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Sample records for scan detects quantitative

  1. 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.

  2. Sex-specific variability and a 'cage effect' independently mask a neuropathic pain quantitative trait locus detected in a whole genome scan.

    PubMed

    Devor, Marshall; Gilad, Amit; Arbilly, Michal; Nissenbaum, Jonathan; Yakir, Benjamin; Raber, Pnina; Minert, Anne; Pisanté, Anne; Darvasi, Ariel

    2007-08-01

    Sex and environment may dramatically affect genetic studies, and thus should be carefully considered. Beginning with two inbred mouse strains with contrasting phenotype in the neuroma model of neuropathic pain (autotomy), we established a backcross population on which we conducted a genome-wide scan. The backcross population was partially maintained in small social groups and partially in isolation. The genome scan detected one previously reported quantitative trait locus (QTL) on chromosome 15 (pain1), but no additional QTLs were found. Interestingly, group caging introduced phenotypic noise large enough to completely mask the genetic effect of the chromosome 15 QTL. The reason appears to be that group-caging animals from the low-autotomy strain together with animals from the high-autotomy strain dramatically increases autotomy in the otherwise low-autotomy mice (males or females). The converse, suppression of pain behaviour in the high-autotomy strain when caged with the low-autotomy strain was also observed, but only in females. Even in isolated mice, the genetic effect of the chromosome 15 QTL was significant only in females. To determine why, we evaluated autotomy levels of females in 12 different inbred stains of mice and compared them to previously reported levels for males. Strikingly larger environmental variation was observed in males than in females for this pain phenotype. The high baseline variance in males can explain the difficulty in detecting the genetic effect, which was readily seen in females. Our study emphasizes the importance of sex and environment in the genetic analysis of pain. PMID:17686043

  3. 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. PMID:16862444

  4. 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.

  5. Quantitative analysis of CT scans of ceramic candle filters

    SciTech Connect

    Ferer, M.V.; Smith, D.H.

    1996-12-31

    Candle filters are being developed to remove coal ash and other fine particles (<15{mu}m) from hot (ca. 1000 K) gas streams. In the present work, a color scanner was used to digitize hard-copy CT X-ray images of cylindrical SiC filters, and linear regressions converted the scanned (color) data to a filter density for each pixel. These data, with the aid of the density of SiC, gave a filter porosity for each pixel. Radial averages, density-density correlation functions, and other statistical analyses were performed on the density data. The CT images also detected the presence and depth of cracks that developed during usage of the filters. The quantitative data promise to be a very useful addition to the color images.

  6. Scanning tunneling microscopy on rough surfaces-quantitative image analysis

    NASA Astrophysics Data System (ADS)

    Reiss, G.; Brückl, H.; Vancea, J.; Lecheler, R.; Hastreiter, E.

    1991-07-01

    In this communication, the application of scanning tunneling microscopy (STM) for a quantitative evaluation of roughnesses and mean island sizes of polycrystalline thin films is discussed. Provided strong conditions concerning the resolution are satisfied, the results are in good agreement with standard techniques as, for example, transmission electron microscopy. Owing to its high resolution, STM can supply a better characterization of surfaces than established methods, especially concerning the roughness. Microscopic interpretations of surface dependent physical properties thus can be considerably improved by a quantitative analysis of STM images.

  7. Acute osteomyelitis: advantage of white cell scans in early detection

    SciTech Connect

    Raptopoulos, V.; Doherty, P.W.; Goss, T.P.; King, M.A.; Johnson, K.; Gantz, N.M.

    1982-12-01

    Acute osteomyelitis was induced in 18 rabbits after direct injection of a solution of Staphylococcus aureus culture into a proximal tibial metaphysis. Serial plain radiographs and radionuclide studies with /sup 111/In oxide labeled while blood cells and /sup 99m/Tc methylene diphosphonate were performed over the next 4 weeks. Visual and quantitative analysis by measuring the isotope activity of /sup 111/In and /sup 99m/Tc over the infected tibias as compared with the opposite bones revealed that the white blood cell scans were positive in 15 (83%) of the 18 rabbits during the first week after injection of the microorganism. During the same period, the /sup 99m/Tc bone scans were positive in only 22% of the animals (p less than 0.005). In the animals that survived, both white blood cell and bone scans were positive during the second week, and thereafter, the bone scans revealed consistently higher activity than was observed with white blood cell scans. Computed tomography performed in six rabbits revealed an increased attenuation coefficient of the medullary cavities in the infected bones of four animals during the first week and of one more during the second week. Plain radiographs became positive after the 12th day. Results indicate that in patients with suspected acute osteomyelitis, white blood cell scans and probably computed tomography can detect the disease earlier than /sup 99m/Tc bone scans and plain radiographs.

  8. Object detection in side scan sonar

    NASA Astrophysics Data System (ADS)

    Wang, Wenwu; Cheng, Binbin; Chen, Yao

    2015-12-01

    Automatic target detection is a challenging task as the response from an underwater target may vary greatly depending on its configuration, sonar parameters and the environment. We propose a Z- test algorithm for target detection in side scan sonar image which avoids this problem that covers the variation in the target response. A Z-test is performed on the means of the pixel gray levels within and outside the window area, a detection being called when the value of test statistic feature exceeds a certain threshold. The algorithm is formulated for real-time execution on limited memory commercial-of-the-shelf platforms and is capable of detection objects on the seabed-bottom.

  9. 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.

  10. 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

  11. 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. PMID:23976803

  12. Circle detection using scan lines and histograms

    NASA Astrophysics Data System (ADS)

    Chen, Ming; Zhang, Feng; Du, Zhenhong; Liu, Renyi

    2013-11-01

    Circle detection is significant in image processing and pattern recognition. We present a new algorithm for detecting circles, which is based on the global geometric symmetry of circles. First, the horizontal and vertical midpoint histograms of the edge image are obtained by using scan lines. Then, we apply the peak-finding algorithm to the midpoint histograms to look for the center of the circle. The normalized radius histogram is finally used to verify the existence of the circle and extract its radius. Synthetic images with different levels of pepper noise and real images containing several circles have been taken to test the performance. Experimental results demonstrate that the proposed algorithm has the advantage of computational efficiency as compared with the randomized Hough transform and some other algorithms.

  13. 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. PMID:26686661

  14. 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.

  15. 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.

  16. Quantitative multiplex detection of pathogen biomarkers

    SciTech Connect

    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.

  17. 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.

  18. 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. PMID:27085947

  19. Brazilian Amazonia Deforestation Detection Using Spatio-Temporal Scan Statistics

    NASA Astrophysics Data System (ADS)

    Vieira, C. A. O.; Santos, N. T.; Carneiro, A. P. S.; Balieiro, A. A. S.

    2012-07-01

    The spatio-temporal models, developed for analyses of diseases, can also be used for others fields of study, including concerns about forest and deforestation. The aim of this paper is to quantitatively check priority areas in order to combat deforestation on the Amazon forest, using the space-time scan statistic. The study area location is at the south of the Amazonas State and cover around 297.183 kilometre squares, including the municipality of Boca do Acre, Labrea, Canutama, Humaita, Manicore, Novo Aripuana e Apui County on the north region of Brazil. This area has showed a significant change for land cover, which has increased the number of deforestation's alerts. Therefore this situation becomes a concern and gets more investigation, trying to stop factors that increase the number of cases in the area. The methodology includes the location and year that deforestation's alert occurred. These deforestation's alerts are mapped by the DETER (Detection System of Deforestation in Real Time in Amazonia), which is carry out by the Brazilian Space Agency (INPE). The software SatScanTM v7.0 was used in order to define space-time permutation scan statistic for detection of deforestation cases. The outcome of this experiment shows an efficient model to detect space-time clusters of deforestation's alerts. The model was efficient to detect the location, the size, the order and characteristics about activities at the end of the experiments. Two clusters were considered actives and kept actives up to the end of the study. These clusters are located in Canutama and Lábrea County. This quantitative spatial modelling of deforestation warnings allowed: firstly, identifying actives clustering of deforestation, in which the environment government official are able to concentrate their actions; secondly, identifying historic clustering of deforestation, in which the environment government official are able to monitoring in order to avoid them to became actives again; and finally

  20. 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.

  1. Detecting and Quantitating Physiological Endoplasmic Reticulum Stress

    PubMed Central

    Qi, Ling; Yang, Liu; Chen, Hui

    2012-01-01

    Unfolded protein response (UPR) is a key cellular defense mechanism associated with many human “conformational” diseases, including heart diseases, neurodegeneration and metabolic syndrome. One of the major obstacles that have hindered our further understanding of physiological UPR and its future therapeutic potential is our inability to detect and quantitate ER stress and UPR activation under physiological and pathological conditions, where ER stress is perceivably very mild. Here we describe a Phos-tag-based Western blot approach that allows for direct visualization and quantitative assessment of mild ER stress and UPR signaling, directly at the levels of UPR sensors, in various in vivo conditions. This method will likely pave the foundation for future studies on physiological UPR, aid in the diagnosis of ER-associated diseases and facilitate therapeutic strategies targeting UPR in vivo. PMID:21266248

  2. Bone scanning in the detection of occult fractures

    SciTech Connect

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

    1981-07-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    SciTech Connect

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

    2013-01-01

    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. 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.

  5. Quantitative characterization of crosstalk effects for friction force microscopy with scan-by-probe SPMs.

    PubMed

    Prunici, Pavel; Hess, Peter

    2008-06-01

    If the photodetector and cantilever of an atomic force microscope (AFM) are not properly adjusted, crosstalk effects will appear. These effects disturb measurements of the absolute vertical and horizontal cantilever deflections, which are involved in friction force microscopy (FFM). A straightforward procedure is proposed to study quantitatively crosstalk effects observed in scan-by-probe SPMs. The advantage of this simple, fast, and accurate procedure is that no hardware change or upgrade is needed. The results indicate that crosstalk effects depend not only on the alignment of the detector but also on the cantilever properties, position, and detection conditions. The measurements may provide information on the origin of the crosstalk effect. After determination of its magnitude, simple correction formulas can be applied to correct the crosstalk effects and then the single-load wedge method, using a commercially available grating, can be employed for accurate calibration of the lateral force. PMID:18035500

  6. 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.

  7. 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

    2016-02-25

    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. PMID:26879591

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

    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.

  9. 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

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

    PubMed

    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

  11. 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.

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

    NASA Astrophysics Data System (ADS)

    Yankovich, Andrew B.

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

  13. 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. PMID:11669531

  14. Optical digital coherent detection technology enabled flexible and ultra-fast quantitative phase imaging.

    PubMed

    Feng, Yuan-Hua; Lu, Xing; Song, Lu; Guo, Xiaojie; Wang, Yawei; Zhu, Linyan; Sui, Qi; Li, Jianping; Shi, Kebin; Li, Zhaohui

    2016-07-25

    Quantitative phase imaging has been an important labeling-free microscopy modality for many biomedical and material science applications. In which, ultra-fast quantitative phase imaging is indispensable for dynamic or transient characteristics analysis. Conventional wide field optical interferometry is a common scheme for quantitative phase imaging, while its data acquisition rate is usually hindered by the frame rate of arrayed detector. By utilizing novel balanced-photo-detector based digital optics coherent detection techniques, we report on a method of constructing ultra-fast quantitative phase microscopy at the line-scan rate of 100 MHz with ~2 μm spatial resolution. PMID:27464166

  15. 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. PMID:20036873

  16. Scanning quantum dot microscopy: A quantitative method to measure local electrostatic potential near surfaces

    NASA Astrophysics Data System (ADS)

    Green, Matthew F. B.; Wagner, Christian; Leinen, Philipp; Deilmann, Thorsten; Krüger, Peter; Rohlfing, Michael; Tautz, F. Stefan; Temirov, Ruslan

    2016-08-01

    In this paper we review a recently introduced microscopy technique, scanning quantum dot microscopy (SQDM), which delivers quantitative maps of local electrostatic potential near surfaces in three dimensions. The key to achieving SQDM imaging is the functionalization of a scanning probe microscope tip with a π-conjugated molecule that acts as a gateable QD. Mapping of electrostatic potential with SQDM is performed by gating the QD by the bias voltage applied to the scanning probe microscope junction and registering changes of the QD charge state with frequency-modulated atomic force microscopy.

  17. 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.

  18. 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

  19. 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.

  20. Fast and Accurate Detection of Multiple Quantitative Trait Loci

    PubMed Central

    Nettelblad, Carl; Holmgren, Sverker

    2013-01-01

    Abstract We present a new computational scheme that enables efficient and reliable quantitative trait loci (QTL) scans for experimental populations. Using a standard brute-force exhaustive search effectively prohibits accurate QTL scans involving more than two loci to be performed in practice, at least if permutation testing is used to determine significance. Some more elaborate global optimization approaches, for example, DIRECT have been adopted earlier to QTL search problems. Dramatic speedups have been reported for high-dimensional scans. However, since a heuristic termination criterion must be used in these types of algorithms, the accuracy of the optimization process cannot be guaranteed. Indeed, earlier results show that a small bias in the significance thresholds is sometimes introduced. Our new optimization scheme, PruneDIRECT, is based on an analysis leading to a computable (Lipschitz) bound on the slope of a transformed objective function. The bound is derived for both infinite- and finite-size populations. Introducing a Lipschitz bound in DIRECT leads to an algorithm related to classical Lipschitz optimization. Regions in the search space can be permanently excluded (pruned) during the optimization process. Heuristic termination criteria can thus be avoided. Hence, PruneDIRECT has a well-defined error bound and can in practice be guaranteed to be equivalent to a corresponding exhaustive search. We present simulation results that show that for simultaneous mapping of three QTLS using permutation testing, PruneDIRECT is typically more than 50 times faster than exhaustive search. The speedup is higher for stronger QTL. This could be used to quickly detect strong candidate eQTL networks. PMID:23919387

  1. Quantitative Imaging of Rapidly Decaying Evanescent Fields Using Plasmonic Near-Field Scanning Optical Microscopy

    PubMed Central

    Zhang, Zhen; Ahn, Phillip; Dong, Biqin; Balogun, Oluwaseyi; Sun, Cheng

    2013-01-01

    Non-propagating evanescent fields play an important role in the development of nano-photonic devices. While detecting the evanescent fields in far-field can be accomplished by coupling it to the propagating waves, in practice they are measured in the presence of unwanted propagating background components. It leads to a poor signal-to-noise ratio and thus to errors in quantitative analysis of the local evanescent fields. Here we report on a plasmonic near-field scanning optical microscopy (p-NSOM) technique that incorporates a nanofocusing probe for adiabatic focusing of propagating surface plasmon polaritons at the probe apex, and for enhanced coupling of evanescent waves to the far-field. In addition, a harmonic demodulation technique is employed to suppress the contribution of the background. Our experimental results show strong evidence of background free near-field imaging using the new p-NSOM technique. Furthermore, we present measurements of surface plasmon cavity modes, and quantify their contributing sources using an analytical model. PMID:24076563

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

    PubMed Central

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

    2003-01-01

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

  3. Acute osteomyelitis: advantage of white cell scans in early detection. [Rabbits

    SciTech Connect

    Raptopoulos, V.; Doherty, P.W.; Goss, T.P.; King, M.A.; Johnson, K.; Gantz, N.M.

    1982-12-01

    Acute osteomyelitis was induced in 18 rabbits after direct injection of a solution of Staphylococcus aureus culture into a proximal tibial metaphysis. Serial plain radiographs and radionuclide studies with indium-111 oxine labeled white blood cells and technetium-99m methylene diphosphonate were performed over the next 4 weeks. Visual and quantitative analysis by measuring the isotope activity of /sup 111/In and /sup 99m/Tc over the infected tibias as compared with the opposite bones revealed that the white blood cell scans were positive in 15 (83%) of the 18 rabbits during the first week after injection of the microorganism. During the same period, the /sup 99m/Tc bone scans were positive in only 22% of the animals (p < 0.005). In the animals that survived, both white blood cell and bone scans were positive during the second week, and thereafter, the bone scans revealed consistently higher activity than was observed with white blood cell scans. Computed tomography performed in six rabbits revealed an increased attentuation coefficient of the medullary cavities of the infected bones of four animals during the first week and of one more during the second week. Plain radiographs became positive after the 12th day. Results indicate that in patients with suspected acute osteomyelitis, white blood cell scans and probably computed tomography can detect the disease earlier than /sup 99m/Tc bone scans and plain radiographs.

  4. Ultrasensitive immunoassay for prostate specific antigen using scanning tunneling microscopy-based electrical detection

    NASA Astrophysics Data System (ADS)

    Choi, Jeong-Woo; Oh, Byung-Keun; Jang, Yong-Hark; Kang, Da-Yeon

    2008-07-01

    We characterized a vertically configured electrical detection system that used scanning tunneling microscopy (STM) to detect antigen-antibody binding. This technique could be used to easily construct a multiple measurement system in a protein chip. We utilized immunocomplexes comprised of our model protein, prostate specific antigen (PSA), corresponding antibody fragments, and gold nanoparticle-antibody conjugates. The electrical tunneling current between the STM tip and these complexes exhibited a peaklike pulse, the frequency of which depended on the surface density of the bound complexes. We could therefore quantitatively measure PSA concentrations as low as 10fg/mL using periodogram analysis of this peak frequency.

  5. Detecting damage in steel with scanning SQUID microscopy

    SciTech Connect

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

    2001-09-04

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

  6. 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.

  7. 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.

  8. Quantitative determination of enzyme activity in single cells by scanning microelectrode coupled with a nitrocellulose film-covered microreactor by means of a scanning electrochemical microscope.

    PubMed

    Zhang, Xiaoli; Sun, Fuchan; Peng, Xuewei; Jin, Wenrui

    2007-02-01

    An electrochemical method for quantitative determination of enzyme activity in single cells was developed by scanning a microelectrode (ME) over a nitrocellulose film-covered microreactor with micropores by means of a scanning electrochemical microscope (SECM). Peroxidase (PO) in neutrophils was chosen as the model system. The microreactor consisted of a microwell with a solution and a nitrocellulose film with micropores. A single cell perforated by digitonin was injected into the microwell. After the perforated cell was lysed and allowed to dry, physiological buffer saline (PBS) containing hydroquinone (H2Q) and H2O2 as substrates of the enzyme-catalyzed reaction was added in the microwell. The microwell containing the extract of the lysed cell and the enzyme substrates was covered with Parafilm to prevent evaporation. The solution in the microwell was incubated for 20 min. In this case, the released PO from the cell converted H2Q into benzoquinone (BQ). Then, the Parafilm was replaced by a nitrocellulose film with micropores to fabricate the microreactor. The microreactor was placed in an electrochemical cell containing PBS, H2Q, and H2O2. After a 10-microm-radius Au ME was inserted into the electrochemical cell and approached down to the microreactor, the ME was scanned along the central line across the microreactor by means of a SECM. The scan curve with a peak was obtained by detecting BQ that diffused out from the microreactor through the micropores on the nitrocellulose film. PO activity could be quantified on the basis of the peak current on the scan curve using a calibration curve. This method had two obvious advantages: no electrode fouling and no oxygen interference. PMID:17263362

  9. 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.

  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. [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). PMID:16948447

  12. Quantitative spectroscopic imaging for non-invasive early cancer detection.

    PubMed

    Yu, Chung-Chieh; Lau, Condon; O'Donoghue, Geoffrey; Mirkovic, Jelena; McGee, Sasha; Galindo, Luis; Elackattu, Alphi; Stier, Elizabeth; Grillone, Gregory; Badizadegan, Kamran; Dasari, Ramachandra R; Feld, Michael S

    2008-09-29

    We report a fully quantitative spectroscopy imaging instrument for wide area detection of early cancer (dysplasia). This instrument provides quantitative maps of tissue biochemistry and morphology, making it a potentially powerful surveillance tool for objective early cancer detection. We describe the design, construction, calibration, and first clinical application of this new system. We demonstrate its accuracy using physical tissue models. We validate its diagnostic ability on a resected colon adenoma, and demonstrate feasibility of in vivo imaging in the oral cavity. PMID:18825262

  13. Quantitative assessment of automatic reconstructions of branching systems obtained from laser scanning

    PubMed Central

    Boudon, Frédéric; Preuksakarn, Chakkrit; Ferraro, Pascal; Diener, Julien; Nacry, Philippe; Nikinmaa, Eero; Godin, Christophe

    2014-01-01

    Background and Aims Automatic acquisition of plant architecture is a major challenge for the construction of quantitative models of plant development. Recently, 3-D laser scanners have made it possible to acquire 3-D images representing a sampling of an object's surface. A number of specific methods have been proposed to reconstruct plausible branching structures from this new type of data, but critical questions remain regarding their suitability and accuracy before they can be fully exploited for use in biological applications. Methods In this paper, an evaluation framework to assess the accuracy of tree reconstructions is presented. The use of this framework is illustrated on a selection of laser scans of trees. Scanned data were manipulated by experienced researchers to produce reference tree reconstructions against which comparisons could be made. The evaluation framework is given two tree structures and compares both their elements and their topological organization. Similar elements are identified based on geometric criteria using an optimization algorithm. The organization of these elements is then compared and their similarity quantified. From these analyses, two indices of geometrical and structural similarities are defined, and the automatic reconstructions can thus be compared with the reference structures in order to assess their accuracy. Key Results The evaluation framework that was developed was successful at capturing the variation in similarities between two structures as different levels of noise were introduced. The framework was used to compare three different reconstruction methods taken from the literature, and allowed sensitive parameters of each one to be determined. The framework was also generalized for the evaluation of root reconstruction from 2-D images and demonstrated its sensitivity to higher architectural complexity of structure which was not detected with a global evaluation criterion. Conclusions The evaluation framework

  14. 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

  15. Lesion detection and quantitation of positron emission mammography

    SciTech Connect

    Qi, Jinyi; Huesman, Ronald H.

    2001-12-01

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

  16. The detection and quantitation of protein oligomerization.

    PubMed

    Gell, David A; Grant, Richard P; Mackay, Joel P

    2012-01-01

    There are many different techniques available to biologists and biochemists that can be used to detect and characterize the self-association of proteins. Each technique has strengths and weaknesses and it is often useful to combine several approaches to maximize the former and minimize the latter. Here we review a range of methodologies that identify protein self-association and/or allow the stoichiometry and affinity of the interaction to be determined, placing an emphasis on what type of information can be obtained and outlining the advantages and disadvantages involved. In general, in vitro biophysical techniques, such as size exclusion chromatography, analytical ultracentrifugation, scattering techniques, NMR spectroscopy, isothermal titration calorimetry, fluorescence anisotropy and mass spectrometry, provide information on stoichiometry and/or binding affinities. Other approaches such as cross-linking, fluorescence methods (e.g., fluorescence correlation spectroscopy, FCS; Förster resonance energy transfer, FRET; fluorescence recovery after photobleaching, FRAP; and proximity imaging, PRIM) and complementation approaches (e.g., yeast two hybrid assays and bimolecular fluorescence complementation, BiFC) can be used to detect protein self-association in a cellular context. PMID:22949109

  17. X-ray-excited photoelectron detection using a scanning tunneling microscope

    SciTech Connect

    Rose, V.; Freeland, J. W.; Gray, K. E.; Streiffer, S. K.

    2008-05-12

    Detection of x-ray-enhanced electrons emitted by synchrotron radiation with the tip of a scanning tunneling microscope has the potential to open a path to high-resolution microscopy with chemical sensitivity. Nonresonant photoejected electrons typically yield a current background of a few hundred picoamperes at a bare tip. Coating the tip with an insulating boron nitride film can effectively reduce this background. In this configuration, we have quantitatively studied the bias dependent photoelectron collection for tip/sample separations of 400-1600 nm, where quantum mechanical tunneling does not contribute.

  18. Quantitative Detection of Spiroplasma Citri by Real Time PCR

    Technology Transfer Automated Retrieval System (TEKTRAN)

    There is a need to develop an accurate and rapid method to detect Spiroplasma citri, the causal agent of citrus stubborn disease for use in epidemiology studies. Quantitative real-time PCR was developed for detection of S. citri. Two sets of primers based on sequences from the P58 putative adhesin ...

  19. 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. PMID:19695816

  20. Detection of Creep displacement along the North Anatolian Fault by ScanSAR-ScanSAR Interferometry

    NASA Astrophysics Data System (ADS)

    Deguchi, Tomonori

    North Anatolian Fault (NAF) has several records of a huge earthquake occurrence in the last one century, which is well-known as a risky active fault. Some signs indicating a creep displacement could be observed on the Ismetpasa segment. The fault with creep deformation is aseismic and never generates the large scale earthquakes. But the scale and rate of fault creep are important factors to watch the fault behavior and to understand the cycle of earthquake. The author had investigated the distribution of spatial and temporal change on the ground motion due to fault creep in the surrounding of the Ismetpasa by InSAR time series analysis using PALSAR datasets from 2007 until 2011. As a result, the land deformation that the northern and southern parts of the fault have slipped to east and west at a rate of 7.5 and 6.5 mm/year in line of sight respectively were obviously detected. These results had good agreement with GPS data. In addition, it became clear that the fault creep along the NAF extended 61 km in east to west direction. In this study, the author applied ScanSAR-ScanSAR Interferometry using PALSAR data to the Ismetpasa segment of NAF.

  1. [Quantitative Detection of Chinese Cabbage Clubroot Based on FTIR Spectroscopy].

    PubMed

    Wang, Wei-ping; Chai, A-li; Shi, Yan-xia; Xie, Xue-wen; Li, Bao-ju

    2015-05-01

    Clubroot, caused by Plasmodiophora brassicae, is considered the most devastating soilborne disease in Brassica crops. It has emerged as a serious disease threatening the cruciferous crop production industry in China. Nowadays, the detection techniques for P. brassicae are laborious, time-consuming and low sensitivity. Rapid and effective detection methods are needed. The objective of this study is to develop a Fourier transform infrared spectrometer (FTIR) technique for detection of P. brassicae effectively and accurately. FTIR and Real-time PCR techniques were applied in quantitative detection of P. brassicae. Chinese cabbages were inoculated with P. brassicae. By analyzing the FTIR spectra of P. brassicae, infected clubroots and healthy roots, three specific bands 1 105, 1 145 and 1 228 cm-1 were selected. According to the correlation between the peak areas at these sensitive bands and Real-time PCR Ct value, quantitative evaluation model of P. brassicae was established based on FTIR y=34. 17 +12. 24x - 9. 81x2 - 6. 05x3, r=0. 98 (p<0. 05). To validate accuracy of the model, 10 clubroot samples were selected randomly from field, and detected by FTIR spectrum model, the results showed that the average error is 1. 60%. This demonstrated that the FTIR technology is an available one for the quantitative detection of P. brassicae in clubroot, and it provides a new method for quantitative and quickly detection of Chinese cabbage clubroot. PMID:26415436

  2. 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.

  3. X-ray scan detection for cargo integrity

    NASA Astrophysics Data System (ADS)

    Valencia, Juan; Miller, Steve

    2011-04-01

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

  4. 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.

  5. 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).

  6. 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.

  7. 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.

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

    PubMed

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

    2016-01-19

    Compared with routine microscopy imaging of a few analytes at a time, rapid scanning through the whole sample area of a microscope slide to locate every single target object offers many advantages in terms of simplicity, speed, throughput, and potential for robust quantitative analysis. Existing techniques that accommodate solid-phase samples incorporating individual micrometer-sized targets generally rely on digital microscopy and image analysis, with intrinsically low throughput and reliability. Here, we report an advanced on-the-fly stage scanning method to achieve high-precision target location across the whole slide. By integrating X- and Y-axis linear encoders to a motorized stage as the virtual "grids" that provide real-time positional references, we demonstrate an orthogonal scanning automated microscopy (OSAM) technique which can search a coverslip area of 50 × 24 mm(2) in just 5.3 min and locate individual 15 μm lanthanide luminescent microspheres with standard deviations of 1.38 and 1.75 μm in X and Y directions. Alongside implementation of an autofocus unit that compensates the tilt of a slide in the Z-axis in real time, we increase the luminescence detection efficiency by 35% with an improved coefficient of variation. We demonstrate the capability of advanced OSAM for robust quantification of luminescence intensities and lifetimes for a variety of micrometer-scale luminescent targets, specifically single down-shifting and upconversion microspheres, crystalline microplates, and color-barcoded microrods, as well as quantitative suspension array assays of biotinylated-DNA functionalized upconversion nanoparticles. PMID:26669618

  9. Quantitative annular dark field scanning transmission electron microscopy for nanoparticle atom-counting: What are the limits?

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

    Quantitative atomic resolution annular dark field scanning transmission electron microscopy (ADF STEM) has become a powerful technique for nanoparticle atom-counting. However, a lot of nanoparticles provide a severe characterisation challenge because of their limited size and beam sensitivity. Therefore, quantitative ADF STEM may greatly benefit from statistical detection theory in order to optimise the instrumental microscope settings such that the incoming electron dose can be kept as low as possible whilst still retaining single-atom precision. The principles of detection theory are used to quantify the probability of error for atom-counting. This enables us to decide between different image performance measures and to optimise the experimental detector settings for atom-counting in ADF STEM in an objective manner. To demonstrate this, ADF STEM imaging of an industrial catalyst has been conducted using the near-optimal detector settings. For this experiment, we discussed the limits for atomcounting diagnosed by combining a thorough statistical method and detailed image simulations.

  10. Prospective image registration for automated scan prescription of follow-up knee images in quantitative studies.

    PubMed

    Goldenstein, Janet; Schooler, Joseph; Crane, Jason C; Ozhinsky, Eugene; Pialat, Jean-Baptiste; Carballido-Gamio, Julio; Majumdar, Sharmila

    2011-06-01

    Consistent scan prescription for MRI of the knee is very important for accurate comparison of images in a longitudinal study. However, consistent scan region selection is difficult due to the complexity of the knee joint. We propose a novel method for registering knee images using a mutual information registration algorithm to align images in a baseline and follow-up exam. The output of the registration algorithm, three translations and three Euler angles, is then used to redefine the region to be imaged and acquire an identical oblique imaging volume in the follow-up exam as in the baseline. This algorithm is robust to articulation of the knee and anatomical abnormalities due to disease (e.g., osteophytes). The registration method is performed only on the distal femur and is not affected by the proximal tibia or soft tissues. We have incorporated this approach in a clinical MR system and have demonstrated its utility in automatically obtaining consistent scan regions between baseline and follow-up examinations, thus improving the precision of quantitative evaluation of cartilage. Results show an improvement with prospective registration in the coefficient of variation for cartilage thickness, cartilage volume and T2 relaxation measurements. PMID:21546186

  11. Improved Detection Sensitivity of Line-Scanning Optical Coherence Microscopy

    PubMed Central

    Chen, Yu; Huang, Shu-Wei; Zhou, Chao; Potsaid, Benjamin; Fujimoto, James G.

    2012-01-01

    Optical coherence microscopy (OCM) is a promising technology for high-resolution cellular-level imaging in human tissues. Line-scanning OCM is a new form of OCM that utilizes line-field illumination for parallel detection. In this study, we demonstrate improved detection sensitivity by using an achromatic design for line-field generation. This system operates at 830-nm wavelength with 82-nm bandwidth. The measured axial resolution is 3.9 μm in air (corresponding to ~2.9 μm in tissue), and the transverse resolutions are 2.1 μm along the line-field illumination direction and 1.7 μm perpendicular to line illumination direction. The measured sensitivity is 98 dB with 25 line averages, resulting in an imaging speed of ~2 frames/s (516 lines/s). Real-time, cellular-level imaging of scattering tissues is demonstrated using human-colon specimens. PMID:22685379

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

    PubMed

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

    2012-05-22

    Understanding energy dissipation at the nanoscale requires the ability to probe temperature fields with nanometer resolution. Here, we describe an ultra-high vacuum (UHV)-based scanning thermal microscope (SThM) technique that is capable of quantitatively mapping temperature fields with ∼15 mK temperature resolution and ∼10 nm spatial resolution. In this technique, a custom fabricated atomic force microscope (AFM) cantilever, with a nanoscale Au-Cr thermocouple integrated into the tip of the probe, is used to measure temperature fields of surfaces. Operation in an UHV environment eliminates parasitic heat transport between the tip and the sample enabling quantitative measurement of temperature fields on metal and dielectric surfaces with nanoscale resolution. We demonstrate the capabilities of this technique by directly imaging thermal fields in the vicinity of a 200 nm wide, self-heated, Pt line. Our measurements are in excellent agreement with computational results-unambiguously demonstrating the quantitative capabilities of the technique. UHV-SThM techniques will play an important role in the study of energy dissipation in nanometer-sized electronic and photonic devices and the study of phonon and electron transport at the nanoscale. PMID:22530657

  13. Intracellular subsurface imaging using a hybrid shear-force feedback/scanning quantitative phase microscopy technique

    NASA Astrophysics Data System (ADS)

    Edward, Kert

    Quantitative phase microscopy (QPM) allows for the imaging of translucent or transparent biological specimens without the need for exogenous contrast agents. This technique is usually applied towards the investigation of simple cells such as red blood cells which are typically enucleated and can be considered to be homogenous. However, most biological cells are nucleated and contain other interesting intracellular organelles. It has been established that the physical characteristics of certain subsurface structures such as the shape and roughness of the nucleus is well correlated with onset and progress of pathological conditions such as cancer. Although the acquired quantitative phase information of biological cells contains surface information as well as coupled subsurface information, the latter has been ignored up until now. A novel scanning quantitative phase imaging system unencumbered by 2pi ambiguities is hereby presented. This system is incorporated into a shear-force feedback scheme which allows for simultaneous phase and topography determination. It will be shown how subsequent image processing of these two data sets allows for the extraction of the subsurface component in the phase data and in vivo cell refractometry studies. Both fabricated samples and biological cells ranging from rat fibroblast cells to malaria infected human erythrocytes were investigated as part of this research. The results correlate quite well with that obtained via other microscopy techniques.

  14. 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.

  15. 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..

  16. 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.

  17. SCAN+

    Energy Science and Technology Software Center (ESTSC)

    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 determinemore » 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.« less

  18. Thickness-dependent thin-film resistivity: Application of quantitative scanning-tunneling-microscopy imaging

    NASA Astrophysics Data System (ADS)

    Reiss, G.; Hastreiter, E.; Brückl, H.; Vancea, J.

    1991-02-01

    The dependence of thin-film resistivity on the thickness is known to be strongly influenced by the interaction of the conduction electrons with the surface. Great efforts have been made in recent years, mainly concerning the quantum-mechanical description of the surface scattering. Detailed discussions of this problem, however, suffer from the lack of information concerning the real topography of thin-film surfaces. The development of scanning tunneling microscopy (STM) now gives the chance of direct, quantitative imaging. In this paper, we use the topographic information of STM to improve the fitting of theoretical descriptions to the measured thickness-dependence of the resistivity. The transport parameters obtained from these calculations show a high degree of physical consistency.

  19. Quantitative X-ray dark-field and phase tomography using single directional speckle scanning technique

    NASA Astrophysics Data System (ADS)

    Wang, Hongchang; Kashyap, Yogesh; Sawhney, Kawal

    2016-03-01

    X-ray dark-field contrast tomography can provide important supplementary information inside a sample to the conventional absorption tomography. Recently, the X-ray speckle based technique has been proposed to provide qualitative two-dimensional dark-field imaging with a simple experimental arrangement. In this letter, we deduce a relationship between the second moment of scattering angle distribution and cross-correlation degradation of speckle and establish a quantitative basis of X-ray dark-field tomography using single directional speckle scanning technique. In addition, the phase contrast images can be simultaneously retrieved permitting tomographic reconstruction, which yields enhanced contrast in weakly absorbing materials. Such complementary tomography technique can allow systematic investigation of complex samples containing both soft and hard materials.

  20. Quantitative scanning electron microscopic autoradiography of inhaled /sup 239/PuO/sub 2/

    SciTech Connect

    Sanders, C.L.; Lauhala, K.E.; McDonald, K.E.

    1989-03-01

    We have applied the scanning electron microscope (SEM) to obtain autoradiographs of particles of /sup 239/PuO/sub 2/ deposited in rat lung. The technique was used to obtain quantitative information on the clearance rates of particles from the alveoli, bronchioles and trachea up to 240 d after exposure. At all times, the concentration of particles on the surface of the bronchioles was an order of magnitude greater than on the tracheal surface. The clearance of Pu from both regions followed a biphasic pattern, similar to that obtained by radiometric analysis of the whole lung. Most of the radiation dose to the bronchiolar epithelium originated from Pu particles in peribronchiolar alveoli in which they were preferentially retained, compared to other alveolar regions. The prolonged retention of particles in the peribronchiolar alveoli may be a significant factor in the induction of lung carcinomas.

  1. 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.

  2. Quantitative analysis of sharp-force trauma: an application of scanning electron microscopy in forensic anthropology.

    PubMed

    Bartelink, E J; Wiersema, J M; Demaree, R S

    2001-11-01

    Scanning electron microscopy (SEM) has occasionally been used by anthropologists and forensic scientists to look at morphological characteristics that certain implements leave on bone. However, few studies have addressed techniques or protocols for assessing quantitative differences between tool marks on bone made by different bladed implements. In this study, the statistical variation in cut mark width was examined between control and test samples on bone using a scalpel blade, paring knife, and kitchen utility knife. Statistically significant differences (p < .0005) were found between cut marks made by the same knife under control and test conditions for all three knife types used in the study. When the control sample and test samples were examined individually for differences in mean variation between knife types, significant differences were also found (p < .0005). While significant differences in cut mark width were found, caution should be used in trying to classify individual cut marks as being inflicted by a particular implement, due to the overlap in cut mark width that exists between different knife types. When combined, both quantitative and qualitative analyses of cut marks should prove to be more useful in trying to identify a suspect weapon. Furthermore, the application of SEM can be particularly useful for assessing many of these features. PMID:11714137

  3. Analytic Validation of the Automated Bone Scan Index as an Imaging Biomarker to Standardize Quantitative Changes in Bone Scans of Patients with Metastatic Prostate Cancer

    PubMed Central

    Anand, Aseem; Morris, Michael J.; Kaboteh, Reza; Båth, Lena; Sadik, May; Gjertsson, Peter; Lomsky, Milan; Edenbrandt, Lars; Minarik, David; Bjartell, Anders

    2016-01-01

    A reproducible and quantitative imaging biomarker is needed to standardize the evaluation of changes in bone scans of prostate cancer patients with skeletal metastasis. We performed a series of analytic validation studies to evaluate the performance of the automated bone scan index (BSI) as an imaging biomarker in patients with metastatic prostate cancer. Methods Three separate analytic studies were performed to evaluate the accuracy, precision, and reproducibility of the automated BSI. Simulation study: bone scan simulations with predefined tumor burdens were created to assess accuracy and precision. Fifty bone scans were simulated with a tumor burden ranging from low to high disease confluence (0.10–13.0 BSI). A second group of 50 scans was divided into 5 subgroups, each containing 10 simulated bone scans, corresponding to BSI values of 0.5, 1.0, 3.0, 5.0, and 10.0. Repeat bone scan study: to assess the reproducibility in a routine clinical setting, 2 repeat bone scans were obtained from metastatic prostate cancer patients after a single 600-MBq 99mTc-methylene diphosphonate injection. Follow-up bone scan study: 2 follow-up bone scans of metastatic prostate cancer patients were analyzed to determine the interobserver variability between the automated BSIs and the visual interpretations in assessing changes. The automated BSI was generated using the upgraded EXINI boneBSI software (version 2). The results were evaluated using linear regression, Pearson correlation, Cohen κ measurement, coefficient of variation, and SD. Results Linearity of the automated BSI interpretations in the range of 0.10–13.0 was confirmed, and Pearson correlation was observed at 0.995 (n = 50; 95% confidence interval, 0.99–0.99; P < 0.0001). The mean coefficient of variation was less than 20%. The mean BSI difference between the 2 repeat bone scans of 35 patients was 0.05 (SD = 0.15), with an upper confidence limit of 0.30. The interobserver agreement in the automated BSI

  4. [Application of near-infrared absorption spectrum scanning techniques in gas quantitative measurement].

    PubMed

    Ding, Hui; Liang, Jian-Qi; Cui, Jun-Hong; Wu, Xiang-Nan; Li, Xian-Li

    2010-03-01

    A practical gas sensing system utilizing absorption spectrum scanning techniques was developed. Using the narrow-band transmission of a fiber tunable filter (TOF) and wavelength modulation technique, the so-called cross-sensing effects of the traditional spectrum absorption based gas sensor were reduced effectively and thus the target gas was detected sensitively and selectively. In order to reduce the effects of nonlinearity of TOF on the measurement results and improve the system stability in operation, the reflection spectrum of a reference FBG was monitored and employed to control the modulation region and center of TOF wavelength precisely. Moreover, a kind of weak signal detecting circuits was developed to detect the weak response signal of the system with high sensitivity. The properties of the proposed system were demonstrated experimentally by detection of acetylene. Approximate linear relationships between the system responses and the input acetylene concentrations were demonstrated by experiments. The minimum detectable acetylene of 5 x 10(-6), with signal-noise ratio of 3, was also achieved by experiments. PMID:20496683

  5. Rapid and quantitative detection of hepatitis B virus

    PubMed Central

    Liu, Yue-Ping; Yao, Chun-Yan

    2015-01-01

    Despite availability of a universal vaccine, hepatitis B virus (HBV) infection has a huge impact on public health worldwide. Accurate and timely diagnosis of HBV infection is needed. Rapid developments have been made in the diagnostic and monitoring methods for HBV infection, including serological and molecular assays. In clinical practice, qualitative hepatitis B surface antigen (HBsAg) testing has long served as a diagnostic marker for individuals infected with HBV. More recently, HBsAg level has been used to predict treatment outcome when determined early during treatment or at baseline. However, identification of HBV DNA positive cases that do not have detectable HBsAg has encouraged the application of molecular tests. Hence, combination of quantitative detection of HBV DNA and HBsAg can be used to discriminate patients during the course of HBV infection and to monitor therapy. This article reviews the most commonly used quantitative methods for HBsAg and HBV DNA. PMID:26576084

  6. 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

  7. 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. PMID:27231641

  8. 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.

  9. 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.

  10. Genome-scan analysis for quantitative trait loci in an F2 tilapia hybrid.

    PubMed

    Cnaani, A; Zilberman, N; Tinman, S; Hulata, G; Ron, M

    2004-09-01

    We searched for genetic linkage between DNA markers and quantitative trait loci (QTLs) for innate immunity, response to stress, biochemical parameters of blood, and fish size in an F2 population derived from an interspecific tilapia hybrid (Oreochromis mossambicusx O. aureus). A family of 114 fish was scanned for 40 polymorphic microsatellite DNA markers and two polymorphic genes, covering approximately 80% of the tilapia genome. These fish had previously been phenotyped for seven immune-response traits and six blood parameters. Critical values for significance were P <0.05 with the false discovery rate (FDR) controlled at 40%. The genome-scan analysis resulted in 35 significant marker-trait associations, involving 26 markers in 16 linkage groups. In a second experiment, nine markers were re-sampled in a second family of 79 fish of the same species hybrid. Seven markers (GM180, GM553, MHC-I, UNH848, UNH868, UNH898 and UNH925) in five linkage groups (LG 1, 3, 4, 22 and 23) were associated with stress response traits. An additional six markers (GM47, GM552, UNH208, UNH881, UNH952, UNH998) in five linkage groups (LG 4, 16, 19, 20 and 23) were verified for their associations with immune response traits, by linkage to several different traits. The portion of variance explained by each QTL was 11% on average, with a maximum of 29%. The average additive effect of QTLs was 0.2 standard deviation units of stress response traits and fish size, with a maximum of 0.33. In three linkage groups (LG 1, 3 and 23) markers were associated with stress response, body weight and sex determination, confirming the location of QTLs reported by several other studies. PMID:15449174

  11. Towards quantitative modelling of surface deformation of polymer micro-structures under tactile scanning measurement

    NASA Astrophysics Data System (ADS)

    Li, Zhi; Brand, Uwe; Ahbe, Thomas

    2014-04-01

    Contact stylus-based surface profilometry is capable of topography measurement whilst being independent of the physical, electrical and optical properties of the materials under test, and has therefore become an indispensable tool for dimensional measurement of transparent specimens. However, large measurement deviations will appear when soft specimens, especially specimens made of polymers, are measured by contact stylus profilometry. In this paper the surface deformation behaviour of two polymers for molding and one photoresist, i.e. Ormocomp, Ormoclad and SU-8, under different tactile measurement conditions have been experimentally investigated. An empirical analytical model is hereby proposed for the prediction of surface deformation of soft specimens under tactile (sliding) contact. Preliminary experimental results demonstrate that the proposed five-parameter model is applicable for describing the deformation behaviour of these thermoplastic materials under the scanning speed ranging from 2 to 200 μm s-1 and the probing force varying from 5 to 500 μN. In addition, thanks to quantitative topographical measurements of the layer thickness of the aforementioned photoresists, the scratch behaviour and the time-dependent mechanical properties of these materials have also been experimentally determined.

  12. Quantitative characterization of the surface topography of rolled sheets by laser scanning microscopy and fourier transformation

    NASA Astrophysics Data System (ADS)

    Gjønnes, Liv

    1996-08-01

    The surface of twin-roll cast aluminum sheets undergoes dramatic changes during cold rolling. This is mainly due to variables in the roll gap, topography of the rolls, lubrication, material properties, and in particular the initial structure and topography of the cast sheet. Therefore, it is important to have means to quantitatively describe the changes in the surface structure of each pass and from pass to pass in order to optimize the desired final surface structure. To achieve this, the laser scanning microscope (LSM) with its confocal technique has been employed to image the three-dimensional (3-D) topography and to digitize the image for further computer analysis. The digitization of the image is primarily motivated by the need to introduce a Fourier transformation of the surface topography. The method is effective in describing qualitative periodic trends in the surface features. Information is gained on the shape and periodicities as well as roughness directionality. For instance, grooves and cross hatches and their remnants can be followed from one pass to the other. Important characteristics of the surface topography such as rolling ridges and shingles can also easily be characterized.

  13. A genome-wide linkage scan for iron phenotype quantitative trait loci: the HEIRS Family Study.

    PubMed

    Acton, R T; Snively, B M; Barton, J C; McLaren, C E; Adams, P C; Rich, S S; Eckfeldt, J H; Press, R D; Sholinsky, P; Leiendecker-Foster, C; McLaren, G D; Speechley, M R; Harris, E L; Dawkins, F W; Gordeuk, V R

    2007-06-01

    Iron overload phenotypes in persons with and without hemochromatosis are variable. To investigate this further, probands with hemochromatosis or evidence of elevated iron stores and their family members were recruited for a genome-wide linkage scan to identify potential quantitative trait loci (QTL) that contribute to variation in transferrin saturation (TS), unsaturated iron-binding capacity (UIBC), and serum ferritin (SF). Genotyping utilized 402 microsatellite markers with average spacing of 9 cM. A total of 943 individuals, 64% Caucasian, were evaluated from 174 families. After adjusting for age, gender, and race/ethnicity, there was evidence for linkage of UIBC to chromosome 4q logarithm of the odds (LOD) = 2.08, p = 0.001) and of UIBC (LOD = 9.52), TS (LOD = 4.78), and SF (LOD = 2.75) to the chromosome 6p region containing HFE (each p < 0.0001). After adjustments for HFE genotype and other covariates, there was evidence of linkage of SF to chromosome 16p (LOD = 2.63, p = 0.0007) and of UIBC to chromosome 5q (LOD = 2.12, p = 0.002) and to chromosome 17q (LOD = 2.19, p = 0.002). We conclude that these regions should be considered for fine mapping studies to identify QTL that contribute to variation in SF and UIBC. PMID:17539901

  14. Uracil on Cu(110): A quantitative structure determination by energy-scanned photoelectron diffraction

    NASA Astrophysics Data System (ADS)

    Duncan, D. A.; Unterberger, W.; Kreikemeyer-Lorenzo, D.; Woodruff, D. P.

    2011-07-01

    The local adsorption site of the nucleobase uracil on Cu(110) has been determined quantitatively by energy-scanned photoelectron diffraction (PhD). Qualitative inspection of the O 1s and N 1s soft x-ray photoelectron spectra, PhD modulation spectra, and O K-edge near-edge x-ray adsorption fine structure indicate that uracil bonds to the surface through its nitrogen and oxygen constituent atoms, each in near atop sites, with the molecular plane essentially perpendicular to surface and aligned along the close packed [1overline 1 0] azimuth. Multiple scattering simulations of the PhD spectra confirm and refine this geometry. The Cu-N bondlength is 1.96 ± 0.04 Å, while the Cu-O bondlengths of the two inequivalent O atoms are 1.93 ± 0.04 Å and 1.96 ± 0.04 Å, respectively. The molecule is twisted out of the [1overline 1 0]direction by 11 ± 5°.

  15. Analysis of quantitative phase detection based on optical information processing

    NASA Astrophysics Data System (ADS)

    Tao, Wang; Tu, Jiang-Chen; Chun, Kuang-Tao; Yu, Han-Wang; Xin, Du

    2009-07-01

    Phase object exists widely in nature, such as biological cells, optical components, atmospheric flow field and so on. The phase detection of objects has great significance in the basic research, nondestructive testing, aerospace, military weapons and other areas. The usual methods of phase object detection include interference method, grating method, schlieren method, and phase-contrast method etc. These methods have their own advantages, but they also have some disadvantages on detecting precision, environmental requirements, cost, detection rate, detection range, detection linearity in various applications, even the most sophisticated method-phase contrast method mainly used in microscopic structure, lacks quantitative analysis of the size of the phase of the object and the relationship between the image contrast and the optical system. In this paper, various phase detection means and the characteristics of different applications are analyzed based on the optical information processing, and a phase detection system based on optical filtering is formed. Firstly the frequency spectrum of the phase object is achieved by Fourier transform lens in the system, then the frequency spectrum is changed reasonably by the filter, at last the image which can represent the phase distribution through light intensity is achieved by the inverse Fourier transform. The advantages and disadvantages of the common used filters such as 1/4 wavelength phase filter, high-pass filter and edge filter are analyzed, and their phase resolution is analyzed in the same optical information processing system, and the factors impacting phase resolution are pointed out. The paper draws a conclusion that there exists an optimal filter which makes the detect accuracy best for any application. At last, we discussed how to design an optimal filter through which the ability of the phase testing of optical information processing system can be improved most.

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

    SciTech Connect

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

    1982-07-15

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

  17. 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.

  18. Driving With Hemianopia: IV. Head Scanning and Detection at Intersections in a Simulator

    PubMed Central

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

    2014-01-01

    Purpose. Using a driving simulator, we examined the effects of homonymous hemianopia (HH) on head scanning behaviors at intersections and evaluated the role of inadequate head scanning in detection failures. Methods. Fourteen people with complete HH and without cognitive decline or visual neglect and 12 normally sighted (NV) current drivers participated. They drove in an urban environment following predetermined routes, which included multiple intersections. Head scanning behaviors were quantified at T-intersections (n = 32) with a stop or yield sign. Participants also performed a pedestrian detection task. The relationship between head scanning and detection was examined at 10 intersections. Results. For HH drivers, the first scan was more likely to be toward the blind than the seeing hemifield. They also made a greater proportion of head scans overall to the blind side than did the NV drivers to the corresponding side (P = 0.003). However, head scan magnitudes of HH drivers were smaller than those of the NV group (P < 0.001). Drivers with HH had impaired detection of blind-side pedestrians due either to not scanning in the direction of the pedestrian or to an insufficient scan magnitude (left HH detected only 46% and right HH 8% at the extreme left and right of the intersection, respectively). Conclusions. Drivers with HH demonstrated compensatory head scan patterns, but not scan magnitudes. Inadequate scanning resulted in blind-side detection failures, which might place HH drivers at increased risk for collisions at intersections. Scanning training tailored to specific problem areas identified in this study might be beneficial. PMID:24474265

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

    PubMed Central

    2012-01-01

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

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

    PubMed Central

    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.

  1. 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

  2. Mechanical properties, density and quantitative CT scan data of trabecular bone with and without metastases.

    PubMed

    Kaneko, Tadashi S; Bell, Jason S; Pejcic, Marina R; Tehranzadeh, Jamshid; Keyak, Joyce H

    2004-04-01

    Pathologic fracture of the hip due to metastatic lesions in bone is a serious problem. This study examined the effect of metastatic lesions on the material properties and quantitative computed tomography (QCT) data of trabecular bone. Twelve distal femora were obtained, four with lytic and/or blastic metastatic lesions (group L), four without lesions but from donors who died from breast, prostate, or lung cancer (group NL), and four from donors with no cancer (group NC). Each specimen was CT scanned, and 56, 15x15x15-mm cubes of trabecular bone were cut. QCT density (rho(QCT)), compressive elastic modulus (E), compressive yield and ultimate strengths (S(y) and S(u)), and ash density (rho(ash)) of each cube were determined. Regression analysis was performed between rho(ash) and E, S(y), S(u) and rho(QCT), and analysis of covariance was used to identify differences between groups. Power relationships that did not depend on group (p >/= 0.1) were found between E and rho(ash) (0.74 /= 0.94; p<0.001). rho(ash) was strongly related to rho(QCT) (r >/= 0.99; p<0.001). These results indicate that metastatic disease does not significantly impair the ability of QCT to provide an accurate and precise estimate of rho(ash) that can be used to estimate mechanical properties of trabecular bone with and without metastases. PMID:14996564

  3. Effect of random coincidences for quantitative cardiac PET studies using 3D oxygen-15 water scans

    NASA Astrophysics Data System (ADS)

    Bouchareb, Y.; Thielemans, K.; Spinks, T.; Rimoldi, O.; Camici, P. G.

    2006-03-01

    The effect of random coincidences estimation methods on the quantitative accuracy of iterative and analytic reconstruction methods to determine myocardial blood flow (MBF) in PET studies using H II 15O has been investigated. Dynamic scans were acquired on the EXACT3D PET scanner on pigs after H II 15O injection (resting and dipyridamoleinduced stress). Radioactive microspheres (MS) were used to provide a "gold standard" of MBF values. The online subtraction (OS) and maximum likelihood (ML) methods for estimating randoms were combined with (i) 3D-RP, (ii) FORE + attenuation-weighted OSEM, (iii) FORE-FBP and (iv) 3D-OSEM. Factor images were generated and resliced to short axis images; 16 ROIs were defined in the left myocardium and 2 ROIs in the left and right cavities. ROIs were projected onto the dynamic images to extract time-activity-curves, which were then fitted to a single compartment model to estimate absolute MBF. Microsphere measurements were obtained in a similar way and 64 pairs of measurements were made. The ML method improved the SNR of 3D-RP, FORE-FBP, FORE-OSEM, and 3D-OSEM by 8%, 8%, 7% and 3% respectively. Compared to the OS method, the ML method improved the accuracy of coronary flow reserve values of 3DOSEM, 3D-RP, FORE-OSEM and FORE-FBP by 9%, 7%, 1% and 3% respectively. Regression analysis provided better correlation with 3D-OSEM and FORE-OSEM when combined with the ML method. We conclude that the ML method for estimating randoms combined with 3D-OSEM and FORE-OSEM delivers the best performance for absolute quantification of MBF using H II 15O when compared with microsphere measurements.

  4. Comparison of the scanning linear estimator (SLE) and ROI methods for quantitative SPECT imaging

    NASA Astrophysics Data System (ADS)

    Könik, Arda; Kupinski, Meredith; Hendrik Pretorius, P.; King, Michael A.; Barrett, Harrison H.

    2015-08-01

    In quantitative emission tomography, tumor activity is typically estimated from calculations on a region of interest (ROI) identified in the reconstructed slices. In these calculations, unpredictable bias arising from the null functions of the imaging system affects ROI estimates. The magnitude of this bias depends upon the tumor size and location. In prior work it has been shown that the scanning linear estimator (SLE), which operates on the raw projection data, is an unbiased estimator of activity when the size and location of the tumor are known. In this work, we performed analytic simulation of SPECT imaging with a parallel-hole medium-energy collimator. Distance-dependent system spatial resolution and non-uniform attenuation were included in the imaging simulation. We compared the task of activity estimation by the ROI and SLE methods for a range of tumor sizes (diameter: 1-3 cm) and activities (contrast ratio: 1-10) added to uniform and non-uniform liver backgrounds. Using the correct value for the tumor shape and location is an idealized approximation to how task estimation would occur clinically. Thus we determined how perturbing this idealized prior knowledge impacted the performance of both techniques. To implement the SLE for the non-uniform background, we used a novel iterative algorithm for pre-whitening stationary noise within a compact region. Estimation task performance was compared using the ensemble mean-squared error (EMSE) as the criterion. The SLE method performed substantially better than the ROI method (i.e. EMSE(SLE) was 23-174 times lower) when the background is uniform and tumor location and size are known accurately. The variance of the SLE increased when a non-uniform liver texture was introduced but the EMSE(SLE) continued to be 5-20 times lower than the ROI method. In summary, SLE outperformed ROI under almost all conditions that we tested.

  5. Comparison of the scanning linear estimator (SLE) and ROI methods for quantitative SPECT imaging.

    PubMed

    Könik, Arda; Kupinski, Meredith; Pretorius, P Hendrik; King, Michael A; Barrett, Harrison H

    2015-08-21

    In quantitative emission tomography, tumor activity is typically estimated from calculations on a region of interest (ROI) identified in the reconstructed slices. In these calculations, unpredictable bias arising from the null functions of the imaging system affects ROI estimates. The magnitude of this bias depends upon the tumor size and location. In prior work it has been shown that the scanning linear estimator (SLE), which operates on the raw projection data, is an unbiased estimator of activity when the size and location of the tumor are known. In this work, we performed analytic simulation of SPECT imaging with a parallel-hole medium-energy collimator. Distance-dependent system spatial resolution and non-uniform attenuation were included in the imaging simulation. We compared the task of activity estimation by the ROI and SLE methods for a range of tumor sizes (diameter: 1-3 cm) and activities (contrast ratio: 1-10) added to uniform and non-uniform liver backgrounds. Using the correct value for the tumor shape and location is an idealized approximation to how task estimation would occur clinically. Thus we determined how perturbing this idealized prior knowledge impacted the performance of both techniques. To implement the SLE for the non-uniform background, we used a novel iterative algorithm for pre-whitening stationary noise within a compact region. Estimation task performance was compared using the ensemble mean-squared error (EMSE) as the criterion. The SLE method performed substantially better than the ROI method (i.e. EMSE(SLE) was 23-174 times lower) when the background is uniform and tumor location and size are known accurately. The variance of the SLE increased when a non-uniform liver texture was introduced but the EMSE(SLE) continued to be 5-20 times lower than the ROI method. In summary, SLE outperformed ROI under almost all conditions that we tested. PMID:26247228

  6. 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.

  7. Hyperspectral imaging and quantitative analysis for prostate cancer detection

    PubMed Central

    Akbari, Hamed; Halig, Luma V.; Schuster, David M.; Osunkoya, Adeboye; Master, Viraj; Nieh, Peter T.; Chen, Georgia Z.

    2012-01-01

    Abstract. Hyperspectral imaging (HSI) is an emerging modality for various medical applications. Its spectroscopic data might be able to be used to noninvasively detect cancer. Quantitative analysis is often necessary in order to differentiate healthy from diseased tissue. We propose the use of an advanced image processing and classification method in order to analyze hyperspectral image data for prostate cancer detection. The spectral signatures were extracted and evaluated in both cancerous and normal tissue. Least squares support vector machines were developed and evaluated for classifying hyperspectral data in order to enhance the detection of cancer tissue. This method was used to detect prostate cancer in tumor-bearing mice and on pathology slides. Spatially resolved images were created to highlight the differences of the reflectance properties of cancer versus those of normal tissue. Preliminary results with 11 mice showed that the sensitivity and specificity of the hyperspectral image classification method are 92.8% to 2.0% and 96.9% to 1.3%, respectively. Therefore, this imaging method may be able to help physicians to dissect malignant regions with a safe margin and to evaluate the tumor bed after resection. This pilot study may lead to advances in the optical diagnosis of prostate cancer using HSI technology. PMID:22894488

  8. Hyperspectral imaging and quantitative analysis for prostate cancer detection

    NASA Astrophysics Data System (ADS)

    Akbari, Hamed; Halig, Luma V.; Schuster, David M.; Osunkoya, Adeboye; Master, Viraj; Nieh, Peter T.; Chen, Georgia Z.; Fei, Baowei

    2012-07-01

    Hyperspectral imaging (HSI) is an emerging modality for various medical applications. Its spectroscopic data might be able to be used to noninvasively detect cancer. Quantitative analysis is often necessary in order to differentiate healthy from diseased tissue. We propose the use of an advanced image processing and classification method in order to analyze hyperspectral image data for prostate cancer detection. The spectral signatures were extracted and evaluated in both cancerous and normal tissue. Least squares support vector machines were developed and evaluated for classifying hyperspectral data in order to enhance the detection of cancer tissue. This method was used to detect prostate cancer in tumor-bearing mice and on pathology slides. Spatially resolved images were created to highlight the differences of the reflectance properties of cancer versus those of normal tissue. Preliminary results with 11 mice showed that the sensitivity and specificity of the hyperspectral image classification method are 92.8% to 2.0% and 96.9% to 1.3%, respectively. Therefore, this imaging method may be able to help physicians to dissect malignant regions with a safe margin and to evaluate the tumor bed after resection. This pilot study may lead to advances in the optical diagnosis of prostate cancer using HSI technology.

  9. Hyperspectral imaging and quantitative analysis for prostate cancer detection.

    PubMed

    Akbari, Hamed; Halig, Luma V; Schuster, David M; Osunkoya, Adeboye; Master, Viraj; Nieh, Peter T; Chen, Georgia Z; Fei, Baowei

    2012-07-01

    Hyperspectral imaging (HSI) is an emerging modality for various medical applications. Its spectroscopic data might be able to be used to noninvasively detect cancer. Quantitative analysis is often necessary in order to differentiate healthy from diseased tissue. We propose the use of an advanced image processing and classification method in order to analyze hyperspectral image data for prostate cancer detection. The spectral signatures were extracted and evaluated in both cancerous and normal tissue. Least squares support vector machines were developed and evaluated for classifying hyperspectral data in order to enhance the detection of cancer tissue. This method was used to detect prostate cancer in tumor-bearing mice and on pathology slides. Spatially resolved images were created to highlight the differences of the reflectance properties of cancer versus those of normal tissue. Preliminary results with 11 mice showed that the sensitivity and specificity of the hyperspectral image classification method are 92.8% to 2.0% and 96.9% to 1.3%, respectively. Therefore, this imaging method may be able to help physicians to dissect malignant regions with a safe margin and to evaluate the tumor bed after resection. This pilot study may lead to advances in the optical diagnosis of prostate cancer using HSI technology. PMID:22894488

  10. Quantitative Trait Loci (QTL) Detection in Multicross Inbred Designs

    PubMed Central

    Crepieux, Sébastien; Lebreton, Claude; Servin, Bertrand; Charmet, Gilles

    2004-01-01

    Mapping quantitative trait loci in plants is usually conducted using a population derived from a cross between two inbred lines. The power of such QTL detection and the parameter estimates depend largely on the choice of the two parental lines. Thus, the QTL detected in such populations represent only a small part of the genetic architecture of the trait. In addition, the effects of only two alleles are characterized, which is of limited interest to the breeder, while common pedigree breeding material remains unexploited for QTL mapping. In this study, we extend QTL mapping methodology to a generalized framework, based on a two-step IBD variance component approach, applicable to any type of breeding population obtained from inbred parents. We then investigate with simulated data mimicking conventional breeding programs the influence of different estimates of the IBD values on the power of QTL detection. The proposed method would provide an alternative to the development of specifically designed recombinant populations, by utilizing the genetic variation actually managed by plant breeders. The use of these detected QTL in assisting breeding would thus be facilitated. PMID:15579720

  11. 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.

  12. Nanoplasmonic Quantitative Detection of Intact Viruses from Unprocessed Whole Blood

    PubMed Central

    Inci, Fatih; Tokel, Onur; Wang, ShuQi; Gurkan, Umut Atakan; Tasoglu, Savas; Kuritzkes, Daniel R.; Demirci, Utkan

    2013-01-01

    Infectious diseases such as HIV and Hepatitis B infection pose an omnipresent threat to global health. Reliable, fast, accurate and sensitive platforms that can be deployed at the point-of-care (POC) in multiple settings, such as airports and offices for detection of infectious pathogens are essential for the management of epidemics and possible biological attacks. To the best of our knowledge, no viral load technology adaptable to the POC settings exists today due to critical technical and biological challenges. Here, we present for the first time a broadly applicable technology for quantitative, nanoplasmonic-based intact virus detection at clinically relevant concentrations. The sensing platform is based on unique nanoplasmonic properties of nanoparticles utilizing immobilized antibodies to selectively capture rapidly evolving viral subtypes. We demonstrate the capture, detection and quantification of multiple HIV subtypes (A, B, C, D, E, G, and subtype panel) with high repeatability, sensitivity and specificity down to 98 ± 39 copies/mL (i.e., subtype D) using spiked whole blood samples and clinical discarded HIV-infected patient whole blood samples validated by the gold standard, i.e., RT-qPCR. This platform technology offers an assay time of 1 hour and 10 minutes (1 hour for capture, 10 minutes for detection and data analysis). The presented platform is also able to capture intact viruses at high efficiency using immuno-surface chemistry approaches directly from whole blood samples without any sample preprocessing steps such as spin-down or sorting. Evidence is presented showing the system to be accurate, repeatable and reliable. Additionally, the presented platform technology can be broadly adapted to detect other pathogens having reasonably well-described biomarkers by adapting the surface chemistry. Thus, this broadly applicable detection platform holds great promise to be implemented potentially at POC settings, hospital and primary care settings. PMID

  13. EpiScan: online seizure detection for epilepsy monitoring units.

    PubMed

    Hartmann, Manfred M; Fürbass, Franz; Perko, Hannes; Skupch, Ana; Lackmayer, Katharina; Baumgartner, Christoph; Kluge, Tilmann

    2011-01-01

    An online seizure detection algorithm for long-term EEG monitoring is presented, which is based on a periodic waveform analysis detecting rhythmic EEG patterns and an adaptation module automatically adjusting the algorithm to patient-specific EEG properties. The algorithm was evaluated using 4.300 hours of unselected EEG recordings from 48 patients with temporal lobe epilepsy. For 66% of the patients the algorithm detected 100% of the seizures. A mean sensitivity of 83% was achieved. An average of 7.2 false alarms within 24 hours for unselected EEG makes the algorithm attractive for epilepsy monitoring units. PMID:22255730

  14. Quantitative analysis and application of tip position modulation-scanning electrochemical microscopy.

    PubMed

    Edwards, Martin A; Whitworth, Anna L; Unwin, Patrick R

    2011-03-15

    Tip position modulation (TPM) involves moving the ultramicroelectrode (UME) tip of a scanning electrochemical microscope (SECM) perpendicular to the substrate in a sinusoidal fashion with a small amplitude compared to the tip/sample separation. The UME, which serves as the working electrode in a conventional voltammetric setup, is held at a potential to detect a species in solution at a transport-limited rate and the resulting current (ac and dc) is measured. This paper shows that tip-induced convection is an important factor in TPM. A model has been developed that describes the TPM response for the most challenging case of an inert substrate, where tip-induced convective effects compared to diffusion are greatest. The model provides an improved description of the ac response compared to existing treatment, as evidenced by the analysis of TPM-SECM approach curves (current-distance characteristics). The extension of the model to SECM-induced transfer is considered and it is shown that one can extract highly precise information on the permeability of a sample from such measurements, for which experiments and theory are compared. The prospects for using the technique more widely are highlighted and routes to improving the theoretical analysis further are briefly discussed. PMID:21322581

  15. Combination of detection and estimation tasks using channelized scanning linear observer for CT imaging systems

    NASA Astrophysics Data System (ADS)

    Tseng, Hsin-Wu; Fan, Jiahua; Kupinski, Matthew A.

    2015-03-01

    Maintaining or even improving image quality while lowering patient dose is always the desire in clinical CT imaging. Iterative reconstruction (IR) algorithms have been designed to help reduce dose and/or provide better image quality. In this work, the channelized scanning linear observer (CSLO) is applied to study the combination of detection and estimation task performance using CT image data. The purpose of this work is to design a task-­-based approach to quantitatively evaluate image-­-quality for different reconstruction algorithms. Low-­-contrast objects embedded in head-­-size and body-­-size phantoms are imaged multiple times and reconstructed by FBP and an IR algorithm for this study. Independent signal present and absent ROIs cropped from images are channelized by Difference of Gauss channels for CSLO training and testing. Estimation receiver operating characteristic (EROC) curves and the area under EROC curve (EAUC) are calculated by CSLO as the figure of merit. The One-­- Shot method is used to compute the variance of the EAUC values. Results suggest that the IR algorithm studied in this work could efficiently reduce the dose approximately 54% to achieve an image quality comparable to conventional FBP reconstruction for the combined detection and estimation tasks.

  16. Detecting Gene-Environment Interactions for a Quantitative Trait in a Genome-Wide Association Study.

    PubMed

    Zhang, Pingye; Lewinger, Juan Pablo; Conti, David; Morrison, John L; Gauderman, W James

    2016-07-01

    A genome-wide association study (GWAS) typically is focused on detecting marginal genetic effects. However, many complex traits are likely to be the result of the interplay of genes and environmental factors. These SNPs may have a weak marginal effect and thus unlikely to be detected from a scan of marginal effects, but may be detectable in a gene-environment (G × E) interaction analysis. However, a genome-wide interaction scan (GWIS) using a standard test of G × E interaction is known to have low power, particularly when one corrects for testing multiple SNPs. Two 2-step methods for GWIS have been previously proposed, aimed at improving efficiency by prioritizing SNPs most likely to be involved in a G × E interaction using a screening step. For a quantitative trait, these include a method that screens on marginal effects [Kooperberg and Leblanc, 2008] and a method that screens on variance heterogeneity by genotype [Paré et al., 2010] In this paper, we show that the Paré et al. approach has an inflated false-positive rate in the presence of an environmental marginal effect, and we propose an alternative that remains valid. We also propose a novel 2-step approach that combines the two screening approaches, and provide simulations demonstrating that the new method can outperform other GWIS approaches. Application of this method to a G × Hispanic-ethnicity scan for childhood lung function reveals a SNP near the MARCO locus that was not identified by previous marginal-effect scans. PMID:27230133

  17. Fast detection of deletion breakpoints using quantitative PCR.

    PubMed

    Abildinova, Gulshara; Abdrakhmanova, Zhanara; Tuchinsky, Helena; Nesher, Elimelech; Pinhasov, Albert; Raskin, Leon

    2016-06-16

    The routine detection of large and medium copy number variants (CNVs) is well established. Hemizygotic deletions or duplications in the large Duchenne muscular dystrophy DMD gene responsible for Duchenne and Becker muscular dystrophies are routinely identified using multiple ligation probe amplification and array-based comparative genomic hybridization. These methods only map deleted or duplicated exons, without providing the exact location of breakpoints. Commonly used methods for the detection of CNV breakpoints include long-range PCR and primer walking, their success being limited by the deletion size, GC content and presence of DNA repeats. Here, we present a strategy for detecting the breakpoints of medium and large CNVs regardless of their size. The hemizygous deletion of exons 45-50 in the DMD gene and the large autosomal heterozygous PARK2 deletion were used to demonstrate the workflow that relies on real-time quantitative PCR to narrow down the deletion region and Sanger sequencing for breakpoint confirmation. The strategy is fast, reliable and cost-efficient, making it amenable to widespread use in genetic laboratories. PMID:27333265

  18. Fast detection of deletion breakpoints using quantitative PCR

    PubMed Central

    Abildinova, Gulshara; Abdrakhmanova, Zhanara; Tuchinsky, Helena; Nesher, Elimelech; Pinhasov, Albert; Raskin, Leon

    2016-01-01

    Abstract The routine detection of large and medium copy number variants (CNVs) is well established. Hemizygotic deletions or duplications in the large Duchenne muscular dystrophy DMD gene responsible for Duchenne and Becker muscular dystrophies are routinely identified using multiple ligation probe amplification and array-based comparative genomic hybridization. These methods only map deleted or duplicated exons, without providing the exact location of breakpoints. Commonly used methods for the detection of CNV breakpoints include long-range PCR and primer walking, their success being limited by the deletion size, GC content and presence of DNA repeats. Here, we present a strategy for detecting the breakpoints of medium and large CNVs regardless of their size. The hemizygous deletion of exons 45-50 in the DMD gene and the large autosomal heterozygous PARK2 deletion were used to demonstrate the workflow that relies on real-time quantitative PCR to narrow down the deletion region and Sanger sequencing for breakpoint confirmation. The strategy is fast, reliable and cost-efficient, making it amenable to widespread use in genetic laboratories. PMID:27560363

  19. Fast detection of deletion breakpoints using quantitative PCR.

    PubMed

    Abildinova, Gulshara; Abdrakhmanova, Zhanara; Tuchinsky, Helena; Nesher, Elimelech; Pinhasov, Albert; Raskin, Leon

    2016-01-01

    The routine detection of large and medium copy number variants (CNVs) is well established. Hemizygotic deletions or duplications in the large Duchenne muscular dystrophy DMD gene responsible for Duchenne and Becker muscular dystrophies are routinely identified using multiple ligation probe amplification and array-based comparative genomic hybridization. These methods only map deleted or duplicated exons, without providing the exact location of breakpoints. Commonly used methods for the detection of CNV breakpoints include long-range PCR and primer walking, their success being limited by the deletion size, GC content and presence of DNA repeats. Here, we present a strategy for detecting the breakpoints of medium and large CNVs regardless of their size. The hemizygous deletion of exons 45-50 in the DMD gene and the large autosomal heterozygous PARK2 deletion were used to demonstrate the workflow that relies on real-time quantitative PCR to narrow down the deletion region and Sanger sequencing for breakpoint confirmation. The strategy is fast, reliable and cost-efficient, making it amenable to widespread use in genetic laboratories. PMID:27560363

  20. Detection model modeling and application for batch scans of cone-beam computed tomography

    NASA Astrophysics Data System (ADS)

    Huang, Kuidong; Zhang, Dinghua; Li, Mingjun; Wang, Kuyu

    2009-07-01

    Aiming at the artifact corrections for batch scans in Cone-Beam Computed Tomography (CBCT) system, the concept of detection model is proposed. Expressing the prior knowledge of CT system and scanned object properties by the detection model, the rapid artifact corrections are achieved based on the object knowledge, which can save the machine consumption, enhance the detection efficiency and improve the correction effect. Based on the Digital Radiography (DR) imaging conditions remained basically unchanged in the batch scans, the modeling method of detection model is established by getting the relevant information through the detected scanning for one of a batch of parts. Finally, the processing flow of CBCT scans and artifact corrections of a batch of parts based on the detection model is given, and some key problems in the flow are discussed to improve the practical operability of the method. The experimental result shows that the modeling method of detection model is feasible, and the rapid CBCT scans and effective artifact corrections can be realized based on the obtained detection model.

  1. 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

  2. Cluster detection of diseases in heterogeneous populations: an alternative to scan methods.

    PubMed

    Ramis, Rebeca; Gómez-Barroso, Diana; López-Abente, Gonzalo

    2014-05-01

    Cluster detection has become an important part of the agenda of epidemiologists and public health authorities, the identification of high- and low-risk areas is fundamental in the definition of public health strategies and in the suggestion of potential risks factors. Currently, there are different cluster detection techniques available, the most popular being those using windows to scan the areas within the studied region. However, when these areas are heterogeneous in populations' sizes, scan window methods can lead to inaccurate conclusions. In order to perform cluster detection over heterogeneously populated areas, we developed a method not based on scanning windows but instead on standard mortality ratios (SMR) using irregular spatial aggregation (ISA). Its extension, i.e. irregular spatial aggregation with covariates (ISAC), includes covariates with residuals from Poisson regression. We compared the performance of the method with the flexible shaped spatial scan statistic (FlexScan) using mortality data for stomach and bladder cancer for 8,098 Spanish towns. The results show a collection of clusters for stomach and bladder cancer similar to that detected by ISA and FlexScan. However, in general, clusters detected by FlexScan were bigger and include towns with SMR, which were not statistically significant. For bladder cancer, clusters detected by ISAC differed from those detected by ISA and FlexScan in shape and location. The ISA and ISAC methods could be an alternative to the traditional scan window methods for cluster detection over aggregated data when the areas under study are heterogeneous in terms of population. The simplicity and flexibility of the methods make them more attractive than methods based on more complicated algorithms. PMID:24893029

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

    NASA Astrophysics Data System (ADS)

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

    2012-01-01

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

  4. Automated detection of rare-event pathogens through time-gated luminescence scanning microscopy.

    PubMed

    Lu, Yiqing; Jin, Dayong; Leif, Robert C; Deng, Wei; Piper, James A; Yuan, Jingli; Duan, Yusheng; Huo, Yujing

    2011-05-01

    Many microorganisms have a very low threshold (<10 cells) to trigger infectious diseases, and, in these cases, it is important to determine the absolute cell count in a low-cost and speedy fashion. Fluorescent microscopy is a routine method; however, one fundamental problem has been associated with the existence in the sample of large numbers of nontarget particles, which are naturally autofluorescent, thereby obscuring the visibility of target organisms. This severely affects both direct visual inspection and the automated microscopy based on computer pattern recognition. We report a novel strategy of time-gated luminescent scanning for accurate counting of rare-event cells, which exploits the large difference in luminescence lifetimes between the lanthanide biolabels, >100 μs, and the autofluorescence backgrounds, <0.1 μs, to render background autofluorescence invisible to the detector. Rather than having to resort to sophisticated imaging analysis, the background-free feature allows a single-element photomultiplier to locate rare-event cells, so that requirements for data storage and analysis are minimized to the level of image confirmation only at the final step. We have evaluated this concept in a prototype instrument using a 2D scanning stage and applied it to rare-event Giardia detection labeled by a europium complex. For a slide area of 225 mm(2) , the time-gated scanning method easily reduced the original 40,000 adjacent elements (0.075 mm × 0.075 mm) down to a few "elements of interest" containing the Giardia cysts. We achieved an averaged signal-to-background ratio of 41.2 (minimum ratio of 12.1). Such high contrasts ensured the accurate mapping of all the potential Giardia cysts free of false positives or negatives. This was confirmed by the automatic retrieving and time-gated luminescence bioimaging of these Giardia cysts. Such automated microscopy based on time-gated scanning can provide novel solutions for quantitative diagnostics in advanced

  5. Comparison of envelope detection techniques in coherence scanning interferometry.

    PubMed

    Gianto, G; Salzenstein, F; Montgomery, P

    2016-08-20

    The aim of this work is to make a comparison of the most current signal processing techniques used to analyze the fringe signal in coherence scanning interferometry (CSI), a major technique for optical surface roughness measurements. We focus here on classical AM-FM signal-processing algorithms such as the Hilbert transform (HT), the five-sample adaptive (FSA), and the continuous wavelet transform (CWT). We have recently also introduced a new family of compact and robust algorithms using the Teager-Kaiser energy operator (TKEO). We propose an improved version of TKEO using a combination of different techniques of pre-filtering and demodulation processing to remove the noise and offset component and to retrieve the fringe envelope to either determine the surface height information or to separate adjacent transparent layers. In particular, as a pre-filtering approach, we have focused on empirical mode decomposition in combination with the Savitzky-Golay filter. An added Gaussian post-filtering is helpful for a precise peak extraction. The experimental results show that TKEO performs better than CWT in terms of computation time and provides a better surface extraction than HT and FSA. Results have been obtained on synthetic and real data taken from a layer of resin on a silicon substrate. PMID:27557001

  6. CW THz scanning transmission imaging for concealed object detection

    NASA Astrophysics Data System (ADS)

    Li, Qi; Yao, Rui; Yin, Qiguo; Ding, Shenghui; Wang, Qi

    2009-07-01

    In the paper, the two-dimensional THz imaging methods are described. The SIFIR-50 FPL Far-Infrared Laser is used as the THz source. The output frequency is 2.5THz in the experiment, because the THz laser operates steadily at this frequency. The P4-42 detector works at room temperature and offers relatively high sensitivity. The software of THz imaging system is self-designed, and it plays a crucial role in this imaging system because it controls nearly all the operations of this system, including the two-dimensional scanning, image data collection, image data storage, image display and image processing. Utilizing this setup, THz transmission images of concealed objects are obtained. In the experiment, a bottle cap and a plastic board covered by reflective materials are chosen as the imaging objects; paper and Teflon are placed before the object to test the transmission imaging effect. The experimental results show that this imaging system can generate clear images.

  7. Quantitative phase imaging applied to laser damage detection and analysis.

    PubMed

    Douti, Dam-Bé L; Chrayteh, Mhamad; Aknoun, Sherazade; Doualle, Thomas; Hecquet, Christophe; Monneret, Serge; Gallais, Laurent

    2015-10-01

    We investigate phase imaging as a measurement method for laser damage detection and analysis of laser-induced modification of optical materials. Experiments have been conducted with a wavefront sensor based on lateral shearing interferometry associated with a high-magnification optical microscope. The system has been used for the in-line observation of optical thin films and bulk samples, laser irradiated in two different conditions: 500 fs pulses at 343 and 1030 nm, and millisecond to second irradiation with a CO2 laser at 10.6 μm. We investigate the measurement of the laser-induced damage threshold of optical material by detection and phase changes and show that the technique realizes high sensitivity with different optical path measurements lower than 1 nm. Additionally, the quantitative information on the refractive index or surface modification of the samples under test that is provided by the system has been compared to classical metrology instruments used for laser damage or laser ablation characterization (an atomic force microscope, a differential interference contrast microscope, and an optical surface profiler). An accurate in-line measurement of the morphology of laser-ablated sites, from few nanometers to hundred microns in depth, is shown. PMID:26479612

  8. Comparison of qualitative and quantitative analysis of T2-weighted MRI scans in chronic-progressive multiple sclerosis

    NASA Astrophysics Data System (ADS)

    Adams, Hans-Peter; Wagner, Simone; Koziol, James A.

    1998-06-01

    Magnetic resonance imaging (MRI) is routinely used for the diagnosis of multiple sclerosis (MS), and for objective assessment of the extent of disease as a marker of treatment efficacy in MS clinical trials. The purpose of this study is to compare the evaluation of T2-weighted MRI scans in MS patients using a semi-automated quantitative technique with an independent assessment by a neurologist. Baseline, 6- month, and 12-month T2-weighted MRI scans from 41 chronic progressive MS patients were examined. The lesion volume ranged from 0.50 to 51.56 cm2 (mean: 8.08 cm2). Reproducibility of the quantitative technique was assessed by the re-evaluation of a random subset of 20 scans, the coefficient of variation of the replicate determinations was 8.2%. The reproducibility of the neurologist evaluations was assessed by the re-evaluation of a random subset of 10 patients. The rank correlation between the results of the two methods was 0.097, which did not significantly differ from zero. Disease-related activity in T2-weighted MRI scans is a multi-dimensional construct, and is not adequately summarized solely by determination of lesion volume. In this setting, image analysis software should not only support storage and retrieval as sets of pixels, but should also support links to an anatomical dictionary.

  9. Based on line scan CCD print image detection system

    NASA Astrophysics Data System (ADS)

    Zhang, Lifeng; Xie, Kai; Li, Tong

    2015-12-01

    In this paper, a new method based on machine vision is proposed for the defects of the traditional manual inspection of the quality of printed matter. With the aid of on line array CCD camera for image acquisition, using stepper motor as a sampling of drive circuit. Through improvement of driving circuit, to achieve the different size or precision image acquisition. In the terms of image processing, the standard image registration algorithm then, because of the characteristics of CCD-image acquisition, rigid body transformation is usually used in the registration, so as to achieve the detection of printed image.

  10. 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.

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

    SciTech Connect

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

    1987-09-01

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

  12. Technetium-99m Bone Scan and Panoramic Radiography in Detection of Bone Invasion by Oral Carcinoma

    PubMed Central

    John, Ani

    2014-01-01

    Objective: The correct extension of cancer in the bone usually remains undetected on static imaging which may lead to inadequate or over excision. The conventional radiography as well as other anatomical imaging modalities like computed tomography, magnetic resonance imaging often fails to detect functional changes in the bone. However, bone scinitigraphy is highly sensitive in detecting earlier changes in the bone but lack anatomical definition. The purpose of the study was to evaluate the accuracy of combining technetium-99m bone scan and panoramic radiography (Tc scan/PR) over using single diagnostic modality in detection of jaw bone invasion by oral carcinomas. The accuracy of these imaging modalities either alone or in combination were determined by comparing with the histopathological findings. Materials and Methods: Twenty patients with biopsy-proven oral malignant tumors were randomly selected from Oral Medicine and Radiology department over a period of two years. All patients were investigated preoperatively by Tc scan and PR. Lewis – Jones’s designed diagnostic criterion was applied on Tc scan/PR to evaluate bone involvement by cancer. To test the accuracy of Tc scan, PR and Tc scan/PR, their results were compared with the histopathological findings of resected specimen. Results: Hybrid Tc scan/PR had higher specificity, accuracy and positive predictive value (83.3%, 94.7%, 92.8%) than Tc scan alone (50%, 84.2%, 81.2%) and higher sensitivity and negative predictive value (100%, 100%) than PR (69.2%, 55.5%). Conclusion: Combination of Tc scan and PR was more accurate in detecting jaw bone invasion by oral squamous cell carcinoma than Tc scan and PR alone. PMID:24995244

  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. 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.

  15. Towards Alignment Independent Quantitative Assessment of Homology Detection

    PubMed Central

    Kliger, Yossef

    2006-01-01

    Identification of homologous proteins provides a basis for protein annotation. Sequence alignment tools reliably identify homologs sharing high sequence similarity. However, identification of homologs that share low sequence similarity remains a challenge. Lowering the cutoff value could enable the identification of diverged homologs, but also introduces numerous false hits. Methods are being continuously developed to minimize this problem. Estimation of the fraction of homologs in a set of protein alignments can help in the assessment and development of such methods, and provides the users with intuitive quantitative assessment of protein alignment results. Herein, we present a computational approach that estimates the amount of homologs in a set of protein pairs. The method requires a prevalent and detectable protein feature that is conserved between homologs. By analyzing the feature prevalence in a set of pairwise protein alignments, the method can estimate the number of homolog pairs in the set independently of the alignments' quality. Using the HomoloGene database as a standard of truth, we implemented this approach in a proteome-wide analysis. The results revealed that this approach, which is independent of the alignments themselves, works well for estimating the number of homologous proteins in a wide range of homology values. In summary, the presented method can accompany homology searches and method development, provides validation to search results, and allows tuning of tools and methods. PMID:17205117

  16. Line-scan hyperspectral imaging for real-time on-line poultry fecal detection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The preliminary results demonstrated that high speed line-scan hyperspectral imaging system has a potential for real-time online fecal detection during poultry processing. To improve detection accuracy, fully calibrated images both spatially and spectrally were acquired for further processing. In ad...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The preliminary results demonstrated that high speed line-scan hyperspectral imaging system has a potential for real-time online fecal detection during poultry processing. To improve detection accuracy, fully calibrated images both spatially and spectrally were acquired for further processing. In ad...

  18. AB021. Validation of real-world, non-research thoracic CT scans for quantitative analysis of COPD

    PubMed Central

    Dandurand, Ronald J.; Dandurand, Myriam; San José Estépar, Raúl; Bourbeau, Jean; Eidelman, David H.

    2016-01-01

    Background Quantitative CT (QCT) imaging plays an important role in phenotyping COPD and uses the voxel density histogram to measure total lung volume (TLV) and emphysema surrogates: low attenuation area (LAA) and lung density (LD). LD is often volume corrected using the predicted total lung capacity (TLC) to compensate for submaximal inspiration prior to image acquisition. QCT is carried out with careful attention to quality control including scanner make/model, calibration frequency, lung volume, acquisition protocol, and the use of contrast, and bears a financial and radiation cost. We wished to determine if: (I) thoracic CT scans acquired for clinical indications on a variety of scanners from different centres with varying calibration frequency, acquisition protocols and only simple breath holding instructions could yield reproducible data; (II) volume correcting LAA and LD using the pulmonary function test (PFT) measured TLC would compensate for submaximal inspiration better than using the predicted TLC; and (III) contrast infusion causes predictable changes in the QCT metrics TLV, LAA and LD. Methods A total of 82 subjects (67 COPD, 15 non-COPD) from a community respirology practice had at least 2 CT scans judged free of significant infiltrates, performed on 10 different models of scanner in 7 different community hospitals or radiology centres for clinical indications within a 13-month period and had pulmonary function tests performed respecting ATS criteria within 14 months of at least 1 CT scan. Images were analysed with Airway Inspector in ITALIC FONT (airwayinspector.acil-bwh.org) for LAA [<-950 Hounsfield Unit (HU)], LD (at 15th percentile + 1,000 HU) and TLV. 46 paired non-contrast scans (NC/NC) and 42 paired contrast/non-contrast scans (C/NC, 23 CT angio with early infusion, 19 routine contrast with late infusion) were used to construct identity plots for TLV, LAA, LD, and LAA and LD corrected for both predicted TLC and PFT measured TLC. LAA was volume

  19. Application of line scanning thermography for the detection of interlaminar disbonds in sandwich composite structures

    NASA Astrophysics Data System (ADS)

    Ley, Obdulia; Chung, Simon; Schutte, Jaco; Caiazzo, Anthony; Godinez, Valery; Bandos, Bruce

    2010-04-01

    An innovative Line Scanning Thermography (LST) inspection method is being developed as part of a Structural Damage Assessment System to access the health of in-service composite structures. The system utilizes a line heat source to thermally excite the surface inspected and an infrared detector to record the transient surface temperature variation and to detect regions of increased heat resistance associated to interlaminar disbonds, cracks and other imperfections found in composites structures. In this study our efforts towards the applications of LST for the analysis of carbon fiber sandwich composites will be discussed. The LST technique provides a quick and efficient methodology to scan wide areas rapidly. The scanning protocols developed for the detection of sub-surface disbonds (delamination) in composite sandwich parts will be presented. The results presented correspond to scans of test coupons with manufactured defects.

  20. Detection of Gold Nanoparticles Aggregation Growth Induced by Nucleic Acid through Laser Scanning Confocal Microscopy

    PubMed Central

    Gary, Ramla; Carbone, Giovani; Petriashvili, Gia; De Santo, Maria Penelope; Barberi, Riccardo

    2016-01-01

    The gold nanoparticle (GNP) aggregation growth induced by deoxyribonucleic acid (DNA) is studied by laser scanning confocal and environmental scanning electron microscopies. As in the investigated case the direct light scattering analysis is not suitable, we observe the behavior of the fluorescence produced by a dye and we detect the aggregation by the shift and the broadening of the fluorescence peak. Results of laser scanning confocal microscopy images and the fluorescence emission spectra from lambda scan mode suggest, in fact, that the intruding of the hydrophobic moiety of the probe within the cationic surfactants bilayer film coating GNPs results in a Förster resonance energy transfer. The environmental scanning electron microscopy images show that DNA molecules act as template to assemble GNPs into three-dimensional structures which are reminiscent of the DNA helix. This study is useful to design better nanobiotechnological devices using GNPs and DNA. PMID:26907286

  1. Detection of Gold Nanoparticles Aggregation Growth Induced by Nucleic Acid through Laser Scanning Confocal Microscopy.

    PubMed

    Gary, Ramla; Carbone, Giovani; Petriashvili, Gia; De Santo, Maria Penelope; Barberi, Riccardo

    2016-01-01

    The gold nanoparticle (GNP) aggregation growth induced by deoxyribonucleic acid (DNA) is studied by laser scanning confocal and environmental scanning electron microscopies. As in the investigated case the direct light scattering analysis is not suitable, we observe the behavior of the fluorescence produced by a dye and we detect the aggregation by the shift and the broadening of the fluorescence peak. Results of laser scanning confocal microscopy images and the fluorescence emission spectra from lambda scan mode suggest, in fact, that the intruding of the hydrophobic moiety of the probe within the cationic surfactants bilayer film coating GNPs results in a Förster resonance energy transfer. The environmental scanning electron microscopy images show that DNA molecules act as template to assemble GNPs into three-dimensional structures which are reminiscent of the DNA helix. This study is useful to design better nanobiotechnological devices using GNPs and DNA. PMID:26907286

  2. Scan-rescan reproducibility of quantitative assessment of inflammatory carotid atherosclerotic plaque using dynamic contrast-enhanced 3T CMR in a multi-center study

    PubMed Central

    2014-01-01

    Background The aim of this study is to investigate the inter-scan reproducibility of kinetic parameters in atherosclerotic plaque using dynamic contrast-enhanced (DCE) cardiovascular magnetic resonance (CMR) in a multi-center setting at 3T. Methods Carotid arteries of 51 subjects from 15 sites were scanned twice within two weeks on 3T scanners using a previously described DCE-CMR protocol. Imaging data with protocol compliance and sufficient image quality were analyzed to generate kinetic parameters of vessel wall, expressed as transfer constant (Ktrans) and plasma volume (vp). The inter-scan reproducibility was evaluated using intra-class correlation coefficient (ICC) and coefficient of variation (CV). Power analysis was carried out to provide sample size estimations for future prospective study. Results Ten (19.6%) subjects were found to suffer from protocol violation, and another 6 (11.8%) had poor image quality (n = 6) in at least one scan. In the 35 (68.6%) subjects with complete data, the ICCs of Ktrans and vp were 0.65 and 0.28, respectively. The CVs were 25% and 62%, respectively. The ICC and CV for vp improved to 0.73 and 28% in larger lesions with analyzed area larger than 25 mm2. Power analysis based on the measured CV showed that 50 subjects per arm are sufficient to detect a 20% difference in change of Ktrans over time between treatment arms with 80% power without consideration of the dropout rate. Conclusion The result of this study indicates that quantitative measurement from DCE-CMR is feasible to detect changes with a relatively modest sample size in a prospective multi-center study despite the limitations. The relative high dropout rate suggested the critical needs for intensive operator training, optimized imaging protocol, and strict quality control in future studies. PMID:25084698

  3. Scanning image detection (SID) system for conventional transmission electron microscope (CTEM) images.

    PubMed

    Tanji, T; Tomita, M; Kobayashi, H

    1990-08-01

    A new image detection system has been developed to display transmission electron microscope (TEM) images on a CRT without a video camera system. Deflection coils placed in both the upper space of an objective lens and in the lower space of the first intermediate lens scan a small electron probe simultaneously. The electrical signal acquired through an improved scintillator and a photomultiplier is synchronized with the scanning signal and displayed in a similar fashion to a conventional scanning TEM (STEM) instrument. A preliminary system using a 100 kV conventional TEM (CTEM) equipped with a hairpin-type electron gun, produced an image with a spatial resolution of 1 nm. PMID:2391565

  4. Automatic landmark detection and scan range delimitation for topogram images using hierarchical network

    NASA Astrophysics Data System (ADS)

    Zhang, Wei; Mantlic, Frederic; Zhou, Shaohua K.

    2010-03-01

    The topogram is a 2D projection image of human body formed using a Computed Tomography (CT) scanner. It could be used to delimitate the desired scan range for further precise 3D CT scan. In this paper, we present a robust and efficient system for automatically determining scan ranges and their associated anatomical landmarks for topogram images. The system could handle the cases when only about 50% of the desired regions are visible. The robustness of our system can be attributed to three key ingredients: 1. The detection is based on a hierarchical network; 2. Network optimization is based on sequentially optimizing a set of subnetworks; 3. The detection probability is further refined based on the detection context. Extensive experiments (including external testing) on over 1000 topogram images show that our approach works robustly and efficiently even on very challenging data.

  5. 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)

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

    PubMed

    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

    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

  8. 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.

  9. 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.

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

    PubMed

    Jentsch, Holger; Mozaffari, Eshan; Jonas, Ludwig

    2013-08-01

    The aim of this study was to quantify the influence of different mouth rinses on dental plaque. Wearing splints with enamel pieces 24 volunteers rinsed with essential oils, amine/stannous fluoride, or chlorhexidine digluconate (0.12%) mouth rinses. After 24, 48, 72, and 96 h the enamel pieces were analyzed by scanning electron microscopy. The counts of cocci and bacilli in different plaque layers and the plaque thickness were almost similar using essential oils and amine/stannous fluoride. These results differed significantly from those of chlorhexidine digluconate mouth rinses. The results for plaque thickness were without significant differences between the groups at any appointment. PMID:23758106

  11. 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.

  12. 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.

  13. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

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

  15. Automatic detection of axillary lymphadenopathy on CT scans of untreated chronic lymphocytic leukemia patients

    NASA Astrophysics Data System (ADS)

    Liu, Jiamin; Hua, Jeremy; Chellappa, Vivek; Petrick, Nicholas; Sahiner, Berkman; Farooqui, Mohammed; Marti, Gerald; Wiestner, Adrian; Summers, Ronald M.

    2012-03-01

    Patients with chronic lymphocytic leukemia (CLL) have an increased frequency of axillary lymphadenopathy. Pretreatment CT scans can be used to upstage patients at the time of presentation and post-treatment CT scans can reduce the number of complete responses. In the current clinical workflow, the detection and diagnosis of lymph nodes is usually performed manually by examining all slices of CT images, which can be time consuming and highly dependent on the observer's experience. A system for automatic lymph node detection and measurement is desired. We propose a computer aided detection (CAD) system for axillary lymph nodes on CT scans in CLL patients. The lung is first automatically segmented and the patient's body in lung region is extracted to set the search region for lymph nodes. Multi-scale Hessian based blob detection is then applied to detect potential lymph nodes within the search region. Next, the detected potential candidates are segmented by fast level set method. Finally, features are calculated from the segmented candidates and support vector machine (SVM) classification is utilized for false positive reduction. Two blobness features, Frangi's and Li's, are tested and their free-response receiver operating characteristic (FROC) curves are generated to assess system performance. We applied our detection system to 12 patients with 168 axillary lymph nodes measuring greater than 10 mm. All lymph nodes are manually labeled as ground truth. The system achieved sensitivities of 81% and 85% at 2 false positives per patient for Frangi's and Li's blobness, respectively.

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

    PubMed

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

    2013-12-30

    Symptom dimensions of schizophrenia are likely to be the intermediate phenotypes under the control of disease-susceptibility genes, or separate traits related to disease-modifier genes. This study aimed to identify chromosomal loci linked to symptom dimensions of schizophrenia through genome-wide quantitative trait locus (QTL) linkage analysis. The study subjects consisted of 56 families with 183 members including 123 affected individuals. Symptom evaluations were performed on lifetime basis. Through principal component factor analysis, eight quantitative phenotypes representing symptom dimensions were identified. Genotyping was done for 6008 SNP markers, and genome-wide QTL linkage analysis was performed. No symptom dimension showed a significant linkage attaining genome-wide empirical thresholds. We observed seven regions yielding linkage signals attaining genome-wide empirical thresholds for suggestive linkage (NPL Z score = 2.78-3.49); chromosome 15q26.1 for 'non-paranoid delusion factor', 2p24.3 and 7q31.1 for 'prodromal impairment factor', 1q32.1, 9p21.3, and 9q31.2 for 'negative symptom factor', and 10p13 for 'disorganization factor'. Among these loci, chromosome 2p24.3 and 1q32.1 overlap with susceptibility loci of schizophrenia identified in our previous linkage studies. This study suggests the existence of genetic loci related to various clinical features of schizophrenia. Further genetic analyses for these dimensional phenotypes are warranted. PMID:24035701

  17. 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.

  18. Frequency-scanning MALDI linear ion trap mass spectrometer for large biomolecular ion detection.

    PubMed

    Lu, I-Chung; Lin, Jung Lee; Lai, Szu-Hsueh; Chen, Chung-Hsuan

    2011-11-01

    This study presents the first report on the development of a matrix-assisted laser desorption ionization (MALDI) linear ion trap mass spectrometer for large biomolecular ion detection by frequency scan. We designed, installed, and tested this radio frequency (RF) scan linear ion trap mass spectrometer and its associated electronics to dramatically extend the mass region to be detected. The RF circuit can be adjusted from 300 to 10 kHz with a set of operation amplifiers. To trap the ions produced by MALDI, a high pressure of helium buffer gas was employed to quench extra kinetic energy of the heavy ions produced by MALDI. The successful detection of the singly charged secretory immunoglobulin A ions indicates that the detectable mass-to-charge ratio (m/z) of this system can reach ~385 000 or beyond. PMID:21932813

  19. Quantitative discrimination of water and hydrocarbons in porous media by magnetization prepared centric-scan SPRITE.

    PubMed

    Li, Linqing; Marica, Florin; Chen, Quan; MacMillan, Bryce; Balcom, Bruce J

    2007-06-01

    MRI has considerable potential as a non-destructive probe of porous media, offering the possibility of rapid quantification of local oil and water content. This potential has not yet, however, been completely realized. In this paper, we explore a general magnetization preparation approach to the discrimination of water and oil in a model, representative, porous medium. These measurements have, as a common element, a centric scan pure phase encode readout based on the SPRITE methodology. Magnetization preparation permits facile T1, T2 and diffusion coefficient mapping as the basis for oil and water discrimination. Diffusion coefficient mapping proved to be the most robust approach to discrimination of oil and water. These methods are illustrated through static experiments and a dynamic immiscible fluid displacement experiment. PMID:17428712

  20. 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.

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

    PubMed

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

    2014-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  3. 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.

  4. On the power for linkage detection using a test based on scan statistics.

    PubMed

    Hernández, Sonia; Siegmund, David O; de Gunst, Mathisca

    2005-04-01

    We analyze some aspects of scan statistics, which have been proposed to help for the detection of weak signals in genetic linkage analysis. We derive approximate expressions for the power of a test based on moving averages of the identity by descent allele sharing proportions for pairs of relatives at several contiguous markers. We confirm these approximate formulae by simulation. The results show that when there is a single trait-locus on a chromosome, the test based on the scan statistic is slightly less powerful than that based on the customary allele sharing statistic. On the other hand, if two genes having a moderate effect on a trait lie close to each other on the same chromosome, scan statistics improve power to detect linkage. PMID:15772104

  5. Dark-Field Scanning Transmission Ion Microscopy via Direct Detection of Transmitted Helium Ions with a Multichannel Plate

    NASA Astrophysics Data System (ADS)

    Woehl, Taylor; White, Ryan; Keller, Robert

    A multichannel plate was used as an ion sensitive transmission detector in a commercial helium ion microscope for annular dark-field imaging of nanomaterials, i.e. scanning transmission ion microscopy. In contrast to previous transmission helium ion microscopy approaches that used secondary electron conversion holders, our new approach directly detects transmitted helium ions on an annular detector. Monte Carlo simulations are used to predict detector collection angles at which annular dark-field images with atomic number contrast are obtained. We demonstrate atomic number contrast imaging via scanning transmission ion imaging of silica-coated gold nanoparticles and magnetite nanoparticles. While the resolution of this transmission technique is limited by beam broadening in the substrate, we image magnetite nanoparticles with high contrast on a relatively thick silicon nitride substrate. We expect this new approach to annular dark-field scanning transmission ion microscopy will open avenues for more quantitative ion imaging techniques, such as direct mass-thickness determination, and advance fundamental understanding of underlying ion scattering mechanisms leading to image formation.

  6. Detection of gait events using an F-Scan in-shoe pressure measurement system.

    PubMed

    Catalfamo, Paola; Moser, David; Ghoussayni, Salim; Ewins, David

    2008-10-01

    A portable system capable of accurate detection of initial contact (IC) and foot off (FO) without adding encumbrance to the subject would be extremely useful in many gait analysis applications. Force platforms represent the gold standard method for determining these events and other methods including foot switches and kinematic data have also been proposed. These approaches, however, present limitations in terms of the number of steps that can be analysed per trial, the portability for outdoor measurements or the information needed beforehand. The purpose of this study was to evaluate the F-Scan((R)) Mobile pressure measurement system when detecting IC and FO. Two methods were used, one was the force detection (FD) in-built algorithm used by F-Scan software and a new area detection (AD) method using the loaded area during the gait cycle. Both methods were tested in ten healthy adults and compared with the detection provided by a kinetic detection (KT) algorithm. The absolute mean differences between KT and FD were (mean+/-standard deviation) 42+/-11 ms for IC and 37+/-11 ms for FO. The absolute mean differences between KT and AD were 22+/-9 ms for IC and 10+/-4 ms for FO. The AD method remained closer to KT detection for all subjects providing sufficiently accurate detection of both events and presenting advantages in terms of portability, number of steps analysed per trial and practicality as to make it a system of choice for gait event detection. PMID:18468441

  7. 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.

  8. 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.

  9. 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.

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

    PubMed

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

    2015-08-21

    In this paper, we present a smartphone-readable barcode assay for the qualitative detection of methyl parathion residues, a toxic organophosphorus pesticide that is popularly used in agriculture worldwide. The detection principle is based on the irreversible inhibition of the enzymatic activity of acetylcholinesterase (AchE) by methyl parathion; AchE catalytically hydrolyzes acetylthiocholine iodine to thiocholine that in turn dissociates dithiobis-nitrobenzoate to produce a yellow product (deprotonated thio-nitrobenzoate). The yellow intensity of the product was confirmed to be inversely dependent on the concentration of the pesticide. We have designed a barcode-formatted assay chip by using a PDMS (polydimethylsiloxane) channel plate (as the reaction reservoir), situated under a printed partial barcode, to complete the whole barcode such that it can be directly read by a barcode scanning app installed on a smartphone. The app is able to qualitatively present the result of the pesticide test; the absence or a low concentration of methyl parathion results in the barcode reading as "-", identifying the test as negative for pesticides. Upon obtaining a positive result (the app reads a "+" character), the captured image can be further analyzed to quantitate the methyl parathion concentration in the sample. Besides the portability and simplicity, this mobile-app based colorimetric barcode assay compares favorably with the standard spectrophotometric method. PMID:26087169

  11. Quantitative scanning thermal microscopy based on determination of thermal probe dynamic resistance.

    PubMed

    Bodzenta, J; Juszczyk, J; Chirtoc, M

    2013-09-01

    Resistive thermal probes used in scanning thermal microscopy provide high spatial resolution of measurement accompanied with high sensitivity to temperature changes. At the same time their sensitivity to variations of thermal conductivity of a sample is relatively low. In typical dc operation mode the static resistance of the thermal probe is measured. It is shown both analytically and experimentally that the sensitivity of measurement can be improved by a factor of three by measuring the dynamic resistance of a dc biased probe superimposed with small ac current. The dynamic resistance can be treated as a complex value. Its amplitude represents the slope of the static voltage-current U-I characteristic for a given I while its phase describes the delay between the measured ac voltage and applied ac current component in the probe. The phase signal also reveals dependence on the sample thermal conductivity. Signal changes are relatively small but very repeatable. In contrast, the difference between dynamic and static resistance has higher sensitivity (the same maximum value as that of the 2nd and 3rd harmonics), and also much higher amplitude than higher harmonics. The proposed dc + ac excitation scheme combines the benefits of dc excitation (mechanical stability of probe-sample contact, average temperature control) with those of ac excitation (base-line stability, rejection of ambient temperature influence, high sensitivity, lock-in signal processing), when the experimental conditions prohibit large ac excitation. PMID:24089831

  12. 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.

  13. Importance of quantum correction for the quantitative simulation of photoexcited scanning tunneling spectra of semiconductor surfaces

    NASA Astrophysics Data System (ADS)

    Schnedler, M.; Dunin-Borkowski, R. E.; Ebert, Ph.

    2016-05-01

    Photoexcited scanning tunneling spectroscopy is a promising technique for the determination of carrier concentrations, surface photovoltages, and potentials of semiconductors with atomic spatial resolution. However, extraction of the desired quantities requires computation of the electrostatic potential induced by the proximity of the tip and the tunnel current. This calculation is based on an accurate solution of the Poisson as well as the continuity equations for the tip-vacuum-semiconductor system. For this purpose, the carrier current densities are modeled by classical drift and diffusion equations. However, for small tip radii and highly doped materials, the drift and diffusion transport model significantly overestimates a semiconductor's carrier concentration near the surface, making the quantification of physical properties impossible. In this paper, we apply quantum correction to the drift and diffusion model, in order to account for the so-called quantum compressibility, i.e., reduced compressibility of the carrier gas due to the Pauli principle, in the region of the tip-induced band bending. We compare carrier concentrations, potentials, and tunnel currents derived with and without quantum correction for GaN (10 1 ¯0 ) and GaAs(110) surfaces to demonstrate its necessity.

  14. 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.

  15. Quantitative high-angle annular dark field scanning transmission electron microscopy for materials science

    NASA Astrophysics Data System (ADS)

    Petrova, Rumyana V.

    Scanning transmission electron microscopy (STEM) has been widely used for characterization of materials; to identify micro- and nano-structures within a sample and to analyze crystal and defect structures. High-angle annular dark field (HAADF) STEM imaging using atomic number (Z) contrast has proven capable of resolving atomic structures with better than 2 A lateral resolution. In this work, the HAADF STEM imaging mode is used in combination with multislice simulations. This combination is applied to the investigation of the temperature dependence of the intensity collected by the HAADF detector in silicon, and to convergent beam electron diffraction (CBED) to measure the degree of chemical order in intermetallic nanoparticles. The experimental and simulation results on the high-angle scattering of 300 keV electrons in crystalline silicon provide a new contribution to the understanding of the temperature dependence of the HAADF intensity. In the case of 300 keV, the average high-angle scattered intensity slightly decreases as the temperature increases from 100 K to 300 K, and this is different from the temperature dependence at 100 keV and 200 keV where HAADF intensity increases with temperature, as had been previously reported by other workers. The L10 class of hard magnetic materials has attracted continuous attention as a candidate for high-density magnetic recording media, as this phase is known to have large magnetocrystalline anisotropy, with magnetocrystalline anisotropy constant, Ku, strongly dependent on the long-range chemical order parameter, S. A new method is developed to assess the degree of chemical order in small FePt L1 0 nanoparticles by implementing a CBED diffraction technique. Unexpectedly, the degree of order of individual particles is highly variable and not a simple function of particle size or sample composition. The particle-to-particle variability observed is an important new aspect to the understanding of phase transformations in

  16. 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.

  17. 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.

  18. Surface sensitivity in scanning transmission x-ray microspectroscopy using secondary electron detection.

    PubMed

    Hub, C; Wenzel, S; Raabe, J; Ade, H; Fink, R H

    2010-03-01

    The successful integration of electron detection into an existing scanning transmission x-ray microspectroscope (STXM) at the Swiss Light Source is demonstrated. In conventional x-ray detection using a photomultiplier, STXM offers mainly bulk sensitivity combined with high lateral resolution. However, by implementation of a channeltron electron multiplier, the surface sensitivity can be established by the detection of secondary electrons emitted from the sample upon resonant excitation. We describe the experimental setup and discuss several relevant aspects, in particular the schemes to correct for self-absorption in the specimen due to back illumination in case of thicker films. PMID:20370182

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

  20. 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.

  1. 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.

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

    PubMed Central

    Hashmi, Faiz R.; Elfandi, Khaled O.

    2016-01-01

    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. PMID:27433300

  3. 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. PMID:27433300

  4. Confocal scanning laser microscopy with complementary 3D image analysis allows quantitative studies of functional state of ionoregulatory cells in the Nile tilapia (Oreochromis niloticus) following salinity challenge.

    PubMed

    Fridman, Sophie; Rana, Krishen J; Bron, James E

    2013-04-01

    The development of a novel three-dimensional image analysis technique of stacks generated by confocal laser scanning microscopy is described allowing visualization of mitochondria-rich cells (MRCs) in the seawater-adapted Nile tilapia in relation to their spatial location. This method permits the assessment and classification of both active and nonactive MRCs based on the distance of the top of the immunopositive cell from the epithelial surface. In addition, this technique offers the potential for informative and quantitative studies, for example, densitometric and morphometric measurements based on MRC functional state. Confocal scanning laser microscopy used with triple staining whole-mount immunohistochemistry was used to detect integumental MRCs in the yolk-sac larvae tail of the Nile tilapia following transfer from freshwater to elevated salinities, that is, 12.5 and 20 ppt. Mean active MRC volume was always significantly larger and displayed a greater staining intensity (GLM; P<0.05) than nonactive MRCs. Following transfer, the percentage of active MRCs was seen to increase as did MRC volume (GLM; P<0.05). PMID:23390074

  5. 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.

  6. Alternating current measurements in scanning electrochemical microscopy, part 2: detection of adsorbates.

    PubMed

    Trinh, Dao; Keddam, Michel; Novoa, Xosé Ramón; Vivier, Vincent

    2011-08-01

    A scanning electrochemical microscope (SECM) in ac mode is used for the characterisation of the adsorption process during the hydrogen evolution reaction (HER) in sulfuric acid solution. It is shown that this technique allows quantitative analysis of the adsorption process, and measurements of the differential capacitance with the frequency as parameter are obtained. The time constant for relaxation of adsorbed hydrogen (H(ads)) is approximately 2 Hz, and analysis of the Nyquist plot allows direct evaluation of the charge involved. In addition, the direct comparison of the usual electrochemical impedance data and ac-SECM results obtained simultaneously permits characterisation of processes occurring at the surface and in solution. PMID:21630411

  7. Detection of quantitative trait loci for growth and carcass composition in cattle.

    PubMed

    Casas, E; Shackelford, S D; Keele, J W; Koohmaraie, M; Smith, T P L; Stone, R T

    2003-12-01

    The objective of the present study was to detect quantitative trait loci for economically important traits in a family from a Bos indicus x Bos taurus sire. A Brahman x Hereford sire was used to develop a half-sib family (n = 547). The sire was mated to Bos taurus cows. Traits analyzed were birth (kg) and weaning weights (kg); hot carcass weight (kg); marbling score; longissimus area (cm2); USDA yield grade; estimated kidney, pelvic, and heart fat (%); fat thickness (cm); fat yield (%); and retail product yield (%). Meat tenderness was measured as Warner-Bratzler shear force (kg) at 3 and 14 d postmortem. Two hundred and thirty-eight markers were genotyped in 185 offspring. One hundred and thirty markers were used to genotype the remaining 362 offspring. A total of 312 markers were used in the final analysis. Seventy-four markers were common to both groups. Significant QTL (expected number of false-positives < 0.05) were observed for birth weight and longissimus area on chromosome 5, for longissimus area on chromosome 6, for retail product yield on chromosome 9, for birth weight on chromosome 21, and for marbling score on chromosome 23. Evidence suggesting (expected number of false-positives < 1) the presence of QTL was detected for several traits. Putative QTL for birth weight were detected on chromosomes 1, 2, and 3, and for weaning weight on chromosome 29. For hot carcass weight, QTL were detected on chromosomes 10, 18, and 29. Four QTL for yield grade were identified on chromosomes 2, 11, 14, and 19. Three QTL for fat thickness were detected on chromosomes 2, 3, 7, and 14. For marbling score, QTL were identified on chromosomes 3, 10, 14, and 27. Four QTL were identified for retail product yield on chromosomes 12, 18, 19, and 29. A QTL for estimated kidney, pelvic, and heart fat was detected on chromosome 15, and a QTL for meat tenderness measured as Warner-Bratzler shear force at 3 d postmortem was identified on chromosome 20. Two QTL were detected for meat

  8. 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.

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

    PubMed Central

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

    2015-01-01

    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. PMID:25872047

  10. Reliability of void detection in structural ceramics by use of scanning laser acoustic microscopy

    NASA Technical Reports Server (NTRS)

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

    1986-01-01

    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.

  11. 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.

  12. Reliability of void detection in structural ceramics by use of scanning laser acoustic microscopy

    SciTech Connect

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

    1986-05-01

    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. 20 references.

  13. 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

  14. 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.

  15. Technetium pyrophosphate scanning in the detection of acute myocardial infarction: clinical experience.

    PubMed Central

    Ko, P.; Kostuk, W. J.; Deatrich, D.

    1977-01-01

    Technetium-99m-stannous pyrophosphate (99mTc-PYP) accumulates in acutely infarcted myocardium and can be detected by scintiscanning. The clinical value of 99mTc-PYP scintiscanning was studied in 83 patients 6 hours to 21 days after the onset of acute chest pain. In 12 patients with normal electrocardiograms and serum enzyme values no uptake of 99mTc-PYP was detected on the scintigrams. Of 44 patients with electrocardiographic or enzyme evidence, or both, of acute myocardial infarction the scintigrams were positive in 31, "questionable" in 2 and negative in 11; no positive scan was obtained within 12 hours of the onset of pain, and the scans generally remained positive for up to 5 days. In 24 patients with evidence of prolonged myocardial ischemia the scans were positive in 2, questionable in 4 and negative in 18. The scans were negative in each of three patients with acute or constrictive pericarditis. Localization by electrocardiography and scintiscanning correlated nearly perfectly for transmural infarcts but subendocardial infarcts could not always be localized precisely by scintiscanning. The infarct area (total area of 99mTc-PYP uptake) correlated well with the peak serum value of creatine phosphokinase. Images FIG. 1 FIG. 2 FIG. 3 FIG. 5 PMID:189887

  16. A capillary holder for scanning detection of capillary isoelectric focusing with laser-induced fluorescence.

    PubMed

    Takahashi, Katsuyoshi; Maruo, Yuji; Kitamori, Takehiko; Shimura, Kiyohito

    2009-02-01

    A holder for a 12 cm long capillary was designed for scanning LIF detection of CIEF. The polyimide coat of a fused-silica capillary has been removed, and 1.5 mm diameter flanges have been attached near both ends. The holder is fixed on the stage of a fluorescence microscope via a translational stage, and a capillary guide is directly fixed on the microscope stage. The guide has a groove and a pressure plate for the capillary to slide in. The holder has two pulling plates with slits of 1 mm to accept the capillary just inside the flanges. The slits and the groove of the guide have been aligned. The motion of the translational stage brings the pulling plate into contact with the flange at the pulled side, and slides the capillary through the guide. The other end of the capillary is free and produces no strain on the capillary. When the motion of the stage is reversed, an unstrained contact is achieved at the other end. The baseline noise from scanning was only 50% larger than that without scanning. The fluorescence-signal variation during scanning was about 4% of the total signal, which was about twice that without scanning. PMID:19142915

  17. High bandwidth secondary electron detection in variable pressure scanning electron microscopy using a Frisch grid

    NASA Astrophysics Data System (ADS)

    Morgan, S. W.; Phillips, M. R.

    2008-03-01

    The bandwidth and contrast of secondary electron (SE) images obtained using variable pressure scanning electron microscopy are enhanced when a grounded Frisch grid is placed between the SE detecting anode and the negatively biased stage. The improvement in SE image quality occurs as a consequence of the grounded Frisch grid electrostatically screening the 'slow' induced ion current signal, generated below the grid, from the induced current detected above the grid by the anode. Ion induced artefacts, such as image smearing at fast scan rates, are virtually eliminated using a Frisch grid. Gas amplification data are presented to illustrate that gas gain can be optimized by varying the Frisch grid-stage (amplification region) separation Frisch grid-anode (drift region) separation and stage bias.

  18. 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

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

    SciTech Connect

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

    2005-11-07

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

  20. 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.

  1. An electrochemical immunosensor for quantitative detection of ficolin-3.

    PubMed

    San, Lili; Zeng, Dongdong; Song, Shiping; Zuo, Xiaolei; Zhang, Huan; Wang, Chenguang; Wu, Jiarui; Mi, Xianqiang

    2016-06-24

    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. PMID:27183363

  2. 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.

  3. Detection of vertical root fractures in endodontically treated teeth by a cone beam computed tomography scan.

    PubMed

    Hassan, Bassam; Metska, Maria Elissavet; Ozok, Ahmet Rifat; van der Stelt, Paul; Wesselink, Paul Rudolf

    2009-05-01

    Our aim was to compare the accuracy of cone beam computed tomography (CBCT) scans and periapical radiographs (PRs) in detecting vertical root fractures (VRFs) and to assess the influence of root canal filling (RCF) on fracture visibility. Eighty teeth were endodontically prepared and divided into four groups. The teeth in groups A and B were artificially fractured, and teeth in groups C and D were not. Groups A and C were root filled. Four observers evaluated the CBCT scans and PR images. Sensitivity and specificity for VRF detection of CBCT were 79.4% and 92.5% and for PR were 37.1% and 95%, respectively. The specificity of CBCT was reduced (p = 0.032) by the presence of RCF, but its overall accuracy was not influenced (p = 0.654). Both the sensitivity (p = 0.006) and overall accuracy (p = 0.008) of PRs were reduced by the presence of RCF. The results showed an overall higher accuracy for CBCT (0.86) scans than PRs (0.66) for detecting VRF. PMID:19410091

  4. Solid-phase sequence scanning for drug resistance detection in tuberculosis.

    PubMed

    Head, S R; Parikh, K; Rogers, Y H; Bishai, W; Goelet, P; Boyce-Jacino, M T

    1999-04-01

    DNA chip arrays hold considerable promise for diagnostic sequencing of polymerase chain reaction (PCR) products. To date, however, arrays have been relatively expensive, complex to use and difficult to interpret, preventing their adaptation to the clinical lab. A moderate density array method has been developed that enables efficient, easy-to-interpret and robust solid-phase PCR product sequencing. Here, the results of Mycobacterium tuberculosis rifampin resistance mutation detection by primer-extension-based sequence scanning of the rpo B gene of M. tuberculosis are presented. Rifampin resistant clinical isolates were identified in as little as 1 h post PCR amplification with visual results detection. PMID:10208797

  5. 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.

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

    NASA Astrophysics Data System (ADS)

    Wang, Tai-Chi; Phoa, Frederick Kin Hing

    2016-03-01

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

  7. 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. PMID:27153003

  8. A new method of building footprints detection using airborne laser scanning data and multispectral image

    NASA Astrophysics Data System (ADS)

    Luo, Yiping; Jiang, Ting; Gao, Shengli; Wang, Xin

    2010-10-01

    It presents a new approach for detecting building footprints in a combination of registered aerial image with multispectral bands and airborne laser scanning data synchronously obtained by Leica-Geosystems ALS40 and Applanix DACS-301 on the same platform. A two-step method for building detection was presented consisting of selecting 'building' candidate points and then classifying candidate points. A digital surface model(DSM) derived from last pulse laser scanning data was first filtered and the laser points were classified into classes 'ground' and 'building or tree' based on mathematic morphological filter. Then, 'ground' points were resample into digital elevation model(DEM), and a Normalized DSM(nDSM) was generated from DEM and DSM. The candidate points were selected from 'building or tree' points by height value and area threshold in nDSM. The candidate points were further classified into building points and tree points by using the support vector machines(SVM) classification method. Two classification tests were carried out using features only from laser scanning data and associated features from two input data sources. The features included height, height finite difference, RGB bands value, and so on. The RGB value of points was acquired by matching laser scanning data and image using collinear equation. The features of training points were presented as input data for SVM classification method, and cross validation was used to select best classification parameters. The determinant function could be constructed by the classification parameters and the class of candidate points was determined by determinant function. The result showed that associated features from two input data sources were superior to features only from laser scanning data. The accuracy of more than 90% was achieved for buildings in first kind of features.

  9. AB029. The clinical significance of RigiScan plus detection

    PubMed Central

    Gao, Bing; Mu, Hongtao; Zhang, Zhichao; Yuan, Yiming; Peng, Jing; Xin, Zhongcheng; Guo, Yinglu

    2016-01-01

    Erectile dysfunction (ED) is a common disease in male outpatient service, the penis hardness testing of ED in the clinical diagnosis has important significance, past some detection methods, such as nocturnal penile tumescence monitoring (NPT) due to time-consuming is not easy in outpatient service and a vasodilator agent intervention tests such as color Doppler detection due to the injection of drugs in the penis is difficult for patients to accept. In 1965 night rapid eye movement sleep phase 3–5 times of penile erection phenomenon was first reported by Fisher, in 1970 the night monitoring instrument of penis erectile hardness is used for evaluation of male erectile function. In 1985 researchers reported the RigiScan plus software was used to record of nocturnal erection, 1994 this method was gradually improved and used in clinical application by Levine. Sol reported that after taking sildenafil the patient was given audio-visual stimulation to induce the penis erects, then the RigiScan plus was used to record erection hardness in 2006. Due to the complexity of the etiology of ED, for the evaluation of penile erectile function should also be in many ways any single check has its limitations, the drug combined with audio-visual sense stimulation induced penile erection hardness monitoring (AVSS + RigiScan plus) in newly diagnosed patients with erectile function has a certain significance. Compared with AVSS + RigiScan examination, NPT is more expensive, time-consuming, and cumbersome, and patients feel unwell. And AVSS + RigiScan is simple, effective, easy, cheap, and the diagnostic accuracy rate matching to NPT, it is suitable for routine examination of patients with newly diagnosed ED.

  10. Towards a quantitative prediction of the blob detection rate

    NASA Astrophysics Data System (ADS)

    Fuchert, G.; Carralero, D.; Manz, P.; Stroth, U.; Wolfrum, E.; ASDEX Upgrade Team

    2016-05-01

    To estimate the particle and energy flux to the plasma facing components of a future fusion power plant, the transport carried by filaments of increased pressure, called blobs, is of critical importance. To understand this transport the rate of the filaments has to be known. The novel approach presented here allows the prediction of both the blob generation and detection rates based on background plasma parameters only. The prediction is in a good overall agreement with recent experiments in ASDEX Upgrade.

  11. 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

  12. Lateral resolution improvement of laser-scanning imaging for nano defects detection

    NASA Astrophysics Data System (ADS)

    Yokozeki, Hiroki; Kudo, Ryota; Takahashi, Satoru; Takamasu, Kiyoshi

    2014-08-01

    Demand for higher efficiency in the semiconductor manufacturing industry is continually increasing. In particular, nano defects measurement on patterned or bare Si semiconductor wafer surfaces is an important quality control factor for realizing high productivity and reliability of semiconductor device fabrication. Optical methods and electron beam methods are conventionally used for the inspection of semiconductor wafers. Because they are nondestructive and suitable for high-throughput inspection, optical methods are preferable to electron beam methods such as scanning electron microscopy, transmission electron microscopy, and so on. However, optical methods generally have an essential disadvantage about lateral spatial resolution than electron beam methods, because of the diffraction limit depending on the optical wavelength. In this research, we aim to develop a novel laser-scanning imaging method that can be applied to nano-/micro manufacturing processes such as semiconductor wafer surface inspection to allow lateral spatial super-resolution imaging with resolution beyond the diffraction limit. In our proposed method, instead of detecting the light intensity value from the beam spot on the inspection surface, the light intensity distribution, which is formed with infinity corrected optical system, coming from the beam spot on the inspection surface is detected. In addition, nano scale shifts in the beam spot are applied for laser spot scanning using a conventional laser-scanning method in which the spots are shifted at about a 100 nm pitch. By detecting multiple light intensity distributions due to the nano scale shifts, a super-resolution image reconstruction with resolution beyond the diffraction limit can be expected. In order to verify the feasibility of the proposed method, several numerical simulations were carried out.

  13. Quantitative computed tomography detects peripheral airway disease in asthmatic children.

    PubMed

    Jain, Neal; Covar, Ronina A; Gleason, Melanie C; Newell, John D; Gelfand, Erwin W; Spahn, Joseph D

    2005-09-01

    The aim of this study was to compare air-trapping as quantified by high-resolution computed tomography (HRCT) of the chest with measures of lung function and airway inflammation in children with mild to moderate asthma. Plethysmography indices, respiratory resistance, and reactance before and after bronchodilator with impulse oscillation (IOS), exhaled nitric oxide (eNO), total eosinophil count (TEC), and serum eosinophil cationic protein (ECP) levels were measured in 21 subjects. A single-cut HRCT image at end-expiration was obtained. Air-trapping was quantified and expressed in terms of the pixel index (PI) by determining the percentage of pixels in lung fields below -856 and -910 Hounsfeld units (HU). Pairwise linear correlations between PI and other parameters were evaluated. Subjects had only mild airflow limitation based on prebronchodilator forced expiratory volume in 1 sec (FEV(1)), but were hyperinflated and had air-trapping based on elevated total lung capacity (TLC) and residual volume (RV)/TLC ratio, respectively. The PI at -856 HU was positively correlated with % predicted TLC, total gas volume (TGV), and ECP level, and was inversely correlated with FEV(1)/forced vital capacity (FVC) and % predicted forced expiratory flow between 25-75% FVC (FEF(25-75)). The PI at -910 HU correlated similarly with these variables, and also correlated positively with IOS bronchodilator reversibility. This data suggest that quantitative HRCT may be a useful tool in the evaluation of peripheral airflow obstruction in children with asthma. PMID:16015663

  14. 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.

  15. Spatial scanning for anomaly detection in acoustic emission testing of an aerospace structure

    NASA Astrophysics Data System (ADS)

    Hensman, James; Worden, Keith; Eaton, Mark; Pullin, Rhys; Holford, Karen; Evans, Sam

    2011-10-01

    Acoustic emission (AE) monitoring of engineering structures potentially provides a convenient, cost-effective means of performing structural health monitoring. Networks of AE sensors can be easily and unobtrusively installed upon structures, giving the ability to detect and locate damage-related strain releases ('events') in the structure. Use of the technique is not widespread due to the lack of a simple and effective method for detecting abnormal activity levels: the sensitivity of AE sensor networks is such that events unrelated to damage are prevalent in most applications. In this publication, we propose to monitor AE activity in a structure using a spatial scanning statistic, developed and used effectively in the field of epidemiology. The technique is demonstrated on an aerospace structure - an Airbus A320 main landing gear fitting - undergoing fatigue loading, and the method is compared to existing techniques. Despite its simplicity, the scanning statistic proves to be an extremely effective tool in detecting the onset of damage in the structure: it requires little to no user intervention or expertise, is inexpensive to compute and has an easily interpretable output. Furthermore, the generic nature of the method allows the technique to be used in a variety of monitoring scenarios, to detect damage in a wide range of structures.

  16. Prospective evaluation of radionuclide scanning in detection of intestinal necrosis in neonatal necrotizing enterocolitis.

    PubMed

    Haase, G M; Sfakianakis, G N; Lobe, T E; Boles, E T

    1981-06-01

    The ability of external imaging to demonstrate intestinal infarction in neonatal necrotizing enterocolitis (NEC) was prospectively evaluated. The radiopharmaceutical technetium--99m diphosphonate was injected intravenously and the patients subsequently underwent abdominal scanning. Clinical patient care and interpretation of the images were entirely independent throughout the study. Of 33 studies, 7 were positive, 4 were suspicious, and 22 were negative. One false positive study detected ischemia without transmural infarction. The second false positive scan occurred postoperatively and was due to misinterpretation of the hyperactivity along the surgical incision. None of the suspicious cases had damaged bowel. The two false negative studies clearly failed to demonstrate frank intestinal necrosis. The presence of very small areas of infarction, errors in technical settings, subjective interpretation of scans and delayed clearance of the radionuclide in a critically ill neonate may all limit the accuracy of external abdominal scanning. However, in spite of an error rate of 12%, it is likely that this technique will enhance the present clinical, laboratory, and radiologic parameters of patient management in NEC. PMID:7019410

  17. Automatic scanning of nuclear emulsions with wide-angle acceptance for nuclear fragment detection

    NASA Astrophysics Data System (ADS)

    Fukuda, T.; Fukunaga, S.; Ishida, H.; Kodama, K.; Matsuo, T.; Mikado, S.; Ogawa, S.; Shibuya, H.; Sudo, J.

    2013-01-01

    Nuclear emulsion, a tracking detector with sub-micron position resolution, has played a successful role in the field of particle physics and the analysis speed has been substantially improved by the development of automated scanning systems. This paper describes a newly developed automated scanning system and its application to the analysis of nuclear fragments emitted almost isotropically in nuclear evaporation. This system is able to recognize tracks of nuclear fragments up to |tan θ| < 3.0 (where θ is the track angle with respect to the perpendicular to the emulsion film), while existing systems have an angular acceptance limited to |tan θ| < 0.6. The automatic scanning for such a large angle track in nuclear emulsion is the first trial. Furthermore the track recognition algorithm is performed by a powerful Graphics Processing Unit (GPU) for the first time. This GPU has a sufficient computing power to process large area scanning data with a wide angular acceptance and enough flexibility to allow the tuning of the recognition algorithm. This new system will in particular be applied in the framework of the OPERA experiment: the background in the sample of τ decay candidates due to hadronic interactions will be reduced by a better detection of the emitted nuclear fragments.

  18. Quantitative detection of settled dust over green canopy

    NASA Astrophysics Data System (ADS)

    Brook, Anna

    2016-04-01

    The main task of environmental and geoscience applications are efficient and accurate quantitative classification of earth surfaces and spatial phenomena. In the past decade, there has been a significant interest in employing hyperspectral unmixing in order to retrieve accurate quantitative information latent in hyperspectral imagery data. Recently, the ground-truth and laboratory measured spectral signatures promoted by advanced algorithms are proposed as a new path toward solving the unmixing problem of hyperspectral imagery in semi-supervised fashion. This paper suggests that the sensitivity of sparse unmixing techniques provides an ideal approach to extract and identify dust settled over/upon green vegetation canopy using hyperspectral airborne data. Atmospheric dust transports a variety of chemicals, some of which pose a risk to the ecosystem and human health (Kaskaoutis, et al., 2008). Many studies deal with the impact of dust on particulate matter (PM) and atmospheric pollution. Considering the potential impact of industrial pollutants, one of the most important considerations is the fact that suspended PM can have both a physical and a chemical impact on plants, soils, and water bodies. Not only can the particles covering surfaces cause physical distortion, but particles of diverse origin and different chemistries can also serve as chemical stressors and cause irreversible damage. Sediment dust load in an indoor environment can be spectrally assessed using reflectance spectroscopy (Chudnovsky and Ben-Dor, 2009). Small amounts of particulate pollution that may carry a signature of a forthcoming environmental hazard are of key interest when considering the effects of pollution. According to the most basic distribution dynamics, dust consists of suspended particulate matter in a fine state of subdivision that are raised and carried by wind. In this context, it is increasingly important to first, understand the distribution dynamics of pollutants, and

  19. Detectable distance calculations for a visual navigation system using a scanning semiconductor laser with electronic pumping.

    PubMed

    Kaloshin, G A; Shishkin, S A

    2011-07-10

    Results of detectable distance calculations for a visual navigation system based on a scanning semiconductor laser with electronic pumping (SSLEP) are presented. A semiconductor crystal in the laser is pumped with an electron beam, which is scanned across the crystal in the television-frame scan mode. The navigation system forms three orientation sectors with radiation wavelengths λ=0.52, 0.57, and 0.63 μm. Herein, calculations of energetic characteristics of output radiation are performed for the navigation system described above. The calculations were performed using the Range software package, which considers microphysical and optical characteristics of aerosol and observation path geometry for the case of coastal environment. Finally, comparison of results of the calculations with data obtained in marine and flight experiments is presented. It is demonstrated that minor discrepancies between calculated and measured values of detectable distance are observed in the coastal haze at lower values of meteorological visibility range S(m). As S(m) increases, the discrepancies become significant. PMID:21743551

  20. Auto-alignment of knee MR scout scans through redundant, adaptive and hierarchical anatomy detection.

    PubMed

    Zhan, Yiqiang; Dewan, Maneesh; Zhou, Xiang Sean

    2011-01-01

    3D knee magnetic resonance (MR) scout scan is an emerging imaging sequence that facilitates technicians in aligning the imaging planes of diagnostic high resolution MR scans. In this paper, we propose a method to automate this process with the goal of improving the accuracy, robustness and speed of the workflow. To tackle the various challenges coming from MR knee scout scans, our auto-alignment method is built upon a redundant, adaptive and hierarchical anatomy detection system. More specifically, we learn 1) a hierarchical redudant set of anatomy detectors, and 2) ensemble of group-wise spatial configurations across different anatomies, from training data. These learned statistics are integrated into a comprehensive objective function optimized using an expectation-maximization (EM) framework. The optimization provides a new framework for hierarchical detection and adaptive selection of anatomy primitives to derive optimal alignment. Being extensively validated on 744 clinical datasets, our method achieves high accuracy (sub-voxel alignment error), robustness (to severe diseases or imaging artifacts) and fast speed ( 5 sees for 10 alignments). PMID:21761650

  1. Analytical bioconjugates, aptamers, enable specific quantitative detection of Listeria monocytogenes.

    PubMed

    Lee, Sang-Hee; Ahn, Ji-Young; Lee, Kyeong-Ah; Um, Hyun-Ju; Sekhon, Simranjeet Singh; Sun Park, Tae; Min, Jiho; Kim, Yang-Hoon

    2015-06-15

    As a major human pathogen in the Listeria genus, Listeria monocytogenes causes the bacterial disease listeriosis, which is a serious infection caused by eating food contaminated with the bacteria. We have developed an aptamer-based sandwich assay (ABSA) platform that demonstrates a promising potential for use in pathogen detection using aptamers as analytical bioconjugates. The whole-bacteria SELEX (WB-SELEX) strategy was adopted to generate aptamers with high affinity and specificity against live L. monocytogenes. Of the 35 aptamer candidates tested, LMCA2 and LMCA26 reacted to L. monocytogenes with high binding, and were consequently chosen as sensing probes. The ABSA platform can significantly enhance the sensitivity by employing a very specific aptamer pair for the sandwich complex. The ABSA platform exhibited a linear response over a wide concentration range of L. monocytogenes from 20 to 2×10(6) CFU per mL and was closely correlated with the following relationship: y=9533.3x+1542.3 (R(2)=0.99). Our proposed ABSA platform also provided excellent specificity for the tests to distinguish L. monocytogenes from other Listeria species and other bacterial genera (3 Listeria spp., 4 Salmonella spp., 2 Vibrio spp., 3 Escherichia coli and 3 Shigella spp.). Improvements in the sensitivity and specificity have not only facilitated the reliable detection of L. monocytogenes at extremely low concentrations, but also allowed for the development of a 96-well plate-based routine assay platform for multivalent diagnostics. PMID:25590973

  2. Target-responsive DNAzyme cross-linked hydrogel for visual quantitative detection of lead.

    PubMed

    Huang, Yishun; Ma, Yanli; Chen, Yahong; Wu, Xuemeng; Fang, Luting; Zhu, Zhi; Yang, Chaoyong James

    2014-11-18

    Because of the severe health risks associated with lead pollution, rapid, sensitive, and portable detection of low levels of Pb(2+) in biological and environmental samples is of great importance. In this work, a Pb(2+)-responsive hydrogel was prepared using a DNAzyme and its substrate as cross-linker for rapid, sensitive, portable, and quantitative detection of Pb(2+). Gold nanoparticles (AuNPs) were first encapsulated in the hydrogel as an indicator for colorimetric analysis. In the absence of lead, the DNAzyme is inactive, and the substrate cross-linker maintains the hydrogel in the gel form. In contrast, the presence of lead activates the DNAzyme to cleave the substrate, decreasing the cross-linking density of the hydrogel and resulting in dissolution of the hydrogel and release of AuNPs for visual detection. As low as 10 nM Pb(2+) can be detected by the naked eye. Furthermore, to realize quantitative visual detection, a volumetric bar-chart chip (V-chip) was used for quantitative readout of the hydrogel system by replacing AuNPs with gold-platinum core-shell nanoparticles (Au@PtNPs). The Au@PtNPs released from the hydrogel upon target activation can efficiently catalyze the decomposition of H2O2 to generate a large volume of O2. The gas pressure moves an ink bar in the V-chip for portable visual quantitative detection of lead with a detection limit less than 5 nM. The device was able to detect lead in digested blood with excellent accuracy. The method developed can be used for portable lead quantitation in many applications. Furthermore, the method can be further extended to portable visual quantitative detection of a variety of targets by replacing the lead-responsive DNAzyme with other DNAzymes. PMID:25340621

  3. 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.

  4. 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

  5. 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.

  6. Improving global feature detectabilities through scan range splitting for untargeted metabolomics by high-performance liquid chromatography-Orbitrap mass spectrometry.

    PubMed

    Ranninger, Christina; Schmidt, Lukas E; Rurik, Marc; Limonciel, Alice; Jennings, Paul; Kohlbacher, Oliver; Huber, Christian G

    2016-08-01

    Untargeted metabolomics aims at obtaining quantitative information on the highest possible number of low-molecular biomolecules present in a biological sample. Rather small changes in mass spectrometric spectrum acquisition parameters may have a significant influence on the detectabilities of metabolites in untargeted global-scale studies by means of high-performance liquid chromatography-mass spectrometry (HPLC-MS). Employing whole cell lysates of human renal proximal tubule cells, we present a systematic global-scale study of the influence of mass spectrometric scan parameters and post-acquisition data treatment on the number and intensity of metabolites detectable in whole cell lysates. Ion transmission and ion collection efficiencies in an Orbitrap-based mass spectrometer basically depend on the m/z range scanned, which, ideally, requires different instrument settings for the respective mass ranges investigated. Therefore, we split a full scan range of m/z 50-1000 relevant for metabolites into two separate segments (m/z 50-200 and m/z 200-1,000), allowing an independent tuning of the ion transmission parameters for both mass ranges. Three different implementations, involving either scanning from m/z 50-1000 in a single scan, or scanning from m/z 50-200 and from m/z 200-1000 in two alternating scans, or performing two separate HPLC-MS runs with m/z 50-200 and m/z 200-1000 scan ranges were critically assessed. The detected features were subjected to rigorous background filtering and quality control in order to obtain reliable metabolite features for subsequent differential quantification. The most efficient approach in terms of feature number, which forms the basis for statistical analysis, identification, and for generating biological hypotheses, was the separate analysis of two different mass ranges. This lead to an increase in the number of detectable metabolite features, especially in the higher mass range (m/z greater than 400), by 2.5 (negative mode) to 6

  7. Comparison of Droplet Digital PCR and Quantitative PCR Assays for Quantitative Detection of Xanthomonas citri Subsp. citri.

    PubMed

    Zhao, Yun; Xia, Qingyan; Yin, Youping; Wang, Zhongkang

    2016-01-01

    Droplet digital polymerase chain reaction (ddPCR) is a novel molecular biology technique providing absolute quantification of target nucleic acids without the need for an external calibrator. Despite its emerging applications in medical diagnosis, there are few reports of its use for the detection of plant pathogens. This work was designed to assess the diagnosis potential of the ddPCR for absolute quantitative detection of Xanthomonas citri subsp. citri, a quarantine plant pathogenic bacterium that causes citrus bacterial canker in susceptible Citrus species. We transferred an established quantitative PCR (qPCR) assay for citrus bacterial canker diagnosis directly to the ddPCR format and compared the performance of the two methods. The qPCR assay has a broader dynamic range compared to the ddPCR assay and the ddPCR assay has a significantly higher degree of sensitivity compared to the qPCR assay. The influence of PCR inhibitors can be reduced considerably in the ddPCR assay because the collection of end-point fluorescent signals and the counting of binomial events (positive or negative droplets) are associated with a Poisson algorithm. The ddPCR assay also shows lower coefficient of variation compared to the qPCR assay especially in low target concentration. The linear association of the measurements by ddPCR and qPCR assays is strong (Pearson correlation = 0.8633; P<0.001). Receiver operating characteristic analysis indicates the ddPCR methodology is a more robust approach for diagnosis of citrus bacterial canker. In summary, the results demonstrated that the ddPCR assay has the potential for the quantitative detection of X. citri subsp. citri with high precision and accuracy as compared with the results from qPCR assay. Further studies are required to evaluate and validate the value of ddPCR technology in the diagnosis of plant disease and quarantine applications. PMID:27427975

  8. 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

  9. 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.

  10. Development of a c-scan photoacoutsic imaging probe for prostate cancer detection

    NASA Astrophysics Data System (ADS)

    Valluru, Keerthi S.; Chinni, Bhargava K.; Rao, Navalgund A.; Bhatt, Shweta; Dogra, Vikram S.

    2011-03-01

    Prostate cancer is the second leading cause of death in American men after lung cancer. The current screening procedures include Digital Rectal Exam (DRE) and Prostate Specific Antigen (PSA) test, along with Transrectal Ultrasound (TRUS). All suffer from low sensitivity and specificity in detecting prostate cancer in early stages. There is a desperate need for a new imaging modality. We are developing a prototype transrectal photoacoustic imaging probe to detect prostate malignancies in vivo that promises high sensitivity and specificity. To generate photoacoustic (PA) signals, the probe utilizes a high energy 1064 nm laser that delivers light pulses onto the prostate at 10Hz with 10ns duration through a fiber optic cable. The designed system will generate focused C-scan planar images using acoustic lens technology. A 5 MHz custom fabricated ultrasound sensor array located in the image plane acquires the focused PA signals, eliminating the need for any synthetic aperture focusing. The lens and sensor array design was optimized towards this objective. For fast acquisition times, a custom built 16 channel simultaneous backend electronics PCB has been developed. It consists of a low-noise variable gain amplifier and a 16 channel ADC. Due to the unavailability of 2d ultrasound arrays, in the current implementation several B-scan (depth-resolved) data is first acquired by scanning a 1d array, which is then processed to reconstruct either 3d volumetric images or several C-scan planar images. Experimental results on excised tissue using a in-vitro prototype of this technology are presented to demonstrate the system capability in terms of resolution and sensitivity.

  11. Electrophoretic capture and detection of nanoparticles at the opening of a membrane pore using scanning electrochemical microscopy.

    PubMed

    Lee, Sungwon; Zhang, Yanhui; White, Henry S; Harrell, C Chad; Martin, Charles R

    2004-10-15

    Stochastic electrophoretic capture of individual nanometer-scale particles at the small opening of a conically shaped nanopore in a synthetic membrane is described. Particle capture is sensed using a scanning electrochemical microscope (SECM) to measure the decrease in the transport rate of a redox-active molecule through the pore. The SECM tip is positioned at the larger backside opening of pore and used to amperometrically monitor the transport rate prior, during, and after particle capture. Following capture, the particle is released by electrophoretically driving it out of the pore opening and back into the solution. The capture and release method is demonstrated by detection of charged polystyrene spheres (43-150-nm diameter) using a polycarbonate membrane with conically shaped pores, the small opening of the pore having a diameter of 60 nm. The inverse of the time to capture polystyrene spheres increases with particle concentration over the range 10(8)-10(10) particles/mL. Selective detection based on nanoparticle charge and size is also demonstrated. A quantitative theoretical description of the rate of particle capture is presented, and the physical mechanism of particle capture, based on the balance of electrostatic and entropic forces, is considered. PMID:15481960

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. Single-scan coherent detection with enhanced time resolution for arbitrarily polarized terahertz wave

    NASA Astrophysics Data System (ADS)

    Lv, Zhihui; Zhang, Dongwen; Meng, Chao; Sun, Lin; Zhou, Zhaoyan; Zhao, Zengxiu; Yuan, Jianmin

    2012-12-01

    We present an enhanced scheme of polarization-sensitive THz-ABCD which can provide about twice broader bandwidth than the conventional method. In our experiment using a 26 fs laser pulse, compared with 0.3~40 THz in the conventional scheme, bandwidth coverage from 0.3 to 80 THz has been achieved in the resolution-enhanced scheme. It also should have to be noted the terahertz source may also restrict the detection bandwidth. Employing the polarizationsensitive technology, the polarization in time domain, as well as the field amplitude, can be achieved with just one single scan.

  18. 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

  19. Quantitation of brain perfusion with {sup 99m}{Tc}-bicisate and single SPECT scan: Comparison with microsphere measurements

    SciTech Connect

    Pupi, A.; De Cristofaro, T.R.; Passeri, A.; Castagnoli, A.; Bacciottini, L.; Bottoncetti, A.; Dal Pozzo, G.; Santoro, G.M.; Antoniucci, D.

    1994-01-01

    This study describes and validates in a preliminary manner a method to measure the steady-state influx constant (K{sub 1}) of {sup 99m}{Tc}-bicisate with one single photon emission computed tomography (SPECT) scan. The method is based on the analysis of the arterial concentration of the radioactivity. The results of this quantitation procedure were compared with regional CBF (rCBF) measurements made using {sup 99m}{Tc}-microspheres (MI). Two quantitative indexes of perfusion, fractional brain uptake (FBU) and normalized (with cerebellum) brain uptake (NBU), were also evaluated. Two SPECT studies were performed on seven cardiovascular patients who had no signs of neurological disease. In the first of these, {sup 99m}{Tc}-bicisate was used, while in the other, which was performed 2 days later, MI were injected into the left heart ventricle. The values of the FBU, NBU, and K{sub 1} of {sup 99m}{Tc}-bicisate were calculated in several gray and white matter brain regions of interest (ROIs) and compared with the rCBF values measured with MI in coupled ROIs. Mean FBU values were 0.00008 {+-} 0.00002 and 0.00004 {+-} 0.00001 in the gray and the white matter, respectively. Mean NBU values were 0.99 {+-} 0.04 and 0.54 {+-} 0.05, mean K{sub 1} values were 0.36 {+-} 0.06 and 0.19 {+-} 0.03 ml g{sup {minus}1} min{sup {minus}1} and mean rCBF values were 0.51 {+-} 0.04 and 0.27 {+-} 0.04 ml g{sup {minus}1} min{sup {minus}1} in gray and white matter, respectively. Analysis of variance of the regression gave different F values for the regressions with rCBF of FBU (F = 19, n = 126), NBU (F = 289, n = 112), and K{sub 1}(F = 117, n = 112), and K{sub 1}(F = 117, n = 126). The regression of K{sub 1} versus rCBF was K{sub 1} = 0.08 {+-} 0.55 rCBF. 25 refs., 5 figs., 2 tabs.

  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. 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.

  2. Detection of lying tree stems from airborne laser scanning data using a line template matching algorithm

    NASA Astrophysics Data System (ADS)

    Lindberg, E.; Hollaus, M.; Mücke, W.; Fransson, J. E. S.; Pfeifer, N.

    2013-10-01

    Dead wood is an important habitat characteristic in forests. However, dead wood lying on the ground below a canopy is difficult to detect from remotely sensed data. Data from airborne laser scanning include measurement of surfaces below the canopy, thus offering the potential to model objects on the ground. This paper describes a new line template matching algorithm for detecting lines along the ground. The line template matching is done directly to the laser point cloud and results in a raster showing the support of the line in each raster cell. Line elements are vectorized based on the raster to represent lying tree stems. The results have been validated versus field-measured lying tree stems. The number of detected lines was 845, of which 268 could be automatically linked to the 651 field-measured stems. The line template matching produced a raster which visually showed linear elements in areas where lying tree stems where present, but the result is difficult to compare with the field measurements due to positioning errors. The study area contained big piles of storm-felled trees in some places, which made it an unusually complex test site. Longer line structures such as ditches and roads also resulted in detected lines and further analysis is needed to avoid this, for example by specifically detecting longer lines and removing them.

  3. 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.

  4. 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

  5. Computerized lung nodule detection on screening CT scans: performance on juxta-pleural and internal nodules

    NASA Astrophysics Data System (ADS)

    Sahiner, Berkman; Hadjiiski, Lubomir M.; Chan, Heang-Ping; Zhou, Chuan; Wei, Jun

    2006-03-01

    We are developing a computer-aided detection (CAD) system for lung nodules in thoracic CT volumes. Our CAD system includes an adaptive 3D pre-screening algorithm to segment suspicious objects, and a false-positive (FP) reduction stage to classify the segmented objects as true nodules or normal lung structures. We found that the effectiveness of the FP reduction stage was limited by the different characteristics of the objects in the internal and the juxta-pleural (JP) regions. The purpose of this study was to evaluate object characteristics in the internal and JP regions of a lung CT scan, and to develop different FP reduction classifiers for JP and internal objects. Our FP reduction technique utilized shape, grayscale, and gradient features, as well as the scores of a newly-developed neural network trained on the eigenvalues of the Hessian matrix in a volume of interest containing the suspicious object. We designed an algorithm to automatically label the objects as internal or JP. Based on a training set of 75 CT scans containing internal and JP nodules, two FP classifiers were trained separately for objects in the two types of lung regions. The system performance was evaluated on an independent test set of 27 low dose screening scans. An experienced chest radiologist identified 64 solid nodules (mean diameter: 5.3 mm, range: 3.0-12.9 mm) on the test cases, of which 33 were internal and 31 were JP. Our adaptive 3D prescreening algorithm detected 28 internal and 29 JP nodules. At 80% sensitivity, the average number of FPs was 3.9 and 9.7 in the internal and JP regions per scan, respectively. In comparison, a classifier designed to work on both types of nodules had an average of 29.4 FPs per scan at the same sensitivity. Our results indicate that it is more effective to use two different classifiers for JP and internal nodules because of their different characteristics. FPs in the JP region were more difficult to distinguish from true nodules. Further investigation

  6. 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.

  7. 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.

  8. 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. PMID:26724038

  9. Detection of quantitative trait loci for meat quality traits in cattle.

    PubMed

    Gutiérrez-Gil, B; Wiener, P; Nute, G R; Burton, D; Gill, J L; Wood, J D; Williams, J L

    2008-02-01

    A whole-genome scan was carried out to detect quantitative trait loci (QTL) affecting sensory, organoleptic, physical and chemical properties of meat. The study used phenotypic data from 235 second-generation cross-bred bull calves of a Charolais x Holstein experimental population. Loin muscle samples were evaluated for yield force, intramuscular fat and nitrogen contents, myofibrillar fragmentation index, haem pigment concentration, moisture content and pH at 24 h postmortem. A sensory assessment was performed on grilled loin and roasted silverside joints by trained panellists. A linear regression analysis based on 165 markers revealed 35 QTL at the 5% chromosome-wide significance level (20 for sensory traits and 15 for physical and chemical traits), five of which were highly significant (F-value: > or =9). The most significant QTL was located on chromosome 6 (with the best likely position at 39 cM) and affected haem pigment concentration. The Holstein allele for this QTL was associated with an increase of 0.53 SD in the haem scores. A QTL for pH(24h) was identified on chromosome 14 (at 40 cM) and a QTL for moisture content was identified on chromosome 22 (at 21 cM). Two highly significant QTL were identified for sensory panel-assessed traits: beef odour intensity (grilled sample) on chromosome 10 (at 119 cM), and juiciness (roast sample) on chromosome 16 (at 70 cM). The proportion of phenotypic variance explained by the significant QTL ranged from 3.6% (for nitrogen content on chromosome 10) to 9.5% (for juiciness, roast sample on chromosome 16). PMID:18254735

  10. SkinScan©: A PORTABLE LIBRARY FOR MELANOMA DETECTION ON HANDHELD DEVICES.

    PubMed

    Wadhawan, Tarun; Situ, Ning; Lancaster, Keith; Yuan, Xiaojing; Zouridakis, George

    2011-03-30

    We have developed a portable library for automated detection of melanoma termed SkinScan© that can be used on smartphones and other handheld devices. Compared to desktop computers, embedded processors have limited processing speed, memory, and power, but they have the advantage of portability and low cost. In this study we explored the feasibility of running a sophisticated application for automated skin cancer detection on an Apple iPhone 4. Our results demonstrate that the proposed library with the advanced image processing and analysis algorithms has excellent performance on handheld and desktop computers. Therefore, deployment of smartphones as screening devices for skin cancer and other skin diseases can have a significant impact on health care delivery in underserved and remote areas. PMID:21892382

  11. Novel ac Heating-dc Detection Method for Active Thermoelectric Scanning Thermal Microscopy

    NASA Astrophysics Data System (ADS)

    Miao, Tingting; Ma, Weigang; Zhang, Xing

    2015-11-01

    A novel and reliable ac heating-dc detection method is developed for active thermoelectric scanning thermal microscopy, which can map out local thermal property imaging by point-heating and point-sensing with nanoscale spatial resolution. The thermoelectric probe is electrically heated by an ac current, and the corresponding dc thermoelectric voltage is detected. Using the measured dc voltage, the temperature information can be extracted with the known Seebeck coefficient of the thermoelectric probe. The validity and accuracy of this method have been verified by a 25.4 \\upmu m thick K-type thermocouple by both experiment and numerical simulation in high vacuum and in air. The experimental results show that the proposed method is reliable and convenient to monitor the temperature of the junction.

  12. Segmentation-Based Ground Points Detection from Mobile Laser Scanning Point Cloud

    NASA Astrophysics Data System (ADS)

    Lin, X.; Zhang, J.

    2015-06-01

    In most Mobile Laser Scanning (MLS) applications, filtering is a necessary step. In this paper, a segmentation-based filtering method is proposed for MLS point cloud, where a segment rather than an individual point is the basic processing unit. Particularly, the MLS point cloud in some blocks are clustered into segments by a surface growing algorithm, then the object segments are detected and removed. A segment-based filtering method is employed to detect the ground segments. Two MLS point cloud datasets are used to evaluate the proposed method. Experiments indicate that, compared with the classic progressive TIN (Triangulated Irregular Network) densification algorithm, the proposed method is capable of reducing the omission error, the commission error and total error by 3.62%, 7.87% and 5.54% on average, respectively.

  13. 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

  14. 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. PMID:27188424

  15. Enhanced ratio of signals enables digital mutation scanning for rare allele detection.

    PubMed

    Castellanos-Rizaldos, Elena; Paweletz, Cloud; Song, Chen; Oxnard, Geoffrey R; Mamon, Harvey; Jänne, Pasi A; Makrigiorgos, G Mike

    2015-05-01

    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. 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

  17. High-throughput baggage scanning employing x-ray diffraction for accurate explosives detection

    NASA Astrophysics Data System (ADS)

    Green, Michael C.; Partain, Larry D.

    2003-07-01

    X-ray systems dominate the installed base of airport baggage scanning systems for explosives detection. The majority are conveyer systems with projection line scanners. These systems can achieve a high throughput but exhibit a high false positive rate and require significant operator involvement. Systems employing computed tomography (CT) are currently being installed at a rapid rate. These can provide good discrimination of levels of xray absorption coefficient and can largely circumvent superimposition effects. Nonetheless CT measures only x-ray absorption coefficient per voxel which does not provide a means of specific material identification resulting in many false positives, and it is relatively straightforward to configure explosive materials so that they are undetectable by CT systems. Diffraction-based x-ray systems present a solution to this problem. They detect and measure atomic layer spacings in crystalline and microcrystalline materials with high sensitivity. This provides a means of specific material identification. The majority of explosive compounds are well crystallized solids at room temperature. X-ray diffraction systems using both conventional wavelength-dispersive diffraction and fixed-angle, multi-wavelength diffraction for improved throughput are described. Large-area, flat-panel x-ray detector technology coupled with an extended x-ray source will permit a full 3D volumetric x-ray diffraction scan of a bag in a single pass, (patent pending).

  18. 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.

  19. Liquid crystal-based sensors for selective and quantitative detection of nitrogen dioxide.

    PubMed

    Sen, Avijit; Kupcho, Kurt A; Grinwald, Bart A; Vantreeck, Heidi J; Acharya, Bharat R

    2013-03-01

    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

  20. 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.

  1. Extending the detectability index to quantitative imaging performance: applications in tomosynthesis and CT

    NASA Astrophysics Data System (ADS)

    Richard, Samuel; Chen, Baiyu; Samei, Ehsan

    2010-04-01

    This study aimed to extend Fourier-based imaging metrics for the modeling of quantitative imaging performance. Breast tomosynthesis was used as a platform for investigating acquisition and processing parameters (e.g., acquisition angle and dose) that can significantly affect 3D signal and noise, and consequently quantitative imaging performance. The detectability index was computed using the modulation transfer function and noise-power spectrum combined with a Fourier description of imaging task. Three imaging tasks were considered: detection, area estimation (in coronal slice), and volume estimation of a 4 mm diameter spherical target. Task functions for size estimation were generated by using measured performance of the maximum-likelihood estimator as training data. The detectability index computed with the size estimation tasks correlated well with precision measurements for area and volume estimation over a fairly broad range of imaging conditions and provided a meaningful figure of merit for quantitative imaging performance. Furthermore, results highlighted that optimal breast tomosynthesis acquisition parameters depend significantly on imaging task. Mass detection was optimal at an acquisition angle of 85° while area and volume estimation for the same mass were optimal at ~100° and 125° acquisition angles, respectively. These findings provide key initial validation that the Fourier-based detectability index extended to estimation tasks can represent a meaningful metric and predictor of quantitative imaging performance.

  2. Detection and Classification of Changes in Buildings from Airborne Laser Scanning Data

    NASA Astrophysics Data System (ADS)

    Xu, S.; Vosselman, G.; Oude Elberink, S.

    2013-10-01

    Building change detection serves to investigate illegal buildings. Illegal built or removed structures, especially those concealed among gable roofs such as dormers, are difficult to track among potentially millions of buildings. Nevertheless, they can be efficiently located in changed areas. An approach is proposed to automatically detect and classify changes in buildings from two epochs of Airborne Laser Scanning Data. Both datasets are classified into water, ground, building, vegetation and undefined objects in advance. After generalization of a 3D surface separation map, we verify changes by making rules on the separation map. Changes belonging to buildings are then classified into roof, wall, dormers, vehicles, construction above roof and undefined objects. As the ALS data has accuracy in strip difference of lower than 5 cm within the same epoch and from different epochs, changes that are larger than 10 cm were detected. Building changes, which areas are larger than 4 m2, are identified as change. By inspection, nearly all changes are detected and approximately 80% changes are correctly classified.

  3. 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.

  4. Increased Detection of Colorectal Polyps in Screening Colonoscopy Using High Definition i-SCAN Compared with Standard White Light

    PubMed Central

    Kim, Woo Jung; Park, Sang Young; Park, Iksoo; Lee, Wook Jin; Park, Jaechan; Chon, Nuri; Oh, Tak Geun; Kim, Kwang Hyun

    2016-01-01

    Background/Aims: The aim of this study was to evaluate the efficacy of high definition (HD) i-SCAN for colorectal polyp detection in screening colonoscopy. Methods: We retrospectively analyzed the records of 501 patients who had undergone screening colonoscopy performed by three endoscopists with either HD i-SCAN (n=149) or standard white light (n=352) from January 2, 2014 through June 30, 2014. Patient information and inter-endoscopist variation as well as polyp number, endoscopic findings, and pathologic characteristics were reviewed. Results: The detection rates of colorectal and neoplastic polyps were significantly higher using HD i-SCAN than standard white light colonoscopy (52% vs. 38.1%, p=0.004 for colorectal polyps; and 37.2% vs. 27.9%, p=0.041 for neoplastic polyps). Analysis of endoscopic findings revealed no difference in detected polyp size between HD i-SCAN and standard white light colonoscopy (4.59±2.35 mm vs. 4.82±2.81 mm, p=0.739), but non-protruding polyps were more commonly detected by i-SCAN than by standard white light colonoscopy (24.6% vs. 13.5%, p=0.007). Conclusions: Colonoscopy using HD i-SCAN had a significantly higher detection rate of colorectal polyps, including neoplastic polyps, because of improved sensitivity for detecting non-protruding lesions. PMID:26855927

  5. Predicting outbreak detection in public health surveillance: quantitative analysis to enable evidence-based method selection.

    PubMed

    Buckeridge, David L; Okhmatovskaia, Anna; Tu, Samson; O'Connor, Martin; Nyulas, Csongor; Musen, Mark A

    2008-01-01

    Public health surveillance is critical for accurate and timely outbreak detection and effective epidemic control. A wide range of statistical algorithms is used for surveillance, and important differences have been noted in the ability of these algorithms to detect outbreaks. The evidence about the relative performance of these algorithms, however, remains limited and mainly qualitative. Using simulated outbreak data, we developed and validated quantitative models for predicting the ability of commonly used surveillance algorithms to detect different types of outbreaks. The developed models accurately predict the ability of different algorithms to detect different types of outbreaks. These models enable evidence-based algorithm selection and can guide research into algorithm development. PMID:18999264

  6. Predicting Outbreak Detection in Public Health Surveillance: Quantitative Analysis to Enable Evidence-Based Method Selection

    PubMed Central

    Buckeridge, David L.; Okhmatovskaia, Anna; Tu, Samson; O’Connor, Martin; Nyulas, Csongor; Musen, Mark A.

    2008-01-01

    Public health surveillance is critical for accurate and timely outbreak detection and effective epidemic control. A wide range of statistical algorithms is used for surveillance, and important differences have been noted in the ability of these algorithms to detect outbreaks. The evidence about the relative performance of these algorithms, however, remains limited and mainly qualitative. Using simulated outbreak data, we developed and validated quantitative models for predicting the ability of commonly used surveillance algorithms to detect different types of outbreaks. The developed models accurately predict the ability of different algorithms to detect different types of outbreaks. These models enable evidence-based algorithm selection and can guide research into algorithm development. PMID:18999264

  7. 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. PMID:27087003

  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. N-Scan®: New Vibro-Modulation System for Crack Detection, Monitoring and Characterization

    NASA Astrophysics Data System (ADS)

    Zagrai, Andrei; Donskoy, Dimitri; Lottiaux, Jean-Louis

    2004-02-01

    In recent years, an innovative vibro-modulation technique has been introduced for the detection of contact-type interfaces such as cracks, debondings, and delaminations. The technique utilizes the effect of nonlinear interaction of ultrasound and vibrations at the interface of the defect. Vibration varies the contact area of the interface, modulating a passing ultrasonic wave. The modulation manifests itself as additional side-band spectral components with the combination frequencies in the spectrum of the received signal. The presence of these components allows for the detection and differentiation of the contact-type defects from other structural and material inhomogeneities. The vibro-modulation technique has been implemented in the N-SCAN® damage detection system providing a cost effective solution for the complex NDT problems. N-SCAN® proved to be very effective for damage detection and characterization in structures and structural components of simple and complex geometries made of steel, aluminum, composites, and other materials. Examples include 24 foot-long gun barrels, stainless steel pipes used in nuclear power plants, aluminum automotive parts, steel train couplers, etc. This paper describes the basic principles of the nonlinear vibro-modulation NDE technique, some theoretical background for nonlinear interaction, and justification of signal processing algorithms. The laboratory experiment is presented for a set of specimens with the calibrated cracks and the quantitative characterization of fatigue damage is given in terms of a modulation index. The paper also discusses examples of practical implementation and application of the technique.

  10. 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

  11. 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

  12. 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

  13. 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.

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

    PubMed Central

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

    2012-01-01

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

  15. 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. PMID:18710880

  16. DETECTION OF RENIBACTERIUM SALMONINARUM IN CHINOOK SALMON ONCORHYNCHUS TSHAWYTSCHA USING QUANTITATIVE PCR.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We have developed a quantitative PCR assay to detect varying levels of Renibacterium salmoninarum, the causative agent of bacterial kidney disease (BKD). This assay allows for the direct enumeration of bacterial DNA or RNA copy number within tissues and body fluids. The assay can be applied nonletha...

  17. DETECTION AND QUANTITATION OF SOLENOPSIS INVICTA VIRUS IN FIRE ANTS BY REAL-TIME PCR

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A quantitative real-time PCR (QPCR) method was developed to detect and quantify the amount of Solenopsis invicta virus (SINV) infecting individual ants of Solenopsis invicta. The two-step method utilized a gene-specific oligonucleotide primer targeting the SINV RNA-dependent RNA polymerase (RdRp) f...

  18. Type-A influenza virus detection and quantitation by real-time RT-PCR

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Real-time RT-PCR (RRT-PCR) is a relatively new technology which has been used for AIV detection since the early 2000’s for routine surveillance, during outbreaks and for research. Some of the advantages of RRT-PCR are: quantitative nature, scalability, cost, high sensitivity, high specificity, and ...

  19. PCR detection and quantitation of predominant anaerobic bacteria in human and animal fecal samples

    SciTech Connect

    Wang, Rong-Fu; Cao, Wei-Wen; Cerniglia, C.E.

    1996-04-01

    PCR procedures based on 16S rRNA genen sequence specific for 12 anaerobic bacteria that predominate in the human intestinal tract were developed and used for quantitative detection of these species in human feces and animal feces. The reported PCR procedure including the fecal sample preparation method is simplified and rapid and eliminates the DNA isolation steps.

  20. 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. ...

  1. Single Laboratory Comparison of Quantitative Real-time PCR Assays for the Detection of Fecal Pollution

    EPA Science Inventory

    There are numerous quantitative real-time PCR (qPCR) assays available to detect and enumerate fecal pollution in ambient waters. Each assay employs distinct primers and probes that target different rRNA genes and microorganisms leading to potential variations in concentration es...

  2. Quantitative Detection of Listeria monocytogenes in Biofilms by Real-Time PCR

    PubMed Central

    Guilbaud, Morgan; de Coppet, Pierre; Bourion, Fabrice; Rachman, Cinta; Prévost, Hervé; Dousset, Xavier

    2005-01-01

    A quantitative method based on a real-time PCR assay to enumerate Listeria monocytogenes in biofilms was developed. The specificity for L. monocytogenes of primers targeting the listeriolysin gene was demonstrated using a SYBR Green I real-time PCR assay. The number of L. monocytogenes detected growing in biofilms was 6 × 102 CFU/cm2. PMID:15812058

  3. 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...

  4. 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...

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

    PubMed Central

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

    2008-01-01

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

  6. 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...

  7. Application of quantitative PCR assays to detection of human Bacteroides species in the intestines of pigs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    When evaluating the efficacy of probiotic bacteria, it is beneficial to know whether a fed bacterium reaches the appropriate location in the digestive tract. Use of quantitative PCR could detect specific bacteria in a sample with a complex microbial community. In order to determine whether three Bac...

  8. Detecting shallow mixing heights in two coastal locations with a scanning Doppler lidar

    NASA Astrophysics Data System (ADS)

    Vakkari, Ville; O'Connor, Ewan J.; Nisantzi, Argyro; Mamouri, Rodanthi E.; Hadjimitsis, Diofantos Gl.

    2015-04-01

    Turbulent mixing is one of the most important processes in the lower troposphere for climate, weather and air quality. A key parameter describing turbulent mixing in atmosphere is mixing height, i.e. the height of the layer that is constantly in contact with the surface. Doppler lidar offers a way to observe the vertical wind velocity profile with a high enough time resolution to retrieve information on turbulent mixing. However, Doppler lidars cannot retrieve wind velocity measurements below an instrument-specific threshold, typically 100 - 200 metres. Here, we introduce a method for identifying mixing heights below the vertical minimum range of a scanning Doppler lidar. The new method for detecting shallow mixing height is based on velocity variance in low elevation angle conical scanning, i.e. vertical azimuth display (VAD) scanning, which provides simultaneously the horizontal wind profile. This method is applied to measurements in two very different coastal environments: Limassol, Cyprus during summer; and Loviisa, Finland during winter. At Limassol the measurements were carried out from 22 August to 15 October 2013 at the Cyprus University of Technology campus, 600 metres NE from the Mediterranean Sea shoreline. At Loviisa, the measurement campaign took place from 10 December 2013 to 17 March 2014 on a 2000 m long, 500 m wide island in the Baltic Sea archipelago. At both locations, the new method agrees well with mixing heights derived from turbulent kinetic energy dissipation rate profiles obtained from vertically-pointing Doppler lidar measurements. Furthermore, when the vertically pointing measurements indicated the mixing height to be below the Doppler lidar minimum range, the VADs indicated a shallow mixing height on 87 % of the time at Loviisa and on 58 % of the time at Limassol. At Limassol such low mixing heights occurred only during the night; at Loviisa very low mixing heights were also common during the day.

  9. 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

  10. Streamed Vertical Rectangle Detection in Terrestrial Laser Scans for Facade Database Production

    NASA Astrophysics Data System (ADS)

    Demantké, J.; Vallet, B.; Paparoditis, N.

    2012-07-01

    A reliable and accurate facade database would be a major asset in applications such as localization of autonomous vehicles, registration and fine building modeling. Mobile mapping devices now provide the data required to create such a database, but efficient methods should be designed in order to tackle the enormous amount of data collected by such means (a million point per second for hours of acquisition). Another important limitation is the presence of numerous objects in urban scenes of many different types. This paper proposes a method that overcomes these two issues: - The facade detection algorithm is streamed: the data is processed in the order it was acquired. More precisely, the input data is split into overlapping blocks which are analysed in turn to extract facade parts. Close overlapping parts are then merged in order to recover the full facade rectangle. - The geometry of the neighborhood of each point is analysed to define a probability that the point belongs to a vertical planar patch. This probability is then injected in a RANdom SAmple Consensus (RANSAC) algorithm both in the sampling step and in the hypothesis validation, in order to favour the most reliable candidates. This ensures much more robustness against outliers during the facade detection. This way, the main vertical rectangles are detected without any prior knowledge about the data. The only assumptions are that the facades are roughly planar and vertical. The method has been successfully tested on a large dataset in Paris. The facades are detected despite the presence of trees occluding large areas of some facades. The robustness and accuracy of the detected facade rectangles makes them useful for localization applications and for registration of other scans of the same city or of entire city models.

  11. Automated urban change detection using scanned cartographic and satellite image data

    USGS Publications Warehouse

    Spooner, Jeffrey D.

    1991-01-01

    The objective of this study was to develop a digital procedure to measure the amount of urban change that has occurred in an area since the publication of its corresponding 1:24,000-scale topographic map. Traditional change detection techniques are dependent upon the visual comparison of high-altitude aerial photographs or, more recently, satellite image data to a corresponding map. Analytical change detection techniques typically involve the digital comparison of satellite images to one another. As a result of this investigation, a new technique has been developed that analytically compares the most recently published map to a corresponding digital satellite image. Scanned cartographic and satellite image data are combined in a single file with a structural component derived from the satellite image. This investigation determined that with this combination of data the spectral characteristics of urban change are predictable. A supervised classification was used to detect and delimit urban change. Although it was not intended to identify the specific nature of any change, this procedure does provide a means of differentiating between areas that have or have not experienced urbanization to determine appropriate map revision strategies.

  12. 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.

  13. A real-time 3D scanning system for pavement rutting and pothole detections

    NASA Astrophysics Data System (ADS)

    Li, Qingguang; Yao, Ming; Yao, Xun; Yu, Wurong; Xu, Bugao

    2009-08-01

    Rutting and pothole are the common pavement distress problems that need to be timely inspected and repaired to ensure ride quality and safe traffic. This paper introduces a real-time, automated inspection system devoted for detecting these distress features using high-speed transverse scanning. The detection principle is based on the dynamic generation and characterization of 3D pavement profiles obtained from structured light measurements. The system implementation mainly involves three tasks: multi-view coplanar calibration, sub-pixel laser stripe location, and pavement distress recognition. The multi-view coplanar scheme was employed in the calibration procedure to increase the feature points and to make the points distributed across the field of view of the camera, which greatly improves the calibration precision. The laser stripe locating method was implemented in four steps: median filtering, coarse edge detection, fine edge adjusting, stripe curve mending and interpolation by cubic splines. The pavement distress recognition algorithms include line segment approximation of the profile, searching for the feature points, and parameters calculations. The parameter data of a curve segment between two feature points, such as width, depth and length, were used to differentiate rutting, pothole, and pothole under different constraints. The preliminary experiment results show that the system is capable of locating these pavement distresses, and meets the needs for real-time and accurate pavement inspection.

  14. Detecting pruning of individual stems using Airborne Laser Scanning data captured from an Unmanned Aerial Vehicle

    NASA Astrophysics Data System (ADS)

    Wallace, Luke; Watson, Christopher; Lucieer, Arko

    2014-08-01

    Modern forest management involves implementing optimal pruning regimes. These regimes aim to achieve the highest quality timber in the shortest possible rotation period. Although a valuable addition to forest management activities, tracking the application of these treatments in the field to ensure best practice management is not economically viable. This paper describes the use of Airborne Laser Scanner (ALS) data to track the rate of pruning in a Eucalyptus globulus stand. Data is obtained from an Unmanned Aerial Vehicle (UAV) and we describe automated processing routines that provide a cost-effective alternative to field sampling. We manually prune a 500 m2 plot to 2.5 m above the ground at rates of between 160 and 660 stems/ha. Utilising the high density ALS data, we first derived crown base height (CBH) with an RMSE of 0.60 m at each stage of pruning. Variability in the measurement of CBH resulted in both false positive (mean rate of 11%) and false negative detection (3.5%), however, detected rates of pruning of between 96% and 125% of the actual rate of pruning were achieved. The successful automated detection of pruning within this study highlights the suitability of UAV laser scanning as a cost-effective tool for monitoring forest management activities.

  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. 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

  17. Multiresolution neural networks for mine detection in side scan sonar images

    NASA Astrophysics Data System (ADS)

    Guo, Weiming; Szymczak, William G.

    1998-09-01

    Statistical and neural network algorithms are used to separate mine targets from clutter in side scan sonar images. In these images, a typical target usually contains in excess of 100 pixels filled with salt and pepper noise. This translates into a problem of classifying in a complicated high dimensional space, which is very difficult if not impossible to solve. Therefore, a typical mine detection algorithm contains three stages preceding the classification algorithm: noise reduction, clutter rejection, and feature extraction. These pre-processing steps would reduce the dimension of the feature space by an order of magnitude. Side scan sonar images are known to be contaminated with noise and mine like clutter. The major challenge is to select and measure the features of the potential targets. This is frequently done by fractal and/or Fourier analysis. Recently, wavelet analysis has also been used successfully as a tool for feature extraction. However, there are few analytical rules to guide the selection of features. In this paper, we investigate a new integrated feature extraction and classification algorithm that first enhances a potential target using variational based algorithms, and then transforms the enhanced image into a set of wavelet channels. We use the multichannel information as inputs to a feed-forward neural network. This new classifier has the advantage of extracting not only the local features but also the background features through higher scale wavelet channels. Results are compared for different network designs.

  18. 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.

  19. 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. PMID:25173605

  20. Mobile, scanning x-ray source for mine detection using backscattered x-rays

    SciTech Connect

    Shope, S.; Lockwood, G.; Bishop, L.; Selph, M.; Jojola, J.; Wavrik, R.; Turman, B.; Wehlburg, J.

    1997-04-01

    A continuously operating, scanning x-ray machine is being developed for landmine detection using backscattered x-rays. The source operates at 130 kV and 650 mA. The x-rays are formed by electrons striking a high Z target. Target shape is an approximate 5 cm wide by 210 cm long racetrack. The electron beam is scanned across this target with electromagnets. There are 105, 1-cm by 1-cm collimators in each leg of the racetrack for a total of 210 collimators. The source is moved in the forward direction(the direction perpendicular to the 210-cm dimension) at 3 mi/h. The forward velocity and collimator spacing are such that a grid of collimated x-rays are projected at normal incidence to the soil. The spacing between the collimators and the ground results in a 2-cm by 2-cm x-ray pixel on the ground. A unique detector arrangement of collimated and uncollimated detectors allows surface features to be recognized and removed, leaving an image of a buried landmine. Another detector monitors the uncollimated x-ray output and is used to normalize the source output. The mine detector is being prepared for an Advanced Technology Demonstration (ATD). The ATD is scheduled for midyear of 1998. The results of the source performance in pre ATD tests will be presented.

  1. ac driving amplitude dependent systematic error in scanning Kelvin probe microscope measurements: Detection and correction

    SciTech Connect

    Wu Yan; Shannon, Mark A.

    2006-04-15

    The dependence of the contact potential difference (CPD) reading on the ac driving amplitude in scanning Kelvin probe microscope (SKPM) hinders researchers from quantifying true material properties. We show theoretically and demonstrate experimentally that an ac driving amplitude dependence in the SKPM measurement can come from a systematic error, and it is common for all tip sample systems as long as there is a nonzero tracking error in the feedback control loop of the instrument. We further propose a methodology to detect and to correct the ac driving amplitude dependent systematic error in SKPM measurements. The true contact potential difference can be found by applying a linear regression to the measured CPD versus one over ac driving amplitude data. Two scenarios are studied: (a) when the surface being scanned by SKPM is not semiconducting and there is an ac driving amplitude dependent systematic error; (b) when a semiconductor surface is probed and asymmetric band bending occurs when the systematic error is present. Experiments are conducted using a commercial SKPM and CPD measurement results of two systems: platinum-iridium/gap/gold and platinum-iridium/gap/thermal oxide/silicon are discussed.

  2. 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.

  3. Unsuspected pneumonia detected by increased lung uptake on 111In-ibritumomab tiuxetan scan.

    PubMed

    Hwang, Misun; Joyce, Judith M; Klein, Herbert; Hou, Jing-Zhou

    2012-10-01

    99Y-ibritumomab tiuxetan (Zevalin) is a CD20-targeted radioimmunotherapy for the treatment of B-cell non-Hodgkin lymphoma approved by the FDA in 2002. The acquisition of an 111In ibritumomab tiuxetan scan (bioscan) to confirm normal biodistribution before treatment with 99Y-ibritumomab tiuxetan was initially required in the United States until November 2011. This is the first documented example of abnormal biodistribution due to unsuspected pneumonia detected by increased lung uptake on the bioscan. The pneumonia was treated and resolved before 99Y Zevalin, avoiding potential harm and indicating that a screening chest x-ray may be appropriate when a bioscan is not performed. PMID:22955077

  4. 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.

  5. The influence of scan mode and circle fitting on tree stem detection, stem diameter and volume extraction from terrestrial laser scans

    NASA Astrophysics Data System (ADS)

    Pueschel, Pyare; Newnham, Glenn; Rock, Gilles; Udelhoven, Thomas; Werner, Willy; Hill, Joachim

    2013-03-01

    Terrestrial laser scanning (TLS) has been used to estimate a number of biophysical and structural vegetation parameters. Of these stem diameter is a primary input to traditional forest inventory. While many experimental studies have confirmed the potential for TLS to successfully extract stem diameter, the estimation accuracies differ strongly for these studies - due to differences in experimental design, data processing and test plot characteristics. In order to provide consistency and maximize estimation accuracy, a systematic study into the impact of these variables is required. To contribute to such an approach, 12 scans were acquired with a FARO photon 120 at two test plots (Beech, Douglas fir) to assess the effects of scan mode and circle fitting on the extraction of stem diameter and volume. An automated tree stem detection algorithm based on the range images of single scans was developed and applied to the data. Extraction of stem diameter was achieved by slicing the point cloud and fitting circles to the slices using three different algorithms (Lemen, Pratt and Taubin), resulting in diameter profiles for each detected tree. Diameter at breast height (DBH) was determined using both the single value for the diameter fitted at the nominal breast height and by a linear fit of the stem diameter vertical profile. The latter is intended to reduce the influence of outliers and errors in the ground level determination. TLS-extracted DBH was compared to tape-measured DBH. Results show that tree stems with an unobstructed view to the scanner can be successfully extracted automatically from range images of the TLS data with detection rates of 94% for Beech and 96% for Douglas fir. If occlusion of trees is accounted for stem detection rates decrease to 85% (Beech) and 84% (Douglas fir). As far as the DBH estimation is concerned, both DBH extraction methods yield estimates which agree with reference measurements, however, the linear fit based approach proved to be more

  6. 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.

  7. Quantitative risk assessment & leak detection criteria for a subsea oil export pipeline

    NASA Astrophysics Data System (ADS)

    Zhang, Fang-Yuan; Bai, Yong; Badaruddin, Mohd Fauzi; Tuty, Suhartodjo

    2009-06-01

    A quantitative risk assessment (QRA) based on leak detection criteria (LDC) for the design of a proposed subsea oil export pipeline is presented in this paper. The objective of this QRA/LDC study was to determine if current leak detection methodologies were sufficient, based on QRA results, while excluding the use of statistical leak detection; if not, an appropriate LDC for the leak detection system would need to be established. The famous UK PARLOC database was used for the calculation of pipeline failure rates, and the software POSVCM from MMS was used for oil spill simulations. QRA results revealed that the installation of a statistically based leak detection system (LDS) can significantly reduce time to leak detection, thereby mitigating the consequences of leakage. A sound LDC has been defined based on QRA study results and comments from various LDS vendors to assist the emergency response team (ERT) to quickly identify and locate leakage and employ the most effective measures to contain damage.

  8. Quantitation of virus using laser-based scanning of near-infrared fluorophores replaces manual plate reading in a virus titration assay.

    PubMed

    Weldon, Sally K; Mischnick, Shawn L; Urlacher, Teresa M; Ambroz, Kristi L H

    2010-09-01

    A method was developed for quantitation of a virus titration assay for minimally cytopathic and noncytopathic viruses that utilizes laser-based scanning of near-infrared (NIR) fluorophores. This automated method bypasses the need for manual plate reading thus eliminating human bias and error. The image data is translated by LI-COR's Odyssey software into numerical data which is used directly in the virus titer calculations. PMID:20438762

  9. 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

  10. Quantitative PCR for detection of DNA damage in mitochondrial DNA of the fission yeast Schizosaccharomyces pombe.

    PubMed

    Senoo, Takanori; Yamanaka, Mayumi; Nakamura, Atori; Terashita, Tomoki; Kawano, Shinji; Ikeda, Shogo

    2016-08-01

    Quantitative polymerase chain reaction (QPCR) has been employed to detect DNA damage and repair in mitochondrial DNA (mtDNA) of human and several model organisms. The assay also permits the quantitation of relative mtDNA copy number in cells. Here, we developed the QPCR assay primers and reaction conditions for the fission yeast Schizosaccharomyces pombe, an important model of eukaryote biology, not previously described. Under these conditions, long targets (approximately 10kb) in mtDNA were quantitatively amplified using 0.1ng of crude DNA templates without isolation of mitochondria and mtDNA. Quantitative detection of oxidative DNA damage in mtDNA was illustrated by using a DNA template irradiated with UVA in the presence of riboflavin. The damage to mtDNA in S. pombe cells treated with hydrogen peroxide and paraquat was also quantitatively measured. Finally, we found that mtDNA copy number in S. pombe cells increased after transition into a stationary phase and that the damage to mtDNA due to endogenous cellular processes accumulated during chronological aging. PMID:27236021

  11. Structural damage detection using higher-order finite elements and a scanning laser vibrometer

    NASA Astrophysics Data System (ADS)

    Jin, Si

    In contrast to conventional non-destructive evaluation methods, dynamics-based damage detection methods are capable of rapid integrity evaluation of large structures and have received considerable attention from aerospace, mechanical, and civil engineering communities in recent years. However, the identifiable damage size using dynamics-based methods is determined by the number of sensors used, level of measurement noise, accuracy of structural models, and signal processing techniques. In this thesis we study dynamics of structures with damage and then derive and experimentally verify new model-independent structural damage detection methods that can locate small damage to structures. To find sensitive damage detection parameters we develop a higher-order beam element that enforces the continuity of displacements, slopes, bending moments, and shear forces at all nodes, and a higher-order rectangular plate element that enforces the continuity of displacements, slopes, and bending and twisting moments at all nodes. These two elements are used to study the dynamics of beams and plates. Results show that high-order spatial derivatives of high-frequency modes are important sensitive parameters that can locate small structural damage. Unfortunately the most powerful and popular structural modeling technique, the finite element method, is not accurate in predicting high-frequency responses. Hence, a model-independent method using dynamic responses obtained from high density measurements is concluded to be the best approach. To increase measurement density and reduce noise a Polytec PI PSV-200 scanning laser vibrometer is used to provide non-contact, dense, and accurate measurements of structural vibration velocities. To avoid the use of structural models and to extract sensitive detection parameters from experimental data, a brand-new structural damage detection method named BED (Boundary-Effect Detection) is developed for pinpointing damage locations using Operational

  12. 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. PMID:26224395

  13. 3D change detection at street level using mobile laser scanning point clouds and terrestrial images

    NASA Astrophysics Data System (ADS)

    Qin, Rongjun; Gruen, Armin

    2014-04-01

    Automatic change detection and geo-database updating in the urban environment are difficult tasks. There has been much research on detecting changes with satellite and aerial images, but studies have rarely been performed at the street level, which is complex in its 3D geometry. Contemporary geo-databases include 3D street-level objects, which demand frequent data updating. Terrestrial images provides rich texture information for change detection, but the change detection with terrestrial images from different epochs sometimes faces problems with illumination changes, perspective distortions and unreliable 3D geometry caused by the lack of performance of automatic image matchers, while mobile laser scanning (MLS) data acquired from different epochs provides accurate 3D geometry for change detection, but is very expensive for periodical acquisition. This paper proposes a new method for change detection at street level by using combination of MLS point clouds and terrestrial images: the accurate but expensive MLS data acquired from an early epoch serves as the reference, and terrestrial images or photogrammetric images captured from an image-based mobile mapping system (MMS) at a later epoch are used to detect the geometrical changes between different epochs. The method will automatically mark the possible changes in each view, which provides a cost-efficient method for frequent data updating. The methodology is divided into several steps. In the first step, the point clouds are recorded by the MLS system and processed, with data cleaned and classified by semi-automatic means. In the second step, terrestrial images or mobile mapping images at a later epoch are taken and registered to the point cloud, and then point clouds are projected on each image by a weighted window based z-buffering method for view dependent 2D triangulation. In the next step, stereo pairs of the terrestrial images are rectified and re-projected between each other to check the geometrical

  14. Detection and semi-quantitative measurement of lung cancer metabolic activity by whole body PET

    SciTech Connect

    Tse, K.K.M.; Buchpiguel, C.A.; Alavi, J.B.

    1994-05-01

    Conventional radiologic and nuclear medicine techniques have been shown to have a limited role in the staging and monitoring of disease activity in patients with lung cancer. Both qualitative and semi-quantitative position emission tomography (PET) using the F-18 FDG technique have been applied to determine the clinical utility of whole body PET-FDG imaging in lung cancer. Nineteen whole body FDG PET scans were performed in 18 patients; 17 with lung cancer (15 non-small cell and 2 small cell) and 1 with squamous cell carcinoma of the trachea.

  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

    2016-04-01

    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. PMID:26928571

  16. 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

  17. Dual channel detection of ultra low concentration of bacteria in real time by scanning FCS.

    PubMed

    Altamore, Ilaria; Lanzano, Luca; Gratton, Enrico

    2013-06-01

    We describe a novel method to detect very low concentrations of bacteria in water. Our device consists of a portable horizontal geometry small confocal microscope with large pinhole and a holder for cylindrical cuvettes containing the sample. Two motors provide a fast rotational and slow vertical motion of the cuvette so the device looks like a simplified flow cytometer without flow. To achieve high sensitivity the design has two detection channels. Bacteria are stained by two different nucleic acid dyes and excited with two different lasers. Data are analyzed with a correlation filter based on particle passage pattern recognition. The passage of a particle through the illumination volume is compared with a Gaussian pattern in both channels. The width of the Gaussian correlates with the time of passage of the particle so one particle is counted when the algorithm finds a match with a Gaussian in both channels. The concentration of particles in the sample is deduced from the total number of coincident hits and the total volume scanned. This portable setup provides higher sensitivity, low cost and it could have a wide use ranging from clinical applications to pollution monitors and water and air quality control. PMID:24039347

  18. Detection of hydrogen peroxide produced during electrochemical oxygen reduction using scanning electrochemical microscopy.

    PubMed

    Shen, Yan; Träuble, Markus; Wittstock, Gunther

    2008-02-01

    The substrate-generation/tip-collection mode of scanning electrochemical microscopy was used to detect hydrogen peroxide formed as an intermediate during oxygen reduction at various electrodes. The experiment is conceptually similar to rotating ring-disk experiments but does not require the production of a ring-disk assembly for the specific electrode material in question. In order to limit the extension of the diffusion layer above the sample, the sample electrode potential is pulsed while the Pt ultramicroelectrode probe (UME) is held at a constant potential for oxidative amperometric detection of hydrogen peroxide. The signal at UME is influenced by the sample region within the diffusion length of hydrogen peroxide during the pulse of 2.5 s. The method is tested with three model electrodes showing different behavior with respect to the oxygen reduction reaction (ORR) in acidic solution. Simple analytical models were used to extract effective rate constants for the most important reaction paths of ORR at gold and palladium-cobalt samples from the chronoamperometric response of the UME to a reduction pulse at the sample electrode. PMID:18179180

  19. Power and sample size estimation for epigenome-wide association scans to detect differential DNA methylation

    PubMed Central

    Tsai, Pei-Chien; Bell, Jordana T

    2015-01-01

    Background: Epigenome-wide association scans (EWAS) are under way for many complex human traits, but EWAS power has not been fully assessed. We investigate power of EWAS to detect differential methylation using case-control and disease-discordant monozygotic (MZ) twin designs with genome-wide DNA methylation arrays. Methods and Results: We performed simulations to estimate power under the case-control and discordant MZ twin EWAS study designs, under a range of epigenetic risk effect sizes and conditions. For example, to detect a 10% mean methylation difference between affected and unaffected subjects at a genome-wide significance threshold of P = 1 × 10−6, 98 MZ twin pairs were required to reach 80% EWAS power, and 112 cases and 112 controls pairs were needed in the case-control design. We also estimated the minimum sample size required to reach 80% EWAS power under both study designs. Our analyses highlighted several factors that significantly influenced EWAS power, including sample size, epigenetic risk effect size, the variance of DNA methylation at the locus of interest and the correlation in DNA methylation patterns within the twin sample. Conclusions: We provide power estimates for array-based DNA methylation EWAS under case-control and disease-discordant MZ twin designs, and explore multiple factors that impact on EWAS power. Our results can help guide EWAS experimental design and interpretation for future epigenetic studies. PMID:25972603

  20. Development of Parallel Image Detection System Using Annular Pupils for Scanning Transmission Electron Microscope

    SciTech Connect

    Matsutani, Takaomi; Taya, Masaki; Ikuta, Takashi; Tanaka, Takeo; Kimura, Yoshihide; Takai, Yoshizo; Kawasaki, Tadahiro; Ichihashi, Mikio

    2010-10-13

    A parallel image detection system using an annular pupil for electron optics were developed to realize an increase in the depth of focus, aberration-free imaging and separation of amplitude and phase images under scanning transmission electron microscopy (STEM). Apertures for annular pupils able to suppress high-energy electron scattering were developed using a focused ion beam (FIB) technique. The annular apertures were designed with outer diameter of oe 40 {mu}m and inner diameter of oe32 {mu}m. A taper angle varying from 20 deg. to 1 deg. was applied to the slits of the annular apertures to suppress the influence of high-energy electron scattering. Each azimuth angle image on scintillator was detected by a multi-anode photomultiplier tube assembly through 40 optical fibers bundled in a ring shape. To focus the image appearing on the scintillator on optical fibers, an optical lens relay system attached with CCD camera was developed. The system enables the taking of 40 images simultaneously from different scattered directions.

  1. CWA stand-off detection, a new figure-of-merit: the field surface scanning rate

    NASA Astrophysics Data System (ADS)

    Bernascolle, Philippe F.

    2013-05-01

    All the manufacturers of stand-off CWA detectors communicate on the "same" characteristics. And one can find these parameters in the comparison table published between all the different products [1]. These characteristics are for example the maximum detection range, the number of different detectable compounds, the weight, the price, etc… All these parameters are good to compare products between them, but they omit one very important point: the reaction time in case of an unexpected incoming chemical threat, in the case of the surveillance application. To answer this important question, we imagine a new parameter: the Field Surface Scanning Rate (FSSR). This value is a classical parameter in astronomical survey, use by astronomers to compare the performance of different telescopes, they compute the quantity of sky (in sky square degrees) analyzed per unit of time by the system. In this paper we will compare this new figure-of-merit, the FSSR, of some commercially off the shelf stand-off detector. The comparison between classical FTIR system and gas imaging system in term of FSSR will be presented.

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

    PubMed

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

    2011-01-01

    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 assay can reliably detect BoNT/A with a similar sensitivity as the MBA. PMID:21130748

  3. 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

  4. A combined algorithm for T-wave alternans qualitative detection and quantitative measurement

    PubMed Central

    2013-01-01

    Background T-wave alternans (TWA) provides a noninvasive and clinically useful marker for the risk of sudden cardiac death (SCD). Current most widely used TWA detection algorithms work in two different domains: time and frequency. The disadvantage of the spectral analytical techniques is that they treat the alternans signal as a stationary wave with a constant amplitude and a phase. They cannot detect non-stationary characteristics of the signal. The temporal domain methods are sensitive to the alignment of the T-waves. In this study, we sought to develop a robust combined algorithm (CA) to assess T-wave alternans, which can qualitatively detect and quantitatively measure TWA in time domain. Methods The T wave sequences were extracted and the total energy of each T wave within the specified time-frequency region was calculated. The rank-sum test was applied to the ranked energy sequences of T waves to detect TWA qualitatively. The ECG containing TWA was quantitatively analyzed with correlation method. Results Simulation test result proved a mean sensitivity of 91.2% in detecting TWA, and for the SNR not less than 30 dB, the accuracy rate of detection achieved 100%. The clinical data experiment showed that the results from this method vs. spectral method had the correlation coefficients of 0.96. Conclusions A novel TWA analysis algorithm utilizing the wavelet transform and correlation technique is presented in this paper. TWAs are not only correctly detected qualitatively in frequency domain by energy value of T waves, but the alternans frequency and amplitude in temporal domain are measured quantitatively. PMID:23311454

  5. 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. PMID:26720916

  6. Quantitative Detection of Trace Explosive Vapors by Programmed Temperature Desorption Gas Chromatography-Electron Capture Detector

    PubMed Central

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

    2014-01-01

    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. PMID:25145416

  7. Fast wavelength-scanning interferometry technique with derivative detection of quadrature signals

    NASA Astrophysics Data System (ADS)

    Číp, O.; Mikel, B.; Lazar, J.

    2006-04-01

    We present a laser interferometer where a narrow-line width tuneable VCSEL laser (Vertical-Cavity Surface-Emitting Laser) working at 760 nm is used. For the detection of an absolute distance, we have used a fast wavelength-scanning interferometry technique. In the first part of the work we introduce the absolute laser interferometer as a demonstrator for research of a digital detection of quadrature signals (X-cos and Y-sin). This interferometer uses polarized beams and magnitude division of interference fringes. The wavelength of VCSEL laser is swept with the mode-hop free tuning range more than 1.2 nm, by means of the amplitude modulation of the injection current. At the same time, the operating temperature of the VCSEL is stabilized with a fast digital temperature controller. We control the wavelength value and whole tuning process of the laser with the frequency lock to selected modes of an external Fabry-Perot etalon. Except the frequency lock, the Fabry-Perot mode spectrum identifies wavelength-tuning interval of VCSEL during each sweep. A digital signal processor (DSP) is heart of the control and detection system. It samples intensity signal from Fabry- Perot etalon and X-Y quadrature signals from the detection unit of the interferometer. After 1 nm sweep of the VCSEL wavelength, we obtain a number of passed interference fringes and the number of passed Fabry-Perot resonance modes, at the same time. On basis of these measured quantities we are able to calculate the instantaneous value of the optical path length difference between the measuring and reference arm of the demonstrational interferometer. The other part of the work is oriented to research and experimental testing of the digital detection of quadrature signals (X-cos and Y-sin) processed only on basis of one intensity signal (X-axis) that is produced by a simple photo-detector. On basis of traditional inversion function arctan(Y/X) we are able to determine instantaneous phase between interference

  8. 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

  9. Quantification of HIV-1 using multiple quantitative polymerase chain reaction standards and bioluminometric detection.

    PubMed

    Nygren, M; Ronaghi, M; Nyrén, P; Albert, J; Lundeberg, J

    2001-01-01

    A non-gel-based quantification assay based on competitive PCR and bioluminometric detection has been developed. Samples containing human immunodeficiency virus type 1 (HIV-1) DNA and three quantitative standards at discrete concentrations were coamplified by PCR with primers annealing in the polymerase gene region. The quantitative standards contained the same primer binding sequences and had the same amplicon length as the wild-type DNA, but differed in an internal homopolymeric stretch (A, C, or T) over three base pairs. The PCR products were captured onto a solid support and treated with NaOH to separate the strands. Discrimination between the wild-type DNA and the three quantitative standard amplicons was achieved on the solid support by four parallel extension reactions with 3'-end specific primers. Inorganic pyrophosphate (PPi) released as a result of successful extension was converted to ATP by ATP sulfurylase and the level of ATP was sensed by firefly luciferase, generating a proportional amount of visible light which was detected by a luminometer. Here, we show that the obtained calibration curves, using the signal intensities of the three quantitative standards, enabled determination of the amount of target HIV-1 DNA. PMID:11141303

  10. Quantitative Thallium-201 exercise scintigraphy for detection of coronary artery disease

    SciTech Connect

    Berger, B.C.; Watson, D.D.; Taylor, G.J.; Craddock, G.B.; Martin, R.P.; Teates, C.D.; Beller, G.A.

    1981-07-01

    In 140 patients with chest pain quantitation of regional myocardial Tl-201 activity was performed by serial scintigraphic images after treadmill exercise. Criteria for an abnormal thallium scintigram included: (a) greater than or equal to 25% persistent reduction in Tl-201 uptake in anterolateral, anteroseptal, posterolateral, and inferoapical segments, or greater than or equal to 35% reduction in the inferior segment; (b) an initial defect with delayed redistribution; and (c) abnormal Tl-201 washout. Of 110 patients with significant coronary artery disease (CAD), 100 had abnormal Tl-201 scintigrams, while 27 of 30 patients with angiographically normal coronary arteries had normal scintigrams; 91% sensitivity, 90% specificity, and 97% predictive accuracy. Sensitivity and specificity were not significantly different when the 95 patients with diagnostic (greater than or equal to 85% maximum heart rate) and 45 with inconclusive (less than or equal to 85% maximum HR) Ex tests were compared. Comparison of qualitative and quantitative image analyses in a subset of these patients showed that both specificity and multivessel disease prediction were greater when the quantitative approach was used (90 against 73% and 78 against 39%, respectively). Sensitivity for CAD detection was reduced by 10% with visual interpretation alone. Thus, quantitative exercise Tl-201 scintigraphy appears highly sensitive and specific for CAD detection in patients with chest pain.

  11. 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. PMID:27607947

  12. 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.

  13. Terahertz absorbance spectrum fitting method for quantitative detection of concealed contraband

    NASA Astrophysics Data System (ADS)

    Wang, Yingxin; Zhao, Ziran; Chen, Zhiqiang; Kang, Kejun; Feng, Bing; Zhang, Yan

    2007-12-01

    We present a quantitative method for the nondestructive detection of concealed contraband based on terahertz transmission spectroscopy. Without knowing the prior information of barrier materials, the amount of concealed contraband can be extracted by approximating the terahertz absorbance spectrum of the barrier material with a low-order polynomial and then fitting the measured absorbance spectrum of the inspected object with the polynomial and the known standard spectrum of this kind of contraband. We verify the validity of this method using a sample of explosive 1,3,5-trinitro-s-triazine (RDX) covered with several different barrier materials which are commonly encountered in actual inspection, and good agreement between the calculated and actual value of the amount of RDX is obtained for the experiments performed under both nitrogen and air atmospheres. This indicates that the presented method can achieve quantitative detection of hidden contraband, which is important for security inspection applications.

  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. Bone scanning.

    PubMed

    Greenfield, L D; Bennett, L R

    1975-03-01

    Scanning is based on the uptake of a nuclide by the crystal lattice of bone and is related to bone blood flow. Cancer cells do not take up the tracer. Normally, the scan visualizes the highly vascular bones. Scans are useful and are indicated in metastatic bone disease, primary bone tumors, hematologic malignancies and some non-neoplastic diseases. The scan is more sensitive than x-ray in the detection of malignant diseases of the skeleton. PMID:1054210

  16. 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. PMID:26356762

  17. Detection and quantitation of low abundance oligosaccharides in recombinant monoclonal antibodies.

    PubMed

    Ponniah, Gomathinayagam; Nowak, Christine; Gonzalez, Nidia; Miano, Dino; Liu, Hongcheng

    2015-03-01

    Oligosaccharides are critical for structural integrity, stability, and biological functions of recombinant monoclonal antibodies. It is relatively easy to characterize, quantify, and determine the impact of major glycoforms. While challenging to detect and quantify, certain low abundance oligosaccharides are highly relevant to the stability and functions of recombinant monoclonal antibodies. Methods were established in this study based on enzymatic digestion to consolidate peaks of the same type of oligosaccharides by removing heterogeneity and thus increase detectability of low abundance peaks. Endo H was used to collapse high mannose oligosaccharides to a single peak of GlcNAc for ease of detection and quantitation. β-Galactosidase and β-N-acetylhexosaminidase were used to convert complex oligosaccharides into two peaks containing either GlcNAc2Man3Fuc or GlcNAc2Man3, which simplified the chromatograms and data analysis. More importantly, low abundance hybrid oligosaccharides can only be detected and qualified after β-galactosidase and β-N-acetylhexosaminidase digestion. Detection and quantitation of low abundance oligosaccharides can also be achieved using a combination of all three enzymes. These methods can be applied to the development of recombinant monoclonal antibody therapeutics. PMID:25647617

  18. Simple, sensitive, and quantitative electrochemical detection method for paper analytical devices.

    PubMed

    Scida, Karen; Cunningham, Josephine C; Renault, Christophe; Richards, Ian; Crooks, Richard M

    2014-07-01

    We report a new type of paper analytical device that provides quantitative electrochemical output and detects concentrations as low as 767 fM. The model analyte is labeled with silver nanoparticles (AgNPs), which provide 250,000-fold amplification. AgNPs eliminate the need for enzymatic amplification, thereby improving device stability and response time. The use of magnetic beads to preconcentrate the AgNPs at the detection electrode further improves sensitivity. Response time is improved by incorporation of a hollow channel, which increases the flow rate in the device by a factor of 7 and facilitates the use of magnetic beads. A key reaction necessary for label detection is made possible by the presence of a slip layer, a fluidic switch that can be actuated by manually slipping a piece of paper. The design of the device is versatile and should be useful for detection of proteins, nucleic acids, and microbes. PMID:24918259

  19. Development of a computer-aided diagnostic scheme for detection of interval changes in successive whole-body bone scans

    SciTech Connect

    Shiraishi, Junji; Li Qiang; Appelbaum, Daniel; Pu Yonglin; Doi, Kunio

    2007-01-15

    Bone scintigraphy is the most frequent examination among various diagnostic nuclear medicine procedures. It is a well-established imaging modality for the diagnosis of osseous metastasis and for monitoring osseous tumor response to chemotherapy and radiation therapy. Although the sensitivity of bone scan examinations for detection of bone abnormalities has been considered to be relatively high, it is time consuming to identify multiple lesions such as bone metastases of prostate and breast cancers. In addition, it is very difficult to detect subtle interval changes between two successive abnormal bone scans, because of variations in patient conditions, the accumulation of radioisotopes during each examination, and the image quality of gamma cameras. Therefore, we developed a new computer-aided diagnostic (CAD) scheme for the detection of interval changes in successive whole-body bone scans by use of a temporal subtraction image which was obtained with a nonlinear image-warping technique. We carried out 58 pairs of successive bone scans in which each scan included both posterior and anterior views. We determined 107 'gold-standard' interval changes among the 58 pairs based on the consensus of three radiologists. Our computerized scheme consisted of seven steps, i.e., initial image density normalization on each image, image matching for the paired images, temporal subtraction by use of the nonlinear image-warping technique, initial detection of interval changes by use of temporal-subtraction images, image feature extraction of candidates of interval changes, rule-based tests by use of 16 image features for removing some false positives, and display of the computer output for identified interval changes. One hundred seven gold standard interval changes included 71 hot lesions (uptake was increased compared with the previous scan, or there was new uptake in the current scan) and 36 cold lesions (uptake was decreased or disappeared) for anterior and posterior views. The

  20. Development of a computer-aided diagnostic scheme for detection of interval changes in successive whole-body bone scans.

    PubMed

    Shiraishi, Junji; Li, Qiang; Appelbaum, Daniel; Pu, Yonglin; Doi, Kunio

    2007-01-01

    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

  1. 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. PMID:27326831

  2. 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.

  3. Imaging via complete cantilever dynamic detection: general dynamic mode imaging and spectroscopy in scanning probe microscopy.

    PubMed

    Somnath, Suhas; Collins, Liam; Matheson, Michael A; Sukumar, Sreenivas R; Kalinin, Sergei V; Jesse, Stephen

    2016-10-14

    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. PMID:27607339

  4. LiDAR scan and smart piezo layer combined damage detection

    NASA Astrophysics Data System (ADS)

    Chen, Shenen; Chung, Howard; Park, Youngjin

    2013-04-01

    The motivation of this study is to determine a technique to completely describe the damage state of large deformed structures commonly found during forensic investigations. The combination of Laser Detecting and Ranging (LiDAR) and Piezoelectric (PZT) Sensing Technologies for damage quantification is suggested to generate the full-field description of large deformation of a plate. The test subject is a 16 inch by 16 inch aluminum plate subjected to different damage scenarios. LiDAR is a static scanning laser that provides a 3-dimensional picture of the object. Smart Layer is a commercial PZT actuator/sensor network system that generates stress waves for internal damage evaluation. Both techniques were applied to the test plate after damages are introduced. In order to effectively analyze the results, the images for each test were superimposed. Frequencies that depicted the best interpretation of damage in the direct path images were superimposed with the 3-dimensional LiDAR images. Four damage scenarios were imposed on an aluminum plate including saw cuts at different depths using an electric saw. The final damage is a severe bending of the plate. The bending of the specimen produced an image that located the most severe damage directly under the left hand portion and directly above the right hand portion of the bend.

  5. 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. PMID:26538617

  6. 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.

  7. 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.

  8. A new total body scanning system for automatic change detection in multiple pigmented skin lesions.

    PubMed

    Korotkov, Konstantin; Quintana, Josep; Puig, Susana; Malvehy, Josep; Garcia, Rafael

    2015-01-01

    The detection of newly appearing and changing pigmented skin lesions (PSLs) is essential for timely diagnosis of cutaneous melanoma. Total body skin examination (TBSE) procedures, currently practiced for this purpose, can be extremely time-consuming for patients with numerous lesions. In addition, these procedures are prone to subjectivity when selecting PSLs for baseline image comparison, increasing the risk of missing a developing cancer. To address this issue, we propose a new photogrammetry-based total body scanning system allowing for skin surface image acquisition using cross-polarized light. Equipped with 21 high-resolution cameras and a turntable, this scanner automatically acquires a set of overlapping images, covering 85%-90% of the patient's skin surface. These images are used for the automated mapping of PSLs and their change estimation between explorations. The maps produced relate images of individual lesions with their locations on the patient's body, solving the body-to-image and image-to-image correspondence problem in TBSEs. Currently, the scanner is limited to patients with sparse body hair and, for a complete skin examination, the scalp, palms, soles and inner arms should be photographed manually. The initial tests of the scanner showed that it can be successfully applied for automated mapping and temporal monitoring of multiple lesions: PSLs relevant for follow-up were repeatedly mapped in several explorations. Moreover, during the baseline image comparison, all lesions with artificially induced changes were correctly identified as "evolved." PMID:25222947

  9. Scanning electrochemical microscopy of model neurons: imaging and real-time detection of morphological changes.

    PubMed

    Liebetrau, Johanna M; Miller, Heather M; Baur, John E; Takacs, Sara A; Anupunpisit, Vipavee; Garris, Paul A; Wipf, David O

    2003-02-01

    Living PC12 cells, a model cell type for studying neuronal function, were imaged using the negative feedback mode of a scanning electrochemical microscope (SECM). Six biocompatible redox mediators were successfully identified from a large pool of candidates and were then used for imaging PC12 cells before and after exposure to nerve growth factor (NGF). When exposed to NGF, cells differentiate into a neuron phenotype by growing narrow neurites (1-2 microm wide) that can extend > 100 microm from the cell proper. We demonstrate that carbon fiber electrodes with reduced tip diameters can be used for imaging both the cell proper and these neurites. Regions of decreased current, possibly resulting from raised features not identifiable by light microscopy, are clearly evident in the SECM images. Changes in the morphology of undifferentiated PC12 cells could be detected in real time with the SECM. After exposure to hypotonic and hypertonic solutions, reversible changes in cell height of <2 microm were measured. PMID:12585485

  10. Imaging via complete cantilever dynamic detection: General dynamic mode imaging and spectroscopy in scanning probe microscopy

    DOE PAGESBeta

    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 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

  11. 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

    2016-01-01

    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

  12. 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

  13. Indium 111-labeled leukocyte scanning for detection of prosthetic vascular graft infection

    SciTech Connect

    Lawrence, P.F.; Dries, D.J.; Alazraki, N.; Albo, D. Jr.

    1985-01-01

    Recent animal and human studies have suggested that positive indium 111-labeled leukocyte scans may help establish the diagnosis of vascular graft infection; however, there is little information available about the predictive value of both positive and negative leukocyte scans in larger groups of patients. In this study 31 indium 111 leukocyte scans were performed prior to definitive treatment in 21 patients with suspected vascular graft infections. Patients with more than one leukocyte scan performed had either anatomically distinct sites of infection or rescanning of a potentially infected site after definitive treatment. Scans were performed according to the method of Baker et al., attaching 500 muCi of indium 111 to leukocytes with imaging 24 hours later. All patients with positive scans underwent surgical exploration of the area of leukocyte accumulation, with documentation of purulence and culture of the graft. Patients with negative scans were treated as if scan results were indeterminate and underwent surgical exploration for usual clinical indications; if no exploration was performed, the patient was followed up closely for at least 1 year. Twelve of 12 positive scans showed purulence or culture evidence of infection with three different organisms; in 15 instances of negative scans, two operations were performed with one infection noted, whereas no patient without surgery has had a graft infection at 10 months follow-up. In addition to localizing graft infections, two scans demonstrated a nonvascular site of infection. Positive scans also helped determine the extent of infection along the graft, allowing better planning of the surgical procedure. These results indicate that indium 111-labeled leukocyte scans help document and localize prosthetic vascular graft infections.

  14. ScanIndel: a hybrid framework for indel detection via gapped alignment, split reads and de novo assembly.

    PubMed

    Yang, Rendong; Nelson, Andrew C; Henzler, Christine; Thyagarajan, Bharat; Silverstein, Kevin A T

    2015-01-01

    Comprehensive identification of insertions/deletions (indels) across the full size spectrum from second generation sequencing is challenging due to the relatively short read length inherent in the technology. Different indel calling methods exist but are limited in detection to specific sizes with varying accuracy and resolution. We present ScanIndel, an integrated framework for detecting indels with multiple heuristics including gapped alignment, split reads and de novo assembly. Using simulation data, we demonstrate ScanIndel's superior sensitivity and specificity relative to several state-of-the-art indel callers across various coverage levels and indel sizes. ScanIndel yields higher predictive accuracy with lower computational cost compared with existing tools for both targeted resequencing data from tumor specimens and high coverage whole-genome sequencing data from the human NIST standard NA12878. Thus, we anticipate ScanIndel will improve indel analysis in both clinical and research settings. ScanIndel is implemented in Python, and is freely available for academic use at https://github.com/cauyrd/ScanIndel. PMID:26643039

  15. Rapid tests for detection and quantitation of Enterococcus contamination in recreational waters.

    PubMed

    Morgan, Rhian; Morris, Ceri; Livzey, Kristin; Hogan, James; Buttigieg, Neil; Pollner, Reinhold; Kacian, Daniel; Weeks, Ian

    2007-05-01

    Presently, growth-based tests are used for the detection and quantitation of microbiological contaminants in the environment. These tests take a minimum of 24 h to generate a result, which compromises the ability to take the most appropriate action. This report describes a rapid test for Enterococcus in recreational water as an indicator of faecal contamination. This method involves (1) isolation and lysis of the target organism, (2) purification of ribosomal RNA (rRNA) from the lysate and (3) amplification and detection of the purified rRNA. rRNA is used as the target since, in contrast to DNA, there are hundreds to thousands of copies in the cell. The rRNA is purified from the lysate by target capture onto magnetic microspheres, which removes interfering substances present in the sample. The rRNA is then quantitated using transcription-mediated amplification (TMA) with real-time homogeneous detection of amplicon using a fluorescent oligonucleotide probe. Compared to polymerase chain reaction (PCR) amplification, TMA is isothermal, more rapid, and ideally suited to RNA detection. The test described here demonstrates sensitive detection and quantitation of enterococci over a wide dynamic range with a high level of analytical specificity. The latter is particularly important for accurate and relevant monitoring both for protecting public health and for source tracking. Many conventional microbiological tests are time-consuming, exhibit limited dynamic range and are known to lack specificity. This assay demonstrates the advantages achievable by the application of TMA of rRNA targets to current environmental testing challenges. PMID:17492087

  16. Automated detection of pulmonary nodules from whole lung helical CT scans: performance comparison for isolated and attached nodules

    NASA Astrophysics Data System (ADS)

    Enquobahrie, Andinet A.; Reeves, Anthony P.; Yankelevitz, David F.; Henschke, Claudia I.

    2004-05-01

    The objective of this research is to evaluate and compare the performance of our automated detection algorithm on isolated and attached nodules in whole lung CT scans. Isolated nodules are surrounded by the lung parenchyma with no attachment to large solid structures such as the chest wall or mediastinum surface, while attached nodules are adjacent to these structures. The detection algorithm involves three major stages. First, the region of the image space where pulmonary nodules are to be found is identified. This involves segmenting the lung region and generating the pleural surface. In the second stage, which is the hypothesis generation stage, nodule candidate locations are identified and their sizes are estimated. The nodule candidates are successively refined in the third stage a sequence of filters of increasing complexity. The algorithm was tested on a dataset containing 250 low-dose whole lung CT scans with 2.5mm slice thickness. A scan is composed of images covering the whole lung region for a single person. The dataset was partitioned into 200 and 50 scans for training and testing the algorithm. Only solid nodules were considered in this study. Experienced chest radiologists identified a total of 447 solid nodules. 345 and 102 of the nodules were from the training and testing datasets respectively. 126(28.2%) of the nodules in the dataset were attached nodules. The detection performance was then evaluated separately for isolated and attached nodule types considering different size ranges. For nodules 3mm and larger, the algorithm achieved a sensitivity of 97.8% with 2.0 false positives (FPs) per scan and 95.7% with 19.3 FPs per scan for isolated and attached nodules respectively. For nodules 4mm and larger, a sensitivity of 96.6% with 1.5 FP per scan and a 100% sensitivity with 13 FPs per scan were obtained for isolated and attached nodule types respectively. The results show that our algorithm detects isolated and attached nodules with comparable

  17. Quantitative assessment of colon distention for polyp detection in CT virtual colonoscopy

    NASA Astrophysics Data System (ADS)

    Van Uitert, Robert; Bitter, Ingmar; Summers, Ronald M.; Choi, J. Richard; Pickhardt, Perry J.

    2006-03-01

    Virtual colonoscopy is becoming a more prevalent way to diagnose colon cancer. One of the critical elements in detecting cancerous polyps using virtual colonoscopy, especially in conjunction with computer-aided detection of polyps, is that the colon be sufficiently distended. We have developed an automatic method to determine from a CT scan what percentage of the colon is distended by 1cm or larger and compared our method with a radiologist's assessment of quality of the scan with respect to successful colon polyp detection. A radiologist grouped 41 CT virtual colonoscopy scans into three groups according to the degree of colonic distention, "well", "medium", and "poor". We also employed a subvoxel accurate centerline algorithm and a subvoxel accurate distance transform to each dataset to measure the colon distention along the centerline. To summarize the colonic distention with a single value relevant for polyp detection, the distention score, we recorded the percentage of centerline positions in which the colon distention was 1cm or larger. We then compared the radiologist's assessment and the computed results. The sorting of all datasets according to the distention score agreed with the radiologist's assessment. The "poor" cases had a mean and standard deviation score of 78.4% +/- 5.2%, the "medium" cases measured 88.7% +/- 1.9%, and the "well" cases 98.8% +/- 1.5%. All categories were shown to be significantly different from each other using unpaired two sample t-tests. The presented colonic distention score is an accurate method for assessing the quality of colonic distention for CT colonography.

  18. 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

  19. 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

  20. Quantitative Detection of Clostridium perfringens in the Broiler Fowl Gastrointestinal Tract by Real-Time PCR

    PubMed Central

    Wise, Mark G.; Siragusa, Gregory R.

    2005-01-01

    Strains of Clostridium perfringens are a frequent cause of food-borne disease and gas gangrene and are also associated with necrotic enteritis in chickens. To detect and quantify the levels of C. perfringens in the chicken gastrointestinal tract, a quantitative real-time PCR assay utilizing a fluorogenic, hydrolysis-type probe was developed and utilized to assay material retrieved from the broiler chicken cecum and ileum. Primers and probe were selected following an alignment of 16S rDNA sequences from members of cluster I of the genus Clostridium, and proved to be specific for C. perfringens. The assay could detect approximately 50 fg of C. perfringens genomic DNA and approximately 20 cells in pure culture. Measurements of the analytical sensitivity determined with spiked intestinal contents indicated that the consistent limit of detection with ileal samples was approximately 102 CFU/g of ileal material, but only about 104 CFU/g of cecal samples. The decreased sensitivity with the cecal samples was due to the presence of an unidentified chemical PCR inhibitor(s) in the cecal DNA purifications. The assay was utilized to rapidly detect and quantify C. perfringens levels in the gut tract of broiler chickens reared without supplementary growth-promoting antibiotics that manifested symptoms of necrotic enteritis. The results illustrated that quantitative real-time PCR correlates well with quantification via standard plate counts in samples taken from the ileal region of the gastrointestinal tract. PMID:16000804

  1. Validation of a quantitative PCR assay for detection and quantification of 'Candidatus Xenohaliotis californiensis'.

    PubMed

    Friedman, Carolyn S; Wight, Nate; Crosson, Lisa M; White, Samuel J; Strenge, Robyn M

    2014-04-01

    Withering syndrome (WS), a serious disease affecting abalone Haliotis spp., is caused by infection from an intracellular Rickettsia-like organism (WS-RLO). Diagnosis of the disease currently relies on a combination of histological examination and molecular methods (in situ hybridization, standard PCR, and sequence analysis). However, these techniques only provide a semi-quantitative assessment of bacterial load. We created a real-time quantitative PCR (qPCR) assay to specifically identify and enumerate bacterial loads of WS-RLO in abalone tissue, fecal, and seawater samples based on 16S rDNA gene copy numbers. The qPCR assay designed to detect DNA of the WS-RLO was validated according to standards set by the World Organisation for Animal Health. Standard curves derived from purified plasmid dilutions were linear across 7 logs of concentration, and efficiencies ranged from 90.2 to 97.4%. The limit of detection was 3 gene copies per reaction. Diagnostic sensitivity was 100% and specificity was 99.8%. The qPCR assay was robust, as evidenced by its high level of repeatability and reproducibility. This study has shown for the first time that WS-RLO DNA can be detected and quantified in abalone tissue, fecal, and seawater samples. The ability to detect and quantify RLO gene copies in a variety of materials will enable us to better understand transmission dynamics in both farmed and natural environments. PMID:24695238

  2. 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. PMID:26274894

  3. 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. PMID:26468325

  4. A Slot Blot Immunoassay for Quantitative Detection of Plasmodium falciparum Circumsporozoite Protein in Mosquito Midgut Oocyst

    PubMed Central

    Kumar, Sanjai; Zheng, Hong; Deng, Bingbing; Mahajan, Babita; Grabias, Bryan; Kozakai, Yukiko; Morin, Merribeth J.; Locke, Emily; Birkett, Ashley; Miura, Kazutoyo; Long, Carole

    2014-01-01

    There is still a need for sensitive and reproducible immunoassays for quantitative detection of malarial antigens in preclinical and clinical phases of vaccine development and in epidemiology and surveillance studies, particularly in the vector host. Here we report the results of sensitivity and reproducibility studies for a research-grade, quantitative enhanced chemiluminescent-based slot blot assay (ECL-SB) for detection of both recombinant Plasmodium falciparum circumsporozoite protein (rPfCSP) and native PfCSP from Oocysts (Pf Oocyst) developing in the midguts of Anopheles stephensi mosquitoes. The ECL-SB detects as little as 1.25 pg of rPfCSP (linear range of quantitation 2.5–20 pg; R2 = 0.9505). We also find the earliest detectable expression of native PfCSP in Pf Oocyst by ECL-SB occurs on day 7 post feeding with infected blood meal. The ECL-SB was able to detect approximately as few as 0.5 day 8 Pf Oocysts (linear quantitation range 1–4, R2 = 0.9795) and determined that one Pf Oocyst expressed approximately 2.0 pg (0.5–3 pg) of native PfCSP, suggesting a similar range of detection for recombinant and native forms of Pf CSP. The ECL-SB is highly reproducible; the Coefficient of Variation (CV) for inter-assay variability for rPf CSP and native PfCSP were 1.74% and 1.32%, respectively. The CVs for intra-assay variability performed on three days for rPf CSP were 2.41%, 0.82% and 2% and for native Pf CSP 1.52%, 0.57%, and 1.86%, respectively. In addition, the ECL-SB was comparable to microscopy in determining the P. falciparum prevalence in mosquito populations that distinctly contained either high and low midgut Pf Oocyst burden. In whole mosquito samples, estimations of positivity for P. falciparum in the high and low burden groups were 83.3% and 23.3% by ECL-SB and 85.7% and 27.6% by microscopy. Based on its performance characteristics, ECL-SB could be valuable in vaccine development and to measure the parasite prevalence in mosquitoes and

  5. 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.

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

    PubMed

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

    2006-10-21

    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. PMID:17019042

  7. 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...

  8. 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.

  9. Methods for quantitative detection of antibody-induced complement activation on red blood cells.

    PubMed

    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 - fatal(1). 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 lysis(1-4). 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

  10. 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

  11. A revisited hemolytic assay for palytoxin detection: Limitations for its quantitation in mussels.

    PubMed

    Brovedani, Valentina; Sosa, Silvio; Poli, Mark; Forino, Martino; Varello, Katia; Tubaro, Aurelia; Pelin, Marco

    2016-09-01

    Palytoxin (PLTX) and its analogues have been detected as seafood contaminants associated with a series of human foodborne poisonings. Due to a number of fatalities ascribed to the ingestion of PLTX-contaminated marine organisms, the development of methods for its detection in seafood has been recommended by the European Food Safety Authority (EFSA). Due to its feasibility, the spectrophotometric hemolytic assay is widely used to detect PLTX in different matrices, even though a standardized protocol is still lacking. Thus, on the basis of available assay procedures, a new standardized protocol was set up using purified human erythrocytes exposed to PLTX (working range: 3.9 × 10(-10)-2.5 × 10(-8) M) in a K(+)-free phosphate buffered saline solution, employing a 5 h incubation at 41 °C. An intra-laboratory characterization demonstrated its sensitivity (limit of detection, LOD = 1.4 × 10(-10) M and quantitation, LOQ = 3.4 × 10(-10) M), accuracy (bias = -0.8%), repeatability (RSDr = 15% and 6% for intra- and inter-day repeatability, respectively) and specificity. However, the standardized method seems not to be suitable for PLTX quantitation in complex matrices, such as mussel (Mytilus galloprovincialis) extracts, at least below the limit suggested by EFSA (30 μg PLTXs/Kg shellfish meat). Thus, the hemolytic assay for PLTX quantitation in seafood should be used only after a careful evaluation of the specific matrix effects. PMID:27343702

  12. Tree Scanning

    PubMed Central

    Templeton, Alan R.; Maxwell, Taylor; Posada, David; Stengård, Jari H.; Boerwinkle, Eric; Sing, Charles F.

    2005-01-01

    We use evolutionary trees of haplotypes to study phenotypic associations by exhaustively examining all possible biallelic partitions of the tree, a technique we call tree scanning. If the first scan detects significant associations, additional rounds of tree scanning are used to partition the tree into three or more allelic classes. Two worked examples are presented. The first is a reanalysis of associations between haplotypes at the Alcohol Dehydrogenase locus in Drosophila melanogaster that was previously analyzed using a nested clade analysis, a more complicated technique for using haplotype trees to detect phenotypic associations. Tree scanning and the nested clade analysis yield the same inferences when permutation testing is used with both approaches. The second example is an analysis of associations between variation in various lipid traits and genetic variation at the Apolipoprotein E (APOE) gene in three human populations. Tree scanning successfully identified phenotypic associations expected from previous analyses. Tree scanning for the most part detected more associations and provided a better biological interpretative framework than single SNP analyses. We also show how prior information can be incorporated into the tree scan by starting with the traditional three electrophoretic alleles at APOE. Tree scanning detected genetically determined phenotypic heterogeneity within all three electrophoretic allelic classes. Overall, tree scanning is a simple, powerful, and flexible method for using haplotype trees to detect phenotype/genotype associations at candidate loci. PMID:15371364

  13. 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.

  14. Nanomolar colorimetric quantitative detection of Fe(3+) and PPi with high selectivity.

    PubMed

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

    2016-04-15

    A novel rhodamine and 8-hydroxyquinoline-based derivative was synthesized, which is shown to act as a colorimetric chemosensor for Fe(3+) 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 (<1min). Fe(3+) can be detected quantitatively in the concentration range from 6.7 to 16μM and the detection limit (LOD) on UV-vis response of the sensor can be as low as 15nM. The 'in situ' prepared Fe(3+) complex (1⋅Fe) showed high selectivity toward PPi against many common anions, and sensitivity (the LOD can be as low as 71nM). In addition, both the chemosensor and the 'in situ' prepared Fe(3+) complex are reusable for the detection of Fe(3+) and PPi respectively. PMID:26878355

  15. 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. PMID:22285626

  16. 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

  17. A competitive enzyme immunoassay for the quantitative detection of cocaine from banknotes and latent fingermarks.

    PubMed

    van der Heide, Susan; Garcia Calavia, Paula; Hardwick, Sheila; Hudson, Simon; Wolff, Kim; Russell, David A

    2015-05-01

    A sensitive and versatile competitive enzyme immunoassay (cEIA) has been developed for the quantitative detection of cocaine in complex forensic samples. Polyclonal anti-cocaine antibody was purified from serum and deposited onto microtiter plates. The concentration of the cocaine antibody adsorbed onto the plates, and the dilution of the cocaine-HRP hapten were both studied to achieve an optimised immunoassay. The method was successfully used to quantify cocaine in extracts taken from both paper currency and latent fingermarks. The limit of detection (LOD) of 0.162ngmL(-1) achieved with the assay compares favourably to that of conventional chromatography-mass spectroscopy techniques, with an appropriate sensitivity for the quantification of cocaine at the low concentrations present in some forensic samples. The cEIA was directly compared to LC-MS for the analysis of ten UK banknote samples. The results obtained from both techniques were statistically similar, suggesting that the immunoassay was unaffected by cross-reactivity with potentially interfering compounds. The cEIA was used also for the detection of cocaine in extracts from latent fingermarks. The results obtained were compared to the cocaine concentrations detected in oral fluid sampled from the same individual. Using the cEIA, we have shown, for the first time, that endogeneously excreted cocaine can be detected and quantified from a single latent fingermark. Additionally, it has been shown that the presence of cocaine, at similar concentrations, in more than one latent fingermark from the same individual can be linked with those concentrations found in oral fluid. These results show that detection of drugs in latent fingermarks could directly indicate whether an individual has consumed the drug. The specificity and feasibility of measuring low concentrations of cocaine in complex forensic samples demonstrate the effectiveness and robustness of the assay. The immunoassay presents a simple and cost

  18. Quantitative PCR for detection of Nosema bombycis in single silkworm eggs and newly hatched larvae.

    PubMed

    Fu, Zhangwuke; He, Xiangkang; Cai, Shunfeng; Liu, Han; He, Xinyi; Li, Mingqian; Lu, Xingmeng

    2016-01-01

    Pebrine disease is the only mandatory quarantine item in sericultural production due to its destructive consequences. So far, the mother moth microscopic examination method established by Pasteur (1870) remains the only detection method for screening for the causative agent Nosema bombycis (N. bombycis). Because pebrine is a horizontal and vertical transmission disease, it is better to inspect silkworm eggs and newly hatched larvae to investigate the infection rate, vertical transmission rate and spore load of the progenies. There is a rising demand for a more direct, effective and accurate detection approach in the sericultural industry. Here, we developed a molecular detection approach based on real-time quantitative PCR (qPCR) for pebrine inspection in single silkworm eggs and newly hatched larvae. Targeting the small-subunit rRNA gene of N. bombycis, this assay showed high sensitivity and reproducibility. Ten spores in a whole sample or 0.1 spore DNA (1 spore DNA represents the DNA content of one N. bombycis spore) in a reaction system was estimated as the detection limit of the isolation and real-time qPCR procedure. Silkworm egg tissues impact the detection sensitivity but are not significant in single silkworm egg detection. Of 400 samples produced by infected moths, 167 and 195 were scored positive by light microscopy and real-time qPCR analysis, respectively. With higher accuracy and the potential capability of high-throughput screening, this method is anticipated to be adaptable for pebrine inspection and surveillance in the sericultural industry. In addition, this method can be applied to ecology studies of N. bombycis-silkworm interactions due to its quantitative function. PMID:26658327

  19. 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

  20. Rapid Detection of Ceratocystis platani Inoculum by Quantitative Real-Time PCR Assay

    PubMed Central

    Ghelardini, Luisa; Belbahri, Lassaâd; Quartier, Marion; Santini, Alberto

    2013-01-01

    Ceratocystis platani is the causal agent of canker stain of plane trees, a lethal disease able to kill mature trees in one or two successive growing seasons. The pathogen is a quarantine organism and has a negative impact on anthropogenic and natural populations of plane trees. Contaminated sawdust produced during pruning and sanitation fellings can contribute to disease spread. The goal of this study was to design a rapid, real-time quantitative PCR assay to detect a C. platani airborne inoculum. Airborne inoculum traps (AITs) were placed in an urban setting in the city of Florence, Italy, where the disease was present. Primers and TaqMan minor groove binder (MGB) probes were designed to target cerato-platanin (CP) and internal transcribed spacer 2 (ITS2) genes. The detection limits of the assay were 0.05 pg/μl and 2 fg/μl of fungal DNA for CP and ITS, respectively. Pathogen detection directly from AITs demonstrated specificity and high sensitivity for C. platani, detecting DNA concentrations as low as 1.2 × 10−2 to 1.4 × 10−2 pg/μl, corresponding to ∼10 conidia per ml. Airborne inoculum traps were able to detect the C. platani inoculum within 200 m of the closest symptomatic infected plane tree. The combination of airborne trapping and real-time quantitative PCR assay provides a rapid and sensitive method for the specific detection of a C. platani inoculum. This technique may be used to identify the period of highest risk of pathogen spread in a site, thus helping disease management. PMID:23811499

  1. Empyema of the gallbladder detected by gallium scan and abdominal ultrasonography

    SciTech Connect

    Garcia, O.M.; Kovac, A.; Plauche, W.E.

    1981-08-01

    A case history of patient with a abnormal gallium uptake and sonogram in the region of the gallbladder is described. The abnormality was interpreted as empyema of the gallbladder and later proven surgically. A liver-spleen scan was normal except for slight prominence of the hilar structures. Gallium citrate Ga-67 scans done at 24 and 48 hours showed a persistent area of increased tracer localization around the gallbladder with a central clear zone in the latter scan. Ultrasonography revealed poor definition and slight thickening of the gallbladder wall. Because of the lack of specificity of gallium scans, the combination of ultrasonic imaging and gallium uptake scans appears much superior in diagnostic efficiency than either of the two alone. The sequence of performing these two examinations does not seem to be critical though it was prefered that the scintigraphy precede the sonography.

  2. 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

  3. 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.

  4. A genome-wide linkage scan for quantitative trait loci influencing the craniofacial complex in humans(Homo sapiens sapiens)

    PubMed Central

    Sherwood, Richard J.; Duren, Dana L.; Mahaney, Michael C.; Blangero, John; Dyer, Thomas D.; Cole, Shelley A.; Czerwinski, Stefan A.; Chumlea, Wm. Cameron; Siervogel, Roger M.; Choh, Audrey C.; Nahhas, Ramzi W.; Lee, Miryoung; Towne, Bradford

    2011-01-01

    The genetic architecture of the craniofacial complex has been the subject of intense scrutiny because of the high frequency of congenital malformations. Numerous animal models have been used to document the early development of the craniofacial complex, but few studies have focused directly on the genetic underpinnings of normal variation in the human craniofacial complex. The current study examines 80 quantitative traits derived from lateral cephalographs of 981 participants in the Fels Longitudinal Study, Wright State University, Dayton, Ohio. Quantitative genetic analyses were conducted using the SOLAR analytic platform, a maximum-likelihood variance components method that incorporates all familial information for parameter estimation. Heritability estimates were significant and of moderate to high magnitude for all craniofacial traits. Additionally, significant quantitative trait loci (QTL) were identified for 10 traits from the three developmental components (basicranium, splanchnocranium, and neurocranium) of the craniofacial complex. These QTL were found on chromosomes 3, 6, 11, 12, and 14. This study of the genetic architecture of the craniofacial complex elucidates fundamental information of the genetic architecture of the craniofacial complex in humans. PMID:21328561

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

    PubMed

    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

  6. Profiling and Quantitation of Bacterial Carotenoids by Liquid Chromatography and Photodiode Array Detection

    PubMed Central

    Nelis, H. J.; De Leenheer, A. P.

    1989-01-01

    An analytical method for the profiling and quantitative determination of carotenoids in bacteria is described. Exhaustive extraction of the pigments from four selected bacterial strains required treatment of the cells with potassium hydroxide or liquefied phenol or both before the addition of the extracting solvent (methanol or diethyl ether). The carotenoids in the extracts were separated by nonaqueous reversed-phase liquid chromatography in conjunction with photodiode array absorption detection. The identity of a peak was considered definitive only when both its retention time and absorption spectrum, before and after chemical reactions, matched those of a reference component. In the absence of the latter, most peaks could be tentatively identified. Two examples illustrate how in the analysis of pigmented bacteria errors may result from using nonchromatographic procedures or liquid chromatographic methods lacking sufficient criteria for peak identification. Carotenoids of interest were determined quantitatively when the authentic reference substance was available or, alternatively, were determined semiquantitatively. PMID:16348068

  7. Detecting surface changes of slope to channel coupling in an alpine catchment using terrestrial laser scanning

    NASA Astrophysics Data System (ADS)

    Rascher, Eric; Sass, Oliver

    2015-04-01

    Understanding the evolution and functions of a river system and interpreting the morphology and the dynamics of the channel is a key factor in fluvial geomorphology. For this purpose it is essential to analyse the processes of sediment input and output within and between river reaches and to detect the various forms of storage types on hillslopes and in the channel network. From these processes catchment scale sediment fluxes are derived and result in sediment budgets showing the amount and motion of sediment through the system. Sediment connectivity is a highly important characteristic of catchments when sediment transfer processes are studied. In this context, connectivity controls the sediment fluxes throughout the landscape which means the transfer of sediment from sediment sources to sinks and particularly the potential of a particle to move through the system. This study focuses on slope to channel coupling in the Johnsbach Valley, a typical, non-glaciated alpine catchment in the eastern Austrian Alps. The valley covers an area of 65 km² with altitudes ranging from 584 m a.s.l. at the outlet to 2369 m a.s.l. (Hochtor). The valley is drained by the Johnsbach River which originates in a crystalline bedrock dominated part of the catchment. After approximately 10 km of the distance downstream the lithology changes to calcareous bedrock. In this part of the Johnsbach Valley most of the sediment contributing areas are situated. To detect slope to channel coupling surface changes were measured and mass balances were quantified by terrestrial laser scanning using a RIEGL LMS-Z620. Four field sites were chosen were side channels are directly connected to the main fluvial system. Additionally two field sites show sediment movement in between the side channels. Field campaigns were carried out in September and October of 2013 as well as in April, July, August and October of 2014. First results show that sediment contribution from the side channels and erosion of

  8. 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

  9. 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

  10. 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. PMID:25749798

  11. Methods for the Specific Detection and Quantitation of Amyloid-β Oligomers in Cerebrospinal Fluid.

    PubMed

    Schuster, Judith; Funke, Susanne Aileen

    2016-05-01

    Protein misfolding and aggregation are fundamental features of the majority of neurodegenerative diseases, like Alzheimer's disease (AD), Parkinson's disease, frontotemporal dementia, and prion diseases. Proteinaceous deposits in the brain of the patient, e.g., amyloid plaques consisting of the amyloid-β (Aβ) peptide and tangles composed of tau protein, are the hallmarks of AD. Soluble oligomers of Aβ and tau play a fundamental role in disease progression, and specific detection and quantification of the respective oligomeric proteins in cerebrospinal fluid may provide presymptomatically detectable biomarkers, paving the way for early diagnosis or even prognosis. Several studies on the development of techniques for the specific detection of Aβ oligomers were published, but some of the existing tools do not yet seem to be satisfactory, and the study results are contradicting. The detection of oligomers is challenging due to their polymorphous and unstable nature, their low concentration, and the presence of competing proteins and Aβ monomers in body fluids. Here, we present an overview of the current state of the development of methods for Aβ oligomer specific detection and quantitation. The methods are divided in the three subgroups: (i) enzyme linked immunosorbent assays (ELISA), (ii) methods for single oligomer detection, and (iii) others, which are mainly biosensor based methods. PMID:27163804

  12. High sensitivity detection of active botulinum neurotoxin by glyco-quantitative polymerase chain-reaction.

    PubMed

    Kwon, Seok Joon; Jeong, Eun Ji; Yoo, Yung Choon; Cai, Chao; Yang, Gi-Hyeok; Lee, Jae Chul; Dordick, Jonathan S; Linhardt, Robert J; Lee, Kyung Bok

    2014-03-01

    The sensitive detection of highly toxic botulinum neurotoxin (BoNT) from Clostridium botulinum is of critical importance because it causes human illnesses if foodborne or introduced in wounds and as an iatrogenic substance. Moreover, it has been recently considered a possible biological warfare agent. Over the past decade, significant progress has been made in BoNT detection technologies, including mouse lethality assays, enzyme-linked immunosorbent assays, and endopeptidase assays and by mass spectrometry. Critical assay requirements, including rapid assay, active toxin detection, sensitive and accurate detection, still remain challenging. Here, we present a novel method to detect active BoNTs using a Glyco-quantitative polymerase chain-reaction (qPCR) approach. Sialyllactose, which interacts with the binding-domain of BoNTs, is incorporated into a sialyllactose-DNA conjugate as a binding-probe for active BoNT and recovered through BoNT-immunoprecipitation. Glyco-qPCR analysis of the bound sialyllactose-DNA is then used to detect low attomolar concentrations of BoNT and attomolar to femtomolar concentrations of BoNT in honey, the most common foodborne source of infant botulism. PMID:24506443

  13. 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%.

  14. Native denaturation differential scanning fluorimetry: Determining the effect of urea using a quantitative real-time thermocycler.

    PubMed

    Childers, Christine L; Green, Stuart R; Dawson, Neal J; Storey, Kenneth B

    2016-09-01

    The effect of protein stability on kinetic function is monitored with many techniques that often require large amounts of expensive substrates and specialized equipment not universally available. We present differential scanning fluorimetry (DSF), a simple high-throughput assay performed in real-time thermocyclers, as a technique for analysis of protein unfolding. Furthermore, we demonstrate a correlation between the half-maximal rate of protein unfolding (Knd), and protein unfolding by urea (I50). This demonstrates that DSF methods can determine the structural stability of an enzyme's active site and can compare the relative structural stability of homologous enzymes with a high degree of sequence similarity. PMID:27296634

  15. 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

  16. 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. PMID:24048535

  17. Detection, monitoring, and quantitative analysis of wildfires with the BIRD satellite

    NASA Astrophysics Data System (ADS)

    Oertel, Dieter A.; Briess, Klaus; Lorenz, Eckehard; Skrbek, Wolfgang; Zhukov, Boris

    2004-02-01

    Increasing concern about environment and interest to avoid losses led to growing demands on space borne fire detection, monitoring and quantitative parameter estimation of wildfires. The global change research community intends to quantify the amount of gaseous and particulate matter emitted from vegetation fires, peat fires and coal seam fires. The DLR Institute of Space Sensor Technology and Planetary Exploration (Berlin-Adlershof) developed a small satellite called BIRD (Bi-spectral Infrared Detection) which carries a sensor package specially designed for fire detection. BIRD was launched as a piggy-back satellite on October 22, 2001 with ISRO"s Polar Satellite Launch Vehicle (PSLV). It is circling the Earth on a polar and sun-synchronous orbit at an altitude of 572 km and it is providing unique data for detailed analysis of high temperature events on Earth surface. The BIRD sensor package is dedicated for high resolution and reliable fire recognition. Active fire analysis is possible in the sub-pixel domain. The leading channel for fire detection and monitoring is the MIR channel at 3.8 μm. The rejection of false alarms is based on procedures using MIR/NIR (Middle Infra Red/Near Infra Red) and MIR/TIR (Middle Infra Red/Thermal Infra Red) radiance ratio thresholds. Unique results of BIRD wildfire detection and analysis over fire prone regions in Australia and Asia will be presented. BIRD successfully demonstrates innovative fire recognition technology for small satellites which permit to retrieve quantitative characteristics of active burning wildfires, such as the equivalent fire temperature, fire area, radiative energy release, fire front length and fire front strength.

  18. Tentative method for the qualitative detection and quantitative assessment of air contamination by drugs.

    PubMed

    Buogo, A; Eboli, V

    1972-06-01

    A method for detecting and measuring air contamination by drugs is described which uses an electrostatic bacterial air sampler, sprayers for micronizing drugs, and Mueller-Hinton medium seeded with a highly susceptible strain of Sarcina lutea. Three antibiotics (penicillin, tetracycline, aminosidine) and a sulfonamide (sulfapyrazine) were identified by pretreating portions of medium, showing no bacterial growth, with penicillinase or p-aminobenzoic acid solution and subsequently determining how both drug(-) susceptible and drug-resistant strains of Staphylococcus aureus were affected by this pretreatment. Quantitative determinations were also attempted by measuring the size of the inhibition zones. PMID:4483536

  19. Tentative Method for the Qualitative Detection and Quantitative Assessment of Air Contamination by Drugs

    PubMed Central

    Buogo, A.; Eboli, V.

    1972-01-01

    A method for detecting and measuring air contamination by drugs is described which uses an electrostatic bacterial air sampler, sprayers for micronizing drugs, and Mueller-Hinton medium seeded with a highly susceptible strain of Sarcina lutea. Three antibiotics (penicillin, tetracycline, aminosidine) and a sulfonamide (sulfapyrazine) were identified by pretreating portions of medium, showing no bacterial growth, with penicillinase or p-aminobenzoic acid solution and subsequently determining how both drug- susceptible and drug-resistant strains of Staphylococcus aureus were affected by this pretreatment. Quantitative determinations were also attempted by measuring the size of the inhibition zones. Images PMID:4483536

  20. 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.

  1. 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. PMID:26011500

  2. Enzyme-Based Test Strips for Visual or Photographic Detection and Quantitation of Gaseous Sulfur Mustard.

    PubMed

    Bidmanova, Sarka; Steiner, Mark-Steven; Stepan, Martin; Vymazalova, Kamila; Gruber, Michael A; Duerkop, Axel; Damborsky, Jiri; Prokop, Zbynek; Wolfbeis, Otto S

    2016-06-01

    Sulfur mustard is a chemical agent of high military and terroristic significance. No effective antidote exists, and sulfur mustard can be fairly easily produced in large quantity. Rapid field testing of sulfur mustard is highly desirable. Existing analytical devices for its detection are available but can suffer from low selectivity, laborious sample preparation, and/or the need for complex instrumentation. We describe a new kind of test strip for rapid detection of gaseous sulfur mustard that is based on its degradation by the enzyme haloalkane dehalogenase that is accompanied by a change of local pH. This change can be detected using pH indicators contained in the strips whose color changes from blue-green to yellow within 10 min. In addition to visual read-out, we also demonstrate quantitative reflectometric readout by using a conventional digital camera based on red-green-blue data acquisition. Organic haloalkanes, such as 1,2-dichloroethane, have a negligible interfering effect. The visual limit of detection is 20 μg/L, and the one for red-green-blue read-out is as low as 3 μg/L. The assays have good reproducibility ±6% and ±2% for interday assays and intraday assays, respectively. The strips can be stored for at least 6 months without loss of function. They are disposable and can be produced fairly rapidly and at low costs. Hence, they represent a promising tool for in-field detection of sulfur mustard. PMID:27118397

  3. 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.

  4. IDENTIFICATION AND QUANTITATION OF ALKYLATED NUCLEOBASIS BY HIGH-PERFORMANCE LIQUID CHROMATOGRAPHY WITH UV PHOTODIODE ARRAY DETECTION

    EPA Science Inventory

    The application of UV diode array detection in high-performance liquid chromatographic (HPLC) identification and quantitation of several classes of synthetic and commercially available alkylated nucleobases is investigated. uantitative spectral overlays of these compounds to meth...

  5. 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

  6. 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.

  7. Rapid, specific and quantitative assays for the detection of the endophytic bacterium Methylobacterium mesophilicum in plants.

    PubMed

    Lacava, P T; Li, W B; Araújo, W L; Azevedo, J L; Hartung, J S

    2006-06-01

    Xylella fastidiosa is a xylem-limited bacterium that causes citrus variegated chlorosis disease in sweet orange. There is evidence that X. fastidiosa interacts with endophytic bacteria present in the xylem of sweet orange, and that these interactions, particularly with Methylobacterium mesophilicum, may affect disease progress. However, these interactions cannot be evaluated in detail until efficient methods for detection and enumeration of these bacteria in planta are developed. We have previously developed standard and quantitative PCR-based assays specific for X. fastidiosa using the LightCycler system [Li, W.B., Pria Jr., L.P.M.W.D., X. Qin, and J.S. Hartung, 2003. Presence of Xylella fastidiosa in sweet orange fruit and seeds and its transmission to seedlings. Phytopathology 93:953-958.], and now report the development of both standard and quantitative PCR assays for M. mesophilicum. The assays are specific for M. mesophilicum and do not amplify DNA from other species of Methylobacterium or other bacteria commonly associated with citrus or plant tissue. Other bacteria tested included Curtobacterium flaccumfaciens, Pantoea agglomerans, Enterobacter cloacae, Bacillus sp., X. fastidiosa, Xanthomonas axonopodis pv. citri, and Candidatus Liberibacter asiaticus. We have demonstrated that with these methods we can quantitatively monitor the colonization of xylem by M. mesophilicum during the course of disease development in plants artificially inoculated with both bacteria. PMID:16266765

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

    PubMed

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

    2009-07-01

    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

  9. Early detection of cervical cancer among Native American women: a qualitative supplement to a quantitative study.

    PubMed

    Messer, L; Steckler, A; Dignan, M

    1999-08-01

    The North Carolina Native American Cervical Cancer Prevention Project was a 5-year (1989-1995) National Cancer Institute-funded, community-based, early detection of cervical cancer intervention implemented among two Native American tribes in North Carolina: the eastern band of the Cherokee Indians and the Lumbee. The initial quantitative analysis of the intervention showed modest effects and found that the intervention had different effects in the two communities. Due to the equivocal findings, a retrospective qualitative study was conducted. The qualitative study found that two types of factors influenced the intervention's results. The first were project and intervention characteristics, and the second were community and cultural factors over which the project had no control. The community and cultural factors took two forms: enhancers, which contributed to greater intervention effect, and attenuators, which created barriers to success. Examples of each factor are presented, and implications for cervical cancer detection among Native American women are discussed. PMID:10435237

  10. Real-time cellular analysis for quantitative detection of functional Clostridium difficile toxin in stool.

    PubMed

    Huang, Bin; Li, Haijing; Jin, Dazhi; Stratton, Charles W; Tang, Yi-Wei

    2014-04-01

    Rapid and accurate diagnosis and monitoring of Clostridium difficile infection (CDI) is critical for patient care and infection control. We will briefly review current laboratory techniques for the diagnosis of CDI and identify aspects needing improvement. We will also introduce a real-time cellular analysis (RTCA) assay developed for the diagnosis and monitoring of CDI using electronic impedance to assess the cell status. The RTCA assay uses impedance measurement to detect minute physiological changes in cells cultured on gold microelectrodes embedded in glass substrates in the bottom of microtiter wells. This assay has been adapted for quantitative detection of C. difficile functional toxin directly from stool specimens. Compared to conventional techniques and molecular assays, the RTCA assay provides a valuable tool for the diagnosis of CDI as well as for the assessment of clinical severity and for monitoring therapeutic efficacies. PMID:24649817

  11. Detecting Polychlorinated Biphenyls by Ah Receptor and Fluorescence Quantitative PCR with Exonuclease

    NASA Astrophysics Data System (ADS)

    Zhao, Xiaoxiang; Zhuang, Huisheng

    2010-11-01

    Tetrachlorobiphenyls as ligands were cultivated with goldfish, Ah receptors were extracted from the liver of goldfish and purified by hydroxyapatite. The complex of TCB ligands-receptors were analyzed by Surface Plasmon Resonance. DNA probes were amplified by PCR using Primers F1 and F2 with the DNA recognition site of responsive enhancer. DNA probes bound to the complex were not digested by exonuclease. The DNA that bound to the complex was quantified by real time PCR. A standard curve with TCB concentration to Ct values was obtained in the range of 10-12mol/L to 10-8 mol/L, according to TCB concentration in samples. The detection limit of the assay was below 10-12mol/L of TCB. Compared with HPLC, this assay is much more sensitive. These results suggest that fluorescence quantitative PCR with exonuclease by Ah receptors fits for detection of trace PCB.

  12. Detection and quantitation of resveratrol in tomato fruit (Lycopersicon esculentum Mill.).

    PubMed

    Ragab, Amr S; Van Fleet, Jennifer; Jankowski, Boris; Park, Joon-Hyun; Bobzin, Steven C

    2006-09-20

    Resveratrol is a stilbene phytoalexin well-known for its presence in grape, wine, and peanut. As a result of its antioxidant and chemopreventative properties, it has gained much attention as a functional food ingredient. A gas chromatography-mass spectrometry method for the detection of resveratrol, its 3-glucopyranoside piceid, and the cis isomers of both compounds has been developed and used to quantitate the levels of these compounds in the skin of commercially available tomato fruit (Lycopersicon esculentum Mill.). The resveratrol concentration remains relatively stable during fruit maturation, reaching a maximum concentration in the skin of 18.4 +/- 1.6 microg/g dry weight at 4 weeks postbreaker. No stilbenes were detected in the flesh of tomato fruit. PMID:16968079

  13. Rapid method for glutathione quantitation using high-performance liquid chromatography with coulometric electrochemical detection.

    PubMed

    Bayram, Banu; Rimbach, Gerald; Frank, Jan; Esatbeyoglu, Tuba

    2014-01-15

    A rapid, sensitive, and direct method (without derivatization) was developed for the detection of reduced glutathione (GSH) in cultured hepatocytes (HepG2 cells) using high-performance liquid chromatography with electrochemical detection (HPLC-ECD). The method was validated according to the guidelines of the U.S. Food and Drug Administration in terms of linearity, lower limit of quantitation (LOQ), lower limit of detection (LOD), precision, accuracy, recovery, and stabilities of GSH standards and quality control samples. The total analysis time was 5 min, and the retention time of GSH was 1.78 min. Separation was carried out isocratically using 50 mM sodium phosphate (pH 3.0) as a mobile phase with a fused-core column. The detector response was linear between 0.01 and 80 μmol/L, and the regression coefficient (R(2)) was >0.99. The LOD for GSH was 15 fmol, and the intra- and interday recoveries ranged between 100.7 and 104.6%. This method also enabled the rapid detection (in 4 min) of other compounds involved in GSH metabolism such as uric acid, ascorbic acid, and glutathione disulfite. The optimized and validated HPLC-ECD method was successfully applied for the determination of GSH levels in HepG2 cells treated with buthionine sulfoximine (BSO), an inhibitor, and α-lipoic acid (α-LA), an inducer of GSH synthesis. As expected, the amount of GSH concentration-dependently decreased with BSO and increased with α-LA treatments in HepG2 cells. This method could also be useful for the quantitation of GSH, uric acid, ascorbic acid, and glutathione disulfide in other biological matrices such as tissue homogenates and blood. PMID:24328299

  14. Passive mass transport for direct and quantitative SERS detection using purified silica encapsulated metal nanoparticles

    NASA Astrophysics Data System (ADS)

    Shrestha, Binaya Kumar

    This thesis focuses on understanding implications of nanomaterial quality control and mass transport through internally etched silica coated nanoparticles for direct and quantitative molecular detection using surface enhanced Raman scattering (SERS). Prior to use, bare nanoparticles (partially or uncoated with silica) are removal using column chromatography to improve the quality of these nanomaterials and their SERS reproducibility. Separation of silica coated nanoparticles with two different diameters is achieved using Surfactant-free size exclusion chromatography with modest fractionation. Next, selective molecular transport is modeled and monitored using SERS and evaluated as a function of solution ionic strength, pH, and polarity. Molecular detection is achieved when the analytes first partition through the silica membrane then interact with the metal surface at short distances (i.e., less than 2 nm). The SERS intensities of unique molecular vibrational modes for a given molecule increases as the number of molecules that bind to the metal surface increases and are enhanced via both chemical and electromagnetic enhancement mechanisms as long as the vibrational mode has a component of polarizability tensor along the surface normal. SERS signals increase linearly with molecular concentration until the three-dimensional SERS-active volume is saturated with molecules. Implications of molecular orientation as well as surface selection rules on SERS intensities of molecular vibrational modes are studied to improve quantitative and reproducible SERS detection using internally etched Ag Au SiO2 nanoparticles. Using the unique vibrational modes, SERS intensities for p-aminothiophenol as a function of metal core compositions and plasmonics are studied. By understanding molecular transport mechanisms through internally etched silica matrices coated on metal nanoparticles, important experimental and materials design parameters are learned, which can be subsequently applied

  15. Quantitative photoelectrochemical detection of biological affinity reaction: biotin-avidin interaction.

    PubMed

    Dong, Dong; Zheng, Dong; Wang, Fu-Quan; Yang, Xi-Qiang; Wang, Na; Li, Yuan-Guang; Guo, Liang-Hong; Cheng, Jing

    2004-01-15

    Quantitative detection of a biological affinity reaction, the biotin/avidin recognition, was achieved using our newly developed photoelectrochemical analytical system. The system is based on the operation mechanism of the well-developed dye-sensitized photoelectrochemical solar cells and comprises a ruthenium tris(2,2'-bipyridine) (Ru-bipy) derivative as the photoelectrochemical signal-generating molecule, oxalate as the sacrificial electron donor, and tin oxide nanoparticle as the semiconductor electrode material. To perform the affinity reaction, avidin was immobilized on SnO(2) electrode by passive adsorption. Biotin-linked bovine serum albumin (BSA) was labeled with an NHS-ester derivative of Ru-bipy. After binding of BSA to the surface-immobilized avidin through biotin, photoelectrochemical measurement was carried out in the presence of oxalate. Anodic photocurrent was turned on and off repeatedly by control of incidental light. The action spectrum of the photocurrent resembled the absorption spectrum of Ru-bipy, proving the photocurrent was generated from the metal complex. A linear relationship between photocurrent and BSA concentration was obtained in the range of 1-100 microg/mL. This is the first case of quantitative photoelectrochemical detection of a biological affinity interaction. PMID:14719905

  16. Fast wide-field photothermal and quantitative phase cell imaging with optical lock-in detection

    PubMed Central

    Eldridge, Will J.; Meiri, Amihai; Sheinfeld, Adi; Rinehart, Matthew T.; Wax, Adam

    2014-01-01

    We present a fast, wide-field holography system for detecting photothermally excited gold nanospheres with combined quantitative phase imaging. An interferometric photothermal optical lock-in approach (POLI) is shown to improve SNR for detecting nanoparticles (NPs) on multiple substrates, including a monolayer of NPs on a silanized coverslip, and NPs bound to live cells. Furthermore, the set up allowed for co-registered quantitative phase imaging (QPI) to be acquired in an off-axis holographic set-up. An SNR of 103 was obtained for NP-tagging of epidermal growth factor receptor (EGFR) in live cells with a 3 second acquisition, while an SNR of 47 was seen for 20 ms acquisition. An analysis of improvements in SNR due to averaging multiple frames is presented, which suggest that residual photothermal signal can be a limiting factor. The combination of techniques allows for high resolution imaging of cell structure via QPI with the ability to identify receptor expression via POLI. PMID:25136482

  17. 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

  18. Quantitative Surface Chirality Detection with Sum Frequency Generation Vibrational Spectroscopy: Twin Polarization Angle Approach

    SciTech Connect

    Wei, Feng; Xu, Yanyan; Guo, Yuan; Liu, Shi-lin; Wang, Hongfei

    2009-12-27

    Here we report a novel twin polarization angle (TPA) approach in the quantitative chirality detection with the surface sum-frequency generation vibrational spectroscopy (SFG-VS). Generally, the achiral contribution dominates the surface SFG-VS signal, and the pure chiral signal is usually two or three orders of magnitude smaller. Therefore, it has been difficult to make quantitative detection and analysis of the chiral contributions to the surface SFG- VS signal. In the TPA method, by varying together the polarization angles of the incoming visible light and the sum frequency signal at fixed s or p polarization of the incoming infrared beam, the polarization dependent SFG signal can give not only direct signature of the chiral contribution in the total SFG-VS signal, but also the accurate measurement of the chiral and achiral components in the surface SFG signal. The general description of the TPA method is presented and the experiment test of the TPA approach is also presented for the SFG-VS from the S- and R-limonene chiral liquid surfaces. The most accurate degree of chiral excess values thus obtained for the 2878 cm⁻¹ spectral peak of the S- and R-limonene liquid surfaces are (23.7±0.4)% and ({25.4±1.3)%, respectively.

  19. 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. PMID:24154926

  20. In-vivo Tumor detection using diffusion reflection measurements of targeted gold nanorods - a quantitative study.

    PubMed

    Ankri, Rinat; Duadi, Hamootal; Motiei, Menachem; Fixler, Dror

    2012-03-01

    The ability to quantitatively and non-invasively detect nanoparticles has important implications on their development as an in-vivo cancer diagnostic tool. The Diffusion Reflection (DR) method is a simple, non-invasive imaging technique which has been proven useful for the investigation of tissue's optical parameters. In this study, Monte Carlo (MC) simulations, tissue-like phantom experiments and in-vivo measurements of the reflected light intensity from tumor bearing mice are presented. Following intravenous injection of antibody conjugated poly (ethylene glycol)-coated (PEGylated) gold nanorods (GNR) to tumor-bearing mice, accumulation of GNR in the tumor was clearly detected by the DR profile of the tumor. The ability of DR measurements to quantitate in-vivo the concentration of the GNR in the tumor was demonstrated and validated with Flame Atomic Absorption spectroscopy results. With GNR as absorbing contrast agents, DR has important potential applications in the image guided therapy of superficial tumors such as head and neck cancer, breast cancer and melanoma. PMID:22234916

  1. 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.

  2. 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

    2016-01-01

    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

  3. Quantitative detection of nitroxyl upon trapping with glutathione and labeling with a specific fluorogenic reagent.

    PubMed

    Johnson, Gail M; Chozinski, Tyler J; Salmon, Debra J; Moghaddam, Alan D; Chen, Hsin Chih; Miranda, Katrina M

    2013-10-01

    Donors of nitroxyl (HNO) have shown promise for treatment of stroke, heart failure, alcoholism and cancer. However, comparing the pharmacological capacities of various donors is difficult without first quantifying the amount of HNO released from each donor. Detection and quantitation of HNO has been complicated by the rapid self-consumption of HNO through irreversible dimerization, poor selectivity of trapping agents against other nitrogen oxides, and/or low sensitivity towards HNO. Here, an assay is described for the trapping of HNO by glutathione (GSH) followed by labeling of GSH with the fluorogenic agent, naphthalene-2,3-dicarboxaldehyde (NDA), and subsequent quantitation by fluorescence difference. The newly developed assay was used to validate the pH-dependence of HNO release from isopropylamine NONOate (IPA/NO), which is a dual donor of HNO and NO at physiological pH. Furthermore, varied assay conditions were utilized to suggest the ratios of the products of the reaction of GSH with HNO. At intracellular concentrations of GSH, the disulfide (GSSG) was the major product, but significant concentrations of glutathione sulfinamide (GS(O)NH₂) were also detected. This suggests that GS(O)NH₂, which is a selective biomarker of HNO, may be produced in concentrations that are amenable to in vivo analysis. PMID:23685286

  4. DetectTLC: Automated Reaction Mixture Screening Utilizing Quantitative Mass Spectrometry Image Feature

    PubMed Central

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

    2016-01-01

    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. PMID:26508443

  5. 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.

  6. 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. PMID:26508443

  7. 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. PMID:26562485

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

    DOE PAGESBeta

    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

  9. 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%.

  10. 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%.

  11. Automatic detection of the myocardial boundaries of the right and left ventricles in MR cardio perfusion scans

    NASA Astrophysics Data System (ADS)

    Spreeuwers, Luuk J.; Breeuwer, Marcel M.

    2001-07-01

    Recent advances in Magnetic Resonance Imaging allow fast recording of contrast enhanced myocardial perfusion scans. MR perfusion scans are made by recording, during a period of 20-40 seconds a number of short-axis slices through the myocardium. The scanning is triggered by the patient's ECG typically resulting in one set of slices per heart beat. For the perfusion analysis, the myocardial boundaries must be traced in all images Currently this is done manually, a tedious procedure, prone to inter- and intra-observer variability. In this paper a method for automatic detection of myocardial boundaries is proposed. This results in a considerable time reduction of the analysis and is an important step towards automatic analysis of cardiac MR perfusion scans. The most important consideration in the proposed approach is the use of not only spatial-intensity information, but also intensity-time and shape information to realize a robust segmentation. The procedure was tested on a total of 30 image sequences from 14 different scans. From 26 out of 30 sequences the myocardial boundaries were correctly found. The remaining 4 sequences were of very low quality and would most likely not be used for analysis.

  12. 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%.

  13. 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.

  14. Nuclear Scans

    MedlinePlus

    ... functions inside your body. They use a special camera that detects radioactivity. Before the test, you receive ... you lie still on a table while the camera makes images. Most scans take 20 to 45 ...

  15. 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.

  16. Genome wide scan for quantitative trait loci affecting tick resistance in cattle (Bos taurus × Bos indicus)

    PubMed Central

    2010-01-01

    Background In tropical countries, losses caused by bovine tick Rhipicephalus (Boophilus) microplus infestation have a tremendous economic impact on cattle production systems. Genetic variation between Bos taurus and Bos indicus to tick resistance and molecular biology tools might allow for the identification of molecular markers linked to resistance traits that could be used as an auxiliary tool in selection programs. The objective of this work was to identify QTL associated with tick resistance/susceptibility in a bovine F2 population derived from the Gyr (Bos indicus) × Holstein (Bos taurus) cross. Results Through a whole genome scan with microsatellite markers, we were able to map six genomic regions associated with bovine tick resistance. For most QTL, we have found that depending on the tick evaluation season (dry and rainy) different sets of genes could be involved in the resistance mechanism. We identified dry season specific QTL on BTA 2 and 10, rainy season specific QTL on BTA 5, 11 and 27. We also found a highly significant genome wide QTL for both dry and rainy seasons in the central region of BTA 23. Conclusions The experimental F2 population derived from Gyr × Holstein cross successfully allowed the identification of six highly significant QTL associated with tick resistance in cattle. QTL located on BTA 23 might be related with the bovine histocompatibility complex. Further investigation of these QTL will help to isolate candidate genes involved with tick resistance in cattle. PMID:20433753

  17. 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. © 2015 International Society for Advancement of Cytometry. PMID:26013098

  18. A genome-wide sib-pair scan for quantitative language traits reveals linkage to chromosomes 10 and 13

    PubMed Central

    Evans, P. D.; Mueller, K. L.; Gamazon, E. R.; Cox, N. J.; Tomblin, J. B.

    2016-01-01

    Although there is considerable evidence that individual differences in language development are highly heritable, there have been few genome-wide scans to locate genes associated with the trait. Previous analyses of language impairment have yielded replicable evidence for linkage to regions on chromosomes 16q, 19q, 13q (within lab) and at 13q (between labs). Here we report the first linkage study to screen the continuum of language ability, from normal to disordered, as found in the general population. 383 children from 147 sib-ships (214 sib-pairs) were genotyped on the Illumina® Linkage IVb Marker Panel using three composite language-related phenotypes and a measure of phonological memory (PM). Two regions (10q23.33; 13q33.3) yielded genome-wide significant peaks for linkage with PM. A peak suggestive of linkage was also found at 17q12 for the overall language composite. This study presents two novel genetic loci for the study of language development and disorders, but fails to replicate findings by previous groups. Possible reasons for this are discussed. PMID:25997078

  19. The binding of cellulase variants to dislocations: a semi-quantitative analysis based on CLSM (confocal laser scanning microscopy) images.

    PubMed

    Hidayat, Budi J; Weisskopf, Carmen; Felby, Claus; Johansen, Katja S; Thygesen, Lisbeth G

    2015-12-01

    Binding of enzymes to the substrate is the first step in enzymatic hydrolysis of lignocellulose, a key process within biorefining. During this process elongated plant cells such as fibers and tracheids have been found to break into segments at irregular cell wall regions known as dislocations or slip planes. Here we study whether cellulases bind to dislocations to a higher extent than to the surrounding cell wall. The binding of fluorescently labelled cellobiohydrolases and endoglucanases to filter paper fibers was investigated using confocal laser scanning microscopy and a ratiometric method was developed to assess and quantify the abundance of the binding of cellulases to dislocations as compared to the surrounding cell wall. Only Humicola insolens EGV was found to have stronger binding preference to dislocations than to the surrounding cell wall, while no difference in binding affinity was seen for any of the other cellulose variants included in the study (H. insolens EGV variants, Trichoderma reesei CBHI, CBHII and EGII). This result favours the hypothesis that fibers break at dislocations during the initial phase of hydrolysis mostly due to mechanical failure rather than as a result of faster degradation at these locations. PMID:26626331

  20. Assessment of aircraft structural integrity by detecting disbonds through ultrasonic scanning

    NASA Technical Reports Server (NTRS)

    Abedin, M. N.; Prabhu, D. R.; Winfree, W. P.

    1992-01-01

    A study of nondestructive evaluation of aircraft bonded joints using the contact scanning technique is presented. Reflected signals acquired through the contacting transducer characterize the test region as being bonded or disbonded. Ultrasonic signals are attenuated more rapidly in the bonded regions when compared to disbonded regions. A peak amplitude based method and an artificial neural network are used to classify the signals. Results obtained using an artificial neural network exhibited significant insensitivity to signal variation when compared to the peak amplitude. Very good agreement is observed between results obtained using the present technique and those obtained using immersion scanning.

  1. Electron detection characteristics of a slow-scan CCD camera, imaging plates and film, and electron image restoration.

    PubMed

    Zuo, J M

    2000-05-01

    Electron detection characteristics are summarized for the slow scan CCD (SSC) camera, imaging plates, and film. The advantage of each detector is demonstrated with the selected examples of electron diffraction and imaging. The Richardson-Lucy algorithm for image restoration is described and tested for images recorded with the SSC camera. The effectiveness of image restoration is demonstrated for the recorded high-resolution lattice image, energy-loss spectrum, and convergent beam electron diffraction (CBED) pattern. PMID:10816266

  2. Glucose encapsulating liposome for signal amplification for quantitative detection of biomarkers with glucometer readout.

    PubMed

    Zhao, Yuting; Du, Dan; Lin, Yuehe

    2015-10-15

    A new technology was developed to quantitatively detect a broad range of disease biomarkers and proven to be portable, economical, and conveniently accessible. Measurements were performed based on releasing encapsulated glucose from antibody-tagged liposomes and subsequently detecting the released glucose using a commercial personal glucose meter (GM). The innovative aspect of this approach lies in the quantification of target biomarkers through the detection of glucose, thus expanding the applicability of the GM by broadening the range of target biomarkers instead of detecting only one analyte, glucose. Because of the bilayer membrane of liposomes, which can accommodate tens of thousands of glucose molecules, the sensitivity was greatly enhanced by using glucose encapsulating liposomes as a signal output and an amplifier. Here, the model analyte, protein 53 phosphorylated on Serine 15 (phospho-p53(15)), was captured by primary antibodies bound on magnetic Fe3O4 nanoparticles and then recognized by reporting antibodies conjugated to glucose encapsulating liposomes. Finally, the target phospho-p53(15) was detected by lysing the bound liposomes to release the encapsulated glucose (4 × 10(5) glucose molecules per liposome), which is detected with the GM. This approach was demonstrated to be a universal technology that can be easily produced to quantify a wide variety of biomarkers in medical diagnostics, food safety, public health, and environmental monitoring. In the near future, it is expected that these sensors, in combination with a portable GM, can be used in many fields such as physicians' laboratories, hospitals and the common household. PMID:26005847

  3. Enhanced detection of surface-associated bacteria in indoor environments by quantitative PCR.

    PubMed

    Buttner, M P; Cruz-Perez, P; Stetzenbach, L D

    2001-06-01

    Methods for detecting microorganisms on surfaces are needed to locate biocontamination sources and to relate surface and airborne concentrations. Research was conducted in an experimental room to evaluate surface sampling methods and quantitative PCR (QPCR) for enhanced detection of a target biocontaminant present on flooring materials. QPCR and culture analyses were used to quantitate Bacillus subtilis (Bacillus globigii) endospores on vinyl tile, commercial carpet, and new and soiled residential carpet with samples obtained by four surface sampling methods: a swab kit, a sponge swipe, a cotton swab, and a bulk method. The initial data showed that greater overall sensitivity was obtained with the QPCR than with culture analysis; however, the QPCR results for bulk samples from residential carpet were negative. The swab kit and the sponge swipe methods were then tested with two levels of background biological contamination consisting of Penicillium chrysogenum spores. The B. subtilis values obtained by the QPCR method were greater than those obtained by culture analysis. The differences between the QPCR and culture data were significant for the samples obtained with the swab kit for all flooring materials except soiled residential carpet and with the sponge swipe for commercial carpet. The QPCR data showed that there were no significant differences between the swab kit and sponge swipe sampling methods for any of the flooring materials. Inhibition of QPCR due solely to biological contamination of flooring materials was not evident. However, some degree of inhibition was observed with the soiled residential carpet, which may have been caused by the presence of abiotic contaminants, alone or in combination with biological contaminants. The results of this research demonstrate the ability of QPCR to enhance detection and enumeration of biocontaminants on surface materials and provide information concerning the comparability of currently available surface sampling

  4. 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

  5. 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

    2016-01-01

    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

  6. 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.

  7. 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

    2016-03-01

    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.

  8. High-sensitivity piezoelectric tube sensor for shear-force detection in scanning near-field optical microscopy

    NASA Astrophysics Data System (ADS)

    Lindfors, K.; Kapulainen, M.; Ryytty, P.; Kaivola, M.

    2004-11-01

    An easy-to-implement non-optical shear-force detection setup for tip-sample distance regulation in scanning near-field optical microscopy is demonstrated. The detection method is based on attaching the near-field probe to a piezoelectric tube resulting in excellent mechanical contact between tip and detector. The main advantages of the method are good signal-to-background contrast and thus potential for high sensitivity. The method is demonstrated by obtaining approach curves of silicon surfaces. The suitability for optical experiments is further shown by measuring the near-field intensity distribution of the emission of a semiconductor laser.

  9. 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.

  10. Quantitative charge state analysis of manganese biominerals in aqueous suspension using scanning transmission X-ray microscopy (STXM)

    NASA Astrophysics Data System (ADS)

    Pecher, K.; McCubbery, D.; Kneedler, E.; Rothe, J.; Bargar, J.; Meigs, G.; Cox, L.; Nealson, K.; Tonner, B.

    2003-03-01

    We have applied Scanning Transmission Soft X-ray Microscopy (STXM) to investigate the charge state distribution of Mn in two kinds of Mn-biominerals, Mn nodules collected from Lake Michigan sediments and Mn precipitates formed by spores of a marine bacillus SG-1 under transport limited reaction conditions. A data analysis technique was developed, which allows for extraction of spatially resolved 2-d charge state maps of manganese on a submicron level. We find that the charge state of Mn dominates the spectral shape of L-edge spectra of environmentally important single oxidation state Mn minerals and that spectra of mixed oxidation state oxides can be modelled by a combination of appropriate single oxidation state reference spectra. Two-dimensional maps of charge state distributions clearly reveal domains of different oxidation states within single particles of Mn-micronodules. Spots of preferred accumulation of Mn(II) were found, which indicates biogenic precipitation of Mn(II)-species as a first step of nodule formation. The presence of Mn(III) in the studied sediment samples suggests the involvement of one-electron oxidation processes and reaction conditions which inhibit or slow down the disproportionation of Mn(III)-products. Under transport limited conditions, Mn oxidation products formed by spores of the marine bacillus SG-1 can vary from cell to cell. The presence of significant amounts of Mn(III) containing species points to the involvement of one-electron oxidation reactions as in the case of the micro-nodules. Our technique and the results obtained form a new basis for the mechanistic understanding of the formation of Mn biominerals in the environment.

  11. Hormonal regulation of capillary fenestrae in the rat adrenal cortex: quantitative studies using objective lens staging scanning electron microscopy.

    PubMed

    Apkarian, R P; Curtis, J C

    1986-01-01

    High magnification studies of the fenestrated capillary endothelium in the zona fasciculata (ZF) of rat adrenal glands were performed using the objective lens stage of an analytical scanning electron microscope (SEM) equipped with a lanthanum hexaboride emitter (LaB6). Resolution of surface substructure of the luminal membrane obtained with specimens decorated with gold/palladium (Au/Pd) was compared with that observed in others sputter coated with tantalum (Ta). High magnification (50,000x) of the fenestrated endothelium demonstrates that tantalum coating of the cryofractured adrenals improves the substructural detail compared to that seen in Au/Pd decorated specimens. The procedures used in specimen preparation, metal deposition and secondary electron imaging (SEI) are described. Quality imaging achieved using the objective lens stage is a result of the elimination of the SE-III component derived from backscattered electrons. Rat adrenals exhibited uniformly patent capillaries. High magnification micrographs of capillary walls were randomly recorded in two morphometric studies of the fenestral content of capillaries in the rat adrenal cortex. Adrenocorticotropic hormone (ACTH), when administered to rats following dexamethasone (DEX) treatment, significantly reduced the fenestrae/micron 2 of endothelial surface and increased the mean size of fenestrae. After hypophysectomy, the number of fenestrae/micron 2 declined over 48 h; within 2 h after ACTH was given to rats hypophysectomized 48 hours earlier, the fenestrae/micron 2 had increased two-fold. These studies indicate that ACTH plays an important role in modulating fenestral content of the capillary endothelium in the adrenal cortex. PMID:3027881

  12. Toward quantitative STM: Scanning tunneling microscopy study of structure and dynamics of adsorbates on transition metal surfaces

    SciTech Connect

    Dunphy, J.C.

    1995-05-01

    STM was applied to chemisorbed S layers on Re(000l) and Mo(100) surfaces. As function of coverage on both these surfaces, S orders into several different overlayer structures, which have been studied by dynamic LEED. STM images of all these structures were obtained. Approximate location of S atoms in the structures was determined by inspecting the images, especially the regions containing defects. Results are in agreement with LEED except for the p(2{times}l) overlayer of sulfur on Mo(100). The STM images were compared to calculations made with Electron Scattering Quantum Chemistry (ESQC) theory. Variation of contrast in experimental images is explained as a result of changes in STM tip termination structure. STM image contrast is a result of changes in the interference between different paths for the tunneling electrons. The simplest structure on the Mo(100) surface was used as a model for developing and testing a method of quantitative structure determination with the STM. Experimental STM images acquired under a range of tunneling conditions were compared to theoretical calculations of the images as a function of surface structure to determine the structure which best fit. Results matched within approximately 0.1 Angstroms a LEED structural determination. At lower S coverage, diffusion of S atoms over the Re(0001) surface and the lateral interaction between these atoms were investigated by application of a new image analysis technique. The interaction between the S and a coadsorbed CO layer was also studied, and CO was found to induce compression of the S overlayer. A similar result was found for Au deposited on the sulfur covered Mo(100) surface. The interaction between steps on the Mo surface was found to be influenced by S adsorption and this observation was interpreted with the theory of equilibrium crystal shape. Design of an STM instrument which operates at cryogenic and variable sample temperatures, and its future applications, are described.

  13. 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.

  14. Quantitative and sensitive detection of rare mutations using droplet-based microfluidics.

    PubMed

    Pekin, Deniz; Skhiri, Yousr; Baret, Jean-Christophe; Le Corre, Delphine; Mazutis, Linas; Salem, Chaouki Ben; Millot, Florian; El Harrak, Abdeslam; Hutchison, J Brian; Larson, Jonathan W; Link, Darren R; Laurent-Puig, Pierre; Griffiths, Andrew D; Taly, Valérie

    2011-07-01

    Somatic mutations within tumoral DNA can be used as highly specific biomarkers to distinguish cancer cells from their normal counterparts. These DNA biomarkers are potentially useful for the diagnosis, prognosis, treatment and follow-up of patients. In order to have the required sensitivity and specificity to detect rare tumoral DNA in stool, blood, lymph and other patient samples, a simple, sensitive and quantitative procedure to measure the ratio of mutant to wild-type genes is required. However, techniques such as dual probe TaqMan(®) assays and pyrosequencing, while quantitative, cannot detect less than ∼1% mutant genes in a background of non-mutated DNA from normal cells. Here we describe a procedure allowing the highly sensitive detection of mutated DNA in a quantitative manner within complex mixtures of DNA. The method is based on using a droplet-based microfluidic system to perform digital PCR in millions of picolitre droplets. Genomic DNA (gDNA) is compartmentalized in droplets at a concentration of less than one genome equivalent per droplet together with two TaqMan(®) probes, one specific for the mutant and the other for the wild-type DNA, which generate green and red fluorescent signals, respectively. After thermocycling, the ratio of mutant to wild-type genes is determined by counting the ratio of green to red droplets. We demonstrate the accurate and sensitive quantification of mutated KRAS oncogene in gDNA. The technique enabled the determination of mutant allelic specific imbalance (MASI) in several cancer cell-lines and the precise quantification of a mutated KRAS gene in the presence of a 200,000-fold excess of unmutated KRAS genes. The sensitivity is only limited by the number of droplets analyzed. Furthermore, by one-to-one fusion of drops containing gDNA with any one of seven different types of droplets, each containing a TaqMan(®) probe specific for a different KRAS mutation, or wild-type KRAS, and an optical code, it was possible to

  15. 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

  16. 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.

  17. Scan direction induced charging dynamics and the application for detection of gate to S/D shorts in logic devices

    NASA Astrophysics Data System (ADS)

    Lei, Ming; Tian, Qing; Wu, Kevin; Zhao, Yan

    2016-03-01

    Gate to source/drain (S/D) short is the most common and detrimental failure mechanism for advanced process technology development in Metal-Oxide-Semiconductor-Field-Effect-Transistor (MOSFET) device manufacturing. Especially for sub-1Xnm nodes, MOSFET device is more vulnerable to gate-S/D shorts due to the aggressive scaling. The detection of this kind of electrical short defect is always challenging for in-line electron beam inspection (EBI), especially new shorting mechanisms on atomic scale due to new material/process flow implementation. The second challenge comes from the characterization of the shorts including identification of the exact shorting location. In this paper, we demonstrate unique scan direction induced charging dynamics (SDCD) phenomenon which stems from the transistor level response from EBI scan at post metal contact chemical-mechanical planarization (CMP) layers. We found that SDCD effect is exceptionally useful for gate-S/D short induced voltage contrast (VC) defect detection, especially for identification of shorting locations. The unique SDCD effect signatures of gate-S/D shorts can be used as fingerprint for ground true shorting defect detection. Correlation with other characterization methods on the same defective location from EBI scan shows consistent results from various shorting mechanism. A practical work flow to implement the application of SDCD effect for in-line EBI monitor of critical gate-S/D short defects is also proposed, together with examples of successful application use cases which mostly focus on static random-access memory (SRAM) array regions. Although the capability of gate-S/D short detection as well as expected device response is limited to passing transistors and pull-down transistors due to the design restriction from standard 6-cell SRAM structure, SDCD effect is proven to be very effective for gate-S/D short induced VC defect detection as well as yield learning for advanced technology development.

  18. 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

  19. Large-scale gold nanoparticle superlattice and its SERS properties for the quantitative detection of toxic carbaryl.

    PubMed

    Wu, Lina; Wang, Zhijiang; Shen, Baozhong

    2013-06-21

    Large scale and well-ordered gold nanoparticle superlattices were fabricated by self-assembly as an active substrate for surface-enhanced Raman scattering (SERS) that can quantitatively detect carbaryl with a detection limit of 1 ppm. These fabricated superlattices with a dimension of several hundred micrometers exhibited high, reproducible SERS activity. PMID:23674317

  20. Tools for the Quantitative Analysis of Sedimentation Boundaries Detected by Fluorescence Optical Analytical Ultracentrifugation

    PubMed Central

    Zhao, Huaying; Casillas, Ernesto; Shroff, Hari; Patterson, George H.; Schuck, Peter

    2013-01-01

    Fluorescence optical detection in sedimentation velocity analytical ultracentrifugation allows the study of macromolecules at nanomolar concentrations and below. This has significant promise, for example, for the study of systems of high-affinity protein interactions. Here we describe adaptations of the direct boundary modeling analysis approach implemented in the software SEDFIT that were developed to accommodate unique characteristics of the confocal fluorescence detection system. These include spatial gradients of signal intensity due to scanner movements out of the plane of rotation, temporal intensity drifts due to instability of the laser and fluorophores, and masking of the finite excitation and detection cone by the sample holder. In an extensive series of experiments with enhanced green fluorescent protein ranging from low nanomolar to low micromolar concentrations, we show that the experimental data provide sufficient information to determine the parameters required for first-order approximation of the impact of these effects on the recorded data. Systematic deviations of fluorescence optical sedimentation velocity data analyzed using conventional sedimentation models developed for absorbance and interference optics are largely removed after these adaptations, resulting in excellent fits that highlight the high precision of fluorescence sedimentation velocity data, thus allowing a more detailed quantitative interpretation of the signal boundaries that is otherwise not possible for this system. PMID:24204779

  1. 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.

  2. RNA-seq analysis for detecting quantitative trait-associated genes.

    PubMed

    Seo, Minseok; Kim, Kwondo; Yoon, Joon; Jeong, Jin Young; Lee, Hyun-Jeong; Cho, Seoae; Kim, Heebal

    2016-01-01

    Many recent RNA-seq studies were focused mainly on detecting the differentially expressed genes (DEGs) between two or more conditions. In contrast, only a few attempts have been made to detect genes associated with quantitative traits, such as obesity index and milk yield, on RNA-seq experiment with large number of biological replicates. This study illustrates the linear model application on trait associated genes (TAGs) detection in two real RNA-seq datasets: 89 replicated human obesity related data and 21 replicated Holsteins' milk production related RNA-seq data. Based on these two datasets, the performance between suggesting methods, such as ordinary regression and robust regression, and existing methods: DESeq2 and Voom, were compared. The results indicate that suggesting methods have much lower false discoveries compared to the precedent two group comparisons based approaches in our simulation study and qRT-PCR experiment. In particular, the robust regression outperforms existing DEG finding method as well as ordinary regression in terms of precision. Given the current trend in RNA-seq pricing, we expect our methods to be successfully applied in various RNA-seq studies with numerous biological replicates that handle continuous response traits. PMID:27071914

  3. Quantitative 3D-KPFM imaging with simultaneous electrostatic force and force gradient detection

    NASA Astrophysics Data System (ADS)

    Collins, L.; Okatan, M. B.; Li, Q.; Kravenchenko, I. I.; Lavrik, N. V.; Kalinin, S. V.; Rodriguez, B. J.; Jesse, S.

    2015-05-01

    Kelvin probe force microscopy (KPFM) is a powerful characterization technique for imaging local electrochemical and electrostatic potential distributions and has been applied across a broad range of materials and devices. Proper interpretation of the local KPFM data can be complicated, however, by convolution of the true surface potential under the tip with additional contributions due to long range capacitive coupling between the probe (e.g. cantilever, cone, tip apex) and the sample under test. In this work, band excitation (BE)-KPFM is used to negate such effects. In contrast to traditional single frequency KPFM, multifrequency BE-KPFM is shown to afford dual sensitivity to both the electrostatic force and the force gradient detection, analogous to simultaneous amplitude modulated and frequency modulated KPFM imaging. BE-KPFM is demonstrated on a Pt/Au/SiOx test structure and electrostatic force gradient detection is found to lead to an improved lateral resolution compared to electrostatic force detection. Finally, a 3D-KPFM imaging technique is developed. Force volume (FV) BE-KPFM allows the tip-sample distance dependence of the electrostatic interactions (force and force gradient) to be recorded at each point across the sample surface. As such, FVBE-KPFM provides a much needed pathway towards complete tip-sample capacitive de-convolution in KPFM measurements and will enable quantitative surface potential measurements with nanoscale resolution.

  4. 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.

  5. Towards an optimized platform for the detection, enrichment, and semi-quantitation circulating tumor cells.

    PubMed

    Molloy, T J; Bosma, A J; van't Veer, Laura J

    2008-11-01

    Metastasis describes the process of migration of a frequently clinically occult circulating tumor cell (CTC) from the primary lesion to a new location and the subsequent formation of an overt growth. We and others have shown that the detection and quantitation of these cells has significant prognostic value, however there still remains no consensus as to the optimal methods to achieve this. The work described herein therefore considered various techniques, from storage and sample processing to data acquisition and analysis, to find an optimal combination of methods for an effective and practical platform for the detection of CTCs in peripheral blood. A dual-antigen epithelial cell enrichment procedure followed by a multi-marker QPCR analysis demonstrated the highest sensitivity and specificity, with the ability to detect as few as 10 tumor cells from a background of 10(6) peripheral blood mononuclear cells. Using these techniques in conjunction with a quadratic linear discriminant analysis (QDA) resulted in a platform able to generate this data and then combine it a single score for each patient, in which positivity reflected tumor cell presence, and negativity represented tumor cell absence. This assay was able to correctly determine tumor cell presence or absence in 100% of healthy controls and 84% of metastatic patients in a validation cohort of 39 individuals. This platform represents a highly sensitive and specific assay which could augment current routine assays for CTCs in the clinic. PMID:18213476

  6. Rapid quantitative detection of Aeromonas hydrophila strains associated with disease outbreaks in catfish aquaculture.

    PubMed

    Griffin, Matt J; Goodwin, Andrew E; Merry, Gwenn E; Liles, Mark R; Williams, Malachi A; Ware, Cynthia; Waldbieser, Geoffrey C

    2013-07-01

    A new strain of Aeromonas hydrophila has been implicated in significant losses in farm-raised catfish. Outbreaks attributable to this new strain began in Alabama in the summer of 2009 and have spread to Arkansas and Mississippi in subsequent years. These outbreaks mostly afflicted market-sized fish and resulted in considerable losses in short periods of time. The present research was designed to develop an expeditious diagnostic procedure to detect the new strains of A. hydrophila due to the rapid onset and biosecurity concerns associated with this new disease. A discriminatory quantitative polymerase chain reaction assay was developed using gene sequences unique to the virulent strains identified in a related comparative genomic study. Using this assay, suspect colonies on a culture plate can be positively identified as the new strain within 2 hr. The assay is repeatable and reproducible with a linear dynamic range covering 8 orders of magnitude and a sensitivity of approximately 7 copies of target DNA in a 15-µl reaction. In addition, the assay is able to detect and quantify the virulent strain from catfish tissues (0.025 g), pond water (40 ml), and sediments (0.25 g) with a sensitivity limit of approximately 100 bacteria in a sample. This assay provides rapid discrimination between the new virulent strain and more common A. hydrophila and is useful for epidemiological studies involving the detection and quantification of the virulent strain in environmental samples and fish tissues. PMID:23847227

  7. 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

  8. RNA-seq analysis for detecting quantitative trait-associated genes

    PubMed Central

    Seo, Minseok; Kim, Kwondo; Yoon, Joon; Jeong, Jin Young; Lee, Hyun-Jeong; Cho, Seoae; Kim, Heebal

    2016-01-01

    Many recent RNA-seq studies were focused mainly on detecting the differentially expressed genes (DEGs) between two or more conditions. In contrast, only a few attempts have been made to detect genes associated with quantitative traits, such as obesity index and milk yield, on RNA-seq experiment with large number of biological replicates. This study illustrates the linear model application on trait associated genes (TAGs) detection in two real RNA-seq datasets: 89 replicated human obesity related data and 21 replicated Holsteins’ milk production related RNA-seq data. Based on these two datasets, the performance between suggesting methods, such as ordinary regression and robust regression, and existing methods: DESeq2 and Voom, were compared. The results indicate that suggesting methods have much lower false discoveries compared to the precedent two group comparisons based approaches in our simulation study and qRT-PCR experiment. In particular, the robust regression outperforms existing DEG finding method as well as ordinary regression in terms of precision. Given the current trend in RNA-seq pricing, we expect our methods to be successfully applied in various RNA-seq studies with numerous biological replicates that handle continuous response traits. PMID:27071914

  9. On the quantitative evaluation of edge detection schemes and their comparison with human performance. [image processing of satellite photographs

    NASA Technical Reports Server (NTRS)

    Fram, J. R.; Deutsch, E. S.

    1975-01-01

    A technique for the quantitative evaluation of edge detection schemes is presented. It is used to assess the performance of three such schemes using a specially-generated set of images containing noise. The ability of human subjects to distinguish the edges in the presence of noise is also measured and compared with that of the edge detection schemes. The edge detection schemes are used on a high-resolution satellite photograph with varying degrees of noise added in order to relate the quantitative comparison to real-life imagery.

  10. A study of the relation between the limit of detection and the limit of quantitation in inductively coupled plasma spectrochemistry

    NASA Astrophysics Data System (ADS)

    Carré, M.; Excoffier, S.; Mermet, J. M.

    1997-12-01

    The limit of quantitation based on a repeatability threshold concept is compared with the limit of detection in induction coupled plasma atomic emission spectrometry (ICP-AES) and induction coupled plasma mass spectrometry (ICP-MS). A 5%-based limit of quantitation would normally correspond to 10 times the 3-σ based limit of detection. However, because of a possible lack of linearity of the calibration graph at low concentrations, some additional noise not taken into consideration and the possible use of time-correlated multichannel detection, this ratio of 10 cannot be used in every case. It is suggested that a suitable way of determining the limit of quantitation is to establish the plot of the percentage relative standard deviation (RSD) of the net signal as a function of the concentration in a range from the limit of detection to 50 times this limit.

  11. TaqMan probe array for quantitative detection of DNA targets

    PubMed Central

    Liu, Heping; Wang, Hong; Shi, Zhiyang; Wang, Hua; Yang, Chaoyong; Silke, Spering; Tan, Weihong; Lu, Zuhong

    2006-01-01

    To date real-time quantitative PCR and gene expression microarrays are the methods of choice for quantification of nucleic acids. Herein, we described a unique fluorescence resonance energy transfer-based microarray platform for real-time quantification of nucleic acid targets that combines advantages of both and reduces their limitations. A set of 3′ amino-modified TaqMan probes were designed and immobilized on a glass slide composing a regular microarray pattern, and used as probes in the consecutive PCR carried out on the surface. During the extension step of the PCR, 5′ nuclease activity of DNA polymerase will cleave quencher dyes of the immobilized probe in the presence of nucleic acids targets. The increase of fluorescence intensities generated by the change in physical distance between reporter fluorophore and quencher moiety of the probes were collected by a confocal scanner. Using this new approach we successfully monitored five different pathogenic genomic DNAs and analyzed the dynamic characteristics of fluorescence intensity changes on the TaqMan probe array. The results indicate that the TaqMan probe array on a planar glass slide monitors DNA targets with excellent specificity as well as high sensitivity. This set-up offers the great advantage of real-time quantitative detection of DNA targets in a parallel array format.

  12. 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.

  13. 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.

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

    DOE PAGESBeta

    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 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

  15. 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. PMID:26210470

  16. 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. Copyright © 2016 John Wiley & Sons, Ltd. PMID:27041659

  17. Quantitative detection of human spermatogonia for optimization of spermatogonial stem cell culture

    PubMed Central

    Zheng, Y.; Thomas, A.; Schmidt, C.M.; Dann, C.T.

    2014-01-01

    STUDY QUESTION Can human spermatogonia be detected in long-term primary testicular cell cultures using validated, germ cell-specific markers of spermatogonia? SUMMARY ANSWER Germ cell-specific markers of spermatogonia/spermatogonial stem cells (SSCs) are detected in early (1–2 weeks) but not late (> 6 weeks) primary testicular cell cultures; somatic cell markers are detected in late primary testicular cell cultures. WHAT IS KNOWN ALREADY The development of conditions for human SSC culture is critically dependent on the ability to define cell types unequivocally and to quantify spermatogonia/SSCs. Growth by somatic cells presents a major challenge in the establishment of SSC cultures and therefore markers that define spermatogonia/SSCs, but are not also expressed by testicular somatic cells, are essential for accurate characterization of SSC cultures. STUDY DESIGN, SIZE, DURATION Testicular tissue from eight organ donors with normal spermatogenesis was used for assay validation and establishing primary testicular cell cultures. PARTICIPANTS/MATERIALS, SETTING, METHODS Immunofluorescence analysis of normal human testicular tissue was used to validate antibodies (UTF1, SALL4, DAZL and VIM) and then the antibodies were used to demonstrate that primary testicular cells cultured in vitro for 1–2 weeks were composed of somatic cells and rare germ cells. Primary testicular cell cultures were further characterized by comparing to testicular somatic cell cultures using quantitative reverse transcriptase PCR (UTF1, FGFR3, ZBTB16, GPR125, DAZL, GATA4 and VIM) and flow cytometry (CD9 and SSEA4). MAIN RESULTS AND THE ROLE OF CHANCE UTF1, FGFR3, DAZL and ZBTB16 qRT–PCR and SSEA4 flow cytometry were validated for the sensitive, quantitative and specific detection of germ cells. In contrast, GPR125 mRNA and CD9 were found to be not specific to germ cells because they were also expressed in testicular somatic cell cultures. While the germ cell-specific markers were detected in

  18. Detection and quantitative determination of diethylene glycol in ethyl alcohol using gamma- ray spectroscopy.

    PubMed

    Udagani, Chikkappa; Ramesh, Thimmasandra Narayan

    2015-08-01

    Determination of the toxic diethylene glycol contamination in ethyl alcohol demands a rapid, accurate and reliable method. Diethylene glycol (DEG) ingestion, accidental or intentional, can lead to death. Clinical and analytical methods used to detect diethylene glycol in alcohol require several hours to days due to tedious instrument handling and measurements. Enzymatic assays face difficulty due to analytic problems. As an alternative method of data analysis, we have used γ-ray spectroscopic method to estimate the diethylene glycol contamination in alcohol by monitoring the variation in the linear and mass attenuation coefficients. This method is simple, robust, portable and can provide reliable and quantitative information about the ethyl alcohol adulterated with diethylene glycol which is of broader interest to society. PMID:26243958

  19. 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.

  20. 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

    2016-03-01

    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. PMID:26842653

  1. 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

  2. Quantum error correction and detection: Quantitative analysis of a coherent-state amplitude-damping code

    NASA Astrophysics Data System (ADS)

    Wickert, Ricardo; van Loock, Peter

    2014-05-01

    We reexamine a non-Gaussian quantum error-correction code designed to protect optical coherent-state qubits against errors due to an amplitude-damping channel. We improve on a previous result [R. Wickert, N. K. Bernardes, and P. van Loock, Phys. Rev. A 81, 062344 (2010), 10.1103/PhysRevA.81.062344] by providing a tighter upper bound on the performance attained when considering realistic assumptions, which constrain the operation of the gates employed in the scheme. The quantitative characterization is performed through measures of fidelity and concurrence, the latter obtained by employing the code as an entanglement distillation protocol. We find that, when running the code in fully deterministic error-correction mode, direct transmission can only be beaten for certain combinations of channel and input state parameters. In contrast, in error-detection mode, the usage of higher repetition encodings remains beneficial throughout, however, at the expense of diminishing success probabilities.

  3. Mapping of quantitative trait loci for blood pressure and cardiac mass in the rat by genome scanning of recombinant inbred strains.

    PubMed Central

    Pravenec, M; Gauguier, D; Schott, J J; Buard, J; Kren, V; Bila, V; Szpirer, C; Szpirer, J; Wang, J M; Huang, H

    1995-01-01

    In the HXB and BXH recombinant inbred strains derived from the spontaneously hypertensive rat and the normotensive Brown Norway rat, we determined the strain distribution patterns of 500 genetic markers to scan the rodent genome for quantitative trait loci regulating cardiac mass and blood pressure. The markers spanned approximately 1,139 cM of the genome and were tested for correlations with left ventricular mass adjusted for body weight, and with systolic, diastolic, and mean arterial pressures. The marker for the dopamine 1A receptor (Drd1a) on chromosome 17 showed the strongest correlation with left ventricular heart weight (P = .00038, r = -0.59) and the relationship to heart weight was independent of blood pressure. The markers showing the strongest correlations with systolic, diastolic, and mean arterial pressure were D19Mit7 on chromosome 19 (P = .0012, r = .55), D2N35 on chromosome 2 (P = .0008, r = .56), and Il6 on chromosome 4 (P = .0018, r = .53), respectively. These studies demonstrate that the HXB and BXH strains can be effectively used for genome scanning studies of complex traits and have revealed several chromosome regions that may be involved in the genetic control of blood pressure and cardiac mass in the rat. PMID:7560090

  4. 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.

  5. Rigorous quantitative elemental microanalysis by scanning electron microscopy/energy dispersive x-ray spectrometry (SEM/EDS) with spectrum processing by NIST DTSA-II

    NASA Astrophysics Data System (ADS)

    Newbury, Dale E.; Ritchie, Nicholas W. M.

    2014-09-01

    Quantitative electron-excited x-ray microanalysis by scanning electron microscopy/silicon drift detector energy dispersive x-ray spectrometry (SEM/SDD-EDS) is capable of achieving high accuracy and high precision equivalent to that of the high spectral resolution wavelength dispersive x-ray spectrometer even when severe peak interference occurs. The throughput of the SDD-EDS enables high count spectra to be measured that are stable in calibration and resolution (peak shape) across the full deadtime range. With this high spectral stability, multiple linear least squares peak fitting is successful for separating overlapping peaks and spectral background. Careful specimen preparation is necessary to remove topography on unknowns and standards. The standards-based matrix correction procedure embedded in the NIST DTSA-II software engine returns quantitative results supported by a complete error budget, including estimates of the uncertainties from measurement statistics and from the physical basis of the matrix corrections. NIST DTSA-II is available free for Java-platforms at: http://www.cstl.nist.gov/div837/837.02/epq/dtsa2/index.html).

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

    SciTech Connect

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

    2008-09-15

    We develop the theoretical description of 3{omega} 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{sub 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 3{omega} signal variations as small as -1.75% in amplitude and 0.60 deg. in phase upon heating the sample from room temperature to 100 deg. 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 3{omega} phase information is used quantitatively as well. The static, calibrated 3{omega} measurements are complementary to 3{omega} 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.

  7. 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. PMID:23890654

  8. A comparison of digitally scanned radiographs with conventional film for the detection of small endodontic instruments.

    PubMed

    Fuge, K N; Stuck, A M; Love, R M

    1998-03-01

    The use of computers in dentistry is becoming common as a practice tool for a diverse number of tasks, including the storage and enhancement of intra-oral radiographs. Several systems of digital radiography are available to produce a digital image including irradiation of a charged-couple device and scanning conventional radiographs. This study compared various digital images of scanned periapical radiographs with the original radiographs to determine whether the digitized images offered any advantage when viewing small files at the radiographic apex. Twenty extracted permanent molar teeth were prepared by gaining straight line access to the root canals and a ISO size 06 K-file was intro