factor', 2p24.3 and 7q31.1 for 'prodromal impairment factor', 1q32.1, 9p21.3, and 9q31.2 for 'negative symptom factor', and 10p13 for 'disorganization factor'. Among these loci, chromosome 2p24.3 and 1q32.1 overlap with susceptibility loci of schizophrenia identified in our previous linkage studies. This study suggests the existence of genetic loci related to various clinical features of schizophrenia. Further genetic analyses for these dimensional phenotypes are warranted. © 2013 Published by Elsevier Ireland Ltd.

  8. Quantitative peptide binding motifs for 19 human and mouse MHC class I molecules derived using positional scanning combinatorial peptide libraries

    PubMed Central

    Sidney, John; Assarsson, Erika; Moore, Carrie; Ngo, Sandy; Pinilla, Clemencia; Sette, Alessandro; Peters, Bjoern

    2008-01-01

    Background It has been previously shown that combinatorial peptide libraries are a useful tool to characterize the binding specificity of class I MHC molecules. Compared to other methodologies, such as pool sequencing or measuring the affinities of individual peptides, utilizing positional scanning combinatorial libraries provides a baseline characterization of MHC molecular specificity that is cost effective, quantitative and unbiased. Results Here, we present a large-scale application of this technology to 19 different human and mouse class I alleles. These include very well characterized alleles (e.g. HLA A*0201), alleles with little previous data available (e.g. HLA A*3201), and alleles with conflicting previous reports on specificity (e.g. HLA A*3001). For all alleles, the positional scanning combinatorial libraries were able to elucidate distinct binding patterns defined with a uniform approach, which we make available here. We introduce a heuristic method to translate this data into classical definitions of main and secondary anchor positions and their preferred residues. Finally, we validate that these matrices can be used to identify candidate MHC binding peptides and T cell epitopes in the vaccinia virus and influenza virus systems, respectively. Conclusion These data confirm, on a large scale, including 15 human and 4 mouse class I alleles, the efficacy of the positional scanning combinatorial library approach for describing MHC class I binding specificity and identifying high affinity binding peptides. These libraries were shown to be useful for identifying specific primary and secondary anchor positions, and thereby simpler motifs, analogous to those described by other approaches. The present study also provides matrices useful for predicting high affinity binders for several alleles for which detailed quantitative descriptions of binding specificity were previously unavailable, including A*3001, A*3201, B*0801, B*1501 and B*1503. PMID:18221540

  9. Interactive algorithms for the segmentation and quantitation of 3-D MRI brain scans.

    PubMed

    Freeborough, P A; Fox, N C; Kitney, R I

    1997-05-01

    Interactive algorithms are an attractive approach to the accurate segmentation of 3D brain scans as they potentially improve the reliability of fully automated segmentation while avoiding the labour intensiveness and inaccuracies of manual segmentation. We present a 3D image analysis package (MIDAS) with a novel architecture enabling highly interactive segmentation algorithms to be implemented as add on modules. Interactive methods based on intensity thresholding, region growing and the constrained application of morphological operators are also presented. The methods involve the application of constraints and freedoms on the algorithms coupled with real time visualisation of the effect. This methodology has been applied to the segmentation, visualisation and measurement of the whole brain and a small irregular neuroanatomical structure, the hippocampus. We demonstrate reproducible and anatomically accurate segmentations of these structures. The efficacy of one method in measuring volume loss (atrophy) of the hippocampus in Alzheimer's disease is shown and is compared to conventional methods.

  10. PREHISTORICAL Pediculus humanus capitis INFESTATION: QUANTITATIVE DATA AND LOW VACUUM SCANNING MICROSCOPY

    PubMed Central

    Dutra, Juliana M.F.; Alves, Arthur Daniel; Pessanha, Thaila; Rachid, Rachel; de Souza, Wanderley; Linardi, Pedro Marcos; Ferreira, Luiz Fernando; de Souza, Sheila Mendonça; Araujo, Adauto

    2014-01-01

    A pre-Columbian Peruvian scalp was examined decades ago by a researcher from the Oswaldo Cruz Foundation. Professor Olympio da Fonseca Filho described nits and adult lice attached to hair shafts and commented about the origin of head lice infestations on mankind. This same scalp was sent to our laboratory and is the subject of the present paper. Analysis showed a massive infestation with nine eggs/cm2 and an impressive number of very well preserved adult lice. The infestation age was roughly estimated as nine months before death based on the distance of nits from the hair root and the medium rate of hair growth. A small traditional textile was associated with the scalp, possibly part of the funerary belongings. Other morphological aspects visualized by low-vacuum scanning electron microscopy are also presented here for adults and nits. PMID:24626412

  11. Prehistorical Pediculus humanus capitis infestation: quantitative data and low vacuum scanning microscopy.

    PubMed

    Dutra, Juliana M F; Alves, Arthur Daniel; Pessanha, Thaila; Rachid, Rachel; Souza, Wanderley de; Linardi, Pedro Marcos; Ferreira, Luiz Fernando; Souza, Sheila Mendonça de; Araujo, Adauto

    2014-01-01

    A pre-Columbian Peruvian scalp was examined decades ago by a researcher from the Oswaldo Cruz Foundation. Professor Olympio da Fonseca Filho described nits and adult lice attached to hair shafts and commented about the origin of head lice infestations on mankind. This same scalp was sent to our laboratory and is the subject of the present paper. Analysis showed a massive infestation with nine eggs/cm2 and an impressive number of very well preserved adult lice. The infestation age was roughly estimated as nine months before death based on the distance of nits from the hair root and the medium rate of hair growth. A small traditional textile was associated with the scalp, possibly part of the funerary belongings. Other morphological aspects visualized by low-vacuum scanning electron microscopy are also presented here for adults and nits.

  12. Acquisition of quantitative physiological data and computerized image reconstruction using a single scan TV system

    NASA Technical Reports Server (NTRS)

    Baily, N. A.

    1976-01-01

    A single-scan radiography system has been interfaced to a minicomputer, and the combined system has been used with a variety of fluoroscopic systems and image intensifiers available in clinical facilities. The system's response range is analyzed, and several applications are described. These include determination of the gray scale for typical X-ray-fluoroscopic-television chains, measurement of gallstone volume in patients, localization of markers or other small anatomical features, determinations of organ areas and volumes, computer reconstruction of tomographic sections of organs in motion, and computer reconstruction of transverse axial body sections from fluoroscopic images. It is concluded that this type of system combined with a minimum of statistical processing shows excellent capabilities for delineating small changes in differential X-ray attenuation.

  13. Acquisition of quantitative physiological data and computerized image reconstruction using a single scan TV system

    NASA Technical Reports Server (NTRS)

    Baily, N. A.

    1976-01-01

    A single-scan radiography system has been interfaced to a minicomputer, and the combined system has been used with a variety of fluoroscopic systems and image intensifiers available in clinical facilities. The system's response range is analyzed, and several applications are described. These include determination of the gray scale for typical X-ray-fluoroscopic-television chains, measurement of gallstone volume in patients, localization of markers or other small anatomical features, determinations of organ areas and volumes, computer reconstruction of tomographic sections of organs in motion, and computer reconstruction of transverse axial body sections from fluoroscopic images. It is concluded that this type of system combined with a minimum of statistical processing shows excellent capabilities for delineating small changes in differential X-ray attenuation.

  14. Quantitative Z-contrast imaging in the scanning transmission electron microscope with size-selected clusters

    NASA Astrophysics Data System (ADS)

    Wang, Z. W.; Li, Z. Y.; Park, S. J.; Abdela, A.; Tang, D.; Palmer, R. E.

    2011-08-01

    This paper describes a new approach of quantification of annular-dark-field or Z-contrast image intensity as a function of inner acceptance angle of the detector in a scanning transmission electron microscope. By using size-selected nanoclusters of Pd (Z = 46) and Au (Z = 79), it is shown experimentally that the exponent in the power law I ˜ Zα varies strongly between 1.2 and 1.8 as the collection angle changes from 14 to 103 mrad. The result is discussed in line with existing theoretical models. Factors, such as cluster size, structure, and orientation as well as the detector geometry, are also discussed for potential use of the work.

  15. Concentration dependent red shift: qualitative and quantitative investigation of motor oils by synchronous fluorescence scan.

    PubMed

    Patra, D; Mishra, A K

    2001-01-05

    Synchronous fluorescence scan (SFS) has been described as a successful technique to characterize Motor oils like diesel, petrol, kerosene, 2T oil and Mobil. The concentration dependent investigation of Motor oils shows a red shift in lambda(SFS)(max). Using red shift of lambda(SFS)(max), a method has been developed to quantify Motor oil in the concentration range 5-100% v/v. The concentration dependent overall rate of energy transfer of Motor oil gives a unique behavioral change according to the oil type and SFS is a simpler spectroscopic method to qualitatively differentiate between heavy and light oil. The molecular interaction of polycyclic aromatic compounds (PACs) in fluorophoric mixtures like resonance energy transfer and self-quenching via solvent collision has been clearly explained by SFS method. Effect of solvent and external quencher molecule on Motor oils has also been studied. Nitrobenzene is found to be a selective quencher for PACs of Motor oils.

  16. Quantitative analysis of the lamina cribrosa in vivo using a scanning laser opthalmoscope.

    PubMed

    Bhandari, A; Fontana, L; Fitzke, F W; Hitchings, R A

    1997-01-01

    Structural changes in the lamina cribrosa have been implicated in the pathogenesis of glaucomatous optic nerve atrophy. The purpose of this study was to develop a method for morphometric analysis of the lamina cribrosa pores in vivo, using a scanning laser ophthalmoscope. A prototype Zeiss confocal laser scanning ophthalmoscope was used to acquire images of the lamina cribrosa. The images were digitised and aligned to compensate for eye movements. Thirty-two consecutive images were averaged to reduce noise. The images were processed to adjust for luminance gradients prior to segmentation and analysis. Details of the image processing are described. The end result of processing the images was a binary (black and white) image that can be used for automated computer assisted measurements. The pores of the lamina cribrosa are well represented and retain their overall shape in the binary image, as judged by superimposing the binary image on the unprocessed image. We also established the repeatability, reproducibility and intercession variability of this technique. Repeated images of the internal lamina cribrosa of 10 patients were acquired by two observers in two separate visits, and the images were processed before automated computer measurements. The parameters evaluated were number of pores, area covered by the pores and area covered by the visible lamina cribrosa. The coefficient of variation for number of pores, pore area and lamina area was 6.9%, 2.1% and 4.3% for observer A and 5.5%, 2.1% and 5.8% for observer B. Pearson product moment correlation coefficient between the two observers was 0.94, 0.99 and 0.97 for the above parameters respectively. There was no significant difference between the measurements on visit 1 and 2 for both observers. The technique described allows, for the first time, in vivo morphometry of the internal lamina cribrosa surface. This method has good reproducibility, suggesting future clinical applications.

  17. Quantitative analysis of high-resolution computed tomography scans in severe asthma subphenotypes

    PubMed Central

    Gupta, Sumit; Siddiqui, Salman; Haldar, Pranab; Entwisle, James J; Mawby, Dean; Wardlaw, Andrew J; Bradding, Peter; Pavord, Ian D; Green, Ruth H

    2010-01-01

    Background Severe asthma is a heterogeneous condition. Airway remodelling is a feature of severe asthma and can be determined by the assessment of high-resolution computed tomography (HRCT) scans. The aim of this study was to assess whether airway remodelling is restricted to specific subphenotypes of severe asthma. Methods A retrospective analysis was performed of HRCT scans from subjects who had attended a single-centre severe asthma clinic between 2003 and 2008. The right upper lobe apical segmental bronchus (RB1) dimensions were measured and the clinical and sputum inflammatory characteristics associated with RB1 geometry were assessed by univariate and multivariate regression analyses. Longitudinal sputum data were available and were described as area under the time curve (AUC). Comparisons were made in RB1 geometry across subjects in four subphenotypes determined by cluster analysis, smokers and non-smokers, and subjects with and without persistent airflow obstruction. Results Ninety-nine subjects with severe asthma and 16 healthy controls were recruited. In the subjects with severe asthma the RB1 percentage wall area (%WA) was increased (p=0.009) and lumen area (LA)/body surface area (BSA) was decreased (p=0.008) compared with controls but was not different across the four subphenotypes. Airway geometry was not different between smokers and non-smokers and RB1 %WA was increased in those with persistent airflow obstruction. RB1 %WA in severe asthma was best associated with airflow limitation and persistent neutrophilic airway inflammation (model R2=0.27, p=0.001). Conclusions Airway remodelling of proximal airways occurs in severe asthma and is associated with impaired lung function and neutrophilic airway inflammation. PMID:20805170

  18. Autoblocker: a system for detecting and blocking of network scanning based on analysis of netflow data

    SciTech Connect

    Bobyshev, A.; Lamore, D.; Demar, P.; /Fermilab

    2004-12-01

    In a large campus network, such at Fermilab, with tens of thousands of nodes, scanning initiated from either outside of or within the campus network raises security concerns. This scanning may have very serious impact on network performance, and even disrupt normal operation of many services. In this paper we introduce a system for detecting and automatic blocking excessive traffic of different kinds of scanning, DoS attacks, virus infected computers. The system, called AutoBlocker, is a distributed computing system based on quasi-real time analysis of network flow data collected from the border router and core switches. AutoBlocker also has an interface to accept alerts from IDS systems (e.g. BRO, SNORT) that are based on other technologies. The system has multiple configurable alert levels for the detection of anomalous behavior and configurable trigger criteria for automated blocking of scans at the core or border routers. It has been in use at Fermilab for about 2 years, and has become a very valuable tool to curtail scan activity within the Fermilab campus network.

  19. A system for automatically scanning tissue culture dishes to detect fluorescently labeled cell colonies

    NASA Astrophysics Data System (ADS)

    Goldstein, Seth R.; Guan-Xiong, Zhou; Siegel, Ruth E.; Brownstein, Michael J.

    1989-07-01

    A microprocessor-controlled system has been developed to automatically scan tissue culture dishes in order to detect and locate fluorescently labeled cell colonies for subsequent cloning. An X-Y recorder mechanism moves an 80-mm-diam dish in a raster scan through a stationary laser beam adjacent to a photomultiplier tube equipped with an emission filter. Front-end electronics processes the PMT signal to screen out small-scale fluorescent artifacts of selectable size (e.g., <0.2 mm). Appropriate signals are input to the computer which then interrupts the raster scan to perform a limited fine scan of the dish to accurately localize the fluorescent spot position. An additional artifact test using a different filter is then performed. The underside of the dish is scribed at the location of spots that pass this test. Using fluorescein as a label, fluorescence as low as 25% above intrinsic cell background fluorescence can be detected. The fluorescence signal level threshhold can be set (e.g., 70% above intrinsic cell background) to within an accuracy of approximately 15% of intrinsic cell background fluorescence, and the system will reliably find colonies with a signal exceeding that level. With the above typical values, the number of false positives is typically less than five per dish and the time to completely scan an 80-mm-diam tissue culture dish is 2-4 min.

  20. Quantitative measurement of adhesion of ink on plastic films with a Nano Indenter and a Scanning Probe Microscope

    NASA Astrophysics Data System (ADS)

    Shen, Weidian

    2005-03-01

    Plastic film packaging is widely used these days, especially in the convenience food industry due to its flexibility, boilability, and microwavability. Almost every package is printed with ink. The adhesion of ink on plastic films merits increasing attention to ensure quality packaging. However, inks and plastic films are polymeric materials with complicated molecular structures. The thickness of the jelly-like ink is only 500nm or less, and the thickness of the soft and flexible film is no more than 50μm, which make the quantitative measurement of their adhesion very challenging. Up to now, no scientific quantitative measurement method for the adhesion of ink on plastic films has been documented. We have tried a technique, in which a Nano-Indenter and a Scanning Probe Microscope were used to evaluate the adhesion strength of ink deposited on plastic films, quantitatively, as well as examine the configurations of adhesion failure. It was helpful in better understanding the adhesion mechanism, thus giving direction as to how to improve the adhesion.

  1. Investigation into the quantitative and qualitative characteristics of choroidal melanoma through magnetic resonance imaging and B-scan ultrasound.

    PubMed

    Papayiannis, Vassilis; Tsaousis, Konstantinos T; Kouskouras, Constantinos A; Haritanti, Afroditi; Diakonis, Vasilios F; Tsinopoulos, Ioannis T

    2017-01-01

    To investigate the homogeneity and vascularity of choroidal melanoma through magnetic resonance imaging (MRI) and brightness modulation (B-mode) ultrasound scan and their correlation with dimensions of tumor, as well as to measure the sensitivity of both modalities in retinal detachment (RD) detection. This retrospective chart review included patients diagnosed with choroidal melanoma. All these patients underwent MRI scans using T2-weighted (T2-WI) and T1-weighted (T1-WI) sequences, before and after an intravenous injection of paramagnetic contrast material. The patients were also examined using a B-mode ultrasound scan, and the results from both modalities were compared (tumor homogeneity, tumor height, tumor base diameter, and tumor vascularity). Forty-two patients (mean age=65.33±12.51 years) with choroidal melanoma were included in the study. Homogeneity was confirmed in 16 patients through ultrasound scan, in 19 patients through T1-WI sequence, in 21 patients through T2-WI sequence, and in 25 patients through T1-WI sequence + contrast (gadolinium). Patients with homogenous tumors presented with lower (P=0.0045) mean height than that of those with nonhomogenous tumors, whereas no statistically significant difference was found for base diameter measurements (P=0.056). Patients with tumors of high vascularity presented with greater mean height (P=0.000638) and greater mean base diameter compared with those with tumors of low vascularity (P=0.019543). RD was detected in 26 patients through T1-WI sequence, in 13 patients through T2-WI sequence, in 26 patients through T1-WI sequence + contrast, and in 32 patients through ultrasound scan, which proved to be the most sensitive modality. The height of choroidal melanoma was positively correlated with tumor's homogeneity. Melanomas of greater height were found to be less homogenous, due to increased degeneration and higher occurrence of intratumoral hemorrhage. In addition, choroidal melanoma's height was also

  2. Investigation into the quantitative and qualitative characteristics of choroidal melanoma through magnetic resonance imaging and B-scan ultrasound

    PubMed Central

    Papayiannis, Vassilis; Tsaousis, Konstantinos T; Kouskouras, Constantinos A; Haritanti, Afroditi; Diakonis, Vasilios F; Tsinopoulos, Ioannis T

    2017-01-01

    Objective To investigate the homogeneity and vascularity of choroidal melanoma through magnetic resonance imaging (MRI) and brightness modulation (B-mode) ultrasound scan and their correlation with dimensions of tumor, as well as to measure the sensitivity of both modalities in retinal detachment (RD) detection. Materials and methods This retrospective chart review included patients diagnosed with choroidal melanoma. All these patients underwent MRI scans using T2-weighted (T2-WI) and T1-weighted (T1-WI) sequences, before and after an intravenous injection of paramagnetic contrast material. The patients were also examined using a B-mode ultrasound scan, and the results from both modalities were compared (tumor homogeneity, tumor height, tumor base diameter, and tumor vascularity). Results Forty-two patients (mean age=65.33±12.51 years) with choroidal melanoma were included in the study. Homogeneity was confirmed in 16 patients through ultrasound scan, in 19 patients through T1-WI sequence, in 21 patients through T2-WI sequence, and in 25 patients through T1-WI sequence + contrast (gadolinium). Patients with homogenous tumors presented with lower (P=0.0045) mean height than that of those with nonhomogenous tumors, whereas no statistically significant difference was found for base diameter measurements (P=0.056). Patients with tumors of high vascularity presented with greater mean height (P=0.000638) and greater mean base diameter compared with those with tumors of low vascularity (P=0.019543). RD was detected in 26 patients through T1-WI sequence, in 13 patients through T2-WI sequence, in 26 patients through T1-WI sequence + contrast, and in 32 patients through ultrasound scan, which proved to be the most sensitive modality. Conclusion The height of choroidal melanoma was positively correlated with tumor’s homogeneity. Melanomas of greater height were found to be less homogenous, due to increased degeneration and higher occurrence of intratumoral hemorrhage. In

  3. Quantitative assessment of lesion detection accuracy, resolution, and reconstruction algorithms in neutron stimulated emission computed tomography.

    PubMed

    Lakshmanan, Manu N; Kapadia, Anuj J

    2012-07-01

    We present a quantitative analysis of the image quality obtained using filtered back-projection (FBP) with Ram-Lak filtering and maximum likelihood-expectation maximization (ML-EM)-with no post-reconstruction filtering in either case-in neutron stimulated emission computed tomography (NSECT) imaging using Monte Carlo simulations in the context of clinically relevant models of liver iron overload. The ratios of pixel intensities for several regions of interest and lesion shape detection using an active-contours segmentation algorithm are assessed for accuracy across different scanning configurations and reconstruction algorithms. The modulation transfer functions (MTFs) are also computed for the cases under study and are applied to determine a minimum detectable lesion spacing as a form of sensitivity analysis. The accuracy of NSECT imaging in measuring relative tissue concentration is presented for simulated clinical liver cases. When using the 15th iteration, ML-EM provides at least 25% better resolution than FBP and proves to be highly robust under low-signal high-noise conditions prevalent in NSECT. However, FBP gives more accurate lesion pixel intensity ratios and size estimates in some cases; due to advantages provided by both reconstruction algorithms, it is worth exploring the development of an algorithm that is a hybrid of the two. We also show that NSECT imaging can be used to accurately detect 3-cm lesions in backgrounds that are a significant fraction (one-quarter) of the concentration of the lesion, down to a 4-cm spacing between lesions.

  4. Ultrasonography and indium 111 white blood cell scanning for the detection of intraabdominal abscesses

    SciTech Connect

    Carroll, B.; Silverman, P.M.; Goodwin, D.A.; McDougall, I.R.

    1981-07-01

    Ultrasound and indium 111 white blood cell scanning were performed on 163 patients with suspected intraabdominal abscesses. In all but one case, intraabdominal abscesses were correctly identified by one or both tests; conversely, no patient was falsely diagnosed by both tests to have an abscess. Sonography was useful in those patients with focal symptoms, and frequently identified nonabscess causes for fever. White cell scanning was valuable when focal signs were absent, and frequently identified extraabdominal sources of sepsis. The two imaging modalities are complementary and provide a highly accurate and sensitive means of intraabdominal abscess detection.

  5. Reliability of scanning laser acoustic microscopy for detecting internal voids in structural ceramics

    NASA Technical Reports Server (NTRS)

    Roth, D. J.; Baaklini, G. Y.

    1986-01-01

    The reliability of 100 MHz scanning laser acoustic microscopy (SLAM) for detecting internal voids in sintered specimens of silicon nitride and silicon carbide was evaluated. The specimens contained artificially implanted voids and were positioned at depths ranging up to 2 mm below the specimen surface. Detection probability of 0.90 at a 0.95 confidence level was determined as a function of material, void diameter, and void depth. The statistical results presented for void detectability indicate some of the strengths and limitations of SLAM as a nondestructive evaluation technique for structural ceramics.

  6. Automatic concrete cracks detection and mapping of terrestrial laser scan data

    NASA Astrophysics Data System (ADS)

    Rabah, Mostafa; Elhattab, Ahmed; Fayad, Atef

    2013-12-01

    Terrestrial laser scanning has become one of the standard technologies for object acquisition in surveying engineering. The high spatial resolution of imaging and the excellent capability of measuring the 3D space by laser scanning bear a great potential if combined for both data acquisition and data compilation. Automatic crack detection from concrete surface images is very effective for nondestructive testing. The crack information can be used to decide the appropriate rehabilitation method to fix the cracked structures and prevent any catastrophic failure. In practice, cracks on concrete surfaces are traced manually for diagnosis. On the other hand, automatic crack detection is highly desirable for efficient and objective crack assessment. The current paper submits a method for automatic concrete cracks detection and mapping from the data that was obtained during laser scanning survey. The method of cracks detection and mapping is achieved by three steps, namely the step of shading correction in the original image, step of crack detection and finally step of crack mapping and processing steps. The detected crack is defined in a pixel coordinate system. To remap the crack into the referred coordinate system, a reverse engineering is used. This is achieved by a hybrid concept of terrestrial laser-scanner point clouds and the corresponding camera image, i.e. a conversion from the pixel coordinate system to the terrestrial laser-scanner or global coordinate system. The results of the experiment show that the mean differences between terrestrial laser scan and the total station are about 30.5, 16.4 and 14.3 mms in x, y and z direction, respectively.

  7. Quantitative Mapping of Pore Fraction Variations in Silicon Nitride Using an Ultrasonic Contact Scan Technique

    NASA Technical Reports Server (NTRS)

    Roth, Don J.; Kiser, James D.; Swickard, Suzanne M.; Szatmary, Steven A.; Kerwin, David P.

    1993-01-01

    An ultrasonic scan procedure using the pulse-echo contact configuration was employed to obtain maps of pore fraction variations in sintered silicon nitride samples in terms of ultrasonic material properties. Ultrasonic velocity, attenuation coefficient, and reflection coefficient images were obtained simultaneously over a broad band of frequencies (e.g., 30 to 110 MHz) by using spectroscopic analysis. Liquid and membrane (dry) coupling techniques and longitudinal and shear-wave energies were used. The major results include the following: Ultrasonic velocity (longitudinal and shear wave) images revealed and correlated with the extent of average through-thickness pore fraction variations in the silicon nitride disks. Attenuation coefficient images revealed pore fraction nonuniformity due to the scattering that occurred at boundaries between regions of high and low pore fraction. Velocity and attenuation coefficient images were each nearly identical for machined and polished disks, making the method readily applicable to machined materials. Velocity images were similar for wet and membrane coupling. Maps of apparent Poisson's ratio constructed from longitudinal and shear-wave velocities quantified Poisson's ratio variations across a silicon nitride disk. Thermal wave images of a disk indicated transient thermal behavior variations that correlated with observed variations in pore fraction and velocity and attenuation coefficients.

  8. Quantitative model for near-field scanning microwave microscopy: application to metrology of thin film dielectrics.

    PubMed

    Reznik, Alexander N; Talanov, Vladimir V

    2008-11-01

    We have experimentally verified a recently proposed theoretical model for near-field microwave microscopy of multilayer media. The model addresses a near-field microwave probe as an electrically small antenna with a Gaussian-like current distribution that has a single characteristic length scale on the order of the probe size. Electrodynamic response of an antenna is calculated using Green functions in the form of integral transforms for electric and magnetic fields (both quasistatic and propagating), which are generated by a pointlike dipole. Experimental data were obtained at 4 GHz using a near-field scanning microwave microscope with aperture size of approximately 5 microm for a set of six SiO(2) films with thickness ranging from 0.1 to 1.5 microm. For each sample the probe resonant frequency was both measured and simulated as a function of the tip-sample distance, and good agreement between the theory and experimental data was observed. It was found that the model is capable of determining thin film dielectric constant with accuracy of approximately 5%-7%.

  9. A paper/polymer hybrid microfluidic microplate for rapid quantitative detection of multiple disease biomarkers

    NASA Astrophysics Data System (ADS)

    Sanjay, Sharma T.; Dou, Maowei; Sun, Jianjun; Li, Xiujun

    2016-07-01

    Enzyme linked immunosorbent assay (ELISA) is one of the most widely used laboratory disease diagnosis methods. However, performing ELISA in low-resource settings is limited by long incubation time, large volumes of precious reagents, and well-equipped laboratories. Herein, we developed a simple, miniaturized paper/PMMA (poly(methyl methacrylate)) hybrid microfluidic microplate for low-cost, high throughput, and point-of-care (POC) infectious disease diagnosis. The novel use of porous paper in flow-through microwells facilitates rapid antibody/antigen immobilization and efficient washing, avoiding complicated surface modifications. The top reagent delivery channels can simply transfer reagents to multiple microwells thus avoiding repeated manual pipetting and costly robots. Results of colorimetric ELISA can be observed within an hour by the naked eye. Quantitative analysis was achieved by calculating the brightness of images scanned by an office scanner. Immunoglobulin G (IgG) and Hepatitis B surface Antigen (HBsAg) were quantitatively analyzed with good reliability in human serum samples. Without using any specialized equipment, the limits of detection of 1.6 ng/mL for IgG and 1.3 ng/mL for HBsAg were achieved, which were comparable to commercial ELISA kits using specialized equipment. We envisage that this simple POC hybrid microplate can have broad applications in various bioassays, especially in resource-limited settings.

  10. A paper/polymer hybrid microfluidic microplate for rapid quantitative detection of multiple disease biomarkers

    PubMed Central

    Sanjay, Sharma T.; Dou, Maowei; Sun, Jianjun; Li, XiuJun

    2016-01-01

    Enzyme linked immunosorbent assay (ELISA) is one of the most widely used laboratory disease diagnosis methods. However, performing ELISA in low-resource settings is limited by long incubation time, large volumes of precious reagents, and well-equipped laboratories. Herein, we developed a simple, miniaturized paper/PMMA (poly(methyl methacrylate)) hybrid microfluidic microplate for low-cost, high throughput, and point-of-care (POC) infectious disease diagnosis. The novel use of porous paper in flow-through microwells facilitates rapid antibody/antigen immobilization and efficient washing, avoiding complicated surface modifications. The top reagent delivery channels can simply transfer reagents to multiple microwells thus avoiding repeated manual pipetting and costly robots. Results of colorimetric ELISA can be observed within an hour by the naked eye. Quantitative analysis was achieved by calculating the brightness of images scanned by an office scanner. Immunoglobulin G (IgG) and Hepatitis B surface Antigen (HBsAg) were quantitatively analyzed with good reliability in human serum samples. Without using any specialized equipment, the limits of detection of 1.6 ng/mL for IgG and 1.3 ng/mL for HBsAg were achieved, which were comparable to commercial ELISA kits using specialized equipment. We envisage that this simple POC hybrid microplate can have broad applications in various bioassays, especially in resource-limited settings. PMID:27456979

  11. Heel Ultrasound Scan in Detecting Osteoporosis in Low Trauma Fracture Patients.

    PubMed

    Hashmi, Faiz R; Elfandi, Khaled O

    2016-06-27

    Osteoporosis is the most common metabolic disease with significant impact on the morbidity and mortality of affected patients. Osteoporosis has a significant impact on the economy worldwide. The aim of this study was to find out whether heel ultrasound is as good as central bone densitometry scanning in diagnosing osteoporosis in patients who are at high risk of osteoporosis. This was a prospective study of patients comparing heel ultrasound to central bone densitometry scanning (dual X-ray absorptiometry, DEXA) in patients. The recruited patients attended for a DEXA scan of the left hip and lumbar spine. All subjects had an ultrasound of the left heel using the quantitative heel ultrasound machine. The results of DEXA scan were blinded from the results of ultrasound and vice versa. There were 59 patients who took part in the study, 12 men and 47 women. The mean age was 66 years (SD 11.9) and mean weight was 62.5 kg (SD 10.7). The sensitivity and specificity of the ultrasound heel test to predict osteoporosis were 53% (95%CI: 29-77) and 86% (95%CI: 75-96) respectively. Specificity for predicting bone mineral density (BMD)-defined osteoporosis was high (86%), but sensitivity was low (53%). A heel ultrasound result in the osteoporotic range was highly predictive of BMD-defined osteoporosis. A positive ultrasound heel test in high risk patients is more useful in ruling in osteoporosis than a negative test to rule out osteoporosis.

  12. Quantitative microstructural imaging by scanning Laue x-ray micro- and nanodiffraction

    DOE PAGES

    Chen, Xian; Dejoie, Catherine; Jiang, Tengfei; ...

    2016-06-08

    We present that local crystal structure, crystal orientation, and crystal deformation can all be probed by Laue diffraction using a submicron x-ray beam. This technique, employed at a synchrotron facility, is particularly suitable for fast mapping the mechanical and microstructural properties of inhomogeneous multiphase polycrystalline samples, as well as imperfect epitaxial films or crystals. As synchrotron Laue x-ray microdiffraction enters its 20th year of existence and new synchrotron nanoprobe facilities are being built and commissioned around the world, we take the opportunity to overview current capabilities as well as the latest technical developments. Fast data collection provided by state-of-the-art areamore » detectors and fully automated pattern indexing algorithms optimized for speed make it possible to map large portions of a sample with fine step size and obtain quantitative images of its microstructure in near real time. Lastly, we extrapolate how the technique is anticipated to evolve in the near future and its potential emerging applications at a free-electron laser facility.« less

  13. Quantitative microstructural imaging by scanning Laue x-ray micro- and nanodiffraction

    SciTech Connect

    Chen, Xian; Dejoie, Catherine; Jiang, Tengfei; Ku, Ching-Shun; Tamura, Nobumichi

    2016-06-08

    We present that local crystal structure, crystal orientation, and crystal deformation can all be probed by Laue diffraction using a submicron x-ray beam. This technique, employed at a synchrotron facility, is particularly suitable for fast mapping the mechanical and microstructural properties of inhomogeneous multiphase polycrystalline samples, as well as imperfect epitaxial films or crystals. As synchrotron Laue x-ray microdiffraction enters its 20th year of existence and new synchrotron nanoprobe facilities are being built and commissioned around the world, we take the opportunity to overview current capabilities as well as the latest technical developments. Fast data collection provided by state-of-the-art area detectors and fully automated pattern indexing algorithms optimized for speed make it possible to map large portions of a sample with fine step size and obtain quantitative images of its microstructure in near real time. Lastly, we extrapolate how the technique is anticipated to evolve in the near future and its potential emerging applications at a free-electron laser facility.

  14. Rapid super-resolution line-scanning microscopy through virtually structured detection.

    PubMed

    Zhi, Yanan; Lu, Rongwen; Wang, Benquan; Zhang, Qiuxiang; Yao, Xincheng

    2015-04-15

    Virtually structured detection (VSD) has been demonstrated to break the diffraction limit in scanning laser microscopy (SLM). VSD provides an easy, low-cost, and phase-artifact-free strategy to achieve super-resolution imaging. However, practical application of this method is challenging due to a limited image acquisition speed. We report here the combination of VSD and line-scanning microscopy (LSM) to improve the image acquisition speed. A motorized dove prism was used to achieve automatic control of four-angle (i.e., 0°, 45°, 90°, and 135°) scanning, thus ensuring isotropic resolution improvement. Both an optical resolution target and a living frog eyecup were used to verify resolution enhancement.

  15. Effect of Intrafraction Prostate Motion on Proton Pencil Beam Scanning Delivery: A Quantitative Assessment

    SciTech Connect

    Tang, Shikui; Deville, Curtiland; McDonough, James; Tochner, Zelig; Wang, Ken Kang-Hsin; Vapiwala, Neha; Both, Stefan

    2013-10-01

    Purpose: To assess the dosimetric impact caused by the interplay between intrafraction prostate motion and the intermittent delivery of proton pencil beam scanning (PBS). Methods and Materials: A cohort of 10 prostate patients was treated with PBS using a bilateral single-field uniform dose (SFUD) modality. Bilateral intensity-modulated proton therapy (IMPT) plans were generated for comparison. Because beam-on time in PBS was intermittent, the actual beam-on time was determined from treatment logs. Prostate motion was generalized according to real-time Calypso tracking data from our previously reported prospective photon trial. We investigated potential dose deviations by considering the interplay effect resulting from the worst-case scenario motion and the PBS delivery sequence. Results: For both bilateral-field SFUD and IMPT plans, clinical target volume (CTV) D{sub 99}% coverage was degraded <2% owing to prostate intrafraction motion when averaged over the course of treatment, but was >10% for the worst fraction. The standard deviation of CTV D{sub 99}% distribution was approximately 1.2%. The CTV coverage of individual fields in SFUD plans degraded as time elapsed after the initial alignment, owing to prostate drift. Intensity-modulated proton therapy and SFUD demonstrated comparable results when bilateral opposed fields were used. Single-field SFUD plans that were repainted twice, which could reduce half of the treatment time, resulted in similar CTV coverage as bilateral-field plans. Conclusions: Intrafraction prostate motion affects the actual delivered dose to CTV; however, when averaged over the course of treatment, CTV D{sub 99}% coverage degraded only approximately 2% even for the worst-case scenario. The IMPT plan results are comparable to those of the SFUD plan, and similar coverage can be achieved if treated by SFUD 1 lateral field per day when rescanning the field twice to shorten the treatment time and mitigate intrafraction motion.

  16. Quantitative Two-Dimensional Dopant Profile Measurement on Semiconductors by Scanning Probe Microscopy.

    NASA Astrophysics Data System (ADS)

    Huang, Yunji

    1995-01-01

    A Scanning Capacitance Microscope (SCM) has been built to measure two-dimensional (2D) dopant density profiles on semiconductor materials. A quasi-one-dimensional(1D) analytical model has been constructed for inverting the measured SCM data to dopant profile. Local Capacitance -Voltage (C-V) measurements have been performed on n ^+/n and p^+/n ion implanted silicon wafers and systematic results have been obtained. Dopant profile measurements by SCM have been performed on both top surfaces and cross-sectional surfaces of ion implanted silicon wafers. After inversion, a good agreement has been found between the SCM profile and the profiles obtained by other independent methods such as Secondary Ion Mass Spectrometry (SIMS), Spreading Resistance Profiling (SRP), and process simulation (SUPREM IV). The dissertation presented here consists of four chapters. The first chapter introduces the dopant profile measurement and gives a review of existing doping profiling methods. The advantages of SCM for dopant profile measurement are discussed in this chapter. The second chapter concentrates on the instrumentation of SCM, SCM tip preparation, and silicon sample preparation for dopant profile measurement by SCM. The third chapter describes the tip/sample modeling by which the measured capacitance signal is inverted to dopant profile. The calculation of the electrostatic force between a tip and semiconductor sample as a function of dopant density is also presented in this chapter. Finally, in the fourth chapter, the SCM measurement results are presented and the inverted 2D profiles are compared with the results obtained by other independent methods. A discussion about measurement sensitivity, spatial resolution, modeling errors, and future works is presented.

  17. Scanning Laser Entoptic Perimetry for the Detection of Age-Related Macular Degeneration

    PubMed Central

    Freeman, William R.; El-Bradey, Mohamed; Plummer, Daniel J.

    2006-01-01

    Objective To determine the sensitivity and specificity of scanning laser entoptic perimetry for detecting visual function damage due to age-related macular degeneration (ARMD). Methods We measured the presence or absence of visual field disturbances by entoptic perimetry and determined the severity of ARMD based on masked readings of fundus photographs. A prospective masked study comparing the findings of entoptic perimetry with fundus photographs was performed. We recruited 91 patients with ARMD and 24 patients without ARMD during ophthalmologic visits. An appropriate institutional review board approval was obtained for the project. The main outcome measure was the detection of visual scotomata. Results Scanning laser entoptic perimetry had an overall sensitivity of 82% and a specificity of 100% for the detection of ARMD. The sensitivity for early stages of the disease is greater than 70%, and increases to above 90% for moderate to late stages. Conclusion Scanning laser entoptic perimetry is a specific and sensitive test for detecting ARMD, even at the earliest stages when patients are typically asymptomatic. PMID:15534125

  18. Line-scan hyperspectral imaging for real-time poultry fecal detection

    NASA Astrophysics Data System (ADS)

    Park, Bosoon; Yoon, Seung-Chul; Windham, William R.; Lawrence, Kurt C.; Heitschmidt, G. W.; Kim, Moon S.; Chao, Kaunglin

    2010-04-01

    The ARS multispectral imaging system with three-band common aperture camera was able to inspect fecal contaminants in real-time mode during poultry processing. Recent study has demonstrated several image processing methods including binning, cuticle removal filter, median filter, and morphological analysis in real-time mode could remove false positive errors. The ARS research groups and their industry partner are now merging the fecal detection and systemically disease detection systems onto a common platform using line-scan hyperspectral imaging system. This system will aid in commercialization by creating one hyperspectral imaging system with user-defined wavelengths that can be installed in different locations of the processing line to solve significant food safety problems. Therefore, this research demonstrated the feasibility of line-scan hyperspectral imaging system in terms of processing speed and detection accuracy for a real-time, on-line fecal detection at current processing speed (140 birds per minute) of commercial poultry plant. The newly developed line-scan hyperspectral imaging system could improve Food Safety Inspection Service (FSIS)'s poultry safety inspection program significantly.

  19. Automated Guided-Wave Scanning Developed to Characterize Materials and Detect Defects

    NASA Technical Reports Server (NTRS)

    Martin, Richard E.; Gyekenyeski, Andrew L.; Roth, Don J.

    2004-01-01

    The Nondestructive Evaluation (NDE) Group of the Optical Instrumentation Technology Branch at the NASA Glenn Research Center has developed a scanning system that uses guided waves to characterize materials and detect defects. The technique uses two ultrasonic transducers to interrogate the condition of a material. The sending transducer introduces an ultrasonic pulse at a point on the surface of the specimen, and the receiving transducer detects the signal after it has passed through the material. The aim of the method is to correlate certain parameters in both the time and frequency domains of the detected waveform to characteristics of the material between the two transducers. The scanning system is shown. The waveform parameters of interest include the attenuation due to internal damping, waveform shape parameters, and frequency shifts due to material changes. For the most part, guided waves are used to gauge the damage state and defect growth of materials subjected to various mechanical or environmental loads. The technique has been applied to polymer matrix composites, ceramic matrix composites, and metal matrix composites as well as metallic alloys. Historically, guided wave analysis has been a point-by-point, manual technique with waveforms collected at discrete locations and postprocessed. Data collection and analysis of this type limits the amount of detail that can be obtained. Also, the manual movement of the sensors is prone to user error and is time consuming. The development of an automated guided-wave scanning system has allowed the method to be applied to a wide variety of materials in a consistent, repeatable manner. Experimental studies have been conducted to determine the repeatability of the system as well as compare the results obtained using more traditional NDE methods. The following screen capture shows guided-wave scan results for a ceramic matrix composite plate, including images for each of nine calculated parameters. The system can

  20. Reliability of void detection in structural ceramics using scanning laser acoustic microscopy

    NASA Technical Reports Server (NTRS)

    Roth, D. J.; Klima, S. J.; Kiser, J. D.; Baaklini, G. Y.

    1985-01-01

    The reliability of scanning laser acoustic microscopy (SLAM) for detecting surface voids in structural ceramic test specimens was statistically evaluated. Specimens of sintered silicon nitride and sintered silicon carbide, seeded with surface voids, were examined by SLAM at an ultrasonic frequency of 100 MHz in the as fired condition and after surface polishing. It was observed that polishing substantially increased void detectability. Voids as small as 100 micrometers in diameter were detected in polished specimens with 0.90 probability at a 0.95 confidence level. In addition, inspection times were reduced up to a factor of 10 after polishing. The applicability of the SLAM technique for detection of naturally occurring flaws of similar dimensions to the seeded voids is discussed. A FORTRAN program listing is given for calculating and plotting flaw detection statistics.

  1. A novel full-angle scanning light scattering profiler to quantitatively evaluate forward and backward light scattering from intraocular lenses

    SciTech Connect

    Walker, Bennett N.; James, Robert H.; Ilev, Ilko K.; Calogero, Don

    2015-09-15

    Glare, glistenings, optical defects, dysphotopsia, and poor image quality are a few of the known deficiencies of intraocular lenses (IOLs). All of these optical phenomena are related to light scatter. However, the specific direction that light scatters makes a critical difference between debilitating glare and a slightly noticeable decrease in image quality. Consequently, quantifying the magnitude and direction of scattered light is essential to appropriately evaluate the safety and efficacy of IOLs. In this study, we introduce a full-angle scanning light scattering profiler (SLSP) as a novel approach capable of quantitatively evaluating the light scattering from IOLs with a nearly 360° view. The SLSP method can simulate in situ conditions by controlling the parameters of the light source including angle of incidence. This testing strategy will provide a more effective nonclinical approach for the evaluation of IOL light scatter.

  2. A novel full-angle scanning light scattering profiler to quantitatively evaluate forward and backward light scattering from intraocular lenses.

    PubMed

    Walker, Bennett N; James, Robert H; Calogero, Don; Ilev, Ilko K

    2015-09-01

    Glare, glistenings, optical defects, dysphotopsia, and poor image quality are a few of the known deficiencies of intraocular lenses (IOLs). All of these optical phenomena are related to light scatter. However, the specific direction that light scatters makes a critical difference between debilitating glare and a slightly noticeable decrease in image quality. Consequently, quantifying the magnitude and direction of scattered light is essential to appropriately evaluate the safety and efficacy of IOLs. In this study, we introduce a full-angle scanning light scattering profiler (SLSP) as a novel approach capable of quantitatively evaluating the light scattering from IOLs with a nearly 360° view. The SLSP method can simulate in situ conditions by controlling the parameters of the light source including angle of incidence. This testing strategy will provide a more effective nonclinical approach for the evaluation of IOL light scatter.

  3. How do trees grow? Response from the graphical and quantitative analyses of computed tomography scanning data collected on stem sections.

    PubMed

    Dutilleul, Pierre; Han, Li Wen; Beaulieu, Jean

    2014-06-01

    Tree growth, as measured via the width of annual rings, is used for environmental impact assessment and climate back-forecasting. This fascinating natural process has been studied at various scales in the stem (from cell and fiber within a growth ring, to ring and entire stem) in one, two, and three dimensions. A new approach is presented to study tree growth in 3D from stem sections, at a scale sufficiently small to allow the delineation of reliable limits for annual rings and large enough to capture directional variation in growth rates. The technology applied is computed tomography scanning, which provides - for one stem section - millions of data (indirect measures of wood density) that can be mapped, together with a companion measure of dispersion and growth ring limits in filigree. Graphical and quantitative analyses are reported for white spruce trees with circular vs non-circular growth. Implications for dendroclimatological research are discussed.

  4. [Identification and quantitative determination of baclofen in human blood by HPLC with mass spectrometry detection].

    PubMed

    Dukova, O A; Kotlovsky, M Yu; Pokrovsky, A A; Suvorova, E V; Shivrina, T G; Krasnov, E A; Efremov, A A

    2016-03-01

    A method of identification and quantitative determination of baclofen in blood by HPLC with mass spectrometry detection has been developed. It is characterized by high sensitivity, specificity, linearity, accuracy, reproducibility, and a low detection for quantitative determination. The method has been used for diagnostics of acute baclofen poisoning in patients.

  5. Maximum linkage space-time permutation scan statistics for disease outbreak detection.

    PubMed

    Costa, Marcelo A; Kulldorff, Martin

    2014-06-10

    In disease surveillance, the prospective space-time permutation scan statistic is commonly used for the early detection of disease outbreaks. The scanning window that defines potential clusters of diseases is cylindrical in shape, which does not allow incorporating into the cluster shape potential factors that can contribute to the spread of the disease, such as information about roads, landscape, among others. Furthermore, the cylinder scanning window assumes that the spatial extent of the cluster does not change in time. Alternatively, a dynamic space-time cluster may indicate the potential spread of the disease through time. For instance, the cluster may decrease over time indicating that the spread of the disease is vanishing. This paper proposes two irregularly shaped space-time permutation scan statistics. The cluster geometry is dynamically created using a graph structure. The graph can be created to include nearest-neighbor structures, geographical adjacency information or any relevant prior information regarding the contagious behavior of the event under surveillance. The new methods are illustrated using influenza cases in three New England states, and compared with the cylindrical version. A simulation study is provided to investigate some properties of the proposed arbitrary cluster detection techniques. We have successfully developed two new space-time permutation scan statistics methods with irregular shapes and improved computational performance. The results demonstrate the potential of these methods to quickly detect disease outbreaks with irregular geometries. Future work aims at performing intensive simulation studies to evaluate the proposed methods using different scenarios, number of cases, and graph structures.

  6. Maximum linkage space-time permutation scan statistics for disease outbreak detection

    PubMed Central

    2014-01-01

    Background In disease surveillance, the prospective space-time permutation scan statistic is commonly used for the early detection of disease outbreaks. The scanning window that defines potential clusters of diseases is cylindrical in shape, which does not allow incorporating into the cluster shape potential factors that can contribute to the spread of the disease, such as information about roads, landscape, among others. Furthermore, the cylinder scanning window assumes that the spatial extent of the cluster does not change in time. Alternatively, a dynamic space-time cluster may indicate the potential spread of the disease through time. For instance, the cluster may decrease over time indicating that the spread of the disease is vanishing. Methods This paper proposes two irregularly shaped space-time permutation scan statistics. The cluster geometry is dynamically created using a graph structure. The graph can be created to include nearest-neighbor structures, geographical adjacency information or any relevant prior information regarding the contagious behavior of the event under surveillance. Results The new methods are illustrated using influenza cases in three New England states, and compared with the cylindrical version. A simulation study is provided to investigate some properties of the proposed arbitrary cluster detection techniques. Conclusion We have successfully developed two new space-time permutation scan statistics methods with irregular shapes and improved computational performance. The results demonstrate the potential of these methods to quickly detect disease outbreaks with irregular geometries. Future work aims at performing intensive simulation studies to evaluate the proposed methods using different scenarios, number of cases, and graph structures. PMID:24916839

  7. Tunable PIE and synchronized gating detections by FastFLIM for quantitative microscopy measurements of fast dynamics of single molecules

    NASA Astrophysics Data System (ADS)

    Sun, Yuansheng; Coskun, Ulas; Ferreon, Allan Chris; Barbieri, Beniamino; Liao, Shih-Chu Jeff

    2016-03-01

    The crosstalk between two fluorescent species causes problems in fluorescence microscopy imaging, especially for quantitative measurements such as co-localization, Förster resonance energy transfer (FRET), fluorescence cross correlation spectroscopy (FCCS). In laser scanning confocal microscopy, the lasers can be switched on and off by acousto-optic tunable filters (AOTF) in the microsecond scale for alternative line scanning in order to avoid the crosstalk while minimizing the time delay between two lasers on the same pixel location. In contrast, the pulsed interleaved excitation (PIE) technique synchronizes two pulsed lasers of different wavelengths in the nanosecond scale to enable measuring superfast dynamics of two fluorescent species simultaneously and yet quantitatively without the crosstalk contamination. This feature is critical for many cell biology applications, e.g. accurate determination of stoichiometry in FRET measurements for studying protein-protein interactions or cell signal events, detection of weaker bindings in FCCS by eliminating the false cross correlation due to the crosstalk. The PIE has been used with the time correlated single photon counting (TCSPC) electronics. Here, we describe a novel PIE development using the digital frequency domain (DFD) technique -- FastFLIM, which provides tunable PIE setups and synchronized gating detections, tailored and optimized to specific applications. A few PIE setups by FastFLIM and measurement examples are described. Combined with the sensitivity of Alba and Q2 systems, the PIE allowed us to quantitatively measure the fast dynamics of single molecules.

  8. Using Information From Prior Satellite Scans to Improve Cloud Detection Near the Day-Night Terminator

    NASA Technical Reports Server (NTRS)

    Yost, Christopher R.; Minnis, Patrick; Trepte, Qing Z.; Palikonda, Rabindra; Ayers, Jeffrey K.; Spangenberg, Doulas A.

    2012-01-01

    With geostationary satellite data it is possible to have a continuous record of diurnal cycles of cloud properties for a large portion of the globe. Daytime cloud property retrieval algorithms are typically superior to nighttime algorithms because daytime methods utilize measurements of reflected solar radiation. However, reflected solar radiation is difficult to accurately model for high solar zenith angles where the amount of incident radiation is small. Clear and cloudy scenes can exhibit very small differences in reflected radiation and threshold-based cloud detection methods have more difficulty setting the proper thresholds for accurate cloud detection. Because top-of-atmosphere radiances are typically more accurately modeled outside the terminator region, information from previous scans can help guide cloud detection near the terminator. This paper presents an algorithm that uses cloud fraction and clear and cloudy infrared brightness temperatures from previous satellite scan times to improve the performance of a threshold-based cloud mask near the terminator. Comparisons of daytime, nighttime, and terminator cloud fraction derived from Geostationary Operational Environmental Satellite (GOES) radiance measurements show that the algorithm greatly reduces the number of false cloud detections and smoothes the transition from the daytime to the nighttime clod detection algorithm. Comparisons with the Geoscience Laser Altimeter System (GLAS) data show that using this algorithm decreases the number of false detections by approximately 20 percentage points.

  9. Quantitative detection of settled dust over green canopy

    NASA Astrophysics Data System (ADS)

    Brook, Anna

    2016-04-01

    NMF (SS-NMF), 6) Alternating Least-Square (ALS), and 2) Lin's Projected Gradient (LPG). The performance is evaluated on real hyperspectral imagery data via detailed experimental assessment. The study showed that in certain compression tasks content-adapted sparse representation is provided by state-of-the-art solutions. The NMF algorithm estimates endmembers that are used to remove spurious information. If computationally feasible, it should include interaction terms to make the model more flexible. The optimal NMF algorithms, such as ALS and LPG, are assumed to be the simplest methods that achieve the minimum error on the test set. In summary, this work shows that sediment dust can be assessed using airborne HSI data, making it a potentially powerful tool for environmental studies. References Keshava, N., Mustard, J. (2002). Spectral unmixing. IEEE Signal Process. Mag., 19(1), 44-57. Chudnovsky, A., & Ben-Dor, E. (2009). Reflectance spectroscopy as a tool for settled dust monitoring in office environment. International Journal of Environment and Waste Management, 4(1), 32-49. Brook, A. (2014). Quantitative Detection of Settled dust over Green Canopy using Sparse Unmixing of Airborne Hyperspectral Data. IEEE-Whispers 6th Workshop on Hyperspectral Image and Signal Processing: Evolution in Remote Sensing, 2014, Switzerland, 4-8. Keshava, N., Mustard, J. (2002). Spectral unmixing. IEEE Signal Process. Mag., 19(1), 44-57. Bioucas-Dias et al. (2012). Hyperspectral unmixing overview: Geometrical, statistical, and sparse regression-based approaches, IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing, 5(2), 354 -379.

  10. Integrated scanning laser ophthalmoscopy and optical coherence tomography for quantitative multimodal imaging of retinal degeneration and autofluorescence

    NASA Astrophysics Data System (ADS)

    Issaei, Ali; Szczygiel, Lukasz; Hossein-Javaheri, Nima; Young, Mei; Molday, L. L.; Molday, R. S.; Sarunic, M. V.

    2011-03-01

    Scanning Laser Ophthalmoscopy (SLO) and Coherence Tomography (OCT) are complimentary retinal imaging modalities. Integration of SLO and OCT allows for both fluorescent detection and depth- resolved structural imaging of the retinal cell layers to be performed in-vivo. System customization is required to image rodents used in medical research by vision scientists. We are investigating multimodal SLO/OCT imaging of a rodent model of Stargardt's Macular Dystrophy which is characterized by retinal degeneration and accumulation of toxic autofluorescent lipofuscin deposits. Our new findings demonstrate the ability to track fundus autofluorescence and retinal degeneration concurrently.

  11. Ultrasonic enrichment of microspheres for ultrasensitive biomedical analysis in confocal laser-scanning fluorescence detection

    NASA Astrophysics Data System (ADS)

    Wiklund, M.; Toivonen, J.; Tirri, M.; Hänninen, P.; Hertz, H. M.

    2004-07-01

    An ultrasonic particle concentrator based on a standing-wave hemispherical resonator is combined with confocal laser-scanning fluorescence detection. The goal is to perform ultrasensitive biomedical analysis by concentration of biologically active microspheres. The standing-wave resonator consists of a 4 MHz focusing ultrasonic transducer combined with the optically transparent plastic bottom of a disposable 96-well microplate platform. The ultrasonic particle concentrator collects suspended microspheres into dense, single-layer aggregates at well-defined positions in the sample vessel of the microplate, and the fluorescence from the aggregates is detected by the confocal laser-scanning system. The biochemical properties of the system are investigated using a microsphere-based human thyroid stimulating hormone assay.

  12. Scanning Light Scattering Profiler (SLPS) Based Methodology to Quantitatively Evaluate Forward and Backward Light Scattering from Intraocular Lenses.

    PubMed

    Walker, Bennett N; James, Robert H; Calogero, Don; Ilev, Ilko K

    2017-06-06

    The scanning light scattering profiler (SLSP) methodology has been developed for the full-angle quantitative evaluation of forward and backward light scattering from intraocular lenses (IOLs) using goniophotometer principles. This protocol describes the SLSP platform and how it employs a 360° rotational photodetector sensor that is scanned around an IOL sample while recording the intensity and location of scattered light as it passes through the IOL medium. The SLSP platform can be used to predict, non-clinically, the propensity for current and novel IOL designs and materials to induce light scatter. Non-clinical evaluation of light scattering properties of IOLs can significantly reduce the number of patient complaints related to unwanted glare, glistening, optical defects, poor image quality, and other phenomena associated with the unintended light scattering. Future studies should be conducted to correlate SLSP data with clinical results to help identify which measured light scatter is most problematic for patients that have undergone cataract surgery subsequent to IOL implantation.

  13. Detection of Fatigue Damage Prior to Crack Initiation withScanning SQUID Microscopy

    SciTech Connect

    Lee, Tae-Kyu; Morris Jr., J.W.; Lee, Seungkyun; Clarke, John

    2005-11-07

    The remanence fields of fatigued ferritic steel specimens were measured using a scanning microscope based on a high transition temperature Superconducting Quantum Interference Device (SQUID). The results show an overall increase of remanence until dislocation density saturates and an additional local remanence increase after saturation during cyclic loading. Because of the combined magnetic and spatial resolution of the SQUID microscope, these local changes of dislocation structures can be detected before a crack actually initiates, and identify the sites where crack nucleation will occur.

  14. Real time coarse orientation detection in MR scans using multi-planar deep convolutional neural networks

    NASA Astrophysics Data System (ADS)

    Bhatia, Parmeet S.; Reda, Fitsum; Harder, Martin; Zhan, Yiqiang; Zhou, Xiang Sean

    2017-02-01

    Automatically detecting anatomy orientation is an important task in medical image analysis. Specifically, the ability to automatically detect coarse orientation of structures is useful to minimize the effort of fine/accurate orientation detection algorithms, to initialize non-rigid deformable registration algorithms or to align models to target structures in model-based segmentation algorithms. In this work, we present a deep convolution neural network (DCNN)-based method for fast and robust detection of the coarse structure orientation, i.e., the hemi-sphere where the principal axis of a structure lies. That is, our algorithm predicts whether the principal orientation of a structure is in the northern hemisphere or southern hemisphere, which we will refer to as UP and DOWN, respectively, in the remainder of this manuscript. The only assumption of our method is that the entire structure is located within the scan's field-of-view (FOV). To efficiently solve the problem in 3D space, we formulated it as a multi-planar 2D deep learning problem. In the training stage, a large number coronal-sagittal slice pairs are constructed as 2-channel images to train a DCNN to classify whether a scan is UP or DOWN. During testing, we randomly sample a small number of coronal-sagittal 2-channel images and pass them through our trained network. Finally, coarse structure orientation is determined using majority voting. We tested our method on 114 Elbow MR Scans. Experimental results suggest that only five 2-channel images are sufficient to achieve a high success rate of 97.39%. Our method is also extremely fast and takes approximately 50 milliseconds per 3D MR scan. Our method is insensitive to the location of the structure in the FOV.

  15. Quantitating morphological changes in biological samples during scanning electron microscopy sample preparation with correlative super-resolution microscopy

    PubMed Central

    Huang, Tao; Jorgens, Danielle M.; Nickerson, Andrew; Lin, Li-Jung; Pelz, Joshua; Gray, Joe W.; López, Claudia S.

    2017-01-01

    Sample preparation is critical to biological electron microscopy (EM), and there have been continuous efforts on optimizing the procedures to best preserve structures of interest in the sample. However, a quantitative characterization of the morphological changes associated with each step in EM sample preparation is currently lacking. Using correlative EM and superresolution microscopy (SRM), we have examined the effects of different drying methods as well as osmium tetroxide (OsO4) post-fixation on cell morphology during scanning electron microscopy (SEM) sample preparation. Here, SRM images of the sample acquired under hydrated conditions were used as a baseline for evaluating morphological changes as the sample went through SEM sample processing. We found that both chemical drying and critical point drying lead to a mild cellular boundary retraction of ~60 nm. Post-fixation by OsO4 causes at least 40 nm additional boundary retraction. We also found that coating coverslips with adhesion molecules such as fibronectin prior to cell plating helps reduce cell distortion from OsO4 post-fixation. These quantitative measurements offer useful information for identifying causes of cell distortions in SEM sample preparation and improving current procedures. PMID:28562683

  16. Quantitating morphological changes in biological samples during scanning electron microscopy sample preparation with correlative super-resolution microscopy.

    PubMed

    Zhang, Ying; Huang, Tao; Jorgens, Danielle M; Nickerson, Andrew; Lin, Li-Jung; Pelz, Joshua; Gray, Joe W; López, Claudia S; Nan, Xiaolin

    2017-01-01

    Sample preparation is critical to biological electron microscopy (EM), and there have been continuous efforts on optimizing the procedures to best preserve structures of interest in the sample. However, a quantitative characterization of the morphological changes associated with each step in EM sample preparation is currently lacking. Using correlative EM and superresolution microscopy (SRM), we have examined the effects of different drying methods as well as osmium tetroxide (OsO4) post-fixation on cell morphology during scanning electron microscopy (SEM) sample preparation. Here, SRM images of the sample acquired under hydrated conditions were used as a baseline for evaluating morphological changes as the sample went through SEM sample processing. We found that both chemical drying and critical point drying lead to a mild cellular boundary retraction of ~60 nm. Post-fixation by OsO4 causes at least 40 nm additional boundary retraction. We also found that coating coverslips with adhesion molecules such as fibronectin prior to cell plating helps reduce cell distortion from OsO4 post-fixation. These quantitative measurements offer useful information for identifying causes of cell distortions in SEM sample preparation and improving current procedures.

  17. Three-dimension scanning micro pulse lidar for detecting haze space distribution

    NASA Astrophysics Data System (ADS)

    Li, Shichun; Yan, Qing; Wei, Pengpeng; Xin, Wenhui; Hua, Dengxin

    2015-10-01

    Aim to the current situation that the haze distribution detection is limited by network of point-type instruments, a three dimension scanning micro pulse lidar is researched on the basis of the Mie scattering theory of atmospheric particles. In order to strengthen detective ability of fine particles having a significant effect on human respiratory system, we choose a diode-pumped Nd:YAG solid laser with 532-nm wavelength and wind cooled technique as excited optical source to actualize lidar miniaturization. The pulse energy of 50 μJ and pulse repetitive frequency of 1 kHz are configured to ensure the eye-safety and high temporal-spatial resolution, while the lidar operates in the horizontal scanning mode. A Cassegrain telescope with clear aperture of 254 mm is utilized to collect the backscattering signal for portable multi-location observation. The lidar echo signal is filtered through an interference filter with passed bandwidth of 0.2 nm to implement all-time efficient detection. The experimental observation of atmospheric particle distribution is carried out in horizontal scanning mode. Each plane- position-indication of atmospheric particle distribution contains approximately 300 profiles in the horizontal plane within 6-min interval. Experimental results show that this lidar prototype can probe the space distribution of atmospheric particle with the range of 6 km, and that the influence of industrial production on the atmospheric particle density is 2-3 times as much as that of human activity.

  18. A smartphone-readable barcode assay for the detection and quantitation of pesticide residues.

    PubMed

    Guo, Juan; Wong, Jessica X H; Cui, Caie; Li, Xiaochun; Yu, Hua-Zhong

    2015-08-21

    In this paper, we present a smartphone-readable barcode assay for the qualitative detection of methyl parathion residues, a toxic organophosphorus pesticide that is popularly used in agriculture worldwide. The detection principle is based on the irreversible inhibition of the enzymatic activity of acetylcholinesterase (AchE) by methyl parathion; AchE catalytically hydrolyzes acetylthiocholine iodine to thiocholine that in turn dissociates dithiobis-nitrobenzoate to produce a yellow product (deprotonated thio-nitrobenzoate). The yellow intensity of the product was confirmed to be inversely dependent on the concentration of the pesticide. We have designed a barcode-formatted assay chip by using a PDMS (polydimethylsiloxane) channel plate (as the reaction reservoir), situated under a printed partial barcode, to complete the whole barcode such that it can be directly read by a barcode scanning app installed on a smartphone. The app is able to qualitatively present the result of the pesticide test; the absence or a low concentration of methyl parathion results in the barcode reading as "-", identifying the test as negative for pesticides. Upon obtaining a positive result (the app reads a "+" character), the captured image can be further analyzed to quantitate the methyl parathion concentration in the sample. Besides the portability and simplicity, this mobile-app based colorimetric barcode assay compares favorably with the standard spectrophotometric method.

  19. Detecting tectonic tremor through frequency scanning at a single station: Application to the Cascadia margin

    NASA Astrophysics Data System (ADS)

    Sit, Stefany; Brudzinski, Michael; Kao, Honn

    2012-11-01

    The discovery of episodic tremor and slip (ETS) spurred increased instrumentation and investigation of the Cascadia margin, which is now typified by the seismic phenomena. We utilize established detection and location techniques already present in the region to guide the development of a new single station detection method. While detailed network-wide investigations have led to exciting discoveries on the source location and migration patterns of tectonic tremor, single station detection has the ability to expand our search for tremor to more subduction zones and tectonic settings where instrumentation is not widely available. Our frequency scanning technique bandpass filters seismic data into three categories, 2-5 Hz, 10-15 Hz, and 0.02-0.1 Hz, where we expect prominent signals produced by tectonic tremor, local earthquakes, and surface waves, respectively. We combine amplitudes in each category into a ratio to determine tremor detection for a given hour. Results from our technique are evaluated in two ways: 1) combined in a network setting to compare with prominent location and detection methods and 2) assessed at an individual station and compared with other techniques that are capable of single station tremor detection. Network-wide processing over a two-year time period in both northern and southern Cascadia reveals common identification of larger ETS episodes when comparing our technique to both envelope waveform and combined single station detection methods. We find slight variations in the total duration of tremor and the onset timing between the different techniques, which may be due to the varying stations included in each technique. Frequency scanning identifies more inter-ETS episodes than envelope waveform and single station methods, particularly in the more sparsely instrumented region of southern Oregon. Our method also reduces erroneous signals more commonly found in other single station methods, discerned through comparison of nearby seismograms

  20. Computer-assisted quantitative evaluation of bisphosphonate treatment for Paget's disease of bone using the bone scan index

    PubMed Central

    Nagano, Satoshi; Nakamura, Shunsuke; Shimada, Hirofumi; Yokouchi, Masahiro; Setoguchi, Takao; Ishidou, Yasuhiro; Sasaki, Hiromi; Komiya, Setsuro

    2016-01-01

    The purpose of the present study was to analyze the effect of treatment of Paget's disease of bone (PDB) with bone scintigraphy using a computer-assisted diagnosis system (BONENAVI) that quantitatively evaluates bone metabolism. Seven patients with PDB (three male, four female; average age, 60 years; age range, 33–80 years) underwent bone scintigraphy and measurement of serum alkaline phosphatase (ALP), bone-specific ALP (BAP), serum cross-linked N-telopeptide (NTx) of type I collagen, urinary NTx, and deoxypyridinoline (DPD) before and after bisphosphonate treatment. Bone scan index (BSI), artificial neural network (ANN) value, and hotspot number (HSn) were calculated using BONENAVI software. Mean follow-up period was 22 months (range, 11–35 months). Among three BONENAVI parameters (ANN, BSI, and HSn), only BSI was significantly lower after bisphosphonate treatment as compared with before. All bone metabolic markers excluding DPD were significantly lower following bisphosphonate treatment than before. Bone formation markers (ALP and BAP) were significantly lower than bone resorption markers (U-NTx and S-NTx). The correlation of BONENAVI parameters with four bone metabolic markers was analyzed before and after bisphosphonate treatment. Before treatment, the majority of the four markers did not correlate with the BONENAVI parameters. In contrast, post-treatment ALP, BAP, and U-NTx were significantly correlated with BSI and HSn. To the best of our knowledge, this is the first study to evaluate the treatment of PDB by bone scintigraphy using a computer-assisted diagnosis system that quantitatively evaluates bone metabolism. The findings demonstrated that, using BONENAVI software, bone scintigraphy is able to quantitatively and spatially evaluate the bisphosphonate treatment effect, particularly in patients with polyostotic PDB. PMID:28105116

  1. Quantitative assessment of image artifacts from root filling materials on CBCT scans made using several exposure parameters.

    PubMed

    Rabelo, Katharina Alves; Cavalcanti, Yuri Wanderley; de Oliveira Pinto, Martina Gerlane; Sousa Melo, Saulo Leonardo; Campos, Paulo Sérgio Flores; de Andrade Freitas Oliveira, Luciana Soares; de Melo, Daniela Pita

    2017-09-01

    To quantify artifacts from different root filling materials in cone-beam computed tomography (CBCT) images acquired using different exposure parameters. Fifteen single-rooted teeth were scanned using 8 different exposure protocols with 3 different filling materials and once without filling material as a control group. Artifact quantification was performed by a trained observer who made measurements in the central axial slice of all acquired images in a fixed region of interest using ImageJ. Hyperdense artifacts, hypodense artifacts, and the remaining tooth area were identified, and the percentages of hyperdense and hypodense artifacts, remaining tooth area, and tooth area affected by the artifacts were calculated. Artifacts were analyzed qualitatively by 2 observers using the following scores: absence (0), moderate presence (1), and high presence (2) for hypodense halos, hypodense lines, and hyperdense lines. Two-way ANOVA and the post-hoc Tukey test were used for quantitative and qualitative artifact analysis. The Dunnet test was also used for qualitative analysis. The significance level was set at P<.05. There were no significant interactions among the exposure parameters in the quantitative or qualitative analysis. Significant differences were observed among the studied filling materials in all quantitative analyses. In the qualitative analyses, all materials differed from the control group in terms of hypodense and hyperdense lines (P<.05). Fiberglass posts did not differ statistically from the control group in terms of hypodense halos (P>.05). Different exposure parameters did not affect the objective or subjective observations of artifacts in CBCT images; however, the filling materials used in endodontic restorations did affect both types of assessments.

  2. A scanning method for detecting clustering pattern of both attribute and structure in social networks

    NASA Astrophysics Data System (ADS)

    Wang, Tai-Chi; Phoa, Frederick Kin Hing

    2016-03-01

    Community/cluster is one of the most important features in social networks. Many cluster detection methods were proposed to identify such an important pattern, but few were able to identify the statistical significance of the clusters by considering the likelihood of network structure and its attributes. Based on the definition of clustering, we propose a scanning method, originated from analyzing spatial data, for identifying clusters in social networks. Since the properties of network data are more complicated than those of spatial data, we verify our method's feasibility via simulation studies. The results show that the detection powers are affected by cluster sizes and connection probabilities. According to our simulation results, the detection accuracy of structure clusters and both structure and attribute clusters detected by our proposed method is better than that of other methods in most of our simulation cases. In addition, we apply our proposed method to some empirical data to identify statistically significant clusters.

  3. Scanning laser entoptic perimetry for the detection of visual defects associated with diabetic retinopathy

    PubMed Central

    El‐Bradey, M; Plummer, D J; Uwe‐Bartsch, D; Freeman, W R

    2006-01-01

    Aim To determine the sensitivity and specificity of entoptic perimetry for diagnosing diabetic retinopathy at all levels of severity. Methods A prospective clinical study at the Shiley Eye Center, University of California, and San Diego. 30 patients with photographically documented diabetic retinopathy and 24 controls with a similar age distribution. Sensitivity and specificity of entoptic perimetry were computed for detecting clinically significant macular oedema within the central 120 degree radius of the fovea compared to fundus photographs. Results Entoptic perimetry can detect clinically significant diabetic retinopathy with a sensitivity of 0.88 and specificity of 1.00. Entoptic perimetry can detect the earliest stages of diabetic retinopathy with a sensitivity of 0.86. Conclusion Scanning laser entoptic perimetry is an effective tool for detecting visual function loss caused by diabetic retinopathy. PMID:16361659

  4. Highly Sensitive Electrical Detection of HIV-1 Virus Based on Scanning Tunneling Microscopy.

    PubMed

    Lee, Jin-Ho; Kim, Byung-Chan; Oh, Byung-Keun; Choi, Jeong-Woo

    2015-02-01

    A highly sensitive immunosensor based on scanning tunneling microscopy (STM) was developed for the first time to detect living material such as HIV-1 virus by gold (Au) nanoparticle and fragmented antibody complex. Fragmented antibodies were pre-immobilized on the Au surface, then HIV-1 virus like particles (HIV-1 VLPs) and Au-nanoparticle and fragmented antibody complexes were applied to develop sandwich assay. The developed surface morphology and the current profile of fabricated immunosensing element were characterized by Raman spectroscopy and investigated with STM. The power spectrum derived from the current profile was found to be related with concentrations of HIV-1 VLPs. Using the electrical detection method based on current mapping profile of STM, living material such as virus, HIV-1 VLPs, was able to be detected successfully. The proposed technique can be a promising method to construct the highly sensitive and efficient sensor for detecting viruses and other living materials.

  5. Fiber-Optic Array Scanning Technology (FAST) for Detection and Molecular Characterization of Circulating Tumor Cells.

    PubMed

    Ao, Zheng; Liu, Xiaohe

    2017-01-01

    Circulating tumor cell (CTC) as an important component in "liquid biopsy" holds crucial clinical relevance in cancer prognosis, treatment efficiency evaluation, prediction and potentially early detection. Here, we present a Fiber-optic Array Scanning Technology (FAST) that enables antigen-agnostic, size-agnostic detection of CTC. By immunofluorescence staining detection of a combination of a panel of markers, FAST technology can be applied to detect rare CTC in non-small cell lung cancer (NSCLC) setting with high sensitivity and specificity. In combination with Automated Digital Microscopy (ADM) platform, companion markers on CTC such as Vimentin and Programmed death-ligand 1 (PD-L1) can also be analyzed to further characterize these CTCs. FAST data output is also compatible with downstream single cell picking platforms. Single cell can be isolated post ADM confirmation and used for "actionable" genetic mutations analysis.

  6. Dark-Field Scanning Transmission Ion Microscopy via Detection of Forward-Scattered Helium Ions with a Microchannel Plate.

    PubMed

    Woehl, Taylor J; White, Ryan M; Keller, Robert R

    2016-06-01

    A microchannel plate was used as an ion sensitive detector in a commercial helium ion microscope (HIM) for dark-field transmission imaging of nanomaterials, i.e. scanning transmission ion microscopy (STIM). In contrast to previous transmission HIM approaches that used secondary electron conversion holders, our new approach detects forward-scattered helium ions on a dedicated annular shaped ion sensitive detector. Minimum collection angles between 125 mrad and 325 mrad were obtained by varying the distance of the sample from the microchannel plate detector during imaging. Monte Carlo simulations were used to predict detector angular ranges at which dark-field images with atomic number contrast could be obtained. We demonstrate atomic number contrast imaging via scanning transmission ion imaging of silica-coated gold nanoparticles and magnetite nanoparticles. Although the resolution of STIM is known to be degraded by beam broadening in the substrate, we imaged magnetite nanoparticles with high contrast on a relatively thick silicon nitride substrate. We expect this new approach to annular dark-field STIM will open avenues for more quantitative ion imaging techniques and advance fundamental understanding of underlying ion scattering mechanisms leading to image formation.

  7. Wave propagation models for quantitative defect detection by ultrasonic methods

    NASA Astrophysics Data System (ADS)

    Srivastava, Ankit; Bartoli, Ivan; Coccia, Stefano; Lanza di Scalea, Francesco

    2008-03-01

    Ultrasonic guided wave testing necessitates of quantitative, rather than qualitative, information on flaw size, shape and position. This quantitative diagnosis ability can be used to provide meaningful data to a prognosis algorithm for remaining life prediction, or simply to generate data sets for a statistical defect classification algorithm. Quantitative diagnostics needs models able to represent the interaction of guided waves with various defect scenarios. One such model is the Global-Local (GL) method, which uses a full finite element discretization of the region around a flaw to properly represent wave diffraction, and a suitable set of wave functions to simulate regions away from the flaw. Displacement and stress continuity conditions are imposed at the boundary between the global and the local regions. In this paper the GL method is expanded to take advantage of the Semi-Analytical Finite Element (SAFE) method in the global portion of the waveguide. The SAFE method is efficient because it only requires the discretization of the cross-section of the waveguide to obtain the wave dispersion solutions and it can handle complex structures such as multilayered sandwich panels. The GL method is applied to predicting quantitatively the interaction of guided waves with defects in aluminum and composites structural components.

  8. A CAD of fully automated colonic polyp detection for contrasted and non-contrasted CT scans.

    PubMed

    Tulum, Gökalp; Bolat, Bülent; Osman, Onur

    2017-04-01

    Computer-aided detection (CAD) systems are developed to help radiologists detect colonic polyps over CT scans. It is possible to reduce the detection time and increase the detection accuracy rates by using CAD systems. In this paper, we aimed to develop a fully integrated CAD system for automated detection of polyps that yields a high polyp detection rate with a reasonable number of false positives. The proposed CAD system is a multistage implementation whose main components are: automatic colon segmentation, candidate detection, feature extraction and classification. The first element of the algorithm includes a discrete segmentation for both air and fluid regions. Colon-air regions were determined based on adaptive thresholding, and the volume/length measure was used to detect air regions. To extract the colon-fluid regions, a rule-based connectivity test was used to detect the regions belong to the colon. Potential polyp candidates were detected based on the 3D Laplacian of Gaussian filter. The geometrical features were used to reduce false-positive detections. A 2D projection image was generated to extract discriminative features as the inputs of an artificial neural network classifier. Our CAD system performs at 100% sensitivity for polyps larger than 9 mm, 95.83% sensitivity for polyps 6-10 mm and 85.71% sensitivity for polyps smaller than 6 mm with 5.3 false positives per dataset. Also, clinically relevant polyps ([Formula: see text]6 mm) were identified with 96.67% sensitivity at 1.12 FP/dataset. To the best of our knowledge, the novel polyp candidate detection system which determines polyp candidates with LoG filters is one of the main contributions. We also propose a new 2D projection image calculation scheme to determine the distinctive features. We believe that our CAD system is highly effective for assisting radiologist interpreting CT.

  9. [Research progress of real-time quantitative PCR method for group A rotavirus detection].

    PubMed

    Guo, Yan-Qing; Li, Dan-Di; Duan, Zhao-Jun

    2013-11-01

    Group A rotavirus is one of the most significant etiological agents which causes acute gastroenteritis among infants and young children worldwide. So far, several method which includes electron microscopy (EM), enzyme immunoassay (EIA), reverse transcription-polymerase chain reaction (RT-PCR)and Real-time Quantitative PCR has been established for the detection of rotavirus. Compared with other methods, Real-time quantitative PCR have advantages in specificity, sensitivity, genotyping and quantitative accuracy. This article shows a overview of the application of real-time quantitative PCR technique to detecte group A rotavirus.

  10. Oil detection in RADARSAT-2 quad-polarization imagery: implications for ScanSAR performance

    NASA Astrophysics Data System (ADS)

    Cheng, Angela; Arkett, Matt; Zagon, Tom; De Abreu, Roger; Mueller, Derek; Vachon, Paris; Wolfe, John

    2011-11-01

    Environment Canada's Integrated Satellite Tracking of Pollution (ISTOP) program uses RADARSAT-2 data to vector pollution surveillance assets to areas where oil discharges/spills are suspected in support of enforcement and/or cleanup efforts. RADARSAT-2's new imaging capabilities and ground system promises significant improvement's in ISTOP's ability to detect and report on oil pollution. Of specific interest is the potential of dual polarization ScanSAR data acquired with VV polarization to improve the detection of oil pollution compared to data acquired with HH polarization, and with VH polarization to concurrently detect ship targets. A series of 101 RADARSAT-2 fine quad images were acquired over Coal Oil Point, near Santa Barbara, California where a seep field naturally releases hydrocarbons. The oil and gas releases in this region are visible on the sea surface and have been well documented allowing for the remote sensing of a constant source of oil at a fixed location. Although the make-up of the oil seep field could be different from that of oil spills, it provides a representative target that can be routinely imaged under a variety of wind conditions. Results derived from the fine quad imagery with a lower noise floor were adjusted to mimic the noise floor limitations of ScanSAR. In this study it was found that VV performed better than HH for oil detection, especially at higher incidence angles.

  11. Seismic Event Identification Using Scanning Detection: A Comparison of Denoising and Classification Methods

    NASA Astrophysics Data System (ADS)

    Rowe, C. A.; MacCarthy, J. K.; Giudicepietro, F.

    2005-12-01

    Automatic detection and classification methods are increasingly important in observatory operations, as the volume and rate of incoming data exceed the capacity of human analysis staff to process the data in near-real-time. We explore the success of scanning detection for similar event identification in a variety of seismic waveform catalogs. Several waveform pre-processing methods are applied to previously recorded events which are scanned through triggered and continuous waveform catalogs to determine the success and false alarm rate for detections of repeating signals. Pre-processing approaches include adaptive, cross-coherency filtering, adaptive, auto-associative neural network filtering, discrete wavelet package decomposition and linear predictive coding as well as suites of standard bandpass filters. Classification / detection methods for the various pre-processed signals are applied to investigate the robustness of the individual and combined approaches. The classifiers as applied to the processed waveforms include dendrogram-based clustering and neural network classifiers. We will present findings for the various combinations of methods as applied to tectonic earthquakes, mine blasts and volcanic seismicity.

  12. Application of hotspot detection using spatial scan statistic: Study of criminality in Indonesia

    NASA Astrophysics Data System (ADS)

    Runadi, Taruga; Widyaningsih, Yekti

    2017-03-01

    According to the police registered data, the number of criminal cases tends to fluctuate during 2011 to 2013. It means there is no significant reduction cases number of criminal acts during that period. Local government needs to observe whether their area was a high risk of criminal case. The objectives of this study are to detect hotspot area of certain criminal cases using spatial scan statistic. This study analyzed the data of 22 criminal types cases based on province in Indonesia that occurred during 2013. The data was obtained from Badan Pusat Statistik (BPS) that was released in 2014. Hotspot detection was performed according to the likelihood ratio of the Poisson model using SaTScanTM software and then mapped using R. The spatial scan statistic method successfully detected provinces that was categorized as hotspot for 22 crime types cases being analyzed with p-value less than 0.05. The local governments of province that were detected as hotspot area of certain crime cases should provide more attention to improve security quality.

  13. Detecting fixation on a target using time-frequency distributions of a retinal birefringence scanning signal

    PubMed Central

    2013-01-01

    Background The fovea, which is the most sensitive part of the retina, is known to have birefringent properties, i.e. it changes the polarization state of light upon reflection. Existing devices use this property to obtain information on the orientation of the fovea and the direction of gaze. Such devices employ specific frequency components that appear during moments of fixation on a target. To detect them, previous methods have used solely the power spectrum of the Fast Fourier Transform (FFT), which, unfortunately, is an integral method, and does not give information as to where exactly the events of interest occur. With very young patients who are not cooperative enough, this presents a problem, because central fixation may be present only during very short-lasting episodes, and can easily be missed by the FFT. Method This paper presents a method for detecting short-lasting moments of central fixation in existing devices for retinal birefringence scanning, with the goal of a reliable detection of eye alignment. Signal analysis is based on the Continuous Wavelet Transform (CWT), which reliably localizes such events in the time-frequency plane. Even though the characteristic frequencies are not always strongly expressed due to possible artifacts, simple topological analysis of the time-frequency distribution can detect fixation reliably. Results In all six subjects tested, the CWT allowed precise identification of both frequency components. Moreover, in four of these subjects, episodes of intermittent but definitely present central fixation were detectable, similar to those in Figure 4. A simple FFT is likely to treat them as borderline cases, or entirely miss them, depending on the thresholds used. Conclusion Joint time-frequency analysis is a powerful tool in the detection of eye alignment, even in a noisy environment. The method is applicable to similar situations, where short-lasting diagnostic events need to be detected in time series acquired by means of

  14. Reduction of false positives by extracting fuzzy rules from data for polyp detection in CTC scans

    NASA Astrophysics Data System (ADS)

    Siddique, Musib M.; Zheng, Yalin; Yang, Xiaoyun; Beddoe, Gareth

    2008-03-01

    This paper presents an adaptive neural network based Fuzzy Inference System (ANFIS) to reduce the false positive (FP) rate of detected colonic polyps in Computed Tomography Colonography (CTC) scans. Extracted fuzzy rules establish linguistically interpretable relationships in the data that are easy to understand, validate, and extend. The system takes several features identified from regions extracted by a segmentation algorithm and decides whether the regions are true polyps. In the training phase, subtractive clustering is used to down-sample the negative regions in order to get balanced data. The rule extraction method is based on estimating clusters in the data using the subtractive clustering algorithm; each cluster obtained corresponds to a fuzzy rule that maps a region in the input space to an output class. After the number of rules and initial rule parameters are obtained by cluster estimation, the rule parameters are optimized using a hybrid learning algorithm which is a combination of least-squares estimation with back propagation. The evolved Sugeno-type FIS has been tested on a total of 129 scans with 99 polyps of sizes 5-15 mm by experienced radiologists. The results indicate that for 93% detection sensitivity (on polyps), the evolved FIS method is able to remove 88% of FPs generated by the segmentation algorithm leaving 7.5 FP per scan. The high sensitivity rate of our results show the promise of neuro-fuzzy classifiers as an aid for interpreting CTC examinations.

  15. High spatial resolution confocal microscope with independent excitation and detection scanning capabilities.

    PubMed

    Marcet, S; Ouellet-Plamondon, C; Francoeur, S

    2009-06-01

    We present the design of a confocal microscope adapted for optical spectroscopy and imaging at cryogenic temperatures. This system is based on the existing approach of partly inserting the optical components of the microscope inside a helium-bath cryostat. It provides a spatial resolution approaching the diffraction limit with a mechanical stability allowing uninterrupted integration times exceeding 10 h and allows keeping track of a single emitter for unlimited periods of time. Furthermore, our design allows scanning the excitation spot and detection area independently of the sample position. This feature provides the means to perform probeless transport experiments on one-dimensional nanostructures. The scanning capabilities of this microscope are fully detailed and characterized using the photoluminescence of single nitrogen dyads at 4.5 K.

  16. Temperature scans/cycles for the detection of low abundant DNA point mutations on microarrays.

    PubMed

    Pingel, Julia; Buhot, Arnaud; Calemczuk, Roberto; Livache, Thierry

    2012-01-15

    The possibility to detect low abundant DNA point mutations is essential for early cancer diagnosis and/or prognosis. Furthermore, in order to be less invasive, the somatic mutations are not only sought in tumor extract samples but also from body fluids or stools rendering their content even more diluted compared to the wild type sequences. In this short communication, we propose two protocols based on temperature scans or cycles for the enrichment of the mutation strands hybridized on microarrays. We predict numerically and confirm experimentally a 10-fold increase in the fraction of mutated DNA hybridized on the microarray compared to the sample content. Coupled to more standard solution phase enrichment techniques, it would be possible to lower by one order of magnitude the current detection limit with the advantage of multiple mutation detections offered by the microarray technology. Copyright © 2011 Elsevier B.V. All rights reserved.

  17. Photoacoustic signal simulation and detection optimization based on laser-scanning optical-resolution photoacoustic microscopy

    NASA Astrophysics Data System (ADS)

    Li, Lin; Du, Yi; Zhao, Qingliang; Li, Qian; Chai, Xinyu; Zhou, Chuanqing

    2014-11-01

    Laser-scanning optical-resolution photoacoustic microscopy (LSOR-PAM) has a high application potential in ophthalmology and other clinical fields because of its high resolution and imaging speed. The stationary unfocused ultrasonic transducer of this system decides the efficiency and field of view (FOV) of photoacoustic signal detection, but the refraction and attenuation of laser generated photoacoustic signal in different tissue mediums will cause signal strength and direction distribution uneven. In this study, we simulated the photoacoustic signal propagation and detection in compound medium models with different tissue parameters using k-space method based on LSOR-PAM imaging principle. The results show a distance related signal strength attenuation and FOV changes related to transducer angle. Our study provides a method for photoacoustic signal detection optimization for different complex tissue structure with LSOR-PAM.

  18. Detection of bladder cancer: comparison of low-dose scans with AIDR 3D and routine-dose scans with FBP on the excretory phase in CT urography

    PubMed Central

    Tsuboyama, Takahiro; Kumano, Seishi; Inada, Yuki; Koyama, Mitsuhiro; Azuma, Haruhito; Narumi, Yoshifumi

    2016-01-01

    Objective: To prospectively compare the detection of bladder cancer between low-dose scans with adaptive iterative dose reduction three dimensional projection (AIDR 3D) and routine-dose scans with filtered back projection (FBP) on the excretory phase (EP) in CT urography. Methods: 42 patients were included. Routine- and low-dose EP were performed in each patient. Routine-dose images were reconstructed with FBP, and low-dose images were reconstructed with AIDR 3D. Two radiologists scored confidence levels for the presence or absence of bladder cancer using a 5-point scale. The CT dose index of each EP was measured, and the dose reduction was calculated. Results: Sensitivity, specificity and accuracy were 86.4%, 95.0% and 90.5% on routine-dose scans and were 86.4%, 90.0% and 88.1% on low-dose scans, respectively. There was no significant difference (p; not significant, 1.00 and 1.00, respectively). The average CT dose index was 8.07 and 2.63 mGy on routine- and low-dose scans, and the ratio of dose reduction was 67.6%. Conclusion: The detection of bladder cancer on low-dose scans with AIDR 3D is almost equal to that on routine-dose scans with FBP on the EP, with nearly 70% dose reduction. Advances in knowledge: Using AIDR 3D, the radiation dose may be reduced on the EP in CT urography for the detection of bladder cancer. PMID:26642306

  19. Ultrasound detection of pneumothorax compared with chest X-ray and computed tomography scan.

    PubMed

    Nagarsheth, Khanjan; Kurek, Stanley

    2011-04-01

    Pneumothorax after trauma can be a life threatening injury and its care requires expeditious and accurate diagnosis and possible intervention. We performed a prospective, single blinded study with convenience sampling at a Level I trauma center comparing thoracic ultrasound with chest X-ray and CT scan in the detection of traumatic pneumothorax. Trauma patients that received a thoracic ultrasound, chest X-ray, and chest CT scan were included in the study. The chest X-rays were read by a radiologist who was blinded to the thoracic ultrasound results. Then both were compared with CT scan results. One hundred and twenty-five patients had a thoracic ultrasound performed in the 24-month period. Forty-six patients were excluded from the study due to lack of either a chest X-ray or chest CT scan. Of the remaining 79 patients there were 22 positive pneumothorax found by CT and of those 18 (82%) were found on ultrasound and 7 (32%) were found on chest X-ray. The sensitivity of thoracic ultrasound was found to be 81.8 per cent and the specificity was found to be 100 per cent. The sensitivity of chest X-ray was found to be 31.8 per cent and again the specificity was found to be 100 per cent. The negative predictive value of thoracic ultrasound for pneumothorax was 0.934 and the negative predictive value for chest X-ray for pneumothorax was found to be 0.792. We advocate the use of chest ultrasound for detection of pneumothorax in trauma patients.

  20. Detection of coronary calcifications from computed tomography scans for automated risk assessment of coronary artery disease

    SciTech Connect

    Isgum, Ivana; Rutten, Annemarieke; Prokop, Mathias; Ginneken, Bram van

    2007-04-15

    A fully automated method for coronary calcification detection from non-contrast-enhanced, ECG-gated multi-slice computed tomography (CT) data is presented. Candidates for coronary calcifications are extracted by thresholding and component labeling. These candidates include coronary calcifications, calcifications in the aorta and in the heart, and other high-density structures such as noise and bone. A dedicated set of 64 features is calculated for each candidate object. They characterize the object's spatial position relative to the heart and the aorta, for which an automatic segmentation scheme was developed, its size and shape, and its appearance, which is described by a set of approximated Gaussian derivatives for which an efficient computational scheme is presented. Three classification strategies were designed. The first one tested direct classification without feature selection. The second approach also utilized direct classification, but with feature selection. Finally, the third scheme employed two-stage classification. In a computationally inexpensive first stage, the most easily recognizable false positives were discarded. The second stage discriminated between more difficult to separate coronary calcium and other candidates. Performance of linear, quadratic, nearest neighbor, and support vector machine classifiers was compared. The method was tested on 76 scans containing 275 calcifications in the coronary arteries and 335 calcifications in the heart and aorta. The best performance was obtained employing a two-stage classification system with a k-nearest neighbor (k-NN) classifier and a feature selection scheme. The method detected 73.8% of coronary calcifications at the expense of on average 0.1 false positives per scan. A calcium score was computed for each scan and subjects were assigned one of four risk categories based on this score. The method assigned the correct risk category to 93.4% of all scans.

  1. Multiple Regression Analysis of Sib-Pair Data on Reading to Detect Quantitative Trait Loci.

    ERIC Educational Resources Information Center

    Fulker, D. W.; And Others

    1991-01-01

    Applies an extension of an earlier multiple regression model for twin analysis to the problem of detecting linkage in a quantitative trait. Detects a number of possible linkages, indicating that the approach is effective. Discusses detecting genotype-environment interaction and the issue of power. (RS)

  2. Improving global feature detectabilities through scan range splitting for untargeted metabolomics by high-performance liquid chromatography-Orbitrap mass spectrometry.

    PubMed

    Ranninger, Christina; Schmidt, Lukas E; Rurik, Marc; Limonciel, Alice; Jennings, Paul; Kohlbacher, Oliver; Huber, Christian G

    2016-08-03

    Untargeted metabolomics aims at obtaining quantitative information on the highest possible number of low-molecular biomolecules present in a biological sample. Rather small changes in mass spectrometric spectrum acquisition parameters may have a significant influence on the detectabilities of metabolites in untargeted global-scale studies by means of high-performance liquid chromatography-mass spectrometry (HPLC-MS). Employing whole cell lysates of human renal proximal tubule cells, we present a systematic global-scale study of the influence of mass spectrometric scan parameters and post-acquisition data treatment on the number and intensity of metabolites detectable in whole cell lysates. Ion transmission and ion collection efficiencies in an Orbitrap-based mass spectrometer basically depend on the m/z range scanned, which, ideally, requires different instrument settings for the respective mass ranges investigated. Therefore, we split a full scan range of m/z 50-1000 relevant for metabolites into two separate segments (m/z 50-200 and m/z 200-1,000), allowing an independent tuning of the ion transmission parameters for both mass ranges. Three different implementations, involving either scanning from m/z 50-1000 in a single scan, or scanning from m/z 50-200 and from m/z 200-1000 in two alternating scans, or performing two separate HPLC-MS runs with m/z 50-200 and m/z 200-1000 scan ranges were critically assessed. The detected features were subjected to rigorous background filtering and quality control in order to obtain reliable metabolite features for subsequent differential quantification. The most efficient approach in terms of feature number, which forms the basis for statistical analysis, identification, and for generating biological hypotheses, was the separate analysis of two different mass ranges. This lead to an increase in the number of detectable metabolite features, especially in the higher mass range (m/z greater than 400), by 2.5 (negative mode) to 6

  3. A Space–Time Permutation Scan Statistic for Disease Outbreak Detection

    PubMed Central

    2005-01-01

    Background The ability to detect disease outbreaks early is important in order to minimize morbidity and mortality through timely implementation of disease prevention and control measures. Many national, state, and local health departments are launching disease surveillance systems with daily analyses of hospital emergency department visits, ambulance dispatch calls, or pharmacy sales for which population-at-risk information is unavailable or irrelevant. Methods and Findings We propose a prospective space–time permutation scan statistic for the early detection of disease outbreaks that uses only case numbers, with no need for population-at-risk data. It makes minimal assumptions about the time, geographical location, or size of the outbreak, and it adjusts for natural purely spatial and purely temporal variation. The new method was evaluated using daily analyses of hospital emergency department visits in New York City. Four of the five strongest signals were likely local precursors to citywide outbreaks due to rotavirus, norovirus, and influenza. The number of false signals was at most modest. Conclusion If such results hold up over longer study times and in other locations, the space–time permutation scan statistic will be an important tool for local and national health departments that are setting up early disease detection surveillance systems. PMID:15719066

  4. Automated kidney detection for 3D ultrasound using scan line searching

    NASA Astrophysics Data System (ADS)

    Noll, Matthias; Nadolny, Anne; Wesarg, Stefan

    2016-04-01

    Ultrasound (U/S) is a fast and non-expensive imaging modality that is used for the examination of various anatomical structures, e.g. the kidneys. One important task for automatic organ tracking or computer-aided diagnosis is the identification of the organ region. During this process the exact information about the transducer location and orientation is usually unavailable. This renders the implementation of such automatic methods exceedingly challenging. In this work we like to introduce a new automatic method for the detection of the kidney in 3D U/S images. This novel technique analyses the U/S image data along virtual scan lines. Here, characteristic texture changes when entering and leaving the symmetric tissue regions of the renal cortex are searched for. A subsequent feature accumulation along a second scan direction produces a 2D heat map of renal cortex candidates, from which the kidney location is extracted in two steps. First, the strongest candidate as well as its counterpart are extracted by heat map intensity ranking and renal cortex size analysis. This process exploits the heat map gap caused by the renal pelvis region. Substituting the renal pelvis detection with this combined cortex tissue feature increases the detection robustness. In contrast to model based methods that generate characteristic pattern matches, our method is simpler and therefore faster. An evaluation performed on 61 3D U/S data sets showed, that in 55 cases showing none or minor shadowing the kidney location could be correctly identified.

  5. Simultaneous Detection and Tracking of Pedestrian from Panoramic Laser Scanning Data

    NASA Astrophysics Data System (ADS)

    Xiao, Wen; Vallet, Bruno; Schindler, Konrad; Paparoditis, Nicolas

    2016-06-01

    Pedestrian traffic flow estimation is essential for public place design and construction planning. Traditional data collection by human investigation is tedious, inefficient and expensive. Panoramic laser scanners, e.g. Velodyne HDL-64E, which scan surroundings repetitively at a high frequency, have been increasingly used for 3D object tracking. In this paper, a simultaneous detection and tracking (SDAT) method is proposed for precise and automatic pedestrian trajectory recovery. First, the dynamic environment is detected using two different methods, Nearest-point and Max-distance. Then, all the points on moving objects are transferred into a space-time (x, y, t) coordinate system. The pedestrian detection and tracking amounts to assign the points belonging to pedestrians into continuous trajectories in space-time. We formulate the point assignment task as an energy function which incorporates the point evidence, trajectory number, pedestrian shape and motion. A low energy trajectory will well explain the point observations, and have plausible trajectory trend and length. The method inherently filters out points from other moving objects and false detections. The energy function is solved by a two-step optimization process: tracklet detection in a short temporal window; and global tracklet association through the whole time span. Results demonstrate that the proposed method can automatically recover the pedestrians trajectories with accurate positions and low false detections and mismatches.

  6. Performance Analysis of a Pole and Tree Trunk Detection Method for Mobile Laser Scanning Data

    NASA Astrophysics Data System (ADS)

    Lehtomäki, M.; Jaakkola, A.; Hyyppä, J.; Kukko, A.; Kaartinen, H.

    2011-09-01

    Dense point clouds can be collected efficiently from large areas using mobile laser scanning (MLS) technology. Accurate MLS data can be used for detailed 3D modelling of the road surface and objects around it. The 3D models can be utilised, for example, in street planning and maintenance and noise modelling. Utility poles, traffic signs, and lamp posts can be considered an important part of road infrastructure. Poles and trees stand out from the environment and should be included in realistic 3D models. Detection of narrow vertical objects, such as poles and tree trunks, from MLS data was studied. MLS produces huge amounts of data and, therefore, processing methods should be as automatic as possible and for the methods to be practical, the algorithms should run in an acceptable time. The automatic pole detection method tested in this study is based on first finding point clusters that are good candidates for poles and then separating poles and tree trunks from other clusters using features calculated from the clusters and by applying a mask that acts as a model of a pole. The method achieved detection rates of 77.7% and 69.7% in the field tests while 81.0% and 86.5% of the detected targets were correct. Pole-like targets that were surrounded by other objects, such as tree trunks that were inside branches, were the most difficult to detect. Most of the false detections came from wall structures, which could be corrected in further processing.

  7. Noncontact-mode scanning capacitance force microscopy towards quantitative two-dimensional carrier profiling on semiconductor devices

    SciTech Connect

    Kimura, Kenjiro; Kobayashi, Kei; Matsushige, Kazumi; Usuda, Koji; Yamada, Hirofumi

    2007-02-19

    Scanning capacitance force microscopy (SCFM) is a promising tool for investigation of two-dimensional carrier density distribution on semiconducting devices. Its sensitivity is strongly dependent on the Q factor of the mechanical resonance mode of the cantilever. Therefore, measurement in vacuum is more appropriate for increasing the sensitivity. In this letter, the authors describe noncontact-mode (NC) SCFM which is combined with the frequency modulation detection method and its signal characteristics. The authors derived a quasiquantitative calibration curve which correlates to the amplitude signal in NC-SCFM to the dopant density. Using the calibration curve, the authors obtained a quasiquantitative two-dimensional dopant density distribution map on a cross-sectional transistor device.

  8. Design and Development of a Scanning Airborne Direct Detection Doppler Lidar System

    NASA Technical Reports Server (NTRS)

    Gentry, Bruce; McGill, Matthew; Schwemmer, Geary; Hardesty, Michael; Brewer, Alan; Wilkerson, Thomas; Atlas, Robert; Sirota, Marcos; Lindemann, Scott

    2006-01-01

    In the fall of 2005 we began developing an airborne scanning direct detection molecular Doppler lidar. The instrument is being built as part of the Tropospheric Wind Lidar Technology Experiment (TWiLiTE), a three year project selected by the NASA Earth Sun Technology Office under the Instrument Incubator Program. The TWiLiTE project is a collaboration involving scientists and engineers from NASA Goddard Space Flight Center, NOAA ESRL, Utah State University Space Dynamics Lab, Michigan Aerospace Corporation and Sigma Space Corporation. The TWiLiTE instrument will leverage significant research and development investments made by NASA Goddard and it's partners in the past several years in key lidar technologies and sub-systems (lasers, telescopes, scanning systems, detectors and receivers) required to enable spaceborne global wind lidar measurement. These sub-systems will be integrated into a complete molecular direct detection Doppler wind lidar system designed for autonomous operation on a high altitude aircraft, such as the NASA WB57. The WB57 flies at an altitude of 18 km and from this vantage point the nadir viewing Doppler lidar will be able to profile winds through the full troposphere. The TWiLiTE integrated airborne Doppler lidar instrument will be the first demonstration of a airborne scanning direct detection Doppler lidar and will serve as a critical milestone on the path to a future spaceborne tropospheric wind system. In addition to being a technology testbed for space based tropospheric wind lidar, when completed the TWiLiTE high altitude airborne lidar will be used for studying mesoscale dynamics and storm research (e.g. winter storms, hurricanes) and could be used for calibration and validation of satellite based wind systems such as ESA's Aeolus Atmospheric Dynamics Mission. The TWiLiTE Doppler lidar will have the capability to profile winds in clear air from the aircraft altitude of 18 km to the surface with 250 m vertical resolution and < 2mls

  9. Terrestrial laser scanning for detection of landfill gas: a pilot study

    NASA Astrophysics Data System (ADS)

    Reshetyuk, Yuriy; Mårtensson, Stig-Göran

    2014-04-01

    Methane built up in landfills as a result of breaking down of organic materials can be a renewable energy source if it is taken advantage of. The aim of research presented in this paper is to detect landfill gas (that contains methane) by means of terrestrial laser scanning. The hypothesis is that where no surface leakage has been reported, the landfill gas will expand or migrate. Therefore, it is possible to detect it through repeated scanning of the same area and comparison of Digital Terrain Models (DTMs) generated from the point clouds. Only the most significant movements, i.e. vertical, are of interest in this case. During September-November 2011, a small area at Forsbacka landfill in the vicinity of Gävle was scanned 10 times. Epoch-to-epoch comparisons of the resulting DTMs have shown two significant changes (-27 and +19 mm) in elevation of the surface, and it is not impossible that they are caused by migrating landfill gas. The method tested in this study is deemed to be rigorous and accurate for detecting small-scale swell-shrink behaviour of the ground surface (in our case a landfill surface). However, both data processing and interpretation of the results have been considerably complicated by presence of low vegetation (weeds) on the study site, which was dificult to filter away completely from the data. Based on our pilot study, we recommend that a larger area and a longer period of time are chosen to give basis for more grounded conclusions about presence of landfill gas.

  10. Routine early CT scanning after craniotomy: is it effective for the early detection of postoperative intracranial hematoma?

    PubMed

    Wen, Liang; Yang, Xiao-Feng; Jiang, Hao; Wang, Hao; Zhan, Ren-Ya

    2016-08-01

    Postoperative intracranial hematoma (POIH) is a frequent sequela secondary to cranial surgery. The role of routine early postoperative computed tomography (CT) scanning in the detection of POIH remains controversial. The study was aimed at analyzing the effect of routine early CT scanning after craniotomy for the early detection of POIH. Routine early postoperative CT scanning was performed at our institute, and a retrospective study was conducted to analyze the data. POIH was defined as an intracranial hematoma requiring surgical management. A total of 1,148 patients undergoing craniotomy were included in this study; 28 of these patients developed POIH. The majority of POIH cases (15/28, 54 %) were detected during the first 6 h following craniotomy. A routine CT scan was performed on all included patients but two; however, CT scans detected only 16 POIH cases. During the first 6 h, the rate at which CT scans detected POIH was 1.9 % (15/786); subsequently, the rate decreased to only 0.3 % (1/360; p < 0.05, compared with the rate during the first 6 h). Among patients without clinical manifestations, the rate at which the routine post-craniotomy CT scan detected POIH was only 0.7 % (5/721) (p < 0.05, compared with the incidence of POIH). Finally, among high-risk POIH patients, the POIH-positive rate of routine CT scanning was elevated. It appears that routine early CT scan is ineffective for the detection of POIH in patients undergoing craniotomy. However, if the strategy for routine scanning can be improved, its effect may be beneficial.

  11. Acousto-optical deflection-based whole channel scanning for microchip isoelectric focusing with laser-induced fluorescence detection.

    PubMed

    Sanders, J C; Huang, Z; Landers, J P

    2001-12-01

    This paper describes the development of a technique amenable to the separation of proteins on a microchip by isoelectric focusing (IEF) with entire channel scanning laser-induced fluorescence detection using acousto-optical deflection (AOD). The ability to use AOD to scan the portions of or the entire length of an IEF separation channel allows for high-speed analysis since the mobilization step is circumvented with this technique. Employing no moving parts eliminates mechanical noise and, not only is there no loss of resolution, AOD scanning can potentially increase resolution. The ability of AOD to provide ultra-fast scanning rates (kHz timescale) allows for real-time imaging of the focusing process. This is demonstrated with the separation of naturally fluorescent proteins using entire channel (total scanning range of 2.4 cm) AOD-mediated scanning laser-induced fluorescence detection.

  12. Lanthanum Deposition in the Stomach: Usefulness of Scanning Electron Microscopy for Its Detection.

    PubMed

    Iwamuro, Masaya; Urata, Haruo; Tanaka, Takehiro; Ando, Akemi; Nada, Takahiro; Kimura, Kosuke; Yamauchi, Kenji; Kusumoto, Chiaki; Otsuka, Fumio; Okada, Hiroyuki

    2017-02-01

    After having been treated with lanthanum carbonate administration for 4 years for hyperphosphatemia, a 75-year-old Japanese woman undergoing hemodialysis was diagnosed with lanthanum phosphate deposition in the stomach. The deposition, seen as white microgranules, was observed using esophagogastroduodenoscopy with magnifying observation. To the best of our knowledge, these are the minutest endoscopy images of lanthanum phosphate deposition in the gastric mucosa. Scanning electron microscopy (SEM) observation enabled easier identification of the deposited material, which was visible as bright areas. The present case suggests the usefulness of SEM observation in the detection of lanthanum phosphate deposition in the gastrointestinal tract.

  13. Quantitative and sensitive RNA based detection of Bacillus spores

    PubMed Central

    Osmekhina, Ekaterina; Shvetsova, Antonina; Ruottinen, Maria; Neubauer, Peter

    2014-01-01

    The fast and reliable detection of bacterial spores is of great importance and still remains a challenge. Here we describe a direct RNA-based diagnostic method for the specific detection of viable bacterial spores which does not depends on an enzymatic amplification step and therefore is directly appropriate for quantification. The procedure includes the following steps: (i) heat activation of spores, (ii) germination and enrichment cultivation, (iii) cell lysis, and (iv) analysis of 16S rRNA in crude cell lysates using a sandwich hybridization assay. The sensitivity of the method is dependent on the cultivation time and the detection limit; it is possible to detect 10 spores per ml when the RNA analysis is performed after 6 h of enrichment cultivation. At spore concentrations above 106 spores per ml the cultivation time can be shortened to 30 min. Total analysis times are in the range of 2–8 h depending on the spore concentration in samples. The developed procedure is optimized at the example of Bacillus subtilis spores but should be applicable to other organisms. The new method can easily be modified for other target RNAs and is suitable for specific detection of spores from known groups of organisms. PMID:24653718

  14. A quantitative study of 3D-scanning frequency and Δd of tracking points on the tooth surface

    PubMed Central

    Li, Hong; Lyu, Peijun; Sun, Yuchun; Wang, Yong; Liang, Xiaoyue

    2015-01-01

    Micro-movement of human jaws in the resting state might influence the accuracy of direct three-dimensional (3D) measurement. Providing a reference for sampling frequency settings of intraoral scanning systems to overcome this influence is important. In this study, we measured micro-movement, or change in distance (∆d), as the change in position of a single tracking point from one sampling time point to another in five human subjects. ∆d of tracking points on incisors at 7 sampling frequencies was judged against the clinical accuracy requirement to select proper sampling frequency settings. The curve equation was then fit quantitatively between ∆d median and the sampling frequency to predict the trend of ∆d with increasing f. The difference of ∆d among the subjects and the difference between upper and lower incisor feature points of the same subject were analyzed by a non-parametric test (α = 0.05). Significant differences of incisor feature points were noted among different subjects and between upper and lower jaws of the same subject (P < 0.01). Overall, ∆d decreased with increasing frequency. When the frequency was 60 Hz, ∆d nearly reached the clinical accuracy requirement. Frequencies higher than 60 Hz did not significantly decrease Δd further. PMID:26400112

  15. An electrochemical immunosensor for quantitative detection of ficolin-3

    NASA Astrophysics Data System (ADS)

    San, Lili; Zeng, Dongdong; Song, Shiping; Zuo, Xiaolei; Zhang, Huan; Wang, Chenguang; Wu, Jiarui; Mi, Xianqiang

    2016-06-01

    Diabetes mellitus (DM) is one of the most common metabolic disorders in the world, of which more than 90% is type-2 diabetes mellitus (T2DM). There is a rather urgent need for reliable, sensitive and quick detection techniques in clinical application of T2DM. Ficolin-3 is a potential biomarker of T2DM, because serum ficolin-3 levels are associated with insulin resistance and predict the incidence of T2DM. Herein, a sandwich-type electrochemical immunosensor was developed for the detection of ficolin-3 in human serum. Cyclic voltammetry and the amperometric current versus time were used to characterize the performance of the immunosensor. Under optimal conditions, the detection limitation of ficolin-3 was 100 ng ml-1 and the linear dynamic range was between 2 and 50 μg ml-1. The method has ideal accuracy, excellent stability and selectivity and has wide application prospects in clinical research.

  16. Combined frequency modulated atomic force microscopy and scanning tunneling microscopy detection for multi-tip scanning probe microscopy applications.

    PubMed

    Morawski, Ireneusz; Spiegelberg, Richard; Korte, Stefan; Voigtländer, Bert

    2015-12-01

    A method which allows scanning tunneling microscopy (STM) tip biasing independent of the sample bias during frequency modulated atomic force microscopy (AFM) operation is presented. The AFM sensor is supplied by an electronic circuit combining both a frequency shift signal and a tunneling current signal by means of an inductive coupling. This solution enables a control of the tip potential independent of the sample potential. Individual tip biasing is specifically important in order to implement multi-tip STM/AFM applications. An extensional quartz sensor (needle sensor) with a conductive tip is applied to record simultaneously topography and conductivity of the sample. The high resonance frequency of the needle sensor (1 MHz) allows scanning of a large area of the surface being investigated in a reasonably short time. A recipe for the amplitude calibration which is based only on the frequency shift signal and does not require the tip being in contact is presented. Additionally, we show spectral measurements of the mechanical vibration noise of the scanning system used in the investigations.

  17. Combined frequency modulated atomic force microscopy and scanning tunneling microscopy detection for multi-tip scanning probe microscopy applications

    NASA Astrophysics Data System (ADS)

    Morawski, Ireneusz; Spiegelberg, Richard; Korte, Stefan; Voigtländer, Bert

    2015-12-01

    A method which allows scanning tunneling microscopy (STM) tip biasing independent of the sample bias during frequency modulated atomic force microscopy (AFM) operation is presented. The AFM sensor is supplied by an electronic circuit combining both a frequency shift signal and a tunneling current signal by means of an inductive coupling. This solution enables a control of the tip potential independent of the sample potential. Individual tip biasing is specifically important in order to implement multi-tip STM/AFM applications. An extensional quartz sensor (needle sensor) with a conductive tip is applied to record simultaneously topography and conductivity of the sample. The high resonance frequency of the needle sensor (1 MHz) allows scanning of a large area of the surface being investigated in a reasonably short time. A recipe for the amplitude calibration which is based only on the frequency shift signal and does not require the tip being in contact is presented. Additionally, we show spectral measurements of the mechanical vibration noise of the scanning system used in the investigations.

  18. Combined frequency modulated atomic force microscopy and scanning tunneling microscopy detection for multi-tip scanning probe microscopy applications

    SciTech Connect

    Morawski, Ireneusz; Spiegelberg, Richard; Korte, Stefan; Voigtländer, Bert

    2015-12-15

    A method which allows scanning tunneling microscopy (STM) tip biasing independent of the sample bias during frequency modulated atomic force microscopy (AFM) operation is presented. The AFM sensor is supplied by an electronic circuit combining both a frequency shift signal and a tunneling current signal by means of an inductive coupling. This solution enables a control of the tip potential independent of the sample potential. Individual tip biasing is specifically important in order to implement multi-tip STM/AFM applications. An extensional quartz sensor (needle sensor) with a conductive tip is applied to record simultaneously topography and conductivity of the sample. The high resonance frequency of the needle sensor (1 MHz) allows scanning of a large area of the surface being investigated in a reasonably short time. A recipe for the amplitude calibration which is based only on the frequency shift signal and does not require the tip being in contact is presented. Additionally, we show spectral measurements of the mechanical vibration noise of the scanning system used in the investigations.

  19. Quantitative analysis of arterial flow properties for detection of non-calcified plaques in ECG-gated coronary CT angiography

    NASA Astrophysics Data System (ADS)

    Wei, Jun; Zhou, Chuan; Chan, Heang-Ping; Chughtai, Aamer; Agarwal, Prachi; Kuriakose, Jean; Hadjiiski, Lubomir; Patel, Smita; Kazerooni, Ella

    2015-03-01

    We are developing a computer-aided detection system to assist radiologists in detection of non-calcified plaques (NCPs) in coronary CT angiograms (cCTA). In this study, we performed quantitative analysis of arterial flow properties in each vessel branch and extracted flow information to differentiate the presence and absence of stenosis in a vessel segment. Under rest conditions, blood flow in a single vessel branch was assumed to follow Poiseuille's law. For a uniform pressure distribution, two quantitative flow features, the normalized arterial compliance per unit length (Cu) and the normalized volumetric flow (Q) along the vessel centerline, were calculated based on the parabolic Poiseuille solution. The flow features were evaluated for a two-class classification task to differentiate NCP candidates obtained by prescreening as true NCPs and false positives (FPs) in cCTA. For evaluation, a data set of 83 cCTA scans was retrospectively collected from 83 patient files with IRB approval. A total of 118 NCPs were identified by experienced cardiothoracic radiologists. The correlation between the two flow features was 0.32. The discriminatory ability of the flow features evaluated as the area under the ROC curve (AUC) was 0.65 for Cu and 0.63 for Q in comparison with AUCs of 0.56-0.69 from our previous luminal features. With stepwise LDA feature selection, volumetric flow (Q) was selected in addition to three other luminal features. With FROC analysis, the test results indicated a reduction of the FP rates to 3.14, 1.98, and 1.32 FPs/scan at sensitivities of 90%, 80%, and 70%, respectively. The study indicated that quantitative blood flow analysis has the potential to provide useful features for the detection of NCPs in cCTA.

  20. Multiplexed paper test strip for quantitative bacterial detection.

    PubMed

    Hossain, S M Zakir; Ozimok, Cory; Sicard, Clémence; Aguirre, Sergio D; Ali, M Monsur; Li, Yingfu; Brennan, John D

    2012-06-01

    Rapid, sensitive, on-site detection of bacteria without a need for sophisticated equipment or skilled personnel is extremely important in clinical settings and rapid response scenarios, as well as in resource-limited settings. Here, we report a novel approach for selective and ultra-sensitive multiplexed detection of Escherichia coli (non-pathogenic or pathogenic) using a lab-on-paper test strip (bioactive paper) based on intracellular enzyme (β-galactosidase (B-GAL) or β-glucuronidase (GUS)) activity. The test strip is composed of a paper support (0.5 × 8 cm), onto which either 5-bromo-4-chloro-3-indolyl-β-D: -glucuronide sodium salt (XG), chlorophenol red β-galactopyranoside (CPRG) or both and FeCl(3) were entrapped using sol-gel-derived silica inks in different zones via an ink-jet printing technique. The sample was lysed and assayed via lateral flow through the FeCl(3) zone to the substrate area to initiate rapid enzyme hydrolysis of the substrate, causing a change from colorless-to-blue (XG hydrolyzed by GUS, indication of nonpathogenic E. coli) and/or yellow to red-magenta (CPRG hydrolyzed by B-GAL, indication of total coliforms). Using immunomagnetic nanoparticles for selective preconcentration, the limit of detection was ~5 colony-forming units (cfu) per milliliter for E. coli O157:H7 and ~20 cfu/mL for E. coli BL21, within 30 min without cell culturing. Thus, these paper test strips could be suitable for detection of viable total coliforms and pathogens in bathing water samples. Moreover, inclusion of a culturing step allows detection of less than 1 cfu in 100 mL within 8 h, making the paper tests strips relevant for detection of multiple pathogens and total coliform bacteria in beverage and food samples.

  1. Dual-detection confocal microscopy: high-speed surface profiling without depth scanning

    NASA Astrophysics Data System (ADS)

    Lee, Dong-Ryoung; Gweon, Dae-Gab; Yoo, Hongki

    2016-03-01

    We propose a new method for three-dimensional (3-D) imaging without depth scanning that we refer to as the dual-detection confocal microscopy (DDCM). Compared to conventional confocal microscopy, DDCM utilizes two pinholes of different sizes. DDCM generates two axial response curves which have different stiffness according to the pinhole diameters. The two axial response curves can draw the characteristics curve of the system which shows the relationship between the axial position of the sample and the intensity ratio. Utilizing the characteristic curve, the DDCM reconstructs a 3-D surface profile with a single 2-D scanning. The height of each pixel is calculated by the intensity ratio of the pixel and the intensity ratio curve. Since the height information can be obtained directly from the characteristic curve without depth scanning, a major advantage of DDCM over the conventional confocal microscopy is a speed. The 3-D surface profiling time is dramatically reduced. Furthermore, DDCM can measure 3-D images without the influence of the sample condition since the intensity ratio is independent of the quantum yield and reflectance. We present two types of DDCM, such as a fluorescence microscopy and a reflectance microscopy. In addition, we extend the measurement range axially by varying the pupil function. Here, we demonstrate the working principle of DDCM and the feasibility of the proposed methods.

  2. sup 111 In-labeled nonspecific immunoglobulin scanning in the detection of focal infection

    SciTech Connect

    Rubin, R.H.; Fischman, A.J.; Callahan, R.J.; Khaw, B.A.; Keech, F.; Ahmad, M.; Wilkinson, R.; Strauss, H.W. )

    1989-10-05

    We performed radionuclide scanning after the intravenous injection of human IgG labeled with indium-111 in 128 patients with suspected focal sites of inflammation. Localization of 111In-labeled IgG correlated with clinical findings in 51 infected patients (21 with abdominal or pelvic infections, 11 with intravascular infections, 7 with pulmonary infections, and 12 with skeletal infections). Infecting organisms included gram-positive bacteria, gram-negative bacteria, Pneumocystis carinii, Mycoplasma pneumoniae, and Candida albicans. No focal localization of 111In-labeled IgG was observed in 63 patients without infection. There were five false negative results, and nine results were unusable. Serial scans were carried out in eight patients: continued localization correctly predicted relapse in six, and the absence of localization indicated resolution in two. To determine whether 111In-labeled IgG localization was specific for inflammation, we studied 16 patients with cancer. Focal localization occurred in 13 of these patients (5 with melanomas, 5 with gynecologic cancers, and 1 each with lymphoma, prostate cancer, and malignant fibrous histiocytoma). No localization was seen in patients with renal or colon cancer or metastatic medullary carcinoma of the thyroid. We conclude that 111In-labeled IgG imaging is effective for the detection of focal infection and that serial scans may be useful in assessing therapeutic efficacy. This technique may also be helpful in the evaluation of certain cancers.

  3. Magnetic Ligation Method for Quantitative Detection of MicroRNAs

    PubMed Central

    Liong, Monty; Im, Hyungsoon; Majmudar, Maulik D.; Aguirre, Aaron D.; Sebas, Matthew; Lee, Hakho; Weissleder, Ralph

    2014-01-01

    A magnetic ligation method is utilized for the detection of microRNAs amongst a complex biological background without polymerase chain reaction or nucleotide modification. The sandwich probes assay can be adapted to analyze a panel of microRNAs associated with cardiovascular diseases in heart tissue samples. PMID:24532323

  4. The colorimetric detection and quantitation of total protein.

    PubMed

    Krohn, Randall I

    2011-09-01

    Protein quantification is an important step for handling protein samples for isolation and characterization; it is a prerequisite step before submitting proteins for chromatographic, electrophoretic, or immunochemical analysis and separation. Colorimetric methods are fast, simple, and not laborious. This unit describes a number of assays able to detect protein concentrations in the low microgram to milligram per milliliter ranges in a variety of formats.

  5. Computerized lung nodule detection on screening CT scans: performance on juxta-pleural and internal nodules

    NASA Astrophysics Data System (ADS)

    Sahiner, Berkman; Hadjiiski, Lubomir M.; Chan, Heang-Ping; Zhou, Chuan; Wei, Jun

    2006-03-01

    We are developing a computer-aided detection (CAD) system for lung nodules in thoracic CT volumes. Our CAD system includes an adaptive 3D pre-screening algorithm to segment suspicious objects, and a false-positive (FP) reduction stage to classify the segmented objects as true nodules or normal lung structures. We found that the effectiveness of the FP reduction stage was limited by the different characteristics of the objects in the internal and the juxta-pleural (JP) regions. The purpose of this study was to evaluate object characteristics in the internal and JP regions of a lung CT scan, and to develop different FP reduction classifiers for JP and internal objects. Our FP reduction technique utilized shape, grayscale, and gradient features, as well as the scores of a newly-developed neural network trained on the eigenvalues of the Hessian matrix in a volume of interest containing the suspicious object. We designed an algorithm to automatically label the objects as internal or JP. Based on a training set of 75 CT scans containing internal and JP nodules, two FP classifiers were trained separately for objects in the two types of lung regions. The system performance was evaluated on an independent test set of 27 low dose screening scans. An experienced chest radiologist identified 64 solid nodules (mean diameter: 5.3 mm, range: 3.0-12.9 mm) on the test cases, of which 33 were internal and 31 were JP. Our adaptive 3D prescreening algorithm detected 28 internal and 29 JP nodules. At 80% sensitivity, the average number of FPs was 3.9 and 9.7 in the internal and JP regions per scan, respectively. In comparison, a classifier designed to work on both types of nodules had an average of 29.4 FPs per scan at the same sensitivity. Our results indicate that it is more effective to use two different classifiers for JP and internal nodules because of their different characteristics. FPs in the JP region were more difficult to distinguish from true nodules. Further investigation

  6. Analysis of Scanning Electron Microscopy Images To Investigate Adsorption Processes Responsible for Detection of Cancer Biomarkers.

    PubMed

    Rodrigues, Valquiria da Cruz; Comin, Cesar H; Soares, Juliana Coatrini; Soares, Andrey Coatrini; Melendez, Matias Eliseo; Fregnani, José Humberto T G; Carvalho, André Lopes; Costa, Luciano da F; Oliveira, Osvaldo N

    2017-02-22

    Adsorption processes are responsible for detection of cancer biomarkers in biosensors (and immunosensors), which can be captured with various principles of detection. In this study, we used a biosensor made with nanostructured films of polypyrrole and p53 antibodies, and image analysis of scanning electron microscopy data made it possible to correlate morphological changes of the biosensor with the concentration of cells containing the cancer biomarker p53. The selectivity of the biosensor was proven by distinguishing images obtained with exposure of the biosensor to cells containing the biomarker from those acquired with cells that did not contain it. Detection was confirmed with cyclic voltammetry measurements, while the adsorption of the p53 biomarker was probed with polarization-modulated infrared reflection absorption (PM-IRRAS) and a quartz crystal microbalance (QCM). Adsorption is described using the Langmuir-Freundlich model, with saturation taking place at a concentration of 100 Ucells/mL. Taken together, our results point to novel ways to detect biomarkers or any type of analyte for which detection is based on adsorption as is the case of the majority of biosensors.

  7. a Feasibility Study on Use of Generic Mobile Laser Scanning System for Detecting Asphalt Pavement Cracks

    NASA Astrophysics Data System (ADS)

    Chen, Xinqu; Li, Jonathan

    2016-06-01

    This study aims to automatically detect pavement cracks on urban roads by employing the 3D point clouds acquired by a mobile laser scanning (MLS) system. Our method consists of four steps: ground point filtering, high-pass convolution, matched filtering, and noise removal. First, a voxel-based upward growing method is applied to construct Digital Terrain Model (DTM) of the road surface. Then, a high-pass filter convolutes the DTM to detect local elevation changes that may embed cracking information. Next, a two-step matched filter is applied to extract crack features. Lastly, a noise removal process is conducted to refine the results. Instead of using MLS intensity, this study takes advantages of the MLS elevation information to perform automated crack detection from large-volume, mixed-density, unstructured MLS point clouds. Four types of cracks including longitudinal, transvers, random, and alligator cracks are detected. Our results demonstrated that the proposed method works well with the RIEGL VMX-450 point clouds and can detect cracks in moderate-to-severe severity (13 - 25 mm) within a 200 m by 30 m urban road segment located in Kingston, Ontario, at one time. Due to the resolution capability, small cracks with slight severity remain unclear in the MLS point cloud.

  8. Confocal laser scanning microscopy detection of chlorophylls and carotenoids in chloroplasts and chromoplasts of tomato fruit.

    PubMed

    D'Andrea, Lucio; Amenós, Montse; Rodríguez-Concepción, Manuel

    2014-01-01

    Plant cells are unique among eukaryotic cells because of the presence of plastids, including chloroplasts and chromoplasts. Chloroplasts are found in green tissues and harbor the photosynthetic machinery (including chlorophyll molecules), while chromoplasts are present in non-photosynthetic tissues and accumulate large amounts of carotenoids. During tomato fruit development, chloroplasts are converted into chromoplasts that accumulate high levels of lycopene, a linear carotenoid responsible for the characteristic red color of ripe fruit. Here, we describe a simple and fast method to detect both types of fully differentiated plastids (chloroplasts and chromoplasts), as well as intermediate stages, in fresh tomato fruits. The method is based on the differential autofluorescence of chlorophylls and carotenoids (lycopene) detected by Confocal Laser Scanning Microscopy.

  9. Single Tree Detection from Airborne Laser Scanning Data Using a Marked Point Process Based Method

    NASA Astrophysics Data System (ADS)

    Zhang, J.; Sohn, G.; Brédif, M.

    2013-05-01

    Tree detection and reconstruction is of great interest in large-scale city modelling. In this paper, we present a marked point process model to detect single trees from airborne laser scanning (ALS) data. We consider single trees in ALS recovered canopy height model (CHM) as a realization of point process of circles. Unlike traditional marked point process, we sample the model in a constraint configuration space by making use of image process techniques. A Gibbs energy is defined on the model, containing a data term which judge the fitness of the model with respect to the data, and prior term which incorporate the prior knowledge of object layouts. We search the optimal configuration through a steepest gradient descent algorithm. The presented hybrid framework was test on three forest plots and experiments show the effectiveness of the proposed method.

  10. Modeling and minimizing interference from corneal birefringence in retinal birefringence scanning for foveal fixation detection

    PubMed Central

    Irsch, Kristina; Gramatikov, Boris; Wu, Yi-Kai; Guyton, David

    2011-01-01

    Utilizing the measured corneal birefringence from a data set of 150 eyes of 75 human subjects, an algorithm and related computer program, based on Müller-Stokes matrix calculus, were developed in MATLAB for assessing the influence of corneal birefringence on retinal birefringence scanning (RBS) and for converging upon an optical/mechanical design using wave plates (“wave-plate-enhanced RBS”) that allows foveal fixation detection essentially independently of corneal birefringence. The RBS computer model, and in particular the optimization algorithm, were verified with experimental human data using an available monocular RBS-based eye fixation monitor. Fixation detection using wave-plate-enhanced RBS is adaptable to less cooperative subjects, including young children at risk for developing amblyopia. PMID:21750772

  11. Modeling and minimizing interference from corneal birefringence in retinal birefringence scanning for foveal fixation detection.

    PubMed

    Irsch, Kristina; Gramatikov, Boris; Wu, Yi-Kai; Guyton, David

    2011-07-01

    Utilizing the measured corneal birefringence from a data set of 150 eyes of 75 human subjects, an algorithm and related computer program, based on Müller-Stokes matrix calculus, were developed in MATLAB for assessing the influence of corneal birefringence on retinal birefringence scanning (RBS) and for converging upon an optical/mechanical design using wave plates ("wave-plate-enhanced RBS") that allows foveal fixation detection essentially independently of corneal birefringence. The RBS computer model, and in particular the optimization algorithm, were verified with experimental human data using an available monocular RBS-based eye fixation monitor. Fixation detection using wave-plate-enhanced RBS is adaptable to less cooperative subjects, including young children at risk for developing amblyopia.

  12. MRI findings of new uptake in the femoral head detected on follow-up bone scans.

    PubMed

    Kim, Seong Ho; Yoo, Hye Jin; Kang, Yusuhn; Choi, Ja-Young; Hong, Sung Hwan

    2015-03-01

    OBJECTIVE. The purpose of this article is to suggest clinical indications for MRI in patients with breast cancer who have new uptake lesions in the femoral head on follow-up bone scans, by evaluating the incidence and causes of new uptake lesions. MATERIALS AND METHODS. Between January 2002 and July 2013, a total of 145 patients with breast cancer who showed new uptake in the femoral head on follow-up bone scans were included in our study. They were classified into two groups: group 1 consisted of 125 patients without known bone metastases, and group 2 consisted of 20 patients who already had bone metastases other than that in the femoral head. The Fisher exact test was performed for the statistical analysis. Thereafter, we reviewed MR images for characterization of the new abnormal uptake in the femoral head. RESULTS. New uptake lesions in the femoral head were metastatic in only 4.8% (6/125) of group 1 patients but in 75% (15/20) of group 2 patients (p < 0.0001). In both groups, no patient with a single uptake lesion in the femoral head had bone metastasis, whereas all patients with more than five new uptake lesions, including those of the femoral head, showed bone metastasis. Most MRI diagnoses for new uptake in the femoral head were fibrocystic change (15/30, 50%) and subchondral fracture (11/30, 36.7%). CONCLUSION. Most of the new uptake lesions in the femoral head detected on the follow-up bone scans in patients with breast cancer were benign. However, MRI could be considered in patients with known bone metastasis or with multiple new uptake lesions on bone scans.

  13. Gravity driven high throughput phase detecting cytometer based on quantitative interferometric microscopy

    NASA Astrophysics Data System (ADS)

    Xue, Liang; Wang, Shouyu; Yan, Keding; Sun, Nan; Ferraro, Pietro; Li, Zhenhua; Liu, Fei

    2014-04-01

    Phase distribution detection of cells and tissues is concerned since it is an important auxiliary method for observing biological samples. High speed and large amount cell detection is needed for its high detecting efficiency. In this paper, we have proposed a simple large scale biological sample phase detection device called gravity driven high throughput phase detecting cytometer based on quantitative interferometric microscopy to obtain flowing red blood cells phase. The system could realize high throughput phase detecting and statistical analysis with high detecting speed and in real time. The statistical characteristics of red blood cells could be obtained which might be helpful for biological analysis and disease detection. We believe this method is a powerful tool to quantitatively measure the phase distribution of biological samples.

  14. Design of the scanning mode coated glass color difference online detection system

    NASA Astrophysics Data System (ADS)

    Bi, Weihong; Zhang, Yu; Wang, Dajiang; Zhang, Baojun; Fu, Guangwei

    2008-03-01

    A design of scanning mode coated glass color difference online detection system was introduced. The system consisted of color difference data acquirement part and orbit control part. The function of the color difference data acquirement part was to acquire glass spectral reflectance and then processed them to get the color difference value. Using fiber for light guiding, the reflected light from surface of glass was transmitted into light division part, and the dispersive light was imaged on linear CCD, and then the output signals from the CCD was sampled pixel by pixel, and the spectral reflectance of coated glass was obtained finally. Then, the acquired spectral reflectance signals was sent to industrial personal computer through USB interface, using standard color space and color difference formula nominated by International Commission on Illumination (CIE) in 1976 to process these signals, and the reflected color parameter and color difference of coated glass was gained in the end. The function of the orbit control part was to move the detection probe by way of transverse scanning mode above the glass strip, and control the measuring start-stop time of the color difference data acquirement part at the same time. The color difference data acquirement part of the system was put on the orbit which is after annealing area in coated glass production line, and the protected fiber probe was placed on slide of the orbit. Using single chip microcomputer to control transmission mechanism of the slide, which made the slide move by way of transverse scanning mode on the glass strip, meanwhile, the color difference data acquirement part of the system was also controlled by the single chip microcomputer, and it made the acquirement part measure color difference data when the probe reached the needed working speed and required place on the glass strip. The scanning mode coated glass color difference online detection system can measure color parameter and color difference of

  15. Enhanced Ratio of Signals Enables Digital Mutation Scanning for Rare Allele Detection

    PubMed Central

    Castellanos-Rizaldos, Elena; Paweletz, Cloud; Song, Chen; Oxnard, Geoffrey R.; Mamon, Harvey; Jänne, Pasi A.; Makrigiorgos, G. Mike

    2016-01-01

    The use of droplet digital PCR (ddPCR) for low-level DNA mutation detection in cancer, prenatal diagnosis, and infectious diseases is growing rapidly. However, although ddPCR has been implemented successfully for detection of rare mutations at pre-determined positions, no ddPCR adaptation for mutation scanning exists. Yet, frequently, clinically relevant mutations reside on multiple sequence positions in tumor suppressor genes or complex hotspot mutations in oncogenes. Here, we describe a combination of coamplification at lower denaturation temperature PCR (COLD-PCR) with ddPCR that enables digital mutation scanning within approximately 50-bp sections of a target amplicon. Two FAM/HEX-labeled hydrolysis probes matching the wild-type sequence are used during ddPCR. The ratio of FAM/HEX-positive droplets is constant when wild-type amplicons are amplified but deviates when mutations anywhere under the FAM or HEX probes are present. To enhance the change in FAM/HEX ratio, we employed COLD-PCR cycling conditions that enrich mutation-containing amplicons anywhere on the sequence. We validated COLD-ddPCR on multiple mutations in TP53 and in EGFR using serial mutation dilutions and cell-free circulating DNA samples, and demonstrate detection down to approximately 0.2% to 1.2% mutation abundance. COLD-ddPCR enables a simple, rapid, and robust two-fluorophore detection method for the identification of multiple mutations during ddPCR and potentially can identify unknown DNA variants present in the target sequence. PMID:25772705

  16. Birt-Hogg-Dube syndrome prospectively detected by review of chest computed tomography scans

    PubMed Central

    Park, Hye Jung; Park, Chul Hwan; Lee, Sang Eun; Lee, Geun Dong; Byun, Min Kwang; Lee, Sungsoo; Lee, Kyung-A; Kim, Tae Hoon; Kim, Seong Han; Yang, Seo Yeon; Kim, Hyung Jung; Ahn, Chul Min

    2017-01-01

    Purpose Birt-Hogg-Dube syndrome (BHD) is a rare disorder caused by mutations in the gene that encodes folliculin (FLCN) and is inherited in an autosomal dominant manner. BHD is commonly accompanied by fibrofolliculomas, renal tumors, multiple pulmonary cysts, and spontaneous pneumothorax. The aim of this study was to detect BHD prospectively in patients undergoing chest computed tomography (CT) scans and to evaluate further the characteristics of BHD in Korea. Methods We prospectively checked and reviewed the chest CT scans obtained for 10,883 patients at Gangnam Severance Hospital, Seoul, Korea, from June 1, 2015 to May 31, 2016. Seventeen patients met the study inclusion criteria and underwent screening for FLCN mutation to confirm BHD. We analyzed the characteristics of the patients confirmed to have BHD and those for a further 6 patients who had previously been described in Korea. Results Six (0.06%) of the 10,883 patients reviewed were diagnosed with BHD. There was no difference in demographic or clinical features between the patients with BHD (n = 6) and those without BHD (n = 11). Pneumothorax was present in 50% of the patients with BHD but typical skin and renal lesions were absent. The maximum size of the cysts in the BHD group (median 39.4 mm; interquartile range [IQR] 11.4 mm) was significantly larger than that in the non-BHD group (median 15.8 mm; IQR 7.8 mm; P = 0.001). Variable morphology was seen in 100.0% of the cysts in the BHD group but in only 18.2% of the cysts in the non-BHD group (P = 0.002). Nine (95%) of the total of 12 Korean patients with BHD had experienced pneumothorax. Typical skin and renal lesions were present in 20.0% of patients with BHD. Conclusions Our findings suggest that BHD can be detected if chest CT scans are read in detail. PMID:28151982

  17. Scanning elastic scattering spectroscopy detects metastatic breast cancer in sentinel lymph nodes

    NASA Astrophysics Data System (ADS)

    Austwick, Martin R.; Clark, Benjamin; Mosse, Charles A.; Johnson, Kristie; Chicken, D. Wayne; Somasundaram, Santosh K.; Calabro, Katherine W.; Zhu, Ying; Falzon, Mary; Kocjan, Gabrijela; Fearn, Tom; Bown, Stephen G.; Bigio, Irving J.; Keshtgar, Mohammed R. S.

    2010-07-01

    A novel method for rapidly detecting metastatic breast cancer within excised sentinel lymph node(s) of the axilla is presented. Elastic scattering spectroscopy (ESS) is a point-contact technique that collects broadband optical spectra sensitive to absorption and scattering within the tissue. A statistical discrimination algorithm was generated from a training set of nearly 3000 clinical spectra and used to test clinical spectra collected from an independent set of nodes. Freshly excised nodes were bivalved and mounted under a fiber-optic plate. Stepper motors raster-scanned a fiber-optic probe over the plate to interrogate the node's cut surface, creating a 20×20 grid of spectra. These spectra were analyzed to create a map of cancer risk across the node surface. Rules were developed to convert these maps to a prediction for the presence of cancer in the node. Using these analyses, a leave-one-out cross-validation to optimize discrimination parameters on 128 scanned nodes gave a sensitivity of 69% for detection of clinically relevant metastases (71% for macrometastases) and a specificity of 96%, comparable to literature results for touch imprint cytology, a standard technique for intraoperative diagnosis. ESS has the advantage of not requiring a pathologist to review the tissue sample.

  18. Automated surface-scanning detection of pathogenic bacteria on fresh produce

    NASA Astrophysics Data System (ADS)

    Horikawa, Shin; Du, Songtao; Liu, Yuzhe; Chen, I.-Hsuan; Xi, Jianguo; Crumpler, Michael S.; Sirois, Donald L.; Best, Steve R.; Wikle, Howard C.; Chin, Bryan A.

    2017-05-01

    This paper investigates the effects of surface-scanning detector position on the resonant frequency and signal amplitude of a wireless magnetoelastic (ME) biosensor for direct pathogen detection on solid surfaces. The experiments were conducted on the surface of a flat polyethylene (PE) plate as a model study. An ME biosensor (1 mm × 0.2 mm × 30 μm) was placed on the PE surface, and a surface-scanning detector was brought close and aligned to the sensor for wireless resonant frequency measurement. The position of the detector was accurately controlled by using a motorized three-axis translation system (i.e., controlled X, Y, and Z positions). The results showed that the resonant frequency variations of the sensor were -125 to +150 Hz for X and Y detector displacements of +/-600 μm and Z displacements of +100 to +500 μm. These resonant frequency variations were small compared to the sensor's initial resonant frequency (< 0.007% of 2.2 MHz initial resonant frequency) measured at the detector home position, indicating high accuracy of the measurement. In addition, the signal amplitude was, as anticipated, found to decrease exponentially with increasing detection distance (i.e., Z distance). Finally, additional experiments were conducted on the surface of cucumbers. Similar results were obtained.

  19. Fast Edge Detection and Segmentation of Terrestrial Laser Scans Through Normal Variation Analysis

    NASA Astrophysics Data System (ADS)

    Che, E.; Olsen, M. J.

    2017-09-01

    Terrestrial Laser Scanning (TLS) utilizes light detection and ranging (lidar) to effectively and efficiently acquire point cloud data for a wide variety of applications. Segmentation is a common procedure of post-processing to group the point cloud into a number of clusters to simplify the data for the sequential modelling and analysis needed for most applications. This paper presents a novel method to rapidly segment TLS data based on edge detection and region growing. First, by computing the projected incidence angles and performing the normal variation analysis, the silhouette edges and intersection edges are separated from the smooth surfaces. Then a modified region growing algorithm groups the points lying on the same smooth surface. The proposed method efficiently exploits the gridded scan pattern utilized during acquisition of TLS data from most sensors and takes advantage of parallel programming to process approximately 1 million points per second. Moreover, the proposed segmentation does not require estimation of the normal at each point, which limits the errors in normal estimation propagating to segmentation. Both an indoor and outdoor scene are used for an experiment to demonstrate and discuss the effectiveness and robustness of the proposed segmentation method.

  20. Coronary calcium scanning independently detects coronary artery disease in asymptomatic firefighters: a prospective study.

    PubMed

    Santora, Lawrence J; Pillutla, Priya; Norris, Teresa; Santora, Rina; Brandt, Richard; Jenkins, Mark; Robinson, Mary; Santora, Nicole; Budoff, Matthew J

    2013-01-01

    Sudden cardiac death is the leading cause of death among firefighters in the United States. Fire departments commonly maintain physical examination protocols, often with exercise stress testing, to detect risk of coronary heart disease. We sought to determine whether coronary calcium detected by electron beam computed tomography (EBCT) adds incremental risk stratification beyond the traditional risk factors in asymptomatic community-based firefighters. Three hundred ninety nine asymptomatic firefighters underwent a coronary calcium scan on a GE/Imatron C-150 Ultrafast EBCT scanner, using standardized imaging protocols. Framingham risk factor data were obtained on each patient by using a questionnaire. Agatston scores were derived and compared with national database of Agatston scores for asymptomatic populations on the basis of age and sex, allowing determination of a calcium percentile for each score. Coronary calcium was found only in men >34 years of age. Of the 53% who had positive scans (Agatston score > 0), 87% had higher than average Agatston scores compared with a national database (P < 0.01). Agatston score above the 75th percentile was found in 57% of firefighters. No correlation was observed between traditional risk factors and those with and without coronary calcium. Firefighters have a high burden of calcified coronary atherosclerosis, greater than anticipated on the basis of age and coronary risk factors. Copyright © 2013 Society of Cardiovascular Computed Tomography. Published by Elsevier Inc. All rights reserved.

  1. DETECTION AND QUANTITATION OF FALLOUT PARTICLES IN A HUMAN LUNG.

    PubMed

    WEGST, A V; PELLETIER, C A; WHIPPLE, G H

    1964-02-28

    Portions of an adult human lung were studied by autoradiography in order to detect the presence of fallout particles. The radioactivity in the remainder of the tissue was determined with a gamma-ray spectrometer. Four particles were found and their activities were determined. From the measurement for total-fission-product activity in the lung tissue it was calculated that there were approximately 264 particles in the right lung at the time of death.

  2. Optimization of Quantitative PCR Methods for Enteropathogen Detection.

    PubMed

    Liu, Jie; Gratz, Jean; Amour, Caroline; Nshama, Rosemary; Walongo, Thomas; Maro, Athanasia; Mduma, Esto; Platts-Mills, James; Boisen, Nadia; Nataro, James; Haverstick, Doris M; Kabir, Furqan; Lertsethtakarn, Paphavee; Silapong, Sasikorn; Jeamwattanalert, Pimmada; Bodhidatta, Ladaporn; Mason, Carl; Begum, Sharmin; Haque, Rashidul; Praharaj, Ira; Kang, Gagandeep; Houpt, Eric R

    2016-01-01

    Detection and quantification of enteropathogens in stool specimens is useful for diagnosing the cause of diarrhea but is technically challenging. Here we evaluate several important determinants of quantification: specimen collection, nucleic acid extraction, and extraction and amplification efficiency. First, we evaluate the molecular detection and quantification of pathogens in rectal swabs versus stool, using paired flocked rectal swabs and whole stool collected from 129 children hospitalized with diarrhea in Tanzania. Swabs generally yielded a higher quantification cycle (Cq) (average 29.7, standard deviation 3.5 vs. 25.3 ± 2.9 from stool, P<0.001) but were still able to detect 80% of pathogens with a Cq < 30 in stool. Second, a simplified total nucleic acid (TNA) extraction procedure was compared to separate DNA and RNA extractions and showed 92% (318/344) sensitivity and 98% (951/968) specificity, with no difference in Cq value for the positive results (ΔCq(DNA+RNA-TNA) = -0.01 ± 1.17, P = 0.972, N = 318). Third, we devised a quantification scheme that adjusts pathogen quantity to the specimen's extraction and amplification efficiency, and show that this better estimates the quantity of spiked specimens than the raw target Cq. In sum, these methods for enteropathogen quantification, stool sample collection, and nucleic acid extraction will be useful for laboratories studying enteric disease.

  3. Optimization of Quantitative PCR Methods for Enteropathogen Detection

    PubMed Central

    Liu, Jie; Gratz, Jean; Amour, Caroline; Nshama, Rosemary; Walongo, Thomas; Maro, Athanasia; Mduma, Esto; Platts-Mills, James; Boisen, Nadia; Nataro, James; Haverstick, Doris M.; Kabir, Furqan; Lertsethtakarn, Paphavee; Silapong, Sasikorn; Jeamwattanalert, Pimmada; Bodhidatta, Ladaporn; Mason, Carl; Begum, Sharmin; Haque, Rashidul; Praharaj, Ira; Kang, Gagandeep; Houpt, Eric R.

    2016-01-01

    Detection and quantification of enteropathogens in stool specimens is useful for diagnosing the cause of diarrhea but is technically challenging. Here we evaluate several important determinants of quantification: specimen collection, nucleic acid extraction, and extraction and amplification efficiency. First, we evaluate the molecular detection and quantification of pathogens in rectal swabs versus stool, using paired flocked rectal swabs and whole stool collected from 129 children hospitalized with diarrhea in Tanzania. Swabs generally yielded a higher quantification cycle (Cq) (average 29.7, standard deviation 3.5 vs. 25.3 ± 2.9 from stool, P<0.001) but were still able to detect 80% of pathogens with a Cq < 30 in stool. Second, a simplified total nucleic acid (TNA) extraction procedure was compared to separate DNA and RNA extractions and showed 92% (318/344) sensitivity and 98% (951/968) specificity, with no difference in Cq value for the positive results (ΔCq(DNA+RNA-TNA) = -0.01 ± 1.17, P = 0.972, N = 318). Third, we devised a quantification scheme that adjusts pathogen quantity to the specimen’s extraction and amplification efficiency, and show that this better estimates the quantity of spiked specimens than the raw target Cq. In sum, these methods for enteropathogen quantification, stool sample collection, and nucleic acid extraction will be useful for laboratories studying enteric disease. PMID:27336160

  4. Impact of number of repeated scans on model observer performance for a low-contrast detection task in CT

    NASA Astrophysics Data System (ADS)

    Ma, Chi; Yu, Lifeng; Chen, Baiyu; Vrieze, Thomas; Favazza, Christopher; Leng, Shuai; McCollough, Cynthia

    2015-03-01

    In previous investigations on CT image quality, channelized Hotelling observer (CHO) models have been shown to well represent human observer performance in several phantom-based detection/discrimination tasks. In these studies, a large number of independent images was necessary to estimate the expectation images and covariance matrices for each test condition. The purpose of this study is to investigate how the number of repeated scans affects the precision and accuracy of the CHO's performance in a signal-known-exactly detection task. A phantom containing 21 low-contrast objects (3 contrast levels and 7 sizes) was scanned with a 128-slice CT scanner at three dose levels. For each dose level, 100 independent images were acquired for each test condition. All images were reconstructed using filtered-backprojection (FBP) and a commercial iterative reconstruction algorithm. For each combination of dose level and reconstruction method, the low-contrast detectability, quantified with the area under receiver operating characteristic curve (Az), was calculated using a previously validated CHO model. To determine the dependency of CHO performance on the number of repeated scans, the Az value was calculated for different number of channel filters, for each object size and contrast, and for different dose/reconstruction settings using all 100 repeated scans. The Az values were also calculated using randomly selected subsets of the scans (from 10 to 90 scans with an increment of 10 scans). Using the Az from the 100 scans as the reference, the accuracy of Az values calculated from a fewer number of scans was determined and the minimal number of scans was subsequently derived. For the studied signal-known-exactly detection task, results demonstrated that, the minimal number of scans depends on dose level, object size and contrast level, and channel filters.

  5. Quantitative Laughter Detection, Measurement, and Classification-A Critical Survey.

    PubMed

    Cosentino, Sarah; Sessa, Salvatore; Takanishi, Atsuo

    2016-01-01

    The study of human nonverbal social behaviors has taken a more quantitative and computational approach in recent years due to the development of smart interfaces and virtual agents or robots able to interact socially. One of the most interesting nonverbal social behaviors, producing a characteristic vocal signal, is laughing. Laughter is produced in several different situations: in response to external physical, cognitive, or emotional stimuli; to negotiate social interactions; and also, pathologically, as a consequence of neural damage. For this reason, laughter has attracted researchers from many disciplines. A consequence of this multidisciplinarity is the absence of a holistic vision of this complex behavior: the methods of analysis and classification of laughter, as well as the terminology used, are heterogeneous; the findings sometimes contradictory and poorly documented. This survey aims at collecting and presenting objective measurement methods and results from a variety of different studies in different fields, to contribute to build a unified model and taxonomy of laughter. This could be successfully used for advances in several fields, from artificial intelligence and human-robot interaction to medicine and psychiatry.

  6. Detection of cardiomyopathy in an animal model using quantitative autoradiography

    SciTech Connect

    Kubota, K.; Som, P.; Oster, Z.H.; Brill, A.B.; Goodman, M.M.; Knapp, F.F. Jr.; Atkins, H.L.; Sole, M.J.

    1988-10-01

    A fatty acid analog (15-p-iodophenyl)-3,3 dimethyl-pentadecanoic acid (DMIPP) was studied in cardiomyopathic (CM) and normal age-matched Syrian hamsters. Dual tracer quantitative wholebody autoradiography (QARG) with DMIPP and 2-(/sup 14/C(U))-2-deoxy-2-fluoro-D-glucose (FDG) or with FDG and /sup 201/Tl enabled comparison of the uptake of a fatty acid and a glucose analog with the blood flow. These comparisons were carried out at the onset and mid-stage of the disease before congestive failure developed. Groups of CM and normal animals were treated with verapamil from the age of 26 days, before the onset of the disease for 41 days. In CM hearts, areas of decreased DMIPP uptake were seen. These areas were much larger than the decrease in uptake of FDG or /sup 201/Tl. In early CM only minimal changes in FDG or /sup 201/Tl uptake were observed as compared to controls. Treatment of CM-prone animals with verapamil prevented any changes in DMIPP, FDG, or /sup 201/Tl uptake. DMIPP seems to be a more sensitive indicator of early cardiomyopathic changes as compared to /sup 201/Tl or FDG. The trial of DMIPP and SPECT in the diagnosis of human disease, as well as for monitoring the effects of drugs which may prevent it seems to be warranted.

  7. QEMSCAN° (Quantitative Evaluation of Minerals by Scanning Electron Microscopy): capability and application to fracture characterization in geothermal systems

    NASA Astrophysics Data System (ADS)

    Ayling, B.; Rose, P. E.; Zemach, E.; Drakos, P. S.; Petty, S.

    2011-12-01

    Fractures are important conduits for fluids in geothermal systems, and the creation and maintenance of fracture permeability is a fundamental aspect of EGS (Engineered Geothermal System) development. Hydraulic or chemical stimulation techniques are often employed to achieve this. In the case of chemical stimulation, an understanding of the minerals present in the fractures themselves is desirable to better design a stimulation effort (i.e. which chemical to use and how much). Borehole televiewer surveys provide important information about regional and local stress regimes and fracture characteristics (e.g. fracture aperture), and XRD is useful for examining bulk rock mineralogy, but neither technique is able to quantify the distribution of these minerals in fractures. QEMSCAN° is a fully-automated micro-analysis system that enables quantitative chemical analysis of materials and generation of high-resolution mineral maps and images as well as porosity structure. It uses a scanning electron microscopy platform (SEM) with an electron beam source in combination with four energy-dispersive X-ray spectrometers (EDS). The measured backscattered electron and electron-induced secondary X-ray emission spectra are used to classify sample mineralogy. Initial applications of QEMSCAN° technology were predominantly in the minerals industry and application to geothermal problems has remained limited to date. In this pilot study, the potential application of QEMSCAN° technology to fracture characterization was evaluated using samples of representative mineralized fractures in two geothermal systems (Newberry Volcano, Oregon and Brady's geothermal field, Nevada). QEMSCAN° results were compared with XRD and petrographic techniques. Nine samples were analyzed from each field, collected from the drill core in the 1000-1500 m depth range in two shallow wells (GEO-N2 at Newberry Volcano and BCH-3 at Brady's). The samples were prepared as polished thin sections for QEMSCAN° analysis

  8. Genome-wide quantitative trait locus association scan of general cognitive ability using pooled DNA and 500K single nucleotide polymorphism microarrays

    PubMed Central

    Butcher, L M; Davis, O S P; Craig, I W; Plomin, R

    2008-01-01

    General cognitive ability (g), which refers to what cognitive abilities have in common, is an important target for molecular genetic research because multivariate quantitative genetic analyses have shown that the same set of genes affects diverse cognitive abilities as well as learning disabilities. In this first autosomal genome-wide association scan of g, we used a two-stage quantitative trait locus (QTL) design with pooled DNA to screen more than 500 000 single nucleotide polymorphisms (SNPs) on microarrays, selecting from a sample of 7000 7-year-old children. In stage 1, we screened for allele frequency differences between groups pooled for low and high g. In stage 2, 47 SNPs nominated in stage 1 were tested by individually genotyping an independent sample of 3195 individuals, representative of the entire distribution of g scores in the full 7000 7-year-old children. Six SNPs yielded significant associations across the normal distribution of g, although only one SNP remained significant after a false discovery rate of 0.05 was imposed. However, none of these SNPs accounted for more than 0.4% of the variance of g, despite 95% power to detect associations of that size. It is likely that QTL effect sizes, even for highly heritable traits such as cognitive abilities and disabilities, are much smaller than previously assumed. Nonetheless, an aggregated ‘SNP set’ of the six SNPs correlated 0.11 (P < 0.00000003) with g. This shows that future SNP sets that will incorporate many more SNPs could be useful for predicting genetic risk and for investigating functional systems of effects from genes to brain to behavior. PMID:18067574

  9. A genome scan for Plasmodium falciparum malaria identifies quantitative trait loci on chromosomes 5q31, 6p21.3, 17p12, and 19p13.

    PubMed

    Brisebarre, Audrey; Kumulungui, Brice; Sawadogo, Serge; Atkinson, Alexandre; Garnier, Séverine; Fumoux, Francis; Rihet, Pascal

    2014-05-28

    Genome-wide studies have mapped several loci controlling Plasmodium falciparum mild malaria and parasitaemia, only two of them being significant at the genome level. The objective of the present study was to identify malaria resistance loci in individuals living in Burkina Faso. A genome scan that involved 314 individuals belonging to 63 families was performed. Markers located within chromosomes 6p21.3 and 17p12 were genotyped in 247 additional individuals belonging to 55 families. The linkage and the association of markers with parasitaemia and mild malaria were assessed by using the maximum-likelihood binomial method extended to quantitative trait linkage and the quantitative trait disequilibrium test, respectively. Multipoint linkage analysis showed a significant linkage of mild malaria to chromosome 6p21.3 (LOD score 3.73, P = 1.7 10-5), a suggestive linkage of mild malaria to chromosome 19p13.12 (LOD score 2.50, P = 3.5 10-4), and a suggestive linkage of asymptomatic parasitaemia to chromosomes 6p21.3 (LOD score 2.36, P = 4.9 10-4) and 17p12 (LOD score 2.87, P = 1.4 10-4). Genome-wide family-based association analysis revealed a significant association between three chromosome 5q31 markers and asymptomatic parasitaemia, whereas there was no association with mild malaria. When taking into account 247 additional individuals, a significant linkage of asymptomatic parasitaemia to chromosome 17p12 (LOD score 3.6, P = 2 10-5) was detected. A new genome-wide significant malaria locus on chromosome 17p12 and a new suggestive locus on chromosome 19p13.12 are reported. Moreover, there was evidence that confirmed the influence of chromosomes 5q31 and 6p21.3 as loci controlling mild malaria or asymptomatic parasitaemia.

  10. A genome scan for quantitative trait loci affecting the length of small intestine in a White Duroc x Chinese Erhualian intercross resource population.

    PubMed

    Gao, J; Ren, J; Zhou, L H; Ren, D R; Li, L; Xiao, S J; Yang, B; Huang, L S

    2010-04-01

    The small intestine is a vital organ in animal gastrointestinal system, in which a large variety of nutrients are absorbed. To identify quantitative trait loci (QTL) for the length of porcine small intestine, phenotypic values were measured in 1034 individuals at 240 d from a White Duroc x Chinese Erhualian intercross F(2) population. The length of small intestine showed strong correlation with growth traits and carcass length in the F2 population. A whole-genome scan was performed based on 183 microsatellites covering the pig genome in the F(2) population. A total of 10 QTL for this trait were identified on 8 pig chromosomes (SSC), including four 1% genome-wide significant QTL on SSC2, 4, 7 and 8, one 5% genome-wide significant QTL on SSC12, and five 5% chromosome-wide significant QTL on SSC5, 7, 13 and 14. The Erhualian alleles were generally associated with shorter length of the small intestine except the alleles on SSC7 and 13. The QTL on SSC4 overlapped with the previously reported QTL for the length of small intestine. Several significant QTL on SSC2, 8, and 12 were consistent with previous reports. The significant QTL detected on SSC7 was reported for the first time. All QTL identified in this study corresponded to the known region significantly associated with growth traits, supporting the important role of the length of small intestine in pig growth.

  11. Defect Detection of Fiberglass Composite Laminates (FGCL) with Ultrasonic A-Scan Signal Measurement

    NASA Astrophysics Data System (ADS)

    Mahmod, M. F.; Abu Bakar, Elmi; Othman, A. R.

    2016-02-01

    Fiberglass composite laminates are widely used in many industries, due to its advantages of high specific strength and high specific modulus. Invisible defect such as delamination and inclusion may cause composite structural failure. Therefore, several research on ultrasonic testing for composite material defect detection have been done for the past few years. However, improper parameter setup may lead to significant error to determine the behavior of defects. In this paper, the intensive study on defect detection with ultrasonic single crystal immersion transducer has been conducted. In general, the defects detection thru acquired signal is determine the behavior of defects through the certain ultrasonic parameter setup such as sound velocity, pulse width, gain, sampling rate and transducer distance with specimen surface. Furthermore, an A-scan signal interpretation for FGCL defect detection is demonstrated and illustrated. This research is focusing on for FGCL with maximum thickness up to 10 mm in ambient temperature. The result shows an appropriate ultrasonic parameter will result better signal interpretation analysis.

  12. Detecting benzoyl peroxide in wheat flour by line-scan macro-scale Raman chemical imaging

    NASA Astrophysics Data System (ADS)

    Qin, Jianwei; Kim, Moon S.; Chao, Kuanglin; Gonzalez, Maria; Cho, Byoung-Kwan

    2017-05-01

    Excessive use of benzoyl peroxide (BPO, a bleaching agent) in wheat flour can destroy flour nutrients and cause diseases to consumers. A macro-scale Raman chemical imaging method was developed for direct detection of BPO mixed in the wheat flour. A 785 nm line laser was used in a line-scan Hyperspectral Raman imaging system. Raman images were collected from wheat flour mixed with BPO at eight concentrations (w/w) from 50 to 6,400 ppm. A sample holder (150×100×2 mm3) was used to present a thin layer (2 mm thick) of the powdered sample for image acquisition. A baseline correction method was used to correct the fluctuating fluorescence signals from the wheat flour. To isolate BPO particles from the flour background, a simple thresholding method was applied to the single-band fluorescence-free images at a unique Raman peak wavenumber (i.e., 1001 cm-1) preselected for the BPO detection. Chemical images were created to detect and map the BPO particles. Limit of detection for the BPO was estimated in the order of 50 ppm, which is on the same level with regulatory standards.

  13. Digitally generated excitation and near-baseband quadrature detection of rapid scan EPR signals

    PubMed Central

    Quine, Richard W.; Rinard, George A.; Eaton, Sandra S.; Eaton, Gareth R.

    2014-01-01

    The use of multiple synchronized outputs from an AWG provides the opportunity to perform EPR experiments differently than by conventional EPR. We report a method for reconstructing the quadrature EPR spectrum from periodic signals that are generated with sinusoidal magnetic field modulation such as continuous wave (CW), multiharmonic, or rapid scan experiments. The signal is down-converted to an intermediate frequency (IF) that is less than the field scan or field modulation frequency and then digitized in a single channel. This method permits use of a high-pass analog filter before digitization to remove the strong non-EPR signal at the IF, that might otherwise overwhelm the digitizer. The IF is the difference between two synchronized X-band outputs from a Tektronix AWG 70002A arbitrary waveform generator (AWG), one of which is for excitation and the other is the reference for down-conversion. To permit signal averaging, timing was selected to give an exact integer number of full cycles for each frequency. In the experiments reported here the IF was 5 kHz and the scan frequency was 40 kHz. To produce sinusoidal rapid scans with a scan frequency eight times IF, a third synchronized output generated a square wave that was converted to a sine wave. The timing of the data acquisition with a Bruker SpecJet II was synchronized by an external clock signal from the AWG. The baseband quadrature signal in the frequency domain was reconstructed. This approach has the advantages that (i) the non-EPR response at the carrier frequency is eliminated, (ii) both real and imaginary EPR signals are reconstructed from a single physical channel to produce an ideal quadrature signal, and (iii) signal bandwidth does not increase relative to baseband detection. Spectra were obtained by deconvolution of the reconstructed signals for solid BDPA (1,3-bisdiphenylene-2-phenylallyl) in air, 0.2 mM trityl OX63 in water, 15N perdeuterated tempone, and a nitroxide with a 0.5 G partially

  14. Digitally generated excitation and near-baseband quadrature detection of rapid scan EPR signals

    NASA Astrophysics Data System (ADS)

    Tseitlin, Mark; Yu, Zhelin; Quine, Richard W.; Rinard, George A.; Eaton, Sandra S.; Eaton, Gareth R.

    2014-12-01

    The use of multiple synchronized outputs from an arbitrary waveform generator (AWG) provides the opportunity to perform EPR experiments differently than by conventional EPR. We report a method for reconstructing the quadrature EPR spectrum from periodic signals that are generated with sinusoidal magnetic field modulation such as continuous wave (CW), multiharmonic, or rapid scan experiments. The signal is down-converted to an intermediate frequency (IF) that is less than the field scan or field modulation frequency and then digitized in a single channel. This method permits use of a high-pass analog filter before digitization to remove the strong non-EPR signal at the IF, that might otherwise overwhelm the digitizer. The IF is the difference between two synchronized X-band outputs from a Tektronix AWG 70002A, one of which is for excitation and the other is the reference for down-conversion. To permit signal averaging, timing was selected to give an exact integer number of full cycles for each frequency. In the experiments reported here the IF was 5 kHz and the scan frequency was 40 kHz. To produce sinusoidal rapid scans with a scan frequency eight times IF, a third synchronized output generated a square wave that was converted to a sine wave. The timing of the data acquisition with a Bruker SpecJet II was synchronized by an external clock signal from the AWG. The baseband quadrature signal in the frequency domain was reconstructed. This approach has the advantages that (i) the non-EPR response at the carrier frequency is eliminated, (ii) both real and imaginary EPR signals are reconstructed from a single physical channel to produce an ideal quadrature signal, and (iii) signal bandwidth does not increase relative to baseband detection. Spectra were obtained by deconvolution of the reconstructed signals for solid BDPA (1,3-bisdiphenylene-2-phenylallyl) in air, 0.2 mM trityl OX63 in water, 15N perdeuterated tempone, and a nitroxide with a 0.5 G partially

  15. Digitally generated excitation and near-baseband quadrature detection of rapid scan EPR signals.

    PubMed

    Tseitlin, Mark; Yu, Zhelin; Quine, Richard W; Rinard, George A; Eaton, Sandra S; Eaton, Gareth R

    2014-10-30

    The use of multiple synchronized outputs from an arbitrary waveform generator (AWG) provides the opportunity to perform EPR experiments differently than by conventional EPR. We report a method for reconstructing the quadrature EPR spectrum from periodic signals that are generated with sinusoidal magnetic field modulation such as continuous wave (CW), multiharmonic, or rapid scan experiments. The signal is down-converted to an intermediate frequency (IF) that is less than the field scan or field modulation frequency and then digitized in a single channel. This method permits use of a high-pass analog filter before digitization to remove the strong non-EPR signal at the IF, that might otherwise overwhelm the digitizer. The IF is the difference between two synchronized X-band outputs from a Tektronix AWG 70002A, one of which is for excitation and the other is the reference for down-conversion. To permit signal averaging, timing was selected to give an exact integer number of full cycles for each frequency. In the experiments reported here the IF was 5kHz and the scan frequency was 40kHz. To produce sinusoidal rapid scans with a scan frequency eight times IF, a third synchronized output generated a square wave that was converted to a sine wave. The timing of the data acquisition with a Bruker SpecJet II was synchronized by an external clock signal from the AWG. The baseband quadrature signal in the frequency domain was reconstructed. This approach has the advantages that (i) the non-EPR response at the carrier frequency is eliminated, (ii) both real and imaginary EPR signals are reconstructed from a single physical channel to produce an ideal quadrature signal, and (iii) signal bandwidth does not increase relative to baseband detection. Spectra were obtained by deconvolution of the reconstructed signals for solid BDPA (1,3-bisdiphenylene-2-phenylallyl) in air, 0.2mM trityl OX63 in water, (15)N perdeuterated tempone, and a nitroxide with a 0.5G partially-resolved proton

  16. Automatic Feature Detection, Description and Matching from Mobile Laser Scanning Data and Aerial Imagery

    NASA Astrophysics Data System (ADS)

    Hussnain, Zille; Oude Elberink, Sander; Vosselman, George

    2016-06-01

    In mobile laser scanning systems, the platform's position is measured by GNSS and IMU, which is often not reliable in urban areas. Consequently, derived Mobile Laser Scanning Point Cloud (MLSPC) lacks expected positioning reliability and accuracy. Many of the current solutions are either semi-automatic or unable to achieve pixel level accuracy. We propose an automatic feature extraction method which involves utilizing corresponding aerial images as a reference data set. The proposed method comprise three steps; image feature detection, description and matching between corresponding patches of nadir aerial and MLSPC ortho images. In the data pre-processing step the MLSPC is patch-wise cropped and converted to ortho images. Furthermore, each aerial image patch covering the area of the corresponding MLSPC patch is also cropped from the aerial image. For feature detection, we implemented an adaptive variant of Harris-operator to automatically detect corner feature points on the vertices of road markings. In feature description phase, we used the LATCH binary descriptor, which is robust to data from different sensors. For descriptor matching, we developed an outlier filtering technique, which exploits the arrangements of relative Euclidean-distances and angles between corresponding sets of feature points. We found that the positioning accuracy of the computed correspondence has achieved the pixel level accuracy, where the image resolution is 12cm. Furthermore, the developed approach is reliable when enough road markings are available in the data sets. We conclude that, in urban areas, the developed approach can reliably extract features necessary to improve the MLSPC accuracy to pixel level.

  17. Target-responsive DNAzyme cross-linked hydrogel for visual quantitative detection of lead.

    PubMed

    Huang, Yishun; Ma, Yanli; Chen, Yahong; Wu, Xuemeng; Fang, Luting; Zhu, Zhi; Yang, Chaoyong James

    2014-11-18

    Because of the severe health risks associated with lead pollution, rapid, sensitive, and portable detection of low levels of Pb(2+) in biological and environmental samples is of great importance. In this work, a Pb(2+)-responsive hydrogel was prepared using a DNAzyme and its substrate as cross-linker for rapid, sensitive, portable, and quantitative detection of Pb(2+). Gold nanoparticles (AuNPs) were first encapsulated in the hydrogel as an indicator for colorimetric analysis. In the absence of lead, the DNAzyme is inactive, and the substrate cross-linker maintains the hydrogel in the gel form. In contrast, the presence of lead activates the DNAzyme to cleave the substrate, decreasing the cross-linking density of the hydrogel and resulting in dissolution of the hydrogel and release of AuNPs for visual detection. As low as 10 nM Pb(2+) can be detected by the naked eye. Furthermore, to realize quantitative visual detection, a volumetric bar-chart chip (V-chip) was used for quantitative readout of the hydrogel system by replacing AuNPs with gold-platinum core-shell nanoparticles (Au@PtNPs). The Au@PtNPs released from the hydrogel upon target activation can efficiently catalyze the decomposition of H2O2 to generate a large volume of O2. The gas pressure moves an ink bar in the V-chip for portable visual quantitative detection of lead with a detection limit less than 5 nM. The device was able to detect lead in digested blood with excellent accuracy. The method developed can be used for portable lead quantitation in many applications. Furthermore, the method can be further extended to portable visual quantitative detection of a variety of targets by replacing the lead-responsive DNAzyme with other DNAzymes.

  18. Genome scan linkage analysis identifies quantitative trait loci affecting serum clinical-chemical traits in Korean native chicken.

    PubMed

    Seo, Dong-Won; Park, Hee-Bok; Jin, Shil; Cahyadi, Muhammad; Choi, Nuri; Heo, Kang-Nyeong; Jo, Cheorun; Lee, Jun-Heon

    2016-07-01

    Alterations in robustness- and health-related traits lead to physiological changes, such as changes in the serum clinical chemical parameters in individuals. Therefore, clinical-chemical traits can be used as biomarkers to examine the health status of chickens. The aim of the present study was to detect the quantitative trait loci (QTLs) influencing eight clinical-chemical traits (glucose, total protein, creatinine, high-density lipoprotein cholesterol, total cholesterol, glutamic oxaloacetic transaminase, glutamic pyruvic transaminase, and α-amylase) in an F1 nuclear families comprising 83 F0 founders and 585 F1 progeny of Korean native chickens. Genotypic data on 135 DNA markers representing 26 autosomes have been generated for this resource pedigree. The total length of the map was 2729.4 cM. We used a multipoint variance component linkage approach to identify QTLs for the traits. A significant QTL affecting serum α-amylase levels was identified on chicken chromosome (GGA) 7 [logarithm of odds (LOD) = 3.02, P value = 1.92 × 10(-4)]. Additionally, we detected several suggestive linkage signals for the levels of total cholesterol, glutamic oxaloacetic transaminase, glutamic pyruvic transaminase, and creatinine on GGA 4, 12, 13, and 15. In this study, serum α-amylase levels related significant QTL was mapped on GGA7 and cholesterol, glutamic oxaloacetic transaminase, glutamic pyruvic transaminase, and creatinine traits related suggestive QTLs were detected on GGA4, 12, 13 and 15, respectively. Further verification and fine mapping of these identified QTLs can provide valuable information for understanding the variations of clinical chemical trait in chickens.

  19. Clinical experience with the radioisotope varicocele scan as a screening method for the detection of subclinical varicoceles

    SciTech Connect

    Wheatley, J.K.; Fajman, W.A.; Witten, F.R.

    1982-07-01

    The association of varicoceles and subfertility has been well documented. Although varicoceles remain the most common surgically correctable cause of male infertility the diagnosis of small varicoceles remains a challenge. We evaluated 40 men with an isotope blood pooling scan. Seven volunteers served as either positive or negative controls. Complete correlation between physical findings and the isotope scan was found. The 6 patients with obvious clinical varicoceles and a stress pattern on semen analysis all had positive scans. The 18 patients with a stress pattern and who were clinically suspected of having a varicocele all had positive scans. Of 9 patients evaluated for infertility with a stress pattern but no clinical evidence of varicocele 6 had positive scans. We believe that the isotope scan will prove to be a useful procedure in the detection of nonpalpable varicoceles in selected subfertile men.

  20. New quantitative detection of pathogens in heterogeneous environmental samples

    NASA Astrophysics Data System (ADS)

    Lee, Eun-Hee; Wang, Xiaofang; Mitchell, Kristi; Chae, Seon-Ha; Son, Ahjeong

    2015-04-01

    Quantum dots and magnetic beads based genomic assay (NanoGene assay) has been developed for sensitive and inhibition resistant gene quantification to achieve in-situ bacteria monitoring in environmental samples. In this study, eaeA gene of pathogenic E. coli O157:H7 was quantified. The result demonstrated the excellent sensitivity (i.e., limit of detection: 87 gene copies for dsDNA and 890 zeptomolar for ssDNA) in the presence of nonspecific microbial populations (Kim et al., 2010; 2011a). The feasibility of the developed gene quantification for non-laboratory environment usage (in-situ use) was investigated. Therefore, DNA hybridization was achieved at ambient temperature and minimum agitation, and the analysis was completed within hours. Most importantly, the NanoGene assay demonstrated the resistance to the presence of naturally occurring inhibitors (humic acids, cations) and residual reagents (surfactants, alcohols) from DNA extraction (Kim et al., 2011b). The assay was also applied to humic acids laden soils (7 types of soils with various amount of organic matters) and successfully quantified 105 to 108 CFU of E. coli O157:H7 per gram soil (R2 = 0.99). The results indicate that the presented NanoGene assay is suitable for further development as an in-situ bacteria monitoring method for working with heterogeneous environmental samples (Wang et al., 2013). Another aspect of the method is to transform the NanoGene assay into a portable device that can be used as a pathogenic bacteria detector in environment. The project consisted of the first inline fluidic components development and characterization as well as the first integration effort on a briefcase platform for the in-situ pathogen detection system (IPDS) (Mitchell et al., 2014). Our long term vision is to further miniaturize the briefcase platform implementation of the IPDS and to commercialize the handheld version of the IPDS.

  1. Analytical bioconjugates, aptamers, enable specific quantitative detection of Listeria monocytogenes.

    PubMed

    Lee, Sang-Hee; Ahn, Ji-Young; Lee, Kyeong-Ah; Um, Hyun-Ju; Sekhon, Simranjeet Singh; Sun Park, Tae; Min, Jiho; Kim, Yang-Hoon

    2015-06-15

    As a major human pathogen in the Listeria genus, Listeria monocytogenes causes the bacterial disease listeriosis, which is a serious infection caused by eating food contaminated with the bacteria. We have developed an aptamer-based sandwich assay (ABSA) platform that demonstrates a promising potential for use in pathogen detection using aptamers as analytical bioconjugates. The whole-bacteria SELEX (WB-SELEX) strategy was adopted to generate aptamers with high affinity and specificity against live L. monocytogenes. Of the 35 aptamer candidates tested, LMCA2 and LMCA26 reacted to L. monocytogenes with high binding, and were consequently chosen as sensing probes. The ABSA platform can significantly enhance the sensitivity by employing a very specific aptamer pair for the sandwich complex. The ABSA platform exhibited a linear response over a wide concentration range of L. monocytogenes from 20 to 2×10(6) CFU per mL and was closely correlated with the following relationship: y=9533.3x+1542.3 (R(2)=0.99). Our proposed ABSA platform also provided excellent specificity for the tests to distinguish L. monocytogenes from other Listeria species and other bacterial genera (3 Listeria spp., 4 Salmonella spp., 2 Vibrio spp., 3 Escherichia coli and 3 Shigella spp.). Improvements in the sensitivity and specificity have not only facilitated the reliable detection of L. monocytogenes at extremely low concentrations, but also allowed for the development of a 96-well plate-based routine assay platform for multivalent diagnostics. Copyright © 2015 Elsevier B.V. All rights reserved.

  2. Quantitative detection of bovine and porcine gelatin difference using surface plasmon resonance based biosensor

    NASA Astrophysics Data System (ADS)

    Wardani, Devy P.; Arifin, Muhammad; Suharyadi, Edi; Abraha, Kamsul

    2015-05-01

    Gelatin is a biopolymer derived from collagen that is widely used in food and pharmaceutical products. Due to some religion restrictions and health issues regarding the gelatin consumption which is extracted from certain species, it is necessary to establish a robust, reliable, sensitive and simple quantitative method to detect gelatin from different parent collagen species. To the best of our knowledge, there has not been a gelatin differentiation method based on optical sensor that could detect gelatin from different species quantitatively. Surface plasmon resonance (SPR) based biosensor is known to be a sensitive, simple and label free optical method for detecting biomaterials that is able to do quantitative detection. Therefore, we have utilized SPR-based biosensor to detect the differentiation between bovine and porcine gelatin in various concentration, from 0% to 10% (w/w). Here, we report the ability of SPR-based biosensor to detect difference between both gelatins, its sensitivity toward the gelatin concentration change, its reliability and limit of detection (LOD) and limit of quantification (LOQ) of the sensor. The sensor's LOD and LOQ towards bovine gelatin concentration are 0.38% and 1.26% (w/w), while towards porcine gelatin concentration are 0.66% and 2.20% (w/w), respectively. The results show that SPR-based biosensor is a promising tool for detecting gelatin from different raw materials quantitatively.

  3. A sandwich assay for quantitative detection of transcription factors in cell lysate.

    PubMed

    Fang, Zhiyuan; Zhang, Wenjuan; Ge, Chenchen; Liu, Jie; Lie, Puchang; Zeng, Lingwen

    2012-09-21

    A double-stranded DNA (dsDNA) mediated sandwich assay was developed for quantitative detection of transcription factors. The detection limit for human recombinant c-jun protein is 2.5 ng, and for c-jun protein the limit is as low as 0.625 μg of cell lysate.

  4. Rapid Detection and Quantitative Estimation of Type A Botulinum Toxin by Electroimmunodiffusion

    PubMed Central

    Miller, Carol A.; Anderson, Arthur W.

    1971-01-01

    An experimental system is described for the detection and quantitative estimation of type A botulinum toxin by electroimmunodiffusion. The method is shown to be rapid, specific, and quantitative. As little as 14 mouse LD50 per 0.1 ml of type A toxin was detected within 2 hr. When applied to experimentally contaminated foods such as canned tuna, pumpkin, spinach, green beans, and sausage, the technique detected botulinum toxin rapidly and identified it as to type and quantity. A specific rabbit type A antitoxin was produced for this in vitro system since the equine antitoxin (Center for Disease Control) tested in this experiment was found to be unsuitable. Images PMID:5005291

  5. Quantitative aspects of rare earth metal determinations using capillary electrophoresis with indirect absorbance detection

    SciTech Connect

    Colburn, B.A.; Starnes, S.D.; Sepaniak, M.J.

    1995-04-01

    The practical utility of capillary zone electrophoresis with indirect absorbance detection is examined for the separation and quantitation of rare earth metals. Various imidazole derivatives are investigated as to their suitability as running buffer (displaceable) detection ions with {alpha}-hydroxyisobutyric acid functioning as a chelating agent to enhance separations. Parameters important for quantitative analysis, such as limits of detection, relative standard deviation of peak areas, efficiency, resolution, peak shape and linear dynamic range are presented. The influence of sample matrix, method of injection, and background ion identity on these parameters are investigated and discussed.

  6. Detection of beta-amyloid (1-42) on protein array based on electrical detection technique using scanning tunneling microscopy.

    PubMed

    Choi, Jeong-Woo; Islam, A T M Kamrul; Lee, Jin-Ho; Song, Joon Myong; Oh, Byung-Keun

    2011-05-01

    In this study an immuno-array for Abeta42 based on scanning tunneling microscopy (STM) was developed using conjugated gold nanoparticle (Au-NP) and antibody (Ab) complex. Fragmented monoclonal Ab against Abeta42 was allowed to immobilize on the Au-dot arrays followed by its target protein Abeta42 and Au NP and Ab complex. The surface structure of Au-NP and Ab complex on Au-dots was investigated with Atomic Force Microscopy and the current profile of fabricated immunosensing element was investigated with STM. The power spectrum derived from the current profile was found to be increasing with higher concentrations of Abeta42 having a detection limit of 100 fg/ml. The proposed technique can be a promising method to construct the highly sensitive and efficient protein chip of immunosensors arrays.

  7. Comparison of Droplet Digital PCR and Quantitative PCR Assays for Quantitative Detection of Xanthomonas citri Subsp. citri

    PubMed Central

    Yin, Youping; Wang, Zhongkang

    2016-01-01

    Droplet digital polymerase chain reaction (ddPCR) is a novel molecular biology technique providing absolute quantification of target nucleic acids without the need for an external calibrator. Despite its emerging applications in medical diagnosis, there are few reports of its use for the detection of plant pathogens. This work was designed to assess the diagnosis potential of the ddPCR for absolute quantitative detection of Xanthomonas citri subsp. citri, a quarantine plant pathogenic bacterium that causes citrus bacterial canker in susceptible Citrus species. We transferred an established quantitative PCR (qPCR) assay for citrus bacterial canker diagnosis directly to the ddPCR format and compared the performance of the two methods. The qPCR assay has a broader dynamic range compared to the ddPCR assay and the ddPCR assay has a significantly higher degree of sensitivity compared to the qPCR assay. The influence of PCR inhibitors can be reduced considerably in the ddPCR assay because the collection of end-point fluorescent signals and the counting of binomial events (positive or negative droplets) are associated with a Poisson algorithm. The ddPCR assay also shows lower coefficient of variation compared to the qPCR assay especially in low target concentration. The linear association of the measurements by ddPCR and qPCR assays is strong (Pearson correlation = 0.8633; P<0.001). Receiver operating characteristic analysis indicates the ddPCR methodology is a more robust approach for diagnosis of citrus bacterial canker. In summary, the results demonstrated that the ddPCR assay has the potential for the quantitative detection of X. citri subsp. citri with high precision and accuracy as compared with the results from qPCR assay. Further studies are required to evaluate and validate the value of ddPCR technology in the diagnosis of plant disease and quarantine applications. PMID:27427975

  8. Detecting distortion: bridging visual and quantitative reasoning on similarity tasks

    NASA Astrophysics Data System (ADS)

    Cox, Dana C.; Lo, Jane-Jane

    2014-03-01

    This study is focused on identifying and describing the reasoning patterns of middle grade students when examining potentially similar figures. Described here is a framework that includes 11 strategies that students used during clinical interview to differentiate similar and non-similar figures. Two factors were found to influence the strategies students selected: the complexity of the figures being compared and the type of distortion present in nonsimilar pairings. Data from this study support the theory that distortions are identified as a dominant property of figures and that students use the presence and absence of distortion to visually decide if two figures are similar. Furthermore, this study shows that visual reasoning is not as primitive or nonconstructive as represented in earlier literature and supports students who are developing numeric reasoning strategies. This illuminates possible pathways students may take when advancing from using visual and additive reasoning strategies to using multiplicative proportional reasoning on similarity tasks. In particular, distortion detection is a visual activity that enables students to reflect upon and evaluate the validity and accuracy of differentiation and quantify perceived relationships leading to ratio. This study has implications for curriculum developers as well as future research.

  9. Optical aptasensors for quantitative detection of small biomolecules: a review.

    PubMed

    Feng, Chunjing; Dai, Shuang; Wang, Lei

    2014-09-15

    Aptasensors are aptamer-based biosensors with excellent recognition capability towards a wide range of targets. Specially, there have been ever-growing interests in the development of aptasensors for the detection of small molecules. This phenomenon is contributed to two reasons. On one hand, small biomolecules play an important role in living organisms with many kinds of biological function, such as antiarrhythmic effect and vasodilator activity of adenosine. On the other hand, the concentration of small molecules can be an indicator for disease diagnosis, for example, the concentration of ATP is closely associated with cell injury and cell viability. As a potential analysis tool in the construction of aptasensors, optical analysis has attracted much more interest of researchers due to its high sensitivity, quick response and simple operation. Besides, it promises the promotion of aptasensors in performance toward a new level. Review the development of optical aptasensors for small biomolecules will give readers an overall understanding of its progress and provide some theoretical guidelines for its future development. Hence, we give a mini-review on the advance of optical aptasensors for small biomolecules. This review focuses on recent achievements in the design of various optical aptasensors for small biomolecules, containing fluorescence aptasensors, colorimetric aptasensors, chemiluminescence aptasensors and other optical aptasensors.

  10. The influence of scan mode and circle fitting on tree stem detection, stem diameter and volume extraction from terrestrial laser scans

    NASA Astrophysics Data System (ADS)

    Pueschel, Pyare; Newnham, Glenn; Rock, Gilles; Udelhoven, Thomas; Werner, Willy; Hill, Joachim

    2013-03-01

    Terrestrial laser scanning (TLS) has been used to estimate a number of biophysical and structural vegetation parameters. Of these stem diameter is a primary input to traditional forest inventory. While many experimental studies have confirmed the potential for TLS to successfully extract stem diameter, the estimation accuracies differ strongly for these studies - due to differences in experimental design, data processing and test plot characteristics. In order to provide consistency and maximize estimation accuracy, a systematic study into the impact of these variables is required. To contribute to such an approach, 12 scans were acquired with a FARO photon 120 at two test plots (Beech, Douglas fir) to assess the effects of scan mode and circle fitting on the extraction of stem diameter and volume. An automated tree stem detection algorithm based on the range images of single scans was developed and applied to the data. Extraction of stem diameter was achieved by slicing the point cloud and fitting circles to the slices using three different algorithms (Lemen, Pratt and Taubin), resulting in diameter profiles for each detected tree. Diameter at breast height (DBH) was determined using both the single value for the diameter fitted at the nominal breast height and by a linear fit of the stem diameter vertical profile. The latter is intended to reduce the influence of outliers and errors in the ground level determination. TLS-extracted DBH was compared to tape-measured DBH. Results show that tree stems with an unobstructed view to the scanner can be successfully extracted automatically from range images of the TLS data with detection rates of 94% for Beech and 96% for Douglas fir. If occlusion of trees is accounted for stem detection rates decrease to 85% (Beech) and 84% (Douglas fir). As far as the DBH estimation is concerned, both DBH extraction methods yield estimates which agree with reference measurements, however, the linear fit based approach proved to be more

  11. Effective Detection of Sub-Surface Archeological Features from Laser Scanning Point Clouds and Imagery Data

    NASA Astrophysics Data System (ADS)

    Fryskowska, A.; Kedzierski, M.; Walczykowski, P.; Wierzbicki, D.; Delis, P.; Lada, A.

    2017-08-01

    The archaeological heritage is non-renewable, and any invasive research or other actions leading to the intervention of mechanical or chemical into the ground lead to the destruction of the archaeological site in whole or in part. For this reason, modern archeology is looking for alternative methods of non-destructive and non-invasive methods of new objects identification. The concept of aerial archeology is relation between the presence of the archaeological site in the particular localization, and the phenomena that in the same place can be observed on the terrain surface form airborne platform. One of the most appreciated, moreover, extremely precise, methods of such measurements is airborne laser scanning. In research airborne laser scanning point cloud with a density of 5 points/sq. m was used. Additionally unmanned aerial vehicle imagery data was acquired. Test area is located in central Europe. The preliminary verification of potentially microstructures localization was the creation of digital terrain and surface models. These models gave an information about the differences in elevation, as well as regular shapes and sizes that can be related to the former settlement/sub-surface feature. The paper presents the results of the detection of potentially sub-surface microstructure fields in the forestry area.

  12. Elimination Voltammetry with Linear Scan as a New Detection Method for DNA Sensors

    PubMed Central

    Trnkova, Libuse; Jelen, Frantisek; Petrlova, Jitka; Adam, Vojtech; Potesil, David; Kizek, Rene

    2005-01-01

    The paper describes successful coupling of adsorptive transfer stripping (AdTS) and elimination voltammetry with linear scan (EVLS) for the resolution of reduction signals of cytosine (C) and adenine (A) residues in hetero-oligodeoxynucleotides (ODNs). Short ODNs (9-mers and 20-mers) were adsorbed from a small volume on a hanging mercury drop electrode (HMDE). After washing of the ODN-modified electrode by water and its transferring to an electrochemical cell, voltammetric curves were measured. The AdTS EVLS was able to determine of C/A ratio of ODNs through the elimination function conserving the diffusion current component and eliminating kinetic and charging current components. This function, which provides the elimination signal in a peak-counterpeak form, increased the current sensitivity for A and C resolution, and for the recognition of bases sequences in ODN chains. Optimal conditions of elimination experiments such as pH, time of adsorption, and scan rate were found. The combination of EVLS with AdTS procedure can be considered as a new detection method in a DNA sensor.

  13. Super-Resolution Scanning Laser Microscopy Based on Virtually Structured Detection.

    PubMed

    Zhi, Yanan; Wang, Benquan; Yao, Xincheng

    2015-01-01

    Light microscopy plays a key role in biological studies and medical diagnosis. The spatial resolution of conventional optical microscopes is limited to approximately half the wavelength of the illumination light as a result of the diffraction limit. Several approaches-including confocal microscopy, stimulated emission depletion microscopy, stochastic optical reconstruction microscopy, photoactivated localization microscopy, and structured illumination microscopy-have been established to achieve super-resolution imaging. However, none of these methods is suitable for the super-resolution ophthalmoscopy of retinal structures because of laser safety issues and inevitable eye movements. We recently experimentally validated virtually structured detection (VSD) as an alternative strategy to extend the diffraction limit. Without the complexity of structured illumination, VSD provides an easy, low-cost, and phase artifact-free strategy to achieve super-resolution in scanning laser microscopy. In this article we summarize the basic principles of the VSD method, review our demonstrated single-point and line-scan super-resolution systems, and discuss both technical challenges and the potential of VSD-based instrumentation for super-resolution ophthalmoscopy of the retina.

  14. Super-Resolution Scanning Laser Microscopy Based on Virtually Structured Detection

    PubMed Central

    Zhi, Yanan; Wang, Benquan; Yao, Xincheng

    2016-01-01

    Light microscopy plays a key role in biological studies and medical diagnosis. The spatial resolution of conventional optical microscopes is limited to approximately half the wavelength of the illumination light as a result of the diffraction limit. Several approaches—including confocal microscopy, stimulated emission depletion microscopy, stochastic optical reconstruction microscopy, photoactivated localization microscopy, and structured illumination microscopy—have been established to achieve super-resolution imaging. However, none of these methods is suitable for the super-resolution ophthalmoscopy of retinal structures because of laser safety issues and inevitable eye movements. We recently experimentally validated virtually structured detection (VSD) as an alternative strategy to extend the diffraction limit. Without the complexity of structured illumination, VSD provides an easy, low-cost, and phase artifact–free strategy to achieve super-resolution in scanning laser microscopy. In this article we summarize the basic principles of the VSD method, review our demonstrated single-point and line-scan super-resolution systems, and discuss both technical challenges and the potential of VSD-based instrumentation for super-resolution ophthalmoscopy of the retina. PMID:27480461

  15. Detection of redshifted HI from the Epoch of Reionization using drift scans

    NASA Astrophysics Data System (ADS)

    Paul, S.; Patwa, A. K.; Sethi, S.; Dwarakanath, K. S.

    2016-07-01

    The detection of redshifted HI from the Epoch of Reionization (EoR) is one of the outstanding aims of modern day observational cosmology. Like many other radio interferometers, EoR research is one of the major science goals of MWA. We, at RRI have been involved in EoR research from past few years. We have successfully developed an independent pipeline to extract the delay power spectra from MWA tracking observation. We, simultaneously have been progressing towards the set up of another pipeline to obtain the power spectra from drift scan observation. We seek, based on our existing endeavors, 30 hours of drift scan data from MWA observing time 2016B. Our aims are to attain both 2d (k_perp,k_parallel) & 1d (k) power spectra, also to study various foreground removal and noise reduction strategies. The new 'hex configuration' of MWA would be a favorable feature for this effort, owing to many short spacing & redundant baselines, which are essential requirements for EoR science.

  16. Hyperspectral imaging fluorescence excitation scanning for detecting colorectal cancer: pilot study

    NASA Astrophysics Data System (ADS)

    Leavesley, Silas J.; Wheeler, Mikayla; Lopez, Carmen; Baker, Thomas; Favreau, Peter F.; Rich, Thomas C.; Rider, Paul F.; Boudreaux, Carole W.

    2016-03-01

    Optical spectroscopy and hyperspectral imaging have shown the theoretical potential to discriminate between cancerous and non-cancerous tissue with high sensitivity and specificity. To date, these techniques have not been able to be effectively translated to endoscope platforms. Hyperspectral imaging of the fluorescence excitation spectrum represents a new technology that may be well-suited for endoscopic implementation. However, the feasibility of detecting differences between normal and cancerous mucosa using fluorescence excitation-scanning hyperspectral imaging has not been evaluated. The objective of this pilot study was to evaluate the changes in the fluorescence excitation spectrum of resected specimen pairs of colorectal adenocarcinoma and normal colorectal mucosa. Patients being treated for colorectal adenocarcinoma were enrolled. Representative adenocarcinoma and normal colonic mucosa specimens were collected from each case. Specimens were flash frozen in liquid nitrogen. Adenocarcinoma was confirmed by histologic evaluation of H&E permanent sections. Hyperspectral image data of the fluorescence excitation of adenocarcinoma and surrounding normal tissue were acquired using a custom microscope configuration previously developed in our lab. Results demonstrated consistent spectral differences between normal and cancerous tissues over the fluorescence excitation spectral range of 390-450 nm. We conclude that fluorescence excitation-scanning hyperspectral imaging may offer an alternative approach for differentiating adenocarcinoma and surrounding normal mucosa of the colon. Future work will focus on expanding the number of specimen pairs analyzed and will utilize fresh tissues where possible, as flash freezing and reconstituting tissues may have altered the autofluorescence properties.

  17. Targeted detection of murine colonic dysplasia in vivo with flexible multispectral scanning fiber endoscopy

    NASA Astrophysics Data System (ADS)

    Miller, Sharon J.; Lee, Cameron M.; Joshi, Bishnu P.; Gaustad, Adam; Seibel, Eric J.; Wang, Thomas D.

    2012-02-01

    Gastrointestinal cancers are heterogeneous and can overexpress several protein targets that can be imaged simultaneously on endoscopy using multiple molecular probes. We aim to demonstrate a multispectral scanning fiber endoscope for wide-field fluorescence detection of colonic dysplasia. Excitation at 440, 532, and 635 nm is delivered into a single spiral scanning fiber, and fluorescence is collected by a ring of light-collecting optical fibers placed around the instrument periphery. Specific-binding peptides are selected with phage display technology using the CPC;Apc mouse model of spontaneous colonic dysplasia. Validation of peptide specificity is performed on flow cytometry and in vivo endoscopy. The peptides KCCFPAQ, AKPGYLS, and LTTHYKL are selected and labeled with 7-diethylaminocoumarin-3-carboxylic acid (DEAC), 5-carboxytetramethylrhodamine (TAMRA), and CF633, respectively. Separate droplets of KCCFPAQ-DEAC, AKPGYLS-TAMRA, and LTTHYKL-CF633 are distinguished at concentrations of 100 and 1 μM. Separate application of the fluorescent-labeled peptides demonstrate specific binding to colonic adenomas. The average target/background ratios are 1.71+/-0.19 and 1.67+/-0.12 for KCCFPAQ-DEAC and AKPGYLS-TAMRA, respectively. Administration of these two peptides together results in distinct binding patterns in the blue and green channels. Specific binding of two or more peptides can be distinguished in vivo using a novel multispectral endoscope to localize colonic dysplasia on real-time wide-field imaging.

  18. Label-free detection of nucleic acid and protein microarrays by scanning Kelvin nanoprobe.

    PubMed

    Thompson, Michael; Cheran, Larisa-Emilia; Zhang, Mingquan; Chacko, Melissa; Huo, Hong; Sadeghi, Saman

    2005-02-15

    A high-resolution scanning Kelvin nanoprobe is introduced as an alternative technique to the conventional fluorescence and mass spectrometric detection methods currently employed in nucleic acid and protein microarray technology. The new instrument is capable of the highly sensitive discernment of surface biochemical events taking place at molecular level such as nucleic acid hybridization and antibody-antigen interaction. The method involves measurement of changes in work function and surface potential instigated by such interactions. Being a label-free and non-contact technique, the structure, spatial configuration, local properties or function of the molecular system under study are not affected, nor perturbed by intercalating dyes, a strong electric field or ionizing beam. Subsequent to scanning, the microarray can be examined by other alternative approaches. Nucleic acids and proteins have been printed in microarray format on slides with a gold film in place using gold-sulphur interactive chemistry. Hybridization of nucleic acids for complementary and mismatched configurations shows consistent and reproducible values of work function. Differentiation of single internal mismatches is demonstrated. Protein concentration and formation of antibody-antigen pairs can be visualized and examined with high sensitivity and good inter-spot reproducibility.

  19. Detection of a magnetic bead by hybrid nanodevices using scanning gate microscopy

    NASA Astrophysics Data System (ADS)

    Corte-León, H.; Krzysteczko, P.; Marchi, F.; Motte, J.-F.; Manzin, A.; Schumacher, H. W.; Antonov, V.; Kazakova, O.

    2016-05-01

    Hybrid ferromagnetic(Py)/non-magnetic metal(Au) junctions with a width of 400 nm are studied by magnetotransport measurements, magnetic scanning gate microscopy (SGM) with a magnetic bead (MB) attached to the probe, and micromagnetic simulations. In the transverse geometry, the devices demonstrate a characteristic magnetoresistive behavior that depends on the direction of the in plane magnetic field, with minimum/maximum variation when the field is applied parallel/perpendicular to the Py wire. The SGM is performed with a NdFeB bead of 1.6 μm diameter attached to the scanning probe. Our results demonstrate that the hybrid junction can be used to detect this type of MB. A rough approximation of the sensing volume of the junction has the shape of elliptical cylinder with the volume of ˜1.51 μm3. Micromagnetic simulations coupled to a magnetotransport model including anisotropic magnetoresistance and planar Hall effects are in good agreement with the experimental findings, enabling the interpretation of the SGM images.

  20. Geometry and intensity based culvert detection in mobile laser scanning point clouds

    NASA Astrophysics Data System (ADS)

    Lin, Yi; Hyyppa, Juha

    2010-11-01

    Mobile laser scanning (MLS), which recently has been developing so quickly as a promising technology for mapping and remote sensing (RS), offers a good means to measure the fundamental geographic data, e.g. culverts, for urban planning and road engineering. This study as the first try presents a new automatic method to detect culverts in MLS point clouds, in which actually only partial characterization of this category of objects can be presented due to the restricted scanning zenith of MLS. The schematic is based on the raster-form of the data, and the digital terrain models (DTMs) with multi-leveled resolutions are first yielded by local minimum filtering. Then, the common layout of the expanded areas containing culverts is generalized as the theoretical basis, and the schematic components are derived to deploy the concrete judgment. The geometry and intensity information about culverts are both utilized to determine the real locations from coarse- to fine-scales. Numerical analysis based on the real-measured MLS data at the Espoonlahti test site has basically validated the proposed approach. Concretely, the statistical errors of the retrieved lengths and widths of the pedestrian culverts are less than 9% and 16% compared to the real ones individually, notwithstanding the inner heights innately in-accessible.

  1. Streamed Vertical Rectangle Detection in Terrestrial Laser Scans for Facade Database Production

    NASA Astrophysics Data System (ADS)

    Demantké, J.; Vallet, B.; Paparoditis, N.

    2012-07-01

    A reliable and accurate facade database would be a major asset in applications such as localization of autonomous vehicles, registration and fine building modeling. Mobile mapping devices now provide the data required to create such a database, but efficient methods should be designed in order to tackle the enormous amount of data collected by such means (a million point per second for hours of acquisition). Another important limitation is the presence of numerous objects in urban scenes of many different types. This paper proposes a method that overcomes these two issues: - The facade detection algorithm is streamed: the data is processed in the order it was acquired. More precisely, the input data is split into overlapping blocks which are analysed in turn to extract facade parts. Close overlapping parts are then merged in order to recover the full facade rectangle. - The geometry of the neighborhood of each point is analysed to define a probability that the point belongs to a vertical planar patch. This probability is then injected in a RANdom SAmple Consensus (RANSAC) algorithm both in the sampling step and in the hypothesis validation, in order to favour the most reliable candidates. This ensures much more robustness against outliers during the facade detection. This way, the main vertical rectangles are detected without any prior knowledge about the data. The only assumptions are that the facades are roughly planar and vertical. The method has been successfully tested on a large dataset in Paris. The facades are detected despite the presence of trees occluding large areas of some facades. The robustness and accuracy of the detected facade rectangles makes them useful for localization applications and for registration of other scans of the same city or of entire city models.

  2. Targeted detection of murine colonic dysplasia in vivo with flexible multispectral scanning fiber endoscopy

    NASA Astrophysics Data System (ADS)

    Joshi, Bishnu P.; Miller, Sharon J.; Lee, Cameron; Gustad, Adam; Seibel, Eric J.; Wang, Thomas D.

    2012-02-01

    We demonstrate a multi-spectral scanning fiber endoscope (SFE) that collects fluorescence images in vivo from three target peptides that bind specifically to murine colonic adenomas. This ultrathin endoscope was demonstrated in a genetically engineered mouse model of spontaneous colorectal adenomas based on somatic Apc (adenomatous polyposis coli) gene inactivation. The SFE delivers excitation at 440, 532, 635 nm with <2 mW per channel. The target 7-mer peptides were conjugated to visible organic dyes, including 7-Diethylaminocoumarin-3-carboxylic acid (DEAC) (λex=432 nm, λem=472 nm), 5-Carboxytetramethylrhodamine (5-TAMRA) (λex=535 nm, λem=568 nm), and CF-633 (λex=633 nm, λem=650 nm). Target peptides were first validated using techniques of pfu counting, flow cytometry and previously established methods of fluorescence endoscopy. Peptides were applied individually or in combination and detected with fluorescence imaging. The ability to image multiple channels of fluorescence concurrently was successful for all three channels in vitro, while two channels were resolved simultaneously in vivo. Selective binding of the peptide was evident to adenomas and not to adjacent normal-appearing mucosa. Multispectral wide-field fluorescence detection using the SFE is achievable, and this technology has potential to advance early cancer detection and image-guided therapy in human patients by simultaneously visualizing multiple over expressed molecular targets unique to dysplasia.

  3. Improved eye-fixation detection using polarization-modulated retinal birefringence scanning, immune to corneal birefringence.

    PubMed

    Irsch, Kristina; Gramatikov, Boris I; Wu, Yi-Kai; Guyton, David L

    2014-04-07

    We present an improved method for remote eye-fixation detection, using a polarization-modulated approach to retinal birefringence scanning (RBS), without the need for individual calibration or separate background measurements and essentially independent of corneal birefringence. Polarization-modulated RBS detects polarization changes generated in modulated polarized light passing through a unique pattern of nerve fibers identifying and defining the retinal region where fixation occurs (the fovea). A proof-of-concept demonstration in human eyes suggests that polarization-modulated RBS has the potential to reliably detect true foveal fixation on a specified point with an accuracy of at least ± 0.75°, and that it can be applied to the general population, including individuals with sub-optimal eyes and young children, where early diagnosis of visual problems can be critical. As could be employed in an eye-controlled display or in other devices, polarization-modulated RBS also enables and paves the way for new and reliable eye-fixation-evoked human-machine interfaces.

  4. Quantitative evaluation of ultrasonic C-scan image in acoustically homogeneous and layered anisotropic materials using three dimensional ray tracing method.

    PubMed

    Kolkoori, Sanjeevareddy; Hoehne, Christian; Prager, Jens; Rethmeier, Michael; Kreutzbruck, Marc

    2014-02-01

    Quantitative evaluation of ultrasonic C-scan images in homogeneous and layered anisotropic austenitic materials is of general importance for understanding the influence of anisotropy on wave fields during ultrasonic non-destructive testing and evaluation of these materials. In this contribution, a three dimensional ray tracing method is presented for evaluating ultrasonic C-scan images quantitatively in general homogeneous and layered anisotropic austenitic materials. The directivity of the ultrasonic ray source in general homogeneous columnar grained anisotropic austenitic steel material (including layback orientation) is obtained in three dimensions based on Lamb's reciprocity theorem. As a prerequisite for ray tracing model, the problem of ultrasonic ray energy reflection and transmission coefficients at an interface between (a) isotropic base material and anisotropic austenitic weld material (including layback orientation), (b) two adjacent anisotropic weld metals and (c) anisotropic weld metal and isotropic base material is solved in three dimensions. The influence of columnar grain orientation and layback orientation on ultrasonic C-scan image is quantitatively analyzed in the context of ultrasonic testing of homogeneous and layered austenitic steel materials. The presented quantitative results provide valuable information during ultrasonic characterization of homogeneous and layered anisotropic austenitic steel materials. Copyright © 2013 Elsevier B.V. All rights reserved.

  5. Detection and quantitation of Agrotis baculoviruses in mixed infections.

    PubMed

    Wennmann, Jörg T; Jehle, Johannes A

    2014-03-01

    At least four distinct baculoviruses, namely the Agrotis segetum nucleopolyhedrovirus A (AgseNPV-A), the A. segetum nucleopolyhedrovirus B (AgseNPV-B), the Agrotis ipsilon nucleopolyhedrovirus (AgipNPV) and the A. segetum granulovirus (AgseGV) have been isolated from larval stages (cutworms) of the species A. segetum and A. ipsilon (Lepidoptera: Noctuidae), which are serious soil pests in agriculture. Cutworms can become infected by at least one of these four baculoviruses and also co-infections of A. segetum larvae with AgseNPV-B and AgseGV are observed under laboratory conditions. Because of their adaption to common hosts and the occurrence in mixed infections, these viruses have a considerable potential as biological control agents of cutworms and are suitable objects to decipher the co-evolution and population dynamics of baculoviruses in mixed infections. However, to facilitate studies on these viruses a reliable tool for detection and identification is essential. A method based on highly specific oligonucleotide primers for multiplex polymerase chain reaction (PCR) that led to the amplification of discriminating fragments of the polyhedrin (polh) and granulin (gran) gene of AgseNPV-A, AgseNPV-B, AgipNPV and AgseGV, was established. Furthermore, the AgseNPV-B and AgseGV specific pairs of primers were applied in real-time PCR (qPCR) for AgseNPV-B/AgseGV ratio determination in samples of mixed infections. It is demonstrated further that for quantifying NPVs and GVs in mixed infections, the method of occlusion body isolation is most crucial and significantly influences the results. Copyright © 2013 Elsevier B.V. All rights reserved.

  6. EN FACE VERSUS 12-LINE RADIAL OPTICAL COHERENCE TOMOGRAPHY SCAN PATTERNS FOR DETECTION OF MACULAR FLUID IN NEOVASCULAR AGE-RELATED MACULAR DEGENERATION.

    PubMed

    Adam, Murtaza K; Shahlaee, Abtin; Samara, Wasim A; Maguire, Joseph I; Ho, Allen C; Hsu, Jason

    2017-08-14

    To compare fluid detection of autosegmented en face to 12-line radial spectral domain optical coherence tomography scan patterns in neovascular age-related macular degeneration. Retrospective observational case series. Sixty-seven patients (94 eyes) with neovascular age-related macular degeneration underwent autosegmented en face optical coherence tomography (with associated 304-line raster scan) and 12-line radial scan patterns. Sensitivity and specificity of fluid detection for en face scan and 12-line radial scans were determined by combining radial and 304-line raster scans as a gold standard. Two hundred and fifty-eight en face and 12-line radial spectral domain optical coherence tomography scans were interpreted. Seventy-five scans (58.1%) had fluid, whereas 54 scans (41.9%) did not. En face scan pattern fluid detection sensitivity and specificity was 89.3% and 61.1%, respectively. Twelve-line radial scan pattern fluid detection sensitivity and specificity was 97.3% and 100%, respectively. The difference in fluid detection between scan patterns was statistically significant (P = 0.01). Decreased central macular thickness was associated with false-positive (P = 0.035) and false-negative (P = 0.01) fluid detection on en face scans. En face optical coherence tomography alone is not as sensitive or specific as the 12-line radial scan pattern in detecting fluid in neovascular age-related macular degeneration. En face scans should be corroborated with other optical coherence tomography protocols to guide clinical decision making.

  7. Detecting degradation in Ni-based superalloy Udimet520 with scanning SQUID microscopy

    NASA Astrophysics Data System (ADS)

    Isawa, K.; Igarashi, Y.; Hayashi, M.; Sato, F.; Ogota, S.; Hasegawa, S.; Miyaguchi, K.

    2010-11-01

    In order to develop a new method for detecting degradation nondestructively in Udimet520 (U520), which is used for blades of aircraft jet-engine components and land-based gas turbines, fractured and interrupted samples in low-cycle fatigue (LCF) and creep tests were studied using scanning SQUID microscopy (SSM). High temperature LCF and creep experiments on U520 were conducted to obtain various samples with different damage level. Simultaneously, we also examined the artificially degraded samples by optical microscopy, electron backscattering diffraction, and hardness measurements to ensure the damage level. On the basis of the magnetic permeability data, the virgin sample is nonmagnetic. However, for the artificially damaged samples, the observation of magnetic signals on the field maps indicates the potential of SSM to evaluate the degradation in U520 superalloy nondestructively.

  8. Detecting Distributed Scans Using High-Performance Query-DrivenVisualization

    SciTech Connect

    Stockinger, Kurt; Bethel, E. Wes; Campbell, Scott; Dart, Eli; Wu,Kesheng

    2006-09-01

    Modern forensic analytics applications, like network trafficanalysis, perform high-performance hypothesis testing, knowledgediscovery and data mining on very large datasets. One essential strategyto reduce the time required for these operations is to select only themost relevant data records for a given computation. In this paper, wepresent a set of parallel algorithms that demonstrate how an efficientselection mechanism -- bitmap indexing -- significantly speeds up acommon analysist ask, namely, computing conditional histogram on verylarge datasets. We present a thorough study of the performancecharacteristics of the parallel conditional histogram algorithms. Asacase study, we compute conditional histograms for detecting distributedscans hidden in a dataset consisting of approximately 2.5 billion networkconnection records. We show that these conditional histograms can becomputed on interactive timescale (i.e., in seconds). We also show how toprogressively modify the selection criteria to narrow the analysis andfind the sources of the distributed scans.

  9. Development and Evaluation of Roadside/Obstacle Detection Method Using 3D Scanned Data Processing

    NASA Astrophysics Data System (ADS)

    Yamamoto, Hiroshi; Ishii, Yoshinori; Yamazaki, Katsuyuki

    In this paper, we have reported the development of a snowblower support system which can safely navigate snowblowers, even during a whiteout, with the combination of a very accurate GPS system, so called RTK-GPS, and a unique and highly accurate map of roadsides and obstacles on roads. Particularly emphasized new techniques in this paper are ways to detect accurate geographical positions of roadsides and obstacles by utilizing and analyzing 3D laser scanned data, whose data has become available in recent days. The experiment has shown that the map created by the methods and RTK-GPS can sufficiently navigate snowblowers, whereby a secure and pleasant social environment can be archived in snow areas of Japan. In addition, proposed methods are expected to be useful for other systems such as a quick development of a highly accurate road map, a safely navigation of a wheeled chair, and so on.

  10. Spectral imaging technique for retinal perfusion detection using confocal scanning laser ophthalmoscopy

    NASA Astrophysics Data System (ADS)

    Rasta, Seyed Hossein; Manivannan, Ayyakkannu; Sharp, Peter F.

    2012-11-01

    To evaluate retinal perfusion in the human eye, a dual-wavelength confocal scanning laser ophthalmoscope (cSLO) was developed that provides spectral imaging of the fundus using a combination of red (670 nm) and near-infrared (810 nm) wavelengths. The image of the ocular fundus was analyzed to find out if quantitative measurements of the reflectivity of tissue permit assessment of the oxygen perfusion of tissue. We explored problems that affect the reproducibility of patient measurements such as non-uniformity errors on the image. For the first time, an image processing technique was designed and used to minimize the errors of oxygen saturation measurements by illumination correction in retina wide field by increasing SNR. Retinal images were taken from healthy and diabetic retinopathy eyes using the cSLO with a confocal aperture of 100 μm. The ratio image (RI) of red/IR, as oxygen saturation (SO2) index, was calculated for normal eyes. The image correction technique improved the reproducibility of the measurements. Average RI intensity variation of healthy retina tissue was determined within a range of about 5.5%. The capability of the new technique to discriminate oxygenation levels of retinal artery and vein was successfully demonstrated and showed good promise in the diagnosis of the perfused retina.

  11. Spectral imaging technique for retinal perfusion detection using confocal scanning laser ophthalmoscopy.

    PubMed

    Rasta, Seyed Hossein; Manivannan, Ayyakkannu; Sharp, Peter F

    2012-11-01

    To evaluate retinal perfusion in the human eye, a dual-wavelength confocal scanning laser ophthalmoscope (cSLO) was developed that provides spectral imaging of the fundus using a combination of red (670 nm) and near-infrared (810 nm) wavelengths. The image of the ocular fundus was analyzed to find out if quantitative measurements of the reflectivity of tissue permit assessment of the oxygen perfusion of tissue. We explored problems that affect the reproducibility of patient measurements such as non-uniformity errors on the image. For the first time, an image processing technique was designed and used to minimize the errors of oxygen saturation measurements by illumination correction in retina wide field by increasing SNR. Retinal images were taken from healthy and diabetic retinopathy eyes using the cSLO with a confocal aperture of 100 μm. The ratio image (RI) of red/IR, as oxygen saturation (SO2) index, was calculated for normal eyes. The image correction technique improved the reproducibility of the measurements. Average RI intensity variation of healthy retina tissue was determined within a range of about 5.5%. The capability of the new technique to discriminate oxygenation levels of retinal artery and vein was successfully demonstrated and showed good promise in the diagnosis of the perfused retina.

  12. Quantitative surface acoustic wave detection based on colloidal gold nanoparticles and their bioconjugates.

    PubMed

    Chiu, Chi-Shun; Gwo, Shangjr

    2008-05-01

    The immobilization scheme of monodispersed gold nanoparticles (10-nm diameter) on piezoelectric substrate surfaces using organosilane molecules as cross-linkers has been developed for lithium niobate (LiNbO3) and silicon oxide (SiO2)/gold-covered lithium tantalate (LiTaO3) of Rayleigh and guided shear horizontal- (guided SH) surface acoustic wave (SAW) sensors. In this study, comparative measurements of gold nanoparticle adsorption kinetics using high-resolution field-emission scanning electron microscopy and SAW sensors allow the frequency responses of SAW sensors to be quantitatively correlated with surface densities of adsorbed nanoparticles. Using this approach, gold nanoparticles are used as the "nanosized mass standards" to scale the mass loading in a wide dynamical range. Rayleigh-SAW and guided SH-SAW sensors are employed here to monitor the surface mass changes on the device surfaces in gas and liquid phases, respectively. The mass sensitivity ( approximately 20 Hz.cm2/ng) of Rayleigh-SAW device (fundamental oscillation frequency of 113.3 MHz in air) is more than 2 orders of magnitude higher than that of conventional 9-MHz quartz crystal microbalance sensors. Furthermore, in situ (aqueous solutions), real-time measurements of adsorption kinetics for both citrate-stabilized gold nanoparticles and DNA-gold nanoparticle conjugates are also demonstrated by guided SH-SAW (fundamental oscillation frequency of 121.3 MHz). By comparing frequency shifts between the adsorption cases of gold nanoparticles and DNA-gold nanoparticle conjugates, the average number of bound oligonucleotides per gold nanoparticle can also be determined. The high mass sensitivity ( approximately 6 Hz.cm2/ng) of guided SH-SAW sensors and successful detection of DNA-gold nanoparticle conjugates paves the way for real-time biosensing in liquids using nanoparticle-enhanced SAW devices.

  13. Correction of inter-scan motion artifacts in quantitative R1 mapping by accounting for receive coil sensitivity effects.

    PubMed

    Papp, Daniel; Callaghan, Martina F; Meyer, Heiko; Buckley, Craig; Weiskopf, Nikolaus

    2016-11-01

    Inter-scan motion causes differential receive field modulation between scans, leading to errors when they are combined to quantify MRI parameters. We present a robust and efficient method that accounts for inter-scan motion by removing this modulation before parameter quantification. Five participants moved between two high-resolution structural scans acquired with different flip angles. Before each high-resolution scan, the effective relative sensitivity of the receive head coil was estimated by combining two rapid low-resolution scans acquired receiving on each of the body and head coils. All data were co-registered and sensitivity variations were removed from the high-resolution scans by division with the effective relative sensitivity. R1 maps with and without this correction were calculated and compared against reference maps unaffected by inter-scan motion. Even after coregistration, inter-scan motion significantly biased the R1 maps, leading to spurious variation in R1 in brain tissue and deviations with respect to a no-motion reference. The proposed correction scheme reduced the error to within the typical scan-rescan error observed in datasets unaffected by motion. Inter-scan motion negatively impacts the accuracy and precision of R1 mapping. We present a validated correction method that accounts for position-specific receive field modulation. Magn Reson Med 76:1478-1485, 2016. © 2015 The Authors. Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © The Authors. Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine.

  14. 3D change detection at street level using mobile laser scanning point clouds and terrestrial images

    NASA Astrophysics Data System (ADS)

    Qin, Rongjun; Gruen, Armin

    2014-04-01

    Automatic change detection and geo-database updating in the urban environment are difficult tasks. There has been much research on detecting changes with satellite and aerial images, but studies have rarely been performed at the street level, which is complex in its 3D geometry. Contemporary geo-databases include 3D street-level objects, which demand frequent data updating. Terrestrial images provides rich texture information for change detection, but the change detection with terrestrial images from different epochs sometimes faces problems with illumination changes, perspective distortions and unreliable 3D geometry caused by the lack of performance of automatic image matchers, while mobile laser scanning (MLS) data acquired from different epochs provides accurate 3D geometry for change detection, but is very expensive for periodical acquisition. This paper proposes a new method for change detection at street level by using combination of MLS point clouds and terrestrial images: the accurate but expensive MLS data acquired from an early epoch serves as the reference, and terrestrial images or photogrammetric images captured from an image-based mobile mapping system (MMS) at a later epoch are used to detect the geometrical changes between different epochs. The method will automatically mark the possible changes in each view, which provides a cost-efficient method for frequent data updating. The methodology is divided into several steps. In the first step, the point clouds are recorded by the MLS system and processed, with data cleaned and classified by semi-automatic means. In the second step, terrestrial images or mobile mapping images at a later epoch are taken and registered to the point cloud, and then point clouds are projected on each image by a weighted window based z-buffering method for view dependent 2D triangulation. In the next step, stereo pairs of the terrestrial images are rectified and re-projected between each other to check the geometrical

  15. Combining Frequency Doubling Technology Perimetry and Scanning Laser Polarimetry for Glaucoma Detection.

    PubMed

    Mwanza, Jean-Claude; Warren, Joshua L; Hochberg, Jessica T; Budenz, Donald L; Chang, Robert T; Ramulu, Pradeep Y

    2015-01-01

    To determine the ability of frequency doubling technology (FDT) and scanning laser polarimetry with variable corneal compensation (GDx-VCC) to detect glaucoma when used individually and in combination. One hundred ten normal and 114 glaucomatous subjects were tested with FDT C-20-5 screening protocol and the GDx-VCC. The discriminating ability was tested for each device individually and for both devices combined using GDx-NFI, GDx-TSNIT, number of missed points of FDT, and normal or abnormal FDT. Measures of discrimination included sensitivity, specificity, area under the curve (AUC), Akaike's information criterion (AIC), and prediction confidence interval lengths. For detecting glaucoma regardless of severity, the multivariable model resulting from the combination of GDx-TSNIT, number of abnormal points on FDT (NAP-FDT), and the interaction GDx-TSNIT×NAP-FDT (AIC: 88.28, AUC: 0.959, sensitivity: 94.6%, specificity: 89.5%) outperformed the best single-variable model provided by GDx-NFI (AIC: 120.88, AUC: 0.914, sensitivity: 87.8%, specificity: 84.2%). The multivariable model combining GDx-TSNIT, NAP-FDT, and interaction GDx-TSNIT×NAP-FDT consistently provided better discriminating abilities for detecting early, moderate, and severe glaucoma than the best single-variable models. The multivariable model including GDx-TSNIT, NAP-FDT, and the interaction GDx-TSNIT×NAP-FDT provides the best glaucoma prediction compared with all other multivariable and univariable models. Combining the FDT C-20-5 screening protocol and GDx-VCC improves glaucoma detection compared with using GDx or FDT alone.

  16. Combining Frequency Doubling Technology Perimetry and Scanning Laser Polarimetry for Glaucoma Detection

    PubMed Central

    Mwanza, Jean-Claude; Warren, Joshua L.; Hochberg, Jessica T.; Budenz, Donald L.; Chang, Robert T.; Ramulu, Pradeep Y.

    2014-01-01

    Purpose To determine the ability of frequency doubling technology (FDT) and scanning laser polarimetry with variable corneal compensation (GDx-VCC) to detect glaucoma when used individually and in combination. Methods One hundred and ten normal and 114 glaucomatous subjects were tested with FDT C-20-5 screening protocol and the GDx-VCC. The discriminating ability was tested for each device individually and for both devices combined using GDx-NFI, GDx-TSNIT, number of missed points of FDT, and normal or abnormal FDT. Measures of discrimination included sensitivity, specificity, area under the curve (AUC), Akaike’s information criterion (AIC), and prediction confidence interval lengths (PIL). Results For detecting glaucoma regardless of severity, the multivariable model resulting from the combination of GDX-TSNIT, number of abnormal points on FDT (NAP-FDT), and the interaction GDx-TSNIT * NAP-FDT (AIC: 88.28, AUC: 0.959, sensitivity: 94.6%, specificity: 89.5%) outperformed the best single variable model provided by GDx-NFI (AIC: 120.88, AUC: 0.914, sensitivity: 87.8%, specificity: 84.2%). The multivariable model combining GDx-TSNIT, NAPFDT, and interaction GDx-TSNIT*NAP-FDT consistently provided better discriminating abilities for detecting early, moderate and severe glaucoma than the best single variable models. Conclusions The multivariable model including GDx-TSNIT, NAP-FDT, and the interaction GDX-TSNIT * NAP-FDT provides the best glaucoma prediction compared to all other multivariable and univariable models. Combining the FDT C-20-5 screening protocol and GDx-VCC improves glaucoma detection compared to using GDx or FDT alone. PMID:24777046

  17. Imaging and quantitative data acquisition of biological cell walls with Atomic Force Microscopy and Scanning Acoustic Microscopy

    SciTech Connect

    Tittmann, B. R.; Xi, X.

    2014-09-01

    This chapter demonstrates the feasibility of Atomic Force Microscopy (AFM) and High Frequency Scanning Acoustic Microscopy (HF-SAM) as tools to characterize biological tissues. Both the AFM and the SAM have shown to provide imaging (with different resolution) and quantitative elasticity measuring abilities. Plant cell walls with minimal disturbance and under conditions of their native state have been examined with these two kinds of microscopy. After descriptions of both the SAM and AFM, their special features and the typical sample preparation is discussed. The sample preparation is focused here on epidermal peels of onion scales and celery epidermis cells which were sectioned for the AFM to visualize the inner surface (closest to the plasma membrane) of the outer epidermal wall. The nm-wide cellulose microfibrils orientation and multilayer structure were clearly observed. The microfibril orientation and alignment tend to be more organized in older scales compared with younger scales. The onion epidermis cell wall was also used as a test analog to study cell wall elasticity by the AFM nanoindentation and the SAM V(z) feature. The novelty in this work was to demonstrate the capability of these two techniques to analyze isolated, single layered plant cell walls in their natural state. AFM nanoindentation was also used to probe the effects of Ethylenediaminetetraacetic acid (EDTA), and calcium ion treatment to modify pectin networks in cell walls. The results suggest a significant modulus increase in the calcium ion treatment and a slight decrease in EDTA treatment. To complement the AFM measurements, the HF-SAM was used to obtain the V(z) signatures of the onion epidermis. These measurements were focused on documenting the effect of pectinase enzyme treatment. The results indicate a significant change in the V(z) signature curves with time into the enzyme treatment. Thus AFM and HF-SAM open the door to a systematic nondestructive structure and mechanical property

  18. Trimodal detection of early childhood caries using laser light scanning and fluorescence spectroscopy: clinical prototype

    PubMed Central

    Kim, Amy S.; Ridge, Jeremy S.; Nelson, Leonard Y.; Berg, Joel H.; Seibel, Eric J.

    2013-01-01

    Abstract. There is currently a need for a safe and effective way to detect and diagnose early stages of childhood caries. A multimodal optical clinical prototype for diagnosing caries demineralization in vivo has been developed. The device can be used to quickly image and screen for any signs of demineralized enamel by obtaining high-resolution and high-contrast surface images using a 405-nm laser as the illumination source, as well as obtaining autofluorescence and bacterial fluorescence images. When a suspicious region of demineralization is located, the device also performs dual laser fluorescence spectroscopy using 405- and 532-nm laser excitation. An autofluorescence ratio of the two excitation lasers is computed and used to quantitatively diagnose enamel health. The device was tested on five patients in vivo as well as on 28 extracted teeth with clinically diagnosed carious lesions. The device was able to provide detailed images that highlighted the lesions identified by the clinicians. The autofluorescence spectroscopic ratios obtained from the extracted teeth successfully quantitatively discriminated between sound and demineralized enamel. PMID:23986369

  19. Quantitative proteomics: assessing the spectrum of in-gel protein detection methods

    PubMed Central

    Gauci, Victoria J.; Wright, Elise P.

    2010-01-01

    Proteomics research relies heavily on visualization methods for detection of proteins separated by polyacrylamide gel electrophoresis. Commonly used staining approaches involve colorimetric dyes such as Coomassie Brilliant Blue, fluorescent dyes including Sypro Ruby, newly developed reactive fluorophores, as well as a plethora of others. The most desired characteristic in selecting one stain over another is sensitivity, but this is far from the only important parameter. This review evaluates protein detection methods in terms of their quantitative attributes, including limit of detection (i.e., sensitivity), linear dynamic range, inter-protein variability, capacity for spot detection after 2D gel electrophoresis, and compatibility with subsequent mass spectrometric analyses. Unfortunately, many of these quantitative criteria are not routinely or consistently addressed by most of the studies published to date. We would urge more rigorous routine characterization of stains and detection methodologies as a critical approach to systematically improving these critically important tools for quantitative proteomics. In addition, substantial improvements in detection technology, particularly over the last decade or so, emphasize the need to consider renewed characterization of existing stains; the quantitative stains we need, or at least the chemistries required for their future development, may well already exist. PMID:21686332

  20. Application of quantitative signal detection in the Dutch spontaneous reporting system for adverse drug reactions.

    PubMed

    van Puijenbroek, Eugène; Diemont, Willem; van Grootheest, Kees

    2003-01-01

    The primary aim of spontaneous reporting systems (SRSs) is the timely detection of unknown adverse drug reactions (ADRs), or signal detection. Generally this is carried out by a systematic manual review of every report sent to an SRS. Statistical analysis of the data sets of an SRS, or quantitative signal detection, can provide additional information concerning a possible relationship between a drug and an ADR. We describe the role of quantitative signal detection and the way it is applied at the Netherlands Pharmacovigilance Centre Lareb. Results of the statistical analysis are implemented in the traditional case-by-case analysis. In addition, for data-mining purposes, a list of associations of ADRs and suspected drugs that are disproportionally present in the database is periodically generated. Finally, quantitative signal generation can be used to study more complex relationships, such as drug-drug interactions and syndromes. The results of quantitative signal detection should be considered as an additional source of information, complementary to the traditional analysis. Techniques for the detection of drug interactions and syndromes offer a new challenge for pharmacovigilance in the near future.

  1. Comparison of staining techniques for scanning electron microscopic detection of ultrastructural protuberances on cellulolytic bacteria.

    PubMed

    Blair, B G; Anderson, K L

    1998-03-01

    Cell surface protuberances found on cellulolytic bacteria, but not on noncellulolytic bacteria, can be detected by scanning electron microscopy. Cationized ferritin typically has been used as a stain to increase the microscopic resolution of these protuberances; however, as a cation it binds only to negatively charged molecules. Thus, binding of cationized ferritin to cell surface molecules can be affected by the cell's physiological state. We incubated the noncellulolytic bacterium, Clostridium beijerinckii, in different media at various temperatures to obtain cells with different growth rates and physiological states. Staining of these cells with cationized ferritin showed that slower growing cells exhibited more protuberant structures than faster growing cells. This provided a clear correlation of ultrastructural protuberances with physiological changes associated with growth rate. On the other hand, cells stained with osmium tetroxide exhibited no protuberant structures regardless of growth rate. Because various cations are known to induce aggregation of surface proteins on some cellulolytic Clostridia, we incubated the cellulolytic bacterium, Clostridium cellulovorans, in media containing glucose, cellobiose, or cellulose. Ultrastructural protuberances were evident on all cells stained with cationized ferritin, but extensive protuberances were detected only on cells grown in cellulose and stained with osmium tetroxide. For cells stained with cationized ferritin, the presence of ultrastructural protuberances was correlated with growth rate rather than induction of cellulolytic systems. By contrast, cells stained with osmium tetroxide showed a clear correlation between protuberant structures and cellulolytic activity.

  2. Genome-wide scans detect adaptation to aridity in a widespread forest tree species.

    PubMed

    Steane, Dorothy A; Potts, Brad M; McLean, Elizabeth; Prober, Suzanne M; Stock, William D; Vaillancourt, René E; Byrne, Margaret

    2014-05-01

    Patterns of adaptive variation within plant species are best studied through common garden experiments, but these are costly and time-consuming, especially for trees that have long generation times. We explored whether genome-wide scanning technology combined with outlier marker detection could be used to detect adaptation to climate and provide an alternative to common garden experiments. As a case study, we sampled nine provenances of the widespread forest tree species, Eucalyptus tricarpa, across an aridity gradient in southeastern Australia. Using a Bayesian analysis, we identified a suite of 94 putatively adaptive (outlying) sequence-tagged markers across the genome. Population-level allele frequencies of these outlier markers were strongly correlated with temperature and moisture availability at the site of origin, and with population differences in functional traits measured in two common gardens. Using the output from a canonical analysis of principal coordinates, we devised a metric that provides a holistic measure of genomic adaptation to aridity that could be used to guide assisted migration or genetic augmentation.

  3. New noise reduction method for reducing CT scan dose: Combining Wiener filtering and edge detection algorithm

    NASA Astrophysics Data System (ADS)

    Anam, Choirul; Haryanto, Freddy; Widita, Rena; Arif, Idam

    2015-09-01

    New noise reduction method for reducing dose of CT scans has been proposed. The new method is expected to address the major problems in the noise reduction algorithm, i.e. the decreasing in the spatial resolution of the image. The proposed method was developed by combining adaptive Wiener filtering and edge detection algorithms. The first step, the image was filtered with a Wiener filter. Separately, edge detection operation performed on the original image using the Prewitt method. The next step, a new image was generated based on the edge detection operation. At the edge area, the image was taken from the original image, while at the non-edge area, the image was taken from the image that had been filtered with a Wiener filter. The new method was tested on a CT image of the spatial resolution phantom, which was scanned by different current-time multiplication, namely 80, 130 and 200 mAs, while other exposure factors were kept in constant conditions. The spatial resolution phantom consists of six sets of bar pattern made of plexi-glass and separated at some distance by water. The new image quality assessed from the amount of noise and the magnitude of spatial resolution. Noise was calculated by determining the standard deviation of the homogeneous regions, while the spatial resolution was assessed by observation of the area sets of the bar pattern. In addition, to evaluate the performance of this new method has also been tested on patient CT images. From the measurements, the new method can reduce the noise to an average 64.85%, with a spatial resolution does not decrease significantly. Visually, the third set bar on the image phantom (the distance between the bar 1.0 mm) can still be distinguished, as well as on the original image. Meanwhile, if the image is only processed using Wiener filter, the second set bar (the distance between the bar 1.3 mm) are distinguishable. Testing this new method to patient image, its results in relatively the same. Thus, using this

  4. Automatic Detection and Quantification of Tree-in-Bud (TIB) Opacities From CT Scans

    PubMed Central

    Yao, Jianhua; Wu, Albert; Caban, Jesus; Palmore, Tara N.; Suffredini, Anthony F.; Aras, Omer; Mollura, Daniel J.

    2012-01-01

    This study presents a novel computer-assisted detection (CAD) system for automatically detecting and precisely quantifying abnormal nodular branching opacities in chest computed tomography (CT), termed tree-in-bud (TIB) opacities by radiology literature. The developed CAD system in this study is based on 1) fast localization of candidate imaging patterns using local scale information of the images, and 2) Möobius invariant feature extraction method based on learned local shape and texture properties of TIB patterns. For fast localization of candidate imaging patterns, we use ball-scale filtering and, based on the observation of the pattern of interest, a suitable scale selection is used to retain only small size patterns. Once candidate abnormality patterns are identified, we extract proposed shape features from regions where at least one candidate pattern occupies. The comparative evaluation of the proposed method with commonly used CAD methods is presented with a dataset of 60 chest CTs (laboratory confirmed 39 viral bronchiolitis human parainfluenza CTs and 21 normal chest CTs). The quantitative results are presented as the area under the receiver operator characteristics curves and a computer score (volume affected by TIB) provided as an output of the CAD system. In addition, a visual grading scheme is applied to the patient data by three well-trained radiologists. Inter-observer and observer–computer agreements are obtained by the relevant statistical methods over different lung zones. Experimental results demonstrate that the proposed CAD system can achieve high detection rates with an overall accuracy of 90.96%.Moreover, correlations of observer–observer (R2 = 0.8848,p <0.01) and observer–CAD agreements (R2 = 0.824,p <0.01) validate the feasibility of the use of the proposed CAD system in detecting and quantifying TIB patterns. PMID:22434795

  5. Liquid crystal-based sensors for selective and quantitative detection of nitrogen dioxide

    PubMed Central

    Sen, Avijit; Kupcho, Kurt A.; Grinwald, Bart A.; VanTreeck, Heidi J.; Acharya, Bharat R.

    2013-01-01

    A highly sensitive nitrogen dioxide (NO2) sensor based on orientational transition of a thin film of liquid crystal (LC) supported on a gold surface is reported. Transport of NO2 molecules through the LC film to the LC-gold interface induces an orientation transition in the LC film. The dynamic behavior of the sensor response exhibits a concentration-dependent response rate that is employed to generate an algorithm for quantitative determination of unknown concentrations. Sensitive, selective and reversible detection with minimal effects of environmental fluctuations suggest that these sensors can be used for quantitative NO2 detection for a number of applications. PMID:23526230

  6. Developing the Quantitative Histopathology Image Ontology (QHIO): A case study using the hot spot detection problem.

    PubMed

    Gurcan, Metin N; Tomaszewski, John; Overton, James A; Doyle, Scott; Ruttenberg, Alan; Smith, Barry

    2017-02-01

    Interoperability across data sets is a key challenge for quantitative histopathological imaging. There is a need for an ontology that can support effective merging of pathological image data with associated clinical and demographic data. To foster organized, cross-disciplinary, information-driven collaborations in the pathological imaging field, we propose to develop an ontology to represent imaging data and methods used in pathological imaging and analysis, and call it Quantitative Histopathological Imaging Ontology - QHIO. We apply QHIO to breast cancer hot-spot detection with the goal of enhancing reliability of detection by promoting the sharing of data between image analysts.

  7. Non-invasive and high-sensitivity scanning detection of magnetic nanoparticles in animals using high-Tc scanning superconducting-quantum-interference-device biosusceptometry.

    PubMed

    Chieh, J J; Hong, C Y

    2011-08-01

    Although magnetic nanoparticles (MNPs) have been widely applied to animals in biomedicine, MNPs within animals should be examined in real time, in vivo, and without bio-damaged possibility to evaluate whether the bio-function of MNPs is valid or to further controls the biomedicinal process because of accompanying complex problems such as MNPs distribution and MNPs biodegradation. The non-invasive and high-sensitivity scanning detection of MNPs in animals using ac susceptometry based on a high-T(c) superconducting quantum interference device (SQUID) is presented. The non-invasive results and biopsy results show good agreement, and two gold-standard biomedicine methods, Prussian blue stain and inductively coupled plasma, prove the magnetic results. This confirms that the future clinical diagnosis of bio-functional MNPs could be operated by using scanning SQUID biosusceptometry as conveniently as an ultrasonic probe.

  8. Non-invasive and high-sensitivity scanning detection of magnetic nanoparticles in animals using high-Tc scanning superconducting-quantum-interference-device biosusceptometry

    NASA Astrophysics Data System (ADS)

    Chieh, J. J.; Hong, C. Y.

    2011-08-01

    Although magnetic nanoparticles (MNPs) have been widely applied to animals in biomedicine, MNPs within animals should be examined in real time, in vivo, and without bio-damaged possibility to evaluate whether the bio-function of MNPs is valid or to further controls the biomedicinal process because of accompanying complex problems such as MNPs distribution and MNPs biodegradation. The non-invasive and high-sensitivity scanning detection of MNPs in animals using ac susceptometry based on a high-Tc superconducting quantum interference device (SQUID) is presented. The non-invasive results and biopsy results show good agreement, and two gold-standard biomedicine methods, Prussian blue stain and inductively coupled plasma, prove the magnetic results. This confirms that the future clinical diagnosis of bio-functional MNPs could be operated by using scanning SQUID biosusceptometry as conveniently as an ultrasonic probe.

  9. Quantitative weaknesses of the Marcus-Hush theory of electrode kinetics revealed by Reverse Scan Square Wave Voltammetry: The reduction of 2-methyl-2-nitropropane at mercury microelectrodes

    NASA Astrophysics Data System (ADS)

    Laborda, Eduardo; Wang, Yijun; Henstridge, Martin C.; Martínez-Ortiz, Francisco; Molina, Angela; Compton, Richard G.

    2011-08-01

    The Marcus-Hush and Butler-Volmer kinetic electrode models are compared experimentally by studying the reduction of 2-methyl-2-nitropropane in acetonitrile at mercury microelectrodes using Reverse Scan Square Wave Voltammetry. This technique is found to be very sensitive to the electrode kinetics and to permit critical comparison of the two models. The Butler-Volmer model satisfactorily fits the experimental data whereas Marcus-Hush does not quantitatively describe this redox system.

  10. [Quantitative Approach to Melamine Detection in Egg White with Surface-Enhanced Raman Spectroscopy].

    PubMed

    Wang, Qiao-hua; Liu, Ya-li; Ma, Mei-hu; Wang, Hong

    2015-04-01

    Due to the harmfulness of melamine to human, the quantitative detection of melamine in egg is very necessary. In the present study, the surface enhanced Raman spectra technology combined with chemometric analysis method was used to conduct melamine quantitative detection in egg white. Firstly, the melamine egg sample could be got by the method of artificial feeding hens usingdifferent feeding formulation. Then the surface enhanced Raman spectra of egg white was determined using portable Raman spectroscopy (Opto Trace RamTracer-200) and Raman enhancement reagents, and the melamine content within the white eggs was measured with gas chromatography mass spectrometry technology. The software of Raman Analyzer was used for baseline correction of Raman spectra. The correlation coefficient method was used to choose 320 spectral variables from the surface enhanced Raman spectroscopy as input variables to establish partial least squares quantitative calibration model . And the peaks-decomposition method was used to establish peaks-decomposition quantitative calibration model. Both models selected 90 and 44 samples respectively as calibration sets and validation sets during model establishment, and both models achieved good prediction effect. The determination coefficient between predicted values of partial least squares quantitative calibration model and measured values of gas chromatography mass spectrometry was 0.856, and root mean square error of prediction was 1.547. The determination coefficient was 0.947 and RMSEP was 0.893 for the peaks-decomposition quantitative calibration model. This study demonstrated that the method can effectively quantitatively detect melamine in eggs. Testing a sample only takes 15 minutes, which can provide a new way for the melamine egg detection.

  11. Mueller matrix microscope: a quantitative tool to facilitate detections and fibrosis scorings of liver cirrhosis and cancer tissues.

    PubMed

    Wang, Ye; He, Honghui; Chang, Jintao; He, Chao; Liu, Shaoxiong; Li, Migao; Zeng, Nan; Wu, Jian; Ma, Hui

    2016-07-01

    Today the increasing cancer incidence rate is becoming one of the biggest threats to human health.Among all types of cancers, liver cancer ranks in the top five in both frequency and mortality rate all over the world. During the development of liver cancer, fibrosis often evolves as part of a healing process in response to liver damage, resulting in cirrhosis of liver tissues. In a previous study, we applied the Mueller matrix microscope to pathological liver tissue samples and found that both the Mueller matrix polar decomposition (MMPD) and Mueller matrix transformation (MMT) parameters are closely related to the fibrous microstructures. In this paper,we take this one step further to quantitatively facilitate the fibrosis detections and scorings of pathological liver tissue samples in different stages from cirrhosis to cancer using the Mueller matrix microscope. The experimental results of MMPD and MMT parameters for the fibrotic liver tissue samples in different stages are measured and analyzed. We also conduct Monte Carlo simulations based on the sphere birefringence model to examine in detail the influence of structural changes in different fibrosis stages on the imaging parameters. Both the experimental and simulated results indicate that the polarized light microscope and transformed Mueller matrix parameter scan provide additional quantitative information helpful for fibrosis detections and scorings of liver cirrhosis and cancers. Therefore, the polarized light microscope and transformed Mueller matrix parameters have a good application prospect in liver cancer diagnosis.

  12. Field emission scanning electron microscopy (FE-SEM) as an approach for nanoparticle detection inside cells.

    PubMed

    Havrdova, M; Polakova, K; Skopalik, J; Vujtek, M; Mokdad, A; Homolkova, M; Tucek, J; Nebesarova, J; Zboril, R

    2014-12-01

    When developing new nanoparticles for bio-applications, it is important to fully characterize the nanoparticle's behavior in biological systems. The most common techniques employed for mapping nanoparticles inside cells include transmission electron microscopy (TEM) and scanning transmission electron microscopy (STEM). These techniques entail passing an electron beam through a thin specimen. STEM or TEM imaging is often used for the detection of nanoparticles inside cellular organelles. However, lengthy sample preparation is required (i.e., fixation, dehydration, drying, resin embedding, and cutting). In the present work, a new matrix (FTO glass) for biological samples was used and characterized by field emission scanning electron microscopy (FE-SEM) to generate images comparable to those obtained by TEM. Using FE-SEM, nanoparticle images were acquired inside endo/lysosomes without disruption of the cellular shape. Furthermore, the initial steps of nanoparticle incorporation into the cells were captured. In addition, the conductive FTO glass endowed the sample with high stability under the required accelerating voltage. Owing to these features of the sample, further analyses could be performed (material contrast and energy-dispersive X-ray spectroscopy (EDS)), which confirmed the presence of nanoparticles inside the cells. The results showed that FE-SEM can enable detailed characterization of nanoparticles in endosomes without the need for contrast staining or metal coating of the sample. Images showing the intracellular distribution of nanoparticles together with cellular morphology can give important information on the biocompatibility and demonstrate the potential of nanoparticle utilization in medicine. Copyright © 2014 Elsevier Ltd. All rights reserved.

  13. Detection and Characterization of Package Defects and Integrity Failure using Dynamic Scanning Infrared Thermography (DSIRT).

    PubMed

    Morris, Scott A

    2016-02-01

    A dynamic scanning infrared thermography (DSIRT) system developed at the Univ. of Illinois Urbana-Champaign (UIUC) Packaging Lab relies on variation in transient thermal artifacts to indicate defects, and offers the possibility of characterization of many types of materials and structures. These include newer polymer and laminate-based structures for shelf-stable foods that lack a reliable, nondestructive method for inspection, which is a continuing safety issue. Preliminary trials were conducted on a polyester/aluminum foil/polypropylene retort pouch laminate containing artificially-induced failed seal and insulating inclusion defects ranging from 1 to 10 mm wide in the plane of the seal. The samples were placed in relative motion to a laterally positioned infrared laser, inducing heating through the plane of the seal. The emergent thermal artifact on the obverse side was sensed using either a bolometer camera or a thermopile sensor, with thermal anomalies indicating potential defects and the results of each sensors were compared. The bolometer camera detected defects to the limit of its measured optical resolution-approximately 1 mm at 20 cm-although the lower-resolution thermopile sensors were only capable of detecting 5 mm defects even at closer distances of approximately 5 mm. In addition, a supplementary magnification system was fitted to the bolometer camera which increased resolution but reduced field of view and would require a much higher frame rate to be useful. Automatic processing of the image data rapidly detected the model defects and can lead to development of an automated inspection system.  Much higher material throughput speeds are feasible using faster instruments, and the system is scalable. © 2015 Institute of Food Technologists®

  14. GeneScanning analysis of Ig/TCR gene rearrangements to detect clonality in canine lymphomas.

    PubMed

    Gentilini, Fabio; Calzolari, Claudia; Turba, Maria E; Bettini, Giuliano; Famigli-Bergamini, Paolo

    2009-01-15

    The diagnosis of canine lymphoma is achieved using morphological and immunological methods. In a certain percentage of cases, difficulties in making a definitive diagnosis of lymphoproliferative disorders may occur despite extensive immunophenotyping. Therefore, additional diagnostics, such as molecular assessment of Ig/TCR gene rearrangements clonality, may confirm the final diagnosis. Polyacrylamide gel electrophoresis and heteroduplex analysis have already been proven to be suitable for detecting clonality but are cumbersome and labor-intensive. In the present study, GeneScanning analysis of PCR products originating from different primer sets targeting different regions of Ig and TCR was validated in improving sensitivity as well as in reducing the turnaround time of gene rearrangement assays. GeneScanning exploits 5' fluorescently labelled primers for the automated and fast analysis of PCR products either as singleplex or multiplex runs. Initially, the assay was set up using DNA purified from normal tissues (n=6), hyperplastic/reactive tissues (n=10) and a small set of immunophenotyped lymphoma samples (n=12). The optimized methods were then used in a large set of 96 canine lymphoma samples. Normal and hyperplastic/reactive lymphoid tissues showed typically polyclonal or, occasionally, oligoclonal PCR products. Lymphoma samples showed monoclonal peaks arranged as a single or, occasionally, a double narrow base peak sometimes embedded in a polyclonal background. In all immunophenotyped cases, an Ig or TCR clonal finding corresponded to B- and T-cell lymphomas, respectively. Overall, 94/96 (97.9%) samples showed clonal Ig/TCR clonal rearrangements among which clonal Ig was found in 61/96 (63.5%) of samples and clonal TCR in 33/35 Ig negative samples (34.4% of all cases). In one out of ten randomly chosen cases, both Ig and TCR clonal gene rearrangements were found. Among the factors affecting assay accuracy, DNA quality has been shown to be critical and the

  15. A genome scan for quantitative trait loci affecting cyanogenic potential of cassava root in an outbred population

    PubMed Central

    2011-01-01

    Background Cassava (Manihot esculenta Crantz) can produce cyanide, a toxic compound, without self-injury. That ability was called the cyanogenic potential (CN). This project aimed to identify quantitative trait loci (QTL) associated with the CN in an outbred population derived from 'Hanatee' × 'Huay Bong 60', two contrasting cultivars. CN was evaluated in 2008 and in 2009 at Rayong province, and in 2009 at Lop Buri province, Thailand. CN was measured using a picrate paper kit. QTL analysis affecting CN was performed with 303 SSR markers. Results The phenotypic values showed continuous variation with transgressive segregation events with more (115 ppm) and less CN (15 ppm) than either parent ('Hanatee' had 33 ppm and 'Huay Bong 60' had 95 ppm). The linkage map consisted of 303 SSR markers, on 27 linkage groups with a map that encompassed 1,328 cM. The average marker interval was 5.8 cM. Five QTL underlying CN were detected. CN08R1from 2008 at Rayong, CN09R1and CN09R2 from 2009 at Rayong, and CN09L1 and CN09L2 from 2009 at Lop Buri were mapped on linkage group 2, 5, 10 and 11, respectively. Among all the identified QTL, CN09R1 was the most significantly associated with the CN trait with LOD score 5.75 and explained the greatest percentage of phenotypic variation (%Expl.) of 26%. Conclusions Five new QTL affecting CN were successfully identified from 4 linkage groups. Discovery of these QTL can provide useful markers to assist in cassava breeding and studying genes affecting the trait. PMID:21609492

  16. Surface scanning inspection system particle detection dependence on aluminum film morphology

    NASA Astrophysics Data System (ADS)

    Prater, Walter; Tran, Natalie; McGarvey, Steve

    2012-03-01

    Physical vapor deposition (PVD) aluminum films present unique challenges when detecting particulate defects with a Surface Scanning Inspection System (SSIS). Aluminum (Al) films 4500Å thick were deposited on 300mm particle grade bare Si wafers at two temperatures using a Novellus Systems INOVA® NExT,.. Film surface roughness and morphology measurements were performed using a Veeco Vx310® atomic force microscope (AFM). AFM characterization found the high deposition temperature (TD) Al roughness (Root Mean Square 16.5 nm) to be five-times rougher than the low-TD Al roughness (rms 3.7 nm). High-TD Al had grooves at the grain boundaries that were measured to be 20 to 80 nm deep. Scanning electron microscopy (SEM) examination, with a Hitachi RS6000 defect review SEM, confirmed the presence of pronounced grain grooves. SEM images established that the low-TD filmed wafers have fine grains (0.1 to 0.3 um diameter) and the high-TD film wafers have fifty-times larger equiaxed plateletshape grains (5 to 15 um diameter). Calibrated Poly-Styrene Latex (PSL) spheres ranging in size from 90 nm to 1 μm were deposited in circular patterns on the wafers using an aerosol deposition chamber. PSL sphere depositions at each spot were controlled to yield 2000 to 5000 counts. A Hitachi LS9100® dark field full wafer SSIS was used to experimentally determine the relationship of the PSL sphere scattered light intensity with S-polarized light, a measure of scattering cross-section, with respect to the calibrated PSL sphere diameter. Comparison of the SSIS scattered light versus PSL spot size calibration curves shows two distinct differences. Scattering cross-section (intensity) of the PSL spheres increased on the low-TD Al film with smooth surface roughness and the low-TD Al film defect detection sensitivity was 126 nm compared to 200 nm for the rougher high- TD Al film. This can be explained by the higher signal to noise attributed to the smooth low-TD Al. Dark field defect detection on

  17. QUANTITATIVE VS. CONVENTIONAL PCR FOR DETECTION OF HUMAN ADENOVIRUSES IN WATER AND SEDIMENT SAMPLES

    PubMed Central

    STAGGEMEIER, Rodrigo; BORTOLUZZI, Marina; HECK, Tatiana Moraes da Silva; SPILKI, Fernando Rosado; ALMEIDA, Sabrina Esteves de Matos

    2015-01-01

    SUMMARY Human Adenoviruses (HAdV) are notably resistant in the environment. These agents may serve as effective indicators of fecal contamination, and may act as causative agents of a number of different diseases in human beings. Conventional polymerase chain reaction (PCR) and, more recently, quantitative PCR (qPCR) are widely used for detection of viral agents in environmental matrices. In the present study PCR and SYBR(r)Green qPCR assays were compared for detection of HAdV in water (55) and sediments (20) samples of spring and artesian wells, ponds and streams, collected from dairy farms. By the quantitative methodology HAdV were detected in 87.3% of the water samples and 80% of the sediments, while by the conventional PCR 47.3% and 35% were detected in water samples and sediments, respectively. PMID:26422153

  18. QUANTITATIVE VS. CONVENTIONAL PCR FOR DETECTION OF HUMAN ADENOVIRUSES IN WATER AND SEDIMENT SAMPLES.

    PubMed

    Staggemeier, Rodrigo; Bortoluzzi, Marina; Heck, Tatiana Moraes da Silva; Spilki, Fernando Rosado; Almeida, Sabrina Esteves de Matos

    2015-01-01

    Human Adenoviruses (HAdV) are notably resistant in the environment. These agents may serve as effective indicators of fecal contamination, and may act as causative agents of a number of different diseases in human beings. Conventional polymerase chain reaction (PCR) and, more recently, quantitative PCR (qPCR) are widely used for detection of viral agents in environmental matrices. In the present study PCR and SYBR(r)Green qPCR assays were compared for detection of HAdV in water (55) and sediments (20) samples of spring and artesian wells, ponds and streams, collected from dairy farms. By the quantitative methodology HAdV were detected in 87.3% of the water samples and 80% of the sediments, while by the conventional PCR 47.3% and 35% were detected in water samples and sediments, respectively.

  19. [Quantitative specific detection of Staphylococcus aureus based on recombinant lysostaphin and ATP bioluminescence].

    PubMed

    Li, Yuyuan; Mi, Zhiqiang; An, Xiaoping; Zhou, Yusen; Tong, Yigang

    2014-08-01

    Quantitative specific detection of Staphylococcus aureus is based on recombinant lysostaphin and ATP bioluminescence. To produce recombinant lysostaphin, the lysostaphin gene was chemically synthesized and inserted it into prokaryotic expression vector pQE30, and the resulting expression plasmid pQE30-Lys was transformed into E. coli M15 for expressing lysostaphin with IPTG induction. The recombinant protein was purified by Ni(2+)-NTA affinity chromatography. Staphylococcus aureus was detected by the recombinant lysostaphin with ATP bioluminescence, and plate count method. The results of the two methods were compared. The recombinant lysostaphin was successfully expressed, and a method of quantitative specific detection of S. aureus has been established, which showed a significant linear correlation with the colony counting. The detection method developed has good perspective to quantify S. aureus.

  20. Lock-in-detection-free line-scan stimulated Raman scattering microscopy for near video-rate Raman imaging.

    PubMed

    Wang, Zi; Zheng, Wei; Huang, Zhiwei

    2016-09-01

    We report on the development of a unique lock-in-detection-free line-scan stimulated Raman scattering microscopy technique based on a linear detector with a large full well capacity controlled by a field-programmable gate array (FPGA) for near video-rate Raman imaging. With the use of parallel excitation and detection scheme, the line-scan SRS imaging at 20 frames per second can be acquired with a ∼5-fold lower excitation power density, compared to conventional point-scan SRS imaging. The rapid data communication between the FPGA and the linear detector allows a high line-scanning rate to boost the SRS imaging speed without the need for lock-in detection. We demonstrate this lock-in-detection-free line-scan SRS imaging technique using the 0.5 μm polystyrene and 1.0 μm poly(methyl methacrylate) beads mixed in water, as well as living gastric cancer cells.

  1. Evaluation of a quantitative plasma PCR plate assay for detecting cytomegalovirus infection in marrow transplant recipients.

    PubMed Central

    Gallez-Hawkins, G M; Tegtmeier, B R; ter Veer, A; Niland, J C; Forman, S J; Zaia, J A

    1997-01-01

    A plasma PCR test, using a nonradioactive PCR plate assay, was evaluated for detection of human cytomegalovirus reactivation. This assay was compared to Southern blotting and found to perform well. As a noncompetitive method of quantitation, it was similar to a competitive method for detecting the number of genome copies per milliliter of plasma in marrow transplant recipients. This is a technically simplified assay with potential for adaptation to automation. PMID:9041438

  2. A genome scan for Plasmodium falciparum malaria identifies quantitative trait loci on chromosomes 5q31, 6p21.3, 17p12, and 19p13

    PubMed Central

    2014-01-01

    Background Genome-wide studies have mapped several loci controlling Plasmodium falciparum mild malaria and parasitaemia, only two of them being significant at the genome level. The objective of the present study was to identify malaria resistance loci in individuals living in Burkina Faso. Methods A genome scan that involved 314 individuals belonging to 63 families was performed. Markers located within chromosomes 6p21.3 and 17p12 were genotyped in 247 additional individuals belonging to 55 families. The linkage and the association of markers with parasitaemia and mild malaria were assessed by using the maximum-likelihood binomial method extended to quantitative trait linkage and the quantitative trait disequilibrium test, respectively. Results Multipoint linkage analysis showed a significant linkage of mild malaria to chromosome 6p21.3 (LOD score 3.73, P = 1.7 10−5), a suggestive linkage of mild malaria to chromosome 19p13.12 (LOD score 2.50, P = 3.5 10−4), and a suggestive linkage of asymptomatic parasitaemia to chromosomes 6p21.3 (LOD score 2.36, P = 4.9 10−4) and 17p12 (LOD score 2.87, P = 1.4 10−4). Genome-wide family-based association analysis revealed a significant association between three chromosome 5q31 markers and asymptomatic parasitaemia, whereas there was no association with mild malaria. When taking into account 247 additional individuals, a significant linkage of asymptomatic parasitaemia to chromosome 17p12 (LOD score 3.6, P = 2 10−5) was detected. Conclusion A new genome-wide significant malaria locus on chromosome 17p12 and a new suggestive locus on chromosome 19p13.12 are reported. Moreover, there was evidence that confirmed the influence of chromosomes 5q31 and 6p21.3 as loci controlling mild malaria or asymptomatic parasitaemia. PMID:24884991

  3. Systematic Assessment of Survey Scan and MS2-Based Abundance Strategies for Label-Free Quantitative Proteomics Using High-Resolution MS Data

    PubMed Central

    2015-01-01

    Survey-scan-based label-free method have shown no compelling benefit over fragment ion (MS2)-based approaches when low-resolution mass spectrometry (MS) was used, the growing prevalence of high-resolution analyzers may have changed the game. This necessitates an updated, comparative investigation of these approaches for data acquired by high-resolution MS. Here, we compared survey scan-based (ion current, IC) and MS2-based abundance features including spectral-count (SpC) and MS2 total-ion-current (MS2-TIC), for quantitative analysis using various high-resolution LC/MS data sets. Key discoveries include: (i) study with seven different biological data sets revealed only IC achieved high reproducibility for lower-abundance proteins; (ii) evaluation with 5-replicate analyses of a yeast sample showed IC provided much higher quantitative precision and lower missing data; (iii) IC, SpC, and MS2-TIC all showed good quantitative linearity (R2 > 0.99) over a >1000-fold concentration range; (iv) both MS2-TIC and IC showed good linear response to various protein loading amounts but not SpC; (v) quantification using a well-characterized CPTAC data set showed that IC exhibited markedly higher quantitative accuracy, higher sensitivity, and lower false-positives/false-negatives than both SpC and MS2-TIC. Therefore, IC achieved an overall superior performance than the MS2-based strategies in terms of reproducibility, missing data, quantitative dynamic range, quantitative accuracy, and biomarker discovery. PMID:24635752

  4. Systematic assessment of survey scan and MS2-based abundance strategies for label-free quantitative proteomics using high-resolution MS data.

    PubMed

    Tu, Chengjian; Li, Jun; Sheng, Quanhu; Zhang, Ming; Qu, Jun

    2014-04-04

    Survey-scan-based label-free method have shown no compelling benefit over fragment ion (MS2)-based approaches when low-resolution mass spectrometry (MS) was used, the growing prevalence of high-resolution analyzers may have changed the game. This necessitates an updated, comparative investigation of these approaches for data acquired by high-resolution MS. Here, we compared survey scan-based (ion current, IC) and MS2-based abundance features including spectral-count (SpC) and MS2 total-ion-current (MS2-TIC), for quantitative analysis using various high-resolution LC/MS data sets. Key discoveries include: (i) study with seven different biological data sets revealed only IC achieved high reproducibility for lower-abundance proteins; (ii) evaluation with 5-replicate analyses of a yeast sample showed IC provided much higher quantitative precision and lower missing data; (iii) IC, SpC, and MS2-TIC all showed good quantitative linearity (R(2) > 0.99) over a >1000-fold concentration range; (iv) both MS2-TIC and IC showed good linear response to various protein loading amounts but not SpC; (v) quantification using a well-characterized CPTAC data set showed that IC exhibited markedly higher quantitative accuracy, higher sensitivity, and lower false-positives/false-negatives than both SpC and MS2-TIC. Therefore, IC achieved an overall superior performance than the MS2-based strategies in terms of reproducibility, missing data, quantitative dynamic range, quantitative accuracy, and biomarker discovery.

  5. High Resolution Trichromatic Road Surface Scanning with a Line Scan Camera and Light Emitting Diode Lighting for Road-Kill Detection

    PubMed Central

    Lopes, Gil; Ribeiro, A. Fernando; Sillero, Neftalí; Gonçalves-Seco, Luís; Silva, Cristiano; Franch, Marc; Trigueiros, Paulo

    2016-01-01

    This paper presents a road surface scanning system that operates with a trichromatic line scan camera with light emitting diode (LED) lighting achieving road surface resolution under a millimeter. It was part of a project named Roadkills—Intelligent systems for surveying mortality of amphibians in Portuguese roads, sponsored by the Portuguese Science and Technology Foundation. A trailer was developed in order to accommodate the complete system with standalone power generation, computer image capture and recording, controlled lighting to operate day or night without disturbance, incremental encoder with 5000 pulses per revolution attached to one of the trailer wheels, under a meter Global Positioning System (GPS) localization, easy to utilize with any vehicle with a trailer towing system and focused on a complete low cost solution. The paper describes the system architecture of the developed prototype, its calibration procedure, the performed experimentation and some obtained results, along with a discussion and comparison with existing systems. Sustained operating trailer speeds of up to 30 km/h are achievable without loss of quality at 4096 pixels’ image width (1 m width of road surface) with 250 µm/pixel resolution. Higher scanning speeds can be achieved by lowering the image resolution (120 km/h with 1 mm/pixel). Computer vision algorithms are under development to operate on the captured images in order to automatically detect road-kills of amphibians. PMID:27104535

  6. High Resolution Trichromatic Road Surface Scanning with a Line Scan Camera and Light Emitting Diode Lighting for Road-Kill Detection.

    PubMed

    Lopes, Gil; Ribeiro, A Fernando; Sillero, Neftalí; Gonçalves-Seco, Luís; Silva, Cristiano; Franch, Marc; Trigueiros, Paulo

    2016-04-19

    This paper presents a road surface scanning system that operates with a trichromatic line scan camera with light emitting diode (LED) lighting achieving road surface resolution under a millimeter. It was part of a project named Roadkills-Intelligent systems for surveying mortality of amphibians in Portuguese roads, sponsored by the Portuguese Science and Technology Foundation. A trailer was developed in order to accommodate the complete system with standalone power generation, computer image capture and recording, controlled lighting to operate day or night without disturbance, incremental encoder with 5000 pulses per revolution attached to one of the trailer wheels, under a meter Global Positioning System (GPS) localization, easy to utilize with any vehicle with a trailer towing system and focused on a complete low cost solution. The paper describes the system architecture of the developed prototype, its calibration procedure, the performed experimentation and some obtained results, along with a discussion and comparison with existing systems. Sustained operating trailer speeds of up to 30 km/h are achievable without loss of quality at 4096 pixels' image width (1 m width of road surface) with 250 µm/pixel resolution. Higher scanning speeds can be achieved by lowering the image resolution (120 km/h with 1 mm/pixel). Computer vision algorithms are under development to operate on the captured images in order to automatically detect road-kills of amphibians.

  7. Quantitative PCR for Detection and Enumeration of Genetic Markers of Bovine Fecal Pollution

    EPA Science Inventory

    Accurate assessment of health risks associated with bovine (cattle) fecal pollution requires a reliable host-specific genetic marker and a rapid quantification method. We report the development of quantitative PCR assays for the detection of two recently described cow feces-spec...

  8. Comparative analysis of techniques for detection of quiescent Botrytis cinerea in grapes by quantitative PCR

    USDA-ARS?s Scientific Manuscript database

    Quantitative PCR (qPCR) can be used to detect and monitor pathogen colonization, but early attempts to apply the technology to quiescent Botrytis cinerea infections of grape berries identified some specific limitations. In this study, four DNA extraction methods, two tissue-grinding methods, two gra...

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

    PubMed

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

    2008-10-01

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

  10. Quantitative PCR for Detection and Enumeration of Genetic Markers of Bovine Fecal Pollution

    EPA Science Inventory

    Accurate assessment of health risks associated with bovine (cattle) fecal pollution requires a reliable host-specific genetic marker and a rapid quantification method. We report the development of quantitative PCR assays for the detection of two recently described cow feces-spec...

  11. A new molecular diagnostic tool for quantitatively detecting and genotyping “Candidatus Liberibacter species”

    USDA-ARS?s Scientific Manuscript database

    A new molecular diagnostic method was developed for quantitative detection of “Candidatus Liberibacter” species associated with citrus Huanglongbing (“Ca. Liberibacter asiaticus”, “Ca. Liberibacter africanus” and “Ca. Liberibacter americanus”) and potato zebra chip disorder (“Ca. Liberibacter solana...

  12. A visual volumetric hydrogel sensor enables quantitative and sensitive detection of copper ions.

    PubMed

    Wu, Rui; Zhang, Shenghai; Lyu, Jitong; Lu, Fang; Yue, Xuanfeng; Lv, Jiagen

    2015-05-11

    We propose a visual volumetric sensor with 5,6-dicarboxylic fluorescein cross-linked amine-functionalized polyacrylamide hydrogel. The sensor undergoes volume response to Cu(2+) ions at the μM level, which enables naked-eye quantitative detection by reading the graduation on a pipette.

  13. QUANTITATIVE DETECTION OF ENVIRONMENTALLY IMPORTANT DYES USING DIODE LASER/FIBER-OPTIC RAMAN

    EPA Science Inventory

    A compact diode laser/fiber-optic Raman spectrometer is used for quantitative detection of environmentally important dyes. This system is based on diode laser excitation at 782 mm, fiber optic probe technology, an imaging spectrometer, and state-of-the-art scientific CCD camera. ...

  14. Single Laboratory Comparison of Quantitative Real-time PCR Assays for the Detection of Fecal Pollution

    EPA Science Inventory

    There are numerous quantitative real-time PCR (qPCR) assays available to detect and enumerate fecal pollution in ambient waters. Each assay employs distinct primers and probes that target different rRNA genes and microorganisms leading to potential variations in concentration es...

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

    PubMed Central

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

    2008-01-01

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

  16. QUANTITATIVE DETECTION OF ENVIRONMENTALLY IMPORTANT DYES USING DIODE LASER/FIBER-OPTIC RAMAN

    EPA Science Inventory

    A compact diode laser/fiber-optic Raman spectrometer is used for quantitative detection of environmentally important dyes. This system is based on diode laser excitation at 782 mm, fiber optic probe technology, an imaging spectrometer, and state-of-the-art scientific CCD camera. ...

  17. The value of positron emission tomography scanning in the detection of subclinical metastatic melanoma.

    PubMed

    Acland, K M; O'Doherty, M J; Russell-Jones, R

    2000-04-01

    We have undertaken a retrospective analysis of all positron emission tomography (PET) scans carried out at St Thomas' Hospital, London, since 1994 to establish the sensitivity and specificity of this radiologic technique in cutaneous malignant melanoma. In particular, we have identified those patients with primary cutaneous malignant melanoma in whom PET scanning revealed in-transit or regional spread to nodes and those patients with known regional spread in whom PET scanning revealed distant metastases. We defined our false-negative results as a negative scan result with positive histology or subsequent clinical progression of disease. False-positive results were defined as a suspect scan with negative histology or no subsequent progression of disease. PET scanning had an overall sensitivity of 78% and specificity of 87%; however, subset analysis (M. D. Anderson staging system) showed a sensitivity of 50% for stage I disease (34 patients and 35 scans) and 33% for stage II disease (9 patients and 9 scans) with specificities of 87% and 100%, respectively. For stage III disease (16 patients and 17 scans), PET showed a sensitivity of 93% and specificity of 50%. Overall, 35% of patients with true-positive scans had their disease restaged. We can conclude therefore that PET is valuable as a staging procedure in patients with known regional spread but is suboptimal in the prediction of outcome in stage I or stage II disease.

  18. Automatic registration of pelvic computed tomography data and magnetic resonance scans including a full circle method for quantitative accuracy evaluation.

    PubMed

    van Herk, M; de Munck, J C; Lebesque, J V; Muller, S; Rasch, C; Touw, A

    1998-10-01

    The purpose of this study is to develop a method for registration of CT and MR scans of the pelvis with minimal user interaction and to obtain a means for objective quantification of the registration accuracy of clinical data without markers. CT scans were registered with proton density MR scans using chamfer matching on automatically segmented bone. A fixed threshold was used to segment CT, while morphological filters were used to segment MR. The method was tested with transverse and coronal MR scans of 18 patients and sagittal MR scans of 8 patients. The registration accuracy was estimated by comparing (triangulating) registrations of a single CT scan with MR in different orientations in a "full circle." For example, CT is first matched on transverse MR, next transverse MR is matched independently on coronal MR, and finally coronal MR is matched independently on CT. The product of the three transformations is the identity if all matching steps are perfect. Deviations from identity occur both due to random errors and due to some types of systematic errors. MR was registered on MR (to close the "circle") by minimization of rms voxel value differences. CT-MR registration takes about 1 min, including user interaction. The random error for CT-MR registration with transverse or coronal MR was 0.5 mm in translation and 0.4 degree in rotation (standard deviation) for each axis. A systematic registration error of about 1 mm was demonstrated along the MR frequency encoding direction, which is attributed to the chemical shift. In conclusion, the presented algorithm efficiently and accurately registers pelvic CT and MR scans on bone. The "full circle" method provides an estimate of the registration accuracy on clinical data.

  19. Development of a computer-aided diagnostic scheme for detection of interval changes in successive whole-body bone scans

    SciTech Connect

    Shiraishi, Junji; Li Qiang; Appelbaum, Daniel; Pu Yonglin; Doi, Kunio

    2007-01-15

    Bone scintigraphy is the most frequent examination among various diagnostic nuclear medicine procedures. It is a well-established imaging modality for the diagnosis of osseous metastasis and for monitoring osseous tumor response to chemotherapy and radiation therapy. Although the sensitivity of bone scan examinations for detection of bone abnormalities has been considered to be relatively high, it is time consuming to identify multiple lesions such as bone metastases of prostate and breast cancers. In addition, it is very difficult to detect subtle interval changes between two successive abnormal bone scans, because of variations in patient conditions, the accumulation of radioisotopes during each examination, and the image quality of gamma cameras. Therefore, we developed a new computer-aided diagnostic (CAD) scheme for the detection of interval changes in successive whole-body bone scans by use of a temporal subtraction image which was obtained with a nonlinear image-warping technique. We carried out 58 pairs of successive bone scans in which each scan included both posterior and anterior views. We determined 107 'gold-standard' interval changes among the 58 pairs based on the consensus of three radiologists. Our computerized scheme consisted of seven steps, i.e., initial image density normalization on each image, image matching for the paired images, temporal subtraction by use of the nonlinear image-warping technique, initial detection of interval changes by use of temporal-subtraction images, image feature extraction of candidates of interval changes, rule-based tests by use of 16 image features for removing some false positives, and display of the computer output for identified interval changes. One hundred seven gold standard interval changes included 71 hot lesions (uptake was increased compared with the previous scan, or there was new uptake in the current scan) and 36 cold lesions (uptake was decreased or disappeared) for anterior and posterior views. The

  20. Fast-Scan Cyclic Voltammetry (FSCV) Detection of Endogenous Octopamine in Drosophila melanogaster Ventral Nerve Cord.

    PubMed

    Pyakurel, Poojan; Privman Champaloux, Eve; Venton, B Jill

    2016-08-17

    Octopamine is an endogenous biogenic amine neurotransmitter, neurohormone, and neuromodulator in invertebrates and has functional analogy with norepinephrine in vertebrates. Fast-scan cyclic voltammetry (FSCV) can detect rapid changes in neurotransmitters, but FSCV has not been optimized for octopamine detection in situ. The goal of this study was to characterize octopamine release in the ventral nerve cord of Drosophila larvae for the first time. A FSCV waveform was optimized so that the potential for octopamine oxidation would not be near the switching potential where interferences can occur. Endogenous octopamine release was stimulated by genetically inserting either the ATP sensitive channel, P2X2, or the red-light sensitive channelrhodopsin, CsChrimson, into cells expressing tyrosine decarboxylase (TDC), an octopamine synthesis enzyme. To ensure that release is due to octopamine and not the precursor tyramine, the octopamine synthesis inhibitor disulfiram was applied, and the signal decreased by 80%. Stimulated release was vesicular, and a 2 s continuous light stimulation of CsChrimson evoked 0.22 ± 0.03 μM of octopamine release in the larval ventral nerve cord. Repeated stimulations were stable with 2 or 5 min interstimulation times. With pulsed stimulations, the release was dependent on the frequency of applied light pulse. An octopamine transporter has not been identified, and blockers of the dopamine transporter and serotonin transporter had no significant effect on the clearance time of octopamine, suggesting that they do not take up octopamine. This study shows that octopamine can be monitored in Drosophila, facilitating future studies of how octopamine release functions in the insect brain.

  1. Picometer stable scan mechanism for gravitational wave detection in space: LISA PAAM

    NASA Astrophysics Data System (ADS)

    Pijnenburg, Joep; Rijnveld, Niek; Sheard, Benjamin

    Picometer stable scan mechanism for gravitational wave detection in space: LISA PAAM Detection and observation of gravitational waves requires extreme stability in the frequency range 1E-4 to 1 Hz. The Laser Interferometer Space Antenna (LISA) mission will attain this by creating a giant interferometer in space, based on free floating proof masses in three spacecrafts. Due to orbit evolution and time delay in the interferometer arms, the direction of transmitted light changes. To solve this problem, an extremely stable Point Ahead Angle Mechanism (PAAM) was designed, built and tested. The PAAM concept is based on a rotatable mirror. The critical requirements are the contri-bution to the optical path delay (less than 1.4 pm / rt Hz) and the angular jitter (less than 8 nrad / rt Hz). To meet these requirements, the PAAM is designed for extreme mechanical and thermal stability. Extreme mechanical stability is achieved by manufacturing a monolithical Haberland hinge mechanism out of Ti-6Al-4V, through high precision wire erosion. Cross-talk is minimized by separation of the mirror rotation and actuation by a strut, resulting in a min-imum of parasitical forces. Extreme thermal stability is realized by placing the thermal center on the surface of the mirror. Because of piezo actuator noise and leakage, the PAAM has to be controlled in closed-loop. To meet the requirements in the low frequencies, an active target charge integration capacitance-to-digital converter is used. Interferometric measurements with a triangular resonant cavity in high vacuum proved that the PAAM meets the requirements. The critical component in the performance is the low frequency capacitive sensor noise.

  2. The source of moving particles in parafoveal capillaries detected by adaptive optics scanning laser ophthalmoscopy.

    PubMed

    Uji, Akihito; Hangai, Masanori; Ooto, Sotaro; Takayama, Kohei; Arakawa, Naoko; Imamura, Hiroshi; Nozato, Koji; Yoshimura, Nagahisa

    2012-01-20

    To investigate the source of moving particles in parafoveal capillaries detected by adaptive optics scanning laser ophthalmoscopy (AO-SLO). AO-SLO videos were acquired from the parafoveal areas of eyes of healthy subjects. The gray-scale values inside and outside the moving particles were measured and compared. Thereafter, successive frames of the captured videos were analyzed under higher magnification to detect changes in the gray values of bright spots inside the capillaries, before and during passage of the particles. Simultaneously, changes in the gray values of areas without the bright spots were measured for comparison. Then, the authors analyzed the packing arrangements of the bright spots in the particles, and measured the particle velocity using spatiotemporal images of the target capillary. There were no significant differences in the gray values between the moving particles and the cone mosaic outside the parafoveal capillaries adjacent to the particles. The gray value of the bright spots in the dark shadow of the vessels increased when the particles passed through, while the dark areas without bright spots remained dark. There were no significant differences in the packing arrangements between the bright spots and surrounding cone mosaic. Further, the concordance rate of packing arrangements of bright spots between two consecutive moving particles in the capillary was 95.8%. The mean particle velocity was 1.34 ± 0.42 mm/s. The particles moving in the capillaries are suggested to be reflections of photoreceptor aggregates that pass through circulating transparent objects such as leukocytes or plasma gaps.

  3. Use of differential scanning calorimetry to detect canola oil (Brassica napus L.) adulterated with lard stearin.

    PubMed

    Marikkar, Jalaldeen Mohammed Nazrim; Rana, Sohel

    2014-01-01

    A study was conducted to detect and quantify lard stearin (LS) content in canola oil (CaO) using differential scanning calorimetry (DSC). Authentic samples of CaO were obtained from a reliable supplier and the adulterant LS were obtained through a fractional crystallization procedure as reported previously. Pure CaO samples spiked with LS in levels ranging from 5 to 15% (w/w) were analyzed using DSC to obtain their cooling and heating profiles. The results showed that samples contaminated with LS at 5% (w/w) level can be detected using characteristic contaminant peaks appearing in the higher temperature regions (0 to 70°C) of the cooling and heating curves. Pearson correlation analysis of LS content against individual DSC parameters of the adulterant peak namely peak temperature, peak area, peak onset temperature indicated that there were strong correlations between these with the LS content of the CaO admixtures. When these three parameters were engaged as variables in the execution of the stepwise regression procedure, predictive models for determination of LS content in CaO were obtained. The predictive models obtained with single DSC parameter had relatively lower coefficient of determination (R(2) value) and higher standard error than the models obtained using two DSC parameters in combination. This study concluded that the predictive models obtained with peak area and peak onset temperature of the adulteration peak would be more accurate for prediction of LS content in CaO based on the highest coefficient of determination (R(2) value) and smallest standard error.

  4. Detection of conserved segments in proteins: iterative scanning of sequence databases with alignment blocks.

    PubMed Central

    Tatusov, R L; Altschul, S F; Koonin, E V

    1994-01-01

    We describe an approach to analyzing protein sequence databases that, starting from a single uncharacterized sequence or group of related sequences, generates blocks of conserved segments. The procedure involves iterative database scans with an evolving position-dependent weight matrix constructed from a coevolving set of aligned conserved segments. For each iteration, the expected distribution of matrix scores under a random model is used to set a cutoff score for the inclusion of a segment in the next iteration. This cutoff may be calculated to allow the chance inclusion of either a fixed number or a fixed proportion of false positive segments. With sufficiently high cutoff scores, the procedure converged for all alignment blocks studied, with varying numbers of iterations required. Different methods for calculating weight matrices from alignment blocks were compared. The most effective of those tested was a logarithm-of-odds, Bayesian-based approach that used prior residue probabilities calculated from a mixture of Dirichlet distributions. The procedure described was used to detect novel conserved motifs of potential biological importance. Images PMID:7991589

  5. Urban Road Detection in Airbone Laser Scanning Point Cloud Using Random Forest Algorithm

    NASA Astrophysics Data System (ADS)

    Kaczałek, B.; Borkowski, A.

    2016-06-01

    The objective of this research is to detect points that describe a road surface in an unclassified point cloud of the airborne laser scanning (ALS). For this purpose we use the Random Forest learning algorithm. The proposed methodology consists of two stages: preparation of features and supervised point cloud classification. In this approach we consider ALS points, representing only the last echo. For these points RGB, intensity, the normal vectors, their mean values and the standard deviations are provided. Moreover, local and global height variations are taken into account as components of a feature vector. The feature vectors are calculated on a basis of the 3D Delaunay triangulation. The proposed methodology was tested on point clouds with the average point density of 12 pts/m2 that represent large urban scene. The significance level of 15% was set up for a decision tree of the learning algorithm. As a result of the Random Forest classification we received two subsets of ALS points. One of those groups represents points belonging to the road network. After the classification evaluation we achieved from 90% of the overall classification accuracy. Finally, the ALS points representing roads were merged and simplified into road network polylines using morphological operations.

  6. Automatic fracture detection based on Terrestrial Laser Scanning data: A new method and case study

    NASA Astrophysics Data System (ADS)

    Cao, Ting; Xiao, Ancheng; Wu, Lei; Mao, Liguang

    2017-09-01

    Terrestrial Laser Scanning (TLS), widely known as light detection and ranging (LiDAR) technology, is increasingly used to obtain rapidly three-dimensional (3-D) geometry or highly detailed digital terrain models with millimetric point precision and accuracy. In this contribution, we proposed a simple and unbiased approach to identify fractures directly from 3-D surface model of natural outcrops generated from TLS data and thus acquire surface density, which can provide important supplement data for fracture related research. One outcrop from the Shizigou anticline in the Qaidam Basin (NW China) is taken as the case to validate the method and obtain optimal parameters, according to the references of surface density measured in the field and from the photos taken by high-resolution camera. The results show that with suitable parameters, the proposed method can identify most structural fractures quickly, providing a solution of extracting structural fractures from virtual outcrops based on TLS data. Furthermore, it will help a lot in analyzing the development of fractures and other related fields.

  7. CHARACTERISING THE EOS SLOT-SCANNING SYSTEM WITH THE EFFECTIVE DETECTIVE QUANTUM EFFICIENCY.

    PubMed

    Clavel, A H; Monnin, P; Létang, J M; Verdun, F R; Darbon, A

    2016-06-01

    As opposed to the standard detective quantum efficiency (DQE), effective DQE (eDQE) is a figure of merit that allows comparing the performances of imaging systems in the presence of scatter rejection devices. The geometry of the EOS™ slot-scanning system is such that the detector is self-collimated and rejects scattered radiation. In this study, the EOS system was characterised using the eDQE in imaging conditions similar to those used in clinical practice: with phantoms of different widths placed in the X-ray beam, for various incident air kerma and tube voltages corresponding to the phantom thickness. Scatter fractions in EOS images were extremely low, around 2 % for all configurations. Maximum eDQE values spanned 9-14.8 % for a large range of air kerma at the detector plane from 0.01 to 1.34 µGy. These figures were obtained with non-optimised EOS setting but still over-performed most of the maximum eDQEs recently assessed for various computed radiology and digital radiology systems with antiscatter grids.

  8. Line-scan Raman microscopy complements optical coherence tomography for tumor boundary detection

    NASA Astrophysics Data System (ADS)

    Sudheendran, Narendran; Qi, Ji; Young, Eric D.; Lazar, Alexander J.; Lev, Dina C.; Pollock, Raphael E.; Larin, Kirill V.; Shih, Wei-Chuan

    2014-10-01

    Current technique for tumor resection requires biopsy of the tumor region and histological confirmation before the surgeon can be certain that the entire tumor has been resected. This confirmation process is time consuming both for the surgeon and the patient and also requires sacrifice of healthy tissue, motivating the development of novel technologies which can enable real-time detection of tumor-healthy tissue boundary for faster and more efficient surgeries. In this study, the potential of combining structural information from optical coherence tomography (OCT) and molecular information from line-scan Raman microscopy (LSRM) for such an application is presented. The results show a clear presence of boundary between myxoid liposarcoma and normal fat which is easily identifiable both from structural and molecular information. In cases where structural images are indistinguishable, for example, in normal fat and well differentiated liposarcoma (WDLS) or gastrointestinal sarcoma tumor (GIST) and myxoma, distinct molecular spectra have been obtained. The results suggest LSRM can effectively complement OCT to tumor boundary demarcation with high specificity.

  9. Buried mine detection using fractal geometry analysis to the LWIR successive line scan data image

    NASA Astrophysics Data System (ADS)

    Araki, Kan

    2012-06-01

    We have engaged in research on buried mine/IED detection by remote sensing method using LWIR camera. A IR image of a ground, containing buried objects can be assumed as a superimposed pattern including thermal scattering which may depend on the ground surface roughness, vegetation canopy, and effect of the sun light, and radiation due to various heat interaction caused by differences in specific heat, size, and buried depth of the objects and local temperature of their surrounding environment. In this cumbersome environment, we introduce fractal geometry for analyzing from an IR image. Clutter patterns due to these complex elements have oftentimes low ordered fractal dimension of Hausdorff Dimension. On the other hand, the target patterns have its tendency of obtaining higher ordered fractal dimension in terms of Information Dimension. Random Shuffle Surrogate method or Fourier Transform Surrogate method is used to evaluate fractional statistics by applying shuffle of time sequence data or phase of spectrum. Fractal interpolation to each line scan was also applied to improve the signal processing performance in order to evade zero division and enhance information of data. Some results of target extraction by using relationship between low and high ordered fractal dimension are to be presented.

  10. Imaging via complete cantilever dynamic detection: General dynamic mode imaging and spectroscopy in scanning probe microscopy

    SciTech Connect

    Somnath, Suhas; Collins, Liam; Matheson, Michael A.; Sukumar, Sreenivas R.; Kalinin, Sergei V.; Jesse, Stephen

    2016-09-08

    We develop and implement a multifrequency spectroscopy and spectroscopic imaging mode, referred to as general dynamic mode (GDM), that captures the complete spatially- and stimulus dependent information on nonlinear cantilever dynamics in scanning probe microscopy (SPM). GDM acquires the cantilever response including harmonics and mode mixing products across the entire broadband cantilever spectrum as a function of excitation frequency. GDM spectra substitute the classical measurements in SPM, e.g. amplitude and phase in lock-in detection. Here, GDM is used to investigate the response of a purely capacitively driven cantilever. We use information theory techniques to mine the data and verify the findings with governing equations and classical lock-in based approaches. We explore the dependence of the cantilever dynamics on the tip–sample distance, AC and DC driving bias. This approach can be applied to investigate the dynamic behavior of other systems within and beyond dynamic SPM. In conclusion, GDM is expected to be useful for separating the contribution of different physical phenomena in the cantilever response and understanding the role of cantilever dynamics in dynamic AFM techniques.

  11. Nanoparticle Enhanced MRI Scanning to Detect Cellular Inflammation in Experimental Chronic Renal Allograft Rejection

    PubMed Central

    Alam, S. R.; Tse, G. H.; Stirrat, C.; MacGillivray, T. J.; Lennen, R. J.; Jansen, M. A.; Newby, D. E.; Marson, L.; Henriksen, P. A.

    2015-01-01

    Objectives. We investigated whether ultrasmall paramagnetic particles of iron oxide- (USPIO-) enhanced magnetic resonance imaging (MRI) can detect experimental chronic allograft damage in a murine renal allograft model. Materials and Methods. Two cohorts of mice underwent renal transplantation with either a syngeneic isograft or allograft kidney. MRI scanning was performed prior to and 48 hours after USPIO infusion using T2∗-weighted protocols. R2∗ values were calculated to indicate the degree of USPIO uptake. Native kidneys and skeletal muscle were imaged as reference tissues and renal explants analysed by histology and electron microscopy. Results. R2∗ values in the allograft group were higher compared to the isograft group when indexed to native kidney (median 1.24 (interquartile range: 1.12 to 1.36) versus 0.96 (0.92 to 1.04), P < 0.01). R2∗ values were also higher in the allograft transplant when indexed to skeletal muscle (6.24 (5.63 to 13.51)) compared to native kidney (2.91 (1.11 to 6.46) P < 0.05). Increased R2∗ signal in kidney allograft was associated with macrophage and iron staining on histology. USPIO were identified within tissue resident macrophages on electron microscopy. Conclusion. USPIO-enhanced MRI identifies macrophage. PMID:25954516

  12. Imaging via complete cantilever dynamic detection: general dynamic mode imaging and spectroscopy in scanning probe microscopy

    NASA Astrophysics Data System (ADS)

    Somnath, Suhas; Collins, Liam; Matheson, Michael A.; Sukumar, Sreenivas R.; Kalinin, Sergei V.; Jesse, Stephen

    2016-10-01

    We develop and implement a multifrequency spectroscopy and spectroscopic imaging mode, referred to as general dynamic mode (GDM), that captures the complete spatially- and stimulus dependent information on nonlinear cantilever dynamics in scanning probe microscopy (SPM). GDM acquires the cantilever response including harmonics and mode mixing products across the entire broadband cantilever spectrum as a function of excitation frequency. GDM spectra substitute the classical measurements in SPM, e.g. amplitude and phase in lock-in detection. Here, GDM is used to investigate the response of a purely capacitively driven cantilever. We use information theory techniques to mine the data and verify the findings with governing equations and classical lock-in based approaches. We explore the dependence of the cantilever dynamics on the tip–sample distance, AC and DC driving bias. This approach can be applied to investigate the dynamic behavior of other systems within and beyond dynamic SPM. GDM is expected to be useful for separating the contribution of different physical phenomena in the cantilever response and understanding the role of cantilever dynamics in dynamic AFM techniques.

  13. Imaging via complete cantilever dynamic detection: General dynamic mode imaging and spectroscopy in scanning probe microscopy

    SciTech Connect

    Somnath, Suhas; Collins, Liam; Matheson, Michael A.; Sukumar, Sreenivas R.; Kalinin, Sergei V.; Jesse, Stephen

    2016-09-08

    We develop and implement a multifrequency spectroscopy and spectroscopic imaging mode, referred to as general dynamic mode (GDM), that captures the complete spatially- and stimulus dependent information on nonlinear cantilever dynamics in scanning probe microscopy (SPM). GDM acquires the cantilever response including harmonics and mode mixing products across the entire broadband cantilever spectrum as a function of excitation frequency. GDM spectra substitute the classical measurements in SPM, e.g. amplitude and phase in lock-in detection. Here, GDM is used to investigate the response of a purely capacitively driven cantilever. We use information theory techniques to mine the data and verify the findings with governing equations and classical lock-in based approaches. We explore the dependence of the cantilever dynamics on the tip–sample distance, AC and DC driving bias. This approach can be applied to investigate the dynamic behavior of other systems within and beyond dynamic SPM. In conclusion, GDM is expected to be useful for separating the contribution of different physical phenomena in the cantilever response and understanding the role of cantilever dynamics in dynamic AFM techniques.

  14. Imaging via complete cantilever dynamic detection: General dynamic mode imaging and spectroscopy in scanning probe microscopy

    DOE PAGES

    Somnath, Suhas; Collins, Liam; Matheson, Michael A.; ...

    2016-09-08

    We develop and implement a multifrequency spectroscopy and spectroscopic imaging mode, referred to as general dynamic mode (GDM), that captures the complete spatially- and stimulus dependent information on nonlinear cantilever dynamics in scanning probe microscopy (SPM). GDM acquires the cantilever response including harmonics and mode mixing products across the entire broadband cantilever spectrum as a function of excitation frequency. GDM spectra substitute the classical measurements in SPM, e.g. amplitude and phase in lock-in detection. Here, GDM is used to investigate the response of a purely capacitively driven cantilever. We use information theory techniques to mine the data and verify themore » findings with governing equations and classical lock-in based approaches. We explore the dependence of the cantilever dynamics on the tip–sample distance, AC and DC driving bias. This approach can be applied to investigate the dynamic behavior of other systems within and beyond dynamic SPM. In conclusion, GDM is expected to be useful for separating the contribution of different physical phenomena in the cantilever response and understanding the role of cantilever dynamics in dynamic AFM techniques.« less

  15. Computerized lung nodule detection: comparison of performance for low-dose and standard-dose helical CT scans

    NASA Astrophysics Data System (ADS)

    Armato, Samuel G., III; Giger, Maryellen L.; Doi, Kunio; Bick, Ulrich; MacMahon, Heber

    2001-07-01

    The vast amount of image data acquired during a computed tomography (CT) scan makes lung nodule detection a burdensome task. Moreover, the growing acceptance of low-dose CT for lung cancer screening promises to further impact radiologists' workloads. Therefore, we have developed a computerized method to automatically analyze structures within a CT scan and identify those structures that represent lung nodules. Gray-level thresholding is performed to segment the lungs in each section to produce a segmented lung volume, which is then iteratively thresholded. At each iteration, remaining voxels are grouped into contiguous three-dimensional structures. Structures that satisfy a volume criterion then become nodule candidates. The set of nodule candidates is subjected to feature analysis. To distinguish candidates representing nodule and non-nodule structures, a rule-based approach is combined with an automated classifier. This method was applied to 43 standard-dose (diagnostic) CT scans and 13 low-dose CT scans. The method achieved an overall detection sensitivity of 71% with 1.5 false-positive detections per section on the standard-dose database and 71% sensitivity with 1.2 false-positive detections per section on the low-dose database. This automated method demonstrates promising performance in its ability to accurately detect lung nodules in standard-dose and low-dose CT images.

  16. Detection of Cervical Cancer Biomarker Patterns in Blood Plasma and Urine by Differential Scanning Calorimetry and Mass Spectrometry

    PubMed Central

    Garbett, Nichola C.; Merchant, Michael L.; Helm, C. William; Jenson, Alfred B.; Klein, Jon B.; Chaires, Jonathan B.

    2014-01-01

    Improved methods for the accurate identification of both the presence and severity of cervical intraepithelial neoplasia (CIN) and extent of spread of invasive carcinomas of the cervix (IC) are needed. Differential scanning calorimetry (DSC) has recently been shown to detect specific changes in the thermal behavior of blood plasma proteins in several diseases. This methodology is being explored to provide a complementary approach for screening of cervical disease. The present study evaluated the utility of DSC in differentiating between healthy controls, increasing severity of CIN and early and advanced IC. Significant discrimination was apparent relative to the extent of disease with no clear effect of demographic factors such as age, ethnicity, smoking status and parity. Of most clinical relevance, there was strong differentiation of CIN from healthy controls and IC, and amongst patients with IC between FIGO Stage I and advanced cancer. The observed disease-specific changes in DSC profiles (thermograms) were hypothesized to reflect differential expression of disease biomarkers that subsequently bound to and affected the thermal behavior of the most abundant plasma proteins. The effect of interacting biomarkers can be inferred from the modulation of thermograms but cannot be directly identified by DSC. To investigate the nature of the proposed interactions, mass spectrometry (MS) analyses were employed. Quantitative assessment of the low molecular weight protein fragments of plasma and urine samples revealed a small list of peptides whose abundance was correlated with the extent of cervical disease, with the most striking plasma peptidome data supporting the interactome theory of peptide portioning to abundant plasma proteins. The combined DSC and MS approach in this study was successful in identifying unique biomarker signatures for cervical cancer and demonstrated the utility of DSC plasma profiles as a complementary diagnostic tool to evaluate cervical cancer

  17. Detection of cervical cancer biomarker patterns in blood plasma and urine by differential scanning calorimetry and mass spectrometry.

    PubMed

    Garbett, Nichola C; Merchant, Michael L; Helm, C William; Jenson, Alfred B; Klein, Jon B; Chaires, Jonathan B

    2014-01-01

    Improved methods for the accurate identification of both the presence and severity of cervical intraepithelial neoplasia (CIN) and extent of spread of invasive carcinomas of the cervix (IC) are needed. Differential scanning calorimetry (DSC) has recently been shown to detect specific changes in the thermal behavior of blood plasma proteins in several diseases. This methodology is being explored to provide a complementary approach for screening of cervical disease. The present study evaluated the utility of DSC in differentiating between healthy controls, increasing severity of CIN and early and advanced IC. Significant discrimination was apparent relative to the extent of disease with no clear effect of demographic factors such as age, ethnicity, smoking status and parity. Of most clinical relevance, there was strong differentiation of CIN from healthy controls and IC, and amongst patients with IC between FIGO Stage I and advanced cancer. The observed disease-specific changes in DSC profiles (thermograms) were hypothesized to reflect differential expression of disease biomarkers that subsequently bound to and affected the thermal behavior of the most abundant plasma proteins. The effect of interacting biomarkers can be inferred from the modulation of thermograms but cannot be directly identified by DSC. To investigate the nature of the proposed interactions, mass spectrometry (MS) analyses were employed. Quantitative assessment of the low molecular weight protein fragments of plasma and urine samples revealed a small list of peptides whose abundance was correlated with the extent of cervical disease, with the most striking plasma peptidome data supporting the interactome theory of peptide portioning to abundant plasma proteins. The combined DSC and MS approach in this study was successful in identifying unique biomarker signatures for cervical cancer and demonstrated the utility of DSC plasma profiles as a complementary diagnostic tool to evaluate cervical cancer