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Sample records for scan detects quantitative

  1. 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.

  2. 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.

  3. 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.

  4. 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)

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  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. 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.

  12. 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.

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. [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).

  18. 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.

  19. 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.

  20. 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.

  1. Computer-aided quantitative bone scan assessment of prostate cancer treatment response

    PubMed Central

    Brown, Matthew S.; Chu, Gregory H.; Kim, Hyun J.; Allen-Auerbach, Martin; Poon, Cheryce; Bridges, Juliette; Vidovic, Adria; Ramakrishna, Bharath; Ho, Judy; Morris, Michael J.; Larson, Steven M.; Scher, Howard I.; Goldin, Jonathan G.

    2012-01-01

    Objective The development and evaluation of a computer-aided bone scan analysis technique to quantify changes in tumor burden and assess treatment effects in prostate cancer clinical trials. Methods We have developed and report on a commercial fully automated computer-aided detection system. Using this system, scan images were intensity normalized, then lesions identified and segmented by anatomic region-specific intensity thresholding. Detected lesions were compared against expert markings to assess the accuracy of the computer-aided detection system. The metrics Bone Scan Lesion Area, Bone Scan Lesion Intensity, and Bone Scan Lesion Count were calculated from identified lesions, and their utility in assessing treatment effects was evaluated by analyzing before and after scans from metastatic castration-resistant prostate cancer patients: 10 treated and 10 untreated. In this study, patients were treated with cabozantinib, a MET/VEGF inhibitor resulting in high rates of resolution of bone scan abnormalities. Results Our automated computer-aided detection system identified bone lesion pixels with 94% sensitivity, 89% specificity, and 89% accuracy. Significant differences in changes from baseline were found between treated and untreated groups in all assessed measurements derived by our system. The most significant measure, Bone Scan Lesion Area, showed a median (interquartile range) change from baseline at week 6 of 7.13% (27.61) in the untreated group compared with −73.76% (45.38) in the cabozantinib-treated group (P = 0.0003). Conclusions Our system accurately and objectively identified and quantified metastases in bone scans, allowing for interpatient and intrapatient comparison. It demonstrates potential as an objective measurement of treatment effects, laying the foundation for validation against other clinically relevant outcome measures. PMID:22367858

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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).

  2. 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.

  3. 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.

  4. 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.

  5. 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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 ...

  7. 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.

  8. 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.

  9. 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..

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. Bone Scan Index: A Quantitative Treatment Response Biomarker for Castration-Resistant Metastatic Prostate Cancer

    PubMed Central

    Dennis, Elizabeth R.; Jia, Xiaoyu; Mezheritskiy, Irina S.; Stephenson, Ryan D.; Schoder, Heiko; Fox, Josef J.; Heller, Glenn; Scher, Howard I.; Larson, Steven M.; Morris, Michael J.

    2012-01-01

    Purpose There is currently no imaging biomarker for metastatic prostate cancer. The bone scan index (BSI) is a promising candidate, being a reproducible, quantitative expression of tumor burden seen on bone scintigraphy. Prior studies have shown the prognostic value of a baseline BSI. This study tested whether treatment-related changes in BSI are prognostic for survival and compared BSI to prostate-specific antigen (PSA) as an outcome measure. Patients and Methods We retrospectively examined serial bone scans from patients with castration-resistant metastatic prostate cancer (CRMPC) enrolled in four clinical trials. We calculated BSI at baseline and at 3 and 6 months on treatment and performed univariate and bivariate analyses of PSA, BSI, and survival. Results Eighty-eight patients were scanned, 81 of whom have died. In the univariate analysis, the log percent change in BSI from baseline to 3 and 6 months on treatment prognosticated for survival (hazard ratio [HR], 2.44; P = .0089 and HR, 2.54; P < .001, respectively). A doubling in BSI resulted in a 1.9-fold increase in risk of death. Log percent change in PSA at 6 months on treatment was also associated with survival (HR, 1.298; P = .013). In the bivariate analysis, change in BSI while adjusting for PSA was prognostic at 3 and 6 months on treatment (HR, 2.368; P = .012 and HR, 2.226; P = .002, respectively), but while adjusting for BSI, PSA was not prognostic. Conclusion These data furnish early evidence that on-treatment changes in BSI are a response indicator and support further exploration of bone scintigraphy as an imaging biomarker in CRMPC. PMID:22231045

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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.

  2. 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

  3. 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.

  4. 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.

  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. 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.

  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

    2017-01-17

    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 × 10(20) neutrons cm(-)(2) The quantitatively measured size distribution (average loop size = 3.6 ± 2.1 nm), number density of the dislocation loops (3.6 × 10(22) m(-3)) and dislocation density (7.8 × 10(13) 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. A genome scan for quantitative trait loci affecting body conformation traits in Spanish Churra dairy sheep.

    PubMed

    Gutiérrez-Gil, B; Alvarez, L; de la Fuente, L F; Sanchez, J P; San Primitivo, F; Arranz, J J

    2011-08-01

    A genome scan for chromosomal regions influencing body conformation traits was conducted for a population of Spanish Churra dairy sheep following a daughter design. A total of 739 ewes from 11 half-sib sire families were included in the study. The ewes were scored for the 5 linear traits used in the breeding scheme of the Churra breed to assess body conformation: stature, rear legs-rear view, foot angle, rump width, and general appearance. All the animals, including the 11 sires, were genotyped for 181 microsatellite markers evenly distributed across the 26 sheep autosomes. Using the yield deviations of the raw scores adjusted for fixed factors as phenotypic measurements, a quantitative trait loci (QTL) analysis was performed on the basis of a multi-marker regression method. Seven suggestive QTL were identified on chromosomes Ovis aries (OAR)2, OAR5, OAR16, OAR23, and OAR26, but none reached a genome-wise significance level. Putative QTL were identified for all of the traits analyzed, except for general appearance score. The suggestive QTL showing the highest test statistic influenced rear legs-rear view and was localized on OAR16, close to the growth hormone receptor coding gene, GHR. Some of the putative linkage associations reported here are consistent with previously reported QTL in cattle for similar traits. To the best of our knowledge, this study provides the first report of QTL for body conformation traits in dairy sheep; further studies will be needed to confirm and redefine the linkage associations reported herein. It is expected that future genome-wide association analyses of larger families will help identify genes underlying these putative genetic effects and provide useful markers for marker-assisted selection of such functional traits.

  17. 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.

  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. 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.

  20. 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.

  1. 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.

  2. 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

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. [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.

  17. 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.

  18. Association Between a Quantitative CT Scan Measure of Brain Edema and Outcome After Cardiac Arrest

    PubMed Central

    Metter, Robert B.; Rittenberger, Jon C.; Guyette, Francis X.; Callaway, Clifton W.

    2011-01-01

    Background Cerebral edema is one physical change associated with brain injury and decreased survival after cardiac arrest. Edema appears on computed tomography (CT) scan of the brain as decreased x-ray attenuation by gray matter. This study tested whether the gray matter attenuation to white matter attenuation ratio (GWR) was associated with survival and functional recovery. Methods Subjects were patients hospitalized after cardiac arrest at a single institution between 1/1/2005 and 7/30/2010. Subjects were included if they had non-traumatic cardiac arrest and a non-contrast CT scan within 24 hours after cardiac arrest. Attenuation (Hounsfield Units) was measured in gray matter (caudate nucleus, putamen, thalamus, and cortex) and in white matter (internal capsule, corpus callosum and centrum semiovale). The GWR was calculated for basal ganglia and cerebrum. Outcomes included survival and functional status at hospital discharge. Results For 680 patients, 258 CT scans were available, but 18 were excluded because of hemorrhage (10), intravenous contrast (3) or technical artifact (5), leaving 240 CT scans for analysis. Lower GWR values were associated with lower initial Glasgow Coma Scale motor score. Overall survival was 36%, but decreased with decreasing GWR. The average of basal ganglia and cerebrum GWR provided the best discrimination. Only 2/58 subjects with average GWR<1.20 survived and both were treated with hypothermia. The association of GWR with functional outcome was completely explained by mortality when GWR<1.20. Conclusions Subjects with severe cerebral edema, defined by GWR<1.20, have very low survival with conventional care, including hypothermia. GWR estimates pre-treatment likelihood of survival after cardiac arrest. PMID:21592642

  19. 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.

  20. 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

  1. 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.

  2. 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)

  3. 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.

  4. 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

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. DMSO increases mutation-scanning detection sensitivity in clinical samples using high resolution melting

    PubMed Central

    Song, Chen; Castellanos-Rizaldos, Elena; Bejar, Rafael; Ebert, Benjamin L.; Makrigiorgos, G. Mike

    2016-01-01

    BACKGROUND Mutation scanning provides the simplest, lowest cost method for identifying DNA variations on single PCR amplicons, and it may be performed prior to sequencing to avoid screening of non-informative wild type samples. High resolution melting (HRM) is the most commonly used method for mutation scanning. However, by using PCR-HRM mutations below ≈ 3–10% that can still be clinically significant may often be missed. Therefore, enhancing HRM detection sensitivity is important for mutation scanning and its clinical application. METHODS We used serial dilution of TP53 exon 8 mutation containing cell lines to demonstrate the improvement in detection sensitivity for conventional-PCR-HRM in the presence of DMSO. We also conducted full-COLD-PCR to further enrich low-level mutations prior to HRM±DMSO and employed droplet-digital PCR to derive the optimal conditions for mutation enrichment. Both conventional-PCR-HRM and full-COLD-PCR-HRM ±DMSO were used for mutation scanning in TP53 exon 8 in cancer samples containing known mutations and in myelodysplastic syndrome samples with unknown mutations. Mutations in other genes were also examined. RESULTS The detection sensitivity of PCR-HRM-scanning increases 2–5-fold in the presence of DMSO, depending also on mutation type and sequence context, and can typically detect mutation abundance of about 1%. When mutation enrichment is applied during amplification using full-COLD-PCR and followed by HRM in the presence of DMSO, mutations with 0.2–0.3% mutation abundance in TP53 exon 8 can be detected. CONCLUSIONS DMSO improves HRM mutation scanning sensitivity. When full-COLD-PCR is employed, followed by DMSO-HRM, the overall improvement is about 20-fold as compared to conventional PCR-HRM. PMID:26432802

  13. 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

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  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. 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. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. [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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. 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

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. 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)

  16. 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.

  17. 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.

  18. 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

  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. 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

  2. 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.

  3. 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.

  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. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. 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.

  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. 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.

  14. 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

  15. 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.

  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. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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

  3. 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.

  4. 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.

  5. 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

  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. 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.

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. 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.

  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. 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. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. 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.

  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. 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.

  12. 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

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. 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

  20. 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.

  1. 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

  2. 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.

  3. [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.

  4. 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.

  5. 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

  6. 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

  7. 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

  8. 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. ...

  9. A new molecular diagnostic tool for quantitatively detecting and genotyping “Candidatus Liberibacter species”

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  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. 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.

  12. Comparative analysis of techniques for detection of quiescent Botrytis cinerea in grapes by quantitative PCR

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. Step-scan T cell-based differential Fourier transform infrared photoacoustic spectroscopy (DFTIR-PAS) for detection of ambient air contaminants

    NASA Astrophysics Data System (ADS)

    Liu, Lixian; Mandelis, Andreas; Huan, Huiting; Melnikov, Alexander

    2016-10-01

    A step-scan differential Fourier transform infrared photoacoustic spectroscopy (DFTIR-PAS) using a commercial FTIR spectrometer was developed theoretically and experimentally for air contaminant monitoring. The configuration comprises two identical, small-size and low-resonance-frequency T cells satisfying the conflicting requirements of low chopping frequency and limited space in the sample compartment. Carbon dioxide (CO2) IR absorption spectra were used to demonstrate the capability of the DFTIR-PAS method to detect ambient pollutants. A linear amplitude response to CO2 concentrations from 100 to 10,000 ppmv was observed, leading to a theoretical detection limit of 2 ppmv. The differential mode was able to suppress the coherent noise, thereby imparting the DFTIR-PAS method with a better signal-to-noise ratio and lower theoretical detection limit than the single mode. The results indicate that it is possible to use step-scan DFTIR-PAS with T cells as a quantitative method for high sensitivity analysis of ambient contaminants.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. Lateral flow immunoassay for quantitative detection of ractopamine in swine urine.

    PubMed

    Ren, Mei Ling; Chen, Xue Lan; Li, Chao Hui; Xu, Bo; Liu, Wen Juan; Xu, Heng Yi; Xiong, Yong Hua

    2014-02-01

    A strip reader based lateral flow immunoassay (LFIA) was established for the rapid and quantitative detection of ractopamine (RAC) in swine urine. The ratio of the optical densities (ODs) of the test line (AT) to that of the control line (AC) was used to effectively minimize interference among strips and sample variations. The linear range for the quantitative detection of RAC was 0.2 ng/mL to 3.5 ng/mL with a median inhibitory concentration (IC50) of 0.59 ± 0.06 ng/mL. The limit of detection (LOD) of the LFIA was 0.13 ng/mL. The intra-assay recovery rates were 92.97%, 97.25%, and 107.41%, whereas the inter-assay rates were 80.07%, 108.17%, and 93.7%, respectively.

  12. Application of image processing for terahertz time domain spectroscopy imaging quantitative detection

    NASA Astrophysics Data System (ADS)

    Li, Li-juan; Wang, Sheng; Ren, Jiao-jiao; Zhou, Ming-xing; Zhao, Duo

    2015-03-01

    According to nondestructive testing principle for the terahertz time domain spectroscopy Imaging, using digital image processing techniques, through Terahertz time-domain spectroscopy system collected images and two-dimensional datas and using a range of processing methods, including selecting regions of interest, contrast enhancement, edge detection, and defects being detected. In the paper, Matlab programming is been use to defect recognition of Terahertz, by figuring out the pixels to determine defects defect area and border length, roundness, diameter size. Through the experiment of the qualitative analysis and quantitative calculation of Matlab image processing, this method of detection of defects of geometric dimension of the sample to get a better result.

  13. Paper diagnostic device for quantitative electrochemical detection of ricin at picomolar levels.

    PubMed

    Cunningham, Josephine C; Scida, Karen; Kogan, Molly R; Wang, Bo; Ellington, Andrew D; Crooks, Richard M

    2015-01-01

    We report a paper-based assay platform for detection of ricin a chain. The paper platform is assembled by simple origami paper folding. The sensor is based on quantitative, electrochemical detection of silver nanoparticle labels linked to a magnetic microbead support via a ricin immunosandwich. Importantly, ricin was detected at concentrations as low as 34 pM. Additionally, the assay is robust, even in the presence of 100-fold excess hoax materials. Finally, the device is easily remediated after use by incineration. The cost of the device, not including reagents, is just $0.30. The total assay time, including formation of the immunosandwich, is 9.5 min.

  14. Quantitative ventilation-perfusion lung scans in infants and children: utility of a submicronic radiolabeled aerosol to assess ventilation

    SciTech Connect

    O'Brodovich, H.M.; Coates, G.

    1984-09-01

    The quantitative assessment of regional pulmonary ventilation and perfusion provides useful information regarding lung function. Its use in infants and young children, however, has been minimal because of practical and technical limitations when the distribution of ventilation is assessed by radioactive gases. In 16 infants and children we used an inexpensive commercially available nebulizer to produce a submicronic aerosol labeled with 99mtechnetium-diethylenetriamine pentacetic acid to assess ventilation quantitatively, and intravenous injections of 99mtechnetium-labeled macroaggregates of albumin to assess pulmonary perfusion quantitatively. Studies were safely completed in both ambulatory and critically ill patients, including two premature infants who had endotracheal tubes in place for ventilatory support. No sedation or patient cooperation is required. This technique enables any department of nuclear medicine to measure regional pulmonary ventilation and perfusion in infants and children.

  15. Distance-based microfluidic quantitative detection methods for point-of-care testing.

    PubMed

    Tian, Tian; Li, Jiuxing; Song, Yanling; Zhou, Leiji; Zhu, Zhi; Yang, Chaoyong James

    2016-04-07

    Equipment-free devices with quantitative readout are of great significance to point-of-care testing (POCT), which provides real-time readout to users and is especially important in low-resource settings. Among various equipment-free approaches, distance-based visual quantitative detection methods rely on reading the visual signal length for corresponding target concentrations, thus eliminating the need for sophisticated instruments. The distance-based methods are low-cost, user-friendly and can be integrated into portable analytical devices. Moreover, such methods enable quantitative detection of various targets by the naked eye. In this review, we first introduce the concept and history of distance-based visual quantitative detection methods. Then, we summarize the main methods for translation of molecular signals to distance-based readout and discuss different microfluidic platforms (glass, PDMS, paper and thread) in terms of applications in biomedical diagnostics, food safety monitoring, and environmental analysis. Finally, the potential and future perspectives are discussed.

  16. Functionalized Magnetic Nanoparticles for the Detection and Quantitative Analysis of Cell Surface Antigen

    PubMed Central

    Shahbazi-Gahrouei, Daryoush; Abdolahi, Mohammad; Zarkesh-Esfahani, Sayyed Hamid; Laurent, Sophie; Sermeus, Corine; Gruettner, Cordula

    2013-01-01

    Cell surface antigens as biomarkers offer tremendous potential for early diagnosis, prognosis, and therapeutic response in a variety of diseases such as cancers. In this research, a simple, rapid, accurate, inexpensive, and easily available in vitro assay based on magnetic nanoparticles and magnetic cell separation principle was applied to identify and quantitatively analyze the cell surface antigen expression in the case of prostate cancer cells. Comparing the capability of the assay with flow cytometry as a gold standard method showed similar results. The results showed that the antigen-specific magnetic cell separation with antibody-coated magnetic nanoparticles has high potential for quantitative cell surface antigen detection and analysis. PMID:23484112

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

    PubMed

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

    2016-06-01

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

  18. Genome-wide scans to detect positive selection in Large White and Tongcheng pigs.

    PubMed

    Li, Xiuling; Yang, Songbai; Tang, Zhonglin; Li, Kui; Rothschild, Max F; Liu, Bang; Fan, Bin

    2014-06-01

    Due to the direction, intensity, duration and consistency of genetic selection, especially recent artificial selection, the production performance of domestic pigs has been greatly changed. Therefore, we reasoned that there must be footprints or selection signatures that had been left during domestication. In this study, with porcine 60K BeadChip genotyping data from both commercial Large White and local Chinese Tongcheng pigs, we calculated the extended haplotype homozygosity values of the two breeds using the long-range haplotype method to detect selection signatures. We found 34 candidate regions, including 61 known genes, from Large White pigs and 25 regions comprising 57 known genes from Tongcheng pigs. Many selection signatures were found on SSC1, SSC4, SSC7 and SSC14 regions in both populations. According to quantitative trait loci and network pathway analyses, most of the regions and genes were linked to growth, reproduction and immune responses. In addition, the average genetic differentiation coefficient FST was 0.254, which means that there had already been a significant differentiation between the breeds. The findings from this study can contribute to further research on molecular mechanisms of pig evolution and domestication and also provide valuable references for improvement of their breeding and cultivation.

  19. A scanning laser source and a microcantilever ultrasound receiver for detection of surface flaws in microdevices

    NASA Astrophysics Data System (ADS)

    Sohn, Younghoon; Krishnaswamy, Sridhar

    2005-05-01

    In recent work at Northwestern University, we have shown that near-field scattering of ultrasound generated by a Scanning Laser Source (SLS) can be used to effectively identify surface flaws in macroscale structures. In past work, the laser ultrasound source was in the near-field of a scatterer and a piezoelectric detector was used to measure the ultrasound in the far field. It was observed that distinct variations are observed in the far-field signals as the SLS scans past surface-breaking flaws. These changes were attributed to the near-field scatterer redirecting parts of the ultrasonic beam (which might otherwise have gone into the bulk of the object) towards the far-field detector. We now propose an extension of the SLS approach to map defects in microdevices by bringing both the generator and the receiver to the near-field scattering region of the defects. For the purpose of near-field ultrasound measurement, the receiving transducer has to be made very small as well. To facilitate this, silicon microcantilever probes are fabricated and their acoustical characteristics are first investigated. Silicon cantilevers with tip and chip body are fabricated using isotropic reactive ion etching and anisotropic KOH etching. To characterize the free cantilever vibration, the chip body with the microcantilever is excited by an ultrasonic transducer and a Michelson interferometer is used to monitor the cantilever motion. The fundamental frequency of the microcantilever is measured and compared with analytically calculated fundamental frequency assuming the cross sections of the cantilevers are rectangular. Next, the performance of the fabricated microcantilevers as ultrasound detectors is investigated. The microcantilever is used essentially as a profilometer by contacting it to the specimen surface. Surface and bulk acoustic waves are generated with specific narrowband frequencies and the surface ultrasonic displacements are detected using the microcantilever probe. Next

  20. Sensitive and quantitative detection of botulinum neurotoxin in neurons derived from mouse embryonic stem cells

    PubMed Central

    Pellett, Sabine; Du, Zhong-wei; Pier, Christina L.; Tepp, William H.; Zhang, Su-chun; Johnson, Eric A.

    2010-01-01

    Botulinum neurotoxins (BoNTs), the most poisonous protein toxins known, represent a serious bioterrorism threat but are also used as a unique and important bio-pharmaceutical to treat an increasing myriad of neurological disorders. The only currently accepted detection method by the United States Food and Drug Administration for biological activity of BoNTs and for potency determination of pharmaceutical preparations is the mouse bioassay (MBA). Recent advances have indicated that cell-based assays using primary neuronal cells can provide an equally sensitive and robust detection platform as the MBA to reliably and quantitatively detect biologically active BoNTs. This study reports for the first time a BoNT detection assay using mouse embryonic stem cells to produce a neuronal cell culture. The data presented indicate that this assaycan reliably detect BoNT/A with a similar sensitivity as the MBA. PMID:21130748

  1. Qualitative and quantitative PCR methods for detection of three lines of genetically modified potatoes.

    PubMed

    Rho, Jae Kyun; Lee, Theresa; Jung, Soon-Il; Kim, Tae-San; Park, Yong-Hwan; Kim, Young-Mi

    2004-06-02

    Qualitative and quantitative polymerase chain reaction (PCR) methods have been developed for the detection of genetically modified (GM) potatoes. The combination of specific primers for amplification of the promoter region of Cry3A gene, potato leafroll virus replicase gene, and potato virus Y coat protein gene allows to identify each line of NewLeaf, NewLeaf Y, and NewLeaf Plus GM potatoes. Multiplex PCR method was also established for the simple and rapid detection of the three lines of GM potato in a mixture sample. For further quantitative detection, the realtime PCR method has been developed. This method features the use of a standard plasmid as a reference molecule. Standard plasmid contains both a specific region of the transgene Cry3A and an endogenous UDP-glucose pyrophosphorylase gene of the potato. The test samples containing 0.5, 1, 3, and 5% GM potatoes were quantified by this method. At the 3.0% level of each line of GM potato, the relative standard deviations ranged from 6.0 to 19.6%. This result shows that the above PCR methods are applicable to detect GM potatoes quantitatively as well as qualitatively.

  2. Rapid and quantitative detection of C-reactive protein based on quantum dots and immunofiltration assay

    PubMed Central

    Zhang, Pengfei; Bao, Yan; Draz, Mohamed Shehata; Lu, Huiqi; Liu, Chang; Han, Huanxing

    2015-01-01

    Convenient and rapid immunofiltration assays (IFAs) enable on-site “yes” or “no” determination of disease markers. However, traditional IFAs are commonly qualitative or semi-quantitative and are very limited for the efficient testing of samples in field diagnostics. Here, we overcome these limitations by developing a quantum dots (QDs)-based fluorescent IFA for the quantitative detection of C-reactive proteins (CRP). CRP, the well-known diagnostic marker for acute viral and bacterial infections, was used as a model analyte to demonstrate performance and sensitivity of our developed QDs-based IFA. QDs capped with both polyethylene glycol (PEG) and glutathione were used as fluorescent labels for our IFAs. The presence of the surface PEG layer, which reduced the non-specific protein interactions, in conjunction with the inherent optical properties of QDs, resulted in lower background signal, increased sensitivity, and ability to detect CRP down to 0.79 mg/L with only 5 µL serum sample. In addition, the developed assay is simple, fast and can quantitatively detect CRP with a detection limit up to 200 mg/L. Clinical test results of our QD-based IFA are well correlated with the traditional latex enhance immune-agglutination aggregation. The proposed QD-based fluorescent IFA is very promising, and potentially will be adopted for multiplexed immunoassay and in field point-of-care test. PMID:26491289

  3. Rapid and quantitative detection of C-reactive protein based on quantum dots and immunofiltration assay.

    PubMed

    Zhang, Pengfei; Bao, Yan; Draz, Mohamed Shehata; Lu, Huiqi; Liu, Chang; Han, Huanxing

    2015-01-01

    Convenient and rapid immunofiltration assays (IFAs) enable on-site "yes" or "no" determination of disease markers. However, traditional IFAs are commonly qualitative or semi-quantitative and are very limited for the efficient testing of samples in field diagnostics. Here, we overcome these limitations by developing a quantum dots (QDs)-based fluorescent IFA for the quantitative detection of C-reactive proteins (CRP). CRP, the well-known diagnostic marker for acute viral and bacterial infections, was used as a model analyte to demonstrate performance and sensitivity of our developed QDs-based IFA. QDs capped with both polyethylene glycol (PEG) and glutathione were used as fluorescent labels for our IFAs. The presence of the surface PEG layer, which reduced the non-specific protein interactions, in conjunction with the inherent optical properties of QDs, resulted in lower background signal, increased sensitivity, and ability to detect CRP down to 0.79 mg/L with only 5 µL serum sample. In addition, the developed assay is simple, fast and can quantitatively detect CRP with a detection limit up to 200 mg/L. Clinical test results of our QD-based IFA are well correlated with the traditional latex enhance immune-agglutination aggregation. The proposed QD-based fluorescent IFA is very promising, and potentially will be adopted for multiplexed immunoassay and in field point-of-care test.

  4. The development of line-scan image recognition algorithms for the detection of frass on mature tomatoes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In this research, a multispectral algorithm derived from hyperspectral line-scan fluorescence imaging under violet LED excitation was developed for the detection of frass contamination on mature tomatoes. The algorithm utilized the fluorescence intensities at two wavebands, 664 nm and 690 nm, for co...

  5. A simple but precise method for quantitative measurement of the quality of the laser focus in a scanning optical microscope

    PubMed Central

    MACRAE, K.; TRAVIS, C.; AMOR, R.; NORRIS, G.; WILSON, S.H.; OPPO, G.‐L.; MCCONNELL, G.

    2015-01-01

    Summary We report a method for characterizing the focussing laser beam exiting the objective in a laser scanning microscope. This method provides the size of the optical focus, the divergence of the beam, the ellipticity and the astigmatism. We use a microscopic‐scale knife edge in the form of a simple transmission electron microscopy grid attached to a glass microscope slide, and a light‐collecting optical fibre and photodiode underneath the specimen. By scanning the laser spot from a reflective to a transmitting part of the grid, a beam profile in the form of an error function can be obtained and by repeating this with the knife edge at different axial positions relative to the beam waist, the divergence and astigmatism of the postobjective laser beam can be obtained. The measured divergence can be used to quantify how much of the full numerical aperture of the lens is used in practice. We present data of the beam radius, beam divergence, ellipticity and astigmatism obtained with low (0.15, 0.7) and high (1.3) numerical aperture lenses and lasers commonly used in confocal and multiphoton laser scanning microscopy. Our knife‐edge method has several advantages over alternative knife‐edge methods used in microscopy including that the knife edge is easy to prepare, that the beam can be characterized also directly under a cover slip, as necessary to reduce spherical aberrations for objectives designed to be used with a cover slip, and it is suitable for use with commercial laser scanning microscopes where access to the laser beam can be limited. PMID:25864964

  6. Detection Of Multilayer Cavities By Employing RC-DTH Air Hammer System And Cavity Auto Scanning Laser System

    NASA Astrophysics Data System (ADS)

    Luo, Yongjiang; Li, Lijia; Peng, Jianming; Yin, Kun; Li, Peng; Gan, Xin; Zhao, Letao; Su, Wei

    2015-12-01

    The subterranean cavities are seriously threatened to construction and mining safety, and it's important to obtain the exact localization and dimensions of subterranean cavities for the planning of geotechnical and mining activities. Geophysical investigation is an alternative method for cavity detection, but it usually failed for the uncertainly solution of information and data obtained by Geophysical methods. Drilling is considered as the most accurate method for cavity detection. However, the conventional drilling methods can only be used for single cavity detection, and there is no effective solution for multilayer cavities detection have been reported. In this paper, a reverse circulation (RC) down-the-hole (DTH) air hammer system with a special structured drill bit is built and a cavity auto scanning laser system based on laser range finding technique was employed to confirm the localization and dimensions of the cavities. This RC-DTH air hammer system allows drilling through the upper cavities and putting the cavity auto scanning laser system into the cavity area through the central passage of the drill tools to protect the detection system from collapsing of borehole wall. The RC-DTH air hammer system was built, and field tests were conducted in Lanxian County Iron Ore District, which is located in Lv Liang city of Shan Xi province, the northwest of china. Field tests show that employing the RC-DTH air hammer system assisted by the cavity auto scanning laser system is an efficiency method to detect multilayer cavities.

  7. Quantitative detection of trace explosive vapors by programmed temperature desorption gas chromatography-electron capture detector.

    PubMed

    Field, Christopher R; Lubrano, Adam; Woytowitz, Morgan; Giordano, Braden C; Rose-Pehrsson, Susan L

    2014-07-25

    The direct liquid deposition of solution standards onto sorbent-filled thermal desorption tubes is used for the quantitative analysis of trace explosive vapor samples. The direct liquid deposition method yields a higher fidelity between the analysis of vapor samples and the analysis of solution standards than using separate injection methods for vapors and solutions, i.e., samples collected on vapor collection tubes and standards prepared in solution vials. Additionally, the method can account for instrumentation losses, which makes it ideal for minimizing variability and quantitative trace chemical detection. Gas chromatography with an electron capture detector is an instrumentation configuration sensitive to nitro-energetics, such as TNT and RDX, due to their relatively high electron affinity. However, vapor quantitation of these compounds is difficult without viable vapor standards. Thus, we eliminate the requirement for vapor standards by combining the sensitivity of the instrumentation with a direct liquid deposition protocol to analyze trace explosive vapor samples.

  8. Quantitative and sensitive detection of GNAS mutations causing mccune-albright syndrome with next generation sequencing.

    PubMed

    Narumi, Satoshi; Matsuo, Kumihiro; Ishii, Tomohiro; Tanahashi, Yusuke; Hasegawa, Tomonobu

    2013-01-01

    Somatic activating GNAS mutations cause McCune-Albright syndrome (MAS). Owing to low mutation abundance, mutant-specific enrichment procedures, such as the peptide nucleic acid (PNA) method, are required to detect mutations in peripheral blood. Next generation sequencing (NGS) can analyze millions of PCR amplicons independently, thus it is expected to detect low-abundance GNAS mutations quantitatively. In the present study, we aimed to develop an NGS-based method to detect low-abundance somatic GNAS mutations. PCR amplicons encompassing exons 8 and 9 of GNAS, in which most activating mutations occur, were sequenced on the MiSeq instrument. As expected, our NGS-based method could sequence the GNAS locus with very high read depth (approximately 100,000) and low error rate. A serial dilution study with use of cloned mutant and wildtype DNA samples showed a linear correlation between dilution and measured mutation abundance, indicating the reliability of quantification of the mutation. Using the serially diluted samples, the detection limits of three mutation detection methods (the PNA method, NGS, and combinatory use of PNA and NGS [PNA-NGS]) were determined. The lowest detectable mutation abundance was 1% for the PNA method, 0.03% for NGS and 0.01% for PNA-NGS. Finally, we analyzed 16 MAS patient-derived leukocytic DNA samples with the three methods, and compared the mutation detection rate of them. Mutation detection rate of the PNA method, NGS and PNA-NGS in 16 patient-derived peripheral blood samples were 56%, 63% and 75%, respectively. In conclusion, NGS can detect somatic activating GNAS mutations quantitatively and sensitively from peripheral blood samples. At present, the PNA-NGS method is likely the most sensitive method to detect low-abundance GNAS mutation.

  9. Dual color fluorescence quantitative detection of specific single-stranded DNA with molecular beacons and nucleic acid dye SYBR Green I.

    PubMed

    Xiang, Dong-Shan; Zhou, Guo-Hua; Luo, Ming; Ji, Xing-Hu; He, Zhi-Ke

    2012-08-21

    We have developed a dual color fluorescence quantitative detection method for specific single-stranded DNA with molecular beacons (MBs) and nucleic acid dye SYBR Green I by synchronous scanning fluorescence spectrometry. It is demonstrated by a reverse-transcription oligonucleotide sequence (target DNA, 33 bases) of RNA fragment of human immunodeficiency virus (HIV) as a model system. In the absence of target DNA, the MBs are in the stem-closed state, the fluorescence of 5-carboxy-X-rhodamine (ROX) is quenched by black hole quencher-2 (BHQ-2), and the interaction between SYBR Green I and the MBs is very weak. At this time the fluorescence signals of ROX and SYBR Green I are all very weak. In the presence of target DNA, MBs hybridize with target DNA and form a double-strand structure, the fluorophore ROX is separated from the quencher BHQ-2, and the fluorescence of ROX recovers. At the same time, SYBR Green I binds to hybridized dsDNA, whose fluorescence intensity is significantly enhanced. Thus, dual color fluorescence quantitative detection for the target DNA can be realized by synchronous scanning fluorescence spectrometry. In this strategy, the fluorescence signal of SYBR Green I is far larger than that of ROX, so the quantitative analysis of target DNA with the fluorescence intensity of SYBR Green I can significantly improve the detection sensitivity. In addition, the false-positive signals of MBs do not affect the fluorescence signals of nucleic acid dye SYBR Green I. Thereby, in the analysis of complex samples, quantitative analysis of target DNA with SYBR Green I can avoid the false-positive signals of MBs and improve the detection accuracy.

  10. DETECTING SELECTION IN NATURAL POPULATIONS: MAKING SENSE OF GENOME SCANS AND TOWARDS ALTERNATIVE SOLUTIONS

    PubMed Central

    Haasl, Ryan J.; Payseur, Bret A.

    2016-01-01

    Genomewide scans for natural selection (GWSS) have become increasingly common over the last 15 years due to increased availability of genome-scale genetic data. Here, we report a representative survey of GWSS from 1999 to present and find that (i) between 1999 and 2009, 35 of 49 (71%) GWSS focused on human, while from 2010 to present, only 38 of 83 (46%) of GWSS focused on human, indicating increased focus on nonmodel organisms; (ii) the large majority of GWSS incorporate interpopulation or interspecific comparisons using, for example FST, cross-population extended haplotype homozygosity or the ratio of nonsynonymous to synonymous substitutions; (iii) most GWSS focus on detection of directional selection rather than other modes such as balancing selection; and (iv) in human GWSS, there is a clear shift after 2004 from microsatellite markers to dense SNP data. A survey of GWSS meant to identify loci positively selected in response to severe hypoxic conditions support an approach to GWSS in which a list of a priori candidate genes based on potential selective pressures are used to filter the list of significant hits a posteriori. We also discuss four frequently ignored determinants of genomic heterogeneity that complicate GWSS: mutation, recombination, selection and the genetic architecture of adaptive traits. We recommend that GWSS methodology should better incorporate aspects of genomewide heterogeneity using empirical estimates of relevant parameters and/or realistic, whole-chromosome simulations to improve interpretation of GWSS results. Finally, we argue that knowledge of potential selective agents improves interpretation of GWSS results and that new methods focused on correlations between environmental variables and genetic variation can help automate this approach. PMID:26224644

  11. Detection of Aspens Using High Resolution Aerial Laser Scanning Data and Digital Aerial Images

    PubMed Central

    Säynäjoki, Raita; Packalén, Petteri; Maltamo, Matti; Vehmas, Mikko; Eerikäinen, Kalle

    2008-01-01

    The aim was to use high resolution Aerial Laser Scanning (ALS) data and aerial images to detect European aspen (Populus tremula L.) from among other deciduous trees. The field data consisted of 14 sample plots of 30 m × 30 m size located in the Koli National Park in the North Karelia, Eastern Finland. A Canopy Height Model (CHM) was interpolated from the ALS data with a pulse density of 3.86/m2, low-pass filtered using Height-Based Filtering (HBF) and binarized to create the mask needed to separate the ground pixels from the canopy pixels within individual areas. Watershed segmentation was applied to the low-pass filtered CHM in order to create preliminary canopy segments, from which the non-canopy elements were extracted to obtain the final canopy segmentation, i.e. the ground mask was analysed against the canopy mask. A manual classification of aerial images was employed to separate the canopy segments of deciduous trees from those of coniferous trees. Finally, linear discriminant analysis was applied to the correctly classified canopy segments of deciduous trees to classify them into segments belonging to aspen and those belonging to other deciduous trees. The independent variables used in the classification were obtained from the first pulse ALS point data. The accuracy of discrimination between aspen and other deciduous trees was 78.6%. The independent variables in the classification function were the proportion of vegetation hits, the standard deviation of in pulse heights, accumulated intensity at the 90th percentile and the proportion of laser points reflected at the 60th height percentile. The accuracy of classification corresponded to the validation results of earlier ALS-based studies on the classification of individual deciduous trees to tree species. PMID:27873799

  12. Detection of morphological changes in cliff face surrounding a waterfall using terrestrial laser scanning and unmanned aerial system

    NASA Astrophysics Data System (ADS)

    Hayakawa, Yuichi S.; Obanawa, Hiroyuki

    2015-04-01

    Waterfall or bedrock knickpoint appears as an erosional front in bedrock rivers forming deep v-shaped valley downstream. Following the rapid fluvial erosion of waterfall, rockfalls and gravita-tional collapses often occur in surrounding steep cliffs. Although morphological changes of such steep cliffs are sometimes visually observed, quantitative and precise measurements of their spatio-temporal distribution have been limited due to the difficulties in direct access to such cliffs if with classical measurement methods. However, for the clarification of geomorphological processes oc-curring in the cliffs, multi-temporal mapping of the cliff face at a high resolution is necessary. Re-mote sensing approaches are therefore suitable for the topographic measurements and detection of changes in such inaccessible cliffs. To achieve accurate topographic mapping of cliffs around a wa-terfall, here we perform multi-temporal terrestrial laser scanning (TLS), as well as structure-from-motion multi-view stereo (SfM-MVS) photogrammetry based on unmanned aerial system (UAS). The study site is Kegon Falls in central Japan, having a vertical drop of surface water from top of its overhanging cliff, as well as groundwater outflows from its lower portions. The bedrock is composed of alternate layers of andesite lava and conglomerates. Minor rockfalls in the cliffs are often ob-served by local people. The latest major rockfall occurred in 1986, causing ca. 8-m upstream propa-gation of the waterfall lip. This provides a good opportunity to examine the changes in the surround-ing cliffs following the waterfall recession. Multi-time point clouds were obtained by TLS measure-ment over years, and the three-dimensional changes of the rock surface were detected, uncovering the locus of small rockfalls and gully developments. Erosion seems particularly frequent in relatively weak the conglomerates layer, whereas small rockfalls seems to have occurred in the andesite layers. Also, shadows in the

  13. Surface characterization of dialyzer polymer membranes by imaging ToF-SIMS and quantitative XPS line scans

    PubMed Central

    Holzweber, Markus; Lippitz, Andreas; Krueger, Katharina; Jankowski, Joachim; Unger, Wolfgang E. S.

    2015-01-01

    The surfaces of polymeric dialyzer membranes consisting of polysulfone and poly-vinylpyrrolidone were investigated regarding the lateral distribution and quantitative surface composition using time-of-flight secondary-ion-mass-spectrometry and x-ray photoelectron spectroscopy. Knowledge of the distribution and composition on the outer surface region is of utmost importance for understanding the biocompatibility of such dialyzer membranes. Both flat membranes and hollow fiber membranes were studied. PMID:25711334

  14. Quantitative detection of defects based on Markov-PCA-BP algorithm using pulsed infrared thermography technology

    NASA Astrophysics Data System (ADS)

    Tang, Qingju; Dai, Jingmin; Liu, Junyan; Liu, Chunsheng; Liu, Yuanlin; Ren, Chunping

    2016-07-01

    Quantitative detection of debonding defects' diameter and depth in TBCs has been carried out using pulsed infrared thermography technology. By combining principal component analysis with neural network theory, the Markov-PCA-BP algorithm was proposed. The principle and realization process of the proposed algorithm was described. In the prediction model, the principal components which can reflect most characteristics of the thermal wave signal were set as the input, and the defect depth and diameter was set as the output. The experimental data from pulsed infrared thermography tests of TBCs with flat bottom hole defects was selected as the training and testing sample. Markov-PCA-BP predictive system was arrived, based on which both the defect depth and diameter were identified accurately, which proved the effectiveness of the proposed method for quantitative detection of debonding defects in TBCs.

  15. Quantitative surface enhanced Raman scattering detection based on the ``sandwich'' structure substrate

    NASA Astrophysics Data System (ADS)

    Zhang, Junmeng; Qu, Shengchun; Zhang, Lisheng; Tang, Aiwei; Wang, Zhanguo

    2011-08-01

    A sandwich structured substrate was designed for quantitative molecular detection using surface enhanced Raman scattering (SERS), in which the probe molecule was sandwiched between silver nanoparticles (SNPs) and silver nanoarrays. The SNPs was prepared using Lee-Meisel method, and the silver nanoarrays was fabricated on porous anodic aluminum oxide (AAO) using electrodepositing method. The SERS studies show that the sandwich structured substrate exhibits good stability and reproducibility, and the detection sensitivity of Rhodamine 6G (R6G) and Melamine can respectively reach up to 10 -19 M and 10 -9 M, which is improved greatly as compared to other SERS substrates. The improved SERS sensitivity is closely associated with the stronger electromagnetic field enhancement, which stems from localized surface plasmon (LSP) coupling between the two silver nanostructures. Furthermore, the SERS intensity increased almost linearly as the mother concentration increased, which indicates that such a sandwich structure may be used as a good SERS substrate for quantitative analysis.

  16. Detection and quantitation of proteoglycans extracted from cell culture medium and cultured cartilage slices

    SciTech Connect

    Hronowski, L.J.; Anastassiades, T.P.

    1988-11-01

    Detection and quantitation of extracted proteoglycans, by staining with the dye Alcian blue on cellulose acetate followed by dissolution of the stained cellulose acetate strips in dimethyl sulfoxide containing 0.5% (v/v) sulfuric acid for absorbance measurement, is described. It is shown that, in the present system, the dye uptake by the proteoglycan is dependent only on the glycosaminoglycan content of the proteoglycan. The method is applied to the quantitation and characterization of proteoglycans and glycosaminoglycans, which have been extracted from radiolabeled bovine ankle cartilage and from mononuclear cell supernatant and which have been separated by DEAE-Sephacel column chromatography. The high sensitivity of the method allows detection of proteoglycans in 25-microliters samples of solutions containing as little as 1 microgram of glycosaminoglycan per milliliter of solution.

  17. Detection, characterization and quantitation of coxsackievirus A16 using polyclonal antibodies against recombinant capsid subunit proteins.

    PubMed

    Liu, Qingwei; Ku, Zhiqiang; Cai, Yicun; Sun, Bing; Leng, Qibin; Huang, Zhong

    2011-04-01

    Coxsackievirus A16 (CVA16), together with enterovirus type 71 (EV71), is responsible for most cases of hand, foot and mouth disease (HFMD) worldwide. Recent findings suggest that the recombination between CVA16 and EV71, and co-circulation of these two viruses may have contributed to the increase of HFMD cases in China over the past few years. Thus, for CVA16, further understanding of its virology, epidemiology and development of diagnostic tests and vaccines are of importance. The present study aimed to develop reagents and protocols for the detection, characterization and quantitation of CVA16. Recombinant CVA16 capsid subunit proteins VP0, VP3 and truncated VP1, were produced in Escherichia coli and used to immunize guinea pigs to generate polyclonal antibodies. The resultant three antisera detected specifically CVA16 propagated in Vero cells by immunostaining, ELISA and Western blotting. The antisera was used to show that CVA16 capsids were composed of correctly processed VP0, VP1 and VP3 subunits, and were present in the form of efficiently assembled particles. A method for the quantitation of the yield of CVA16 in Vero cells was established based on a Western blotting protocol using the recombinant VP0 as a reference standard and anti-VP0 as the detection antibody. This study shows the development and validation of reagents and methods, for qualitative and quantitative determination of CVA16, which are essential for the development of vaccines.

  18. Detection of circulating tumor cells using GeneScan analysis for antigen receptor gene rearrangements in canine lymphoma patients

    PubMed Central

    HIYOSHI-KANEMOTO, Saaya; GOTO-KOSHINO, Yuko; FUKUSHIMA, Kenjiro; TAKAHASHI, Masashi; KANEMOTO, Hideyuki; UCHIDA, Kazuyuki; FUJINO, Yasuhito; OHNO, Koichi; TSUJIMOTO, Hajime

    2016-01-01

    The presence of circulating tumor cells (CTCs) serves as a prognostic marker and indicator of disease relapse, as well as a means of evaluating treatment efficacy in human and canine lymphoma patients. As an extension of our previous study for the construction of clinically useful GeneScan system, we utilized the GeneScan system for detecting CTCs in canine lymphoma patients. Samples from the primary lesion and peripheral blood mononuclear cells (PBMCs) were obtained from 32 dogs with lymphoma at initial diagnosis. All samples were subjected to polymerase chain reaction (PCR) for antigen receptor gene rearrangements (PARR) followed by GeneScan analysis. Common clonal rearrangements with identical amplified fragments were detected in both the primary lesion and PBMCs in 19 of the 32 dogs (59.4%). However, the detection rate of CTCs varied among the anatomical classification of lymphoma studied. GeneScan analysis following PARR would facilitate studies on determining the clinical significance of CTCs in canine lymphoma patients. PMID:26888583

  19. An ECL-PCR method for quantitative detection of point mutation

    NASA Astrophysics Data System (ADS)

    Zhu, Debin; Xing, Da; Shen, Xingyan; Chen, Qun; Liu, Jinfeng

    2005-04-01

    A new method for identification of point mutations was proposed. Polymerase chain reaction (PCR) amplification of a sequence from genomic DNA was followed by digestion with a kind of restriction enzyme, which only cut the wild-type amplicon containing its recognition site. Reaction products were detected by electrochemiluminescence (ECL) assay after adsorption of the resulting DNA duplexes to the solid phase. One strand of PCR products carries biotin to be bound on a streptavidin-coated microbead for sample selection. Another strand carries Ru(bpy)32+ (TBR) to react with tripropylamine (TPA) to emit light for ECL detection. The method was applied to detect a specific point mutation in H-ras oncogene in T24 cell line. The results show that the detection limit for H-ras amplicon is 100 fmol and the linear range is more than 3 orders of magnitude, thus, make quantitative analysis possible. The genotype can be clearly discriminated. Results of the study suggest that ECL-PCR is a feasible quantitative method for safe, sensitive and rapid detection of point mutation in human genes.

  20. Microwave-accelerated bioassay technique for rapid and quantitative detection of biological and environmental samples.

    PubMed

    Mohammed, Muzaffer; Syed, Maleeha F; Aslan, Kadir

    2016-01-15

    Quantitative detection of molecules of interest from biological and environmental samples in a rapid manner, particularly with a relevant concentration range, is imperative to the timely assessment of human diseases and environmental issues. In this work, we employed the microwave-accelerated bioassay (MAB) technique, which is based on the combined use of circular bioassay platforms and microwave heating, for rapid and quantitative detection of Glial Fibrillary Acidic Protein (GFAP) and Shiga like toxin (STX 1). The proof-of-principle use of the MAB technique with the circular bioassay platforms for the rapid detection of GFAP in buffer based on colorimetric and fluorescence readouts was demonstrated with a 900W kitchen microwave. We also employed the MAB technique with a new microwave system (called the iCrystal system) for the detection of GFAP from mice with brain injuries and STX 1 from a city water stream. Control bioassays included the commercially available gold standard bioassay kits run at room temperature. Our results show that the lower limit of detection (LLOD) of the colorimetric and fluorescence based bioassays for GFAP was decreased by ~1000 times using the MAB technique and our circular bioassay platforms as compared to the commercially available bioassay kits. The overall bioassay time for GFAP and STX 1 was reduced from 4h using commercially available bioassay kits to 10min using the MAB technique.

  1. Validation of quantitative and qualitative methods for detecting allergenic ingredients in processed foods in Japan.

    PubMed

    Sakai, Shinobu; Adachi, Reiko; Akiyama, Hiroshi; Teshima, Reiko

    2013-06-19

    A labeling system for food allergenic ingredients was established in Japan in April 2002. To monitor the labeling, the Japanese government announced official methods for detecting allergens in processed foods in November 2002. The official methods consist of quantitative screening tests using enzyme-linked immunosorbent assays (ELISAs) and qualitative confirmation tests using Western blotting or polymerase chain reactions (PCR). In addition, the Japanese government designated 10 μg protein/g food (the corresponding allergenic ingredient soluble protein weight/food weight), determined by ELISA, as the labeling threshold. To standardize the official methods, the criteria for the validation protocol were described in the official guidelines. This paper, which was presented at the Advances in Food Allergen Detection Symposium, ACS National Meeting and Expo, San Diego, CA, Spring 2012, describes the validation protocol outlined in the official Japanese guidelines, the results of interlaboratory studies for the quantitative detection method (ELISA for crustacean proteins) and the qualitative detection method (PCR for shrimp and crab DNAs), and the reliability of the detection methods.

  2. Microwave-Accelerated Bioassay Technique for Rapid and Quantitative Detection of Biological and Environmental Samples

    PubMed Central

    Mohammed, Muzaffer; Syed, Maleeha F.; Aslan, Kadir

    2015-01-01

    Quantitative detection of molecules of interest from biological and environmental samples in a rapid manner, particularly with a relevant concentration range, is imperative to the timely assessment of human diseases and environmental issues. In this work, we employed the microwave-accelerated bioassay (MAB) technique, which is based on the combined use of circular bioassay platforms and microwave heating, for rapid and quantitative detection of Glial Fibrillary Acidic Protein (GFAP) and Shiga like toxin (STX 1). The proof-of-principle use of the MAB technique with the circular bioassay platforms for the rapid detection of GFAP in buffer based on colorimetric and fluorescence readouts was demonstrated with a 900 W kitchen microwave. We also employed the MAB technique with a new microwave system (called the iCrystal system) for the detection of GFAP from mice with brain injuries and STX 1 from a city water stream. Control bioassays included the commercially available gold standard bioassay kits run at room temperature. Our results show that the lower limit of detection (LLOD) of the colorimetric and fluorescence based bioassays for GFAP was decreased by ~1,000 times using the MAB technique and our circular bioassay platforms as compared to the commercially available bioassay kits. The overall bioassay time for GFAP and STX 1 was reduced from 4 hours using commercially available bioassay kits to 10 minutes using the MAB technique. PMID:26356762

  3. Comparison of standard, quantitative and digital PCR in the detection of enterotoxigenic Bacteroides fragilis.

    PubMed

    Purcell, Rachel V; Pearson, John; Frizelle, Frank A; Keenan, Jacqueline I

    2016-09-30

    Gut colonization with enterotoxigenic Bacteroides fragilis (ETBF) appears to be associated with the development of colorectal cancer. However, differences in carriage rates are seen with various testing methods and sampling sites. We compared standard PCR, SYBR green and TaqMan quantitative PCR (qPCR) and digital PCR (dPCR) in detecting the B. fragilis toxin (bft) gene from cultured ETBF, and from matched luminal and faecal stool samples from 19 colorectal cancer patients. Bland-Altman analysis found that all three quantitative methods performed comparably in detecting bft from purified bacterial DNA, with the same limits of detection (<1 copy/μl). However, SYBR qPCR under-performed compared to TaqMan qPCR and dPCR in detecting bft in clinical stool samples; 13/38 samples were reported positive by SYBR, compared to 35 and 36 samples by TaqMan and dPCR, respectively. TaqMan qPCR and dPCR gave bft copy numbers that were 48-fold and 75-fold higher for the same samples than SYBR qPCR, respectively (p < 0.001). For samples that were bft-positive in both fecal and luminal stools, there was no difference in relative abundance between the sites, by any method tested. From our findings, we recommend the use of TaqMan qPCR as the preferred method to detect ETBF from clinical stool samples.

  4. TDI imaging and scanning moiré for online defect detection

    NASA Astrophysics Data System (ADS)

    Sajan, M. R.; Tay, C. J.; Shang, H. M.; Asundi, A.

    1997-09-01

    This paper explains the application of scanning moiré in association with TDI (Time Delay and Integration) imaging for complete peripheral inspection of cylindrical objects. Based on the structured light technique, a grating pattern modulated by deformations, such as dents on the surface of a rotating cylindrical object, is recorded using a TDI camera. The illumination system consists of an intensity modulated, line generating laser diode aligned at an angle to the camera axis. By using the TDI option for recording every nth line, an online scanning moiré pattern is generated. After providing a simple explanation of the scanning moiré, the effects of object rotation speed and TDI scan speed on the fringe pattern are discussed and demonstrated. The techniques presented here offer low cost solutions to industrial machine vision tasks related to peripheral imaging and inspection of cylindrical objects.

  5. DEVELOPMENT OF SEMI-QUANTITATIVE PCR ASSAYS FOR THE DETECTION AND ENUMERATION OF GAMBIERDISCUS SPECIES (GONYAULACALES, DINOPHYCEAE)(1).

    PubMed

    Vandersea, Mark W; Kibler, Steven R; Holland, William C; Tester, Patricia A; Schultz, Thomas F; Faust, Maria A; Holmes, Michael J; Chinain, Mirelle; Wayne Litaker, R

    2012-08-01

    Ciguatera fish poisoning (CFP) is a serious health problem in tropical regions and is caused by the bioaccumulation of lipophilic toxins produced by dinoflagellates in the genus Gambierdiscus. Gambierdiscus species are morphologically similar and are difficult to distinguish from one another even when using scanning electron microscopy. Improved identification and detection methods that are sensitive and rapid are needed to identify toxic species and investigate potential distribution and abundance patterns in relation to incidences of CFP. This study presents the first species-specific, semi-quantitative polymerase chain reaction (qPCR) assays that can be used to address these questions. These assays are specific for five Gambierdiscus species and one undescribed ribotype. The assays utilized a SYBR green format and targeted unique sequences found within the SSU, ITS, and the D1/D3 LSU ribosomal domains. Standard curves were constructed using known concentrations of cultured cells and 10-fold serial dilutions of rDNA PCR amplicons containing the target sequence for each specific assay. Assay sensitivity and accuracy were tested using DNA extracts purified from known concentrations of multiple Gambierdiscus species. The qPCR assays were used to assess Gambierdiscus species diversity and abundance in samples collected from nearshore areas adjacent to Ft. Pierce and Jupiter, Florida USA. The results indicated that the practical limit of detection for each assay was 10 cells per sample. Most interestingly, the qPCR analysis revealed that as many as four species of Gambierdiscus were present in a single macrophyte sample.

  6. Signal Processing and Its Effect on Scanning Efficiencies for a Field Instrument for Detecting Low-energy Radiation.

    PubMed

    Marianno, Craig M

    2015-07-01

    Signal processing within a radiation detector affects detection efficiency. Currently, organizations such as private industry, the U.S. Navy, Army, and Air Force are coupling some detector systems with data collection devices to survey large land areas for radioactive contamination. As detector technology has advanced and analog data collection has turned to digital, signal processing is becoming prevalent in some instruments. Using a NIST traceable (241)Am source, detection efficiency for a field instrument for detecting low-energy radiation (FIDLER) was examined for both a static and scanning mode. Experimental results were compared to Monte Carlo-generated efficiencies. Stationary data compared nicely to the theoretical results. Conversely, scanning detection efficiencies were considerably different from their theoretical counterparts. As speed increased, differences in detection efficiency approached two orders of magnitude. To account for these differences, a quasi time-dependent Monte Carlo simulation was created mimicking the signal processing undertaken by the FIDLER detection system. By including signal processing, experimental results fell within the bounds of the Monte Carlo-generated efficiencies, thus demonstrating the negative effects of such processing on detection efficiencies.

  7. A novel spherical shell filter for reducing false positives in automatic detection of pulmonary nodules in thoracic CT scans

    NASA Astrophysics Data System (ADS)

    van de Leemput, Sil; Dorssers, Frank; Ehteshami Bejnordi, Babak

    2015-03-01

    Early detection of pulmonary nodules is crucial for improving prognosis of patients with lung cancer. Computer-aided detection of lung nodules in thoracic computed tomography (CT) scans has a great potential to enhance the performance of the radiologist in detecting nodules. In this paper we present a computer-aided lung nodule detection system for computed tomography (CT) scans that works in three steps. The system first segments the lung using thresholding and hole filling. From this segmentation the system extracts candidate nodules using Laplacian of Gaussian. To reject false positives among the detected candidate nodules, multiple established features are calculated. We propose a novel feature based on a spherical shell filter, which is specifically designed to distinguish between vascular structures and nodular structures. The performance of the proposed CAD system was evaluated by partaking in the ANODE09 challenge, which presents a platform for comparing automatic nodule detection programs. The results from the challenge show that our CAD system ranks third among the submitted works, demonstrating the efficacy of our proposed CAD system. The results also show that our proposed spherical shell filter in combination with conventional features can significantly reduce the number of false positives from the detected candidate nodules.

  8. QUANTITATIVE ASSESSMENT OF BETA CELL APOPTOSIS AND CELL COMPOSITION OF ISOLATED, UNDISRUPTED HUMAN ISLETS BY LASER SCANNING CYTOMETRY

    PubMed Central

    Todorov, Ivan; Nair, Indu; Avakian-Mansoorian, Alina; Rawson, Jeffrey; Omori, Keiko; Ito, Taihei; Valiente, Luis; Iglesias-Meza, Itzia; Orr, Chris; Shiang, Keh D.; Ferreri, Kevin; Al-Abdullah, Ismail H.; Mullen, Yoko; Kandeel, Fouad

    2010-01-01

    Background Assays for assessing human islet cell quality which provide results prior to transplantation would be very beneficial to improving outcomes for islet transplantation therapy. Parameters such as percent beta cell apoptosis and cell composition are found to vary markedly between different islet preparations, and may serve as markers of islet quality. We have developed fluorescence-based assays using laser scanning cytometry (LSC) for assessing beta cell apoptosis and islet cell composition on serial sections of intact isolated islets. Methods Isolated human islets were fixed in formalin and embedded in paraffin. Serial sections were immunostained for the pancreatic hormones, acinar and ductal cell markers. DNA fragmentation was used to label apoptotic cells. Stained cells were quantified using an iCys laser scanning cytometer. Results Islet preparations from 102 human pancreatic islet isolations were analyzed. For the whole set of islet preparations we found a mean islet cell composition of 54.5±1.2% insulin positive; 33.9±1.2% glucagon; 12.1±0.7% somatostatin and 1.5±0.2% pancreatic polypeptide positive cells. The apoptotic beta cells were 2.85±0.4% with a range of 0.27% to 18.3%. The percentage of apoptotic beta cells correlated well (p<0.0001, n=59) with results obtained in vivo by transplantation of the corresponding islets in diabetic NODscid mice. Conclusions The analysis of whole, non-dissociated islets for cell composition and beta cell apoptosis using LSC is giving reliable and reproducible results and could be done both before islet transplantation, as well as on preserved cell blocks at any future time. Thus, they can be a powerful tool for islet quality assessment. PMID:20697327

  9. Detection of human brain tumor infiltration with quantitative stimulated Raman scattering microscopy.

    PubMed

    Ji, Minbiao; Lewis, Spencer; Camelo-Piragua, Sandra; Ramkissoon, Shakti H; Snuderl, Matija; Venneti, Sriram; Fisher-Hubbard, Amanda; Garrard, Mia; Fu, Dan; Wang, Anthony C; Heth, Jason A; Maher, Cormac O; Sanai, Nader; Johnson, Timothy D; Freudiger, Christian W; Sagher, Oren; Xie, Xiaoliang Sunney; Orringer, Daniel A

    2015-10-14

    Differentiating tumor from normal brain is a major barrier to achieving optimal outcome in brain tumor surgery. New imaging techniques for visualizing tumor margins during surgery are needed to improve surgical results. We recently demonstrated the ability of stimulated Raman scattering (SRS) microscopy, a nondestructive, label-free optical method, to reveal glioma infiltration in animal models. We show that SRS reveals human brain tumor infiltration in fresh, unprocessed surgical specimens from 22 neurosurgical patients. SRS detects tumor infiltration in near-perfect agreement with standard hematoxylin and eosin light microscopy (κ = 0.86). The unique chemical contrast specific to SRS microscopy enables tumor detection by revealing quantifiable alterations in tissue cellularity, axonal density, and protein/lipid ratio in tumor-infiltrated tissues. To ensure that SRS microscopic data can be easily used in brain tumor surgery, without the need for expert interpretation, we created a classifier based on cellularity, axonal density, and protein/lipid ratio in SRS images capable of detecting tumor infiltration with 97.5% sensitivity and 98.5% specificity. Quantitative SRS microscopy detects the spread of tumor cells, even in brain tissue surrounding a tumor that appears grossly normal. By accurately revealing tumor infiltration, quantitative SRS microscopy holds potential for improving the accuracy of brain tumor surgery.

  10. Detection of human brain tumor infiltration with quantitative stimulated Raman scattering microscopy

    PubMed Central

    Ji, Minbiao; Lewis, Spencer; Camelo-Piragua, Sandra; Ramkissoon, Shakti H.; Snuderl, Matija; Venneti, Sriram; Fisher-Hubbard, Amanda; Garrard, Mia; Fu, Dan; Wang, Anthony C.; Heth, Jason A.; Maher, Cormac O.; Sanai, Nader; Johnson, Timothy D.; Freudiger, Christian W.; Sagher, Oren; Xie, Xiaoliang Sunney; Orringer, Daniel A.

    2016-01-01

    Differentiating tumor from normal brain is a major barrier to achieving optimal outcome in brain tumor surgery. New imaging techniques for visualizing tumor margins during surgery are needed to improve surgical results. We recently demonstrated the ability of stimulated Raman scattering (SRS) microscopy, a non-destructive, label-free optical method, to reveal glioma infiltration in animal models. Here we show that SRS reveals human brain tumor infiltration in fresh, unprocessed surgical specimens from 22 neurosurgical patients. SRS detects tumor infiltration in near-perfect agreement with standard hematoxylin and eosin light microscopy (κ=0.86). The unique chemical contrast specific to SRS microscopy enables tumor detection by revealing quantifiable alterations in tissue cellularity, axonal density and protein:lipid ratio in tumor-infiltrated tissues. To ensure that SRS microscopic data can be easily used in brain tumor surgery, without the need for expert interpretation, we created a classifier based on cellularity, axonal density and protein:lipid ratio in SRS images capable of detecting tumor infiltration with 97.5% sensitivity and 98.5% specificity. Importantly, quantitative SRS microscopy detects the spread of tumor cells, even in brain tissue surrounding a tumor that appears grossly normal. By accurately revealing tumor infiltration, quantitative SRS microscopy holds potential for improving the accuracy of brain tumor surgery. PMID:26468325

  11. Portable SERS-enabled micropipettes for microarea sampling and reliably quantitative detection of surface organic residues.

    PubMed

    Fang, Wei; Zhang, Xinwei; Chen, Yong; Wan, Liang; Huang, Weihua; Shen, Aiguo; Hu, Jiming

    2015-09-15

    We report the first microsampling device for reliably quantitative, label-free and separation-free detection of multicomponents of surface organic residues (SORs) by means of a quality controllable surface-enhanced Raman scattering (SERS)-enabled micropipette. The micropipette is comprised of a drawn glass capillary with a tiny orifice (∼50 μm) at the distal tip, where the specially designed nanorattles (NRs) are compactly coated on the inner wall surface. SERS signals of 4-mercapto benzoic acid (MBA) anchored inside the internal gap of NRs could be used to evaluate and control the quality of micropipettes and, therefore, allow us to overcome the limitations of a reliably quantitative SERS assay using traditional substrates without an internal standard. By dropping a trace extraction agent on targeting SORs located on a narrow surface, the capillary and SERS functionalities of these micropipettes allow on-site microsampling via capillary action and subsequent multiplex distinction/detection due to their molecularly narrow Raman peaks. For example, 8 nM thiram (TMTD), 8 nM malachite green (MG), and 1.5 μM (400 ppb) methyl parathion (MPT) on pepper and cucumber peels have been simultaneously detected in a wide detection range. The portable SERS-enabled device could potentially be facilely incorporated with liquid-liquid or solid phase micro-extracting devices for a broader range of applications in rapid and field analysis of food/public/environment security related SORs.

  12. Aerosol Plume Detection Algorithm Based on Image Segmentation of Scanning Atmospheric Lidar Data

    SciTech Connect

    Weekley, R. Andrew; Goodrich, R. Kent; Cornman, Larry B.

    2016-04-01

    An image-processing algorithm has been developed to identify aerosol plumes in scanning lidar backscatter data. The images in this case consist of lidar data in a polar coordinate system. Each full lidar scan is taken as a fixed image in time, and sequences of such scans are considered functions of time. The data are analyzed in both the original backscatter polar coordinate system and a lagged coordinate system. The lagged coordinate system is a scatterplot of two datasets, such as subregions taken from the same lidar scan (spatial delay), or two sequential scans in time (time delay). The lagged coordinate system processing allows for finding and classifying clusters of data. The classification step is important in determining which clusters are valid aerosol plumes and which are from artifacts such as noise, hard targets, or background fields. These cluster classification techniques have skill since both local and global properties are used. Furthermore, more information is available since both the original data and the lag data are used. Performance statistics are presented for a limited set of data processed by the algorithm, where results from the algorithm were compared to subjective truth data identified by a human.

  13. Aerosol Plume Detection Algorithm Based on Image Segmentation of Scanning Atmospheric Lidar Data

    DOE PAGES

    Weekley, R. Andrew; Goodrich, R. Kent; Cornman, Larry B.

    2016-04-06

    An image-processing algorithm has been developed to identify aerosol plumes in scanning lidar backscatter data. The images in this case consist of lidar data in a polar coordinate system. Each full lidar scan is taken as a fixed image in time, and sequences of such scans are considered functions of time. The data are analyzed in both the original backscatter polar coordinate system and a lagged coordinate system. The lagged coordinate system is a scatterplot of two datasets, such as subregions taken from the same lidar scan (spatial delay), or two sequential scans in time (time delay). The lagged coordinatemore » system processing allows for finding and classifying clusters of data. The classification step is important in determining which clusters are valid aerosol plumes and which are from artifacts such as noise, hard targets, or background fields. These cluster classification techniques have skill since both local and global properties are used. Furthermore, more information is available since both the original data and the lag data are used. Performance statistics are presented for a limited set of data processed by the algorithm, where results from the algorithm were compared to subjective truth data identified by a human.« less

  14. Aerosol Plume Detection Algorithm Based on Image Segmentation of Scanning Atmospheric Lidar Data

    SciTech Connect

    Weekley, R. Andrew; Goodrich, R. Kent; Cornman, Larry B.

    2016-04-06

    An image-processing algorithm has been developed to identify aerosol plumes in scanning lidar backscatter data. The images in this case consist of lidar data in a polar coordinate system. Each full lidar scan is taken as a fixed image in time, and sequences of such scans are considered functions of time. The data are analyzed in both the original backscatter polar coordinate system and a lagged coordinate system. The lagged coordinate system is a scatterplot of two datasets, such as subregions taken from the same lidar scan (spatial delay), or two sequential scans in time (time delay). The lagged coordinate system processing allows for finding and classifying clusters of data. The classification step is important in determining which clusters are valid aerosol plumes and which are from artifacts such as noise, hard targets, or background fields. These cluster classification techniques have skill since both local and global properties are used. Furthermore, more information is available since both the original data and the lag data are used. Performance statistics are presented for a limited set of data processed by the algorithm, where results from the algorithm were compared to subjective truth data identified by a human.

  15. Quantitative ultrasound imaging detects degenerative changes in articular cartilage surface and subchondral bone

    NASA Astrophysics Data System (ADS)

    Saarakkala, Simo; Laasanen, Mikko S.; Jurvelin, Jukka S.; Töyräs, Juha

    2006-10-01

    Previous studies have suggested that quantitative ultrasound imaging could sensitively diagnose degeneration of the articular surface and changes in the subchondral bone during the development of osteoarthrosis (OA). We have recently introduced a new parameter, ultrasound roughness index (URI), for the quantification of cartilage surface roughness, and successfully tested it with normal and experimentally degraded articular surfaces. In this in vitro study, the applicability of URI was tested in bovine cartilage samples with spontaneously developed tissue degeneration. Simultaneously, we studied the sensitivity of quantitative ultrasound imaging to detect degenerative changes in the cartilage-bone interface. For reference, histological degenerative grade of the cartilage samples was determined. Mechanical reference measurements were also conducted. Cartilage surface roughness (URI) was significantly (p < 0.05) higher in histologically degenerated samples with inferior mechanical properties. Ultrasound reflection at the cartilage-bone interface was also significantly (p < 0.05) increased in degenerated samples. Furthermore, it was quantitatively confirmed that ultrasound attenuation in the overlying cartilage significantly affects the measured ultrasound reflection values from the cartilage-bone interface. To conclude, the combined ultrasound measurement of the cartilage surface roughness and ultrasound reflection at the cartilage-bone interface complement each other, and may together enable more sensitive and quantitative diagnosis of early OA or follow up after surgical cartilage repair.

  16. Genomic resources and their influence on the detection of the signal of positive selection in genome scans.

    PubMed

    Manel, S; Perrier, C; Pratlong, M; Abi-Rached, L; Paganini, J; Pontarotti, P; Aurelle, D

    2016-01-01

    Genome scans represent powerful approaches to investigate the action of natural selection on the genetic variation of natural populations and to better understand local adaptation. This is very useful, for example, in the field of conservation biology and evolutionary biology. Thanks to Next Generation Sequencing, genomic resources are growing exponentially, improving genome scan analyses in non-model species. Thousands of SNPs called using Reduced Representation Sequencing are increasingly used in genome scans. Besides, genome sequences are also becoming increasingly available, allowing better processing of short-read data, offering physical localization of variants, and improving haplotype reconstruction and data imputation. Ultimately, genome sequences are also becoming the raw material for selection inferences. Here, we discuss how the increasing availability of such genomic resources, notably genome sequences, influences the detection of signals of selection. Mainly, increasing data density and having the information of physical linkage data expand genome scans by (i) improving the overall quality of the data, (ii) helping the reconstruction of demographic history for the population studied to decrease false-positive rates and (iii) improving the statistical power of methods to detect the signal of selection. Of particular importance, the availability of a high-quality reference genome can improve the detection of the signal of selection by (i) allowing matching the potential candidate loci to linked coding regions under selection, (ii) rapidly moving the investigation to the gene and function and (iii) ensuring that the highly variable regions of the genomes that include functional genes are also investigated. For all those reasons, using reference genomes in genome scan analyses is highly recommended.

  17. Automated detection of nodules attached to the pleural and mediastinal surface in low-dose CT scans

    NASA Astrophysics Data System (ADS)

    van Ginneken, Bram; Tan, Andre; Murphy, Keelin; de Hoop, Bart-Jan; Prokop, Mathias

    2008-03-01

    This paper presents a new computer-aided detection scheme for lung nodules attached to the pleural or mediastinal surface in low dose CT scans. First the lungs are automatically segmented and smoothed. Any connected set of voxels attached to the wall - with each voxel above minus 500 HU and the total object within a specified volume range - was considered a candidate finding. For each candidate, a refined segmentation was computed using morphological operators to remove attached structures. For each candidate, 35 features were defined, based on their position in the lung and relative to other structures, and the shape and density within and around each candidate. In a training procedure an optimal set of 15 features was determined with a k-nearest-neighbor classifier and sequential floating forward feature selection. The algorithm was trained with a data set of 708 scans from a lung cancer screening study containing 224 pleural nodules and tested on an independent test set of 226 scans from the same program with 58 pleural nodules. The algorithm achieved a sensitivity of 52% with an average of 0.76 false positives per scan. At 2.5 false positive marks per scan, the sensitivity increased to 80%.

  18. Comparison of bone scan and radiograph sensitivity in the detection of steroid-induced ischemic necrosis of bone

    SciTech Connect

    Conklin, J.J.; Alderson, P.O.; Zizic, T.M.; Hungerford, D.S.; Densereaux, J.Y.; Gober, A.; Wagner, H.N.

    1983-04-01

    A prospective study of bone scanning for detection of ischemic necrosis of bone (INB) was performed in 36 patients (97% female, age range 16-36 yrs.) with systemic lupus erythematosis (SLE). Since the hips, knees, and shoulders are usually affected by INB in patients with SLE, 300 K converging collimator images of these joints were obtained on film and in digital format 2 to 3 hours after the injection of 20 mCi (740 MBq) of Tc-99m methylene diphosphonate. All patients underwent radiography of the joints, and 10 had intraosseous pressure determinations in the marrow space of affected joints (n . 31) for independent assessment of INB. Scans showed abnormally increased joint activity in 28 of the 36 patients. A total of 97 joints showed abnormalities, 19% in the hips, 34% in the knees, and 47% in the shoulders. Twenty-four of 27 joints with elevated bone marrow pressure (BMP) had abnormal scans (sensitivity . 89%), and scans were abnormal in 2 of 4 joints with normal pressures (specificity . 50%). The positive predictive value of the scans compared with BMP measurements was 92% (24/26). Eleven of 27 joints with abnormal BMP had abnormal radiographs, a sensitivity of 41%.

  19. Comparison of bone scan and radiograph sensitivity in the detection of steroid-induced ischemic necrosis of bone

    SciTech Connect

    Conklin, J.J.; Alderson, P.O.; Zizic, T.M.; Hungerford, D.S.; Densereaux, J.Y.; Gober, A.; Wagner, H.N.

    1983-04-01

    A prospective study of bone scanning for detection of ischemic necrosis of bone (INB) was performed in 36 patients (97% female, age range 16-36 yrs.) with systemic lupus erythematosis (SLE). Since the hips, knees, and shoulders are usually affected by INB in patients with SLE, 300 K converging collimator images of these joints were obtained on film and in digital format 2 to 3 hours after the injection of 20 mCi (740 MBq) of Tc-99m methylene diphosphonate. All patients underwent radiography of the joints, and 10 had intraosseous pressure determinations in the marrow space of affected joints (n=31) for independent assessment of INB. Scans showed abnormally increased joint activity in 28 of the 36 patients. A total of 97 joints showed abnormalities, 19% in the hips, 34% in the knees, and 47% in the shoulders. Twenty-four of 27 joints with elevated bone marrow pressure (BMP) had abnormal scans (sensitivity = 89%), and scans were abnormal in 2 of 4 joints with normal pressures (specificity = 50%). The positive predicitive value of the scans compared with BMP measurements was 92% (24/26). Eleven of 27 joints with abnormal BMP had abnormal radiographs, a sensitivity of 41%.

  20. Quantitative detection of residual porcine host cell DNA by real-time PCR.

    PubMed

    Chang, Jen-Ting; Chen, Yu-Chen; Chou, Yu-Chi; Wang, Shih-Rong

    2014-03-01

    All biological products are derived from complex living systems and are often mixed with large numbers of impurities. For reasons of safety, residual host-cell DNA must be eliminated during processing. To assay host-cell DNA content in biopharmaceutical products derived from porcine sources, this study applies the quantitative real-time polymerase chain reaction (Q-PCR) method. The optimized assay in this study is based on the pol region of the porcine endogenous retrovirus (PERV). Assay validation results demonstrate that the proposed assay has appropriate accuracy, preciseness, reproducibility, and sensitivity. Primer and probe specificity are evaluated in real-time Q-PCR reactions using genomic DNA from rabbit, mouse, cat, hamster, monkey, human cell, yeast, and Escherichia coli as templates. The sensitivity of real-time Q-PCR is determined using genomic DNA from the porcine kidney cell line. The reliable detection range is within 0.5-10(5) pg/reaction. The limit of quantitation is 500 fg. The sensitivity of the assay meets the authority criterion. Moreover, the assay is applied to determine the level of host-cell DNA in recombinant human coagulation factor IX (rhFIX) from transgenic pigs. The real-time Q-PCR assay is thus a promising new tool for quantitative detection and clearance validation of residual porcine DNA when manufacturing recombinant therapeutics.

  1. Methods for Quantitative Detection of Antibody-induced Complement Activation on Red Blood Cells

    PubMed Central

    Meulenbroek, Elisabeth M.; Wouters, Diana; Zeerleder, Sacha

    2014-01-01

    Antibodies against red blood cells (RBCs) can lead to complement activation resulting in an accelerated clearance via complement receptors in the liver (extravascular hemolysis) or leading to intravascular lysis of RBCs. Alloantibodies (e.g. ABO) or autoantibodies to RBC antigens (as seen in autoimmune hemolytic anemia, AIHA) leading to complement activation are potentially harmful and can be - especially when leading to intravascular lysis - fatal1. Currently, complement activation due to (auto)-antibodies on RBCs is assessed in vitro by using the Coombs test reflecting complement deposition on RBC or by a nonquantitative hemolytic assay reflecting RBC lysis1-4. However, to assess the efficacy of complement inhibitors, it is mandatory to have quantitative techniques. Here we describe two such techniques. First, an assay to detect C3 and C4 deposition on red blood cells that is induced by antibodies in patient serum is presented. For this, FACS analysis is used with fluorescently labeled anti-C3 or anti-C4 antibodies. Next, a quantitative hemolytic assay is described. In this assay, complement-mediated hemolysis induced by patient serum is measured making use of spectrophotometric detection of the released hemoglobin. Both of these assays are very reproducible and quantitative, facilitating studies of antibody-induced complement activation. PMID:24514151

  2. Calibration-free quantitation in microchip zone electrophoresis with conductivity detection.

    PubMed

    Noblitt, Scott D; Henry, Charles S

    2015-08-01

    The relationship between electrophoretic mobility and molar conductivity has previously led to speculation on achieving quantitation in zone electrophoresis without calibration curves when using conductivity detection. However, little work in this area has been pursued, possibly because of the breakdown of simple sensitivity-mobility relationships when working with partially protonated species. This topic is revisited with the aid of electrophoretic simulation software that produces facile predictions of analyte sensitivity relative to an internal standard. Calibration curve slopes for over 50 analyte/internal standard/BGE combinations were measured with both unbiased and electrokinetically biased injections using microchip electrophoresis with conductivity detection. The results were compared to theoretical expectations as computed with PeakMaster software. Good agreement was observed, with some systems being predicted with quantitative accuracy while others showed significant deviations. Some mechanisms that can lead to deviations from theory are demonstrated, but the causes for some discrepancies are still not understood. Overall, this work exhibits another useful application for simulation software, particularly for disposable devices where device-specific calibration curves cannot be collected. It also serves as quantitative validation for some outputs of PeakMaster simulation software.

  3. Quantitation of HIV-1 by real-time amplification and detection

    NASA Astrophysics Data System (ADS)

    Jung, Paul M.; Yang, Naiquan; Kroeger, Paul E.

    1998-04-01

    A model assay for HIV-1 using a non-competitive internal standard in quantitative RT-PCR was coupled with real-time detection of both analyte and internal standard (IS) signals in a closed system. Real-time detection by the PE-ABI Prism 7700 relied on TaqMan probes specific for HIV and IS. The exogenous, non-competitive IS RNA was added in the same, known amount to a series of HIV RNA standards. The threshold cycle ratio from this internal standard calibration curve was used in the quantitation of HIV. Two configurations of reporter labels were compared. The HEX-HIV:FAM-IS system was the most precise, with nearly half-log discrimination over a range of 102 through 105 copies HIV-1 RNA. The FAM- HIV:HEX-IS system was less precise, but more sensitive and resistant to sample inhibition. The analysis of these signals and their impact on the range and precision of HIV quantitation is discussed. The design and synthesis of the fluorescently-labelled probes is also described.

  4. Automated Detection of P. falciparum Using Machine Learning Algorithms with Quantitative Phase Images of Unstained Cells

    PubMed Central

    Park, Han Sang; Rinehart, Matthew T.; Walzer, Katelyn A.; Chi, Jen-Tsan Ashley; Wax, Adam

    2016-01-01

    Malaria detection through microscopic examination of stained blood smears is a diagnostic challenge that heavily relies on the expertise of trained microscopists. This paper presents an automated analysis method for detection and staging of red blood cells infected by the malaria parasite Plasmodium falciparum at trophozoite or schizont stage. Unlike previous efforts in this area, this study uses quantitative phase images of unstained cells. Erythrocytes are automatically segmented using thresholds of optical phase and refocused to enable quantitative comparison of phase images. Refocused images are analyzed to extract 23 morphological descriptors based on the phase information. While all individual descriptors are highly statistically different between infected and uninfected cells, each descriptor does not enable separation of populations at a level satisfactory for clinical utility. To improve the diagnostic capacity, we applied various machine learning techniques, including linear discriminant classification (LDC), logistic regression (LR), and k-nearest neighbor classification (NNC), to formulate algorithms that combine all of the calculated physical parameters to distinguish cells more effectively. Results show that LDC provides the highest accuracy of up to 99.7% in detecting schizont stage infected cells compared to uninfected RBCs. NNC showed slightly better accuracy (99.5%) than either LDC (99.0%) or LR (99.1%) for discriminating late trophozoites from uninfected RBCs. However, for early trophozoites, LDC produced the best accuracy of 98%. Discrimination of infection stage was less accurate, producing high specificity (99.8%) but only 45.0%-66.8% sensitivity with early trophozoites most often mistaken for late trophozoite or schizont stage and late trophozoite and schizont stage most often confused for each other. Overall, this methodology points to a significant clinical potential of using quantitative phase imaging to detect and stage malaria infection

  5. Low-level mixing height detection in coastal locations with a scanning Doppler lidar

    NASA Astrophysics Data System (ADS)

    Vakkari, V.; O'Connor, E. J.; Nisantzi, A.; Mamouri, R. E.; Hadjimitsis, D. G.

    2015-04-01

    Mixing layer height (MLH) is one of the key parameters in describing lower tropospheric dynamics and capturing its diurnal variability is crucial, especially for interpreting surface observations. In this paper we introduce a method for identifying MLH below the minimum range of a scanning Doppler lidar when operated at vertical. The method we propose is based on velocity variance in low-elevation-angle conical scanning and is applied to measurements in two very different coastal environments: Limassol, Cyprus, during summer and Loviisa, Finland, during winter. At both locations, the new method agrees well with MLH derived from turbulent kinetic energy dissipation rate profiles obtained from vertically pointing measurements. The low-level scanning routine frequently indicated non-zero MLH less than 100 m above the surface. Such low MLHs were more common in wintertime Loviisa on the Baltic Sea coast than during summertime in Mediterranean Limassol.

  6. Signal Processing Variables for Optimization of Flaw Detection in Composites Using Ultrasonic Guided Wave Scanning

    NASA Technical Reports Server (NTRS)

    Roth, Don J.; Cosgriff, Laura M.; Martin, Richard E.; Teemer, LeTarrie

    2004-01-01

    This study analyzes the effect of signal processing variables on the ability of the ultrasonic guided wave scan method at NASA Glenn Research Center to distinguish various flaw conditions in ceramic matrix composites samples. In the ultrasonic guided wave scan method, several time- and frequency-domain parameters are calculated from the ultrasonic guided wave signal at each scan location to form images. The parameters include power spectral density, centroid mean time, total energy (zeroth moment), centroid frequency, and ultrasonic decay rate. A number of signal processing variables are available to the user when calculating these parameters. These signal processing variables include 1) the time portion of the time-domain waveform processed, 2) integration type for the properties requiring integrations, 3) bounded versus unbounded integrations, 4) power spectral density window type, 5) and the number of time segments chosen if using the short-time fourier transform to calculate ultrasonic decay rate. Flaw conditions examined included delamination, cracking, and density variation.

  7. Mining three-dimensional anthropometric body surface scanning data for hypertension detection.

    PubMed

    Chiu, Chaochang; Hsu, Kuang-Hung; Hsu, Pei-Lun; Hsu, Chi-I; Lee, Po-Chi; Chiou, Wen-Ko; Liu, Thu-Hua; Chuang, Yi-Chou; Hwang, Chorng-Jer

    2007-05-01

    Hypertension is a major disease, being one of the top ten causes of death in Taiwan. The exploration of three-dimensional (3-D) anthropometry scanning data along with other existing subject medical profiles using data mining techniques becomes an important research issue for medical decision support. This research attempts to construct a prediction model for hypertension using anthropometric body surface scanning data. This research adopts classification trees to reveal the relationship between a subject's 3-D scanning data and hypertension disease using the hybrid of the association rule algorithm (ARA) and genetic algorithms (GAs) approach. The ARA is adopted to obtain useful clues based on which the GA is able to proceed its searching tasks in a more efficient way. The proposed approach was experimented and compared with a regular genetic algorithm in predicting a subject's hypertension disease. Better computational efficiency and more accurate prediction results from the proposed approach are demonstrated.

  8. A self-referential outlier detection method for quantitative motor unit action potential analysis.

    PubMed

    Sheean, Geoffrey L

    2012-04-01

    Quantitative MUAP analysis is often based on outlier detection, in the case of neurogenic conditions, the finding of MUAPs that are larger than the limit determined from a reference normal population. Such reference data is available from only a few sources and for only a few muscles. It would be desirable if muscles could serve as their own controls. The Henneman size principle determines the order of recruitment, following an exponential distribution of twitch force, motor neurone, motor unit, and MUAP size. Therefore, an outlier could be detected by being too large for the level of recruitment, as judged by its size relative to the other MUAPs. This would improve the sensitivity of detecting neurogenic muscles and obviate the need for external reference data.

  9. Nanomolar colorimetric quantitative detection of Fe3 + and PPi with high selectivity

    NASA Astrophysics Data System (ADS)

    Li, Zhanxian; Li, Haixia; Shi, Caixia; Yu, Mingming; Wei, Liuhe; Ni, Zhonghai

    2016-04-01

    A novel rhodamine and 8-hydroxyquinoline-based derivative was synthesized, which is shown to act as a colorimetric chemosensor for Fe3 + in aqueous solution with high selectivity over various environmentally and biologically relevant metal ions and anions with a distinct color change from colorless to pink in very fast response time (< 1 min). Fe3 + can be detected quantitatively in the concentration range from 6.7 to 16 μM and the detection limit (LOD) on UV-vis response of the sensor can be as low as 15 nM. The 'in situ' prepared Fe3 + complex (1 ṡ Fe) showed high selectivity toward PPi against many common anions, and sensitivity (the LOD can be as low as 71 nM). In addition, both the chemosensor and the 'in situ' prepared Fe3 + complex are reusable for the detection of Fe3 + and PPi respectively.

  10. Quantitative multiplex detection of biomarkers on a waveguide-based biosensor using quantum dots

    SciTech Connect

    Xie, Hongzhi; Mukundan, Harshini; Martinez, Jennifer S; Swanson, Basil I; Anderson, Aaron S; Grace, Kevin

    2009-01-01

    The quantitative, simultaneous detection of multiple biomarkers with high sensitivity and specificity is critical for biomedical diagnostics, drug discovery and biomarker characterization [Wilson 2006, Tok 2006, Straub 2005, Joos 2002, Jani 2000]. Detection systems relying on optical signal transduction are, in general, advantageous because they are fast, portable, inexpensive, sensitive, and have the potential for multiplex detection of analytes of interest. However, conventional immunoassays for the detection of biomarkers, such as the Enzyme Linked Immunosorbant Assays (ELISAs) are semi-quantitative, time consuming and insensitive. ELISA assays are also limited by high non-specific binding, especially when used with complex biological samples such as serum and urine (REF). Organic fluorophores that are commonly used in such applications lack photostability and possess a narrow Stoke's shift that makes simultaneous detection of multiple fluorophores with a single excitation source difficult, thereby restricting their use in multiplex assays. The above limitations with traditional assay platforms have resulted in the increased use of nanotechnology-based tools and techniques in the fields of medical imaging [ref], targeted drug delivery [Caruthers 2007, Liu 2007], and sensing [ref]. One such area of increasing interest is the use of semiconductor quantum dots (QDs) for biomedical research and diagnostics [Gao and Cui 2004, Voura 2004, Michalet 2005, Chan 2002, Jaiswal 2004, Gao 2005, Medintz 2005, So 2006 2006, Wu 2003]. Compared to organic dyes, QDs provide several advantages for use in immunoassay platforms, including broad absorption bands with high extinction coefficients, narrow and symmetric emission bands with high quantum yields, high photostablility, and a large Stokes shift [Michalet 2005, Gu 2002]. These features prompted the use of QDs as probes in biodetection [Michalet 2005, Medintz 2005]. For example, Jaiswal et al. reported long term multiple color

  11. Fast real-time polymerase chain reaction for quantitative detection of Lactobacillus delbrueckii bacteriophages in milk.

    PubMed

    Martín, Maria Cruz; del Rio, Beatriz; Martínez, Noelia; Magadán, Alfonso H; Alvarez, Miguel A

    2008-12-01

    One of the main microbiological problems of the dairy industry is the susceptibility of starter bacteria to virus infections. Lactobacillus delbrueckii, a component of thermophilic starter cultures used in the manufacture of several fermented dairy products, including yogurt, is also sensitive to bacteriophage attacks. To avoid the problems associated with these viruses, quick and sensitive detection methods are necessary. In the present study, a fast real-time quantitative polymerase chain reaction assay for the direct detection and quantification of L. delbrueckii phages in milk was developed. A set of primers and a TaqMan MGB probe was designed, based on the lysin gene sequence of different L. delbrueckii phages. The results show the proposed method to be a rapid (total processing time 30 min), specific and highly sensitive technique for detecting L. delbrueckii phages in milk.

  12. A quantitative immunopolymerase chain reaction method for detection of vegetative insecticidal protein in genetically modified crops.

    PubMed

    Kumar, Rajesh

    2011-10-12

    Vegetative insecticidal protein (Vip) is being employed for transgenic expression in selected crops such as cotton, brinjal, and corn. For regulatory compliance, there is a need for a sensitive and reliable detection method, which can distinguish between approved and nonapproved genetically modified (GM) events and quantify GM contents as well. A quantitative immunopolymerase chain reaction (IPCR) method has been developed for the detection and quantification of Vip protein in GM crops. The developed assay displayed a detection limit of 1 ng/mL (1 ppb) and linear quantification range between 10 and 1000 ng/mL of Vip-S protein. The sensitivity of the assay was found to be 10 times higher than an analogous enzyme-linked immunosorbent assay for Vip-S protein. The results suggest that IPCR has the potential to become a standard method to quantify GM proteins.

  13. Incidental detection of superior sternal cleft on Technetium-99m methylene diphosphonate bone scan

    PubMed Central

    Aland, Nusrat IJ; Pawar, Shwetal Uday; Tilve, Gundu Hari

    2013-01-01

    A sternal cleft is an extremely rare developmental anomaly, which results from failure of fusion of sternal bars which contribute to the formation of the sternum. Most cases are diagnosed in early childhood, where it is associated with serious other midline defects. A sternal cleft is seen as a photopenic area on technetium-99m methylene diphosphonate bone scan and can be confused with other conditions. We report an extremely rare case of isolated upper sternal cleft in a 45-years-old male, found incidentally on Tc-99m MDP bone scan. PMID:24163521

  14. Detection of Luminescent Nanodiamonds Using a Scanning Near-Field Optical Microscope with an Aperture Probe

    NASA Astrophysics Data System (ADS)

    Shershulin, V. A.; Samoylenko, S. R.; Shenderova, O. A.; Vlasov, I. I.; Konov, V. I.

    2016-09-01

    Scanning near-fi eld optical microscopy (SNOM) with an aperture probe has been used to map the luminescence of isolated submicron diamond crystallites. 532-nm laser light was used to excite luminescence of nitrogen-vacancy (NV) centers. The sizes of the analyzed diamond crystallites were determined with an atomic-force microscope. The optical resolution for the lateral dimensions of the luminescing diamond crystallites was doubled on going from confocal luminescence microscopy to scanning near-fi eld optical microscopy with a 290-nm probe aperture diameter.

  15. Molecular detection of Mikrocytos mackini in Pacific oysters using quantitative PCR.

    PubMed

    Polinski, Mark; Lowe, Geoff; Meyer, Gary; Corbeil, Serge; Colling, Axel; Caraguel, Charles; Abbott, Cathryn L

    2015-01-01

    Mikrocytos mackini is an internationally regulated pathogen and causative agent of Denman Island disease in Pacific oysters Crassostrea gigas. Recent phylogenetic breakthroughs have placed this parasite within a highly divergent and globally distributed eukaryotic lineage that has been designated a new taxonomic order, Mikrocytida. The discovery of this new radiation of parasites is accompanied by a heightened awareness of the many knowledge gaps that exist with respect to the general biology, epizootiology, and potential impact of mikrocytid parasites on hosts, ecosystems, and commercial fisheries. It has also highlighted current shortcomings regarding our ability to detect these organisms. In this study, we developed a species-specific, sensitive, and quantitative method for detecting M. mackini DNA from host tissues using probe-based real-time qPCR technology. A limit of sensitivity between 2 and 5 genome copy equivalents was achieved in a reaction matrix containing ≥ 40 ng/μL host gDNA without inhibition. This detection proved superior to existing methods based on conventional PCR, histology or gross pathology and is the first species-specific diagnostic test for M. mackini. Quantitative assessment of parasite DNA using this assay remained accurate to between 10 and 50 copies identifying that during infection, M. mackini DNA was significantly more prevalent in hemolymph, labial palp, and mid-body cross-sections compared to mantle or adductor muscle. DNA extracted from a mid-body cross-section also provided the highest likelihood for detection during diagnostic screening of infected oysters. Taken together, these findings provide strong analytical evidence for the adoption of qPCR as the new reference standard for detecting M. mackini and give preliminary insight into the distribution of the parasite within host tissues. Standardised operating methodologies for sample collection and qPCR testing are provided to aid in the international regulatory diagnosis of

  16. Qualitative and Quantitative Assays for Detection and Characterization of Protein Antimicrobials

    PubMed Central

    Farris, M. Heath; Ford, Kara A.; Doyle, Richard C.

    2016-01-01

    Initial evaluations of large microbial libraries for potential producers of novel antimicrobial proteins require both qualitative and quantitative methods to screen for target enzymes prior to investing greater research effort and resources. The goal of this protocol is to demonstrate two complementary assays for conducting these initial evaluations. The microslide diffusion assay provides an initial or simple detection screen to enable the qualitative and rapid assessment of proteolytic activity against an array of both viable and heat-killed bacterial target substrates. As a counterpart, the increased sensitivity and reproducibility of the dye-release assay provides a quantitative platform for evaluating and comparing environmental influences affecting the hydrolytic activity of protein antimicrobials. The ability to label specific heat-killed cell culture substrates with Remazol brilliant blue R dye expands this capability to tailor the dye-release assay to characterize enzymatic activity of interest. PMID:27166738

  17. Quantum dots assisted laser desorption/ionization mass spectrometric detection of carbohydrates: qualitative and quantitative analysis.

    PubMed

    Bibi, Aisha; Ju, Huangxian

    2016-04-01

    A quantum dots (QDs) assisted laser desorption/ionization mass spectrometric (QDA-LDI-MS) strategy was proposed for qualitative and quantitative analysis of a series of carbohydrates. The adsorption of carbohydrates on the modified surface of different QDs as the matrices depended mainly on the formation of hydrogen bonding, which led to higher MS intensity than those with conventional organic matrix. The effects of QDs concentration and sample preparation method were explored for improving the selective ionization process and the detection sensitivity. The proposed approach offered a new dimension to the application of QDs as matrices for MALDI-MS research of carbohydrates. It could be used for quantitative measurement of glucose concentration in human serum with good performance. The QDs served as a matrix showed the advantages of low background, higher sensitivity, convenient sample preparation and excellent stability under vacuum. The QDs assisted LDI-MS approach has promising application to the analysis of carbohydrates in complex biological samples.

  18. Nanobarcoded superparamagnetic iron oxide nanoparticles for nanomedicine: Quantitative studies of cell-nanoparticle interactions by scanning image cytometry.

    PubMed

    Eustaquio, Trisha; Leary, James F

    2016-02-01

    Oligonucleotide-functionalized nanoparticles (NPs) are promising agents for nanomedicine, but the potential in vitro nanotoxicity that may arise from such conjugates has yet to be evaluated in a dose response manner. Since nanomedicine functions on the single-cell level, measurements of nanotoxicity should also be performed as such. In vitro single-cell nanotoxicity assays based on scanning image cytometry are used to study a specific type of oligo-functionalized NP, "nanobarcoded" superparamagnetic iron oxide NPs (NB-SPIONs). The selected panel of single-cell assays measures well-known modes of nanotoxicity--apoptosis, necrosis, generation of reactive oxygen species (ROS), and cell number. Using these assays, the cytotoxicity of two sizes of NB-SPIONs (10 nm and 30 nm core size) was compared to the parent NP, carboxylated SPIONs (COOH-SPIONs). The results suggest that the conjugated NB confers a biocompatible coating that protects against cytotoxicity at very high SPION doses, but both NB- and COOH-SPIONs of either size generally have low in vitro cytotoxicity at physiologically relevant doses.

  19. Event-specific quantitative detection of nine genetically modified maizes using one novel standard reference molecule.

    PubMed

    Yang, Litao; Guo, Jinchao; Pan, Aihu; Zhang, Haibo; Zhang, Kewei; Wang, Zhengming; Zhang, Dabing

    2007-01-10

    With the development of genetically modified organism (GMO) detection techniques, the Polymerase Chain Reaction (PCR) technique has been the mainstay for GMO detection, and real-time PCR is the most effective and important method for GMO quantification. An event-specific detection strategy based on the unique and specific integration junction sequences between the host plant genome DNA and the integrated gene is being developed for its high specificity. This study establishes the event-specific detection methods for TC1507 and CBH351 maizes. In addition, the event-specific TaqMan real-time PCR detection methods for another seven GM maize events (Bt11, Bt176, GA21, MON810, MON863, NK603, and T25) were systematically optimized and developed. In these PCR assays, the fluorescent quencher, TAMRA, was dyed on the T-base of the probe at the internal position to improve the intensity of the fluorescent signal. To overcome the difficulties in obtaining the certified reference materials of these GM maizes, one novel standard reference molecule containing all nine specific integration junction sequences of these GM maizes and the maize endogenous reference gene, zSSIIb, was constructed and used for quantitative analysis. The limits of detection of these methods were 20 copies for these different GM maizes, the limits of quantitation were about 20 copies, and the dynamic ranges for quantification were from 0.05 to 100% in 100 ng of DNA template. Furthermore, nine groups of the mixed maize samples of these nine GM maize events were quantitatively analyzed to evaluate the accuracy and precision. The accuracy expressed as bias varied from 0.67 to 28.00% for the nine tested groups of GM maize samples, and the precision expressed as relative standard deviations was from 0.83 to 26.20%. All of these indicated that the established event-specific real-time PCR detection systems and the reference molecule in this study are suitable for the identification and quantification of these GM

  20. Quantitative analysis of PEG-functionalized colloidal gold nanoparticles using charged aerosol detection.

    PubMed

    Smith, Mackensie C; Crist, Rachael M; Clogston, Jeffrey D; McNeil, Scott E

    2015-05-01

    Surface characteristics of a nanoparticle, such as functionalization with polyethylene glycol (PEG), are critical to understand and achieve optimal biocompatibility. Routine physicochemical characterization such as UV-vis spectroscopy (for gold nanoparticles), dynamic light scattering, and zeta potential are commonly used to assess the presence of PEG. However, these techniques are merely qualitative and are not sensitive enough to distinguish differences in PEG quantity, density, or presentation. As an alternative, two methods are described here which allow for quantitative measurement of PEG on PEGylated gold nanoparticles. The first, a displacement method, utilizes dithiothreitol to displace PEG from the gold surface. The dithiothreitol-coated gold nanoparticles are separated from the mixture via centrifugation, and the excess dithiothreitol and dissociated PEG are separated through reversed-phase high-performance liquid chromatography (RP-HPLC). The second, a dissolution method, utilizes potassium cyanide to dissolve the gold nanoparticles and liberate PEG. Excess CN(-), Au(CN)2 (-), and free PEG are separated using RP-HPLC. In both techniques, the free PEG can be quantified against a standard curve using charged aerosol detection. The displacement and dissolution methods are validated here using 2-, 5-, 10-, and 20-kDa PEGylated 30-nm colloidal gold nanoparticles. Further value in these techniques is demonstrated not only by quantitating the total PEG fraction but also by being able to be adapted to quantitate the free unbound PEG and the bound PEG fractions. This is an important distinction, as differences in the bound and unbound PEG fractions can affect biocompatibility, which would not be detected in techniques that only quantitate the total PEG fraction.

  1. Novel automatic detection of pleura and B-lines (comet-tail artifacts) on in vivo lung ultrasound scans

    NASA Astrophysics Data System (ADS)

    Moshavegh, Ramin; Hansen, Kristoffer Lindskov; Møller Sørensen, Hasse; Hemmsen, Martin Christian; Ewertsen, Caroline; Nielsen, Michael Bachmann; Jensen, Jørgen Arendt

    2016-04-01

    This paper presents a novel automatic method for detection of B-lines (comet-tail artifacts) in lung ultrasound scans. B-lines are the most commonly used artifacts for analyzing the pulmonary edema. They appear as laser-like vertical beams, which arise from the pleural line and spread down without fading to the edge of the screen. An increase in their number is associated with presence of edema. All the scans used in this study were acquired using a BK3000 ultrasound scanner (BK Ultrasound, Denmark) driving a 192-element 5:5 MHz wide linear transducer (10L2W, BK Ultrasound). The dynamic received focus technique was employed to generate the sequences. Six subjects, among those three patients after major surgery and three normal subjects, were scanned once and Six ultrasound sequences each containing 50 frames were acquired. The proposed algorithm was applied to all 300 in-vivo lung ultrasound images. The pleural line is first segmented on each image and then the B-line artifacts spreading down from the pleural line are detected and overlayed on the image. The resulting 300 images showed that the mean lateral distance between B-lines detected on images acquired from patients decreased by 20% in compare with that of normal subjects. Therefore, the method can be used as the basis of a method of automatically and qualitatively characterizing the distribution of B-lines.

  2. Evaluation of various real-time reverse transcription quantitative PCR assays for norovirus detection.

    PubMed

    Yoo, Ju Eun; Lee, Cheonghoon; Park, SungJun; Ko, GwangPyo

    2017-02-01

    Human noroviruses are widespread and contagious viruses causing nonbacterial gastroenteritis. Real-time reverse transcription quantitative PCR (real-time RT-qPCR) is currently the gold standard for sensitive and accurate detection for these pathogens and serves as a critical tool in outbreak prevention and control. Different surveillance teams, however, may use different assays and variability in specimen conditions may lead to disagreement in results. Furthermore, the norovirus genome is highly variable and continuously evolving. These issues necessitate the re-examination of the real-time RT-qPCR's robustness in the context of accurate detection as well as the investigation of practical strategies to enhance assay performance. Four widely referenced real-time RT-qPCR assays (Assay A-D) were simultaneously performed to evaluate characteristics such as PCR efficiency, detection limit, as well as sensitivity and specificity with RT-PCR, and to assess the most accurate method for detecting norovirus genogroups I and II. Overall, Assay D was evaluated to be the most precise and accurate assay in this study. A Zen internal quencher, which decreases nonspecific fluorescence during the PCR reaction, was added to Assay D's probe which further improved assay performance. This study compared several detection assays for noroviruses and an improvement strategy based on such comparisons provided useful characterizations of a highly optimized real-time RT-qPCR assay for norovirus detection.

  3. Hepatocellular carcinoma detection by gallium scan and subsequent treatment by gallium maltolate: rationale and case study.

    PubMed

    Bernstein, Lawrence R; van der Hoeven, Jacobus J M; Boer, Robbert O

    2011-07-01

    Gallium is antiproliferative to many types of cancer, due primarily to its ability to act as a non-functional mimic of ferric iron (Fe(3+)). Because Fe(3+) is needed for ribonucleotide reductase activity--and thus DNA synthesis--gallium can inhibit DNA production and cell division. Diagnostic gallium scans have shown that hepatocellular carcinoma (HCC) is commonly avid for gallium. Furthermore, in vitro studies have found that gallium nitrate, and particularly gallium maltolate (GaM), have dose-dependent antiproliferative activity against HCC cell lines. Rationale thus exists to use GaM, an orally active compound that has been well tolerated in Phase I clinical trials, to treat patients whose HCC is gallium-avid in a gallium scan. Because gallium absorbed from orally administered GaM is bound predominately to serum transferrin, which travels to all tissues in the body, GaM has the potential to treat even distant metastases. A patient with advanced HCC (20 × 10 cm primary tumor, ascites around liver and spleen, resistant to Nexavar(®) (sorafenib)), whose cancer was highly gallium-avid in a (67)Ga-scan, was treated with oral gallium maltolate at 1500 mg/day q.d. After four weeks of treatment, the patient had a large reduction in pain, with greatly increased mobility and quality of life, and significantly lowered serum bilirubin and inflammation-related liver enzymes. At eight weeks, CT scans showed apparent necrosis of the tumor.

  4. Quantitation of tetrahydrocannabinol in hair using immunoassay and liquid chromatography with tandem mass spectrometric detection.

    PubMed

    Coulter, Cynthia; Taruc, Margaux; Tuyay, James; Moore, Christine

    2009-05-01

    A quantitative analytical procedure for the determination of Delta(9)-tetrahydrocannabinol (THC) in hair has been developed and validated using liquid chromatography with tandem mass spectral detection (LC-MS/MS). Specimens that were determined as containing cannabinoids following immunoassay testing were quantified using solid-phase extraction followed by liquid chromatographic separation and tandem mass spectral detection in positive electrospray ionization mode. For confirmation, two transitions were monitored and one ratio determined. Samples being reported as positive were required to have both transitions present, the ratio of quantifying transition to qualifying transition being within 20% of that determined from known calibration standards. The limit of quantitation and the limit of detection was 10 pg/mg. The percentage recovery of the THC from hair at 20 pg/mg was 56% and a matrix effect of the hair showed an ion suppression percentage of -51%. The immunochemical screening method was performed following a rapid aqueous extraction, requiring only 10 mg of hair; the confirmatory procedure required 20 mg of hair. The methods were applied to proficiency specimens from the Society of Hair Testing, which had been received in August 2008.

  5. Development of Multiplexed Real-Time Quantitative PCR Assay for Detecting Human Adenoviruses

    PubMed Central

    Huang, Meei-Li; Nguy, Long; Ferrenberg, James; Boeckh, Michael; Cent, Anne; Corey, Lawrence

    2008-01-01

    Adenoviruses (AdV) have been associated with a wide variety of human disease and are increasingly recognized as viral pathogens that can cause significant morbidity and mortality in immunocompromised patients. Early detection of AdV DNA in plasma and sterile fluids has been shown to be useful for identifying patients at risk for invasive AdV disease. Due to the large number of existing Adv types, few real-time quantitative AdV PCR assays published effectively cover all AdV types. We designed a series of AdV PCR primers and probes and empirically multiplexed them into two separate real-time PCR assays to quantitatively detect all 49 serotypes of human AdV (Types 1-49) available from ATCC. We then subsequently multiplexed all the primers and probes into one reaction. The sensitivity of these assays was determined to be less than 10 copies per reaction (500 copies/ml plasma). In a retrospective evaluation we detected all 84 clinical AdV isolates isolated in cell culture from patients undergoing hematopoietic stem cell transplant (HSCT) between 1981 and 1987. Prospective analysis of 46 consecutive clinical samples submitted for adenovirus testing showed greater sensitivity and equal specificity of the AdV PCR than viral culture. This real time PCR assay allows rapid, sensitive and specific quantification of all currently defined adenoviruses into either two or one multiplex assay for clinical samples. PMID:18707838

  6. Quantitative detection of the colloidal gold immunochromatographic strip in HSV color space

    NASA Astrophysics Data System (ADS)

    Wu, Yuanshu; Gao, Yueming; Du, Min

    2014-09-01

    In this paper, a fast, reliable and accurate quantitative detection method for the colloidal gold immunochromatographic strip(GICA) is presented. An image acquisition device which is mainly composed of annular LED source, zoom ratio lens, and 10bit CMOS image sensors with 54.5dB SNR is designed for the detection. Firstly, the test line is extracted from the strip window through using the H component peak points of the HSV space as the clustering centers via the Fuzzy C-Means(FCM) clustering method. Then, a two dimensional eigenvalue composed with the hue(H) and saturation(S) of HSV space was proposed to improve the accuracy of the quantitative detection. At last, the experiment of human chorionic gonadotropin(HCG) with the concentration range 0-500mIU/mL is carried out. The results show that the linear correlation coefficient between this method and optical density(OD) values measured by the fiber optical sensor reach 96.74%. Meanwhile, the linearity of fitting curve constructed with concentration was greater than 95.00%.

  7. Highly sensitive detection of glucose: A quantitative approach employing nanorods assembled plasmonic substrate.

    PubMed

    Chen, Qiulan; Fu, Yu; Zhang, Weihong; Ye, Suibo; Zhang, Hao; Xie, Fangyan; Gong, Li; Wei, Zhanxiao; Jin, Haoyu; Chen, Jian

    2017-04-01

    Sensitive glucose detection enables indirect blood glucose sensing through easily accessible biofluids such as saliva and sweat. In this work, silver coated gold nanorods (Au@Ag NRs) were synthesized and used to prepare plasmonic substrate for surface-enhanced Raman spectroscopy (SERS) to leverage highly sensitive detection of glucose for quantitative analysis. By synthetically manipulating of gold NRs and the outer silver shell, the size and aspect ratio of Au@Ag NRs were optimized, and the plasmon resonance wavelength was tuned to approximately the excitation wavelength. 4-Mercaptophenyl-boronic acid (4-MPBA) and 4-Cyanophenylboronic acid (4-CPBA) were used as primary and secondary receptors respectively to specifically capture glucose molecules. The distinct Raman peak at 2226cm(-1) of the cyano group in 4-CPBA was used as a signal reporter for glucose sensing. It is located in a biological silent region (1800-2800cm(-1)), thus offering specific sensing of glucose, without the interference of other endogenous molecules. Our results showed that the SERS substrate was long-term stable. Glucose in urine solution with additive glucose was quantitatively and specifically determined, with the detection limit down to 10(-8)M. Further experiments using urine from mild diabetes shows positive results, demonstrating the feasibility of clinical use.

  8. Toxin screening in phytoplankton: detection and quantitation using MALDI triple quadrupole mass spectrometry.

    PubMed

    Sleno, Lekha; Volmer, Dietrich A

    2005-03-01

    The investigation of a MALDI triple quadrupole instrument for the analysis of spirolide toxins in phytoplankton samples is described in this study. A high-frequency (kHz) laser was employed for MALDI, generating a semicontinuous ion beam, thus taking advantage of the high duty cycle obtained in sensitive triple quadrupole MRM experiments. Initially, several experimental parameters such as type of organic matrix and concentration, solvent composition, and matrix-to-analyte ratio were optimized, and their impact on sensitivity and precision of the obtained ion currents for a reference spirolide, 13-desmethyl-C, was studied. In all quantitative experiments, excellent linearities in the concentration range between 0.01 and 1.75 microg/mL were obtained, with R2 values of 0.99 or higher. The average precision of the quantitative MALDI measurements was 7.4+/-2.4% RSD. No systematic errors were apparent with this method as shown by a direct comparison to an electrospray LC/MS/MS method. Most importantly, the MALDI technique was very fast; each sample spot was analyzed in less than 5 s as compared to several minutes with the electrospray assay. To demonstrate the potential of the MALDI triple quadrupole method, its application to quantitative analysis in several different phytoplankton samples was investigated, including crude extracts and samples from mass-triggered fractionation experiments. 13-Desmethyl spirolide C was successfully quantified in these complex samples at concentration levels from 0.05 to 90.4 microg/mL (prior to dilution to have samples fall within the dynamic range of the method) without extensive sample preparation steps. The versatility of the MALDI triple quadrupole method was also exhibited for the identification of unknown spirolide analogues. Through the use of dedicated linked scan functions such as precursor ion and neutral loss scans, several spirolide compounds were tentatively identified directly from the crude extract, without the usual time

  9. Detection of porosity in glass ceramic matrix composites using an ultrasonic multiple-gate C-scan technique

    SciTech Connect

    Stubbs, D.A.; Zawada, L.P.

    1996-07-01

    Ceramic matrix composite (CMC) plates consisting of silicon carbide fibers in a barium magnesium aluminosilicate matrix (SiC/BMAS) were obtained for mechanical and thermal properties characterization. Each plate had dimensions of 150 x 150 x 3 mm (6 x 6 x 0.12 in.) from which mechanical test specimens, each 150 mm (6 in.) long, were to be cut. To ensure that the material was properly consolidated and free of porosity, the plates were inspected using an ultrasonic multiple-gate C-scan technique previously developed for graphite epoxy composites. This technique allowed the placement of multiple peak-detection gates between the front and back surface echoes on the A-scan signal. Because each gate recorded the amplitude variation for a very narrow time-of-flight range, the frequent fluctuations in signal amplitude due to the inhomogeneity of the material affected one or two gates at times, while the other gates remained sensitive to small amplitude signals from defects. The increased sensitivity allowed the detection of very small material defects such as porosity. Using this technique for each plate revealed an isolated area of manufacturing abnormalities, presumed to be porosity, near the center of one plate. Based on the C-scan information, the pattern for cutting out the mechanical test specimens was altered and the region containing the abnormalities was sectioned, polished, and optically inspected. Optical microscopy clearly showed extensive porosity and a region of poor consolidation in the matrix material at the depth indicated by the C-scans. Details of the multiple-gate ultrasonic C-scan technique, results of the ultrasonic evaluation, and destructive analysis are discussed.

  10. Quantitative detection of Vibrio cholera toxin by real-time and dynamic cytotoxicity monitoring.

    PubMed

    Jin, Dazhi; Luo, Yun; Zheng, Min; Li, Haijing; Zhang, Jing; Stampfl, Melinda; Xu, Xiao; Ding, Gangqiang; Zhang, Yanjun; Tang, Yi-Wei

    2013-12-01

    We report here the quantitative detection of Vibrio cholerae toxin (CT) in isolates and stool specimens by dynamic monitoring of the full course of CT-mediated cytotoxicity in a real-time cell analysis (RTCA) system. Four cell lines, including Y-1 mouse adrenal tumor cells, Chinese hamster ovary (CHO) cells, small intestine epithelial (FHs74Int) cells, and mouse adrenal gland (PC12-Adh) cells, were evaluated for their suitability for CT-induced cytotoxicity testing. Among them, the Y-1 line was demonstrated to be the most sensitive for CT-mediated cytotoxicity, with limits of detection of 7.0 pg/ml for purified CT and 0.11 ng/ml for spiked CT in pooled negative stool specimens. No CT-mediated cytotoxicity was observed for nontoxigenic V. cholerae, non-V. cholerae species, or non-V. cholerae enterotoxins. The CT-RTCA assay was further validated with 100 stool specimens consecutively collected from patients with diarrhea and 200 V. cholerae isolates recovered from patients and the environment, in comparison to a reference using three detection methods. The CT-RTCA assay had sensitivities and specificities of 97.5% and 100.0%, respectively, for V. cholerae isolates and 90.0% and 97.2% for stool specimens. For stool specimens spiked with CT concentrations ranging from 3.5 pg/ml to 1.8 ng/ml, the inoculation-to-detection time was 1.12 ± 0.38 h, and the values were inversely correlated with CT concentrations (ρ = -1; P = 0.01). The results indicate that the CT-RTCA assay with the Y-1 cell line provides a rapid and sensitive tool for the quantitative detection of CT activities in clinical specimens.

  11. Detection and differentiation of human parvovirus variants by commercial quantitative real-time PCR tests.

    PubMed

    Hokynar, Kati; Norja, Päivi; Laitinen, Harri; Palomäki, Pekka; Garbarg-Chenon, Antoine; Ranki, Annamari; Hedman, Klaus; Söderlund-Venermo, Maria

    2004-05-01

    Parvovirus B19 causes a variety of diseases in humans, with outcomes ranging from asymptomatic to severe, such as chronic anemia in immunocompromised patients or fetal hydrops and death after maternal infection during pregnancy. The virus may be transmitted via plasma-derived products. According to the results of solvent-detergent safety studies, an upper limit of B19 DNA in plasma pools was recently defined. To restrict the input of B19 virus into production pools, a quantitative nucleic acid test is a prerequisite. We examined the suitability of the two commercial quantitative B19 PCR tests, LightCycler-Parvovirus B19 quantification kit (Roche Diagnostics) and RealArt Parvo B19 LC PCR (Artus) for detection, quantification, and differentiation of the three known B19 genotypes, including the newly described erythrovirus variants (genotypes 2 and 3). The former kit was highly sensitive for genotype 1 but was not suitable for detection of genotype 2 or one of two genotype 3 strains. The latter kit detected and differentiated all three genotypes, albeit with lower sensitivity for one of the genotype-3 strains. We furthermore assessed the prevalence of the three B19 virus genotypes in blood donors, by screening pooled plasma samples derived from 140,160 Finnish blood-donor units. None of the pools contained detectable levels of B19 virus genotypes 2 or 3. The origin, mode of transmission, and clinical significance of these genotypes are unknown and deserve further study. The RealArt Parvo B19 LC PCR is suitable for detection, quantification, and differentiation of all three B19 virus genotypes in molecular and clinical research.

  12. Nanometer-scale, quantitative composition mappings of InGaN layers from a combination of scanning transmission electron microscopy and energy dispersive x-ray spectroscopy.

    PubMed

    Pantzas, K; Patriarche, G; Troadec, D; Gautier, S; Moudakir, T; Suresh, S; Largeau, L; Mauguin, O; Voss, P L; Ougazzaden, A

    2012-11-16

    Using elastic scattering theory we show that a small set of energy dispersive x-ray spectroscopy (EDX) measurements is sufficient to experimentally evaluate the scattering function of electrons in high-angle annular dark field scanning transmission microscopy (HAADF-STEM). We then demonstrate how to use this function to transform qualitative HAADF-STEM images of InGaN layers into precise, quantitative chemical maps of the indium composition. The maps obtained in this way combine the resolution of HAADF-STEM and the chemical precision of EDX. We illustrate the potential of such chemical maps by using them to investigate nanometer-scale fluctuations in the indium composition and their impact on the growth of epitaxial InGaN layers.

  13. The effect of probe inaccuracies on the quantitative model-based analysis of high angle annular dark field scanning transmission electron microscopy images.

    PubMed

    Martinez, G T; De Backer, A; Rosenauer, A; Verbeeck, J; Van Aert, S

    2014-08-01

    Quantitative structural and chemical information can be obtained from high angle annular dark field scanning transmission electron microscopy (HAADF STEM) images when using statistical parameter estimation theory. In this approach, we assume an empirical parameterized imaging model for which the total scattered intensities of the atomic columns are estimated. These intensities can be related to the material structure or composition. Since the experimental probe profile is assumed to be known in the description of the imaging model, we will explore how the uncertainties in the probe profile affect the estimation of the total scattered intensities. Using multislice image simulations, we analyze this effect for Cs corrected and non-Cs corrected microscopes as a function of inaccuracies in cylindrically symmetric aberrations, such as defocus and spherical aberration of third and fifth order, and non-cylindrically symmetric aberrations, such as 2-fold and 3-fold astigmatism and coma.

  14. Electromechanical Detection in Scanning Probe Microscopy: Tip Models and Materials Contrast

    SciTech Connect

    Eliseev, E. A.; Kalinin, Sergei V; Jesse, Stephen; Bravina, S. L.; Morozovska, A. N.

    2007-01-01

    The rapid development of nanoscience and nanotechnology in the last two decades was stimulated by the emergence of scanning probe microscopy techniques capable of accessing local material properties, including transport, mechanical, and electromechanical behaviors, on the nanoscale. Here, we analyze the general principles of electromechanical probing by piezoresponse force microscopy (PFM), a scanning probe technique applicable to a broad range of piezoelectric and ferroelectric materials. The relationship between vertical and lateral PFM signals and material properties is derived analytically for two cases: transversally isotropic piezoelectric materials in the limit of weak elastic anisotropy, and anisotropic piezoelectric materials in the limit of weak elastic and dielectric anisotropies. The integral representations for PFM response for fully anisotropic material are also obtained. The image formation mechanism for conventional (e.g., sphere and cone) and multipole tips corresponding to emerging shielded and strip-line-type probes is analyzed. Possible applications for orientation imaging on the nanoscale and molecular resolution imaging are discussed.

  15. [Quantitative analysis method of natural gas combustion process combining wavelength selection and outlier spectra detection].

    PubMed

    Cao, Hui; Hu, Luo-Na; Zhou, Yan

    2012-10-01

    The present paper uses a combination method of wavelength selection and outlier spectra detection for quantitative analysis of nature gas combustion process based on its near infrared spectra. According to the statistical distribution of partial least squares (PLS) model coefficients and prediction errors, the method realized wavelength selection and outlier spectra detection, respectively. In contrast with PLS, PLS after leave-one-out for outlier detection (LOO-PLS), uninformative variable elimination by PLS (UVE-PLS) and UVE-PLS after leave-one-out for outlier detection (LOO-UVE-PLS), the root-mean-squared error of prediction (RMSEP) based on the method for CH4 prediction model is reduced by 14.33%, 14.33%, 10.96% and 12.21%; the RMSEP value for CO prediction model is reduced by 67.26%, 72.58%, 11.32% and 4.52%; the RMSEP value for CO2 prediction model is reduced by 5.95%, 19.7%, 36.71% and 4.04% respectively. Experimental results demonstrate that the method can significantly decrease the number of selected wavelengths, reduce model complexity and effectively detect outlier spectra. The established prediction model of analytes is more accurate as well as robust.

  16. Quantitative PCR and Digital PCR for Detection of Ascaris lumbricoides Eggs in Reclaimed Water

    PubMed Central

    Santísima-Trinidad, Ana Belén; Bornay-Llinares, Fernando Jorge; Martín González, Marcos; Pascual Valero, José Antonio; Ros Muñoz, Margarita

    2017-01-01

    The reuse of reclaimed water from wastewater depuration is a widespread and necessary practice in many areas around the world and must be accompanied by adequate and continuous quality control. Ascaris lumbricoides is one of the soil-transmitted helminths (STH) with risk for humans due to its high infectivity and an important determinant of transmission is the inadequacy of water supplies and sanitation. The World Health Organization (WHO) recommends a limit equal to or lower than one parasitic helminth egg per liter, to reuse reclaimed water for unrestricted irrigation. We present two new protocols of DNA extraction from large volumes of reclaimed water. Quantitative PCR (qPCR) and digital PCR (dPCR) were able to detect low amounts of A. lumbricoides eggs. By using the first extraction protocol, which processes 500 mL of reclaimed water, qPCR can detect DNA concentrations as low as one A. lumbricoides egg equivalent, while dPCR can detect DNA concentrations as low as five A. lumbricoides egg equivalents. By using the second protocol, which processes 10 L of reclaimed water, qPCR was able to detect DNA concentrations equivalent to 20 A. lumbricoides eggs. This fact indicated the importance of developing new methodologies to detect helminth eggs with higher sensitivity and precision avoiding possible human infection risks. PMID:28377928

  17. A Quantitative PCR Protocol for Detection of Oxyspirura petrowi in Northern Bobwhites (Colinus virginianus)

    PubMed Central

    Kistler, Whitney M.; Parlos, Julie A.; Peper, Steven T.; Dunham, Nicholas R.; Kendall, Ronald J.

    2016-01-01

    Oxyspirura petrowi is a parasitic nematode that infects wild birds. This parasite has a broad host range, but has recently been reported in high prevalences from native Galliformes species in the United States. In order to better understand the impact O. petrowi has on wild bird populations, we developed a quantitative PCR protocol to detect infections in wild northern bobwhites (Colinus virginianus). We used paired fecal and cloacal swab samples from wild caught and experimentally infected northern bobwhites and matching fecal float data from experimentally infected birds to validate our assay. Overall we detected more positive birds from fecal samples than the paired cloacal swabs and there was strong agreement between the qPCR results from fecal samples and from fecal flotation (84%; κ = 0.69 [0.53–0.84 95% CI]). We also detected O. petrowi DNA in ten replicates of samples spiked with one O. petrowi egg. This qPCR assay is an effective assay to detect O. petrowi infections in wild birds. Our results suggest that fecal samples are the most appropriate sample for detecting infections; although, cloacal swabs can be useful for determining if O. petrowi is circulating in a population. PMID:27893772

  18. Accurate detection and quantitation of heteroplasmic mitochondrial point mutations by pyrosequencing.

    PubMed

    White, Helen E; Durston, Victoria J; Seller, Anneke; Fratter, Carl; Harvey, John F; Cross, Nicholas C P

    2005-01-01

    Disease-causing mutations in mitochondrial DNA (mtDNA) are typically heteroplasmic and therefore interpretation of genetic tests for mitochondrial disorders can be problematic. Detection of low level heteroplasmy is technically demanding and it is often difficult to discriminate between the absence of a mutation or the failure of a technique to detect the mutation in a particular tissue. The reliable measurement of heteroplasmy in different tissues may help identify individuals who are at risk of developing specific complications and allow improved prognostic advice for patients and family members. We have evaluated Pyrosequencing technology for the detection and estimation of heteroplasmy for six mitochondrial point mutations associated with the following diseases: Leber's hereditary optical neuropathy (LHON), G3460A, G11778A, and T14484C; mitochondrial encephalopathy with lactic acidosis and stroke-like episodes (MELAS), A3243G; myoclonus epilepsy with ragged red fibers (MERRF), A8344G, and neurogenic muscle weakness, ataxia, and retinitis pigmentosa (NARP)/Leighs: T8993G/C. Results obtained from the Pyrosequencing assays for 50 patients with presumptive mitochondrial disease were compared to those obtained using the commonly used diagnostic technique of polymerase chain reaction (PCR) and restriction enzyme digestion. The Pyrosequencing assays provided accurate genotyping and quantitative determination of mutational load with a sensitivity and specificity of 100%. The MELAS A3243G mutation was detected reliably at a level of 1% heteroplasmy. We conclude that Pyrosequencing is a rapid and robust method for detecting heteroplasmic mitochondrial point mutations.

  19. Quantitative PCR and Digital PCR for Detection of Ascaris lumbricoides Eggs in Reclaimed Water.

    PubMed

    Acosta Soto, Lucrecia; Santísima-Trinidad, Ana Belén; Bornay-Llinares, Fernando Jorge; Martín González, Marcos; Pascual Valero, José Antonio; Ros Muñoz, Margarita

    2017-01-01

    The reuse of reclaimed water from wastewater depuration is a widespread and necessary practice in many areas around the world and must be accompanied by adequate and continuous quality control. Ascaris lumbricoides is one of the soil-transmitted helminths (STH) with risk for humans due to its high infectivity and an important determinant of transmission is the inadequacy of water supplies and sanitation. The World Health Organization (WHO) recommends a limit equal to or lower than one parasitic helminth egg per liter, to reuse reclaimed water for unrestricted irrigation. We present two new protocols of DNA extraction from large volumes of reclaimed water. Quantitative PCR (qPCR) and digital PCR (dPCR) were able to detect low amounts of A. lumbricoides eggs. By using the first extraction protocol, which processes 500 mL of reclaimed water, qPCR can detect DNA concentrations as low as one A. lumbricoides egg equivalent, while dPCR can detect DNA concentrations as low as five A. lumbricoides egg equivalents. By using the second protocol, which processes 10 L of reclaimed water, qPCR was able to detect DNA concentrations equivalent to 20 A. lumbricoides eggs. This fact indicated the importance of developing new methodologies to detect helminth eggs with higher sensitivity and precision avoiding possible human infection risks.

  20. Quantitative PCR detection of Batrachochytrium dendrobatidis DNA from sediments and water

    USGS Publications Warehouse

    Kirshtein, J.D.; Anderson, C.W.; Wood, J.S.; Longcore, J.E.; Voytek, M.A.

    2007-01-01

    The fungal pathogen Batrachochytrium dendrobatidis (Bd) causes chytridiomycosis, a disease implicated in amphibian declines on 5 continents. Polymerase chain reaction (PCR) primer sets exist with which amphibians can be tested for this disease, and advances in sampling techniques allow non-invasive testing of animals. We developed filtering and PCR based quantitative methods by modifying existing PCR assays to detect Bd DNA in water and sediments, without the need for testing amphibians; we tested the methods at 4 field sites. The SYBR based assay using Boyle primers (SYBR/Boyle assay) and the Taqman based assay using Wood primers performed similarly with samples generated in the laboratory (Bd spiked filters), but the SYBR/Boyle assay detected Bd DNA in more field samples. We detected Bd DNA in water from 3 of 4 sites tested, including one pond historically negative for chytridiomycosis. Zoospore equivalents in sampled water ranged from 19 to 454 l-1 (nominal detection limit is 10 DNA copies, or about 0.06 zoospore). We did not detect DNA of Bd from sediments collected at any sites. Our filtering and amplification methods provide a new tool to investigate critical aspects of Bd in the environment. ?? Inter-Research 2007.

  1. Detecting submerged objects: the application of side scan sonar to forensic contexts.

    PubMed

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

    2013-09-10

    Forensic personnel must deal with numerous challenges when searching for submerged objects. While traditional water search methods have generally involved using dive teams, remotely operated vehicles (ROVs), and water scent dogs for cases involving submerged objects and bodies, law enforcement is increasingly integrating multiple methods that include geophysical technologies. There are numerous advantages for integrating geophysical technologies, such as side scan sonar and ground penetrating radar (GPR), with more traditional search methods. Overall, these methods decrease the time involved searching, in addition to increasing area searched. However, as with other search methods, there are advantages and disadvantages when using each method. For example, in instances with excessive aquatic vegetation or irregular bottom terrain, it may not be possible to discern a submersed body with side scan sonar. As a result, forensic personnel will have the highest rate of success during searches for submerged objects when integrating multiple search methods, including deploying multiple geophysical technologies. The goal of this paper is to discuss the methodology of various search methods that are employed for submerged objects and how these various methods can be integrated as part of a comprehensive protocol for water searches depending upon the type of underwater terrain. In addition, two successful case studies involving the search and recovery of a submerged human body using side scan sonar are presented to illustrate the successful application of integrating a geophysical technology with divers when searching for a submerged object.

  2. A quantitative strategy to detect changes in accessibility of protein regions to chemical modification on heterodimerization

    PubMed Central

    Dreger, Mathias; Leung, Bo Wah; Brownlee, George G; Deng, Tao

    2009-01-01

    We describe a method for studying quantitative changes in accessibility of surface lysine residues of the PB1 subunit of the influenza RNA polymerase as a result of association with the PA subunit to form a PB1-PA heterodimer. Our method combines two established methods: (i) the chemical modification of surface lysine residues of native proteins by N-hydroxysuccinimidobiotin (NHS-biotin) and (ii) the stable isotope labeling of amino acids in cell culture (SILAC) followed by tryptic digestion and mass spectrometry. By linking the chemical modification with the SILAC methodology for the first time, we obtain quantitative data on chemical modification allowing subtle changes in accessibility to be described. Five regions in the PB1 monomer showed altered reactivity to NHS-biotin when compared with the [PB1-PA] heterodimer. Mutational analysis of residues in two such regions—at K265 and K481 of PB1, which were about three- and twofold, respectively, less accessible to biotinylation in the PB1-PA heterodimer compared with the PB1 monomer, demonstrated that both K265 and K481 were crucial for polymerase function. This novel assay of quantitative profiling of biotinylation patterns (Q-POP assay) highlights likely conformational changes at important functional sites, as observed here for PB1, and may provide information on protein–protein interaction interfaces. The Q-POP assay should be a generally applicable approach and may detect novel functional sites suitable for targeting by drugs. PMID:19517532

  3. Quantitative detection of astaxanthin and cantaxanthin in Atlantic salmon by resonance Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Ermakov, Igor V.; Ermakova, Maia R.; Gellermann, Werner

    2006-02-01

    Two major carotenoids species found in salmonids muscle tissues are astaxanthin and cantaxanthin. They are taken up from fish food and are responsible for the attractive red-orange color of salmon filet. Since carotenoids are powerful antioxidants and biomarkers of nutrient consumption, they are thought to indicate fish health and resistance to diseases in fish farm environments. Therefore, a rapid, accurate, quantitative optical technique for measuring carotenoid content in salmon tissues is of economic interest. We demonstrate the possibility of using fast, selective, quantitative detection of astaxanthin and cantaxanthin in salmon muscle tissues, employing resonance Raman spectroscopy. Analyzing strong Raman signals originating from the carbon-carbon double bond stretch vibrations of the carotenoid molecules under blue laser excitation, we are able to characterize quantitatively the concentrations of carotenoids in salmon muscle tissue. To validate the technique, we compared Raman data with absorption measurements of carotenoid extracts in acetone. A close correspondence was observed in absorption spectra for tissue extract in acetone and a pure astaxanthin solution. Raman results show a linear dependence between Raman and absorption data. The proposed technique holds promise as a method of rapid screening of carotenoid levels in fish muscle tissues and may be attractive for the fish farm industry to assess the dietary status of salmon, risk for infective diseases, and product quality control.

  4. Whole-genome scan for quantitative trait loci associated with birth weight, gestation length and passive immune transfer in a Holstein x Jersey crossbred population.

    PubMed

    Maltecca, C; Weigel, K A; Khatib, H; Cowan, M; Bagnato, A

    2009-02-01

    We herein report results from a daughter design genome-scan study aiming to identify quantitative trait loci (QTL) associated with birth weight, direct gestation length and passive immune transfer in a backcross (Holstein x Jersey) x Holstein population. Two-hundred and seventy-six calves, offspring of seven crossbred sires, were genotyped for 161 microsatellite markers distributed along the 29 bovine autosomes. The genome scan was performed through interval mapping using an animal model in order to identify QTL accounting for phenotypic differences between individual animals. Based on significant chi-squared values, we identified putative QTL on BTA7 and BTA14 for gestation length, on BTA2, BTA6 and BTA14 for birth weight and on BTA20 for passive immune transfer. In total, these QTL accounted for 12%, 18% and 1% of the phenotypic variance in gestation length, birth weight and passive immune transfer respectively. We also report results from a supplementary and independent influential grand-daughter Holstein family. In this family, findings on BTA7 and BTA14 for direct gestation length were in agreement with results in the crossbred population. Two other regions on BTA6 and BTA21 putatively underlying QTL for direct gestation length variability were discovered with this analysis.

  5. Development and application of quantitative detection method for viral hemorrhagic septicemia virus (VHSV) genogroup IVa.

    PubMed

    Kim, Jong-Oh; Kim, Wi-Sik; Kim, Si-Woo; Han, Hyun-Ja; Kim, Jin Woo; Park, Myoung Ae; Oh, Myung-Joo

    2014-05-23

    Viral hemorrhagic septicemia virus (VHSV) is a problematic pathogen in olive flounder (Paralichthys olivaceus) aquaculture farms in Korea. Thus, it is necessary to develop a rapid and accurate diagnostic method to detect this virus. We developed a quantitative RT-PCR (qRT-PCR) method based on the nucleocapsid (N) gene sequence of Korean VHSV isolate (Genogroup IVa). The slope and R² values of the primer set developed in this study were -0.2928 (96% efficiency) and 0.9979, respectively. Its comparison with viral infectivity calculated by traditional quantifying method (TCID₅₀) showed a similar pattern of kinetic changes in vitro and in vivo. The qRT-PCR method reduced detection time compared to that of TCID₅₀, making it a very useful tool for VHSV diagnosis.

  6. Development and Application of Quantitative Detection Method for Viral Hemorrhagic Septicemia Virus (VHSV) Genogroup IVa

    PubMed Central

    Kim, Jong-Oh; Kim, Wi-Sik; Kim, Si-Woo; Han, Hyun-Ja; Kim, Jin Woo; Park, Myoung Ae; Oh, Myung-Joo

    2014-01-01

    Viral hemorrhagic septicemia virus (VHSV) is a problematic pathogen in olive flounder (Paralichthys olivaceus) aquaculture farms in Korea. Thus, it is necessary to develop a rapid and accurate diagnostic method to detect this virus. We developed a quantitative RT-PCR (qRT-PCR) method based on the nucleocapsid (N) gene sequence of Korean VHSV isolate (Genogroup IVa). The slope and R2 values of the primer set developed in this study were −0.2928 (96% efficiency) and 0.9979, respectively. Its comparison with viral infectivity calculated by traditional quantifying method (TCID50) showed a similar pattern of kinetic changes in vitro and in vivo. The qRT-PCR method reduced detection time compared to that of TCID50, making it a very useful tool for VHSV diagnosis. PMID:24859343

  7. Feasibility of quantitative lung perfusion by 4D CT imaging by a new dynamic-scanning protocol in an animal model

    NASA Astrophysics Data System (ADS)

    Wang, Yang; Goldin, Jonathan G.; Abtin, Fereidoun G.; Brown, Matt; McNitt-Gray, Mike

    2008-03-01

    The purpose of this study is to test a new dynamic Perfusion-CT imaging protocol in an animal model and investigate the feasibility of quantifying perfusion of lung parenchyma to perform functional analysis from 4D CT image data. A novel perfusion-CT protocol was designed with 25 scanning time points: the first at baseline and 24 scans after a bolus injection of contrast material. Post-contrast CT scanning images were acquired with a high sampling rate before the first blood recirculation and then a relatively low sampling rate until 10 minutes after administrating contrast agent. Lower radiation techniques were used to keep the radiation dose to an acceptable level. 2 Yorkshire swine with pulmonary emboli underwent this perfusion- CT protocol at suspended end inspiration. The software tools were designed to measure the quantitative perfusion parameters (perfusion, permeability, relative blood volume, blood flow, wash-in & wash-out enhancement) of voxel or interesting area of lung. The perfusion values were calculated for further lung functional analysis and presented visually as contrast enhancement maps for the volume being examined. The results show increased CT temporal sampling rate provides the feasibility of quantifying lung function and evaluating the pulmonary emboli. Differences between areas with known perfusion defects and those without perfusion defects were observed. In conclusion, the techniques to calculate the lung perfusion on animal model have potential application in human lung functional analysis such as evaluation of functional effects of pulmonary embolism. With further study, these techniques might be applicable in human lung parenchyma characterization and possibly for lung nodule characterization.

  8. Development of a quantitative PCR for detection of Lactobacillus plantarum starters during wine malolactic fermentation.

    PubMed

    Cho, Gyu-Sung; Krauss, Sabrina; Huch, Melanie; Du Toit, Maret; Franz, Charles M A P

    2011-12-01

    A quantitative, real-time PCR method was developed to enumerate Lactobacillus plantarum IWBT B 188 during the malolactic fermentation (MLF) in Grauburgunder wine. The qRT-PCR was strain-specific, as it was based on primers targeting a plasmid DNA sequence, or it was L. plantarum-specific, as it targeted a chromosomally located plantaricin gene sequence. Two 50 l wine fermentations were prepared. One was inoculated with 15 g/hl Saccharomyces cerevisiae, followed by L. plantarum IWBT B 188 at 3.6 × 10(6) CFU/ml, whereas the other was not inoculated (control). Viable cell counts were performed for up to 25 days on MRS agar, and the same cells were enumerated by qRT-PCR with both the plasmid or chromosomally encoded gene primers. The L. plantarum strain survived under the harsh conditions in the wine fermentation at levels above 10(5)/ml for approx. 10 days, after which cell numbers decreased to levels of 10(3) CFU/ml at day 25, and to below the detection limit after day 25. In the control, no lactic acid bacteria could be detected throughout the fermentation, with the exception of two sampling points where ca. 1 × 10(2) CFU/ml was detected. The minimum detection level for quantitative PCR in this study was 1 × 10(2) to 1 × 10(3) CFU/ml. The qRT-PCR results determined generally overestimated the plate count results by about 1 log unit, probably as a result of the presence of DNA from dead cells. Overall, qRT-PCR appeared to be well suited for specifically enumerating Lactobacillus plantarum starter cultures in the MLF in wine.

  9. DetectTLC: Automated Reaction Mixture Screening Utilizing Quantitative Mass Spectrometry Image Features.

    PubMed

    Kaddi, Chanchala D; Bennett, Rachel V; Paine, Martin R L; Banks, Mitchel D; Weber, Arthur L; Fernández, Facundo M; Wang, May D

    2016-02-01

    Full characterization of complex reaction mixtures is necessary to understand mechanisms, optimize yields, and elucidate secondary reaction pathways. Molecular-level information for species in such mixtures can be readily obtained by coupling mass spectrometry imaging (MSI) with thin layer chromatography (TLC) separations. User-guided investigation of imaging data for mixture components with known m/z values is generally straightforward; however, spot detection for unknowns is highly tedious, and limits the applicability of MSI in conjunction with TLC. To accelerate imaging data mining, we developed DetectTLC, an approach that automatically identifies m/z values exhibiting TLC spot-like regions in MS molecular images. Furthermore, DetectTLC can also spatially match m/z values for spots acquired during alternating high and low collision-energy scans, pairing product ions with precursors to enhance structural identification. As an example, DetectTLC is applied to the identification and structural confirmation of unknown, yet significant, products of abiotic pyrazinone and aminopyrazine nucleoside analog synthesis. Graphical Abstract ᅟ.

  10. DetectTLC: Automated Reaction Mixture Screening Utilizing Quantitative Mass Spectrometry Image Features

    NASA Astrophysics Data System (ADS)

    Kaddi, Chanchala D.; Bennett, Rachel V.; Paine, Martin R. L.; Banks, Mitchel D.; Weber, Arthur L.; Fernández, Facundo M.; Wang, May D.

    2016-02-01

    Full characterization of complex reaction mixtures is necessary to understand mechanisms, optimize yields, and elucidate secondary reaction pathways. Molecular-level information for species in such mixtures can be readily obtained by coupling mass spectrometry imaging (MSI) with thin layer chromatography (TLC) separations. User-guided investigation of imaging data for mixture components with known m/z values is generally straightforward; however, spot detection for unknowns is highly tedious, and limits the applicability of MSI in conjunction with TLC. To accelerate imaging data mining, we developed DetectTLC, an approach that automatically identifies m/z values exhibiting TLC spot-like regions in MS molecular images. Furthermore, DetectTLC can also spatially match m/z values for spots acquired during alternating high and low collision-energy scans, pairing product ions with precursors to enhance structural identification. As an example, DetectTLC is applied to the identification and structural confirmation of unknown, yet significant, products of abiotic pyrazinone and aminopyrazine nucleoside analog synthesis.

  11. Detection accuracy of condylar bony defects in Promax 3D cone beam CT images scanned with different protocols

    PubMed Central

    Zhang, Z-L; Cheng, J-G; Li, G; Shi, X-Q; Zhang, J-Z; Zhang, Z-Y; Ma, X-C

    2013-01-01

    Objectives: To investigate and compare the detection accuracy of bony defects on the condylar surface of the temporomandibular joint (TMJ) in cone beam CT (CBCT) images scanned with standard and large view protocols on the same machine. Methods: 21 dry human skulls with 42 TMJs were scanned with the large view and standard view protocols of the CBCT scanner Promax 3D (Planmeca, Helsinki, Finland). Seven observers evaluated all the images for the presence or absence of defects on the surface of the condyle. Using the macroscopic examination of condylar defects as the gold standard, receiver operating characteristic (ROC) analysis was performed. Results: Macroscopic examination revealed that, of the 42 condyles, 18 were normal and 24 had a defect on the surface of the condyles. Areas under the ROC curves for the large view and the standard view group of CBCT images were 0.739 and 0.720, respectively, and no significant difference was found between the two groups of images (p = 0.902). Neither the interobserver nor the intraobserver variability were significant. Conclusions: The two scanning protocols provided by the CBCT scanner Promax 3D were reliable and comparable with detection of condylar defects. PMID:23420852

  12. The development of a line-scan imaging algorithm for the detection of fecal contamination on leafy geens

    NASA Astrophysics Data System (ADS)

    Yang, Chun-Chieh; Kim, Moon S.; Chuang, Yung-Kun; Lee, Hoyoung

    2013-05-01

    This paper reports the development of a multispectral algorithm, using the line-scan hyperspectral imaging system, to detect fecal contamination on leafy greens. Fresh bovine feces were applied to the surfaces of washed loose baby spinach leaves. A hyperspectral line-scan imaging system was used to acquire hyperspectral fluorescence images of the contaminated leaves. Hyperspectral image analysis resulted in the selection of the 666 nm and 688 nm wavebands for a multispectral algorithm to rapidly detect feces on leafy greens, by use of the ratio of fluorescence intensities measured at those two wavebands (666 nm over 688 nm). The algorithm successfully distinguished most of the lowly diluted fecal spots (0.05 g feces/ml water and 0.025 g feces/ml water) and some of the highly diluted spots (0.0125 g feces/ml water and 0.00625 g feces/ml water) from the clean spinach leaves. The results showed the potential of the multispectral algorithm with line-scan imaging system for application to automated food processing lines for food safety inspection of leafy green vegetables.

  13. Temperature-dependent quantitative 3omega scanning thermal microscopy: Local thermal conductivity changes in NiTi microstructures induced by martensite-austenite phase transition.

    PubMed

    Chirtoc, M; Gibkes, J; Wernhardt, R; Pelzl, J; Wieck, A

    2008-09-01

    We develop the theoretical description of 3omega signals from the resistive Wollaston thermal probe (ThP) of a scanning thermal microscope (SThM) in terms of an equivalent low-pass filter. The normalized amplitude and phase frequency spectra are completely characterized by a single parameter, the crossover frequency f(c)(k) depending on the sample thermal conductivity k. The application concerns polycrystalline NiTi shape memory alloy microstructured by focused Ga ion beam milling and implantation. The calibration of the ThP combined with a novel two-step normalization procedure allowed quantitative exploitation of 3omega signal variations as small as -1.75% in amplitude and 0.60 degrees in phase upon heating the sample from room temperature to 100 degrees C. This corresponds to k increase of 23.9% that is consistent with the expected thermal conductivity variation due to martensite-austenite structural phase transition. To our knowledge this is for the first time that SThM 3omega phase information is used quantitatively as well. The static, calibrated 3omega measurements are complementary to 3omega SThM images of the patterned sample surface. The local SThM measurement of temperature-dependent thermal conductivity opens the possibility to imaging structural phase transitions at submicron scale.

  14. Identification and quantitation of Bacillus globigii using metal enhanced electrochemical detection and capillary biosensor.

    PubMed

    Mwilu, Samuel K; Aluoch, Austin O; Miller, Seth; Wong, Paula; Sadik, Omowunmi A; Fatah, Alim A; Arcilesi, Richard D

    2009-09-15

    Presented herein are two detection strategies for the identification and quantification of Bacillus globigii, a spore forming nonpathogenic simulant of Bacillus anthracis. The first strategy involves a label-free, metal-enhanced electrochemical immunosensor for the quantitative detection of Bacillus globigii (atrophaeus). The immunosensor comprises of antibacillus globigii (BG) antibody self-assembled onto a gold quartz crystal electrode via cystamine bond. A solid-phase monolayer of silver underpotentially deposited onto the cystamine modified-Au-electrode surface is used as the redox probe. The monolayer was also generated by adsorbing silver nanoparticles on the gold electrode. When the antibody-modified electrode is exposed to BG spores, the antibody-antigen (Ab-Ag) complex formed insulated the electrode surface toward the silver redox probe. The variation of redox current was found to be proportional to the concentration of the BG spores between 1 x 10(2)-3.5 x 10(4) spores/mL. A detection limit of 602 spores/mL was obtained, which is well-below the infectious dose of anthrax spores at 2.5 x 10(5) spores/mL. The second approach involves the use of ultrasensitive portable capillary biosensor (UPAC) to detect the spores. The capillary is an enclosed system that acts as the flow cell, the waveguide, and the solid support for immobilized bimolecular probes. An evanescent excitation generates a signal from an antigen-antibody-fluorophore complex, which propagates along the capillary and is guided to the detector. A limit of detection of 112 spores/mL was reported using the UPAC sensor. Both methods showed lower detection limits compared to the conventional ELISA. The effect of potential interferants tested using Bacillus pumilus confirmed the selectivity for the analyte. This work should allow the first responders to rapidly detect and quantify Bacillus globigii spores at concentrations that are well-below the infectious dose.

  15. Detection of parent-of-origin effects for quantitative traits using general pedigree data.

    PubMed

    He, Hai-Qiang; Mao, Wei-Gao; Pan, Dongdong; Zhou, Ji-Yuan; Chen, Ping-Yan; Fung, Wing Kam

    2014-08-01

    Genomic imprinting is a genetic phenomenon in which certain alleles are differentially expressed in a parent-of-origin-specific manner, and plays an important role in the study of complex traits. For a diallelic marker locus in human, the parentalasymmetry tests Q-PAT(c) with any constant c were developed to detect parent-of-origin effects for quantitative traits. However, these methods can only be applied to deal with nuclear families and thus are not suitable for extended pedigrees. In this study, by making no assumption about the distribution of the quantitative trait, we first propose the pedigree parentalasymmetry tests Q-PPAT(c) with any constant c for quantitative traits to test for parent-of-origin effects based on nuclear families with complete information from general pedigree data, in the presence of association between marker alleles under study and quantitative traits. When there are any genotypes missing in pedigrees, we utilize Monte Carlo (MC) sampling and estimation and develop the Q-MCPPAT(c) statistics to test for parent-of-origin effects. Various simulation studies are conducted to assess the performance of the proposed methods, for different sample sizes, genotype missing rates, degrees of imprinting effects and population models. Simulation results show that the proposed methods control the size well under the null hypothesis of no parent-of-origin effects and Q-PPAT(c) are robust to population stratification. In addition, the power comparison demonstrates that Q-PPAT(c) and Q-MCPPAT(c) for pedigree data are much more powerful than Q-PAT(c) only using two-generation nuclear families selected from extended pedigrees.

  16. A Room Temperature Ultrasensitive Magnetoelectric Susceptometer for Quantitative Tissue Iron Detection

    NASA Astrophysics Data System (ADS)

    Xi, Hao; Qian, Xiaoshi; Lu, Meng-Chien; Mei, Lei; Rupprecht, Sebastian; Yang, Qing X.; Zhang, Q. M.

    2016-07-01

    Iron is a trace mineral that plays a vital role in the human body. However, absorbing and accumulating excessive iron in body organs (iron overload) can damage or even destroy an organ. Even after many decades of research, progress on the development of noninvasive and low-cost tissue iron detection methods is very limited. Here we report a recent advance in a room-temperature ultrasensitive biomagnetic susceptometer for quantitative tissue iron detection. The biomagnetic susceptometer exploits recent advances in the magnetoelectric (ME) composite sensors that exhibit an ultrahigh AC magnetic sensitivity under the presence of a strong DC magnetic field. The first order gradiometer based on piezoelectric and magnetostrictive laminate (ME composite) structure shows an equivalent magnetic noise of 0.99 nT/rt Hz at 1 Hz in the presence of a DC magnetic field of 0.1 Tesla and a great common mode noise rejection ability. A prototype magnetoelectric liver susceptometry has been demonstrated with liver phantoms. The results indicate its output signals to be linearly responsive to iron concentrations from normal iron dose (0.05 mg Fe/g liver phantom) to 5 mg Fe/g liver phantom iron overload (100X overdose). The results here open up many innovative possibilities for compact-size, portable, cost-affordable, and room-temperature operated medical systems for quantitative determinations of tissue iron.

  17. Quantitative single-molecule detection of protein based on DNA tetrahedron fluorescent nanolabels.

    PubMed

    Ding, Yongshun; Liu, Xingti; Zhu, Jing; Wang, Lei; Jiang, Wei

    2014-07-01

    A highly sensitive method for single-molecule quantitative detection of human IgG is presented by the employment of a new fluorescent nanolabel. In this method, fluorescent nanolabels were assembled by inserting SYBR Green I into DNA tetrahedron nanostructure. The bio-nanolabels were attached to the streptavidin-antihuman antibody by a specific reaction between biotin and streptavidin. The antibody was combined with the target antigen, human IgG, which was immobilized on the silanized glass subtrate surface. Finally, epi-fluorescence microscopy (EFM) coupled with an electron multiplying charge-coupled device was employed for fluorescence imaging. The fluorescent spots corresponding to single protein molecule on images were counted and further used for the quantitative detection. It was found that the new nanolabel shows good photostability, biocompatiblity and exhibits no blinking compared to traditional labels like fluorescence dyes and quantum dot (QDs). In addition, the number of fluorescence spots on the images has a linear relationship with the concentration of human IgG in the range of 3.0×10(-14) to 1.0×10(-12)mol L(-1). What is more, this method showed an excellent specificity and a low matrix effect.

  18. Quantitative detection of tetracycline residues in honey by a simple sensitive immunoassay.

    PubMed

    Jeon, Moonsun; Rhee Paeng, Insook

    2008-09-26

    Tetracyclines (TCs) are widely used for prevention and control of infectious diseases and have a great activity against variety of Gram-positive and Gram-negative bacteria. Due to the widespread use of TCs in animal husbandry, it can lead to an increase the risk of TCs remaining in human food. To protect consumers, many countries have set acceptable tolerance levels for these drugs. Therefore, it is necessary to establish a suitable analytical technique with specificity, sensitivity and simplicity. The biotin-avidin mediated ELISA method was performed to determine TC residues in honey quantitatively. By using PBS-EDTA assay buffer at pH 7.2, a honey solution of TC standard was prepared and diluted. And no additional pre-treatment of sample was required in this method. The limit of detection and limit of quantitation of the optimized method were 3.98 x 10(-10)M (0.19 mugL(-1)) and 7.94 x 10(-10)M (0.38 mugL(-1)), respectively, and the dynamic range was from 1.52 mugL(-1) to 152 mugL(-1) of TC in honey. No cross-reactivity was observed with the structurally similar compounds, and mean percent recoveries of TC spiked in honey ranged from 95% to 101%. Compared to other methods, this method was superior in terms of detection limit, dynamic range, and % recovery with simple sample-preparation.

  19. A Room Temperature Ultrasensitive Magnetoelectric Susceptometer for Quantitative Tissue Iron Detection

    PubMed Central

    Xi, Hao; Qian, Xiaoshi; Lu, Meng-Chien; Mei, Lei; Rupprecht, Sebastian; Yang, Qing X.; Zhang, Q. M.

    2016-01-01

    Iron is a trace mineral that plays a vital role in the human body. However, absorbing and accumulating excessive iron in body organs (iron overload) can damage or even destroy an organ. Even after many decades of research, progress on the development of noninvasive and low-cost tissue iron detection methods is very limited. Here we report a recent advance in a room-temperature ultrasensitive biomagnetic susceptometer for quantitative tissue iron detection. The biomagnetic susceptometer exploits recent advances in the magnetoelectric (ME) composite sensors that exhibit an ultrahigh AC magnetic sensitivity under the presence of a strong DC magnetic field. The first order gradiometer based on piezoelectric and magnetostrictive laminate (ME composite) structure shows an equivalent magnetic noise of 0.99 nT/rt Hz at 1 Hz in the presence of a DC magnetic field of 0.1 Tesla and a great common mode noise rejection ability. A prototype magnetoelectric liver susceptometry has been demonstrated with liver phantoms. The results indicate its output signals to be linearly responsive to iron concentrations from normal iron dose (0.05 mg Fe/g liver phantom) to 5 mg Fe/g liver phantom iron overload (100X overdose). The results here open up many innovative possibilities for compact-size, portable, cost-affordable, and room-temperature operated medical systems for quantitative determinations of tissue iron. PMID:27465206

  20. A Room Temperature Ultrasensitive Magnetoelectric Susceptometer for Quantitative Tissue Iron Detection.

    PubMed

    Xi, Hao; Qian, Xiaoshi; Lu, Meng-Chien; Mei, Lei; Rupprecht, Sebastian; Yang, Qing X; Zhang, Q M

    2016-07-28

    Iron is a trace mineral that plays a vital role in the human body. However, absorbing and accumulating excessive iron in body organs (iron overload) can damage or even destroy an organ. Even after many decades of research, progress on the development of noninvasive and low-cost tissue iron detection methods is very limited. Here we report a recent advance in a room-temperature ultrasensitive biomagnetic susceptometer for quantitative tissue iron detection. The biomagnetic susceptometer exploits recent advances in the magnetoelectric (ME) composite sensors that exhibit an ultrahigh AC magnetic sensitivity under the presence of a strong DC magnetic field. The first order gradiometer based on piezoelectric and magnetostrictive laminate (ME composite) structure shows an equivalent magnetic noise of 0.99 nT/rt Hz at 1 Hz in the presence of a DC magnetic field of 0.1 Tesla and a great common mode noise rejection ability. A prototype magnetoelectric liver susceptometry has been demonstrated with liver phantoms. The results indicate its output signals to be linearly responsive to iron concentrations from normal iron dose (0.05 mg Fe/g liver phantom) to 5 mg Fe/g liver phantom iron overload (100X overdose). The results here open up many innovative possibilities for compact-size, portable, cost-affordable, and room-temperature operated medical systems for quantitative determinations of tissue iron.

  1. Surface-enhanced Raman scattering for quantitative detection of ethyl carbamate in alcoholic beverages.

    PubMed

    Yang, Danting; Zhou, Haibo; Ying, Yibin; Niessner, Reinhard; Haisch, Christoph

    2013-11-01

    Ethyl carbamate, a by-product of fermentation and storage with widespread occurrence in fermented food and alcoholic beverages, is a compound potentially toxic to humans. In this work, a new approach for quantitative detection of ethyl carbamate in alcoholic beverages, based on surface-enhanced Raman scattering (SERS), is reported. Individual silver-coated gold nanoparticle colloids are used as SERS amplifiers, yielding high Raman enhancement of ethyl carbamate in three kinds of alcoholic beverages (vodka, Obstler, and white rum). The characteristic band at 1,003 cm(-1), which is the strongest and best reproducible peak in the SERS spectra, was used for quantitative evaluation of ethyl carbamate. The limit of detection, which corresponds to a signal-to-noise ratio of 3, was 9.0 × 10(-9) M (0.8 μg · L(-1)), 1.3 × 10(-7) M (11.6 μg · L(-1)), and 7.8 × 10(-8) M (6.9 μg · L(-1)), respectively. Surface-enhanced Raman spectroscopy offers great practical potential for the in situ assessment and identification of ethyl carbamate in the alcoholic beverage industry.

  2. Quantitative determination of selenium and mercury, and an ICP-MS semi-quantitative scan of other elements in samples of eagle tissues collected from the Pacific Northwest--Summer 2011

    USGS Publications Warehouse

    May, Thomas; Walther, Mike; Brumbaugh, William

    2013-01-01

    Eagle tissues from dead eagle carcasses were collected by U.S. Fish and Wildlife Service personnel at various locations in the Pacific Northwest as part of a study to document the occurrence of metal and metalloid contaminants. A group of 182 eagle tissue samples, consisting of liver, kidney, brain, talon, feather, femur, humerus, and stomach contents, were quantitatively analyzed for concentrations of selenium and mercury by atomic absorption techniques, and for other elements by semi-quantitative scan with an inductively coupled plasma-mass spectrometer. For the various tissue matrices analyzed by an ICP-MS semiquantitative scan, some elemental concentrations (micrograms per gram dry weight) were quite variable within a particular matrix; notable observations were as follows: lead concentrations ranged from 0.2 to 31 in femurs, 0.1 to 29 in humeri, 0.1 to 54 in talons, less than (<) 0.05 to 120 in livers, <0.05 to 34 in kidneys, and 0.05 to 8 in brains; copper concentrations ranged from 5 to 9 in feathers, 8 to 47 in livers, 7 to 43 in kidneys, and 7 to 28 in brains; cadmium concentrations ranged from 0.1 to 10 in kidneys. In stomach contents, concentrations of vanadium ranged from 0.08 to 5, chromium 2 to 34, manganese 1 to 57, copper 2 to 69, arsenic <0.05 to 6, rubidium 1 to 13, and barium <0.5 to 18. Selenium concentrations from highest to lowest based on the matrix mean were as follows: kidney, liver, feather, brain, stomach content, talon, femur, and humerus. For mercury, the highest to lowest concentrations were feather, liver, talon, brain, stomach content, femur, and humerus.

  3. Automated detection and quantification of micronodules in thoracic CT scans to identify subjects at risk for silicosis

    NASA Astrophysics Data System (ADS)

    Jacobs, C.; Opdam, S. H. T. T.; van Rikxoort, E. M.; Mets, O. M.; Rooyackers, J.; de Jong, P. A.; Prokop, M.; van Ginneken, B.

    2014-03-01

    Silica dust-exposed individuals are at high risk of developing silicosis, a fatal and incurable lung disease. The presence of disseminated micronodules on thoracic CT is the radiological hallmark of silicosis but locating micronodules, to identify subjects at risk, is tedious for human observers. We present a computer-aided detection scheme to automatically find micronodules and quantify micronodule load. The system used lung segmentation, template matching, and a supervised classification scheme. The system achieved a promising sensitivity of 84% at an average of 8.4 false positive marks per scan. In an independent data set of 54 CT scans in which we defined four risk categories, the CAD system automatically classified 83% of subjects correctly, and obtained a weighted kappa of 0.76.

  4. A new narrow-beam, multi-frequency, scanning radiometer and its application to in-flight icing detection

    NASA Astrophysics Data System (ADS)

    Serke, David J.; Reed, Kimberly A.; Negus, James; Blanchette, Levi; Ware, Randolph; Kennedy, Patrick C.

    2017-03-01

    A one degree beamwidth, multi-frequency (20 to 30 and 89GHz), dual-polarization radiometer with full azimuth and elevation scanning capabilities was built with the purpose of improving the detection of in-flight icing hazards to aircraft in the near airport environment. This goal was achieved by collocating the radiometer with Colorado State University's CHILL polarized Doppler radar and leveraging the similar beamwidth and volume scan regiments of the two instruments. The collocated instruments allowed for the liquid water path and water vapor measurements derived from the radiometer to be merged with the radar moment fields to determine microphysical and water phase characteristics aloft. The radiometer was field tested at Colorado State University's CHILL radar site near Greeley, Colorado during the summer of 2009. Instrument design, calibration, and initial field testing results are discussed in this paper.

  5. A New Narrowbeam, Multi-Frequency Scanning Radiometer and Its Application to In-Flight Icing Detection

    NASA Technical Reports Server (NTRS)

    Serke, David J.; Solheim, Frederick; Ware, Randolph; Politovich, Marcia K.; Brunkow, David; Bowie, Robert

    2010-01-01

    A narrow-beam (1 degree beamwidth), multi-channel (20 to 30 and 89 GHz), polarized (89 vertical and horizontal) radiometer with full azimuth and elevation scanning capabilities has been built with the purpose of improving the detection of in-flight icing hazards to aircraft in the near airport environment. This goal was achieved by co-locating the radiometer with Colorado State University's CHILL polarized Doppler radar and taking advantage of similar beamwidth and volume scan regiments. In this way, the liquid water path and water vapor measurements derived from the radiometer were merged with CHILL's moment fields to provide diagnoses of water phase and microphysics aloft. The radiometer was field tested at Colorado State University's CHILL radar site near Greeley, Colorado, during the summer of 2009. Instrument design, calibration and initial field testing results are discussed in this paper

  6. ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins

    PubMed Central

    de Castro, Edouard; Sigrist, Christian J. A.; Gattiker, Alexandre; Bulliard, Virginie; Langendijk-Genevaux, Petra S.; Gasteiger, Elisabeth; Bairoch, Amos; Hulo, Nicolas

    2006-01-01

    ScanProsite——is a new and improved version of the web-based tool for detecting PROSITE signature matches in protein sequences. For a number of PROSITE profiles, the tool now makes use of ProRules—context-dependent annotation templates—to detect functional and structural intra-domain residues. The detection of those features enhances the power of function prediction based on profiles. Both user-defined sequences and sequences from the UniProt Knowledgebase can be matched against custom patterns, or against PROSITE signatures. To improve response times, matches of sequences from UniProtKB against PROSITE signatures are now retrieved from a pre-computed match database. Several output modes are available including simple text views and a rich mode providing an interactive match and feature viewer with a graphical representation of results. PMID:16845026

  7. Rapid and precise scanning helium ion microscope milling of solid-state nanopores for biomolecule detection

    SciTech Connect

    Yang, Jijin; Ferranti, David C; Stern, Lewis A; Sanford, Colin A; Huang, Jason; Ren, Zheng; Qin, Lu-Chang; Hall, Adam R

    2011-06-10

    We report the formation of solid-state nanopores using a scanning helium ion microscope. The fabrication process offers the advantage of high sample throughput along with fine control over nanopore dimensions, producing single pores with diameters below 4 nm. Electronic noise associated with ion transport through the resultant pores is found to be comparable with levels measured on devices made with the established technique of transmission electron microscope milling. We demonstrate the utility of our nanopores for biomolecular analysis by measuring the passage of double-strand DNA.

  8. Real-time PCR assay for rapid qualitative and quantitative detection of Entamoeba histolytica.

    PubMed

    Orosz, Erika; Perkátai, Katalin; Kapusinszky, Beatrix; Farkas, Agnes; Kucsera, István

    2012-12-01

    Simple real-time PCR assay with one set of primer and probe for rapid, sensitive qualitative and quantitative detection of Entamoeba histolytica has been used. Consensus sequences were used to amplify a species-specific region of the 16S rRNA gene, and fluorescence resonance energy transfer hybridization probes were used for detection in a LightCycler platform (Roche). The anchor probe sequence was designed to be a perfect match for the 16S rRNA gene of Entamoeba species, while the acceptor probe sequence was designed for Entamoeba histolytica, which allowed differentiation. The performed characteristics of the real-time PCR assay were compared with ELISA antigen and microscopical detection from 77 samples of individuals with suspected clinical diagnosis of imported E. histolytica infection. Stool and liver abscess pus samples were examined with analytical sensitivity of 5 parasites per PCR reaction. The melting curve means Tms (standard deviation) in clinical isolates were 54°C. The real-time assay was 100% sensitive and specific for differentiation of Entamoeba histolytica, compared with conventional ELISA or microscopy. This real-time PCR assay with melting curve analysis is rapid, and specific for the detection and differentiation of Entamoeba histolytica. The suitability for routine use of this assay in clinical diagnostic laboratories is discussed.

  9. Utility of Real-Time Quantitative Polymerase Chain Reaction in Detecting Mycobacterium tuberculosis

    PubMed Central

    Zhang, Mingxin; Zhang, Hui

    2017-01-01

    This study aimed to assess the value of real-time quantitative polymerase chain reaction (RT-qPCR) for the detection of Mycobacterium tuberculosis (MTB). Samples from 192 patients with suspected MTB were examined by RT-qPCR and an improved Löwenstein–Jensen (L-J) culture method. To evaluate the diagnostic usefulness of RT-qPCR in detecting MTB, a receiver operating characteristic (ROC) curve for RT-qPCR was generated, and the area under the curve (AUC) as well as a cutoff value was calculated. Using the L-J culture method as the gold standard, accuracy of the RT-qPCR method for detecting MTB was 92.7%, with sensitivity and specificity of 62.5% and 97.02%, respectively. In comparison with the improved L-J culture method, the AUC of RT-qPCR ROC curve was 0.957, which was statistically significant (p < 0.001). The Youden Index reached the maximum value (0.88) for gene copy number of 794.5 IU/mL, which was used as the cutoff value. RT-qPCR detection of MTB yielded results consistent with those of the improved L-J culture method, with high accuracy. RT-qPCR may be used as an auxiliary method for etiological diagnosis of tuberculosis. PMID:28168192

  10. Quantitative GSTP1 methylation and the detection of prostate adenocarcinoma in sextant biopsies.

    PubMed

    Harden, Susan V; Sanderson, Harriette; Goodman, Steven N; Partin, Alan A W; Walsh, Patrick C; Epstein, Jonathan I; Sidransky, David

    2003-11-05

    Hypermethylation of the 5' promoter region of the glutathione S-transferase pi gene (GSTP1) occurs at a very high frequency in prostate adenocarcinoma. We compared the results of blinded histologic review of sextant biopsy samples from 72 excised prostates with those obtained using a quantitative methylation-specific polymerase chain reaction assay (QMSP) for GSTP1. Formal surgical pathologic review of the resected prostates was used to determine the number of patients with (n = 61) and without (n = 11) prostate cancer. Histology alone detected prostate carcinoma with 64% sensitivity (95% confidence interval [CI] = 51% to 76%) and 100% specificity (95% CI = 72% to 100%), whereas the combination of histology and GSTP1 QMSP at an assay threshold greater than 10 detected prostate carcinoma with 75% sensitivity (95% CI = 63% to 86%) and 100% specificity (95% CI = 72% to 100%), an 11% improvement (95% CI = 5% to 22%) in sensitivity over histology alone. The combination of histology and GSTP1 QMSP at an assay threshold greater than 5 detected prostate adenocarcinoma with 79% sensitivity (95% CI = 68% to 89%), a 15% improvement (95% CI = 7% to 26%) over histology alone. Thus, GSTP1 QMSP improved the sensitivity of histologic review of random needle biopsies for prostate cancer diagnosis. Further studies should determine whether detection of GSTP1 hypermethylation in a biopsy sample with normal histology indicates the need for an early repeat biopsy at the same site.

  11. Automatic detection and quantitative analysis of cells in the mouse primary motor cortex

    NASA Astrophysics Data System (ADS)

    Meng, Yunlong; He, Yong; Wu, Jingpeng; Chen, Shangbin; Li, Anan; Gong, Hui

    2014-09-01

    Neuronal cells play very important role on metabolism regulation and mechanism control, so cell number is a fundamental determinant of brain function. Combined suitable cell-labeling approaches with recently proposed three-dimensional optical imaging techniques, whole mouse brain coronal sections can be acquired with 1-μm voxel resolution. We have developed a completely automatic pipeline to perform cell centroids detection, and provided three-dimensional quantitative information of cells in the primary motor cortex of C57BL/6 mouse. It involves four principal steps: i) preprocessing; ii) image binarization; iii) cell centroids extraction and contour segmentation; iv) laminar density estimation. Investigations on the presented method reveal promising detection accuracy in terms of recall and precision, with average recall rate 92.1% and average precision rate 86.2%. We also analyze laminar density distribution of cells from pial surface to corpus callosum from the output vectorizations of detected cell centroids in mouse primary motor cortex, and find significant cellular density distribution variations in different layers. This automatic cell centroids detection approach will be beneficial for fast cell-counting and accurate density estimation, as time-consuming and error-prone manual identification is avoided.

  12. Quantitative trait loci detection of Edwardsiella tarda resistance in Japanese flounder Paralichthys olivaceus using bulked segregant analysis

    NASA Astrophysics Data System (ADS)

    Wang, Xiaoxia; Xu, Wenteng; Liu, Yang; Wang, Lei; Sun, Hejun; Wang, Lei; Chen, Songlin

    2016-11-01

    In recent years, Edwardsiella tarda has become one of the most deadly pathogens of Japanese flounder ( Paralichthys olivaceus), causing serious annual losses in commercial production. In contrast to the rapid advances in the aquaculture of P. olivaceus, the study of E. tarda resistance-related markers has lagged behind, hindering the development of a disease-resistant strain. Thus, a marker-trait association analysis was initiated, combining bulked segregant analysis (BSA) and quantitative trait loci (QTL) mapping. Based on 180 microsatellite loci across all chromosomes, 106 individuals from the F1333 (♀: F0768 ×♂: F0915) (Nomenclature rule: F+year+family number) were used to detect simple sequence repeats (SSRs) and QTLs associated with E. tarda resistance. After a genomic scan, three markers (Scaffold 404-21589, Scaffold 404-21594 and Scaffold 270-13812) from the same linkage group (LG)-1 exhibited a significant difference between DNA, pooled/bulked from the resistant and susceptible groups (P <0.001). Therefore, 106 individuals were genotyped using all the SSR markers in LG1 by single marker analysis. Two different analytical models were then employed to detect SSR markers with different levels of significance in LG1, where 17 and 18 SSR markers were identified, respectively. Each model found three resistance-related QTLs by composite interval mapping (CIM). These six QTLs, designated qE1-6, explained 16.0%-89.5% of the phenotypic variance. Two of the QTLs, qE-2 and qE-4, were located at the 66.7 cM region, which was considered a major candidate region for E. tarda resistance. This study will provide valuable data for further investigations of E. tarda resistance genes and facilitate the selective breeding of disease-resistant Japanese flounder in the future.

  13. Detection of multivessel disease in patients with sustained myocardial infarction by thallium 201 myocardial scintigraphy: No additional value of quantitative analysis

    SciTech Connect

    Niemeyer, M.G.; Pauwels, E.K.; van der Wall, E.E.; Cramer, M.J.; Verzijlbergen, J.F.; Zwinderman, A.H.; Ascoop, C.A. )

    1989-01-01

    This study was performed to determine the value of visual and quantitative thallium 201 scintigraphy for the detection of multivessel disease in 67 patients with a sustained transmural myocardial infarction. Also the viability of the myocardial regions corresponding to pathologic Q-waves was evaluated. Of the 67 patients, 51 patients had multivessel coronary artery disease (76%). The sensitivity of the exercise test was 53%, of thallium scintigraphy 69%, when interpreted visually, and 67%, when analysed quantitatively. The specificity of these methods was 69%, 56%, and 50%, respectively. Sixty-two infarct-related flow regions were detected by visual analysis of the thallium scans, total redistribution was observed in 11/62 (18%) of patients, partial redistribution in 26/62 (42%), and no redistribution in 25/62 (40%) of patients. The infarct-related areas with total redistribution on the thallium scintigrams were more likely to be associated with normal or hypokinetic wall motion (7/11: 64%) than the areas with a persistent defect (7/25:28%) (P = 0.05), which were more related with akinetic or dyskinetic wall motion. Based on our results, it is concluded that (1) both visual and quantitative analysis of thallium exercise scintigraphy have limited value to predict the presence or absence of multivessel coronary artery disease in patients with sustained myocardial infarction, and (2) exercise-induced thallium redistribution may occur within the infarct zone, suggesting the presence of viable but jeopardized myocardium in presumed fibrotic myocardial areas.

  14. Immunomagnetic quantitative immuno-PCR for detection of less than one HIV-1 virion.

    PubMed

    Barletta, Janet; Bartolome, Amelita; Constantine, Niel T

    2009-05-01

    Methods that allow the accurate and reliable detection of ultra-low molecular levels of proteins using techniques such as quantitative immuno-PCR (qIPCR) have demonstrated numerous technical difficulties. Protein detection methods lose specificity when the protein target is immersed within a matrix of thousands of molecules having wide ranges of concentrations. In addition, sensitivities are limited because of high background signals. To validate the performance of an immunomagnetic bead qIPCR method designed to remove the 'matrix' effect for HIV-1 p24 antigen detection, regression analyses were performed using samples from patients infected with HIV-1 diluted to approximately 100-1000, 10-100, 1-10, and 0.1-1.0 HIV-1 p24 Ag molecules/reaction. The number of HIV-1 p24 Ag molecules was derived from quantified HIV-1 RNA determinations. The modified immunomagnetic qIPCR bead assay demonstrated a limit of quantification of 10-100 HIV-1 p24 molecules per reaction, with an average correlation coefficient of 0.948+/-0.028 over a 4-log dynamic range. This method detects less than one HIV-1 virion (a limit of detection unreported previously for HIV-1), and thus, has the potential to identify HIV-1 infection and monitor the dynamics of the disease course earlier than nucleic acid methods. The immunomagnetic qIPCR bead assay is a simple and inexpensive method for ultra-low protein detection of infectious agents, toxins, and cancer markers at a level unrecognized previously using any enzymatic or molecular method.

  15. Genome Scans for Detecting Footprints of Local Adaptation Using a Bayesian Factor Model

    PubMed Central

    Duforet-Frebourg, Nicolas; Bazin, Eric; Blum, Michael G.B.

    2014-01-01

    There is a considerable impetus in population genomics to pinpoint loci involved in local adaptation. A powerful approach to find genomic regions subject to local adaptation is to genotype numerous molecular markers and look for outlier loci. One of the most common approaches for selection scans is based on statistics that measure population differentiation such as FST. However, there are important caveats with approaches related to FST because they require grouping individuals into populations and they additionally assume a particular model of population structure. Here, we implement a more flexible individual-based approach based on Bayesian factor models. Factor models capture population structure with latent variables called factors, which can describe clustering of individuals into populations or isolation-by-distance patterns. Using hierarchical Bayesian modeling, we both infer population structure and identify outlier loci that are candidates for local adaptation. In order to identify outlier loci, the hierarchical factor model searches for loci that are atypically related to population structure as measured by the latent factors. In a model of population divergence, we show that it can achieve a 2-fold or more reduction of false discovery rate compared with the software BayeScan or with an FST approach. We show that our software can handle large data sets by analyzing the single nucleotide polymorphisms of the Human Genome Diversity Project. The Bayesian factor model is implemented in the open-source PCAdapt software. PMID:24899666

  16. Assessing principal component regression prediction of neurochemicals detected with fast-scan cyclic voltammetry.

    PubMed

    Keithley, Richard B; Wightman, R Mark

    2011-06-07

    Principal component regression is a multivariate data analysis approach routinely used to predict neurochemical concentrations from in vivo fast-scan cyclic voltammetry measurements. This mathematical procedure can rapidly be employed with present day computer programming languages. Here, we evaluate several methods that can be used to evaluate and improve multivariate concentration determination. The cyclic voltammetric representation of the calculated regression vector is shown to be a valuable tool in determining whether the calculated multivariate model is chemically appropriate. The use of Cook's distance successfully identified outliers contained within in vivo fast-scan cyclic voltammetry training sets. This work also presents the first direct interpretation of a residual color plot and demonstrated the effect of peak shifts on predicted dopamine concentrations. Finally, separate analyses of smaller increments of a single continuous measurement could not be concatenated without substantial error in the predicted neurochemical concentrations due to electrode drift. Taken together, these tools allow for the construction of more robust multivariate calibration models and provide the first approach to assess the predictive ability of a procedure that is inherently impossible to validate because of the lack of in vivo standards.

  17. Empirical Bayes scan statistics for detecting clusters of disease risk variants in genetic studies.

    PubMed

    McCallum, Kenneth J; Ionita-Laza, Iuliana

    2015-12-01

    Recent developments of high-throughput genomic technologies offer an unprecedented detailed view of the genetic variation in various human populations, and promise to lead to significant progress in understanding the genetic basis of complex diseases. Despite this tremendous advance in data generation, it remains very challenging to analyze and interpret these data due to their sparse and high-dimensional nature. Here, we propose novel applications and new developments of empirical Bayes scan statistics to identify genomic regions significantly enriched with disease risk variants. We show that the proposed empirical Bayes methodology can be substantially more powerful than existing scan statistics methods especially so in the presence of many non-disease risk variants, and in situations when there is a mixture of risk and protective variants. Furthermore, the empirical Bayes approach has greater flexibility to accommodate covariates such as functional prediction scores and additional biomarkers. As proof-of-concept we apply the proposed methods to a whole-exome sequencing study for autism spectrum disorders and identify several promising candidate genes.

  18. Development of fast line scanning imaging algorithm for diseased chicken detection

    NASA Astrophysics Data System (ADS)

    Yang, Chun-Chieh; Chao, Kuanglin; Chen, Yud-Ren; Kim, Moon S.

    2005-11-01

    A hyperspectral line-scan imaging system for automated inspection of wholesome and diseased chickens was developed and demonstrated. The hyperspectral imaging system consisted of an electron-multiplying charge-coupled-device (EMCCD) camera and an imaging spectrograph. The system used a spectrograph to collect spectral measurements across a pixel-wide vertical linear field of view through which moving chicken carcasses passed. After a series of image calibration procedures, the hyperspectral line-scan images were collected for chickens on a laboratory simulated processing line. From spectral analysis, four key wavebands for differentiating between wholesome and systemically diseased chickens were selected: 413 nm, 472 nm, 515 nm, and 546 nm, and a reference waveband, 622 nm. The ratio of relative reflectance between each key wavelength and the reference wavelength was calculated as an image feature. A fuzzy logic-based algorithm utilizing the key wavebands was developed to identify individual pixels on the chicken surface exhibiting symptoms of systemic disease. Two differentiation methods were built to successfully differentiate 72 systemically diseased chickens from 65 wholesome chickens.

  19. Quantitative Detection of Trace Malachite Green in Aquiculture Water Samples by Extractive Electrospray Ionization Mass Spectrometry

    PubMed Central

    Fang, Xiaowei; Yang, Shuiping; Chingin, Konstantin; Zhu, Liang; Zhang, Xinglei; Zhou, Zhiquan; Zhao, Zhanfeng

    2016-01-01

    Exposure to malachite green (MG) may pose great health risks to humans; thus, it is of prime importance to develop fast and robust methods to quantitatively screen the presence of malachite green in water. Herein the application of extractive electrospray ionization mass spectrometry (EESI-MS) has been extended to the trace detection of MG within lake water and aquiculture water, due to the intensive use of MG as a biocide in fisheries. This method has the advantage of obviating offline liquid-liquid extraction or tedious matrix separation prior to the measurement of malachite green in native aqueous medium. The experimental results indicate that the extrapolated detection limit for MG was ~3.8 μg·L−1 (S/N = 3) in lake water samples and ~0.5 μg·L−1 in ultrapure water under optimized experimental conditions. The signal intensity of MG showed good linearity over the concentration range of 10–1000 μg·L−1. Measurement of practical water samples fortified with MG at 0.01, 0.1 and 1.0 mg·L−1 gave a good validation of the established calibration curve. The average recoveries and relative standard deviation (RSD) of malachite green in lake water and Carassius carassius fish farm effluent water were 115% (6.64% RSD), 85.4% (9.17% RSD) and 96.0% (7.44% RSD), respectively. Overall, the established EESI-MS/MS method has been demonstrated suitable for sensitive and rapid (<2 min per sample) quantitative detection of malachite green in various aqueous media, indicating its potential for online real-time monitoring of real life samples. PMID:27529262

  20. Quantitative Detection of Trace Malachite Green in Aquiculture Water Samples by Extractive Electrospray Ionization Mass Spectrometry.

    PubMed

    Fang, Xiaowei; Yang, Shuiping; Chingin, Konstantin; Zhu, Liang; Zhang, Xinglei; Zhou, Zhiquan; Zhao, Zhanfeng

    2016-08-11

    Exposure to malachite green (MG) may pose great health risks to humans; thus, it is of prime importance to develop fast and robust methods to quantitatively screen the presence of malachite green in water. Herein the application of extractive electrospray ionization mass spectrometry (EESI-MS) has been extended to the trace detection of MG within lake water and aquiculture water, due to the intensive use of MG as a biocide in fisheries. This method has the advantage of obviating offline liquid-liquid extraction or tedious matrix separation prior to the measurement of malachite green in native aqueous medium. The experimental results indicate that the extrapolated detection limit for MG was ~3.8 μg·L(-1) (S/N = 3) in lake water samples and ~0.5 μg·L(-1) in ultrapure water under optimized experimental conditions. The signal intensity of MG showed good linearity over the concentration range of 10-1000 μg·L(-1). Measurement of practical water samples fortified with MG at 0.01, 0.1 and 1.0 mg·L(-1) gave a good validation of the established calibration curve. The average recoveries and relative standard deviation (RSD) of malachite green in lake water and Carassius carassius fish farm effluent water were 115% (6.64% RSD), 85.4% (9.17% RSD) and 96.0% (7.44% RSD), respectively. Overall, the established EESI-MS/MS method has been demonstrated suitable for sensitive and rapid (<2 min per sample) quantitative detection of malachite green in various aqueous media, indicating its potential for online real-time monitoring of real life samples.

  1. Quantitative detection of powdered activated carbon in wastewater treatment plant effluent by thermogravimetric analysis (TGA).

    PubMed

    Krahnstöver, Therese; Plattner, Julia; Wintgens, Thomas

    2016-09-15

    For the elimination of potentially harmful micropollutants, powdered activated carbon (PAC) adsorption is applied in many wastewater treatment plants (WWTP). This holds the risk of PAC leakage into the WWTP effluent and desorption of contaminants into natural water bodies. In order to assess a potential PAC leakage, PAC concentrations below several mg/L have to be detected in the WWTP effluent. None of the methods that are used for water analysis today are able to differentiate between activated carbon and solid background matrix. Thus, a selective, quantitative and easily applicable method is still needed for the detection of PAC residues in wastewater. In the present study, a method was developed to quantitatively measure the PAC content in wastewater by using filtration and thermogravimetric analysis (TGA), which is a well-established technique for the distinction between different solid materials. For the sample filtration, quartz filters with a temperature stability up to 950 °C were used. This allowed for sensitive and well reproducible measurements, as the TGA was not affected by the presence of the filter. The sample's mass fractions were calculated by integrating the mass decrease rate obtained by TGA in specific, clearly identifiable peak areas. A two-step TGA heating method consisting of N2 and O2 atmospheres led to a good differentiation between PAC and biological background matrix, thanks to the reduction of peak overlapping. A linear correlation was found between a sample's PAC content and the corresponding peak areas under N2 and O2, the sample volume and the solid mass separated by filtration. Based on these findings, various wastewater samples from different WWTPs were then analyzed by TGA with regard to their PAC content. It was found that, compared to alternative techniques such as measurement of turbidity or total suspended solids, the newly developed TGA method allows for a quantitative and selective detection of PAC concentrations down to 0

  2. Scanning thermal microscopy based on a modified atomic force microscope combined with pyroelectric detection

    NASA Astrophysics Data System (ADS)

    Antoniow, J.-S.; Chirtoc, M.; Trannoy, N.; Raphael, O.; Pelzl, J.

    2005-06-01

    We propose a novel approach in scanning thermal microscopy of layered samples. The thermal probe (ThP) (Wollaston wire) acts as a local a.c. heat source at the front of a sample layer deposited on a pyroelectric (PE) sensor. The PE signal is proportional to the heat wave transmitted through the sample. The ThP and PE signals can be used to generate complementary thermal conductivity maps and with some restrictions, thermal diffusivity maps of the sample. Additionally, the topography map is obtained in the usual way from the atomic force microscope. We give the theoretical background for the interpretation of PE signal obtained at low and at high frequency, and we demonstrate that it carries information on the thermal diffusivity of a test sample (12 μm thick PET polymer sheet). Finally, we discuss the contributions of heat transfer channels between ThP and sample, and the role of contact thermal resistance.

  3. Placental-site trophoblastic tumor with PET scan-detected surgically treated lung metastasis.

    PubMed

    Nieves, Lucybeth; Hoffman, James; Allen, Gretchen; Currie, John; Sorosky, Joel I

    2008-06-01

    Metastatic placental-site trophoblastic tumor (PSTT) continues to be a diagnostic and management dilemma due to its relative resistance to chemotherapy and the difficulties in diagnosing such a rare tumor. We describe a 35-year-old woman with PSTT presenting with irregular bleeding and a mass in the lung. Dilation and curettage provided the diagnosis of PSTT by frozen section of the specimen. Subsequently, a total abdominal hysterectomy was performed and the patient received three cycles of EMA-CO (etoposide, methotrexate, actinomycin D, cyclophosphamide, and vincristine) Positron emission tomography (PET) scan confirmed a persistent lung nodule that was treated with wedge resection. She is currently in clinical remission. Surgery may have a role in salvaging a patient with persistent PET-positive disease after chemotherapy.

  4. Scanning Electron Microscope Mapping System Developed for Detecting Surface Defects in Fatigue Specimens

    NASA Technical Reports Server (NTRS)

    Bonacuse, Peter J.; Kantzos, Peter T.

    2002-01-01

    An automated two-degree-of-freedom specimen positioning stage has been developed at the NASA Glenn Research Center to map and monitor defects in fatigue specimens. This system expedites the examination of the entire gauge section of fatigue specimens so that defects can be found using scanning electron microscopy (SEM). Translation and rotation stages are driven by microprocessor-based controllers that are, in turn, interfaced to a computer running custom-designed software. This system is currently being used to find and record the location of ceramic inclusions in powder metallurgy materials. The mapped inclusions are periodically examined during interrupted fatigue experiments. The number of cycles to initiate cracks from these inclusions and the rate of growth of initiated cracks can then be quantified. This information is necessary to quantify the effect of this type of defect on the durability of powder metallurgy materials. This system was developed with support of the Ultra Safe program.

  5. Incidental detection of gastrointestinal stromal tumor by Tc-99m MDP bone scan.

    PubMed

    Shepherd, Timothy M; Idakoji, Ibrahim A; Pampaloni, Miguel H

    2012-02-01

    This case demonstrates extraosseous 99m-technetium methylene diphosphonate (Tc-99m MDP) accumulation from a gastrointestinal stromal tumor. A 75-year-old woman underwent a temporal bone CT for conductive hearing loss that showed sclerosis in the right occipital condyle. Follow-up Tc-99m MDP bone scan for osseous metastases instead showed a mass-like extraosseous accumulation of Tc-99m MDP in the anterior left upper quadrant. Differential diagnoses included gastric cancer, lymphoma, metastatic melanoma, systemic hypercalcemia, or heterotopic mesenteric ossification. Contrast CT showed a well-circumscribed mass arising from the stomach, and subsequent pathology confirmed gastrointestinal stromal tumor. These tumors rarely can contain osteoclast-like giant cells and should be considered for extraosseous Tc-99m MDP accumulation.

  6. Concomitant use of Congo red staining and confocal laser scanning microscopy to detect amyloidosis in oral biopsy: A clinicopathological study of 16 patients.

    PubMed

    Scivetti, Michele; Favia, Gianfranco; Fatone, Laura; Maiorano, Eugenio; Crincoli, Vito

    2016-01-01

    Twenty oral biopsies from 16 patients were analyzed both by traditional microscopy and by confocal laser scanning microscopy. Using conventional histopathological techniques, the diagnosis of amyloidosis was confirmed only in 15 biopsies. Using confocal laser scanning microscopy, amyloid deposits were detected in all of the samples. The current study shows that confocal laser scanning analysis helps to identify minimal amyloid deposits that could be overlooked using traditional microscopy, thus raising the sensitivity of oral biopsy up to 100%.

  7. Simultaneous detection of influenza viruses A and B using real-time quantitative PCR.

    PubMed

    van Elden, L J; Nijhuis, M; Schipper, P; Schuurman, R; van Loon, A M

    2001-01-01

    Since influenza viruses can cause severe illness, timely diagnosis is important for an adequate intervention. The available rapid detection methods either lack sensitivity or require complex laboratory manipulation. This study describes a rapid, sensitive detection method that can be easily applied to routine diagnosis. This method simultaneously detects influenza viruses A and B in specimens of patients with respiratory infections using a TaqMan-based real-time PCR assay. Primers and probes were selected from highly conserved regions of the matrix protein gene of influenza virus A and the hemagglutinin gene segment of influenza virus B. The applicability of this multiplex PCR was evaluated with 27 influenza virus A and 9 influenza virus B reference strains and isolates. In addition, the specificity of the assay was assessed using eight reference strains of other respiratory viruses (parainfluenza viruses 1 to 3, respiratory syncytial virus Long strain, rhinoviruses 1A and 14, and coronaviruses OC43 and 229E) and 30 combined nose and throat swabs from asymptomatic subjects. Electron microscopy-counted stocks of influenza viruses A and B were used to develop a quantitative PCR format. Thirteen copies of viral RNA were detected for influenza virus A, and 11 copies were detected for influenza virus B, equaling 0.02 and 0.006 50% tissue culture infective doses, respectively. The diagnostic efficacy of the multiplex TaqMan-based PCR was determined by testing 98 clinical samples. This real-time PCR technique was found to be more sensitive than the combination of conventional viral culturing and shell vial culturing.

  8. Quantitative analysis of electrically detected Ramsey fringes in P-doped Si

    NASA Astrophysics Data System (ADS)

    Greenland, P. T.; Matmon, G.; Villis, B. J.; Bowyer, E. T.; Li, Juerong; Murdin, B. N.; van der Meer, A. F. G.; Redlich, B.; Pidgeon, C. R.; Aeppli, G.

    2015-10-01

    This work describes detection of the laser preparation and subsequent coherent manipulation of the quantum states of orbital levels of donors in doped Si, by measuring the voltage drop across an irradiated Si sample. This electrical signal, which arises from thermal ionization of excited orbital states, and which is detected on a millisecond time scale by a voltmeter, leads to much more sensitive detection than can be had using optical methods, but has not before been quantitatively described from first principles. We present here a unified theory which relates the voltage drop across the sample to the wave function of the excited donors, and compare its predictions to experiments in which pairs of picosecond pulses from the Dutch free-electron laser FELIX are used to resonantly and coherently excite P donors in Si. Although the voltage drop varies on a millisecond time scale we are able to measure Ramsey oscillation of the excitation on a picosecond time scale, thus confirming that the donor wave function, and not just its excited state population, is crucial in determining the electrical signal. We are also able to extract the recombination rate coefficient to the ground state of the donor as well as the photoionization cross section of the excited state and phonon induced thermal ionization rate from the excited state. These quantities, which were previously of limited interest, are here shown to be important in the description of electrical detection, which, in our unoptimized configuration, is sensitive enough to enable us to detect the excitation of ˜107 donors.

  9. Comparison of point target detection algorithms for space-based scanning infrared sensors

    NASA Astrophysics Data System (ADS)

    Namoos, Omar M.; Schulenburg, Nielson W.

    1995-09-01

    The tracking of resident space objects (RSO) by space-based sensors can lead to engagements that result in stressing backgrounds. These backgrounds, including hard earth, earth limb, and zodiacal, pose various difficulties for signal processing algorithms designed to detect and track the target with a minimum of false alarms. Simulated RSO engagements were generated using the Strategic Scene Generator Model and a sensor model to create focal plane scenes. Using this data, the performance of several detection algorithms has been quantified for space, earth limb and cluttered hard earth backgrounds. These algorithms consist of an adaptive spatial filter, a transversal (matched) filters, and a median variance (nonlinear) filter. Signal-to-clutter statistics of the filtered scenes are compared to those of the unfiltered scene. False alarm and detection results are included. Based on these findings, a suggested processing software architectures design is hypothesized.

  10. Gold Nanoparticle Labeling Based ICP-MS Detection/Measurement of Bacteria, and Their Quantitative Photothermal Destruction

    PubMed Central

    Lin, Yunfeng

    2015-01-01

    Bacteria such as Salmonella and E. coli present a great challenge in public health care in today’s society. Protection of public safety against bacterial contamination and rapid diagnosis of infection require simple and fast assays for the detection and elimination of bacterial pathogens. After utilizing Salmonella DT104 as an example bacterial strain for our investigation, we report a rapid and sensitive assay for the qualitative and quantitative detection of bacteria by using antibody affinity binding, popcorn shaped gold nanoparticle (GNPOPs) labeling, surfance enchanced Raman spectroscopy (SERS), and inductively coupled plasma mass spectrometry (ICP-MS) detection. For qualitative analysis, our assay can detect Salmonella within 10 min by Raman spectroscopy; for quantitative analysis, our assay has the ability to measure as few as 100 Salmonella DT104 in a 1 mL sample (100 CFU/mL) within 40 min. Based on the quantitative detection, we investigated the quantitative destruction of Salmonella DT104, and the assay’s photothermal efficiency in order to reduce the amount of GNPOPs in the assay to ultimately to eliminate any potential side effects/toxicity to the surrounding cells in vivo. Results suggest that our assay may serve as a promising candidate for qualitative and quantitative detection and elimination of a variety of bacterial pathogens. PMID:26417447

  11. Quantitative surface-enhanced Raman spectroscopy of dipicolinic acid--towards rapid anthrax endospore detection.

    PubMed

    Bell, Steven E J; Mackle, Joseph N; Sirimuthu, Narayana M S

    2005-04-01

    Dipicolinic acid (DPA) is an excellent marker compound for bacterial spores, including those of Bacillus anthracis (anthrax). Surface-enhanced Raman spectroscopy (SERS) potentially has the sensitivity and discrimination needed for trace DPA analysis, but mixing DPA solutions with citrate-reduced silver colloid only yielded measurable SERS spectra at much higher (>80 ppm) concentrations than would be desirable for anthrax detection. Aggregation of the colloid with halide salts eliminated even these small DPA bands but aggregation with Na2SO4(aq) resulted in a remarkable increase in the DPA signals. With sulfate aggregation even 1 ppm solutions gave detectable signals with 10 s accumulation times, which is in the sensitivity range required. Addition of CNS- as an internal standard allowed quantitative DPA analysis, plotting the intensity of the strong DPA 1010 cm(-1) band (normalised to the ca. 2120 cm(-1) CNS- band) against DPA concentration gave a linear calibration (R2 = 0.986) over the range 0-50 ppm DPA. The inclusion of thiocyanate also allows false negatives due to accidental deactivation of the enhancing medium to be detected.

  12. Detection of yellow fever virus: a comparison of quantitative real-time PCR and plaque assay.

    PubMed

    Bae, Hi-Gung; Nitsche, Andreas; Teichmann, Anette; Biel, Stefan S; Niedrig, Matthias

    2003-06-30

    Yellow fever virus quantitation is performed routinely by cultivation of virus containing samples using susceptible cells. Counting of the resulting plaques provides a marker for the number of infectious particles present in the sample. This assay usually takes up to 5 days before results are obtained and must be carried out under L2 or L3 laboratory conditions, depending on the yellow fever virus strain used. For clinical diagnosis of yellow fever virus infections the cell culture-based approach takes too long and is of limited practical relevance. Recently, due to its considerable sensitivity, PCR has become a promising method for virus detection. However, whilst PCR can detect virus-specific nucleic acids, it does not allow conclusions to be drawn regarding the infectious potential of the virus detected. Nonetheless, for diagnostic purposes, a rapid, specific and sensitive virus PCR is preferable. Therefore, two independent yellow fever virus-specific real-time PCR assays were established and compared the viral RNA loads to the results of a traditional plaque assay. The estimated ratio of yellow fever virus genomes to infectious particles was between 1000:1 and 5000:1; both approaches displayed a comparable precision of <45%. A significant correlation between genome number as determined by real-time PCR and the corresponding number of plaques in paired samples was found with a Pearson coefficient of correlation of r=0.88 (P<0.0001).

  13. Organic Substances Interfere with Reverse Transcription-Quantitative PCR-Based Virus Detection in Water Samples

    PubMed Central

    Katayama, Hiroyuki; Furumai, Hiroaki

    2014-01-01

    Reverse transcription (RT)-PCR-based virus detection from water samples is occasionally hampered by organic substances that are coconcentrated during virus concentration procedures. To characterize these organic substances, samples containing commercially available humic acid, which is known to inhibit RT-PCR, and river water samples were subjected to adsorption-elution-based virus concentration using an electronegative membrane. In this study, the samples before, during, and after the concentration were analyzed in terms of organic properties and virus detection efficiencies. Two out of the three humic acid solutions resulted in RT-quantitative PCR (qPCR) inhibition that caused >3-log10-unit underestimation of spiked poliovirus. Over 60% of the organics contained in the two solutions were recovered in the concentrate, while over 60% of the organics in the uninhibited solution were lost during the concentration process. River water concentrates also caused inhibition of RT-qPCR. Organic concentrations in the river water samples increased by 2.3 to 3.9 times after the virus concentration procedure. The inhibitory samples contained organic fractions in the 10- to 100-kDa size range, which are suspected to be RT-PCR inhibitors. According to excitation-emission matrices, humic acid-like and protein-like fractions were also recovered from river water concentrates, but these fractions did not seem to affect virus detection. Our findings reveal that detailed organic analyses are effective in characterizing inhibitory substances. PMID:25527552

  14. Quantitative analysis and detection of adulteration in pork using near-infrared spectroscopy

    NASA Astrophysics Data System (ADS)

    Fan, Yuxia; Cheng, Fang; Xie, Lijuan

    2010-04-01

    Authenticity is an important food quality criterion. Rapid methods for confirming authenticity or detecting adulteration are increasingly demanded by food processors and consumers. Near infrared (NIR) spectroscopy has been used to detect economic adulteration in pork . Pork samples were adulterated with liver and chicken in 10% increments. Prediction and quantitative analysis were done using raw data and pretreatment spectra. The optimal prediction result was achieved by partial least aquares(PLS) regression with standard normal variate(SNV) pretreatment for pork adulterated with liver samples, and the correlation coefficient(R value), the root mean square error of calibration(RMSEC) and the root mean square error of prediction (RMSEP) were 0.97706, 0.0673 and 0.0732, respectively. The best model for pork meat adulterated with chicken samples was obtained by PLS with the raw spectra, and the correlation coefficient(R value), RMSEP and RMSEC were 0.98614, 0.0525, and 0.122, respectively. The result shows that NIR technology can be successfully used to detect adulteration in pork meat adulterated with liver and chicken.

  15. Detection and Quantitation of Succinimide in Intact Protein via Hydrazine Trapping and Chemical Derivatization

    PubMed Central

    KLAENE, JOSHUA J.; NI, WENQIN; ALFARO, JOSHUA F.; ZHOU, ZHAOHUI SUNNY

    2014-01-01

    Formation of aspartyl succinimide (Asu) is a common post-translational modification (PTM) of protein pharmaceuticals under acidic conditions. We present a method to detect and quantitate succinimide in intact protein via hydrazine trapping and chemical derivatization. Succinimide, which is labile under typical analytical conditions, is first trapped with hydrazine to form stable hydrazide and can be directly analyzed by mass spectrometry. The resulting aspartyl hydrazide can be selectively derivatized by various tags, such as fluorescent rhodamine sulfonyl chloride that absorbs strongly in the visible region (570 nm). Our tagging strategy allows the labeled protein to be analyzed by orthogonal methods, including HPLC-UV, LC-MS, and SDS-PAGE coupled with fluorescence imaging. A unique advantage of our method is that variants containing succinimide, after derivatization, can be readily resolved via either affinity enrichment or chromatographic separation. This allows further investigation of individual factors in a complex protein mixture that affect succinimide formation. Some additional advantages imparted by fluorescence labeling include, the facile detection of the intact protein without proteolytic digestion to peptides; and high sensitivity, e.g. without optimization 0.41% succinimide was readily detected. As such, our method should be useful for rapid screening, optimization of formulation conditions and related processes relevant to protein pharmaceuticals. PMID:25043726

  16. A miniaturized optoelectronic system for rapid quantitative label-free detection of harmful species in food

    NASA Astrophysics Data System (ADS)

    Raptis, Ioannis; Misiakos, Konstantinos; Makarona, Eleni; Salapatas, Alexandros; Petrou, Panagiota; Kakabakos, Sotirios; Botsialas, Athanasios; Jobst, Gerhard; Haasnoot, Willem; Fernandez-Alba, Amadeo; Lees, Michelle; Valamontes, Evangelos

    2016-03-01

    Optical biosensors have emerged in the past decade as the most promising candidates for portable, highly-sensitive bioanalytical systems that can be employed for in-situ measurements. In this work, a miniaturized optoelectronic system for rapid, quantitative, label-free detection of harmful species in food is presented. The proposed system has four distinctive features that can render to a powerful tool for the next generation of Point-of-Need applications, namely it accommodates the light sources and ten interferometric biosensors on a single silicon chip of a less-than-40mm2 footprint, each sensor can be individually functionalized for a specific target analyte, the encapsulation can be performed at the wafer-scale, and finally it exploits a new operation principle, Broad-band Mach-Zehnder Interferometry to ameliorate its analytical capabilities. Multi-analyte evaluation schemes for the simultaneous detection of harmful contaminants, such as mycotoxins, allergens and pesticides, proved that the proposed system is capable of detecting within short time these substances at concentrations below the limits imposed by regulatory authorities, rendering it to a novel tool for the near-future food safety applications.

  17. Detection of wheel rim by immersion scan of phased array ultrasonic flaw testing

    NASA Astrophysics Data System (ADS)

    Cai, Yi-He; Guo, Jian-qiang; Wang, Ze-yong; Gao, Xiao-rong; Jiang, Xiang-dong; Li, Xi

    2015-02-01

    In order to achieve the in-service detection to high speed train wheel rims, this article analyzed the effects of the number of array elements to image focusing and image quality using water immersion ultrasonic phased array technology. Also, the effects of the depth of water to detecting technique had been researched. According to the results of the experiments, the number of optimal array elements, the corresponding thickness of immersion layer, and the optimal range of water's depth had been obtained. Thus, appropriate references had been provided to water immersion ultrasonic phased array testing.

  18. [Clinical significance of ID4 methylation detection by quantitative methylation-specific PCR in acute leukemia].

    PubMed

    Liu, Yang; Zhong, Wen-Wen; Kang, Hui-Yuan; Wang, Li-Li; Lu, Xue-Chun; Yu, Li; Zhu, Hong-Li

    2014-06-01

    The advances of treatment improved the prognosis of the patients with acute leukemia (AL) in the last decade, but the lack of general biomarker for predicting relapse in AL, which is one of the most important factors influencing the survival and prognosis. DNA methylation of ID4 gene promoter occurred frequently in patients with AL and was found to be highly related to the tumor progression. Based on the previous work of the setup of methylation-specific quantitative PCR system for ID4 gene, this study was designed to investigate the relation between the quantitative indicator of methylation density, percentage of methylation reference(PMR) value, and different disease status of AL. PMR of ID4 was detected by MS-PCR in bone marrow (BM) samples of 17 healthy persons and 54 AL patients in the status of newly diagnosis, complete remission and disease relapse. The results showed that at different disease status, PMR value in newly diagnosed group was significantly lower than that in complete remission group (P = 0.031). Among serial samples, PMR value remained very low at the status of patients with continuous complete remission (<1.5‰), and increased along with the accumulation of tumor cells at relapse. In 1 relapse case, the abnormal rise of PMR value occurred prior to morphological relapse. PMR value seemed to be related to body tumor cell load. It is concluded that the quantitative indicator of methylation density and PMR value may reflect the change of tumor cell load in acute leukemia patients. Dynamic monitoring of PMR maybe predict leukemia relapse.

  19. Development of the scanning system to detect the concentration of oxy- and deoxy-hemoglobin by tracking the head

    NASA Astrophysics Data System (ADS)

    Ko, Woo Seok; Darwish, Naser; Gratton, Enrico; Kim, Soo Hyun

    2005-04-01

    We measure the concentration of oxy-, deoxy- and total hemoglobin by using the frequency-domain, near-infrared spectroscopy(NIRS) scanner. It is a non-invasive instrument that can provide real-time measurements of the changes in concentration. It can provide a diagnostic tool for the study of the brain in infants and children. However, it is difficult to apply it to the baby's head because of the contact of the probe on the soft baby's head. Therefore, we suggest the NIRS scanning system that can track the baby' head movement and detect NIRS parameters on the same position of the head. This system has three key components. The vision system performs the pattern matching for tracking the head by using the normalized cross correlation method with the target as a cross-line on the head during the diagnostic experiment. We can use the change of the position of the baby's head to re-target the light by the scanning system that uses four laser sources, a wavelength selector, and an x-y scanner. The detector system analyzes the resulting signal from the head using the diffusion model. Therefore, NIRS scanning system can provide a diagnostic tool to measure the changes of the NIRS parameters for the study of the baby's brain.

  20. Obstacle Avoidance, Visual Detection Performance, and Eye-Scanning Behavior of Glaucoma Patients in a Driving Simulator: A Preliminary Study

    PubMed Central

    Prado Vega, Rocío; van Leeuwen, Peter M.; Rendón Vélez, Elizabeth; Lemij, Hans G.; de Winter, Joost C. F.

    2013-01-01

    The objective of this study was to evaluate differences in driving performance, visual detection performance, and eye-scanning behavior between glaucoma patients and control participants without glaucoma. Glaucoma patients (n = 23) and control participants (n = 12) completed four 5-min driving sessions in a simulator. The participants were instructed to maintain the car in the right lane of a two-lane highway while their speed was automatically maintained at 100 km/h. Additional tasks per session were: Session 1: none, Session 2: verbalization of projected letters, Session 3: avoidance of static obstacles, and Session 4: combined letter verbalization and avoidance of static obstacles. Eye-scanning behavior was recorded with an eye-tracker. Results showed no statistically significant differences between patients and control participants for lane keeping, obstacle avoidance, and eye-scanning behavior. Steering activity, number of missed letters, and letter reaction time were significantly higher for glaucoma patients than for control participants. In conclusion, glaucoma patients were able to avoid objects and maintain a nominal lane keeping performance, but applied more steering input than control participants, and were more likely than control participants to miss peripherally projected stimuli. The eye-tracking results suggest that glaucoma patients did not use extra visual search to compensate for their visual field loss. Limitations of the study, such as small sample size, are discussed. PMID:24146975

  1. Quantitative Phase Fraction Detection in Organic Photovoltaic Materials through EELS Imaging

    SciTech Connect

    Dyck, Ondrej; Hu, Sheng; Das, Sanjib; Keum, Jong; Xiao, Kai; Khomami, Bamin; Duscher, Gerd

    2015-11-24

    Organic photovoltaic materials have recently seen intense interest from the research community. Improvements in device performance are occurring at an impressive rate; however, visualization of the active layer phase separation still remains a challenge. Our paper outlines the application of two electron energy-loss spectroscopic (EELS) imaging techniques that can complement and enhance current phase detection techniques. Specifically, the bulk plasmon peak position, often used to produce contrast between phases in energy filtered transmission electron microscopy (EFTEM), is quantitatively mapped across a sample cross section. One complementary spectrum image capturing the carbon and sulfur core loss edges is compared with the plasmon peak map and found to agree quite well, indicating that carbon and sulfur density differences between the two phases also allows phase discrimination. Additionally, an analytical technique for determining absolute atomic areal density is used to produce an absolute carbon and sulfur areal density map. We also show how these maps may be re-interpreted as a phase ratio map, giving quantitative information about the purity of the phases within the junction.

  2. Quantitative Phase Fraction Detection in Organic Photovoltaic Materials through EELS Imaging

    DOE PAGES

    Dyck, Ondrej; Hu, Sheng; Das, Sanjib; ...

    2015-11-24

    Organic photovoltaic materials have recently seen intense interest from the research community. Improvements in device performance are occurring at an impressive rate; however, visualization of the active layer phase separation still remains a challenge. Our paper outlines the application of two electron energy-loss spectroscopic (EELS) imaging techniques that can complement and enhance current phase detection techniques. Specifically, the bulk plasmon peak position, often used to produce contrast between phases in energy filtered transmission electron microscopy (EFTEM), is quantitatively mapped across a sample cross section. One complementary spectrum image capturing the carbon and sulfur core loss edges is compared with themore » plasmon peak map and found to agree quite well, indicating that carbon and sulfur density differences between the two phases also allows phase discrimination. Additionally, an analytical technique for determining absolute atomic areal density is used to produce an absolute carbon and sulfur areal density map. We also show how these maps may be re-interpreted as a phase ratio map, giving quantitative information about the purity of the phases within the junction.« less

  3. Quantitative detection of nitric oxide in exhaled human breath by extractive electrospray ionization mass spectrometry

    NASA Astrophysics Data System (ADS)

    Pan, Susu; Tian, Yong; Li, Ming; Zhao, Jiuyan; Zhu, Lanlan; Zhang, Wei; Gu, Haiwei; Wang, Haidong; Shi, Jianbo; Fang, Xiang; Li, Penghui; Chen, Huanwen

    2015-03-01

    Exhaled nitric oxide (eNO) is a useful biomarker of various physiological conditions, including asthma and other pulmonary diseases. Herein a fast and sensitive analytical method has been developed for the quantitative detection of eNO based on extractive electrospray ionization mass spectrometry (EESI-MS). Exhaled NO molecules selectively reacted with 2-phenyl-4, 4, 5, 5-tetramethylimidazoline-1-oxyl-3-oxide (PTIO) reagent, and eNO concentration was derived based on the EESI-MS response of 1-oxyl-2-phenyl-4, 4, 5, 5-tetramethylimidazoline (PTI) product. The method allowed quantification of eNO below ppb level (~0.02 ppbv) with a relative standard deviation (RSD) of 11.6%. In addition, eNO levels of 20 volunteers were monitored by EESI-MS over the time period of 10 hrs. Long-term eNO response to smoking a cigarette was recorded, and the observed time-dependent profile was discussed. This work extends the application of EESI-MS to small molecules (<30 Da) with low proton affinity and collision-induced dissociation efficiency, which are usually poorly visible by conventional ion trap mass spectrometers. Long-term quantitative profiling of eNO by EESI-MS opens new possibilities for the research of human metabolism and clinical diagnosis.

  4. On-chip quantitative detection of pathogen genes by autonomous microfluidic PCR platform.

    PubMed

    Tachibana, Hiroaki; Saito, Masato; Shibuya, Shogo; Tsuji, Koji; Miyagawa, Nobuyuki; Yamanaka, Keiichiro; Tamiya, Eiichi

    2015-12-15

    Polymerase chain reaction (PCR)-based genetic testing has become a routine part of clinical diagnoses and food testing. In these fields, rapid, easy-to-use, and cost-efficient PCR chips are expected to be appeared for providing such testing on-site. In this study, a new autonomous disposable plastic microfluidic PCR chip was created, and was utilized for quantitative detection of pathogenic microorganisms. To control the capillary flow of the following solution in the PCR microchannel, a driving microchannel was newly designed behind the PCR microchannel. This allowed the effective PCR by simply dropping the PCR solution onto the inlet without any external pumps. In order to achieve disposability, injection-molded cyclo-olefin polymer (COP) of a cost-competitive plastic was used for the PCR chip. We discovered that coating the microchannel walls with non-ionic surfactant produced a suitable hydrophilic surface for driving the capillary flow through the 1250-mm long microchannel. As a result, quantitative real-time PCR with the lowest initial concentration of human, Escherichia coli (E. coli), and pathogenic E. coli O157 genomic DNA of 4, 0.0019, 0.031 pg/μl, respectively, was successfully achieved in less than 18 min. Our results indicate that the platform presented in this study provided a rapid, easy-to-use, and low-cost real-time PCR system that could be potentially used for on-site gene testing.

  5. Quantitative polymerase chain reaction (PCR) for detection of aquatic animal pathogens in a diagnostic laboratory setting

    USGS Publications Warehouse

    Purcell, Maureen K.; Getchell, Rodman G.; McClure, Carol A.; Weber, S.E.; Garver, Kyle A.

    2011-01-01

    Real-time, or quantitative, polymerase chain reaction (qPCR) is quickly supplanting other molecular methods for detecting the nucleic acids of human and other animal pathogens owing to the speed and robustness of the technology. As the aquatic animal health community moves toward implementing national diagnostic testing schemes, it will need to evaluate how qPCR technology should be employed. This review outlines the basic principles of qPCR technology, considerations for assay development, standards and controls, assay performance, diagnostic validation, implementation in the diagnostic laboratory, and quality assurance and control measures. These factors are fundamental for ensuring the validity of qPCR assay results obtained in the diagnostic laboratory setting.

  6. Quantitative detection of pharmaceuticals using a combination of paper microfluidics and wavelength modulated Raman spectroscopy.

    PubMed

    Craig, Derek; Mazilu, Michael; Dholakia, Kishan

    2015-01-01

    Raman spectroscopy has proven to be an indispensable technique for the identification of various types of analytes due to the fingerprint vibration spectrum obtained. Paper microfluidics has also emerged as a low cost, easy to fabricate and portable approach for point of care testing. However, due to inherent background fluorescence, combining Raman spectroscopy with paper microfluidics is to date an unmet challenge in the absence of using surface enhanced mechanisms. We describe the first use of wavelength modulated Raman spectroscopy (WMRS) for analysis on a paper microfluidics platform. This study demonstrates the ability to suppress the background fluorescence of the paper using WMRS and the subsequent implementation of this technique for pharmaceutical analysis. The results of this study demonstrate that it is possible to discriminate between both paracetamol and ibuprofen, whilst, also being able to detect the presence of each analyte quantitatively at nanomolar concentrations.

  7. Cell death detection by quantitative three-dimensional single-cell tomography

    PubMed Central

    Cheng, Nai-Chia; Hsieh, Tsung-Hsun; Wang, Yu-Ta; Lai, Chien-Chih; Chang, Chia-Kai; Lin, Ming-Yi; Huang, Ding-Wei; Tjiu, Jeng-Wei; Huang, Sheng-Lung

    2012-01-01

    Ultrahigh-resolution optical coherence tomography (UR-OCT) has been used for the first time to our knowledge to study single-cell basal cell carcinoma (BCC) in vitro. This noninvasive, in situ, label-free technique with deep imaging depth enables three-dimensional analysis of scattering properties of single cells with cellular spatial resolution. From three-dimensional UR-OCT imaging, live and dead BCC cells can be easily identified based on morphological observation. We developed a novel method to automatically extract characteristic parameters of a single cell from data volume, and quantitative comparison and parametric analysis were performed. The results demonstrate the capability of UR-OCT to detect cell death at the cellular level. PMID:23024905

  8. Quantitative polymerase chain reaction (PCR) for detection of aquatic animal pathogens in a diagnostic laboratory setting.

    PubMed

    Purcell, Maureen K; Getchell, Rodman G; McClure, Carol A; Garver, Kyle A

    2011-09-01

    Real-time, or quantitative, polymerase chain reaction (qPCR) is quickly supplanting other molecular methods for detecting the nucleic acids of human and other animal pathogens owing to the speed and robustness of the technology. As the aquatic animal health community moves toward implementing national diagnostic testing schemes, it will need to evaluate how qPCR technology should be employed. This review outlines the basic principles of qPCR technology, considerations for assay development, standards and controls, assay performance, diagnostic validation, implementation in the diagnostic laboratory, and quality assurance and control measures. These factors are fundamental for ensuring the validity of qPCR assay results obtained in the diagnostic laboratory setting.

  9. Detection and quantitation of pea and soy-derived proteins in calf milk replacers.

    PubMed

    Schoonderwoerd, M; Misra, V

    1989-01-01

    Preruminant calves on several farms had diarrhea nonresponsive to treatment and were doing poorly, despite being fed a high quality calf milk replacer. Because these reconstituted milk replacers always had a sediment, they were suspected of containing insoluble nonmilk-derived proteins. Microscopic examination of the milk replacer, however, did not show any evidence of starch granules. We therefore analyzed the samples by SDS PAGE. We were able to identify and quantitate pea protein in calf milk replacers in which all the protein was supposedly milk-derived. We were also able to differentiate polypeptides derived from pea and soy. We concluded that PAGE is a sensitive technique for detecting nonmilk-derived proteins in calf milk replacers.

  10. Quantitative Detection of Pharmaceuticals Using a Combination of Paper Microfluidics and Wavelength Modulated Raman Spectroscopy

    PubMed Central

    Craig, Derek; Mazilu, Michael; Dholakia, Kishan

    2015-01-01

    Raman spectroscopy has proven to be an indispensable technique for the identification of various types of analytes due to the fingerprint vibration spectrum obtained. Paper microfluidics has also emerged as a low cost, easy to fabricate and portable approach for point of care testing. However, due to inherent background fluorescence, combining Raman spectroscopy with paper microfluidics is to date an unmet challenge in the absence of using surface enhanced mechanisms. We describe the first use of wavelength modulated Raman spectroscopy (WMRS) for analysis on a paper microfluidics platform. This study demonstrates the ability to suppress the background fluorescence of the paper using WMRS and the subsequent implementation of this technique for pharmaceutical analysis. The results of this study demonstrate that it is possible to discriminate between both paracetamol and ibuprofen, whilst, also being able to detect the presence of each analyte quantitatively at nanomolar concentrations. PMID:25938464

  11. Quantitative carbon detector for enhanced detection of molecules in foods, pharmaceuticals, cosmetics, flavors, and fuels.

    PubMed

    Beach, Connor A; Krumm, Christoph; Spanjers, Charles S; Maduskar, Saurabh; Jones, Andrew J; Dauenhauer, Paul J

    2016-03-07

    Analysis of trace compounds, such as pesticides and other contaminants, within consumer products, fuels, and the environment requires quantification of increasingly complex mixtures of difficult-to-quantify compounds. Many compounds of interest are non-volatile and exhibit poor response in current gas chromatography and flame ionization systems. Here we show the reaction of trimethylsilylated chemical analytes to methane using a quantitative carbon detector (QCD; the Polyarc™ reactor) within a gas chromatograph (GC), thereby enabling enhanced detection (up to 10×) of highly functionalized compounds including carbohydrates, acids, drugs, flavorants, and pesticides. Analysis of a complex mixture of compounds shows that the GC-QCD method exhibits faster and more accurate analysis of complex mixtures commonly encountered in everyday products and the environment.

  12. Detection of quantitative trait loci in outbred populations with incomplete marker data.

    PubMed Central

    Bink, M C; Van Arendonk, J A

    1999-01-01

    Augmentation of marker genotypes for ungenotyped individuals is implemented in a Bayesian approach via the use of Markov chain Monte Carlo techniques. Marker data on relatives and phenotypes are combined to compute conditional posterior probabilities for marker genotypes of ungenotyped individuals. The presented procedure allows the analysis of complex pedigrees with ungenotyped individuals to detect segregating quantitative trait loci (QTL). Allelic effects at the QTL were assumed to follow a normal distribution with a covariance matrix based on known QTL position and identity by descent probabilities derived from flanking markers. The Bayesian approach estimates variance due to the single QTL, together with polygenic and residual variance. The method was empirically tested through analyzing simulated data from a complex granddaughter design. Ungenotyped dams were related to one or more sons or grandsires in the design. Heterozygosity of the marker loci and size of QTL were varied. Simulation results indicated a significant increase in power when ungenotyped dams were included in the analysis. PMID:9872977

  13. Quantitative film detection of 3H and 14C in polyacrylamide gels by fluorography.

    PubMed

    Laskey, R A; Mills, A D

    1975-08-15

    Methods which use the scintillator PPO to record film images of 3H in chromatograms and polyacrylamide gels (fluorography) have been described elsewhere. This paper demonstrates that pre-exposure of the film to a brief flash of light greatly increases the sensitivity of fluorography. Pre-exposure also permits quantitative interpretation of the film image, because it corrects the non-linear relationship between radioactivity of the sample and absorbance of the film image. Therefore the distribution of radioactivity in the sample is accurately represented by microdensitometry of the image obtained on pre-exposed film. Using pre-exposed film 300 dis. 3H/min or 30 dis. 14C/min can be detected in a band in a gel in a 24-h exposure. The Appendix describes revisions and extensions of existing fluorographic procedures, including application to agarose gels and a rapid procedure for recovering PPO for re-use.

  14. Overcoming the detection bandwidth limit in precision spectroscopy: The analytical apparatus function for a stepped frequency scan

    NASA Astrophysics Data System (ADS)

    Rohart, François

    2017-01-01

    In a previous paper [Rohart et al., Phys Rev A 2014;90(042506)], the influence of detection-bandwidth properties on observed line-shapes in precision spectroscopy was theoretically modeled for the first time using the basic model of a continuous sweeping of the laser frequency. Specific experiments confirmed general theoretical trends but also revealed several insufficiencies of the model in case of stepped frequency scans. As a consequence in as much as up-to-date experiments use step-by-step frequency-swept lasers, a new model of the influence of the detection-bandwidth is developed, including a realistic timing of signal sampling and frequency changes. Using Fourier transform techniques, the resulting time domain apparatus function gets a simple analytical form that can be easily implemented in line-shape fitting codes without any significant increase of computation durations. This new model is then considered in details for detection systems characterized by 1st and 2nd order bandwidths, underlining the importance of the ratio of detection time constant to frequency step duration, namely for the measurement of line frequencies. It also allows a straightforward analysis of corresponding systematic deviations on retrieved line frequencies and broadenings. Finally, a special attention is paid to consequences of a finite detection-bandwidth in Doppler Broadening Thermometry, namely to experimental adjustments required for a spectroscopic determination of the Boltzmann constant at the 1-ppm level of accuracy. In this respect, the interest of implementing a Butterworth 2nd order filter is emphasized.

  15. Bag-of-visual-phrases and hierarchical deep models for traffic sign detection and recognition in mobile laser scanning data

    NASA Astrophysics Data System (ADS)

    Yu, Yongtao; Li, Jonathan; Wen, Chenglu; Guan, Haiyan; Luo, Huan; Wang, Cheng

    2016-03-01

    This paper presents a novel algorithm for detection and recognition of traffic signs in mobile laser scanning (MLS) data for intelligent transportation-related applications. The traffic sign detection task is accomplished based on 3-D point clouds by using bag-of-visual-phrases representations; whereas the recognition task is achieved based on 2-D images by using a Gaussian-Bernoulli deep Boltzmann machine-based hierarchical classifier. To exploit high-order feature encodings of feature regions, a deep Boltzmann machine-based feature encoder is constructed. For detecting traffic signs in 3-D point clouds, the proposed algorithm achieves an average recall, precision, quality, and F-score of 0.956, 0.946, 0.907, and 0.951, respectively, on the four selected MLS datasets. For on-image traffic sign recognition, a recognition accuracy of 97.54% is achieved by using the proposed hierarchical classifier. Comparative studies with the existing traffic sign detection and recognition methods demonstrate that our algorithm obtains promising, reliable, and high performance in both detecting traffic signs in 3-D point clouds and recognizing traffic signs on 2-D images.

  16. Application of terrestrial laser scanning for detection of ground surface deformation in small mud volcano (Murono, Japan)

    NASA Astrophysics Data System (ADS)

    Hayakawa, Yuichi S.; Kusumoto, Shigekazu; Matta, Nobuhisa

    2016-07-01

    We perform terrestrial laser scanning (TLS) to detect changes in surface morphology of a mud volcano in Murono, north-central Japan. The study site underwent significant deformation by a strong earthquake in 2011, and the surface deformation has continued in the following years. The point cloud datasets were obtained by TLS at three different times in 2011, 2013 and 2014. Those point clouds were aligned by cloud-based registration, which minimizes the closest point distance of point clouds of unchanged ground features, and the TLS-based point cloud data appear to be suitable for detecting centimeter-order deformations in the central domain of the mud volcano, as well as for measurements of topographic features including cracks of paved ground surface. The spatial patterns and accumulative amount of the vertical deformation during 2011-2014 captured by TLS correspond well with those previously reported based on point-based leveling surveys, supporting the validity of TLS survey.

  17. Nondestructive testing based on scanning-from-heating approach: application to nonthrough defect detection and fiber orientation assessment

    NASA Astrophysics Data System (ADS)

    Belkacemi, Mohamed; Stolz, Christophe; Mathieu, Alexandre; Lemaitre, Guillaume; Massich, Joan; Aubreton, Olivier

    2015-11-01

    Today, industries ensure the quality of their manufactured products through computer vision techniques and nonconventional imaging. Three-dimensional (3-D) scanners and nondestructive testing (NDT) systems are commonly used independently for such applications. Furthermore, these approaches combined constitute hybrid systems, providing a 3-D reconstruction and NDT analysis. These systems, however, suffer from drawbacks such as errors during the data fusion and higher cost for manufacturers. In an attempt to solve these problems, a single active thermography system based on scanning-from-heating is proposed in this paper. In addition to 3-D digitization of the object, our contributions are twofold: (1) the nonthrough defect detection for a homogeneous metallic object and (2) fiber orientation assessment for a long fiber composite material. The experiments on steel and aluminum plates show that our method achieves the detection of nonthrough defects. Additionally, the estimation of the fiber orientation is evaluated on carbon-fiber composite material.

  18. A Case Study Correlating Innovative Gamma Ray Scanning Detection Systems Data to Surface Soil Gamma Spectrometry Results - 13580

    SciTech Connect

    Thompson, Shannon; Rodriguez, Rene; Billock, Paul; Lit, Peter

    2013-07-01

    HydroGeoLogic (HGL), Inc. completed a United States Environmental Protection Agency (USEPA) study to characterize radiological contamination at a site near Canoga Park, California. The characterized area contained 470 acres including the site of a prototype commercial nuclear reactor and other nuclear design, testing, and support operations from the 1950's until 1988 [1]. The site history included radiological releases during operation followed by D and D activities. The characterization was conducted under an accelerated schedule and the results will support the project remediation. The project has a rigorous cleanup to background agenda and does not allow for comparison to risk-based guidelines. To target soil sample locations, multiple lines of evidence were evaluated including a gamma radiation survey, geophysical surveys, historical site assessment, aerial photographs, and former worker interviews. Due to the time since production and decay, the primary gamma emitting radionuclide remaining is cesium-137 (Cs-137). The gamma ray survey covered diverse, rugged terrain using custom designed sodium iodide thallium-activated (NaI(Tl)) scintillation detection systems. The survey goals included attaining 100% ground surface coverage and detecting gamma radiation as sensitively as possible. The effectiveness of innovative gamma ray detection systems was tested by correlating field Cs-137 static count ratios to Cs-137 laboratory gamma spectrometry results. As a case study, the area encompassing the former location of the first nuclear power station in the U. S. was scanned, and second by second global positioning system (GPS)-linked gamma spectral data were evaluated by examining total count rate and nuclide-specific regions of interest. To compensate for Compton scattering from higher energy naturally occurring radionuclides (U-238, Th-232 and their progeny, and K-40), count rate ratios of anthropogenic nuclide-specific regions of interest to the total count rate were

  19. Potential effect of CAD systems on the detection of actionable nodules in chest CT scans during routine reporting

    NASA Astrophysics Data System (ADS)

    Wormanns, Dag; Beyer, Florian; Butzbach, Arnauld; Zierott, Livia; Heindel, Walter

    2006-03-01

    The purpose of the presented study was to determine the impact of two different CAD systems used as concur-rent reader for detection of actionable nodules (>4 mm) on the interpretation of chest CT scans during routine reporting. Fifty consecutive MDCT scans (1 mm or 1.25 mm slice thickness, 0.8 mm reconstruction increment) were se-lected from clinical routine. All cases were read by a resident and a staff radiologist, and a written report was available in the radiology information system (RIS). The RIS report mentioned at least one actionable pulmonary nodule in 18 cases (50%) and did not report any pulmonary nodule in the remaining 32 cases. Two different recent CAD systems were independently applied to the 50 CT scans as concurrent reader with two radiologists: Siemens LungCare NEV and MEDIAN CAD-Lung. Two radiologists independently reviewed the CAD results and determined if a CAD result was a true positive or a false positive finding. Patients were classified into two groups: in group A if at least one actionable nodule was detected and in group B if no actionable nodules were found. The effect of CAD on routine reporting was simulated as set union of the findings of routine reporting and CAD thus applying CAD as concurrent reader. According to the RIS report group A (patients with at least one actionable nodule) contained 18 cases (36% of all 50 cases), and group B contained 32 cases. Application of a CAD system as concurrent reader resulted in detec-tion of additional CT scans with actionable nodules and reclassification into group A in 16 resp. 18 cases (radi-ologist 1 resp. radiologist 2) with Siemens NEV and in 19 resp. 18 cases with MEDIAN CAD-Lung. In seven cases MEDIAN CAD-Lung and in four cases Siemens NEV reclassified a case into group A while the other CAD system missed the relevant finding. Sensitivity on a nodule (>4 mm) base was .45 for Siemens NEV and .55 for MEDIAN CAD-Lung; the difference was not yet significant (p=.077). In our study use of CAD

  20. Dual core quantum dots for highly quantitative ratiometric detection of trypsin activity in cystic fibrosis patients

    NASA Astrophysics Data System (ADS)

    Castelló Serrano, Iván; Stoica, Georgiana; Matas Adams, Alba; Palomares, Emilio

    2014-10-01

    We present herein two colour encoded silica nanospheres (2nanoSi) for the fluorescence quantitative ratiometric determination of trypsin in humans. Current detection methods for cystic fibrosis diagnosis are slow, costly and suffer from false positives. The 2nanoSi proved to be a highly sensitive, fast (minutes), and single-step approach nanosensor for the screening and diagnosis of cystic fibrosis, allowing the quantification of trypsin concentrations in a wide range relevant for clinical applications (25-350 μg L-1). Furthermore, as trypsin is directly related to the development of cystic fibrosis (CF), different human genotypes, i.e. CF homozygotic, CF heterozygotic, and unaffected, respectively, can be determined using our 2nanoSi nanospheres. We anticipate the 2nanoSi system to be a starting point for non-invasive, easy-to-use and cost effective ratiometric fluorescent biomarkers for recessive genetic diseases like human cystic fibrosis. In a screening program in which the goal is to detect disease and also the carrier status, early diagnosis could be of great help.We present herein two colour encoded silica nanospheres (2nanoSi) for the fluorescence quantitative ratiometric determination of trypsin in humans. Current detection methods for cystic fibrosis diagnosis are slow, costly and suffer from false positives. The 2nanoSi proved to be a highly sensitive, fast (minutes), and single-step approach nanosensor for the screening and diagnosis of cystic fibrosis, allowing the quantification of trypsin concentrations in a wide range relevant for clinical applications (25-350 μg L-1). Furthermore, as trypsin is directly related to the development of cystic fibrosis (CF), different human genotypes, i.e. CF homozygotic, CF heterozygotic, and unaffected, respectively, can be determined using our 2nanoSi nanospheres. We anticipate the 2nanoSi system to be a starting point for non-invasive, easy-to-use and cost effective ratiometric fluorescent biomarkers for

  1. Detection of human herpesvirus 8 by quantitative polymerase chain reaction: development and standardisation of methods

    PubMed Central

    2012-01-01

    Background Human herpesvirus 8 (HHV-8), the aetiological agent of Kaposi’s sarcoma (KS), multicentric Castleman’s disease (MCD), and primary effusion lymphoma (PEL) is rare in Australia, but endemic in Sub-Saharan Africa, parts of South-east Asia and Oceania. While the treatment of external KS lesions can be monitored by clinical observation, the internal lesions of KS, MCD and PEL require extensive and expensive internal imaging, or autopsy. In patients with MCD and PEL, if HHV-8 viraemia is not reduced quickly, ~50% die within 24 months. HHV-8 qPCR is a valuable tool for monitoring HHV-8 viraemia, but is not available in many parts of the world, including those with high prevalence of KS and HHV-8. Methods A new molecular facility with stringent three-phase workflow was established, adhering to NPAAC and CLSI guidelines. Three fully validated quantitative assays were developed: two for detection and quantification of HHV-8; one for GAPDH, necessary for normalisation of viral loads in tissue and peripheral blood. Results The HHV-8 ORF73 and ORF26 qPCR assays were 100% specific. All qPCR assays, displayed a broad dynamic range (102 to 1010 copies/μL TE Buffer) with a limit of detection of 4.85x103, 5.61x102, and 2.59x102 copies/μL TE Buffer and a limit of quantification of 4.85x103, 3.01x102, and 1.38x102 copies/μL TE Buffer for HHV-8 ORF73, HHV-8 ORF26, and GAPDH respectively. The assays were tested on a panel of 35 KS biopsies from Queensland. All were HHV-8 qPCR positive with average viral load of 2.96x105 HHV-8 copies/μL DNA extract (range: 4.37x103 to 1.47x106 copies/μL DNA extract): When normalised these equate to an average viral load of 2.44x104 HHV-8 copies/103 cells (range: 2.20x102 to 7.38x105 HHV-8 copies/103 cells). Conclusions These are the first fully optimised, validated and MIQE compliant HHV-8 qPCR assays established in Australia. They worked well for qualitative detection of HHV-8 in archival tissue, and are well-suited for

  2. Detection of Progressive Retinal Nerve Fiber Layer Loss in Glaucoma Using Scanning Laser Polarimetry with Variable Corneal Compensation

    PubMed Central

    Medeiros, Felipe A.; Alencar, Luciana M.; Zangwill, Linda M.; Bowd, Christopher; Vizzeri, Gianmarco; Sample, Pamela A.; Weinreb, Robert N.

    2010-01-01

    Purpose To evaluate the ability of scanning laser polarimetry with variable corneal compensation to detect progressive retinal nerve fiber layer (RNFL) loss in glaucoma patients and patients suspected of having the disease. Methods This was an observational cohort study that included 335 eyes of 195 patients. Images were obtained annually with the GDx VCC scanning laser polarimeter, along with optic disc stereophotographs and standard automated perimetry (SAP) visual fields. The median follow-up time was 3.94 years. Progression was determined using commercial software for SAP and by masked assessment of optic disc stereophotographs performed by expert graders. Random coefficient models were used to evaluate the relationship between RNFL thickness measurements over time and progression as determined by SAP and/or stereophotographs. Results From the 335 eyes, 34 (10%) showed progression over time by stereophotographs and/or SAP. Average GDx VCC measurements decreased significantly over time for both progressors as well as non-progressors. However, the rate of decline was significantly higher in the progressing group (−0.70 μm/year) compared to the non-progressing group (−0.14 μm/year; P = 0.001). Black race and male sex were significantly associated with higher rates of RNFL loss during follow-up. Conclusions The GDx VCC scanning laser polarimeter was able to identify longitudinal RNFL loss in eyes that showed progression in optic disc stereophotographs and/or visual fields. These findings suggest that this technology could be useful to detect and monitor progressive disease in patients with established diagnosis of glaucoma or suspected of having the disease. PMID:19029038

  3. Optimization of Quantitative Detection of Cytomegalovirus DNA in Plasma by Real-Time PCR

    PubMed Central

    Boeckh, Michael; Huang, MeeiLi; Ferrenberg, James; Stevens-Ayers, Terry; Stensland, Laurence; Garrett Nichols, W.; Corey, Lawrence

    2004-01-01

    Previous studies have shown that detection of cytomegalovirus (CMV) DNA in plasma is less sensitive than the antigenemia assay for CMV surveillance in blood. In 1,983 blood samples, plasma PCR assays with three different primer sets (UL125 alone, UL126 alone, and UL55/UL123-exon 4) were compared to the pp65 antigenemia assay and blood cultures. Plasma PCR detected CMV more frequently in blood specimens than either the antigenemia assay or cultures, but of the three PCR assays, the double-primer assay (UL55/UL123-exon 4) performed best with regard to sensitivity, specificity, and predictive values compared to antigenemia: 122 of 151 antigenemia-positive samples were detected (sensitivity, 80.1%), and there were 122 samples that were PCR positive-antigenemia negative (specificity, 93%). Samples with discrepant results had a low viral load (median, 0.5 cells per slide; 1,150 copies per ml) and were often obtained from patients receiving antiviral therapy. CMV could be detected by other methods in 15 of 29 antigenemia positive-PCR negative samples compared to 121 of 122 PCR positive-antigenemia negative samples (P < 0.001). On a per-subject basis, 21 of 25 patients (antigenemia positive-PCR negative) and all 57 (PCR positive-antigenemia negative) could be confirmed at different time points during follow-up. The higher sensitivity of the double-primer assay resulted in earlier detection compared to antigenemia in a time-to-event analysis of 42 CMV-seropositive stem cell transplant recipients, and two of three patients with CMV disease who were antigenemia negative were detected by plasma PCR prior to the onset of disease. Interassay variability was low, and the dynamic range was >5 log10. Automated DNA extraction resulted in high reproducibility, accurate CMV quantitation (R = 0.87, P < 0.001), improved sensitivity, and increased speed of sample processing. Thus, primer optimization and improved DNA extraction techniques resulted in a plasma-based PCR assay that is

  4. Detection of microcystin-producing cyanobacteria in Missisquoi Bay, Quebec, Canada, using quantitative PCR.

    PubMed

    Fortin, Nathalie; Aranda-Rodriguez, Rocio; Jing, Hongmei; Pick, Frances; Bird, David; Greer, Charles W

    2010-08-01

    Toxic cyanobacterial blooms, as well as their increasing global occurrence, pose a serious threat to public health, domestic animals, and livestock. In Missisquoi Bay, Lake Champlain, public health advisories have been issued from 2001 to 2009, and local microcystin concentrations found in the lake water regularly exceeded the Canadian drinking water guideline of 1.5 microg liter(-1). A quantitative PCR (Q-PCR) approach was developed for the detection of blooms formed by microcystin-producing cyanobacteria. Primers were designed for the beta-ketoacyl synthase (mcyD(KS)) and the first dehydratase domain (mcyD(DH)) of the mcyD gene, involved in microcystin synthesis. The Q-PCR method was used to track the toxigenic cyanobacteria in Missisquoi Bay during the summers of 2006 and 2007. Two toxic bloom events were detected in 2006: more than 6.5 x 10(4) copies of the mcyD(KS) gene ml(-1) were detected in August, and an average of 4.0 x 10(4) copies ml(-1) were detected in September, when microcystin concentrations were more than 4 microg liter(-1) and approximately 2 microg liter(-1), respectively. Gene copy numbers and total microcystin concentrations (determined by enzyme-linked immunosorbent assay [ELISA]) were highly correlated in the littoral (r = 0.93, P < 0.001) and the pelagic station (r = 0.87, P < 0.001) in 2006. In contrast to the situation in 2006, a cyanobacterial bloom occurred only in late summer-early fall of 2007, reaching only 3 x 10(2) mcyD(KS) copies ml(-1), while the microcystin concentration was barely detectable. The Q-PCR method allowed the detection of microcystin-producing cyanobacteria when toxins and toxigenic cyanobacterial abundance were still below the limit of detection by high-pressure liquid chromatography (HPLC) and microscopy. Toxin gene copy numbers grew exponentially at a steady rate over a period of 7 weeks. Onshore winds selected for cells with a higher cell quota of microcystin. This technique could be an effective approach for

  5. Population structure of eleven Spanish ovine breeds and detection of selective sweeps with BayeScan and hapFLK.

    PubMed

    Manunza, A; Cardoso, T F; Noce, A; Martínez, A; Pons, A; Bermejo, L A; Landi, V; Sànchez, A; Jordana, J; Delgado, J V; Adán, S; Capote, J; Vidal, O; Ugarte, E; Arranz, J J; Calvo, J H; Casellas, J; Amills, M

    2016-06-07

    The goals of the current work were to analyse the population structure of 11 Spanish ovine breeds and to detect genomic regions that may have been targeted by selection. A total of 141 individuals were genotyped with the Infinium 50 K Ovine SNP BeadChip (Illumina). We combined this dataset with Spanish ovine data previously reported by the International Sheep Genomics Consortium (N = 229). Multidimensional scaling and Admixture analyses revealed that Canaria de Pelo and, to a lesser extent, Roja Mallorquina, Latxa and Churra are clearly differentiated populations, while the remaining seven breeds (Ojalada, Castellana, Gallega, Xisqueta, Ripollesa, Rasa Aragonesa and Segureña) share a similar genetic background. Performance of a genome scan with BayeScan and hapFLK allowed us identifying three genomic regions that are consistently detected with both methods i.e. Oar3 (150-154 Mb), Oar6 (4-49 Mb) and Oar13 (68-74 Mb). Neighbor-joining trees based on polymorphisms mapping to these three selective sweeps did not show a clustering of breeds according to their predominant productive specialization (except the local tree based on Oar13 SNPs). Such cryptic signatures of selection have been also found in the bovine genome, posing a considerable challenge to understand the biological consequences of artificial selection.

  6. Population structure of eleven Spanish ovine breeds and detection of selective sweeps with BayeScan and hapFLK

    PubMed Central

    Manunza, A.; Cardoso, T. F.; Noce, A.; Martínez, A.; Pons, A.; Bermejo, L. A.; Landi, V.; Sànchez, A.; Jordana, J.; Delgado, J. V.; Adán, S.; Capote, J.; Vidal, O.; Ugarte, E.; Arranz, J. J.; Calvo, J. H.; Casellas, J.; Amills, M.

    2016-01-01

    The goals of the current work were to analyse the population structure of 11 Spanish ovine breeds and to detect genomic regions that may have been targeted by selection. A total of 141 individuals were genotyped with the Infinium 50 K Ovine SNP BeadChip (Illumina). We combined this dataset with Spanish ovine data previously reported by the International Sheep Genomics Consortium (N = 229). Multidimensional scaling and Admixture analyses revealed that Canaria de Pelo and, to a lesser extent, Roja Mallorquina, Latxa and Churra are clearly differentiated populations, while the remaining seven breeds (Ojalada, Castellana, Gallega, Xisqueta, Ripollesa, Rasa Aragonesa and Segureña) share a similar genetic background. Performance of a genome scan with BayeScan and hapFLK allowed us identifying three genomic regions that are consistently detected with both methods i.e. Oar3 (150–154 Mb), Oar6 (4–49 Mb) and Oar13 (68–74 Mb). Neighbor-joining trees based on polymorphisms mapping to these three selective sweeps did not show a clustering of breeds according to their predominant productive specialization (except the local tree based on Oar13 SNPs). Such cryptic signatures of selection have been also found in the bovine genome, posing a considerable challenge to understand the biological consequences of artificial selection. PMID:27272025

  7. Genomewide linkage scan of hand osteoarthritis in female twin pairs showing replication of quantitative trait loci on chromosomes 2 and 19

    PubMed Central

    Livshits, Gregory; Kato, Bernet S; Zhai, Guangju; Hart, Deborah J; Hunter, David; MacGregor, Alex J; Williams, Frances M K; Spector, Tim D

    2007-01-01

    Background and objective Until recently, there has been little agreement between conflicting results of osteoarthritis (OA) linkage. The purpose of this study was to conduct a whole‐genome linkage scan to identify susceptibility loci for idiopathic hand OA in a large, population‐based sample of females. Methods Two OA‐related radiographic phenotypes DIP (distal interphalangeal joints)‐OA and Tot‐KL (Kellgren‐Lawrence score for both hands) chosen a priori were examined on 538 (269 pairs) monozygous and 1256 (628 pairs) dizygous (DZ) females. A genome‐wide scan using microsatellite markers spaced 10 cM apart was performed on 1028 DZ twins. First, the heritability of the two OA phenotypes was estimated. Next, multipoint linkage analysis was conducted using a modified version of the Haseman–Elston method in a generalised linear model. Results Heritability for DIP‐OA and Tot‐KL was found to be 47.6% and 67.4%, respectively. A genome‐wide scan produced reliable evidence of significant linkage of DIP‐OA on chromosome 2 at 90 cM (logarithmic odds ratio (LOD) = 2.90) and for Tot‐KL on chromosome 19 at 65 cM (LOD = 4.26). These results are in agreement with data published previously. Several other significant linkage peaks were observed—for example, on chromosome 1 at 250 cM and on chromosome 3 at 30 cM—but were confirmed less reliably. Conclusion This is one of the largest OA linkage studies performed to date and provides clear evidence for linkage at two quantitative trait loci (on chromosome 2 at 90 cM and on chromosome 19 at 65 cM). As the results were robust and replicated in previous smaller studies, the fine mapping of these regions is a logical next step to pinpoint potential susceptibility gene(s) of interest. PMID:17127684

  8. A Scanning Transmission Electron Microscopy (STEM) Approach to Analyzing Large Volumes of Tissue to Detect Nanoparticles

    PubMed Central

    Kempen, Paul J.; Thakor, Avnesh S.; Zavaleta, Cristina; Gambhir, Sanjiv S.; Sinclair, Robert

    2013-01-01

    The use of nanoparticles for the diagnosis and treatment of cancer requires the complete characterization of their toxicity, including accurately locating them within biological tissues. Owing to their size, traditional light microscopy techniques are unable to resolve them. Transmission electron microscopy provides the necessary spatial resolution to image individual nanoparticles in tissue but is severely limited by the very small analysis volume, usually on the order of tens of cubic microns. In this work we developed a scanning transmission electron microscopy (STEM) approach to analyze large volumes of tissue for the presence of polyethylene glycol coated Raman-active-silica-gold-nanoparticles (PEG-R-Si-Au-NPs). This approach utilizes the simultaneous bright and dark field imaging capabilities of STEM along with careful control of the image contrast settings to readily identify PEG-R-Si-Au-NPs in mouse liver tissue without the need for additional time consuming analytical characterization. We utilized this technique to analyze 243,000 µm3 of mouse liver tissue for the presence of PEG-R-Si-Au-NPs. Nanoparticles injected into the mice intravenously via the tail-vein accumulated in the liver while those injected intrarectally did not, indicating that they remain in the colon and do not pass through the colon wall into the systemic circulation. PMID:23803218

  9. Obstacle detection and spectral discrimination using multi-wavelength motionless wide angle laser scanning.

    PubMed

    Sahba, Kaveh; Alameh, Kamal E; Smith, Clifton L

    2008-04-14

    Static laser scanning over a wide angle is demonstrated by ranging to 20 laser beams generated by a novel cylindrical quasi-cavity waveguide, using laser triangulation. Baseline distances and outgoing angles unique to each laser beam are calculated by modelling the triangulation arrangement using a system of linear equations and plotting principal rays. The quasi-cavity waveguide, imaging lens and focal plane are also plotted. The system is calibrated by finding optimal values for uncertain instrumental parameters using constrained non-linear optimization. Distances calculated over 5m indoors result in accuracies above 93%. Discrete laser spectroscopy using 640nm and 785nm laser diodes is also demonstrated. Both injected laser beams follow the same optical path through the quasi-cavity waveguide, enabling spectral measurements to be made from the same point on an object for both wavelengths. The reflected red and infrared laser light is digitally recorded by a CCD imager and differences in reflected intensity enable discrimination between various natural objects. This provides more complete information about the perturbing object, including its 3D coordinates as well as limited identification of its surface material.

  10. A scanning transmission electron microscopy approach to analyzing large volumes of tissue to detect nanoparticles.

    PubMed

    Kempen, Paul J; Thakor, Avnesh S; Zavaleta, Cristina; Gambhir, Sanjiv S; Sinclair, Robert

    2013-10-01

    The use of nanoparticles for the diagnosis and treatment of cancer requires the complete characterization of their toxicity, including accurately locating them within biological tissues. Owing to their size, traditional light microscopy techniques are unable to resolve them. Transmission electron microscopy provides the necessary spatial resolution to image individual nanoparticles in tissue, but is severely limited by the very small analysis volume, usually on the order of tens of cubic microns. In this work, we developed a scanning transmission electron microscopy (STEM) approach to analyze large volumes of tissue for the presence of polyethylene glycol-coated Raman-active-silica-gold-nanoparticles (PEG-R-Si-Au-NPs). This approach utilizes the simultaneous bright and dark field imaging capabilities of STEM along with careful control of the image contrast settings to readily identify PEG-R-Si-Au-NPs in mouse liver tissue without the need for additional time-consuming analytical characterization. We utilized this technique to analyze 243,000 mm³ of mouse liver tissue for the presence of PEG-R-Si-Au-NPs. Nanoparticles injected into the mice intravenously via the tail vein accumulated in the liver, whereas those injected intrarectally did not, indicating that they remain in the colon and do not pass through the colon wall into the systemic circulation.

  11. Moving Object Detection Using Scanning Camera on a High-Precision Intelligent Holder

    PubMed Central

    Chen, Shuoyang; Xu, Tingfa; Li, Daqun; Zhang, Jizhou; Jiang, Shenwang

    2016-01-01

    During the process of moving object detection in an intelligent visual surveillance system, a scenario with complex background is sure to appear. The traditional methods, such as “frame difference” and “optical flow”, may not able to deal with the problem very well. In such scenarios, we use a modified algorithm to do the background modeling work. In this paper, we use edge detection to get an edge difference image just to enhance the ability of resistance illumination variation. Then we use a “multi-block temporal-analyzing LBP (Local Binary Pattern)” algorithm to do the segmentation. In the end, a connected component is used to locate the object. We also produce a hardware platform, the core of which consists of the DSP (Digital Signal Processor) and FPGA (Field Programmable Gate Array) platforms and the high-precision intelligent holder. PMID:27775671

  12. Quantitative Assessment of Detection Frequency for the INL Ambient Air Monitoring Network

    SciTech Connect

    Sondrup, A. Jeffrey; Rood, Arthur S.

    2014-11-01

    A quantitative assessment of the Idaho National Laboratory (INL) air monitoring network was performed using frequency of detection as the performance metric. The INL air monitoring network consists of 37 low-volume air samplers in 31 different locations. Twenty of the samplers are located on INL (onsite) and 17 are located off INL (offsite). Detection frequencies were calculated using both BEA and ESER laboratory minimum detectable activity (MDA) levels. The CALPUFF Lagrangian puff dispersion model, coupled with 1 year of meteorological data, was used to calculate time-integrated concentrations at sampler locations for a 1-hour release of unit activity (1 Ci) for every hour of the year. The unit-activity time-integrated concentration (TICu) values were calculated at all samplers for releases from eight INL facilities. The TICu values were then scaled and integrated for a given release quantity and release duration. All facilities modeled a ground-level release emanating either from the center of the facility or at a point where significant emissions are possible. In addition to ground-level releases, three existing stacks at the Advanced Test Reactor Complex, Idaho Nuclear Technology and Engineering Center, and Material and Fuels Complex were also modeled. Meteorological data from the 35 stations comprising the INL Mesonet network, data from the Idaho Falls Regional airport, upper air data from the Boise airport, and three-dimensional gridded data from the weather research forecasting model were used for modeling. Three representative radionuclides identified as key radionuclides in INL’s annual National Emission Standards for Hazardous Air Pollutants evaluations were considered for the frequency of detection analysis: Cs-137 (beta-gamma emitter), Pu-239 (alpha emitter), and Sr-90 (beta emitter). Source-specific release quantities were calculated for each radionuclide, such that the maximum inhalation dose at any publicly accessible sampler or the National

  13. Quantum-dot submicrobead-based immunochromatographic assay for quantitative and sensitive detection of zearalenone.

    PubMed

    Duan, Hong; Chen, Xuelan; Xu, Wei; Fu, Jinhua; Xiong, Yonghua; Wang, Andrew

    2015-01-01

    Mycotoxin pollutants are commonly related to cereal products and cause fatal threats in food safety, and therefore require simple and sensitive detection. In this work, quantum-dot (QD) submicrobeads (QBs) were synthesized by encapsulating CdSe/ZnS QDs using the microemulsion technique. The resultant QBs, with approximately 2800 times brighter luminescence than the corresponding QDs, were explored as novel fluorescent probes in the immunochromatographic assay (ICA) for sensitive and quantitative detection of zearalenone (ZEN) in corns. Various parameters that influenced the sensitivity and stability of QB-based ICA (QB-ICA) were investigated and optimized. The optimal QB-ICA exhibits good dynamic linear detection for ZEN over the range of 0.125 ng/mL to 10 ng/mL with a median inhibitory concentration of 1.01±0.09 ng/mL (n=3). The detection limits for ZEN in a standard solution and real corn sample (dilution ratio of 1:30) are 0.0625 ng/mL and 3.6 µg/kg, respectively, which is much better than that of a previously reported gold nanoparticle-based ICA method. Forty-six natural corn samples are assayed using both QB-ICA and enzyme-linked immunosorbent assay. The two methods show a highly significant correlation (R(2)=0.92). Nine ZEN-contaminated samples were further confirmed with liquid chromatography-tandem mass spectrometry (LC-MS/MS), and the QB-ICA results also exhibited good agreement with LC-MS/MS method. In brief, this work demonstrates that QB-ICA is capable of rapid, sensitive screening of toxins in food analysis, and shows great promise for point-of-care testing of other analytes.

  14. High dynamic range detection of Chlamydia trachomatis growth by direct quantitative PCR of the infected cells.

    PubMed

    Eszik, Ildikó; Lantos, Ildikó; Önder, Kamil; Somogyvári, Ferenc; Burián, Katalin; Endrész, Valéria; Virok, Dezső P

    2016-01-01

    Chlamydiae are obligate intracellular bacteria developing in an intracytoplasmic niche, the inclusion. Chlamydia growth measurement by inclusion counting is a key task in the development of novel antichlamydial antibiotics and in vaccine studies. Most of the current counting methods rely on the immunofluorescent staining of the inclusions and either manual or automatic microscopy detection and enumeration. The manual method is highly labor intensive, while the automatic methods are either medium-throughput or require automatic microscopy. The sensitive and specific PCR technology could be an effective method for growth related chlamydial DNA detection; however the currently described PCR approaches have a major limitation, the requirement of purification of DNA or RNA from the infected cells. This limitation makes this approach unfeasible for high-throughput screenings. To overcome this, we developed a quantitative PCR (qPCR) method for the detection of Chlamydia trachomatis DNA directly from the infected HeLa cells. With our method we were able to detect the bacterial growth in a 4 log scale (multiplicity of infection (MOI): 64 to 0.0039), with high correlation between the biological and technical replicates. As a further proof of the method, we applied the direct qPCR for antibiotic minimum inhibitory concentration (MIC) measurements. The measured MICs of moxifloxacin, tetracycline, clarithromycin and compound PCC00213 were 0.031 μg/ml, 0.031 μg/ml, 0.0039 μg/ml and 6.2 μg/ml respectively, identical or close to the already published MIC values. Our direct qPCR method for chlamydial growth and antibiotic MIC determination is less time-consuming, more objective and more sensitive than the currently applied manual or automatic fluorescent microscopy- based methods.

  15. Computer-aided detection system for lung cancer in computed tomography scans: Review and future prospects

    PubMed Central

    2014-01-01

    Introduction The goal of this paper is to present a critical review of major Computer-Aided Detection systems (CADe) for lung cancer in order to identify challenges for future research. CADe systems must meet the following requirements: improve the performance of radiologists providing high sensitivity in the diagnosis, a low number of false positives (FP), have high processing speed, present high level of automation, low cost (of implementation, training, support and maintenance), the ability to detect different types and shapes of nodules, and software security assurance. Methods The relevant literature related to “CADe for lung cancer” was obtained from PubMed, IEEEXplore and Science Direct database. Articles published from 2009 to 2013, and some articles previously published, were used. A systemic analysis was made on these articles and the results were summarized. Discussion Based on literature search, it was observed that many if not all systems described in this survey have the potential to be important in clinical practice. However, no significant improvement was observed in sensitivity, number of false positives, level of automation and ability to detect different types and shapes of nodules in the studied period. Challenges were presented for future research. Conclusions Further research is needed to improve existing systems and propose new solutions. For this, we believe that collaborative efforts through the creation of open source software communities are necessary to develop a CADe system with all the requirements mentioned and with a short development cycle. In addition, future CADe systems should improve the level of automation, through integration with picture archiving and communication systems (PACS) and the electronic record of the patient, decrease the number of false positives, measure the evolution of tumors, evaluate the evolution of the oncological treatment, and its possible prognosis. PMID:24713067

  16. Mediastinal lymph node detection on thoracic CT scans using spatial prior from multi-atlas label fusion

    NASA Astrophysics Data System (ADS)

    Liu, Jiamin; Zhao, Jocelyn; Hoffman, Joanne; Yao, Jianhua; Zhang, Weidong; Turkbey, Evrim B.; Wang, Shijun; Kim, Christine; Summers, Ronald M.

    2014-03-01

    Lymph nodes play an important role in clinical practice but detection is challenging due to low contrast surrounding structures and variable size and shape. We propose a fully automatic method for mediastinal lymph node detection on thoracic CT scans. First, lungs are automatically segmented to locate the mediastinum region. Shape features by Hessian analysis, local scale, and circular transformation are computed at each voxel. Spatial prior distribution is determined based on the identification of multiple anatomical structures (esophagus, aortic arch, heart, etc.) by using multi-atlas label fusion. Shape features and spatial prior are then integrated for lymph node detection. The detected candidates are segmented by curve evolution. Characteristic features are calculated on the segmented lymph nodes and support vector machine is utilized for classification and false positive reduction. We applied our method to 20 patients with 62 enlarged mediastinal lymph nodes. The system achieved a significant improvement with 80% sensitivity at 8 false positives per patient with spatial prior compared to 45% sensitivity at 8 false positives per patient without a spatial prior.

  17. Detection of secondary phases in duplex stainless steel by magnetic force microscopy and scanning Kelvin probe force microscopy

    SciTech Connect

    Ramírez-Salgado, J.; Domínguez-Aguilar, M.A.; Castro-Domínguez, B.; Hernández-Hernández, P.; Newman, R.C.

    2013-12-15

    The secondary phase transformations in a commercial super duplex stainless steel were investigated by micro-chemical analyses and high resolution scanning probe microscopy. Energy dispersive X-ray and electron probe detected ferrite and austenite as well as secondary phases in unetched aged duplex stainless steel type 25Cr-7Ni-3Mo. Volta potential indicated that nitride and sigma appeared more active than ferrite, while secondary austenite and austenite presented a nobler potential. Reversal order in nobility is thought to be attributable to the potential ranking provided by oxide nature diversity as a result of secondary phase surface compositions on steel. After eutectoid transformation, secondary austenite was detected by electron probe microanalysis, whereas atomic force microscopy distinguished this phase from former austenite by image contrast. Magnetic force microscopy revealed a “ghosted