WorldWideScience

Sample records for scan detects quantitative

  1. Quantitative Detection of Benzoyl Peroxide in Wheat Flour Using Line-Scan Macroscale Raman Chemical Imaging.

    Science.gov (United States)

    Qin, Jianwei; Kim, Moon S; Chao, Kuanglin; Gonzalez, Maria; Cho, Byoung-Kwan

    2017-11-01

    A high-throughput Raman chemical imaging method was developed for direct inspection of benzoyl peroxide (BPO) mixed in wheat flour. A 5 W, 785 nm line laser (240 mm long and 1 mm wide) was used as a Raman excitation source in a push-broom Raman imaging system. Hyperspectral Raman images were collected in a wavenumber range of 103-2881 cm-1 from dry wheat flour mixed with BPO at eight concentrations (w/w) from 50 to 6400 ppm. A sample holder with a sampling volume of 150 × 100 × 2 mm3 was used to present a thin layer (2 mm thick) of the powdered sample for line-scan image acquisition with a spatial resolution of 0.2 mm. A baseline correction method based on adaptive iteratively reweighted penalized least squares was used to remove the fluctuating fluorescence signals from the wheat flour. To isolate BPO particles from the flour background, a simple thresholding method was applied to the single-band fluorescence-free images at a unique Raman peak wavenumber (i.e., 1001 cm-1) preselected for the BPO detection. Chemical images were created to detect and map the BPO particles. Limit of detection for the BPO was estimated in the order of 50 ppm, which is on the same level with regulatory standards. Pixel concentrations were calculated from the percentages of the BPO pixels in the chemical images. High correlation was found between the pixel concentrations and the mass concentrations of the BPO, indicating that the Raman chemical imaging method can be used for quantitative detection of the BPO mixed in the wheat flour.

  2. Genome Scan Detects Quantitative Trait Loci Affecting Female Fertility Traits in Danish and Swedish Holstein Cattle

    DEFF Research Database (Denmark)

    Höglund, Johanna Karolina; Guldbrandtsen, B; Su, G

    2009-01-01

    microsatellite markers. Single trait breeding values were used for 12 traits relating to female fertility and female reproductive disorders. Data were analyzed by least squares regression analysis within and across families. Twenty-six QTL were detected on 17 different chromosomes. The best evidence was found......Data from the joint Nordic breeding value prediction for Danish and Swedish Holstein grandsire families were used to locate quantitative trait loci (QTL) for female fertility traits in Danish and Swedish Holstein cattle. Up to 36 Holstein grandsires with over 2,000 sons were genotyped for 416...

  3. Quantitative detection of gold nanoparticles on individual, unstained cancer cells by Scanning Electron Microscopy

    NARCIS (Netherlands)

    Hartsuiker, Liesbeth; van Es, Peter; Petersen, Wilhelmina; van Leeuwen, Ton; Terstappen, Leonardus Wendelinus Mathias Marie; Otto, Cornelis

    2011-01-01

    Gold nanoparticles are rapidly emerging for use in biomedical applications. Characterization of the interaction and delivery of nanoparticles to cells through microscopy is important. Scanning electron microscopes have the intrinsic resolution to visualize gold nanoparticles on cells. A novel sample

  4. Thin-layer chromatography with UV-scanning detection for quantitative analysis of coal-derived products

    Energy Technology Data Exchange (ETDEWEB)

    Vela, J.; Cebolla, V.L.; Membrado, L.; Ferrando, A.C. [University of Zaragoza, Zaragoza (Spain). Dept. of Analytical Chemistry

    1998-07-01

    Quantitative analysis of hydrocarbon groups (HGTA) is important in the characterization of products derived from coal conversion. The heaviest products are usually analyzed by thin-layer chromatography with flame-ionization detection (TLC-FID). TLC with ultraviolet (UV) scanning densitometry was investigated as an alternative to TLC-FID for the rapid determination of aromatic, polar, and noneluted compounds in coal-derived products. The results obtained show that TLC-UV is adequate in terms of speed, repeatability, and quantitative analysis, and furnishes results similar to those obtained by TLC-FID. Preparative TLC enables isolation of fractions suitable for preparative purposes and is less time-consuming (hours rather than days) than LC methods. Rapid calibration of TLC-UV is possible by use of fractions isolated by preparative TLC (derived from the actual fossil fuels to be analyzed) as external standards. A method of fast internal calibration has been tested for hydrocarbon group-type analysis. Direct acquisition of UV spectra from the separated peaks can be used to determine whether this method of calibration is applicable to the sample.

  5. QUANTITATIVE CONFOCAL LASER SCANNING MICROSCOPY

    Directory of Open Access Journals (Sweden)

    Merete Krog Raarup

    2011-05-01

    Full Text Available This paper discusses recent advances in confocal laser scanning microscopy (CLSM for imaging of 3D structure as well as quantitative characterization of biomolecular interactions and diffusion behaviour by means of one- and two-photon excitation. The use of CLSM for improved stereological length estimation in thick (up to 0.5 mm tissue is proposed. The techniques of FRET (Fluorescence Resonance Energy Transfer, FLIM (Fluorescence Lifetime Imaging Microscopy, FCS (Fluorescence Correlation Spectroscopy and FRAP (Fluorescence Recovery After Photobleaching are introduced and their applicability for quantitative imaging of biomolecular (co-localization and trafficking in live cells described. The advantage of two-photon versus one-photon excitation in relation to these techniques is discussed.

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

    Science.gov (United States)

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

    2007-07-01

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

  7. Quantitative bone scanning after asymptomatic Charnley arthroplasty

    Energy Technology Data Exchange (ETDEWEB)

    Mullaji, A.B. (University Department of Orthopedic and Accident Surgery, Royal Liverpool University Hospital, Lierpool (United Kingdom)); Tood, R.C. (Department of Orthopedics, Black Notley Hospital, Braintree (United Kingdom)); Robinson, S. (Department of MedicaL Physics, Colchester General Hospital, Colchester (United Kingdom)); Critchley, M. (Department of Nuclear Medicine, Royal Liverpool University Hospital, Liverpool (United Kingdom))

    1994-06-01

    To establish the normal pattern of postoperative tracer uptake we performed 73 [sup 99m]technetium methylene disphosphonate scans following primary Charnley hip replacements for arthrosis in 68 patients without clinical, hematological and radiographic complications. The patients were divided into 7 subgroups according to the period, 6-24 months, between surgery and scan. There were 10-12 patients in each subgroup. A high-resolution gamma camera with a large filed of view was used. Ratios of uptake in each of 10 peri-prosthetic zones to normal bone were calculated. Femoral uptake was found to decrease in linear fashion from 6 to 12 months after surgery. Thereafter the uptake remained unaltered at levels nearly twice the normal ones in the greater trochanter and nearly 1.5 times in the lesser trochanter, returning to almost normal levels in other zones. Acetabular uptake remained elevated throughout. (au) (20 refs.).

  8. Quantitative measurements of autofluorescence with the scanning laser ophthalmoscope.

    Science.gov (United States)

    Delori, François; Greenberg, Jonathan P; Woods, Russell L; Fischer, Jörg; Duncker, Tobias; Sparrow, Janet; Smith, R Theodore

    2011-12-09

    To evaluate the feasibility and reliability of a standardized approach for quantitative measurements of fundus autofluorescence (AF) in images obtained with a confocal scanning laser ophthalmoscope (cSLO). AF images (30°) were acquired in 34 normal subjects (age range, 20-55 years) with two different cSLOs (488-nm excitation) equipped with an internal fluorescent reference to account for variable laser power and detector sensitivity. The gray levels (GLs) of each image were calibrated to the reference, the zero GL, and the magnification, to give quantified autofluorescence (qAF). Images from subjects and fixed patterns were used to test detector linearity with respect to fluorescence intensity, the stability of qAF with change in detector gain, field uniformity, effect of refractive error, and repeatability. qAF was independent of detector gain and laser power over clinically relevant ranges, provided that detector gain was adjusted to maintain exposures within the linear detection range (GL instruments was Quantitative AF imaging appears feasible. It may enhance understanding of retinal degeneration, serve as a diagnostic aid and as a sensitive marker of disease progression, and provide a tool to monitor the effects of therapeutic interventions.

  9. Quantitative phase imaging with scanning holographic microscopy: an experimental assessment.

    Science.gov (United States)

    Indebetouw, Guy; Tada, Yoshitaka; Leacock, John

    2006-11-28

    This paper demonstrates experimentally how quantitative phase information can be obtained in scanning holographic microscopy. Scanning holography can operate in both coherent and incoherent modes, simultaneously if desired, with different detector geometries. A spatially integrating detector provides an incoherent hologram of the object's intensity distribution (absorption and/or fluorescence, for example), while a point detector in a conjugate plane of the pupil provides a coherent hologram of the object's complex amplitude, from which a quantitative measure of its phase distribution can be extracted. The possibility of capturing simultaneously holograms of three-dimensional specimens, leading to three-dimensional reconstructions with absorption contrast, reflectance contrast, fluorescence contrast, as was previously demonstrated, and quantitative phase contrast, as shown here for the first time, opens up new avenues for multimodal imaging in biological studies.

  10. Quantitative phase imaging with scanning holographic microscopy: an experimental assesment

    Directory of Open Access Journals (Sweden)

    Tada Yoshitaka

    2006-11-01

    Full Text Available Abstract This paper demonstrates experimentally how quantitative phase information can be obtained in scanning holographic microscopy. Scanning holography can operate in both coherent and incoherent modes, simultaneously if desired, with different detector geometries. A spatially integrating detector provides an incoherent hologram of the object's intensity distribution (absorption and/or fluorescence, for example, while a point detector in a conjugate plane of the pupil provides a coherent hologram of the object's complex amplitude, from which a quantitative measure of its phase distribution can be extracted. The possibility of capturing simultaneously holograms of three-dimensional specimens, leading to three-dimensional reconstructions with absorption contrast, reflectance contrast, fluorescence contrast, as was previously demonstrated, and quantitative phase contrast, as shown here for the first time, opens up new avenues for multimodal imaging in biological studies.

  11. Lumber Scanning System for Surface Defect Detection

    Science.gov (United States)

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

    1992-01-01

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

  12. Quantitative linkage genome scan for atopy in a large collection of Caucasian families

    DEFF Research Database (Denmark)

    Webb, BT; van den Oord, E; Akkari, A

    2007-01-01

    Quantitative phenotypes correlated with a complex disorder offer increased power to detect linkage in comparison to affected-unaffected classifications. Asthma is a complex disorder characterized by periods of bronchial obstruction and increased bronchial hyper reactivity. In childhood and early...... represents one of the biggest genome scans so far reported for asthma related phenotypes. This study also demonstrates the utility of increased sample sizes and quantitative phenotypes in linkage analysis of complex disorders....

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

    Science.gov (United States)

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

    2008-11-25

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

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

    Science.gov (United States)

    Sindern, Sven; Meyer, F. Michael

    2016-09-01

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

  15. Automatic change detection using mobile laser scanning

    Science.gov (United States)

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

    Science.gov (United States)

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

    2016-08-01

    Although liquid chromatography with mass spectrometry in full scan mode can obtain all the signals simultaneously in a large range and low cost, it is rarely used in quantitative analysis due to several problems such as chromatographic drifts and peak overlap. In this paper, we propose a Tchebichef moment method for the simultaneous quantitative analysis of three active compounds in Qingrejiedu oral liquid based on three-dimensional spectra in full scan mode of liquid chromatography with mass spectrometry. After the Tchebichef moments were calculated directly from the spectra, the quantitative linear models for three active compounds were established by stepwise regression. All the correlation coefficients were more than 0.9978. The limits of detection and limits of quantitation were less than 0.11 and 0.49 μg/mL, respectively. The intra- and interday precisions were less than 6.54 and 9.47%, while the recovery ranged from 102.56 to 112.15%. Owing to the advantages of multi-resolution and inherent invariance properties, Tchebichef moments could provide favorable results even in the situation of peaks shifting and overlapping, unknown interferences and noise signals, so it could be applied to the analysis of three-dimensional spectra in full scan mode of liquid chromatography with mass spectrometry. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. BRAZILIAN AMAZONIA DEFORESTATION DETECTION USING SPATIO-TEMPORAL SCAN STATISTICS

    Directory of Open Access Journals (Sweden)

    C. A. O. Vieira

    2012-07-01

    Full Text Available 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

  18. MutScan: fast detection and visualization of target mutations by scanning FASTQ data.

    Science.gov (United States)

    Chen, Shifu; Huang, Tanxiao; Wen, Tiexiang; Li, Hong; Xu, Mingyan; Gu, Jia

    2018-01-22

    Some types of clinical genetic tests, such as cancer testing using circulating tumor DNA (ctDNA), require sensitive detection of known target mutations. However, conventional next-generation sequencing (NGS) data analysis pipelines typically involve different steps of filtering, which may cause miss-detection of key mutations with low frequencies. Variant validation is also indicated for key mutations detected by bioinformatics pipelines. Typically, this process can be executed using alignment visualization tools such as IGV or GenomeBrowse. However, these tools are too heavy and therefore unsuitable for validating mutations in ultra-deep sequencing data. We developed MutScan to address problems of sensitive detection and efficient validation for target mutations. MutScan involves highly optimized string-searching algorithms, which can scan input FASTQ files to grab all reads that support target mutations. The collected supporting reads for each target mutation will be piled up and visualized using web technologies such as HTML and JavaScript. Algorithms such as rolling hash and bloom filter are applied to accelerate scanning and make MutScan applicable to detect or visualize target mutations in a very fast way. MutScan is a tool for the detection and visualization of target mutations by only scanning FASTQ raw data directly. Compared to conventional pipelines, this offers a very high performance, executing about 20 times faster, and offering maximal sensitivity since it can grab mutations with even one single supporting read. MutScan visualizes detected mutations by generating interactive pile-ups using web technologies. These can serve to validate target mutations, thus avoiding false positives. Furthermore, MutScan can visualize all mutation records in a VCF file to HTML pages for cloud-friendly VCF validation. MutScan is an open source tool available at GitHub: https://github.com/OpenGene/MutScan.

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

    Science.gov (United States)

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

    2017-09-13

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

  20. Variation of quantitative emphysema measurements from CT scans

    Science.gov (United States)

    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. Quantitative multiplex detection of pathogen biomarkers

    Science.gov (United States)

    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.

  2. Quantitative multiplex detection of pathogen biomarkers

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    Science.gov (United States)

    Siria, Alessandro; Niguès, Antoine

    2017-09-14

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

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

    Science.gov (United States)

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

    2000-01-01

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

  5. A flexibly shaped spatial scan statistic for detecting clusters

    Directory of Open Access Journals (Sweden)

    Takahashi Kunihiko

    2005-05-01

    Full Text Available Abstract Background The spatial scan statistic proposed by Kulldorff has been applied to a wide variety of epidemiological studies for cluster detection. This scan statistic, however, uses a circular window to define the potential cluster areas and thus has difficulty in correctly detecting actual noncircular clusters. A recent proposal by Duczmal and Assunção for detecting noncircular clusters is shown to detect a cluster of very irregular shape that is much larger than the true cluster in our experiences. Methods We propose a flexibly shaped spatial scan statistic that can detect irregular shaped clusters within relatively small neighborhoods of each region. The performance of the proposed spatial scan statistic is compared to that of Kulldorff's circular spatial scan statistic with Monte Carlo simulation by considering several circular and noncircular hot-spot cluster models. For comparison, we also propose a new bivariate power distribution classified by the number of regions detected as the most likely cluster and the number of hot-spot regions included in the most likely cluster. Results The circular spatial scan statistics shows a high level of accuracy in detecting circular clusters exactly. The proposed spatial scan statistic is shown to have good usual powers plus the ability to detect the noncircular hot-spot clusters more accurately than the circular one. Conclusion The proposed spatial scan statistic is shown to work well for small to moderate cluster size, up to say 30. For larger cluster sizes, the method is not practically feasible and a more efficient algorithm is needed.

  6. Scanning the macula for detecting glaucoma

    Directory of Open Access Journals (Sweden)

    Viquar U Begum

    2014-01-01

    Full Text Available Background: With the advent of spectral domain optical coherence tomography (SDOCT, there has been a renewed interest in macular region for detection of glaucoma. However, most macular SDOCT parameters currently are thickness parameters which evaluate thinning of the macular layers but do not quantify the extent of area over which the thinning has occurred. We therefore calculated a new macular parameter, "ganglion cell complex surface abnormality ratio (GCC SAR" that represented the surface area over which the macular thickness was decreased. Purpose: To evaluate the ability of SAR in detecting perimetric and preperimetric glaucoma. Design: Retrospective image analysis. Materials and Methods: 68 eyes with perimetric glaucoma, 62 eyes with preperimetric glaucoma and 165 control eyes underwent GCC imaging with SDOCT. SAR was calculated as the ratio of the abnormal to total area on the GCC significance map. Statistical Analysis: Diagnostic ability of SAR in glaucoma was compared against that of the standard parameters generated by the SDOCT software using area under receiver operating characteristic curves (AUC and sensitivities at fixed specificities. Results: AUC of SAR (0.91 was statistically significantly better than that of GCC average thickness (0.86, P = 0.001 and GCC global loss volume (GLV; 0.88, P = 0.01 in differentiating perimetric glaucoma from control eyes. In differentiating preperimetric glaucoma from control eyes, AUC of SAR (0.72 was comparable to that of GCC average thickness (0.70, P > 0.05 and GLV (0.72, P > 0.05. Sensitivities at specificities of 80% and 95% of SAR were comparable (P > 0.05 for all comparisons to that of GCC average thickness and GLV in diagnosing perimetric and preperimetric glaucoma. Conclusion: GCC SAR had a better ability to diagnose perimetric glaucoma compared to the SDOCT software provided global GCC parameters. However, in diagnosing preperimetric glaucoma, the ability of SAR was similar to that of

  7. Automated model-based quantitative analysis of phantoms with spherical inserts in FDG PET scans.

    Science.gov (United States)

    Ulrich, Ethan J; Sunderland, John J; Smith, Brian J; Mohiuddin, Imran; Parkhurst, Jessica; Plichta, Kristin A; Buatti, John M; Beichel, Reinhard R

    2018-01-01

    Quality control plays an increasingly important role in quantitative PET imaging and is typically performed using phantoms. The purpose of this work was to develop and validate a fully automated analysis method for two common PET/CT quality assurance phantoms: the NEMA NU-2 IQ and SNMMI/CTN oncology phantom. The algorithm was designed to only utilize the PET scan to enable the analysis of phantoms with thin-walled inserts. We introduce a model-based method for automated analysis of phantoms with spherical inserts. Models are first constructed for each type of phantom to be analyzed. A robust insert detection algorithm uses the model to locate all inserts inside the phantom. First, candidates for inserts are detected using a scale-space detection approach. Second, candidates are given an initial label using a score-based optimization algorithm. Third, a robust model fitting step aligns the phantom model to the initial labeling and fixes incorrect labels. Finally, the detected insert locations are refined and measurements are taken for each insert and several background regions. In addition, an approach for automated selection of NEMA and CTN phantom models is presented. The method was evaluated on a diverse set of 15 NEMA and 20 CTN phantom PET/CT scans. NEMA phantoms were filled with radioactive tracer solution at 9.7:1 activity ratio over background, and CTN phantoms were filled with 4:1 and 2:1 activity ratio over background. For quantitative evaluation, an independent reference standard was generated by two experts using PET/CT scans of the phantoms. In addition, the automated approach was compared against manual analysis, which represents the current clinical standard approach, of the PET phantom scans by four experts. The automated analysis method successfully detected and measured all inserts in all test phantom scans. It is a deterministic algorithm (zero variability), and the insert detection RMS error (i.e., bias) was 0.97, 1.12, and 1.48 mm for phantom

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

    Science.gov (United States)

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

    2015-05-07

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

  9. Quantitative three-dimensional ice roughness from scanning electron microscopy

    Science.gov (United States)

    Butterfield, Nicholas; Rowe, Penny M.; Stewart, Emily; Roesel, David; Neshyba, Steven

    2017-03-01

    We present a method for inferring surface morphology of ice from scanning electron microscope images. We first develop a novel functional form for the backscattered electron intensity as a function of ice facet orientation; this form is parameterized using smooth ice facets of known orientation. Three-dimensional representations of rough surfaces are retrieved at approximately micrometer resolution using Gauss-Newton inversion within a Bayesian framework. Statistical analysis of the resulting data sets permits characterization of ice surface roughness with a much higher statistical confidence than previously possible. A survey of results in the range -39°C to -29°C shows that characteristics of the roughness (e.g., Weibull parameters) are sensitive not only to the degree of roughening but also to the symmetry of the roughening. These results suggest that roughening characteristics obtained by remote sensing and in situ measurements of atmospheric ice clouds can potentially provide more facet-specific information than has previously been appreciated.

  10. Influence analysis in quantitative trait loci detection.

    Science.gov (United States)

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

    2014-07-01

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

  11. Transmission environmental scanning electron microscope with scintillation gaseous detection device

    Energy Technology Data Exchange (ETDEWEB)

    Danilatos, Gerasimos, E-mail: gerry@danilatos.com [ESEM Research Laboratory, 28 Wallis Parade, North Bondi, NSW 2026 (Australia); Kollia, Mary [Laboratory of Electron Microscopy and Microanalysis, School of Natural Sciences, University of Patras, GR-26504 Patras (Greece); Dracopoulos, Vassileios [Foundation for Research & Technology-Hellas (FORTH), Institute of Chemical Engineering Sciences (ICE-HT), Stadiou Str., Platani P.O.Box 1414, GR-26504 Patras (Greece)

    2015-03-15

    A transmission environmental scanning electron microscope with use of a scintillation gaseous detection device has been implemented. This corresponds to a transmission scanning electron microscope but with addition of a gaseous environment acting both as environmental and detection medium. A commercial type of low vacuum machine has been employed together with appropriate modifications to the detection configuration. This involves controlled screening of various emitted signals in conjunction with a scintillation gaseous detection device already provided with the machine for regular surface imaging. Dark field and bright field imaging has been obtained along with other detection conditions. With a progressive series of modifications and tests, the theory and practice of a novel type of microscopy is briefly shown now ushering further significant improvements and developments in electron microscopy as a whole. - Highlights: • Novel scanning transmission electron microscopy (STEM) with an environmental scanning electron microscope (ESEM) called TESEM. • Use of the gaseous detection device (GDD) in scintillation mode that allows high resolution bright and dark field imaging in the TESEM. • Novel approach towards a unification of both vacuum and environmental conditions in both bulk/surface and transmission mode of electron microscopy.

  12. Hybrid detection of lung nodules on CT scan images

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Lin; Tan, Yongqiang; Schwartz, Lawrence H.; Zhao, Binsheng, E-mail: bz2166@columbia.edu [Department of Radiology, Columbia University Medical Center, 630 West 168th Street, New York, New York 10032 (United States)

    2015-09-15

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

  13. Processing of Graphene combining Optical Detection and Scanning Probe Lithography

    Directory of Open Access Journals (Sweden)

    Zimmermann Sören

    2015-01-01

    Full Text Available This paper presents an experimental setup tailored for robotic processing of graphene with in-situ vision based control. A robust graphene detection approach is presented applying multiple image processing operations of the visual feedback provided by a high-resolution light microscope. Detected graphene flakes can be modified using a scanning probe based lithographical process that is directly linked to the in-situ optical images. The results of this process are discussed with respect to further application scenarios.

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

    Science.gov (United States)

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

    2012-06-10

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

  15. Bremstrahlung Detection and Chamber Obstruction Localisation Using Scanning Radiation Detectors

    CERN Document Server

    Naylor, G A; Robinson, D

    2005-01-01

    Radiation monitors consisting of scintillating plastic coupled to photomultipliers are used for diagnostic purposes. By scanning such a detector or a radiation scatterer, two applications are demonstrated: i) Monitoring of vacuum chamber conditioning by monitoring gas Bremstrahlung from residual gas. ii) Localisation of beam interception (beam losses) by longitudinal scanning of a radiation detector. The measurement of gas pressure inside long, small cross section, vacuum vessels is difficult due to the distance between the centre of the vacuum vessel and vacuum gauges (leading to a low vacuum conductance). The narrow beam of gamma Bremstrahlung radiation is intercepted by scanning tungsten blades in the beam line front-end allowing a radiation shower to be detected outside the vacuum vessel proportional to the gas pressure in the corresponding storage ring straight section. A second detector mounted on rails can be moved over a length of 6.5m parallel to the ESRF storage ring so as to localise regions of bea...

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

    Science.gov (United States)

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

    2016-03-01

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

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    Wang, Chunliang; Lundström, Claes

    2016-02-01

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

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

    Science.gov (United States)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Watanabe, Norio; Tsuburaya, Yuji; Shimada, Akihiro; Aoki, Sadao [Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8573 (Japan)

    2016-01-28

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

  1. Quantitative linkage genome scan for atopy in a large collection of Caucasian families

    NARCIS (Netherlands)

    Webb, Bradley T.; van den Oord, Edwin; Akkari, Anthony; Wilton, Steve; Ly, Tina; Duv, Rachael; Barnes, Kathleen C.; Carlsen, Karin; Gerritsen, Jorrit; Lenney, Warren; Silverman, Michael; Sly, Peter; Sundy, John; Tsanakas, John; von Berg, Andrea; Whyte, Moira; Blumenthal, Malcolm; Vestbo, Jorgen; Middleton, Lefkos; Helms, Peter J.; Anderson, Wayne H.; Pillai, Sreekumar G.

    Quantitative phenotypes correlated with a complex disorder offer increased power to detect linkage in comparison to affected-unaffected classifications. Asthma is a complex disorder characterized by periods of bronchial obstruction and increased bronchial hyper reactivity. In childhood and early

  2. Detection Mechanism of Parallel Defect using Scanning Inductive Thermography

    Science.gov (United States)

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

    2017-06-01

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

  3. Fault detection by surface seismic scanning tunneling macroscope: Field test

    KAUST Repository

    Hanafy, Sherif M.

    2014-08-05

    The seismic scanning tunneling macroscope (SSTM) is proposed for detecting the presence of near-surface impedance anomalies and faults. Results with synthetic data are consistent with theory in that scatterers closer to the surface provide brighter SSTM profiles than those that are deeper. The SSTM profiles show superresolution detection if the scatterers are in the near-field region of the recording line. The field data tests near Gulf of Aqaba, Haql, KSA clearly show the presence of the observable fault scarp, and identify the subsurface presence of the hidden faults indicated in the tomograms. Superresolution detection of the fault is achieved, even when the 35 Hz data are lowpass filtered to the 5-10 Hz band.

  4. Linear and Nonlinear Damage Detection Using a Scanning Laser Vibrometer

    Directory of Open Access Journals (Sweden)

    Steve Vanlanduit

    2002-01-01

    Full Text Available Because a Scanning Laser Vibrometer (SLV can perform vibration measurements with a high spatial resolution, it is an ideal instrument to accurately locate damage in a structure. Unfortunately, the use of linear damage detection features, as for instance FRFs or modal parameters, does not always lead to a successful identification of the damage location. Measurement noise and nonlinear distortions can make the damage detection procedure difficult. In this article, a combined linear-nonlinear strategy to detect and locate damage in a structure with the aid of a SLV, will be proposed. To minimize the effect of noise, the modal parameters will be estimated using a Maximum Likelihood Estimator (MLE. Both noise and nonlinear distortion levels are extracted using the residuals of a two-dimensional spline fit. The validation of the technique will be performed on SLV measurements of a delaminated composite plate.

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

    Science.gov (United States)

    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

  6. Detecting positive selection from genome scans of linkage disequilibrium

    Directory of Open Access Journals (Sweden)

    Rogers Alan R

    2010-01-01

    Full Text Available Abstract Background Though a variety of linkage disequilibrium tests have recently been introduced to measure the signal of recent positive selection, the statistical properties of the various methods have not been directly compared. While most applications of these tests have suggested that positive selection has played an important role in recent human history, the results of these tests have varied dramatically. Results Here, we evaluate the performance of three statistics designed to detect incomplete selective sweeps, LRH and iHS, and ALnLH. To analyze the properties of these tests, we introduce a new computational method that can model complex population histories with migration and changing population sizes to simulate gene trees influenced by recent positive selection. We demonstrate that iHS performs substantially better than the other two statistics, with power of up to 0.74 at the 0.01 level for the variation best suited for full genome scans and a power of over 0.8 at the 0.01 level for the variation best suited for candidate gene tests. The performance of the iHS statistic was robust to complex demographic histories and variable recombination rates. Genome scans involving the other two statistics suffer from low power and high false positive rates, with false discovery rates of up to 0.96 for ALnLH. The difference in performance between iHS and ALnLH, did not result from the properties of the statistics, but instead from the different methods for mitigating the multiple comparison problem inherent in full genome scans. Conclusions We introduce a new method for simulating genealogies influenced by positive selection with complex demographic scenarios. In a power analysis based on this method, iHS outperformed LRH and ALnLH in detecting incomplete selective sweeps. We also show that the single-site iHS statistic is more powerful in a candidate gene test than the multi-site statistic, but that the multi-site statistic maintains a low

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

    Science.gov (United States)

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

    2017-08-01

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

  8. AN AUTOMATED ROAD ROUGHNESS DETECTION FROM MOBILE LASER SCANNING DATA

    Directory of Open Access Journals (Sweden)

    P. Kumar

    2017-05-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

  10. X-ray scan detection for cargo integrity

    Science.gov (United States)

    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.

  11. Aptasensors for quantitative detection of Salmonella Typhimurium.

    Science.gov (United States)

    Ansari, Najmeh; Yazdian-Robati, Rezvan; Shahdordizadeh, Mahin; Wang, Zhouping; Ghazvini, Kiarash

    2017-09-15

    Salmonella is one of the most frequent causes of food borne infectious disease. Among nearly 2500 documented serotypes are reported, Salmonella Typhimurium is the number one serotype associated with salmonellosis worldwide. Many different methods have been developed for the detection and quantification of S. typhimurium. Most of these assays are usually expensive, time consuming and require difficult sample preparation steps. Therefore, it is necessary to develop rapid, robust, cost-effective and sensitive alternative detection methods. In the last years, aptasensors, used for detection of S. typhimurium in different samples. In this review, recent advances and applications of aptasensors for the detection and quantification of S. typhimurium in details have been summarized. Copyright © 2017 Elsevier Inc. All rights reserved.

  12. PEDESTRIAN DETECTION BY LASER SCANNING AND DEPTH IMAGERY

    Directory of Open Access Journals (Sweden)

    A. Barsi

    2016-06-01

    Full Text Available 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.

  13. Quantitative imaging of electrospun fibers by PeakForce Quantitative NanoMechanics atomic force microscopy using etched scanning probes.

    Science.gov (United States)

    Chlanda, Adrian; Rebis, Janusz; Kijeńska, Ewa; Wozniak, Michal J; Rozniatowski, Krzysztof; Swieszkowski, Wojciech; Kurzydlowski, Krzysztof J

    2015-05-01

    Electrospun polymeric submicron and nanofibers can be used as tissue engineering scaffolds in regenerative medicine. In physiological conditions fibers are subjected to stresses and strains from the surrounding biological environment. Such stresses can cause permanent deformation or even failure to their structure. Therefore, there is a growing necessity to characterize their mechanical properties, especially at the nanoscale. Atomic force microscopy is a powerful tool for the visualization and probing of selected mechanical properties of materials in biomedical sciences. Image resolution of atomic force microscopy techniques depends on the equipment quality and shape of the scanning probe. The probe radius and aspect ratio has huge impact on the quality of measurement. In the presented work the nanomechanical properties of four different polymer based electrospun fibers were tested using PeakForce Quantitative NanoMechanics atomic force microscopy, with standard and modified scanning probes. Standard, commercially available probes have been modified by etching using focused ion beam (FIB). Results have shown that modified probes can be used for mechanical properties mapping of biomaterial in the nanoscale, and generate nanomechanical information where conventional tips fail. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

    Science.gov (United States)

    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.

  15. Computational tools for quantitative breast morphometry based on 3D scans.

    Science.gov (United States)

    Chen, D; Chittajallu, D R; Passalis, G; Kakadiaris, I A

    2010-05-01

    Quantitative analysis of breast morphometry is critical to breast plastic surgery. Recently, three-dimensional (3D) photography has emerged as a strong new alternative for breast morphometry analysis in comparison to other existing techniques. 3D photography enables the capture of the entire breast surface topology virtually in a single snapshot and without any direct contact with the patient, thus causing minimal discomfort. In this paper, we present a set of computational tools for the quantitative analysis of two key morphological properties of the breast that are of interest to breast plastic surgery based on 3D scans, namely breast shape and volume. The breast shape is modeled using a compact geometric model capable of capturing the global shape of the breast with very few parameters. Specifically, the shape model is deduced by applying a set of five global deformations to a geometric primitive. These deformations, defined using very intuitive parameters, closely model the key shape variables that surgeons inherently use to describe the overall shape of the breast. Patient-specific parameters of the breast shape model are automatically recovered by fitting a generic breast shape model to the 3D scan of the patient's breast using a physics-based deformable model framework. The mean error of fit between the automatically fitted shape model and the actual breast surface for 12 subjects varied between 0.9 and 2.6 mm. These results are very encouraging considering the fact that only 17 parameters are used to determine the shape of the breast. The breast volume is estimated automatically by first localizing the breast on a 3D scan of the patient's torso and then computing the volume enclosed between an interpolated breast-less torso surface and the actual breast. The volume estimated by the proposed method was found to be within the intra-operator variability among five segmentation trials performed manually by an expert on 3D torso scans of three subjects.

  16. Compositional analysis of GaAs/AlGaAs heterostructures using quantitative scanning transmission electron microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Kauko, H.; Helvoort, A. T. J. van [Department of Physics, Norwegian University of Science and Technology (NTNU), Trondheim (Norway); Zheng, C. L.; Glanvill, S. [Monash Centre for Electron Microscopy, Monash University, VIC 3800 (Australia); Zhu, Y.; Etheridge, J., E-mail: joanne.etheridge@monash.edu [Monash Centre for Electron Microscopy, Monash University, VIC 3800 (Australia); Department of Materials Engineering, Monash University, VIC 3800 (Australia); Dwyer, C. [Monash Centre for Electron Microscopy, Monash University, VIC 3800 (Australia); Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons, and Peter Grünberg Institute, Forschungszentrum Jülich, D-52425 Jülich (Germany); Munshi, A. M.; Fimland, B. O. [Department of Electronics and Telecommunications, Norwegian University of Science and Technology (NTNU), Trondheim (Norway)

    2013-12-02

    We demonstrate a method for compositional mapping of Al{sub x}Ga{sub 1–x}As heterostructures with high accuracy and unit cell spatial resolution using quantitative high angle annular dark field scanning transmission electron microscopy. The method is low dose relative to spectroscopic methods and insensitive to the effective source size and higher order lens aberrations. We apply the method to study the spatial variation in Al concentration in cross-sectioned GaAs/AlGaAs core-shell nanowires and quantify the concentration in the Al-rich radial band and the AlGaAs shell segments.

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

    Science.gov (United States)

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

    2017-06-01

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

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

    Science.gov (United States)

    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..

  19. Detecting Terrain Stoniness From Airborne Laser Scanning Data †

    Directory of Open Access Journals (Sweden)

    Paavo Nevalainen

    2016-08-01

    Full Text Available Three methods to estimate the presence of ground surface stones from publicly available Airborne Laser Scanning (ALS point clouds are presented. The first method approximates the local curvature by local linear multi-scale fitting, and the second method uses Discrete-Differential Gaussian curvature based on the ground surface triangulation. The third baseline method applies Laplace filtering to Digital Elevation Model (DEM in a 2 m regular grid data. All methods produce an approximate Gaussian curvature distribution which is then vectorized and classified by logistic regression. Two training data sets consisted of 88 and 674 polygons of mass-flow deposits, respectively. The locality of the polygon samples is a sparse canopy boreal forest, where the density of ALS ground returns is sufficiently high to reveal information about terrain micro-topography. The surface stoniness of each polygon sample was categorized for supervised learning by expert observation on the site. The leave-pair-out (L2O cross-validation of the local linear fit method results in the area under curve A U C = 0 . 74 and A U C = 0 . 85 on two data sets, respectively. This performance can be expected to suit real world applications such as detecting coarse-grained sediments for infrastructure construction. A wall-to-wall predictor based on the study was demonstrated.

  20. Quantitative linkage genome scan for atopy in a large collection of Caucasian families

    DEFF Research Database (Denmark)

    Webb, BT; van den Oord, E; Akkari, A

    2007-01-01

    Quantitative phenotypes correlated with a complex disorder offer increased power to detect linkage in comparison to affected-unaffected classifications. Asthma is a complex disorder characterized by periods of bronchial obstruction and increased bronchial hyper reactivity. In childhood and early...... adulthood, asthma is frequently associated also with quantitative measures of atopy. Genome wide quantitative multipoint linkage analysis was conducted for serum IgE levels and percentage of positive skin prick test (SPT(per)) using three large groups of families originally ascertained for asthma....... In this report, 438 and 429 asthma families were informative for linkage using IgE and SPT(per) which represents 690 independent families. Suggestive linkage (LOD >/= 2) was found on chromosomes 1, 3, and 8q with maximum LODs of 2.34 (IgE), 2.03 (SPT(per)), and 2.25 (IgE) near markers D1S1653, D3S2322-D3S1764...

  1. Gold nanoparticle immunochromatographic assay for quantitative detection of urinary RBP

    Directory of Open Access Journals (Sweden)

    XU Kuan

    2013-04-01

    Full Text Available A rapid quantitative detection of urinary RBP was established by using nano-gold immunochromatography (sandwich method and trisodium citrate reduction method and a rapid immunochromatographic test strip was developed. Theimmunochromatographic test strip can quantitatively detect RBP within 15 minutes. The detection limit was 150ng/mL and detection range was from 150 to 5000 ng/mL. There were no cross-reactions with others kidney disease markers,such as urinary albumin (ALB,transferrin protein (TRF,β2-microglobulin (β2-MG,urinary fiber connecting protein (FN,and lysozyme (LZM. The results indicate that it is a quick and simple method with strong specificity,high sensitivity,and wide detection range. The rapid detection method will have extensive clinical applications in the early diagnosis of proximal tubular damage,kidney disease,diabetic nephropathy,and process monitoring.

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

    Science.gov (United States)

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

    2013-01-01

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

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

    Science.gov (United States)

    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.

  4. Three-dimensional quantitative ultrasound for detecting lymph node metastases.

    Science.gov (United States)

    Saegusa-Beecroft, Emi; Machi, Junji; Mamou, Jonathan; Hata, Masaki; Coron, Alain; Yanagihara, Eugene T; Yamaguchi, Tadashi; Oelze, Michael L; Laugier, Pascal; Feleppa, Ernest J

    2013-07-01

    Detection of metastases in lymph nodes (LNs) is critical for cancer management. Conventional histological methods may miss metastatic foci. To date, no practical means of evaluating the entire LN volume exists. The aim of this study was to develop fast, reliable, operator-independent, high-frequency, quantitative ultrasound (QUS) methods for evaluating LNs over their entire volume to effectively detect LN metastases. We scanned freshly excised LNs at 26 MHz and digitally acquired echo-signal data over the entire three-dimensional (3D) volume. A total of 146 LNs of colorectal, 26 LNs of gastric, and 118 LNs of breast cancer patients were enrolled. We step-sectioned LNs at 50-μm intervals and later compared them with 13 QUS estimates associated with tissue microstructure. Linear-discriminant analysis classified LNs as metastatic or nonmetastatic, and we computed areas (Az) under receiver-operator characteristic curves to assess classification performance. The QUS estimates and cancer probability values derived from discriminant analysis were depicted in 3D images for comparison with 3D histology. Of 146 LNs of colorectal cancer patients, 23 were metastatic; Az = 0.952 ± 0.021 (95% confidence interval [CI]: 0.911-0.993); sensitivity = 91.3% (specificity = 87.0%); and sensitivity = 100% (specificity = 67.5%). Of 26 LNs of gastric cancer patients, five were metastatic; Az = 0.962 ± 0.039 (95% CI: 0.807-1.000); sensitivity = 100% (specificity = 95.3%). A total of 17 of 118 LNs of breast cancer patients were metastatic; Az = 0.833 ± 0.047 (95% CI: 0.741-0.926); sensitivity = 88.2% (specificity = 62.5%); sensitivity = 100% (specificity = 50.5%). 3D cancer probability images showed good correlation with 3D histology. These results suggest that operator- and system-independent QUS methods allow reliable entire-volume LN evaluation for detecting metastases. 3D cancer probability images can help pathologists identify metastatic foci that could be missed using conventional

  5. 3D quantitative ultrasound for detecting lymph-node metastases

    Science.gov (United States)

    Saegusa-Beecroft, Emi; Machi, Junji; Mamou, Jonathan; Hata, Masaki; Coron, Alain; Yanagihara, Eugene T.; Yamaguchi, Tadashi; Oelze, Michael L.; Laugier, Pascal; Feleppa, Ernest

    2013-01-01

    BACKGROUND Detection of metastases in lymph nodes (LNs) is critical for cancer management. Conventional histological methods may miss metastatic foci. Currently, no practical means of entire LN-volume evaluation exists. The aim of this study is to develop fast, reliable, operator-independent, high-frequency, quantitative-ultrasound (QUS) methods for evaluating LNs over their entire volumes for effectively detecting LN metastases. MATERIALS AND METHODS Freshly excised LNs were scanned at 26 MHz and echo-signal data were digitally acquired over the entire three-dimensional (3D) volume. 146 LNs of colorectal-, 26 LNs of gastric-, and 118 LNs of breast-cancer patients were enrolled. LNs were step-sectioned at 50-μm intervals and later compared to 13 QUS estimates associated with tissue microstructure. Linear-discriminant analysis classified LNs as metastatic or non-metastatic, and areas (Az) under receiver-operator characteristic (ROC) curves were computed to assess classification performance. QUS-estimates and cancer-probability values derived from discriminant analysis were depicted in 3D images for comparison with 3D histology. RESULTS 23/146 LNs of colorectal-cancer patients were metastatic; Az = 0.952 ± 0.021 (95% CI: 0.911 to 0.993); sensitivity 91.3% (specificity 87.0%); sensitivity 100% (specificity 67.5%). 5/26 LNs of gastric-cancer patients were metastatic; Az = 0.962 ± 0.039 (95% CI: 0.807 to 1.000); sensitivity 100% (specificity 95.3%). 17/118 LNs of breast-cancer patients were metastatic; Az = 0.833 ± 0.047 (95% CI: 0.741 to 0.926); sensitivity 88.2% (specificity 62.5%); sensitivity 100% (specificity 50.5%). 3D cancer-probability images showed good correlation with 3D histology. CONCLUSIONS These results suggest that operator- and system-independent QUS methods will allow reliable entire-volume LN evaluation for detecting metastases. 3D cancer-probability images can help pathologists identify metastatic foci that could be missed using conventional

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

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Hongchang, E-mail: hongchang.wang@diamond.ac.uk; Kashyap, Yogesh; Sawhney, Kawal [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom)

    2016-03-21

    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.

  7. Quantitative radio-isotope scanning in ankylosing spondylitis: a clinical, laboratory and computerised tomographic study

    Energy Technology Data Exchange (ETDEWEB)

    Taylor, H.G.; Gadd, R.; Beswick, E.J.; Venkateswaran, M.; Dawes, P.T. (Staffordshire Rheumatology Centre, Haywood Hospital, Stoke-on-Trent (United Kingdom))

    1991-01-01

    Quantitative sacroiliac and lumbar spine radio-isotope (Tc-99m MDP) scans were performed in 42 patients with ankylosing spondylitis, and repeated 12 months later in 25. Clinical and laboratory assessments as well as computerised tomographic (CT) scans of the sacroiliac joints (SIJ) and lateral lumbar spine x-rays, were performed. Bone (using the L3/4 area of the lumbar spine, sacrum, SIJ's and knee) to soft tissue (ST) ratios all correlated strongly with each other. Patients with high SIJ:ST ratios had significantly greater low-back stiffness (p<0.05). Change in serum IgA levels correlated negatively with change in bone: ST ratios. There was no relationship between bone: ST ratios and any other clinical or laboratory variables. The change in SIJ:ST ratios correlated positively with change in CT erosion score (p<0.05) and negatively with change in CT ankylosis score (p<0.05). (au) 24 refs., 2 figs., 1 tbl.

  8. Quantitative analysis of CT scan in degenerative diseases of the nervous system

    Energy Technology Data Exchange (ETDEWEB)

    Matsuoka, Yukihiko; Yamamoto, Hiroko; Sobue, Itsuro.

    1988-05-01

    Quantitative analysis was made on cranial CT scans of 142 patients with spinocerebellar degeneration (SCD), 16 with dentato-rubro-pallido-luysian atrophy (DRPLA), 12 with Huntington's chorea (HC), and four with chorea-acanthocytosis (CA). One hundred sex- and age-matched persons without any neurologic signs served as controls. Regarding parameters for atrophy in the infratentorial brain tissue, there was statistically significant difference between the SCD group and the control group. This indicated remarkable atrophy in the cerebellum and brain stem in SCD. According to subgroups of SCD, both bilateral atrophy of the pons and dilation of the prepontine cistern were significantly greater in the group of sporadic olivo-ponto-cerebellar atrophy than the group of Menzel type of olivo-ponto-cerebellar atrophy. The subgroup of hereditary spastic paraplegia had the mildest atrophy of the brain on CT, although there was still a significant atrophy compared with controls. In the DRPLA group, finding in the infratentorial brain tissue were similar to those in the SCD group. The HC group was characterized by having the greatest atrophy in the lateral ventricle, especially the caudate nuclei. Similar findings were seen in the CA group, although atrophy was generally mild. The results indicate the usefulness of quantitative analysis on CT in the diagnosis of degenerative diseases of the nervous system. (Namekawa, K.).

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

    Science.gov (United States)

    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 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 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.

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

    Science.gov (United States)

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

    2013-11-01

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

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

    Science.gov (United States)

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

    2016-01-01

    Selective breeding of dogs has resulted in repeated artificial selection on breed-specific morphological phenotypes. A number of quantitative trait loci associated with these phenotypes have been identified in genetic mapping studies. We analysed the population genomic signatures observed around the causal mutations for 12 of these loci in 25 dog breeds, for which we genotyped 25 individuals in each breed. By measuring the population frequencies of the causal mutations in each breed, we identified those breeds in which specific mutations most likely experienced positive selection. These instances were then used as positive controls for assessing the performance of popular statistics to detect selection from population genomic data. We found that artificial selection during dog domestication has left characteristic signatures in the haplotype and nucleotide polymorphism patterns around selected loci that can be detected in the genotype data from a single population sample. However, the sensitivity and accuracy at which such signatures were detected varied widely between loci, the particular statistic used and the choice of analysis parameters. We observed examples of both hard and soft selective sweeps and detected strong selective events that removed genetic diversity almost entirely over regions >10 Mbp. Our study demonstrates the power and limitations of selection scans in populations with high levels of linkage disequilibrium due to severe founder effects and recent population bottlenecks. © 2015 John Wiley & Sons Ltd.

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

    Science.gov (United States)

    Kellner, Kenneth F; Swihart, Robert K

    2014-01-01

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

  13. If brain scans really detected deception, who would volunteer to be scanned?

    Science.gov (United States)

    Spence, Sean A; Hope-Urwin, Alexandra; Lankappa, Sudheer T; Woodhead, Jean; Burgess, Jenny C L; Mackay, Alice V

    2010-09-01

    Recent neuroimaging studies investigating the neural correlates of deception among healthy people, have raised the possibility that such methods may eventually be applied during legal proceedings. Were this so, who would volunteer to be scanned? We report a "natural experiment" casting some light upon this question. Following broadcast of a television series describing our team's investigative neuroimaging of deception in 2007, we received unsolicited (public) correspondence for 12 months. Using a customized template to examine this material, three independent assessors unanimously rated 30 of an initial 56 communications as unequivocally constituting requests for a "scan" (to demonstrate their author's "innocence"). Compared with the rest, these index communications were more likely to originate from incarcerated males, who were also more likely to engage in further correspondence. Hence, in conclusion, if neuroimaging were to become an acceptable means of demonstrating innocence then incarcerated males may well constitute those volunteering for such investigation. © 2010 American Academy of Forensic Sciences.

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

    Energy Technology Data Exchange (ETDEWEB)

    Kalugin, Nikolai G. (New Mexico Tech, Socorro, NM); Gonzales, Edward; Kalichava, Irakli (New Mexico Tech, Socorro, NM); Gin, Aaron V.; Wickey, Lee (New Mexico Tech, Socorro, NM); Del Barga, Christopher (New Mexico Tech, Socorro, NM); Talanov, Vladimir V. (Neocera, LLC, Beltsville, MD); Shaner, Eric Arthur

    2010-07-01

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

  15. Is scanning electron microscopy/energy dispersive X-ray spectrometry (SEM/EDS) quantitative?

    Science.gov (United States)

    Newbury, Dale E; Ritchie, Nicholas W M

    2013-01-01

    Scanning electron microscopy/energy dispersive X-ray spectrometry (SEM/EDS) is a widely applied elemental microanalysis method capable of identifying and quantifying all elements in the periodic table except H, He, and Li. By following the "k-ratio" (unknown/standard) measurement protocol development for electron-excited wavelength dispersive spectrometry (WDS), SEM/EDS can achieve accuracy and precision equivalent to WDS and at substantially lower electron dose, even when severe X-ray peak overlaps occur, provided sufficient counts are recorded. Achieving this level of performance is now much more practical with the advent of the high-throughput silicon drift detector energy dispersive X-ray spectrometer (SDD-EDS). However, three measurement issues continue to diminish the impact of SEM/EDS: (1) In the qualitative analysis (i.e., element identification) that must precede quantitative analysis, at least some current and many legacy software systems are vulnerable to occasional misidentification of major constituent peaks, with the frequency of misidentifications rising significantly for minor and trace constituents. (2) The use of standardless analysis, which is subject to much broader systematic errors, leads to quantitative results that, while useful, do not have sufficient accuracy to solve critical problems, e.g. determining the formula of a compound. (3) EDS spectrometers have such a large volume of acceptance that apparently credible spectra can be obtained from specimens with complex topography that introduce uncontrolled geometric factors that modify X-ray generation and propagation, resulting in very large systematic errors, often a factor of ten or more. © Wiley Periodicals, Inc.

  16. Videodensitometric quantitative angiography after coronary balloon angioplasty, compared to edge-detection quantitative angiography and intracoronary ultrasound imaging

    NARCIS (Netherlands)

    Peters, R. J.; Kok, W. E.; Pasterkamp, G.; von Birgelen, C.; Prins, M. [=Martin H.; Serruys, P. W.

    2000-01-01

    AIMS: To assess the value of videodensitometric quantification of the coronary lumen after angioplasty by comparison to two other techniques of coronary artery lumen quantification. METHODS AND RESULTS: Videodensitometric quantitative angiography, edge detection quantitative angiography and 30 MHz

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

    Energy Technology Data Exchange (ETDEWEB)

    Van Aert, S., E-mail: sandra.vanaert@ua.ac.be [Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp (Belgium); Verbeeck, J. [Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp (Belgium); Erni, R. [National Center for Electron Microscopy, Ernest Orlando Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS 72R0150, Berkeley, CA 94720 (United States); Bals, S. [Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp (Belgium); Luysberg, M. [Institute of Solid State Research and Ernst Ruska Center for Microscopy and Spectroscopy with Electrons, Helmholtz Research Center Juelich, 52425 Juelich (Germany); Dyck, D. Van; Tendeloo, G. Van [Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp (Belgium)

    2009-09-15

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

  18. Quantitative radio-isotope scanning of the sacroiliac joints in ankylosing spondylitis

    Energy Technology Data Exchange (ETDEWEB)

    Skaar, O.; Dale, K.; Lindegaard, M.W.; Foerre, O.; Kaass, E. (Oslo Sanitetsforening Rheumatism Hospital (Norway). Dept. of Radiology, General Dept. Norwegian Radium Hospital, Oslo (Norway). Dept. of Nuclear Medicine)

    1992-03-01

    A method for applying {sup 99m}Tc-MDP for dynamic and static quantitative radioisotope scanning (QRS) of the sacroiliac joints (SI) in early progressive sacroiliitis in ankylosing spondylitis (AS) is described. In a prospective study, 2 groups of male AS patients were investigated, one with increased elevated erythrocytic sedimentation rate (ERS) (group A, n = 7) and one with normal ERS (group B, n = 8). In both groups an increased uptake of the radiotracer was found in the static part of the study versus a control group C (n = 9). An increased uptake versus group C was also found for group A in the dynamic part of the study (p = 0.01) while there was no significant difference dynamically between group B and C. The results of the dynamic study in group A indicate ERS to be a parameter of inflammatory activity in the SI joints. The study also seems to indicate QRS to be a valuable diagnostic method in early AS without definite radiographic changes in the SI joints. (orig.).

  19. Tree Root System Characterization and Volume Estimation by Terrestrial Laser Scanning and Quantitative Structure Modeling

    Directory of Open Access Journals (Sweden)

    Aaron Smith

    2014-12-01

    Full Text Available The accurate characterization of three-dimensional (3D root architecture, volume, and biomass is important for a wide variety of applications in forest ecology and to better understand tree and soil stability. Technological advancements have led to increasingly more digitized and automated procedures, which have been used to more accurately and quickly describe the 3D structure of root systems. Terrestrial laser scanners (TLS have successfully been used to describe aboveground structures of individual trees and stand structure, but have only recently been applied to the 3D characterization of whole root systems. In this study, 13 recently harvested Norway spruce root systems were mechanically pulled from the soil, cleaned, and their volumes were measured by displacement. The root systems were suspended, scanned with TLS from three different angles, and the root surfaces from the co-registered point clouds were modeled with the 3D Quantitative Structure Model to determine root architecture and volume. The modeling procedure facilitated the rapid derivation of root volume, diameters, break point diameters, linear root length, cumulative percentages, and root fraction counts. The modeled root systems underestimated root system volume by 4.4%. The modeling procedure is widely applicable and easily adapted to derive other important topological and volumetric root variables.

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

    Science.gov (United States)

    Hassa-Roudsari, Majid; Goff, H Douglas

    2012-01-01

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

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

    Science.gov (United States)

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

    2017-04-01

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

  2. A Highly Sensitive Immunochromatographic Strip Test for Rapid and Quantitative Detection of Saikosaponin d

    Directory of Open Access Journals (Sweden)

    Yue Zhang

    2018-02-01

    Full Text Available A quantitative lateral-flow immunoassay using gold nanoparticles (AuNPs conjugated with a monoclonal antibody (MAb against saikosaponin d (SSd was developed for the analysis of SSd. The AuNPs were prepared in our laboratory. The AuNPs were polyhedral, with an average diameter of approximately 18 nm. We used the conjugation between AuNPs and MAbs against SSd to prepare immunochromatographic strips (ICSs. For the quantitative experiment, the strips with the test results were scanned using a membrane strip reader, and a detection curve (regression equation, y = −0.113ln(x + 1.5451, R2 = 0.983, representing the averages of the scanned data, was obtained. This curve was linear from 96 ng/mL to 150 μg/mL, and the IC50 value was 10.39 μg/mL. In this study, we bring the concept of POCT (point-of-care testing to the measurement of TCM compounds, and this is the first report of quantitative detection of SSd by an ICS.

  3. A flexibly shaped space-time scan statistic for disease outbreak detection and monitoring

    Directory of Open Access Journals (Sweden)

    Tango Toshiro

    2008-04-01

    Full Text Available Abstract Background Early detection of disease outbreaks enables public health officials to implement disease control and prevention measures at the earliest possible time. A time periodic geographical disease surveillance system based on a cylindrical space-time scan statistic has been used extensively for disease surveillance along with the SaTScan software. In the purely spatial setting, many different methods have been proposed to detect spatial disease clusters. In particular, some spatial scan statistics are aimed at detecting irregularly shaped clusters which may not be detected by the circular spatial scan statistic. Results Based on the flexible purely spatial scan statistic, we propose a flexibly shaped space-time scan statistic for early detection of disease outbreaks. The performance of the proposed space-time scan statistic is compared with that of the cylindrical scan statistic using benchmark data. In order to compare their performances, we have developed a space-time power distribution by extending the purely spatial bivariate power distribution. Daily syndromic surveillance data in Massachusetts, USA, are used to illustrate the proposed test statistic. Conclusion The flexible space-time scan statistic is well suited for detecting and monitoring disease outbreaks in irregularly shaped areas.

  4. Internal fingerprint zone detection in optical coherence tomography fingertip scans

    CSIR Research Space (South Africa)

    Darlow, LN

    2015-04-01

    Full Text Available details and tests a k-means clustering approach for papillary junction detection. All tested metrics are of a standard comparable to the measured human error. The technique presented in this research is highly successful in detection of the location...

  5. LIBS experiments for quantitative detection of retained fuel

    Directory of Open Access Journals (Sweden)

    F. Colao

    2017-08-01

    Here we present the results of the Double Pulse LIBS (DP-LIBS probing of deuterated samples with the simultaneous optical detection by medium-resolution and high-resolution spectrometer. Deuterium emission at 656.1nm has been detected then the elemental composition has been quantified by applying the Calibration Free (CF approach. The obtained results demonstrate that the DP-LIBS technique combined with CF analysis is suitable for the quantitative determination of tritium content inside the PFCs of next fusion devices like ITER.

  6. Scan statistics with local vote for target detection in distributed system

    Science.gov (United States)

    Luo, Junhai; Wu, Qi

    2017-12-01

    Target detection has occupied a pivotal position in distributed system. Scan statistics, as one of the most efficient detection methods, has been applied to a variety of anomaly detection problems and significantly improves the probability of detection. However, scan statistics cannot achieve the expected performance when the noise intensity is strong, or the signal emitted by the target is weak. The local vote algorithm can also achieve higher target detection rate. After the local vote, the counting rule is always adopted for decision fusion. The counting rule does not use the information about the contiguity of sensors but takes all sensors' data into consideration, which makes the result undesirable. In this paper, we propose a scan statistics with local vote (SSLV) method. This method combines scan statistics with local vote decision. Before scan statistics, each sensor executes local vote decision according to the data of its neighbors and its own. By combining the advantages of both, our method can obtain higher detection rate in low signal-to-noise ratio environment than the scan statistics. After the local vote decision, the distribution of sensors which have detected the target becomes more intensive. To make full use of local vote decision, we introduce a variable-step-parameter for the SSLV. It significantly shortens the scan period especially when the target is absent. Analysis and simulations are presented to demonstrate the performance of our method.

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

    DEFF Research Database (Denmark)

    Abbott, Diana; Li, Yi-Ju; Guggenheim, Jeremy A

    2012-01-01

    To investigate quantitative trait loci linked to refractive error, we performed a genome-wide quantitative trait linkage analysis using single nucleotide polymorphism markers and family data from five international sites.......To investigate quantitative trait loci linked to refractive error, we performed a genome-wide quantitative trait linkage analysis using single nucleotide polymorphism markers and family data from five international sites....

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

  10. Diffusing capacity for carbon monoxide correlates best with tissue volume from quantitative CT scanning analysis.

    Science.gov (United States)

    Barjaktarevic, Igor; Springmeyer, Steven; Gonzalez, Xavier; Sirokman, William; Coxson, Harvey O; Cooper, Christopher B

    2015-06-01

    Quantitative analysis of high-resolution chest CT scan (QCT) is an established method for determining the severity and distribution of lung parenchymal destruction inpatients with emphysema. Diffusing capacity of the lung for carbon monoxide (D(LCO)) is a traditional physiologic measure of emphysema severity and is probably influenced more by destruction of the alveolar capillary bed than by membrane diffusion per se. We reasoned that D(LCO) should correlate with tissue volume from QCT. A total of 460 patients with upper-lobe-predominant emphysema were enrolled in the study. Th e mean (SD) of percent predicted values for FEV 1 , total lung capacity, and D(LCO) were 30.6% (8.0%), 129.5% (18.1%), and 6.7% (13.1%), respectively. QCT was performed using custom soft ware; the relationship between D(LCO) and various metrics from QCT were evaluated using Pearson correlation coefficients. On average, whole-body plethysmography volumes were higher by 841 mL compared with QCT-calculated total lung volume. However, there was a strong correlation between these measurements (r=0.824, P lung volume (r=0.314, Pvolume (r=0.498, Plung with low density (-950 Hounsfield units) (r=-0.337, Pvolume,supporting the hypothesis that pulmonary capillary blood volume is the main determinant of D(LCO) in the human lung. Th e relationships between D(LCO) and various anatomic metrics of lung parenchymal destruction from QCT inform our understanding of the relationship between structure and function of the human lung.

  11. Detection of in vitro proximal caries in storage phosphor plate radiographs scanned with different resolutions

    NARCIS (Netherlands)

    Li, G.; Berkhout, W.E.R.; Sanderink, G.C.H.; Martins, M.; van der Stelt, P.F.

    2008-01-01

    Objectives: To investigate the effect of the scanning resolution of storage phosphor plate (SPP) radiographs on the detection of proximal caries lesions. Methods: 10 dentists evaluated 72 proximal surfaces of premolars with respect to caries from SPP radiographs scanned with theoretical spatial

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

    Directory of Open Access Journals (Sweden)

    Takeshi Hara

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

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

    Science.gov (United States)

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

    2015-01-01

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

  14. Range image segmentation for tree detection in forest scans

    Directory of Open Access Journals (Sweden)

    A. Bienert

    2013-10-01

    Full Text Available To make a tree-wise analysis inside a forest stand, the trees have to be identified. An interactive segmentation is often labourintensive and time-consuming. Therefore, an automatic detection process will aspired using a range image. This paper presents a method for the segmentation of range images extracted from terrestrial laser scanner point clouds of forest stands. After range image generation the segmentation is carried out with a connectivity analysis using the differences of the range values as homogeneity criterion. Subsequently, the tree detection is performed interactively by analysing one horizontal image line. When passing objects with a specific width, the object indicates a potential tree. By using the edge points of a segmented pixel group the tree position and diameter is calculated. Results from one test site are presented to show the performance of the method.

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

    Science.gov (United States)

    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.

  16. Catenary System Detection, Localization and Classification Using Mobile Scanning Data

    Directory of Open Access Journals (Sweden)

    Elżbieta Pastucha

    2016-09-01

    Full Text Available This paper presents a new method for detecting, locating and classifying overhead contact systems (catenary systems in point clouds collected by mobile mapping systems (MMS on rail roads. Contrary to many other application types, railway embankments are highly regulated and standardized. Railway infrastructure geometric relations remain roughly unchanged within established regions and have similarities between them. The newly-developed method exploits both these characteristics, as well as the survey process. There are several steps in this approach. Firstly, it restricts the search for catenaries relative to the distance to registered MMS trajectory, then finds possible support structures according to the density of points above the track. Subsequently, the method verifies the structures’ presence and classifies the points with the use of the RANSAC algorithm. It establishes the presence of cantilevers, as well as poles or structural beams, depending on the type of detected support structure. The method also determines the coordinates of the identified object on the ground. Finally, a classification is clarified with the use of a modified DBSCAN algorithm. The design method has been verified with data collected in four surveys where the cumulative length of the route was almost 90 km. Over 97% of support structures were correctly detected, and out of these, over 95% were completely classified.

  17. Quantitative optical imaging for the detection of early cancer

    Science.gov (United States)

    Wu, Tao

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

  18. Quantitative analysis of intrusion detection systems: Snort and Suricata

    Science.gov (United States)

    White, Joshua S.; Fitzsimmons, Thomas; Matthews, Jeanna N.

    2013-05-01

    Given competing claims, an objective head-to-head comparison of the performance of both the Snort R and Suricata Intrusion Detection Systems is needed. In this paper, we present a comprehensive quantitative comparison of the two systems. We have developed a rigorous testing framework that examines the performance of both systems as we scale system resources. Our results show that a single instance of Suricata is able to deliver substantially higher performance than a corresponding single instance of Snort. This paper describes in detail both the testing framework capabilities, tests performed and results found.

  19. Detection of in vitro proximal caries in storage phosphor plate radiographs scanned with different resolutions.

    Science.gov (United States)

    Li, G; Berkhout, W E R; Sanderink, G C H; Martins, M; van der Stelt, P F

    2008-09-01

    To investigate the effect of the scanning resolution of storage phosphor plate (SPP) radiographs on the detection of proximal caries lesions. 10 dentists evaluated 72 proximal surfaces of premolars with respect to caries from SPP radiographs scanned with theoretical spatial resolutions of: (1) the Digora FMX at 7.8 lp mm(-1); (2) the Digora Optime at both 7.8 lp mm(-1) and 12.5 lp mm(-1); and (3) the Dürr VistaScan at 10 lp mm(-1) and 20 lp mm(-1), respectively. The lesions were validated by histological examination. Receiver operating characteristic (ROC) analysis was employed. The A(z) value for the radiographs scanned with the Dürr VistaScan at 10 lp mm(-1) is significantly lower than those for the other series of radiographs (P = 0.000). For SPP radiographs, an increased theoretical spatial resolution per se is not related to an improved detection of proximal caries.

  20. Automatic detection of Hyperreflective Foci in optical coherence tomography B-scans using Morphological Component Analysis.

    Science.gov (United States)

    Mokhtari, Marzieh; Ghasemi Kamasi, Zeinab; Rabbani, Hossein

    2017-07-01

    Hyperreflective Foci (HF) is one of the most common complications distributed in cross-sectional images of patients with Diabetic Macular Edema (DME). Scanning Laser Ophthalmoscope (SLO) images usually consists of several B-scans that represent a cross-sectional reconstruction of a plane through the anterior or posterior regions of retina. In each B-scan, HFs are geometrically distinct constituents in different retinal layers. Since the intensity levels of HFs and many other subjects in B-scans are the same, in this paper we try to separate HFs from other objects by detection of the point and curve singularities in each B-scan. The decomposition algorithm presented in this paper is based on sparse image representation of B-scans using Morphological Component Analysis (MCA) technique. By using curvelet transform and Daubechies wavelet basis, two different over-complete dictionaries are constructed which represent two various aspects of B-scans. The HFs are more distinguished in reconstructed image with wavelet dictionary and other objects are mostly detectable by curvelet dictionary. So, HFs can be detected by applying an optimum threshold criterion on reconstructed image by wavelet atoms. Finally, the false positive points are reduced by removing the candidate points in RNFL and RPE layers, which are automatically segmented based on ridgelet transform. Our simulation results on 1924 HFs show that sensitivity and specificity for HF detection is 91.0% and 100%, respectively.

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

    Science.gov (United States)

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

    2016-03-01

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

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

    Science.gov (United States)

    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

  3. Evaluation of mouse tail-vein injections both qualitatively and quantitatively on small-animal PET tail scans.

    Science.gov (United States)

    Vines, Douglass C; Green, David E; Kudo, Gen; Keller, Harald

    2011-12-01

    Quantitative small-animal PET of mice requires successful delivery of radiotracers into the venous system. Intravenous injection of radiotracers via lateral tail veins is the most commonly used method of administration and can be technically challenging. Evaluation of the quality of an intravenous injection is necessary to determine whether small-animal PET is quantitatively accurate. The purpose of this study was to evaluate and compare the quality of 50 consecutive intravenous injections into mouse tail veins using both quantitative and qualitative methods. During (18)F-FDG intravenous injection, qualitative assessment of the injection was performed and classified according to specific criteria as good, intermediate, or poor. Small-animal PET scans of the body and tail were acquired, and tail injection sites were quantitatively assessed in terms of percentage injected dose per gram and classified as low, medium, or high uptake of (18)F-FDG. Qualitative and quantitative methods were compared. To assess baseline amounts of (18)F-FDG in the tail without a tail injection, 3 additional mice were injected by the intraperitoneal method, imaged, and quantitatively assessed in the same manner. The in vivo imaging data were validated on 7 additional mice by sacrificing them after scans, removing their tails, rescanning the tails, and then measuring the tail radioactivity ex vivo in a γ-counter and correlating it with the in vivo amount. Validation of in vivo imaging to ex vivo data yielded an excellent correlation, with an r(2) value of 0.95. Comparison of qualitative and quantitative methods yielded 45 matching results (42 good and low, 2 intermediate and medium, and 1 poor and high). There were 5 cases of mismatching results (1 false-negative and 4 false-positive) between qualitative and quantitative methods. Low-uptake tail injections were comparable to the intraperitoneal injection values. Using qualitative methods, accuracy was true 90% (45/50) of the time. The

  4. A genome scan for quantitative trait loci and imprinted regions affecting reproduction in pigs.

    Science.gov (United States)

    Holl, J W; Cassady, J P; Pomp, D; Johnson, R K

    2004-12-01

    Quantitative trait loci for reproductive traits in a three-generation resource population of a cross between low-indexing pigs from a control line and high-indexing pigs from a line selected 10 generations for increased index of ovulation rate and embryonic survival are reported. Phenotypic data were collected in F2 females for birth weight (BWT, n = 428), weaning weight (WWT, n = 405), age at puberty (AP, n = 295), ovulation rate (OR, n = 423), number of fully formed pigs (FF, n = 370), number of pigs born alive (NBA, n = 370), number of mummified pigs (MUM, n = 370), and number of stillborn pigs (NSB, n = 370). Grandparent, F1, and F2 animals were genotyped for 151 microsatellite markers. Sixteen putative QTL (P reproductive traits were identified in previous analyses of these data with single QTL line-cross models. Data were reanalyzed with multiple QTL models, including imprinting effects. Data also were analyzed with half-sib models. Permutation was used to establish genome-wide significance levels ( = 0.01, 0.05, and 0.10). Thirty-one putative QTL for reproductive traits and two QTL for birth weight were identified (P < 0.10). One Mendelian QTL for FF (P < 0.05), one for NBA (P < 0.05), three for NSB (P < 0.05), three for NN (P < 0.05), seven for AP (P < 0.10), five for MUM (P < 0.10), and one for BWT (P < 0.10) were found. Partial imprinting of QTL affecting OR (P < 0.01), BWT (P < 0.05), and MUM (P < 0.05) was detected. There were four paternally expressed QTL for NN (P < 0.10) and one each for AP (P < 0.05) and MUM (P < 0.10). Maternally expressed QTL affecting NSB (P < 0.10), NN (P < 0.10), and MUM (P < 0.10) were detected. No QTL were detected with half-sib analyses. Multiple QTL models with imprinting effects are more appropriate for analyzing F2 data than single Mendelian QTL line-cross models.

  5. Rapid-scan Fourier-transform coherent anti-Stokes Raman scattering spectroscopy with heterodyne detection.

    Science.gov (United States)

    Hiramatsu, Kotaro; Luo, Yizhi; Ideguchi, Takuro; Goda, Keisuke

    2017-11-01

    High-speed Raman spectroscopy has become increasingly important for analyzing chemical dynamics in real time. To address the need, rapid-scan Fourier-transform coherent anti-Stokes Raman scattering (FT-CARS) spectroscopy has been developed to realize broadband CARS measurements at a scan rate of more than 20,000 scans/s. However, the detection sensitivity of FT-CARS spectroscopy is inherently low due to the limited number of photons detected during each scan. In this Letter, we show our experimental demonstration of enhanced sensitivity in rapid-scan FT-CARS spectroscopy by heterodyne detection. Specifically, we implemented heterodyne detection by superposing the CARS electric field with an external local oscillator (LO) for their interference. The CARS signal was amplified by simply increasing the power of the LO without the need for increasing the incident power onto the sample. Consequently, we achieved enhancement in signal intensity and the signal-to-noise ratio by factors of 39 and 5, respectively, compared to FT-CARS spectroscopy with homodyne detection. The sensitivity-improved rapid-scan FT-CARS spectroscopy is expected to enable the sensitive real-time observation of chemical dynamics in a broad range of settings, such as combustion engines and live biological cells.

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

    Directory of Open Access Journals (Sweden)

    He Junkun

    2012-06-01

    Full Text Available Abstract 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 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 liposomes allows nonspecific DNA in the assay medium to be degraded with DNase I prior to quantification of the encapsulated reporter by PCR, which reduces false-positive results and improves quantitative accuracy. The ability to

  7. The efficacy of i-SCAN for detecting reflux esophagitis: a prospective randomized controlled trial.

    Science.gov (United States)

    Kang, H S; Hong, S N; Kim, Y S; Park, H S; Kim, B K; Lee, J H; Kim, S I; Lee, T Y; Kim, J H; Lee, S Y; Sung, I K; Shim, C S

    2013-01-01

    New imaging technologies have been applied in endoscopy to improve the detection and differentiation of subtle mucosal changes using a digital contrast method. Among them, i-SCAN technology is the most recently developed image-enhancing technology. We investigated whether i-SCAN could improve the detection rate of reflux esophagitis. Interobserver agreement between endoscopists was compared with conventional white light (WL) endoscopic examination. We performed a prospective randomized controlled trial. A consecutive series of 514 subjects that underwent an esophagogastroduodenoscopy for health inspection were enrolled and randomized into the i-SCAN group (n = 246) and WL group (n = 268). An esophagogastroduodenoscopy with video recording was used for detecting reflux esophagitis, and reflux esophagitis were categorized by the modified Los Angeles (LA) classification. The total number of reflux esophagitis identified by WL and i-SCAN was 58 (21.7%) and 74 (30.1%), respectively. The diagnostic yield of reflux esophagitis was significantly higher (P = 0.034) in the i-SCAN group (30.1%) as compared to the WL group (21.6%). Using the modified LA classification, the detection rate of minimal changes was significantly higher (P = 0.017) in the i-SCAN group (11.8%) as compared to the WL group (5.6%), but the detection rates of LA-A and LA-B were not significantly different between the two groups (P = 0.897 and P = 0.311, respectively). After comparison of the interobserver agreement using randomly selected video clips, the i-SCAN group showed better agreement than the WL group (Kappa value, 0.793 vs. 0.473). Compared to WL endoscopy, applying i-SCAN in daily practice can improve the diagnostic yield of reflux esophagitis by detecting more minimal changes in the squamo-columnar junction of the esophagus and can improve the interobserver agreement of the modified Los Angeles classification.

  8. Phase imaging and detection in pseudo-heterodyne scattering scanning near-field optical microscopy measurements.

    Science.gov (United States)

    Moreno, Camilo; Alda, Javier; Kinzel, Edward; Boreman, Glenn

    2017-02-01

    When considering the pseudo-heterodyne mode for detection of the modulus and phase of the near field from scattering scanning near-field optical microscopy (s-SNOM) measurements, processing only the modulus of the signal may produce an undesired constraint in the accessible values of the phase of the near field. A two-dimensional analysis of the signal provided by the data acquisition system makes it possible to obtain phase maps over the whole [0, 2π) range. This requires post-processing of the data to select the best coordinate system in which to represent the data along the direction of maximum variance. The analysis also provides a quantitative parameter describing how much of the total variance is included within the component selected for calculation of the modulus and phase of the near field. The dependence of the pseudo-heterodyne phase on the mean position of the reference mirror is analyzed, and the evolution of the global phase is extracted from the s-SNOM data. The results obtained from this technique compared well with the expected maps of the near-field phase obtained from simulations.

  9. Laser-scanning velocimetry: A confocal microscopy method for quantitative measurement of cardiovascular performance in zebrafish embryos and larvae

    Directory of Open Access Journals (Sweden)

    Linney Elwood

    2007-07-01

    Full Text Available Abstract Background The zebrafish Danio rerio is an important model system for drug discovery and to study cardiovascular development. Using a laser-scanning confocal microscope, we have developed a non-invasive method of measuring cardiac performance in zebrafish embryos and larvae that obtains cardiovascular parameters similar to those obtained using Doppler echocardiography in mammals. A laser scan line placed parallel to the path of blood in the dorsal aorta measures blood cell velocity, from which cardiac output and indices of vascular resistance and contractility are calculated. Results This technique, called laser-scanning velocimetry, was used to quantify the effects of pharmacological, developmental, and genetic modifiers of cardiac function. Laser-scanning velocimetry was applied to analyze the cardiovascular effects of morpholino knockdown of osmosensing scaffold for MEKK3 (OSM, which when mutated causes the human vascular disease cerebral cavernous malformations. OSM-deficient embryos had a constricted aortic arch and markedly increased peak cell velocity, a characteristic indicator of aortic stenosis. Conclusion These data validate laser-scanning velocimetry as a quantitative tool to measure cardiovascular performance for pharmacological and genetic analysis in zebrafish, which requires no specialized equipment other than a laser-scanning confocal microscope.

  10. Quantitative detection of well-based DNA array using switchable lanthanide luminescence

    Energy Technology Data Exchange (ETDEWEB)

    Karhunen, Ulla, E-mail: umskar@utu.fi [Division of Biotechnology, University of Turku, Tykistökatu 6A, Sixth Floor, FI-20520 Turku (Finland); Soikkeli, Minna; Lahdenperä, Susanne; Soukka, Tero [Division of Biotechnology, University of Turku, Tykistökatu 6A, Sixth Floor, FI-20520 Turku (Finland)

    2013-04-15

    Highlights: ► Oligonucleotide hybridization switches on lanthanide luminescence. ► The binary probe technology enables wash-free nucleic acid array. ► Detection of both synthetic targets and PCR-amplified E. coli DNA is demonstrated. -- Abstract: In this report a novel wash-free method for multiplexed DNA detection is demonstrated employing target specific probe pairs and switchable lanthanide luminescence technology on a solid-phase array. Four oligonucleotide capture probes, conjugated at 3′ to non-luminescent lanthanide ion carrier chelate, were immobilized as a small array on the bottom of a microtiter plate well onto which a mix of corresponding detection probes, conjugated at 5′ to a light absorbing antenna ligand, were added. In the presence of complementary target nucleic acid both the spotted capture probe and the liquid-phase detection probe hybridize adjacently on the target. Consequently the two non-luminescent label molecules self-assemble and form a luminescent mixed lanthanide chelate complex. Lanthanide luminescence is thereafter measured without a wash step from the spots by scanning in time-resolved mode. The homogeneous solid-phase array-based method resulted in quantitative detection of synthetic target oligonucleotides with 0.32 nM and 0.60 nM detection limits in a single target and multiplexed assay, respectively, corresponding to 3× SD of the background. Also qualitative detection of PCR-amplified target from Escherichia coli is described.

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

    Science.gov (United States)

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

    2017-03-01

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

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

    Directory of Open Access Journals (Sweden)

    Maximilian Gahr

    2017-01-01

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

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

    Science.gov (United States)

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

    2017-01-05

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

  14. Contribution of Metal Layer Thickness for Quantitative Backscattered Electron Imaging of Field Emission Scanning Electron Microscopy

    National Research Council Canada - National Science Library

    Kim, Hyonchol; Takei, Hiroyuki; Negishi, Tsutomu; Kudo, Masato; Terazono, Hideyuki; Yasuda, Kenji

    2012-01-01

    ...) imaging in field emission scanning electron microscopy (FE-SEM) were studied to evaluate the potential of using these particles as simultaneously distinguishable labels of target molecules in FE-SEM studies...

  15. Retrieving the Quantitative Chemical Information at Nanoscale from Scanning Electron Microscope Energy Dispersive X-ray Measurements by Machine Learning

    Science.gov (United States)

    Jany, B. R.; Janas, A.; Krok, F.

    2017-11-01

    The quantitative composition of metal alloy nanowires on InSb(001) semiconductor surface and gold nanostructures on germanium surface is determined by blind source separation (BSS) machine learning (ML) method using non negative matrix factorization (NMF) from energy dispersive X-ray spectroscopy (EDX) spectrum image maps measured in a scanning electron microscope (SEM). The BSS method blindly decomposes the collected EDX spectrum image into three source components, which correspond directly to the X-ray signals coming from the supported metal nanostructures, bulk semiconductor signal and carbon background. The recovered quantitative composition is validated by detailed Monte Carlo simulations and is confirmed by separate cross-sectional TEM EDX measurements of the nanostructures. This shows that SEM EDX measurements together with machine learning blind source separation processing could be successfully used for the nanostructures quantitative chemical composition determination.

  16. Limit of Blank, Limit of Detection and Limit of Quantitation

    Science.gov (United States)

    Armbruster, David A; Pry, Terry

    2008-01-01

    Summary Limit of Blank (LoB), Limit of Detection (LoD), and Limit of Quantitation (LoQ) are terms used to describe the smallest concentration of a measurand that can be reliably measured by an analytical procedure.LoB is the highest apparent analyte concentration expected to be found when replicates of a blank sample containing no analyte are tested.LoB = meanblank + 1.645(SDblank)LoD is the lowest analyte concentration likely to be reliably distinguished from the LoB and at which detection is feasible. LoD is determined by utilising both the measured LoB and test replicates of a sample known to contain a low concentration of analyte.LoD = LoB + 1.645(SD low concentration sample)LoQ is the lowest concentration at which the analyte can not only be reliably detected but at which some predefined goals for bias and imprecision are met. The LoQ may be equivalent to the LoD or it could be at a much higher concentration. PMID:18852857

  17. Using Cognitive Control in Software Defined Networking for Port Scan Detection

    Science.gov (United States)

    2017-07-01

    ARL-TR-8059 ● July 2017 US Army Research Laboratory Using Cognitive Control in Software -Defined Networking for Port Scan...Cognitive Control in Software -Defined Networking for Port Scan Detection by Vinod K Mishra Computational and Information Sciences Directorate, ARL...Technical Report 3. DATES COVERED (From - To) 15 June–31 July 2016 4. TITLE AND SUBTITLE Using Cognitive Control in Software -Defined Networking for

  18. The Role of Gallium Scanning in the Detection of Bone and Joint Sepsis

    OpenAIRE

    Gavin, Anna; Laird, J. D.; Roberts, S D

    1984-01-01

    The value of gallium (67Ga) scanning in the diagnosis of septic disease of bone or joint was assessed in 34 patients. The results show a sensitivity of 60 per cent and specificity of 64 per cent. The low accuracy of this method for the detection of bone and joint sepsis (62 per cent) means that gallium scanning can be used only as an adjunct to other investigative techniques.

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

    Science.gov (United States)

    He, Jiaze; Yuan, Fuh-Gwo

    2016-10-01

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

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

    Science.gov (United States)

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

    2016-12-01

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

  1. An exploratory study to detect Ménière’s disease in conventional MRI scans using radiomics

    Directory of Open Access Journals (Sweden)

    E. L. van den Burg

    2016-11-01

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

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

    Science.gov (United States)

    Hwang, Gwangseok; Chung, Jaehun; Kwon, Ohmyoung

    2014-11-01

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

  3. Real-time underwater object detection based on an electrically scanned high-resolution sonar

    DEFF Research Database (Denmark)

    Henriksen, Lars

    1994-01-01

    The paper describes an approach to real time detection and tracking of underwater objects, using image sequences from an electrically scanned high-resolution sonar. The use of a high resolution sonar provides a good estimate of the location of the objects, but strains the computers on board......, because of the high rate of raw data. The amount of data can be cut down by decreasing the scanned area, but this reduces the possibility of planning an optimal path. In the paper methods are described, that maintains the wide area of detection, without significant loss of precision or speed. This is done...

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

    Science.gov (United States)

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

    2016-05-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

  6. DETECTION OF WATER SURFACES IN FULL-WAVEFORM LASER SCANNING DATA

    Directory of Open Access Journals (Sweden)

    A. Schmidt

    2012-09-01

    Full Text Available Airborne laser scanning has become a standard method for recording topographic data. A new generation of laser scanners digitises the complete waveform of the backscattered signal and thus offers the possibility of analysing the signal shape. As a product of the laser scanning, a digital surface model (DSM or a digital terrain model (DTM can be derived. In water regions, data acquisition by laser scanning is limited to the water surface because the near-infrared laser pulses hardly penetrate water. Therefore, a height model generated from laser scanner point clouds over water regions does not represent the actual terrain. The generation of a DTM thus requires the detection of water surfaces. In this study, a method for the detection and classification of water surfaces in airborne laser scanning data is proposed. The method works with both geometrical features (e.g. height or height variation and characteristics of the pulses derived from the full waveform of the returned signal (e.g. intensity or pulse width. In our strategy, based on fuzzy logic, all classification parameters are derived automatically from training areas. According to their statistical distributions, the features are considered with individual weights. The aim of this paper is to analyse crucial features for classification and to investigate the potential of full waveform laser scanning data for this application. We present results from different areas with lakes and rivers, analysing the contribution of the individual groups of features for the detection of water surfaces.

  7. High Speed Scanning Ion Conductance Microscopy for Quantitative Analysis of Nanoscale Dynamics of Microvilli.

    Science.gov (United States)

    Ida, Hiroki; Takahashi, Yasufumi; Kumatani, Akichika; Shiku, Hitoshi; Matsue, Tomokazu

    2017-06-06

    Observation of nanoscale structure dynamics on cell surfaces is essential to understanding cell functions. Hopping-mode scanning ion conductance microscopy (SICM) was used to visualize the topography of fragile convoluted nanoscale structures on cell surfaces under noninvasive conditions. However, conventional hopping mode SICM does not have sufficient temporal resolution to observe cell-surface dynamics in situ because of the additional time required for performing vertical probe movements of the nanopipette. Here, we introduce a new scanning algorithm for high speed SICM measurements using low capacitance and high-resonance-frequency piezo stages. As a result, a topographic image is taken within 18 s with a 64 × 64 pixel resolution at 10 × 10 μm. The high speed SICM is applied to the characterization of microvilli dynamics on surfaces, which shows clear structural changes after the epidermal growth factor stimulation.

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

    Directory of Open Access Journals (Sweden)

    Mostafa Rabah

    2013-12-01

    The current paper submits a method for automatic concrete cracks detection and mapping from the data that was obtained during laser scanning survey. The method of cracks detection and mapping is achieved by three steps, namely the step of shading correction in the original image, step of crack detection and finally step of crack mapping and processing steps. The detected crack is defined in a pixel coordinate system. To remap the crack into the referred coordinate system, a reverse engineering is used. This is achieved by a hybrid concept of terrestrial laser-scanner point clouds and the corresponding camera image, i.e. a conversion from the pixel coordinate system to the terrestrial laser-scanner or global coordinate system. The results of the experiment show that the mean differences between terrestrial laser scan and the total station are about 30.5, 16.4 and 14.3 mms in x, y and z direction, respectively.

  9. Direct Observation of Sr Vacancies in SrTiO_{3} by Quantitative Scanning Transmission Electron Microscopy

    Directory of Open Access Journals (Sweden)

    Honggyu Kim

    2016-12-01

    Full Text Available Unveiling the identity, spatial configuration, and microscopic structure of point defects is one of the key challenges in materials science. Here, we demonstrate that quantitative scanning transmission electron microscopy (STEM can be used to directly observe Sr vacancies in SrTiO_{3} and to determine the atom column relaxations around them. By combining recent advances in quantitative STEM, including variable-angle, high-angle annular dark-field imaging and rigid registration methods, with frozen phonon multislice image simulations, we identify which Sr columns contain vacancies and quantify the number of vacancies in them. Picometer precision measurements of the surrounding atom column positions show that the nearest-neighbor Ti atoms are displaced away from the Sr vacancies. The results open up a new methodology for studying the microscopic mechanisms by which point defects control materials properties.

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

    Science.gov (United States)

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

    2017-05-01

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

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

    Science.gov (United States)

    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.

  12. Towards alignment independent quantitative assessment of homology detection.

    Directory of Open Access Journals (Sweden)

    Avihay Apatoff

    Full Text Available 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.

  13. Radioiodine scan index: A simplified, quantitative treatment response parameter for metastatic thyroid carcinoma

    Energy Technology Data Exchange (ETDEWEB)

    Oh, Jong Ryool; Ahn, Byeong Cheol; Jeong, Shin Young; Lee, Sang Woo; Lee, Jae Tae [Dept. of Nuclear Medicine, Kyungpook National University School of Medicine and Hospital, Daegu (Korea, Republic of)

    2015-09-15

    We aimed to develop and validate a simplified, novel quantification method for radioiodine whole-body scans (WBSs) as a predictor for the treatment response in differentiated thyroid carcinoma (DTC) patients with distant metastasis. We retrospectively reviewed serial WBSs after radioiodine treatment from 2008 to 2011 in patients with metastatic DTC. For standardization of TSH simulation, only a subset of patients whose TSH level was fully enhanced (TSH > 80 mU/l) was enrolled. The radioiodine scan index (RSI) was calculated by the ratio of tumor-to-brain uptake. We compared correlations between the RSI and TSH-stimulated serum thyroglobulin (TSH{sub sT}g) level and between the RSI and Tg reduction rate of consecutive radioiodine treatments. A total of 30 rounds of radioiodine treatment for 15 patients were eligible. Tumor histology was 11 papillary and 4 follicular subtypes. The TSH{sub sT}g level was mean 980 ng/ml (range, 0.5–11,244). The Tg reduction rate after treatment was a mean of −7 % (range, −90 %–210 %). Mean RSI was 3.02 (range, 0.40–10.97). RSI was positively correlated with the TSH{sub sT}g level (R2 = 0.3084, p = 0.001) and negatively correlated with the Tg reduction rate (R2 = 0.2993, p = 0.037). The regression equation to predict treatment response was as follows: Tg reduction rate = −14.581 × RSI + 51.183. Use of the radioiodine scan index derived from conventional WBS is feasible to reflect the serum Tg level in patients with metastatic DTC, and it may be useful for predicting the biologic treatment response after radioiodine treatment.

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

    Directory of Open Access Journals (Sweden)

    Papayiannis V

    2017-08-01

    Full Text Available Vassilis Papayiannis,1 Konstantinos T Tsaousis,2,3 Constantinos A Kouskouras,4 Afroditi Haritanti,4 Vasilios F Diakonis,5 Ioannis T Tsinopoulos2 1Department of Radiology, Papageorgiou General Hospital, 2Department of Ophthalmology, Aristotle University of Thessaloniki, Thessaloniki, Greece; 3John A Moran Eye Center, University of Utah, Salt Lake City, UT, USA; 4Department of Radiology, AHEPA Aristotle University Hospital of Thessaloniki, Thessaloniki, Greece; 5Bascom Palmer Eye Institute, Miller School of Medicine, University of Miami, Miami, FL, USA Objective: To investigate the homogeneity and vascularity of choroidal melanoma through magnetic resonance imaging (MRI and brightness modulation (B-mode ultrasound scan and their correlation with dimensions of tumor, as well as to measure the sensitivity of both modalities in retinal detachment (RD detection.Materials and methods: This retrospective chart review included patients diagnosed with choroidal melanoma. All these patients underwent MRI scans using T2-weighted (T2-WI and T1-weighted (T1-WI sequences, before and after an intravenous injection of paramagnetic contrast material. The patients were also examined using a B-mode ultrasound scan, and the results from both modalities were compared (tumor homogeneity, tumor height, tumor base diameter, and tumor vascularity.Results: Forty-two patients (mean age =65.33±12.51 years with choroidal melanoma were included in the study. Homogeneity was confirmed in 16 patients through ultrasound scan, in 19 patients through T1-WI sequence, in 21 patients through T2-WI sequence, and in 25 patients through T1-WI sequence + contrast (gadolinium. Patients with homogenous tumors presented with lower (P=0.0045 mean height than that of those with nonhomogenous tumors, whereas no statistically significant difference was found for base diameter measurements (P=0.056. Patients with tumors of high vascularity presented with greater mean height (P=0.000638 and

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    Science.gov (United States)

    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.

  17. Damage Detection on Thin-walled Structures Utilizing Laser Scanning and Standing Waves

    Energy Technology Data Exchange (ETDEWEB)

    Kang, Se Hyeok; Jeon, Jun Young; Kim, Du Hwan; Park, Gyuhae [Chonnam Nat’l Univ., Gwangju (Korea, Republic of); Kang, To; Han, Soon Woo [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2017-05-15

    This paper describes wavenumber filtering for damage detection using single-frequency standing wave excitation and laser scanning sensing. An embedded piezoelectric sensor generates ultrasonic standing waves, and the responses are measured using a laser Doppler vibrometer and mirror tilting device. After scanning, newly developed damage detection techniques based on wavenumber filtering are applied to the full standing wave field. To demonstrate the performance of the proposed techniques, several experiments were performed on composite plates with delamination and aluminum plates with corrosion damage. The results demonstrated that the developed techniques could be applied to various structures to localize the damage, with the potential to improve the damage detection capability at a high interrogation speed.

  18. Low-Level Detection of Poly(amidoamine PAMAM Dendrimers Using Immunoimaging Scanning Probe Microscopy

    Directory of Open Access Journals (Sweden)

    Chevelle A. Cason

    2012-01-01

    Full Text Available Immunoimaging scanning probe microscopy was utilized for the low-level detection and quantification of biotinylated G4 poly(amidoamine PAMAM dendrimers. Results were compared to those of high-performance liquid chromatography (HPLC and found to provide a vastly improved analytical method for the low-level detection of dendrimers, improving the limit of detection by a factor of 1000 (LOD=2.5×10−13 moles. The biorecognition method is reproducible and shows high specificity and good accuracy. In addition, the capture assay platform shows a promising approach to patterning dendrimers for nanotechnology applications.

  19. Low-Level Detection of Poly(amidoamine) PAMAM Dendrimers Using Immunoimaging Scanning Probe Microscopy.

    Science.gov (United States)

    Cason, Chevelle A; Fabré, Thomas A; Buhrlage, Andrew; Haik, Kristi L; Bullen, Heather A

    2012-01-01

    Immunoimaging scanning probe microscopy was utilized for the low-level detection and quantification of biotinylated G4 poly(amidoamine) PAMAM dendrimers. Results were compared to those of high-performance liquid chromatography (HPLC) and found to provide a vastly improved analytical method for the low-level detection of dendrimers, improving the limit of detection by a factor of 1000 (LOD = 2.5 × 10(-13) moles). The biorecognition method is reproducible and shows high specificity and good accuracy. In addition, the capture assay platform shows a promising approach to patterning dendrimers for nanotechnology applications.

  20. Quantitative vertebral fracture detection on DXA images using shape and appearance models.

    Science.gov (United States)

    Roberts, Martin; Cootes, Tim; Pacheco, Elisa; Adams, Judith

    2007-10-01

    Current quantitative morphometric methods of vertebral fracture detection lack specificity, particularly with mild fractures. We use more detailed shape and texture information to develop quantitative classifiers. The detailed shape and appearance of vertebrae on 360 lateral dual energy x-ray absorptiometry scans were statistically modeled, thus producing a set of shape and appearance parameters for each vertebra. The vertebrae were given a "gold standard" classification using a consensus reading by two radiologists. Linear discriminants were trained on the vertebral shape and appearance parameters. The appearance-based classifiers gave significantly better specificity than shape-based methods in all regions of the spine (overall specificity 92% at a sensitivity of 95%), while using the full shape parameters slightly improved specificity in the thoracic spine compared with using three standard height ratios. The main improvement was in the detection of mild fractures. Performance varied over different regions of the spine. False-positive rates at 95% sensitivity for the lumbar, mid-thoracic (T12-T10) and upper thoracic (T9-T7) regions were 2.9%, 14.6%, and 5.5%, respectively, compared with 6.4%, 32.6%, and 21.1% for three-height morphometry. The appearance and shape parameters of statistical models could provide more powerful quantitative classifiers of osteoporotic vertebral fracture, particularly mild fractures. False positive rates can be substantially reduced at high sensitivity by using an appearance-based classifier, because this can better distinguish between mild fractures and some kinds of non-fracture shape deformities.

  1. Flip-registration procedure of three-dimensional laser surface scanning images on quantitative evaluation of facial asymmetries.

    Science.gov (United States)

    Yu, Zheyuan; Mu, Xiongzheng; Feng, Shengzhi; Han, Jiayi; Chang, Tisheng

    2009-01-01

    The aim of the study was to find a proper method that may evaluate the severity of facial asymmetry quickly and accessibly in clinics. The three-dimensional image data of facial asymmetry patients were collected with three-dimensional laser surface scanning, and the desired therapy outcomes were simulated in computers by flip-registration procedure. The discrepancy between desired results and initial images was calculated automatically, and a colored hypsography was printed. A questionnaire was given to both the patient and the craniofacial surgeon to examine the symmetry, accessibility, achievability, and helpfulness of these outcomes. The three-dimensional image data offered by laser surface scanning were accurate and convenient. The desired results were reliable and acceptable to the patients. The colored hypsography was clear and accessible and achieved high appreciations from the surgeons. Three-dimensional laser surface scanning together with flip registration procedure can evaluate the severity of facial asymmetry quickly, quantitatively, and effectively with an achievable outcome. It is welcomed by the craniofacial surgeons and has a great potential in clinic application.

  2. Quantitative detection of settled coal dust over green canopy

    Science.gov (United States)

    Brook, Anna; Sahar, Nir

    2017-04-01

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

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

    Science.gov (United States)

    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.

  4. Detection of bladder cancer: comparison of low-dose scans with AIDR 3D and routine-dose scans with FBP on the excretory phase in CT urography.

    Science.gov (United States)

    Juri, Hiroshi; Tsuboyama, Takahiro; Kumano, Seishi; Inada, Yuki; Koyama, Mitsuhiro; Azuma, Haruhito; Narumi, Yoshifumi

    2016-01-01

    To prospectively compare the detection of bladder cancer between low-dose scans with adaptive iterative dose reduction three dimensional projection (AIDR 3D) and routine-dose scans with filtered back projection (FBP) on the excretory phase (EP) in CT urography. 42 patients were included. Routine- and low-dose EP were performed in each patient. Routine-dose images were reconstructed with FBP, and low-dose images were reconstructed with AIDR 3D. Two radiologists scored confidence levels for the presence or absence of bladder cancer using a 5-point scale. The CT dose index of each EP was measured, and the dose reduction was calculated. Sensitivity, specificity and accuracy were 86.4%, 95.0% and 90.5% on routine-dose scans and were 86.4%, 90.0% and 88.1% on low-dose scans, respectively. There was no significant difference (p; not significant, 1.00 and 1.00, respectively). The average CT dose index was 8.07 and 2.63 mGy on routine- and low-dose scans, and the ratio of dose reduction was 67.6%. The detection of bladder cancer on low-dose scans with AIDR 3D is almost equal to that on routine-dose scans with FBP on the EP, with nearly 70% dose reduction. Using AIDR 3D, the radiation dose may be reduced on the EP in CT urography for the detection of bladder cancer.

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

    Energy Technology Data Exchange (ETDEWEB)

    De Backer, A.; Martinez, G.T. [Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp (Belgium); MacArthur, K.E.; Jones, L. [Department of Materials, University of Oxford, 16 Parks Road, Oxford OX1 3PH (United Kingdom); Béché, A. [Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp (Belgium); Nellist, P.D. [Department of Materials, University of Oxford, 16 Parks Road, Oxford OX1 3PH (United Kingdom); Van Aert, S., E-mail: sandra.vanaert@uantwerpen.be [Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp (Belgium)

    2015-04-15

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

  6. Automated Detection of Healthy and Diseased Aortae from Images Obtained by Contrast-Enhanced CT Scan

    Directory of Open Access Journals (Sweden)

    Michael Gayhart

    2013-01-01

    Full Text Available Purpose. We developed the next stage of our computer assisted diagnosis (CAD system to aid radiologists in evaluating CT images for aortic disease by removing innocuous images and highlighting signs of aortic disease. Materials and Methods. Segmented data of patient’s contrast-enhanced CT scan was analyzed for aortic dissection and penetrating aortic ulcer (PAU. Aortic dissection was detected by checking for an abnormal shape of the aorta using edge oriented methods. PAU was recognized through abnormally high intensities with interest point operators. Results. The aortic dissection detection process had a sensitivity of 0.8218 and a specificity of 0.9907. The PAU detection process scored a sensitivity of 0.7587 and a specificity of 0.9700. Conclusion. The aortic dissection detection process and the PAU detection process were successful in removing innocuous images, but additional methods are necessary for improving recognition of images with aortic disease.

  7. Image processing based detection of lung cancer on CT scan images

    Science.gov (United States)

    Abdillah, Bariqi; Bustamam, Alhadi; Sarwinda, Devvi

    2017-10-01

    In this paper, we implement and analyze the image processing method for detection of lung cancer. Image processing techniques are widely used in several medical problems for picture enhancement in the detection phase to support the early medical treatment. In this research we proposed a detection method of lung cancer based on image segmentation. Image segmentation is one of intermediate level in image processing. Marker control watershed and region growing approach are used to segment of CT scan image. Detection phases are followed by image enhancement using Gabor filter, image segmentation, and features extraction. From the experimental results, we found the effectiveness of our approach. The results show that the best approach for main features detection is watershed with masking method which has high accuracy and robust.

  8. Quantitative lung perfusion scintigraphy and detection of intrapulmonary shunt in liver cirrhosis

    Energy Technology Data Exchange (ETDEWEB)

    Hosono, Makoto; Machida, Kikuo; Honda, Norinari; Takahashi, Takeo; Kashimada, Akio; Osada, Hisato; Murata, Osamu; Ohtawa, Nobuyuki; Nishimura, Keiichiro [Saitama Medical School, Kawagoe (Japan). Saitama Medical Center

    2002-12-01

    Frequent association between liver cirrhosis and hypoxemia has been well documented. It is mostly attributable to intrapulmonary shunt due to dilation of pulmonary vasculature. We preformed quantitative lung perfusion scintigraphy to detect an intrapulmonary shunt in cirrhosis patients. Prior to injection, Tc-99m MAA was applied to thin layer chromatography for quality control. Three cirrhosis patients who had hypoxemia were examined as well as 11 control subjects. After intravenous injection (i.v.) injection of Tc-99m MAA, whole body anterior and posterior images were taken at 5 min in patients with cirrhosis and at 8 time points up to 60 min in control subjects. Regions of interest were placed at the bilateral lungs and the whole body, and pulmonary accumulation was calculated. All the control subjects demonstrated more than 90% of radioactivity in the lungs until 20 min. In contrast, all the patients showed values less than 80% at 5 min. In the cirrhosis patients with hypoxemia, the presence of intrapulmonary shunt was confirmed on quantitative lung perfusion scan. In control subjects, pulmonary accumulation of Tc-99m MAA dropped as a function of time and became less than 90% after 30 min. The timing of measurements is essential in evaluating intrapulmonary shunt. (author)

  9. Oil spill detection in northern Europe using ScanSAR data

    Energy Technology Data Exchange (ETDEWEB)

    Pedersen, J.P. [Tromso Satellite Station, Tromso (Norway); Bauna, T.; Enoksen, R.T.; Seljelv, L.G.; Landmark, F.

    1998-12-31

    In 1991 a project was initiated at the Norwegian Space Centre in which ERS-1 SAR data was used for detecting oil spills at sea. The goal of the project was to develop service infrastructure for near real-time processing, analysis and distribution. It was shown that satellite data is capable of establishing early warning of illegal oil spills. A total of 15 RADARSAT scenes from the ScanSAR modes covering Norwegian and Baltic Sea water were acquired under the RADARSAT Application Development and Research Opportunity (ADRO) program. Several of the scenes show oil spills at the sea surface. The results demonstrated overall detection capabilities of ScanSAR better than expected.

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

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Shikui, E-mail: TangS@uphs.upenn.edu [Department of Radiation Oncology, University of Pennsylvania, Philadelphia, Pennsylvania (United States); Deville, Curtiland; McDonough, James; Tochner, Zelig [Department of Radiation Oncology, University of Pennsylvania, Philadelphia, Pennsylvania (United States); Wang, Ken Kang-Hsin [Department of Radiation Oncology, University of Pennsylvania, Philadelphia, Pennsylvania (United States); Department of Radiation Oncology and Molecular Radiation Sciences, The Johns Hopkins University, Baltimore, Maryland (United States); Vapiwala, Neha; Both, Stefan [Department of Radiation Oncology, University of Pennsylvania, Philadelphia, Pennsylvania (United States)

    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.

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

    Science.gov (United States)

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

    2017-02-01

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

  12. Atlantoaxial Ankylosis Detected on Neck CT Scans in a Patient with Ankylosing Spondylitis: A Case Report

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Jeong Ah; Lee, Seung Hun; Joo, Kyung Bin [Dept. of Radiology, Seoul Hospital, Hanyang University College of Medicine, Seoul (Korea, Republic of); Ryu, Jeong Ah [Dept. of Radiology, Guri Hospital, Hanyang University College of Medicine, Guri (Korea, Republic of); Kim, Tae Hwan [Dept. of Rheynmatology, Seoul Hospital, Hanyang University College of Medicine, Seoul (Korea, Republic of)

    2011-07-15

    Ankylosing spondylitis is a chronic inflammatory disorder of unknown cause that principally affects the axial skeleton. The cervical spine is also vulnerable to this disease process and the characteristic feature of cervical involvement is atlantoaxial subluxation. However, only a few cases of atlantoaxial ankylosis have been reported to date. We report a case of atlantoaxial ankylosis in a patient with ankylosing spondylitis with radiologic findings incidentally detected on neck CT scans.

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

    Science.gov (United States)

    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.

  14. Quantitative detection of settled dust over green canopy

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    Tulum, Gökalp; Bolat, Bülent; Osman, Onur

    2017-04-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Rabelo, Katharina Alves; Cavalcanti, Yuri Wanderley; De Oliveira Pinto, Martina Gerlane; De Melo, Daniela Pita [Dept. of Oral Diagnosis, State University of Paraiba, Campina Grande (Brazil); Melo, Saulo Leonardo Sousa [Dept. of Oral Pathology, Radiology and Medicine, University of Iowa, Iowa City (United States); Campos, Paulo Sergio Flores; De Andrade Freitas Oliveira, Luciana Soares [Federal University of Bahia, Salvador (Brazil)

    2017-09-15

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

  19. Advanced Approach of Material Region Detections on Fibre-Reinforced Concrete CT-Scans

    Directory of Open Access Journals (Sweden)

    Marek Pecha

    2017-01-01

    Full Text Available Detections of material regions on CT-scans of solids are commonly treated manually by an expert. Although such manual detections have many advantages, some amount of human error is also incorporated. Moreover, expert opinions may vary significantly. We present an application of the k-means++ clustering as an alternative option to manual way of material area detections. k-means++ clustering is derived from k-means (the method of vector quantization, originally from signal processing, popular for cluster analysis in data mining and image processing communities. The algorithm s main advantages are its simple implementation and fast convergence to a local optimum of an objective function. We benchmark the suggested approach on transverse CT-scans of a fibre-reinforced concrete solid. Moreover, we introduce a technique for processing air distribution, such that the appropriate pixels detected as the pixels of air are converted into pixels representing concrete. The technique is based on the connected component algorithm. Benchmark and results of proposed method conclude the paper.

  20. Oil detection in RADARSAT-2 quad-polarization imagery: implications for ScanSAR performance

    Science.gov (United States)

    Cheng, Angela; Arkett, Matt; Zagon, Tom; De Abreu, Roger; Mueller, Derek; Vachon, Paris; Wolfe, John

    2011-11-01

    Environment Canada's Integrated Satellite Tracking of Pollution (ISTOP) program uses RADARSAT-2 data to vector pollution surveillance assets to areas where oil discharges/spills are suspected in support of enforcement and/or cleanup efforts. RADARSAT-2's new imaging capabilities and ground system promises significant improvement's in ISTOP's ability to detect and report on oil pollution. Of specific interest is the potential of dual polarization ScanSAR data acquired with VV polarization to improve the detection of oil pollution compared to data acquired with HH polarization, and with VH polarization to concurrently detect ship targets. A series of 101 RADARSAT-2 fine quad images were acquired over Coal Oil Point, near Santa Barbara, California where a seep field naturally releases hydrocarbons. The oil and gas releases in this region are visible on the sea surface and have been well documented allowing for the remote sensing of a constant source of oil at a fixed location. Although the make-up of the oil seep field could be different from that of oil spills, it provides a representative target that can be routinely imaged under a variety of wind conditions. Results derived from the fine quad imagery with a lower noise floor were adjusted to mimic the noise floor limitations of ScanSAR. In this study it was found that VV performed better than HH for oil detection, especially at higher incidence angles.

  1. Quantitative Indicators for Behaviour Drift Detection from Home Automation Data.

    Science.gov (United States)

    Veronese, Fabio; Masciadri, Andrea; Comai, Sara; Matteucci, Matteo; Salice, Fabio

    2017-01-01

    Smart Homes diffusion provides an opportunity to implement elderly monitoring, extending seniors' independence and avoiding unnecessary assistance costs. Information concerning the inhabitant behaviour is contained in home automation data, and can be extracted by means of quantitative indicators. The application of such approach proves it can evidence behaviour changes.

  2. A quantitative acoustic microscope with multiple detection modes.

    Science.gov (United States)

    Weaver, J R; Daft, C W; Briggs, G D

    1989-01-01

    An acoustic microscope that permits operation with both toneburst and impulse excitation of the lens is presented. Either mode can be selected and combined with mechanical scanning in any direction. In the impulse-excited mode, the specular and Rayleigh signals from the sample are resolved in time, and analysis is performed to obtain surface wave propagation parameters. The power of the simultaneous application of these techniques is illustrated by measurements on specimens of intact and fractured glass and duraluminum. Reflection and transmission coefficients for a crack are measured, and conclusions are drawn about V(z) processing. These results are significant because the images of cracks produced by the conventional toneburst scanning acoustic microphone (SAM) tend to be complex. Diffraction from the tips of cracks is observed in the microscope.

  3. Real time quantitative amplification detection on a microarray: towards high multiplex quantitative PCR.

    NARCIS (Netherlands)

    Pierik, A.; Moamfa, M; van Zelst, M.; Clout, D.; Stapert, H.; Dijksman, Johan Frederik; Broer, D.; Wimberger-Friedl, R.

    2012-01-01

    Quantitative real-time polymerase chain reaction (qrtPCR) is widely used as a research and diagnostic tool. Notwithstanding its many powerful features, the method is limited in the degree of multiplexing to about 6 due to spectral overlap of the available fluorophores. A new method is presented that

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

    Science.gov (United States)

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

    2013-11-01

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

  5. Incidental detection of colorectal lesions by FDG PET/CT scans in melanoma patients.

    Science.gov (United States)

    Young, Christopher J; Zahid, Assad; Choy, Ian; Thompson, John F; Saw, Robyn P M

    2017-11-01

    Increased use of PET/CT scans in oncology patients has raised detection of Colorectal incidentalomas (CIs). The frequency and diagnostic outcomes of identifying these lesions in melanoma patients have not previously been studied. This studies primary objective was to determine the prevalence of CIs found on PET/CT scans in melanoma patients. The secondary objectives were to correlate the PET/CT findings with the pathology found at colonoscopy, and identify which patients were referred for colonoscopy. A retrospective analysis of patients identified from the prospectively collected research database of Melanoma Institute Australia. 2509 patients with melanoma underwent PET/CT scans between 2001 and 2013. The prevalence of CIs, the correlation of lesions, and the survival of patients who underwent colonoscopy versus patients who did not were analyzed. The prevalence of CIs in melanoma patients who had PET/CT scans was 3.2%. Forty-five of the 81 (56%) patients with CIs underwent colonoscopy. Of these, premalignant or malignant disease was found in 58%. Patients with previous metastatic melanoma were significantly less likely to be referred for colonoscopy. Patients undergoing colonoscopy had significantly better survival, as did those without previous distant metastases before the CIs were found, and those without any metastases at the time the CIs were found. These factors were not significant on multivariate analysis. The prevalence of incidental colorectal lesions identified on PET/CT scans in melanoma patients was found to be equivalent to that in the general cancer population. Patients undergoing colonoscopy had better survival than those who did not. Copyright © 2017 Elsevier Ltd, BASO ~ The Association for Cancer Surgery, and the European Society of Surgical Oncology. All rights reserved.

  6. Automated kidney detection for 3D ultrasound using scan line searching

    Science.gov (United States)

    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.

  7. Application of scanning laser Doppler vibrometry for delamination detection in composite structures

    Science.gov (United States)

    Kudela, Pawel; Wandowski, Tomasz; Malinowski, Pawel; Ostachowicz, Wieslaw

    2017-12-01

    In this paper application of scanning laser Doppler vibrometry for delamination detection in composite structures was presented. Delamination detection was based on a guided wave propagation method. In this papers results from numerical and experimental research were presented. In the case of numerical research, the Spectral Element Method (SEM) was utilized, in which a mesh was composed of 3D spectral elements. SEM model included also a piezoelectric transducer. In the experimental research guided waves were excited using the piezoelectric transducer whereas the sensing process was conducted using scanning laser Doppler vibrometer (SLDV). Analysis of guided wave propagation and its interaction with delamination was based on a full wavefield approach. Attention was focused on interactions of guided waves with delamination manifested by A0 mode reflection, A0 mode entrapment, and S0/A0 mode conversion. Delamination was simulated by a teflon insert located between plies of composite material. Results of interaction with symmetrically and nonsymmetrical placed delamination (in respect to the composite sample thickness) were presented. Moreover, the authors investigated different size of delaminations. Damage detection was based on a new signal processing algorithm proposed by the authors. In this approach the weighted RMS was utilized selectively. It means that the summation in RMS formula was performed only for a specially selected time instances. Results for simple composite panels, panel with honeycomb core, and real stiffened composite panel from the aircraft were presented.

  8. Quantitative PCR detection of feline morbillivirus in cat urine samples.

    Science.gov (United States)

    Furuya, Tetsuya; Wachi, Akiko; Sassa, Yukiko; Omatsu, Tsutomu; Nagai, Makoto; Fukushima, Ryuji; Shibutani, Makoto; Yamaguchi, Tomohiro; Uematsu, Yosuke; Shirota, Kinji; Mizutani, Tetsuya

    2016-01-01

    Feline morbillivirus (FmoPV) is a new virus species and its detection is important, since correlation has been reported between FmoPV virus infection and tubulointerstitial nephritis in cats. Here, we report a real-time reverse transcription (RT)-PCR system that can detect the FmoPV L-gene sequence with more than 10-time higher sensitivity than a conventional PCR system, resulting in detection of less than 10 copies of the template DNA. The total FmoPV positive rate of urine samples from veterinary clinics and hospitals in Japan was 15.1% (25/166) using this system. This study demonstrates usefulness of the real-time RT-PCR system for detection of FmoPV for cat urine samples.

  9. Quantitative Emboli Detection Using Nonlinear Ultrasound Technique Project

    Data.gov (United States)

    National Aeronautics and Space Administration — We propose to develop a new and innovative method for the detection and classification of emboli flowing into the brain through Carotid arteries, specifically for...

  10. Quantitative Ischemia Detection During Cardiac MR Stress Testing

    National Research Council Canada - National Science Library

    Kraitchman, D

    2001-01-01

    .... During a second ischemic episode, conventional cine wall motion images were acquired. The time from occlusion to the detection of ischemia by each MR technique, as well as ECG ischemic alterations, was determined...

  11. Combined frequency modulated atomic force microscopy and scanning tunneling microscopy detection for multi-tip scanning probe microscopy applications

    Science.gov (United States)

    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.

  12. High resolution surface scanning of Thick-GEM for single photo-electron detection

    Science.gov (United States)

    Hamar, G.; Varga, D.

    2012-12-01

    An optical system for high resolution scanning of TGEM UV photon detection systems is introduced. The structure exploits the combination of a single Au-coated TGEM under study, and an asymmetric MWPC (Close Cathode Chamber) as post-amplification stage. A pulsed UV LED source with emission down to 240 nm has been focused to a spot of 0.07 mm on the TGEM surface, and single photo-electron charge spectra has been recorded over selected two dimensional regions. This way, the TGEM gain (order of 10-100) and TGEM photo-electron detection efficiency is clearly separated, unlike in case of continuous illumination. The surface structure connected to the TGEM photon detection is well observable, including inefficiencies in the holes and at the symmetry points between holes. The detection efficiency as well as the gas gain are fluctuating from hole to hole. The gain is constant in the hexagon around any hole, pointing to the fact that the gain depends on hole geometry, and less on the position where the electron enters. The detection probability map strongly changes with the field strength above the TGEM surface, in relation to the change of the actual surface field configuration. The results can be confronted with position-dependent simulations of TGEM electron transfer and gas multiplication.

  13. SINGLE TREE DETECTION FROM AIRBORNE LASER SCANNING DATA USING A MARKED POINT PROCESS BASED METHOD

    Directory of Open Access Journals (Sweden)

    J. Zhang

    2013-05-01

    Full Text Available Tree detection and reconstruction is of great interest in large-scale city modelling. In this paper, we present a marked point process model to detect single trees from airborne laser scanning (ALS data. We consider single trees in ALS recovered canopy height model (CHM as a realization of point process of circles. Unlike traditional marked point process, we sample the model in a constraint configuration space by making use of image process techniques. A Gibbs energy is defined on the model, containing a data term which judge the fitness of the model with respect to the data, and prior term which incorporate the prior knowledge of object layouts. We search the optimal configuration through a steepest gradient descent algorithm. The presented hybrid framework was test on three forest plots and experiments show the effectiveness of the proposed method.

  14. Modeling and minimizing interference from corneal birefringence in retinal birefringence scanning for foveal fixation detection.

    Science.gov (United States)

    Irsch, Kristina; Gramatikov, Boris; Wu, Yi-Kai; Guyton, David

    2011-07-01

    Utilizing the measured corneal birefringence from a data set of 150 eyes of 75 human subjects, an algorithm and related computer program, based on Müller-Stokes matrix calculus, were developed in MATLAB for assessing the influence of corneal birefringence on retinal birefringence scanning (RBS) and for converging upon an optical/mechanical design using wave plates ("wave-plate-enhanced RBS") that allows foveal fixation detection essentially independently of corneal birefringence. The RBS computer model, and in particular the optimization algorithm, were verified with experimental human data using an available monocular RBS-based eye fixation monitor. Fixation detection using wave-plate-enhanced RBS is adaptable to less cooperative subjects, including young children at risk for developing amblyopia.

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

    Science.gov (United States)

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

    2016-06-01

    Diabetes mellitus (DM) is one of the most common metabolic disorders in the world, of which more than 90% is type-2 diabetes mellitus (T2DM). There is a rather urgent need for reliable, sensitive and quick detection techniques in clinical application of T2DM. Ficolin-3 is a potential biomarker of T2DM, because serum ficolin-3 levels are associated with insulin resistance and predict the incidence of T2DM. Herein, a sandwich-type electrochemical immunosensor was developed for the detection of ficolin-3 in human serum. Cyclic voltammetry and the amperometric current versus time were used to characterize the performance of the immunosensor. Under optimal conditions, the detection limitation of ficolin-3 was 100 ng ml-1 and the linear dynamic range was between 2 and 50 μg ml-1. The method has ideal accuracy, excellent stability and selectivity and has wide application prospects in clinical research.

  16. Multiplexed paper test strip for quantitative bacterial detection.

    Science.gov (United States)

    Hossain, S M Zakir; Ozimok, Cory; Sicard, Clémence; Aguirre, Sergio D; Ali, M Monsur; Li, Yingfu; Brennan, John D

    2012-06-01

    Rapid, sensitive, on-site detection of bacteria without a need for sophisticated equipment or skilled personnel is extremely important in clinical settings and rapid response scenarios, as well as in resource-limited settings. Here, we report a novel approach for selective and ultra-sensitive multiplexed detection of Escherichia coli (non-pathogenic or pathogenic) using a lab-on-paper test strip (bioactive paper) based on intracellular enzyme (β-galactosidase (B-GAL) or β-glucuronidase (GUS)) activity. The test strip is composed of a paper support (0.5 × 8 cm), onto which either 5-bromo-4-chloro-3-indolyl-β-D: -glucuronide sodium salt (XG), chlorophenol red β-galactopyranoside (CPRG) or both and FeCl(3) were entrapped using sol-gel-derived silica inks in different zones via an ink-jet printing technique. The sample was lysed and assayed via lateral flow through the FeCl(3) zone to the substrate area to initiate rapid enzyme hydrolysis of the substrate, causing a change from colorless-to-blue (XG hydrolyzed by GUS, indication of nonpathogenic E. coli) and/or yellow to red-magenta (CPRG hydrolyzed by B-GAL, indication of total coliforms). Using immunomagnetic nanoparticles for selective preconcentration, the limit of detection was ~5 colony-forming units (cfu) per milliliter for E. coli O157:H7 and ~20 cfu/mL for E. coli BL21, within 30 min without cell culturing. Thus, these paper test strips could be suitable for detection of viable total coliforms and pathogens in bathing water samples. Moreover, inclusion of a culturing step allows detection of less than 1 cfu in 100 mL within 8 h, making the paper tests strips relevant for detection of multiple pathogens and total coliform bacteria in beverage and food samples.

  17. Enhanced Ratio of Signals Enables Digital Mutation Scanning for Rare Allele Detection

    Science.gov (United States)

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

    2016-01-01

    The use of droplet digital PCR (ddPCR) for low-level DNA mutation detection in cancer, prenatal diagnosis, and infectious diseases is growing rapidly. However, although ddPCR has been implemented successfully for detection of rare mutations at pre-determined positions, no ddPCR adaptation for mutation scanning exists. Yet, frequently, clinically relevant mutations reside on multiple sequence positions in tumor suppressor genes or complex hotspot mutations in oncogenes. Here, we describe a combination of coamplification at lower denaturation temperature PCR (COLD-PCR) with ddPCR that enables digital mutation scanning within approximately 50-bp sections of a target amplicon. Two FAM/HEX-labeled hydrolysis probes matching the wild-type sequence are used during ddPCR. The ratio of FAM/HEX-positive droplets is constant when wild-type amplicons are amplified but deviates when mutations anywhere under the FAM or HEX probes are present. To enhance the change in FAM/HEX ratio, we employed COLD-PCR cycling conditions that enrich mutation-containing amplicons anywhere on the sequence. We validated COLD-ddPCR on multiple mutations in TP53 and in EGFR using serial mutation dilutions and cell-free circulating DNA samples, and demonstrate detection down to approximately 0.2% to 1.2% mutation abundance. COLD-ddPCR enables a simple, rapid, and robust two-fluorophore detection method for the identification of multiple mutations during ddPCR and potentially can identify unknown DNA variants present in the target sequence. PMID:25772705

  18. Small Submersible Robust Microflow Cytometer for Quantitative Detection of Phytoplankton Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Translume will develop an extremely robust, inexpensive micro flow cytometer (mFCM) for quantitative detection of phytoplankton. This device will be designed to be...

  19. Quantitative thickness measurement of polarity-inverted piezoelectric thin-film layer by scanning nonlinear dielectric microscopy

    Science.gov (United States)

    Odagawa, Hiroyuki; Terada, Koshiro; Tanaka, Yohei; Nishikawa, Hiroaki; Yanagitani, Takahiko; Cho, Yasuo

    2017-10-01

    A quantitative measurement method for a polarity-inverted layer in ferroelectric or piezoelectric thin film is proposed. It is performed nondestructively by scanning nonlinear dielectric microscopy (SNDM). In SNDM, linear and nonlinear dielectric constants are measured using a probe that converts the variation of capacitance related to these constants into the variation of electrical oscillation frequency. In this paper, we describe a principle for determining the layer thickness and some calculation results of the output signal, which are related to the radius of the probe tip and the thickness of the inverted layer. Moreover, we derive an equation that represents the relationship between the output signal and the oscillation frequency of the probe and explain how to determine the thickness from the measured frequency. Experimental results in Sc-doped AlN piezoelectric thin films that have a polarity-inverted layer with a thickness of 1.5 µm fabricated by radio frequency magnetron sputtering showed a fairly good value of 1.38 µm for the thickness of the polarity-inverted layer.

  20. Birt-Hogg-Dube syndrome prospectively detected by review of chest computed tomography scans.

    Directory of Open Access Journals (Sweden)

    Hye Jung Park

    Full Text Available Birt-Hogg-Dube syndrome (BHD is a rare disorder caused by mutations in the gene that encodes folliculin (FLCN and is inherited in an autosomal dominant manner. BHD is commonly accompanied by fibrofolliculomas, renal tumors, multiple pulmonary cysts, and spontaneous pneumothorax. The aim of this study was to detect BHD prospectively in patients undergoing chest computed tomography (CT scans and to evaluate further the characteristics of BHD in Korea.We prospectively checked and reviewed the chest CT scans obtained for 10,883 patients at Gangnam Severance Hospital, Seoul, Korea, from June 1, 2015 to May 31, 2016. Seventeen patients met the study inclusion criteria and underwent screening for FLCN mutation to confirm BHD. We analyzed the characteristics of the patients confirmed to have BHD and those for a further 6 patients who had previously been described in Korea.Six (0.06% of the 10,883 patients reviewed were diagnosed with BHD. There was no difference in demographic or clinical features between the patients with BHD (n = 6 and those without BHD (n = 11. Pneumothorax was present in 50% of the patients with BHD but typical skin and renal lesions were absent. The maximum size of the cysts in the BHD group (median 39.4 mm; interquartile range [IQR] 11.4 mm was significantly larger than that in the non-BHD group (median 15.8 mm; IQR 7.8 mm; P = 0.001. Variable morphology was seen in 100.0% of the cysts in the BHD group but in only 18.2% of the cysts in the non-BHD group (P = 0.002. Nine (95% of the total of 12 Korean patients with BHD had experienced pneumothorax. Typical skin and renal lesions were present in 20.0% of patients with BHD.Our findings suggest that BHD can be detected if chest CT scans are read in detail.

  1. Noninvasive in vivo detection and quantification of Demodex mites by confocal laser scanning microscopy.

    Science.gov (United States)

    Sattler, E C; Maier, T; Hoffmann, V S; Hegyi, J; Ruzicka, T; Berking, C

    2012-11-01

    In many Demodex-associated skin diseases Demodex mites are present in abundance and seem to be at least partially pathogenic. So far all diagnostic approaches such as scraping or standardized superficial skin biopsy are (semi-)invasive and may cause discomfort to the patient. To see whether confocal laser scanning microscopy (CLSM) - a noninvasive method for the visualization of superficial skin layers - is able to detect and quantify D. folliculorum in facial skin of patients with rosacea. Twenty-five patients (34-72 years of age) with facial rosacea and 25 age- and sex-matched normal controls were examined by CLSM. Mosaics of 8 × 8 mm and 5 × 5 mm were created by scanning horizontal layers of lesional skin and quantification of mites per follicle and per area as well as follicles per area was performed. In all patients D. folliculorum could be detected by CLSM and presented as roundish or lengthy cone-shaped structures. CLSM allowed the quantification of Demodex mites and revealed significant differences (P Demodex mites noninvasively in facial skin of patients with rosacea. © 2012 The Authors. BJD © 2012 British Association of Dermatologists.

  2. Detecting Changes in Forest Structure over Time with Bi-Temporal Terrestrial Laser Scanning Data

    Directory of Open Access Journals (Sweden)

    Timo Melkas

    2012-10-01

    Full Text Available Changes to stems caused by natural forces and timber harvesting constitute an essential input for many forestry-related applications and ecological studies, especially forestry inventories based on the use of permanent sample plots. Conventional field measurement is widely acknowledged as being time-consuming and labor-intensive. More automated and efficient alternatives or supportive methods are needed. Terrestrial laser scanning (TLS has been demonstrated to be a promising method in forestry field inventories. Nevertheless, the applicability of TLS in recording changes in the structure of forest plots has not been studied in detail. This paper presents a fully automated method for detecting changes in forest structure over time using bi-temporal TLS data. The developed method was tested on five densely populated forest plots including 137 trees and 50 harvested trees in point clouds. The present study demonstrated that 90 percent of tree stem changes could be automatically located from single-scan TLS data. These changes accounted for 92 percent of the changed basal area. The results indicate that the processing of TLS data collected at different times to detect tree stem changes can be fully automated.

  3. Scanning elastic scattering spectroscopy detects metastatic breast cancer in sentinel lymph nodes

    Science.gov (United States)

    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.

  4. Defect Detection of Fiberglass Composite Laminates (FGCL) with Ultrasonic A-Scan Signal Measurement

    Science.gov (United States)

    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.

  5. Automatic Detection of Small Single Trees in the Forest-Tundra Ecotone Using Airborne Laser Scanning

    Directory of Open Access Journals (Sweden)

    Nadja Stumberg

    2014-10-01

    Full Text Available A large proportion of Norway’s land area is occupied by the forest-tundra ecotone. The vegetation of this temperature-sensitive ecosystem between mountain forest and the alpine zone is expected to be highly affected by climate change and effective monitoring techniques are required. For the detection of such small pioneer trees, airborne laser scanning (ALS has been proposed as a useful tool employing laser height data. The objective of this study was to assess the capability of an unsupervised classification for automated monitoring programs of small individual trees using high-density ALS data. Field and ALS data were collected along a 1500 km long transect stretching from northern to southern Norway. Different laser and tree height thresholds were tested in various combinations within an unsupervised classification of tree and nontree raster cells employing different cell sizes. Suitable initial cell sizes for the exclusion of large treeless areas as well as an optimal cell size for tree cell detection were determined. High rates of successful tree cell detection involved high levels of commission error at lower laser height thresholds, however, exceeding the 20 cm laser height threshold, the rates of commission error decreased substantially with a still satisfying rate of successful tree cell detection.

  6. Detecting benzoyl peroxide in wheat flour by line-scan macro-scale Raman chemical imaging

    Science.gov (United States)

    Qin, Jianwei; Kim, Moon S.; Chao, Kuanglin; Gonzalez, Maria; Cho, Byoung-Kwan

    2017-05-01

    Excessive use of benzoyl peroxide (BPO, a bleaching agent) in wheat flour can destroy flour nutrients and cause diseases to consumers. A macro-scale Raman chemical imaging method was developed for direct detection of BPO mixed in the wheat flour. A 785 nm line laser was used in a line-scan Hyperspectral Raman imaging system. Raman images were collected from wheat flour mixed with BPO at eight concentrations (w/w) from 50 to 6,400 ppm. A sample holder (150×100×2 mm3) was used to present a thin layer (2 mm thick) of the powdered sample for image acquisition. A baseline correction method was used to correct the fluctuating fluorescence signals from the wheat flour. To isolate BPO particles from the flour background, a simple thresholding method was applied to the single-band fluorescence-free images at a unique Raman peak wavenumber (i.e., 1001 cm-1) preselected for the BPO detection. Chemical images were created to detect and map the BPO particles. Limit of detection for the BPO was estimated in the order of 50 ppm, which is on the same level with regulatory standards.

  7. Optimization of Quantitative PCR Methods for Enteropathogen Detection.

    Directory of Open Access Journals (Sweden)

    Jie Liu

    Full Text Available 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.

  8. Impact of number of repeated scans on model observer performance for a low-contrast detection task in computed tomography.

    Science.gov (United States)

    Ma, Chi; Yu, Lifeng; Chen, Baiyu; Favazza, Christopher; Leng, Shuai; McCollough, Cynthia

    2016-04-01

    Channelized Hotelling observer (CHO) models have been shown to correlate well with human observers for several phantom-based detection/classification tasks in clinical computed tomography (CT). A large number of repeated scans were used to achieve an accurate estimate of the model's template. The purpose of this study is to investigate how the experimental and CHO model parameters affect the minimum required number of repeated scans. A phantom containing 21 low-contrast objects was scanned on a 128-slice CT scanner at three dose levels. Each scan was repeated 100 times. For each experimental configuration, the low-contrast detectability, quantified as the area under receiver operating characteristic curve, [Formula: see text], was calculated using a previously validated CHO with randomly selected subsets of scans, ranging from 10 to 100. Using [Formula: see text] from the 100 scans as the reference, the accuracy from a smaller number of scans was determined. Our results demonstrated that the minimum number of repeated scans increased when the radiation dose level decreased, object size and contrast level decreased, and the number of channels increased. As a general trend, it increased as the low-contrast detectability decreased. This study provides a basis for the experimental design of task-based image quality assessment in clinical CT using CHO.

  9. Quantitative Laughter Detection, Measurement, and Classification-A Critical Survey.

    Science.gov (United States)

    Cosentino, Sarah; Sessa, Salvatore; Takanishi, Atsuo

    2016-01-01

    The study of human nonverbal social behaviors has taken a more quantitative and computational approach in recent years due to the development of smart interfaces and virtual agents or robots able to interact socially. One of the most interesting nonverbal social behaviors, producing a characteristic vocal signal, is laughing. Laughter is produced in several different situations: in response to external physical, cognitive, or emotional stimuli; to negotiate social interactions; and also, pathologically, as a consequence of neural damage. For this reason, laughter has attracted researchers from many disciplines. A consequence of this multidisciplinarity is the absence of a holistic vision of this complex behavior: the methods of analysis and classification of laughter, as well as the terminology used, are heterogeneous; the findings sometimes contradictory and poorly documented. This survey aims at collecting and presenting objective measurement methods and results from a variety of different studies in different fields, to contribute to build a unified model and taxonomy of laughter. This could be successfully used for advances in several fields, from artificial intelligence and human-robot interaction to medicine and psychiatry.

  10. Clinical experience with the radioisotope varicocele scan as a screening method for the detection of subclinical varicoceles

    Energy Technology Data Exchange (ETDEWEB)

    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.

  11. Automatic registration of pelvic computed tomography data and magnetic resonance scans including a full circle method for quantitative accuracy evaluation

    NARCIS (Netherlands)

    van Herk, M.; de Munck, J. C.; Lebesque, J. V.; Muller, S.; Rasch, C.; Touw, A.

    1998-01-01

    The purpose of this study is to develop a method for registration of CT and MR scans of the pelvis with minimal user interaction and to obtain a means for objective quantification of the registration accuracy of clinical data without markers. CT scans were registered with proton density MR scans

  12. STREAMED VERTICAL RECTANGLE DETECTION IN TERRESTRIAL LASER SCANS FOR FACADE DATABASE PRODUCTION

    Directory of Open Access Journals (Sweden)

    J. Demantké

    2012-07-01

    Full Text Available 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.

  13. A novel versatile microbiosensor for local hydrogen detection by means of scanning photoelectrochemical microscopy.

    Science.gov (United States)

    Zhao, Fangyuan; Conzuelo, Felipe; Hartmann, Volker; Li, Huaiguang; Stapf, Stefanie; Nowaczyk, Marc M; Rögner, Matthias; Plumeré, Nicolas; Lubitz, Wolfgang; Schuhmann, Wolfgang

    2017-08-15

    The development of a versatile microbiosensor for hydrogen detection is reported. Carbon-based microelectrodes were modified with a [NiFe]-hydrogenase embedded in a viologen-modified redox hydrogel for the fabrication of a sensitive hydrogen biosensor By integrating the microbiosensor in a scanning photoelectrochemical microscope, it was capable of serving simultaneously as local light source to initiate photo(bio)electrochemical reactions while acting as sensitive biosensor for the detection of hydrogen. A hydrogen evolution biocatalyst based on photosystem 1-platinum nanoparticle biocomplexes embedded into a specifically designed redox polymer was used as a model for proving the capability of the developed hydrogen biosensor for the detection of hydrogen upon localized illumination. The versatility and sensitivity of the proposed microbiosensor as probe tip allows simplification of the set-up used for the evaluation of complex electrochemical processes and the rapid investigation of local photoelectrocatalytic activity of biocatalysts towards light-induced hydrogen evolution. Copyright © 2017 Elsevier B.V. All rights reserved.

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

    Science.gov (United States)

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

    2015-06-15

    As a major human pathogen in the Listeria genus, Listeria monocytogenes causes the bacterial disease listeriosis, which is a serious infection caused by eating food contaminated with the bacteria. We have developed an aptamer-based sandwich assay (ABSA) platform that demonstrates a promising potential for use in pathogen detection using aptamers as analytical bioconjugates. The whole-bacteria SELEX (WB-SELEX) strategy was adopted to generate aptamers with high affinity and specificity against live L. monocytogenes. Of the 35 aptamer candidates tested, LMCA2 and LMCA26 reacted to L. monocytogenes with high binding, and were consequently chosen as sensing probes. The ABSA platform can significantly enhance the sensitivity by employing a very specific aptamer pair for the sandwich complex. The ABSA platform exhibited a linear response over a wide concentration range of L. monocytogenes from 20 to 2×10(6) CFU per mL and was closely correlated with the following relationship: y=9533.3x+1542.3 (R(2)=0.99). Our proposed ABSA platform also provided excellent specificity for the tests to distinguish L. monocytogenes from other Listeria species and other bacterial genera (3 Listeria spp., 4 Salmonella spp., 2 Vibrio spp., 3 Escherichia coli and 3 Shigella spp.). Improvements in the sensitivity and specificity have not only facilitated the reliable detection of L. monocytogenes at extremely low concentrations, but also allowed for the development of a 96-well plate-based routine assay platform for multivalent diagnostics. Copyright © 2015 Elsevier B.V. All rights reserved.

  15. New quantitative detection of pathogens in heterogeneous environmental samples

    Science.gov (United States)

    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.

  16. A new approach for using genome scans to detect recent positive selection in the human genome.

    Directory of Open Access Journals (Sweden)

    Kun Tang

    2007-07-01

    Full Text Available Genome-wide scanning for signals of recent positive selection is essential for a comprehensive and systematic understanding of human adaptation. Here, we present a genomic survey of recent local selective sweeps, especially aimed at those nearly or recently completed. A novel approach was developed for such signals, based on contrasting the extended haplotype homozygosity (EHH profiles between populations. We applied this method to the genome single nucleotide polymorphism (SNP data of both the International HapMap Project and Perlegen Sciences, and detected widespread signals of recent local selection across the genome, consisting of both complete and partial sweeps. A challenging problem of genomic scans of recent positive selection is to clearly distinguish selection from neutral effects, given the high sensitivity of the test statistics to departures from neutral demographic assumptions and the lack of a single, accurate neutral model of human history. We therefore developed a new procedure that is robust across a wide range of demographic and ascertainment models, one that indicates that certain portions of the genome clearly depart from neutrality. Simulations of positive selection showed that our tests have high power towards strong selection sweeps that have undergone fixation. Gene ontology analysis of the candidate regions revealed several new functional groups that might help explain some important interpopulation differences in phenotypic traits.

  17. Effective Detection of Sub-Surface Archeological Features from Laser Scanning Point Clouds and Imagery Data

    Science.gov (United States)

    Fryskowska, A.; Kedzierski, M.; Walczykowski, P.; Wierzbicki, D.; Delis, P.; Lada, A.

    2017-08-01

    The archaeological heritage is non-renewable, and any invasive research or other actions leading to the intervention of mechanical or chemical into the ground lead to the destruction of the archaeological site in whole or in part. For this reason, modern archeology is looking for alternative methods of non-destructive and non-invasive methods of new objects identification. The concept of aerial archeology is relation between the presence of the archaeological site in the particular localization, and the phenomena that in the same place can be observed on the terrain surface form airborne platform. One of the most appreciated, moreover, extremely precise, methods of such measurements is airborne laser scanning. In research airborne laser scanning point cloud with a density of 5 points/sq. m was used. Additionally unmanned aerial vehicle imagery data was acquired. Test area is located in central Europe. The preliminary verification of potentially microstructures localization was the creation of digital terrain and surface models. These models gave an information about the differences in elevation, as well as regular shapes and sizes that can be related to the former settlement/sub-surface feature. The paper presents the results of the detection of potentially sub-surface microstructure fields in the forestry area.

  18. EFFECTIVE DETECTION OF SUB-SURFACE ARCHEOLOGICAL FEATURES FROM LASER SCANNING POINT CLOUDS AND IMAGERY DATA

    Directory of Open Access Journals (Sweden)

    A. Fryskowska

    2017-08-01

    Full Text Available The archaeological heritage is non-renewable, and any invasive research or other actions leading to the intervention of mechanical or chemical into the ground lead to the destruction of the archaeological site in whole or in part. For this reason, modern archeology is looking for alternative methods of non-destructive and non-invasive methods of new objects identification. The concept of aerial archeology is relation between the presence of the archaeological site in the particular localization, and the phenomena that in the same place can be observed on the terrain surface form airborne platform. One of the most appreciated, moreover, extremely precise, methods of such measurements is airborne laser scanning. In research airborne laser scanning point cloud with a density of 5 points/sq. m was used. Additionally unmanned aerial vehicle imagery data was acquired. Test area is located in central Europe. The preliminary verification of potentially microstructures localization was the creation of digital terrain and surface models. These models gave an information about the differences in elevation, as well as regular shapes and sizes that can be related to the former settlement/sub-surface feature. The paper presents the results of the detection of potentially sub-surface microstructure fields in the forestry area.

  19. On the detection of imprinted quantitative trait loci in experimental crosses of outbred species

    NARCIS (Netherlands)

    Koning, de D.J.; Bovenhuis, H.; Arendonk, van J.A.M.

    2002-01-01

    In this article, the quantitative genetic aspects of imprinted genes and statistical properties of methods to detect imprinted QTL are studied. Different models to detect imprinted QTL and to distinguish between imprinted and Mendelian QTL were compared in a simulation study. Mendelian and imprinted

  20. On the detection of imprinting quantitative trait loci in experimental crosses of outbred species

    NARCIS (Netherlands)

    Koning, de D.J.; Bovenhuis, H.; Arendonk, van J.A.M.

    2002-01-01

    In this article, the quantitative genetic aspects of imprinted genes and statistical properties of methods to detect imprinted QTL are studied. Different models to detect imprinted QTL and to distinguish between imprinted and Mendelian QTL were compared in a simulation study. Mendelian and imprinted

  1. Quantitative detection of bovine and porcine gelatin difference using surface plasmon resonance based biosensor

    Science.gov (United States)

    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.

  2. EN FACE VERSUS 12-LINE RADIAL OPTICAL COHERENCE TOMOGRAPHY SCAN PATTERNS FOR DETECTION OF MACULAR FLUID IN NEOVASCULAR AGE-RELATED MACULAR DEGENERATION.

    Science.gov (United States)

    Adam, Murtaza K; Shahlaee, Abtin; Samara, Wasim A; Maguire, Joseph I; Ho, Allen C; Hsu, Jason

    2017-08-14

    To compare fluid detection of autosegmented en face to 12-line radial spectral domain optical coherence tomography scan patterns in neovascular age-related macular degeneration. Retrospective observational case series. Sixty-seven patients (94 eyes) with neovascular age-related macular degeneration underwent autosegmented en face optical coherence tomography (with associated 304-line raster scan) and 12-line radial scan patterns. Sensitivity and specificity of fluid detection for en face scan and 12-line radial scans were determined by combining radial and 304-line raster scans as a gold standard. Two hundred and fifty-eight en face and 12-line radial spectral domain optical coherence tomography scans were interpreted. Seventy-five scans (58.1%) had fluid, whereas 54 scans (41.9%) did not. En face scan pattern fluid detection sensitivity and specificity was 89.3% and 61.1%, respectively. Twelve-line radial scan pattern fluid detection sensitivity and specificity was 97.3% and 100%, respectively. The difference in fluid detection between scan patterns was statistically significant (P = 0.01). Decreased central macular thickness was associated with false-positive (P = 0.035) and false-negative (P = 0.01) fluid detection on en face scans. En face optical coherence tomography alone is not as sensitive or specific as the 12-line radial scan pattern in detecting fluid in neovascular age-related macular degeneration. En face scans should be corroborated with other optical coherence tomography protocols to guide clinical decision making.

  3. Scanning of Open Data for Detection of Emerging Organized Crime Threats

    DEFF Research Database (Denmark)

    Pastor Pastor, Raquel; Larsen, Henrik Legind

    2017-01-01

    In fighting organized crime, open data provide an important source for both detecting emerging threats, as well as forecasting future threats. This allows the police to plan their resources and capacity for countering the threats in due time to prevent it or at least to mitigate its effects....... A vital part of a system supporting the police analysts for this purpose is an efficient and effective system for scanning the open data providing information about the relevant factors in the environment. This chapter presents the ePOOLICE project, aimed at developing a solution, the “ePOOLICE system...... in deploying such systems. One of the outcomes from the end-user evaluation of the prototype was the desire to integrate internal data to support not only strategic, but also operational analysis and investigation....

  4. Detecting Distributed Scans Using High-Performance Query-DrivenVisualization

    Energy Technology Data Exchange (ETDEWEB)

    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.

  5. Optical aptasensors for quantitative detection of small biomolecules: a review.

    Science.gov (United States)

    Feng, Chunjing; Dai, Shuang; Wang, Lei

    2014-09-15

    Aptasensors are aptamer-based biosensors with excellent recognition capability towards a wide range of targets. Specially, there have been ever-growing interests in the development of aptasensors for the detection of small molecules. This phenomenon is contributed to two reasons. On one hand, small biomolecules play an important role in living organisms with many kinds of biological function, such as antiarrhythmic effect and vasodilator activity of adenosine. On the other hand, the concentration of small molecules can be an indicator for disease diagnosis, for example, the concentration of ATP is closely associated with cell injury and cell viability. As a potential analysis tool in the construction of aptasensors, optical analysis has attracted much more interest of researchers due to its high sensitivity, quick response and simple operation. Besides, it promises the promotion of aptasensors in performance toward a new level. Review the development of optical aptasensors for small biomolecules will give readers an overall understanding of its progress and provide some theoretical guidelines for its future development. Hence, we give a mini-review on the advance of optical aptasensors for small biomolecules. This review focuses on recent achievements in the design of various optical aptasensors for small biomolecules, containing fluorescence aptasensors, colorimetric aptasensors, chemiluminescence aptasensors and other optical aptasensors. Copyright © 2014 Elsevier B.V. All rights reserved.

  6. Data Handling and Validation in Automated Detection of Food Toxicants Using Full Scan GC-MS and LC-MS

    NARCIS (Netherlands)

    Mol, H.; Lommen, A.; Zomer, P.; Kamp, van der H.; Lee, van der M.; Gerssen, A.

    2010-01-01

    Generic methods based on chromatography with full scan MS detection are maturing. Progress has been made in the development of software for automated detection or identification of the analytes, but this still is the bottleneck inhibiting implementation for routine analysis. Validation of

  7. Multiplexed Detection and Quantitation of Extracellular Vesicle RNA Expression Using NanoString.

    Science.gov (United States)

    Shukla, Neha; Yan, Irene K; Patel, Tushar

    2018-01-01

    Several different types of RNA molecules such as microRNAs (miRNAs) have been detected within extracellular vesicles in the circulation. The detection and potential utility of these as disease biomarkers requires the ability to detect their presence with adequate sensitivity and to quantitate their expression. The potential for circulating miRNA to serve as biomarkers can be evaluated through their detection in association with specific disease states. Multiplexed detection of several miRNA simultaneously can be useful for discovery studies. We describe the analysis of miRNA from biological fluids like plasma and serum using the Nanostring nCounter platform. Assays can be used to quantitate the expression of miRNA using direct detection based on hybridization to target specific color-coded probes followed by counting each color-coded barcode digitally.

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

    Science.gov (United States)

    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

  9. Detection and quantitation of genetically modified maize (Bt-176 transgenic maize) by applying ligation detection reaction and universal array technology.

    Science.gov (United States)

    Bordoni, Roberta; Mezzelani, Alessandra; Consolandi, Clarissa; Frosini, Andrea; Rizzi, Ermanno; Castiglioni, Bianca; Salati, Claudia; Marmiroli, Nelson; Marchelli, Rosangela; Rossi Bernardi, Luigi; Battaglia, Cristina; De Bellis, Gianluca

    2004-03-10

    We have applied the ligation detection reaction (LDR) combined with a universal array approach to the detection and quantitation of the polymerase chain reaction (PCR) amplified cry1A(b) gene from Bt-176 transgenic maize. We demonstrated excellent specificity and high sensitivity. Down to 0.5 fmol (nearly 60 pg) of PCR amplified transgenic material was unequivocally detected with excellent linearity within the 0.1-2.0% range with respect to wild-type maize. We suggest the feasibility of extending the LDR/universal array format to detect in parallel several transgenic sequences that are being developed for food applications.

  10. Combining Frequency Doubling Technology Perimetry and Scanning Laser Polarimetry for Glaucoma Detection.

    Science.gov (United States)

    Mwanza, Jean-Claude; Warren, Joshua L; Hochberg, Jessica T; Budenz, Donald L; Chang, Robert T; Ramulu, Pradeep Y

    2015-01-01

    To determine the ability of frequency doubling technology (FDT) and scanning laser polarimetry with variable corneal compensation (GDx-VCC) to detect glaucoma when used individually and in combination. One hundred ten normal and 114 glaucomatous subjects were tested with FDT C-20-5 screening protocol and the GDx-VCC. The discriminating ability was tested for each device individually and for both devices combined using GDx-NFI, GDx-TSNIT, number of missed points of FDT, and normal or abnormal FDT. Measures of discrimination included sensitivity, specificity, area under the curve (AUC), Akaike's information criterion (AIC), and prediction confidence interval lengths. For detecting glaucoma regardless of severity, the multivariable model resulting from the combination of GDx-TSNIT, number of abnormal points on FDT (NAP-FDT), and the interaction GDx-TSNIT×NAP-FDT (AIC: 88.28, AUC: 0.959, sensitivity: 94.6%, specificity: 89.5%) outperformed the best single-variable model provided by GDx-NFI (AIC: 120.88, AUC: 0.914, sensitivity: 87.8%, specificity: 84.2%). The multivariable model combining GDx-TSNIT, NAP-FDT, and interaction GDx-TSNIT×NAP-FDT consistently provided better discriminating abilities for detecting early, moderate, and severe glaucoma than the best single-variable models. The multivariable model including GDx-TSNIT, NAP-FDT, and the interaction GDx-TSNIT×NAP-FDT provides the best glaucoma prediction compared with all other multivariable and univariable models. Combining the FDT C-20-5 screening protocol and GDx-VCC improves glaucoma detection compared with using GDx or FDT alone.

  11. Design of Pixellated CMOS Photon Detector for Secondary Electron Detection in the Scanning Electron Microscope

    Directory of Open Access Journals (Sweden)

    Joon Huang Chuah

    2011-01-01

    Full Text Available This paper presents a novel method of detecting secondary electrons generated in the scanning electron microscope (SEM. The method suggests that the photomultiplier tube (PMT, traditionally used in the Everhart-Thornley (ET detector, is to be replaced with a configurable multipixel solid-state photon detector offering the advantages of smaller dimension, lower supply voltage and power requirements, and potentially cheaper product cost. The design of the proposed detector has been implemented using a standard 0.35 μm CMOS technology with optical enhancement. This microchip comprises main circuit constituents of an array of photodiodes connecting to respective noise-optimised transimpedance amplifiers (TIAs, a selector-combiner (SC circuit, and a postamplifier (PA. The design possesses the capability of detecting photons with low input optical power in the range of 1 nW with 100 μm × 100 μm sized photodiodes and achieves a total amplification of 180 dBΩ at the output.

  12. Fast quantitative detection of thiram using surface-enhanced Raman scattering and support vector machine regression

    Science.gov (United States)

    Weng, Shizhuang; Yuan, Baohong; Zhu, Zede; Huang, Linsheng; Zhang, Dongyan; Zheng, Ling

    2016-03-01

    As a novel and ultrasensitive detection technology that had advantages of fingerprint effect, high speed and low cost, surface-enhanced Raman scattering (SERS) was used to develop the regression models for the fast quantitative detection of thiram by support vector machine regression (SVR) in the paper. Meanwhile, three parameter optimization methods, which were grid search (GS), genetic algorithm (GA) and particle swarm optimization (PSO), were employed to optimize the internal parameters of SVR. Furthermore, the influence of the spectral number, spectral wavenumber range and principal component analysis (PCA) on the quantitative detection was also discussed. Firstly, the experiments demonstrate the proposed method can realize the fast and quantitative detection of thiram, and the best result is obtained by GS-SVR with the spectra of the range of characteristic peak which are processed by PCA. And the effect of GS, GA, PSO on the parameter optimization is similar, but the analysis time has a great difference in which GS is the fastest. Considering the analysis accuracy and time simultaneously, the spectral number of samples over each concentration should be set to 50. Then, developing the quantitative model with the spectra of range of characteristic peak can reduce analysis time on the promise of ensuring the detection accuracy. Additionally, PCA can further reduce the detection error through reserving the main information of the spectra data and eliminating the noise.

  13. Optimisation of qualitative and semi-quantitative detection of genetically modified crops by PCR

    Directory of Open Access Journals (Sweden)

    Tomáš Vyhnánek

    2009-01-01

    Full Text Available For qualitative and semi-quantitative detection of genetically modified crops we selected the detection of the frequently used promoter 35S CaMV. To optimise the method we used two commercially available genotypes of maize from the company Monsanto (USA, i.e. the transgenic hybrid Bt-maize line MON810 and a genetically non-modified control (isogenic line to MON810. We tested the pri­mers and PCR programmes described by Greiner et al. (2005 and Hernandéz et al. (2005. When applying PCR methods of detection of Bt-maize the first step was to optimise the protocol for the detection of the maize genome and detection of the specific sites of genetically modified MON810 maize. For detection of the maize genome we selected the primers IVR1-F and IVR1-R (invertase gene which verify the presence of the maize genome by a 226 bp product. For qualitative detection of the insert of Bt-maize MON810 the primer pairs VW01/VW03 (Greiner et al., 2005 and BT03/BT04 (Hernandéz et al., 2005 were used to detect the 35S CaMV promoter. Products of the size 178 bp and 280 bp, respectively, verify its presence. Based on the results of qualitative PCR we selected the primers VW01/VW03 for semi-quantitative detection of the amount of DNA of Bt-maize. For semi-quantitative PCR we have chosen sampling of the amplification product in the 30th cycle of the PCR reaction. In the genetically unmodified control a detection limit of 1% of admixture of Bt-maize was determined when using semi-quantitative PCR. The same primers as for semi-quantitative PCR were also used for multiplex PCR but with half the concentration of primers for standard PCR. This protocol however will have to be further optimised. The presented results introduce PCR methods for qualitative and semi-quantitative detection of DNA of the genetically modified Bt-maize MON810 which can also be used for other GM crops containing the 35S CaMV promoter. It could be suitable to use these methods for the

  14. Imaging and quantitative data acquisition of biological cell walls with Atomic Force Microscopy and Scanning Acoustic Microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Tittmann, B. R. [Penn State; Xi, X. [Penn State

    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

  15. Flow cytometric immunobead assay for quantitative detection of platelet autoantibodies in immune thrombocytopenia patients.

    Science.gov (United States)

    Zhai, Juping; Ding, Mengyuan; Yang, Tianjie; Zuo, Bin; Weng, Zhen; Zhao, Yunxiao; He, Jun; Wu, Qingyu; Ruan, Changgeng; He, Yang

    2017-10-23

    Platelet autoantibody detection is critical for immune thrombocytopenia (ITP) diagnosis and prognosis. Therefore, we aimed to establish a quantitative flow cytometric immunobead assay (FCIA) for ITP platelet autoantibodies evaluation. Capture microbeads coupled with anti-GPIX, -GPIb, -GPIIb, -GPIIIa and P-selectin antibodies were used to bind the platelet-bound autoantibodies complex generated from plasma samples of 250 ITP patients, 163 non-ITP patients and 243 healthy controls, a fluorescein isothiocyanate (FITC)-conjugated secondary antibody was the detector reagent and mean fluorescence intensity (MFI) signals were recorded by flow cytometry. Intra- and inter-assay variations of the quantitative FCIA assay were assessed. Comparisons of the specificity, sensitivity and accuracy between quantitative and qualitative FCIA or monoclonal antibody immobilization of platelet antigen (MAIPA) assay were performed. Finally, treatment process was monitored by our quantitative FCIA in 8 newly diagnosed ITPs. The coefficient of variations (CV) of the quantitative FCIA assay were respectively 9.4, 3.8, 5.4, 5.1 and 5.8% for anti-GPIX, -GPIb, -GPIIIa, -GPIIb and -P-selectin autoantibodies. Elevated levels of autoantibodies against platelet glycoproteins GPIX, GPIb, GPIIIa, GPIIb and P-selectin were detected by our quantitative FCIA in ITP patients compared to non-ITP patients or healthy controls. The sensitivity, specificity and accuracy of our quantitative assay were respectively 73.13, 81.98 and 78.65% when combining all 5 autoantibodies, while the sensitivity, specificity and accuracy of MAIPA assay were respectively 41.46, 90.41 and 72.81%. A quantitative FCIA assay was established. Reduced levels of platelet autoantibodies could be confirmed by our quantitative FCIA in ITP patients after corticosteroid treatment. Our quantitative assay is not only good for ITP diagnosis but also for ITP treatment monitoring.

  16. Incidental detection of adult polycystic kidney disease on routine bone scan

    Energy Technology Data Exchange (ETDEWEB)

    Axelrod, M.S.; Maayan, M.L.

    1989-04-01

    A routine bone scan performed on a 36-y old male incidentally demonstrated enlarged kidneys with multifocal areas of radionuclide concentration suggestive of polycystic kidneys. Further evaluation using ultrasonography, CT scan, and a /sup 99m/Tc-GHA renal scan confirmed the initial impression. The routine evaluation of the kidneys on a bone scan is emphasized as a simple method of identifying previously unsuspected renal structural abnormalities. (orig.).

  17. Field emission scanning electron microscopy (FE-SEM) as an approach for nanoparticle detection inside cells.

    Science.gov (United States)

    Havrdova, M; Polakova, K; Skopalik, J; Vujtek, M; Mokdad, A; Homolkova, M; Tucek, J; Nebesarova, J; Zboril, R

    2014-12-01

    When developing new nanoparticles for bio-applications, it is important to fully characterize the nanoparticle's behavior in biological systems. The most common techniques employed for mapping nanoparticles inside cells include transmission electron microscopy (TEM) and scanning transmission electron microscopy (STEM). These techniques entail passing an electron beam through a thin specimen. STEM or TEM imaging is often used for the detection of nanoparticles inside cellular organelles. However, lengthy sample preparation is required (i.e., fixation, dehydration, drying, resin embedding, and cutting). In the present work, a new matrix (FTO glass) for biological samples was used and characterized by field emission scanning electron microscopy (FE-SEM) to generate images comparable to those obtained by TEM. Using FE-SEM, nanoparticle images were acquired inside endo/lysosomes without disruption of the cellular shape. Furthermore, the initial steps of nanoparticle incorporation into the cells were captured. In addition, the conductive FTO glass endowed the sample with high stability under the required accelerating voltage. Owing to these features of the sample, further analyses could be performed (material contrast and energy-dispersive X-ray spectroscopy (EDS)), which confirmed the presence of nanoparticles inside the cells. The results showed that FE-SEM can enable detailed characterization of nanoparticles in endosomes without the need for contrast staining or metal coating of the sample. Images showing the intracellular distribution of nanoparticles together with cellular morphology can give important information on the biocompatibility and demonstrate the potential of nanoparticle utilization in medicine. Copyright © 2014 Elsevier Ltd. All rights reserved.

  18. Detection and Segmentation of Small Trees in the Forest-Tundra Ecotone Using Airborne Laser Scanning

    Directory of Open Access Journals (Sweden)

    Marius Hauglin

    2016-05-01

    Full Text Available Due to expected climate change and increased focus on forests as a potential carbon sink, it is of interest to map and monitor even marginal forests where trees exist close to their tolerance limits, such as small pioneer trees in the forest-tundra ecotone. Such small trees might indicate tree line migrations and expansion of the forests into treeless areas. Airborne laser scanning (ALS has been suggested and tested as a tool for this purpose and in the present study a novel procedure for identification and segmentation of small trees is proposed. The study was carried out in the Rollag municipality in southeastern Norway, where ALS data and field measurements of individual trees were acquired. The point density of the ALS data was eight points per m2, and the field tree heights ranged from 0.04 to 6.3 m, with a mean of 1.4 m. The proposed method is based on an allometric model relating field-measured tree height to crown diameter, and another model relating field-measured tree height to ALS-derived height. These models are calibrated with local field data. Using these simple models, every positive above-ground height derived from the ALS data can be related to a crown diameter, and by assuming a circular crown shape, this crown diameter can be extended to a crown segment. Applying this model to all ALS echoes with a positive above-ground height value yields an initial map of possible circular crown segments. The final crown segments were then derived by applying a set of simple rules to this initial “map” of segments. The resulting segments were validated by comparison with field-measured crown segments. Overall, 46% of the field-measured trees were successfully detected. The detection rate increased with tree size. For trees with height >3 m the detection rate was 80%. The relatively large detection errors were partly due to the inherent limitations in the ALS data; a substantial fraction of the smaller trees was hit by no or just a few

  19. Detection accuracy of proximal caries by phosphor plate and cone-beam computerized tomography images scanned with different resolutions.

    Science.gov (United States)

    Cheng, Jun-Ge; Zhang, Zhi-Ling; Wang, Xiao-Yan; Zhang, Zu-Yan; Ma, Xu-Chen; Li, Gang

    2012-08-01

    This study was carried out to assess whether the spatial resolution has an impact on the detection accuracy of proximal caries in flat panel CBCT (cone beam computerized tomography) images and if the detection accuracy can be improved by flat panel CBCT images scanned with high spatial resolution when compared to digital intraoral images. The CBCT test images of 45 non-restored human permanent teeth were respectively scanned with the ProMax 3D and the DCT Pro scanners at different resolutions. Digital images were obtained with a phosphor plate imaging system Digora Optime. Eight observers evaluated all the test images for carious lesion within the 90 proximal surfaces. With the histological examination serving as the reference standard, observer performances were evaluated by receiver operating characteristic (ROC) curves. The areas under the ROC curves were analyzed with two-way analysis of variance. No significant differences were found among the CBCT images and between CBCT and digital images when only proximal enamel caries was detected (p = 0.989). With respect to the detection of proximal dentinal caries, significant difference was found between CBCT and digital images (p proximal caries in flat panel CBCT images. The flat panel CBCT images scanned with high spatial resolution did not improve the detection accuracy of proximal enamel caries compared to digital intraoral images. CBCT images scanned with high spatial resolutions could not be used for proximal caries detection.

  20. Effect of the degree of liver inflammation on FibroScan detection

    Directory of Open Access Journals (Sweden)

    Fan LI

    2011-11-01

    Full Text Available Objective To observe the effect of the degree of liver inflammation on transient elastography(FibroScan detection value(FS.Methods A total of 282 patients with chronic hepatitis from 302 Hospital of PLA from April 2009 to December 2010 were enrolled in the current study.The patients were subjected to histologic examination of a liver biopsy and FibroScan detection.The patients were divided into two groups according to stage of fibrosis F0-2 and F3-4 to compare the FS values of the patients with different degrees of inflammation.The patients were divided into the G1-2 group and G3-4 group according to grade of histologic inflammation,and Receive Operating Characteristic(ROC curve were drawn for the two patient groups to diagnose liver cirrhosis using the FS values and to analyze the correlation between the FS value of patients with the different degrees of inflammation.Results Up to 115 patients had histologic inflammation grade(G1,109 patients had grade 2,54 had grade 3,and 4 patients had grade 4.Their FS values were 6.4(2.9,35.0,11.6(2.9,45.0,15.1(5.2,75.0,and 61.5(45.0,75.0,respectively.Significant differences were observed among the groups(P < 0.001,H=107.5.Among the patients in groups F0-2 and F3-4,the FS value increased with the degree of inflammation(P < 0.001.The area under the curve was 0.853 and 0.897 for the patients of G1-2 and G3-4 groups,respectively,using the FS value to diagnose liver cirrhosis.The FS threshold limit value was 17.7kPa and 18.7kPa,respectively.Conclusion Liver inflammation is one of the factors that affect FS values.The threshold limit for FS in diagnosing liver cirrhosis among patients with different degrees of liver inflammation varies.

  1. A genome scan for quantitative trait loci affecting cyanogenic potential of cassava root in an outbred population

    Science.gov (United States)

    2011-01-01

    Background Cassava (Manihot esculenta Crantz) can produce cyanide, a toxic compound, without self-injury. That ability was called the cyanogenic potential (CN). This project aimed to identify quantitative trait loci (QTL) associated with the CN in an outbred population derived from 'Hanatee' × 'Huay Bong 60', two contrasting cultivars. CN was evaluated in 2008 and in 2009 at Rayong province, and in 2009 at Lop Buri province, Thailand. CN was measured using a picrate paper kit. QTL analysis affecting CN was performed with 303 SSR markers. Results The phenotypic values showed continuous variation with transgressive segregation events with more (115 ppm) and less CN (15 ppm) than either parent ('Hanatee' had 33 ppm and 'Huay Bong 60' had 95 ppm). The linkage map consisted of 303 SSR markers, on 27 linkage groups with a map that encompassed 1,328 cM. The average marker interval was 5.8 cM. Five QTL underlying CN were detected. CN08R1from 2008 at Rayong, CN09R1and CN09R2 from 2009 at Rayong, and CN09L1 and CN09L2 from 2009 at Lop Buri were mapped on linkage group 2, 5, 10 and 11, respectively. Among all the identified QTL, CN09R1 was the most significantly associated with the CN trait with LOD score 5.75 and explained the greatest percentage of phenotypic variation (%Expl.) of 26%. Conclusions Five new QTL affecting CN were successfully identified from 4 linkage groups. Discovery of these QTL can provide useful markers to assist in cassava breeding and studying genes affecting the trait. PMID:21609492

  2. High Resolution Trichromatic Road Surface Scanning with a Line Scan Camera and Light Emitting Diode Lighting for Road-Kill Detection

    Directory of Open Access Journals (Sweden)

    Gil Lopes

    2016-04-01

    Full Text Available 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.

  3. QUANTITATIVE VS. CONVENTIONAL PCR FOR DETECTION OF HUMAN ADENOVIRUSES IN WATER AND SEDIMENT SAMPLES

    Directory of Open Access Journals (Sweden)

    Rodrigo STAGGEMEIER

    2015-08-01

    Full Text Available SUMMARY Human Adenoviruses (HAdV are notably resistant in the environment. These agents may serve as effective indicators of fecal contamination, and may act as causative agents of a number of different diseases in human beings. Conventional polymerase chain reaction (PCR and, more recently, quantitative PCR (qPCR are widely used for detection of viral agents in environmental matrices. In the present study PCR and SYBR(rGreen qPCR assays were compared for detection of HAdV in water (55 and sediments (20 samples of spring and artesian wells, ponds and streams, collected from dairy farms. By the quantitative methodology HAdV were detected in 87.3% of the water samples and 80% of the sediments, while by the conventional PCR 47.3% and 35% were detected in water samples and sediments, respectively.

  4. Delamination detection by Multi-Level Wavelet Processing of Continuous Scanning Laser Doppler Vibrometry data

    Science.gov (United States)

    Chiariotti, P.; Martarelli, M.; Revel, G. M.

    2017-12-01

    A novel non-destructive testing procedure for delamination detection based on the exploitation of the simultaneous time and spatial sampling provided by Continuous Scanning Laser Doppler Vibrometry (CSLDV) and the feature extraction capability of Multi-Level wavelet-based processing is presented in this paper. The processing procedure consists in a multi-step approach. Once the optimal mother-wavelet is selected as the one maximizing the Energy to Shannon Entropy Ratio criterion among the mother-wavelet space, a pruning operation aiming at identifying the best combination of nodes inside the full-binary tree given by Wavelet Packet Decomposition (WPD) is performed. The pruning algorithm exploits, in double step way, a measure of the randomness of the point pattern distribution on the damage map space with an analysis of the energy concentration of the wavelet coefficients on those nodes provided by the first pruning operation. A combination of the point pattern distributions provided by each node of the ensemble node set from the pruning algorithm allows for setting a Damage Reliability Index associated to the final damage map. The effectiveness of the whole approach is proven on both simulated and real test cases. A sensitivity analysis related to the influence of noise on the CSLDV signal provided to the algorithm is also discussed, showing that the processing developed is robust enough to measurement noise. The method is promising: damages are well identified on different materials and for different damage-structure varieties.

  5. Nanoparticle Enhanced MRI Scanning to Detect Cellular Inflammation in Experimental Chronic Renal Allograft Rejection

    Directory of Open Access Journals (Sweden)

    S. R. Alam

    2015-01-01

    Full Text Available Objectives. We investigated whether ultrasmall paramagnetic particles of iron oxide- (USPIO- enhanced magnetic resonance imaging (MRI can detect experimental chronic allograft damage in a murine renal allograft model. Materials and Methods. Two cohorts of mice underwent renal transplantation with either a syngeneic isograft or allograft kidney. MRI scanning was performed prior to and 48 hours after USPIO infusion using T2∗-weighted protocols. R2∗ values were calculated to indicate the degree of USPIO uptake. Native kidneys and skeletal muscle were imaged as reference tissues and renal explants analysed by histology and electron microscopy. Results. R2∗ values in the allograft group were higher compared to the isograft group when indexed to native kidney (median 1.24 (interquartile range: 1.12 to 1.36 versus 0.96 (0.92 to 1.04, P<0.01. R2∗ values were also higher in the allograft transplant when indexed to skeletal muscle (6.24 (5.63 to 13.51 compared to native kidney (2.91 (1.11 to 6.46 P<0.05. Increased R2∗ signal in kidney allograft was associated with macrophage and iron staining on histology. USPIO were identified within tissue resident macrophages on electron microscopy. Conclusion. USPIO-enhanced MRI identifies macrophage.

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

    Science.gov (United States)

    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."

  7. PAVEMENT DISTRESS DETECTION WITH PICUCHA METHODOLOGY FOR AREA-SCAN CAMERAS AND DARK IMAGES

    Directory of Open Access Journals (Sweden)

    Reus Salini

    2017-04-01

    Full Text Available The PICture Unsupervised Classification with Human Analysis (PICUCHA refers to a hybrid human-artificial intelligence methodology for pavement distresses assessment. It combines the human flexibility to recognize patterns and features in images with the neural network ability to expand such recognition to large volumes of images. In this study, the PICUCHA performance was tested with images taken with area-scan cameras and flash light illumination over a pavement with dark textures. These images are particularly challenging for the analysis because of the lens distortion and non-homogeneous illumination, generating artificial joints that happened at random positions inside the image cells. The chosen images were previously analyzed by other software without success because of the dark coluor. The PICUCHA algorithms could analyze the images with no noticeable problem and without any image pre-processing, such as contrast or brightness adjustments. Because of the special procedure used by the pavement engineer for the key patterns description, the distresses detection accuracy of the PICUCHA for the particular image set could reach 100%.

  8. Line-scan Raman microscopy complements optical coherence tomography for tumor boundary detection

    Science.gov (United States)

    Sudheendran, Narendran; Qi, Ji; Young, Eric D.; Lazar, Alexander J.; Lev, Dina C.; Pollock, Raphael E.; Larin, Kirill V.; Shih, Wei-Chuan

    2014-10-01

    Current technique for tumor resection requires biopsy of the tumor region and histological confirmation before the surgeon can be certain that the entire tumor has been resected. This confirmation process is time consuming both for the surgeon and the patient and also requires sacrifice of healthy tissue, motivating the development of novel technologies which can enable real-time detection of tumor-healthy tissue boundary for faster and more efficient surgeries. In this study, the potential of combining structural information from optical coherence tomography (OCT) and molecular information from line-scan Raman microscopy (LSRM) for such an application is presented. The results show a clear presence of boundary between myxoid liposarcoma and normal fat which is easily identifiable both from structural and molecular information. In cases where structural images are indistinguishable, for example, in normal fat and well differentiated liposarcoma (WDLS) or gastrointestinal sarcoma tumor (GIST) and myxoma, distinct molecular spectra have been obtained. The results suggest LSRM can effectively complement OCT to tumor boundary demarcation with high specificity.

  9. Automatic fracture detection based on Terrestrial Laser Scanning data: A new method and case study

    Science.gov (United States)

    Cao, Ting; Xiao, Ancheng; Wu, Lei; Mao, Liguang

    2017-09-01

    Terrestrial Laser Scanning (TLS), widely known as light detection and ranging (LiDAR) technology, is increasingly used to obtain rapidly three-dimensional (3-D) geometry or highly detailed digital terrain models with millimetric point precision and accuracy. In this contribution, we proposed a simple and unbiased approach to identify fractures directly from 3-D surface model of natural outcrops generated from TLS data and thus acquire surface density, which can provide important supplement data for fracture related research. One outcrop from the Shizigou anticline in the Qaidam Basin (NW China) is taken as the case to validate the method and obtain optimal parameters, according to the references of surface density measured in the field and from the photos taken by high-resolution camera. The results show that with suitable parameters, the proposed method can identify most structural fractures quickly, providing a solution of extracting structural fractures from virtual outcrops based on TLS data. Furthermore, it will help a lot in analyzing the development of fractures and other related fields.

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

    Science.gov (United States)

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

    2015-12-07

    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.

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

    Science.gov (United States)

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

    2016-10-01

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

  12. Detection of cervical cancer biomarker patterns in blood plasma and urine by differential scanning calorimetry and mass spectrometry.

    Directory of Open Access Journals (Sweden)

    Nichola C Garbett

    Full Text Available Improved methods for the accurate identification of both the presence and severity of cervical intraepithelial neoplasia (CIN and extent of spread of invasive carcinomas of the cervix (IC are needed. Differential scanning calorimetry (DSC has recently been shown to detect specific changes in the thermal behavior of blood plasma proteins in several diseases. This methodology is being explored to provide a complementary approach for screening of cervical disease. The present study evaluated the utility of DSC in differentiating between healthy controls, increasing severity of CIN and early and advanced IC. Significant discrimination was apparent relative to the extent of disease with no clear effect of demographic factors such as age, ethnicity, smoking status and parity. Of most clinical relevance, there was strong differentiation of CIN from healthy controls and IC, and amongst patients with IC between FIGO Stage I and advanced cancer. The observed disease-specific changes in DSC profiles (thermograms were hypothesized to reflect differential expression of disease biomarkers that subsequently bound to and affected the thermal behavior of the most abundant plasma proteins. The effect of interacting biomarkers can be inferred from the modulation of thermograms but cannot be directly identified by DSC. To investigate the nature of the proposed interactions, mass spectrometry (MS analyses were employed. Quantitative assessment of the low molecular weight protein fragments of plasma and urine samples revealed a small list of peptides whose abundance was correlated with the extent of cervical disease, with the most striking plasma peptidome data supporting the interactome theory of peptide portioning to abundant plasma proteins. The combined DSC and MS approach in this study was successful in identifying unique biomarker signatures for cervical cancer and demonstrated the utility of DSC plasma profiles as a complementary diagnostic tool to evaluate

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

    NARCIS (Netherlands)

    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

    2016-01-01

    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

  14. Quantitative Detection of Respiratory Chlamydia pneumoniae Infection by Real-Time PCR

    OpenAIRE

    Kuoppa, Yvonne; Boman, Jens; Scott, Lena; Kumlin, Urban; Eriksson, Iréne; Allard, Annika

    2002-01-01

    Real-time PCR was evaluated as a quantitative diagnostic method for Chlamydia pneumoniae infection using different respiratory samples. Real-time PCR had efficiency equal to or better than that of nested touchdown PCR. This study confirmed sputum as the best sampling material to detect an ongoing C. pneumoniae infection.

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

    Science.gov (United States)

    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...

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

    Science.gov (United States)

    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.

  17. Systematic assessment of survey scan and MS2-based abundance strategies for label-free quantitative proteomics using high-resolution MS data.

    Science.gov (United States)

    Tu, Chengjian; Li, Jun; Sheng, Quanhu; Zhang, Ming; Qu, Jun

    2014-04-04

    Survey-scan-based label-free method have shown no compelling benefit over fragment ion (MS2)-based approaches when low-resolution mass spectrometry (MS) was used, the growing prevalence of high-resolution analyzers may have changed the game. This necessitates an updated, comparative investigation of these approaches for data acquired by high-resolution MS. Here, we compared survey scan-based (ion current, IC) and MS2-based abundance features including spectral-count (SpC) and MS2 total-ion-current (MS2-TIC), for quantitative analysis using various high-resolution LC/MS data sets. Key discoveries include: (i) study with seven different biological data sets revealed only IC achieved high reproducibility for lower-abundance proteins; (ii) evaluation with 5-replicate analyses of a yeast sample showed IC provided much higher quantitative precision and lower missing data; (iii) IC, SpC, and MS2-TIC all showed good quantitative linearity (R(2) > 0.99) over a >1000-fold concentration range; (iv) both MS2-TIC and IC showed good linear response to various protein loading amounts but not SpC; (v) quantification using a well-characterized CPTAC data set showed that IC exhibited markedly higher quantitative accuracy, higher sensitivity, and lower false-positives/false-negatives than both SpC and MS2-TIC. Therefore, IC achieved an overall superior performance than the MS2-based strategies in terms of reproducibility, missing data, quantitative dynamic range, quantitative accuracy, and biomarker discovery.

  18. Detection of Ground Clutter from Weather Radar Using a Dual-Polarization and Dual-Scan Method

    Directory of Open Access Journals (Sweden)

    Mohammad-Hossein Golbon-Haghighi

    2016-06-01

    Full Text Available A novel dual-polarization and dual-scan (DPDS classification algorithm is developed for clutter detection in weather radar observations. Two consecutive scans of dual-polarization radar echoes are jointly processed to estimate auto- and cross-correlation functions. Discriminants are then defined and estimated in order to separate clutter from weather based on their physical and statistical properties. An optimal Bayesian classifier is used to make a decision on clutter presence from the estimated discriminant functions. The DPDS algorithm is applied to the data collected with the KOUN polarimetric radar and compared with the existing detection methods. It is shown that the DPDS algorithm yields a higher probability of detection and lower false alarm rate in clutter detection.

  19. Application of quantitative PCR for the detection of microorganisms in water.

    Science.gov (United States)

    Botes, Marelize; de Kwaadsteniet, Michéle; Cloete, Thomas Eugene

    2013-01-01

    The occurrence of microorganisms in water due to contamination is a health risk and control thereof is a necessity. Conventional detection methods may be misleading and do not provide rapid results allowing for immediate action. The quantitative polymerase chain reaction (qPCR) method has proven to be an effective tool to detect and quantify microorganisms in water within a few hours. Quantitative PCR assays have recently been developed for the detection of specific adeno- and polyomaviruses, bacteria and protozoa in different water sources. The technique is highly sensitive and able to detect low numbers of microorganisms. Quantitative PCR can be applied for microbial source tracking in water sources, to determine the efficiency of water and wastewater treatment plants and act as a tool for risk assessment. Different qPCR assays exist depending on whether an internal control is used or whether measurements are taken at the end of the PCR reaction (end-point qPCR) or in the exponential phase (real-time qPCR). Fluorescent probes are used in the PCR reaction to hybridise within the target sequence to generate a signal and, together with specialised systems, quantify the amount of PCR product. Quantitative reverse transcription polymerase chain reaction (q-RT-PCR) is a more sensitive technique that detects low copy number RNA and can be applied to detect, e.g. enteric viruses and viable microorganisms in water, and measure specific gene expression. There is, however, a need to standardise qPCR protocols if this technique is to be used as an analytical diagnostic tool for routine monitoring. This review focuses on the application of qPCR in the detection of microorganisms in water.

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

    Science.gov (United States)

    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.

  1. Improved detection and biopsy of solid liver lesions using pulse-inversion ultrasound scanning and contrast agent infusion

    DEFF Research Database (Denmark)

    Skjoldbye, B.; Pedersen, Morten Høgholm; Struckmann, J.

    2002-01-01

    The purpose of this study was to assess the ability of pulse-inversion ultrasound (US) scanning (PIUS), combined with an IV contrast agent, to detect malignant liver lesions and its impact on patient management (resectability). Additionally, to determine the feasibility of US-guided biopsy of new...

  2. The Role of Conventional Bronchoscopy in the Workup of Suspicious CT Scan Screen-Detected Pulmonary Nodules

    NARCIS (Netherlands)

    van't Westeinde, Susan C.; Horeweg, Nanda; Vernhout, Rene M.; Groen, Harry J. M.; Lammers, Jan-Willem J.; Weenink, Carla; Nackaerts, Kristiaan; Oudkerk, Matthijs; Mali, Willem; Thunnissen, Frederik B.; de Koning, Harry J.; van Klaveren, Rob J.

    Background: Up to 50% of the participants in CT scan lung cancer screening trials have at least one pulmonary nodule. To date, the role of conventional bronchoscopy in the workup of suspicious screen-detected pulmonary nodules is unknown. If a bronchoscopic evaluation could be eliminated, the

  3. The role of conventional bronchoscopy in the workup of suspicious CT scan screen-detected pulmonary nodules

    NARCIS (Netherlands)

    S.C. van 't Westeinde (Susan); N. Horeweg (Nanda); R. Vernhout (Rene); H.J.M. Groen (Henk); J.-W.J. Lammers (Jan-Willem); C. Weenink (Carla); K. Nackaerts (Kristiaan); M. Oudkerk (Matthijs); W.P. Mali (Willem); F.B.J.M. Thunnissen (Frederik); H.J. de Koning (Harry); R.J. van Klaveren (Rob)

    2012-01-01

    textabstractBackground: Up to 50% of the participants in CT scan lung cancer screening trials have at least one pulmonary nodule. To date, the role of conventional bronchoscopy in the workup of suspicious screen-detected pulmonary nodules is unknown. If a bronchoscopic evaluation could be

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

    NARCIS (Netherlands)

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

    2014-01-01

    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

  5. Correlation analysis of cortical geometry of tibia and humerus of white leghorns using clinical quantitative computed tomography and microcomputed tomography scans.

    Science.gov (United States)

    Regmi, P; Cox, A G; Robison, C I; Karcher, D M

    2017-08-01

    Peripheral quantitative computed tomography (QCT) has been used in poultry bone research in recent years to analyze cortical and cross-sectional geometry. For QCT to be used as a standard research tool for analysis of bones of laying hens (cortical thickness correlate the cortical parameters measured using clinical CT scans with the measurements from micro-CT, the current gold standard. A total of 15 tibiae and 14 humeri of Lohmann White hens was scanned using clinical CT and micro-CT. Reconstruction of the scans generated images with final voxel resolution of 195 μm for clinical CT scans and 46 μm for micro-CT scans. Cortical and total area were measured using MIMICS® software at proximal, middle, and distal locations of 20 mm sections of humerus diaphysis and 30 mm sections of tibia diaphysis. The total area for proximal and middle locations as well as proximal cortical area measurements for humeri produced strong correlation coefficients (R ≥ 0.70). Moderate strength correlation coefficients (R = 0.40 to 0.60) in humeri were seen in middle and distal cortical areas. Distal total area in humeri displayed a weak correlation coefficient (R ≤ 0.3; P = 0.25). Overall, tibiae demonstrated a weaker correlation. Proximal and middle cortical areas indicated moderate correlation coefficients (R = 0.40 to 0.60), while proximal and middle total areas accompanied by distal cortical and total area displayed weak correlation coefficients (R ≤ 0.3). Only the middle cortical area measurement for tibiae was significant (P = 0.03). These results indicate stronger correlation for humeri measurements among the scans than tibia. Overall, cross-sectional area measurements were only low to moderately correlated between clinical and micro-CT scans. © 2017 Poultry Science Association Inc.

  6. Early Detection of Brain Pathology Suggestive of Early AD Using Objective Evaluation of FDG-PET Scans

    Directory of Open Access Journals (Sweden)

    James C. Patterson

    2011-01-01

    Full Text Available The need for early detection of AD becomes critical as disease-modifying agents near the marketplace. Here, we present results from a study focused on improvement in detection of metabolic deficits related to neurodegenerative changes consistent with possible early AD with statistical evaluation of FDG-PET brain images. We followed 31 subjects at high risk or diagnosed with MCI/AD for 3 years. 15 met criteria for diagnosis of MCI, and five met criteria for AD. FDG-PET scans were completed at initiation and termination of the study. PET scans were read clinically and also evaluated objectively using Statistical Parametric Mapping (SPM. Using standard clinical evaluation of the FDG-PET scans, 11 subjects were detected, while 18 were detected using SPM evaluation. These preliminary results indicate that objective analyses may improve detection; however, early detection in at-risk normal subjects remains tentative. Several FDA-approved software packages are available that use objective analyses, thus the capacity exists for wider use of this method for MCI/AD.

  7. Western blot assay for quantitative and qualitative antigen detection in vaccine development.

    Science.gov (United States)

    Kumar, Sanjai; Zheng, Hong; Mahajan, Babita; Kozakai, Yukiko; Morin, Merribeth; Locke, Emily

    2014-05-01

    Immunological methods for quantitative measurement, antigenic characterization, and monitoring the stability of active immunogenic component(s) are a critical need in the vaccine development process. This unit describes an enhanced chemiluminescence-based western blot for quantitative detection of Plasmodium falciparum circumsporozoite protein (PfCSP), a major malaria candidate vaccine antigen. The most salient features of this assay are its high sensitivity and reproducibility; it can reliably detect ∼5 to 10 pg PfCSP expressed on native parasites or recombinantly expressed in Escherichia coli. Although described for a specific vaccine antigen, this assay should be applicable for any antigen-antibody combination for which relevant detection reagents are available. Detailed stepwise experimental procedures and methods for data acquisition and analysis are described. Copyright © 2014 John Wiley & Sons, Inc.

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

    Science.gov (United States)

    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. Copyright © 2016 Elsevier B.V. All rights reserved.

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

    Science.gov (United States)

    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

  10. Scanning laser polarimetry and optical coherence tomography for detection of retinal nerve fiber layer defects.

    Science.gov (United States)

    Oh, Jong-Hyun; Kim, Yong Yeon

    2009-09-01

    To compare the ability of scanning laser polarimetry with variable corneal compensation (GDx-VCC) and Stratus optical coherence tomography (OCT) to detect photographic retinal nerve fiber layer (RNFL) defects. This retrospective cross-sectional study included 45 eyes of 45 consecutive glaucoma patients with RNFL defects in red-free fundus photographs. The superior and inferior temporal quadrants in each eye were included for data analysis separately. The location and presence of RNFL defects seen in red-free fundus photographs were compared with those seen in GDx-VCC deviation maps and OCT RNFL analysis maps for each quadrant. Of the 90 quadrants (45 eyes), 31 (34%) had no apparent RNFL defects, 29 (32%) had focal RNFL defects, and 30 (33%) had diffuse RNFL defects in red-free fundus photographs. The highest agreement between GDx-VCC and red-free photography was 73% when we defined GDx-VCC RNFL defects as a cluster of three or more color-coded squares (p<5%) along the traveling line of the retinal nerve fiber in the GDx-VCC deviation map (kappa value, 0.388; 95% confidence interval (CI), 0.195 to 0.582). The highest agreement between OCT and red-free photography was 85% (kappa value, 0.666; 95% CI, 0.506 to 0.825) when a value of 5% outside the normal limit for the OCT analysis map was used as a cut-off value for OCT RNFL defects. According to the kappa values, the agreement between GDx-VCC deviation maps and red-free photography was poor, whereas the agreement between OCT analysis maps and red-free photography was good.

  11. Single ion impact detection and scanning probe aligned ion implantation for quantum bit formation

    Energy Technology Data Exchange (ETDEWEB)

    Weis, Christoph D.

    2011-10-04

    Quantum computing and quantum information processing is a promising path to replace classical information processing via conventional computers which are approaching fundamental physical limits. Instead of classical bits, quantum bits (qubits) are utilized for computing operations. Due to quantum mechanical phenomena such as superposition and entanglement, a completely different way of information processing is achieved, enabling enhanced performance for certain problem sets. Various proposals exist on how to realize a quantum bit. Among them are electron or nuclear spins of defect centers in solid state systems. Two such candidates with spin degree of freedom are single donor atoms in silicon and nitrogen vacancy (NV) defect centers in diamond. Both qubit candidates possess extraordinary qualities which makes them promising building blocks. Besides certain advantages, the qubits share the necessity to be placed precisely in their host materials and device structures. A commonly used method is to introduce the donor atoms into the substrate materials via ion implantation. For this, focused ion beam systems can be used, or collimation techniques as in this work. A broad ion beam hits the back of a scanning probe microscope (SPM) cantilever with incorporated apertures. The high resolution imaging capabilities of the SPM allows the non destructive location of device areas and the alignment of the cantilever and thus collimated ion beam spot to the desired implant locations. In this work, this technique is explored, applied and pushed forward to meet necessary precision requirements. The alignment of the ion beam to surface features, which are sensitive to ion impacts and thus act as detectors, is demonstrated. The technique is also used to create NV center arrays in diamond substrates. Further, single ion impacts into silicon device structures are detected which enables deliberate single ion doping.

  12. Detection of a quantitative trait locus associated with resistance to Ascaris suum infection in pigs.

    Science.gov (United States)

    Skallerup, Per; Nejsum, Peter; Jørgensen, Claus B; Göring, Harald H H; Karlskov-Mortensen, Peter; Archibald, Alan L; Fredholm, Merete; Thamsborg, Stig M

    2012-04-01

    Helminths almost invariably have an over-dispersed distribution in the host population. Human and animal studies have provided evidence suggesting that a large part of this variation is due to host genetic factors. Recently, the heritability for roundworm (Ascaris suum) infection levels in pigs was estimated to be 0.45. We used single nucleotide polymorphism markers to perform a whole-genome scan on 195 pigs experimentally infected with A. suum. A putative quantitative trait locus for worm burden on chromosome 4 covering 2.5 Mbp was identified by measured genotype analysis, although none of the SNPs reached genome-wide significance. To validate the putative quantitative trait locus, we genotyped two of the SNPs within the region in unrelated, informative animals exposed to experimental or natural infections and from which we had worm counts and/or faecal egg counts; the validation studies showed that one of the SNPs (TXNIP) was associated with total worm burden (P < 0.001) and adult worm burden(P < 0.0001), whereas the other SNP (ARNT) was associated with adult worm burden (P < 0.025) in these populations. We were thus able to confirm the existence of the quantitative trait locus on chromosome 4.This is to our knowledge the first report of a quantitative trait locus associated with helminth burden in pigs.

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

    Science.gov (United States)

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

    2016-04-07

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

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

    Science.gov (United States)

    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

  15. Estimation of genetic parameters and detection of quantitative trait loci for metabolites in Danish Holstein milk

    DEFF Research Database (Denmark)

    Buitenhuis, Albert Johannes; Sundekilde, Ulrik; Poulsen, Nina Aagaard

    2013-01-01

    Small components and metabolites in milk are significant for the utilization of milk, not only in dairy food production but also as disease predictors in dairy cattle. This study focused on estimation of genetic parameters and detection of quantitative trait loci for metabolites in bovine milk. F...... for lactic acid to >0.8 for orotic acid and β-hydroxybutyrate. A single SNP association analysis revealed 7 genome-wide significant quantitative trait loci [malonate: Bos taurus autosome (BTA)2 and BTA7; galactose-1-phosphate: BTA2; cis-aconitate: BTA11; urea: BTA12; carnitine: BTA25...

  16. Novel Automatic Detection of Pleura and B-lines (Comet-Tail Artifacts) on In-Vivo Lung Ultrasound Scans

    DEFF Research Database (Denmark)

    Moshavegh, Ramin; Hansen, Kristoffer Lindskov; Møller-Sørensen, Hasse

    2016-01-01

    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......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...

  17. A Low Cost, Electronically Scanned Array (ESA) Antenna Technology for Aviation Hazard Detection and Avoidance Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The proposed project will investigate the feasibility of utilizing ThinKom's low cost electronically scanned array (ESA) antenna concepts to enable affordable...

  18. Development of a scanning micro-pulse lidar for aerosol and cloud detection

    Science.gov (United States)

    Chen, Chao; Wang, Zhangjun; Meng, Xiangqian; Qu, Junle; Du, Libin; Li, Xianxin; Lv, Bin; Kabanov, V. V.

    2014-11-01

    A scanning micro-pulse lidar (MPL) was developed by Institute of Oceanographic Instrumentation, Shandong Academy of Sciences, which can be used for routine observations of optical properties, temporal and spatial variation of atmospheric aerosol and cloud in the lower troposphere. In addition to the optical system design, the design of 3 dimensional (3-D) scanning system controlled by servo motors is analyzed, including servo motor selection and mechanical design. Through the measurements in Qingdao, it is proved that 3-D scanning system can control the lidar azimuth/elevation scanning with high precision. The lidar has good performance and can provide time-height indication (THI), range-height indication (RHI) and plane-position indication (PPI) of lidar signals which can well reflect the temporal and spatial variation of atmospheric aerosol.

  19. Outcome of fetuses with short femur length detected at second trimester malformation scan - a national survey

    DEFF Research Database (Denmark)

    Mathiesen, Jonathan Michael; Aksglaede, Lise; Skibsted, Lillian

    2014-01-01

    To assess the relationship between fetal femur diaphysis length (FL) below the 5th percentile at the second trimester scan and pregnancy outcome, in a population where more than 90 % of women attend first trimester screening.......To assess the relationship between fetal femur diaphysis length (FL) below the 5th percentile at the second trimester scan and pregnancy outcome, in a population where more than 90 % of women attend first trimester screening....

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    Trägårdh, J; Macrae, K; Travis, C; Amor, R; Norris, G; Wilson, S H; Oppo, G-L; McConnell, G

    2015-07-01

    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. © 2015 The Authors Journal of Microscopy © 2015 Royal Microscopical Society.

  3. [Quantitative analysis of the palatal features affected by digit-sucking habit using a laser scanning system].

    Science.gov (United States)

    Ji, Yingjie; Ge, Lihong; Miao, Jiangxia

    2013-08-01

    To investigate the influence of digit-sucking habit on palatal features in pre-school children by using a laser scanning system. Forty pre-school children were chosen according to the results of questionnaires, among which 20 with digit-sucking habit(digit-sucking group) and 20 without any oral habits(control group). Impression of the upper jaw was taken from each child. After laser scanning the plaster casts, and three-dimensional reconstruction by the computer, parameters of anterior and posterior palatal length, width and height were measured, ratios of height/width, length/width and width ratio of anterior and posterior palatal were analyzed. The differences of palatal features between two groups were analyzed by t test. There was statistical significance between digit-sucking group and control group in posterior palatal width, anterior palatal length and anterior palatal height. The ratios of height/width and length/width in both posterior and anterior areas were statistically significant (P features were relatively deeper, narrower and more protrusive in digit-sucking group. The digit-sucking habit may have some deleterious impacts on the palatal features in pre-school children with primary dentition. And it is practical to measure the spacial palatal features by using laser scanning system to some extent.

  4. Scanning of Open Data for Detection of Emerging Organized Crime Threats—The ePOOLICE Project

    DEFF Research Database (Denmark)

    Larsen, Henrik Legind

    2017-01-01

    In fighting organized crime, open data provide an important source for both detecting emerging threats, as well as forecasting future threats. This allows the police to plan their resources and capacity for countering the threats in due time to prevent it or at least to mitigate its effects....... A vital part of a system supporting the police analysts for this purpose is an efficient and effective system for scanning the open data providing information about the relevant factors in the environment. This chapter presents the ePOOLICE project, aimed at developing a solution, the “ePOOLICE system......”, for such a scanning system. Through a prototype demonstrated with use cases, the project provided a proof of concept of an efficient and effective environmental scanning system as part of the early warning system for discovering emerging, as well as likely future, organized crime threats. Main elements...

  5. Detectability of cerebral aneurysms and surrounding vessels by three-dimensional evaluation using helical scanning CT (HES-CT)

    Energy Technology Data Exchange (ETDEWEB)

    Ogura, Yuko; Katada, Kazuhiro; Sano, Hirotoshi; Kato, Yoko; Kanno, Tetsuo; Takeshita, Gen; Koga, Sukehiko (Fujita Health Univ., Toyoake, Aichi (Japan))

    1994-09-01

    Helical scanning CT (HES-CT) is a new technique to enable high-speed volumetric data acquisition. We have applied HES-CT to the diagnosis of cerebral vascular diseases. In our experience, the relationship between the scanning parameters of HES-CT and image quality was complex and reciprocal, so that optimization of the parameters according to the clinical demands was essential. We compared HES-CT with conventional cerebral angiography to determine the detectability of the aneurysm and surrounding vessels, and sought the optimal parameters to delineate small vessels. All aneurysms were detected in multiplanar reconstruction (MPR) images. The smallest one was 3 x 4 mm. MPR images were found to have some advantages over conventional cerebral angiography in delineation of intracranial aneurysms: (1) scanning was over in a short time (30 s), (2) the relationship between the aneurysm and surrounding vessels was easily recognized, (3) the diameter of the neck could be measured, because the neck of the aneurysm and parent artery could be imaged on the same plane without overlapping another vessel, (4) calcified lesions on the aneurysmal wall were detected, and (5) HES-CT was done safety without arterial puncture. However, the detectability of unknown aneurysm was less than the detectability of known aneurysm in MPR images. The 180deg interpolation algorithm and 1 mm slice were effective in detecting small vessels. However, vessels with a diameter less than 1 mm could not be detected by HES-CT. HES-CT was considered to be useful as a supplementary examination to conventional angiography for the diagnosis of intracranial aneurysms. (author).

  6. Rapid quantitative detection of glucose content in glucose injection by reaction headspace gas chromatography.

    Science.gov (United States)

    Xie, Wei-Qi; Gong, Yi-Xian; Yu, Kong-Xian

    2017-10-20

    This work investigates an automated technique for rapid detecting the glucose content in glucose injection by reaction headspace gas chromatography (HS-GC). This method is based on the oxidation reaction of glucose in glucose injection with potassium dichromate. The carbon dioxide (CO 2 ) formed from the oxidation reaction can be quantitatively detected by GC. The results show that the relative standard deviation (RSD) of the present method was within 2.91%, and the measured glucose contents in glucose injection closely match those quantified by the reference method (relative differences glucose content in glucose injection related applications. Copyright © 2017 Elsevier B.V. All rights reserved.

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

    Science.gov (United States)

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

    2005-04-01

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

  8. Microfluidic bead trap as a visual bar for quantitative detection of oligonucleotides.

    Science.gov (United States)

    Zhao, Zichen; Bao, Yuanye; Chu, Lok Ting; Ho, John Kin Lim; Chieng, Ching-Chang; Chen, Ting-Hsuan

    2017-09-26

    We demonstrate a microfluidic bead trap capable of forming a dipstick-type bar visible to the naked eye for simple and quantitative detection of oligonucleotides. We use magnetic microparticles (MMPs) and polystyrene microparticles (PMPs) that are connected and form MMPs-targets-PMPs when target oligonucleotides are present, leaving free PMPs with a number inversely proportional to the amount of targets. Using a capillary flow-driven microfluidic circuitry consisting of a magnetic separator to remove the MMPs-targets-PMPs, the free PMPs can be trapped at the narrowing nozzle downstream, forming a visual bar quantifiable based on the length of PMP accumulation. Such a power-free and instrument-free platform enables a limit of detection at 13 fmol (0.65 nM in 20 μl, S/N = 3) of oligonucleotides and is compatible with single-nucleotide polymorphisms and operation in a complex bio-fluid. Moreover, using DNAzyme as the target oligonucleotide that catalyzes a specific hydrolytic cleavage in the presence of lead ions, we demonstrate a model application that detects lead ions with a limit of detection of 12.2 nM (2.5 μg l-1), providing quantitative and visual detection of lead contamination at resource-limited sites.

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

    Science.gov (United States)

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

    2011-04-01

    Coxsackievirus A16 (CVA16), together with enterovirus type 71 (EV71), is responsible for most cases of hand, foot and mouth disease (HFMD) worldwide. Recent findings suggest that the recombination between CVA16 and EV71, and co-circulation of these two viruses may have contributed to the increase of HFMD cases in China over the past few years. Thus, for CVA16, further understanding of its virology, epidemiology and development of diagnostic tests and vaccines are of importance. The present study aimed to develop reagents and protocols for the detection, characterization and quantitation of CVA16. Recombinant CVA16 capsid subunit proteins VP0, VP3 and truncated VP1, were produced in Escherichia coli and used to immunize guinea pigs to generate polyclonal antibodies. The resultant three antisera detected specifically CVA16 propagated in Vero cells by immunostaining, ELISA and Western blotting. The antisera was used to show that CVA16 capsids were composed of correctly processed VP0, VP1 and VP3 subunits, and were present in the form of efficiently assembled particles. A method for the quantitation of the yield of CVA16 in Vero cells was established based on a Western blotting protocol using the recombinant VP0 as a reference standard and anti-VP0 as the detection antibody. This study shows the development and validation of reagents and methods, for qualitative and quantitative determination of CVA16, which are essential for the development of vaccines. Copyright © 2011 Elsevier B.V. All rights reserved.

  10. Comparison of two different segmentation methods on planar lung perfusion scan with reference to quantitative value on SPECT/CT

    Energy Technology Data Exchange (ETDEWEB)

    Suh, Min Seok; Kang, Yeon Koo; Ha, Seung Gyun [Dept. of Nuclear Medicine, Seoul National University Hospital, Seoul (Korea, Republic of); and others

    2017-06-15

    Until now, there was no single standardized regional segmentation method of planar lung perfusion scan. We compared planar scan based two segmentation methods, which are frequently used in the Society of Nuclear Medicine, with reference to the lung perfusion single photon emission computed tomography (SPECT)/computed tomography (CT) derived values in lung cancer patients. Fifty-five lung cancer patients (male:female, 37:18; age, 67.8 ± 10.7 years) were evaluated. The patients underwent planar scan and SPECT/CT after injection of technetium-99 m macroaggregated albumin (Tc-99 m-MAA). The % uptake and predicted postoperative percentage forced expiratory volume in 1 s (ppoFEV1%) derived from both posterior oblique (PO) and anterior posterior (AP) methods were compared with SPECT/CT derived parameters. Concordance analysis, paired comparison, reproducibility analysis and spearman correlation analysis were conducted. The % uptake derived from PO method showed higher concordance with SPECT/CT derived % uptake in every lobe compared to AP method. Both methods showed significantly different lobar distribution of % uptake compared to SPECT/CT. For the target region, ppoFEV1% measured from PO method showed higher concordance with SPECT/CT, but lower reproducibility compared to AP method. Preliminary data revealed that every method significantly correlated with actual postoperative FEV1%, with SPECT/CT showing the best correlation. The PO method derived values showed better concordance with SPECT/CT compared to the AP method. Both PO and AP methods showed significantly different lobar distribution compared to SPECT/CT. In clinical practice such difference according to different methods and lobes should be considered for more accurate postoperative lung function prediction.

  11. Quantitative Ultrasound Assessment of Duchenne Muscular Dystrophy Using Edge Detection Analysis.

    Science.gov (United States)

    Koppaka, Sisir; Shklyar, Irina; Rutkove, Seward B; Darras, Basil T; Anthony, Brian W; Zaidman, Craig M; Wu, Jim S

    2016-09-01

    The purpose of this study was to investigate the ability of quantitative ultrasound (US) using edge detection analysis to assess patients with Duchenne muscular dystrophy (DMD). After Institutional Review Board approval, US examinations with fixed technical parameters were performed unilaterally in 6 muscles (biceps, deltoid, wrist flexors, quadriceps, medial gastrocnemius, and tibialis anterior) in 19 boys with DMD and 21 age-matched control participants. The muscles of interest were outlined by a tracing tool, and the upper third of the muscle was used for analysis. Edge detection values for each muscle were quantified by the Canny edge detection algorithm and then normalized to the number of edge pixels in the muscle region. The edge detection values were extracted at multiple sensitivity thresholds (0.01-0.99) to determine the optimal threshold for distinguishing DMD from normal. Area under the receiver operating curve values were generated for each muscle and averaged across the 6 muscles. The average age in the DMD group was 8.8 years (range, 3.0-14.3 years), and the average age in the control group was 8.7 years (range, 3.4-13.5 years). For edge detection, a Canny threshold of 0.05 provided the best discrimination between DMD and normal (area under the curve, 0.96; 95% confidence interval, 0.84-1.00). According to a Mann-Whitney test, edge detection values were significantly different between DMD and controls (P < .0001). Quantitative US imaging using edge detection can distinguish patients with DMD from healthy controls at low Canny thresholds, at which discrimination of small structures is best. Edge detection by itself or in combination with other tests can potentially serve as a useful biomarker of disease progression and effectiveness of therapy in muscle disorders.

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

    Science.gov (United States)

    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.

  13. Hotspot detection using space-time scan statistics on children under five years of age in Depok

    Science.gov (United States)

    Verdiana, Miranti; Widyaningsih, Yekti

    2017-03-01

    Some problems that affect the health level in Depok is the high malnutrition rates from year to year and the more spread infectious and non-communicable diseases in some areas. Children under five years old is a vulnerable part of population to get the malnutrition and diseases. Based on this reason, it is important to observe the location and time, where and when, malnutrition in Depok happened in high intensity. To obtain the location and time of the hotspots of malnutrition and diseases that attack children under five years old, space-time scan statistics method can be used. Space-time scan statistic is a hotspot detection method, where the area and time of information and time are taken into account simultaneously in detecting the hotspots. This method detects a hotspot with a cylindrical scanning window: the cylindrical pedestal describes the area, and the height of cylinder describe the time. Cylinders formed is a hotspot candidate that may occur, which require testing of hypotheses, whether a cylinder can be summed up as a hotspot. Hotspot detection in this study carried out by forming a combination of several variables. Some combination of variables provides hotspot detection results that tend to be the same, so as to form groups (clusters). In the case of infant health level in Depok city, Beji health care center region in 2011-2012 is a hotspot. According to the combination of the variables used in the detection of hotspots, Beji health care center is most frequently as a hotspot. Hopefully the local government can take the right policy to improve the health level of children under five in the city of Depok.

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

    Science.gov (United States)

    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.

  15. Field emission scanning electron microscopy (FE-SEM) as an approach for nanoparticle detection inside cells

    Czech Academy of Sciences Publication Activity Database

    Havrdová, M.; Poláková, K.; Skopalík, J.; Vůjtek, M.; Mokdad, A.; Homolková, M.; Tuček, J.; Nebesářová, Jana; Zbořil, R.

    2014-01-01

    Roč. 67, DEC 2014 (2014), s. 149-154 ISSN 0968-4328 Institutional support: RVO:60077344 Keywords : Field emission scanning electronmicroscopy (FE-SEM) * Stem cells * Iron oxide nanoparticles * Cellular morphology * Endosomes * Cell uptake Subject RIV: FD - Oncology ; Hematology Impact factor: 1.988, year: 2014

  16. Detection of sunflower oil in extra virgin olive oil by fast differential scanning calorimetry

    NARCIS (Netherlands)

    Wetten, I.A.; Herwaarden, A.W.; Splinter, R.; Boerrigter-Eenling, R.; Ruth, van S.M.

    2015-01-01

    Extra virgin olive oil (EVOO) is an economically valuable product, due to its high quality and premium price. Therefore it is vulnerable for adulteration by means of the addition of cheaper vegetable oils. Differential scanning calorimetry (DSC) has been suggested as a fast technique for the

  17. Roller-transducer scanning of wooden pallet parts for defect detection

    Science.gov (United States)

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

    2001-01-01

    Ultrasonic scanning experiments were conducted on two species of pallet deckboards using rolling transducers in a pitch-catch arrangement. Sound and unsound knots, cross grain, bark pockets, holes, splits, decay, and wane were characterized using several ultrasound parameters. Almost all parameters displayed sensitivity to defects distinctly from clear wood regions—...

  18. Bladder cancer detection in patients with gross haematuria: Computed tomography urography with enhancement-triggered scan versus flexible cystoscopy.

    Science.gov (United States)

    Helenius, Malin; Brekkan, Einar; Dahlman, Pär; Lönnemark, Maria; Magnusson, Anders

    2015-01-01

    Computed tomography urography (CTU) can be used to direct further investigation of patients if the bladder tumour detection rate is high. The aim of this study was to compare a CTU protocol including an enhancement-triggered scan and flexible cystoscopy for detecting bladder tumours. Patients with gross haematuria undergoing CTU during 2005-2008 were included. For patients younger than 50 years the CTU protocol included unenhanced, enhancement-triggered corticomedullary, and excretory phases. Patients older than 50 years followed the same protocol plus a nephrographic phase. The entire urinary tract was examined in all phases. Of 435 patients, 55 patients were diagnosed with bladder tumour. CTU detected bladder tumour in 48 patients (87%). Five CTU examination reports were false positive. With CTU, sensitivity for finding bladder tumour was 0.87, specificity 0.99, positive predictive value (PPV) 0.91 and negative predictive value (NPV) 0.98. Cystoscopy detected bladder tumour in 48 patients (87%) and had one false-positive finding, resulting in sensitivity of 0.87, specificity 1.0, PPV 0.98 and NPV 0.98. The detection rate of bladder tumours for the CTU protocol including an enhancement-triggered scan was high and comparable to flexible cystoscopy. Hence, this protocol could be used to assess the bladder as the primary investigation and direct further investigation of the patient.

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

    Science.gov (United States)

    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. Copyright © 2015, American Association for the Advancement of Science.

  20. A surface-scanning coil detector for real-time, in-situ detection of bacteria on fresh food surfaces.

    Science.gov (United States)

    Chai, Yating; Horikawa, Shin; Li, Suiqiong; Wikle, Howard C; Chin, Bryan A

    2013-12-15

    Proof-in-principle of a new surface-scanning coil detector has been demonstrated. This new coil detector excites and measures the resonant frequency of free-standing magnetoelastic (ME) biosensors that may now be placed outside the coil boundaries. With this coil design, the biosensors are no longer required to be placed inside the coil before frequency measurement. Hence, this new coil enables bacterial pathogens to be detected on fresh food surfaces in real-time and in-situ. The new coil measurement technique was demonstrated using an E2 phage-coated ME biosensor to detect Salmonella typhimurium on tomato surfaces. Real-time, in-situ detection was achieved with a limit of detection (LOD) statistically determined to be lower than 1.5×10(3) CFU/mm(2) with a confidence level of difference higher than 95% (p<0.05). Copyright © 2013 Elsevier B.V. All rights reserved.

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

    Science.gov (United States)

    Yang, Chun-Chieh; Kim, Moon S.; Millner, Pat; Chao, Kuanglin; Chan, Diane E.

    2012-05-01

    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 computation of the simple ratio function for effective detection of frass contamination. The contamination spots were created on the tomato surfaces using four concentrations of aqueous frass dilutions. The algorithms could detect more than 99% of the 0.2 g/ml and 0.1 g/ml frass contamination spots and successfully differentiated these spots from clean tomato surfaces. The results demonstrated that the simple multispectral fluorescence imaging algorithms based on violet LED excitation can be appropriate to detect frass on tomatoes in high-speed post-harvest processing lines.

  2. A quantitative and diametral analysis of human dentinal tubules at pulp chamber ceiling and floor under scanning electron microscopy.

    Science.gov (United States)

    Kontakiotis, Evangelos G; Tsatsoulis, Ioannis N; Filippatos, Christos G; Agrafioti, Anastasia

    2015-04-01

    The purposes of this study are (i) to evaluate and compare the dentinal tubule density, tubule diameter and percentage area of dentin occupied by tubules at the pulp chamber ceiling and floor; and (ii) to evaluate the effects of age on the number and dimensions of tubule openings. Twelve intact, human mandibular third molars were recruited. Six teeth belonged to patients up to 30 years of age and six teeth belonged to patients over 50 years. Scanning electron microscopic evaluations were made at two different locations: the pulp chamber ceiling and floor. The pulp chamber ceiling presented higher tubule density (P ceiling presents higher tubule density and greater area of exposed tubules. In younger people, the pulp chamber floor presents considerably high tubule diameter. The number and dimensions of dentinal tubule openings significantly decrease with age. © 2014 Australian Society of Endodontology.

  3. Robust SERS spectral analysis for quantitative detection of pycocyanin in biological fluids

    Science.gov (United States)

    Nguyen, Cuong; Thrift, Will; Bhattacharjee, Arunima; Whiteson, Katrine; Hochbaum, Allon; Ragan, Regina

    2017-09-01

    We demonstrate the advantage of using machine learning for surface enhanced Raman scattering (SERS) spectral analysis for quantitative detection of pyocyanin in Luria-Bertani media. Planar Au nanoparticle clusters were selfassembled on PS-b-PMMA diblock copolymer template using EDC crosslinking chemistry and electrohydrodynamic flow to fabricate SERS substrates. Resulting substrates produce uniform SERS response over large area with signal relative standard deviation of 10.8 % over 50 μm × 50 μm region. Taking advantage of the uniformity, 400 SERS spectra were collected at each pyocyanin concentration as training dataset. Tracking the intensity of pyocyanin 1350 cm-1 vibrational band shows linear regime beginning at 10 ppb. PLS analysis was also performed on the same training dataset. Without being explicitly "told" which spectrum to look for, PLS analysis recognizes the SERS spectrum of pyocyanin as its first loading vector even in the presence of other molecules in LB media. PLS regression enables quantitative detection at 1 ppb, 1 order of magnitude earlier than univariate regression. We hope this work will fuel a push toward wider adoption of more sophisticated machine learning algorithms for quantitative analysis of SERS spectra.

  4. Comparison of salivary collection and processing methods for quantitative HHV-8 detection.

    Science.gov (United States)

    Speicher, D J; Johnson, N W

    2014-10-01

    Saliva is a proved diagnostic fluid for the qualitative detection of infectious agents, but the accuracy of viral load determinations is unknown. Stabilising fluids impede nucleic acid degradation, compared with collection onto ice and then freezing, and we have shown that the DNA Genotek P-021 prototype kit (P-021) can produce high-quality DNA after 14 months of storage at room temperature. Here we evaluate the quantitative capability of 10 collection/processing methods. Unstimulated whole mouth fluid was spiked with a mixture of HHV-8 cloned constructs, 10-fold serial dilutions were produced, and samples were extracted and then examined with quantitative PCR (qPCR). Calibration curves were compared by linear regression and qPCR dynamics. All methods extracted with commercial spin columns produced linear calibration curves with large dynamic range and gave accurate viral loads. Ethanol precipitation of the P-021 does not produce a linear standard curve, and virus is lost in the cell pellet. DNA extractions from the P-021 using commercial spin columns produced linear standard curves with wide dynamic range and excellent limit of detection. When extracted with spin columns, the P-021 enables accurate viral loads down to 23 copies μl(-1) DNA. The quantitative and long-term storage capability of this system makes it ideal for study of salivary DNA viruses in resource-poor settings. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

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

    Energy Technology Data Exchange (ETDEWEB)

    Xie, Hongzhi [Los Alamos National Laboratory; Mukundan, Harshini [Los Alamos National Laboratory; Martinez, Jennifer S [Los Alamos National Laboratory; Swanson, Basil I [Los Alamos National Laboratory; Anderson, Aaron S [Los Alamos National Laboratory; Grace, Kevin [Los Alamos National Laboratory

    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

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

    Science.gov (United States)

    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. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. Rapid detection of Ceratocystis platani inoculum by quantitative real-time PCR assay.

    Science.gov (United States)

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

    2013-09-01

    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.

  8. Diagnostic value of saccoradiculography and of cat scan to detect stenosis of the lumbar canal

    Energy Technology Data Exchange (ETDEWEB)

    Arrault, I.; Benoist, M.; Rocolle, J.; Busson, J.; Lassale, B.; Deburge, A.

    1987-10-01

    Radiculographic X-rays and CAT scans of 60 patients operated on for stenosis of the lumbar canal were analysed separately and retrospectively by rheumatologists, a radiologist and surgeons working jointly, without knowledge of findings revealed by surgery. Comparison of findings with a detailed surgical report reveals that in the case of central lumbar canal stenosis, CAT scan provides a higher degree of reliability (72%) in diagnosis than does radiculography (56%). With lateral stenosis of the lateral cleft, reliability of both tests is identical (62%). The diagnostic deficiencies of these two examinations are discussed as well as diagnostic criteria employed and possible avenues of research. Currently, in the case of stenosis of the lumbar canal, it is still necessary to perform both of these examinations in combination and to accept the fact that, in certain cases, only one of the two tests reveals the stenosis, to be able to attain a preoperative rate of correct diagnosis greater than 80%.

  9. Quantitative immunohistochemical method for detection of wheat protein in model sausage

    Directory of Open Access Journals (Sweden)

    Zuzana Řezáčová Lukášková

    2014-01-01

    Full Text Available Since gluten can induce coeliac symptoms in hypersensitive consumers with coeliac disease, it is necessary to label foodstuffs containing it. In order to label foodstuffs, it is essential to find reliable methods to accurately determine the amount of wheat protein in food. The objective of this study was to compare the quantitative detection of wheat protein in model sausages by ELISA and immunohistochemical methods. Immunohistochemistry was combined with stereology to achieve quantitative results. High correlation between addition of wheat protein and compared methods was confirmed. For ELISA method the determined values were r = 0.98, P P < 0.01. Although ELISA is an accredited method, it was not reliable, unlike immunohistochemical methods (stereology SD = 3.1.

  10. Evaluation of Various Real-Time Reverse Transcription Quantitative PCR Assays for Norovirus Detection.

    Science.gov (United States)

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

    2017-04-28

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

  11. A probe-based quantitative PCR assay for detecting Tetracapsuloides bryosalmonae in fish tissue and environmental DNA water samples

    Science.gov (United States)

    Hutchins, Patrick; Sepulveda, Adam; Martin, Renee; Hopper, Lacey

    2017-01-01

    A probe-based quantitative real-time PCR assay was developed to detect Tetracapsuloides bryosalmonae, which causes proliferative kidney disease in salmonid fish, in kidney tissue and environmental DNA (eDNA) water samples. The limits of detection and quantification were 7 and 100 DNA copies for calibration standards and T. bryosalmonae was reliably detected down to 100 copies in tissue and eDNA samples. The assay presented here is a highly sensitive and quantitative tool for detecting T. bryosalmonae with potential applications for tissue diagnostics and environmental detection.

  12. Phase Error Caused by Speed Mismatch Analysis in the Line-Scan Defect Detection by Using Fourier Transform Technique

    Directory of Open Access Journals (Sweden)

    Eryi Hu

    2015-01-01

    Full Text Available The phase error caused by the speed mismatch issue is researched in the line-scan images capturing 3D profile measurement. The experimental system is constructed by a line-scan CCD camera, an object moving device, a digital fringe pattern projector, and a personal computer. In the experiment procedure, the detected object is moving relative to the image capturing system by using a motorized translation stage in a stable velocity. The digital fringe pattern is projected onto the detected object, and then the deformed patterns are captured and recorded in the computer. The object surface profile can be calculated by the Fourier transform profilometry. However, the moving speed mismatch error will still exist in most of the engineering application occasion even after an image system calibration. When the moving speed of the detected object is faster than the expected value, the captured image will be compressed in the moving direction of the detected object. In order to overcome this kind of measurement error, an image recovering algorithm is proposed to reconstruct the original compressed image. Thus, the phase values can be extracted much more accurately by the reconstructed images. And then, the phase error distribution caused by the speed mismatch is analyzed by the simulation and experimental methods.

  13. A novel fluorescence imaging technique combining deconvolution microscopy and spectral analysis for quantitative detection of opportunistic pathogens

    Energy Technology Data Exchange (ETDEWEB)

    Le Puil, Michael [Florida Gulf Coast University; Biggerstaff, John P. [University of Tennessee, Knoxville (UTK); Weidow, B. [University of Tennessee, Knoxville (UTK); Price, Jeffery R [ORNL; Naser, S. [University of Central Florida; White, D.C. [University of Tennessee, Knoxville (UTK); Alberte, R. [Florida Gulf Coast University

    2006-01-01

    A novel fluorescence imaging technique based on deconvolution microscopy and spectral analysis is presented here as an alternative to confocal laser scanning microscopy. It allowed rapid, specific and simultaneous identification of five major opportunistic pathogens, relevant for public health, in suspension and provided quantitative results.

  14. Use of Calculated Physicochemical Properties to Enhance Quantitative Response When Using Charged Aerosol Detection.

    Science.gov (United States)

    Robinson, Max W; Hill, Alan P; Readshaw, Simon A; Hollerton, John C; Upton, Richard J; Lynn, Sean M; Besley, Steve C; Boughtflower, Bob J

    2017-02-07

    Universal quantitative detection without the need for analyte reference standards would offer substantial benefits in many areas of analytical science. The quantitative capability of high-performance liquid chromatography (HPLC) with charged aerosol detection (CAD) was investigated for 50 compounds with a wide range of physical and chemical properties. It is widely believed that CAD is a mass detector. Quantification of the 50 compounds using a generic calibrant and mass calibration achieved an average error of 11.4% relative to 1H NMR. Correction factors are proposed that estimate the relative surface area of particles in the detector, taking into account the effects of the density and charge of analytes. Performing these corrections and quantifying with surface area calibration, rather than mass, shows considerably improved linearity and uniformity of detection, reducing the average error relative to 1H NMR to 7.1%. The accuracy of CAD quantification was most significantly improved for highly dense compounds, with traditional mass calibration showing an average error of 34.7% and the newly proposed surface area calibration showing an average error of 5.8%.

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

    Science.gov (United States)

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

    2014-02-01

    A strip reader based lateral flow immunoassay (LFIA) was established for the rapid and quantitative detection of ractopamine (RAC) in swine urine. The ratio of the optical densities (ODs) of the test line (AT) to that of the control line (AC) was used to effectively minimize interference among strips and sample variations. The linear range for the quantitative detection of RAC was 0.2 ng/mL to 3.5 ng/mL with a median inhibitory concentration (IC50) of 0.59 ± 0.06 ng/mL. The limit of detection (LOD) of the LFIA was 0.13 ng/mL. The intra-assay recovery rates were 92.97%, 97.25%, and 107.41%, whereas the inter-assay rates were 80.07%, 108.17%, and 93.7%, respectively. Copyright © 2014 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

  16. Quantitative detection of epidermal growth factor and interleukin-8 in whole saliva of healthy individuals.

    Science.gov (United States)

    Dafar, Amal; Rico, Paula; Işık, Ayşegül; Jontell, Mats; Cevik-Aras, Hülya

    2014-06-01

    This study aims to create consensus concerning the use of a methodology by which the handling of saliva is standardized and quantitative detection of IL-8 and EGF in whole saliva is achieved. Our study involves evaluating the extent to which the pre-treatment of saliva samples with an anionic detergent - sodium dodecyl sulphate (SDS) - improved detection levels for IL-8 and EGF. Whole saliva samples (n=28) were collected from healthy individuals and a protease inhibitor cocktail was added immediately. They were treated with either SDS or PBS for 20min and were then applied to a sandwich ELISA. Saliva is a complex viscous fluid that requires degrading before the analysis of salivary biomarkers. We found that pre-treatment of samples with SDS significantly increased the detection levels for both EGF (293%) and IL-8 (346%) when compared with PBS-treated pairs (***Psaliva samples with SDS for quantitative analysis (ii) using secretory output instead of concentration in the presentation of results to avoid individual variations and (iii) taking into consideration gender, age and meal intake since these have an impact on the secretory output of salivary proteins. Copyright © 2014 Elsevier B.V. All rights reserved.

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

    Science.gov (United States)

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

    2014-03-01

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

  18. Roller-transducer scanning of wooden pallet parts for defect detection

    Science.gov (United States)

    Kabir, M. F.; Schmoldt, D. L.; Schafer, M. E.

    2001-04-01

    Ultrasonic scanning experiments were conducted on two species of pallet deckboards using rolling transducers in a pitch-catch arrangement. Sound and unsound knots, cross grain, bark pockets, holes, splits, decay, and wane were characterized using several ultrasound parameters. Almost all parameters displayed sensitivity to defects distinctly from clear wood regions—being greatest for unsound knots, bark pockets, decay, holes, splits, and less for sound knots and cross grain. This study supports our conjecture that on-line inspection of wooden pallet parts is possible using rolling-transducer ultrasonic inspection.

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    Lucrecia Acosta Soto

    2017-01-01

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

  1. Sensitive, quantitative, and high-throughput detection of angiogenic markers using shape-coded hydrogel microparticles.

    Science.gov (United States)

    Al-Ameen, Mohammad Ali; Li, Ji; Beer, David G; Ghosh, Gargi

    2015-07-07

    Elevated serum concentrations of angiogenic markers including vascular endothelial growth factor (VEGF), fibroblast growth factor (FGF), and platelet-derived growth factor (PDGF) have been correlated with various clinical disorders including cancer, cardiovascular diseases, diabetes mellitus, and liver fibrosis. In addition, the correlation between the serum concentrations of these factors, clinical diagnosis, prognosis, and response to therapeutic agents is significant. Thereby suggesting high-throughput detection of serum levels of angiogenic markers has important implications in early detection of different clinical disorders as well as for subsequent therapy monitoring. Here, we demonstrate the feasibility of utilization of shape-coded hydrogel microparticle based suspension arrays for quantitative and reproducible measurement of VEGF, FGF, and PDGF in single and multiplexed assays. Bio-inert PEG hydrogel attenuated the background signal thereby improving the sensitivity of the detection method as well as eliminating the need for blocking the proteins. In the singleplexed assay, the detection limits of 1.7 pg ml(-1), 1.4 pg ml(-1), and 1.5 pg ml(-1) for VEGF, FGF, and PDGF respectively indicated that the sensitivity of the developed method exceeds that of the conventional technologies. We also demonstrated that in the multiplexed assays, recovery of the proteins was within 20% of the expected values. The practical applicability of the hydrogel microparticle based detection system was established by demonstrating the ability of the system to quantify the production of VEGF, FGF, and PDGF by breast cancer cells (MDA-MB-231).

  2. [Multiplex quantitative PCR detection for female carrier in an X-linked ichthyosis family].

    Science.gov (United States)

    Zhu, Hai-yan; Li, Hai-bo; Wu, Ling-qian; Zhu, Xiang-yu; Li, Jie; Yang, Ying; Zhu, Rui-fang; Wu, Xing; Duan, Hong-lei; Zhang, Ying; Hu, Ya-li

    2008-12-16

    To analyze the pathogenic mutation of an X-linked ichthyosis (XLI) family, and identify the genetic diagnosis of three probable female carriers in this family. To evaluate the availability of different detect methods for steroid sulfatase (STS) gene mutation. Peripheral blood samples were collected from the family, including the proband, proband's mother, younger sister, and younger female cousin, and 10 males and 10 females as controls. Ordinary PCR was used to detect whether there was STS gene deletion in the male proband. Then, multiplex quantitative fluorescent PCR (QF-PCR) was used to detect the STS gene in the proband and his 3 female family members. Fluorescence in situ hybridization (FISH) was used to authenticate the results of multiplex QF-PCR method. No amplified product of the exons 1-10 of STS gene deletion was detected by ordinary PCR in the proband. The proband's mother was diagnosed as a carrier, but his sister and cousin were diagnosed as normal females by multiplex QF-PCR. FISH confirmed the results of multiplex QF-PCR. Both multiplex QF-PCR and FISH are effective to detect the complete deletion mutation of STS gene and identify the female carrier, and multiplex QF-PCR is more convenient and automatic compared with FISH.

  3. A genome-screen experiment to detect quantitative trait loci affecting resistance to facial eczema disease in sheep.

    Science.gov (United States)

    Phua, S H; Dodds, K G; Morris, C A; Henry, H M; Beattie, A E; Garmonsway, H G; Towers, N R; Crawford, A M

    2009-02-01

    Facial eczema (FE) is a secondary photosensitization disease arising from liver cirrhosis caused by the mycotoxin sporidesmin. The disease affects sheep, cattle, deer and goats, and costs the New Zealand sheep industry alone an estimated NZ$63M annually. A long-term sustainable solution to this century-old FE problem is to breed for disease-resistant animals by marker-assisted selection. As a step towards finding a diagnostic DNA test for FE sensitivity, we have conducted a genome-scan experiment to screen for quantitative trait loci (QTL) affecting this trait in Romney sheep. Four F(1) sires, obtained from reciprocal matings of FE resistant and susceptible selection-line animals, were used to generate four outcross families. The resulting half-sib progeny were artificially challenged with sporidesmin to phenotype their FE traits measured in terms of their serum levels of liver-specific enzymes, namely gamma-glutamyl transferase and glutamate dehydrogenase. In a primary screen using selective genotyping on extreme progeny of each family, a total of 244 DNA markers uniformly distributed over all 26 ovine autosomes (with an autosomal genome coverage of 79-91%) were tested for linkage to the FE traits. Data were analysed using Haley-Knott regression. The primary screen detected one significant and one suggestive QTL on chromosomes 3 and 8 respectively. Both the significant and suggestive QTL were followed up in a secondary screen where all progeny were genotyped and analysed; the QTL on chromosome 3 was significant in this analysis.

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

    Energy Technology Data Exchange (ETDEWEB)

    Dunphy, James Christopher [Univ. of California, Berkeley, CA (United States)

    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(2xl) 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.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

  7. Ossification defects detected in CT scans represent early osteochondrosis in the distal femur of piglets.

    Science.gov (United States)

    Olstad, Kristin; Kongsro, Jørgen; Grindflek, Eli; Dolvik, Nils Ivar

    2014-08-01

    The purpose of the current study was to validate the use of CT for selection against osteochondrosis in pigs by calculating positive predictive value and comparing it to the positive predictive value of macroscopic evaluation, using histological examination as the reference standard. Eighteen male, hereditarily osteochondrosis-predisposed piglets underwent terminal examination at biweekly intervals from the ages of 82-180 days old, including CT scanning, macroscopic, and histological evaluation of the left distal femur. Areas of ischemic chondronecrosis (osteochondrosis) were confirmed in histological sections from 44/56 macroscopically suspected lesions, resulting in a positive predictive value of 79% (95% CI: 67-84%). Suspected lesions, that is; focal, radiolucent defects in the ossification front in CT scans corresponded to areas of ischemic chondronecrosis in 36/36 histologically examined lesions, resulting in a positive predictive value of 100% (95% CI: 90-100%). CT was superior to macroscopic evaluation for diagnosis of early stages of osteochondrosis in the distal femur of piglets. The current histologically validated observations can potentially be extrapolated to diagnostic monitoring of juvenile osteochondritis dissecans in children, or to animal models of human juvenile articular cartilage injury and repair. © 2014 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

  8. AB029. The clinical significance of RigiScan plus detection

    OpenAIRE

    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 phas...

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

    Science.gov (United States)

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

    2014-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Jong-Oh Kim

    2014-05-01

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

  11. Optimal camera and illumination angulations for detection of interproximal caries using quantitative light-induced fluorescence.

    Science.gov (United States)

    Buchalla, W; Lennon, A M; van der Veen, M H; Stookey, G K

    2002-01-01

    The aim of the study was to find the optimal illumination and camera angulations for interproximal use of quantitative light-induced fluorescence (QLF). A multiaxis optical bench was developed and interproximal tooth assemblies were investigated using a modified version of QLF. Extracted human premolars without caries (n = 8) and with interproximal D1, D2 and D3 caries (n = 20) were selected. Tooth-pair models without caries and with interproximal caries of matching size, location, and shape were imaged with varying camera and illumination directions from buccal (0 degrees) to occlusal (90 degrees) to lingual (180 degrees) in steps of 30 degrees using a PC and framegrabber and examined for observed presence. Interproximal lesions could be detected in all teeth, but observed presence was dependent on camera angulation (p caries could be detected with the camera in the 90 degree position. Copyright 2002 S. Karger AG, Basel

  12. Detecting Genetic Interactions for Quantitative Traits Using m-Spacing Entropy Measure

    Directory of Open Access Journals (Sweden)

    Jaeyong Yee

    2015-01-01

    Full Text Available A number of statistical methods for detecting gene-gene interactions have been developed in genetic association studies with binary traits. However, many phenotype measures are intrinsically quantitative and categorizing continuous traits may not always be straightforward and meaningful. Association of gene-gene interactions with an observed distribution of such phenotypes needs to be investigated directly without categorization. Information gain based on entropy measure has previously been successful in identifying genetic associations with binary traits. We extend the usefulness of this information gain by proposing a nonparametric evaluation method of conditional entropy of a quantitative phenotype associated with a given genotype. Hence, the information gain can be obtained for any phenotype distribution. Because any functional form, such as Gaussian, is not assumed for the entire distribution of a trait or a given genotype, this method is expected to be robust enough to be applied to any phenotypic association data. Here, we show its use to successfully identify the main effect, as well as the genetic interactions, associated with a quantitative trait.

  13. Coronary Calcium Scan

    Science.gov (United States)

    ... Back To Health Topics / Coronary Calcium Scan Coronary Calcium Scan Also known as Calcium Scan Test A coronary calcium scan is a CT scan of your heart that detects and measures the amount of calcium in the walls of your coronary arteries. Overview ...

  14. Rapid and quantitative detection of Brucella by up-converting phosphor technology-based lateral-flow assay.

    Science.gov (United States)

    Qu, Qing; Zhu, Ziwen; Wang, Yufei; Zhong, Zhijun; Zhao, Jin; Qiao, Feng; Du, Xinying; Wang, Zhoujia; Yang, Ruifu; Huang, Liuyu; Yu, Yaqin; Zhou, Lei; Chen, Zeliang

    2009-10-01

    A rapid and quantitative up-converting phosphor technology-based later-flow assay (UPT-LF assay) was developed for on-site detection of Brucella. Different Brucella species both in pure cultures and in spiked samples could be quantitatively detected. The detection limit for pure culture was 5 x 10(6)CFU/ml and the sensitivity for different spiked samples ranged from 2.0 x 10(3) to 3.9 x 10(5)CFU/mg. The UPT-LF assay showed high specificity, reproducibility and stability, providing great potential for Brucella on-site detection.

  15. Detecting central fixation by means of artificial neural networks in a pediatric vision screener using retinal birefringence scanning.

    Science.gov (United States)

    Gramatikov, Boris I

    2017-04-27

    Reliable detection of central fixation and eye alignment is essential in the diagnosis of amblyopia ("lazy eye"), which can lead to blindness. Our lab has developed and reported earlier a pediatric vision screener that performs scanning of the retina around the fovea and analyzes changes in the polarization state of light as the scan progresses. Depending on the direction of gaze and the instrument design, the screener produces several signal frequencies that can be utilized in the detection of central fixation. The objective of this study was to compare artificial neural networks with classical statistical methods, with respect to their ability to detect central fixation reliably. A classical feedforward, pattern recognition, two-layer neural network architecture was used, consisting of one hidden layer and one output layer. The network has four inputs, representing normalized spectral powers at four signal frequencies generated during retinal birefringence scanning. The hidden layer contains four neurons. The output suggests presence or absence of central fixation. Backpropagation was used to train the network, using the gradient descent algorithm and the cross-entropy error as the performance function. The network was trained, validated and tested on a set of controlled calibration data obtained from 600 measurements from ten eyes in a previous study, and was additionally tested on a clinical set of 78 eyes, independently diagnosed by an ophthalmologist. In the first part of this study, a neural network was designed around the calibration set. With a proper architecture and training, the network provided performance that was comparable to classical statistical methods, allowing perfect separation between the central and paracentral fixation data, with both the sensitivity and the specificity of the instrument being 100%. In the second part of the study, the neural network was applied to the clinical data. It allowed reliable separation between normal subjects

  16. Behavior Drift Detection Based on Anomalies Identification in Home Living Quantitative Indicators

    Directory of Open Access Journals (Sweden)

    Fabio Veronese

    2018-01-01

    Full Text Available Home Automation and Smart Homes diffusion are providing an interesting opportunity to implement elderly monitoring. This is a new valid technological support to allow in-place aging of seniors by means of a detection system to notify potential anomalies. Monitoring has been implemented by means of Complex Event Processing on live streams of home automation data: this allows the analysis of the behavior of the house inhabitant through quantitative indicators. Different kinds of quantitative indicators for monitoring and behavior drift detection have been identified and implemented using the Esper complex event processing engine. The chosen solution permits us not only to exploit the queries when run “online”, but enables also “offline” (re-execution for testing and a posteriori analysis. Indicators were developed on both real world data and on realistic simulations. Tests were made on a dataset of 180 days: the obtained results prove that it is possible to evidence behavior changes for an evaluation of a person’s condition.

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

    Science.gov (United States)

    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.

  18. Automated Fovea Detection in Spectral Domain Optical Coherence Tomography Scans of Exudative Macular Disease

    Directory of Open Access Journals (Sweden)

    Jing Wu

    2016-01-01

    Full Text Available In macular spectral domain optical coherence tomography (SD-OCT volumes, detection of the foveal center is required for accurate and reproducible follow-up studies, structure function correlation, and measurement grid positioning. However, disease can cause severe obscuring or deformation of the fovea, thus presenting a major challenge in automated detection. We propose a fully automated fovea detection algorithm to extract the fovea position in SD-OCT volumes of eyes with exudative maculopathy. The fovea is classified into 3 main appearances to both specify the detection algorithm used and reduce computational complexity. Based on foveal type classification, the fovea position is computed based on retinal nerve fiber layer thickness. Mean absolute distance between system and clinical expert annotated fovea positions from a dataset comprised of 240 SD-OCT volumes was 162.3 µm in cystoid macular edema and 262 µm in nAMD. The presented method has cross-vendor functionality, while demonstrating accurate and reliable performance close to typical expert interobserver agreement. The automatically detected fovea positions may be used as landmarks for intra- and cross-patient registration and to create a joint reference frame for extraction of spatiotemporal features in “big data.” Furthermore, reliable analyses of retinal thickness, as well as retinal structure function correlation, may be facilitated.

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

    Science.gov (United States)

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

    2014-08-01

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

  20. LASER SCANNING APPLICATION FOR DETECTION OF HUMAN POSTURE DISTORTION DURING MASS EXAMINATIONS

    Directory of Open Access Journals (Sweden)

    R. L. Voinov

    2014-03-01

    Full Text Available Identification of human posture distortion in the early stages is an important task, which makes it possible to adjust the onset of the disease with just exercise and without the use of drugs. Existing methods for monitoring of human posture assessment do not meet modern requirements for speed of data acquisition and processing. Real time evaluation of human posture distortion in static and dynamic modes is possible by using a laser scanner. The paper deals with a three-dimensional laser scanning method for determining human posture. The device designed on the basis of its examination gives the possibility for real-time static and dynamic modes. Characteristic feature of the laser scanner is the presence of automated servo rotatable measuring head in two planes (vertical and horizontal with a density of up to tens of measurement points per square centimeter.

  1. Modern Detection of Prostate Cancer's Bone Metastasis: Is the Bone Scan Era Over?

    Directory of Open Access Journals (Sweden)

    Bertrand Tombal

    2012-01-01

    Full Text Available Prostate cancer cells have an exquisite tropism for bone, which clinically translates into the highest rate of bone metastases amongst male cancers. Although in the latest years there has been an active development of new “bone targeted” therapies, modern diagnostic techniques for bone metastases still relies mostly on 99mTc bone scanning (BS and plain X-ray. BS dramatically lacks specificity and sensitivity. Recent publications using modern imaging technologies have clearly pinpointed that BS grossly underestimates the true prevalence of bone metastasis. In addition BS does not allow tumour measurement and is, therefore, not appropriate to monitor response to therapy. This might be extremely important in patients harbouring high-risk localized disease that are eventually candidate for local therapy. Here we reviewed what are the emerging imaging strategies that are likely to supplant BS and to what extent they can be used in the clinic already.

  2. A quantitative evaluation of pleural effusion on computed tomography scans using B-spline and local clustering level set.

    Science.gov (United States)

    Song, Lei; Gao, Jungang; Wang, Sheng; Hu, Huasi; Guo, Youmin

    2017-05-24

    Estimation of the pleural effusion's volume is an important clinical issue. The existing methods cannot assess it accurately when there is large volume of liquid in the pleural cavity and/or the patient has some other disease (e.g. pneumonia). In order to help solve this issue, the objective of this study is to develop and test a novel algorithm using B-spline and local clustering level set method jointly, namely BLL. The BLL algorithm was applied to a dataset involving 27 pleural effusions detected on chest CT examination of 18 adult patients with the presence of free pleural effusion. Study results showed that average volumes of pleural effusion computed using the BLL algorithm and assessed manually by the physicians were 586 ml±339 ml and 604±352 ml, respectively. For the same patient, the volume of the pleural effusion, segmented semi-automatically, was 101.8% ±4.6% of that was segmented manually. Dice similarity was found to be 0.917±0.031. The study demonstrated feasibility of applying the new BLL algorithm to accurately measure the volume of pleural effusion.

  3. Detection of Nanophyetus salmincola in water, snails, and fish tissues by quantitative polymerase chain reaction

    Science.gov (United States)

    Purcell, Maureen K.; Powers, Rachel L.; Besijn, Bonnie; Hershberger, Paul K.

    2017-01-01

    We report the development and validation of two quantitative PCR (qPCR) assays to detect Nanophyetus salmincola DNA in water samples and in fish and snail tissues. Analytical and diagnostic validation demonstrated good sensitivity, specificity, and repeatability of both qPCR assays. The N. salmincola DNA copy number in kidney tissue was significantly correlated with metacercaria counts based on microscopy. Extraction methods were optimized for the sensitive qPCR detection of N. salmincola DNA in settled water samples. Artificially spiked samples suggested that the 1-cercaria/L threshold corresponded to an estimated log10 copies per liter ≥ 6.0. Significant correlation of DNA copy number per liter and microscopic counts indicated that the estimated qPCR copy number was a good predictor of the number of waterborne cercariae. However, the detection of real-world samples below the estimated 1-cercaria/L threshold suggests that the assays may also detect other N. salmincola life stages, nonintact cercariae, or free DNA that settles with the debris. In summary, the qPCR assays reported here are suitable for identifying and quantifying all life stages of N. salmincola that occur in fish tissues, snail tissues, and water.

  4. Quantitative Comparison of the Sensitivity of Detection of Fluorescent and Bioluminescent Reporters in Animal Models

    Directory of Open Access Journals (Sweden)

    Tamara Troy

    2004-01-01

    Full Text Available Bioluminescent and fluorescent reporters are finding increased use in optical molecular imaging in small animals. In the work presented here, issues related to the sensitivity of in vivo detection are examined for standard reporters. A high-sensitivity imaging system that can detect steady-state emission from both bioluminescent and fluorescent reporters is described. The instrument is absolutely calibrated so that animal images can be analyzed in physical units of radiance allowing more quantitative comparisons to be performed. Background emission from mouse tissue, called autoluminescence and autofluorescence, is measured and found to be an important limitation to detection sensitivity of reporters. Measurements of dual-labeled (bioluminescent/fluorescent reporter systems, including PC-3M-luc/DsRed2-1 and HeLa-luc/PKH26, are shown. The results indicate that although fluorescent signals are generally brighter than bioluminescent signals, the very low autoluminescent levels usually results in superior signal to background ratios for bioluminescent imaging, particularly compared with fluorescent imaging in the green to red part of the spectrum. Fluorescence detection sensitivity improves in the far-red to near-infrared, provided the animals are fed a low-chlorophyll diet to reduce autofluorescence in the intestinal region. The use of blue-shifted excitation filters is explored as a method to subtract out tissue autofluorescence and improve the sensitivity of fluorescent imaging.

  5. Detection of Her-2/neu expression in gastric cancer: Quantitative PCR versus immunohistochemistry.

    Science.gov (United States)

    Zhu, Guang-Jun; Xu, Chun-Wei; Fang, Mei-Yu; Zhang, Yu-Ping; Li, Yang

    2014-11-01

    The aim of this study was to compare quantitative polymerase chain reaction (qPCR) with immunohistochemistry (IHC) for the detection of Her-2 in gastric cancer, and to investigate the correlation between the expression levels of human epidermal growth factor receptor 2 (Her-2) and clinical features. Clinical data from 426 cases of gastric cancer were collected. Her-2 expression levels in cancerous tissue were detected using IHC, and the Her-2/neu gene expression levels were determined by qPCR. The correlation between the expression level of Her-2 and clinical features was investigated. The positive expression rate of Her-2 in cancerous tissue detected using qPCR and IHC was 11.17% (46/412) and 13.38% (57/426), respectively. The positive expression of the Her-2 protein/gene was significantly correlated with the depth of invasion and lymphatic metastasis, as well as the TNM stage (PHer-2 protein/gene and tumor location, age, gender, differentiation degree and Lauren classification (P>0.05). The diagnostic consistency was good between the two methods (κ=0.828). The results indicate that the expression of Her-2/neu is closely associated with the development of gastric cancer. qPCR is a convenient, objective and efficient method, which may be used as an alternative to IHC or fluorescence in situ hybridization for the detection of Her-2/neu gene.

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

    Science.gov (United States)

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

    2012-12-01

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

  7. Obstacle avoidance, visual detection performance, and eye-scanning behavior of glaucoma patients in a driving simulator: a preliminary study.

    Directory of Open Access Journals (Sweden)

    Rocío Prado Vega

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

  8. Pillar[5]arene-Based Supramolecular Plasmonic Thin Films for Label-Free, Quantitative and Multiplex SERS Detection.

    Science.gov (United States)

    Montes-García, Verónica; Gómez-González, Borja; Martínez-Solís, Diego; Taboada, José M; Jiménez-Otero, Norman; de Uña-Álvarez, Jacobo; Obelleiro, Fernando; García-Río, Luis; Pérez-Juste, Jorge; Pastoriza-Santos, Isabel

    2017-08-09

    Novel plasmonic thin films based on electrostatic layer-by-layer (LbL) deposition of citrate-stabilized Au nanoparticles (NPs) and ammonium pillar[5]arene (AP[5]A) have been developed. The supramolecular-induced LbL assembly of the plasmonic nanoparticles yields the formation of controlled hot spots with uniform interparticle distances. At the same time, this strategy allows modulating the density and dimensions of the Au aggregates, and therefore the optical response, on the thin film with the number of AuNP-AP[5]A deposition cycles. Characterization of the AuNP-AP[5]A hybrid platforms as a function of the deposition cycles was performed by means of visible-NIR absorption spectroscopy, and scanning electron and atomic force microscopies, showing larger aggregates with the number of cycles. Additionally, the surface enhanced Raman scattering efficiency of the resulting AuNP-AP[5]A thin films has been investigated for three different laser excitations (633, 785, and 830 nm) and using pyrene as Raman probe. The best performance was shown by the AuNP-AP[5]A film obtained with two deposition cycles ((AuNP-AP[5]A)2) when excited with a 785 laser line. The optical response and SERS efficiency of the thin films were also simulated using the M3 solver and employing computer aided design models built based on SEM images of the different films. The use of host molecules as building blocks to fabricate (AuNP-AP[5]A)2) films has enabled the ultradetection, in liquid and gas phase, of low molecular weight polyaromatic hydrocarbons, PAHs, with no affinity for gold but toward the hydrophobic AP[5]A cavity. Besides, these plasmonic platforms allowed achieving quantitative detection within certain concentration regimes. Finally, the multiplex sensing capabilities of the AuNP-AP[5]A)2 were evaluated for their ability to detect in liquid and gas phase three different PAHs.

  9. The use of the temporal scan statistic to detect methicillin-resistant Staphylococcus aureus clusters in a community hospital.

    Science.gov (United States)

    Faires, Meredith C; Pearl, David L; Ciccotelli, William A; Berke, Olaf; Reid-Smith, Richard J; Weese, J Scott

    2014-07-08

    In healthcare facilities, conventional surveillance techniques using rule-based guidelines may result in under- or over-reporting of methicillin-resistant Staphylococcus aureus (MRSA) outbreaks, as these guidelines are generally unvalidated. The objectives of this study were to investigate the utility of the temporal scan statistic for detecting MRSA clusters, validate clusters using molecular techniques and hospital records, and determine significant differences in the rate of MRSA cases using regression models. Patients admitted to a community hospital between August 2006 and February 2011, and identified with MRSA>48 hours following hospital admission, were included in this study. Between March 2010 and February 2011, MRSA specimens were obtained for spa typing. MRSA clusters were investigated using a retrospective temporal scan statistic. Tests were conducted on a monthly scale and significant clusters were compared to MRSA outbreaks identified by hospital personnel. Associations between the rate of MRSA cases and the variables year, month, and season were investigated using a negative binomial regression model. During the study period, 735 MRSA cases were identified and 167 MRSA isolates were spa typed. Nine different spa types were identified with spa type 2/t002 (88.6%) the most prevalent. The temporal scan statistic identified significant MRSA clusters at the hospital (n=2), service (n=16), and ward (n=10) levels (P ≤ 0.05). Seven clusters were concordant with nine MRSA outbreaks identified by hospital staff. For the remaining clusters, seven events may have been equivalent to true outbreaks and six clusters demonstrated possible transmission events. The regression analysis indicated years 2009-2011, compared to 2006, and months March and April, compared to January, were associated with an increase in the rate of MRSA cases (P ≤ 0.05). The application of the temporal scan statistic identified several MRSA clusters that were not detected by hospital

  10. Detection of circulating tumour cells in peripheral blood with an automated scanning fluorescence microscope.

    Science.gov (United States)

    Ntouroupi, T G; Ashraf, S Q; McGregor, S B; Turney, B W; Seppo, A; Kim, Y; Wang, X; Kilpatrick, M W; Tsipouras, P; Tafas, T; Bodmer, W F

    2008-09-02

    We have developed an automated, highly sensitive and specific method for identifying and enumerating circulating tumour cells (CTCs) in the blood. Blood samples from 10 prostate, 25 colorectal and 4 ovarian cancer patients were analysed. Eleven healthy donors and seven men with elevated serum prostate-specific antigen (PSA) levels but no evidence of malignancy served as controls. Spiking experiments with cancer cell lines were performed to estimate recovery yield. Isolation was performed either by density gradient centrifugation or by filtration, and the CTCs were labelled with monoclonal antibodies against cytokeratins 7/8 and either AUA1 (against EpCam) or anti-PSA. The slides were analysed with the Ikoniscope robotic fluorescence microscope imaging system. Spiking experiments showed that less than one epithelial cell per millilitre of blood could be detected, and that fluorescence in situ hybridisation (FISH) could identify chromosomal abnormalities in these cells. No positive cells were detected in the 11 healthy control samples. Circulating tumour cells were detected in 23 out of 25 colorectal, 10 out of 10 prostate and 4 out of 4 ovarian cancer patients. Five samples (three colorectal and two ovarian) were analysed by FISH for chromosomes 7 and 8 combined and all had significantly more than four dots per cell. We have demonstrated an Ikoniscope based relatively simple and rapid procedure for the clear-cut identification of CTCs. The method has considerable promise for screening, early detection of recurrence and evaluation of treatment response for a wide variety of carcinomas.

  11. Time-resolved detection of surface plasmon polaritons with a scanning tunneling microscope

    DEFF Research Database (Denmark)

    Keil, Ulrich Dieter Felix; Ha, T.; Jensen, Jacob Riis

    1998-01-01

    We present the time-resolved detection of surface plasmon polaritons with an STM. The results indicate that the time resolved signal is due to rectification of coherently superimposed plasmon voltages. The comparison with differential reflectivity measurements shows that the tip itself influences...

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

    Science.gov (United States)

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

    2016-03-01

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

  13. High Dose MicroCT Does Not Contribute Toward Improved MicroPET/CT Image Quantitative Accuracy and Can Limit Longitudinal Scanning of Small Animals

    Directory of Open Access Journals (Sweden)

    Wendy A. McDougald

    2017-10-01

    Full Text Available Obtaining accurate quantitative measurements in preclinical Positron Emission Tomography/Computed Tomography (PET/CT imaging is of paramount importance in biomedical research and helps supporting efficient translation of preclinical results to the clinic. The purpose of this study was two-fold: (1 to investigate the effects of different CT acquisition protocols on PET/CT image quality and data quantification; and (2 to evaluate the absorbed dose associated with varying CT parameters.Methods: An air/water quality control CT phantom, tissue equivalent material phantom, an in-house 3D printed phantom and an image quality PET/CT phantom were imaged using a Mediso nanoPET/CT scanner. Collected data was analyzed using PMOD software, VivoQuant software and National Electric Manufactures Association (NEMA software implemented by Mediso. Measured Hounsfield Unit (HU in collected CT images were compared to the known HU values and image noise was quantified. PET recovery coefficients (RC, uniformity and quantitative bias were also measured.Results: Only less than 2 and 1% of CT acquisition protocols yielded water HU values < −80 and air HU values < −840, respectively. Four out of 11 CT protocols resulted in more than 100 mGy absorbed dose. Different CT protocols did not impact PET uniformity and RC, and resulted in <4% overall bias relative to expected radioactive concentration.Conclusion: Preclinical CT protocols with increased exposure times can result in high absorbed doses to the small animals. These should be avoided, as they do not contributed toward improved microPET/CT image quantitative accuracy and could limit longitudinal scanning of small animals.

  14. Hyperspectral reflectance and fluorescence line-scan imaging system for online detection of fecal contamination on apples

    Science.gov (United States)

    Kim, Moon S.; Cho, Byoung-Kwan; Yang, Chun-Chieh; Chao, Kaunglin; Lefcourt, Alan M.; Chen, Yud-Ren

    2006-10-01

    We have developed nondestructive opto-electronic imaging techniques for rapid assessment of safety and wholesomeness of foods. A recently developed fast hyperspectral line-scan imaging system integrated with a commercial apple-sorting machine was evaluated for rapid detection of animal feces matter on apples. Apples obtained from a local orchard were artificially contaminated with cow feces. For the online trial, hyperspectral images with 60 spectral channels, reflectance in the visible to near infrared regions and fluorescence emissions with UV-A excitation, were acquired from apples moving at a processing sorting-line speed of three apples per second. Reflectance and fluorescence imaging required a passive light source, and each method used independent continuous wave (CW) light sources. In this paper, integration of the hyperspectral imaging system with the commercial applesorting machine and preliminary results for detection of fecal contamination on apples, mainly based on the fluorescence method, are presented.

  15. Automated terrestrial laser scanning with near-real-time change detection - monitoring of the Séchilienne landslide

    Science.gov (United States)

    Kromer, Ryan A.; Abellán, Antonio; Hutchinson, D. Jean; Lato, Matt; Chanut, Marie-Aurelie; Dubois, Laurent; Jaboyedoff, Michel

    2017-05-01

    We present an automated terrestrial laser scanning (ATLS) system with automatic near-real-time change detection processing. The ATLS system was tested on the Séchilienne landslide in France for a 6-week period with data collected at 30 min intervals. The purpose of developing the system was to fill the gap of high-temporal-resolution TLS monitoring studies of earth surface processes and to offer a cost-effective, light, portable alternative to ground-based interferometric synthetic aperture radar (GB-InSAR) deformation monitoring. During the study, we detected the flux of talus, displacement of the landslide and pre-failure deformation of discrete rockfall events. Additionally, we found the ATLS system to be an effective tool in monitoring landslide and rockfall processes despite missing points due to poor atmospheric conditions or rainfall. Furthermore, such a system has the potential to help us better understand a wide variety of slope processes at high levels of temporal detail.

  16. Incremental diagnostic value of combined quantitative and qualitative parameters of magnetocardiography to detect coronary artery disease.

    Science.gov (United States)

    Shin, Eun-Seok; Lam, Yat-Yin; Her, Ae-Young; Brachmann, Johannes; Jung, Friedrich; Park, Jai-Wun

    2017-02-01

    Magnetocardiography (MCG) has been proposed as a non-invasive and functional technique with high accuracy for diagnosis of myocardial ischemia. This study sought to investigate the incremental diagnostic value of combined quantitative and qualitative parameters of MCG to detect coronary artery disease (CAD). Ninety six patients with suspected CAD who underwent coronary angiography were enrolled in the analysis to test the diagnostic accuracy of 2 MCG parameters (a quantitative parameter of the percent change of ST-segment fluctuation score and a qualitative parameter of non-dipole phenomenon). The best cut-off value for the percent change of ST-segment fluctuation score was -51.0%. The accuracy, sensitivity, specificity, positive predictive value, and negative predictive value were 78.1, 73.9, 82.0, 79.1, and 77.4, in the percent change of ST-segment fluctuation score and 86.5, 84.8, 88.0, 86.7, and 86.3 in non-dipole phenomenon. The area under the curve of receiver-operating characteristics was 0.79 for the percent change of ST-segment fluctuation score and 0.86 for non-dipole phenomenon (pquantitative parameter of percent change of ST-segment fluctuation score in the detection of significant CAD. Furthermore, this study found that the incorporation of non-dipole phenomenon into the percent change of ST-segment fluctuation score significantly improved the diagnostic performance of CAD detection. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  17. Detection of Leishmania infantum DNA in conjunctival swabs of cats by quantitative real-time PCR.

    Science.gov (United States)

    Benassi, Julia Cristina; Benvenga, Graziella U; Ferreira, Helena Lage; Pereira, Vanessa F; Keid, Lara B; Soares, Rodrigo; Oliveira, Tricia Maria Ferreira de Sousa

    2017-06-01

    Although some studies have investigated the potential role of cats as a reservoir for Leishmania, their role in the epidemiology of visceral leishmaniasis (VL) is still poorly understood. Molecular diagnostic techniques are an important tool in VL diagnosis, and PCR shows high sensitivity and specificity for Leishmania spp. detection. Quantitative real-time PCR (qPCR) is a method that permits quantitative analysis of a large number of samples, resulting in more sensitive, accurate, and reproducible measurements of specific DNA present in the sample. This study compared real-time PCR (qPCR) and conventional PCR (cPCR) for detection of Leishmania spp. in blood and conjunctival swab (CS) samples of healthy cats from a non-endemic area in the state of São Paulo, Brazil. Of all CS samples, 1.85% (2/108) were positive for Leishmania spp. by both cPCR as qPCR (kappa index = 1), indicating excellent agreement between the two methods. The DNA from the two CS-cPCR- and CS-qPCR-positive samples was further tested with a PCR test amplifying the Leishmania spp. discriminative rRNA internal transcribed spacer 1 (ITS 1), of which one sample generated a 300-350-bp DNA fragment whose size varies according to the Leishmania species. Following sequencing, the fragment showed 100% similarity to a GenBank L. infantum sequence obtained from a cat in Italy. In conclusion, the association of qPCR and CS proved to be effective for detection of Leishmania in cats. Conjunctival swab samples were shown to be a practical and better alternative to blood samples and may be useful in the diagnosis and studies of feline leishmaniasis. Copyright © 2017 Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

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

    2010-01-01

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

  19. Automatic Scanning Detection for Characterization of Dome-Related Seismic Swarms at Mount St. Helens and their Evolution Through Time

    Science.gov (United States)

    MacCarthy, J. K.; Rowe, C. A.

    2005-12-01

    Using the waveform data for Mount St. Helens from October 2004 through April, 2005 available from the IRIS DMC, as well as a special data set including the accelerometer that recorded eleven days of activity on the whaleback dome of St. Helens during February, 2005, we have modified a waveform cross-correlation algorithm previously applied for event clustering and repicking into a correlation scanning detector. This tool is being developed for implementation during routine volcano monitoring, as a means of identifying, characterizing and locating repeating swarm events and quantifying their seismic energy release. Application of the scanning detector to St. Helens data reveals stable swarm-type activity over periods with cross-correlation values exceeding 0.8 for 25 days, within which the repeating events slowly evolve over time. Waveforms show high correlation when as much as 60 s of coda is included in the correlation, suggesting very stable source and path characteristics. We present analysis of waveform evolution and event location stability as determined through the detection and automatic repicking and relocation of correlated events. Evolving seismic waveform characteristics are compared to available information about the ongoing eruption sequence to investigate the correspondence among such observables as deformation, volatile flux (both magmagenic and meteoric), estimated dome volume or magma flux and overall energy partitioning. The correlation-detection tool shows promise for real-time implementation, with the potential to greatly reduce analyst workload and augment on-the-fly characterizations already provided by such routine monitoring tools as RSAM and SSAM.

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

    Directory of Open Access Journals (Sweden)

    Shuoyang Chen

    2016-10-01

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

  1. Multidimensional slit-scan detection of bladder cancer. Preliminary clinical results.

    Science.gov (United States)

    Wheeless, L L; Berkan, T K; Patten, S F; Reeder, J E; Robinson, R D; Eldidi, M M; Hulbert, W C; Frank, I N

    1986-03-01

    A multidimensional slit-scan flow system was developed for the automated recognition of abnormal cells derived from cancer of the uterine cervix and its precursors. It provides great sensitivity in both its ability to recognize cellular abnormality and to deal with the myriad potential causes of false alarms in an automated flow system. While its initial application was the automated recognition of the spectrum of neoplasia in gynecologic cytology samples, a preliminary study was carried out using specimens obtained from the urinary bladder. Cellular material was collected by bladder irrigation and stained with the fluorochrome acridine orange. One hundred fifty-three bladder irrigation specimens, including 115 abnormal specimens containing cells derived from neoplastic lesions of the bladder epithelium, were analyzed. For the purposes of this study, abnormal specimens from the urinary bladder included specimens containing cells derived from the following lesions of the urothelium: dysplasia (atypical hyperplasia), carcinoma-in-situ, and transitional cell carcinoma, grades 1-3. Approximately 50,000 cells were analyzed for most specimens. Of the 38 presumed normal specimens (specimens containing only normal urothelial components), four were instrument classified abnormal. For the 69 specimens containing cells derived from transitional cell carcinoma, grade 1, 1-2, 2, 66 were correctly classified as abnormal while three were classified as normal.(ABSTRACT TRUNCATED AT 250 WORDS)

  2. Magnetic Resonance Angiography and Doppler Scanning for Detecting Atherosclerotic Renal Artery Stenosis

    Directory of Open Access Journals (Sweden)

    Yee-Yung Ng

    2010-06-01

    Conclusion: RDS might still be the diagnostic procedure of choice for screening outpatients for ARAS because it is inexpensive, convenient, able to detect severity, and avoids the use of contrast media. When RDS is negative in aged people who have smoked longer than 20 years, with coronary artery disease or serum creatinine > 4 mg/dL, MRA is recommended for further evaluation of ARAS.

  3. Replicate PCR Testing and Probit Analysis for Detection and Quantitation of Chlamydia pneumoniae in Clinical Specimens

    Science.gov (United States)

    Smieja, M.; Mahony, J. B.; Goldsmith, C. H.; Chong, S.; Petrich, A.; Chernesky, M.

    2001-01-01

    Nucleic acid amplification of clinical specimens with low target concentration has variable sensitivity. We examined whether testing multiple aliquots of extracted DNA increased the sensitivity and reproducibility of Chlamydia pneumoniae detection by PCR. Nested and non-nested C. pneumoniae PCR assays were compared using 10 replicates of 16 serial dilutions of C. pneumoniae ATCC VR-1310. The proportion positive versus the C. pneumoniae concentration was modeled by probit regression analysis. To validate the model, 10 replicates of 26 previously positive patient specimens of peripheral blood mononuclear cells (PBMC), sputum, or nasopharyngeal swabs (NPS) were tested. The proportion of replicates that were positive varied with the concentration of C. pneumoniae in the sample. At concentrations above 5 infection-forming units (IFU)/ml, both nested and non-nested PCR assay sensitivities were 90% or greater. The nested PCR was more sensitive (median detection, 0.35 versus 0.61 IFU/ml; relative median detection, 0.58; 95% confidence interval, 0.31 to 0.99; P = 0.04). In clinical specimens, replicate PCR detected 15 of 26 (nested) versus 1 of 26 (non-nested, P < 0.001). For PBMC specimens, testing 1, 3, or 5 replicates detected 3, 5, or 9 of 10 positive specimens, respectively. Median C. pneumoniae concentrations were estimated at 0.07 IFU/ml for PBMC and at <0.03 IFU/ml for NPS specimens. We conclude that performing 5 or 10 replicates considerably increased the sensitivity and reproducibility of C. pneumoniae PCR and enabled quantitation for clinical specimens. Due to sampling variability, PCR tests done without replication may miss a large proportion of positive specimens, particularly for specimens with small amounts of target C. pneumoniae DNA present. PMID:11325993

  4. Quantitative detection of four pome fruit viruses in apple trees throughout the year

    Directory of Open Access Journals (Sweden)

    Lucie WINKOWSKA

    2016-07-01

    Full Text Available A one-step real-time RT-PCR assay (RT-qPCR with melting curve analysis, using the green fluorescence dye SYBR Green I, was developed to detect and quantify RNA targets from Apple mosaic virus (ApMV, Apple stem grooving virus (ASGV, Apple stem pitting virus (ASPV and Apple chlorotic leaf spot virus (ACLSV in infected apple trees. Single PCR products of 87 bp (ApMV, 70 bp (ASGV, 104 bp (ASPV and 148 bp (ACLSV were obtained, and melting curve analyses revealed distinct melting temperature peaks for each virus. A dilution series using in vitro synthesized transcripts containing the target sequences as standards yielded a reproducible quantitative assay, with a wide dynamic range of detection and low coefficients of variance. The content of selected viruses in apple plant tissues was stable throughout the year, and their accumulation did not significantly change between different plant tissues. The only minor exceptions were for ApMV and ACLSV, in which noticeable differences in their concentrations in various biological material were observed within the year. This divergence did not influence their year-round detectability. This one-step RT-qPCR assay is a valuable tool for year-round diagnostics, and molecular studies of the biology of ApMV, ASGV, ASPV and ACLSV.

  5. Tools for the quantitative analysis of sedimentation boundaries detected by fluorescence optical analytical ultracentrifugation.

    Directory of Open Access Journals (Sweden)

    Huaying Zhao

    Full Text Available 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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

  8. Multiplex, Quantitative, Reverse Transcription PCR Detection of Influenza Viruses Using Droplet Microfluidic Technology

    Directory of Open Access Journals (Sweden)

    Ravi Prakash

    2014-12-01

    Full Text Available Quantitative, reverse transcription, polymerase chain reaction (qRT-PCR is facilitated by leveraging droplet microfluidic (DMF system, which due to its precision dispensing and sample handling capabilities at microliter and lower volumes has emerged as a popular method for miniaturization of the PCR platform. This work substantially improves and extends the functional capabilities of our previously demonstrated single qRT-PCR micro-chip, which utilized a combination of electrostatic and electrowetting droplet actuation. In the reported work we illustrate a spatially multiplexed micro-device that is capable of conducting up to eight parallel, real-time PCR reactions per usage, with adjustable control on the PCR thermal cycling parameters (both process time and temperature set-points. This micro-device has been utilized to detect and quantify the presence of two clinically relevant respiratory viruses, Influenza A and Influenza B, in human samples (nasopharyngeal swabs, throat swabs. The device performed accurate detection and quantification of the two respiratory viruses, over several orders of RNA copy counts, in unknown (blind panels of extracted patient samples with acceptably high PCR efficiency (>94%. The multi-stage qRT-PCR assays on eight panel patient samples were accomplished within 35–40 min, with a detection limit for the target Influenza virus RNAs estimated to be less than 10 RNA copies per reaction.

  9. [Detection of enteric pathogenic bacteria from surface waters by quantitative polymerase chain reaction (QPCR)].

    Science.gov (United States)

    Liu, Yong-Jun; Zhang, Chong-Miao; Wang, Xiao-Chang; Lü, Ying-Jun; Zuo, Li-Li

    2008-05-01

    A rapid quantitative polymerase chain reaction (QPCR) analysis method with universal primers was developed to detect cell densities of the enteric pathogenic bacteria from 5 surface water of Xi'an City for 4 months continuously. And the detection results by QPCR method were compared with counts of coliforms colony-forming units (CFU) determined by membrane filter (MF) analysis. The results showed that QPCR method had an estimated 94% confidence, and detection limit was 2.7 Escherichia coli cells per sample in undiluted DNA extracts. For five surface waters (N = 60), the geometric mean of pathogenic bacteria concentration determined by QPCR was 2.2-5 times of corresponding coliform CFU determined by MF analysis. Using QPCR analysis, these geometric means of pathogenic bacteria concentration ranged from 25 CCE/100 mL to 67 000 CCE/100 mL. Using MF culture analysis, coliforms ranged from 3 CFU/100 mL to 45 000 CFU/100 mL. Regression analysis showed that there was a significant positive correlation between pathogenic bacteria determined by QPCR method and coliforms determined by MF method, the correlation coefficient (r) was 0.983.

  10. Reconstruction of the Magnetkoepfl rockfall event - Detecting rock fall release zones using terrestrial laser scanning, Hohe Tauern, Austria

    Science.gov (United States)

    Hartmeyer, I.; Keuschnig, M.; Delleske, R.; Schrott, L.

    2012-04-01

    Instability of rock faces in high mountain areas is an important risk factor for man and infrastructure, particularly within the context of climate change. Numerous rock fall events in the European Alps suggest an increasing occurrence of mass movements due to rising temperatures in recent years. Within the MOREXPERT project ('Monitoring Expert System for Hazardous Rock Walls') a new long-term monitoring site for mass movement and permafrost interaction has been initiated in the Austrian Alps. The study area is located at the Kitzsteinhorn (Hohe Tauern), a particularly interesting site for the investigation of glacier retreat and potential permafrost degradation and their respective consequences for the stability of alpine rock faces. To detect and quantify changes occurring at the terrain surface an extensive terrestrial laser scanning (TLS) monitoring campaign was started in 2011. TLS creates three-dimensional high-resolution images of the scanned area allowing precise quantification of changes in geometry and volume in steep rock faces over distances of up to several hundreds of meters. Within the TLS monitoring campaign at the Kitzsteinhorn a large number of differently dimensioned rock faces is examined (varying size, slope inclination etc.). Scanned areas include the Kitzsteinhorn northwest and south face, the Magnetkoepfl east face as well as a couple of small rock faces in the vicinity of the summit station. During the night from August 27th to August 28th 2011 a rock fall event was documented by employees of the cable car company. The release zone could not immediately be detected. The east face of the Magnetkoepfl covers approximately 70 meters in height and about 200 meters in width. It is made up of calcareous mica-schist and displays an abundance of well-developed joint sets with large joint apertures. Meteorological data from a weather station located at the same altitude (2.950m) and just 500m away from the release zone show that the rock fall event

  11. Quantitative detection of the free-living amoeba Hartmannella vermiformis in surface water by using real-time PCR

    NARCIS (Netherlands)

    Kuiper, M.W.; Valster, R.M.; Wullings, B.A.; Boonstra, H.; Smidt, H.; Kooij, van der D.

    2006-01-01

    A real-time PCR-based method targeting the 18S rRNA gene was developed for the quantitative detection of Hartmannella vermiformis, a free-living amoeba which is a potential host for Legionella pneumophila in warm water systems and cooling towers. The detection specificity was validated using genomic

  12. Molecular diagnosis of urinary tract infections by semi-quantitative detection of uropathogens in a routine clinical hospital setting

    NARCIS (Netherlands)

    A. van der Zee (Anneke); L.D. Roorda (Lieuwe); G. Bosman (Gerda); J.M. Ossewaarde (Jacobus)

    2016-01-01

    textabstractBackground The objective of our study was the development of a semi-quantitative real-time PCR to detect uropathogens. Two multiplex PCR reactions were designed to detect Escherichia coli, Klebsiella spp., Enterobacter spp., Citrobacter spp., Proteus mirabilis, Enterococcus faecalis, and

  13. Comparative genome scan detects host-related divergent selection in the grasshopper Hesperotettix viridis.

    Science.gov (United States)

    Apple, Jennifer L; Grace, Tony; Joern, Anthony; St Amand, Paul; Wisely, Samantha M

    2010-09-01

    In this study, we used a comparative genome scan to examine patterns of population differentiation with respect to host plant use in Hesperotettix viridis, a Nearctic oligophagous grasshopper locally specialized on various Asteraceae including Solidago, Gutierrezia, and Ericameria. We identified amplified fragment length polymorphism (AFLP) loci with significantly elevated F(ST) (outlier loci) in multiple different-host and same-host comparisons of populations while controlling for geographic distance. By comparing the number and identities of outlier loci in different-host vs. same-host comparisons, we found evidence of host plant-related divergent selection for some population comparisons (Solidago- vs. Gutierrezia-feeders), while other comparisons (Ericameria- vs. Gutierrezia-feeders) failed to demonstrate a strong role for host association in population differentiation. In comparisons of Solidago- vs. Gutierrezia-feeding populations, a relatively high number of outlier loci observed repeatedly in different-host comparisons (35% of all outliers and 2.7% of all 625 AFLP loci) indicated a significant role for host-related selection in contributing to overall genomic differentiation in this grasshopper. Mitochondrial DNA sequence data revealed a star-shaped phylogeny with no host- or geography-related structure, low nucleotide diversity, and high haplotype diversity, suggesting a recent population expansion. mtDNA data do not suggest a long period of isolation in separate glacial refugia but are instead more compatible with a single glacial refugium and more recent divergence in host use. Our study adds to research documenting heterogeneity in differentiation across the genome as a consequence of divergent natural selection, a phenomenon that may occur as part of the process of ecological speciation. © 2010 Blackwell Publishing Ltd.

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

    Science.gov (United States)

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

    2014-03-01

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

  15. Incidental musculoskeletal lesions detected on abdomnopelvic CT scans: A pictorial essay

    Energy Technology Data Exchange (ETDEWEB)

    Song, Eun Jee; Ryu, Kyung Nam; Park, Ji Seon [Dept. of Radiology, Kyung Hee University Hospital, Seoul (Korea, Republic of); Jin, Wook; Park, So Young [Dept. of Radiology, Kyung Hee University Hospital at Gangdong Hospital, Seoul (Korea, Republic of)

    2015-02-15

    Various musculoskeletal findings incidentally detected on abdominopelvic computed tomography (CT) images have risen with the increasing use of abdominopelvic CT; however, it is not uncommon for radiologists to overlook the musculoskeletal system when they examine abdominopelvic CT images. Some musculoskeletal lesions may have more clinical significance than abdominopelvic lesions, although most lesions are of little to no significance. Many osseous lesions can be diagnosed using the bone window setting and reconstructed images. The purpose of this article was to review the wide variety of musculoskeletal lesions depicted on abdominopelvic CT images and to emphasize the use of the bone window setting.

  16. Automated lesion detection on MRI scans using combined unsupervised and supervised methods.

    Science.gov (United States)

    Guo, Dazhou; Fridriksson, Julius; Fillmore, Paul; Rorden, Christopher; Yu, Hongkai; Zheng, Kang; Wang, Song

    2015-10-30

    Accurate and precise detection of brain lesions on MR images (MRI) is paramount for accurately relating lesion location to impaired behavior. In this paper, we present a novel method to automatically detect brain lesions from a T1-weighted 3D MRI. The proposed method combines the advantages of both unsupervised and supervised methods. First, unsupervised methods perform a unified segmentation normalization to warp images from the native space into a standard space and to generate probability maps for different tissue types, e.g., gray matter, white matter and fluid. This allows us to construct an initial lesion probability map by comparing the normalized MRI to healthy control subjects. Then, we perform non-rigid and reversible atlas-based registration to refine the probability maps of gray matter, white matter, external CSF, ventricle, and lesions. These probability maps are combined with the normalized MRI to construct three types of features, with which we use supervised methods to train three support vector machine (SVM) classifiers for a combined classifier. Finally, the combined classifier is used to accomplish lesion detection. We tested this method using T1-weighted MRIs from 60 in-house stroke patients. Using leave-one-out cross validation, the proposed method can achieve an average Dice coefficient of 73.1% when compared to lesion maps hand-delineated by trained neurologists. Furthermore, we tested the proposed method on the T1-weighted MRIs in the MICCAI BRATS 2012 dataset. The proposed method can achieve an average Dice coefficient of 66.5% in comparison to the expert annotated tumor maps provided in MICCAI BRATS 2012 dataset. In addition, on these two test datasets, the proposed method shows competitive performance to three state-of-the-art methods, including Stamatakis et al., Seghier et al., and Sanjuan et al. In this paper, we introduced a novel automated procedure for lesion detection from T1-weighted MRIs by combining both an unsupervised and a

  17. The power to detect genetic linkage for quantitative traits in the Utah CEPH pedigrees.

    Science.gov (United States)

    Malhotra, Alka; Cromer, Kevin; Leppert, Mark F; Hasstedt, Sandra J

    2005-01-01

    Quantitative trait phenotypes and linked marker genotypes were simulated for a range of models with different sets of assumptions based on displacement, prevalence, and heritability of the trait in 30 Utah Centre d'Etude du Polymorphisme Humain (CEPH) families. The gain in power by the addition of 15 families was also estimated by extrapolation. Power was evaluated using both parametric single locus (PSL) models and variance components (VC) methods for two situations: (1) a single marker with 75% heterozygosity and a recombination fraction of 0.05, and (2) a fully informative marker as an approximation to multipoint analysis. When the simulation and analysis models were both dominant with the same prevalence, power > or =80% for lod >3 was estimated when quantitative trait locus variance was > or =40% with a displacement of 2.5 or 3. Power was 5-15% lower for recessive models compared to dominant models. With the addition of 15 families, an average increase in power of 17% and 22% was estimated for the dominant and recessive models, respectively. In PSL analyses, power was estimated at < or =20% when the dominance was misspecified. This investigation delineates parameter conditions under which this unique sample affords adequate power to detect linkage using both PSL and VC methods.

  18. Detection of quasi-periodic processes in complex systems: how do we quantitatively describe their properties?

    Science.gov (United States)

    Nigmatullin, Raoul R.; Khamzin, Airat A.; Tenreiro Machado, J.

    2014-01-01

    It has been shown that in reality at least two general scenarios of data structuring are possible: (a) a self-similar (SS) scenario when the measured data form an SS structure and (b) a quasi-periodic (QP) scenario when the repeated (strongly correlated) data form random sequences that are almost periodic with respect to each other. In the second case it becomes possible to describe their behavior and express a part of their randomness quantitatively in terms of the deterministic amplitude-frequency response belonging to the generalized Prony spectrum. This possibility allows us to re-examine the conventional concept of measurements and opens a new way for the description of a wide set of different data. In particular, it concerns different complex systems when the ‘best-fit’ model pretending to be the description of the data measured is absent but the barest necessity of description of these data in terms of the reduced number of quantitative parameters exists. The possibilities of the proposed approach and detection algorithm of the QP processes were demonstrated on actual data: spectroscopic data recorded for pure water and acoustic data for a test hole. The suggested methodology allows revising the accepted classification of different incommensurable and self-affine spatial structures and finding accurate interpretation of the generalized Prony spectroscopy that includes the Fourier spectroscopy as a partial case.

  19. Quantitative analysis of ginger components in commercial products using liquid chromatography with electrochemical array detection

    Science.gov (United States)

    Shao, Xi; Lv, Lishuang; Parks, Tiffany; Wu, Hou; Ho, Chi-Tang; Sang, Shengmin

    2010-01-01

    For the first time, a sensitive reversed-phase HPLC electrochemical array method has been developed for the quantitative analysis of eight major ginger components ([6]-, [8]-, and [10]-gingerol, [6]-, [8]-, and [10]-shogaol, [6]-paradol, and [1]-dehydrogingerdione) in eleven ginger-containing commercial products. This method was valid with unrivaled sensitivity as low as 7.3 – 20.2 pg of limit of detection and a range of 14.5 to 40.4 pg of limit of quantification. Using this method, we quantified the levels of eight ginger components in eleven different commercial products. Our results found that both levels and ratios among the eight compounds vary greatly in commercial products. PMID:21090746

  20. Monoclonal antibodies for the detection and quantitation of the endogenous plant growth regulator, abscisic acid

    Energy Technology Data Exchange (ETDEWEB)

    Mertens, R.; Weiler, E.W. (Bochum Univ. (Germany, F.R.). Lehrstuhl fuer Pflanzenphysiologie); Deus-Neumann, B. (Muenchen Univ. (Germany, F.R.). Inst. fuer pharmazeutische Biologie)

    1983-08-22

    Monoclonal antibodies (mAB) have been produced which recognize the physiologically active 2-cis-(S)-form of the endogenous plant growth regulator, abscisic acid (ABA). Cross-reaction with the ABA-catabolites, phaseic and dihydrophaseic acid, is negligible, and (R)-ABA, 2-trans-ABA, the ABA-conjugate, ABA-..beta..-D-glucopyranosyl ester, as well as the putative ABA precursor, xanthoxin, are totally unreactive. In addition to being very specific, the mAB exhibit high affinities for 2-cis-(S)-ABA; the K values were 7.9 x 10/sup 9/ l/mol and 3.7 x 10/sup 9/ l/mol for antibodies from two different clones. By mAB-radioimmunoassay (RIA), 4 pg of 2-cis-(S)-ABA (99.5% confidence level) can be detected. mAB-RIA can be used to quantitate ABA directly in unprocessed plant extracts.

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

    Directory of Open Access Journals (Sweden)

    Derek Craig

    Full Text Available 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.

  2. Two-dimensional radial laser scanning for circular marker detection and external mobile robot tracking.

    Science.gov (United States)

    Teixidó, Mercè; Pallejà, Tomàs; Font, Davinia; Tresanchez, Marcel; Moreno, Javier; Palacín, Jordi

    2012-11-28

    This paper presents the use of an external fixed two-dimensional laser scanner to detect cylindrical targets attached to moving devices, such as a mobile robot. This proposal is based on the detection of circular markers in the raw data provided by the laser scanner by applying an algorithm for outlier avoidance and a least-squares circular fitting. Some experiments have been developed to empirically validate the proposal with different cylindrical targets in order to estimate the location and tracking errors achieved, which are generally less than 20 mm in the area covered by the laser sensor. As a result of the validation experiments, several error maps have been obtained in order to give an estimate of the uncertainty of any location computed. This proposal has been validated with a medium-sized mobile robot with an attached cylindrical target (diameter 200 mm). The trajectory of the mobile robot was estimated with an average location error of less than 15 mm, and the real location error in each individual circular fitting was similar to the error estimated with the obtained error maps. The radial area covered in this validation experiment was up to 10 m, a value that depends on the radius of the cylindrical target and the radial density of the distance range points provided by the laser scanner but this area can be increased by combining the information of additional external laser scanners.

  3. Online platform for applying space–time scan statistics for prospectively detecting emerging hot spots of dengue fever

    Directory of Open Access Journals (Sweden)

    Chien-Chou Chen

    2016-11-01

    Full Text Available Abstract Background Cases of dengue fever have increased in areas of Southeast Asia in recent years. Taiwan hit a record-high 42,856 cases in 2015, with the majority in southern Tainan and Kaohsiung Cities. Leveraging spatial statistics and geo-visualization techniques, we aim to design an online analytical tool for local public health workers to prospectively identify ongoing hot spots of dengue fever weekly at the village level. Methods A total of 57,516 confirmed cases of dengue fever in 2014 and 2015 were obtained from the Taiwan Centers for Disease Control (TCDC. Incorporating demographic information as covariates with cumulative cases (365 days in a discrete Poisson model, we iteratively applied space–time scan statistics by SaTScan software to detect the currently active cluster of dengue fever (reported as relative risk in each village of Tainan and Kaohsiung every week. A village with a relative risk >1 and p value <0.05 was identified as a dengue-epidemic area. Assuming an ongoing transmission might continuously spread for two consecutive weeks, we estimated the sensitivity and specificity for detecting outbreaks by comparing the scan-based classification (dengue-epidemic vs. dengue-free village with the true cumulative case numbers from the TCDC’s surveillance statistics. Results Among the 1648 villages in Tainan and Kaohsiung, the overall sensitivity for detecting outbreaks increases as case numbers grow in a total of 92 weekly simulations. The specificity for detecting outbreaks behaves inversely, compared to the sensitivity. On average, the mean sensitivity and specificity of 2-week hot spot detection were 0.615 and 0.891 respectively (p value <0.001 for the covariate adjustment model, as the maximum spatial and temporal windows were specified as 50% of the total population at risk and 28 days. Dengue-epidemic villages were visualized and explored in an interactive map. Conclusions We designed an online analytical tool for

  4. Burden of subclinical heart and lung disease detected on thoracic CT scans of HIV patients on HAART

    Directory of Open Access Journals (Sweden)

    Stefano Zona

    2014-11-01

    -infected individuals even in non-smokers. Reduced CD4 count (hence severity of HIV infection may be an important risk factor for chronic lung and heart disease. Thoracic CT scans may provide an excellent screening tool to detect MLHD in HIV-infected patients.

  5. Quantitative evaluation of peripheral tissue elasticity for ultrasound-detected breast lesions.

    Science.gov (United States)

    Xiao, Y; Yu, Y; Niu, L; Qian, M; Deng, Z; Qiu, W; Zheng, H

    2016-09-01

    To evaluate the diagnostic performance of the quantitative measurement of peripheral tissue elasticity using shear-wave elastography (SWE) in differentiating between benign and malignant breast lesions detected by ultrasonography (US). This study was approved by institutional review board; informed consent was signed from all patients. From June 2012 to April 2014, conventional B-mode US and SWE were performed in 205 breast lesions (78 malignant, 127 benign) of 205 consecutive women (mean age, 41.9±12.3 years; age range, 18-76 years). For each lesion, a rim around its contour was constructed by using a computer-aided tool, including adequate adjacent peripheral tissue. Quantitative elastographic features of the rim (elasticity mean, maximum, standard deviation, and elasticity ratio) as well as Breast Imaging Reporting and Data System (BI-RADS) categories were assessed according to the final histopathological results. Sensitivity, specificity, positive and negative predictive values, and receiver operating characteristic (ROC) curve analysis were performed to evaluate the diagnostic performances for the three data sets (conventional B-mode US alone, SWE features alone, and combined B-mode US and SWE features). SWE features of the peripheral tissue differed significantly between benign and malignant breast lesions (mean±standard deviation [SD]: elasticity mean, 16.1±6.6 versus 43.6±17.8; maximum, 55.4±31.4 versus 150.3±44.6; SD, 8.1±4.1 versus 30±13.8 and elasticity ratio, 1.1±0.2 versus 2±0.7, respectively, all pelastic properties of the peripheral tissue exhibited good discriminatory ability in differentiating US-detected breast lesions and could be used to further stratify low-suspicion lesions within BI-RADS category 3 and 4a to avoid unnecessary biopsy. Copyright © 2016 The Royal College of Radiologists. Published by Elsevier Ltd. All rights reserved.

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

    Science.gov (United States)

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

    2014-10-01

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

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

    Directory of Open Access Journals (Sweden)

    Bassett Anne S

    2005-12-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Sondrup, A. Jeffrey [Idaho National Lab. (INL), Idaho Falls, ID (United States); Rood, Arthur S. [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    2014-11-01

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

  9. Scanning seismic intrusion detection method and apparatus. [monitoring unwanted subterranean entry and departure

    Science.gov (United States)

    Lee, R. D. (Inventor)

    1983-01-01

    An intrusion monitoring system includes an array of seismic sensors, such as geophones, arranged along a perimeter to be monitored for unauthorized intrusion as by surface movement or tunneling. Two wires lead from each sensor to a central monitoring station. The central monitoring station has three modes of operation. In a first mode of operation, the output of all of the seismic sensors is summed into a receiver for amplification and detection. When the amplitude of the summed signals exceeds a certain predetermined threshold value an alarm is sounded. In a second mode of operation, the individual output signals from the sensors are multiplexed into the receiver for sequentially interrogating each of the sensors.

  10. Multitarget Quantitative PCR Improves Detection and Predicts Cultivability of the Pathogen Burkholderia pseudomallei.

    Science.gov (United States)

    Göhler, Andre; Trung, Trinh Thanh; Hopf, Verena; Kohler, Christian; Hartleib, Jörg; Wuthiekanun, Vanaporn; Peacock, Sharon J; Limmathurotsakul, Direk; Tuanyok, Apichai; Steinmetz, Ivo

    2017-04-15

    Burkholderia pseudomallei is present in the environment in many parts of the world and causes the often-fatal disease melioidosis. The sensitive detection and quantification of B. pseudomallei in the environment are a prerequisite for assessing the risk of infection. We recently reported the direct detection of B. pseudomallei in soil samples using a quantitative PCR (qPCR) targeting a single type three secretion system 1 (TTSS1) gene. Here, we extend the qPCR-based analysis of B. pseudomallei in soil by validating novel qPCR gene targets selected from a comparative genomic analysis. Two hundred soil samples from two rice paddies in northeast Thailand were evaluated, of which 47% (94/200) were B. pseudomallei culture positive. The TTSS1 qPCR and two novel qPCR assays that targeted open reading frames (ORFs) BPSS0087 and BPSS0745 exhibited detection rates of 76.5% (153/200), 34.5% (69/200), and 74.5% (150/200), respectively. The combination of TTSS1 and BPSS0745 qPCR increased the detection rate to 90% (180/200). Combining the results of the three qPCR assays and the BPSS1187 nested PCR previously published, all 200 samples were positive by at least one PCR assay. Samples positive by either TTSS1 (n = 153) or BPSS0745 (n = 150) qPCR were more likely to be direct-culture positive, with odds ratios of 4.0 (95% confidence interval [CI], 1.7 to 9.5; P rate in soil samples and predicted culture positivity. This approach has the potential for use as a sensitive environmental screening method for B. pseudomalleiIMPORTANCE The worldwide environmental distribution of the soil bacterium Burkholderia pseudomallei remains to be determined. So far, most environmental studies have relied on culture-based approaches to detect this pathogen. Since current culture methods are laborious, are time consuming, and have limited sensitivity, culture-independent and more sensitive methods are needed. In this study, we show that a B. pseudomallei-specific qPCR approach can detect

  11. Detection of CO2•- in the Electrochemical Reduction of Carbon Dioxide in N,N-Dimethylformamide by Scanning Electrochemical Microscopy.

    Science.gov (United States)

    Kai, Tianhan; Zhou, Min; Duan, Zhiyao; Henkelman, Graeme A; Bard, Allen J

    2017-12-27

    The electrocatalytic reduction of CO2 has been studied extensively and produces a number of products. The initial reaction in the CO2 reduction is often taken to be the 1e formation of the radical anion, CO2•-. However, the electrochemical detection and characterization of CO2•- is challenging because of the short lifetime of CO2•-, which can dimerize and react with proton donors and even mild oxidants. Here, we report the generation and quantitative determination of CO2•- in N,N-dimethylformamide (DMF) with the tip generation/substrate collection (TG/SC) mode of scanning electrochemical microscopy (SECM). CO2 was reduced at a hemisphere-shaped Hg/Pt ultramicroelectrode (UME) or a Hg/Au film UME, which were utilized as the SECM tips. The CO2•- produced can either dimerize to form oxalate within the nanogap between SECM tip and substrate or collected at SECM substrate (e.g., an Au UME). The collection efficiency (CE) for CO2•- depends on the distance (d) between the tip and substrate. The dimerization rate (6.0 × 108 M-1 s-1) and half-life (10 ns) of CO2•- can be evaluated by fitting the collection efficiency vs distance curve. The dimerized species of CO2•-, oxalate, can also be determined quantitatively. Furthermore, the formal potential (E0') and heterogeneous rate constant (k0) for CO2 reduction were determined with different quaternary ammonium electrolytes. The significant difference in k0 is due to a tunneling effect caused by the adsorption of the electrolytes on the electrode surface at negative potentials.

  12. Development and application of a quantitative loop-mediated isothermal amplification method for detecting genetically modified maize MON863.

    Science.gov (United States)

    Huang, Sicong; Xu, Yuancong; Yan, Xinghua; Shang, Ying; Zhu, Pengyu; Tian, Wenying; Xu, Wentao

    2015-01-01

    A SYBR Green I-based quantitative loop-mediated isothermal amplification (LAMP) assay was developed for the rapid detection of genetically modified maize MON863. A set of primers was designed based on the integration region of the Cry3Bb1 and tahsp17 genes. The qualitative and quantitative reaction conditions (dNTPs, betaine, primers, Mg(2+), Bst polymerase, temperature, reaction time) were optimized. The concentrations of Mg(2+) and betaine were found to be important to the LAMP assay. The detection limits of both qualitative and quantitative LAMP for MON863 were as low as 4 haploid genomic DNA, and the LAMP reactions can be completed within 1 h at an isothermal temperature of 65 °C. The results of this study demonstrate that this new SYBR Green I-based quantitative LAMP assay system is reliable, sensitive and accurate. © 2014 Society of Chemical Industry.

  13. AN ENERGY-BASED APPROACH FOR DETECTION AND CHARACTERIZATION OF SUBTLE ENTITIES WITHIN LASER SCANNING POINT-CLOUDS

    Directory of Open Access Journals (Sweden)

    R. Arav

    2016-06-01

    Full Text Available Airborne laser scans present an optimal tool to describe geomorphological features in natural environments. However, a challenge arises in the detection of such phenomena, as they are embedded in the topography, tend to blend into their surroundings and leave only a subtle signature within the data. Most object-recognition studies address mainly urban environments and follow a general pipeline where the data are partitioned into segments with uniform properties. These approaches are restricted to man-made domain and are capable to handle limited features that answer a well-defined geometric form. As natural environments present a more complex set of features, the common interpretation of the data is still manual at large. In this paper, we propose a data-aware detection scheme, unbound to specific domains or shapes. We define the recognition question as an energy optimization problem, solved by variational means. Our approach, based on the level-set method, characterizes geometrically local surfaces within the data, and uses these characteristics as potential field for minimization. The main advantage here is that it allows topological changes of the evolving curves, such as merging and breaking. We demonstrate the proposed methodology on the detection of collapse sinkholes.

  14. A voting-based statistical cylinder detection framework applied to fallen tree mapping in terrestrial laser scanning point clouds

    Science.gov (United States)

    Polewski, Przemyslaw; Yao, Wei; Heurich, Marco; Krzystek, Peter; Stilla, Uwe

    2017-07-01

    This paper introduces a statistical framework for detecting cylindrical shapes in dense point clouds. We target the application of mapping fallen trees in datasets obtained through terrestrial laser scanning. This is a challenging task due to the presence of ground vegetation, standing trees, DTM artifacts, as well as the fragmentation of dead trees into non-collinear segments. Our method shares the concept of voting in parameter space with the generalized Hough transform, however two of its significant drawbacks are improved upon. First, the need to generate samples on the shape's surface is eliminated. Instead, pairs of nearby input points lying on the surface cast a vote for the cylinder's parameters based on the intrinsic geometric properties of cylindrical shapes. Second, no discretization of the parameter space is required: the voting is carried out in continuous space by means of constructing a kernel density estimator and obtaining its local maxima, using automatic, data-driven kernel bandwidth selection. Furthermore, we show how the detected cylindrical primitives can be efficiently merged to obtain object-level (entire tree) semantic information using graph-cut segmentation and a tailored dynamic algorithm for eliminating cylinder redundancy. Experiments were performed on 3 plots from the Bavarian Forest National Park, with ground truth obtained through visual inspection of the point clouds. It was found that relative to sample consensus (SAC) cylinder fitting, the proposed voting framework can improve the detection completeness by up to 10 percentage points while maintaining the correctness rate.

  15. A Colorimetric Sensor for Qualitative Discrimination and Quantitative Detection of Volatile Amines

    Directory of Open Access Journals (Sweden)

    Zhonglin Tang

    2010-06-01

    Full Text Available We have developed a novel colorimetric sensor based on a digital camera and white LED illumination. Colorimetric sensor arrays (CSAs were made from a set of six chemically responsive dyes impregnated on an inert substrate plate by solution casting. Six common amine aqueous solutions, including dimethylamine, triethylamine, diisopropyl-amine, aniline, cyclohexylamine, and pyridine vaporized at 25 °C and six health-related trimethylamine (TMA concentrations including 170 ppm, 51 ppm, 8 ppm, 2 ppm, 125 ppb and 50 ppb were analyzed by the sensor to test its ability for the qualitative discrimination and quantitative detection of volatile amines. We extracted the feature vectors of the CSA's response to the analytes from a fusional color space, which was obtained by conducting a joint search algorithm of sequential forward selection and sequential backward selection (SFS&SBS based on the linear discriminant criteria (LDC in a mixed color space composed of six common color spaces. The principle component analysis (PCA followed by the hierarchical cluser analysis (HCA were utilized to discriminate 12 analytes. Results showed that the colorimetric sensor grouped the six amine vapors and five TMA concentrations correctly, while TMA concentrations of 125 ppb and 50 ppb were indiscriminable from each other. The limitation of detection (LOD of the sensor for TMA was found to be lower than 50 ppb. The CSAs were reusable for TMA concentrations below 8 ppm.

  16. Development of real-time PCR for detection and quantitation of Streptococcus parauberis.

    Science.gov (United States)

    Nguyen, T L; Lim, Y J; Kim, D-H; Austin, B

    2016-01-01

    Streptococcus parauberis is an increasing threat to aquaculture of olive flounder, Paralichthys olivaceus Temminck & Schlegel, in South Korea. We developed a real-time polymerase chain reaction (PCR) method using the TaqMan probe assay to detect and quantify S. parauberis by targeting the gyrB gene sequences, which are effective for molecular analysis of the genus Streptococcus. Our real-time PCR assay is capable of detecting 10 fg of genomic DNA per reaction. The intra- and interassay coefficient of variation (CV) values ranged from 0.42-1.95%, demonstrating that the assay has good reproducibility. There was not any cross-reactivity to Streptococcus iniae or to other streptococcal/lactococcal fish pathogens, such as S. agalactiae and Lactococcus garvieae, indicating that the assay is highly specific to S. parauberis. The results of the real-time PCR assay corresponded well to those of conventional culture assays for S. parauberis from inoculated tissue homogenates (r = 0.957; P < 0.05). Hence, this sensitive and specific real-time PCR is a valuable tool for diagnostic quantitation of S. parauberis in clinical samples. © 2014 John Wiley & Sons Ltd.

  17. A lateral flow assay for quantitative detection of amplified HIV-1 RNA.

    Directory of Open Access Journals (Sweden)

    Brittany A Rohrman

    Full Text Available Although the accessibility of HIV treatment in developing nations has increased dramatically over the past decade, viral load testing to monitor the response of patients receiving therapy is often unavailable. Existing viral load technologies are often too expensive or resource-intensive for poor settings, and there is no appropriate HIV viral load test currently available at the point-of-care in low resource settings. Here, we present a lateral flow assay that employs gold nanoparticle probes and gold enhancement solution to detect amplified HIV RNA quantitatively. Preliminary results show that, when coupled with nucleic acid sequence based amplification (NASBA, this assay can detect concentrations of HIV RNA that match the clinically relevant range of viral loads found in HIV patients. The lateral flow test is inexpensive, simple and rapid to perform, and requires few resources. Our results suggest that the lateral flow assay may be integrated with amplification and sample preparation technologies to serve as an HIV viral load test for low-resource settings.

  18. A Lateral Flow Assay for Quantitative Detection of Amplified HIV-1 RNA

    Science.gov (United States)

    Rohrman, Brittany A.; Leautaud, Veronica; Molyneux, Elizabeth; Richards-Kortum, Rebecca R.

    2012-01-01

    Although the accessibility of HIV treatment in developing nations has increased dramatically over the past decade, viral load testing to monitor the response of patients receiving therapy is often unavailable. Existing viral load technologies are often too expensive or resource-intensive for poor settings, and there is no appropriate HIV viral load test currently available at the point-of-care in low resource settings. Here, we present a lateral flow assay that employs gold nanoparticle probes and gold enhancement solution to detect amplified HIV RNA quantitatively. Preliminary results show that, when coupled with nucleic acid sequence based amplification (NASBA), this assay can detect concentrations of HIV RNA that match the clinically relevant range of viral loads found in HIV patients. The lateral flow test is inexpensive, simple and rapid to perform, and requires few resources. Our results suggest that the lateral flow assay may be integrated with amplification and sample preparation technologies to serve as an HIV viral load test for low-resource settings. PMID:23029134

  19. Simultaneous detection of three fish rhabdoviruses using multiplex real-time quantitative RT-PCR assay.

    Science.gov (United States)

    Liu, Zongxiao; Teng, Yong; Liu, Hong; Jiang, Yulin; Xie, Xiayang; Li, Huifang; Lv, Jiangqiang; Gao, Longying; He, Junqiang; Shi, Xiujie; Tian, Feiyan; Yang, Jingshun; Xie, Congxin

    2008-04-01

    Spring viremia of carp virus (SVCV), infectious hematopoietic necrosis virus (IHNV) and viral hemorrhagic septicemia virus (VHSV) are three important fish rhabdoviruses, causing serious Office International des Epizooties (OIE) classified diseases in wild and farmed fish. Here, a new multiplex real-time quantitative RT-PCR (mqRT-PCR) assay was developed for simultaneous detection, identification and quantification of these three rhabdoviruses. The sets of primers and probes were targeted to conserved regions of glycoprotein (G) gene of SVCV, nucleoprotein (N) gene of IHNV and G gene of VHSV and used to amplify. The sensitivity, specificity and interference test of mqRT-PCR assay was analyzed. It was shown that the detection levels of 100 copies of SVCV, 220 copies of IHNV and 140 copies of VHSV were achieved, and there was no non-specific amplification and cross-reactivity using RNA of pike fry rhabdovirus (PFRV), infectious pancreatic necrosis virus (IPNV) and grass carp reovirus (GCRV). A total of 80 clinical fish samples were tested using the mqRT-PCR assay and the results were confirmed by antigen-capture ELISA and cell culture assay. This assay has the potential to be used for both research applications and diagnosis.

  20. Quantitative lateral flow strip assays as User-Friendly Tools To Detect Biomarker Profiles For Leprosy

    Science.gov (United States)

    van Hooij, Anouk; Tjon Kon Fat, Elisa M.; Richardus, Renate; van den Eeden, Susan J. F.; Wilson, Louis; de Dood, Claudia J.; Faber, Roel; Alam, Korshed; Richardus, Jan Hendrik; Corstjens, Paul L. A. M.; Geluk, Annemieke

    2016-01-01

    Leprosy is a debilitating, infectious disease caused by Mycobacterium leprae. Despite the availability of multidrug therapy, transmission is unremitting. Thus, early identification of M. leprae infection is essential to reduce transmission. The immune response to M. leprae is determined by host genetics, resulting in paucibacillary (PB) and multibacillary (MB) leprosy associated with dominant cellular or humoral immunity, respectively. This spectral pathology of leprosy compels detection of immunity to M. leprae to be based on multiple, diverse biomarkers. In this study we have applied quantitative user friendly lateral flow assays (LFAs) for four immune markers (anti-PGL-I antibodies, IL-10, CCL4 and IP-10) for whole blood samples from a longitudinal BCG vaccination field-trial in Bangladesh. Different biomarker profiles, in contrast to single markers, distinguished M. leprae infected from non-infected test groups, patients from household contacts (HHC) and endemic controls (EC), or MB from PB patients. The test protocol presented in this study merging detection of innate, adaptive cellular as well as humoral immunity, thus provides a convenient tool to measure specific biomarker profiles for M. leprae infection and leprosy utilizing a field-friendly technology. PMID:27682181

  1. Quantitative prediction of perceptual decisions during near-threshold fear detection

    Science.gov (United States)

    Pessoa, Luiz; Padmala, Srikanth

    2005-04-01

    A fundamental goal of cognitive neuroscience is to explain how mental decisions originate from basic neural mechanisms. The goal of the present study was to investigate the neural correlates of perceptual decisions in the context of emotional perception. To probe this question, we investigated how fluctuations in functional MRI (fMRI) signals were correlated with behavioral choice during a near-threshold fear detection task. fMRI signals predicted behavioral choice independently of stimulus properties and task accuracy in a network of brain regions linked to emotional processing: posterior cingulate cortex, medial prefrontal cortex, right inferior frontal gyrus, and left insula. We quantified the link between fMRI signals and behavioral choice in a whole-brain analysis by determining choice probabilities by means of signal-detection theory methods. Our results demonstrate that voxel-wise fMRI signals can reliably predict behavioral choice in a quantitative fashion (choice probabilities ranged from 0.63 to 0.78) at levels comparable to neuronal data. We suggest that the conscious decision that a fearful face has been seen is represented across a network of interconnected brain regions that prepare the organism to appropriately handle emotionally challenging stimuli and that regulate the associated emotional response. decision making | emotion | functional MRI

  2. Detection of Vertical Pole-Like Objects in a Road Environment Using Vehicle-Based Laser Scanning Data

    Directory of Open Access Journals (Sweden)

    Harri Kaartinen

    2010-02-01

    Full Text Available Accurate road environment information is needed in applications such as road maintenance and virtual 3D city modelling. Vehicle-based laser scanning (VLS can produce dense point clouds from large areas efficiently from which the road and its environment can be modelled in detail. Pole-like objects such as traffic signs, lamp posts and tree trunks are an important part of road environments. An automatic method was developed for the extraction of pole-like objects from VLS data. The method was able to find 77.7% of the poles which were found by a manual investigation of the data. Correctness of the detection was 81.0%.

  3. The experiment to detect equivalent optical path difference in independent double aperture interference light path based on step scanning method

    Science.gov (United States)

    Wang, Chaoyan; Chen, Xin-yang; Zheng, Lixin; Ding, Yuanyuan

    2014-11-01

    Fringe test is the method which can detect the relative optical path difference in optical synthetic aperture telescope array. To get to the interference fringes, the two beams of light in the meeting point must be within the coherence length. Step scanning method is within its coherence length, selecting a specific step, changing one-way's optical path of both by changing position of micro displacement actuator. At the same time, every fringe pattern can be recorded. The process of fringe patterns is from appearing to clear to disappearing. Firstly, a particular pixel is selected. Then, we keep tract of the intensity of every picture in the same position. From the intensity change, the best position of relative optical path difference can be made sure. The best position of relative optical path difference is also the position of the clearest fringe. The wavelength of the infrared source is 1290nm and the bandwidth is 63.6nm. In this experiment, the coherence length of infrared source is detected by cube reflection experiment. The coherence length is 30μm by data collection and data processing, and that result of 30μm is less different from the 26μm of theoretical calculated. In order to further test the relative optical path of optical synthetic aperture using step scanning method, the infrared source is placed into optical route of optical synthesis aperture telescope double aperture. The precision position of actuator can be obtained when the fringe is the clearest. By the experiment, we found that the actuating step affects the degree of precision of equivalent optical path. The smaller step size, the more accurate position. But the smaller the step length, means that more steps within the coherence length measurement and the longer time.

  4. Detection of quantitative trait loci for resistance/susceptibility to pseudorabies virus in swine.

    Science.gov (United States)

    Reiner, Gerald; Melchinger, Elke; Kramarova, Marcela; Pfaff, Eberhardt; Büttner, Matthias; Saalmüller, Armin; Geldermann, Hermann

    2002-01-01

    This study describes genetic differences in resistance/susceptibility to pseudorabies virus (PrV) between European Large White and Chinese Meishan pigs, with a mapping of quantitative trait loci (QTL) obtained from a genome-wide scan in F(2) animals. Eighty-nine F(2) pigs were challenged intranasally at 12 weeks with 10(5) p.f.u. of the wild-type PrV strain NIA-3. For QTL analysis, 85 microsatellite markers, evenly spaced on the 18 porcine autosomes and on the pseudoautosomal region of the X chromosome, were genotyped. All pigs developed clinical signs, i.e. fever, from 3 to 7 days p.i. The pure-bred Large White pigs, the F(1) and three-quarters of the F(2) animals, but none of the Meishan pigs, developed neurological symptoms and died or were euthanized. QTLs for appearance/non-appearance of neurological symptoms were found on chromosomes 9, 5, 6 and 13. They explained 10.6-17.9% of F(2) phenotypic variance. QTL effects for rectal temperature after PrV challenge were found on chromosomes 2, 4, 8, 10, 11 and 16. Effects on chromosomes 9, 10 and 11 were significant on a genome-wide level. The results present chromosomal regions that are associated with presence/absence of neurological symptoms as well as temperature course after intranasal challenge with NIA-3. The QTLs are in proximity to important candidate genes that are assumed to play crucial roles in host defence against PrV.

  5. Quantifying B Site Disorder in Polycrystalline and Single Crystal Yb2Ti2O7 Pyrochlore by Quantitative Scanning Transmission Electron Microscopy at Atomic Resolution

    Science.gov (United States)

    Shafieizadeh, Zahra; Xin, Yan; Zhou, Haidong

    The cubic pyrochlore oxides, A2B2O7, have attracted much attention over the past 20 years. A and B ions reside on two distinct interpenetrating lattices of corner-sharing tetrahedral. It has been noticed that the magnetic ground states of Yb2Ti2O7 are sample dependent. It could have long-range ordered collinear ferromagnetic state, or non-collinear ferromagnetic fluctuations, or short ranged fluctuations. In particular, the specific heat shows sharp peaks at 265 mK for polycrystalline samples, but a broad peak at 214 mK to 250 mK for optical floating zone (OFZ) single crystals. Neutron scattering study shows that OFZ single crystals are lightly stuffed pyrochlore with 2.3% Yb on to Ti sites. We have studied this disorder by quantitative scanning electron microscopy at atomic resolution for both polycrystals and single crystals. We have carried out atomic resolution imaging of Yb2Ti2O7 along [110] and by comparing image simulations, we have quantified the Yb atoms on the Ti atomic columns, and compared the disorders for both crystals. We also related the degree of the disorder to their magnetic ground states.

  6. Serial Quantitative PCR Assay for Detection, Species Discrimination, and Quantification of Leishmania spp. in Human Samples▿

    Science.gov (United States)

    Weirather, Jason L.; Jeronimo, Selma M. B.; Gautam, Shalini; Sundar, Shyam; Kang, Mitchell; Kurtz, Melissa A.; Haque, Rashidul; Schriefer, Albert; Talhari, Sinésio; Carvalho, Edgar M.; Donelson, John E.; Wilson, Mary E.

    2011-01-01

    The Leishmania species cause a variety of human disease syndromes. Methods for diagnosis and species differentiation are insensitive and many require invasive sampling. Although quantitative PCR (qPCR) methods are reported for leishmania detection, no systematic method to quantify parasites and determine the species in clinical specimens is established. We developed a serial qPCR strategy to identify and rapidly differentiate Leishmania species and quantify parasites in clinical or environmental specimens. SYBR green qPCR is mainly employed, with corresponding TaqMan assays for validation. The screening primers recognize kinetoplast minicircle DNA of all Leishmania species. Species identification employs further qPCR set(s) individualized for geographic regions, combining species-discriminating probes with melt curve analysis. The assay was sufficient to detect Leishmania parasites, make species determinations, and quantify Leishmania spp. in sera, cutaneous biopsy specimens, or cultured isolates from subjects from Bangladesh or Brazil with different forms of leishmaniasis. The multicopy kinetoplast DNA (kDNA) probes were the most sensitive and useful for quantification based on promastigote standard curves. To test their validity for quantification, kDNA copy numbers were compared between Leishmania species, isolates, and life stages using qPCR. Maxicircle and minicircle copy numbers differed up to 6-fold between Leishmania species, but the differences were smaller between strains of the same species. Amastigote and promastigote leishmania life stages retained similar numbers of kDNA maxi- or minicircles. Thus, serial qPCR is useful for leishmania detection and species determination and for absolute quantification when compared to a standard curve from the same Leishmania species. PMID:22042830

  7. Novel bioluminescent quantitative detection of nucleic acid amplification in real-time.

    Science.gov (United States)

    Gandelman, Olga A; Church, Vicki L; Moore, Cathy A; Kiddle, Guy; Carne, Christopher A; Parmar, Surendra; Jalal, Hamid; Tisi, Laurence C; Murray, James A H

    2010-11-30

    The real-time monitoring of polynucleotide amplification is at the core of most molecular assays. This conventionally relies on fluorescent detection of the amplicon produced, requiring complex and costly hardware, often restricting it to specialised laboratories. Here we report the first real-time, closed-tube luminescent reporter system for nucleic acid amplification technologies (NAATs) enabling the progress of amplification to be continuously monitored using simple light measuring equipment. The Bioluminescent Assay in Real-Time (BART) continuously reports through bioluminescent output the exponential increase of inorganic pyrophosphate (PPi) produced during the isothermal amplification of a specific nucleic acid target. BART relies on the coupled conversion of inorganic pyrophosphate (PPi) produced stoichiometrically during nucleic acid synthesis to ATP by the enzyme ATP sulfurylase, and can therefore be coupled to a wide range of isothermal NAATs. During nucleic acid amplification, enzymatic conversion of PPi released during DNA synthesis into ATP is continuously monitored through the bioluminescence generated by thermostable firefly luciferase. The assay shows a unique kinetic signature for nucleic acid amplifications with a readily identifiable light output peak, whose timing is proportional to the concentration of original target nucleic acid. This allows qualitative and quantitative analysis of specific targets, and readily differentiates between negative and positive samples. Since quantitation in BART is based on determination of time-to-peak rather than absolute intensity of light emission, complex or highly sensitive light detectors are not required. The combined chemistries of the BART reporter and amplification require only a constant temperature maintained by a heating block and are shown to be robust in the analysis of clinical samples. Since monitoring the BART reaction requires only a simple light detector, the iNAAT-BART combination is ideal

  8. Novel bioluminescent quantitative detection of nucleic acid amplification in real-time.

    Directory of Open Access Journals (Sweden)

    Olga A Gandelman

    Full Text Available BACKGROUND: The real-time monitoring of polynucleotide amplification is at the core of most molecular assays. This conventionally relies on fluorescent detection of the amplicon produced, requiring complex and costly hardware, often restricting it to specialised laboratories. PRINCIPAL FINDINGS: Here we report the first real-time, closed-tube luminescent reporter system for nucleic acid amplification technologies (NAATs enabling the progress of amplification to be continuously monitored using simple light measuring equipment. The Bioluminescent Assay in Real-Time (BART continuously reports through bioluminescent output the exponential increase of inorganic pyrophosphate (PPi produced during the isothermal amplification of a specific nucleic acid target. BART relies on the coupled conversion of inorganic pyrophosphate (PPi produced stoichiometrically during nucleic acid synthesis to ATP by the enzyme ATP sulfurylase, and can therefore be coupled to a wide range of isothermal NAATs. During nucleic acid amplification, enzymatic conversion of PPi released during DNA synthesis into ATP is continuously monitored through the bioluminescence generated by thermostable firefly luciferase. The assay shows a unique kinetic signature for nucleic acid amplifications with a readily identifiable light output peak, whose timing is proportional to the concentration of original target nucleic acid. This allows qualitative and quantitative analysis of specific targets, and readily differentiates between negative and positive samples. Since quantitation in BART is based on determination of time-to-peak rather than absolute intensity of light emission, complex or highly sensitive light detectors are not required. CONCLUSIONS: The combined chemistries of the BART reporter and amplification require only a constant temperature maintained by a heating block and are shown to be robust in the analysis of clinical samples. Since monitoring the BART reaction requires only a

  9. Lock-in thermography, penetrant inspection, and scanning electron microscopy for quantitative evaluation of open micro-cracks at the tooth-restoration interface

    Science.gov (United States)

    Streza, M.; Hodisan, I.; Prejmerean, C.; Boue, C.; Tessier, Gilles

    2015-03-01

    The evaluation of a dental restoration in a non-invasive way is of paramount importance in clinical practice. The aim of this study was to assess the minimum detectable open crack at the cavity-restorative material interface by the lock-in thermography technique, at laser intensities which are safe for living teeth. For the analysis of the interface, 18 box-type class V standardized cavities were prepared on the facial and oral surfaces of each tooth, with coronal margins in enamel and apical margins in dentine. The preparations were restored with the Giomer Beautifil (Shofu) in combination with three different adhesive systems. Three specimens were randomly selected from each experimental group and each slice has been analysed by visible, infrared (IR), and scanning electron microscopy (SEM). Lock-in thermography showed the most promising results in detecting both marginal and internal defects. The proposed procedure leads to a diagnosis of micro-leakages having openings of 1 µm, which is close to the diffraction limit of the IR camera. Clinical use of a thermographic camera in assessing the marginal integrity of a restoration becomes possible. The method overcomes some drawbacks of standard SEM or dye penetration testing. The results support the use of an IR camera in dentistry, for the diagnosis of micro-gaps at bio-interfaces.

  10. Enrichment followed by quantitative PCR both for rapid detection and as a tool for quantitative risk assessment of food-borne thermotolerant campylobacters

    DEFF Research Database (Denmark)

    Josefsen, Mathilde Hartmann; Jacobsen, N. R.; Hoorfar, Jeffrey

    2004-01-01

    As part of a large international project for standardization of PCR (Food-PCR; www.pcr.dk), a multiplex, multiplatform, ready-to-go enrichment followed by a real-time PCR method, including an internal amplification control, was developed for detection of food-borne thermotolerant campylobacters...... Organization (ISO)-based culture method by testing low, medium, and high levels of 12 spiked and 66 unspiked, presumably naturally contaminated, chicken rinse samples. In the RotorGene, a positive PCR response was detected in 40 samples of the 66. This was in complete agreement with the enriched ISO culture...... naturally contaminated chicken samples, which indicates PCR's additional potential as a tool for quantitative risk assessment. Signal from the internal amplification control was detected in all culture-negative samples (VIC Ct: 23.1 to 28.1). The method will be taken further and validated...

  11. Quantitative skeletal muscle ultrasonography in children with suspected neuromuscular disease.

    NARCIS (Netherlands)

    Pillen, S.; Scholten, R.R.; Zwarts, M.J.; Verrips, A.

    2003-01-01

    We determined prospectively the diagnostic value of quantitative ultrasonography in detecting neuromuscular disorders in children. Ultrasonographic scans of four muscles were made in 36 children with symptoms or signs suggestive of neuromuscular disease, such as muscle weakness and hypotonia. The

  12. Detection and Monitoring of Acute Myocarditis Applying Quantitative Cardiovascular Magnetic Resonance.

    Science.gov (United States)

    von Knobelsdorff-Brenkenhoff, Florian; Schüler, Johannes; Dogangüzel, Serkan; Dieringer, Matthias A; Rudolph, Andre; Greiser, Andreas; Kellman, Peter; Schulz-Menger, Jeanette

    2017-02-01

    Cardiovascular magnetic resonance based on the Lake Louise Criteria is used to make the diagnosis of acute myocarditis. Novel quantitative parametric mapping techniques promise to overcome some of its limitations. We aimed to evaluate quantitative cardiovascular magnetic resonance to detect and monitor acute myocarditis. Eighteen patients with clinical diagnosis of acute myocarditis (25 years [23-38 years]; 78% males) were prospectively enrolled and repeatedly underwent cardiovascular magnetic resonance at 1.5 T seven days (5-10 days) after symptom onset (FU0), after 5 weeks (FU1), and after 6 months (FU2). Eighteen age- and sex-matched healthy subjects served as controls. Cardiovascular magnetic resonance included imaging of edema, hyperemia, necrosis, and fibrosis using semiquantitative T2-weighted spin echo, T2 mapping, and T1 mapping before and 3 and 10 minutes after gadobutrol administration. Extracellular volume for diffuse and late gadolinium enhancement for focal fibrosis were assessed. Compared with controls, patients had significantly higher global T2 times at FU0 (55.1 ms [53.3-57.2 ms] versus 50.2 ms [49.2-52.0 ms]; PT1 times in patients were elevated acutely (1004 ms [988-1048 ms] versus 975 ms [957-1004 ms]; P=0.002) and remained elevated throughout the follow-up (FU1: 998 ms [990-1027 ms]; P=0.014; FU2: 1000 ms [972-1027 ms]; P=0.044). Global extracellular volume fraction was statistically not different between patients and controls (P=0.057). 77.8% (14/18) of patients had focal late gadolinium enhancement. T2 ratio was significantly elevated in patients with myocarditis at FU0 (2.2 [2.0-2.3] versus 1.6 [1.5-1.7]; Pmyocarditis and healthy controls was 86% for T2>52 ms, 78% for native T1>981 ms, 74% for extracellular volume fraction >0.24, and 100% for T2 ratio >1.9. Although both T2 and T1 mapping reliably detected acute myocarditis, only T2 mapping discriminated between acute and healed stages, underlining the incremental value of T2 mapping.

  13. Quantitative elemental detection of size-segregated particles using laser-induced breakdown spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Zhen Zhen [State Key Laboratory of Multiphase Flow in Power Engineering, Xi' an Jiaotong University, Xi' an 710049 (China); Graduate School of Advanced Technology and Science, The University of Tokushima, Tokushima 770-8501 (Japan); Deguchi, Yoshihiro, E-mail: ydeguchi@tokushima-u.ac.jp [Graduate School of Advanced Technology and Science, The University of Tokushima, Tokushima 770-8501 (Japan); Kuwahara, Masakazu; Taira, Takuya [Graduate School of Advanced Technology and Science, The University of Tokushima, Tokushima 770-8501 (Japan); Zhang, Xiao Bo [State Key Laboratory of Multiphase Flow in Power Engineering, Xi' an Jiaotong University, Xi' an 710049 (China); Graduate School of Advanced Technology and Science, The University of Tokushima, Tokushima 770-8501 (Japan); Yan, Jun Jie; Liu, Ji Ping [State Key Laboratory of Multiphase Flow in Power Engineering, Xi' an Jiaotong University, Xi' an 710049 (China); Watanabe, Hiroaki [Energy Engineering Research Laboratory, Central Research Institute of Electric Power Industry, Kanagawa 240-0196 (Japan); Kurose, Ryoichi [Department of Mechanical Engineering and Science, Kyoto University, Nishikyo-ku, Kyoto 615-8540 (Japan)

    2013-09-01

    In order to simulate coal combustion and develop optimal and stable boiler control systems in real power plants, it is imperative to obtain the detailed information in coal combustion processes as well as to measure species contents in fly ash, which should be controlled and analyzed for enhancing boiler efficiency and reducing environmental pollution. The fly ash consists of oxides (SiO{sub 2}, Al{sub 2}O{sub 3}, Fe{sub 2}O{sub 3}, CaO, and so on), unburned carbon, and other minor elements. Recently laser-induced breakdown spectroscopy (LIBS) technique has been applied to coal combustion and other industrial fields because of the fast response, high sensitivity, real-time and non-contact features. In these applications it is important to measure controlling factors without any sample preparation to maintain the real-time measurement feature. The relation between particle content and particle diameter is also one of the vital researches, because compositions of particles are dependent on their diameter. In this study, we have detected the contents of size-segregated particles using LIBS. Particles were classified by an Anderson cascade impactor and their contents were measured using the output of 1064 nm YAG laser, a spectrograph and an ICCD camera. The plasma conditions such as plasma temperature are dependent on the size of particles and these effects must be corrected to obtain quantitative information. The plasma temperature was corrected by the emission intensity ratio from the same atom. Using this correction method, the contents of particles can be measured quantitatively in fixed experimental parameters. This method was applied to coal and fly ash from a coal-fired burner to measure unburned carbon and other contents according to the particle diameter. The acquired results demonstrate that the LIBS technique is applicable to measure size-segregated particle contents in real time and this method is useful for the analysis of coal combustion and its control

  14. Evaluation of intrapleural contrast-enhanced abdominal pelvic CT-scan in detecting diaphragm injury in stable patients with thoraco-abdominal stab wound: a preliminary study.

    Science.gov (United States)

    Abbasy, Hamid Reza; Panahi, Farzad; Sefidbakht, Sepideh; Akrami, Majid; Paydar, Shahram; Mirhashemi, Sedighe; Bolandparvaz, Shahram; Asaadi, Kambiz; Salahi, Roohollah

    2012-09-01

    Many of the patients with thoraco-abdominal stab wound remain asymptomatic; in this regard, previous studies reported that 7-48% of asymptomatic patients had diaphragm injury (DI). Thoracoscopy or multidetector computed tomography (MDCT) scan is the best method to detect DI. We aimed to evaluate the role of CT scan with intrapleural contrast to rule out DI in stable thoraco-abdominal stab wounds. In a prospective study, we evaluated all haemodynamically stable patients with thoraco-abdominal stab wound, from October 2009 to 2010. Exclusion criteria included patients who needed emergency thoracotomy or laparotomy, those who were haemodynamically unstable and those with blunt trauma or gunshot injury. In the CT-scan department, 500 cc of diluted meglumine diatrozate was transfused into the pleural space via a chest tube and the CT scan was performed from the dome of the diaphragm to the pelvic cavity. In the second step, all patients were taken for thoracoscopy within 24h after admission. The CT-scan slide was considered positive if one of the following signs was found: (1) the diaphragm was obviously injured as seen in CT-scan slides and (2) contrast agent was seen in the peritoneal cavity. Sensitivity and specificity were calculated for CT scan and thoracoscopy. Four out of 40 patients had DI according to thoracoscopy. CT scan with intrapleural contrast predicted diaphragmatic injury correctly in all four patients. Considering thoracoscopy as the gold-standard method, the CT scan had two false-positive cases. The sensitivity of the intrapleural-contrast CT scan was 100% and its specificity was 94.4%. Our study showed that CT scan with intrapleural contrast can be an acceptable approach to rule out DI and limit the use of thoracoscopy for final diagnosis and repair of DI in cases with suspicious or positive CT-scan results, especially in trauma centres with high load of trauma patients and little accessible equipment. Copyright © 2011 Elsevier Ltd. All rights

  15. Sandwich ELISA for quantitative detection of human collagen prolyl 4-hydroxylase

    Directory of Open Access Journals (Sweden)

    Myllyharju Johanna

    2010-06-01

    Full Text Available Abstract Background We describe a method for specific, quantitative and quick detection of human collagen prolyl 4-hydroxylase (C-P4H, the key enzyme for collagen prolyl-4 hydroxylation, in crude samples based on a sandwich ELISA principle. The method is relevant to active C-P4H level monitoring during recombinant C-P4H and collagen production in different expression systems. The assay proves to be specific for the active C-P4H α2β2 tetramer due to the use of antibodies against its both subunits. Thus in keeping with the method C-P4H is captured by coupled to an anti-α subunit antibody magnetic beads and an anti-β subunit antibody binds to the PDI/β subunit of the protein. Then the following holoenzyme detection is accomplished by a goat anti-rabbit IgG labeled with alkaline phosphatase which AP catalyzes the reaction of a substrate transformation with fluorescent signal generation. Results We applied an experimental design approach for the optimization of the antibody concentrations used in the sandwich ELISA. The assay sensitivity was 0.1 ng of C-P4H. The method was utilized for the analysis of C-P4H accumulation in crude cell extracts of E. coli overexpressing C-P4H. The sandwich ELISA signals obtained demonstrated a very good correlation with the detected protein activity levels measured with the standard radioactive assay. The developed assay was applied to optimize C-P4H production in E. coli Origami in a system where the C-P4H subunits expression acted under control by different promoters. The experiments performed in a shake flask fed-batch system (EnBase® verified earlier observations that cell density and oxygen supply are critical factors for the use of the inducer anhydrotetracycline and thus for the soluble C-P4H yield. Conclusions Here we show an example of sandwich ELISA usage for quantifying multimeric proteins. The method was developed for monitoring the amount of recombinant C-P4H tetramer in crude E. coli extracts. Due

  16. SonoNet: Real-Time Detection and Localisation of Fetal Standard Scan Planes in Freehand Ultrasound.

    Science.gov (United States)

    Baumgartner, Christian F; Kamnitsas, Konstantinos; Matthew, Jacqueline; Fletcher, Tara P; Smith, Sandra; Koch, Lisa M; Kainz, Bernhard; Rueckert, Daniel

    2017-11-01

    Identifying and interpreting fetal standard scan planes during 2-D ultrasound mid-pregnancy examinations are highly complex tasks, which require years of training. Apart from guiding the probe to the correct location, it can be equally difficult for a non-expert to identify relevant structures within the image. Automatic image processing can provide tools to help experienced as well as inexperienced operators with these tasks. In this paper, we propose a novel method based on convolutional neural networks, which can automatically detect 13 fetal standard views in freehand 2-D ultrasound data as well as provide a localization of the fetal structures via a bounding box. An important contribution is that the network learns to localize the target anatomy using weak supervision based on image-level labels only. The network architecture is designed to operate in real-time while providing optimal output for the localization task. We present results for real-time annotation, retrospective frame retrieval from saved videos, and localization on a very large and challenging dataset consisting of images and video recordings of full clinical anomaly screenings. We found that the proposed method achieved an average F1-score of 0.798 in a realistic classification experiment modeling real-time detection, and obtained a 90.09% accuracy for retrospective frame retrieval. Moreover, an accuracy of 77.8% was achieved on the localization task.

  17. Detecting element specific electrons from a single cobalt nanocluster with synchrotron x-ray scanning tunneling microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Kersell, Heath; Shirato, Nozomi; Cummings, Marvin; Chang, Hao; Miller, Dean; Rosenmann, Daniel; Hla, Saw-Wai; Rose, Volker

    2017-09-04

    We use a nanofabricated scanning tunneling microscope tip as a detector to investigate local X-ray induced tunneling and electron emission from a single cobalt nanocluster on a Au(111) surface. The tip-detector is positioned a few angstroms above the nanocluster, and ramping the incident X-ray energy across the Co photoabsorption K-edge enables the detection of element specific electrons. Atomic-scale spatial dependent changes in the X-ray absorption cross section are directly measured by taking the X-ray induced current as a function of X-ray energy. From the measured sample and tip currents, element specific X-ray induced current components can be separated and thereby the corresponding yields for the X-ray induced processes of the single cobalt nanocluster can be determined. The detection of element specific synchrotron X-ray induced electrons of a single nanocluster opens a new avenue for materials characterization on a one particle at-a-time basis.

  18. Wavelet entropy and directed acyclic graph support vector machine for detection of patients with unilateral hearing loss in MRI scanning

    Directory of Open Access Journals (Sweden)

    Shuihua Wang

    2016-10-01

    Full Text Available (Aim Sensorineural hearing loss (SNHL is correlated to many neurodegenerative disease. Now more and more computer vision based methods are using to detect it in an automatic way. (Materials We have in total 49 subjects, scanned by 3.0T MRI (Siemens Medical Solutions, Erlangen, Germany. The subjects contain 14 patients with right-sided hearing loss (RHL, 15 patients with left-sided hearing loss (LHL, and 20 healthy controls (HC. (Method We treat this as a three-class classification problem: RHL, LHL, and HC. Wavelet entropy (WE was selected from the magnetic resonance images of each subjects, and then submitted to a directed acyclic graph support vector machine (DAG-SVM. (Results The 10 repetition results of 10-fold cross validation shows 3-level decomposition will yield an overall accuracy of 95.10% for this three-class classification problem, higher than feedforward neural network, decision tree, and naive Bayesian classifier. (Conclusions This computer-aided diagnosis system is promising. We hope this study can attract more computer vision method for detecting hearing loss.

  19. Automated terrestrial laser scanning with near-real-time change detection – monitoring of the Séchilienne landslide

    Directory of Open Access Journals (Sweden)

    R. A. Kromer

    2017-05-01

    Full Text Available We present an automated terrestrial laser scanning (ATLS system with automatic near-real-time change detection processing. The ATLS system was tested on the Séchilienne landslide in France for a 6-week period with data collected at 30 min intervals. The purpose of developing the system was to fill the gap of high-temporal-resolution TLS monitoring studies of earth surface processes and to offer a cost-effective, light, portable alternative to ground-based interferometric synthetic aperture radar (GB-InSAR deformation monitoring. During the study, we detected the flux of talus, displacement of the landslide and pre-failure deformation of discrete rockfall events. Additionally, we found the ATLS system to be an effective tool in monitoring landslide and rockfall processes despite missing points due to poor atmospheric conditions or rainfall. Furthermore, such a system has the potential to help us better understand a wide variety of slope processes at high levels of temporal detail.

  20. Damage detection in composite panels based on mode-converted Lamb waves sensed using 3D laser scanning vibrometer

    Science.gov (United States)

    Pieczonka, Łukasz; Ambroziński, Łukasz; Staszewski, Wiesław J.; Barnoncel, David; Pérès, Patrick

    2017-12-01

    This paper introduces damage identification approach based on guided ultrasonic waves and 3D laser Doppler vibrometry. The method is based on the fact that the symmetric and antisymmetric Lamb wave modes differ in amplitude of the in-plane and out-of-plane vibrations. Moreover, the modes differ also in group velocities and normally they are well separated in time. For a given time window both modes can occur simultaneously only close to the wave source or to a defect that leads to mode conversion. By making the comparison between the in-plane and out-of-plane wave vector components the detection of mode conversion is possible, allowing for superior and reliable damage detection. Experimental verification of the proposed damage identification procedure is performed on fuel tank elements of Reusable Launch Vehicles designed for space exploration. Lamb waves are excited using low-profile, surface-bonded piezoceramic transducers and 3D scanning laser Doppler vibrometer is used to characterize the Lamb wave propagation field. The paper presents theoretical background of the proposed damage identification technique as well as experimental arrangements and results.

  1. Network-based group variable selection for detecting expression quantitative trait loci (eQTL

    Directory of Open Access Journals (Sweden)

    Zhang Xuegong

    2011-06-01

    Full Text Available Abstract Background Analysis of expression quantitative trait loci (eQTL aims to identify the genetic loci associated with the expression level of genes. Penalized regression with a proper penalty is suitable for the high-dimensional biological data. Its performance should be enhanced when we incorporate biological knowledge of gene expression network and linkage disequilibrium (LD structure between loci in high-noise background. Results We propose a network-based group variable selection (NGVS method for QTL detection. Our method simultaneously maps highly correlated expression traits sharing the same biological function to marker sets formed by LD. By grouping markers, complex joint activity of multiple SNPs can be considered and the dimensionality of eQTL problem is reduced dramatically. In order to demonstrate the power and flexibility of our method, we used it to analyze two simulations and a mouse obesity and diabetes dataset. We considered the gene co-expression network, grouped markers into marker sets and treated the additive and dominant effect of each locus as a group: as a consequence, we were able to replicate results previously obtained on the mouse linkage dataset. Furthermore, we observed several possible sex-dependent loci and interactions of multiple SNPs. Conclusions The proposed NGVS method is appropriate for problems with high-dimensional data and high-noise background. On eQTL problem it outperforms the classical Lasso method, which does not consider biological knowledge. Introduction of proper gene expression and loci correlation information makes detecting causal markers more accurate. With reasonable model settings, NGVS can lead to novel biological findings.

  2. Detection of placenta elasticity modulus by quantitative real-time shear wave imaging.

    Science.gov (United States)

    Li, W J; Wei, Z T; Yan, R L; Zhang, Y L

    2012-01-01

    To explore the clinical values in detecting the placental elastic modulus using real-time quantitative shear wave elasticity imaging. A total of 30 women in the late pregnancy stage without complications and having normal, single pregnancies, as well as normal fetal growth, amniotic fluid index, and anterior placenta were selected. A real-time elasticity imaging shear wave ultrasonic diagnostic apparatus was used to randomly select regions of interest at the central and edge of the placenta. The elastography imaging mode was launched to measure the elasticity of the elastic modulus of these placental parts. A total of 15 measured values were obtained at the placental center and edge for each pregnancy case. Umbilical artery and uterine artery pulsatility index (PI) values for 18 cases were also randomly measured. The average value of 30 placental edges of the elastic modulus (n = 15) was (7.60 +/- 1.71) kPa. The average value of the 30 placental central elastic modulus (n = 15 ) was (7.84 +/- 1.68) kPa. No significant difference was observed between placenta central and edge elastic modulus. The PI mean value of umbilical artery in 18 cases was 0.94, whereas the average PI values of the uterine artery was 0.83. No linear correlation was found among the elastic modulus, the placental uterine artery PI values, and the umbilical artery PI values (p > 0.05). No difference between the placental center of normal pregnancies and the edge of the elastic modulus was detected. The elastic modulus of the placenta could be obtained in the best position. The placenta varied greatly between elastic modulus. No correlation was found between the placental elastic modulus, the uterine artery, and umbilical artery PI values. Real-time shear wave elasticity imaging technology can provide morphological evidence of placental function, which may emerge as a new clinical assessment approach.

  3. Detection, quantification and vitality of Listeria monocytogenes in food as determined by quantitative PCR.

    Science.gov (United States)

    Rantsiou, Kalliopi; Alessandria, Valentina; Urso, Rosalinda; Dolci, Paola; Cocolin, Luca

    2008-01-15

    In this paper we describe the development of a quantitative PCR (qPCR) technique to detect, quantify and determine the vitality of Listeria monocytogenes in foods. The method was based on the amplification of the intergenic region spacer (IGS) between the 16S and 23S rRNA genes. A panel of more than 100 strains of Listeria spp. and non-Listeria was used in order to verify the specificity of the primers and Taqman probe and amplification signals were obtained only when L. monocytogenes DNA and RNA were loaded in the qPCR mix. Standard curves were constructed in several food matrices (milk, meat, soft cheese, fermented sausage, cured ham and ready-to-eat salad). The quantification limit was of 10(3)-10(4) cfu/g or ml, while for the determination of vitality it was 10(4)-10(5) cfu/g or ml. After an overnight enrichment in BHI at 37 degrees C also 10 cfu/g or ml could be detected in all the matrices used in this study. When we applied the protocol to food samples collected from the market or from small food processing plants, on a total number of 66 samples, 4 fresh cheeses from raw milk gave positive results prior to the overnight incubation, while 9 samples, of which only one represented by fresh meat and the others by cheeses from raw milk, were positive after the enrichment. Out of the 4 positive samples, only one could be quantified and it was determined to contain 4x10(3) cfu/g.

  4. Fast quantitative PCR, locked nucleic acid probes and reduced volume reactions are effective tools for detecting Batrachochytrium dendrobatidis DNA.

    Science.gov (United States)

    Ruthig, Gregory R; Deridder, Benjamin P

    2012-01-24

    The fungal pathogen Batrachochytrium dendrobatidis threatens amphibian populations around the world. The ability to detect this pathogen on infected animals and in the environment is critical for understanding and controlling this pandemic. We tested several advances in quantitative PCR (qPCR) techniques to detect B. dendrobatidis DNA. We used a fast PCR thermocycler and enzymes that reduced the volume and the duration of the reaction. We also compared a conventional TaqMan minor groove binding (MGB) probe to an identical locked nucleic acid (LNA) counterpart. The fast qPCR reaction had a high degree of sensitivity to B. dendrobatidis DNA. The LNA probe was effective for detecting B. dendrobatidis DNA and produced results -similar to those of the MGB probe. The modifications that we tested can improve the cost, time efficiency and specificity of quantitative PCR as a tool for detecting pathogen DNA.

  5. A simple immunoperoxidase plaque assay to detect and quantitate Marek's disease virus plaques.

    Science.gov (United States)

    Silva, R F; Calvert, J G; Lee, L F

    1997-01-01

    We report an immunoperoxidase-based staining technique that can be used to rapidly and accurately detect and quantitate Marek's disease virus (MDV) plaques. Monolayer cultures were fixed and incubated with a monoclonal antibody specific for MDV. After washing, a second antibody of horseradish peroxidase-conjugated goat anti-mouse IgG was applied, incubated for 1 hr, and washed with phosphate-buffered saline. After the cultures were incubated with diaminobenzidine, CoCl2, and H2O2, the plaques appeared as black spots and were easily seen and counted. Significantly more immunoperoxidase-stained serotype 1 MDV plaques could be counted at 4 days postinoculation than were seen in unstained cultures. With serotype 2 MDV-infected cells, the difference in plaque counts was less dramatic. Nevertheless, at 3 days postinoculation, significantly more stained serotype 2 plaques were seen than unstained plaques. Immunoperoxidase staining of turkey herpesvirus plaques did not increase the sensitivity of viewing plaques. Similar numbers of stained and unstained plaques were seen at 2 days postinoculation. We also demonstrated that we could count serotype-specific MDV plaques in a mixed infection that contained all three serotypes.

  6. Quantitative evaluation of automatic methods for lesions detection in breast ultrasound images

    Science.gov (United States)

    Marcomini, Karem D.; Schiabel, Homero; Carneiro, Antonio Adilton O.

    2013-02-01

    Ultrasound (US) is a useful diagnostic tool to distinguish benign from malignant breast masses, providing more detailed evaluation in dense breasts. Due to the subjectivity in the images interpretation, computer-aid diagnosis (CAD) schemes have been developed, increasing the mammography analysis process to include ultrasound images as complementary exams. As one of most important task in the evaluation of this kind of images is the mass detection and its contours interpretation, automated segmentation techniques have been investigated in order to determine a quite suitable procedure to perform such an analysis. Thus, the main goal in this work is investigating the effect of some processing techniques used to provide information on the determination of suspicious breast lesions as well as their accurate boundaries in ultrasound images. In tests, 80 phantom and 50 clinical ultrasound images were preprocessed, and 5 segmentation techniques were tested. By using quantitative evaluation metrics the results were compared to a reference image delineated by an experienced radiologist. A self-organizing map artificial neural network has provided the most relevant results, demonstrating high accuracy and low error rate in the lesions representation, corresponding hence to the segmentation process for US images in our CAD scheme under tests.

  7. Quantitative determination of non-starch polysaccharides in foods using Gas Chromatography with flame ionization detection.

    Science.gov (United States)

    Ma, Jun; Adler, Lewis; Srzednicki, George; Arcot, Jayashree

    2017-04-01

    A gas chromatographic method was developed for the quantitative determination of the monosaccharides of the soluble, insoluble fractions and the total non-starch polysaccharides (NSPs) content in foods with fat contents of less than 5%. Sample preparation involved enzymatic removal of starch and acid hydrolysis of the NSP to their constituent sugars. The alditol acetate derivatives were analysed on a wide bore capillary column with detection by flame ionization. The method was accurate, with recovery of spiked samples between 93.6% and 102.7% for intra-day analysis and between 93.2% and 104.7% for inter-day analysis. Repeatability was excellent; RSD values from 0.1 to 4.4% and 0.2 to 5.7% were observed from intra-day analysis and inter-day analysis, respectively. The peaks for all neutral sugars were sharp and separation was at baseline resolution with no interfering or co-eluting peaks. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Real time PCR method for simultaneous detection, quantitation and differentiation of capripoxviruses.

    Science.gov (United States)

    Lamien, Charles Euloge; Lelenta, Mamadou; Goger, Wilfried; Silber, Roland; Tuppurainen, Eeva; Matijevic, Mirta; Luckins, Antony George; Diallo, Adama

    2011-01-01

    The genus Capripoxvirus (CaPV) comprises three members namely, sheep poxvirus (SPPV), goat poxvirus (GTPV) and lumpy skin disease virus (LSDV) affecting sheep, goats and cattle, respectively. CaPV infections produce similar symptoms in sheep and goats, and the three viruses cannot be distinguished serologically. Since there are conflicting opinions regarding the host specificity of CaPVs, particularly for goatpox and sheeppox viruses, the development of rapid genotyping tools will facilitate more accurate disease diagnosis and surveillance for better management of capripox outbreaks. This paper describes a species-specific, real time polymerase chain reaction (PCR), based on unique molecular markers that were found in the G-protein-coupled chemokine receptor (GPCR) gene sequences of CaPVs, that uses dual hybridization probes for their simultaneous detection, quantitation and genotyping. The assay can differentiate between CaPV strains based on differences in the melting point temperature (Tm) obtained after fluorescence melting curve analysis (FMCA). It is highly sensitive and presents low intra- and inter-run variation. This real time PCR assay will make a significant contribution to CaPV diagnosis and to the better understanding of the epidemiology of CaPVs by enabling rapid genotyping and gene-based classification of viral strains and unequivocal identification of isolates. Copyright © 2010 Elsevier B.V. All rights reserved.

  9. Rapid detection of Pseudomonas aeruginosa from positive blood cultures by quantitative PCR

    Directory of Open Access Journals (Sweden)

    Cattoir Vincent

    2010-08-01

    Full Text Available Abstract Background Pseudomonas aeruginosa is responsible for numerous bloodstream infections associated with severe adverse outcomes in case of inappropriate initial antimicrobial therapy. The present study was aimed to develop a novel quantitative PCR (qPCR assay, using ecfX as the specific target gene, for the rapid and accurate identification of P. aeruginosa from positive blood cultures (BCs. Methods Over the period August 2008 to June 2009, 100 BC bottles positive for gram-negative bacilli were tested in order to evaluate performances of the qPCR technique with conventional methods as gold standard (i.e. culture and phenotypic identification. Results Thirty-three strains of P. aeruginosa, 53 strains of Enterobactericaeae, nine strains of Stenotrophomonas maltophilia and two other gram-negative species were isolated while 3 BCs were polymicrobial including one mixture containing P. aeruginosa. All P. aeruginosa clinical isolates were detected by qPCR except a single strain in mixed culture. Performances of the qPCR technique were: specificity, 100%; positive predictive value, 100%; negative predictive value, 98.5%; and sensitivity, 97%. Conclusions This reliable technique may offer a rapid (

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

    Science.gov (United States)

    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 (metabolism and clinical diagnosis.

  11. A novel method, digital genome scanning detects KRAS gene amplification in gastric cancers: involvement of overexpressed wild-type KRAS in downstream signaling and cancer cell growth

    Directory of Open Access Journals (Sweden)

    Yanagihara Kazuyoshi

    2009-06-01

    Full Text Available Abstract Background Gastric cancer is the third most common malignancy affecting the general population worldwide. Aberrant activation of KRAS is a key factor in the development of many types of tumor, however, oncogenic mutations of KRAS are infrequent in gastric cancer. We have developed a novel quantitative method of analysis of DNA copy number, termed digital genome scanning (DGS, which is based on the enumeration of short restriction fragments, and does not involve PCR or hybridization. In the current study, we used DGS to survey copy-number alterations in gastric cancer cells. Methods DGS of gastric cancer cell lines was performed using the sequences of 5000 to 15000 restriction fragments. We screened 20 gastric cancer cell lines and 86 primary gastric tumors for KRAS amplification by quantitative PCR, and investigated KRAS amplification at the DNA, mRNA and protein levels by mutational analysis, real-time PCR, immunoblot analysis, GTP-RAS pull-down assay and immunohistochemical analysis. The effect of KRAS knock-down on the activation of p44/42 MAP kinase and AKT and on cell growth were examined by immunoblot and colorimetric assay, respectively. Results DGS analysis of the HSC45 gastric cancer cell line revealed the amplification of a 500-kb region on chromosome 12p12.1, which contains the KRAS gene locus. Amplification of the KRAS locus was detected in 15% (3/20 of gastric cancer cell lines (8–18-fold amplification and 4.7% (4/86 of primary gastric tumors (8–50-fold amplification. KRAS mutations were identified in two of the three cell lines in which KRAS was amplified, but were not detected in any of the primary tumors. Overexpression of KRAS protein correlated directly with increased KRAS copy number. The level of GTP-bound KRAS was elevated following serum stimulation in cells with amplified wild-type KRAS, but not in cells with amplified mutant KRAS. Knock-down of KRAS in gastric cancer cells that carried amplified wild

  12. Localization of proteins in paint cross-sections by scanning electrochemical microscopy as an alternative immunochemical detection technique

    Energy Technology Data Exchange (ETDEWEB)

    Sciutto, Giorgia; Prati, Silvia [Microchemistry and Microscopy Art Diagnostic Laboratory, University of Bologna, Via Guaccimanni 42, Ravenna 48121 (Italy); Department of Chemistry “G. Ciamician”, University of Bologna, Via Selmi, Bologna 2 40126 (Italy); Mazzeo, Rocco, E-mail: rocco.mazzeo@unibo.it [Microchemistry and Microscopy Art Diagnostic Laboratory, University of Bologna, Via Guaccimanni 42, Ravenna 48121 (Italy); Department of Chemistry “G. Ciamician”, University of Bologna, Via Selmi, Bologna 2 40126 (Italy); Zangheri, Martina; Roda, Aldo; Bardini, Luca; Valenti, Giovanni; Rapino, Stefania [Department of Chemistry “G. Ciamician”, University of Bologna, Via Selmi, Bologna 2 40126 (Italy); Marcaccio, Massimo, E-mail: massimo.marcaccio@unibo.it [Department of Chemistry “G. Ciamician”, University of Bologna, Via Selmi, Bologna 2 40126 (Italy)

    2014-06-01

    Highlights: • Advanced immuno-electrochemical detection of proteins in paint samples by SECM. • Analysis performed directly on cross-section with high spatial resolution. • Identification of HRP catalytic activity for a selective location of analyte. • Satisfactory results were obtained for aged real samples. • The way forward for an extensive application of SECM in conservation science is shown. - Abstract: The qualitative identification of proteinaceous substances, as well as their location within a complex paint stratigraphy, is one of the most challenging issues in the characterization of painting materials. Nevertheless, information on paint components represent a crucial task for studies concerning both the ancient painting techniques adopted and the state of conservation, being fundamental investigations for the selection of appropriate conservation actions. The present research was aimed at developing a new detection approach for the immunochemical localization of ovalbumin in paint cross-sections based on the use of scanning electrochemical microscopy (SECM). The immunochemical analyses were performed using an anti-ovalbumin primary antibody and a secondary antibody labelled with horseradish peroxidase (HRP). SECM measurements were performed in feedback mode using benzoquinone (BQ)/hydroquinone (H{sub 2}Q) redox couple. In presence of hydrogen peroxide (H{sub 2}O{sub 2}), HRP catalyzes the re-oxidation of H{sub 2}Q to BQ and the increment of BQ concentration in correspondence of the target protein was detected by SECM through the electrochemical reduction of the regenerated BQ at the microelectrode. Indeed, the localization of ovalbumin was possible thanks to a clear discrimination of SECM currents, achieved by the comparison of the measurements recorded before and after H{sub 2}O{sub 2} administration, based on the HRP on/off approach. The method was evaluated both on samples from standard mocks-up and on a historical sample, collected from a

  13. Wavelet Entropy and Directed Acyclic Graph Support Vector Machine for Detection of Patients with Unilateral Hearing Loss in MRI Scanning.

    Science.gov (United States)

    Wang, Shuihua; Yang, Ming; Du, Sidan; Yang, Jiquan; Liu, Bin; Gorriz, Juan M; Ramírez, Javier; Yuan, Ti-Fei; Zhang, Yudong

    2016-01-01

    Highlights We develop computer-aided diagnosis system for unilateral hearing loss detection in structural magnetic resonance imaging.Wavelet entropy is introduced to extract image global features from brain images. Directed acyclic graph is employed to endow support vector machine an ability to handle multi-class problems.The developed computer-aided diagnosis system achieves an overall accuracy of 95.1% for this three-class problem of differentiating left-sided and right-sided hearing loss from healthy controls. Aim: Sensorineural hearing loss (SNHL) is correlated to many neurodegenerative disease. Now more and more computer vision based methods are using to detect it in an automatic way. Materials: We have in total 49 subjects, scanned by 3.0T MRI (Siemens Medical Solutions, Erlangen, Germany). The subjects contain 14 patients with right-sided hearing loss (RHL), 15 patients with left-sided hearing loss (LHL), and 20 healthy controls (HC). Method: We treat this as a three-class classification problem: RHL, LHL, and HC. Wavelet entropy (WE) was selected from the magnetic resonance images of each subjects, and then submitted to a directed acyclic graph support vector machine (DAG-SVM). Results: The 10 repetition results of 10-fold cross validation shows 3-level decomposition will yield an overall accuracy of 95.10% for this three-class classification problem, higher than feedforward neural network, decision tree, and naive Bayesian classifier. Conclusions: This computer-aided diagnosis system is promising. We hope this study can attract more computer vision method for detecting hearing loss.

  14. Quantitative visualization and detection of skin cancer using dynamic thermal imaging.

    Science.gov (United States)

    Herman, Cila; Cetingul, Muge Pirtini

    2011-05-05

    In 2010 approximately 68,720 melanomas will be diagnosed in the US alone, with around 8,650 resulting in death. To date, the only effective treatment for melanoma remains surgical excision, therefore, the key to extended survival is early detection. Considering the large numbers of patients diagnosed every year and the limitations in accessing specialized care quickly, the development of objective in vivo diagnostic instruments to aid the diagnosis is essential. New techniques to detect skin cancer, especially non-invasive diagnostic tools, are being explored in numerous laboratories. Along with the surgical methods, techniques such as digital photography, dermoscopy, multispectral imaging systems (MelaFind), laser-based systems (confocal scanning laser microscopy, laser doppler perfusion imaging, optical coherence tomography), ultrasound, magnetic resonance imaging, are being tested. Each technique offers unique advantages and disadvantages, many of which pose a compromise between effectiveness and accuracy versus ease of use and cost considerations. Details about these techniques and comparisons are available in the literature. Infrared (IR) imaging was shown to be a useful method to diagnose the signs of certain diseases by measuring the local skin temperature. There is a large body of evidence showing that disease or deviation from normal functioning are accompanied by changes of the temperature of the body, which again affect the temperature of the skin. Accurate data about the temperature of the human body and skin can provide a wealth of information on the processes responsible for heat generation and thermoregulation, in particular the deviation from normal conditions, often caused by disease. However, IR imaging has not been widely recognized in medicine due to the premature use of the technology several decades ago, when temperature measurement accuracy and the spatial resolution were inadequate and sophisticated image processing tools were unavailable

  15. Apricot DNA as an indicator for persipan: detection and quantitation in marzipan using ligation-dependent probe amplification.

    Science.gov (United States)

    Luber, Florian; Demmel, Anja; Hosken, Anne; Busch, Ulrich; Engel, Karl-Heinz

    2012-06-13

    The confectionery ingredient marzipan is exclusively prepared from almond kernels and sugar. The potential use of apricot kernels, so-called persipan, is an important issue for the quality assessment of marzipan. Therefore, a ligation-dependent probe amplification (LPA) assay was developed that enables a specific and sensitive detection of apricot DNA, as an indicator for the presence of persipan. The limit of detection was determined to be 0.1% persipan in marzipan. The suitability of the method was confirmed by the analysis of 20 commercially available food samples. The integration of a Prunus -specific probe in the LPA assay as a reference allowed for the relative quantitation of persipan in marzipan. The limit of quantitation was determined to be 0.5% persipan in marzipan. The analysis of two self-prepared mixtures of marzipan and persipan demonstrated the applicability of the quantitation method at concentration levels of practical relevance for quality control.

  16. A quantitative method for detecting deposits of amyloid A protein in aspirated fat tissue of patients with arthritis

    NARCIS (Netherlands)

    Hazenberg, BPC; Limburg, PC; Bijzet, J.; van Rijswijk, M.H.

    Objective-To describe a new, quantitative, and reproducible method for detecting deposits of amyloid A protein in aspirated fat tissue and to compare it with smears stained with Congo red. Methods-After extraction of at least 30 mg of abdominal fat tissue in guanidine, the amyloid A protein

  17. Technetium-99m human polyclonal immunoglobulin g studies and conventional bone scans to detect active joint inflammation in chronic rheumatoid arthritis

    Energy Technology Data Exchange (ETDEWEB)

    Berna, Ll.; Torres, G.; Estorch, M.; Martinez-Duncker, D.; Carrio, I. (Hospital de Sant Pau, Barcelona (Spain). Dept. of Nuclear Medicine); Diez, C. (Hospital de Sant Pau, Barcelona (Spain). Dept. of Rheumatology)

    1992-03-01

    Rheumatoid arthritis is a chronic polyarthritis in which active inflammed joints coexist with joints in remission. We performed bone scans ({sup 99m}Tc-DPD) and {sup 99m}Tc human polyclonal immunoglobulin G scans ({sup 99m}Tc-IgG) in 18 patients with rheumatoid arthritis to assess the uptake in actively inflammed joints and in joints in which remission after inflammation had occurred. A quantitative analysis of tracer uptake in each joint was performed on both scans. In 123 joints without current active inflammation, an increased {sup 99m}Tc-DPD uptake was observed (2.31{+-}1.27), whereas no {sup 99m}Tc-IgG uptake was noted (1.18{+-}0.32). Some 78 joints with mild pain or swelling exhibited increased {sup 99m}Tc-DPD uptake (2.48{+-}1.14) and increased {sup 99m}Tc-IgG uptake (1.76{+-}0.50; P<0.001), white 21 joints with moderate to severe pain or swelling exhibited increased {sup 99m}Tc-DPD uptake (2.39{+-}0.93) and increased {sup 99m}Tc-IgG uptake (1.79{+-}0.51; P<0.001). In conclusion, {sup 99m}Tc-IgG scans distinguish between joints with and without active inflammation in chronic rheumatoid arthritis, whereas bone scans do not. Thus, {sup 99m}Tc-IgG scans may be useful in identifying joints with current active inflammation in rheumatoid arthritis. (orig.).

  18. Human performance in radiological survey scanning

    Energy Technology Data Exchange (ETDEWEB)

    Brown, W.S. [Brookhaven National Lab., Upton, NY (United States); Abelquist, E.W. [Oak Ridge Inst. for Science and Education, TN (United States)

    1998-03-01

    The probability of detecting residual contamination in the field using portable radiological survey instruments depends not only on the sensitivity of the instrumentation used in scanning, but also on the surveyor`s performance. This report provides a basis for taking human performance into account in determining the minimum level of activity detectable by scanning. A theoretical framework was developed (based on signal detection theory) which allows influences on surveyors to be anticipated and understood, and supports a quantitative assessment of performance. The performance of surveyors under controlled yet realistic field conditions was examined to gain insight into the task and to develop means of quantifying performance. Then, their performance was assessed under laboratory conditions to quantify more precisely their ability to make the required discriminations. The information was used to characterize surveyors` performance in the scanning task and to provide a basis for predicting levels of radioactivity that are likely to be detectable under various conditions by surveyors using portable survey instruments.

  19. Automatic Detection and Classification of Pole-Like Objects for Urban Cartography Using Mobile Laser Scanning Data

    Directory of Open Access Journals (Sweden)

    Celestino Ordóñez

    2017-06-01

    Full Text Available Mobile laser scanning (MLS is a modern and powerful technology capable of obtaining massive point clouds of objects in a short period of time. Although this technology is nowadays being widely applied in urban cartography and 3D city modelling, it has some drawbacks that need to be avoided in order to strengthen it. One of the most important shortcomings of MLS data is concerned with the fact that it provides an unstructured dataset whose processing is very time-consuming. Consequently, there is a growing interest in developing algorithms for the automatic extraction of useful information from MLS point clouds. This work is focused on establishing a methodology and developing an algorithm to detect pole-like objects and classify them into several categories using MLS datasets. The developed procedure starts with the discretization of the point cloud by means of a voxelization, in order to simplify and reduce the processing time in the segmentation process. In turn, a heuristic segmentation algorithm was developed to detect pole-like objects in the MLS point cloud. Finally, two supervised classification algorithms, linear discriminant analysis and support vector machines, were used to distinguish between the different types of poles in the point cloud. The predictors are the principal component eigenvalues obtained from the Cartesian coordinates of the laser points, the range of the Z coordinate, and some shape-related indexes. The performance of the method was tested in an urban area with 123 poles of different categories. Very encouraging results were obtained, since the accuracy rate was over 90%.

  20. Glaucoma progression detection by retinal nerve fiber layer measurement using scanning laser polarimetry: event and trend analysis.

    Science.gov (United States)

    Moon, Byung Gil; Sung, Kyung Rim; Cho, Jung Woo; Kang, Sung Yong; Yun, Sung-Cheol; Na, Jung Hwa; Lee, Youngrok; Kook, Michael S

    2012-06-01

    To evaluate the use of scanning laser polarimetry (SLP, GDx VCC) to measure the retinal nerve fiber layer (RNFL) thickness in order to evaluate the progression of glaucoma. Test-retest measurement variability was determined in 47 glaucomatous eyes. One eye each from 152 glaucomatous patients with at least 4 years of follow-up was enrolled. Visual field (VF) loss progression was determined by both event analysis (EA, Humphrey guided progression analysis) and trend analysis (TA, linear regression analysis of the visual field index). SLP progression was defined as a reduction of RNFL exceeding the predetermined repeatability coefficient in three consecutive exams, as compared to the baseline measure (EA). The slope of RNFL thickness change over time was determined by linear regression analysis (TA). Twenty-two eyes (14.5%) progressed according to the VF EA, 16 (10.5%) by VF TA, 37 (24.3%) by SLP EA and 19 (12.5%) by SLP TA. Agreement between VF and SLP progression was poor in both EA and TA (VF EA vs. SLP EA, k = 0.110; VF TA vs. SLP TA, k = 0.129). The mean (±standard deviation) progression rate of RNFL thickness as measured by SLP TA did not significantly differ between VF EA progressors and non-progressors (-0.224 ± 0.148 µm/yr vs. -0.218 ± 0.151 µm/yr, p = 0.874). SLP TA and EA showed similar levels of sensitivity when VF progression was considered as the reference standard. RNFL thickness as measurement by SLP was shown to be capable of detecting glaucoma progression. Both EA and TA of SLP showed poor agreement with VF outcomes in detecting glaucoma progression.

  1. Automatic Detection and Classification of Pole-Like Objects for Urban Cartography Using Mobile Laser Scanning Data.

    Science.gov (United States)

    Ordóñez, Celestino; Cabo, Carlos; Sanz-Ablanedo, Enoc

    2017-06-22

    Mobile laser scanning (MLS) is a modern and powerful technology capable of obtaining massive point clouds of objects in a short period of time. Although this technology is nowadays being widely applied in urban cartography and 3D city modelling, it has some drawbacks that need to be avoided in order to strengthen it. One of the most important shortcomings of MLS data is concerned with the fact that it provides an unstructured dataset whose processing is very time-consuming. Consequently, there is a growing interest in developing algorithms for the automatic extraction of useful information from MLS point clouds. This work is focused on establishing a methodology and developing an algorithm to detect pole-like objects and classify them into several categories using MLS datasets. The developed procedure starts with the discretization of the point cloud by means of a voxelization, in order to simplify and reduce the processing time in the segmentation process. In turn, a heuristic segmentation algorithm was developed to detect pole-like objects in the MLS point cloud. Finally, two supervised classification algorithms, linear discriminant analysis and support vector machines, were used to distinguish between the different types of poles in the point cloud. The predictors are the principal component eigenvalues obtained from the Cartesian coordinates of the laser points, the range of the Z coordinate, and some shape-related indexes. The performance of the method was tested in an urban area with 123 poles of different categories. Very encouraging results were obtained, since the accuracy rate was over 90%.

  2. Dual Immunomagnetic Nanobeads-Based Lateral Flow Test Strip for Simultaneous Quantitative Detection of Carcinoembryonic Antigen and Neuron Specific Enolase

    Science.gov (United States)

    Lu, Wenting; Wang, Kan; Xiao, Kun; Qin, Weijian; Hou, Yafei; Xu, Hao; Yan, Xinyu; Chen, Yanrong; Cui, Daxiang; He, Jinghua

    2017-01-01

    A novel immunomagnetic nanobeads -based lateral flow test strip was developed for the simultaneous quantitative detection of neuron specific enolase (NSE) and carcinoembryonic antigen (CEA), which are sensitive and specific in the clinical diagnosis of small cell lung cancer. Using this nanoscale method, high saturation magnetization, carboxyl-modified magnetic nanobeads were successfully synthesized. To obtain the immunomagnetic probes, a covalent bioconjugation of the magnetic nanobeads with the antibody of NSE and CEA was carried out. The detection area contained test line 1 and test line 2 which captured the immune complexes sensitively and formed sandwich complexes. In this assay, cross-reactivity results were negative and both NSE and CEA were detected simultaneously with no obvious influence on each other. The magnetic signal intensity of the nitrocellulose membrane was measured by a magnetic assay reader. For quantitative analysis, the calculated limit of detection was 0.094 ng/mL for NSE and 0.045 ng/mL for CEA. One hundred thirty clinical samples were used to validate the test strip which exhibited high sensitivity and specificity. This dual lateral flow test strip not only provided an easy, rapid, simultaneous quantitative detection strategy for NSE and CEA, but may also be valuable in automated and portable diagnostic applications. PMID:28186176

  3. Sensitive and Quantitative Detection of C-Reaction Protein Based on Immunofluorescent Nanospheres Coupled with Lateral Flow Test Strip.

    Science.gov (United States)

    Hu, Jiao; Zhang, Zhi-Ling; Wen, Cong-Ying; Tang, Man; Wu, Ling-Ling; Liu, Cui; Zhu, Lian; Pang, Dai-Wen

    2016-06-21

    Sensitive and quantitative detection of protein biomarkers with a point-of-care (POC) assay is significant for early diagnosis, treatment, and prognosis of diseases. In this paper, a quantitative lateral flow assay with high sensitivity for protein biomarkers was established by utilizing fluorescent nanospheres (FNs) as reporters. Each fluorescent nanosphere (FN) contains 332 ± 8 CdSe/ZnS quantum dots (QDs), leading to its superstrong luminescence, 380-fold higher than that of one QD. Then a detection limit of 27.8 pM C-reaction protein (CRP) could be achieved with an immunofluorescent nanosphere (IFN)-based lateral flow test strip. The assay was 257-fold more sensitive than that with a conventional Au-based lateral flow test strip for CRP detection. Besides, the fluorescence intensity of FNs and bioactivity of IFNs were stable during 6 months of storage. Hence, the assay owns good reproducibility (intra-assay variability of 5.3% and interassay variability of 6.6%). Furthermore, other cancer biomarkers (PSA, CEA, AFP) showed negative results by this method, validating the excellent specificity of the method. Then the assay was successfully applied to quantitatively detect CRP in peripheral blood plasma samples from lung cancer and breast cancer patients, and healthy people, facilitating the diagnosis of lung cancer. It holds a good prospect of POC protein biomarker detection.

  4. Rapid DNA extraction for specific detection and quantitation of Mycobacterium tuberculosis DNA in sputum specimens using taqman assays

    Science.gov (United States)

    Gomez, Diana I.; Mullin, Caroline S.; Mora-Guzmán, Francisco; Crespo-Solis, J. Gonzalo; Fisher-Hoch, Susan P.; McCormick, Joseph B.; Restrepo, Blanca I.

    2011-01-01

    SUMMARY Rapid tuberculosis (TB) detection is critical for disease control, and further quantitation of Mycobacterium tuberculosis (Mtb) in sputum is valuable for epidemiological and clinical studies. We evaluated a simple, robust and cost-efficient in-house DNA extraction and downstream taqman approach for detection and quantitation of Mtb genomes from sputum of newly-diagnosed TB patients and non-TB controls. DNA was extracted using guanidine isothiocyanate and silica-based spin columns in less than 2h, stored frozen, and taqman assays were used to detect Mtb with IS6110 and quantify it targeting RD1 and IS1081. The taqmans had a sensitivity > 95% in 108 culture-confirmed TB patients and specificity of 100% in 43 non-TB controls. Genome counts were correlated with the Mycobacterial Growth Indicator Tubes’ (MGIT) time-to-detection values (1/TTD×1000; rho=0.66; p<0.001) in 91 TB patients (33 excluded with MGIT contamination). This linear relationship was nearly identical between mycobacteria isolated from sputum and H37Rv Mtb grown in-vitro to its log phase. TB treatment between 3 and 7 days was associated with lower 1/TTD×1000 values but not with genome counts. Together, our protocol provides rapid, specific, inexpensive and quantitative detection of Mtb DNA in fresh or stored sputa making it a robust tool for prompt TB diagnosis, and with potential use for clinical and epidemiologic studies. PMID:22088321

  5. A Novel Pretreatment-Free Duplex Chamber Digital PCR Detection System for the Absolute Quantitation of GMO Samples.

    Science.gov (United States)

    Zhu, Pengyu; Wang, Chenguang; Huang, Kunlun; Luo, Yunbo; Xu, Wentao

    2016-03-18

    Digital polymerase chain reaction (PCR) has developed rapidly since it was first reported in the 1990s. However, pretreatments are often required during preparation for digital PCR, which can increase operation error. The single-plex amplification of both the target and reference genes may cause uncertainties due to the different reaction volumes and the matrix effect. In the current study, a quantitative detection system based on the pretreatment-free duplex chamber digital PCR was developed. The dynamic range, limit of quantitation (LOQ), sensitivity and specificity were evaluated taking the GA21 event as the experimental object. Moreover, to determine the factors that may influence the stability of the duplex system, we evaluated whether the pretreatments, the primary and secondary structures of the probes and the SNP effect influence the detection. The results showed that the LOQ was 0.5% and the sensitivity was 0.1%. We also found that genome digestion and single nucleotide polymorphism (SNP) sites affect the detection results, whereas the unspecific hybridization within different probes had little side effect. This indicated that the detection system was suited for both chamber-based and droplet-based digital PCR. In conclusion, we have provided a simple and flexible way of achieving absolute quantitation for genetically modified organism (GMO) genome samples using commercial digital PCR detection systems.

  6. Use of quantitative real-time PCR for direct detection of serratia marcescens in marine and other aquatic environments.

    Science.gov (United States)

    Joyner, Jessica; Wanless, David; Sinigalliano, Christopher D; Lipp, Erin K

    2014-03-01

    Serratia marcescens is the etiological agent of acroporid serratiosis, a distinct form of white pox disease in the threatened coral Acropora palmata. The pathogen is commonly found in untreated human waste in the Florida Keys, which may contaminate both nearshore and offshore waters. Currently there is no direct method for detection of this bacterium in the aquatic or reef environment, and culture-based techniques may underestimate its abundance in marine waters. A quantitative real-time PCR assay was developed to detect S. marcescens directly from environmental samples, including marine water, coral mucus, sponge tissue, and wastewater. The assay targeted the luxS gene and was able to distinguish S. marcescens from other Serratia species with a reliable quantitative limit of detection of 10 cell equivalents (CE) per reaction. The method could routinely discern the presence of S. marcescens for as few as 3 CE per reaction, but it could not be reliably quantified at this level. The assay detected environmental S. marcescens in complex sewage influent samples at up to 761 CE ml(-1) and in septic system-impacted residential canals in the Florida Keys at up to 4.1 CE ml(-1). This detection assay provided rapid quantitative abilities and good sensitivity and specificity, which should offer an important tool for monitoring this ubiquitous pathogen that can potentially impact both human health and coral health.

  7. A Novel Pretreatment-Free Duplex Chamber Digital PCR Detection System for the Absolute Quantitation of GMO Samples

    Directory of Open Access Journals (Sweden)

    Pengyu Zhu

    2016-03-01

    Full Text Available Digital polymerase chain reaction (PCR has developed rapidly since it was first reported in the 1990s. However, pretreatments are often required during preparation for digital PCR, which can increase operation error. The single-plex amplification of both the target and reference genes may cause uncertainties due to the different reaction volumes and the matrix effect. In the current study, a quantitative detection system based on the pretreatment-free duplex chamber digital PCR was developed. The dynamic range, limit of quantitation (LOQ, sensitivity and specificity were evaluated taking the GA21 event as the experimental object. Moreover, to determine the factors that may influence the stability of the duplex system, we evaluated whether the pretreatments, the primary and secondary structures of the probes and the SNP effect influence the detection. The results showed that the LOQ was 0.5% and the sensitivity was 0.1%. We also found that genome digestion and single nucleotide polymorphism (SNP sites affect the detection results, whereas the unspecific hybridization within different probes had little side effect. This indicated that the detection system was suited for both chamber-based and droplet-based digital PCR. In conclusion, we have provided a simple and flexible way of achieving absolute quantitation for genetically modified organism (GMO genome samples using commercial digital PCR detection systems.

  8. Quantitative multiplex assay for simultaneous detection and identification of Indiana and New Jersey serotypes of vesicular stomatitis virus

    DEFF Research Database (Denmark)

    Rasmussen, Thomas Bruun; Uttenthal, Åse; Fernandez, Jovita

    2005-01-01

    In order to establish a rapid and reliable system for the detection of vesicular stomatitis virus (VSV), we developed a quantitative reverse transcription-PCR assay for the detection, quantification, and differentiation of the major serotypes, VSV Indiana and VSV New Jersey, using a closed......-tube multiplex format. The detection system is based on the recently invented primer-probe energy transfer (PriProET) system. A region of the gene encoding the RNA-dependent RNA polymerase was amplified by using VSV-specific primers in the presence of two serotype-specific fluorescent probes. By incorporating...... identification of VSV....

  9. Online platform for applying space-time scan statistics for prospectively detecting emerging hot spots of dengue fever.

    Science.gov (United States)

    Chen, Chien-Chou; Teng, Yung-Chu; Lin, Bo-Cheng; Fan, I-Chun; Chan, Ta-Chien

    2016-11-25

    Cases of dengue fever have increased in areas of Southeast Asia in recent years. Taiwan hit a record-high 42,856 cases in 2015, with the majority in southern Tainan and Kaohsiung Cities. Leveraging spatial statistics and geo-visualization techniques, we aim to design an online analytical tool for local public health workers to prospectively identify ongoing hot spots of dengue fever weekly at the village level. A total of 57,516 confirmed cases of dengue fever in 2014 and 2015 were obtained from the Taiwan Centers for Disease Control (TCDC). Incorporating demographic information as covariates with cumulative cases (365 days) in a discrete Poisson model, we iteratively applied space-time scan statistics by SaTScan software to detect the currently active cluster of dengue fever (reported as relative risk) in each village of Tainan and Kaohsiung every week. A village with a relative risk >1 and p value dengue fever transmission on a weekly basis at the village level by using the routine surveillance data.

  10. Detection of macrophage activity in atherosclerosis in vivo using multichannel, high-resolution laser scanning fluorescence microscopy

    Science.gov (United States)

    Pande, Ashvin N.; Kohler, Rainer; Aikawa, Elena; Weissleder, Ralph; Jaffer, Farouc

    2006-03-01

    Molecular and cellular mechanisms of atherogenesis and its treatment are largely being unraveled by in vitro techniques. We describe methodology to directly image macrophage cell activity in vivo in a murine model of atherosclerosis using laser scanning fluorescence microscopy (LSFM) and a macrophage-targeted, near-infrared fluorescent (NIRF) magnetofluorescent nanoparticle (MFNP). Atherosclerotic apolipoprotein E deficient (apoE -/-) mice (n=10) are injected with MFNP or 0.9% saline, and wild-type mice (n=4) are injected with MFNP as additional controls. After 24 h, common carotid arteries are surgically exposed and prepared for LSFM. Multichannel LSFM of MFNP-enhanced carotid atheroma (5×5-µm in-plane resolution) shows a strong focal NIRF signal, with a plaque target-to-background ratio of 3.9+/-1.8. Minimal NIRF signal is observed in control mice. Spectrally resolved indocyanine green (ICG) fluorescence angiograms confirm the intravascular location of atheroma. On ex vivo fluorescence reflectance imaging, greater NIRF plaque signal is seen in apoE -/- MFNP mice compared to controls (p<0.01). The NIRF signal correlates well with immunostained macrophages, both by stained surface area (r=0.77) and macrophage number (r=0.86). The validated experimental methodology thus establishes a platform for investigating macrophage activity in atherosclerosis in vivo, and has implications for the detection of clinical vulnerable plaques.

  11. On detector linearity and precision of beam shift detection for quantitative differential phase contrast applications

    Energy Technology Data Exchange (ETDEWEB)

    Zweck, Josef, E-mail: josef.zweck@ur.de; Schwarzhuber, Felix; Wild, Johannes; Galioit, Vincent

    2016-09-15

    Differential phase contrast is a STEM imaging mode where minute sideways deflections of the electron probe are monitored, usually by using a position sensitive device (Chapman, 1984 [1]; Lohr et al., 2012 [2]) or, alternatively in some cases, a fast camera (Müller et al., 2012 [3,4]; Yang et al., 2015 [5]; Pennycook et al., 2015 [6]) as a pixelated detector. While traditionally differential phase contrast electron microscopy was mainly focused on investigations of micro-magnetic domain structures and their specific features, such as domain wall widths, etc. (Chapman, 1984 [1]; Chapman et al., 1978, 1981, 1985 [7–9]; Sannomiya et al., 2004 [10]), its usage has recently been extended to mesoscopic (Lohr et al., 2012, 2016 [2,12]; Bauer et al., 2014 [11]; Shibata et al., 2015 [13]) and nano-scale electric fields (Shibata et al., 2012 [14]; Mueller et al., 2014 [15]). In this paper, the various interactions which can cause a beam deflection are reviewed and expanded by two so far undiscussed mechanisms which may be important for biological applications. As differential phase contrast microscopy strongly depends on the ability to detect minute beam deflections we first treat the linearity problem for an annular four quadrant detector and then determine the factors which limit the minimum measurable deflection angle, such as S/N ratio, current density, dwell time and detector geometry. Knowing these factors enables the experimenter to optimize the set-up for optimum performance of the microscope and to get a clear figure for the achievable field resolution error margins. - Highlights: • Detector linearity range determined. • Quantitative treatment of measurement precision for differential phase contrast. • Optimization strategy for detector geometry. • Possible application of differential phase contrast in biology.

  12. A rapid and quantitative method to detect human circulating tumor cells in a preclinical animal model.

    Science.gov (United States)

    Tu, Shih-Hsin; Hsieh, Yi-Chen; Huang, Li-Chi; Lin, Chun-Yu; Hsu, Kai-Wen; Hsieh, Wen-Shyang; Chi, Wei-Ming; Lee, Chia-Hwa

    2017-06-23

    As cancer metastasis is the deadliest aspect of cancer, causing 90% of human deaths, evaluating the molecular mechanisms underlying this process is the major interest to those in the drug development field. Both therapeutic target identification and proof-of-concept experimentation in anti-cancer drug development require appropriate animal models, such as xenograft tumor transplantation in transgenic and knockout mice. In the progression of cancer metastasis, circulating tumor cells (CTCs) are the most critical factor in determining the prognosis of cancer patients. Several studies have demonstrated that measuring CTC-specific markers in a clinical setting (e.g., flow cytometry) can provide a current status of cancer development in patients. However, this useful technique has rarely been applied in the real-time monitoring of CTCs in preclinical animal models. In this study, we designed a rapid and reliable detection method by combining a bioluminescent in vivo imaging system (IVIS) and quantitative polymerase chain reaction (QPCR)-based analysis to measure CTCs in animal blood. Using the IVIS Spectrum CT System with 3D-imaging on orthotropic-developed breast-tumor-bearing mice. In this manuscript, we established a quick and reliable method for measuring CTCs in a preclinical animal mode. The key to this technique is the use of specific human and mouse GUS primers on DNA/RNA of mouse peripheral blood under an absolute qPCR system. First, the high sensitivity of cancer cell detection on IVIS was presented by measuring the luciferase carried MDA-MB-231 cells from 5 to 5x10(11) cell numbers with great correlation (R(2) = 0.999). Next, the MDA-MB-231 cell numbers injected by tail vein and their IVIS radiance signals were strongly corrected with qPCR-calculated copy numbers (R(2) > 0.99). Furthermore, by applying an orthotropic implantation animal model, we successfully distinguished xenograft tumor-bearing mice and control mice with a significant difference (p < 0

  13. Absolute quantitation of proteins by acid hydrolysis combined with amino acid detection by mass spectrometry.

    Science.gov (United States)

    Mirgorodskaya, Olga A; Körner, Roman; Kozmin, Yuri P; Roepstorff, Peter

    2012-01-01

    Amino acid analysis is among the most accurate methods for absolute quantification of proteins and peptides. Here, we combine acid hydrolysis with the addition of isotopically labeled standard amino acids and analysis by mass spectrometry for accurate and sensitive protein quantitation. Quantitation of less than 10 fmol of protein standards with errors below 10% has been demonstrated using this method.

  14. Absolute quantitation of proteins by Acid hydrolysis combined with amino Acid detection by mass spectrometry

    DEFF Research Database (Denmark)

    Mirgorodskaya, Olga A; Körner, Roman; Kozmin, Yuri P

    2012-01-01

    Amino acid analysis is among the most accurate methods for absolute quantification of proteins and peptides. Here, we combine acid hydrolysis with the addition of isotopically labeled standard amino acids and analysis by mass spectrometry for accurate and sensitive protein quantitation....... Quantitation of less than 10 fmol of protein standards with errors below 10% has been demonstrated using this method (1)....

  15. Quantitative trait loci involved in sex determination and body growth in the gilthead sea bream (Sparus aurata L. through targeted genome scan.

    Directory of Open Access Journals (Sweden)

    Dimitrios Loukovitis

    Full Text Available Among vertebrates, teleost fish exhibit a considerably wide range of sex determination patterns that may be influenced by extrinsic parameters. However even for model fish species like the zebrafish Danio rerio the precise mechanisms involved in primary sex determination have not been studied extensively. The zebrafish, a gonochoristic species, is lacking discernible sex chromosomes and the sex of juvenile fish is difficult to determine. Sequential protandrous hermaphrodite species provide distinct determination of the gender and allow studying the sex determination process by looking at the mechanism of sex reversal. This is the first attempt to understand the genetic basis of phenotypic variation for sex determination and body weight in a sequential protandrous hermaphrodite species, the gilthead sea bream (Sparus aurata. This work demonstrates a fast and efficient strategy for Quantitative Trait Loci (QTL detection in the gilthead sea bream, a non-model but target hermaphrodite fish species. Therefore a comparative mapping approach was performed to query syntenies against two other Perciformes, the European sea bass (Dicentrarchus labrax, a gonochoristic species and the Asian sea bass (Lates calcarifer a protandrous hermaphrodite. In this manner two significant QTLs, one QTL affecting both body weight and sex and one QTL affecting sex, were detected on the same linkage group. The co-segregation of the two QTLs provides a genomic base to the observed genetic correlation between these two traits in sea bream as well as in other teleosts. The identification of QTLs linked to sex reversal and growth, will contribute significantly to a better understanding of the complex nature of sex determination in S. aurata where most individuals reverse to the female sex at the age of two years through development and maturation of the ovarian portion of the gonad and regression of the testicular area. [Genomic sequences reported in this manuscript have been

  16. Sensitivity of /sup 67/Ga-scanning in sarcoidosis: Detection of biopsy proven pulmonary lesions radiographically undetectable

    Energy Technology Data Exchange (ETDEWEB)

    Beaumont, D.; Herry, J.Y.; Le Cloirec, J.; Le Jeune, J.J.; de Labarthe, B.

    1982-01-01

    Three cases are reported in which gallium-67 citrate scanning disclosed the presence of pulmonary sarcoid lesions, which were confirmed by open lung biopsy. In all three cases the chest radiograph showed no evidence of pulmonary parenchymal leisons. The present report provides evidence that the gallium-67 scan is more sensitive than radiography in disclosing sarcoid lesions of the lung parenchyma. The scan is useful in the management of sarcoidosis, as it shows progressions or remissions of disease more reliably than chest radiographs.

  17. The detection and influence of food soils on microorganisms on stainless steel using scanning electron microscopy and epifluorescence microscopy.

    Science.gov (United States)

    Whitehead, Kathryn A; Smith, Lindsay A; Verran, Joanna

    2010-07-31

    A range of food soils and components (complex [meat extract, fish extract, and cottage cheese extract]; oils [cholesterol, fish oil, and mixed fatty acids]; proteins [bovine serum albumin (BSA), fish peptones, and casein]; and carbohydrates [glycogen, starch, and lactose]) were deposited onto 304 2B finish stainless steel surfaces at different concentrations (10-0.001%). Scanning electron microscopy (SEM) and epifluorescence microscopy were used to visualise the cell and food soil distribution across the surface. Epifluorescence microscopy was also used to quantify the percentage of a field covered by cells or soil. At 10% concentration, most soils, with the exception of BSA and fish peptone were easily visualised using SEM, presenting differences in gross soil morphology and distribution. When soil was stained with acridine orange and visualised by epifluorescence microscopy, the limit of detection of the method varied between soils, but some (meat, cottage cheese and glycogen) were detected at the lowest concentrations used (0.001%). The decrease in soil concentration did not always relate to the surface coverage measurement. When 10% food soil was applied to a surface with Escherichia coli and compared, cell attachment differed depending on the nature of the soil. The highest percentage coverage of cells was observed on surfaces with fish extract and related products (fish peptone and fish oil), followed by carbohydrates, meat extract/meat protein, cottage cheese/casein and the least to the oils (cholesterol and mixed fatty acids). Cells could not be clearly observed in the presence of some food soils using SEM. Findings demonstrate that food soils heterogeneously covered stainless steel surfaces in differing patterns. The pattern and amount of cell attachment was related to food soil type rather than to the amount of food soil detected. This work demonstrates that in the study of conditioning film and cell retention on the hygienic properties of surfaces, SEM

  18. Computed tomography scan to detect traumatic arthrotomies and identify periarticular wounds not requiring surgical intervention: an improvement over the saline load test.

    Science.gov (United States)

    Konda, Sanjit R; Davidovitch, Roy I; Egol, Kenneth A

    2013-09-01

    To report our experience with computed tomography (CT) scans to detect traumatic arthrotomies of the knee (TAK) joint based on the presence of intra-articular air. Retrospective review. Level I trauma center. Sixty-two consecutive patients (63 knees) underwent a CT scan of the knee in the emergency department and had a minimum of 14 days follow-up. Cohort of 37 patients (37 knees) from the original 62 patients who underwent a saline load test (SLT). CT scan and SLT. Positive traumatic arthrotomy of the knee (+TAK) was defined as operating room (OR) confirmation of an arthrotomy or no intra-articular air on CT scan (-iaCT) (and -SLT if performed) with follow-up revealing a septic knee. Periarticular wound equivalent to no traumatic arthrotomy (pw = (-TAK)) was defined as OR evaluation revealing no arthrotomy or -iaCT (and -SLT if performed) with follow-up revealing no septic knee. All 32 knees with intra-articular air on CT scan (+iaCT) had OR confirmation of a TAK and none of these patients had a knee infection at a mean follow-up of 140.0 ± 279.6 days. None of the 31 patients with -iaCT had a knee infection at a mean follow-up of 291.0 ± 548.1 days. Based on these results, the sensitivity and specificity of the CT scan to detect +TAK and pw = (-TAK) was 100%. In a subgroup of 37 patients that received both a CT scan and the conventional SLT, the sensitivity and specificity of the CT scan was 100% compared with 92% for the SLT (P wounds that do not require surgical intervention and should be considered a valid diagnostic test in the appropriate clinical setting. Diagnostic Level III. See Instructions for Authors for a complete description of levels of evidence.

  19. High definition colonoscopy combined with i-Scan is superior in the detection of colorectal neoplasias compared with standard video colonoscopy: a prospective randomized controlled trial.

    Science.gov (United States)

    Hoffman, A; Sar, F; Goetz, M; Tresch, A; Mudter, J; Biesterfeld, S; Galle, P R; Neurath, M F; Kiesslich, R

    2010-10-01

    Colonoscopy is the accepted gold standard for the detection of colorectal cancer. The aim of the current study was to prospectively compare high definition plus (HD+) colonoscopy with I-Scan functionality (electronic staining) vs. standard video colonoscopy. The primary endpoint was the detection of patients having colon cancer or at least one adenoma. A total of 220 patients due to undergo screening colonoscopy, postpolypectomy surveillance or with a positive occult blood test were randomized in a 1 : 1 ratio to undergo HD+ colonoscopy in conjunction with I-Scan surface enhancement (90i series, Pentax, Tokyo, Japan) or standard video colonoscopy (EC-3870FZK, Pentax). Detected colorectal lesions were judged according to type, location, and size. Lesions were characterized in the HD+ group by using further I-Scan functionality (p- and v-modes) to analyze pattern and vessel architecture. Histology was predicted and biopsies or resections were performed on all identified lesions. HD+ colonoscopy with I-Scan functionality detected significantly more patients with colorectal neoplasia (38 %) compared with standard resolution endoscopy (13 %) (200 patients finally analyzed; 100 per arm). Significantly more neoplastic (adenomatous and cancerous) lesions and more flat adenomas could be detected using high definition endoscopy with surface enhancement. Final histology could be predicted with high accuracy (98.6 %) within the HD+ group. HD+ colonoscopy with I-Scan is superior to standard video colonoscopy in detecting patients with colorectal neoplasia based on this prospective, randomized, controlled trial. © Georg Thieme Verlag KG Stuttgart · New York.

  20. Nearest Neighbor Averaging and its Effect on the Critical Level and Minimum Detectable Concentration for Scanning Radiological Survey Instruments that Perform Facility Release Surveys.

    Energy Technology Data Exchange (ETDEWEB)

    Fournier, Sean Donovan; Beall, Patrick S; Miller, Mark L

    2014-08-01

    Through the SNL New Mexico Small Business Assistance (NMSBA) program, several Sandia engineers worked with the Environmental Restoration Group (ERG) Inc. to verify and validate a novel algorithm used to determine the scanning Critical Level (L c ) and Minimum Detectable Concentration (MDC) (or Minimum Detectable Areal Activity) for the 102F scanning system. Through the use of Monte Carlo statistical simulations the algorithm mathematically demonstrates accuracy in determining the L c and MDC when a nearest-neighbor averaging (NNA) technique was used. To empirically validate this approach, SNL prepared several spiked sources and ran a test with the ERG 102F instrument on a bare concrete floor known to have no radiological contamination other than background naturally occurring radioactive material (NORM). The tests conclude that the NNA technique increases the sensitivity (decreases the L c and MDC) for high-density data maps that are obtained by scanning radiological survey instruments.

  1. Quantitative analysis of epicardial fat volume: effects of scanning protocol and reproducibility of measurements in non-contrast cardiac CT vs. coronary CT angiography.

    Science.gov (United States)

    D'Errico, Luigia; Salituri, Francesco; Ciardetti, Marco; Favilla, Riccardo; Mazzarisi, Alessandro; Coppini, Giuseppe; Bartolozzi, Carlo; Marraccini, Paoli

    2017-06-01

    Several studies have focused on the role of epicardial fat in the pathogenesis of cardiovascular disease (CVD). The main purpose of the study was to evaluate a computerized method for the quantitative analysis of epicardial fat volume (EFV) by non-contrast cardiac CT (NCT) for coronary calcium scan and coronary CT angiography (coronary CTA). Thirty patients (61±12.5 years, 73% male, body mass index (BMI) =25.9±6.3 kg/m2) referred to our Institution for suspected coronary artery disease (CAD) underwent NCT and coronary CTA. Epicardial boundaries were traced by 2 experienced operators (operator 1, operators 2) on 3 and 6 short-axis (SA) slices. EFV was computed with a semi-automatic method using an in-house developed software based on spherical harmonic representation of the epicardial surface. In order to analyze the inter-observer variability both the Coefficient of Repeatability (CR) and Intra Class Correlation (ICC) were computed. The total EFV was 103.62±50.97 and 94.96±67.91 cc in NCT and coronary CTA with non-significant difference (P=0.292). CR error was 10.22 cc for operator 1 and 11.31 cc for operator 2 in NCT and 7.99 cc for operator 1 and 7.75 cc for operator 2 in coronary CTA. To analyze the inter-observer variability CR and ICC were computed. CR was 8.17 and 8.39 cc with NCT and 7.07 and 7.21 cc with CTA for 6 and 3 SA slices respectively. ICC values >0.99 were obtained in all cases. The right ventricular EFV was 67.23±31.4 and 57.41±34.3 cc for NCT and coronary CTA respectively; the corresponding values for left ventricular EFV were 38.01±19.1 and 35.27±25.9 cc. Both NCT and coronary CTA can be used with low intra- and inter-observer variability for computer-assisted measurements of EFV. Cardiac CT may allow a fast and reliable computation of EFV in clinical setting.

  2. A Critical Comparison Between Two Scanning Protocols of High-Resolution Peripheral Quantitative Computed Tomography at the Distal Radius in Adolescents.

    Science.gov (United States)

    Cheuk, Ka-Yee; Tam, Elisa Man-Shan; Yu, Fiona Wai-Ping; Yip, Benjamin Hon-Kei; Hung, Vivian Wing-Yin; Wang, Xiaofang; Ghasem-Zadeh, Ali; Zhu, Tracy Y; Qin, Ling; Cheng, Jack Chun-Yiu; Lam, Tsz-Ping

    2016-01-01

    High-resolution peripheral quantitative computed tomography (HR-pQCT) is a unique technology for assessing bone mineral density and bone microarchitecture. Currently, no universally accepted protocol for selecting the region of interest (ROI) at the distal radius has been established for growing subjects. This study aimed (1) to investigate the differences in HR-pQCT measurements of 2 different ROI protocols applied to the distal radius of healthy adolescents and (2) to identify the least common area of ROI (the least common ROI) between the protocols. Twenty-six boys and 26 girls aged between 13 and 16 yr old were recruited. Nondominant distal radius was scanned by 2 HR-pQCT protocols, namely, the "5-mm protocol," where the distal end of ROI started at 5 mm proximal to a reference line, and the "4% protocol," where the ROI started at 4% of the ulnar length proximal to another reference line. The least common ROI between the 2 protocols was identified and the slice numbering within the common ROI was determined. Bland-Altman plots were used to check the agreement of the least common ROIs between the 2 protocols. Paired t-test and Wilcoxon signed-rank test were used for analysis. In boys, significant differences between protocols were found in most parameters with the maximum difference observed in the cortical area (25.0%, p only for total volumetric bone mineral density (3.6%, p = 0.032). The number of slices in the least common ROI was 66 (60.0%) and 57 (51.8%) in boys and girls, respectively. Good agreements on all HR-pQCT parameters from the least common ROI between the 2 protocols were found. Significant differences in bone parameters were noted between the 2 protocols. When comparing the 2 protocols, observed gender differences could reflect the differences in skeletal growth at the peripubertal period between genders. Least common ROI could be useful for cross-center comparisons and when merging datasets from different centers. Copyright © 2016

  3. Droplet Microfluidics Platform for Highly Sensitive and Quantitative Detection of Malaria-Causing Plasmodium Parasites Based on Enzyme Activity Measurement

    DEFF Research Database (Denmark)

    Juul, Sissel; Nielsen, Christine Juul Fælled; Labouriau, Rodrigo

    2012-01-01

    We present an attractive new system for the specific and sensitive detection of the malaria-causing Plasmodium parasites. The system relies on isothermal conversion of single DNA cleavage–ligation events catalyzed specifically by the Plasmodium enzyme topoisomerase I to micrometer-sized products...... detectable at the single-molecule level. Combined with a droplet microfluidics lab-on-a-chip platform, this design allowed for sensitive, specific, and quantitative detection of all human-malaria-causing Plasmodium species in single drops of unprocessed blood with a detection limit of less than one parasite....../μL. Moreover, the setup allowed for detection of Plasmodium parasites in noninvasive saliva samples from infected patients. During recent years malaria transmission has declined worldwide, and with this the number of patients with low-parasite density has increased. Consequently, the need for accurate...

  4. Detection of urinary stones at reduced radiation exposure: a phantom study comparing computed radiography and a low-dose digital radiography linear slit scanning system

    Science.gov (United States)

    Szucs-Farkas, Zsolt; Chakraborty, D. P.; Thoeny, Harriet C.; Loupatatzis, Christos; Vock, Peter; Harald, Bonel

    2010-01-01

    Objective In this experimental study we assessed the diagnostic performance of linear slit scanning radiography (LSSR) compared to conventional computed radiography (CR) in the detection of urinary calculi in an anthropomorphic phantom imitating patients weighing approximately 58 to 88 kg. Conclusion Compared to computed radiography, LSSR is superior in the detection of urinary stones and may be used for pretreatment localization and follow-up at a lower patient exposure. PMID:19457787

  5. A simple and compact smartphone accessory for quantitative chemiluminescence-based lateral flow immunoassay for salivary cortisol detection.

    Science.gov (United States)

    Zangheri, Martina; Cevenini, Luca; Anfossi, Laura; Baggiani, Claudio; Simoni, Patrizia; Di Nardo, Fabio; Roda, Aldo

    2015-02-15

    We have developed a simple and accurate biosensor based on a chemiluminescent (CL)-lateral flow immunoassay (LFIA) method integrated in a smartphone to quantitatively detect salivary cortisol. The biosensor is based on a direct competitive immunoassay using peroxidase-cortisol conjugate, detected by adding the chemiluminescent substrate luminol/enhancer/hydrogen peroxide. The smartphone camera is used as light detector, for image acquisition and data handling via a specific application. We 3D-printed simple accessories to adapt the smartphone. The system comprises a cartridge, which houses the LFIA strip, and a smartphone adaptor with a plano-convex lens and a cartridge-insertion slot. This provides a mini-darkbox and aligned optical interface between the camera and the LFIA membrane for acquiring CL signals. The method is simple and fast, with a detection limit of 0.3 ng/mL. It provides quantitative analysis in the range of 0.3-60 ng/mL, which is adequate for detecting salivary cortisol in the clinically accepted range. It could thus find application in the growing area of home-self-diagnostic device technology for clinical biomarker monitoring, overcoming the current difficulties in achieving sensitive and quantitative information with conventional systems taking the advantage of smartphone connectivity and the enhanced performance of the included camera. Copyright © 2014 Elsevier B.V. All rights reserved.

  6. A novel CMOS image sensor system for quantitative loop-mediated isothermal amplification assays to detect food-borne pathogens.

    Science.gov (United States)

    Wang, Tiantian; Kim, Sanghyo; An, Jeong Ho

    2017-02-01

    Loop-mediated isothermal amplification (LAMP) is considered as one of the alternatives to the conventional PCR and it is an inexpensive portable diagnostic system with minimal power consumption. The present work describes the application of LAMP in real-time photon detection and quantitative analysis of nucleic acids integrated with a disposable complementary-metal-oxide semiconductor (CMOS) image sensor. This novel system works as an amplification-coupled detection platform, relying on a CMOS image sensor, with the aid of a computerized circuitry controller for the temperature and light sources. The CMOS image sensor captures the light which is passing through the sensor surface and converts into digital units using an analog-to-digital converter (ADC). This new system monitors the real-time photon variation, caused by the color changes during amplification. Escherichia coli O157 was used as a proof-of-concept target for quantitative analysis, and compared with the results for Staphylococcus aureus and Salmonella enterica to confirm the efficiency of the system. The system detected various DNA concentrations of E. coli O157 in a short time (45min), with a detection limit of 10fg/μL. The low-cost, simple, and compact design, with low power consumption, represents a significant advance in the development of a portable, sensitive, user-friendly, real-time, and quantitative analytic tools for point-of-care diagnosis. Copyright © 2016 Elsevier B.V. All rights reserved.

  7. The use of indium-111 labeled platelet scanning for the detection of asymptomatic deep venous thrombosis in a high risk population

    Energy Technology Data Exchange (ETDEWEB)

    Siegel, R.S.; Rae, J.L.; Ryan, N.L.; Edwards, C.; Fortune, W.P.; Lewis, R.J.; Reba, R.C. (George Washington Univ. Medical Center, Washington, DC (USA))

    1989-11-01

    Five hundred indium-111 labeled platelet imaging studies (387 donor and 113 autologous) were performed postoperatively in 473 patients who had undergone total hip replacement, total knee replacement, or internal fixation of a hip fracture to detect occult deep venous thrombosis. All patients had been anticoagulated prophylactically with aspirin, warfarin sodium (Coumadin), or dextran. Thirty-four possible cases of proximal deep venous thrombosis were identified in 28 asymptomatic patients. To verify the scan results, 31 venograms were performed in 25 patients (three refused). In 21 of 31 cases, totally occlusive thrombi were detected; in 5 cases, partially occlusive thrombi were detected; in 5 cases, no thrombus was seen. No patient who had a negative scan nor any patient who had a verified positive scan (and received appropriate heparin therapy) subsequently developed symptoms or signs of pulmonary embolism. One hundred forty-one indium study patients also underwent Doppler ultrasonography/impedance plethysmography (Doppler/IPG) as a comparative non-invasive technique. In 137 cases, the results of the indium study and Doppler/IPG studies were congruent. The indium study had no false negative results that were detected by Doppler/IPG. No patient had any clinically evident toxicity. These results suggest that indium-111 labeled platelet scanning is a safe, noninvasive means for identifying DVT in high risk patients.

  8. Hot-spot detection and calibration of a scanning thermal probe with a noise thermometry gold wire sample

    NARCIS (Netherlands)

    Gaitas, A.; Wolgast, S.; Covington, E.; Kurdak, C.

    2013-01-01

    Measuring the temperature profile of a nanoscale sample using scanning thermal microscopy is challenging due to a scanning probe's non-uniform heating. In order to address this challenge, we have developed a calibration sample consisting of a 1-?m wide gold wire, which can be heated electrically by

  9. Relative value of thallium-201 and iodine-131 scans in the detection of recurrence or distant metastasis of well differentiated thyroid carcinoma.

    Science.gov (United States)

    Lin, J D; Kao, P F; Weng, H F; Lu, W T; Huang, M J

    1998-07-01

    Radioactive iodine (131I) has been found to be more sensitive and more specific than thallium-201 for the detection of distant metastases and thyroid remnants in the neck in cases of well-differentiated thyroid carcinoma. 201Tl has been deemed particularly useful in localizing metastases or recurrence in patients with a negative 131I scan and abnormal levels of serum thyroglobulin (Tg). This study aimed to: (1) determine the value of 201Tl imaging in localizing metastases or recurrence in patients with well-differentiated thyroid carcinoma, and (2) evaluate the false-positive and false-negative results of 131I and 201Tl scintigraphy. Sixty-two thyroid remnant ablated patients who underwent simultaneous postoperative 201Tl and 131I scans and and serum Tg determinations were evaluated. Fifty patients had papillary thyroid carcinomas and 12 had follicular thyroid carcinomas. 201Tl imaging was performed before the 131I studies. Of the 62 patients who underwent 201Tl imaging studies, 24 were found to have positive results, with local recurrence or distant metastases. Patients with positive results in the 201Tl imaging studies tended to be older, were mor often male, had higher Tg levels and had a higher recurrence rate. Of these 24 patients, ten had negative diagnostic or therapeutic 131I scans. Concurrently, serum Tg levels were less than 5 ng/ml in five of these ten patients. Three patients were deemed false positive by 201Tl scans; one had a parotid tumour, one a periodontal abscess and one lung metastasis. Among the 38 patients with negative 201Tl scans, 11 had positive findings on 131I scans. Three had distant metastases: two with lung metastases and one with bone metastases. Patients with false-positive results on 131I scans included those with biliary tract stones, ovarian cysts, and breast secretion. Of the 27 patients with negative 201Tl and 131I scans, 15 had elevated serum Tg levels. Among these, local recurrence followed by lung metastases was manifested in

  10. Relative value of thallium-201 and iodine-131 scans in the detection of recurrence or distant metastasis of well differentiated thyroid carcinoma

    Energy Technology Data Exchange (ETDEWEB)

    Lin Jen-Der; Weng Hsiao-Fen; Lu Wen-Tsoung [Division of Endocrinology and Metabolism, Chang Gung Memorial Hospital (Taiwan, Province of China); Kao Pan-Fu; Huang Miau-Ju [Department of Nuclear Medicine, Chang Gung Memorial Hospital, Taiwan (Taiwan, Province of China)

    1998-07-01

    Radioactive iodine ({sup 131}I) has been found to be more sensitive and more specific than thallium-201 for the detection of distant metastases and thyroid remnants in the neck in cases of well-differentiated thyroid carcinoma. {sup 201}Tl has been deemed particularly useful in localizing metastases or recurrence in patients with a negative {sup 131}I scan and abnormal levels of serum thyroglobulin (Tg). This study aimed to: (1) determine the value of {sup 201}Tl imaging in localizing metastases or recurrence in patients with well-differentiated thyroid carcinoma, and (2) evaluate the false-positive and false-negative results of {sup 131}I and {sup 201}Tl scintigraphy. Sixty-two thyroid remnant ablated patients who underwent simultaneous postoperative {sup 201}Tl and {sup 131}I scans and and serum Tg determinations were evaluated. Fifty patients had papillary thyroid carcinomas and 12 had follicular thyroid carcinomas. {sup 201}Tl imaging was performed before the {sup 131}I studies. Of the 62 patients who underwent {sup 201}Tl imaging studies, 24 were found to have positive results, with local recurrence or distant metastases. Patients with positive results in the {sup 201}Tl imaging studies tended to be older, were mor often male, had higher Tg levels and had a higher recurrence rate. Of these 24 patients, ten had negative diagnostic or therapeutic {sup 131}I scans. Concurrently, serum Tg levels were less than 5 ng/ml in five of these ten patients. Three patients were deemed false positive by {sup 201}Tl scans; one had a parotid tumour, one a periodontal abscess and one lung metastasis. Among the 38 patients with negative {sup 201}Tl scans, 11 had positive findings on {sup 131}I scans. Three had distant metastases: two with lung metastases and one with bone metastases. Patients with false-positive results on {sup 131}I scans included those with biliary tract stones, ovarian cysts, and breast secretion. Of the 27 patients with negative {sup 201}Tl and {sup 131}I

  11. Detection of airbag impact-induced cone photoreceptor damage by adaptive optics scanning laser ophthalmoscopy: a case report.

    Science.gov (United States)

    Kaizu, Yoshihiro; Nakao, Shintaro; Yamaguchi, Muneo; Murakami, Yusuke; Salehi-Had, Hani; Ishibashi, Tatsuro

    2016-07-08

    The purpose of this study was to report a case of traumatic maculopathy with para-central visual field defects following an impact by airbag deployment using adaptive optics scanning laser ophthalmoscopy (AO-SLO). A 51-year-old man was involved in a motor vehicular accident and his left eye was struck by the deployed airbag, resulting in a para-central scotoma. The patient underwent a full ophthalmologic examination, spectral-domain optical coherence tomography (SD-OCT), and imaging with prototype AO-SLO systems (Canon Inc.) at 14 and 22 months after the injury. Images focused on the photoreceptor layer were recorded in the foveal area, and a montage of AO-SLO images was created. On AO-SLO, focal dark areas could be observed in the left eye at 14 months after the injury. The analysis showed that the cone mosaic (cone density, 16503/mm(2); ratio of hexagonal Voronoi domain, 36.3 %; average nearest-neighbor distance (NND)/expected NND, 0.606) was disordered compared with the normal area of the same eye (cone density, 24821/mm(2); ratio of hexagonal Voronoi domain, 44.1 %; average NND/expected NND, 0.739). The cone defect area corresponded to the area of the scotoma. A second AO-SLO was performed on the patient at 22 months after the injury and although there were still areas with reduced cone reflectivity, partial improvement of cone mosaic was detected by AO-SLO at this time point. Partial recovery of damaged cone photoreceptors following closed globe blunt ocular trauma can be documented using AO-SLO longitudinal tracking.

  12. Evaluation of the ScanRDI(R) as a Rapid Alternative to the Pharmacopoeial Sterility Test Method: Comparison of the Limits of Detection.

    Science.gov (United States)

    Smith, Ron; Von Tress, Mark; Tubb, Cheyenne; Vanhaecke, Erwin

    2010-01-01

    Two sterility test methods, the ScanRDI® rapid sterility test and the United States Pharmacopeia/European Pharmacopoeia/Japanese Pharmacopoeia (USP/EP/JP) compendial sterility test, were compared with respect to the limits of detection for the presence of viable microorganisms in aqueous solutions at low inoculation levels. The ScanRDI® system employs a combination of direct fluorescent labeling techniques and solid-phase laser scanning cytometry to rapidly enumerate viable microorganisms from aqueous samples, whereas the compendial sterility test is a qualitative, growth-based method that uses a visual assessment of turbidity to indicate microbial contamination. Eight microorganisms were evaluated, seven compendial microorganisms (Clostridium sporogenes, Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, Bacillus subtilis, Aspergillus niger, Candida albicans) and the Gram-positive anaerobe Propionibacterium acnes. The number of viable organisms was estimated using the ScanRDI® method and the conventional sterility test method using most probable number methodology. The mean difference between the methods was computed and 95% confidence intervals around the mean difference were estimated. The ScanRDI® method was found to be numerically superior and statistically non-inferior to the compendial (USP/EP/JP) sterility test with respect to the limits of detection for all organisms tested.

  13. Detection of lacunar infarction in brain CT-scans: No evidence of bias from accompanying patient information

    Energy Technology Data Exchange (ETDEWEB)

    Bonke, B.; Knippenberg, F.C.E. van; Duivenvoorden, H.J.; Koudstaal, P.J.; Dijkstra, G.; Hilligersberg, R. van; Kappelle, L.J.

    1989-05-01

    Interobserver agreement in assessing brain CT-scans is, in general, high. The extent, however, to which such agreement is caused by bias through knowledge of other clinical details remains uncertain. The hypothesis that observers are somehow prejudiced before assessing ambiguous, CT-scans in this particular situation was tested. Sixteen neurologists and 16 radiologists volunteered to interpret two ambiguous brain CT-scans, with regard to the presence or absence of a lacunar infarct in the region of the internal capsule. The scans were accompanied by 'patient' information that was or was not suggestive of a stroke. These scans were camouflaged by a variety of other scans, to be assessed in the same way, to mask the purpose of the study. I was assumed that the observers, in their assessments of the scans, would somehow let their ratings of the likelihood of a lacunar infarction in or near the internal capsule be subject to the accompanying information. Results showed lower ratings produced by neurologists (i.e., less likelihood of an infarction) than by radiologists in the majority of all assessments, but no bias by the accompanying information.

  14. Genome-scan analysis for genetic mapping of quantitative trait loci underlying birth weight and onset of puberty in doe kids (Capra hircus).

    Science.gov (United States)

    Esmailizadeh, A K

    2014-12-01

    The objective of this study was to locate quantitative trait loci (QTL) causing variation in birth weight and age of puberty of doe kids in a population of Rayini cashmere goats. Four hundred and thirty kids from five half-sib families were genotyped for 116 microsatellite markers located on the caprine autosomes. The traits recorded were birth weight of the male and female kids, body weight at puberty, average daily gain from birth to age of puberty and age at puberty of the doe kids. QTL analysis was conducted using the least squares interval mapping approach. Linkage analysis indicated significant QTL for birth weight on Capra hircus chromosomes (CHI) 4, 5, 6, 18 and 21. Five QTL located on CHI 5, 14 and 29 were associated with age at puberty. Across-family analysis revealed evidence for overlapping QTL affecting birth weight (78 cM), body weight at puberty (72 cM), average daily gain from birth to age of puberty (72 cM) and age at puberty (76 cM) on CHI 5 and overlapping QTL controlling body weight at puberty and age at puberty on CHI 14 at 18-19 cM. The proportion of the phenotypic variance explained by the detected QTL ranged between 7.9% and 14.4%. Confirming some of the previously reported results for birth weight and growth QTL in goats, this study identified more QTL for these traits and is the first report of QTL for onset of puberty in doe kids. © 2014 Stichting International Foundation for Animal Genetics.

  15. Improved assay to detect Plasmodium falciparum using an uninterrupted, semi-nested PCR and quantitative lateral flow analysis

    OpenAIRE

    Ongagna-Yhombi, Serge Y; Corstjens, Paul; Geva, Eran; Abrams, William R.; Barber, Cheryl A.; Malamud, Daniel; Mharakurwa, Sungano

    2013-01-01

    Background A rapid, non-invasive, and inexpensive point-of-care (POC) diagnostic for malaria followed by therapeutic intervention would improve the ability to control infection in endemic areas. Methods A semi-nested PCR amplification protocol is described for quantitative detection of Plasmodium falciparum and is compared to a traditional nested PCR. The approach uses primers that target the P. falciparum dihydrofolate reductase gene. Results This study demonstrates that it is possible to pe...

  16. Detection of Legionella species in environmental water by the quantitative PCR method in combination with ethidium monoazide treatment.

    Science.gov (United States)

    Inoue, Hiroaki; Takama, Tomoko; Yoshizaki, Miwa; Agata, Kunio

    2015-01-01

    We detected Legionella species in 111 bath water samples and 95 cooling tower water samples by using a combination of conventional plate culture, quantitative polymerase chain reaction (qPCR) and qPCR combined with ethidium monoazide treatment (EMA-qPCR) methods. In the case of bath water samples, Legionella spp. were detected in 30 samples by plate culture, in 85 samples by qPCR, and in 49 samples by EMA-qPCR. Of 81 samples determined to be Legionella-negative by plate culture, 56 and 23 samples were positive by qPCR and EMA-qPCR, respectively. Therefore, EMA treatment decreased the number of Legionella-positive bath water samples detected by qPCR. In contrast, EMA treatment had no effect on cooling tower water samples. We therefore expect that EMA-qPCR is a useful method for the rapid detection of viable Legionella spp. from bath water samples.

  17. Detection limits of quantitative and digital PCR assays and their influence in presence-absence surveys of environmental DNA

    Science.gov (United States)

    Hunter, Margaret; Dorazio, Robert M.; Butterfield, John S.; Meigs-Friend, Gaia; Nico, Leo; Ferrante, Jason A.

    2017-01-01

    A set of universal guidelines is needed to determine the limit of detection (LOD) in PCR-based analyses of low concentration DNA. In particular, environmental DNA (eDNA) studies require sensitive and reliable methods to detect rare and cryptic species through shed genetic material in environmental samples. Current strategies for assessing detection limits of eDNA are either too stringent or subjective, possibly resulting in biased estimates of species’ presence. Here, a conservative LOD analysis grounded in analytical chemistry is proposed to correct for overestimated DNA concentrations predominantly caused by the concentration plateau, a nonlinear relationship between expected and measured DNA concentrations. We have used statistical criteria to establish formal mathematical models for both quantitative and droplet digital PCR. To assess the method, a new Grass Carp (Ctenopharyngodon idella) TaqMan assay was developed and tested on both PCR platforms using eDNA in water samples. The LOD adjustment reduced Grass Carp occupancy and detection estimates while increasing uncertainty – indicating that caution needs to be applied to eDNA data without LOD correction. Compared to quantitative PCR, digital PCR had higher occurrence estimates due to increased sensitivity and dilution of inhibitors at low concentrations. Without accurate LOD correction, species occurrence and detection probabilities based on eDNA estimates are prone to a source of bias that cannot be reduced by an increase in sample size or PCR replicates. Other applications also could benefit from a standardized LOD such as GMO food analysis, and forensic and clinical diagnostics.

  18. Comparison of Sensitivity and Quantitation between Microbead Dielectrophoresis-Based DNA Detection and Real-Time PCR

    Directory of Open Access Journals (Sweden)

    Michihiko Nakano

    2017-09-01

    Full Text Available In this study, we describe a microbead-based method using dielectrophoresis (DEP for the fast detection of DNA amplified by polymerase chain reaction (PCR. This electrical method measures the change in impedance caused by DEP-trapped microbeads to which biotinylated target DNA molecules are chemically attached. Using this method, measurements can be obtained within 20 min. Currently, real-time PCR is among the most sensitive methods available for the detection of target DNA, and is often used in the diagnosis of infectious diseases. We therefore compared the quantitation and sensitivity achieved by our method to those achieved with real-time PCR. We found that the microbead DEP-based method exhibited the same detection limit as real-time PCR, although its quantitative detection range was slightly narrower at 10–105 copies/reaction compared with 10–107 copies/reaction for real-time PCR. Whereas real-time PCR requires expensive and complex instruments, as well as expertise in primer design and experimental principles, our novel method is simple to use, inexpensive, and rapid. This method could potentially detect viral and other DNAs efficiently in combination with conventional PCR.

  19. Quantitative detection method for Roundup Ready soybean in food using duplex real-time PCR MGB chemistry.

    Science.gov (United States)

    Samson, Maria Cristina; Gullì, Mariolina; Marmiroli, Nelson

    2010-07-01

    Methodologies that enable the detection of genetically modified organisms (GMOs) (authorized and non-authorized) in food and feed strongly influence the potential for adequate updating and implementation of legislation together with labeling requirements. Quantitative polymerase chain reaction (qPCR) systems were designed to boost the sensitivity and specificity on the identification of GMOs in highly degraded DNA samples; however, such testing will become economically difficult to cope with due to increasing numbers of approved genetically modified (GM) lines. Multiplexing approaches are therefore in development to provide cost-efficient solution. Construct-specific primers and probe were developed for quantitative analysis of Roundup Ready soybean (RRS) event glyphosate-tolerant soybean (GTS) 40-3-2. The lectin gene (Le1) was used as a reference gene, and its specificity was verified. RRS- and Le1-specific quantitative real-time PCR (qRTPCR) were optimized in a duplex platform that has been validated with respect to limit of detection (LOD) and limit of quantification (LOQ), as well as accuracy. The analysis of model processed food samples showed that the degradation of DNA has no adverse or little effects on the performance of quantification assay. In this study, a duplex qRTPCR using TaqMan minor groove binder-non-fluorescent quencher (MGB-NFQ) chemistry was developed for specific detection and quantification of RRS event GTS 40-3-2 that can be used for practical monitoring in processed food products.

  20. Quantitative Detection of Ethanol/Acetone in Complex Solutions Using Raman Spectroscopy Based on Headspace Gas Analysis.

    Science.gov (United States)

    Zhao, Yubin; Yamaguchi, Yoshinori; Liu, Chenchen; Sekine, Shinichi; Dou, Xiaoming

    2017-01-01

    This paper demonstrated the quantitative detection of ethanol and acetone mixtures in complex solutions with Raman spectroscopy based on headspace gas analysis. By analyzing the volatile components in the headspace, their concentrations in liquid solutions were determined. We constructed our own Raman spectroscopy system to detect the headspace gas quantitatively over a solution in a sealed vial. The Raman spectra of the headspace gases over standard solutions were standardized for finding the concentrations of ethanol, acetone, and ethanol-acetone in mixture solutions. The results showed that the concentration of a gaseous component in the headspace gas was proportional to its ratio in the liquid solution. We obtained a linear relationship between the spectral intensity of volatile components in headspace and the concentration of the liquid solutions. Then, we analyzed the alcohol concentration in a white wine and a Chinese liquor called Fen Chiew by measuring the Raman spectra of the headspace gas over their liquids. For the river water sample, we also implemented our headspace gas detection with Raman spectra to obtain the concentration of acetone in the river sample. This work demonstrated the facilitation of headspace gas analysis by the qualitative and quantitative determination of volatile substances from liquid samples using Raman spectroscopy.

  1. Suitability of thin-layer chromatography-flame ionization detection with regard to quantitative characterization of different fossil fuel products. II. Calibration methods concerning quantitative hydrocarbon-group type analysis

    Energy Technology Data Exchange (ETDEWEB)

    Vela, J.; Membrado, L.; Cebolla, V.L.; Ferrando, A.C. [CSIC, Zaragoza (Spain). Inst. de Carboquimica, Dept. de Procesos Quimicos

    1998-10-01

    Time-consuming external standard-based calibration methods are usually performed for hydrocarbon group type analysis (HGTA) of fossil fuels, regardless of the instrumental chromatographic technique. HGTA of a broad variety of coal and petroleum products was performed using a modern thin-layer chromatography-flame ionization detection (TLC-FID) system and a rapid method based on internal normalization. Repeatability, linear intervals, and sample load ranges for quantitative application of this method are given, namely a heavy oil and its derived hydrocracked products, raw and chemically-modified petroleum asphaltenes, a coal-tar pitch, several coal extracts, and coal hydroliquefaction products. Results from external standard calibration and a normalization method (both obtained by TLC-FID) are in agreement, and they are validated using TLC-ultraviolet scanning. The use of the latter demonstrates that TLC-FID can also be applied to products such as coal extracts and hydroliquefaction products, despite these products being more volatile than petroleum asphaltenes or heavy oils. 14 refs., 3 figs., 5 tabs.

  2. Change detection studies of Sagar Island, India, using Indian Remote Sensing Satellite 1C linear imaging self-scan sensor III data

    Digital Repository Service at National Institute of Oceanography (India)

    DineshKumar, P.K.; Gopinath, G.; Laluraj, C.M.; Seralathan, P.; Mitra, D.

    Research 23 6 1498–1502 West Palm Beach, Florida November 2007 Change Detection Studies of Sagar Island, India, using Indian Remote Sensing Satellite 1C Linear Imaging Self-Scan Sensor III Data P.K. Dinesh Kumar † , Girish Gopinath ‡ , C.M. Laluraj † , P...-Scan Sensor III data. Journal of Coastal Research, 23(6), 1498–1502. West Palm Beach (Florida), ISSN 0749-0208. The coastal zone of Sagar Island, India, is subjected to various cyclic and random processes that continuously modify the region. The shoreline...

  3. Detection of airbag impact-induced cone photoreceptor damage by adaptive optics scanning laser ophthalmoscopy: a case report

    National Research Council Canada - National Science Library

    Kaizu, Yoshihiro; Nakao, Shintaro; Yamaguchi, Muneo; Murakami, Yusuke; Salehi-Had, Hani; Ishibashi, Tatsuro

    2016-01-01

    The purpose of this study was to report a case of traumatic maculopathy with para-central visual field defects following an impact by airbag deployment using adaptive optics scanning laser ophthalmoscopy (AO-SLO...

  4. [THE COMPARATIVE ANALYSIS OF RESULTS OF DETECTION OF CARCINOGENIC TYPES OF HUMAN PAPILLOMA VIRUS BY QUALITATIVE AND QUANTITATIVE TESTS].

    Science.gov (United States)

    Kuzmenko, E T; Labigina, A V; Leshenko, O Ya; Rusanov, D N; Kuzmenko, V V; Fedko, L P; Pak, I P

    2015-05-01

    The analysis of results of screening (n = 3208; sexually active citizen aged from 18 to 59 years) was carried out to detect oncogene types of human papilloma virus in using qualitative (1150 females and 720 males) and quantitative (polymerase chain reaction in real-time (843 females and 115 males) techniques. The human papilloma virus of high oncogene type was detected in 65% and 68.4% of females and in 48.6% and 53% of males correspondingly. Among 12 types of human papilloma virus the most frequently diagnosed was human papilloma virus 16 independently of gender of examined and technique of analysis. In females, under application of qualitative tests rate of human papilloma virus 16 made up to 18.3% (n = 280) and under application of quantitative tests Rte of human papilloma virus made up to 14.9% (n = 126; p ≤ 0.05). Under examination of males using qualitative tests rate of human papilloma virus 16 made up to 8.3% (n = 60) and under application of qualitative tests made up to 12.2% (n = 14; p ≥ 0.05). Under application of qualitative tests rate of detection on the rest ofoncogene types of human papilloma virus varied in females from 3.4% to 8.4% and in males from 1.8% to 5.9%. Under application of qualitative tests to females rate of human papilloma virus with high viral load made up to 68.4%, with medium viral load - 2.85% (n = 24) and with low viral load -0.24% (n = 2). Under application of quantitative tests in males rate of detection of types of human papilloma virus made up to 53% and at that in all high viral load was established. In females, the most of oncogene types of human papilloma virus (except for 31, 39, 59) are detected significantly more often than in males.

  5. Comparison of different approaches to quantitative adenovirus detection in stool specimens of hematopoietic stem cell transplant recipients.

    Science.gov (United States)

    Kosulin, K; Dworzak, S; Lawitschka, A; Matthes-Leodolter, S; Lion, T

    2016-12-01

    Adenoviruses almost invariably proliferate in the gastrointestinal tract prior to dissemination, and critical threshold concentrations in stool correlate with the risk of viremia. Monitoring of adenovirus loads in stool may therefore be important for timely initiation of treatment in order to prevent invasive infection. Comparison of a manual DNA extraction kit in combination with a validated in-house PCR assay with automated extraction on the NucliSENS-EasyMAG device coupled with the Adenovirus R-gene kit (bioMérieux) for quantitative adenovirus analysis in stool samples. Stool specimens spiked with adenovirus concentrations in a range from 10E2-10E11 copies/g and 32 adenovirus-positive clinical stool specimens from pediatric stem cell transplant recipients were tested along with appropriate negative controls. Quantitative analysis of viral load in adenovirus-positive stool specimens revealed a median difference of 0.5 logs (range 0.1-2.2) between the detection systems tested and a difference of 0.3 logs (range 0.0-1.7) when the comparison was restricted to the PCR assays only. Spiking experiments showed a detection limit of 102-103adenovirus copies/g stool revealing a somewhat higher sensitivity offered by the automated extraction. The dynamic range of accurate quantitative analysis by both systems investigated was between 103 and 108 virus copies/g. The differences in quantitative analysis of adenovirus copy numbers between the systems tested were primarily attributable to the DNA extraction method used, while the qPCR assays revealed a high level of concordance. Both systems showed adequate performance for detection and monitoring of adenoviral load in stool specimens. Copyright © 2016 Elsevier B.V. All rights reserved.

  6. Quantitative image analysis for the detection of motion artefacts in coronary artery computed tomography

    NARCIS (Netherlands)

    Kristanto, Wisnumurti; van Ooijen, Peter M.; Dikkers, Riksta; Greuter, Marcel J.; Zijlstra, Felix; Oudkerk, Matthijs

    Multi detector-row CT (MDCT), the current preferred method for coronary artery disease assessment, is still affected by motion artefacts. To rule out motion artefacts, qualitative image analysis is usually performed. Our study aimed to develop a quantitative image analysis for motion artefacts

  7. Disposable lateral flow-through strip for smartphone-camera to quantitatively detect alkaline phosphatase activity in milk.

    Science.gov (United States)

    Yu, Ling; Shi, ZhuanZhuan; Fang, Can; Zhang, YuanYuan; Liu, YingShuai; Li, ChangMing

    2015-07-15

    A disposable lateral flow-through strip was developed for smartphone to fast one-step quantitatively detect alkaline phosphatase (ALP) activity in raw milk. The strip comprises two functional components, a conjugation pad loaded with phosphotyrosine-coated gold nanoparticles (AuNPs@Cys-Try-p) and a testing line coated with anti-phosphotryosine antibody (anti-Tyr-p mAb). The dephosphorylation activity of ALP at the testing zone can be quantitatively assayed by monitoring the accumulated AuNPs-induced color changes by smartphone camera, thus providing a highly convenient portable detection method. A trace amount of ALP as low as 0.1UL(-1) with a linear dynamic range of 0.1-150UL(-1) (R(2)=0.999) in pasteurized milk and raw milk can be one-step detected by the developed flow-through strip within 10min, demonstrating the potential of smartphone-based portable sensing device for pathogen detection. This bio-hazards free lateral flow-through testing strip can be also used to fabricate rapid, sensitive and inexpensive enzyme or immunosensors for broad portable clinic diagnosis and food contamination analysis, particularly in point-of-care and daily food quality inspection. Copyright © 2015 Elsevier B.V. All rights reserved.

  8. Smartphone-Based Dual-Modality Imaging System for Quantitative Detection of Color or Fluorescent Lateral Flow Immunochromatographic Strips.

    Science.gov (United States)

    Hou, Yafei; Wang, Kan; Xiao, Kun; Qin, Weijian; Lu, Wenting; Tao, Wei; Cui, Daxiang

    2017-12-01

    Nowadays, lateral flow immunochromatographic assays are increasingly popular as a diagnostic tool for point-of-care (POC) test based on their simplicity, specificity, and sensitivity. Hence, quantitative detection and pluralistic popular application are urgently needed in medical examination. In this study, a smartphone-based dual-modality imaging system was developed for quantitative detection of color or fluorescent lateral flow test strips, which can be operated anywhere at any time. In this system, the white and ultra-violet (UV) light of optical device was designed, which was tunable with different strips, and the Sobel operator algorithm was used in the software, which could enhance the identification ability to recognize the test area from the background boundary information. Moreover, this technology based on extraction of the components from RGB format (red, green, and blue) of color strips or only red format of the fluorescent strips can obviously improve the high-signal intensity and sensitivity. Fifty samples were used to evaluate the accuracy of this system, and the ideal detection limit was calculated separately from detection of human chorionic gonadotropin (HCG) and carcinoembryonic antigen (CEA). The results indicated that smartphone-controlled dual-modality imaging system could provide various POC diagnoses, which becomes a potential technology for developing the next-generation of portable system in the near future.

  9. Smartphone-Based Dual-Modality Imaging System for Quantitative Detection of Color or Fluorescent Lateral Flow Immunochromatographic Strips

    Science.gov (United States)

    Hou, Yafei; Wang, Kan; Xiao, Kun; Qin, Weijian; Lu, Wenting; Tao, Wei; Cui, Daxiang

    2017-04-01

    Nowadays, lateral flow immunochromatographic assays are increasingly popular as a diagnostic tool for point-of-care (POC) test based on their simplicity, specificity, and sensitivity. Hence, quantitative detection and pluralistic popular application are urgently needed in medical examination. In this study, a smartphone-based dual-modality imaging system was developed for quantitative detection of color or fluorescent lateral flow test strips, which can be operated anywhere at any time. In this system, the white and ultra-violet (UV) light of optical device was designed, which was tunable with different strips, and the Sobel operator algorithm was used in the software, which could enhance the identification ability to recognize the test area from the background boundary information. Moreover, this technology based on extraction of the components from RGB format (red, green, and blue) of color strips or only red format of the fluorescent strips can obviously improve the high-signal intensity and sensitivity. Fifty samples were used to evaluate the accuracy of this system, and the ideal detection limit was calculated separately from detection of human chorionic gonadotropin (HCG) and carcinoembryonic antigen (CEA). The results indicated that smartphone-controlled dual-modality imaging system could provide various POC diagnoses, which becomes a potential technology for developing the next-generation of portable system in the near future.

  10. Quantitative comparison of DNA detection by GFP-lac repressor tagging, fluorescence in situ hybridization and immunostaining

    Directory of Open Access Journals (Sweden)

    Rohr Karl

    2007-12-01

    Full Text Available Abstract Background GFP-fusion proteins and immunostaining are methods broadly applied to investigate the three-dimensional organization of cells and cell nuclei, the latter often studied in addition by fluorescence in situ hybridization (FISH. Direct comparisons of these detection methods are scarce, however. Results We provide a quantitative comparison of all three approaches. We make use of a cell line that contains a transgene array of lac operator repeats which are detected by GFP-lac repressor fusion proteins. Thus we can detect the same structure in individual cells by GFP fluorescence, by antibodies against GFP and by FISH with a probe against the transgene array. Anti-GFP antibody detection was repeated after FISH. Our results show that while all four signals obtained from a transgene array generally showed qualitative and quantitative similarity, they also differed in details. Conclusion Each of the tested methods revealed particular strengths and weaknesses, which should be considered when interpreting respective experimental results. Despite the required denaturation step, FISH signals in structurally preserved cells show a surprising similarity to signals generated before denaturation.

  11. Quantitative fucK gene polymerase chain reaction on sputum and nasopharyngeal secretions to detect Haemophilus influenzae pneumonia.

    Science.gov (United States)

    Abdeldaim, Guma M K; Strålin, Kristoffer; Olcén, Per; Blomberg, Jonas; Mölling, Paula; Herrmann, Björn

    2013-06-01

    A quantitative polymerase chain reaction (PCR) for the fucK gene was developed for specific detection of Haemophilus influenzae. The method was tested on sputum and nasopharyngeal aspirate (NPA) from 78 patients with community-acquired pneumonia (CAP). With a reference standard of sputum culture and/or serology against the patient's own nasopharyngeal isolate, H. influenzae etiology was detected in 20 patients. Compared with the reference standard, fucK PCR (using the detection limit 10(5) DNA copies/mL) on sputum and NPA showed a sensitivity of 95.0% (19/20) in both cases, and specificities of 87.9% (51/58) and 89.5% (52/58), respectively. In a receiver operating characteristic curve analysis, sputum fucK PCR was found to be significantly superior to sputum P6 PCR for detection of H. influenzae CAP. NPA fucK PCR was positive in 3 of 54 adult controls without respiratory symptoms. In conclusion, quantitative fucK real-time PCR provides a sensitive and specific identification of H. influenzae in respiratory secretions. Copyright © 2013 Elsevier Inc. All rights reserved.

  12. Qualitative and Quantitative Detection of Botulinum Neurotoxins from Complex Matrices: Results of the First International Proficiency Test

    Directory of Open Access Journals (Sweden)

    Sylvia Worbs

    2015-11-01

    Full Text Available In the framework of the EU project EQuATox, a first international proficiency test (PT on the detection and quantification of botulinum neurotoxins (BoNT was conducted. Sample materials included BoNT serotypes A, B and E spiked into buffer, milk, meat extract and serum. Different methods were applied by the participants combining different principles of detection, identification and quantification. Based on qualitative assays, 95% of all results reported were correct. Successful strategies for BoNT detection were based on a combination of complementary immunological, MS-based and functional methods or on suitable functional in vivo/in vitro approaches (mouse bioassay, hemidiaphragm assay and Endopep-MS assay. Quantification of BoNT/A, BoNT/B and BoNT/E was performed by 48% of participating laboratories. It turned out that precise quantification of BoNT was difficult, resulting in a substantial scatter of quantitative data. This was especially true for results obtained by the mouse bioassay which is currently considered as “gold standard” for BoNT detection. The results clearly demonstrate the urgent need for certified BoNT reference materials and the development of methods replacing animal testing. In this context, the BoNT PT provided the valuable information that both the Endopep-MS assay and the hemidiaphragm assay delivered quantitative results superior to the mouse bioassay.

  13. Qualitative and Quantitative Detection of Botulinum Neurotoxins from Complex Matrices: Results of the First International Proficiency Test.

    Science.gov (United States)

    Worbs, Sylvia; Fiebig, Uwe; Zeleny, Reinhard; Schimmel, Heinz; Rummel, Andreas; Luginbühl, Werner; Dorner, Brigitte G

    2015-11-26

    In the framework of the EU project EQuATox, a first international proficiency test (PT) on the detection and quantification of botulinum neurotoxins (BoNT) was conducted. Sample materials included BoNT serotypes A, B and E spiked into buffer, milk, meat extract and serum. Different methods were applied by the participants combining different principles of detection, identification and quantification. Based on qualitative assays, 95% of all results reported were correct. Successful strategies for BoNT detection were based on a combination of complementary immunological, MS-based and functional methods or on suitable functional in vivo/in vitro approaches (mouse bioassay, hemidiaphragm assay and Endopep-MS assay). Quantification of BoNT/A, BoNT/B and BoNT/E was performed by 48% of participating laboratories. It turned out that precise quantification of BoNT was difficult, resulting in a substantial scatter of quantitative data. This was especially true for results obtained by the mouse bioassay which is currently considered as "gold standard" for BoNT detection. The results clearly demonstrate the urgent need for certified BoNT reference materials and the development of methods replacing animal testing. In this context, the BoNT PT provided the valuable information that both the Endopep-MS assay and the hemidiaphragm assay delivered quantitative results superior to the mouse bioassay.

  14. Highly sensitive and selective lateral flow immunoassay based on magnetic nanoparticles for quantitative detection of carcinoembryonic antigen.

    Science.gov (United States)

    Liu, Fangming; Zhang, Honglian; Wu, Zhenhua; Dong, Haidao; Zhou, Lin; Yang, Dawei; Ge, Yuqing; Jia, Chunping; Liu, Huiying; Jin, Qinghui; Zhao, Jianlong; Zhang, Qiqing; Mao, Hongju

    2016-12-01

    Carcinoembryonic antigen (CEA) is an important biomarker in cancer diagnosis. Here, we present an efficient, selective lateral-flow immunoassay (LFIA) based on magnetic nanoparticles (MNPs) for in situ sensitive and accurate point-of-care detection of CEA. Signal amplification mechanism involved linking of detection MNPs with signal MNPs through biotin-modified single-stranded DNA (ssDNA) and streptavidin. To verify the effectiveness of this modified LFIA system, the sensitivity and specificity were evaluated. Sensitivity evaluation showed a broad detection range of 0.25-1000ng/ml for CEA protein by the modified LFIA, and the limit of detection (LOD) of the modified LFIA was 0.25ng/ml, thus producing significant increase in