Method for enhancing single-trial P300 detection by introducing the complexity degree of image information in rapid serial visual presentation tasks

PubMed Central

Lin, Zhimin; Zeng, Ying; Tong, Li; Zhang, Hangming; Zhang, Chi

2017-01-01

The application of electroencephalogram (EEG) generated by human viewing images is a new thrust in image retrieval technology. A P300 component in the EEG is induced when the subjects see their point of interest in a target image under the rapid serial visual presentation (RSVP) experimental paradigm. We detected the single-trial P300 component to determine whether a subject was interested in an image. In practice, the latency and amplitude of the P300 component may vary in relation to different experimental parameters, such as target probability and stimulus semantics. Thus, we proposed a novel method, Target Recognition using Image Complexity Priori (TRICP) algorithm, in which the image information is introduced in the calculation of the interest score in the RSVP paradigm. The method combines information from the image and EEG to enhance the accuracy of single-trial P300 detection on the basis of traditional single-trial P300 detection algorithm. We defined an image complexity parameter based on the features of the different layers of a convolution neural network (CNN). We used the TRICP algorithm to compute for the complexity of an image to quantify the effect of different complexity images on the P300 components and training specialty classifier according to the image complexity. We compared TRICP with the HDCA algorithm. Results show that TRICP is significantly higher than the HDCA algorithm (Wilcoxon Sign Rank Test, p<0.05). Thus, the proposed method can be used in other and visual task-related single-trial event-related potential detection. PMID:29283998

Correlation between model observers in uniform background and human observers in patient liver background for a low-contrast detection task in CT

NASA Astrophysics Data System (ADS)

Gong, Hao; Yu, Lifeng; Leng, Shuai; Dilger, Samantha; Zhou, Wei; Ren, Liqiang; McCollough, Cynthia H.

2018-03-01

Channelized Hotelling observer (CHO) has demonstrated strong correlation with human observer (HO) in both single-slice viewing mode and multi-slice viewing mode in low-contrast detection tasks with uniform background. However, it remains unknown if the simplest single-slice CHO in uniform background can be used to predict human observer performance in more realistic tasks that involve patient anatomical background and multi-slice viewing mode. In this study, we aim to investigate the correlation between CHO in a uniform water background and human observer performance at a multi-slice viewing mode on patient liver background for a low-contrast lesion detection task. The human observer study was performed on CT images from 7 abdominal CT exams. A noise insertion tool was employed to synthesize CT scans at two additional dose levels. A validated lesion insertion tool was used to numerically insert metastatic liver lesions of various sizes and contrasts into both phantom and patient images. We selected 12 conditions out of 72 possible experimental conditions to evaluate the correlation at various radiation doses, lesion sizes, lesion contrasts and reconstruction algorithms. CHO with both single and multi-slice viewing modes were strongly correlated with HO. The corresponding Pearson's correlation coefficient was 0.982 (with 95% confidence interval (CI) [0.936, 0.995]) and 0.989 (with 95% CI of [0.960, 0.997]) in multi-slice and single-slice viewing modes, respectively. Therefore, this study demonstrated the potential to use the simplest single-slice CHO to assess image quality for more realistic clinically relevant CT detection tasks.

SU-G-IeP4-09: Method of Human Eye Aberration Measurement Using Plenoptic Camera Over Large Field of View

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lv, Yang; Wang, Ruixing; Ma, Haotong

Purpose: The measurement based on Shack-Hartmann wave-front sensor(WFS), obtaining both the high and low order wave-front aberrations simultaneously and accurately, has been applied in the detection of human eyes aberration in recent years. However, Its application is limited by the small field of view (FOV), slight eye movement leads the optical bacon image exceeds the lenslet array which result in uncertain detection error. To overcome difficulties of precise eye location, the capacity of detecting eye wave-front aberration over FOV much larger than simply a single conjugate Hartmann WFS accurately and simultaneously is demanded. Methods: Plenoptic camera’s lenslet array subdivides themore » aperture light-field in spatial frequency domain, capture the 4-D light-field information. Data recorded by plenoptic cameras can be used to extract the wave-front phases associated to the eyes aberration. The corresponding theoretical model and simulation system is built up in this article to discuss wave-front measurement performance when utilizing plenoptic camera as wave-front sensor. Results: The simulation results indicate that the plenoptic wave-front method can obtain both the high and low order eyes wave-front aberration with the same accuracy as conventional system in single visual angle detectionand over FOV much larger than simply a single conjugate Hartmann systems. Meanwhile, simulation results show that detection of eye aberrations wave-front in different visual angle can be achieved effectively and simultaneously by plenoptic method, by both point and extended optical beacon from the eye. Conclusion: Plenoptic wave-front method possesses the feasibility in eye aberrations wave-front detection. With larger FOV, the method can effectively reduce the detection error brought by imprecise eye location and simplify the eye aberrations wave-front detection system comparing with which based on Shack-Hartmann WFS. Unique advantage of the plenoptic method lies in obtaining wave-front in different visual angle simultaneously, which provides an approach in building up 3-D model of eye refractor tomographically. Funded by the key Laboratory of High Power Laser and Physics, CAS Research Project of National University of Defense Technology No. JC13-07-01; National Natural Science Foundation of China No. 61205144.« less

Computerized detection of breast cancer on automated breast ultrasound imaging of women with dense breasts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Drukker, Karen, E-mail: kdrukker@uchicago.edu; Sennett, Charlene A.; Giger, Maryellen L.

2014-01-15

Purpose: Develop a computer-aided detection method and investigate its feasibility for detection of breast cancer in automated 3D ultrasound images of women with dense breasts. Methods: The HIPAA compliant study involved a dataset of volumetric ultrasound image data, “views,” acquired with an automated U-Systems Somo•V{sup ®} ABUS system for 185 asymptomatic women with dense breasts (BI-RADS Composition/Density 3 or 4). For each patient, three whole-breast views (3D image volumes) per breast were acquired. A total of 52 patients had breast cancer (61 cancers), diagnosed through any follow-up at most 365 days after the original screening mammogram. Thirty-one of these patientsmore » (32 cancers) had a screening-mammogram with a clinically assigned BI-RADS Assessment Category 1 or 2, i.e., were mammographically negative. All software used for analysis was developed in-house and involved 3 steps: (1) detection of initial tumor candidates, (2) characterization of candidates, and (3) elimination of false-positive candidates. Performance was assessed by calculating the cancer detection sensitivity as a function of the number of “marks” (detections) per view. Results: At a single mark per view, i.e., six marks per patient, the median detection sensitivity by cancer was 50.0% (16/32) ± 6% for patients with a screening mammogram-assigned BI-RADS category 1 or 2—similar to radiologists’ performance sensitivity (49.9%) for this dataset from a prior reader study—and 45.9% (28/61) ± 4% for all patients. Conclusions: Promising detection sensitivity was obtained for the computer on a 3D ultrasound dataset of women with dense breasts at a rate of false-positive detections that may be acceptable for clinical implementation.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Drukker, Karen, E-mail: kdrukker@uchicago.edu; Sennett, Charlene A.; Giger, Maryellen L.

Purpose: Develop a computer-aided detection method and investigate its feasibility for detection of breast cancer in automated 3D ultrasound images of women with dense breasts. Methods: The HIPAA compliant study involved a dataset of volumetric ultrasound image data, “views,” acquired with an automated U-Systems Somo•V{sup ®} ABUS system for 185 asymptomatic women with dense breasts (BI-RADS Composition/Density 3 or 4). For each patient, three whole-breast views (3D image volumes) per breast were acquired. A total of 52 patients had breast cancer (61 cancers), diagnosed through any follow-up at most 365 days after the original screening mammogram. Thirty-one of these patientsmore » (32 cancers) had a screening-mammogram with a clinically assigned BI-RADS Assessment Category 1 or 2, i.e., were mammographically negative. All software used for analysis was developed in-house and involved 3 steps: (1) detection of initial tumor candidates, (2) characterization of candidates, and (3) elimination of false-positive candidates. Performance was assessed by calculating the cancer detection sensitivity as a function of the number of “marks” (detections) per view. Results: At a single mark per view, i.e., six marks per patient, the median detection sensitivity by cancer was 50.0% (16/32) ± 6% for patients with a screening mammogram-assigned BI-RADS category 1 or 2—similar to radiologists’ performance sensitivity (49.9%) for this dataset from a prior reader study—and 45.9% (28/61) ± 4% for all patients. Conclusions: Promising detection sensitivity was obtained for the computer on a 3D ultrasound dataset of women with dense breasts at a rate of false-positive detections that may be acceptable for clinical implementation.« less

Exploiting Satellite Focal Plane Geometry for Automatic Extraction of Traffic Flow from Single Optical Satellite Imagery

NASA Astrophysics Data System (ADS)

Krauß, T.

2014-11-01

The focal plane assembly of most pushbroom scanner satellites is built up in a way that different multispectral or multispectral and panchromatic bands are not all acquired exactly at the same time. This effect is due to offsets of some millimeters of the CCD-lines in the focal plane. Exploiting this special configuration allows the detection of objects moving during this small time span. In this paper we present a method for automatic detection and extraction of moving objects - mainly traffic - from single very high resolution optical satellite imagery of different sensors. The sensors investigated are WorldView-2, RapidEye, Pléiades and also the new SkyBox satellites. Different sensors require different approaches for detecting moving objects. Since the objects are mapped on different positions only in different spectral bands also the change of spectral properties have to be taken into account. In case the main distance in the focal plane is between the multispectral and the panchromatic CCD-line like for Pléiades an approach for weighted integration to receive mostly identical images is investigated. Other approaches for RapidEye and WorldView-2 are also shown. From these intermediate bands difference images are calculated and a method for detecting the moving objects from these difference images is proposed. Based on these presented methods images from different sensors are processed and the results are assessed for detection quality - how many moving objects can be detected, how many are missed - and accuracy - how accurate is the derived speed and size of the objects. Finally the results are discussed and an outlook for possible improvements towards operational processing is presented.

Embedded Reasoning Supporting Aerospace IVHM

DTIC Science & Technology

2007-01-01

c method (BIT or health assessment algorithm) which the monitoring diagnostic relies on input information tics and Astronautics In the diagram...viewing of the current health state of all monitored subsystems, while also providing a means to probe deeper in the event anomalous operation is...seeks to integrate detection , diagnostic, and prognostic capabilities with a hierarchical diagnostic reasoning architecture into a single

Sensitive and inexpensive digital DNA analysis by microfluidic enrichment of rolling circle amplified single-molecules

PubMed Central

Kühnemund, Malte; Hernández-Neuta, Iván; Sharif, Mohd Istiaq; Cornaglia, Matteo; Gijs, Martin A.M.

2017-01-01

Abstract Single molecule quantification assays provide the ultimate sensitivity and precision for molecular analysis. However, most digital analysis techniques, i.e. droplet PCR, require sophisticated and expensive instrumentation for molecule compartmentalization, amplification and analysis. Rolling circle amplification (RCA) provides a simpler means for digital analysis. Nevertheless, the sensitivity of RCA assays has until now been limited by inefficient detection methods. We have developed a simple microfluidic strategy for enrichment of RCA products into a single field of view of a low magnification fluorescent sensor, enabling ultra-sensitive digital quantification of nucleic acids over a dynamic range from 1.2 aM to 190 fM. We prove the broad applicability of our analysis platform by demonstrating 5-plex detection of as little as ∼1 pg (∼300 genome copies) of pathogenic DNA with simultaneous antibiotic resistance marker detection, and the analysis of rare oncogene mutations. Our method is simpler, more cost-effective and faster than other digital analysis techniques and provides the means to implement digital analysis in any laboratory equipped with a standard fluorescent microscope. PMID:28077562

Electro-optical muzzle flash detection

NASA Astrophysics Data System (ADS)

Krieg, Jürgen; Eisele, Christian; Seiffer, Dirk

2016-10-01

Localizing a shooter in a complex scenario is a difficult task. Acoustic sensors can be used to detect blast waves. Radar technology permits detection of the projectile. A third method is to detect the muzzle flash using electro-optical devices. Detection of muzzle flash events is possible with focal plane arrays, line and single element detectors. In this paper, we will show that the detection of a muzzle flash works well in the shortwave infrared spectral range. Important for the acceptance of an operational warning system in daily use is a very low false alarm rate. Using data from a detector with a high sampling rate the temporal signature of a potential muzzle flash event can be analyzed and the false alarm rate can be reduced. Another important issue is the realization of an omnidirectional view required on an operational level. It will be shown that a combination of single element detectors and simple optics in an appropriate configuration is a capable solution.

Distributed Detection with Collisions in a Random, Single-Hop Wireless Sensor Network

DTIC Science & Technology

2013-05-26

public release; distribution is unlimited. Distributed detection with collisions in a random, single-hop wireless sensor network The views, opinions...1274 2 ABSTRACT Distributed detection with collisions in a random, single-hop wireless sensor network Report Title We consider the problem of... WIRELESS SENSOR NETWORK Gene T. Whipps?† Emre Ertin† Randolph L. Moses† ?U.S. Army Research Laboratory, Adelphi, MD 20783 †The Ohio State University

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tripathi, Ashish; McNulty, Ian; Munson, Todd

We propose a new approach to robustly retrieve the exit wave of an extended sample from its coherent diffraction pattern by exploiting sparsity of the sample's edges. This approach enables imaging of an extended sample with a single view, without ptychography. We introduce nonlinear optimization methods that promote sparsity, and we derive update rules to robustly recover the sample's exit wave. We test these methods on simulated samples by varying the sparsity of the edge-detected representation of the exit wave. Finally, our tests illustrate the strengths and limitations of the proposed method in imaging extended samples.

[Physical methods and molecular biology].

PubMed

Serdiuk, I N

2009-01-01

The review is devoted to the description of the current state of physical and chemical methods used for studying the structural and functional bases of living processes. Special attention is focused on the physical methods that have opened a new page in the research of the structure of biological macromolecules. They include primarily the methods of detecting and manipulating single molecules using optical and magnetic traps. New physical methods, such as two-dimensional infrared spectroscopy, fluorescence correlation spectroscopy and magnetic resonance microscopy are also analyzed briefly in the review. The path that physics and biology have passed for the latest 55 years shows that there is no single method providing all necessary information on macromolecules and their interactions. Each method provides its space-time view of the system. All physical methods are complementary. It is just complementarity that is the fundamental idea justifying the existence in practice of all physical methods, whose description is the aim of the review.

Sensitive and inexpensive digital DNA analysis by microfluidic enrichment of rolling circle amplified single-molecules.

PubMed

Kühnemund, Malte; Hernández-Neuta, Iván; Sharif, Mohd Istiaq; Cornaglia, Matteo; Gijs, Martin A M; Nilsson, Mats

2017-05-05

Single molecule quantification assays provide the ultimate sensitivity and precision for molecular analysis. However, most digital analysis techniques, i.e. droplet PCR, require sophisticated and expensive instrumentation for molecule compartmentalization, amplification and analysis. Rolling circle amplification (RCA) provides a simpler means for digital analysis. Nevertheless, the sensitivity of RCA assays has until now been limited by inefficient detection methods. We have developed a simple microfluidic strategy for enrichment of RCA products into a single field of view of a low magnification fluorescent sensor, enabling ultra-sensitive digital quantification of nucleic acids over a dynamic range from 1.2 aM to 190 fM. We prove the broad applicability of our analysis platform by demonstrating 5-plex detection of as little as ∼1 pg (∼300 genome copies) of pathogenic DNA with simultaneous antibiotic resistance marker detection, and the analysis of rare oncogene mutations. Our method is simpler, more cost-effective and faster than other digital analysis techniques and provides the means to implement digital analysis in any laboratory equipped with a standard fluorescent microscope. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Simultaneous multicolor detection system of the single-molecular microbial antigen by total internal reflection fluorescence microscopy with fluorescent nanocrystal quantum dots

NASA Astrophysics Data System (ADS)

Hoshino, Akiyoshi; Fujioka, Kouki; Yamamoto, Mayu; Manabe, Noriyoshi; Yasuhara, Masato; Suzuki, Kazuo; Yamamoto, Kenji

2005-11-01

Immunological diagnostic methods have been widely performed and showed high performance in molecular and cellular biology, molecular imaging, and medical diagnostics. We have developed novel methods for the fluorescent labeling of several antibodies coupled with fluorescent nanocrystals QDs. In this study we demonstrated that two bacterial toxins, diphtheria toxin and tetanus toxin, were detected simultaneously in the same view field of a cover slip by using directly QD-conjugated antibodies. We have succeeded in detecting bacterial toxins by counting luminescent spots on the evanescent field with using primary antibody conjugated to QDs. In addition, each bacterial toxin in the mixture can be separately detected by single excitation laser with emission band pass filters, and simultaneously in situ pathogen quantification was performed by calculating the luminescent density on the surface of the cover slip. Our results demonstrate that total internal reflection fluorescence microscopy (TIRFM) enables us to distinguish each antigen from mixed samples and can simultaneously quantitate multiple antigens by QD-conjugated antibodies. Bioconjugated QDs could have great potentialities for in practical biomedical applications to develop various high-sensitivity detection systems.

Underwater single beam circumferentially scanning detection system using range-gated receiver and adaptive filter

NASA Astrophysics Data System (ADS)

Tan, Yayun; Zhang, He; Zha, Bingting

2017-09-01

Underwater target detection and ranging in seawater are of interest in unmanned underwater vehicles. This study presents an underwater detection system that synchronously scans a collimated laser beam and a narrow field of view to circumferentially detect an underwater target. Hybrid methods of range-gated and variable step-size least mean squares (VSS-LMS) adaptive filter are proposed to suppress water backscattering. The range-gated receiver eliminates the backscattering of near-field water. The VSS-LMS filter extracts the target echo in the remaining backscattering and the constant fraction discriminator timing method is used to improve ranging accuracy. The optimal constant fraction is selected by analysing the jitter noise and slope of the target echo. The prototype of the underwater detection system is constructed and tested in coastal seawater, then the effectiveness of backscattering suppression and high-ranging accuracy is verified through experimental results and analysis discussed in this paper.

Fast imaging of live organisms with sculpted light sheets

NASA Astrophysics Data System (ADS)

Chmielewski, Aleksander K.; Kyrsting, Anders; Mahou, Pierre; Wayland, Matthew T.; Muresan, Leila; Evers, Jan Felix; Kaminski, Clemens F.

2015-04-01

Light-sheet microscopy is an increasingly popular technique in the life sciences due to its fast 3D imaging capability of fluorescent samples with low photo toxicity compared to confocal methods. In this work we present a new, fast, flexible and simple to implement method to optimize the illumination light-sheet to the requirement at hand. A telescope composed of two electrically tuneable lenses enables us to define thickness and position of the light-sheet independently but accurately within milliseconds, and therefore optimize image quality of the features of interest interactively. We demonstrated the practical benefit of this technique by 1) assembling large field of views from tiled single exposure each with individually optimized illumination settings; 2) sculpting the light-sheet to trace complex sample shapes within single exposures. This technique proved compatible with confocal line scanning detection, further improving image contrast and resolution. Finally, we determined the effect of light-sheet optimization in the context of scattering tissue, devising procedures for balancing image quality, field of view and acquisition speed.

Kernel-Based Sensor Fusion With Application to Audio-Visual Voice Activity Detection

NASA Astrophysics Data System (ADS)

Dov, David; Talmon, Ronen; Cohen, Israel

2016-12-01

In this paper, we address the problem of multiple view data fusion in the presence of noise and interferences. Recent studies have approached this problem using kernel methods, by relying particularly on a product of kernels constructed separately for each view. From a graph theory point of view, we analyze this fusion approach in a discrete setting. More specifically, based on a statistical model for the connectivity between data points, we propose an algorithm for the selection of the kernel bandwidth, a parameter, which, as we show, has important implications on the robustness of this fusion approach to interferences. Then, we consider the fusion of audio-visual speech signals measured by a single microphone and by a video camera pointed to the face of the speaker. Specifically, we address the task of voice activity detection, i.e., the detection of speech and non-speech segments, in the presence of structured interferences such as keyboard taps and office noise. We propose an algorithm for voice activity detection based on the audio-visual signal. Simulation results show that the proposed algorithm outperforms competing fusion and voice activity detection approaches. In addition, we demonstrate that a proper selection of the kernel bandwidth indeed leads to improved performance.

Lensfree in-line holographic detection of bacteria

NASA Astrophysics Data System (ADS)

Poher, V.; Allier, C. P.; Coutard, J. G.; Hervé, L.; Dinten, J. M.

2011-07-01

Due to low light scattering, bacteria are difficult to detect using lensless imaging systems. In order to detect individual bacteria, we report a method based on a thin wetting film imaging that produces a micro-lens effect on top of each bacterium when the sample dries up. The imaging using a high-end CMOS sensor is combined with an in-line holographic reconstruction to improve positive detection rate up to 95% with micron-sized beads at high density of ~103 objects/mm2. The system allows detecting from single bacterium to densely packed objects (103 bacteria/μl) within 10μl sample. As an example, E.coli, Bacillus subtilis and Bacillus thuringiensis, has been successfully detected with strong signal to noise ratio across a 24mm2 field of view.

Brain stem/brain stem occipital bone ratio and the four-line view in nuchal translucency images of fetuses with open spina bifida.

PubMed

Iuculano, Ambra; Zoppi, Maria Angelica; Piras, Alessandra; Arras, Maurizio; Monni, Giovanni

2014-09-10

Abstract Objective: Brain stem depth/brain stem occipital bone distance (BS/BSOB ratio) and the four-line view, in images obtained for nuchal translucency (NT) screening in fetuses with open spina bifida (OSB). Methods: Single center, retrospective study based on the assessment of NT screening images of fetuses with OSB. A ratio between the BS depth and the BSOB distance was calculated (BS/BSOB ratio) and the four-line view observed, and the sensitivity for a BS/BSOB ratio superior/equal to 1, and for the lack of detection of the four-line view were calculated. Results: There were 17 cases of prenatal diagnosis OSB. In six cases, the suspicion on OSB was raised during NT screening, in six cases, the diagnosis was made before 20 weeks and in five cases during anomaly scan. The BS/BSOB ratio was superior/equal to 1 in all 17 cases, and three lines, were visualized in 15/17 images of the OSB cases, being the sensitivity 100% (95% CI, 81 to 100%) and 88% (95% CI, 65 to 96%). Conclusion: Assessment of BS/BSOB ratio and four-line view in NT images is feasible detecting affected by OSB with high sensitivity. The presence of associated anomalies or of an enlarged NT enhances the early detection.

Coronary artery stenosis detection with holographic display of 3D angiograms

NASA Astrophysics Data System (ADS)

Ritman, Erik L.; Schwanke, Todd D.; Simari, Robert D.; Schwartz, Robert S.; Thomas, Paul J.

1995-05-01

The objective of this study was to establish the accuracy of an holographic display approach for detection of stenoses in coronary arteries. The rationale for using an holographic display approach is that multiple angles of view of the coronary arteriogram are provided by a single 'x-ray'-like film, backlit by a special light box. This should be more convenient in that the viewer does not have to page back and forth through a cine angiogram to obtain the multiple angles of view. The method used to test this technique involved viewing 100 3D coronary angiograms. These images were generated from the 3D angiographic images of nine normal coronary arterial trees generated with the Dynamic Spatial Reconstructor (DSR) fast CT scanner. Using our image processing programs, the image of the coronary artery lumen was locally 'narrowed' by an amount and length and at a location determined by a random look-up table. Two independent, blinded, experienced angiographers viewed the holographic displays of these angiograms and recorded their confidence about the presence, location, and severity of the stenoses. This procedure evaluates the sensitivity and specificity of the detection of coronary artery stenoses as a function of the severity, size, and location along the arteries.

Radial line method for rear-view mirror distortion detection

NASA Astrophysics Data System (ADS)

Rahmah, Fitri; Kusumawardhani, Apriani; Setijono, Heru; Hatta, Agus M.; Irwansyah, .

2015-01-01

An image of the object can be distorted due to a defect in a mirror. A rear-view mirror is an important component for the vehicle safety. One of standard parameters of the rear-view mirror is a distortion factor. This paper presents a radial line method for distortion detection of the rear-view mirror. The rear-view mirror was tested for the distortion detection by using a system consisting of a webcam sensor and an image-processing unit. In the image-processing unit, the captured image from the webcam were pre-processed by using smoothing and sharpening techniques and then a radial line method was used to define the distortion factor. It was demonstrated successfully that the radial line method could be used to define the distortion factor. This detection system is useful to be implemented such as in Indonesian's automotive component industry while the manual inspection still be used.

Detection of secondary and backscattered electrons for 3D imaging with multi-detector method in VP/ESEM.

PubMed

Slówko, Witold; Wiatrowski, Artur; Krysztof, Michał

2018-01-01

The paper considers some major problems of adapting the multi-detector method for three-dimensional (3D) imaging of wet bio-medical samples in Variable Pressure/Environmental Scanning Electron Microscope (VP/ESEM). The described method pertains to "single-view techniques", which to create the 3D surface model utilise a sequence of 2D SEM images captured from a single view point (along the electron beam axis) but illuminated from four directions. The basis of the method and requirements resulting from them are given for the detector systems of secondary (SE) and backscattered electrons (BSE), as well as designs of the systems which could work in variable conditions. The problems of SE detection with application of the Pressure Limiting Aperture (PLA) as the signal collector are discussed with respect to secondary electron backscattering by a gaseous environment. However, the authors' attention is turned mainly to the directional BSE detection, realized in two ways. The high take off angle BSE were captured through PLA with use of the quadruple semiconductor detector placed inside the intermediate chamber, while BSE starting at lower angles were detected by the four-folded ionization device working in the sample chamber environment. The latter relied on a conversion of highly energetic BSE into low energetic SE generated on walls and a gaseous environment of the deep discharge gap oriented along the BSE velocity direction. The converted BSE signal was amplified in an ionising avalanche developed in the electric field arranged transversally to the gap. The detector system operation is illustrated with numerous computer simulations and examples of experiments and 3D images. The latter were conducted in a JSM 840 microscope with its combined detector-vacuum equipment which could extend capabilities of this high vacuum instrument toward elevated pressures (over 1kPa) and environmental conditions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Tools for Visualizing HIV in Cure Research.

PubMed

Niessl, Julia; Baxter, Amy E; Kaufmann, Daniel E

2018-02-01

The long-lived HIV reservoir remains a major obstacle for an HIV cure. Current techniques to analyze this reservoir are generally population-based. We highlight recent developments in methods visualizing HIV, which offer a different, complementary view, and provide indispensable information for cure strategy development. Recent advances in fluorescence in situ hybridization techniques enabled key developments in reservoir visualization. Flow cytometric detection of HIV mRNAs, concurrently with proteins, provides a high-throughput approach to study the reservoir on a single-cell level. On a tissue level, key spatial information can be obtained detecting viral RNA and DNA in situ by fluorescence microscopy. At total-body level, advancements in non-invasive immuno-positron emission tomography (PET) detection of HIV proteins may allow an encompassing view of HIV reservoir sites. HIV imaging approaches provide important, complementary information regarding the size, phenotype, and localization of the HIV reservoir. Visualizing the reservoir may contribute to the design, assessment, and monitoring of HIV cure strategies in vitro and in vivo.

Mild Depression Detection of College Students: an EEG-Based Solution with Free Viewing Tasks.

PubMed

Li, Xiaowei; Hu, Bin; Shen, Ji; Xu, Tingting; Retcliffe, Martyn

2015-12-01

Depression is a common mental disorder with growing prevalence; however current diagnoses of depression face the problem of patient denial, clinical experience and subjective biases from self-report. By using a combination of linear and nonlinear EEG features in our research, we aim to develop a more accurate and objective approach to depression detection that supports the process of diagnosis and assists the monitoring of risk factors. By classifying EEG features during free viewing task, an accuracy of 99.1%, which is the highest to our knowledge by far, was achieved using kNN classifier to discriminate depressed and non-depressed subjects. Furthermore, through correlation analysis, comparisons of performance on each electrode were discussed on the availability of single channel EEG recording depression detection system. Combined with wearable EEG collecting devices, our method offers the possibility of cost effective wearable ubiquitous system for doctors to monitor their patients with depression, and for normal people to understand their mental states in time.

An Investigation of the Use of Real-time Image Mosaicing for Facilitating Global Spatial Awareness in Visual Search

NASA Astrophysics Data System (ADS)

Soung Yee, Anthony

Three experiments have been completed to investigate whether and how a software technique called real-time image mosaicing applied to a restricted field of view (FOV) might influence target detection and path integration performance in simulated aerial search scenarios, representing local and global spatial awareness tasks respectively. The mosaiced FOV (mFOV) was compared to single FOV (sFOV) and one with double the single size (dFOV). In addition to advancing our understanding of visual information in mosaicing, the present study examines the advantages and limitations of a number of metrics used to evaluate performance in path integration tasks, with particular attention paid to measuring performance in identifying complex routes. The highlights of the results are summarized as follows, according to Experiments 1 through 3 respectively. 1. A novel response method for evaluating route identification performance was developed. The surmised benefits of the mFOV relative to sFOV and dFOV revealed no significant differences in performance for the relatively simple route shapes tested. Compared to the mFOV and dFOV conditions, target detection performance in the local task was found to be superior in the sFOV condition. 2. In order to appropriately quantify the observed differences in complex route selections made by the participants, a novel analysis method was developed using the Thurstonian Paired Comparisons Method. 3. To investigate the effect of display size and elevation angle (EA) in a complex route environment, a 2x3 experiment was conducted for the two spatial tasks, at a height selected from Experiment 2. Although no significant differences were found in the target detection task, contrasts in the Paired Comparisons Method results revealed that route identification performance were as hypothesised: mFOV > dFOV > sFOV for EA = 90°. Results were similar for EA = 45°, but with mFOV being no different than dFOV. As hypothesised, EA was found to have an effect on route selection performance, with a top down view performing better than an angled view for the mFOV and sFOV conditions.

Learning Oriented Region-based Convolutional Neural Networks for Building Detection in Satellite Remote Sensing Images

NASA Astrophysics Data System (ADS)

Chen, C.; Gong, W.; Hu, Y.; Chen, Y.; Ding, Y.

2017-05-01

The automated building detection in aerial images is a fundamental problem encountered in aerial and satellite images analysis. Recently, thanks to the advances in feature descriptions, Region-based CNN model (R-CNN) for object detection is receiving an increasing attention. Despite the excellent performance in object detection, it is problematic to directly leverage the features of R-CNN model for building detection in single aerial image. As we know, the single aerial image is in vertical view and the buildings possess significant directional feature. However, in R-CNN model, direction of the building is ignored and the detection results are represented by horizontal rectangles. For this reason, the detection results with horizontal rectangle cannot describe the building precisely. To address this problem, in this paper, we proposed a novel model with a key feature related to orientation, namely, Oriented R-CNN (OR-CNN). Our contributions are mainly in the following two aspects: 1) Introducing a new oriented layer network for detecting the rotation angle of building on the basis of the successful VGG-net R-CNN model; 2) the oriented rectangle is proposed to leverage the powerful R-CNN for remote-sensing building detection. In experiments, we establish a complete and bran-new data set for training our oriented R-CNN model and comprehensively evaluate the proposed method on a publicly available building detection data set. We demonstrate State-of-the-art results compared with the previous baseline methods.

Three-dimensional reconstruction from multiple reflected views within a realist painting: an application to Scott Fraser's "Three way vanitas"

NASA Astrophysics Data System (ADS)

Smith, Brandon M.; Stork, David G.; Zhang, Li

2009-01-01

The problem of reconstructing a three-dimensional scene from single or multiple views has been thoroughly studied in the computer vision literature, and recently has been applied to problems in the history of art. Criminisi pioneered the application of single-view metrology to reconstructing the fictive spaces in Renaissance paintings, such as the vault in Masaccio's Trinità and the plaza in Piero della Francesca's Flagellazione. While the vast majority of realist paintings provide but a single view, some provide multiple views, through mirrors depicted within their tableaus. The contemporary American realist Scott Fraser's Three way vanitas is a highly realistic still-life containing three mirrors; each mirror provides a new view of the objects in the tableau. We applied multiple-view reconstruction methods to the direct image and the images reflected by these mirrors to reconstruct the three-dimensional tableau. Our methods estimate virtual viewpoints for each view using the geometric constraints provided by the direct view of the mirror frames, along with the reflected images themselves. Moreover, our methods automatically discover inconsistencies between the different views, including ones that might elude careful scrutiny by eye, for example the fact that the height of the water in the glass differs between the direct view and that in the mirror at the right. We believe our work provides the first application of multiple-view reconstruction to a single painting and will have application to other paintings and questions in the history of art.

Comparison of Four Views to Single-view Ultrasound Protocols to Identify Clinically Significant Pneumothorax.

PubMed

Helland, Gregg; Gaspari, Romolo; Licciardo, Samuel; Sanseverino, Alexandra; Torres, Ulises; Emhoff, Timothy; Blehar, David

2016-10-01

Ultrasound (US) has been shown to be effective at identifying a pneumothorax (PTX); however, the additional value of adding multiple views has not been studied. Single- and four-view protocols have both been described in the literature. The objective of this study was to compare the diagnostic accuracy of single-view versus four-view lung US to detect clinically significant PTX in trauma patients. This was a randomized, prospective trial on trauma patients. Adult patients with acute traumatic injury undergoing computed tomography (CT) scan of the chest were eligible for enrollment. Patients were randomized to a single view or four views of each hemithorax prior to any imaging. USs were performed and interpreted by credentialed physicians using a 7.5-Mhz linear array transducer on a portable US machine with digital clips recorded for later review. Attending radiologist interpretation of the chest CT was reviewed for presence or absence of PTX with descriptions of small foci of air or minimal PTX categorized as clinically insignificant. A total of 260 patients were enrolled over a 2-year period. A total of 139 patients received a single view of each chest wall and 121 patients received four views. There were a total of 49 patients that had a PTX (19%), and 29 of these were clinically significant (11%). In diagnosis of any PTX, both single-view and four-view techniques showed poor sensitivity (54.2 and 68%) but high specificity (99 and 98%). For clinically significant PTX, single-view US demonstrated a sensitivity of 93% (95% confidence interval [CI] = 64.1% to 99.6%) and a specificity of 99.2% (95% CI = 95.5% to 99.9%), with sensitivity of 93.3% (95% CI = 66% to 99.7%) and specificity of 98% (95% CI = 92.1% to 99.7%) for four views. Single-view and four-view chest wall USs demonstrate comparable sensitivity and specificity for PTX. The additional time to obtain four views should be weighed against the absence of additional diagnostic yield over a single view when using US to identify a clinically significant PTX. © 2016 by the Society for Academic Emergency Medicine.

Combined imaging and chemical sensing using a single optical imaging fiber.

PubMed

Bronk, K S; Michael, K L; Pantano, P; Walt, D R

1995-09-01

Despite many innovations and developments in the field of fiber-optic chemical sensors, optical fibers have not been employed to both view a sample and concurrently detect an analyte of interest. While chemical sensors employing a single optical fiber or a noncoherent fiberoptic bundle have been applied to a wide variety of analytical determinations, they cannot be used for imaging. Similarly, coherent imaging fibers have been employed only for their originally intended purpose, image transmission. We herein report a new technique for viewing a sample and measuring surface chemical concentrations that employs a coherent imaging fiber. The method is based on the deposition of a thin, analyte-sensitive polymer layer on the distal surface of a 350-microns-diameter imaging fiber. We present results from a pH sensor array and an acetylcholine biosensor array, each of which contains approximately 6000 optical sensors. The acetylcholine biosensor has a detection limit of 35 microM and a fast (< 1 s) response time. In association with an epifluorescence microscope and a charge-coupled device, these modified imaging fibers can display visual information of a remote sample with 4-microns spatial resolution, allowing for alternating acquisition of both chemical analysis and visual histology.

Optical Detection and Sizing of Single Nano-Particles Using Continuous Wetting Films

PubMed Central

Hennequin, Yves; McLeod, Euan; Mudanyali, Onur; Migliozzi, Daniel; Ozcan, Aydogan; Dinten, Jean-Marc

2013-01-01

The physical interaction between nano-scale objects and liquid interfaces can create unique optical properties, enhancing the signatures of the objects with sub-wavelength features. Here we show that the evaporation on a wetting substrate of a polymer solution containing sub-micrometer or nano-scale particles creates liquid micro-lenses that arise from the local deformations of the continuous wetting film. These micro-lenses have properties similar to axicon lenses that are known to create beams with a long depth of focus. This enhanced depth of focus allows detection of single nanoparticles using a low magnification microscope objective lens, achieving a relatively wide field-of-view, while also lifting the constraints on precise focusing onto the object plane. Hence, by creating these liquid axicon lenses through spatial deformations of a continuous thin wetting film, we transfer the challenge of imaging individual nano-particles to detecting the light focused by these lenses. As a proof of concept, we demonstrate the detection and sizing of single nano-particles (100 and 200 nm), CpGV granuloviruses as well as Staphylococcus epidermidis bacteria over a wide field of view of e.g., 5.10×3.75 mm2 using a ×5 objective lens with a numerical aperture of 0.15. In addition to conventional lens-based microscopy, this continuous wetting film based approach is also applicable to lensfree computational on-chip imaging, which can be used to detect single nano-particles over a large field-of-view of e.g., >20-30 mm2. These results could be especially useful for high-throughput field-analysis of nano-scale objects using compact and cost-effective microscope designs. PMID:23889001

Sustained change blindness to incremental scene rotation: a dissociation between explicit change detection and visual memory.

PubMed

Hollingworth, Andrew; Henderson, John M

2004-07-01

In a change detection paradigm, the global orientation of a natural scene was incrementally changed in 1 degree intervals. In Experiments 1 and 2, participants demonstrated sustained change blindness to incremental rotation, often coming to consider a significantly different scene viewpoint as an unchanged continuation of the original view. Experiment 3 showed that participants who failed to detect the incremental rotation nevertheless reliably detected a single-step rotation back to the initial view. Together, these results demonstrate an important dissociation between explicit change detection and visual memory. Following a change, visual memory is updated to reflect the changed state of the environment, even if the change was not detected.

Accurate Fall Detection in a Top View Privacy Preserving Configuration.

PubMed

Ricciuti, Manola; Spinsante, Susanna; Gambi, Ennio

2018-05-29

Fall detection is one of the most investigated themes in the research on assistive solutions for aged people. In particular, a false-alarm-free discrimination between falls and non-falls is indispensable, especially to assist elderly people living alone. Current technological solutions designed to monitor several types of activities in indoor environments can guarantee absolute privacy to the people that decide to rely on them. Devices integrating RGB and depth cameras, such as the Microsoft Kinect, can ensure privacy and anonymity, since the depth information is considered to extract only meaningful information from video streams. In this paper, we propose an accurate fall detection method investigating the depth frames of the human body using a single device in a top-view configuration, with the subjects located under the device inside a room. Features extracted from depth frames train a classifier based on a binary support vector machine learning algorithm. The dataset includes 32 falls and 8 activities considered for comparison, for a total of 800 sequences performed by 20 adults. The system showed an accuracy of 98.6% and only one false positive.

Time-alternating method based on single-sideband holography with half-zone-plate processing for the enlargement of viewing zones.

PubMed

Mishina, T; Okano, F; Yuyama, I

1999-06-10

The single-sideband method of holography, as is well known, cuts off beams that come from conjugate images for holograms produced in the Fraunhofer region and from objects with no phase components. The single-sideband method with half-zone-plate processing is also effective in the Fresnel region for beams from an object that has phase components. However, this method restricts the viewing zone to a narrow range. We propose a method to improve this restriction by time-alternating switching of hologram patterns and a spatial filter set on the focal plane of a reconstruction lens.

Kernel-aligned multi-view canonical correlation analysis for image recognition

NASA Astrophysics Data System (ADS)

Su, Shuzhi; Ge, Hongwei; Yuan, Yun-Hao

2016-09-01

Existing kernel-based correlation analysis methods mainly adopt a single kernel in each view. However, only a single kernel is usually insufficient to characterize nonlinear distribution information of a view. To solve the problem, we transform each original feature vector into a 2-dimensional feature matrix by means of kernel alignment, and then propose a novel kernel-aligned multi-view canonical correlation analysis (KAMCCA) method on the basis of the feature matrices. Our proposed method can simultaneously employ multiple kernels to better capture the nonlinear distribution information of each view, so that correlation features learned by KAMCCA can have well discriminating power in real-world image recognition. Extensive experiments are designed on five real-world image datasets, including NIR face images, thermal face images, visible face images, handwritten digit images, and object images. Promising experimental results on the datasets have manifested the effectiveness of our proposed method.

Double-observer line transect surveys with Markov-modulated Poisson process models for animal availability.

PubMed

Borchers, D L; Langrock, R

2015-12-01

We develop maximum likelihood methods for line transect surveys in which animals go undetected at distance zero, either because they are stochastically unavailable while within view or because they are missed when they are available. These incorporate a Markov-modulated Poisson process model for animal availability, allowing more clustered availability events than is possible with Poisson availability models. They include a mark-recapture component arising from the independent-observer survey, leading to more accurate estimation of detection probability given availability. We develop models for situations in which (a) multiple detections of the same individual are possible and (b) some or all of the availability process parameters are estimated from the line transect survey itself, rather than from independent data. We investigate estimator performance by simulation, and compare the multiple-detection estimators with estimators that use only initial detections of individuals, and with a single-observer estimator. Simultaneous estimation of detection function parameters and availability model parameters is shown to be feasible from the line transect survey alone with multiple detections and double-observer data but not with single-observer data. Recording multiple detections of individuals improves estimator precision substantially when estimating the availability model parameters from survey data, and we recommend that these data be gathered. We apply the methods to estimate detection probability from a double-observer survey of North Atlantic minke whales, and find that double-observer data greatly improve estimator precision here too. © 2015 The Authors Biometrics published by Wiley Periodicals, Inc. on behalf of International Biometric Society.

Apparatus and method for heterodyne-generated two-dimensional detector array using a single element detector

DOEpatents

Strauss, Charlie E.

1997-01-01

Apparatus and method for heterodyne-generated, two-dimensional detector array using a single detector. Synthetic-array heterodyne detection, permits a single-element optical detector to behave as though it were divided into an array of separate heterodyne detector elements. A fifteen-element synthetic array has successfully been experimentally realized on a single-element detector, permitting all of the array elements to be read out continuously and in parallel from one electrical connection. A CO.sub.2 laser and a single-element HgCdTe photodiode are employed. A different heterodyne local oscillator frequency is incident upon the spatially resolvable regions of the detector surface. Thus, different regions are mapped to different heterodyne beat frequencies. One can determine where the photons were incident on the detector surface even though a single electrical connection to the detector is used. This also prevents the destructive interference that occurs when multiple speckles are imaged (similar to spatial diversity), In coherent LIDAR this permits a larger field of view. An acoustooptic modulator generates the local oscillator frequencies and can achieve adequate spatial separation of optical frequencies of the order of a megahertz apart.

Apparatus and method for heterodyne-generated two-dimensional detector array using a single element detector

DOEpatents

Strauss, C.E.

1997-11-18

Apparatus and method are disclosed for heterodyne-generated, two-dimensional detector array using a single detector. Synthetic-array heterodyne detection, permits a single-element optical detector to behave as though it were divided into an array of separate heterodyne detector elements. A fifteen-element synthetic array has successfully been experimentally realized on a single-element detector, permitting all of the array elements to be read out continuously and in parallel from one electrical connection. A CO{sub 2} laser and a single-element HgCdTe photodiode are employed. A different heterodyne local oscillator frequency is incident upon the spatially resolvable regions of the detector surface. Thus, different regions are mapped to different heterodyne beat frequencies. One can determine where the photons were incident on the detector surface even though a single electrical connection to the detector is used. This also prevents the destructive interference that occurs when multiple speckles are imaged (similar to spatial diversity), In coherent LIDAR this permits a larger field of view. An acoustooptic modulator generates the local oscillator frequencies and can achieve adequate spatial separation of optical frequencies of the order of a megahertz apart. 4 figs.

Dual-view inverted selective plane illumination microscopy (diSPIM) with improved background rejection for accurate 3D digital pathology

NASA Astrophysics Data System (ADS)

Hu, Bihe; Bolus, Daniel; Brown, J. Quincy

2018-02-01

Current gold-standard histopathology for cancerous biopsies is destructive, time consuming, and limited to 2D slices, which do not faithfully represent true 3D tumor micro-morphology. Light sheet microscopy has emerged as a powerful tool for 3D imaging of cancer biospecimens. Here, we utilize the versatile dual-view inverted selective plane illumination microscopy (diSPIM) to render digital histological images of cancer biopsies. Dual-view architecture enabled more isotropic resolution in X, Y, and Z; and different imaging modes, such as adding electronic confocal slit detection (eCSD) or structured illumination (SI), can be used to improve degraded image quality caused by background signal of large, scattering samples. To obtain traditional H&E-like images, we used DRAQ5 and eosin (D&E) staining, with 488nm and 647nm laser illumination, and multi-band filter sets. Here, phantom beads and a D&E stained buccal cell sample have been used to verify our dual-view method. We also show that via dual view imaging and deconvolution, more isotropic resolution has been achieved for optical cleared human prostate sample, providing more accurate quantitation of 3D tumor architecture than was possible with single-view SPIM methods. We demonstrate that the optimized diSPIM delivers more precise analysis of 3D cancer microarchitecture in human prostate biopsy than simpler light sheet microscopy arrangements.

Image Based Mango Fruit Detection, Localisation and Yield Estimation Using Multiple View Geometry

PubMed Central

Stein, Madeleine; Bargoti, Suchet; Underwood, James

2016-01-01

This paper presents a novel multi-sensor framework to efficiently identify, track, localise and map every piece of fruit in a commercial mango orchard. A multiple viewpoint approach is used to solve the problem of occlusion, thus avoiding the need for labour-intensive field calibration to estimate actual yield. Fruit are detected in images using a state-of-the-art faster R-CNN detector, and pair-wise correspondences are established between images using trajectory data provided by a navigation system. A novel LiDAR component automatically generates image masks for each canopy, allowing each fruit to be associated with the corresponding tree. The tracked fruit are triangulated to locate them in 3D, enabling a number of spatial statistics per tree, row or orchard block. A total of 522 trees and 71,609 mangoes were scanned on a Calypso mango orchard near Bundaberg, Queensland, Australia, with 16 trees counted by hand for validation, both on the tree and after harvest. The results show that single, dual and multi-view methods can all provide precise yield estimates, but only the proposed multi-view approach can do so without calibration, with an error rate of only 1.36% for individual trees. PMID:27854271

To See or Not to See: Investigating Detectability of Ganges River Dolphins Using a Combined Visual-Acoustic Survey

PubMed Central

Richman, Nadia I.; Gibbons, James M.; Turvey, Samuel T.; Akamatsu, Tomonari; Ahmed, Benazir; Mahabub, Emile; Smith, Brian D.; Jones, Julia P. G.

2014-01-01

Detection of animals during visual surveys is rarely perfect or constant, and failure to account for imperfect detectability affects the accuracy of abundance estimates. Freshwater cetaceans are among the most threatened group of mammals, and visual surveys are a commonly employed method for estimating population size despite concerns over imperfect and unquantified detectability. We used a combined visual-acoustic survey to estimate detectability of Ganges River dolphins (Platanista gangetica gangetica) in four waterways of southern Bangladesh. The combined visual-acoustic survey resulted in consistently higher detectability than a single observer-team visual survey, thereby improving power to detect trends. Visual detectability was particularly low for dolphins close to meanders where these habitat features temporarily block the view of the preceding river surface. This systematic bias in detectability during visual-only surveys may lead researchers to underestimate the importance of heavily meandering river reaches. Although the benefits of acoustic surveys are increasingly recognised for marine cetaceans, they have not been widely used for monitoring abundance of freshwater cetaceans due to perceived costs and technical skill requirements. We show that acoustic surveys are in fact a relatively cost-effective approach for surveying freshwater cetaceans, once it is acknowledged that methods that do not account for imperfect detectability are of limited value for monitoring. PMID:24805782

To see or not to see: investigating detectability of Ganges River dolphins using a combined visual-acoustic survey.

PubMed

Richman, Nadia I; Gibbons, James M; Turvey, Samuel T; Akamatsu, Tomonari; Ahmed, Benazir; Mahabub, Emile; Smith, Brian D; Jones, Julia P G

2014-01-01

Detection of animals during visual surveys is rarely perfect or constant, and failure to account for imperfect detectability affects the accuracy of abundance estimates. Freshwater cetaceans are among the most threatened group of mammals, and visual surveys are a commonly employed method for estimating population size despite concerns over imperfect and unquantified detectability. We used a combined visual-acoustic survey to estimate detectability of Ganges River dolphins (Platanista gangetica gangetica) in four waterways of southern Bangladesh. The combined visual-acoustic survey resulted in consistently higher detectability than a single observer-team visual survey, thereby improving power to detect trends. Visual detectability was particularly low for dolphins close to meanders where these habitat features temporarily block the view of the preceding river surface. This systematic bias in detectability during visual-only surveys may lead researchers to underestimate the importance of heavily meandering river reaches. Although the benefits of acoustic surveys are increasingly recognised for marine cetaceans, they have not been widely used for monitoring abundance of freshwater cetaceans due to perceived costs and technical skill requirements. We show that acoustic surveys are in fact a relatively cost-effective approach for surveying freshwater cetaceans, once it is acknowledged that methods that do not account for imperfect detectability are of limited value for monitoring.

A multi-view face recognition system based on cascade face detector and improved Dlib

NASA Astrophysics Data System (ADS)

Zhou, Hongjun; Chen, Pei; Shen, Wei

2018-03-01

In this research, we present a framework for multi-view face detect and recognition system based on cascade face detector and improved Dlib. This method is aimed to solve the problems of low efficiency and low accuracy in multi-view face recognition, to build a multi-view face recognition system, and to discover a suitable monitoring scheme. For face detection, the cascade face detector is used to extracted the Haar-like feature from the training samples, and Haar-like feature is used to train a cascade classifier by combining Adaboost algorithm. Next, for face recognition, we proposed an improved distance model based on Dlib to improve the accuracy of multiview face recognition. Furthermore, we applied this proposed method into recognizing face images taken from different viewing directions, including horizontal view, overlooks view, and looking-up view, and researched a suitable monitoring scheme. This method works well for multi-view face recognition, and it is also simulated and tested, showing satisfactory experimental results.

3D digital image correlation using a single 3CCD colour camera and dichroic filter

NASA Astrophysics Data System (ADS)

Zhong, F. Q.; Shao, X. X.; Quan, C.

2018-04-01

In recent years, three-dimensional digital image correlation methods using a single colour camera have been reported. In this study, we propose a simplified system by employing a dichroic filter (DF) to replace the beam splitter and colour filters. The DF can be used to combine two views from different perspectives reflected by two planar mirrors and eliminate their interference. A 3CCD colour camera is then used to capture two different views simultaneously via its blue and red channels. Moreover, the measurement accuracy of the proposed method is higher since the effect of refraction is reduced. Experiments are carried out to verify the effectiveness of the proposed method. It is shown that the interference between the blue and red views is insignificant. In addition, the measurement accuracy of the proposed method is validated on the rigid body displacement. The experimental results demonstrate that the measurement accuracy of the proposed method is higher compared with the reported methods using a single colour camera. Finally, the proposed method is employed to measure the in- and out-of-plane displacements of a loaded plastic board. The re-projection errors of the proposed method are smaller than those of the reported methods using a single colour camera.

Monocular Vision-Based Underwater Object Detection

PubMed Central

Zhang, Zhen; Dai, Fengzhao; Bu, Yang; Wang, Huibin

2017-01-01

In this paper, we propose an underwater object detection method using monocular vision sensors. In addition to commonly used visual features such as color and intensity, we investigate the potential of underwater object detection using light transmission information. The global contrast of various features is used to initially identify the region of interest (ROI), which is then filtered by the image segmentation method, producing the final underwater object detection results. We test the performance of our method with diverse underwater datasets. Samples of the datasets are acquired by a monocular camera with different qualities (such as resolution and focal length) and setups (viewing distance, viewing angle, and optical environment). It is demonstrated that our ROI detection method is necessary and can largely remove the background noise and significantly increase the accuracy of our underwater object detection method. PMID:28771194

Pornographic information of Internet views detection method based on the connected areas

NASA Astrophysics Data System (ADS)

Wang, Huibai; Fan, Ajie

2017-01-01

Nowadays online porn video broadcasting and downloading is very popular. In view of the widespread phenomenon of Internet pornography, this paper proposed a new method of pornographic video detection based on connected areas. Firstly, decode the video into a serious of static images and detect skin color on the extracted key frames. If the area of skin color reaches a certain threshold, use the AdaBoost algorithm to detect the human face. Judge the connectivity of the human face and the large area of skin color to determine whether detect the sensitive area finally. The experimental results show that the method can effectively remove the non-pornographic videos contain human who wear less. This method can improve the efficiency and reduce the workload of detection.

Microfluidic molecular assay platform for the detection of miRNAs, mRNAs, proteins, and post-translational modifications at single-cell resolution

DOE PAGES

Wu, Meiye; Singh, Anup K.

2014-07-15

In this study, cell signaling is a dynamic and complex process. A typical signaling pathway may begin with activation of cell surface receptors, leading to activation kinase cascade that culminates in induction of mRNA and non-coding miRNA production in the nucleus, followed by modulation of mRNA expression by miRNAs in the cytosol, and end with production of proteins in response to the signaling pathway. Signaling pathways involve proteins, miRNA, and mRNAs, along with various forms of transient post-translational modifications, and detecting each type of signaling molecule requires categorically different sample preparation methods such as Western blotting for proteins, PCR formore » nucleic acids, and flow cytometry for post-translational modifications. Since we know that cells in populations behave heterogeneously1, especially in the cases of stem cells, cancer, and hematopoiesis, there is need for a new technology that provides capability to detect and quantify multiple categories of signaling molecules in intact single cells to provide a comprehensive view of the cell’s physiological state. In this technical brief, we describe our microfluidic platform with a portfolio of customized molecular assays that can detect nucleic acids, proteins, and post-translational modifications in single intact cells with >95% reduction in reagent requirement in under 8 hours.« less

Microfluidic molecular assay platform for the detection of miRNAs, mRNAs, proteins, and posttranslational modifications at single-cell resolution.

PubMed

Wu, Meiye; Singh, Anup K

2014-12-01

Cell signaling is a dynamic and complex process. A typical signaling pathway may begin with activation of cell surface receptors, leading to activation of a kinase cascade that culminates in induction of messenger RNA (mRNA) and noncoding microRNA (miRNA) production in the nucleus, followed by modulation of mRNA expression by miRNAs in the cytosol, and end with production of proteins in response to the signaling pathway. Signaling pathways involve proteins, miRNA, and mRNAs, along with various forms of transient posttranslational modifications, and detecting each type of signaling molecule requires categorically different sample preparation methods such as Western blotting for proteins, PCR for nucleic acids, and flow cytometry for posttranslational modifications. Since we know that cells in populations behave heterogeneously,(1) especially in the cases of stem cells, cancer, and hematopoiesis, there is need for a new technology that provides capability to detect and quantify multiple categories of signaling molecules in intact single cells to provide a comprehensive view of the cell's physiological state. In this Technology Brief, we describe our automated microfluidic platform with a portfolio of customized molecular assays that can detect nucleic acids, proteins, and posttranslational modifications in single intact cells with >95% reduction in reagent requirement in under 8 h. © 2014 Society for Laboratory Automation and Screening.

Are 3-D coronal mass ejection parameters from single-view observations consistent with multiview ones?

NASA Astrophysics Data System (ADS)

Lee, Harim; Moon, Y.-J.; Na, Hyeonock; Jang, Soojeong; Lee, Jae-Ok

2015-12-01

To prepare for when only single-view observations are available, we have made a test whether the 3-D parameters (radial velocity, angular width, and source location) of halo coronal mass ejections (HCMEs) from single-view observations are consistent with those from multiview observations. For this test, we select 44 HCMEs from December 2010 to June 2011 with the following conditions: partial and full HCMEs by SOHO and limb CMEs by twin STEREO spacecraft when they were approximately in quadrature. In this study, we compare the 3-D parameters of the HCMEs from three different methods: (1) a geometrical triangulation method, the STEREO CAT tool developed by NASA/CCMC, for multiview observations using STEREO/SECCHI and SOHO/LASCO data, (2) the graduated cylindrical shell (GCS) flux rope model for multiview observations using STEREO/SECCHI data, and (3) an ice cream cone model for single-view observations using SOHO/LASCO data. We find that the radial velocities and the source locations of the HCMEs from three methods are well consistent with one another with high correlation coefficients (≥0.9). However, the angular widths by the ice cream cone model are noticeably underestimated for broad CMEs larger than 100° and several partial HCMEs. A comparison between the 3-D CME parameters directly measured from twin STEREO spacecraft and the above 3-D parameters shows that the parameters from multiview are more consistent with the STEREO measurements than those from single view.

Retinal image mosaicing using the radial distortion correction model

NASA Astrophysics Data System (ADS)

Lee, Sangyeol; Abràmoff, Michael D.; Reinhardt, Joseph M.

2008-03-01

Fundus camera imaging can be used to examine the retina to detect disorders. Similar to looking through a small keyhole into a large room, imaging the fundus with an ophthalmologic camera allows only a limited view at a time. Thus, the generation of a retinal montage using multiple images has the potential to increase diagnostic accuracy by providing larger field of view. A method of mosaicing multiple retinal images using the radial distortion correction (RADIC) model is proposed in this paper. Our method determines the inter-image connectivity by detecting feature correspondences. The connectivity information is converted to a tree structure that describes the spatial relationships between the reference and target images for pairwise registration. The montage is generated by cascading pairwise registration scheme starting from the anchor image downward through the connectivity tree hierarchy. The RADIC model corrects the radial distortion that is due to the spherical-to-planar projection during retinal imaging. Therefore, after radial distortion correction, individual images can be properly mapped onto a montage space by a linear geometric transformation, e.g. affine transform. Compared to the most existing montaging methods, our method is unique in that only a single registration per image is required because of the distortion correction property of RADIC model. As a final step, distance-weighted intensity blending is employed to correct the inter-image differences in illumination encountered when forming the montage. Visual inspection of the experimental results using three mosaicing cases shows our method can produce satisfactory montages.

SU-E-J-142: Performance Study of Automatic Image-Segmentation Algorithms in Motion Tracking Via MR-IGRT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Feng, Y; Olsen, J.; Parikh, P.

2014-06-01

Purpose: Evaluate commonly used segmentation algorithms on a commercially available real-time MR image guided radiotherapy (MR-IGRT) system (ViewRay), compare the strengths and weaknesses of each method, with the purpose of improving motion tracking for more accurate radiotherapy. Methods: MR motion images of bladder, kidney, duodenum, and liver tumor were acquired for three patients using a commercial on-board MR imaging system and an imaging protocol used during MR-IGRT. A series of 40 frames were selected for each case to cover at least 3 respiratory cycles. Thresholding, Canny edge detection, fuzzy k-means (FKM), k-harmonic means (KHM), and reaction-diffusion level set evolution (RD-LSE),more » along with the ViewRay treatment planning and delivery system (TPDS) were included in the comparisons. To evaluate the segmentation results, an expert manual contouring of the organs or tumor from a physician was used as a ground-truth. Metrics value of sensitivity, specificity, Jaccard similarity, and Dice coefficient were computed for comparison. Results: In the segmentation of single image frame, all methods successfully segmented the bladder and kidney, but only FKM, KHM and TPDS were able to segment the liver tumor and the duodenum. For segmenting motion image series, the TPDS method had the highest sensitivity, Jarccard, and Dice coefficients in segmenting bladder and kidney, while FKM and KHM had a slightly higher specificity. A similar pattern was observed when segmenting the liver tumor and the duodenum. The Canny method is not suitable for consistently segmenting motion frames in an automated process, while thresholding and RD-LSE cannot consistently segment a liver tumor and the duodenum. Conclusion: The study compared six different segmentation methods and showed the effectiveness of the ViewRay TPDS algorithm in segmenting motion images during MR-IGRT. Future studies include a selection of conformal segmentation methods based on image/organ-specific information, different filtering methods and their influences on the segmentation results. Parag Parikh receives research grant from ViewRay. Sasa Mutic has consulting and research agreements with ViewRay. Yanle Hu receives travel reimbursement from ViewRay. Iwan Kawrakow and James Dempsey are ViewRay employees.« less

Single DNA imaging and length quantification through a mobile phone microscope

NASA Astrophysics Data System (ADS)

Wei, Qingshan; Luo, Wei; Chiang, Samuel; Kappel, Tara; Mejia, Crystal; Tseng, Derek; Chan, Raymond Yan L.; Yan, Eddie; Qi, Hangfei; Shabbir, Faizan; Ozkan, Haydar; Feng, Steve; Ozcan, Aydogan

2016-03-01

The development of sensitive optical microscopy methods for the detection of single DNA molecules has become an active research area which cultivates various promising applications including point-of-care (POC) genetic testing and diagnostics. Direct visualization of individual DNA molecules usually relies on sophisticated optical microscopes that are mostly available in well-equipped laboratories. For POC DNA testing/detection, there is an increasing need for the development of new single DNA imaging and sensing methods that are field-portable, cost-effective, and accessible for diagnostic applications in resource-limited or field-settings. For this aim, we developed a mobile-phone integrated fluorescence microscopy platform that allows imaging and sizing of single DNA molecules that are stretched on a chip. This handheld device contains an opto-mechanical attachment integrated onto a smartphone camera module, which creates a high signal-to-noise ratio dark-field imaging condition by using an oblique illumination/excitation configuration. Using this device, we demonstrated imaging of individual linearly stretched λ DNA molecules (48 kilobase-pair, kbp) over 2 mm2 field-of-view. We further developed a robust computational algorithm and a smartphone app that allowed the users to quickly quantify the length of each DNA fragment imaged using this mobile interface. The cellphone based device was tested by five different DNA samples (5, 10, 20, 40, and 48 kbp), and a sizing accuracy of <1 kbp was demonstrated for DNA strands longer than 10 kbp. This mobile DNA imaging and sizing platform can be very useful for various diagnostic applications including the detection of disease-specific genes and quantification of copy-number-variations at POC settings.

Detecting presence of cardiovascular disease through mitochondria respiration as depicted through biophotonic emission

PubMed Central

Rizzo, Nancy R.; Hank, Nicole C.; Zhang, Jian

2015-01-01

Aims Increased production of reactive oxygen species (ROS) in mitochondria, play an important role in the cardiovascular system. Furthermore, oxidative metabolism of mitochondria comprised of biophoton emissions, are linked to ROS and oxidative stress. In this review we investigated the association between the ability of ClearViewTM system (ClearView) to indicate the presence or absence of cardiovascular disease through mitochondria respiration as depicted through biophotonic emission. Methods and results One hundred and ninety-five out of the three hundred and fifty-three human subjects enrolled in this prospective, single site study had at least one cardiovascular related diagnosis. Measurements with ClearView consisted of scanning all 10 fingers twice. Images were captured through the ClearView software and analyzed to produce a scale that indicates the presence or absence of cardiovascular disease. The association of ClearView's ability to indicate the presence or absence of cardiovascular disease with a physician's diagnosis was assessed using odds ratios (OR) and area under ROC curve (AUC). Adjusting for age, OR of ClearView measurements conducted with capacitive barrier was 3.44 (95%CI: 2.13, 5.55) and the OR without the capacitive barrier was 2.15 (95%CI: 1.42, 3.23). The OR in men were 5.91 (95%CI: 2.35, 14.85) and 2.88 (95%CI: 1.38, 6.01), adjusting for age and corresponding to with and without capacitive barrier. The OR in women were 3.50 (95%CI: 1.86, 6.59) and 2.09 (95%CI: 1.20, 3.64) with and without capacitive barrier. AUCs for measurements with capacitive barrier were >0.90. Conclusion ClearView detected the presence or absence of cardiovascular disease independent of other conditions. PMID:26722839

Method for the Determination of Aconitum Alkaloids in Dietary Supplements and Raw Materials by Reversed-Phase Liquid Chromatography with Ultraviolet Detection and Confirmation by Tandem Mass Spectrometry: Single-Laboratory Validation

PubMed Central

Tang, Wai-Tong; Wong, Sui-Kay; Law, Tin-Yau; Pang, Kwok-Chu; Sin, Della; Tam, Yin-King

2008-01-01

A study of single-laboratory validation (SLV) of a reversed-phase liquid Chromatography (RP-LC) method was conducted for the determination of diester-diterpene Aconitum alkaloids, viz., aconitine, mesaconitine, and hypaconitine, in a variety of dietary supplements, including single-arid multiple-ingredient dry powder extracts, pills, capsules, and raw materials. The Aconitum alkaloids in the samples were extracted by diethyl ether in the presence of ammonia. After cleanup with solid-phase extraction to remove the matrix interferences, the alkaloids were determined by RP-LC with UV detection at 235 nm, and the results were confirmed by tandem mass Spectrometry. The linear responses for aconitine, mesaconitine, and hypaconitine based on the present LC system ranged from 0.5 to 200 μg/mL. Relative standard deviations of 2.0 to 6.9% were obtained from duplicate analysis of 6 test materials of different matrixes for the 3 Aconitum alkaloids performed by 2 analysts on 5 different days. The recoveries determined for supplements and raw materials spiked with 3 Aconitum alkaloids at levels of 2.5–10 μg/g were in the range of 86–99%. In view of the attainment of satisfactory results for accuracy, precision, and recovery in the SLV study, it is recommended that the method validation process proceed to a collaborative study. PMID:17225594

Nonlinear features for classification and pose estimation of machined parts from single views

NASA Astrophysics Data System (ADS)

Talukder, Ashit; Casasent, David P.

1998-10-01

A new nonlinear feature extraction method is presented for classification and pose estimation of objects from single views. The feature extraction method is called the maximum representation and discrimination feature (MRDF) method. The nonlinear MRDF transformations to use are obtained in closed form, and offer significant advantages compared to nonlinear neural network implementations. The features extracted are useful for both object discrimination (classification) and object representation (pose estimation). We consider MRDFs on image data, provide a new 2-stage nonlinear MRDF solution, and show it specializes to well-known linear and nonlinear image processing transforms under certain conditions. We show the use of MRDF in estimating the class and pose of images of rendered solid CAD models of machine parts from single views using a feature-space trajectory neural network classifier. We show new results with better classification and pose estimation accuracy than are achieved by standard principal component analysis and Fukunaga-Koontz feature extraction methods.

[A quick algorithm of dynamic spectrum photoelectric pulse wave detection based on LabVIEW].

PubMed

Lin, Ling; Li, Na; Li, Gang

2010-02-01

Dynamic spectrum (DS) detection is attractive among the numerous noninvasive blood component detection methods because of the elimination of the main interference of the individual discrepancy and measure conditions. DS is a kind of spectrum extracted from the photoelectric pulse wave and closely relative to the artery blood. It can be used in a noninvasive blood component concentration examination. The key issues in DS detection are high detection precision and high operation speed. The precision of measure can be advanced by making use of over-sampling and lock-in amplifying on the pick-up of photoelectric pulse wave in DS detection. In the present paper, the theory expression formula of the over-sampling and lock-in amplifying method was deduced firstly. Then in order to overcome the problems of great data and excessive operation brought on by this technology, a quick algorithm based on LabVIEW and a method of using external C code applied in the pick-up of photoelectric pulse wave were presented. Experimental verification was conducted in the environment of LabVIEW. The results show that by the method pres ented, the speed of operation was promoted rapidly and the data memory was reduced largely.

Principal axis-based correspondence between multiple cameras for people tracking.

PubMed

Hu, Weiming; Hu, Min; Zhou, Xue; Tan, Tieniu; Lou, Jianguang; Maybank, Steve

2006-04-01

Visual surveillance using multiple cameras has attracted increasing interest in recent years. Correspondence between multiple cameras is one of the most important and basic problems which visual surveillance using multiple cameras brings. In this paper, we propose a simple and robust method, based on principal axes of people, to match people across multiple cameras. The correspondence likelihood reflecting the similarity of pairs of principal axes of people is constructed according to the relationship between "ground-points" of people detected in each camera view and the intersections of principal axes detected in different camera views and transformed to the same view. Our method has the following desirable properties: 1) Camera calibration is not needed. 2) Accurate motion detection and segmentation are less critical due to the robustness of the principal axis-based feature to noise. 3) Based on the fused data derived from correspondence results, positions of people in each camera view can be accurately located even when the people are partially occluded in all views. The experimental results on several real video sequences from outdoor environments have demonstrated the effectiveness, efficiency, and robustness of our method.

The evaluation of single-view and multi-view fusion 3D echocardiography using image-driven segmentation and tracking.

PubMed

Rajpoot, Kashif; Grau, Vicente; Noble, J Alison; Becher, Harald; Szmigielski, Cezary

2011-08-01

Real-time 3D echocardiography (RT3DE) promises a more objective and complete cardiac functional analysis by dynamic 3D image acquisition. Despite several efforts towards automation of left ventricle (LV) segmentation and tracking, these remain challenging research problems due to the poor-quality nature of acquired images usually containing missing anatomical information, speckle noise, and limited field-of-view (FOV). Recently, multi-view fusion 3D echocardiography has been introduced as acquiring multiple conventional single-view RT3DE images with small probe movements and fusing them together after alignment. This concept of multi-view fusion helps to improve image quality and anatomical information and extends the FOV. We now take this work further by comparing single-view and multi-view fused images in a systematic study. In order to better illustrate the differences, this work evaluates image quality and information content of single-view and multi-view fused images using image-driven LV endocardial segmentation and tracking. The image-driven methods were utilized to fully exploit image quality and anatomical information present in the image, thus purposely not including any high-level constraints like prior shape or motion knowledge in the analysis approaches. Experiments show that multi-view fused images are better suited for LV segmentation and tracking, while relatively more failures and errors were observed on single-view images. Copyright © 2011 Elsevier B.V. All rights reserved.

Differential fluorescent staining method for detection of bacteria in blood cultures, cerebrospinal fluid and other clinical specimens.

PubMed

Fazii, P; Ciancaglini, E; Riario Sforza, G

2002-05-01

The aim of this study was to evaluate a differential staining method to distinguish gram-positive from gram-negative bacteria in fluorescence. The method is based on two fluorochromes, one acting in the wavelength of red, i.e. the acridine orange, and another acting in the wavelength of green, i.e. the fluorescein. With this method, gram-positive bacteria appear yellow and gram-negative bacteria appear green. In view of the importance of a rapid aetiological diagnosis in cases of septicaemia, the differential staining method in fluorescence was compared with Gram stain for the detection of bacteria in blood. Of 5,820 blood cultures entered into the study and identified by the Bactec 9120 fluorescent series instrument (Becton Dickinson Europe, France), 774 were positive. Of the 774 positive cultures, 689 yielded only a single organism. The differential staining method in fluorescence detected 626 of the 689 cultures, while Gram stain detected 468. On the basis of these results, the sensitivity of the differential staining method in fluorescence was 90.9%, while that of Gram stain was 67.9%. The difference between the two methods was statistically significant ( P<0.001). The differential fluorescent staining method was more sensitive than Gram stain in the detection of bacteria in blood cultures during the incubation period. This technique provides a rapid, simple and highly sensitive staining method that can be used in conjunction with subculture methods. Whereas subculture requires an incubation period of 18-24 h, the fluorescent staining technique can detect bacteria on the same day that smears are prepared and examined. The differential fluorescent staining method was also evaluated for its ability to detect microorganisms in cerebrospinal fluid and other clinical specimens. The microorganisms were easily detected, even when bacterial counts in the specimens were low.

Enhanced video indirect ophthalmoscopy (VIO) via robust mosaicing.

PubMed

Estrada, Rolando; Tomasi, Carlo; Cabrera, Michelle T; Wallace, David K; Freedman, Sharon F; Farsiu, Sina

2011-10-01

Indirect ophthalmoscopy (IO) is the standard of care for evaluation of the neonatal retina. When recorded on video from a head-mounted camera, IO images have low quality and narrow Field of View (FOV). We present an image fusion methodology for converting a video IO recording into a single, high quality, wide-FOV mosaic that seamlessly blends the best frames in the video. To this end, we have developed fast and robust algorithms for automatic evaluation of video quality, artifact detection and removal, vessel mapping, registration, and multi-frame image fusion. Our experiments show the effectiveness of the proposed methods.

Pump-probe micro-spectroscopy by means of an ultra-fast acousto-optics delay line.

PubMed

Audier, Xavier; Balla, Naveen; Rigneault, Hervé

2017-01-15

We demonstrate femtosecond pump-probe transient absorption spectroscopy using a programmable dispersive filter as an ultra-fast delay line. Combined with fast synchronous detection, this delay line allows for recording of 6 ps decay traces at 34 kHz. With such acquisition speed, we perform single point pump-probe spectroscopy on bulk samples in 80 μs and hyperspectral pump-probe imaging over a field of view of 100 μm in less than a second. The usability of the method is illustrated in a showcase experiment to image and discriminate between two pigments in a mixture.

Comparison of CME three-dimensional parameters derived from single and multi-spacecraft

NASA Astrophysics Data System (ADS)

LEE, Harim; Moon, Yong-Jae; Na, Hyeonock; Jang, Soojeong

2014-06-01

Several geometrical models (e.g., cone and flux rope models) have been suggested to infer three-dimensional parameters of CMEs using multi-view observations (STEREO/SECCHI) and single-view observations (SOHO/LASCO). To prepare for when only single view observations are available, we have made a test whether the cone model parameters from single-view observations are consistent with those from multi-view ones. For this test, we select 35 CMEs which are identified as CMEs, whose angular widths are larger than 180 degrees, by one spacecraft and as limb CMEs by the other ones. For this we use SOHO/LASCO and STEREO/SECCHI data during the period from 2010 December to 2011 July when two spacecraft were separated by 90±10 degrees. In this study, we compare the 3-D parameters of these CMEs from three different methods: (1) a triangulation method using STEREO/SECCHI and SOHO/LASCO data, (2) a Graduated Cylindrical Shell (GCS) flux rope model using STEREO/SECCHI data, and (3) an ice cream cone model using SOHO/LASCO data. The parameters used for comparison are radial velocities, angular widths and source location (angle γ between the propagation direction and the plan of the sky). We find that the radial velocities and the γ-values from three methods are well correlated with one another (CC > 0.8). However, angular widths from the three methods are somewhat different with the correlation coefficients of CC > 0.4. We also find that the correlation coefficients between the locations from the three methods and the active region locations are larger than 0.9, implying that most of the CMEs are radially ejected.

One new method for road data shape change detection

NASA Astrophysics Data System (ADS)

Tang, Luliang; Li, Qingquan; Xu, Feng; Chang, Xiaomeng

2009-10-01

Similarity is a psychological cognition; this paper defines the Difference Distance and puts forward the Similarity Measuring Model for linear spatial data (SMM-L) based on the integration of the Distance View and the Feature Set View which are the views for similarity cognition. Based on the study of the relationship between the spatial data change and the similarity, a change detection algorithm for linear spatial data is developed, and a test on road data change detection is realized.

Single-Camera-Based Method for Step Length Symmetry Measurement in Unconstrained Elderly Home Monitoring.

PubMed

Cai, Xi; Han, Guang; Song, Xin; Wang, Jinkuan

2017-11-01

single-camera-based gait monitoring is unobtrusive, inexpensive, and easy-to-use to monitor daily gait of seniors in their homes. However, most studies require subjects to walk perpendicularly to camera's optical axis or along some specified routes, which limits its application in elderly home monitoring. To build unconstrained monitoring environments, we propose a method to measure step length symmetry ratio (a useful gait parameter representing gait symmetry without significant relationship with age) from unconstrained straight walking using a single camera, without strict restrictions on walking directions or routes. according to projective geometry theory, we first develop a calculation formula of step length ratio for the case of unconstrained straight-line walking. Then, to adapt to general cases, we propose to modify noncollinear footprints, and accordingly provide general procedure for step length ratio extraction from unconstrained straight walking. Our method achieves a mean absolute percentage error (MAPE) of 1.9547% for 15 subjects' normal and abnormal side-view gaits, and also obtains satisfactory MAPEs for non-side-view gaits (2.4026% for 45°-view gaits and 3.9721% for 30°-view gaits). The performance is much better than a well-established monocular gait measurement system suitable only for side-view gaits with a MAPE of 3.5538%. Independently of walking directions, our method can accurately estimate step length ratios from unconstrained straight walking. This demonstrates our method is applicable for elders' daily gait monitoring to provide valuable information for elderly health care, such as abnormal gait recognition, fall risk assessment, etc. single-camera-based gait monitoring is unobtrusive, inexpensive, and easy-to-use to monitor daily gait of seniors in their homes. However, most studies require subjects to walk perpendicularly to camera's optical axis or along some specified routes, which limits its application in elderly home monitoring. To build unconstrained monitoring environments, we propose a method to measure step length symmetry ratio (a useful gait parameter representing gait symmetry without significant relationship with age) from unconstrained straight walking using a single camera, without strict restrictions on walking directions or routes. according to projective geometry theory, we first develop a calculation formula of step length ratio for the case of unconstrained straight-line walking. Then, to adapt to general cases, we propose to modify noncollinear footprints, and accordingly provide general procedure for step length ratio extraction from unconstrained straight walking. Our method achieves a mean absolute percentage error (MAPE) of 1.9547% for 15 subjects' normal and abnormal side-view gaits, and also obtains satisfactory MAPEs for non-side-view gaits (2.4026% for 45°-view gaits and 3.9721% for 30°-view gaits). The performance is much better than a well-established monocular gait measurement system suitable only for side-view gaits with a MAPE of 3.5538%. Independently of walking directions, our method can accurately estimate step length ratios from unconstrained straight walking. This demonstrates our method is applicable for elders' daily gait monitoring to provide valuable information for elderly health care, such as abnormal gait recognition, fall risk assessment, etc.

Robust sky light polarization detection with an S-wave plate in a light field camera.

PubMed

Zhang, Wenjing; Zhang, Xuanzhe; Cao, Yu; Liu, Haibo; Liu, Zejin

2016-05-01

The sky light polarization navigator has many advantages, such as low cost, no decrease in accuracy with continuous operation, etc. However, current celestial polarization measurement methods often suffer from low performance when the sky is covered by clouds, which reduce the accuracy of navigation. In this paper we introduce a new method and structure based on a handheld light field camera and a radial polarizer, composed of an S-wave plate and a linear polarizer, to detect the sky light polarization pattern across a wide field of view in a single snapshot. Each micro-subimage has a special intensity distribution. After extracting the texture feature of these subimages, stable distribution information of the angle of polarization under a cloudy sky can be obtained. Our experimental results match well with the predicted properties of the theory. Because the polarization pattern is obtained through image processing, rather than traditional methods based on mathematical computation, this method is less sensitive to errors of pixel gray value and thus has better anti-interference performance.

Dual-mode switching of a liquid crystal panel for viewing angle control

NASA Astrophysics Data System (ADS)

Baek, Jong-In; Kwon, Yong-Hoan; Kim, Jae Chang; Yoon, Tae-Hoon

2007-03-01

The authors propose a method to control the viewing angle of a liquid crystal (LC) panel using dual-mode switching. To realize both wide viewing angle (WVA) characteristics and narrow viewing angle (NVA) characteristics with a single LC panel, the authors use two different dark states. The LC layer can be aligned homogeneously parallel to the transmission axis of the bottom polarizer for WVA dark state operation, while it can be aligned vertically for NVA dark state operation. The authors demonstrated that viewing angle control can be achieved with a single panel without any loss of contrast at the front.

The optics inside an automated single molecule array analyzer

NASA Astrophysics Data System (ADS)

McGuigan, William; Fournier, David R.; Watson, Gary W.; Walling, Les; Gigante, Bill; Duffy, David C.; Rissin, David M.; Kan, Cheuk W.; Meyer, Raymond E.; Piech, Tomasz; Fishburn, Matthew W.

2014-02-01

Quanterix and Stratec Biomedical have developed an instrument that enables the automated measurement of multiple proteins at concentration ~1000 times lower than existing immunoassays. The instrument is based on Quanterix's proprietary Single Molecule Array technology (Simoa™ ) that facilitates the detection and quantification of biomarkers previously difficult to measure, thus opening up new applications in life science research and in-vitro diagnostics. Simoa is based on trapping individual beads in arrays of femtoliter-sized wells that, when imaged with sufficient resolution, allows for counting of single molecules associated with each bead. When used to capture and detect proteins, this approach is known as digital ELISA (Enzyme-linked immunosorbent assay). The platform developed is a merger of many science and engineering disciplines. This paper concentrates on the optical technologies that have enabled the development of a fully-automated single molecule analyzer. At the core of the system is a custom, wide field-of-view, fluorescence microscope that images arrays of microwells containing single molecules bound to magnetic beads. A consumable disc containing 24 microstructure arrays was developed previously in collaboration with Sony DADC. The system cadence requirements, array dimensions, and requirement to detect single molecules presented significant optical challenges. Specifically, the wide field-of-view needed to image the entire array resulted in the need for a custom objective lens. Additionally, cost considerations for the system required a custom solution that leveraged the image processing capabilities. This paper will discuss the design considerations and resultant optical architecture that has enabled the development of an automated digital ELISA platform.

Combined multi-spectrum and orthogonal Laplacianfaces for fast CB-XLCT imaging with single-view data

NASA Astrophysics Data System (ADS)

Zhang, Haibo; Geng, Guohua; Chen, Yanrong; Qu, Xuan; Zhao, Fengjun; Hou, Yuqing; Yi, Huangjian; He, Xiaowei

2017-12-01

Cone-beam X-ray luminescence computed tomography (CB-XLCT) is an attractive hybrid imaging modality, which has the potential of monitoring the metabolic processes of nanophosphors-based drugs in vivo. Single-view data reconstruction as a key issue of CB-XLCT imaging promotes the effective study of dynamic XLCT imaging. However, it suffers from serious ill-posedness in the inverse problem. In this paper, a multi-spectrum strategy is adopted to relieve the ill-posedness of reconstruction. The strategy is based on the third-order simplified spherical harmonic approximation model. Then, an orthogonal Laplacianfaces-based method is proposed to reduce the large computational burden without degrading the imaging quality. Both simulated data and in vivo experimental data were used to evaluate the efficiency and robustness of the proposed method. The results are satisfactory in terms of both location and quantitative recovering with computational efficiency, indicating that the proposed method is practical and promising for single-view CB-XLCT imaging.

High-speed spatial frequency domain imaging of rat cortex detects dynamic optical and physiological properties following cardiac arrest and resuscitation.

PubMed

Wilson, Robert H; Crouzet, Christian; Torabzadeh, Mohammad; Bazrafkan, Afsheen; Farahabadi, Maryam H; Jamasian, Babak; Donga, Dishant; Alcocer, Juan; Zaher, Shuhab M; Choi, Bernard; Akbari, Yama; Tromberg, Bruce J

2017-10-01

Quantifying rapidly varying perturbations in cerebral tissue absorption and scattering can potentially help to characterize changes in brain function caused by ischemic trauma. We have developed a platform for rapid intrinsic signal brain optical imaging using macroscopically structured light. The device performs fast, multispectral, spatial frequency domain imaging (SFDI), detecting backscattered light from three-phase binary square-wave projected patterns, which have a much higher refresh rate than sinusoidal patterns used in conventional SFDI. Although not as fast as "single-snapshot" spatial frequency methods that do not require three-phase projection, square-wave patterns allow accurate image demodulation in applications such as small animal imaging where the limited field of view does not allow single-phase demodulation. By using 655, 730, and 850 nm light-emitting diodes, two spatial frequencies ([Formula: see text] and [Formula: see text]), three spatial phases (120 deg, 240 deg, and 360 deg), and an overall camera acquisition rate of 167 Hz, we map changes in tissue absorption and reduced scattering parameters ([Formula: see text] and [Formula: see text]) and oxy- and deoxyhemoglobin concentration at [Formula: see text]. We apply this method to a rat model of cardiac arrest (CA) and cardiopulmonary resuscitation (CPR) to quantify hemodynamics and scattering on temporal scales ([Formula: see text]) ranging from tens of milliseconds to minutes. We observe rapid concurrent spatiotemporal changes in tissue oxygenation and scattering during CA and following CPR, even when the cerebral electrical signal is absent. We conclude that square-wave SFDI provides an effective technical strategy for assessing cortical optical and physiological properties by balancing competing performance demands for fast signal acquisition, small fields of view, and quantitative information content.

Compositions and methods for detecting single nucleotide polymorphisms

DOEpatents

Yeh, Hsin-Chih; Werner, James; Martinez, Jennifer S.

2016-11-22

Described herein are nucleic acid based probes and methods for discriminating and detecting single nucleotide variants in nucleic acid molecules (e.g., DNA). The methods include use of a pair of probes can be used to detect and identify polymorphisms, for example single nucleotide polymorphism in DNA. The pair of probes emit a different fluorescent wavelength of light depending on the association and alignment of the probes when hybridized to a target nucleic acid molecule. Each pair of probes is capable of discriminating at least two different nucleic acid molecules that differ by at least a single nucleotide difference. The methods can probes can be used, for example, for detection of DNA polymorphisms that are indicative of a particular disease or condition.

Single-scan patient-specific scatter correction in computed tomography using peripheral detection of scatter and compressed sensing scatter retrieval

PubMed Central

Meng, Bowen; Lee, Ho; Xing, Lei; Fahimian, Benjamin P.

2013-01-01

Purpose: X-ray scatter results in a significant degradation of image quality in computed tomography (CT), representing a major limitation in cone-beam CT (CBCT) and large field-of-view diagnostic scanners. In this work, a novel scatter estimation and correction technique is proposed that utilizes peripheral detection of scatter during the patient scan to simultaneously acquire image and patient-specific scatter information in a single scan, and in conjunction with a proposed compressed sensing scatter recovery technique to reconstruct and correct for the patient-specific scatter in the projection space. Methods: The method consists of the detection of patient scatter at the edges of the field of view (FOV) followed by measurement based compressed sensing recovery of the scatter through-out the projection space. In the prototype implementation, the kV x-ray source of the Varian TrueBeam OBI system was blocked at the edges of the projection FOV, and the image detector in the corresponding blocked region was used for scatter detection. The design enables image data acquisition of the projection data on the unblocked central region of and scatter data at the blocked boundary regions. For the initial scatter estimation on the central FOV, a prior consisting of a hybrid scatter model that combines the scatter interpolation method and scatter convolution model is estimated using the acquired scatter distribution on boundary region. With the hybrid scatter estimation model, compressed sensing optimization is performed to generate the scatter map by penalizing the L1 norm of the discrete cosine transform of scatter signal. The estimated scatter is subtracted from the projection data by soft-tuning, and the scatter-corrected CBCT volume is obtained by the conventional Feldkamp-Davis-Kress algorithm. Experimental studies using image quality and anthropomorphic phantoms on a Varian TrueBeam system were carried out to evaluate the performance of the proposed scheme. Results: The scatter shading artifacts were markedly suppressed in the reconstructed images using the proposed method. On the Catphan©504 phantom, the proposed method reduced the error of CT number to 13 Hounsfield units, 10% of that without scatter correction, and increased the image contrast by a factor of 2 in high-contrast regions. On the anthropomorphic phantom, the spatial nonuniformity decreased from 10.8% to 6.8% after correction. Conclusions: A novel scatter correction method, enabling unobstructed acquisition of the high frequency image data and concurrent detection of the patient-specific low frequency scatter data at the edges of the FOV, is proposed and validated in this work. Relative to blocker based techniques, rather than obstructing the central portion of the FOV which degrades and limits the image reconstruction, compressed sensing is used to solve for the scatter from detection of scatter at the periphery of the FOV, enabling for the highest quality reconstruction in the central region and robust patient-specific scatter correction. PMID:23298098

Automated X-ray image analysis for cargo security: Critical review and future promise.

PubMed

Rogers, Thomas W; Jaccard, Nicolas; Morton, Edward J; Griffin, Lewis D

2017-01-01

We review the relatively immature field of automated image analysis for X-ray cargo imagery. There is increasing demand for automated analysis methods that can assist in the inspection and selection of containers, due to the ever-growing volumes of traded cargo and the increasing concerns that customs- and security-related threats are being smuggled across borders by organised crime and terrorist networks. We split the field into the classical pipeline of image preprocessing and image understanding. Preprocessing includes: image manipulation; quality improvement; Threat Image Projection (TIP); and material discrimination and segmentation. Image understanding includes: Automated Threat Detection (ATD); and Automated Contents Verification (ACV). We identify several gaps in the literature that need to be addressed and propose ideas for future research. Where the current literature is sparse we borrow from the single-view, multi-view, and CT X-ray baggage domains, which have some characteristics in common with X-ray cargo.

Apparatus and method for high dose rate brachytherapy radiation treatment

DOEpatents

Macey, Daniel J.; Majewski, Stanislaw; Weisenberger, Andrew G.; Smith, Mark Frederick; Kross, Brian James

2005-01-25

A method and apparatus for the in vivo location and tracking of a radioactive seed source during and after brachytherapy treatment. The method comprises obtaining multiple views of the seed source in a living organism using: 1) a single PSPMT detector that is exposed through a multiplicity of pinholes thereby obtaining a plurality of images from a single angle; 2) a single PSPMT detector that may obtain an image through a single pinhole or a plurality of pinholes from a plurality of angles through movement of the detector; or 3) a plurality of PSPMT detectors that obtain a plurality of views from different angles simultaneously or virtually simultaneously. The plurality of images obtained from these various techniques, through angular displacement of the various acquired images, provide the information required to generate the three dimensional images needed to define the location of the radioactive seed source within the body of the living organism.

Decay detection in red oak trees using a combination of visual inspection, acoustic testing, and resistance microdrilling

Treesearch

Xiping Wang; R. Bruce Allison

2008-01-01

Arborists are often challenged to identify internal structural defects hidden from view within tree trunks. This article reports the results of a study using a trunk inspection protocol combining visual observation, single-path stress wave testing, acoustic tomography, and resistance microdrilling to detect internal defects. Two century-old red oak (Quercus rubra)...

Miniature curved artificial compound eyes

PubMed Central

Floreano, Dario; Pericet-Camara, Ramon; Viollet, Stéphane; Ruffier, Franck; Brückner, Andreas; Leitel, Robert; Buss, Wolfgang; Menouni, Mohsine; Expert, Fabien; Juston, Raphaël; Dobrzynski, Michal Karol; L’Eplattenier, Geraud; Recktenwald, Fabian; Mallot, Hanspeter A.; Franceschini, Nicolas

2013-01-01

In most animal species, vision is mediated by compound eyes, which offer lower resolution than vertebrate single-lens eyes, but significantly larger fields of view with negligible distortion and spherical aberration, as well as high temporal resolution in a tiny package. Compound eyes are ideally suited for fast panoramic motion perception. Engineering a miniature artificial compound eye is challenging because it requires accurate alignment of photoreceptive and optical components on a curved surface. Here, we describe a unique design method for biomimetic compound eyes featuring a panoramic, undistorted field of view in a very thin package. The design consists of three planar layers of separately produced arrays, namely, a microlens array, a neuromorphic photodetector array, and a flexible printed circuit board that are stacked, cut, and curved to produce a mechanically flexible imager. Following this method, we have prototyped and characterized an artificial compound eye bearing a hemispherical field of view with embedded and programmable low-power signal processing, high temporal resolution, and local adaptation to illumination. The prototyped artificial compound eye possesses several characteristics similar to the eye of the fruit fly Drosophila and other arthropod species. This design method opens up additional vistas for a broad range of applications in which wide field motion detection is at a premium, such as collision-free navigation of terrestrial and aerospace vehicles, and for the experimental testing of insect vision theories. PMID:23690574

Segmentation and detection of breast cancer in mammograms combining wavelet analysis and genetic algorithm.

PubMed

Pereira, Danilo Cesar; Ramos, Rodrigo Pereira; do Nascimento, Marcelo Zanchetta

2014-04-01

In Brazil, the National Cancer Institute (INCA) reports more than 50,000 new cases of the disease, with risk of 51 cases per 100,000 women. Radiographic images obtained from mammography equipments are one of the most frequently used techniques for helping in early diagnosis. Due to factors related to cost and professional experience, in the last two decades computer systems to support detection (Computer-Aided Detection - CADe) and diagnosis (Computer-Aided Diagnosis - CADx) have been developed in order to assist experts in detection of abnormalities in their initial stages. Despite the large number of researches on CADe and CADx systems, there is still a need for improved computerized methods. Nowadays, there is a growing concern with the sensitivity and reliability of abnormalities diagnosis in both views of breast mammographic images, namely cranio-caudal (CC) and medio-lateral oblique (MLO). This paper presents a set of computational tools to aid segmentation and detection of mammograms that contained mass or masses in CC and MLO views. An artifact removal algorithm is first implemented followed by an image denoising and gray-level enhancement method based on wavelet transform and Wiener filter. Finally, a method for detection and segmentation of masses using multiple thresholding, wavelet transform and genetic algorithm is employed in mammograms which were randomly selected from the Digital Database for Screening Mammography (DDSM). The developed computer method was quantitatively evaluated using the area overlap metric (AOM). The mean ± standard deviation value of AOM for the proposed method was 79.2 ± 8%. The experiments demonstrate that the proposed method has a strong potential to be used as the basis for mammogram mass segmentation in CC and MLO views. Another important aspect is that the method overcomes the limitation of analyzing only CC and MLO views. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Using Bi-Seasonal WorldView-2 Multi-Spectral Data and Supervised Random Forest Classification to Map Coastal Plant Communities in Everglades National Park.

PubMed

Wendelberger, Kristie S; Gann, Daniel; Richards, Jennifer H

2018-03-09

Coastal plant communities are being transformed or lost because of sea level rise (SLR) and land-use change. In conjunction with SLR, the Florida Everglades ecosystem has undergone large-scale drainage and restoration, altering coastal vegetation throughout south Florida. To understand how coastal plant communities are changing over time, accurate mapping techniques are needed that can define plant communities at a fine-enough resolution to detect fine-scale changes. We explored using bi-seasonal versus single-season WorldView-2 satellite data to map three mangrove and four adjacent plant communities, including the buttonwood/glycophyte community that harbors the federally-endangered plant Chromolaena frustrata . Bi-seasonal data were more effective than single-season to differentiate all communities of interest. Bi-seasonal data combined with Light Detection and Ranging (LiDAR) elevation data were used to map coastal plant communities of a coastal stretch within Everglades National Park (ENP). Overall map accuracy was 86%. Black and red mangroves were the dominant communities and covered 50% of the study site. All the remaining communities had ≤10% cover, including the buttonwood/glycophyte community. ENP harbors 21 rare coastal species threatened by SLR. The spatially explicit, quantitative data provided by our map provides a fine-scale baseline for monitoring future change in these species' habitats. Our results also offer a method to monitor vegetation change in other threatened habitats.

Using Bi-Seasonal WorldView-2 Multi-Spectral Data and Supervised Random Forest Classification to Map Coastal Plant Communities in Everglades National Park

PubMed Central

Richards, Jennifer H.

2018-01-01

Coastal plant communities are being transformed or lost because of sea level rise (SLR) and land-use change. In conjunction with SLR, the Florida Everglades ecosystem has undergone large-scale drainage and restoration, altering coastal vegetation throughout south Florida. To understand how coastal plant communities are changing over time, accurate mapping techniques are needed that can define plant communities at a fine-enough resolution to detect fine-scale changes. We explored using bi-seasonal versus single-season WorldView-2 satellite data to map three mangrove and four adjacent plant communities, including the buttonwood/glycophyte community that harbors the federally-endangered plant Chromolaena frustrata. Bi-seasonal data were more effective than single-season to differentiate all communities of interest. Bi-seasonal data combined with Light Detection and Ranging (LiDAR) elevation data were used to map coastal plant communities of a coastal stretch within Everglades National Park (ENP). Overall map accuracy was 86%. Black and red mangroves were the dominant communities and covered 50% of the study site. All the remaining communities had ≤10% cover, including the buttonwood/glycophyte community. ENP harbors 21 rare coastal species threatened by SLR. The spatially explicit, quantitative data provided by our map provides a fine-scale baseline for monitoring future change in these species’ habitats. Our results also offer a method to monitor vegetation change in other threatened habitats. PMID:29522476

Advanced wide-field surface plasmon microscopy of single adsorbing nanoparticles

NASA Astrophysics Data System (ADS)

Nizamov, Shavkat; Scherbahn, Vitali; Mirsky, Vladimir M.

2017-05-01

In-situ detection and characterization of nanoparticles in biological media as well as in food or other complex samples is still a big challenge for existing analytical methods. Here we describe a label-free and cost-effective analytical method for detection of nanoparticles in the concentration range 106 -1010 NPs/ml. The proposed method is based on the surface plasmon resonance microscopy (SPRM) with a large field of view ( 1.3mm2 ). It is able to detect and count adsorbing nanoparticles individually, totally up to the hundreds of thousands of NPs on the sensor surface. At constant diffusion conditions the detection rate is proportional to the number concentration of NPs, this provides an approach to determine the NPs concentration. The adsorption of nanoparticle can be manipulated by the surface functionalization, pH and electrolyte concentration of suspensions. Images of detected nanoparticles can be quantified in order to characterize them individually. The image intensity grows quasi-linearly with nanoparticle size for the given material. However, the size and material of nanoparticle cannot be resolved directly from the image. For determination of chemical composition, SPRM can be assisted by electrochemical analysis. In this case, the gold sensor surface is used both as a resonant media for plasmon microscopy and as a working electrode. Under potential sweep, the adsorbed NPs can be subjected to electrochemical dissolution, which is detected optically. The potential of this conversion characterizes the material of NPs.

Lateral variations of the Guerrero-Oaxaca subduction zone (Mexico) derived from weak seismicity (Mb3.5+) detected on a single array at teleseismic distance

NASA Astrophysics Data System (ADS)

Letort, Jean; Retailleau, Lise; Boué, Pierre; Radiguet, Mathilde; Gardonio, Blandine; Cotton, Fabrice; Campillo, Michel

2018-05-01

Detections of pP and sP phase arrivals (the so-called depth phases) at teleseismic distance provide one of the best ways to estimate earthquake focal depth, as the P-pP and the P-sP delays are strongly dependent on the depth. Based on a new processing workflow and using a single seismic array at teleseismic distance, we can estimate the depth of clusters of small events down to magnitude Mb 3.5. Our method provides a direct view of the relative variations of the seismicity depth from an active area. This study focuses on the application of this new methodology to study the lateral variations of the Guerrero subduction zone (Mexico) using the Eielson seismic array in Alaska (USA). After denoising the signals, 1232 Mb 3.5 + events were detected, with clear P, pP, sP and PcP arrivals. A high-resolution view of the lateral variations of the depth of the seismicity of the Guerero-Oaxaca area is thus obtained. The seismicity is shown to be mainly clustered along the interface, coherently following the geometry of the plate as constrained by the receiver-function analysis along the Meso America Subduction Experiment profile. From this study, the hypothesis of tears on the western part of Guerrero and the eastern part of Oaxaca are strongly confirmed by dramatic lateral changes in the depth of the earthquake clusters. The presence of these two tears might explain the observed lateral variations in seismicity, which is correlated with the boundaries of the slow slip events.

Method for Estimating Evaporative Potential (IM/CLO) from ASTM Standard Single Wind Velocity Measures

DTIC Science & Technology

2016-08-10

IM/CLO) FROM ASTM STANDARD SINGLE WIND VELOCITY MEASURES DISCLAIMER The opinions or assertions contained herein are the private views of the...USARIEM TECHNICAL REPORT T16-14 METHOD FOR ESTIMATING EVAPORATIVE POTENTIAL (IM/CLO) FROM ASTM STANDARD SINGLE WIND VELOCITY...ASTM STANDARD SINGLE WIND VELOCITY MEASURES Adam W. Potter Biophysics and Biomedical Modeling Division U.S. Army Research Institute of Environmental

Dim target trajectory-associated detection in bright earth limb background

NASA Astrophysics Data System (ADS)

Chen, Penghui; Xu, Xiaojian; He, Xiaoyu; Jiang, Yuesong

2015-09-01

The intensive emission of earth limb in the field of view of sensors contributes much to the observation images. Due to the low signal-to-noise ratio (SNR), it is a challenge to detect small targets in earth limb background, especially for the detection of point-like targets from a single frame. To improve the target detection, track before detection (TBD) based on the frame sequence is performed. In this paper, a new technique is proposed to determine the target associated trajectories, which jointly carries out background removing, maximum value projection (MVP) and Hough transform. The background of the bright earth limb in the observation images is removed according to the profile characteristics. For a moving target, the corresponding pixels in the MVP image are shifting approximately regularly in time sequence. And the target trajectory is determined by Hough transform according to the pixel characteristics of the target and the clutter and noise. Comparing with traditional frame-by-frame methods, determining associated trajectories from MVP reduces the computation load. Numerical simulations are presented to demonstrate the effectiveness of the approach proposed.

Low-cost soft-copy display accuracy in the detection of pulmonary nodules by single-exposure dual-energy subtraction: comparison with hard-copy viewing.

PubMed

Kido, S; Kuriyama, K; Hosomi, N; Inoue, E; Kuroda, C; Horai, T

2000-02-01

This study endeavored to clarify the usefulness of single-exposure dual-energy subtraction computed radiography (CR) of the chest and the ability of soft-copy images to detect low-contrast simulated pulmonary nodules. Conventional and bone-subtracted CR images of 25 chest phantom image sets with a low-contrast nylon nodule and 25 without a nodule were interpreted by 12 observers (6 radiologists, 6 chest physicians) who rated each on a continuous confidence scale and marked the position of the nodule if one was present. Hard-copy images were 7 x 7-inch laser-printed CR films, and soft-copy images were displayed on a 21-inch noninterlaced color CRT monitor with an optimized dynamic range. Soft-copy images were adjusted to the same size as hard-copy images and were viewed under darkened illumination in the reading room. No significant differences were found between hard- and soft-copy images. In conclusion, the soft-copy images were found to be useful in detecting low-contrast simulated pulmonary nodules.

Handling topological changes during elastic registration : Application to augmented reality in laparoscopic surgery.

PubMed

Paulus, Christoph J; Haouchine, Nazim; Kong, Seong-Ho; Soares, Renato Vianna; Cazier, David; Cotin, Stephane

2017-03-01

Locating the internal structures of an organ is a critical aspect of many surgical procedures. Minimally invasive surgery, associated with augmented reality techniques, offers the potential to visualize inner structures, allowing for improved analysis, depth perception or for supporting planning and decision systems. Most of the current methods dealing with rigid or non-rigid augmented reality make the assumption that the topology of the organ is not modified. As surgery relies essentially on cutting and dissection of anatomical structures, such methods are limited to the early stages of the surgery. We solve this shortcoming with the introduction of a method for physics-based elastic registration using a single view from a monocular camera. Singularities caused by topological changes are detected and propagated to the preoperative model. This significantly improves the coherence between the actual laparoscopic view and the model and provides added value in terms of navigation and decision-making, e.g., by overlaying the internal structures of an organ on the laparoscopic view. Our real-time augmentation method is assessed on several scenarios, using synthetic objects and real organs. In all cases, the impact of our approach is demonstrated, both qualitatively and quantitatively ( http://www.open-cas.org/?q=PaulusIJCARS16 ). The presented approach tackles the challenge of localizing internal structures throughout a complete surgical procedure, even after surgical cuts. This information is crucial for surgeons to improve the outcome for their surgical procedure and avoid complications.

Two-View versus Single-View Shear-Wave Elastography: Comparison of Observer Performance in Differentiating Benign from Malignant Breast Masses.

PubMed

Lee, Su Hyun; Cho, Nariya; Chang, Jung Min; Koo, Hye Ryoung; Kim, Jin You; Kim, Won Hwa; Bae, Min Sun; Yi, Ann; Moon, Woo Kyung

2013-10-28

Purpose To determine whether two-view shear-wave elastography (SWE) improves the performance of radiologists in differentiating benign from malignant breast masses compared with single-view SWE. Materials and Methods This prospective study was conducted with institutional review board approval, and written informed consent was obtained. B-mode ultrasonographic (US) and orthogonal SWE images were obtained for 219 breast masses (136 benign and 83 malignant; mean size, 14.8 mm) in 219 consecutive women (mean age, 47.9 years; range, 20-78 years). Five blinded radiologists independently assessed the likelihood of malignancy for three data sets: B-mode US alone, B-mode US and single-view SWE, and B-mode US and two-view SWE. Interobserver agreement regarding Breast Imaging Reporting and Data System (BI-RADS) category and the area under the receiver operating characteristic curve (AUC) of each data set were compared. Results Interobserver agreement was moderate (κ = 0.560 ± 0.015 [standard error of the mean]) for BI-RADS category assessment with B-mode US alone. When SWE was added to B-mode US, five readers showed substantial interobserver agreement (κ = 0.629 ± 0.017 for single-view SWE; κ = 0.651 ± 0.014 for two-view SWE). The mean AUC of B-mode US was 0.870 (range, 0.855-0.884). The AUC of B-mode US and two-view SWE (average, 0.928; range, 0.904-0.941) was higher than that of B-mode US and single-view SWE (average, 0.900; range, 0.890-0.920), with statistically significant differences for three readers (P ≤ .003). Conclusion The performance of radiologists in differentiating benign from malignant breast masses was improved when B-mode US was combined with two-view SWE compared with that when B-mode US was combined with single-view SWE. © RSNA, 2013 Supplemental material: S1.

Label-free optical detection of single-base mismatches by the combination of nuclease and gold nanoparticles.

PubMed

Liu, Meiying; Yuan, Min; Lou, Xinhui; Mao, Hongju; Zheng, Dongmei; Zou, Ruxing; Zou, Nengli; Tang, Xiangrong; Zhao, Jianlong

2011-07-15

We report here an optical approach that enables highly selective and colorimetric single-base mismatch detection without the need of target modification, precise temperature control or stringent washes. The method is based on the finding that nucleoside monophosphates (dNMPs), which are digested elements of DNA, can better stabilize unmodified gold nanoparticles (AuNPs) than single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) with the same base-composition and concentration. The method combines the exceptional mismatch discrimination capability of the structure-selective nucleases with the attractive optical property of AuNPs. Taking S1 nuclease as one example, the perfectly matched 16-base synthetic DNA target was distinctively differentiated from those with single-base mutation located at any position of the 16-base synthetic target. Single-base mutations present in targets with varied length up to 80-base, located either in the middle or near to the end of the targets, were all effectively detected. In order to prove that the method can be potentially used for real clinic samples, the single-base mismatch detections with two HBV genomic DNA samples were conducted. To further prove the generality of this method and potentially overcome the limitation on the detectable lengths of the targets of the S1 nuclease-based method, we also demonstrated the use of a duplex-specific nuclease (DSN) for color reversed single-base mismatch detection. The main limitation of the demonstrated methods is that it is limited to detect mutations in purified ssDNA targets. However, the method coupled with various convenient ssDNA generation and purification techniques, has the potential to be used for the future development of detector-free testing kits in single nucleotide polymorphism screenings for disease diagnostics and treatments. Copyright © 2011 Elsevier B.V. All rights reserved.

Dynamic ASXL1 Exon Skipping and Alternative Circular Splicing in Single Human Cells

PubMed Central

Natarajan, Sivaraman; Carter, Robert; Brown, Patrick O.

2016-01-01

Circular RNAs comprise a poorly understood new class of noncoding RNA. In this study, we used a combination of targeted deletion, high-resolution splicing detection, and single-cell sequencing to deeply probe ASXL1 circular splicing. We found that efficient circular splicing required the canonical transcriptional start site and inverted AluSx elements. Sequencing-based interrogation of isoforms after ASXL1 overexpression identified promiscuous linear splicing between all exons, with the two most abundant non-canonical linear products skipping the exons that produced the circular isoforms. Single-cell sequencing revealed a strong preference for either the linear or circular ASXL1 isoforms in each cell, and found the predominant exon skipping product is frequently co-expressed with its reciprocal circular isoform. Finally, absolute quantification of ASXL1 isoforms confirmed our findings and suggests that standard methods overestimate circRNA abundance. Taken together, these data reveal a dynamic new view of circRNA genesis, providing additional framework for studying their roles in cellular biology. PMID:27736885

Automatic nipple detection on 3D images of an automated breast ultrasound system (ABUS)

NASA Astrophysics Data System (ADS)

Javanshir Moghaddam, Mandana; Tan, Tao; Karssemeijer, Nico; Platel, Bram

2014-03-01

Recent studies have demonstrated that applying Automated Breast Ultrasound in addition to mammography in women with dense breasts can lead to additional detection of small, early stage breast cancers which are occult in corresponding mammograms. In this paper, we proposed a fully automatic method for detecting the nipple location in 3D ultrasound breast images acquired from Automated Breast Ultrasound Systems. The nipple location is a valuable landmark to report the position of possible abnormalities in a breast or to guide image registration. To detect the nipple location, all images were normalized. Subsequently, features have been extracted in a multi scale approach and classification experiments were performed using a gentle boost classifier to identify the nipple location. The method was applied on a dataset of 100 patients with 294 different 3D ultrasound views from Siemens and U-systems acquisition systems. Our database is a representative sample of cases obtained in clinical practice by four medical centers. The automatic method could accurately locate the nipple in 90% of AP (Anterior-Posterior) views and in 79% of the other views.

Numerical study of ultra-low field nuclear magnetic resonance relaxometry utilizing a single axis magnetometer for signal detection.

PubMed

Vogel, Michael W; Vegh, Viktor; Reutens, David C

2013-05-01

This paper investigates optimal placement of a localized single-axis magnetometer for ultralow field (ULF) relaxometry in view of various sample shapes and sizes. The authors used finite element method for the numerical analysis to determine the sample magnetic field environment and evaluate the optimal location of the single-axis magnetometer. Given the different samples, the authors analysed the magnetic field distribution around the sample and determined the optimal orientation and possible positions of the sensor to maximize signal strength, that is, the power of the free induction decay. The authors demonstrate that a glass vial with flat bottom and 10 ml volume is the best structure to achieve the highest signal out of samples studied. This paper demonstrates the importance of taking into account the combined effects of sensor configuration and sample parameters for signal generation prior to designing and constructing ULF systems with a single-axis magnetometer. Through numerical simulations the authors were able to optimize structural parameters, such as sample shape and size, sensor orientation and location, to maximize the measured signal in ultralow field relaxometry.

Detection of pointing errors with CMOS-based camera in intersatellite optical communications

NASA Astrophysics Data System (ADS)

Yu, Si-yuan; Ma, Jing; Tan, Li-ying

2005-01-01

For very high data rates, intersatellite optical communications hold a potential performance edge over microwave communications. Acquisition and Tracking problem is critical because of the narrow transmit beam. A single array detector in some systems performs both spatial acquisition and tracking functions to detect pointing errors, so both wide field of view and high update rate is required. The past systems tend to employ CCD-based camera with complex readout arrangements, but the additional complexity reduces the applicability of the array based tracking concept. With the development of CMOS array, CMOS-based cameras can employ the single array detector concept. The area of interest feature of the CMOS-based camera allows a PAT system to specify portion of the array. The maximum allowed frame rate increases as the size of the area of interest decreases under certain conditions. A commercially available CMOS camera with 105 fps @ 640×480 is employed in our PAT simulation system, in which only part pixels are used in fact. Beams angle varying in the field of view can be detected after getting across a Cassegrain telescope and an optical focus system. Spot pixel values (8 bits per pixel) reading out from CMOS are transmitted to a DSP subsystem via IEEE 1394 bus, and pointing errors can be computed by the centroid equation. It was shown in test that: (1) 500 fps @ 100×100 is available in acquisition when the field of view is 1mrad; (2)3k fps @ 10×10 is available in tracking when the field of view is 0.1mrad.

Advanced microscopic methods for the detection of adhesion barriers in immunology in medical imaging

NASA Astrophysics Data System (ADS)

Lawrence, Shane

2017-07-01

Advanced methods of microscopy and advanced techniques of analysis stemming therefrom have developed greatly in the past few years.The use of single discrete methods has given way to the combination of methods which means an increase in data for processing to progress to the analysis and diagnosis of ailments and diseases which can be viewed by each and any method.This presentation shows the combination of such methods and gives example of the data which arises from each individual method and the combined methodology and suggests how such data can be streamlined to enable conclusions to be drawn about the particular biological and biochemical considerations that arise.In this particular project the subject of the methodology was human lactoferrin and the relation of the adhesion properties of hlf in the overcoming of barriers to adhesion mainly on the perimeter of the cellular unit and how this affects the process of immunity in any particular case.

Near-isotropic 3D optical nanoscopy with photon-limited chromophores

PubMed Central

Tang, Jianyong; Akerboom, Jasper; Vaziri, Alipasha; Looger, Loren L.; Shank, Charles V.

2010-01-01

Imaging approaches based on single molecule localization break the diffraction barrier of conventional fluorescence microscopy, allowing for bioimaging with nanometer resolution. It remains a challenge, however, to precisely localize photon-limited single molecules in 3D. We have developed a new localization-based imaging technique achieving almost isotropic subdiffraction resolution in 3D. A tilted mirror is used to generate a side view in addition to the front view of activated single emitters, allowing their 3D localization to be precisely determined for superresolution imaging. Because both front and side views are in focus, this method is able to efficiently collect emitted photons. The technique is simple to implement on a commercial fluorescence microscope, and especially suitable for biological samples with photon-limited chromophores such as endogenously expressed photoactivatable fluorescent proteins. Moreover, this method is relatively resistant to optical aberration, as it requires only centroid determination for localization analysis. Here we demonstrate the application of this method to 3D imaging of bacterial protein distribution and neuron dendritic morphology with subdiffraction resolution. PMID:20472826

A novel method to calibrate DOI function of a PET detector with a dual-ended-scintillator readout.

PubMed

Shao, Yiping; Yao, Rutao; Ma, Tianyu

2008-12-01

The detection of depth-of-interaction (DOI) is a critical detector capability to improve the PET spatial resolution uniformity across the field-of-view and will significantly enhance, in particular, small bore system performance for brain, breast, and small animal imaging. One promising technique of DOI detection is to use dual-ended-scintillator readout that uses two photon sensors to detect scintillation light from both ends of a scintillator array and estimate DOI based on the ratio of signals (similar to Anger logic). This approach needs a careful DOI function calibration to establish accurate relationship between DOI and signal ratios, and to recalibrate if the detection condition is shifted due to the drift of sensor gain, bias variations, or degraded optical coupling, etc. However, the current calibration method that uses coincident events to locate interaction positions inside a single scintillator crystal has severe drawbacks, such as complicated setup, long and repetitive measurements, and being prone to errors from various possible misalignments among the source and detector components. This method is also not practically suitable to calibrate multiple DOI functions of a crystal array. To solve these problems, a new method has been developed that requires only a uniform flood source to irradiate a crystal array without the need to locate the interaction positions, and calculates DOI functions based solely on the uniform probability distribution of interactions over DOI positions without knowledge or assumption of detector responses. Simulation and experiment have been studied to validate the new method, and the results show that the new method, with a simple setup and one single measurement, can provide consistent and accurate DOI functions for the entire array of multiple scintillator crystals. This will enable an accurate, simple, and practical DOI function calibration for the PET detectors based on the design of dual-ended-scintillator readout. In addition, the new method can be generally applied to calibrating other types of detectors that use the similar dual-ended readout to acquire the radiation interaction position.

Locating Structural Centers: A Density-Based Clustering Method for Community Detection

PubMed Central

Liu, Gongshen; Li, Jianhua; Nees, Jan P.

2017-01-01

Uncovering underlying community structures in complex networks has received considerable attention because of its importance in understanding structural attributes and group characteristics of networks. The algorithmic identification of such structures is a significant challenge. Local expanding methods have proven to be efficient and effective in community detection, but most methods are sensitive to initial seeds and built-in parameters. In this paper, we present a local expansion method by density-based clustering, which aims to uncover the intrinsic network communities by locating the structural centers of communities based on a proposed structural centrality. The structural centrality takes into account local density of nodes and relative distance between nodes. The proposed algorithm expands a community from the structural center to the border with a single local search procedure. The local expanding procedure follows a heuristic strategy as allowing it to find complete community structures. Moreover, it can identify different node roles (cores and outliers) in communities by defining a border region. The experiments involve both on real-world and artificial networks, and give a comparison view to evaluate the proposed method. The result of these experiments shows that the proposed method performs more efficiently with a comparative clustering performance than current state of the art methods. PMID:28046030

Estimating corresponding locations in ipsilateral breast tomosynthesis views

NASA Astrophysics Data System (ADS)

van Schie, Guido; Tanner, Christine; Karssemeijer, Nico

2011-03-01

To improve cancer detection in mammography, breast exams usually consist of two views per breast. To combine information from both views, radiologists and multiview computer-aided detection (CAD) systems need to match corresponding regions in the two views. In digital breast tomosynthesis (DBT), finding corresponding regions in ipsilateral volumes may be a difficult and time-consuming task for radiologists, because many slices have to be inspected individually. In this study we developed a method to quickly estimate corresponding locations in ipsilateral tomosynthesis views by applying a mathematical transformation. First a compressed breast model is matched to the tomosynthesis view containing a point of interest. Then we decompress, rotate and compress again to estimate the location of the corresponding point in the ipsilateral view. In this study we use a simple elastically deformable sphere model to obtain an analytical solution for the transformation in a given DBT case. The model is matched to the volume by using automatic segmentation of the pectoral muscle, breast tissue and nipple. For validation we annotated 181 landmarks in both views and applied our method to each location. Results show a median 3D distance between the actual location and estimated location of 1.5 cm; a good starting point for a feature based local search method to link lesions for a multiview CAD system. Half of the estimated locations were at most 1 slice away from the actual location, making our method useful as a tool in mammographic workstations to interactively find corresponding locations in ipsilateral tomosynthesis views.

OncoNEM: inferring tumor evolution from single-cell sequencing data.

PubMed

Ross, Edith M; Markowetz, Florian

2016-04-15

Single-cell sequencing promises a high-resolution view of genetic heterogeneity and clonal evolution in cancer. However, methods to infer tumor evolution from single-cell sequencing data lag behind methods developed for bulk-sequencing data. Here, we present OncoNEM, a probabilistic method for inferring intra-tumor evolutionary lineage trees from somatic single nucleotide variants of single cells. OncoNEM identifies homogeneous cellular subpopulations and infers their genotypes as well as a tree describing their evolutionary relationships. In simulation studies, we assess OncoNEM's robustness and benchmark its performance against competing methods. Finally, we show its applicability in case studies of muscle-invasive bladder cancer and essential thrombocythemia.

Single-Image Distance Measurement by a Smart Mobile Device.

PubMed

Chen, Shangwen; Fang, Xianyong; Shen, Jianbing; Wang, Linbo; Shao, Ling

2017-12-01

Existing distance measurement methods either require multiple images and special photographing poses or only measure the height with a special view configuration. We propose a novel image-based method that can measure various types of distance from single image captured by a smart mobile device. The embedded accelerometer is used to determine the view orientation of the device. Consequently, pixels can be back-projected to the ground, thanks to the efficient calibration method using two known distances. Then the distance in pixel is transformed to a real distance in centimeter with a linear model parameterized by the magnification ratio. Various types of distance specified in the image can be computed accordingly. Experimental results demonstrate the effectiveness of the proposed method.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Meiye; Singh, Anup K.

In this study, cell signaling is a dynamic and complex process. A typical signaling pathway may begin with activation of cell surface receptors, leading to activation kinase cascade that culminates in induction of mRNA and non-coding miRNA production in the nucleus, followed by modulation of mRNA expression by miRNAs in the cytosol, and end with production of proteins in response to the signaling pathway. Signaling pathways involve proteins, miRNA, and mRNAs, along with various forms of transient post-translational modifications, and detecting each type of signaling molecule requires categorically different sample preparation methods such as Western blotting for proteins, PCR formore » nucleic acids, and flow cytometry for post-translational modifications. Since we know that cells in populations behave heterogeneously1, especially in the cases of stem cells, cancer, and hematopoiesis, there is need for a new technology that provides capability to detect and quantify multiple categories of signaling molecules in intact single cells to provide a comprehensive view of the cell’s physiological state. In this technical brief, we describe our microfluidic platform with a portfolio of customized molecular assays that can detect nucleic acids, proteins, and post-translational modifications in single intact cells with >95% reduction in reagent requirement in under 8 hours.« less

DETECTION OF PROTEIN ADSORPTION WITH SINGLE WALL CARBON NANOTUBE DEVICE. (R829623)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

Measurement and classification of heart and lung sounds by using LabView for educational use.

PubMed

Altrabsheh, B

2010-01-01

This study presents the design, development and implementation of a simple low-cost method of phonocardiography signal detection. Human heart and lung signals are detected by using a simple microphone through a personal computer; the signals are recorded and analysed using LabView software. Amplitude and frequency analyses are carried out for various phonocardiography pathological cases. Methods for automatic classification of normal and abnormal heart sounds, murmurs and lung sounds are presented. Various cases of heart and lung sound measurement are recorded and analysed. The measurements can be saved for further analysis. The method in this study can be used by doctors as a detection tool aid and may be useful for teaching purposes at medical and nursing schools.

Noise Reduction in Brainwaves by Using Both EEG Signals and Frontal Viewing Camera Images

PubMed Central

Bang, Jae Won; Choi, Jong-Suk; Park, Kang Ryoung

2013-01-01

Electroencephalogram (EEG)-based brain-computer interfaces (BCIs) have been used in various applications, including human–computer interfaces, diagnosis of brain diseases, and measurement of cognitive status. However, EEG signals can be contaminated with noise caused by user's head movements. Therefore, we propose a new method that combines an EEG acquisition device and a frontal viewing camera to isolate and exclude the sections of EEG data containing these noises. This method is novel in the following three ways. First, we compare the accuracies of detecting head movements based on the features of EEG signals in the frequency and time domains and on the motion features of images captured by the frontal viewing camera. Second, the features of EEG signals in the frequency domain and the motion features captured by the frontal viewing camera are selected as optimal ones. The dimension reduction of the features and feature selection are performed using linear discriminant analysis. Third, the combined features are used as inputs to support vector machine (SVM), which improves the accuracy in detecting head movements. The experimental results show that the proposed method can detect head movements with an average error rate of approximately 3.22%, which is smaller than that of other methods. PMID:23669713

Development of a micromanipulation method for single cell isolation of prokaryotes and its application in food safety.

PubMed

Hohnadel, Marisa; Maumy, Myriam; Chollet, Renaud

2018-01-01

For nearly a century, conventional microbiological methods have been standard practice for detecting and identifying pathogens in food. Nevertheless, the microbiological safety of food has improved and various rapid methods have been developed to overcome the limitations of conventional methods. Alternative methods are expected to detect low cell numbers, since the presence in food of even a single cell of a pathogenic organism may be infectious. With respect to low population levels, the performance of a detection method is assessed by producing serial dilutions of a pure bacterial suspension to inoculate representative food matrices with highly diluted bacterial cells (fewer than 10 CFU/ml). The accuracy of data obtained by multiple dilution techniques is not certain and does not exclude some colonies arising from clumps of cells. Micromanipulation techniques to capture and isolate single cells from environmental samples were introduced more than 40 years ago. The main limitation of the current micromanipulation technique is still the low recovery rate for the growth of a single cell in culture medium. In this study, we describe a new single cell isolation method and demonstrate that it can be used successfully to grow various types of microorganism from picked individual cells. Tests with Gram-positive and Gram-negative organisms, including cocci, rods, aerobes, anaerobes, yeasts and molds showed growth recovery rates from 60% to 100% after micromanipulation. We also highlight the use of our method to evaluate and challenge the detection limits of standard detection methods in food samples contaminated by a single cell of Salmonella enterica.

Label-free in-flow detection of single DNA molecules using glass nanopipettes.

PubMed

Gong, Xiuqing; Patil, Amol V; Ivanov, Aleksandar P; Kong, Qingyuan; Gibb, Thomas; Dogan, Fatma; deMello, Andrew J; Edel, Joshua B

2014-01-07

With the view of enhancing the functionality of label-free single molecule nanopore-based detection, we have designed and developed a highly robust, mechanically stable, integrated nanopipette-microfluidic device which combines the recognized advantages of microfluidic systems and the unique properties/advantages of nanopipettes. Unlike more typical planar solid-state nanopores, which have inherent geometrical constraints, nanopipettes can be easily positioned at any point within a microfluidic channel. This is highly advantageous, especially when taking into account fluid flow properties. We show that we are able to detect and discriminate between DNA molecules of varying lengths when motivated through a microfluidic channel, upon the application of appropriate voltage bias across the nanopipette. The effects of applied voltage and volumetric flow rates have been studied to ascertain translocation event frequency and capture rate. Additionally, by exploiting the advantages associated with microfluidic systems (such as flow control and concomitant control over analyte concentration/presence), we show that the technology offers a new opportunity for single molecule detection and recognition in microfluidic devices.

Combined hostile fire and optics detection

NASA Astrophysics Data System (ADS)

Brännlund, Carl; Tidström, Jonas; Henriksson, Markus; Sjöqvist, Lars

2013-10-01

Snipers and other optically guided weapon systems are serious threats in military operations. We have studied a SWIR (Short Wave Infrared) camera-based system with capability to detect and locate snipers both before and after shot over a large field-of-view. The high frame rate SWIR-camera allows resolution of the temporal profile of muzzle flashes which is the infrared signature associated with the ejection of the bullet from the rifle. The capability to detect and discriminate sniper muzzle flashes with this system has been verified by FOI in earlier studies. In this work we have extended the system by adding a laser channel for optics detection. A laser diode with slit-shaped beam profile is scanned over the camera field-of-view to detect retro reflection from optical sights. The optics detection system has been tested at various distances up to 1.15 km showing the feasibility to detect rifle scopes in full daylight. The high speed camera gives the possibility to discriminate false alarms by analyzing the temporal data. The intensity variation, caused by atmospheric turbulence, enables discrimination of small sights from larger reflectors due to aperture averaging, although the targets only cover a single pixel. It is shown that optics detection can be integrated in combination with muzzle flash detection by adding a scanning rectangular laser slit. The overall optics detection capability by continuous surveillance of a relatively large field-of-view looks promising. This type of multifunctional system may become an important tool to detect snipers before and after shot.

New Optics See More With Less

NASA Technical Reports Server (NTRS)

Nabors, Sammy

2015-01-01

NASA offers companies an optical system that provides a unique panoramic perspective with a single camera. NASA's Marshall Space Flight Center has developed a technology that combines a panoramic refracting optic (PRO) lens with a unique detection system to acquire a true 360-degree field of view. Although current imaging systems can acquire panoramic images, they must use up to five cameras to obtain the full field of view. MSFC's technology obtains its panoramic images from one vantage point.

Spatial resolution and chest nodule detection: an interesting incidental finding

NASA Astrophysics Data System (ADS)

Toomey, R. J.; McEntee, M. F.; Ryan, J. T.; Evanoff, M. G.; Hayes, A.; Brennan, P. C.

2010-02-01

This study reports an incidental finding from a larger work. It examines the relationship between spatial resolution and nodule detection for chest radiographs. Twelve examining radiologists with the American Board of Radiology read thirty chest radiographs in two conditions - full (1500 × 1500 pixel) resolution, and 300 × 300 pixel resolution linearly interpolated to 1500 × 1500 pixels. All images were surrounded by a 10-pixel sharp grey border to aid in focussing the observer's eye when viewing the comparatively unsharp interpolated images. Fifteen of the images contained a single simulated pulmonary nodule. Observers were asked to rate their confidence that a nodule was present on each radiograph on a scale of 1 (least confidence, certain no lesion is present) to 6 (most confidence, certain a lesion was present). All other abnormalities were to be ignored. No windowing, levelling or magnification of the images was permitted and viewing distance was constrained to approximately 70cm. Images were displayed on a 3 megapixel greyscale monitor. Receiver operating characteristic (ROC) analysis was applied to the results of the readings using the Dorfman-Berbaum-Metz multiplereader, multiple-case method. No statistically significant differences were found with either readers and cases treated as random or with cases treated as fixed. Low spatial frequency information appears to be sufficient for the detection of chest lesion of the type used in this study.

Single Versus Multiple Events Error Potential Detection in a BCI-Controlled Car Game With Continuous and Discrete Feedback.

PubMed

Kreilinger, Alex; Hiebel, Hannah; Müller-Putz, Gernot R

2016-03-01

This work aimed to find and evaluate a new method for detecting errors in continuous brain-computer interface (BCI) applications. Instead of classifying errors on a single-trial basis, the new method was based on multiple events (MEs) analysis to increase the accuracy of error detection. In a BCI-driven car game, based on motor imagery (MI), discrete events were triggered whenever subjects collided with coins and/or barriers. Coins counted as correct events, whereas barriers were errors. This new method, termed ME method, combined and averaged the classification results of single events (SEs) and determined the correctness of MI trials, which consisted of event sequences instead of SEs. The benefit of this method was evaluated in an offline simulation. In an online experiment, the new method was used to detect erroneous MI trials. Such MI trials were discarded and could be repeated by the users. We found that, even with low SE error potential (ErrP) detection rates, feasible accuracies can be achieved when combining MEs to distinguish erroneous from correct MI trials. Online, all subjects reached higher scores with error detection than without, at the cost of longer times needed for completing the game. Findings suggest that ErrP detection may become a reliable tool for monitoring continuous states in BCI applications when combining MEs. This paper demonstrates a novel technique for detecting errors in online continuous BCI applications, which yields promising results even with low single-trial detection rates.

Single-cell copy number variation detection

PubMed Central

2011-01-01

Detection of chromosomal aberrations from a single cell by array comparative genomic hybridization (single-cell array CGH), instead of from a population of cells, is an emerging technique. However, such detection is challenging because of the genome artifacts and the DNA amplification process inherent to the single cell approach. Current normalization algorithms result in inaccurate aberration detection for single-cell data. We propose a normalization method based on channel, genome composition and recurrent genome artifact corrections. We demonstrate that the proposed channel clone normalization significantly improves the copy number variation detection in both simulated and real single-cell array CGH data. PMID:21854607

TATES: Efficient Multivariate Genotype-Phenotype Analysis for Genome-Wide Association Studies

PubMed Central

van der Sluis, Sophie; Posthuma, Danielle; Dolan, Conor V.

2013-01-01

To date, the genome-wide association study (GWAS) is the primary tool to identify genetic variants that cause phenotypic variation. As GWAS analyses are generally univariate in nature, multivariate phenotypic information is usually reduced to a single composite score. This practice often results in loss of statistical power to detect causal variants. Multivariate genotype–phenotype methods do exist but attain maximal power only in special circumstances. Here, we present a new multivariate method that we refer to as TATES (Trait-based Association Test that uses Extended Simes procedure), inspired by the GATES procedure proposed by Li et al (2011). For each component of a multivariate trait, TATES combines p-values obtained in standard univariate GWAS to acquire one trait-based p-value, while correcting for correlations between components. Extensive simulations, probing a wide variety of genotype–phenotype models, show that TATES's false positive rate is correct, and that TATES's statistical power to detect causal variants explaining 0.5% of the variance can be 2.5–9 times higher than the power of univariate tests based on composite scores and 1.5–2 times higher than the power of the standard MANOVA. Unlike other multivariate methods, TATES detects both genetic variants that are common to multiple phenotypes and genetic variants that are specific to a single phenotype, i.e. TATES provides a more complete view of the genetic architecture of complex traits. As the actual causal genotype–phenotype model is usually unknown and probably phenotypically and genetically complex, TATES, available as an open source program, constitutes a powerful new multivariate strategy that allows researchers to identify novel causal variants, while the complexity of traits is no longer a limiting factor. PMID:23359524

Remote detection of single emitters via optical waveguides

NASA Astrophysics Data System (ADS)

Then, Patrick; Razinskas, Gary; Feichtner, Thorsten; Haas, Philippe; Wild, Andreas; Bellini, Nicola; Osellame, Roberto; Cerullo, Giulio; Hecht, Bert

2014-05-01

The integration of lab-on-a-chip technologies with single-molecule detection techniques may enable new applications in analytical chemistry, biotechnology, and medicine. We describe a method based on the reciprocity theorem of electromagnetic theory to determine and optimize the detection efficiency of photons emitted by single quantum emitters through truncated dielectric waveguides of arbitrary shape positioned in their proximity. We demonstrate experimentally that detection of single quantum emitters via such waveguides is possible, confirming the predicted behavior of the detection efficiency. Our findings blaze the trail towards efficient lensless single-emitter detection compatible with large-scale optofluidic integration.

Monocular correspondence detection for symmetrical objects by template matching

NASA Astrophysics Data System (ADS)

Vilmar, G.; Besslich, Philipp W., Jr.

1990-09-01

We describe a possibility to reconstruct 3-D information from a single view of an 3-D bilateral symmetric object. The symmetry assumption allows us to obtain a " second view" from a different viewpoint by a simple reflection of the monocular image. Therefore we have to solve the correspondence problem in a special case where known feature-based or area-based binocular approaches fail. In principle our approach is based on a frequency domain template matching of the features on the epipolar lines. During a training period our system " learns" the assignment of correspondence models to image features. The object shape is interpolated when no template matches to the image features. This fact is an important advantage of this methodology because no " real world" image holds the symmetry assumption perfectly. To simplify the training process we used single views on human faces (e. g. passport photos) but our system is trainable on any other kind of objects.

Use of amplicon sequencing to improve sensitivity in PCR-based detection of microbial pathogen in environmental samples.

PubMed

Saingam, Prakit; Li, Bo; Yan, Tao

2018-06-01

DNA-based molecular detection of microbial pathogens in complex environments is still plagued by sensitivity, specificity and robustness issues. We propose to address these issues by viewing them as inadvertent consequences of requiring specific and adequate amplification (SAA) of target DNA molecules by current PCR methods. Using the invA gene of Salmonella as the model system, we investigated if next generation sequencing (NGS) can be used to directly detect target sequences in false-negative PCR reaction (PCR-NGS) in order to remove the SAA requirement from PCR. False-negative PCR and qPCR reactions were first created using serial dilutions of laboratory-prepared Salmonella genomic DNA and then analyzed directly by NGS. Target invA sequences were detected in all false-negative PCR and qPCR reactions, which lowered the method detection limits near the theoretical minimum of single gene copy detection. The capability of the PCR-NGS approach in correcting false negativity was further tested and confirmed under more environmentally relevant conditions using Salmonella-spiked stream water and sediment samples. Finally, the PCR-NGS approach was applied to ten urban stream water samples and detected invA sequences in eight samples that would be otherwise deemed Salmonella negative. Analysis of the non-target sequences in the false-negative reactions helped to identify primer dime-like short sequences as the main cause of the false negativity. Together, the results demonstrated that the PCR-NGS approach can significantly improve method sensitivity, correct false-negative detections, and enable sequence-based analysis for failure diagnostics in complex environmental samples. Copyright © 2018 Elsevier B.V. All rights reserved.

A 3D Freehand Ultrasound System for Multi-view Reconstructions from Sparse 2D Scanning Planes

PubMed Central

2011-01-01

Background A significant limitation of existing 3D ultrasound systems comes from the fact that the majority of them work with fixed acquisition geometries. As a result, the users have very limited control over the geometry of the 2D scanning planes. Methods We present a low-cost and flexible ultrasound imaging system that integrates several image processing components to allow for 3D reconstructions from limited numbers of 2D image planes and multiple acoustic views. Our approach is based on a 3D freehand ultrasound system that allows users to control the 2D acquisition imaging using conventional 2D probes. For reliable performance, we develop new methods for image segmentation and robust multi-view registration. We first present a new hybrid geometric level-set approach that provides reliable segmentation performance with relatively simple initializations and minimum edge leakage. Optimization of the segmentation model parameters and its effect on performance is carefully discussed. Second, using the segmented images, a new coarse to fine automatic multi-view registration method is introduced. The approach uses a 3D Hotelling transform to initialize an optimization search. Then, the fine scale feature-based registration is performed using a robust, non-linear least squares algorithm. The robustness of the multi-view registration system allows for accurate 3D reconstructions from sparse 2D image planes. Results Volume measurements from multi-view 3D reconstructions are found to be consistently and significantly more accurate than measurements from single view reconstructions. The volume error of multi-view reconstruction is measured to be less than 5% of the true volume. We show that volume reconstruction accuracy is a function of the total number of 2D image planes and the number of views for calibrated phantom. In clinical in-vivo cardiac experiments, we show that volume estimates of the left ventricle from multi-view reconstructions are found to be in better agreement with clinical measures than measures from single view reconstructions. Conclusions Multi-view 3D reconstruction from sparse 2D freehand B-mode images leads to more accurate volume quantification compared to single view systems. The flexibility and low-cost of the proposed system allow for fine control of the image acquisition planes for optimal 3D reconstructions from multiple views. PMID:21251284

SELFI: an object-based, Bayesian method for faint emission line source detection in MUSE deep field data cubes

NASA Astrophysics Data System (ADS)

Meillier, Céline; Chatelain, Florent; Michel, Olivier; Bacon, Roland; Piqueras, Laure; Bacher, Raphael; Ayasso, Hacheme

2016-04-01

We present SELFI, the Source Emission Line FInder, a new Bayesian method optimized for detection of faint galaxies in Multi Unit Spectroscopic Explorer (MUSE) deep fields. MUSE is the new panoramic integral field spectrograph at the Very Large Telescope (VLT) that has unique capabilities for spectroscopic investigation of the deep sky. It has provided data cubes with 324 million voxels over a single 1 arcmin2 field of view. To address the challenge of faint-galaxy detection in these large data cubes, we developed a new method that processes 3D data either for modeling or for estimation and extraction of source configurations. This object-based approach yields a natural sparse representation of the sources in massive data fields, such as MUSE data cubes. In the Bayesian framework, the parameters that describe the observed sources are considered random variables. The Bayesian model leads to a general and robust algorithm where the parameters are estimated in a fully data-driven way. This detection algorithm was applied to the MUSE observation of Hubble Deep Field-South. With 27 h total integration time, these observations provide a catalog of 189 sources of various categories and with secured redshift. The algorithm retrieved 91% of the galaxies with only 9% false detection. This method also allowed the discovery of three new Lyα emitters and one [OII] emitter, all without any Hubble Space Telescope counterpart. We analyzed the reasons for failure for some targets, and found that the most important limitation of the method is when faint sources are located in the vicinity of bright spatially resolved galaxies that cannot be approximated by the Sérsic elliptical profile. The software and its documentation are available on the MUSE science web service (muse-vlt.eu/science).

A multi points ultrasonic detection method for material flow of belt conveyor

NASA Astrophysics Data System (ADS)

Zhang, Li; He, Rongjun

2018-03-01

For big detection error of single point ultrasonic ranging technology used in material flow detection of belt conveyor when coal distributes unevenly or is large, a material flow detection method of belt conveyor is designed based on multi points ultrasonic counter ranging technology. The method can calculate approximate sectional area of material by locating multi points on surfaces of material and belt, in order to get material flow according to running speed of belt conveyor. The test results show that the method has smaller detection error than single point ultrasonic ranging technology under the condition of big coal with uneven distribution.

Evaluation of collimation and imaging configuration in scintimammography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tsui, B.M.W.; Frey, E.C.; Wessell, D.E.

1996-12-31

Conventional scintimammography (SM) with {sup 99m}Tc sestamibi has been limited to taking a single lateral view of the breast using a parallel-hole high resolution (LEHR) collimator. The collimator is placed close to the breast for best possible spatial resolution. However, the collimator geometry precludes imaging the breast from other views. We evaluated using a pinhole collimator instead of a LEHR collimator in SM for improved spatial resolution and detection efficiency, and to allow additional imaging views. Results from theoretical calculations indicated that pinhole collimators could be designed with higher spatial resolution and detection efficiency than LEHR when imaging small tomore » medium size breasts. The geometrical shape of the pinhole collimator allows imaging of the breasts from both the lateral and craniocaudal views. The dual-view images allow better determination of the location of the tumors within the breast and improved detection of tumors located in the medial region of the breast. A breast model that simulates the shape and composition of the breast and breast tumors with different sizes and locations was added to an existing 3D mathematical cardiac-torso (MCAT) phantom. A cylindrically shaped phantom with 10 cm diameter and spherical inserts with different sizes and {sup 99m}Tc sestamibi uptakes with respect to the background provide physical models of breast with tumors. Simulation studies using the breast and MCAT phantoms and experimental studies using the cylindrical phantom confirmed the utility of the pinhole collimator in SM for improved breast tumor detection.« less

Microfluidic platform for multiplexed detection in single cells and methods thereof

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Meiye; Singh, Anup K.

The present invention relates to a microfluidic device and platform configured to conduct multiplexed analysis within the device. In particular, the device allows multiple targets to be detected on a single-cell level. Also provided are methods of performing multiplexed analyses to detect one or more target nucleic acids, proteins, and post-translational modifications.

Single-trial detection of visual evoked potentials by common spatial patterns and wavelet filtering for brain-computer interface.

PubMed

Tu, Yiheng; Huang, Gan; Hung, Yeung Sam; Hu, Li; Hu, Yong; Zhang, Zhiguo

2013-01-01

Event-related potentials (ERPs) are widely used in brain-computer interface (BCI) systems as input signals conveying a subject's intention. A fast and reliable single-trial ERP detection method can be used to develop a BCI system with both high speed and high accuracy. However, most of single-trial ERP detection methods are developed for offline EEG analysis and thus have a high computational complexity and need manual operations. Therefore, they are not applicable to practical BCI systems, which require a low-complexity and automatic ERP detection method. This work presents a joint spatial-time-frequency filter that combines common spatial patterns (CSP) and wavelet filtering (WF) for improving the signal-to-noise (SNR) of visual evoked potentials (VEP), which can lead to a single-trial ERP-based BCI.

Correlating locations in ipsilateral breast tomosynthesis views using an analytical hemispherical compression model

NASA Astrophysics Data System (ADS)

van Schie, Guido; Tanner, Christine; Snoeren, Peter; Samulski, Maurice; Leifland, Karin; Wallis, Matthew G.; Karssemeijer, Nico

2011-08-01

To improve cancer detection in mammography, breast examinations usually consist of two views per breast. In order to combine information from both views, corresponding regions in the views need to be matched. In 3D digital breast tomosynthesis (DBT), this may be a difficult and time-consuming task for radiologists, because many slices have to be inspected individually. For multiview computer-aided detection (CAD) systems, matching corresponding regions is an essential step that needs to be automated. In this study, we developed an automatic method to quickly estimate corresponding locations in ipsilateral tomosynthesis views by applying a spatial transformation. First we match a model of a compressed breast to the tomosynthesis view containing a point of interest. Then we estimate the location of the corresponding point in the ipsilateral view by assuming that this model was decompressed, rotated and compressed again. In this study, we use a relatively simple, elastically deformable sphere model to obtain an analytical solution for the transformation in a given DBT case. We investigate three different methods to match the compression model to the data by using automatic segmentation of the pectoral muscle, breast tissue and nipple. For validation, we annotated 208 landmarks in both views of a total of 146 imaged breasts of 109 different patients and applied our method to each location. The best results are obtained by using the centre of gravity of the breast to define the central axis of the model, around which the breast is assumed to rotate between views. Results show a median 3D distance between the actual location and the estimated location of 14.6 mm, a good starting point for a registration method or a feature-based local search method to link suspicious regions in a multiview CAD system. Approximately half of the estimated locations are at most one slice away from the actual location, which makes the method useful as a mammographic workstation tool for radiologists to interactively find corresponding locations in ipsilateral tomosynthesis views.

Eye gazing direction inspection based on image processing technique

NASA Astrophysics Data System (ADS)

Hao, Qun; Song, Yong

2005-02-01

According to the research result in neural biology, human eyes can obtain high resolution only at the center of view of field. In the research of Virtual Reality helmet, we design to detect the gazing direction of human eyes in real time and feed it back to the control system to improve the resolution of the graph at the center of field of view. In the case of current display instruments, this method can both give attention to the view field of virtual scene and resolution, and improve the immersion of virtual system greatly. Therefore, detecting the gazing direction of human eyes rapidly and exactly is the basis of realizing the design scheme of this novel VR helmet. In this paper, the conventional method of gazing direction detection that based on Purklinje spot is introduced firstly. In order to overcome the disadvantage of the method based on Purklinje spot, this paper proposed a method based on image processing to realize the detection and determination of the gazing direction. The locations of pupils and shapes of eye sockets change with the gazing directions. With the aid of these changes, analyzing the images of eyes captured by the cameras, gazing direction of human eyes can be determined finally. In this paper, experiments have been done to validate the efficiency of this method by analyzing the images. The algorithm can carry out the detection of gazing direction base on normal eye image directly, and it eliminates the need of special hardware. Experiment results show that the method is easy to implement and have high precision.

Fast methods for analysis of neurotransmitters from single cell and monitoring their releases in central nervous system by capillary electrophoresis, fluorescence microscopy and luminescence imaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Ziqiang

1999-12-10

Fast methods for separation and detection of important neurotransmitters and the releases in central nervous system (CNS) were developed. Enzyme based immunoassay combined with capillary electrophoresis was used to analyze the contents of amino acid neurotransmitters from single neuron cells. The release of amino acid neurotransmitters from neuron cultures was monitored by laser induced fluorescence imaging method. The release and signal transduction of adenosine triphosphate (ATP) in CNS was studied with sensitive luminescence imaging method. A new dual-enzyme on-column reaction method combined with capillary electrophoresis has been developed for determining the glutamate content in single cells. Detection was based onmore » monitoring the laser-induced fluorescence of the reaction product NADH, and the measured fluorescence intensity was related to the concentration of glutamate in each cell. The detection limit of glutamate is down to 10 -8 M level, which is 1 order of magnitude lower than the previously reported detection limit based on similar detection methods. The mass detection limit of a few attomoles is far superior to that of any other reports. Selectivity for glutamate is excellent over most of amino acids. The glutamate content in single human erythrocyte and baby rat brain neurons were determined with this method and results agreed well with literature values.« less

Cascaded automatic target recognition (Cascaded ATR)

NASA Astrophysics Data System (ADS)

Walls, Bradley

2010-04-01

The global war on terror has plunged US and coalition forces into a battle space requiring the continuous adaptation of tactics and technologies to cope with an elusive enemy. As a result, technologies that enhance the intelligence, surveillance, and reconnaissance (ISR) mission making the warfighter more effective are experiencing increased interest. In this paper we show how a new generation of smart cameras built around foveated sensing makes possible a powerful ISR technique termed Cascaded ATR. Foveated sensing is an innovative optical concept in which a single aperture captures two distinct fields of view. In Cascaded ATR, foveated sensing is used to provide a coarse resolution, persistent surveillance, wide field of view (WFOV) detector to accomplish detection level perception. At the same time, within the foveated sensor, these detection locations are passed as a cue to a steerable, high fidelity, narrow field of view (NFOV) detector to perform recognition level perception. Two new ISR mission scenarios, utilizing Cascaded ATR, are proposed.

SISGR: Room Temperature Single-Molecule Detection and Imaging by Stimulated Emission Microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xie, Xiaoliang Sunney

Single-molecule spectroscopy has made considerable impact on many disciplines including chemistry, physics, and biology. To date, most single-molecule spectroscopy work is accomplished by detecting fluorescence. On the other hand, many naturally occurring chromophores, such as retinal, hemoglobin and cytochromes, do not have detectable fluorescence. There is an emerging need for single-molecule spectroscopy techniques that do not require fluorescence. In the last proposal period, we have successfully demonstrated stimulated emission microscopy, single molecule absorption, and stimulated Raman microscopy based on a high-frequency modulation transfer technique. These first-of-a- kind new spectroscopy/microscopy methods tremendously improved our ability to observe molecules that fluorescence weakly,more » even to the limit of single molecule detection for absorption measurement. All of these methods employ two laser beams: one (pump beam) excites a single molecule to a real or virtual excited state, and the other (probe beam) monitors the absorption/emission property of the single. We extract the intensity change of the probe beam with high sensitivity by implementing a high-frequency phase-sensitive detection scheme, which offers orders of magnitude improvement in detection sensitivity over direct absorption/emission measurement. However, single molecule detection based on fluorescence or absorption is fundamentally limited due to their broad spectral response. It is important to explore other avenues in single molecule detection and imaging which provides higher molecular specificity for studying a wide variety of heterogeneous chemical and biological systems. This proposal aimed to achieve single-molecule detection sensitivity with near resonance stimulated Raman scattering (SRS) microscopy. SRS microscopy was developed in our lab as a powerful technique for imaging heterogeneous samples based on their intrinsic vibrational contrasts, which provides much higher molecular specificity than absorption and fluorescence. Current sensitivity limit of SRS microscopy has not yet reached single molecule detection. We proposed to capitalize on our state-of-the-art SRS microscopy and develop near-resonance enhanced SRS for single molecule detection of carotenoids and heme proteins. The specific aims we pursued are: (1) building the next SRS generation microscope that utilizes near resonance enhancement to allow detection and imaging of single molecules with undetectable fluorescence, such as -carotene. (2) using near-resonance SRS as a contrast mechanism to study dye-sensitize semiconductor interface, elucidating the heterogeneous electron ejection kinetics with high spatial and temporal resolution. (3) studying the binding and unbinding of oxygen in single hemoglobin molecules in order to gain molecular level understanding of the long-standing issue of cooperativity. The new methods developed in the fund period of this grant have advanced the detection sensitivity in many aspects. Near-resonance SRS improved the signal by using shorter wavelengths for SRS microscopy. Frequency modulation and multi-color SRS target the reduction of background to improve the chemical specificity of SRS while maintaining the high imaging speed. Time-domain coherent Raman scattering microscopy targets to reduce the noise floor of coherent Raman microscopy. These methods have already demonstrated first-of-a-kind new applications in biology and medical research. However, we are still one order of magnitude away from single molecule limit. It is important to continue to improve the laser specification and develop new imaging methods to finally achieve label-free single molecule microscopy.« less

Novel directed search strategy to detect continuous gravitational waves from neutron stars in low- and high-eccentricity binary systems

NASA Astrophysics Data System (ADS)

Leaci, Paola; Astone, Pia; D'Antonio, Sabrina; Frasca, Sergio; Palomba, Cristiano; Piccinni, Ornella; Mastrogiovanni, Simone

2017-06-01

We describe a novel, very fast and robust, directed search incoherent method (which means that the phase information is lost) for periodic gravitational waves from neutron stars in binary systems. As a directed search, we assume the source sky position to be known with enough accuracy, but all other parameters (including orbital ones) are supposed to be unknown. We exploit the frequency modulation due to source orbital motion to unveil the signal signature by commencing from a collection of time and frequency peaks (the so-called "peakmap"). We validate our algorithm (pipeline), adding 131 artificial continuous-wave signals from pulsars in binary systems to simulated detector Gaussian noise, characterized by a power spectral density Sh=4 ×10-24 Hz-1 /2 in the frequency interval [70, 200] Hz, which is overall commensurate with the advanced detector design sensitivities. The pipeline detected 128 signals, and the weakest signal injected (added) and detected has a gravitational-wave strain amplitude of ˜10-24, assuming one month of gapless data collected by a single advanced detector. We also provide sensitivity estimations, which show that, for a single-detector data covering one month of observation time, depending on the source orbital Doppler modulation, we can detect signals with an amplitude of ˜7 ×10-25. By using three detectors, and one year of data, we would easily gain a factor 3 in sensitivity, translating into being able to detect weaker signals. We also discuss the parameter estimate proficiency of our method, as well as computational budget: sifting one month of single-detector data and 131 Hz-wide frequency range takes roughly 2.4 CPU hours. Hence, the current procedure can be readily applied in ally-sky schemes, sieving in parallel as many sky positions as permitted by the available computational power. Finally, we introduce (ongoing and future) approaches to attain sensitivity improvements and better accuracy on parameter estimates in view of the use on real advanced detector data.

An Accurate Framework for Arbitrary View Pedestrian Detection in Images

NASA Astrophysics Data System (ADS)

Fan, Y.; Wen, G.; Qiu, S.

2018-01-01

We consider the problem of detect pedestrian under from images collected under various viewpoints. This paper utilizes a novel framework called locality-constrained affine subspace coding (LASC). Firstly, the positive training samples are clustered into similar entities which represent similar viewpoint. Then Principal Component Analysis (PCA) is used to obtain the shared feature of each viewpoint. Finally, the samples that can be reconstructed by linear approximation using their top- k nearest shared feature with a small error are regarded as a correct detection. No negative samples are required for our method. Histograms of orientated gradient (HOG) features are used as the feature descriptors, and the sliding window scheme is adopted to detect humans in images. The proposed method exploits the sparse property of intrinsic information and the correlations among the multiple-views samples. Experimental results on the INRIA and SDL human datasets show that the proposed method achieves a higher performance than the state-of-the-art methods in form of effect and efficiency.

Reduced Field of View Diffusion-Weighted Imaging in the Evaluation of Congenital Spine Malformations.

PubMed

Radhakrishnan, Rupa; Betts, Aaron M; Care, Marguerite M; Serai, Suraj; Zhang, Bin; Jones, Blaise V

2016-05-01

Reduced field of view diffusion-weighted imaging (rFOV DWI) is a more recently described technique in the evaluation of spine pathology. In adults, this technique has been shown to increase clinician confidence in identification of diffusion restricting lesions. In this study, we evaluate the image quality and diagnostic confidence of the rFOV DWI technique in pediatric spine MRI. We included patients with MRI of the lumbar spine for suspected congenital abnormalities who had conventional SS-EPI (single shot echo planar imaging) with full field of view (fFOV) and rFOV DWI performed. Images were graded for image quality and observer confidence for detection of lesions with reduced diffusion. Position of the conus and L3 vertebral body measurements were recorded. Comparisons were made between the fFOV and rFOV scores. Fifty children (30 girls, 20 boys) were included (median 3.6 years). Compared to the fFOV images, the rFOV images scored higher in image quality (P < 0.0001) and for confidence in detecting lesions with reduced diffusion (P < 0.0001). The average spread of identified conus position was smaller for in rFOV compared to fFOV (P = 0.0042). There was no significant difference in the L3 vertebral body measurements between the two methods. In rFOV, the anterior aspects of the vertebral bodies were excluded in a few studies due to narrow FOV. rFOV DWI of the lumbar spine in the pediatric population has qualitatively improved image quality and observer confidence for lesion detection when compared to conventional fFOV SS-EPI DWI. Copyright © 2015 by the American Society of Neuroimaging.

Multiple-camera/motion stereoscopy for range estimation in helicopter flight

NASA Technical Reports Server (NTRS)

Smith, Phillip N.; Sridhar, Banavar; Suorsa, Raymond E.

1993-01-01

Aiding the pilot to improve safety and reduce pilot workload by detecting obstacles and planning obstacle-free flight paths during low-altitude helicopter flight is desirable. Computer vision techniques provide an attractive method of obstacle detection and range estimation for objects within a large field of view ahead of the helicopter. Previous research has had considerable success by using an image sequence from a single moving camera to solving this problem. The major limitations of single camera approaches are that no range information can be obtained near the instantaneous direction of motion or in the absence of motion. These limitations can be overcome through the use of multiple cameras. This paper presents a hybrid motion/stereo algorithm which allows range refinement through recursive range estimation while avoiding loss of range information in the direction of travel. A feature-based approach is used to track objects between image frames. An extended Kalman filter combines knowledge of the camera motion and measurements of a feature's image location to recursively estimate the feature's range and to predict its location in future images. Performance of the algorithm will be illustrated using an image sequence, motion information, and independent range measurements from a low-altitude helicopter flight experiment.

Ground-based full-sky imaging polarimeter based on liquid crystal variable retarders.

PubMed

Zhang, Ying; Zhao, Huijie; Song, Ping; Shi, Shaoguang; Xu, Wujian; Liang, Xiao

2014-04-07

A ground-based full-sky imaging polarimeter based on liquid crystal variable retarders (LCVRs) is proposed in this paper. Our proposed method can be used to realize the rapid detection of the skylight polarization information with hemisphere field-of-view for the visual band. The characteristics of the incidence angle of light on the LCVR are investigated, based on the electrically controlled birefringence. Then, the imaging polarimeter with hemisphere field-of-view is designed. Furthermore, the polarization calibration method with the field-of-view multiplexing and piecewise linear fitting is proposed, based on the rotation symmetry of the polarimeter. The polarization calibration of the polarimeter is implemented with the hemisphere field-of-view. This imaging polarimeter is investigated by the experiment of detecting the skylight image. The consistency between the obtained experimental distribution of polarization angle with that due to Rayleigh scattering model is 90%, which confirms the effectivity of our proposed imaging polarimeter.

Design of a single projector multiview 3D display system

NASA Astrophysics Data System (ADS)

Geng, Jason

2014-03-01

Multiview three-dimensional (3D) display is able to provide horizontal parallax to viewers with high-resolution and fullcolor images being presented to each view. Most multiview 3D display systems are designed and implemented using multiple projectors, each generating images for one view. Although this multi-projector design strategy is conceptually straightforward, implementation of such multi-projector design often leads to a very expensive system and complicated calibration procedures. Even for a multiview system with a moderate number of projectors (e.g., 32 or 64 projectors), the cost of a multi-projector 3D display system may become prohibitive due to the cost and complexity of integrating multiple projectors. In this article, we describe an optical design technique for a class of multiview 3D display systems that use only a single projector. In this single projector multiview (SPM) system design, multiple views for the 3D display are generated in a time-multiplex fashion by the single high speed projector with specially designed optical components, a scanning mirror, and a reflective mirror array. Images of all views are generated sequentially and projected via the specially design optical system from different viewing directions towards a 3D display screen. Therefore, the single projector is able to generate equivalent number of multiview images from multiple viewing directions, thus fulfilling the tasks of multiple projectors. An obvious advantage of the proposed SPM technique is the significant reduction of cost, size, and complexity, especially when the number of views is high. The SPM strategy also alleviates the time-consuming procedures for multi-projector calibration. The design method is flexible and scalable and can accommodate systems with different number of views.

WiseView: Visualizing motion and variability of faint WISE sources

NASA Astrophysics Data System (ADS)

Caselden, Dan; Westin, Paul, III; Meisner, Aaron; Kuchner, Marc; Colin, Guillaume

2018-06-01

WiseView renders image blinks of Wide-field Infrared Survey Explorer (WISE) coadds spanning a multi-year time baseline in a browser. The software allows for easy visual identification of motion and variability for sources far beyond the single-frame detection limit, a key threshold not surmounted by many studies. WiseView transparently gathers small image cutouts drawn from many terabytes of unWISE coadds, facilitating access to this large and unique dataset. Users need only input the coordinates of interest and can interactively tune parameters including the image stretch, colormap and blink rate. WiseView was developed in the context of the Backyard Worlds: Planet 9 citizen science project, and has enabled hundreds of brown dwarf candidate discoveries by citizen scientists and professional astronomers.

Topological Relations-Based Detection of Spatial Inconsistency in GLOBELAND30

NASA Astrophysics Data System (ADS)

Kang, S.; Chen, J.; Peng, S.

2017-09-01

Land cover is one of the fundamental data sets on environment assessment, land management and biodiversity protection, etc. Hence, data quality control of land cover is extremely critical for geospatial analysis and decision making. Due to the similar remote-sensing reflectance for some land cover types, omission and commission errors occurred in preliminary classification could result to spatial inconsistency between land cover types. In the progress of post-classification, this error checking mainly depends on manual labour to assure data quality, by which it is time-consuming and labour intensive. So a method required for automatic detection in post-classification is still an open issue. From logical inconsistency point of view, an inconsistency detection method is designed. This method consist of a grids extended 4-intersection model (GE4IM) for topological representation in single-valued space, by which three different kinds of topological relations including disjoint, touch, contain or contained-by are described, and an algorithm of region overlay for the computation of spatial inconsistency. The rules are derived from universal law in nature between water body and wetland, cultivated land and artificial surface. Through experiment conducted in Shandong Linqu County, data inconsistency can be pointed out within 6 minutes through calculation of topological inconsistency between cultivated land and artificial surface, water body and wetland. The efficiency evaluation of the presented algorithm is demonstrated by Google Earth images. Through comparative analysis, the algorithm is proved to be promising for inconsistency detection in land cover data.

Single cell magnetic imaging using a quantum diamond microscope

PubMed Central

Park, H.; Weissleder, R.; Yacoby, A.; Lukin, M. D.; Lee, H.; Walsworth, R. L.; Connolly, C. B.

2015-01-01

We apply a quantum diamond microscope to detection and imaging of immunomagnetically labeled cells. This instrument uses nitrogen-vacancy (NV) centers in diamond for correlated magnetic and fluorescence imaging. Our device provides single-cell resolution and two orders of magnitude larger field of view (~1 mm2) than previous NV imaging technologies, enabling practical applications. To illustrate, we quantify cancer biomarkers expressed by rare tumor cells in a large population of healthy cells. PMID:26098019

Methods and kits for nucleic acid analysis using fluorescence resonance energy transfer

DOEpatents

Kwok, Pui-Yan; Chen, Xiangning

1999-01-01

A method for detecting the presence of a target nucleotide or sequence of nucleotides in a nucleic acid is disclosed. The method is comprised of forming an oligonucleotide labeled with two fluorophores on the nucleic acid target site. The doubly labeled oligonucleotide is formed by addition of a singly labeled dideoxynucleoside triphosphate to a singly labeled polynucleotide or by ligation of two singly labeled polynucleotides. Detection of fluorescence resonance energy transfer upon denaturation indicates the presence of the target. Kits are also provided. The method is particularly applicable to genotyping.

Reduced field-of-view imaging for single-shot MRI with an amplitude-modulated chirp pulse excitation and Fourier transform reconstruction.

PubMed

Li, Jing; Zhang, Miao; Chen, Lin; Cai, Congbo; Sun, Huijun; Cai, Shuhui

2015-06-01

We employ an amplitude-modulated chirp pulse to selectively excite spins in one or more regions of interest (ROIs) to realize reduced field-of-view (rFOV) imaging based on single-shot spatiotemporally encoded (SPEN) sequence and Fourier transform reconstruction. The proposed rFOV imaging method was theoretically analyzed and illustrated with numerical simulation and tested with phantom experiments and in vivo rat experiments. In addition, point spread function was applied to demonstrate the feasibility of the proposed method. To evaluate the proposed method, the rFOV results were compared with those obtained using the EPI method with orthogonal RF excitation. The simulation and experimental results show that the proposed method can image one or two separated ROIs along the SPEN dimension in a single shot with higher spatial resolution, less sensitive to field inhomogeneity, and practically no aliasing artifacts. In addition, the proposed method may produce rFOV images with comparable signal-to-noise ratio to the rFOV EPI images. The proposed method is promising for the applications under severe susceptibility heterogeneities and for imaging separate ROIs simultaneously. Copyright © 2015 Elsevier Inc. All rights reserved.

Balancing precision and risk: should multiple detection methods be analyzed separately in N-mixture models?

USGS Publications Warehouse

Graves, Tabitha A.; Royle, J. Andrew; Kendall, Katherine C.; Beier, Paul; Stetz, Jeffrey B.; Macleod, Amy C.

2012-01-01

Using multiple detection methods can increase the number, kind, and distribution of individuals sampled, which may increase accuracy and precision and reduce cost of population abundance estimates. However, when variables influencing abundance are of interest, if individuals detected via different methods are influenced by the landscape differently, separate analysis of multiple detection methods may be more appropriate. We evaluated the effects of combining two detection methods on the identification of variables important to local abundance using detections of grizzly bears with hair traps (systematic) and bear rubs (opportunistic). We used hierarchical abundance models (N-mixture models) with separate model components for each detection method. If both methods sample the same population, the use of either data set alone should (1) lead to the selection of the same variables as important and (2) provide similar estimates of relative local abundance. We hypothesized that the inclusion of 2 detection methods versus either method alone should (3) yield more support for variables identified in single method analyses (i.e. fewer variables and models with greater weight), and (4) improve precision of covariate estimates for variables selected in both separate and combined analyses because sample size is larger. As expected, joint analysis of both methods increased precision as well as certainty in variable and model selection. However, the single-method analyses identified different variables and the resulting predicted abundances had different spatial distributions. We recommend comparing single-method and jointly modeled results to identify the presence of individual heterogeneity between detection methods in N-mixture models, along with consideration of detection probabilities, correlations among variables, and tolerance to risk of failing to identify variables important to a subset of the population. The benefits of increased precision should be weighed against those risks. The analysis framework presented here will be useful for other species exhibiting heterogeneity by detection method.

Single photon ranging system using two wavelengths laser and analysis of precision

NASA Astrophysics Data System (ADS)

Chen, Yunfei; He, Weiji; Miao, Zhuang; Gu, Guohua; Chen, Qian

2013-09-01

The laser ranging system based on time correlation single photon counting technology and single photon detector has the feature of high precision and low emergent energy etc. In this paper, we established a single photon laser ranging system that use the supercontinuum laser as light source, and two wavelengths (532nm and 830nm) of echo signal as the stop signal. We propose a new method that is capable to improve the single photon ranging system performance. The method is implemented by using two single-photon detectors to receive respectively the two different wavelength signals at the same time. We extracted the firings of the two detectors triggered by the same laser pulse at the same time and then took mean time of the two firings as the combined detection time-of-flight. The detection by two channels using two wavelengths will effectively improve the detection precision and decrease the false alarm probability. Finally, an experimental single photon ranging system was established. Through a lot of experiments, we got the system precision using both single and two wavelengths and verified the effectiveness of the method.

Faint Debris Detection by Particle Based Track-Before-Detect Method

NASA Astrophysics Data System (ADS)

Uetsuhara, M.; Ikoma, N.

2014-09-01

This study proposes a particle method to detect faint debris, which is hardly seen in single frame, from an image sequence based on the concept of track-before-detect (TBD). The most widely used detection method is detect-before-track (DBT), which firstly detects signals of targets from single frame by distinguishing difference of intensity between foreground and background then associate the signals for each target between frames. DBT is capable of tracking bright targets but limited. DBT is necessary to consider presence of false signals and is difficult to recover from false association. On the other hand, TBD methods try to track targets without explicitly detecting the signals followed by evaluation of goodness of each track and obtaining detection results. TBD has an advantage over DBT in detecting weak signals around background level in single frame. However, conventional TBD methods for debris detection apply brute-force search over candidate tracks then manually select true one from the candidates. To reduce those significant drawbacks of brute-force search and not-fully automated process, this study proposes a faint debris detection algorithm by a particle based TBD method consisting of sequential update of target state and heuristic search of initial state. The state consists of position, velocity direction and magnitude, and size of debris over the image at a single frame. The sequential update process is implemented by a particle filter (PF). PF is an optimal filtering technique that requires initial distribution of target state as a prior knowledge. An evolutional algorithm (EA) is utilized to search the initial distribution. The EA iteratively applies propagation and likelihood evaluation of particles for the same image sequences and resulting set of particles is used as an initial distribution of PF. This paper describes the algorithm of the proposed faint debris detection method. The algorithm demonstrates performance on image sequences acquired during observation campaigns dedicated to GEO breakup fragments, which would contain a sufficient number of faint debris images. The results indicate the proposed method is capable of tracking faint debris with moderate computational costs at operational level.

Design and Elementary Evaluation of a Highly-Automated Fluorescence-Based Instrument System for On-Site Detection of Food-Borne Pathogens

PubMed Central

Lu, Zhan; Zhang, Jianyi; Xu, Lizhou; Li, Yanbin; Chen, Siyu; Ye, Zunzhong; Wang, Jianping

2017-01-01

A simple, highly-automated instrument system used for on-site detection of foodborne pathogens based on fluorescence was designed, fabricated, and preliminarily tested in this paper. A corresponding method has been proved effective in our previous studies. This system utilizes a light-emitting diode (LED) to excite fluorescent labels and a spectrometer to record the fluorescence signal from samples. A rotation stage for positioning and switching samples was innovatively designed for high-throughput detection, ten at most in one single run. We also developed software based on LabVIEW for data receiving, processing, and the control of the whole system. In the test of using a pure quantum dot (QD) solution as a standard sample, detection results from this home-made system were highly-relevant with that from a well-commercialized product and even slightly better reproducibility was found. And in the test of three typical kinds of food-borne pathogens, fluorescence signals recorded by this system are highly proportional to the variation of the sample concentration, with a satisfied limit of detection (LOD) (nearly 102–103 CFU·mL−1 in food samples). Additionally, this instrument system is low-cost and easy-to-use, showing a promising potential for on-site rapid detection of food-borne pathogens. PMID:28241478

Design and Elementary Evaluation of a Highly-Automated Fluorescence-Based Instrument System for On-Site Detection of Food-Borne Pathogens.

PubMed

Lu, Zhan; Zhang, Jianyi; Xu, Lizhou; Li, Yanbin; Chen, Siyu; Ye, Zunzhong; Wang, Jianping

2017-02-23

A simple, highly-automated instrument system used for on-site detection of foodborne pathogens based on fluorescence was designed, fabricated, and preliminarily tested in this paper. A corresponding method has been proved effective in our previous studies. This system utilizes a light-emitting diode (LED) to excite fluorescent labels and a spectrometer to record the fluorescence signal from samples. A rotation stage for positioning and switching samples was innovatively designed for high-throughput detection, ten at most in one single run. We also developed software based on LabVIEW for data receiving, processing, and the control of the whole system. In the test of using a pure quantum dot (QD) solution as a standard sample, detection results from this home-made system were highly-relevant with that from a well-commercialized product and even slightly better reproducibility was found. And in the test of three typical kinds of food-borne pathogens, fluorescence signals recorded by this system are highly proportional to the variation of the sample concentration, with a satisfied limit of detection (LOD) (nearly 10²-10³ CFU·mL -1 in food samples). Additionally, this instrument system is low-cost and easy-to-use, showing a promising potential for on-site rapid detection of food-borne pathogens.

A novel method to calibrate DOI function of a PET detector with a dual-ended-scintillator readout

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shao Yiping; Yao Rutao; Ma Tianyu

The detection of depth-of-interaction (DOI) is a critical detector capability to improve the PET spatial resolution uniformity across the field-of-view and will significantly enhance, in particular, small bore system performance for brain, breast, and small animal imaging. One promising technique of DOI detection is to use dual-ended-scintillator readout that uses two photon sensors to detect scintillation light from both ends of a scintillator array and estimate DOI based on the ratio of signals (similar to Anger logic). This approach needs a careful DOI function calibration to establish accurate relationship between DOI and signal ratios, and to recalibrate if the detectionmore » condition is shifted due to the drift of sensor gain, bias variations, or degraded optical coupling, etc. However, the current calibration method that uses coincident events to locate interaction positions inside a single scintillator crystal has severe drawbacks, such as complicated setup, long and repetitive measurements, and being prone to errors from various possible misalignments among the source and detector components. This method is also not practically suitable to calibrate multiple DOI functions of a crystal array. To solve these problems, a new method has been developed that requires only a uniform flood source to irradiate a crystal array without the need to locate the interaction positions, and calculates DOI functions based solely on the uniform probability distribution of interactions over DOI positions without knowledge or assumption of detector responses. Simulation and experiment have been studied to validate the new method, and the results show that the new method, with a simple setup and one single measurement, can provide consistent and accurate DOI functions for the entire array of multiple scintillator crystals. This will enable an accurate, simple, and practical DOI function calibration for the PET detectors based on the design of dual-ended-scintillator readout. In addition, the new method can be generally applied to calibrating other types of detectors that use the similar dual-ended readout to acquire the radiation interaction position.« less

Helicase dependent OnChip-amplification and its use in multiplex pathogen detection.

PubMed

Andresen, Dennie; von Nickisch-Rosenegk, Markus; Bier, Frank F

2009-05-01

The need for fast, specific and sensitive multiparametric detection methods is an ever growing demand in molecular diagnostics. Here we report on a newly developed method, the helicase dependent OnChip amplification (OnChip-HDA). This approach integrates the analysis and detection in one single reaction thus leading to time and cost savings in multiparametric analysis. HDA is an isothermal amplification method that is not depending on thermocycling as known from PCR due to the helicases' ability to unwind DNA double-strands. We have combined the HDA with microarray based detection, making it suitable for multiplex detection. As an example we used the OnChip HDA in single and multiplex amplifications for the detection of the two pathogens N. gonorrhoeae and S. aureus directly on surface bound primers. We have successfully shown the OnChip-HDA and applied it for single- and duplex-detection of the pathogens N. gonorrhoeae and S. aureus. We have developed a new method, the OnChip-HDA for the multiplex detection of pathogens. Its simplicity in reaction setup and potential for miniaturization and multiparametric analysis is advantageous for the integration in miniaturized Lab on Chip systems, e.g. needed in point of care diagnostics.

Integrated Droplet-Based Microextraction with ESI-MS for Removal of Matrix Interference in Single-Cell Analysis.

PubMed

Zhang, Xiao-Chao; Wei, Zhen-Wei; Gong, Xiao-Yun; Si, Xing-Yu; Zhao, Yao-Yao; Yang, Cheng-Dui; Zhang, Si-Chun; Zhang, Xin-Rong

2016-04-29

Integrating droplet-based microfluidics with mass spectrometry is essential to high-throughput and multiple analysis of single cells. Nevertheless, matrix effects such as the interference of culture medium and intracellular components influence the sensitivity and the accuracy of results in single-cell analysis. To resolve this problem, we developed a method that integrated droplet-based microextraction with single-cell mass spectrometry. Specific extraction solvent was used to selectively obtain intracellular components of interest and remove interference of other components. Using this method, UDP-Glc-NAc, GSH, GSSG, AMP, ADP and ATP were successfully detected in single MCF-7 cells. We also applied the method to study the change of unicellular metabolites in the biological process of dysfunctional oxidative phosphorylation. The method could not only realize matrix-free, selective and sensitive detection of metabolites in single cells, but also have the capability for reliable and high-throughput single-cell analysis.

An exact computational method for performance analysis of sequential test algorithms for detecting network intrusions

NASA Astrophysics Data System (ADS)

Chen, Xinjia; Lacy, Fred; Carriere, Patrick

2015-05-01

Sequential test algorithms are playing increasingly important roles for quick detecting network intrusions such as portscanners. In view of the fact that such algorithms are usually analyzed based on intuitive approximation or asymptotic analysis, we develop an exact computational method for the performance analysis of such algorithms. Our method can be used to calculate the probability of false alarm and average detection time up to arbitrarily pre-specified accuracy.

Bisulfite-independent analysis of CpG island methylation enables genome-scale stratification of single cells

PubMed Central

Han, Lin; Wu, Hua-Jun; Zhu, Haiying; Kim, Kun-Yong; Marjani, Sadie L.; Riester, Markus; Euskirchen, Ghia; Zi, Xiaoyuan; Yang, Jennifer; Han, Jasper; Snyder, Michael; Park, In-Hyun; Irizarry, Rafael; Weissman, Sherman M.

2017-01-01

Abstract Conventional DNA bisulfite sequencing has been extended to single cell level, but the coverage consistency is insufficient for parallel comparison. Here we report a novel method for genome-wide CpG island (CGI) methylation sequencing for single cells (scCGI-seq), combining methylation-sensitive restriction enzyme digestion and multiple displacement amplification for selective detection of methylated CGIs. We applied this method to analyzing single cells from two types of hematopoietic cells, K562 and GM12878 and small populations of fibroblasts and induced pluripotent stem cells. The method detected 21 798 CGIs (76% of all CGIs) per cell, and the number of CGIs consistently detected from all 16 profiled single cells was 20 864 (72.7%), with 12 961 promoters covered. This coverage represents a substantial improvement over results obtained using single cell reduced representation bisulfite sequencing, with a 66-fold increase in the fraction of consistently profiled CGIs across individual cells. Single cells of the same type were more similar to each other than to other types, but also displayed epigenetic heterogeneity. The method was further validated by comparing the CpG methylation pattern, methylation profile of CGIs/promoters and repeat regions and 41 classes of known regulatory markers to the ENCODE data. Although not every minor methylation differences between cells are detectable, scCGI-seq provides a solid tool for unsupervised stratification of a heterogeneous cell population. PMID:28126923

High throughput analysis of samples in flowing liquid

DOEpatents

Ambrose, W. Patrick; Grace, W. Kevin; Goodwin, Peter M.; Jett, James H.; Orden, Alan Van; Keller, Richard A.

2001-01-01

Apparatus and method enable imaging multiple fluorescent sample particles in a single flow channel. A flow channel defines a flow direction for samples in a flow stream and has a viewing plane perpendicular to the flow direction. A laser beam is formed as a ribbon having a width effective to cover the viewing plane. Imaging optics are arranged to view the viewing plane to form an image of the fluorescent sample particles in the flow stream, and a camera records the image formed by the imaging optics.

The FLIGHT Drosophila RNAi database

PubMed Central

Bursteinas, Borisas; Jain, Ekta; Gao, Qiong; Baum, Buzz; Zvelebil, Marketa

2010-01-01

FLIGHT (http://flight.icr.ac.uk/) is an online resource compiling data from high-throughput Drosophila in vivo and in vitro RNAi screens. FLIGHT includes details of RNAi reagents and their predicted off-target effects, alongside RNAi screen hits, scores and phenotypes, including images from high-content screens. The latest release of FLIGHT is designed to enable users to upload, analyze, integrate and share their own RNAi screens. Users can perform multiple normalizations, view quality control plots, detect and assign screen hits and compare hits from multiple screens using a variety of methods including hierarchical clustering. FLIGHT integrates RNAi screen data with microarray gene expression as well as genomic annotations and genetic/physical interaction datasets to provide a single interface for RNAi screen analysis and datamining in Drosophila. PMID:20855970

A novel method for detection of phosphorylation in single cells by surface enhanced Raman scattering (SERS) using composite organic-inorganic nanoparticles (COINs).

PubMed

Shachaf, Catherine M; Elchuri, Sailaja V; Koh, Ai Leen; Zhu, Jing; Nguyen, Lienchi N; Mitchell, Dennis J; Zhang, Jingwu; Swartz, Kenneth B; Sun, Lei; Chan, Selena; Sinclair, Robert; Nolan, Garry P

2009-01-01

Detection of single cell epitopes has been a mainstay of immunophenotyping for over three decades, primarily using fluorescence techniques for quantitation. Fluorescence has broad overlapping spectra, limiting multiplexing abilities. To expand upon current detection systems, we developed a novel method for multi-color immuno-detection in single cells using "Composite Organic-Inorganic Nanoparticles" (COINs) Raman nanoparticles. COINs are Surface-Enhanced Raman Scattering (SERS) nanoparticles, with unique Raman spectra. To measure Raman spectra in single cells, we constructed an automated, compact, low noise and sensitive Raman microscopy device (Integrated Raman BioAnalyzer). Using this technology, we detected proteins expressed on the surface in single cells that distinguish T-cells among human blood cells. Finally, we measured intracellular phosphorylation of Stat1 (Y701) and Stat6 (Y641), with results comparable to flow cytometry. Thus, we have demonstrated the practicality of applying COIN nanoparticles for measuring intracellular phosphorylation, offering new possibilities to expand on the current fluorescent technology used for immunoassays in single cells.

A Novel Method for Detection of Phosphorylation in Single Cells by Surface Enhanced Raman Scattering (SERS) using Composite Organic-Inorganic Nanoparticles (COINs)

PubMed Central

Shachaf, Catherine M.; Elchuri, Sailaja V.; Koh, Ai Leen; Zhu, Jing; Nguyen, Lienchi N.; Mitchell, Dennis J.; Zhang, Jingwu; Swartz, Kenneth B.; Sun, Lei; Chan, Selena; Sinclair, Robert; Nolan, Garry P.

2009-01-01

Background Detection of single cell epitopes has been a mainstay of immunophenotyping for over three decades, primarily using fluorescence techniques for quantitation. Fluorescence has broad overlapping spectra, limiting multiplexing abilities. Methodology/Principal Findings To expand upon current detection systems, we developed a novel method for multi-color immuno-detection in single cells using “Composite Organic-Inorganic Nanoparticles” (COINs) Raman nanoparticles. COINs are Surface-Enhanced Raman Scattering (SERS) nanoparticles, with unique Raman spectra. To measure Raman spectra in single cells, we constructed an automated, compact, low noise and sensitive Raman microscopy device (Integrated Raman BioAnalyzer). Using this technology, we detected proteins expressed on the surface in single cells that distinguish T-cells among human blood cells. Finally, we measured intracellular phosphorylation of Stat1 (Y701) and Stat6 (Y641), with results comparable to flow cytometry. Conclusions/Significance Thus, we have demonstrated the practicality of applying COIN nanoparticles for measuring intracellular phosphorylation, offering new possibilities to expand on the current fluorescent technology used for immunoassays in single cells. PMID:19367337

Multiview boosting digital pathology analysis of prostate cancer.

PubMed

Kwak, Jin Tae; Hewitt, Stephen M

2017-04-01

Various digital pathology tools have been developed to aid in analyzing tissues and improving cancer pathology. The multi-resolution nature of cancer pathology, however, has not been fully analyzed and utilized. Here, we develop an automated, cooperative, and multi-resolution method for improving prostate cancer diagnosis. Digitized tissue specimen images are obtained from 5 tissue microarrays (TMAs). The TMAs include 70 benign and 135 cancer samples (TMA1), 74 benign and 89 cancer samples (TMA2), 70 benign and 115 cancer samples (TMA3), 79 benign and 82 cancer samples (TMA4), and 72 benign and 86 cancer samples (TMA5). The tissue specimen images are segmented using intensity- and texture-based features. Using the segmentation results, a number of morphological features from lumens and epithelial nuclei are computed to characterize tissues at different resolutions. Applying a multiview boosting algorithm, tissue characteristics, obtained from differing resolutions, are cooperatively combined to achieve accurate cancer detection. In segmenting prostate tissues, the multiview boosting method achieved≥ 0.97 AUC using TMA1. For detecting cancers, the multiview boosting method achieved an AUC of 0.98 (95% CI: 0.97-0.99) as trained on TMA2 and tested on TMA3, TMA4, and TMA5. The proposed method was superior to single-view approaches, utilizing features from a single resolution or merging features from all the resolutions. Moreover, the performance of the proposed method was insensitive to the choice of the training dataset. Trained on TMA3, TMA4, and TMA5, the proposed method obtained an AUC of 0.97 (95% CI: 0.96-0.98), 0.98 (95% CI: 0.96-0.99), and 0.97 (95% CI: 0.96-0.98), respectively. The multiview boosting method is capable of integrating information from multiple resolutions in an effective and efficient fashion and identifying cancers with high accuracy. The multiview boosting method holds a great potential for improving digital pathology tools and research. Copyright © 2017 Elsevier B.V. All rights reserved.

Multi-resolution statistical image reconstruction for mitigation of truncation effects: application to cone-beam CT of the head

NASA Astrophysics Data System (ADS)

Dang, Hao; Webster Stayman, J.; Sisniega, Alejandro; Zbijewski, Wojciech; Xu, Jennifer; Wang, Xiaohui; Foos, David H.; Aygun, Nafi; Koliatsos, Vassilis E.; Siewerdsen, Jeffrey H.

2017-01-01

A prototype cone-beam CT (CBCT) head scanner featuring model-based iterative reconstruction (MBIR) has been recently developed and demonstrated the potential for reliable detection of acute intracranial hemorrhage (ICH), which is vital to diagnosis of traumatic brain injury and hemorrhagic stroke. However, data truncation (e.g. due to the head holder) can result in artifacts that reduce image uniformity and challenge ICH detection. We propose a multi-resolution MBIR method with an extended reconstruction field of view (RFOV) to mitigate truncation effects in CBCT of the head. The image volume includes a fine voxel size in the (inner) nontruncated region and a coarse voxel size in the (outer) truncated region. This multi-resolution scheme allows extension of the RFOV to mitigate truncation effects while introducing minimal increase in computational complexity. The multi-resolution method was incorporated in a penalized weighted least-squares (PWLS) reconstruction framework previously developed for CBCT of the head. Experiments involving an anthropomorphic head phantom with truncation due to a carbon-fiber holder were shown to result in severe artifacts in conventional single-resolution PWLS, whereas extending the RFOV within the multi-resolution framework strongly reduced truncation artifacts. For the same extended RFOV, the multi-resolution approach reduced computation time compared to the single-resolution approach (viz. time reduced by 40.7%, 83.0%, and over 95% for an image volume of 6003, 8003, 10003 voxels). Algorithm parameters (e.g. regularization strength, the ratio of the fine and coarse voxel size, and RFOV size) were investigated to guide reliable parameter selection. The findings provide a promising method for truncation artifact reduction in CBCT and may be useful for other MBIR methods and applications for which truncation is a challenge.

Large-viewing-angle electroholography by space projection

NASA Astrophysics Data System (ADS)

Sato, Koki; Obana, Kazuki; Okumura, Toshimichi; Kanaoka, Takumi; Nishikawa, Satoko; Takano, Kunihiko

2004-06-01

The specification of hologram image is the full parallax 3D image. In this case we can get more natural 3D image because focusing and convergence are coincident each other. We try to get practical electro-holography system because for conventional electro-holography the image viewing angle is very small. This is due to the limited display pixel size. Now we are developing new method for large viewing angle by space projection method. White color laser is irradiated to single DMD panel ( time shared CGH of RGB three colors ). 3D space screen constructed by very small water particle is used to reconstruct the 3D image with large viewing angle by scattering of water particle.

An Improved Azimuth Angle Estimation Method with a Single Acoustic Vector Sensor Based on an Active Sonar Detection System.

PubMed

Zhao, Anbang; Ma, Lin; Ma, Xuefei; Hui, Juan

2017-02-20

In this paper, an improved azimuth angle estimation method with a single acoustic vector sensor (AVS) is proposed based on matched filtering theory. The proposed method is mainly applied in an active sonar detection system. According to the conventional passive method based on complex acoustic intensity measurement, the mathematical and physical model of this proposed method is described in detail. The computer simulation and lake experiments results indicate that this method can realize the azimuth angle estimation with high precision by using only a single AVS. Compared with the conventional method, the proposed method achieves better estimation performance. Moreover, the proposed method does not require complex operations in frequencydomain and achieves computational complexity reduction.

Can laptops be left inside passenger bags if motion imaging is used in X-ray security screening?

PubMed

Mendes, Marcia; Schwaninger, Adrian; Michel, Stefan

2013-01-01

This paper describes a study where a new X-ray machine for security screening featuring motion imaging (i.e., 5 views of a bag are shown as an image sequence) was evaluated and compared to single view imaging available on conventional X-ray screening systems. More specifically, it was investigated whether with this new technology X-ray screening of passenger bags could be enhanced to such an extent that laptops could be left inside passenger bags, without causing a significant impairment in threat detection performance. An X-ray image interpretation test was created in four different versions, manipulating the factors packing condition (laptop and bag separate vs. laptop in bag) and display condition (single vs. motion imaging). There was a highly significant and large main effect of packing condition. When laptops and bags were screened separately, threat item detection was substantially higher. For display condition, a medium effect was observed. Detection could be slightly enhanced through the application of motion imaging. There was no interaction between display and packing condition, implying that the high negative effect of leaving laptops in passenger bags could not be fully compensated by motion imaging. Additional analyses were carried out to examine effects depending on different threat categories (guns, improvised explosive devices, knives, others), the placement of the threat items (in bag vs. in laptop) and viewpoint (easy vs. difficult view). In summary, although motion imaging provides an enhancement, it is not strong enough to allow leaving laptops in bags for security screening.

Can laptops be left inside passenger bags if motion imaging is used in X-ray security screening?

PubMed Central

Mendes, Marcia; Schwaninger, Adrian; Michel, Stefan

2013-01-01

This paper describes a study where a new X-ray machine for security screening featuring motion imaging (i.e., 5 views of a bag are shown as an image sequence) was evaluated and compared to single view imaging available on conventional X-ray screening systems. More specifically, it was investigated whether with this new technology X-ray screening of passenger bags could be enhanced to such an extent that laptops could be left inside passenger bags, without causing a significant impairment in threat detection performance. An X-ray image interpretation test was created in four different versions, manipulating the factors packing condition (laptop and bag separate vs. laptop in bag) and display condition (single vs. motion imaging). There was a highly significant and large main effect of packing condition. When laptops and bags were screened separately, threat item detection was substantially higher. For display condition, a medium effect was observed. Detection could be slightly enhanced through the application of motion imaging. There was no interaction between display and packing condition, implying that the high negative effect of leaving laptops in passenger bags could not be fully compensated by motion imaging. Additional analyses were carried out to examine effects depending on different threat categories (guns, improvised explosive devices, knives, others), the placement of the threat items (in bag vs. in laptop) and viewpoint (easy vs. difficult view). In summary, although motion imaging provides an enhancement, it is not strong enough to allow leaving laptops in bags for security screening. PMID:24151457

Single-molecule detection: applications to ultrasensitive biochemical analysis

NASA Astrophysics Data System (ADS)

Castro, Alonso; Shera, E. Brooks

1995-06-01

Recent developments in laser-based detection of fluorescent molecules have made possible the implementation of very sensitive techniques for biochemical analysis. We present and discuss our experiments on the applications of our recently developed technique of single-molecule detection to the analysis of molecules of biological interest. These newly developed methods are capable of detecting and identifying biomolecules at the single-molecule level of sensitivity. In one case, identification is based on measuring fluorescence brightness from single molecules. In another, molecules are classified by determining their electrophoretic velocities.

Single Molecules as Optical Probes for Structure and Dynamics

NASA Astrophysics Data System (ADS)

Orrit, Michel

Single molecules and single nanoparticles are convenient links between the nanoscale world and the laboratory. We discuss the limits for their optical detection by three different methods: fluorescence, direct absorption, and photothermal detection. We briefly review some recent illustrations of qualitatively new information gathered from single-molecule signals: intermittency of the fluorescence intensity, acoustic vibrations of nanoparticles (1-100 GHz) or of extended defects in molecular crystals (0.1-1 MHz), and dynamical heterogeneity in glass-forming molecular liquids. We conclude with an outlook of future uses of single-molecule methods in physical chemistry, soft matter, and material science.

Atomic-resolution single-spin magnetic resonance detection concept based on tunneling force microscopy

NASA Astrophysics Data System (ADS)

Payne, A.; Ambal, K.; Boehme, C.; Williams, C. C.

2015-05-01

A study of a force detected single-spin magnetic resonance measurement concept with atomic spatial resolution is presented. The method is based upon electrostatic force detection of spin-selection rule controlled single-electron tunneling between two electrically isolated paramagnetic states. Single-spin magnetic resonance detection is possible by measuring the force detected tunneling charge noise on and off spin resonance. Simulation results of this charge noise, based upon physical models of the tunneling and spin physics, are directly compared to measured atomic force microscopy system noise. The results show that the approach could provide single-spin measurement of electrically isolated qubit states with atomic spatial resolution at room temperature.

Single particle electrochemical sensors and methods of utilization

DOEpatents

Schoeniger, Joseph [Oakland, CA; Flounders, Albert W [Berkeley, CA; Hughes, Robert C [Albuquerque, NM; Ricco, Antonio J [Los Gatos, CA; Wally, Karl [Lafayette, CA; Kravitz, Stanley H [Placitas, NM; Janek, Richard P [Oakland, CA

2006-04-04

The present invention discloses an electrochemical device for detecting single particles, and methods for using such a device to achieve high sensitivity for detecting particles such as bacteria, viruses, aggregates, immuno-complexes, molecules, or ionic species. The device provides for affinity-based electrochemical detection of particles with single-particle sensitivity. The disclosed device and methods are based on microelectrodes with surface-attached, affinity ligands (e.g., antibodies, combinatorial peptides, glycolipids) that bind selectively to some target particle species. The electrodes electrolyze chemical species present in the particle-containing solution, and particle interaction with a sensor element modulates its electrolytic activity. The devices may be used individually, employed as sensors, used in arrays for a single specific type of particle or for a range of particle types, or configured into arrays of sensors having both these attributes.

Sensitivity images for multi-view ultrasonic array inspection

NASA Astrophysics Data System (ADS)

Budyn, Nicolas; Bevan, Rhodri; Croxford, Anthony J.; Zhang, Jie; Wilcox, Paul D.; Kashubin, Artem; Cawley, Peter

2018-04-01

The multi-view total focusing method (TFM) is an imaging technique for ultrasonic full matrix array data that typically exploits ray paths with zero, one or two internal reflections in the inspected object and for all combinations of longitudinal and transverse modes. The fusion of this vast quantity of views is expected to increase the reliability of ultrasonic inspection; however, it is not trivial to determine which views and which areas are the most suited for the detection of a given type and orientation of defect. This work introduces sensitivity images that give the expected response of a defect in any part of the inspected object and for any view. These images are based on a ray-based analytical forward model. They can be used to determine which views and which areas lead to the highest probability of detection of the defect. They can also be used for quantitatively analyzing the effects of the parameters of the inspection (probe angle and position, for example) on the overall probability of detection. Finally, they can be used to rescale TFM images so that the different views have comparable amplitudes. This methodology is applied to experimental data and discussed.

Study of comparison between Ultra-high Frequency (UHF) method and ultrasonic method on PD detection for GIS

NASA Astrophysics Data System (ADS)

Li, Yanran; Chen, Duo; Li, Li; Zhang, Jiwei; Li, Guang; Liu, Hongxia

2017-11-01

GIS (gas insulated switchgear), is an important equipment in power system. Partial discharge plays an important role in detecting the insulation performance of GIS. UHF method and ultrasonic method frequently used in partial discharge (PD) detection for GIS. However, few studies have been conducted on comparison of this two methods. From the view point of safety, it is necessary to investigate UHF method and ultrasonic method for partial discharge in GIS. This paper presents study aimed at clarifying the effect of UHF method and ultrasonic method for partial discharge caused by free metal particles in GIS. Partial discharge tests were performed in laboratory simulated environment. Obtained results show the ability of anti-interference of signal detection and the accuracy of fault localization for UHF method and ultrasonic method. A new method based on UHF method and ultrasonic method of PD detection for GIS is proposed in order to greatly enhance the ability of anti-interference of signal detection and the accuracy of detection localization.

Teacher and Administrator Views on School Principals' Accountability

ERIC Educational Resources Information Center

Argon, Turkan

2015-01-01

The current study aims to identify teacher and administrator views regarding primary school principals' accountability. The case study model, a qualitative research method, was adopted in the study using the holistic single-case design. The working group was composed of a total of 56 individuals, 42 teachers and 14 administrators (11 principals…

SciClone: inferring clonal architecture and tracking the spatial and temporal patterns of tumor evolution.

PubMed

Miller, Christopher A; White, Brian S; Dees, Nathan D; Griffith, Malachi; Welch, John S; Griffith, Obi L; Vij, Ravi; Tomasson, Michael H; Graubert, Timothy A; Walter, Matthew J; Ellis, Matthew J; Schierding, William; DiPersio, John F; Ley, Timothy J; Mardis, Elaine R; Wilson, Richard K; Ding, Li

2014-08-01

The sensitivity of massively-parallel sequencing has confirmed that most cancers are oligoclonal, with subpopulations of neoplastic cells harboring distinct mutations. A fine resolution view of this clonal architecture provides insight into tumor heterogeneity, evolution, and treatment response, all of which may have clinical implications. Single tumor analysis already contributes to understanding these phenomena. However, cryptic subclones are frequently revealed by additional patient samples (e.g., collected at relapse or following treatment), indicating that accurately characterizing a tumor requires analyzing multiple samples from the same patient. To address this need, we present SciClone, a computational method that identifies the number and genetic composition of subclones by analyzing the variant allele frequencies of somatic mutations. We use it to detect subclones in acute myeloid leukemia and breast cancer samples that, though present at disease onset, are not evident from a single primary tumor sample. By doing so, we can track tumor evolution and identify the spatial origins of cells resisting therapy.

SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution

PubMed Central

Dees, Nathan D.; Griffith, Malachi; Welch, John S.; Griffith, Obi L.; Vij, Ravi; Tomasson, Michael H.; Graubert, Timothy A.; Walter, Matthew J.; Ellis, Matthew J.; Schierding, William; DiPersio, John F.; Ley, Timothy J.; Mardis, Elaine R.; Wilson, Richard K.; Ding, Li

2014-01-01

The sensitivity of massively-parallel sequencing has confirmed that most cancers are oligoclonal, with subpopulations of neoplastic cells harboring distinct mutations. A fine resolution view of this clonal architecture provides insight into tumor heterogeneity, evolution, and treatment response, all of which may have clinical implications. Single tumor analysis already contributes to understanding these phenomena. However, cryptic subclones are frequently revealed by additional patient samples (e.g., collected at relapse or following treatment), indicating that accurately characterizing a tumor requires analyzing multiple samples from the same patient. To address this need, we present SciClone, a computational method that identifies the number and genetic composition of subclones by analyzing the variant allele frequencies of somatic mutations. We use it to detect subclones in acute myeloid leukemia and breast cancer samples that, though present at disease onset, are not evident from a single primary tumor sample. By doing so, we can track tumor evolution and identify the spatial origins of cells resisting therapy. PMID:25102416

Volumetric Forest Change Detection Through Vhr Satellite Imagery

NASA Astrophysics Data System (ADS)

Akca, Devrim; Stylianidis, Efstratios; Smagas, Konstantinos; Hofer, Martin; Poli, Daniela; Gruen, Armin; Sanchez Martin, Victor; Altan, Orhan; Walli, Andreas; Jimeno, Elisa; Garcia, Alejandro

2016-06-01

Quick and economical ways of detecting of planimetric and volumetric changes of forest areas are in high demand. A research platform, called FORSAT (A satellite processing platform for high resolution forest assessment), was developed for the extraction of 3D geometric information from VHR (very-high resolution) imagery from satellite optical sensors and automatic change detection. This 3D forest information solution was developed during a Eurostars project. FORSAT includes two main units. The first one is dedicated to the geometric and radiometric processing of satellite optical imagery and 2D/3D information extraction. This includes: image radiometric pre-processing, image and ground point measurement, improvement of geometric sensor orientation, quasiepipolar image generation for stereo measurements, digital surface model (DSM) extraction by using a precise and robust image matching approach specially designed for VHR satellite imagery, generation of orthoimages, and 3D measurements in single images using mono-plotting and in stereo images as well as triplets. FORSAT supports most of the VHR optically imagery commonly used for civil applications: IKONOS, OrbView - 3, SPOT - 5 HRS, SPOT - 5 HRG, QuickBird, GeoEye-1, WorldView-1/2, Pléiades 1A/1B, SPOT 6/7, and sensors of similar type to be expected in the future. The second unit of FORSAT is dedicated to 3D surface comparison for change detection. It allows users to import digital elevation models (DEMs), align them using an advanced 3D surface matching approach and calculate the 3D differences and volume changes between epochs. To this end our 3D surface matching method LS3D is being used. FORSAT is a single source and flexible forest information solution with a very competitive price/quality ratio, allowing expert and non-expert remote sensing users to monitor forests in three and four dimensions from VHR optical imagery for many forest information needs. The capacity and benefits of FORSAT have been tested in six case studies located in Austria, Cyprus, Spain, Switzerland and Turkey, using optical data from different sensors and with the purpose to monitor forest with different geometric characteristics. The validation run on Cyprus dataset is reported and commented.

Potential pitfalls and methods of improving in utero diagnosis of transposition of the great arteries, including the baby bird's beak image.

PubMed

McGahan, John P; Moon-Grady, Anita J; Pahwa, Anokh; Towner, Dena; Rhee-Morris, Laila; Gerscovich, Eugenio O; Fogata, Maria

2007-11-01

The goal of this study was to analyze our recent experience with fetuses with transposition of the great arteries (TGA) to identify potential pitfalls and possible methods to better detect conotruncal anomalies such as TGA. We analyzed all nonreferral obstetric ultrasound examinations in which we performed basic, targeted, or formal fetal echocardiography with a newborn diagnosis of TGA. Nine neonates had TGA. Five of these cases were diagnosed prenatally, and 4 of these had complex congenital heart abnormalities. In these 4 cases, there were abnormalities in the cardiac axis (n = 3), abnormal valves or ventricular size (n = 2), and ventricular septal defects (n = 3) that were detected on the 4-chamber view of the heart. In all cases that were not detected prenatally, both prospective and retrospective reviews of the 4-chamber heart appeared normal. The prospective analyses of the outflow tracts were all interpreted as normal, whereas the retrospective review showed subtle abnormalities such as the "baby bird's beak" image. In review of these cases, there was failure to show the "crisscross" relationship of the outflow tracts. In 1 case, 5 short axis views of the heart, retrospectively showed the artery originating from the left ventricle and bifurcated, representing the pulmonary artery. Transposition of the great arteries may be associated with complex cardiac disease that could be detected on the 4-chamber view of the heart. When the 4-chamber view is normal, it is important to identify the crisscross relationship of the outflow tracts. If this is not done, it is important to document that the pulmonary artery bifurcates and originates from the right ventricle. Five short axis views of the heart may be helpful to detect conotruncal abnormalities.

Improving image quality for digital breast tomosynthesis: an automated detection and diffusion-based method for metal artifact reduction

NASA Astrophysics Data System (ADS)

Lu, Yao; Chan, Heang-Ping; Wei, Jun; Hadjiiski, Lubomir M.; Samala, Ravi K.

2017-10-01

In digital breast tomosynthesis (DBT), the high-attenuation metallic clips marking a previous biopsy site in the breast cause errors in the estimation of attenuation along the ray paths intersecting the markers during reconstruction, which result in interplane and inplane artifacts obscuring the visibility of subtle lesions. We proposed a new metal artifact reduction (MAR) method to improve image quality. Our method uses automatic detection and segmentation to generate a marker location map for each projection (PV). A voting technique based on the geometric correlation among different PVs is designed to reduce false positives (FPs) and to label the pixels on the PVs and the voxels in the imaged volume that represent the location and shape of the markers. An iterative diffusion method replaces the labeled pixels on the PVs with estimated tissue intensity from the neighboring regions while preserving the original pixel values in the neighboring regions. The inpainted PVs are then used for DBT reconstruction. The markers are repainted on the reconstructed DBT slices for radiologists’ information. The MAR method is independent of reconstruction techniques or acquisition geometry. For the training set, the method achieved 100% success rate with one FP in 19 views. For the test set, the success rate by view was 97.2% for core biopsy microclips and 66.7% for clusters of large post-lumpectomy markers with a total of 10 FPs in 58 views. All FPs were large dense benign calcifications that also generated artifacts if they were not corrected by MAR. For the views with successful detection, the metal artifacts were reduced to a level that was not visually apparent in the reconstructed slices. The visibility of breast lesions obscured by the reconstruction artifacts from the metallic markers was restored.

What if we are alone?

NASA Astrophysics Data System (ADS)

Waltham, D.

2013-09-01

The huge number of planets in the observable Universe, and beyond, means that worlds with Earth-like levels of biodiversity are inevitable even if the probability of any give n planet being inhabited is tiny. The corollary of this is that the existence of one such world (the Earth)tells us almost nothing about how common such places are in the Universe. Hence, given the present state of astrobiological know ledge, it is possible that there are no other inhabited planets within the detection-range of any conceivable technology. This is not a popular view currently but the little evidence we have (e.g. the coincidence of stellar-evolution and intelligence-evolution time-scales on Earth [1,2]; indications that many of the Earth's properties may be fine-tuned for complex life [3,4]; the fact that life on Earth was, for most of its history, single-celled [5]) points towards complex life, at least, being rare in the Universe. The plausibility of this "gloomy" view will be tested further incoming decades as we explore Mars, Europa, Titan and other astrobiologically interesting worlds in the Solar System and as we, hopefully, develop ever more sophisticated remote-sensing methods for assessing the biological state of exoplanets. Much thought has been given to the political, social and psychological effects of a positive detection of alien life or even the receiving of a confirmed SETI signal. However, in my view, it is equally important and interesting to consider the impact of negative results. What if we are alone? What if the only other life we find is "primitive"?

Fibre optic system for biochemical and microbiological sensing

NASA Astrophysics Data System (ADS)

Penwill, L. A.; Slater, J. H.; Hayes, N. W.; Tremlett, C. J.

2007-07-01

This poster will discuss state-of-the-art fibre optic sensors based on evanescent wave technology emphasising chemophotonic sensors for biochemical reactions and microbe detection. Devices based on antibody specificity and unique DNA sequences will be described. The development of simple sensor devices with disposable single use sensor probes will be illustrated with a view to providing cost effective field based or point of care analysis of major themes such as hospital acquired infections or bioterrorism events. This presentation will discuss the nature and detection thresholds required, the optical detection techniques investigated, results of sensor trials and the potential for wider commercial application.

Feasibility study on the design of a probe for rectal cancer detection

NASA Technical Reports Server (NTRS)

Anselm, V. J.; Frazer, R. E.; Lecroisset, D. H.; Roseboro, J. A.; Smokler, M. I.

1977-01-01

Rectal examination techniques are considered in terms of detection capability, patient acceptance, and cost reduction. A review of existing clinical techniques are considered in terms of detection capability, patient acceptance, and cost reduction. A review of existing clinical techniques and of relevant aerospace technology included evaluation of the applicability of visual, thermal, ultrasound, and radioisotope modalities of examination. The desired improvements can be obtained by redesigning the proctosigmoidoscope to have reduced size, additional visibility, and the capability of readily providing a color photograph of the entire rectosigmoid mucosa in a single composite view.

A flexible new method for 3D measurement based on multi-view image sequences

NASA Astrophysics Data System (ADS)

Cui, Haihua; Zhao, Zhimin; Cheng, Xiaosheng; Guo, Changye; Jia, Huayu

2016-11-01

Three-dimensional measurement is the base part for reverse engineering. The paper developed a new flexible and fast optical measurement method based on multi-view geometry theory. At first, feature points are detected and matched with improved SIFT algorithm. The Hellinger Kernel is used to estimate the histogram distance instead of traditional Euclidean distance, which is immunity to the weak texture image; then a new filter three-principle for filtering the calculation of essential matrix is designed, the essential matrix is calculated using the improved a Contrario Ransac filter method. One view point cloud is constructed accurately with two view images; after this, the overlapped features are used to eliminate the accumulated errors caused by added view images, which improved the camera's position precision. At last, the method is verified with the application of dental restoration CAD/CAM, experiment results show that the proposed method is fast, accurate and flexible for tooth 3D measurement.

Study of New Method Combined Ultra-High Frequency (UHF) Method and Ultrasonic Method on PD Detection for GIS

NASA Astrophysics Data System (ADS)

Li, Yanran; Chen, Duo; Zhang, Jiwei; Chen, Ning; Li, Xiaoqi; Gong, Xiaojing

2017-09-01

GIS (gas insulated switchgear), is an important equipment in power system. Partial discharge plays an important role in detecting the insulation performance of GIS. UHF method and ultrasonic method frequently used in partial discharge (PD) detection for GIS. It is necessary to investigate UHF method and ultrasonic method for partial discharge in GIS. However, very few studies have been conducted on the method combined this two methods. From the view point of safety, a new method based on UHF method and ultrasonic method of PD detection for GIS is proposed in order to greatly enhance the ability of anti-interference of signal detection and the accuracy of fault localization. This paper presents study aimed at clarifying the effect of the new method combined UHF method and ultrasonic method. Partial discharge tests were performed in laboratory simulated environment. Obtained results show the ability of anti-interference of signal detection and the accuracy of fault localization for this new method combined UHF method and ultrasonic method.

On the uncertainty in single molecule fluorescent lifetime and energy emission measurements

NASA Technical Reports Server (NTRS)

Brown, Emery N.; Zhang, Zhenhua; Mccollom, Alex D.

1995-01-01

Time-correlated single photon counting has recently been combined with mode-locked picosecond pulsed excitation to measure the fluorescent lifetimes and energy emissions of single molecules in a flow stream. Maximum likelihood (ML) and least square methods agree and are optimal when the number of detected photons is large however, in single molecule fluorescence experiments the number of detected photons can be less than 20, 67% of those can be noise and the detection time is restricted to 10 nanoseconds. Under the assumption that the photon signal and background noise are two independent inhomogeneous poisson processes, we derive the exact joint arrival time probably density of the photons collected in a single counting experiment performed in the presence of background noise. The model obviates the need to bin experimental data for analysis, and makes it possible to analyze formally the effect of background noise on the photon detection experiment using both ML or Bayesian methods. For both methods we derive the joint and marginal probability densities of the fluorescent lifetime and fluorescent emission. the ML and Bayesian methods are compared in an analysis of simulated single molecule fluorescence experiments of Rhodamine 110 using different combinations of expected background nose and expected fluorescence emission. While both the ML or Bayesian procedures perform well for analyzing fluorescence emissions, the Bayesian methods provide more realistic measures of uncertainty in the fluorescent lifetimes. The Bayesian methods would be especially useful for measuring uncertainty in fluorescent lifetime estimates in current single molecule flow stream experiments where the expected fluorescence emission is low. Both the ML and Bayesian algorithms can be automated for applications in molecular biology.

On the Uncertainty in Single Molecule Fluorescent Lifetime and Energy Emission Measurements

NASA Technical Reports Server (NTRS)

Brown, Emery N.; Zhang, Zhenhua; McCollom, Alex D.

1996-01-01

Time-correlated single photon counting has recently been combined with mode-locked picosecond pulsed excitation to measure the fluorescent lifetimes and energy emissions of single molecules in a flow stream. Maximum likelihood (ML) and least squares methods agree and are optimal when the number of detected photons is large, however, in single molecule fluorescence experiments the number of detected photons can be less than 20, 67 percent of those can be noise, and the detection time is restricted to 10 nanoseconds. Under the assumption that the photon signal and background noise are two independent inhomogeneous Poisson processes, we derive the exact joint arrival time probability density of the photons collected in a single counting experiment performed in the presence of background noise. The model obviates the need to bin experimental data for analysis, and makes it possible to analyze formally the effect of background noise on the photon detection experiment using both ML or Bayesian methods. For both methods we derive the joint and marginal probability densities of the fluorescent lifetime and fluorescent emission. The ML and Bayesian methods are compared in an analysis of simulated single molecule fluorescence experiments of Rhodamine 110 using different combinations of expected background noise and expected fluorescence emission. While both the ML or Bayesian procedures perform well for analyzing fluorescence emissions, the Bayesian methods provide more realistic measures of uncertainty in the fluorescent lifetimes. The Bayesian methods would be especially useful for measuring uncertainty in fluorescent lifetime estimates in current single molecule flow stream experiments where the expected fluorescence emission is low. Both the ML and Bayesian algorithms can be automated for applications in molecular biology.

Multiratio fusion change detection with adaptive thresholding

NASA Astrophysics Data System (ADS)

Hytla, Patrick C.; Balster, Eric J.; Vasquez, Juan R.; Neuroth, Robert M.

2017-04-01

A ratio-based change detection method known as multiratio fusion (MRF) is proposed and tested. The MRF framework builds on other change detection components proposed in this work: dual ratio (DR) and multiratio (MR). The DR method involves two ratios coupled with adaptive thresholds to maximize detected changes and minimize false alarms. The use of two ratios is shown to outperform the single ratio case when the means of the image pairs are not equal. MR change detection builds on the DR method by including negative imagery to produce four total ratios with adaptive thresholds. Inclusion of negative imagery is shown to improve detection sensitivity and to boost detection performance in certain target and background cases. MRF further expands this concept by fusing together the ratio outputs using a routine in which detections must be verified by two or more ratios to be classified as a true changed pixel. The proposed method is tested with synthetically generated test imagery and real datasets with results compared to other methods found in the literature. DR is shown to significantly outperform the standard single ratio method. MRF produces excellent change detection results that exhibit up to a 22% performance improvement over other methods from the literature at low false-alarm rates.

Comparison of three-view thoracic radiography and computed tomography for detection of pulmonary nodules in dogs with neoplasia.

PubMed

Armbrust, Laura J; Biller, David S; Bamford, Aubrey; Chun, Ruthanne; Garrett, Laura D; Sanderson, Michael W

2012-05-01

To compare the detection of pulmonary nodules by use of 3-view thoracic radiography and CT in dogs with confirmed neoplasia. Prospective case series. 33 dogs of various breeds. 3 interpreters independently evaluated 3-view thoracic radiography images. The location and size of pulmonary nodules were recorded. Computed tomographic scans of the thorax were obtained and evaluated by a single interpreter. The location, size, margin, internal architecture, and density of pulmonary nodules were recorded. Sensitivity, specificity, positive predictive value, and negative predictive value were calculated for thoracic radiography (with CT as the gold standard). 21 of 33 (64%) dogs had pulmonary nodules or masses detected on CT. Of the dogs that had positive CT findings, 17 of 21 (81%) had pulmonary nodules or masses detected on radiographs by at least 1 interpreter. Sensitivity of radiography ranged from 71% to 95%, and specificity ranged from 67% to 92%. Radiography had a positive predictive value of 83% to 94% and a negative predictive value of 65% to 89%. The 4 dogs that were negative for nodules on thoracic radiography but positive on CT were all large-breed to giant-breed dogs with osteosarcoma. CT was more sensitive than radiography for detection of pulmonary nodules. This was particularly evident in large-breed to giant-breed dogs. Thoracic CT is recommended in large-breed to giant-breed dogs with osteosarcoma if the detection of pulmonary nodules will change treatment.

The Morava E-theories of finite general linear groups

NASA Astrophysics Data System (ADS)

Mattafirri, Sara

The feasibility of producing an image of radioactivity distribution within a patient or confined region of space using information carried by the gamma-rays emitted from the source is investigated. The imaging approach makes use of parameters related to the gamma-rays which undergo Compton scattering within a detection system, it does not involve the use of pin-holes, and it employs gamma-rays of energy ranging from a few hundreds of keVs to MeVs. Energy range of the photons and absence of pin-holes aim to provide larger pool of radioisotopes and larger efficiency than other emission imaging modalities, such as single photon emission computed tomography and positron emission tomography, making it possible to investigate larger pool of functions and smaller radioactivity doses. The observables available to produce the image are the gamma-ray position of interaction and energy deposition during Compton scattering within the detection systems. Image reconstruction methodologies such as backprojection and list-mode maximum likelihood expectation maximization algorithm are characterized and applied to produce images of simulated and experimental sources on the basis of the observed parameters. Given the observables and image reconstruction methodologies, imaging systems based on minimizing the variation of the impulse response with position within the field of view are developed. The approach allows imaging of three-dimensional sources when an imaging system which provides full 4 pi view of the object is used and imaging of two-dimensional sources when a single block-type detector which provides one view of the object is used. Geometrical resolution of few millimeters is obtained at few centimeters from the detection system if employing gamma-rays of energy in the order of few hundreds of keVs and current state of the art semi-conductor detectors; At this level of resolution, detection efficiency is in the order of 10-3 at few centimeters from the detector when a single block detector few centimeters in size is used. The resolution significantly improves with increasing energy of the photons and it degrades roughly linearly with increasing distance from the detector; Larger detection efficiency can be obtained at the expenses of resolution or via targeted configurations of the detector. Results pave the way for image reconstruction of practical gamma-ray emitting sources.

Bloodstain detection and discrimination impacted by spectral shift when using an interference filter-based visible and near-infrared multispectral crime scene imaging system

NASA Astrophysics Data System (ADS)

Yang, Jie; Messinger, David W.; Dube, Roger R.

2018-03-01

Bloodstain detection and discrimination from nonblood substances on various substrates are critical in forensic science as bloodstains are a critical source for confirmatory DNA tests. Conventional bloodstain detection methods often involve time-consuming sample preparation, a chance of harm to investigators, the possibility of destruction of blood samples, and acquisition of too little data at crime scenes either in the field or in the laboratory. An imaging method has the advantages of being nondestructive, noncontact, real-time, and covering a large field-of-view. The abundant spectral information provided by multispectral imaging makes it a potential presumptive bloodstain detection and discrimination method. This article proposes an interference filter (IF) based area scanning three-spectral-band crime scene imaging system used for forensic bloodstain detection and discrimination. The impact of large angle of views on the spectral shift of calibrated IFs is determined, for both detecting and discriminating bloodstains from visually similar substances on multiple substrates. Spectral features in the visible and near-infrared portion employed by the relative band depth method are used. This study shows that 1 ml bloodstain on black felt, gray felt, red felt, white cotton, white polyester, and raw wood can be detected. Bloodstains on the above substrates can be discriminated from cola, coffee, ketchup, orange juice, red wine, and green tea.

A 3D freehand ultrasound system for multi-view reconstructions from sparse 2D scanning planes.

PubMed

Yu, Honggang; Pattichis, Marios S; Agurto, Carla; Beth Goens, M

2011-01-20

A significant limitation of existing 3D ultrasound systems comes from the fact that the majority of them work with fixed acquisition geometries. As a result, the users have very limited control over the geometry of the 2D scanning planes. We present a low-cost and flexible ultrasound imaging system that integrates several image processing components to allow for 3D reconstructions from limited numbers of 2D image planes and multiple acoustic views. Our approach is based on a 3D freehand ultrasound system that allows users to control the 2D acquisition imaging using conventional 2D probes.For reliable performance, we develop new methods for image segmentation and robust multi-view registration. We first present a new hybrid geometric level-set approach that provides reliable segmentation performance with relatively simple initializations and minimum edge leakage. Optimization of the segmentation model parameters and its effect on performance is carefully discussed. Second, using the segmented images, a new coarse to fine automatic multi-view registration method is introduced. The approach uses a 3D Hotelling transform to initialize an optimization search. Then, the fine scale feature-based registration is performed using a robust, non-linear least squares algorithm. The robustness of the multi-view registration system allows for accurate 3D reconstructions from sparse 2D image planes. Volume measurements from multi-view 3D reconstructions are found to be consistently and significantly more accurate than measurements from single view reconstructions. The volume error of multi-view reconstruction is measured to be less than 5% of the true volume. We show that volume reconstruction accuracy is a function of the total number of 2D image planes and the number of views for calibrated phantom. In clinical in-vivo cardiac experiments, we show that volume estimates of the left ventricle from multi-view reconstructions are found to be in better agreement with clinical measures than measures from single view reconstructions. Multi-view 3D reconstruction from sparse 2D freehand B-mode images leads to more accurate volume quantification compared to single view systems. The flexibility and low-cost of the proposed system allow for fine control of the image acquisition planes for optimal 3D reconstructions from multiple views.

Bisulfite-independent analysis of CpG island methylation enables genome-scale stratification of single cells.

PubMed

Han, Lin; Wu, Hua-Jun; Zhu, Haiying; Kim, Kun-Yong; Marjani, Sadie L; Riester, Markus; Euskirchen, Ghia; Zi, Xiaoyuan; Yang, Jennifer; Han, Jasper; Snyder, Michael; Park, In-Hyun; Irizarry, Rafael; Weissman, Sherman M; Michor, Franziska; Fan, Rong; Pan, Xinghua

2017-06-02

Conventional DNA bisulfite sequencing has been extended to single cell level, but the coverage consistency is insufficient for parallel comparison. Here we report a novel method for genome-wide CpG island (CGI) methylation sequencing for single cells (scCGI-seq), combining methylation-sensitive restriction enzyme digestion and multiple displacement amplification for selective detection of methylated CGIs. We applied this method to analyzing single cells from two types of hematopoietic cells, K562 and GM12878 and small populations of fibroblasts and induced pluripotent stem cells. The method detected 21 798 CGIs (76% of all CGIs) per cell, and the number of CGIs consistently detected from all 16 profiled single cells was 20 864 (72.7%), with 12 961 promoters covered. This coverage represents a substantial improvement over results obtained using single cell reduced representation bisulfite sequencing, with a 66-fold increase in the fraction of consistently profiled CGIs across individual cells. Single cells of the same type were more similar to each other than to other types, but also displayed epigenetic heterogeneity. The method was further validated by comparing the CpG methylation pattern, methylation profile of CGIs/promoters and repeat regions and 41 classes of known regulatory markers to the ENCODE data. Although not every minor methylation differences between cells are detectable, scCGI-seq provides a solid tool for unsupervised stratification of a heterogeneous cell population. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

VP-Nets : Efficient automatic localization of key brain structures in 3D fetal neurosonography.

PubMed

Huang, Ruobing; Xie, Weidi; Alison Noble, J

2018-04-23

Three-dimensional (3D) fetal neurosonography is used clinically to detect cerebral abnormalities and to assess growth in the developing brain. However, manual identification of key brain structures in 3D ultrasound images requires expertise to perform and even then is tedious. Inspired by how sonographers view and interact with volumes during real-time clinical scanning, we propose an efficient automatic method to simultaneously localize multiple brain structures in 3D fetal neurosonography. The proposed View-based Projection Networks (VP-Nets), uses three view-based Convolutional Neural Networks (CNNs), to simplify 3D localizations by directly predicting 2D projections of the key structures onto three anatomical views. While designed for efficient use of data and GPU memory, the proposed VP-Nets allows for full-resolution 3D prediction. We investigated parameters that influence the performance of VP-Nets, e.g. depth and number of feature channels. Moreover, we demonstrate that the model can pinpoint the structure in 3D space by visualizing the trained VP-Nets, despite only 2D supervision being provided for a single stream during training. For comparison, we implemented two other baseline solutions based on Random Forest and 3D U-Nets. In the reported experiments, VP-Nets consistently outperformed other methods on localization. To test the importance of loss function, two identical models are trained with binary corss-entropy and dice coefficient loss respectively. Our best VP-Net model achieved prediction center deviation: 1.8 ± 1.4 mm, size difference: 1.9 ± 1.5 mm, and 3D Intersection Over Union (IOU): 63.2 ± 14.7% when compared to the ground truth. To make the whole pipeline intervention free, we also implement a skull-stripping tool using 3D CNN, which achieves high segmentation accuracy. As a result, the proposed processing pipeline takes a raw ultrasound brain image as input, and output a skull-stripped image with five detected key brain structures. Copyright © 2018 Elsevier B.V. All rights reserved.

Molecular diagnostics in gastric cancer.

PubMed

Bornschein, Jan; Leja, Marcis; Kupcinskas, Juozas; Link, Alexander; Weaver, Jamie; Rugge, Massimo; Malfertheiner, Peter

2014-01-01

Despite recent advances in individualised targeted therapy, gastric cancer remains one of the most challenging diseases in gastrointestinal oncology. Modern imaging techniques using endoscopic filter devices and in vivo molecular imaging are designed to enable early detection of the cancer and surveillance of patients at risk. Molecular characterisation of the tumour itself as well as of the surrounding inflammatory environment is more sophisticated in the view of tailored therapies and individual prognostic assessment. The broad application of high throughput techniques for the description of genome wide patterns of structural (copy number aberrations, single nucleotide polymorphisms, methylation pattern) and functional (gene expression profiling, proteomics, miRNA) alterations in the cancer tissue lead not only to a better understanding of the tumour biology but also to a description of gastric cancer subtypes independent from classical stratification systems. Biostatistical means are required for the interpretation of the massive amount of data generated by these approaches. In this review we give an overview on the current knowledge of diagnostic methods for detection, description and understanding of gastric cancer disease.

An Improved Azimuth Angle Estimation Method with a Single Acoustic Vector Sensor Based on an Active Sonar Detection System

PubMed Central

Zhao, Anbang; Ma, Lin; Ma, Xuefei; Hui, Juan

2017-01-01

In this paper, an improved azimuth angle estimation method with a single acoustic vector sensor (AVS) is proposed based on matched filtering theory. The proposed method is mainly applied in an active sonar detection system. According to the conventional passive method based on complex acoustic intensity measurement, the mathematical and physical model of this proposed method is described in detail. The computer simulation and lake experiments results indicate that this method can realize the azimuth angle estimation with high precision by using only a single AVS. Compared with the conventional method, the proposed method achieves better estimation performance. Moreover, the proposed method does not require complex operations in frequency-domain and achieves computational complexity reduction. PMID:28230763

Synchronization Design and Error Analysis of Near-Infrared Cameras in Surgical Navigation.

PubMed

Cai, Ken; Yang, Rongqian; Chen, Huazhou; Huang, Yizhou; Wen, Xiaoyan; Huang, Wenhua; Ou, Shanxing

2016-01-01

The accuracy of optical tracking systems is important to scientists. With the improvements reported in this regard, such systems have been applied to an increasing number of operations. To enhance the accuracy of these systems further and to reduce the effect of synchronization and visual field errors, this study introduces a field-programmable gate array (FPGA)-based synchronization control method, a method for measuring synchronous errors, and an error distribution map in field of view. Synchronization control maximizes the parallel processing capability of FPGA, and synchronous error measurement can effectively detect the errors caused by synchronization in an optical tracking system. The distribution of positioning errors can be detected in field of view through the aforementioned error distribution map. Therefore, doctors can perform surgeries in areas with few positioning errors, and the accuracy of optical tracking systems is considerably improved. The system is analyzed and validated in this study through experiments that involve the proposed methods, which can eliminate positioning errors attributed to asynchronous cameras and different fields of view.

Glove perforation rate in vascular surgery--a comparison between single and double gloving.

PubMed

Aarnio, P; Laine, T

2001-05-01

In surgery intact gloves act as a sterile barrier between surgeon and patient. The impermeable gloves protect the surgeon from bloodborne pathogens such as HIV, hepatitis B, and hepatitis C. On the other hand, the surgical wound is protected from micro-organisms from the skin of the surgeon. One objective of this study was to compare puncture rates between the double gloving color indication system and single-use gloves and the other to determine the extent to which glove perforations remain undetected during the course of vascular surgical operations. The study material comprised all gloves used in vascular surgical operations at Satakunta Central Hospital for a period of two months. The analysis was made by the glove type in a prospective and randomised manner. Gloves were tested immediately after the surgical procedure using the approved standardized water-leak method. With this method the glove is filled with water using a special filling tube, and the water-filled glove is then checked for two minutes to detect any holes. The gloves used in this study were either double gloves with indicator, or the standard glove used at our hospital. In 73 operations altogether 200 gloves were tested, half of them were double gloves and half were single gloves. The perforation occurred in the double gloves 3 times and with single gloves 12 times. The overall perforation rate was 15 out of 200 gloves (7.5%). The detection of perforation during surgery was 60%. Most frequently the perforation was located in the second finger of the left hand, 9 out of 15 perforations. In view of the critical importance of safety at work both transmitting the pathogens from the skin of the surgeon to the wound and transmitting the bloodborne pathogens from the patient to the surgeon, it is very important to use double gloving at least in operations where there is a high risk of glove perforation.

Co-Labeling for Multi-View Weakly Labeled Learning.

PubMed

Xu, Xinxing; Li, Wen; Xu, Dong; Tsang, Ivor W

2016-06-01

It is often expensive and time consuming to collect labeled training samples in many real-world applications. To reduce human effort on annotating training samples, many machine learning techniques (e.g., semi-supervised learning (SSL), multi-instance learning (MIL), etc.) have been studied to exploit weakly labeled training samples. Meanwhile, when the training data is represented with multiple types of features, many multi-view learning methods have shown that classifiers trained on different views can help each other to better utilize the unlabeled training samples for the SSL task. In this paper, we study a new learning problem called multi-view weakly labeled learning, in which we aim to develop a unified approach to learn robust classifiers by effectively utilizing different types of weakly labeled multi-view data from a broad range of tasks including SSL, MIL and relative outlier detection (ROD). We propose an effective approach called co-labeling to solve the multi-view weakly labeled learning problem. Specifically, we model the learning problem on each view as a weakly labeled learning problem, which aims to learn an optimal classifier from a set of pseudo-label vectors generated by using the classifiers trained from other views. Unlike traditional co-training approaches using a single pseudo-label vector for training each classifier, our co-labeling approach explores different strategies to utilize the predictions from different views, biases and iterations for generating the pseudo-label vectors, making our approach more robust for real-world applications. Moreover, to further improve the weakly labeled learning on each view, we also exploit the inherent group structure in the pseudo-label vectors generated from different strategies, which leads to a new multi-layer multiple kernel learning problem. Promising results for text-based image retrieval on the NUS-WIDE dataset as well as news classification and text categorization on several real-world multi-view datasets clearly demonstrate that our proposed co-labeling approach achieves state-of-the-art performance for various multi-view weakly labeled learning problems including multi-view SSL, multi-view MIL and multi-view ROD.

Study on Hybrid Image Search Technology Based on Texts and Contents

NASA Astrophysics Data System (ADS)

Wang, H. T.; Ma, F. L.; Yan, C.; Pan, H.

2018-05-01

Image search was studied first here based on texts and contents, respectively. The text-based image feature extraction was put forward by integrating the statistical and topic features in view of the limitation of extraction of keywords only by means of statistical features of words. On the other hand, a search-by-image method was put forward based on multi-feature fusion in view of the imprecision of the content-based image search by means of a single feature. The layered-searching method depended on primarily the text-based image search method and additionally the content-based image search was then put forward in view of differences between the text-based and content-based methods and their difficult direct fusion. The feasibility and effectiveness of the hybrid search algorithm were experimentally verified.

Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads.

PubMed

Sasagawa, Yohei; Danno, Hiroki; Takada, Hitomi; Ebisawa, Masashi; Tanaka, Kaori; Hayashi, Tetsutaro; Kurisaki, Akira; Nikaido, Itoshi

2018-03-09

High-throughput single-cell RNA-seq methods assign limited unique molecular identifier (UMI) counts as gene expression values to single cells from shallow sequence reads and detect limited gene counts. We thus developed a high-throughput single-cell RNA-seq method, Quartz-Seq2, to overcome these issues. Our improvements in the reaction steps make it possible to effectively convert initial reads to UMI counts, at a rate of 30-50%, and detect more genes. To demonstrate the power of Quartz-Seq2, we analyzed approximately 10,000 transcriptomes from in vitro embryonic stem cells and an in vivo stromal vascular fraction with a limited number of reads.

Development and characterization of a handheld hyperspectral Raman imaging probe system for molecular characterization of tissue on mesoscopic scales.

PubMed

St-Arnaud, Karl; Aubertin, Kelly; Strupler, Mathias; Madore, Wendy-Julie; Grosset, Andrée-Anne; Petrecca, Kevin; Trudel, Dominique; Leblond, Frédéric

2018-01-01

Raman spectroscopy is a promising cancer detection technique for surgical guidance applications. It can provide quantitative information relating to global tissue properties associated with structural, metabolic, immunological, and genetic biochemical phenomena in terms of molecular species including amino acids, lipids, proteins, and nucleic acid (DNA). To date in vivo Raman spectroscopy systems mostly included probes and biopsy needles typically limited to single-point tissue interrogation over a scale between 100 and 500 microns. The development of wider field handheld systems could improve tumor localization for a range of open surgery applications including brain, ovarian, and skin cancers. Here we present a novel Raman spectroscopy implementation using a coherent imaging bundle of fibers to create a probe capable of reconstructing molecular images over mesoscopic fields of view. Detection is performed using linear scanning with a rotation mirror and an imaging spectrometer. Different slits widths were tested at the entrance of the spectrometer to optimize spatial and spectral resolution while preserving sufficient signal-to-noise ratios to detect the principal Raman tissue features. The nonbiological samples, calcite and polytetrafluoroethylene (PTFE), were used to characterize the performance of the system. The new wide-field probe was tested on ex vivo samples of calf brain and swine tissue. Raman spectral content of both tissue types were validated with data from the literature and compared with data acquired with a single-point Raman spectroscopy probe. The single-point probe was used as the gold standard against which the new instrument was benchmarked as it has already been thoroughly validated for biological tissue characterization. We have developed and characterized a practical noncontact handheld Raman imager providing tissue information at a spatial resolution of 115 microns over a field of view >14 mm 2 and a spectral resolution of 6 cm -1 over the whole fingerprint region. Typical integration time to acquire an entire Raman image over swine tissue was set to approximately 100 s. Spectra acquired with both probes (single-point and wide-field) showed good agreement, with a Pearson correlation factor >0.85 over different tissue categories. Protein and lipid content of imaged tissue were manifested into the measured spectra which correlated well with previous findings in the literature. An example of quantitative molecular map is presented for swine tissue and calf brain based on the ratio of protein-to-lipid content showing clear delineations between white and gray matter as well as between adipose and muscle tissue. We presented the development of a Raman imaging probe with a field of view of a few millimeters and a spatial resolution consistent with standard surgical imaging methods using an imaging bundle. Spectra acquired with the newly developed system on swine tissue and calf brain correlated well with an establish single-point probe and observed spectral features agreed with previous finding in the literature. The imaging probe has demonstrated its ability to reconstruct molecular images of soft tissues. The approach presented here has a lot of potential for the development of surgical Raman imaging probe to guide the surgeon during cancer surgery. © 2017 American Association of Physicists in Medicine.

Detecting text in natural scenes with multi-level MSER and SWT

NASA Astrophysics Data System (ADS)

Lu, Tongwei; Liu, Renjun

2018-04-01

The detection of the characters in the natural scene is susceptible to factors such as complex background, variable viewing angle and diverse forms of language, which leads to poor detection results. Aiming at these problems, a new text detection method was proposed, which consisted of two main stages, candidate region extraction and text region detection. At first stage, the method used multiple scale transformations of original image and multiple thresholds of maximally stable extremal regions (MSER) to detect the text regions which could detect character regions comprehensively. At second stage, obtained SWT maps by using the stroke width transform (SWT) algorithm to compute the candidate regions, then using cascaded classifiers to propose non-text regions. The proposed method was evaluated on the standard benchmark datasets of ICDAR2011 and the datasets that we made our own data sets. The experiment results showed that the proposed method have greatly improved that compared to other text detection methods.

Medical Student Views of Substance Abuse Treatment, Policy and Training

ERIC Educational Resources Information Center

Agrawal, Shantanu; Everett, Worth W.; Sharma, Sonali

2010-01-01

Purpose: This study examined the impact of medical education on students' views of substance abuse treatment, public policy options and training. Method: A longitudinal survey was conducted on a single-class cohort of 101 students in a major American, urban medical school. The survey was administered in the Spring semesters of the first to third…

Wavefront detection method of a single-sensor based adaptive optics system.

PubMed

Wang, Chongchong; Hu, Lifa; Xu, Huanyu; Wang, Yukun; Li, Dayu; Wang, Shaoxin; Mu, Quanquan; Yang, Chengliang; Cao, Zhaoliang; Lu, Xinghai; Xuan, Li

2015-08-10

In adaptive optics system (AOS) for optical telescopes, the reported wavefront sensing strategy consists of two parts: a specific sensor for tip-tilt (TT) detection and another wavefront sensor for other distortions detection. Thus, a part of incident light has to be used for TT detection, which decreases the light energy used by wavefront sensor and eventually reduces the precision of wavefront correction. In this paper, a single Shack-Hartmann wavefront sensor based wavefront measurement method is presented for both large amplitude TT and other distortions' measurement. Experiments were performed for testing the presented wavefront method and validating the wavefront detection and correction ability of the single-sensor based AOS. With adaptive correction, the root-mean-square of residual TT was less than 0.2 λ, and a clear image was obtained in the lab. Equipped on a 1.23-meter optical telescope, the binary stars with angle distance of 0.6″ were clearly resolved using the AOS. This wavefront measurement method removes the separate TT sensor, which not only simplifies the AOS but also saves light energy for subsequent wavefront sensing and imaging, and eventually improves the detection and imaging capability of the AOS.

Wide field-of-view dual-band multispectral muzzle flash detection

NASA Astrophysics Data System (ADS)

Montoya, J.; Melchor, J.; Spiliotis, P.; Taplin, L.

2013-06-01

Sensor technologies are undergoing revolutionary advances, as seen in the rapid growth of multispectral methodologies. Increases in spatial, spectral, and temporal resolution, and in breadth of spectral coverage, render feasible sensors that function with unprecedented performance. A system was developed that addresses many of the key hardware requirements for a practical dual-band multispectral acquisition system, including wide field of view and spectral/temporal shift between dual bands. The system was designed using a novel dichroic beam splitter and dual band-pass filter configuration that creates two side-by-side images of a scene on a single sensor. A high-speed CMOS sensor was used to simultaneously capture data from the entire scene in both spectral bands using a short focal-length lens that provided a wide field-of-view. The beam-splitter components were arranged such that the two images were maintained in optical alignment and real-time intra-band processing could be carried out using only simple arithmetic on the image halves. An experiment related to limitations of the system to address multispectral detection requirements was performed. This characterized the system's low spectral variation across its wide field of view. This paper provides lessons learned on the general limitation of key hardware components required for multispectral muzzle flash detection, using the system as a hardware example combined with simulated multispectral muzzle flash and background signatures.

Accurate Detection of Methicillin-Resistant Staphylococcus aureus in Mixtures by Use of Single-Bacterium Duplex Droplet Digital PCR.

PubMed

Luo, Jun; Li, Junhua; Yang, Hang; Yu, Junping; Wei, Hongping

2017-10-01

Accurate and rapid identification of methicillin-resistant Staphylococcus aureus (MRSA) is needed to screen MRSA carriers and improve treatment. The current widely used duplex PCR methods are not able to differentiate MRSA from coexisting methicillin-susceptible S. aureus (MSSA) or other methicillin-resistant staphylococci. In this study, we aimed to develop a direct method for accurate and rapid detection of MRSA in clinical samples from open environments, such as nasal swabs. The new molecular assay is based on detecting the cooccurrence of nuc and mecA markers in a single bacterial cell by utilizing droplet digital PCR (ddPCR) with the chimeric lysin ClyH for cell lysis. The method consists of (i) dispersion of an intact single bacterium into nanoliter droplets, (ii) temperature-controlled release of genomic DNA (gDNA) by ClyH at 37°C, and (iii) amplification and detection of the markers ( nuc and mecA ) using standard TaqMan chemistries with ddPCR. Results were analyzed based on MRSA index ratios used for indicating the presence of the duplex-positive markers in droplets. The method was able to achieve an absolute limit of detection (LOD) of 2,900 CFU/ml for MRSA in nasal swabs spiked with excess amounts of Escherichia coli , MSSA, and other mecA -positive bacteria within 4 h. Initial testing of 104 nasal swabs showed that the method had 100% agreement with the standard culture method, while the normal duplex qPCR method had only about 87.5% agreement. The single-bacterium duplex ddPCR assay is rapid and powerful for more accurate detection of MRSA directly from clinical specimens. Copyright © 2017 American Society for Microbiology.

Accurate Detection of Methicillin-Resistant Staphylococcus aureus in Mixtures by Use of Single-Bacterium Duplex Droplet Digital PCR

PubMed Central

Luo, Jun; Li, Junhua; Yang, Hang; Yu, Junping

2017-01-01

ABSTRACT Accurate and rapid identification of methicillin-resistant Staphylococcus aureus (MRSA) is needed to screen MRSA carriers and improve treatment. The current widely used duplex PCR methods are not able to differentiate MRSA from coexisting methicillin-susceptible S. aureus (MSSA) or other methicillin-resistant staphylococci. In this study, we aimed to develop a direct method for accurate and rapid detection of MRSA in clinical samples from open environments, such as nasal swabs. The new molecular assay is based on detecting the cooccurrence of nuc and mecA markers in a single bacterial cell by utilizing droplet digital PCR (ddPCR) with the chimeric lysin ClyH for cell lysis. The method consists of (i) dispersion of an intact single bacterium into nanoliter droplets, (ii) temperature-controlled release of genomic DNA (gDNA) by ClyH at 37°C, and (iii) amplification and detection of the markers (nuc and mecA) using standard TaqMan chemistries with ddPCR. Results were analyzed based on MRSA index ratios used for indicating the presence of the duplex-positive markers in droplets. The method was able to achieve an absolute limit of detection (LOD) of 2,900 CFU/ml for MRSA in nasal swabs spiked with excess amounts of Escherichia coli, MSSA, and other mecA-positive bacteria within 4 h. Initial testing of 104 nasal swabs showed that the method had 100% agreement with the standard culture method, while the normal duplex qPCR method had only about 87.5% agreement. The single-bacterium duplex ddPCR assay is rapid and powerful for more accurate detection of MRSA directly from clinical specimens. PMID:28724560

Selective counting and sizing of single virus particles using fluorescent aptamer-based nanoparticle tracking analysis.

PubMed

Szakács, Zoltán; Mészáros, Tamás; de Jonge, Marien I; Gyurcsányi, Róbert E

2018-05-30

Detection and counting of single virus particles in liquid samples are largely limited to narrow size distribution of viruses and purified formulations. To address these limitations, here we propose a calibration-free method that enables concurrently the selective recognition, counting and sizing of virus particles as demonstrated through the detection of human respiratory syncytial virus (RSV), an enveloped virus with a broad size distribution, in throat swab samples. RSV viruses were selectively labeled through their attachment glycoproteins (G) with fluorescent aptamers, which further enabled their identification, sizing and counting at the single particle level by fluorescent nanoparticle tracking analysis. The proposed approach seems to be generally applicable to virus detection and quantification. Moreover, it could be successfully applied to detect single RSV particles in swab samples of diagnostic relevance. Since the selective recognition is associated with the sizing of each detected particle, this method enables to discriminate viral elements linked to the virus as well as various virus forms and associations.

Probing Enzyme-Surface Interactions via Protein Engineering and Single-Molecule Techniques

DTIC Science & Technology

2017-06-26

SECURITY CLASSIFICATION OF: The overall objective of this research was to exploit protein engineering and fluorescence single-molecule methods to... Engineering and Single-Molecule Techniques The views, opinions and/or findings contained in this report are those of the author(s) and should not...Status: Technology Transfer: Report Date: 1 FINAL REPORT Project Title: Probing Enzyme-Surface Interactions via Protein Engineering and

Methods for Gas Sensing with Single-Walled Carbon Nanotubes

NASA Technical Reports Server (NTRS)

Kaul, Anupama B. (Inventor)

2013-01-01

Methods for gas sensing with single-walled carbon nanotubes are described. The methods comprise biasing at least one carbon nanotube and exposing to a gas environment to detect variation in temperature as an electrical response.

Digital DNA detection based on a compact optofluidic laser with ultra-low sample consumption.

PubMed

Lee, Wonsuk; Chen, Qiushu; Fan, Xudong; Yoon, Dong Ki

2016-11-29

DNA lasers self-amplify optical signals from a DNA analyte as well as thermodynamic differences between sequences, allowing quasi-digital DNA detection. However, these systems have drawbacks, such as relatively large sample consumption and complicated dye labelling. Moreover, although the lasing signal can detect the target DNA, it is superimposed on an unintended fluorescence background, which persists for non-target DNA samples as well. From an optical point of view, it is thus not truly digital detection and requires spectral analysis to identify the target. In this work, we propose and demonstrate an optofluidic laser that has a single layer of DNA molecules as the gain material. A target DNA produces intensive laser emission comparable to existing DNA lasers, while any unnecessary fluorescence background is successfully suppressed. As a result, the target DNA can be detected with a single laser pulse, in a truly digital manner. Since the DNA molecules cover only a single layer on the surface of the laser microcavity, the DNA sample consumption is a few orders of magnitude lower than that of existing DNA lasers. Furthermore, the DNA molecules are stained by simply immersing the microcavity in the intercalating dye solution, and thus the proposed DNA laser is free of any complex dye-labelling process prior to analysis.

Image analysis for the detection of Barré

USDA-ARS?s Scientific Manuscript database

Barré is a major problem for the textile industry. Barré is detectable after fabric is dyed and the detection of barré can depend upon the color of the dyed fabric, lighting conditions, fabric pattern, and/or the color perception of the person viewing the fabric. The standard method for measuring ...

Systematic assessment of the performance of whole-genome amplification for SNP/CNV detection and β-thalassemia genotyping.

PubMed

He, Fei; Zhou, Wanjun; Cai, Ren; Yan, Tizhen; Xu, Xiangmin

2018-04-01

In this study, we aimed to assess the performance of two whole-genome amplification methods, multiple displacement amplification (MDA), and multiple annealing and looping-based amplification cycle (MALBAC), for β-thalassemia genotyping and single-nucleotide polymorphism (SNP)/copy-number variant (CNV) detection using two DNA sequencing assays. We collected peripheral blood, cell lines, and discarded embryos, and carried out MALBAC and MDA on single-cell and five-cell samples. We detected and statistically analyzed differences in the amplification efficiency, positive predictive value, sensitivity, allele dropout (ADO) rate, SNPs, and CV values between the two methods. Through Sanger sequencing at the single-cell and five-cell levels, we showed that both the amplification rate and ADO rate of MDA were better than those using MALBAC, and the sensitivity and positive predictive value obtained from MDA were higher than those from MALBAC for β-thalassemia genotyping. Using next-generation sequencing (NGS) at the single-cell level, we confirmed that MDA has better properties than MALBAC for SNP detection. However, MALBAC was more stable and homogeneous than MDA using low-depth NGS at the single-cell level for CNV detection. We conclude that MALBAC is the better option for CNV detection, while MDA is better suited for SNV detection.

Concept for room temperature single-spin tunneling force microscopy with atomic spatial resolution

NASA Astrophysics Data System (ADS)

Payne, Adam

A study of a force detected single-spin magnetic resonance measurement concept with atomic spatial resolution is presented. The method is based upon electrostatic force detection of spin-selection rule controlled single electron tunneling between two electrically isolated paramagnetic states. Single-spin magnetic resonance detection is possible by measuring the force detected tunneling charge noise on and off spin resonance. Simulation results of this charge noise, based upon physical models of the tunneling and spin physics, are directly compared to measured atomic force microscopy (AFM) system noise. The results show that the approach could provide single-spin measurement of electrically isolated defect states with atomic spatial resolution at room temperature.

Single-molecule two-colour coincidence detection to probe biomolecular associations.

PubMed

Orte, Angel; Clarke, Richard; Klenerman, David

2010-08-01

Two-colour coincidence detection (TCCD) is a form of single-molecule fluorescence developed to sensitively detect and characterize associated biomolecules without any separation, in solution, on the cell membrane and in live cells. In the present short review, we first explain the principles of the method and then describe the application of TCCD to a range of biomedical problems and how this method may be developed further in the future to try to monitor biological processes in live cells.

Performance characteristics of dedicated molecular breast imaging systems at low doses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Long, Zaiyang; Conners, Amy L.; Hunt, Katie N.

Purpose: The purpose of this study was to compare the system performance characteristics and lesion detection capability of two molecular breast imaging (MBI) systems: a multicrystal sodium iodide (NaI)-based single-head system and a cadmium zinc telluride (CZT)-based dual-head system at low administered doses (150–300 MBq) of Tc-99m sestamibi. Methods: System performance characteristics including count sensitivity, uniformity, energy resolution, and spatial resolution were measured using standard NEMA methods, or a modified version thereof in cases where the standard NEMA protocol could not be applied. A contrast-detail phantom with 48 lesions at varying depths from the collimator surface was used to assessmore » lesion contrast-to-noise-ratio (CNR) using background count densities comparable to those observed in patient studies performed with administered doses of 150 MBq Tc-99m sestamibi. Lesions with CNR >3 were deemed to be detectable. Thirty patients undergoing MBI examinations with administered doses of 150–300 MBq were scanned for an additional view on the pixelated NaI system. CNR was calculated for lesions observed on patient images. Background count densities of patient images were measured and compared between the two systems. Results: Over the central field of view, integral and differential uniformity were 6.1% and 4.2%, respectively, for the pixelated NaI system, and 3.8% and 2.7%, respectively, for the CZT system. Count sensitivity was 10.8 kcts/min/MBq for the NaI system and 32.9 kcts/min/MBq for the CZT system. Energy resolution was 13.5% on the pixelated NaI system and 4.5% on the CZT system. Spatial resolution (full-width at half-maximum) for the pixelated NaI detector was 4.2 mm at a distance of 1.2 cm from the collimator and 5.2 mm at 3.1 cm. Spatial resolution of a single CZT detector was 2.9 mm at a distance of 1.2 cm from the collimator and 4.7 mm at 3.1 cm. Effective spatial resolution obtained with dual-head CZT was below 4.7 mm throughout a simulated breast thickness of 6 cm. From contrast-detail phantom images of lesions at distances of 1.5–4.5 cm from the collimator face, the CZT system detected 124 of 144 (86%) of lesions compared to 97 of 144 (67%) with the NaI system. In patient studies, from comparison of the same view with both systems, a total of 7 breast lesions were identified on CZT system in seven patients, and 4 of 7 (57%) were detected on NaI system. Patient image background count densities on the CZT system were on average 3.4 times higher than those on the NaI system. Conclusions: The CZT system demonstrated better uniformity, count sensitivity, spatial resolution, energy resolution, and lesion detection in phantom and patient studies compared to the NaI system. At administered doses of 150–300 MBq Tc-99m sestamibi, patient results obtained with CZT systems may not be directly translatable to NaI systems.« less

A Natural View of Microbial Biodiversity within Hot Spring Cyanobacterial Mat Communities

PubMed Central

Ward, David M.; Ferris, Michael J.; Nold, Stephen C.; Bateson, Mary M.

1998-01-01

This review summarizes a decade of research in which we have used molecular methods, in conjunction with more traditional approaches, to study hot spring cyanobacterial mats as models for understanding principles of microbial community ecology. Molecular methods reveal that the composition of these communities is grossly oversimplified by microscopic and cultivation methods. For example, none of 31 unique 16S rRNA sequences detected in the Octopus Spring mat, Yellowstone National Park, matches that of any prokaryote previously cultivated from geothermal systems; 11 are contributed by genetically diverse cyanobacteria, even though a single cyanobacterial species was suspected based on morphologic and culture analysis. By studying the basis for the incongruity between culture and molecular samplings of community composition, we are beginning to cultivate isolates whose 16S rRNA sequences are readily detected. By placing the genetic diversity detected in context with the well-defined natural environmental gradients typical of hot spring mat systems, the relationship between gene and species diversity is clarified and ecological patterns of species occurrence emerge. By combining these ecological patterns with the evolutionary patterns inherently revealed by phylogenetic analysis of gene sequence data, we find that it may be possible to understand microbial biodiversity within these systems by using principles similar to those developed by evolutionary ecologists to understand biodiversity of larger species. We hope that such an approach guides microbial ecologists to a more realistic and predictive understanding of microbial species occurrence and responsiveness in both natural and disturbed habitats. PMID:9841675

A natural view of microbial biodiversity within hot spring cyanobacterial mat communities

NASA Technical Reports Server (NTRS)

Ward, D. M.; Ferris, M. J.; Nold, S. C.; Bateson, M. M.

1998-01-01

This review summarizes a decade of research in which we have used molecular methods, in conjunction with more traditional approaches, to study hot spring cyanobacterial mats as models for understanding principles of microbial community ecology. Molecular methods reveal that the composition of these communities is grossly oversimplified by microscopic and cultivation methods. For example, none of 31 unique 16S rRNA sequences detected in the Octopus Spring mat, Yellowstone National Park, matches that of any prokaryote previously cultivated from geothermal systems; 11 are contributed by genetically diverse cyanobacteria, even though a single cyanobacterial species was suspected based on morphologic and culture analysis. By studying the basis for the incongruity between culture and molecular samplings of community composition, we are beginning to cultivate isolates whose 16S rRNA sequences are readily detected. By placing the genetic diversity detected in context with the well-defined natural environmental gradients typical of hot spring mat systems, the relationship between gene and species diversity is clarified and ecological patterns of species occurrence emerge. By combining these ecological patterns with the evolutionary patterns inherently revealed by phylogenetic analysis of gene sequence data, we find that it may be possible to understand microbial biodiversity within these systems by using principles similar to those developed by evolutionary ecologists to understand biodiversity of larger species. We hope that such an approach guides microbial ecologists to a more realistic and predictive understanding of microbial species occurrence and responsiveness in both natural and disturbed habitats.

In Situ Hot-Spot Assembly as a General Strategy for Probing Single Biomolecules.

PubMed

Liu, Huiqiao; Li, Qiang; Li, Mingmin; Ma, Sisi; Liu, Dingbin

2017-05-02

Single-molecule detection using surface-enhanced Raman spectroscopy (SERS) has attracted increasing attention in chemical and biomedical analysis. However, it remains a major challenge to probe single biomolecules by means of SERS hot spots owing to the small volume of hot spots and their random distribution on substrates. We here report an in situ hot-spot assembly method as a general strategy for probing single biomolecules. As a proof-of-concept, this proposed strategy was successfully used for the detection of single microRNA-21 (miRNA-21, a potential cancer biomarker) at the single-cell level, showing great capability in differentiating the expression of miRNA-21 in single cancer cells from normal cells. This approach was further extended to single-protein detection. The versatility of the strategy opens an exciting avenue for single-molecule detection of biomarkers of interest and thus holds great promise in a variety of biological and biomedical applications.

Detection of admittivity anomaly on high-contrast heterogeneous backgrounds using frequency difference EIT.

PubMed

Jang, J; Seo, J K

2015-06-01

This paper describes a multiple background subtraction method in frequency difference electrical impedance tomography (fdEIT) to detect an admittivity anomaly from a high-contrast background conductivity distribution. The proposed method expands the use of the conventional weighted frequency difference EIT method, which has been used limitedly to detect admittivity anomalies in a roughly homogeneous background. The proposed method can be viewed as multiple weighted difference imaging in fdEIT. Although the spatial resolutions of the output images by fdEIT are very low due to the inherent ill-posedness, numerical simulations and phantom experiments of the proposed method demonstrate its feasibility to detect anomalies. It has potential application in stroke detection in a head model, which is highly heterogeneous due to the skull.

Iterative nonlinear joint transform correlation for the detection of objects in cluttered scenes

NASA Astrophysics Data System (ADS)

Haist, Tobias; Tiziani, Hans J.

1999-03-01

An iterative correlation technique with digital image processing in the feedback loop for the detection of small objects in cluttered scenes is proposed. A scanning aperture is combined with the method in order to improve the immunity against noise and clutter. Multiple reference objects or different views of one object are processed in parallel. We demonstrate the method by detecting a noisy and distorted face in a crowd with a nonlinear joint transform correlator.

Automatic Calibration Method for Driver’s Head Orientation in Natural Driving Environment

PubMed Central

Fu, Xianping; Guan, Xiao; Peli, Eli; Liu, Hongbo; Luo, Gang

2013-01-01

Gaze tracking is crucial for studying driver’s attention, detecting fatigue, and improving driver assistance systems, but it is difficult in natural driving environments due to nonuniform and highly variable illumination and large head movements. Traditional calibrations that require subjects to follow calibrators are very cumbersome to be implemented in daily driving situations. A new automatic calibration method, based on a single camera for determining the head orientation and which utilizes the side mirrors, the rear-view mirror, the instrument board, and different zones in the windshield as calibration points, is presented in this paper. Supported by a self-learning algorithm, the system tracks the head and categorizes the head pose in 12 gaze zones based on facial features. The particle filter is used to estimate the head pose to obtain an accurate gaze zone by updating the calibration parameters. Experimental results show that, after several hours of driving, the automatic calibration method without driver’s corporation can achieve the same accuracy as a manual calibration method. The mean error of estimated eye gazes was less than 5°in day and night driving. PMID:24639620

Prologue: Reading Comprehension Is Not a Single Ability

ERIC Educational Resources Information Center

Catts, Hugh W.; Kamhi, Alan G.

2017-01-01

Purpose: In this initial article of the clinical forum on reading comprehension, we argue that reading comprehension is not a single ability that can be assessed by one or more general reading measures or taught by a small set of strategies or approaches. Method: We present evidence for a multidimensional view of reading comprehension that…

Validation of Single and Pooled Manure Drag Swabs for the Detection of Salmonella Serovar Enteritidis in Commercial Poultry Houses.

PubMed

Kinde, Hailu; Goodluck, Helen A; Pitesky, Maurice; Friend, Tom D; Campbell, James A; Hill, Ashley E

2015-12-01

Single swabs (cultured individually) are currently used in the Food and Drug Administration (FDA) official method for sampling the environment of commercial laying hens for the detection of Salmonella enterica ssp. serovar Enteritidis (Salmonella Enteritidis). The FDA has also granted provisional acceptance of the National Poultry Improvement Plan's (NPIP) Salmonella isolation and identification methodology for samples taken from table-egg layer flock environments. The NPIP method, as with the FDA method, requires single-swab culturing for the environmental sampling of laying houses for Salmonella Enteritidis. The FDA culture protocol requires a multistep culture enrichment broth, and it is more labor intensive than the NPIP culture protocol, which requires a single enrichment broth. The main objective of this study was to compare the FDA single-swab culturing protocol with that of the NPIP culturing protocol but using a four-swab pool scheme. Single and multi-laboratory testing of replicate manure drag swab sets (n  =  525 and 672, respectively) collected from a Salmonella Enteritidis-free commercial poultry flock was performed by artificially contaminating swabs with either Salmonella Enteritidis phage type 4, 8, or 13a at one of two inoculation levels: low, x¯  = 2.5 CFU (range 2.5-2.7), or medium, x¯  = 10.0 CFU (range 7.5-12). For each replicate, a single swab (inoculated), sets of two swabs (one inoculated and one uninoculated), and sets of four swabs (one inoculated and three uninoculated), testing was conducted using the FDA or NPIP culture method. For swabs inoculated with phage type 8, the NPIP method was more efficient (P < 0.05) for all swab sets at both inoculation levels than the reference method. The single swabs in the NPIP method were significantly (P < 0.05) better than four-pool swabs in detecting Salmonella Enteritidis at the lower inoculation level. In the collaborative study (n  =  13 labs) using Salmonella Enteritidis phage type 13a inoculated swabs, there was no significant difference (P > 0.05) between the FDA method (single swabs) and the pooled NPIP method (four-pool swabs). The study concludes that the pooled NPIP method is not significantly different from the FDA method for the detection of Salmonella Enteritidis in drag swabs in commercial poultry laying houses. Consequently based on the FDA's Salmonella Enteritidis rule for equivalency of different methods, the pooled NPIP method should be considered equivalent. Furthermore, the pooled NPIP method was more efficient and cost effective.

Automatic online spike sorting with singular value decomposition and fuzzy C-mean clustering

PubMed Central

2012-01-01

Background Understanding how neurons contribute to perception, motor functions and cognition requires the reliable detection of spiking activity of individual neurons during a number of different experimental conditions. An important problem in computational neuroscience is thus to develop algorithms to automatically detect and sort the spiking activity of individual neurons from extracellular recordings. While many algorithms for spike sorting exist, the problem of accurate and fast online sorting still remains a challenging issue. Results Here we present a novel software tool, called FSPS (Fuzzy SPike Sorting), which is designed to optimize: (i) fast and accurate detection, (ii) offline sorting and (iii) online classification of neuronal spikes with very limited or null human intervention. The method is based on a combination of Singular Value Decomposition for fast and highly accurate pre-processing of spike shapes, unsupervised Fuzzy C-mean, high-resolution alignment of extracted spike waveforms, optimal selection of the number of features to retain, automatic identification the number of clusters, and quantitative quality assessment of resulting clusters independent on their size. After being trained on a short testing data stream, the method can reliably perform supervised online classification and monitoring of single neuron activity. The generalized procedure has been implemented in our FSPS spike sorting software (available free for non-commercial academic applications at the address: http://www.spikesorting.com) using LabVIEW (National Instruments, USA). We evaluated the performance of our algorithm both on benchmark simulated datasets with different levels of background noise and on real extracellular recordings from premotor cortex of Macaque monkeys. The results of these tests showed an excellent accuracy in discriminating low-amplitude and overlapping spikes under strong background noise. The performance of our method is competitive with respect to other robust spike sorting algorithms. Conclusions This new software provides neuroscience laboratories with a new tool for fast and robust online classification of single neuron activity. This feature could become crucial in situations when online spike detection from multiple electrodes is paramount, such as in human clinical recordings or in brain-computer interfaces. PMID:22871125

Automatic online spike sorting with singular value decomposition and fuzzy C-mean clustering.

PubMed

Oliynyk, Andriy; Bonifazzi, Claudio; Montani, Fernando; Fadiga, Luciano

2012-08-08

Understanding how neurons contribute to perception, motor functions and cognition requires the reliable detection of spiking activity of individual neurons during a number of different experimental conditions. An important problem in computational neuroscience is thus to develop algorithms to automatically detect and sort the spiking activity of individual neurons from extracellular recordings. While many algorithms for spike sorting exist, the problem of accurate and fast online sorting still remains a challenging issue. Here we present a novel software tool, called FSPS (Fuzzy SPike Sorting), which is designed to optimize: (i) fast and accurate detection, (ii) offline sorting and (iii) online classification of neuronal spikes with very limited or null human intervention. The method is based on a combination of Singular Value Decomposition for fast and highly accurate pre-processing of spike shapes, unsupervised Fuzzy C-mean, high-resolution alignment of extracted spike waveforms, optimal selection of the number of features to retain, automatic identification the number of clusters, and quantitative quality assessment of resulting clusters independent on their size. After being trained on a short testing data stream, the method can reliably perform supervised online classification and monitoring of single neuron activity. The generalized procedure has been implemented in our FSPS spike sorting software (available free for non-commercial academic applications at the address: http://www.spikesorting.com) using LabVIEW (National Instruments, USA). We evaluated the performance of our algorithm both on benchmark simulated datasets with different levels of background noise and on real extracellular recordings from premotor cortex of Macaque monkeys. The results of these tests showed an excellent accuracy in discriminating low-amplitude and overlapping spikes under strong background noise. The performance of our method is competitive with respect to other robust spike sorting algorithms. This new software provides neuroscience laboratories with a new tool for fast and robust online classification of single neuron activity. This feature could become crucial in situations when online spike detection from multiple electrodes is paramount, such as in human clinical recordings or in brain-computer interfaces.

Situational Awareness from a Low-Cost Camera System

NASA Technical Reports Server (NTRS)

Freudinger, Lawrence C.; Ward, David; Lesage, John

2010-01-01

A method gathers scene information from a low-cost camera system. Existing surveillance systems using sufficient cameras for continuous coverage of a large field necessarily generate enormous amounts of raw data. Digitizing and channeling that data to a central computer and processing it in real time is difficult when using low-cost, commercially available components. A newly developed system is located on a combined power and data wire to form a string-of-lights camera system. Each camera is accessible through this network interface using standard TCP/IP networking protocols. The cameras more closely resemble cell-phone cameras than traditional security camera systems. Processing capabilities are built directly onto the camera backplane, which helps maintain a low cost. The low power requirements of each camera allow the creation of a single imaging system comprising over 100 cameras. Each camera has built-in processing capabilities to detect events and cooperatively share this information with neighboring cameras. The location of the event is reported to the host computer in Cartesian coordinates computed from data correlation across multiple cameras. In this way, events in the field of view can present low-bandwidth information to the host rather than high-bandwidth bitmap data constantly being generated by the cameras. This approach offers greater flexibility than conventional systems, without compromising performance through using many small, low-cost cameras with overlapping fields of view. This means significant increased viewing without ignoring surveillance areas, which can occur when pan, tilt, and zoom cameras look away. Additionally, due to the sharing of a single cable for power and data, the installation costs are lower. The technology is targeted toward 3D scene extraction and automatic target tracking for military and commercial applications. Security systems and environmental/ vehicular monitoring systems are also potential applications.

A fast and reliable readout method for quantitative analysis of surface-enhanced Raman scattering nanoprobes on chip surface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chang, Hyejin; Jeong, Sinyoung; Ko, Eunbyeol

2015-05-15

Surface-enhanced Raman scattering techniques have been widely used for bioanalysis due to its high sensitivity and multiplex capacity. However, the point-scanning method using a micro-Raman system, which is the most common method in the literature, has a disadvantage of extremely long measurement time for on-chip immunoassay adopting a large chip area of approximately 1-mm scale and confocal beam point of ca. 1-μm size. Alternative methods such as sampled spot scan with high confocality and large-area scan method with enlarged field of view and low confocality have been utilized in order to minimize the measurement time practically. In this study, wemore » analyzed the two methods in respect of signal-to-noise ratio and sampling-led signal fluctuations to obtain insights into a fast and reliable readout strategy. On this basis, we proposed a methodology for fast and reliable quantitative measurement of the whole chip area. The proposed method adopted a raster scan covering a full area of 100 μm × 100 μm region as a proof-of-concept experiment while accumulating signals in the CCD detector for single spectrum per frame. One single scan with 10 s over 100 μm × 100 μm area yielded much higher sensitivity compared to sampled spot scanning measurements and no signal fluctuations attributed to sampled spot scan. This readout method is able to serve as one of key technologies that will bring quantitative multiplexed detection and analysis into practice.« less

Abseq: Ultrahigh-throughput single cell protein profiling with droplet microfluidic barcoding.

PubMed

Shahi, Payam; Kim, Samuel C; Haliburton, John R; Gartner, Zev J; Abate, Adam R

2017-03-14

Proteins are the primary effectors of cellular function, including cellular metabolism, structural dynamics, and information processing. However, quantitative characterization of proteins at the single-cell level is challenging due to the tiny amount of protein available. Here, we present Abseq, a method to detect and quantitate proteins in single cells at ultrahigh throughput. Like flow and mass cytometry, Abseq uses specific antibodies to detect epitopes of interest; however, unlike these methods, antibodies are labeled with sequence tags that can be read out with microfluidic barcoding and DNA sequencing. We demonstrate this novel approach by characterizing surface proteins of different cell types at the single-cell level and distinguishing between the cells by their protein expression profiles. DNA-tagged antibodies provide multiple advantages for profiling proteins in single cells, including the ability to amplify low-abundance tags to make them detectable with sequencing, to use molecular indices for quantitative results, and essentially limitless multiplexing.

Abseq: Ultrahigh-throughput single cell protein profiling with droplet microfluidic barcoding

NASA Astrophysics Data System (ADS)

Shahi, Payam; Kim, Samuel C.; Haliburton, John R.; Gartner, Zev J.; Abate, Adam R.

2017-03-01

Proteins are the primary effectors of cellular function, including cellular metabolism, structural dynamics, and information processing. However, quantitative characterization of proteins at the single-cell level is challenging due to the tiny amount of protein available. Here, we present Abseq, a method to detect and quantitate proteins in single cells at ultrahigh throughput. Like flow and mass cytometry, Abseq uses specific antibodies to detect epitopes of interest; however, unlike these methods, antibodies are labeled with sequence tags that can be read out with microfluidic barcoding and DNA sequencing. We demonstrate this novel approach by characterizing surface proteins of different cell types at the single-cell level and distinguishing between the cells by their protein expression profiles. DNA-tagged antibodies provide multiple advantages for profiling proteins in single cells, including the ability to amplify low-abundance tags to make them detectable with sequencing, to use molecular indices for quantitative results, and essentially limitless multiplexing.

Abseq: Ultrahigh-throughput single cell protein profiling with droplet microfluidic barcoding

PubMed Central

Shahi, Payam; Kim, Samuel C.; Haliburton, John R.; Gartner, Zev J.; Abate, Adam R.

2017-01-01

Proteins are the primary effectors of cellular function, including cellular metabolism, structural dynamics, and information processing. However, quantitative characterization of proteins at the single-cell level is challenging due to the tiny amount of protein available. Here, we present Abseq, a method to detect and quantitate proteins in single cells at ultrahigh throughput. Like flow and mass cytometry, Abseq uses specific antibodies to detect epitopes of interest; however, unlike these methods, antibodies are labeled with sequence tags that can be read out with microfluidic barcoding and DNA sequencing. We demonstrate this novel approach by characterizing surface proteins of different cell types at the single-cell level and distinguishing between the cells by their protein expression profiles. DNA-tagged antibodies provide multiple advantages for profiling proteins in single cells, including the ability to amplify low-abundance tags to make them detectable with sequencing, to use molecular indices for quantitative results, and essentially limitless multiplexing. PMID:28290550

A rapid single-tube protocol for HAV detection by nested real-time PCR.

PubMed

Hu, Yuan; Arsov, Ivica

2014-09-01

Infections by food-borne viruses such as hepatitis A virus (HAV) and norovirus are significant public health concerns worldwide. Since food-borne viruses are rarely confirmed through direct isolation from contaminated samples, highly sensitive molecular techniques remain the methods of choice for the detection of viral genetic material. Our group has previously developed a specific nested real-time PCR (NRT-PCR) assay for HAV detection that improved overall sensitivity. Furthermore in this study, we have developed a single-tube NRT-PCR approach for HAV detection in food samples that reduces the likelihood of cross contamination between tubes during sample manipulation. HAV RNA was isolated from HAV-spiked food samples and HAV-infected cell cultures. All reactions following HAV RNA isolation, including conventional reverse transcriptase PCR, nested-PCR, and RT-PCR were performed in a single tube. Our results demonstrated that all the samples tested positive by RT-PCR and nested-PCR were also positive by a single-tube NRT-PCR. The detection limits observed for HAV-infected cell cultures and HAV-spiked green onions were 0.1 and 1 PFU, respectively. This novel method retained the specificity and robustness of the original NRT-PCR method, while greatly reducing sample manipulation, turnaround time, and the risk of carry-over contamination. Single-tube NRT-PCR thus represents a promising new tool that can potentially facilitate the detection of HAV in foods thereby improving food safety and public health.

Dissecting Transcriptional Heterogeneity in Pluripotency: Single Cell Analysis of Mouse Embryonic Stem Cells.

PubMed

Guedes, Ana M V; Henrique, Domingos; Abranches, Elsa

2016-01-01

Mouse Embryonic Stem cells (mESCs) show heterogeneous and dynamic expression of important pluripotency regulatory factors. Single-cell analysis has revealed the existence of cell-to-cell variability in the expression of individual genes in mESCs. Understanding how these heterogeneities are regulated and what their functional consequences are is crucial to obtain a more comprehensive view of the pluripotent state.In this chapter we describe how to analyze transcriptional heterogeneity by monitoring gene expression of Nanog, Oct4, and Sox2, using single-molecule RNA FISH in single mESCs grown in different cell culture medium. We describe in detail all the steps involved in the protocol, from RNA detection to image acquisition and processing, as well as exploratory data analysis.

Elementary Teachers' Views on the Creative Writing Process: An Evaluation

ERIC Educational Resources Information Center

Akkaya, Nevin

2014-01-01

The goal of this study is to discover and evaluate both the areas of personal interest and the views of 4th and 5th grade classroom teachers regarding the creative writing process. In this study, one of the qualitative study methods, state study, and related to this, single state design which refers to the whole has been chosen. Research was…

Regulation, consultation and divergent community views: the case of access to ART by lesbian and single women.

PubMed

Cannold, Leslie; Gillam, Lynn

2002-05-01

In the many countries which have some form of regulation of ART, a public consultation of some sort is a frequent feature of either the process leading up to regulation or of the regulatory mechanism itself. Not surprisingly, widely divergent views on the moral and political acceptability of ART are expressed during such consultations. And while such diversity of opinion is to be expected, and some even argue welcomed, in pluralist liberal democratic societies, it is often unclear how these divergent community views are and ought to be fed into the opinion-forming and decision-making processes of governments or the bodies that advise them. This article discusses first why regulation of ART may be justified, even when there is radical moral disagreement in the community, and why public consultations should play a central role in the work that advisory bodies undertake in making regulatory recommendations to government. Then, it both proposes and justifies a method for dealing with the contradictory moral views expressed by interested parties during the consultation process. To illustrate this method, the example of the attempt by single and lesbian women to access donor insemination services and ART is used.

Supercontinuum Fourier transform spectrometry with balanced detection on a single photodiode

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goncharov, Vasily V.; Hall, Gregory E., E-mail: gehall@bnl.gov

We demonstrate a method of combining a supercontinuum light source with a commercial Fourier transform spectrometer, using a novel approach to dual-beam balanced detection, implemented with phase-sensitive detection on a single light detector. A 40 dB reduction in the relative intensity noise is achieved for broadband light, analogous to conventional balanced detection methods using two matched photodetectors. Unlike conventional balanced detection, however, this method exploits the time structure of the broadband source to interleave signal and reference pulse trains in the time domain, recording the broadband differential signal at the fundamental pulse repetition frequency of the supercontinuum. The method ismore » capable of real-time correction for instability in the supercontinuum spectral structure over a broad range of wavelengths and is compatible with commercially designed spectrometers. A proof-of-principle experimental setup is demonstrated for weak absorption in the 1500-1600 nm region.« less

Single-molecule detection of proteins with antigen-antibody interaction using resistive-pulse sensing of submicron latex particles

NASA Astrophysics Data System (ADS)

Takakura, T.; Yanagi, I.; Goto, Y.; Ishige, Y.; Kohara, Y.

2016-03-01

We developed a resistive-pulse sensor with a solid-state pore and measured the latex agglutination of submicron particles induced by antigen-antibody interaction for single-molecule detection of proteins. We fabricated the pore based on numerical simulation to clearly distinguish between monomer and dimer latex particles. By measuring single dimers agglutinated in the single-molecule regime, we detected single human alpha-fetoprotein molecules. Adjusting the initial particle concentration improves the limit of detection (LOD) to 95 fmol/l. We established a theoretical model of the LOD by combining the reaction kinetics and the counting statistics to explain the effect of initial particle concentration on the LOD. The theoretical model shows how to improve the LOD quantitatively. The single-molecule detection studied here indicates the feasibility of implementing a highly sensitive immunoassay by a simple measurement method using resistive-pulse sensing.

Nanobarcoding for improved nanoparticle detection in nanomedical biodistribution studies

NASA Astrophysics Data System (ADS)

Eustaquio, Trisha

Determination of the fate of nanoparticles (NPs) in a biological system, or NP biodistribution, is critical in evaluating a NP formulation for nanomedicine. Unlike small-molecule drugs, NPs impose unique challenges in the design of appropriate biodistribution studies due to their small size and subsequent detection signal. Current methods to determine NP biodistribution are greatly inadequate due to their limited detection thresholds. There is an overwhelming need for a sensitive and efficient imaging-based method that can (1) detect and measure small numbers of NPs of various types, ideally single NPs, (2) associate preferential NP uptake with histological cell type by preserving spatial information in samples, and (3) allow for relatively quick and accurate NP detection in in vitro (and possibly ex vivo) samples for comprehensive NP biodistribution studies. Herein, a novel method for improved NP detection is proposed, coined "nanobarcoding." Nanobarcoding utilizes a non-endogenous oligonucleotide, or "nanobarcode" (NB), conjugated to the NP surface to amplify the detection signal from a single NP via in situ polymerase chain reaction (ISPCR), and this signal amplification will facilitate rapid and precise detection of single NPs inside cells over large areas of sample such that more sophisticated studies can be performed on the NP-positive subpopulation. Moreover, nanobarcoding has the potential to be applied to the detection of more than one NP type to study the effects of physicochemical properties, targeting mechanisms, and route of entry on NP biodistribution. The nanobarcoding method was validated in vitro using NB-functionalized superparamagnetic iron oxide NPs (NB-SPIONs) as the model NP type for improved NP detection inside HeLa human cervical cancer cells, a cell line commonly used for ISPCR-mediated detection of human papilloma virus (HPV). Nanotoxicity effects of NB-SPIONs were also evaluated at the single-cell level using LEAP (Laser-Enabled Analysis and Processing, Intrexon, San Diego, CA), and NB-SPIONs were found to be less toxic than its precursor, carboxylated SPIONs (COOH-SPIONs).

Irradiation influence on the detection of genetic-modified soybeans

NASA Astrophysics Data System (ADS)

Villavicencio, A. L. C. H.; Araújo, M. M.; Baldasso, J. G.; Aquino, S.; Konietzny, U.; Greiner, R.

2004-09-01

Three soybean varieties were analyzed to evaluate the irradiation influence on the detection of genetic modification. Samples were treated in a 60Co facility at dose levels of 0, 500, 800, and 1000Gy. The seeds were at first analyzed by Comet Assay as a rapid screening irradiation detection method. Secondly, germination test was performed to detect the viability of irradiated soybeans. Finally, because of its high sensitivity, its specificity and rapidity the polimerase chain reaction was the method applied for genetic modified organism detection. The analysis of DNA by the single technique of microgel electrophoresis of single cells (DNA Comet Assay) showed that DNA damage increased with increasing radiation doses. No negative influence of irradiation on the genetic modification detection was found.

Mouse blood vessel imaging by in-line x-ray phase-contrast imaging

NASA Astrophysics Data System (ADS)

Zhang, Xi; Liu, Xiao-Song; Yang, Xin-Rong; Chen, Shao-Liang; Zhu, Pei-Ping; Yuan, Qing-Xi

2008-10-01

It is virtually impossible to observe blood vessels by conventional x-ray imaging techniques without using contrast agents. In addition, such x-ray systems are typically incapable of detecting vessels with diameters less than 200 µm. Here we show that vessels as small as 30 µm could be detected using in-line phase-contrast x-ray imaging without the use of contrast agents. Image quality was greatly improved by replacing resident blood with physiological saline. Furthermore, an entire branch of the portal vein from the main axial portal vein to the eighth generation of branching could be captured in a single phase-contrast image. Prior to our work, detection of 30 µm diameter blood vessels could only be achieved using x-ray interferometry, which requires sophisticated x-ray optics. Our results thus demonstrate that in-line phase-contrast x-ray imaging, using physiological saline as a contrast agent, provides an alternative to the interferometric method that can be much more easily implemented and also offers the advantage of a larger field of view. A possible application of this methodology is in animal tumor models, where it can be used to observe tumor angiogenesis and the treatment effects of antineoplastic agents.

Pre-impact fall detection system using dynamic threshold and 3D bounding box

NASA Astrophysics Data System (ADS)

Otanasap, Nuth; Boonbrahm, Poonpong

2017-02-01

Fall prevention and detection system have to subjugate many challenges in order to develop an efficient those system. Some of the difficult problems are obtrusion, occlusion and overlay in vision based system. Other associated issues are privacy, cost, noise, computation complexity and definition of threshold values. Estimating human motion using vision based usually involves with partial overlay, caused either by direction of view point between objects or body parts and camera, and these issues have to be taken into consideration. This paper proposes the use of dynamic threshold based and bounding box posture analysis method with multiple Kinect cameras setting for human posture analysis and fall detection. The proposed work only uses two Kinect cameras for acquiring distributed values and differentiating activities between normal and falls. If the peak value of head velocity is greater than the dynamic threshold value, bounding box posture analysis will be used to confirm fall occurrence. Furthermore, information captured by multiple Kinect placed in right angle will address the skeleton overlay problem due to single Kinect. This work contributes on the fusion of multiple Kinect based skeletons, based on dynamic threshold and bounding box posture analysis which is the only research work reported so far.

Easy and Fast Reconstruction of a 3D Avatar with an RGB-D Sensor.

PubMed

Mao, Aihua; Zhang, Hong; Liu, Yuxin; Zheng, Yinglong; Li, Guiqing; Han, Guoqiang

2017-05-12

This paper proposes a new easy and fast 3D avatar reconstruction method using an RGB-D sensor. Users can easily implement human body scanning and modeling just with a personal computer and a single RGB-D sensor such as a Microsoft Kinect within a small workspace in their home or office. To make the reconstruction of 3D avatars easy and fast, a new data capture strategy is proposed for efficient human body scanning, which captures only 18 frames from six views with a close scanning distance to fully cover the body; meanwhile, efficient alignment algorithms are presented to locally align the data frames in the single view and then globally align them in multi-views based on pairwise correspondence. In this method, we do not adopt shape priors or subdivision tools to synthesize the model, which helps to reduce modeling complexity. Experimental results indicate that this method can obtain accurate reconstructed 3D avatar models, and the running performance is faster than that of similar work. This research offers a useful tool for the manufacturers to quickly and economically create 3D avatars for products design, entertainment and online shopping.

A rapid and efficient newly established method to detect COL1A1-PDGFB gene fusion in dermatofibrosarcoma protuberans

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yokoyama, Yoko; Shimizu, Akira; Okada, Etsuko

Highlights: Black-Right-Pointing-Pointer We developed new method to rapidly identify COL1A1-PDGFB fusion in DFSP. Black-Right-Pointing-Pointer New PCR method using a single primer pair detected COL1A1-PDGFB fusion in DFSP. Black-Right-Pointing-Pointer This is the first report of DFSP with a novel COL1A1 breakpoint in exon 5. -- Abstract: The detection of fusion transcripts of the collagen type 1{alpha}1 (COL1A1) and platelet-derived growth factor-BB (PDGFB) genes by genetic analysis has recognized as a reliable and valuable molecular tool for the diagnosis of dermatofibrosarcoma protuberans (DFSP). To detect the COL1A1-PDGFB fusion, almost previous reports performed reverse transcription polymerase chain reaction (RT-PCR) using multiplex forward primersmore » from COL1A1. However, it has possible technical difficulties with respect to the handling of multiple primers and reagents in the procedure. The objective of this study is to establish a rapid, easy, and efficient one-step method of PCR using only a single primer pair to detect the fusion transcripts of the COL1A1 and PDGFB in DFSP. To validate new method, we compared the results of RT-PCR in five patients of DFSP between the previous method using multiplex primers and our established one-step RT-PCR using a single primer pair. In all cases of DFSP, the COL1A1-PDGFB fusion was detected by both previous method and newly established one-step PCR. Importantly, we detected a novel COL1A1 breakpoint in exon 5. The newly developed method is valuable to rapidly identify COL1A1-PDGFB fusion transcripts in DFSP.« less

Ship Detection Based on Multiple Features in Random Forest Model for Hyperspectral Images

NASA Astrophysics Data System (ADS)

Li, N.; Ding, L.; Zhao, H.; Shi, J.; Wang, D.; Gong, X.

2018-04-01

A novel method for detecting ships which aim to make full use of both the spatial and spectral information from hyperspectral images is proposed. Firstly, the band which is high signal-noise ratio in the range of near infrared or short-wave infrared spectrum, is used to segment land and sea on Otsu threshold segmentation method. Secondly, multiple features that include spectral and texture features are extracted from hyperspectral images. Principal components analysis (PCA) is used to extract spectral features, the Grey Level Co-occurrence Matrix (GLCM) is used to extract texture features. Finally, Random Forest (RF) model is introduced to detect ships based on the extracted features. To illustrate the effectiveness of the method, we carry out experiments over the EO-1 data by comparing single feature and different multiple features. Compared with the traditional single feature method and Support Vector Machine (SVM) model, the proposed method can stably achieve the target detection of ships under complex background and can effectively improve the detection accuracy of ships.

Image enhancement of real-time television to benefit the visually impaired.

PubMed

Wolffsohn, James S; Mukhopadhyay, Ditipriya; Rubinstein, Martin

2007-09-01

To examine the use of real-time, generic edge detection, image processing techniques to enhance the television viewing of the visually impaired. Prospective, clinical experimental study. One hundred and two sequential visually impaired (average age 73.8 +/- 14.8 years; 59% female) in a single center optimized a dynamic television image with respect to edge detection filter (Prewitt, Sobel, or the two combined), color (red, green, blue, or white), and intensity (one to 15 times) of the overlaid edges. They then rated the original television footage compared with a black-and-white image displaying the edges detected and the original television image with the detected edges overlaid in the chosen color and at the intensity selected. Footage of news, an advertisement, and the end of program credits were subjectively assessed in a random order. A Prewitt filter was preferred (44%) compared with the Sobel filter (27%) or a combination of the two (28%). Green and white were equally popular for displaying the detected edges (32%), with blue (22%) and red (14%) less so. The average preferred edge intensity was 3.5 +/- 1.7 times. The image-enhanced television was significantly preferred to the original (P < .001), which in turn was preferred to viewing the detected edges alone (P < .001) for each of the footage clips. Preference was not dependent on the condition causing visual impairment. Seventy percent were definitely willing to buy a set-top box that could achieve these effects for a reasonable price. Simple generic edge detection image enhancement options can be performed on television in real-time and significantly enhance the viewing of the visually impaired.

Multiview face detection based on position estimation over multicamera surveillance system

NASA Astrophysics Data System (ADS)

Huang, Ching-chun; Chou, Jay; Shiu, Jia-Hou; Wang, Sheng-Jyh

2012-02-01

In this paper, we propose a multi-view face detection system that locates head positions and indicates the direction of each face in 3-D space over a multi-camera surveillance system. To locate 3-D head positions, conventional methods relied on face detection in 2-D images and projected the face regions back to 3-D space for correspondence. However, the inevitable false face detection and rejection usually degrades the system performance. Instead, our system searches for the heads and face directions over the 3-D space using a sliding cube. Each searched 3-D cube is projected onto the 2-D camera views to determine the existence and direction of human faces. Moreover, a pre-process to estimate the locations of candidate targets is illustrated to speed-up the searching process over the 3-D space. In summary, our proposed method can efficiently fuse multi-camera information and suppress the ambiguity caused by detection errors. Our evaluation shows that the proposed approach can efficiently indicate the head position and face direction on real video sequences even under serious occlusion.

Multimodal autofluorescence detection of cancer: from single cells to living organism

NASA Astrophysics Data System (ADS)

Horilova, J.; Cunderlikova, B.; Cagalinec, M.; Chorvat, D.; Marcek Chorvatova, A.

2018-02-01

Multimodal optical imaging of suspected tissues is showing to be a promising method for distinguishing suspected cancerous tissues from healthy ones. In particular, the combination of steady-state spectroscopic methods with timeresolved fluorescence provides more precise insight into native metabolism when focused on tissue autofluorescence. Cancer is linked to specific metabolic remodelation detectable spectroscopically. In this work, we evaluate possibilities and limitations of multimodal optical cancer detection in single cells, collagen-based 3D cell cultures and in living organisms (whole mice), as a representation of gradually increasing complexity of model systems.

begin{center} MUSIC Algorithms for Rebar Detection

NASA Astrophysics Data System (ADS)

Leone, G.; Solimene, R.

2012-04-01

In this contribution we consider the problem of detecting and localizing small cross section, with respect to the wavelength, scatterers from their scattered field once a known incident field interrogated the scene where they reside. A pertinent applicative context is rebar detection within concrete pillar. For such a case, scatterers to be detected are represented by rebars themselves or by voids due to their lacking. In both cases, as scatterers have point-like support, a subspace projection method can be conveniently exploited [1]. However, as the field scattered by rebars is stronger than the one due to voids, it is expected that the latter can be difficult to be detected. In order to circumvent this problem, in this contribution we adopt a two-step MUltiple SIgnal Classification (MUSIC) detection algorithm. In particular, the first stage aims at detecting rebars. Once rebar are detected, their positions are exploited to update the Green's function and then a further detection scheme is run to locate voids. However, in this second case, background medium encompasses also the rabars. The analysis is conducted numerically for a simplified two-dimensional scalar scattering geometry. More in detail, as is usual in MUSIC algorithm, a multi-view/multi-static single-frequency configuration is considered [2]. Baratonia, G. Leone, R. Pierri, R. Solimene, "Fault Detection in Grid Scattering by a Time-Reversal MUSIC Approach," Porc. Of ICEAA 2011, Turin, 2011. E. A. Marengo, F. K. Gruber, "Subspace-Based Localization and Inverse Scattering of Multiply Scattering Point Targets," EURASIP Journal on Advances in Signal Processing, 2007, Article ID 17342, 16 pages (2007).

The Chandra Source Catalog: Source Variability

NASA Astrophysics Data System (ADS)

Nowak, Michael; Rots, A. H.; McCollough, M. L.; Primini, F. A.; Glotfelty, K. J.; Bonaventura, N. R.; Chen, J. C.; Davis, J. E.; Doe, S. M.; Evans, J. D.; Fabbiano, G.; Galle, E.; Gibbs, D. G.; Grier, J. D.; Hain, R.; Hall, D. M.; Harbo, P. N.; He, X.; Houck, J. C.; Karovska, M.; Lauer, J.; McDowell, J. C.; Miller, J. B.; Mitschang, A. W.; Morgan, D. L.; Nichols, J. S.; Plummer, D. A.; Refsdal, B. L.; Siemiginowska, A. L.; Sundheim, B. A.; Tibbetts, M. S.; Van Stone, D. W.; Winkelman, S. L.; Zografou, P.

2009-01-01

The Chandra Source Catalog (CSC) contains fields of view that have been studied with individual, uninterrupted observations that span integration times ranging from 1 ksec to 160 ksec, and a large number of which have received (multiple) repeat observations days to years later. The CSC thus offers an unprecedented look at the variability of the X-ray sky over a broad range of time scales, and across a wide diversity of variable X-ray sources: stars in the local galactic neighborhood, galactic and extragalactic X-ray binaries, Active Galactic Nuclei, etc. Here we describe the methods used to identify and quantify source variability within a single observation, and the methods used to assess the variability of a source when detected in multiple, individual observations. Three tests are used to detect source variability within a single observation: the Kolmogorov-Smirnov test and its variant, the Kuiper test, and a Bayesian approach originally suggested by Gregory and Loredo. The latter test not only provides an indicator of variability, but is also used to create a best estimate of the variable lightcurve shape. We assess the performance of these tests via simulation of statistically stationary, variable processes with arbitrary input power spectral densities (here we concentrate on results of red noise simulations) at variety of mean count rates and fractional root mean square variabilities relevant to CSC sources. We also assess the false positive rate via simulations of constant sources whose sole source of fluctuation is Poisson noise. We compare these simulations to a preliminary assessment of the variability found in real CSC sources, and estimate the variability sensitivities of the CSC.

The Chandra Source Catalog: Source Variability

NASA Astrophysics Data System (ADS)

Nowak, Michael; Rots, A. H.; McCollough, M. L.; Primini, F. A.; Glotfelty, K. J.; Bonaventura, N. R.; Chen, J. C.; Davis, J. E.; Doe, S. M.; Evans, J. D.; Evans, I.; Fabbiano, G.; Galle, E. C.; Gibbs, D. G., II; Grier, J. D.; Hain, R.; Hall, D. M.; Harbo, P. N.; He, X.; Houck, J. C.; Karovska, M.; Lauer, J.; McDowell, J. C.; Miller, J. B.; Mitschang, A. W.; Morgan, D. L.; Nichols, J. S.; Plummer, D. A.; Refsdal, B. L.; Siemiginowska, A. L.; Sundheim, B. A.; Tibbetts, M. S.; van Stone, D. W.; Winkelman, S. L.; Zografou, P.

2009-09-01

The Chandra Source Catalog (CSC) contains fields of view that have been studied with individual, uninterrupted observations that span integration times ranging from 1 ksec to 160 ksec, and a large number of which have received (multiple) repeat observations days to years later. The CSC thus offers an unprecedented look at the variability of the X-ray sky over a broad range of time scales, and across a wide diversity of variable X-ray sources: stars in the local galactic neighborhood, galactic and extragalactic X-ray binaries, Active Galactic Nuclei, etc. Here we describe the methods used to identify and quantify source variability within a single observation, and the methods used to assess the variability of a source when detected in multiple, individual observations. Three tests are used to detect source variability within a single observation: the Kolmogorov-Smirnov test and its variant, the Kuiper test, and a Bayesian approach originally suggested by Gregory and Loredo. The latter test not only provides an indicator of variability, but is also used to create a best estimate of the variable lightcurve shape. We assess the performance of these tests via simulation of statistically stationary, variable processes with arbitrary input power spectral densities (here we concentrate on results of red noise simulations) at variety of mean count rates and fractional root mean square variabilities relevant to CSC sources. We also assess the false positive rate via simulations of constant sources whose sole source of fluctuation is Poisson noise. We compare these simulations to an assessment of the variability found in real CSC sources, and estimate the variability sensitivities of the CSC.

Recent behavioral history modifies coupling between cell activity and Arc gene transcription in hippocampal CA1 neurons.

PubMed

Guzowski, John F; Miyashita, Teiko; Chawla, Monica K; Sanderson, Jennifer; Maes, Levi I; Houston, Frank P; Lipa, Peter; McNaughton, Bruce L; Worley, Paul F; Barnes, Carol A

2006-01-24

The ability of neurons to alter their transcriptional programs in response to synaptic input is of fundamental importance to the neuroplastic mechanisms underlying learning and memory. Because of technical limitations of conventional gene detection methods, the current view of activity-dependent neural transcription derives from experiments in which neurons are assumed quiescent until a signaling stimulus is given. The present study was designed to move beyond this static model by examining how earlier episodes of neural activity influence transcription of the immediate-early gene Arc. Using a sensitive FISH method that detects primary transcript at genomic alleles, the proportion of hippocampal CA1 neurons that activate transcription of Arc RNA was constant at approximately 40% in response to both a single novel exploration session and daily sessions repeated over 9 days. This proportion is similar to the percentage of active neurons defined electrophysiologically. However, this close correspondence was disrupted in rats exposed briefly, but repeatedly, to the same environment within a single day. Arc transcription in CA1 neurons declined dramatically after as few as four 5-min sessions, despite stable electrophysiological activity during all sessions. Additional experiments indicate that the decrement in Arc transcription occurred at the cellular, rather than synaptic level, and was not simply linked to habituation to novelty. Thus, the neural genomic response is governed by recent, but not remote, cell firing history in the behaving animal. This state-dependence of neuronal transcriptional coupling provides a mechanism of metaplasticity and may regulate capacity for synaptic modification in neural networks.

Commentary on "Reading Comprehension Is Not a Single Ability": Implications for Child Language Intervention

ERIC Educational Resources Information Center

Ukrainetz, Teresa A.

2017-01-01

Purpose: This commentary responds to the implications for child language intervention of Catts and Kamhi's (2017) call to move from viewing reading comprehension as a single ability to recognizing it as a complex constellation of reader, text, and activity. Method: Reading comprehension, as Catts and Kamhi explain, is very complicated. In this…

miRNA detection at single-cell resolution using microfluidic LNA flow-FISH

DOE PAGES

Wu, Meiye; Piccini, Matthew Ernest; Koh, Chung -Yan; ...

2014-08-20

Flow cytometry in combination with fluorescent in situ hybridization (flow-FISH) is a powerful technique that can be utilized to rapidly detect nucleic acids at single-cell resolution without the need for homogenization or nucleic acid extraction. Here, we describe a microfluidic-based method which enables the detection of microRNAs or miRNAs in single intact cells by flow-FISH using locked nucleic acid (LNA)-containing probes. Our method can be applied to all RNA species including mRNA and small noncoding RNA and is suitable for multiplexing with protein immunostaining in the same cell. For demonstration of our method, this chapter details the detection of miR155more » and CD69 protein in PMA and ionomycin-stimulated Jurkat cells. Here, we also include instructions on how to set up a microfluidic chip sample preparation station to prepare cells for imaging and analysis on a commercial flow cytometer or a custom-built micro-flow cytometer.« less

Electrochemical detection of single molecules using abiotic nanopores having electrically tunable dimensions

DOEpatents

Sansinena, Jose-Maria [Los Alamos, NM; Redondo, Antonio [Los Alamos, NM; Olazabal, Virginia [Los Alamos, NM; Hoffbauer, Mark A [Los Alamos, NM; Akhadov, Elshan A [Los Alamos, NM

2009-12-29

A barrier structure for use in an electrochemical stochastic membrane sensor for single molecule detection. The sensor is based upon inorganic nanopores having electrically tunable dimensions. The inorganic nanopores are formed from inorganic materials and an electrically conductive polymer. Methods of making the barrier structure and sensing single molecules using the barrier structure are also described.

Electrochemical detection of single molecules using abiotic nanopores having electrically tunable dimensions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sansinena, Jose-Maria; Redondo, Antonio; Olazabal, Virginia

2017-09-12

A barrier structure for use in an electrochemical stochastic membrane sensor for single molecule detection. The sensor is based upon inorganic nanopores having electrically tunable dimensions. The inorganic nanopores are formed from inorganic materials and an electrically conductive polymer. Methods of making the barrier structure and sensing single molecules using the barrier structure are also described.

Electrochemical detection of single molecules using abiotic nanopores having electrically tunable dimensions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sansinena, Jose-Maria; Redondo, Antonio; Olazabal, Virginia

2017-07-18

A barrier structure for use in an electrochemical stochastic membrane sensor for single molecule detection. The sensor is based upon inorganic nanopores having electrically tunable dimensions. The inorganic nanopores are formed from inorganic materials and an electrically conductive polymer. Methods of making the barrier structure and sensing single molecules using the barrier structure are also described.

Electrochemical detection of single molecules using abiotic nanopores having electrically tunable dimensions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sansinena, Jose-Maria; Redondo, Antonio; Olazabal, Virginia

A barrier structure for use in an electrochemical stochastic membrane sensor for single molecule detection. The sensor is based upon inorganic nanopores having electrically tunable dimensions. The inorganic nanopores are formed from inorganic materials and an electrically conductive polymer. Methods of making the barrier structure and sensing single molecules using the barrier structure are also described.

Detection of kinetic change points in piece-wise linear single molecule motion

NASA Astrophysics Data System (ADS)

Hill, Flynn R.; van Oijen, Antoine M.; Duderstadt, Karl E.

2018-03-01

Single-molecule approaches present a powerful way to obtain detailed kinetic information at the molecular level. However, the identification of small rate changes is often hindered by the considerable noise present in such single-molecule kinetic data. We present a general method to detect such kinetic change points in trajectories of motion of processive single molecules having Gaussian noise, with a minimum number of parameters and without the need of an assumed kinetic model beyond piece-wise linearity of motion. Kinetic change points are detected using a likelihood ratio test in which the probability of no change is compared to the probability of a change occurring, given the experimental noise. A predetermined confidence interval minimizes the occurrence of false detections. Applying the method recursively to all sub-regions of a single molecule trajectory ensures that all kinetic change points are located. The algorithm presented allows rigorous and quantitative determination of kinetic change points in noisy single molecule observations without the need for filtering or binning, which reduce temporal resolution and obscure dynamics. The statistical framework for the approach and implementation details are discussed. The detection power of the algorithm is assessed using simulations with both single kinetic changes and multiple kinetic changes that typically arise in observations of single-molecule DNA-replication reactions. Implementations of the algorithm are provided in ImageJ plugin format written in Java and in the Julia language for numeric computing, with accompanying Jupyter Notebooks to allow reproduction of the analysis presented here.

An efficient heuristic method for dynamic portfolio selection problem under transaction costs and uncertain conditions

NASA Astrophysics Data System (ADS)

Najafi, Amir Abbas; Pourahmadi, Zahra

2016-04-01

Selecting the optimal combination of assets in a portfolio is one of the most important decisions in investment management. As investment is a long term concept, looking into a portfolio optimization problem just in a single period may cause loss of some opportunities that could be exploited in a long term view. Hence, it is tried to extend the problem from single to multi-period model. We include trading costs and uncertain conditions to this model which made it more realistic and complex. Hence, we propose an efficient heuristic method to tackle this problem. The efficiency of the method is examined and compared with the results of the rolling single-period optimization and the buy and hold method which shows the superiority of the proposed method.

An algorithm to estimate building heights from Google street-view imagery using single view metrology across a representational state transfer system

NASA Astrophysics Data System (ADS)

Díaz, Elkin; Arguello, Henry

2016-05-01

Urban ecosystem studies require monitoring, controlling and planning to analyze building density, urban density, urban planning, atmospheric modeling and land use. In urban planning, there are many methods for building height estimation using optical remote sensing images. These methods however, highly depend on sun illumination and cloud-free weather. In contrast, high resolution synthetic aperture radar provides images independent from daytime and weather conditions, although, these images rely on special hardware and expensive acquisition. Most of the biggest cities around the world have been photographed by Google street view under different conditions. Thus, thousands of images from the principal streets of a city can be accessed online. The availability of this and similar rich city imagery such as StreetSide from Microsoft, represents huge opportunities in computer vision because these images can be used as input in many applications such as 3D modeling, segmentation, recognition and stereo correspondence. This paper proposes a novel algorithm to estimate building heights using public Google Street-View imagery. The objective of this work is to obtain thousands of geo-referenced images from Google Street-View using a representational state transfer system, and estimate their average height using single view metrology. Furthermore, the resulting measurements and image metadata are used to derive a layer of heights in a Google map available online. The experimental results show that the proposed algorithm can estimate an accurate average building height map of thousands of images using Google Street-View Imagery of any city.

Holographic elements and curved slit used to enlarge field of view in rocket detection system

NASA Astrophysics Data System (ADS)

Breton, Mélanie; Fortin, Jean; Lessard, Roger A.; Châteauneuf, Marc

2006-09-01

Rocket detection over a wide field of view is an important issue in the protection of light armored vehicle. Traditionally, the detection occurs in UV band, but recent studies have shown the existence of significant emission peaks in the visible and near infrared at rocket launch time. The use of the visible region is interesting in order to reduce the weight and cost of systems. Current methods to detect those specific peaks involve use of interferometric filters. However, they fail to combine wide angle with wavelength selectivity. A linear array of volume holographic elements combined with a curved exit slit is proposed for the development of a wide field of view sensor for the detection of solid propellant motor launch flash. The sensor is envisaged to trigger an active protection system. On the basis of geometric theory, a system has been designed. It consists of a collector, a linear array of holographic elements, a curved slit and a detector. The collector is an off-axis parabolic mirror. Holographic elements are recorded subdividing a hologram film in regions, each individually exposed with a different incidence angle. All regions have a common diffraction angle. The incident angle determines the instantaneous field of view of the elements. The volume hologram performs the function of separating and focusing the diffracted beam on an image plane to achieve wavelength filtering. Conical diffraction property is used to enlarge the field of view in elevation. A curved slit was designed to correspond to oblique incidence of the holographic linear array. It is situated at the image plane and filters the diffracted spectrum toward the sensor. The field of view of the design was calculated to be 34 degrees. This was validated by a prototype tested during a field trial. Results are presented and analyzed. The system succeeded in detecting the rocket launch flash at desired fields of view.

Sensitivity of standing radiographs to detect knee arthritis: a systematic review of Level I studies.

PubMed

Duncan, Stephen T; Khazzam, Michael S; Burnham, Jeremy M; Spindler, Kurt P; Dunn, Warren R; Wright, Rick W

2015-02-01

The purpose of this study was to perform a systematic review of the available literature to define the level of quality evidence for determining the sensitivity and specificity of different radiographic views in detecting knee osteoarthritis and to determine the impact of different grading systems on the ability to detect knee osteoarthritis. A systematic review of the literature was conducted to identify studies that evaluated the standing anteroposterior (AP) and 45° posteroanterior (PA) views for tibiofemoral and patellofemoral arthritis and those comparing the use of the Kellgren-Lawrence versus the joint space narrowing (JSN) radiographic grading systems using arthroscopy as the gold standard. A comprehensive search of PubMed, Scopus, CINAHL, the Cochrane Database, Clinicaltrial.gov, and EMBASE was performed using the keywords "osteoarthritis," "knee," "x-ray," "sensitivity," and "arthroscopy." Six studies were included in the evaluation. The 45° flexion PA view showed a higher sensitivity than the standing AP view for detecting severe arthritis involving either the medial or lateral tibiofemoral compartment. There was no difference in the specificities for the 2 views. The direct comparison of the Kellgren-Lawrence and the JSN radiographic grading systems found no clinical difference between the 2 systems regarding the sensitivities, although the specificity was greater for the JSN system. The ability to detect knee osteoarthritis continues to be difficult without using advanced imaging. However, as an inexpensive screening tool, the 45° flexion PA view is more sensitive than the standing AP view to detect severe tibiofemoral osteoarthritis. When evaluating the radiograph for severe osteoarthritis using either the Kellgren-Lawrence or JSN grading system, there is no clinical difference in the sensitivity between the 2 methods; however, the JSN may be more specific for ruling in severe osteoarthritis in the medial compartment. Level I, systematic review of Level I studies. Copyright © 2015 Arthroscopy Association of North America. Published by Elsevier Inc. All rights reserved.

RNA-templated single-base mutation detection based on T4 DNA ligase and reverse molecular beacon.

PubMed

Tang, Hongxing; Yang, Xiaohai; Wang, Kemin; Tan, Weihong; Li, Huimin; He, Lifang; Liu, Bin

2008-06-15

A novel RNA-templated single-base mutation detection method based on T4 DNA ligase and reverse molecular beacon (rMB) has been developed and successfully applied to identification of single-base mutation in codon 273 of the p53 gene. The discrimination was carried out using allele-specific primers, which flanked the variable position in the target RNA and was ligated using T4 DNA ligase only when the primers perfectly matched the RNA template. The allele-specific primers also carried complementary stem structures with end-labels (fluorophore TAMRA, quencher DABCYL), which formed a molecular beacon after RNase H digestion. One-base mismatch can be discriminated by analyzing the change of fluorescence intensity before and after RNase H digestion. This method has several advantages for practical applications, such as direct discrimination of single-base mismatch of the RNA extracted from cell; no requirement of PCR amplification; performance of homogeneous detection; and easily design of detection probes.

Wavelength modulation spectroscopy--digital detection of gas absorption harmonics based on Fourier analysis.

PubMed

Mei, Liang; Svanberg, Sune

2015-03-20

This work presents a detailed study of the theoretical aspects of the Fourier analysis method, which has been utilized for gas absorption harmonic detection in wavelength modulation spectroscopy (WMS). The lock-in detection of the harmonic signal is accomplished by studying the phase term of the inverse Fourier transform of the Fourier spectrum that corresponds to the harmonic signal. The mathematics and the corresponding simulation results are given for each procedure when applying the Fourier analysis method. The present work provides a detailed view of the WMS technique when applying the Fourier analysis method.

Language Practitioners' Reflections on Method-Based and Post-Method Pedagogies

ERIC Educational Resources Information Center

Soomro, Abdul Fattah; Almalki, Mansoor S.

2017-01-01

Method-based pedagogies are commonly applied in teaching English as a foreign language all over the world. However, in the last quarter of the 20th century, the concept of such pedagogies based on the application of a single best method in EFL started to be viewed with concerns by some scholars. In response to the growing concern against the…

Life detection systems.

NASA Technical Reports Server (NTRS)

Mitz, M. A.

1972-01-01

Some promising newer approaches for detecting microorganisms are discussed, giving particular attention to the integration of different methods into a single instrument. Life detection methods may be divided into biological, chemical, and cytological methods. Biological methods are based on the biological properties of assimilation, metabolism, and growth. Devices for the detection of organic materials are considered, taking into account an instrument which volatilizes, separates, and analyzes a sample sequentially. Other instrumental systems described make use of a microscope and the cytochemical staining principle.

Single Locked Nucleic Acid-Enhanced Nanopore Genetic Discrimination of Pathogenic Serotypes and Cancer Driver Mutations.

PubMed

Tian, Kai; Chen, Xiaowei; Luan, Binquan; Singh, Prashant; Yang, Zhiyu; Gates, Kent S; Lin, Mengshi; Mustapha, Azlin; Gu, Li-Qun

2018-05-22

Accurate and rapid detection of single-nucleotide polymorphism (SNP) in pathogenic mutants is crucial for many fields such as food safety regulation and disease diagnostics. Current detection methods involve laborious sample preparations and expensive characterizations. Here, we investigated a single locked nucleic acid (LNA) approach, facilitated by a nanopore single-molecule sensor, to accurately determine SNPs for detection of Shiga toxin producing Escherichia coli (STEC) serotype O157:H7, and cancer-derived EGFR L858R and KRAS G12D driver mutations. Current LNA applications that require incorporation and optimization of multiple LNA nucleotides. But we found that in the nanopore system, a single LNA introduced in the probe is sufficient to enhance the SNP discrimination capability by over 10-fold, allowing accurate detection of the pathogenic mutant DNA mixed in a large amount of the wild-type DNA. Importantly, the molecular mechanistic study suggests that such a significant improvement is due to the effect of the single-LNA that both stabilizes the fully matched base-pair and destabilizes the mismatched base-pair. This sensitive method, with a simplified, low cost, easy-to-operate LNA design, could be generalized for various applications that need rapid and accurate identification of single-nucleotide variations.

WE-H-BRC-06: A Unified Machine-Learning Based Probabilistic Model for Automated Anomaly Detection in the Treatment Plan Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chang, X; Liu, S; Kalet, A

Purpose: The purpose of this work was to investigate the ability of a machine-learning based probabilistic approach to detect radiotherapy treatment plan anomalies given initial disease classes information. Methods In total we obtained 1112 unique treatment plans with five plan parameters and disease information from a Mosaiq treatment management system database for use in the study. The plan parameters include prescription dose, fractions, fields, modality and techniques. The disease information includes disease site, and T, M and N disease stages. A Bayesian network method was employed to model the probabilistic relationships between tumor disease information, plan parameters and an anomalymore » flag. A Bayesian learning method with Dirichlet prior was useed to learn the joint probabilities between dependent variables in error-free plan data and data with artificially induced anomalies. In the study, we randomly sampled data with anomaly in a specified anomaly space.We tested the approach with three groups of plan anomalies – improper concurrence of values of all five plan parameters and values of any two out of five parameters, and all single plan parameter value anomalies. Totally, 16 types of plan anomalies were covered by the study. For each type, we trained an individual Bayesian network. Results: We found that the true positive rate (recall) and positive predictive value (precision) to detect concurrence anomalies of five plan parameters in new patient cases were 94.45±0.26% and 93.76±0.39% respectively. To detect other 15 types of plan anomalies, the average recall and precision were 93.61±2.57% and 93.78±3.54% respectively. The computation time to detect the plan anomaly of each type in a new plan is ∼0.08 seconds. Conclusion: The proposed method for treatment plan anomaly detection was found effective in the initial tests. The results suggest that this type of models could be applied to develop plan anomaly detection tools to assist manual and automated plan checks. The senior author received research grants from ViewRay Inc. and Varian Medical System.« less

Pattern-Directed Attention in Uncertain Frequency Detection.

DTIC Science & Technology

1983-10-14

performance when compared to a single frequency condition even if the listeners are aware that more than one signal can occur ( Creelman , 1960; Green...be missed. On the-other hand, the multiple band approach, introduced by Green (1958) and modified by Creelman (1960), assumes that listeners base...multiple-band approaches ( Creelman , 1960; Green, 1961; Macmillan & Schwartz, 1975). In general, the two views are difficult to distinguish empirically, and

Interactions between pre-processing and classification methods for event-related-potential classification: best-practice guidelines for brain-computer interfacing.

PubMed

Farquhar, J; Hill, N J

2013-04-01

Detecting event related potentials (ERPs) from single trials is critical to the operation of many stimulus-driven brain computer interface (BCI) systems. The low strength of the ERP signal compared to the noise (due to artifacts and BCI irrelevant brain processes) makes this a challenging signal detection problem. Previous work has tended to focus on how best to detect a single ERP type (such as the visual oddball response). However, the underlying ERP detection problem is essentially the same regardless of stimulus modality (e.g., visual or tactile), ERP component (e.g., P300 oddball response, or the error-potential), measurement system or electrode layout. To investigate whether a single ERP detection method might work for a wider range of ERP BCIs we compare detection performance over a large corpus of more than 50 ERP BCI datasets whilst systematically varying the electrode montage, spectral filter, spatial filter and classifier training methods. We identify an interesting interaction between spatial whitening and regularised classification which made detection performance independent of the choice of spectral filter low-pass frequency. Our results show that pipeline consisting of spectral filtering, spatial whitening, and regularised classification gives near maximal performance in all cases. Importantly, this pipeline is simple to implement and completely automatic with no expert feature selection or parameter tuning required. Thus, we recommend this combination as a "best-practice" method for ERP detection problems.

Use of Protein Biotinylation In Vivo for Immunoelectron Microscopic Localization of a Specific Protein Isoform

PubMed Central

Viens, Antoine; Harper, Francis; Pichard, Evelyne; Comisso, Martine; Pierron, Gérard; Ogryzko, Vasily

2008-01-01

Tagging of proteins in vivo by covalent attachment of a biotin moiety has emerged as a new prospective tool for protein detection and purification. Previously, we established a strategy for expression of in vivo biotinylated proteins in mammalian cells. It is based on coexpression of the protein of interest fused to a short biotin acceptor peptide and biotin ligase BirA cloned in the same vector. We show here that the in vivo biotinylation can be used for immunogold postembedding labeling in immunoelectron microscopy experiments. We show that immunoelectron microscopy with biotinylated nuclear proteins is compatible with a wide range of postembedding methods, facilitating combination of morphological and localization studies in a single experiment. We also show that the method works in both transient transfection and stable cell line expression protocols and can be used for colocalization studies. This manuscript contains online supplemental material at http://www.jhc.org. Please visit this article online to view these materials. (J Histochem Cytochem 56:911–919, 2008) PMID:18574249

Image feature detection and extraction techniques performance evaluation for development of panorama under different light conditions

NASA Astrophysics Data System (ADS)

Patil, Venkat P.; Gohatre, Umakant B.

2018-04-01

The technique of obtaining a wider field-of-view of an image to get high resolution integrated image is normally required for development of panorama of a photographic images or scene from a sequence of part of multiple views. There are various image stitching methods developed recently. For image stitching five basic steps are adopted stitching which are Feature detection and extraction, Image registration, computing homography, image warping and Blending. This paper provides review of some of the existing available image feature detection and extraction techniques and image stitching algorithms by categorizing them into several methods. For each category, the basic concepts are first described and later on the necessary modifications made to the fundamental concepts by different researchers are elaborated. This paper also highlights about the some of the fundamental techniques for the process of photographic image feature detection and extraction methods under various illumination conditions. The Importance of Image stitching is applicable in the various fields such as medical imaging, astrophotography and computer vision. For comparing performance evaluation of the techniques used for image features detection three methods are considered i.e. ORB, SURF, HESSIAN and time required for input images feature detection is measured. Results obtained finally concludes that for daylight condition, ORB algorithm found better due to the fact that less tome is required for more features extracted where as for images under night light condition it shows that SURF detector performs better than ORB/HESSIAN detectors.

Esophageal abnormalities in gastroesophageal reflux disease.

PubMed

Levine, Marc S; Carucci, Laura R

2018-06-01

Fluoroscopic esophagography is a widely available, safe, and inexpensive test for detecting gastroesophageal reflux disease. In this article, we review the technique for performing a high-quality esophagram, including upright, double-contrast views of the esophagus and cardia with high-density barium; prone, single-contrast views of the esophagus with low-density barium; and evaluation of gastroesophageal reflux. We then discuss the radiographic findings associated with gastroesophageal reflux disease, including esophageal dysmotility, reflux esophagitis, peptic strictures, and Barrett's esophagus. Finally, we consider the differential diagnosis for the various radiographic findings associated with this condition. When carefully performed and interpreted, the esophagram is a useful test for evaluating gastroesophageal reflux disease and its complications.

Separation and counting of single molecules through nanofluidics, programmable electrophoresis, and nanoelectrode-gated tunneling and dielectric detection

DOEpatents

Lee, James W.; Thundat, Thomas G.

2006-04-25

An apparatus for carrying out the separation, detection, and/or counting of single molecules at nanometer scale. Molecular separation is achieved by driving single molecules through a microfluidic or nanofluidic medium using programmable and coordinated electric fields. In various embodiments, the fluidic medium is a strip of hydrophilic material on nonconductive hydrophobic surface, a trough produced by parallel strips of hydrophobic nonconductive material on a hydrophilic base, or a covered passageway produced by parallel strips of hydrophobic nonconductive material on a hydrophilic base together with a nonconductive cover on the parallel strips of hydrophobic nonconductive material. The molecules are detected and counted using nanoelectrode-gated electron tunneling methods, dielectric monitoring, and other methods.

nbCNV: a multi-constrained optimization model for discovering copy number variants in single-cell sequencing data.

PubMed

Zhang, Changsheng; Cai, Hongmin; Huang, Jingying; Song, Yan

2016-09-17

Variations in DNA copy number have an important contribution to the development of several diseases, including autism, schizophrenia and cancer. Single-cell sequencing technology allows the dissection of genomic heterogeneity at the single-cell level, thereby providing important evolutionary information about cancer cells. In contrast to traditional bulk sequencing, single-cell sequencing requires the amplification of the whole genome of a single cell to accumulate enough samples for sequencing. However, the amplification process inevitably introduces amplification bias, resulting in an over-dispersing portion of the sequencing data. Recent study has manifested that the over-dispersed portion of the single-cell sequencing data could be well modelled by negative binomial distributions. We developed a read-depth based method, nbCNV to detect the copy number variants (CNVs). The nbCNV method uses two constraints-sparsity and smoothness to fit the CNV patterns under the assumption that the read signals are negatively binomially distributed. The problem of CNV detection was formulated as a quadratic optimization problem, and was solved by an efficient numerical solution based on the classical alternating direction minimization method. Extensive experiments to compare nbCNV with existing benchmark models were conducted on both simulated data and empirical single-cell sequencing data. The results of those experiments demonstrate that nbCNV achieves superior performance and high robustness for the detection of CNVs in single-cell sequencing data.

Development of an Experimental Setup for the Measurement of the Coefficient of Restitution under Vacuum Conditions

PubMed Central

Drücker, Sven; Krautstrunk, Isabell; Paulick, Maria; Saleh, Khashayar; Morgeneyer, Martin; Kwade, Arno

2016-01-01

The Discrete Element Method is used for the simulation of particulate systems to describe and analyze them, to predict and afterwards optimize their behavior for single stages of a process or even an entire process. For the simulation with occurring particle-particle and particle-wall contacts, the value of the coefficient of restitution is required. It can be determined experimentally. The coefficient of restitution depends on several parameters like the impact velocity. Especially for fine particles the impact velocity depends on the air pressure and under atmospheric pressure high impact velocities cannot be reached. For this, a new experimental setup for free-fall tests under vacuum conditions is developed. The coefficient of restitution is determined with the impact and rebound velocity which are detected by a high-speed camera. To not hinder the view, the vacuum chamber is made of glass. Also a new release mechanism to drop one single particle under vacuum conditions is constructed. Due to that, all properties of the particle can be characterized beforehand. PMID:27077671

Development of an Experimental Setup for the Measurement of the Coefficient of Restitution under Vacuum Conditions.

PubMed

Drücker, Sven; Krautstrunk, Isabell; Paulick, Maria; Saleh, Khashayar; Morgeneyer, Martin; Kwade, Arno

2016-03-29

The Discrete Element Method is used for the simulation of particulate systems to describe and analyze them, to predict and afterwards optimize their behavior for single stages of a process or even an entire process. For the simulation with occurring particle-particle and particle-wall contacts, the value of the coefficient of restitution is required. It can be determined experimentally. The coefficient of restitution depends on several parameters like the impact velocity. Especially for fine particles the impact velocity depends on the air pressure and under atmospheric pressure high impact velocities cannot be reached. For this, a new experimental setup for free-fall tests under vacuum conditions is developed. The coefficient of restitution is determined with the impact and rebound velocity which are detected by a high-speed camera. To not hinder the view, the vacuum chamber is made of glass. Also a new release mechanism to drop one single particle under vacuum conditions is constructed. Due to that, all properties of the particle can be characterized beforehand.

Detecting bacteria and Determining Their Susceptibility to Antibiotics by Stochastic Confinement in Nanoliter Droplets using Plug-Based Microfluidics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boedicker, J.; Li, L; Kline, T

2008-01-01

This article describes plug-based microfluidic technology that enables rapid detection and drug susceptibility screening of bacteria in samples, including complex biological matrices, without pre-incubation. Unlike conventional bacterial culture and detection methods, which rely on incubation of a sample to increase the concentration of bacteria to detectable levels, this method confines individual bacteria into droplets nanoliters in volume. When single cells are confined into plugs of small volume such that the loading is less than one bacterium per plug, the detection time is proportional to plug volume. Confinement increases cell density and allows released molecules to accumulate around the cell, eliminatingmore » the pre-incubation step and reducing the time required to detect the bacteria. We refer to this approach as stochastic confinement. Using the microfluidic hybrid method, this technology was used to determine the antibiogram - or chart of antibiotic sensitivity - of methicillin-resistant Staphylococcus aureus (MRSA) to many antibiotics in a single experiment and to measure the minimal inhibitory concentration (MIC) of the drug cefoxitin (CFX) against this strain. In addition, this technology was used to distinguish between sensitive and resistant strains of S. aureus in samples of human blood plasma. High-throughput microfluidic techniques combined with single-cell measurements also enable multiple tests to be performed simultaneously on a single sample containing bacteria. This technology may provide a method of rapid and effective patient-specific treatment of bacterial infections and could be extended to a variety of applications that require multiple functional tests of bacterial samples on reduced timescales.« less

A High Speed Finger-Print Optical Scanning Method

DTIC Science & Technology

2000-01-01

biometrics technologies for authentication, from the view point of convenience and higher security, dactyloscopy is by far the best, much better than the...sensing technologies using static capacitance, thermal or optical detection, the optical detection is by far with the most potential to meet the...present time due to the low resolution of the inherent nature of thermal imaging technique. Besides, this method is easily influenced by environmental

Detection of genetically modified organisms in foods by DNA amplification techniques.

PubMed

García-Cañas, Virginia; Cifuentes, Alejandro; González, Ramón

2004-01-01

In this article, the different DNA amplification techniques that are being used for detecting genetically modified organisms (GMOs) in foods are examined. This study intends to provide an updated overview (including works published till June 2002) on the principal applications of such techniques together with their main advantages and drawbacks in GMO detection in foods. Some relevant facts on sampling, DNA isolation, and DNA amplification methods are discussed. Moreover; these analytical protocols are discuissed from a quantitative point of view, including the newest investigations on multiplex detection of GMOs in foods and validation of methods.

DNA detection and single nucleotide mutation identification using SERS for molecular diagnostics and global health

NASA Astrophysics Data System (ADS)

Ngo, Hoan T.; Gandra, Naveen; Fales, Andrew M.; Taylor, Steve M.; Vo-Dinh, Tuan

2017-02-01

Nucleic acid-based molecular diagnostics at the point-of-care (POC) and in resource-limited settings is still a challenge. We present a sensitive yet simple DNA detection method with single nucleotide polymorphism (SNP) identification capability. The detection scheme involves sandwich hybridization of magnetic beads conjugated with capture probes, target sequences, and ultrabright surface-enhanced Raman Scattering (SERS) nanorattles conjugated with reporter probes. Upon hybridization, the sandwich probes are concentrated at the detection focus controlled by a magnetic system for SERS measurements. The ultrabright SERS nanorattles, consisting of a core and a shell with resonance Raman reporters loaded in the gap space between the core and the shell, serve as SERS tags for ultrasensitive signal detection. Specific DNA sequences of the malaria parasite Plasmodium falciparum and dengue virus 1 (DENV1) were used as the model marker system. Detection limit of approximately 100 attomoles was achieved. Single nucleotide polymorphism (SNP) discrimination of wild type malaria DNA and mutant malaria DNA, which confers resistance to artemisinin drugs, was also demonstrated. The results demonstrate the molecular diagnostic potential of the nanorattle-based method to both detect and genotype infectious pathogens. The method's simplicity makes it a suitable candidate for molecular diagnosis at the POC and in resource-limited settings.

Long-range depth profiling of camouflaged targets using single-photon detection

NASA Astrophysics Data System (ADS)

Tobin, Rachael; Halimi, Abderrahim; McCarthy, Aongus; Ren, Ximing; McEwan, Kenneth J.; McLaughlin, Stephen; Buller, Gerald S.

2018-03-01

We investigate the reconstruction of depth and intensity profiles from data acquired using a custom-designed time-of-flight scanning transceiver based on the time-correlated single-photon counting technique. The system had an operational wavelength of 1550 nm and used a Peltier-cooled InGaAs/InP single-photon avalanche diode detector. Measurements were made of human figures, in plain view and obscured by camouflage netting, from a stand-off distance of 230 m in daylight using only submilliwatt average optical powers. These measurements were analyzed using a pixelwise cross correlation approach and compared to analysis using a bespoke algorithm designed for the restoration of multilayered three-dimensional light detection and ranging images. This algorithm is based on the optimization of a convex cost function composed of a data fidelity term and regularization terms, and the results obtained show that it achieves significant improvements in image quality for multidepth scenarios and for reduced acquisition times.

A six-year record of volcanic ash detection with Envisat MIPAS

NASA Astrophysics Data System (ADS)

Griessbach, S.; Hoffmann, L.; von Hobe, M.; Müller, R.; Spang, R.

2012-04-01

Volcanic ash particles have an impact on the Earth's radiation budget and pose a severe danger to air traffic. Therefore, the ability to detect and characterize volcanic ash layers on a global and altitude-dependent scale is essential. The Michelson Interferometer for Passive Atmospheric Sounding (MIPAS) on-board ESA's Envisat is mainly used for measurements of vertical profiles of atmospheric trace gases. It is also very sensitive to cloud and aerosol particles. We developed a fast, simple, and reliable method to detect volcanic ash using MIPAS spectra. From calculations of volcanic ash and ice particle optical properties, such as extinction coefficients and single scattering albedos as well as simulated MIPAS radiance spectra, we derived two optimal micro windows at 10.5 and 12.1 μm to detect volcanic ash. The calculations were performed with the JUelich RApid Spectral Simulation Code (JURASSIC), which includes a scattering module. Our method applies two radiance thresholds to detect volcanic ash. The first one is derived from a statistical analysis of six years of measured MIPAS radiances in the selected spectral windows. This statistical threshold accounts only for pure volcanic ash detections. The second threshold is derived from simulations of MIPAS radiances with JURASSIC for a broad range of atmospheric conditions and tangent altitudes for volcanic ash and ice particles. The second threshold allows more volcanic ash detections, because it accounts also for mixtures of ice and volcanic ash particles within the instrument's field of view. With the new method major eruptions (from e.g. Chaiten, Okmok, Kasatochi, Sarychev, Eyafjallajökull, Merapi, Grimsvötn, Puyehue-Cordon Caulle, Nabro) as well as several smaller eruptions at mid-latitudes and in polar regions between 2006 - 2011 were clearly identified in the MIPAS data. Trajectory calculations using the Chemical Langangian Model of the Stratosphere (CLaMS) are used to locate a volcanic eruption for each detection. In a case study of the 2011 eruption of the Chilean volcano Puyehue-Cordon Caulle we show how the volcanic ash spreads over the complete southern hemisphere mid-latitudes, is diluted and descends slowly with time. Ash is detected up to two month after the first eruption.

Cest Analysis: Automated Change Detection from Very-High Remote Sensing Images

NASA Astrophysics Data System (ADS)

Ehlers, M.; Klonus, S.; Jarmer, T.; Sofina, N.; Michel, U.; Reinartz, P.; Sirmacek, B.

2012-08-01

A fast detection, visualization and assessment of change in areas of crisis or catastrophes are important requirements for coordination and planning of help. Through the availability of new satellites and/or airborne sensors with very high spatial resolutions (e.g., WorldView, GeoEye) new remote sensing data are available for a better detection, delineation and visualization of change. For automated change detection, a large number of algorithms has been proposed and developed. From previous studies, however, it is evident that to-date no single algorithm has the potential for being a reliable change detector for all possible scenarios. This paper introduces the Combined Edge Segment Texture (CEST) analysis, a decision-tree based cooperative suite of algorithms for automated change detection that is especially designed for the generation of new satellites with very high spatial resolution. The method incorporates frequency based filtering, texture analysis, and image segmentation techniques. For the frequency analysis, different band pass filters can be applied to identify the relevant frequency information for change detection. After transforming the multitemporal images via a fast Fourier transform (FFT) and applying the most suitable band pass filter, different methods are available to extract changed structures: differencing and correlation in the frequency domain and correlation and edge detection in the spatial domain. Best results are obtained using edge extraction. For the texture analysis, different 'Haralick' parameters can be calculated (e.g., energy, correlation, contrast, inverse distance moment) with 'energy' so far providing the most accurate results. These algorithms are combined with a prior segmentation of the image data as well as with morphological operations for a final binary change result. A rule-based combination (CEST) of the change algorithms is applied to calculate the probability of change for a particular location. CEST was tested with high-resolution satellite images of the crisis areas of Darfur (Sudan). CEST results are compared with a number of standard algorithms for automated change detection such as image difference, image ratioe, principal component analysis, delta cue technique and post classification change detection. The new combined method shows superior results averaging between 45% and 15% improvement in accuracy.

A Method for Detecting Circulating Tumor Cells Based on the Measurement of Single-Cell Metabolism in Droplet-Based Microfluidics.

PubMed

Del Ben, Fabio; Turetta, Matteo; Celetti, Giorgia; Piruska, Aigars; Bulfoni, Michela; Cesselli, Daniela; Huck, Wilhelm T S; Scoles, Giacinto

2016-07-18

The number of circulating tumor cells (CTCs) in blood is strongly correlated with the progress of metastatic cancer. Current methods to detect CTCs are based on immunostaining or discrimination of physical properties. Herein, a label-free method is presented exploiting the abnormal metabolic behavior of cancer cells. A single-cell analysis technique is used to measure the secretion of acid from individual living tumor cells compartmentalized in microfluidically prepared, monodisperse, picoliter (pL) droplets. As few as 10 tumor cells can be detected in a background of 200 000 white blood cells and proof-of-concept data is shown on the detection of CTCs in the blood of metastatic patients. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A dual-view digital tomosynthesis imaging technique for improved chest imaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhong, Yuncheng; Lai, Chao-Jen; Wang, Tianpeng

Purpose: Digital tomosynthesis (DTS) has been shown to be useful for reducing the overlapping of abnormalities with anatomical structures at various depth levels along the posterior–anterior (PA) direction in chest radiography. However, DTS provides crude three-dimensional (3D) images that have poor resolution in the lateral view and can only be displayed with reasonable quality in the PA view. Furthermore, the spillover of high-contrast objects from off-fulcrum planes generates artifacts that may impede the diagnostic use of the DTS images. In this paper, the authors describe and demonstrate the use of a dual-view DTS technique to improve the accuracy of themore » reconstructed volume image data for more accurate rendition of the anatomy and slice images with improved resolution and reduced artifacts, thus allowing the 3D image data to be viewed in views other than the PA view. Methods: With the dual-view DTS technique, limited angle scans are performed and projection images are acquired in two orthogonal views: PA and lateral. The dual-view projection data are used together to reconstruct 3D images using the maximum likelihood expectation maximization iterative algorithm. In this study, projection images were simulated or experimentally acquired over 360° using the scanning geometry for cone beam computed tomography (CBCT). While all projections were used to reconstruct CBCT images, selected projections were extracted and used to reconstruct single- and dual-view DTS images for comparison with the CBCT images. For realistic demonstration and comparison, a digital chest phantom derived from clinical CT images was used for the simulation study. An anthropomorphic chest phantom was imaged for the experimental study. The resultant dual-view DTS images were visually compared with the single-view DTS images and CBCT images for the presence of image artifacts and accuracy of CT numbers and anatomy and quantitatively compared with root-mean-square-deviation (RMSD) values computed using the digital chest phantom or the CBCT images as the reference in the simulation and experimental study, respectively. High-contrast wires with vertical, oblique, and horizontal orientations in a PA view plane were also imaged to investigate the spatial resolutions and how the wire signals spread in the PA view and lateral view slice images. Results: Both the digital phantom images (simulated) and the anthropomorphic phantom images (experimentally generated) demonstrated that the dual-view DTS technique resulted in improved spatial resolution in the depth (PA) direction, more accurate representation of the anatomy, and significantly reduced artifacts. The RMSD values corroborate well with visual observations with substantially lower RMSD values measured for the dual-view DTS images as compared to those measured for the single-view DTS images. The imaging experiment with the high-contrast wires shows that while the vertical and oblique wires could be resolved in the lateral view in both single- and dual-view DTS images, the horizontal wire could only be resolved in the dual-view DTS images. This indicates that with single-view DTS, the wire signals spread liberally to off-fulcrum planes and generated wire shadow there. Conclusions: The authors have demonstrated both visually and quantitatively that the dual-view DTS technique can be used to achieve more accurate rendition of the anatomy and to obtain slice images with improved resolution and reduced artifacts as compared to the single-view DTS technique, thus allowing the 3D image data to be viewed in views other than the PA view. These advantages could make the dual-view DTS technique useful in situations where better separation of the objects-of-interest from the off-fulcrum structures or more accurate 3D rendition of the anatomy are required while a regular CT examination is undesirable due to radiation dose considerations.« less

Statistical Deconvolution for Superresolution Fluorescence Microscopy

PubMed Central

Mukamel, Eran A.; Babcock, Hazen; Zhuang, Xiaowei

2012-01-01

Superresolution microscopy techniques based on the sequential activation of fluorophores can achieve image resolution of ∼10 nm but require a sparse distribution of simultaneously activated fluorophores in the field of view. Image analysis procedures for this approach typically discard data from crowded molecules with overlapping images, wasting valuable image information that is only partly degraded by overlap. A data analysis method that exploits all available fluorescence data, regardless of overlap, could increase the number of molecules processed per frame and thereby accelerate superresolution imaging speed, enabling the study of fast, dynamic biological processes. Here, we present a computational method, referred to as deconvolution-STORM (deconSTORM), which uses iterative image deconvolution in place of single- or multiemitter localization to estimate the sample. DeconSTORM approximates the maximum likelihood sample estimate under a realistic statistical model of fluorescence microscopy movies comprising numerous frames. The model incorporates Poisson-distributed photon-detection noise, the sparse spatial distribution of activated fluorophores, and temporal correlations between consecutive movie frames arising from intermittent fluorophore activation. We first quantitatively validated this approach with simulated fluorescence data and showed that deconSTORM accurately estimates superresolution images even at high densities of activated fluorophores where analysis by single- or multiemitter localization methods fails. We then applied the method to experimental data of cellular structures and demonstrated that deconSTORM enables an approximately fivefold or greater increase in imaging speed by allowing a higher density of activated fluorophores/frame. PMID:22677393

A novel method for single bacteria identification by Raman spectroscopy

NASA Astrophysics Data System (ADS)

Schultz, Emmanuelle; Simon, Anne-Catherine; Strola, Samy Andrea; Perenon, Rémi; Espagnon, Isabelle; Allier, Cédric; Claustre, Patricia; Jary, Dorothée.; Dinten, Jean-Marc

2014-03-01

In this paper we present results on single bacteria rapid identification obtained with a low-cost and compact Raman spectrometer. At present, we demonstrate that a 1 minute procedure, including the localization of single bacterium, is sufficient to acquire comprehensive Raman spectrum in the range of 600 to 3300 cm-1. Localization and detection of single bacteria is performed by means of lensfree imaging over a large field of view of 24 mm2. An excitation source of 532 nm and 30 mW illuminates single bacteria to collect Raman signal into a Tornado Spectral Systems prototype spectrometer (HTVS technology). The acquisition time to record a single bacterium spectrum is as low as 10 s owing to the high light throughput of this spectrometer. The spectra processing features different steps for cosmic spikes removal, background subtraction, and gain normalization to correct the residual inducted fluorescence and substrate fluctuations. This allows obtaining a fine chemical fingerprint analysis. We have recorded a total of 1200 spectra over 7 bacterial species (E. coli, Bacillus species, S. epidermis, M. luteus, S. marcescens). The analysis of this database results in a high classification score of almost 90 %. Hence we can conclude that our setup enables automatic recognition of bacteria species among 7 different species. The speed and the sensitivity (<30 minutes for localization and spectra collection of 30 single bacteria) of our Raman spectrometer pave the way for high-throughput and non-destructive real-time bacteria identification assays. This compact and low-cost technology can benefit biomedical, clinical diagnostic and environmental applications.

Three-dimensional thermographic imaging using a virtual wave concept

NASA Astrophysics Data System (ADS)

Burgholzer, Peter; Thor, Michael; Gruber, Jürgen; Mayr, Günther

2017-03-01

In this work, it is shown that image reconstruction methods from ultrasonic imaging can be employed for thermographic signals. Before using these imaging methods, a virtual signal is calculated by applying a local transformation to the temperature evolution measured on a sample surface. The introduced transformation describes all the irreversibility of the heat diffusion process and can be used for every sample shape. To date, one-dimensional methods have been primarily used in thermographic imaging. The proposed two-stage algorithm enables reconstruction in two and three dimensions. The feasibility of this approach is demonstrated through simulations and experiments. For the latter, small steel beads embedded in an epoxy resin are imaged. The resolution limit is found to be proportional to the depth of the structures and to be inversely proportional to the logarithm of the signal-to-noise ratio. Limited-view artefacts can arise if the measurement is performed on a single planar detection surface. These artifacts can be reduced by measuring the thermographic signals from multiple planes, which is demonstrated by numerical simulations and by experiments performed on an epoxy cube.

Detailed Performance Assessment for the ITER ECE Diagnostic

NASA Astrophysics Data System (ADS)

Rowan, W.; Austin, M.; Houshmandyar, S.; Phillips, P.; Beno, J.; Bryant, A.; Ouroua, A.; Weeks, D.; Hubbard, A.; Taylor, G.

2017-10-01

One of the primary diagnostics for electron temperature (Te) measurement on ITER is based on the detection of electron cyclotron emission (ECE) Here we describe the predicted performance of the newly completed ECE diagnostic design by quantitatively following the emission from the plasma to the instruments and including the calibration method to assess accuracy. Operation of the diagnostic at 5.3 T is the main interest here but critical features of the emission spectra for 2.65 T and 1.8 T will be described. ECE will be collected by two very similar optical systems: one a radial view, the other an oblique view. Both measurements are used for Te while the oblique view also allows detection of non-thermal distortion in the electron distribution. An in-vacuum calibration source is included in the front end of each view to calibrate out the effect of any degradation of in-vessel optics. Following collection, the emission is split into orthogonal polarizations and transmitted to the detection instruments via waveguides filled with dry nitrogen, a choice that simplifies construction and analysis. Near the instruments, a switchyard is used to select which polarization and view is detected by each instrument. The design for the radiometer used for 5.3 T will be described in detail. Supported by PPPL/US-DA via subcontract S013464-H to UT Austin.

Specific detection of the toxic dinoflagellates Alexandrium tamarense and Alexandrium catenella from single vegetative cells by a loop-mediated isothermal amplification method.

PubMed

Nagai, Satoshi; Itakura, Shigeru

2012-09-01

In this study, we succeeded in developing a loop-mediated isothermal amplification (LAMP) method that enables sensitive and specific detection of the toxic marine dinoflagellates Alexandrium tamarense and Alexandrium catenella from single cells of both laboratory cultures and naturally blooming cells within 25 min, by monitoring the turbidimeter from the start of the LAMP reaction. The fluorescence intensity was strong enough to allow discrimination between positive and negative results by naked eye under a UV lamp, even in amplified samples from a single cell, by using the LAMP method. Unambiguous detection by naked eye was possible even in half the volume of LAMP cocktail recommended by the manufacturer, suggesting the potential to significantly reduce the cost of Alexandrium monitoring. Therefore, we can conclude that this method is one of the most convenient, sensitive, and cost-effective molecular tools for Alexandrium monitoring. Copyright © 2012 Elsevier B.V. All rights reserved.

A miniaturized NQR spectrometer for a multi-channel NQR-based detection device

NASA Astrophysics Data System (ADS)

Beguš, Samo; Jazbinšek, Vojko; Pirnat, Janez; Trontelj, Zvonko

2014-10-01

A low frequency (0.5-5 MHz) battery operated sensitive pulsed NQR spectrometer with a transmitter power up to 5 W and a total mass of about 3 kg aimed at detecting 14 N NQR signals, predominantly of illicit materials, was designed and assembled. This spectrometer uses a standard software defined radio (SDR) platform for the data acquisition unit. Signal processing is done with the LabView Virtual instrument on a personal computer. We successfully tested the spectrometer by measuring 14 N NQR signals from aminotetrazole monohydrate (ATMH), potassium nitrate (PN), paracetamol (PCM) and trinitrotoluene (TNT). Such a spectrometer is a feasible component of a portable single or multichannel 14 N NQR based detection device.

Self-referenced single-shot THz detection

DOE Office of Scientific and Technical Information (OSTI.GOV)

Russell, Brandon K.; Ofori-Okai, Benjamin K.; Chen, Zhijiang

We demonstrate a self-referencing method to reduce noise in a single-shot terahertz detection scheme. By splitting a single terahertz pulse and using a reflective echelon, both the signal and reference terahertz time-domain waveforms were measured using one laser pulse. Simultaneous acquisition of these waveforms significantly reduces noise originating from shot-to-shot fluctuations. Here, we show that correlation function based referencing, which is not limited to polarization dependent measurements, can achieve a noise floor that is comparable to state-of-the-art polarization-gated balanced detection. Lastly, we extract the DC conductivity of a 30 nm free-standing gold film using a single THz pulse. The measuredmore » value of σ 0 = 1.3 ± 0.4 × 10 7 S m -1 is in good agreement with the value measured by four-point probe, indicating the viability of this method for measuring dynamical changes and small signals.« less

Self-referenced single-shot THz detection

DOE PAGES

Russell, Brandon K.; Ofori-Okai, Benjamin K.; Chen, Zhijiang; ...

2017-06-29

We demonstrate a self-referencing method to reduce noise in a single-shot terahertz detection scheme. By splitting a single terahertz pulse and using a reflective echelon, both the signal and reference terahertz time-domain waveforms were measured using one laser pulse. Simultaneous acquisition of these waveforms significantly reduces noise originating from shot-to-shot fluctuations. Here, we show that correlation function based referencing, which is not limited to polarization dependent measurements, can achieve a noise floor that is comparable to state-of-the-art polarization-gated balanced detection. Lastly, we extract the DC conductivity of a 30 nm free-standing gold film using a single THz pulse. The measuredmore » value of σ 0 = 1.3 ± 0.4 × 10 7 S m -1 is in good agreement with the value measured by four-point probe, indicating the viability of this method for measuring dynamical changes and small signals.« less

Nanopore sensing at ultra-low concentrations using single-molecule dielectrophoretic trapping

NASA Astrophysics Data System (ADS)

Freedman, Kevin J.; Otto, Lauren M.; Ivanov, Aleksandar P.; Barik, Avijit; Oh, Sang-Hyun; Edel, Joshua B.

2016-01-01

Single-molecule techniques are being developed with the exciting prospect of revolutionizing the healthcare industry by generating vast amounts of genetic and proteomic data. One exceptionally promising route is in the use of nanopore sensors. However, a well-known complexity is that detection and capture is predominantly diffusion limited. This problem is compounded when taking into account the capture volume of a nanopore, typically 108-1010 times smaller than the sample volume. To rectify this disproportionate ratio, we demonstrate a simple, yet powerful, method based on coupling single-molecule dielectrophoretic trapping to nanopore sensing. We show that DNA can be captured from a controllable, but typically much larger, volume and concentrated at the tip of a metallic nanopore. This enables the detection of single molecules at concentrations as low as 5 fM, which is approximately a 103 reduction in the limit of detection compared with existing methods, while still maintaining efficient throughput.

Highly sensitive chemiluminescent point mutation detection by circular strand-displacement amplification reaction.

PubMed

Shi, Chao; Ge, Yujie; Gu, Hongxi; Ma, Cuiping

2011-08-15

Single nucleotide polymorphism (SNP) genotyping is attracting extensive attentions owing to its direct connections with human diseases including cancers. Here, we have developed a highly sensitive chemiluminescence biosensor based on circular strand-displacement amplification and the separation by magnetic beads reducing the background signal for point mutation detection at room temperature. This method took advantage of both the T4 DNA ligase recognizing single-base mismatch with high selectivity and the strand-displacement reaction of polymerase to perform signal amplification. The detection limit of this method was 1.3 × 10(-16)M, which showed better sensitivity than that of most of those reported detection methods of SNP. Additionally, the magnetic beads as carrier of immobility was not only to reduce the background signal, but also may have potential apply in high through-put screening of SNP detection in human genome. Copyright © 2011 Elsevier B.V. All rights reserved.

DNAzyme based gap-LCR detection of single-nucleotide polymorphism.

PubMed

Zhou, Li; Du, Feng; Zhao, Yongyun; Yameen, Afshan; Chen, Haodong; Tang, Zhuo

2013-07-15

Fast and accurate detection of single-nucleotide polymorphism (SNP) is thought more and more important for understanding of human physiology and elucidating the molecular based diseases. A great deal of effort has been devoted to developing accurate, rapid, and cost-effective technologies for SNP analysis. However most of those methods developed to date incorporate complicated probe labeling and depend on advanced equipment. The DNAzyme based Gap-LCR detection method averts any chemical modification on probes and circumvents those problems by incorporating a short functional DNA sequence into one of LCR primers. Two kinds of exonuclease are utilized in our strategy to digest all the unreacted probes and release the DNAzymes embedded in the LCR product. The DNAzyme applied in our method is a versatile tool to report the result of SNP detection in colorimetric or fluorometric ways for different detection purposes. Copyright © 2013 Elsevier B.V. All rights reserved.

Detecting delay in visual feedback of an action as a monitor of self recognition.

PubMed

Hoover, Adria E N; Harris, Laurence R

2012-10-01

How do we distinguish "self" from "other"? The correlation between willing an action and seeing it occur is an important cue. We exploited the fact that this correlation needs to occur within a restricted temporal window in order to obtain a quantitative assessment of when a body part is identified as "self". We measured the threshold and sensitivity (d') for detecting a delay between movements of the finger (of both the dominant and non-dominant hands) and visual feedback as seen from four visual perspectives (the natural view, and mirror-reversed and/or inverted views). Each trial consisted of one presentation with minimum delay and another with a delay of between 33 and 150 ms. Participants indicated which presentation contained the delayed view. We varied the amount of efference copy available for this task by comparing performances for discrete movements and continuous movements. Discrete movements are associated with a stronger efference copy. Sensitivity to detect asynchrony between visual and proprioceptive information was significantly higher when movements were viewed from a "plausible" self perspective compared with when the view was reversed or inverted. Further, we found differences in performance between dominant and non-dominant hand finger movements across the continuous and single movements. Performance varied with the viewpoint from which the visual feedback was presented and on the efferent component such that optimal performance was obtained when the presentation was in the normal natural orientation and clear efferent information was available. Variations in sensitivity to visual/non-visual temporal incongruence with the viewpoint in which a movement is seen may help determine the arrangement of the underlying visual representation of the body.

NMR-based urine analysis in rats: prediction of proximal tubule kidney toxicity and phospholipidosis.

PubMed

Lienemann, Kai; Plötz, Thomas; Pestel, Sabine

2008-01-01

The aim of safety pharmacology is early detection of compound-induced side-effects. NMR-based urine analysis followed by multivariate data analysis (metabonomics) identifies efficiently differences between toxic and non-toxic compounds; but in most cases multiple administrations of the test compound are necessary. We tested the feasibility of detecting proximal tubule kidney toxicity and phospholipidosis with metabonomics techniques after single compound administration as an early safety pharmacology approach. Rats were treated orally, intravenously, inhalatively or intraperitoneally with different test compounds. Urine was collected at 0-8 h and 8-24 h after compound administration, and (1)H NMR-patterns were recorded from the samples. Variation of post-processing and feature extraction methods led to different views on the data. Support Vector Machines were trained on these different data sets and then aggregated as experts in an Ensemble. Finally, validity was monitored with a cross-validation study using a training, validation, and test data set. Proximal tubule kidney toxicity could be predicted with reasonable total classification accuracy (85%), specificity (88%) and sensitivity (78%). In comparison to alternative histological studies, results were obtained quicker, compound need was reduced, and very importantly fewer animals were needed. In contrast, the induction of phospholipidosis by the test compounds could not be predicted using NMR-based urine analysis or the previously published biomarker PAG. NMR-based urine analysis was shown to effectively predict proximal tubule kidney toxicity after single compound administration in rats. Thus, this experimental design allows early detection of toxicity risks with relatively low amounts of compound in a reasonably short period of time.

A rapid low-cost high-density DNA-based multi-detection test for routine inspection of meat species.

PubMed

Lin, Chun Chi; Fung, Lai Ling; Chan, Po Kwok; Lee, Cheuk Man; Chow, Kwok Fai; Cheng, Shuk Han

2014-02-01

The increasing occurrence of food frauds suggests that species identification should be part of food authentication. Current molecular-based species identification methods have their own limitations or drawbacks, such as relatively time-consuming experimental steps, expensive equipment and, in particular, these methods cannot identify mixed species in a single experiment. This project proposes an improved method involving PCR amplification of the COI gene and detection of species-specific sequences by hybridisation. Major innovative breakthrough lies in the detection of multiple species, including pork, beef, lamb, horse, cat, dog and mouse, from a mixed sample within a single experiment. The probes used are species-specific either in sole or mixed species samples. As little as 5 pg of DNA template in the PCR is detectable in the proposed method. By designing species-specific probes and adopting reverse dot blot hybridisation and flow-through hybridisation, a low-cost high-density DNA-based multi-detection test suitable for routine inspection of meat species was developed. © 2013.

Effect Size Calculations and Single Subject Designs

ERIC Educational Resources Information Center

Olive, Melissa L.; Smith, Benjamin W.

2005-01-01

This study compared visual analyses with five alternative methods for assessing the magnitude of effect with single subject designs. Each method was successful in detecting intervention effect. When rank ordered, each method was consistent in identifying the participants with the largest effect. We recommend the use of the standard mean difference…

Single molecule targeted sequencing for cancer gene mutation detection.

PubMed

Gao, Yan; Deng, Liwei; Yan, Qin; Gao, Yongqian; Wu, Zengding; Cai, Jinsen; Ji, Daorui; Li, Gailing; Wu, Ping; Jin, Huan; Zhao, Luyang; Liu, Song; Ge, Liangjin; Deem, Michael W; He, Jiankui

2016-05-19

With the rapid decline in cost of sequencing, it is now affordable to examine multiple genes in a single disease-targeted clinical test using next generation sequencing. Current targeted sequencing methods require a separate step of targeted capture enrichment during sample preparation before sequencing. Although there are fast sample preparation methods available in market, the library preparation process is still relatively complicated for physicians to use routinely. Here, we introduced an amplification-free Single Molecule Targeted Sequencing (SMTS) technology, which combined targeted capture and sequencing in one step. We demonstrated that this technology can detect low-frequency mutations using artificially synthesized DNA sample. SMTS has several potential advantages, including simple sample preparation thus no biases and errors are introduced by PCR reaction. SMTS has the potential to be an easy and quick sequencing technology for clinical diagnosis such as cancer gene mutation detection, infectious disease detection, inherited condition screening and noninvasive prenatal diagnosis.

Plume Detection and Plume Top Height Estimation using SLSTR

NASA Astrophysics Data System (ADS)

Virtanen, Timo H.; Kolmonen, Pekka; Sogacheva, Larisa; Rodriguez, Edith; Saponaro, Giulia; de Leeuw, Gerrit

2017-04-01

We present preliminary results on ash and desert dust plume detection and plume top height estimates based on satellite data from the Sea and Land Surface Temperature Radiometer (SLSTR) aboard Sentinel-3, launched in 2016. The methods are based on the previously developed AATSR Correlation Method (ACM) height estimation algorithm, which utilized the data of the preceding similar instrument, Advanced Along Track Scanning Radiometer (AATSR). The height estimate is based on the stereo-viewing capability of SLSTR, which allows to determine the parallax between the satellite's 55° backward and nadir views, and thus the corresponding height. The ash plume detection is based on the brightness temperature difference between between thermal infrared (TIR) channels centered at 11 and 12 μm, which show characteristic signals for both desert dust and ash plumes. The SLSTR instrument provides a unique combination of dual-view capability and a wavelength range from visible to thermal infrared, rendering it an ideal instrument for this work. Accurate information on the volcanic ash position is important for air traffic safety. The ACM algorithm can provide valuable data of both horizontal and vertical ash dispersion. These data may be useful for comparisons with other volcanic ash and desert dust retrieval methods and dispersion models. The current work is being carried out as part of the H2020 project EUNADICS-AV ("European Natural Disaster Coordination and Information System for Aviation"), which started in October 2016.

Integration of single-molecule detection with magnetic separation for multiplexed detection of DNA glycosylases.

PubMed

Li, Chen-Chen; Zhang, Yan; Tang, Bo; Zhang, Chun-Yang

2018-06-05

We combine single-molecule detection with magnetic separation for simultaneous measurement of human 8-oxoG DNA glycosylase 1 (hOGG1) and uracil DNA glycosylase (UDG) based on excision repair-initiated endonuclease IV (Endo IV)-assisted signal amplification. This method can sensitively detect multiple DNA glycosylases, and it can be further applied for the simultaneous measurement of enzyme kinetic parameters and screening of both hOGG1 and UDG inhibitors.

Simultaneous fluorescence and quantitative phase microscopy with single-pixel detectors

NASA Astrophysics Data System (ADS)

Liu, Yang; Suo, Jinli; Zhang, Yuanlong; Dai, Qionghai

2018-02-01

Multimodal microscopy offers high flexibilities for biomedical observation and diagnosis. Conventional multimodal approaches either use multiple cameras or a single camera spatially multiplexing different modes. The former needs expertise demanding alignment and the latter suffers from limited spatial resolution. Here, we report an alignment-free full-resolution simultaneous fluorescence and quantitative phase imaging approach using single-pixel detectors. By combining reference-free interferometry with single-pixel detection, we encode the phase and fluorescence of the sample in two detection arms at the same time. Then we employ structured illumination and the correlated measurements between the sample and the illuminations for reconstruction. The recovered fluorescence and phase images are inherently aligned thanks to single-pixel detection. To validate the proposed method, we built a proof-of-concept setup for first imaging the phase of etched glass with the depth of a few hundred nanometers and then imaging the fluorescence and phase of the quantum dot drop. This method holds great potential for multispectral fluorescence microscopy with additional single-pixel detectors or a spectrometer. Besides, this cost-efficient multimodal system might find broad applications in biomedical science and neuroscience.

Horizontal Directional Drilling-Length Detection Technology While Drilling Based on Bi-Electro-Magnetic Sensing.

PubMed

Wang, Yudan; Wen, Guojun; Chen, Han

2017-04-27

The drilling length is an important parameter in the process of horizontal directional drilling (HDD) exploration and recovery, but there has been a lack of accurate, automatically obtained statistics regarding this parameter. Herein, a technique for real-time HDD length detection and a management system based on the electromagnetic detection method with a microprocessor and two magnetoresistive sensors employing the software LabVIEW are proposed. The basic principle is to detect the change in the magnetic-field strength near a current coil while the drill stem and drill-stem joint successively pass through the current coil forward or backward. The detection system consists of a hardware subsystem and a software subsystem. The hardware subsystem employs a single-chip microprocessor as the main controller. A current coil is installed in front of the clamping unit, and two magneto resistive sensors are installed on the sides of the coil symmetrically and perpendicular to the direction of movement of the drill pipe. Their responses are used to judge whether the drill-stem joint is passing through the clamping unit; then, the order of their responses is used to judge the movement direction. The software subsystem is composed of a visual software running on the host computer and a software running in the slave microprocessor. The host-computer software processes, displays, and saves the drilling-length data, whereas the slave microprocessor software operates the hardware system. A combined test demonstrated the feasibility of the entire drilling-length detection system.

Horizontal Directional Drilling-Length Detection Technology While Drilling Based on Bi-Electro-Magnetic Sensing

PubMed Central

Wang, Yudan; Wen, Guojun; Chen, Han

2017-01-01

The drilling length is an important parameter in the process of horizontal directional drilling (HDD) exploration and recovery, but there has been a lack of accurate, automatically obtained statistics regarding this parameter. Herein, a technique for real-time HDD length detection and a management system based on the electromagnetic detection method with a microprocessor and two magnetoresistive sensors employing the software LabVIEW are proposed. The basic principle is to detect the change in the magnetic-field strength near a current coil while the drill stem and drill-stem joint successively pass through the current coil forward or backward. The detection system consists of a hardware subsystem and a software subsystem. The hardware subsystem employs a single-chip microprocessor as the main controller. A current coil is installed in front of the clamping unit, and two magneto resistive sensors are installed on the sides of the coil symmetrically and perpendicular to the direction of movement of the drill pipe. Their responses are used to judge whether the drill-stem joint is passing through the clamping unit; then, the order of their responses is used to judge the movement direction. The software subsystem is composed of a visual software running on the host computer and a software running in the slave microprocessor. The host-computer software processes, displays, and saves the drilling-length data, whereas the slave microprocessor software operates the hardware system. A combined test demonstrated the feasibility of the entire drilling-length detection system. PMID:28448445

Solid-phase single molecule biosensing using dual-color colocalization of fluorescent quantum dot nanoprobes

NASA Astrophysics Data System (ADS)

Liu, Jianbo; Yang, Xiaohai; Wang, Kemin; Wang, Qing; Liu, Wei; Wang, Dong

2013-10-01

The development of solid-phase surface-based single molecule imaging technology has attracted significant interest during the past decades. Here we demonstrate a sandwich hybridization method for highly sensitive detection of a single thrombin protein at a solid-phase surface based on the use of dual-color colocalization of fluorescent quantum dot (QD) nanoprobes. Green QD560-modified thrombin binding aptamer I (QD560-TBA I) were deposited on a positive poly(l-lysine) assembled layer, followed by bovine serum albumin blocking. It allowed the thrombin protein to mediate the binding of the easily detectable red QD650-modified thrombin binding aptamer II (QD650-TBA II) to the QD560-TBA I substrate. Thus, the presence of the target thrombin can be determined based on fluorescent colocalization measurements of the nanoassemblies, without target amplification or probe separation. The detection limit of this assay reached 0.8 pM. This fluorescent colocalization assay has enabled single molecule recognition in a separation-free detection format, and can serve as a sensitive biosensing platform that greatly suppresses the nonspecific adsorption false-positive signal. This method can be extended to other areas such as multiplexed immunoassay, single cell analysis, and real time biomolecule interaction studies.The development of solid-phase surface-based single molecule imaging technology has attracted significant interest during the past decades. Here we demonstrate a sandwich hybridization method for highly sensitive detection of a single thrombin protein at a solid-phase surface based on the use of dual-color colocalization of fluorescent quantum dot (QD) nanoprobes. Green QD560-modified thrombin binding aptamer I (QD560-TBA I) were deposited on a positive poly(l-lysine) assembled layer, followed by bovine serum albumin blocking. It allowed the thrombin protein to mediate the binding of the easily detectable red QD650-modified thrombin binding aptamer II (QD650-TBA II) to the QD560-TBA I substrate. Thus, the presence of the target thrombin can be determined based on fluorescent colocalization measurements of the nanoassemblies, without target amplification or probe separation. The detection limit of this assay reached 0.8 pM. This fluorescent colocalization assay has enabled single molecule recognition in a separation-free detection format, and can serve as a sensitive biosensing platform that greatly suppresses the nonspecific adsorption false-positive signal. This method can be extended to other areas such as multiplexed immunoassay, single cell analysis, and real time biomolecule interaction studies. Electronic supplementary information (ESI) available: Absorbance and fluorescence spectra of quantum dot nanoprobes, electrophoresis analysis, and experimental setup for fluorescence imaging with dual channels. See DOI: 10.1039/c3nr03291d

Imaging Action Potential in Single Mammalian Neurons by Tracking the Accompanying Sub-Nanometer Mechanical Motion.

PubMed

Yang, Yunze; Liu, Xian-Wei; Wang, Hui; Yu, Hui; Guan, Yan; Wang, Shaopeng; Tao, Nongjian

2018-03-28

Action potentials in neurons have been studied traditionally by intracellular electrophysiological recordings and more recently by the fluorescence detection methods. Here we describe a label-free optical imaging method that can measure mechanical motion in single cells with a sub-nanometer detection limit. Using the method, we have observed sub-nanometer mechanical motion accompanying the action potential in single mammalian neurons by averaging the repeated action potential spikes. The shape and width of the transient displacement are similar to those of the electrically recorded action potential, but the amplitude varies from neuron to neuron, and from one region of a neuron to another, ranging from 0.2-0.4 nm. The work indicates that action potentials may be studied noninvasively in single mammalian neurons by label-free imaging of the accompanying sub-nanometer mechanical motion.

Characteristics of mist 3D screen for projection type electro-holography

NASA Astrophysics Data System (ADS)

Sato, Koki; Okumura, Toshimichi; Kanaoka, Takumi; Koizumi, Shinya; Nishikawa, Satoko; Takano, Kunihiko

2006-01-01

The specification of hologram image is the full parallax 3D image. In this case we can get more natural 3D image because focusing and convergence are coincident each other. We try to get practical electro-holography system because for conventional electro-holography the image viewing angle is very small. This is due to the limited display pixel size. Now we are developing new method for large viewing angle by space projection method. White color laser is irradiated to single DMD panel (time shared CGH of RGB three colors). 3D space screen constructed by very small water particle is used to reconstruct the 3D image with large viewing angle by scattering of water particle.

In Situ Detection of MicroRNA Expression with RNAscope Probes.

PubMed

Yin, Viravuth P

2018-01-01

Elucidating the spatial resolution of gene transcripts provides important insight into potential gene function. MicroRNAs are short, singled-stranded noncoding RNAs that control gene expression through base-pair complementarity with target mRNAs in the 3' untranslated region (UTR) and inhibiting protein expression. However, given their small size of ~22- to 24-nt and low expression levels, standard in situ hybridization detection methods are not amendable for microRNA spatial resolution. Here, I describe a technique that employs RNAscope probe design and propriety amplification technology that provides simultaneous single molecule detection of individual microRNA and its target gene. This method allows for rapid and sensitive detection of noncoding RNA transcripts in frozen tissue sections.

Isothermal circular-strand-displacement polymerization of DNA and microRNA in digital microfluidic devices.

PubMed

Giuffrida, Maria Chiara; Zanoli, Laura Maria; D'Agata, Roberta; Finotti, Alessia; Gambari, Roberto; Spoto, Giuseppe

2015-02-01

Nucleic-acid amplification is a crucial step in nucleic-acid-sequence-detection assays. The use of digital microfluidic devices to miniaturize amplification techniques reduces the required sample volume and the analysis time and offers new possibilities for process automation and integration in a single device. The recently introduced droplet polymerase-chain-reaction (PCR) amplification methods require repeated cycles of two or three temperature-dependent steps during the amplification of the nucleic-acid target sequence. In contrast, low-temperature isothermal-amplification methods have no need for thermal cycling, thus requiring simplified microfluidic-device features. Here, the combined use of digital microfluidics and molecular-beacon (MB)-assisted isothermal circular-strand-displacement polymerization (ICSDP) to detect microRNA-210 sequences is described. MicroRNA-210 has been described as the most consistently and predominantly upregulated hypoxia-inducible factor. The nmol L(-1)-pmol L(-1) detection capabilities of the method were first tested by targeting single-stranded DNA sequences from the genetically modified Roundup Ready soybean. The ability of the droplet-ICSDP method to discriminate between full-matched, single-mismatched, and unrelated sequences was also investigated. The detection of a range of nmol L(-1)-pmol L(-1) microRNA-210 solutions compartmentalized in nanoliter-sized droplets was performed, establishing the ability of the method to detect as little as 10(-18) mol of microRNA target sequences compartmentalized in 20 nL droplets. The suitability of the method for biological samples was tested by detecting microRNA-210 from transfected K562 cells.

Ultrasensitive Single Fluorescence-Labeled Probe-Mediated Single Universal Primer-Multiplex-Droplet Digital Polymerase Chain Reaction for High-Throughput Genetically Modified Organism Screening.

PubMed

Niu, Chenqi; Xu, Yuancong; Zhang, Chao; Zhu, Pengyu; Huang, Kunlun; Luo, Yunbo; Xu, Wentao

2018-05-01

As genetically modified (GM) technology develops and genetically modified organisms (GMOs) become more available, GMOs face increasing regulations and pressure to adhere to strict labeling guidelines. A singleplex detection method cannot perform the high-throughput analysis necessary for optimal GMO detection. Combining the advantages of multiplex detection and droplet digital polymerase chain reaction (ddPCR), a single universal primer-multiplex-ddPCR (SUP-M-ddPCR) strategy was proposed for accurate broad-spectrum screening and quantification. The SUP increases efficiency of the primers in PCR and plays an important role in establishing a high-throughput, multiplex detection method. Emerging ddPCR technology has been used for accurate quantification of nucleic acid molecules without a standard curve. Using maize as a reference point, four heterologous sequences ( 35S, NOS, NPTII, and PAT) were selected to evaluate the feasibility and applicability of this strategy. Surprisingly, these four genes cover more than 93% of the transgenic maize lines and serve as preliminary screening sequences. All screening probes were labeled with FAM fluorescence, which allows the signals from the samples with GMO content and those without to be easily differentiated. This fiveplex screening method is a new development in GMO screening. Utilizing an optimal amplification assay, the specificity, limit of detection (LOD), and limit of quantitation (LOQ) were validated. The LOD and LOQ of this GMO screening method were 0.1% and 0.01%, respectively, with a relative standard deviation (RSD) < 25%. This method could serve as an important tool for the detection of GM maize from different processed, commercially available products. Further, this screening method could be applied to other fields that require reliable and sensitive detection of DNA targets.

Reduction in interval cancer rates following the introduction of two-view mammography in the UK breast screening programme

PubMed Central

Dibden, A; Offman, J; Parmar, D; Jenkins, J; Slater, J; Binysh, K; McSorley, J; Scorfield, S; Cumming, P; Liao, X-H; Ryan, M; Harker, D; Stevens, G; Rogers, N; Blanks, R; Sellars, S; Patnick, J; Duffy, S W

2014-01-01

Background: The introduction of two-view mammography at incident (subsequent) screens in the National Health Service Breast Screening Programme (NHSBSP) has led to an increased number of cancers detected at screen. However, the effect of two-view mammography on interval cancer rates has yet to be assessed. Methods: Routine screening and interval cancer data were collated from all screening programmes in the United Kingdom for women aged 50–64, screened between 1 April 2003 and 31 March 2005. Interval cancer rates were compared based on whether two-view mammography was in use at the last routine screen. Results: The reduction in interval cancers following screening using two-view mammography compared with one view was 0.68 per 1 000 women screened. Overall, this suggests the introduction of two-view mammography at incident screen was accompanied by a 15–20% reduction in interval cancer rates in the NHSBSP. Conclusion: The introduction of two-view mammography at incident screens is associated with a reduction in incidence of interval cancers. This is consistent with previous publications on a contemporaneous increase in screen-detected cancers. The results provide further evidence of the benefit of the use of two-view mammography at incident screens. PMID:24366303

Double-label immunofluorescence method for simultaneous detection of adenovirus and herpes simplex virus from the eye.

PubMed

Walpita, P; Darougar, S

1989-07-01

The development and application of a double-label immunofluorescence method which has the potential to screen for single or dual infections from any site, in single shell vial cultures, is described. In this study, a total of 1,141 ocular specimens were inoculated in shell vials, centrifuged at 15,000 X g for 1 h, incubated at 37 degrees C for 48 h, and fixed in methanol at room temperature for 15 min. The virus inclusions were detected by staining with a double-label indirect immunofluorescence procedure using mixtures of appropriate first antibodies, followed by fluorescein- and rhodamine-conjugated second antibodies. Each specimen was also inoculated in parallel by the conventional virus isolation method. The sensitivity and specificity of the double-label shell vial procedure were comparable to those with the conventional method, and the former test took only 48 h to complete. The test offers a rapid and simple single-vial procedure which allows for individual or simultaneous detection of multiple pathogens. It results in savings in time and cost over the conventional virus isolation method and other shell vial procedures.

Induction-detection electron spin resonance with spin sensitivity of a few tens of spins

DOE Office of Scientific and Technical Information (OSTI.GOV)

Artzi, Yaron; Twig, Ygal; Blank, Aharon

2015-02-23

Electron spin resonance (ESR) is a spectroscopic method that addresses electrons in paramagnetic materials directly through their spin properties. ESR has many applications, ranging from semiconductor characterization to structural biology and even quantum computing. Although it is very powerful and informative, ESR traditionally suffers from low sensitivity, requiring many millions of spins to get a measureable signal with commercial systems using the Faraday induction-detection principle. In view of this disadvantage, significant efforts were made recently to develop alternative detection schemes based, for example, on force, optical, or electrical detection of spins, all of which can reach single electron spin sensitivity.more » This sensitivity, however, comes at the price of limited applicability and usefulness with regard to real scientific and technological issues facing modern ESR which are currently dealt with conventional induction-detection ESR on a daily basis. Here, we present the most sensitive experimental induction-detection ESR setup and results ever recorded that can detect the signal from just a few tens of spins. They were achieved thanks to the development of an ultra-miniature micrometer-sized microwave resonator that was operated at ∼34 GHz at cryogenic temperatures in conjunction with a unique cryogenically cooled low noise amplifier. The test sample used was isotopically enriched phosphorus-doped silicon, which is of significant relevance to spin-based quantum computing. The sensitivity was experimentally verified with the aid of a unique high-resolution ESR imaging approach. These results represent a paradigm shift with respect to the capabilities and possible applications of induction-detection-based ESR spectroscopy and imaging.« less

Photocleavable DNA Barcoding Antibodies for Multiplexed Protein Analysis in Single Cells.

PubMed

Ullal, Adeeti V; Weissleder, Ralph

2015-01-01

We describe a DNA-barcoded antibody sensing technique for single cell protein analysis in which the barcodes are photocleaved and digitally detected without amplification steps (Ullal et al., Sci Transl Med 6:219, 2014). After photocleaving the unique ~70 mer DNA barcodes we use a fluorescent hybridization technology for detection, similar to what is commonly done for nucleic acid readouts. This protocol offers a simple method for multiplexed protein detection using 100+ antibodies and can be performed on clinical samples as well as single cells.

Detection of gait characteristics for scene registration in video surveillance system.

PubMed

Havasi, László; Szlávik, Zoltán; Szirányi, Tamás

2007-02-01

This paper presents a robust walk-detection algorithm, based on our symmetry approach which can be used to extract gait characteristics from video-image sequences. To obtain a useful descriptor of a walking person, we temporally track the symmetries of a person's legs. Our method is suitable for use in indoor or outdoor surveillance scenes. Determining the leading leg of the walking subject is important, and the presented method can identify this from two successive walk steps (one walk cycle). We tested the accuracy of the presented walk-detection method in a possible application: Image registration methods are presented which are applicable to multicamera systems viewing human subjects in motion.

Detection of individual atoms in helium buffer gas and observation of their real-time motion

NASA Technical Reports Server (NTRS)

Pan, C. L.; Prodan, J. V.; Fairbank, W. M., Jr.; She, C. Y.

1980-01-01

Single atoms are detected and their motion measured for the first time to our knowledge by the fluorescence photon-burst method in the presence of large quantities of buffer gas. A single-clipped digital correlator records the photon burst in real time and displays the atom's transit time across the laser beam. A comparison is made of the special requirements for single-atom detection in vacuum and in a buffer gas. Finally, the probability distribution of the bursts from many atoms is measured. It further proves that the bursts observed on resonance are due to single atoms and not simply to noise fluctuations.

High sensitivity fluorescent single particle and single molecule detection apparatus and method

DOEpatents

Mathies, Richard A.; Peck, Konan; Stryer, Lubert

1990-01-01

Apparatus is described for ultrasensitive detection of single fluorescent particles down to the single fluorescent molecule limit in a fluid or on a substrate comprising means for illuminating a predetermined volume of the fluid or area of the substrate whereby to emit light including background light from the fluid and burst of photons from particles residing in the area. The photon burst is detected in real time to generate output representative signal. The signal is received and the burst of energy from the fluorescent particles is distinguished from the background energy to provide an indication of the number, location or concentration of the particles or molecules.

Automated recording of home cage activity and temperature of individual rats housed in social groups: The Rodent Big Brother project

PubMed Central

Tse, Karen; Grant, Claire; Keerie, Amy; Simpson, David J.; Pedersen, John C.; Rimmer, Victoria; Leslie, Lauren; Klein, Stephanie K.; Karp, Natasha A.; Sillito, Rowland; Chartsias, Agis; Lukins, Tim; Heward, James; Vickers, Catherine; Chapman, Kathryn; Armstrong, J. Douglas

2017-01-01

Measuring the activity and temperature of rats is commonly required in biomedical research. Conventional approaches necessitate single housing, which affects their behavior and wellbeing. We have used a subcutaneous radiofrequency identification (RFID) transponder to measure ambulatory activity and temperature of individual rats when group-housed in conventional, rack-mounted home cages. The transponder location and temperature is detected by a matrix of antennae in a baseplate under the cage. An infrared high-definition camera acquires side-view video of the cage and also enables automated detection of vertical activity. Validation studies showed that baseplate-derived ambulatory activity correlated well with manual tracking and with side-view whole-cage video pixel movement. This technology enables individual behavioral and temperature data to be acquired continuously from group-housed rats in their familiar, home cage environment. We demonstrate its ability to reliably detect naturally occurring behavioral effects, extending beyond the capabilities of routine observational tests and conventional monitoring equipment. It has numerous potential applications including safety pharmacology, toxicology, circadian biology, disease models and drug discovery. PMID:28877172

Automated recording of home cage activity and temperature of individual rats housed in social groups: The Rodent Big Brother project.

PubMed

Redfern, William S; Tse, Karen; Grant, Claire; Keerie, Amy; Simpson, David J; Pedersen, John C; Rimmer, Victoria; Leslie, Lauren; Klein, Stephanie K; Karp, Natasha A; Sillito, Rowland; Chartsias, Agis; Lukins, Tim; Heward, James; Vickers, Catherine; Chapman, Kathryn; Armstrong, J Douglas

2017-01-01

Measuring the activity and temperature of rats is commonly required in biomedical research. Conventional approaches necessitate single housing, which affects their behavior and wellbeing. We have used a subcutaneous radiofrequency identification (RFID) transponder to measure ambulatory activity and temperature of individual rats when group-housed in conventional, rack-mounted home cages. The transponder location and temperature is detected by a matrix of antennae in a baseplate under the cage. An infrared high-definition camera acquires side-view video of the cage and also enables automated detection of vertical activity. Validation studies showed that baseplate-derived ambulatory activity correlated well with manual tracking and with side-view whole-cage video pixel movement. This technology enables individual behavioral and temperature data to be acquired continuously from group-housed rats in their familiar, home cage environment. We demonstrate its ability to reliably detect naturally occurring behavioral effects, extending beyond the capabilities of routine observational tests and conventional monitoring equipment. It has numerous potential applications including safety pharmacology, toxicology, circadian biology, disease models and drug discovery.

Interleaved EPI based fMRI improved by multiplexed sensitivity encoding (MUSE) and simultaneous multi-band imaging.

PubMed

Chang, Hing-Chiu; Gaur, Pooja; Chou, Ying-hui; Chu, Mei-Lan; Chen, Nan-kuei

2014-01-01

Functional magnetic resonance imaging (fMRI) is a non-invasive and powerful imaging tool for detecting brain activities. The majority of fMRI studies are performed with single-shot echo-planar imaging (EPI) due to its high temporal resolution. Recent studies have demonstrated that, by increasing the spatial-resolution of fMRI, previously unidentified neuronal networks can be measured. However, it is challenging to improve the spatial resolution of conventional single-shot EPI based fMRI. Although multi-shot interleaved EPI is superior to single-shot EPI in terms of the improved spatial-resolution, reduced geometric distortions, and sharper point spread function (PSF), interleaved EPI based fMRI has two main limitations: 1) the imaging throughput is lower in interleaved EPI; 2) the magnitude and phase signal variations among EPI segments (due to physiological noise, subject motion, and B0 drift) are translated to significant in-plane aliasing artifact across the field of view (FOV). Here we report a method that integrates multiple approaches to address the technical limitations of interleaved EPI-based fMRI. Firstly, the multiplexed sensitivity-encoding (MUSE) post-processing algorithm is used to suppress in-plane aliasing artifacts resulting from time-domain signal instabilities during dynamic scans. Secondly, a simultaneous multi-band interleaved EPI pulse sequence, with a controlled aliasing scheme incorporated, is implemented to increase the imaging throughput. Thirdly, the MUSE algorithm is then generalized to accommodate fMRI data obtained with our multi-band interleaved EPI pulse sequence, suppressing both in-plane and through-plane aliasing artifacts. The blood-oxygenation-level-dependent (BOLD) signal detectability and the scan throughput can be significantly improved for interleaved EPI-based fMRI. Our human fMRI data obtained from 3 Tesla systems demonstrate the effectiveness of the developed methods. It is expected that future fMRI studies requiring high spatial-resolvability and fidelity will largely benefit from the reported techniques.

Highly sensitive and quantitative detection of rare pathogens through agarose droplet microfluidic emulsion PCR at the single-cell level.

PubMed

Zhu, Zhi; Zhang, Wenhua; Leng, Xuefei; Zhang, Mingxia; Guan, Zhichao; Lu, Jiangquan; Yang, Chaoyong James

2012-10-21

Genetic alternations can serve as highly specific biomarkers to distinguish fatal bacteria or cancer cells from their normal counterparts. However, these mutations normally exist in very rare amount in the presence of a large excess of non-mutated analogs. Taking the notorious pathogen E. coli O157:H7 as the target analyte, we have developed an agarose droplet-based microfluidic ePCR method for highly sensitive, specific and quantitative detection of rare pathogens in the high background of normal bacteria. Massively parallel singleplex and multiplex PCR at the single-cell level in agarose droplets have been successfully established. Moreover, we challenged the system with rare pathogen detection and realized the sensitive and quantitative analysis of a single E. coli O157:H7 cell in the high background of 100,000 excess normal K12 cells. For the first time, we demonstrated rare pathogen detection through agarose droplet microfluidic ePCR. Such a multiplex single-cell agarose droplet amplification method enables ultra-high throughput and multi-parameter genetic analysis of large population of cells at the single-cell level to uncover the stochastic variations in biological systems.

A Single-Step Enrichment Medium for Nonchromogenic Isolation of Healthy and Cold-Injured Salmonella spp. from Fresh Vegetables.

PubMed

Kim, Hong-Seok; Choi, Dasom; Kang, Il-Byeong; Kim, Dong-Hyeon; Yim, Jin-Hyeok; Kim, Young-Ji; Chon, Jung-Whan; Oh, Deog-Hwan; Seo, Kun-Ho

2017-02-01

Culture-based detection of nontyphoidal Salmonella spp. in foods requires at least four working days; therefore, new detection methods that shorten the test time are needed. In this study, we developed a novel single-step Salmonella enrichment broth, SSE-1, and compared its detection capability with that of commercial single-step ONE broth-Salmonella (OBS) medium and a conventional two-step enrichment method using buffered peptone water and Rappaport-Vassiliadis soy broth (BPW-RVS). Minimally processed lettuce samples were artificially inoculated with low levels of healthy and cold-injured Salmonella Enteritidis (10 0 or 10 1 colony-forming unit/25 g), incubated in OBS, BPW-RVS, and SSE-1 broths, and streaked on xylose lysine deoxycholate (XLD) agar. Salmonella recoverability was significantly higher in BPW-RVS (79.2%) and SSE-1 (83.3%) compared to OBS (39.3%) (p < 0.05). Our data suggest that the SSE-1 single-step enrichment broth could completely replace two-step enrichment with reduced enrichment time from 48 to 24 h, performing better than commercial single-step enrichment medium in the conventional nonchromogenic Salmonella detection, thus saving time, labor, and cost.

A new effective assay to detect antimicrobial activity of filamentous fungi.

PubMed

Pereira, Eric; Santos, Ana; Reis, Francisca; Tavares, Rui M; Baptista, Paula; Lino-Neto, Teresa; Almeida-Aguiar, Cristina

2013-01-15

The search for new antimicrobial compounds and the optimization of production methods turn the use of antimicrobial susceptibility tests a routine. The most frequently used methods are based on agar diffusion assays or on dilution in agar or broth. For filamentous fungi, the most common antimicrobial activity detection methods comprise the co-culture of two filamentous fungal strains or the use of fungal extracts to test against single-cell microorganisms. Here we report a rapid, effective and reproducible assay to detect fungal antimicrobial activity against single-cell microorganisms. This method allows an easy way of performing a fast antimicrobial screening of actively growing fungi directly against yeast. Because it makes use of an actively growing mycelium, this bioassay also provides a way for studying the production dynamics of antimicrobial compounds by filamentous fungi. The proposed assay is less time consuming and introduces the innovation of allowing the direct detection of fungal antimicrobial properties against single cell microorganisms without the prior isolation of the active substance(s). This is particularly useful when performing large screenings for fungal antimicrobial activity. With this bioassay, antimicrobial activity of Hypholoma fasciculare against yeast species was observed for the first time. Copyright © 2012 Elsevier GmbH. All rights reserved.

Nanolock-Nanopore Facilitated Digital Diagnostics of Cancer Driver Mutation in Tumor Tissue.

PubMed

Wang, Yong; Tian, Kai; Shi, Ruicheng; Gu, Amy; Pennella, Michael; Alberts, Lindsey; Gates, Kent S; Li, Guangfu; Fan, Hongxin; Wang, Michael X; Gu, Li-Qun

2017-07-28

Cancer driver mutations are clinically significant biomarkers. In precision medicine, accurate detection of these oncogenic changes in patients would enable early diagnostics of cancer, individually tailored targeted therapy, and precise monitoring of treatment response. Here we investigated a novel nanolock-nanopore method for single-molecule detection of a serine/threonine protein kinase gene BRAF V600E mutation in tumor tissues of thyroid cancer patients. The method lies in a noncovalent, mutation sequence-specific nanolock. We found that the nanolock formed on the mutant allele/probe duplex can separate the duplex dehybridization procedure into two sequential steps in the nanopore. Remarkably, this stepwise unzipping kinetics can produce a unique nanopore electric marker, with which a single DNA molecule of the cancer mutant allele can be unmistakably identified in various backgrounds of the normal wild-type allele. The single-molecule sensitivity for mutant allele enables both binary diagnostics and quantitative analysis of mutation occurrence. In the current configuration, the method can detect the BRAF V600E mutant DNA lower than 1% in the tumor tissues. The nanolock-nanopore method can be adapted to detect a broad spectrum of both transversion and transition DNA mutations, with applications from diagnostics to targeted therapy.

The Impact of the Implementation of Edge Detection Methods on the Accuracy of Automatic Voltage Reading

NASA Astrophysics Data System (ADS)

Sidor, Kamil; Szlachta, Anna

2017-04-01

The article presents the impact of the edge detection method in the image analysis on the reading accuracy of the measured value. In order to ensure the automatic reading of the measured value by an analog meter, a standard webcam and the LabVIEW programme were applied. NI Vision Development tools were used. The Hough transform was used to detect the indicator. The programme output was compared during the application of several methods of edge detection. Those included: the Prewitt operator, the Roberts cross, the Sobel operator and the Canny edge detector. The image analysis was made for an analog meter indicator with the above-mentioned methods, and the results of that analysis were compared with each other and presented.

Development of a novel single tube nested PCR for enhanced detection of cytomegalovirus DNA from dried blood spots.

PubMed

Atkinson, C; Emery, V C; Griffiths, P D

2014-02-01

Newborn screening for congenital cytomegalovirus (CCMV) using dried blood spots (DBS) has been proposed because many developed countries have DBS screening programmes in place for other diseases. The aim of this study was to develop a rapid, single tube nested polymerase chain reaction (PCR) method for enhanced detection of CMV from DBS compared to existing (single target) real time PCRs. The new method was compared with existing real time PCRs for sensitivity and specificity. Overall sensitivity of the single target PCR assays in both asymptomatic and symptomatic infants with laboratory confirmed congenital CMV was 69% (CMV PCR or culture positive before day 21 of life). In contrast, the single tube nested assay had an increased sensitivity of 81% with100% specificity. Overall the assay detected CMV from a DBS equivalent to an original blood sample which contained 500IU/ml. In conclusion this single tube nested methodology allows simultaneous amplification and detection of CMV DNA in 1.5h removing the associated contamination risk of a two step nested PCR. Owing to its increased sensitivity, it has the potential to be used as a screening assay and ultimately allow early identification and intervention for children with congenital CMV. Copyright © 2013 Elsevier B.V. All rights reserved.

Rapid microscopy measurement of very large spectral images.

PubMed

Lindner, Moshe; Shotan, Zav; Garini, Yuval

2016-05-02

The spectral content of a sample provides important information that cannot be detected by the human eye or by using an ordinary RGB camera. The spectrum is typically a fingerprint of the chemical compound, its environmental conditions, phase and geometry. Thus measuring the spectrum at each point of a sample is important for a large range of applications from art preservation through forensics to pathological analysis of a tissue section. To date, however, there is no system that can measure the spectral image of a large sample in a reasonable time. Here we present a novel method for scanning very large spectral images of microscopy samples even if they cannot be viewed in a single field of view of the camera. The system is based on capturing information while the sample is being scanned continuously 'on the fly'. Spectral separation implements Fourier spectroscopy by using an interferometer mounted along the optical axis. High spectral resolution of ~5 nm at 500 nm could be achieved with a diffraction-limited spatial resolution. The acquisition time is fairly high and takes 6-8 minutes for a sample size of 10mm x 10mm measured under a bright-field microscope using a 20X magnification.

A methodological overview on molecular preimplantation genetic diagnosis and screening: a genomic future?

PubMed

Vendrell, Xavier; Bautista-Llácer, Rosa

2012-12-01

The genetic diagnosis and screening of preimplantation embryos generated by assisted reproduction technology has been consolidated in the prenatal care framework. The rapid evolution of DNA technologies is tending to molecular approaches. Our intention is to present a detailed methodological view, showing different diagnostic strategies based on molecular techniques that are currently applied in preimplantation genetic diagnosis. The amount of DNA from one single, or a few cells, obtained by embryo biopsy is a limiting factor for the molecular analysis. In this sense, genetic laboratories have developed molecular protocols considering this restrictive condition. Nevertheless, the development of whole-genome amplification methods has allowed preimplantation genetic diagnosis for two or more indications simultaneously, like the selection of histocompatible embryos plus detection of monogenic diseases or aneuploidies. Moreover, molecular techniques have permitted preimplantation genetic screening to progress, by implementing microarray-based comparative genome hybridization. Finally, a future view of the embryo-genetics field based on molecular advances is proposed. The normalization, cost-effectiveness analysis, and new technological tools are the next topics for preimplantation genetic diagnosis and screening. Concomitantly, these additions to assisted reproduction technologies could have a positive effect on the schedules of preimplantation studies.

Computerized detection of leukocytes in microscopic leukorrhea images.

PubMed

Zhang, Jing; Zhong, Ya; Wang, Xiangzhou; Ni, Guangming; Du, Xiaohui; Liu, Juanxiu; Liu, Lin; Liu, Yong

2017-09-01

Detection of leukocytes is critical for the routine leukorrhea exam, which is widely used in gynecological examinations. An elevated vaginal leukocyte count in women with bacterial vaginosis is a strong predictor of vaginal or cervical infections. In the routine leukorrhea exam, the counting of leukocytes is primarily performed by manual techniques. However, the viewing and counting of leukocytes from multiple high-power viewing fields on a glass slide under a microscope leads to subjectivity, low efficiency, and low accuracy. To date, many biological cells in stool, blood, and breast cancer have been studied to realize computerized detection; however, the detection of leukocytes in microscopic leukorrhea images has not been studied. Thus, there is an increasing need for computerized detection of leukocytes. There are two key processes in the computerized detection of leukocytes in digital image processing. One is segmentation; the other is intelligent classification. In this paper, we propose a combined ensemble to detect leukocytes in the microscopic leukorrhea image. After image segmentation and selecting likely leukocyte subimages, we obtain the leukocyte candidates. Then, for intelligent classification, we adopt two methods: feature extraction and classification by a support vector machine (SVM); applying a modified convolutional neural network (CNN) to the larger subimages. If different methods classify a candidate in the same category, the process is finished. If not, the outputs of the methods are provided to a classifier to further classify the candidate. After acquiring leukocyte candidates, we attempted three methods to perform classification. The first approach using features and SVM achieved 88% sensitivity, 97% specificity, and 92.5% accuracy. The second method using CNN achieved 95% sensitivity, 84% specificity, and 89.5% accuracy. Then, in the combination approach, we achieved 92% sensitivity, 95% specificity, and 93.5% accuracy. Finally, the images with marked and counted leukocytes were obtained. A novel computerized detection system was developed for automated detection of leukocytes in microscopic images. Different methods resulted in comparable overall qualities by enabling computerized detection of leukocytes. The proposed approach further improved the performance. This preliminary study proves the feasibility of computerized detection of leukocytes in clinical use. © 2017 American Association of Physicists in Medicine.

Single Laboratory Comparison of Host-Specific PCR Assays for the Detection of Bovine Fecal Pollution

EPA Science Inventory

There are numerous PCR-based methods available to detect bovine fecal pollution in ambient waters. Each method targets a different gene and microorganism leading to differences in method performance, making it difficult to determine which approach is most suitable for field appl...

Thin and Slow Smoke Detection by Using Frequency Image

NASA Astrophysics Data System (ADS)

Zheng, Guang; Oe, Shunitiro

In this paper, a new method to detect thin and slow smoke for early fire alarm by using frequency image has been proposed. The correlation coefficient of the frequency image between the current stage and the initial stage are calculated, so are the gray image correlation coefficient of the color image. When the thin smoke close to transparent enters into the camera view, the correlation coefficient of the frequency image becomes small, while the gray image correlation coefficient of the color image hardly change and keep large. When something which is not transparent, like human beings, etc., enters into the camera view, the correlation coefficient of the frequency image becomes small, as well as that of color image. Based on the difference of correlation coefficient between frequency image and color image in different situations, the thin smoke can be detected. Also, considering the movement of the thin smoke, miss detection caused by the illustration change or noise can be avoided. Several experiments in different situations are carried out, and the experimental results show the effect of the proposed method.

[Evaluation of the usefulness of various PCR method variations and nucleic acid hybridization for CMV infection in immunosuppressed patients].

PubMed

Siennicka, J; Trzcińska, A; Litwińska, B; Durlik, M; Seferyńska, I; Pałynyczko, G; Kańtoch, M

2000-01-01

In diagnosis of CMV infection various laboratory methods are used. The methods based on detection of viral nucleic acids have been introduced routinely in many laboratories. The aim of this study was to compare nucleic acid hybridisation method and various variants of PCR methods with respect to their ability to detect CMV DNA. The studied material comprised 60 blood samples from 19 patients including 13 renal transplant recipients and 6 with acute leukaemia. The samples were subjected to hybridisation (Murex Hybrid Capture System CMV DNA) and PCR carried out in 3 variants: with one pair of primers (single PCR), nested PCR and Digene SHARP System with detection of PCR product using a genetic probe in ELISA system. The sensitivity of the variants ranged from 10(0) particles of viral DNA in nested PCR to 10(2) in single PCR. The producer claimed the sensitivity of the hybridisation test to be 3 x 10(5) and it seems to be sufficient for detection of CMV infection. The obtained results show that sensitivity of hybridisation was comparable to that of single PCR and the possibility of obtaining quantitative results makes it superior, on efficacy of antiviral therapy, especially in monitoring CMV infection in immunossuppressed patients and in following the efficacy of antiviral treatment.

Detecting Earthquakes over a Seismic Network using Single-Station Similarity Measures

NASA Astrophysics Data System (ADS)

Bergen, Karianne J.; Beroza, Gregory C.

2018-03-01

New blind waveform-similarity-based detection methods, such as Fingerprint and Similarity Thresholding (FAST), have shown promise for detecting weak signals in long-duration, continuous waveform data. While blind detectors are capable of identifying similar or repeating waveforms without templates, they can also be susceptible to false detections due to local correlated noise. In this work, we present a set of three new methods that allow us to extend single-station similarity-based detection over a seismic network; event-pair extraction, pairwise pseudo-association, and event resolution complete a post-processing pipeline that combines single-station similarity measures (e.g. FAST sparse similarity matrix) from each station in a network into a list of candidate events. The core technique, pairwise pseudo-association, leverages the pairwise structure of event detections in its network detection model, which allows it to identify events observed at multiple stations in the network without modeling the expected move-out. Though our approach is general, we apply it to extend FAST over a sparse seismic network. We demonstrate that our network-based extension of FAST is both sensitive and maintains a low false detection rate. As a test case, we apply our approach to two weeks of continuous waveform data from five stations during the foreshock sequence prior to the 2014 Mw 8.2 Iquique earthquake. Our method identifies nearly five times as many events as the local seismicity catalog (including 95% of the catalog events), and less than 1% of these candidate events are false detections.

Single-tube analysis of DNA methylation with silica superparamagnetic beads.

PubMed

Bailey, Vasudev J; Zhang, Yi; Keeley, Brian P; Yin, Chao; Pelosky, Kristen L; Brock, Malcolm; Baylin, Stephen B; Herman, James G; Wang, Tza-Huei

2010-06-01

DNA promoter methylation is a signature for the silencing of tumor suppressor genes. Most widely used methods to detect DNA methylation involve 3 separate, independent processes: DNA extraction, bisulfite conversion, and methylation detection via a PCR method, such as methylation-specific PCR (MSP). This method includes many disconnected steps with associated losses of material, potentially reducing the analytical sensitivity required for analysis of challenging clinical samples. Methylation on beads (MOB) is a new technique that integrates DNA extraction, bisulfite conversion, and PCR in a single tube via the use of silica superparamagnetic beads (SSBs) as a common DNA carrier for facilitating cell debris removal and buffer exchange throughout the entire process. In addition, PCR buffer is used to directly elute bisulfite-treated DNA from SSBs for subsequent target amplifications. The diagnostic sensitivity of MOB was evaluated by methylation analysis of the CDKN2A [cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4); also known as p16(INK4a)] promoter in serum DNA of lung cancer patients and compared with that of conventional methods. Methylation analysis consisting of DNA extraction followed by bisulfite conversion and MSP was successfully carried out within 9 h in a single tube. The median pre-PCR DNA yield was 6.61-fold higher with the MOB technique than with conventional techniques. Furthermore, MOB increased the diagnostic sensitivity in our analysis of the CDKN2A promoter in patient serum by successfully detecting methylation in 74% of cancer patients, vs the 45% detection rate obtained with conventional techniques. The MOB technique successfully combined 3 processes into a single tube, thereby allowing ease in handling and an increased detection throughput. The increased pre-PCR yield in MOB allowed efficient, diagnostically sensitive methylation detection.

A Lateral Flow Biosensor for the Detection of Single Nucleotide Polymorphisms.

PubMed

Zeng, Lingwen; Xiao, Zhuo

2017-01-01

A lateral flow biosensor (LFB) is introduced for the detection of single nucleotide polymorphisms (SNPs). The assay is composed of two steps: circular strand displacement reaction and lateral flow biosensor detection. In step 1, the nucleotide at SNP site is recognized by T4 DNA ligase and the signal is amplified by strand displacement DNA polymerase, which can be accomplished at a constant temperature. In step 2, the reaction product of step 1 is detected by a lateral flow biosensor, which is a rapid and cost effective tool for nuclei acid detection. Comparing with conventional methods, it requires no complicated machines. It is suitable for the use of point of care diagnostics. Therefore, this simple, cost effective, robust, and promising LFB detection method of SNP has great potential for the detection of genetic diseases, personalized medicine, cancer related mutations, and drug-resistant mutations of infectious agents.

Channelized relevance vector machine as a numerical observer for cardiac perfusion defect detection task

NASA Astrophysics Data System (ADS)

Kalayeh, Mahdi M.; Marin, Thibault; Pretorius, P. Hendrik; Wernick, Miles N.; Yang, Yongyi; Brankov, Jovan G.

2011-03-01

In this paper, we present a numerical observer for image quality assessment, aiming to predict human observer accuracy in a cardiac perfusion defect detection task for single-photon emission computed tomography (SPECT). In medical imaging, image quality should be assessed by evaluating the human observer accuracy for a specific diagnostic task. This approach is known as task-based assessment. Such evaluations are important for optimizing and testing imaging devices and algorithms. Unfortunately, human observer studies with expert readers are costly and time-demanding. To address this problem, numerical observers have been developed as a surrogate for human readers to predict human diagnostic performance. The channelized Hotelling observer (CHO) with internal noise model has been found to predict human performance well in some situations, but does not always generalize well to unseen data. We have argued in the past that finding a model to predict human observers could be viewed as a machine learning problem. Following this approach, in this paper we propose a channelized relevance vector machine (CRVM) to predict human diagnostic scores in a detection task. We have previously used channelized support vector machines (CSVM) to predict human scores and have shown that this approach offers better and more robust predictions than the classical CHO method. The comparison of the proposed CRVM with our previously introduced CSVM method suggests that CRVM can achieve similar generalization accuracy, while dramatically reducing model complexity and computation time.

Tracking single membrane targets of human autoantibodies using single nanoparticle imaging.

PubMed

Jézéquel, Julie; Dupuis, Julien P; Maingret, François; Groc, Laurent

2018-04-21

Over the past decade, an increasing number of neurological and neuropsychiatric diseases have been associated with the expression of autoantibodies directed against neuronal targets, including neurotransmitter receptors. Although cell-based assays are routinely used in clinics to detect the presence of immunoglobulins, such tests often provide heterogeneous outcomes due to their limited sensitivity, especially at low titers. Thus, there is an urging need for new methods allowing the detection of autoantibodies in seropositive patients that cannot always be clinically distinguished from seronegative ones. Here we make a case for single nanoparticle imaging approaches as a highly sensitive antibody detection assay. Through high-affinity interactions between functionalized nanoparticles and autoantibodies that recognize extracellular domains of membrane neuronal targets, single nanoparticle imaging allows a live surface staining of transmembrane proteins and gives access to their surface dynamics. We show here that this method is well-suited to detect low titers of purified immunoglobulin G (IgG) from first-episode psychotic patients and demonstrate that these IgG target glutamatergic N-Methyl-d-Aspartate receptors (NMDAR) in live hippocampal neurons. The molecular behaviors of targeted membrane receptors were indistinguishable from those of endogenous GluN1 NMDAR subunit and were virtually independent of the IgG concentration present in the sample contrary to classical cell-based assays. Single nanoparticle imaging emerges as a real-time sensitive method to detect IgG directed against neuronal surface proteins, which could be used as an additional step to rule out ambiguous seropositivity diagnoses. Copyright © 2018 Elsevier B.V. All rights reserved.

Characterization of x-ray framing cameras for the National Ignition Facility using single photon pulse height analysis.

PubMed

Holder, J P; Benedetti, L R; Bradley, D K

2016-11-01

Single hit pulse height analysis is applied to National Ignition Facility x-ray framing cameras to quantify gain and gain variation in a single micro-channel plate-based instrument. This method allows the separation of gain from detectability in these photon-detecting devices. While pulse heights measured by standard-DC calibration methods follow the expected exponential distribution at the limit of a compound-Poisson process, gain-gated pulse heights follow a more complex distribution that may be approximated as a weighted sum of a few exponentials. We can reproduce this behavior with a simple statistical-sampling model.

Dual Low-Rank Pursuit: Learning Salient Features for Saliency Detection.

PubMed

Lang, Congyan; Feng, Jiashi; Feng, Songhe; Wang, Jingdong; Yan, Shuicheng

2016-06-01

Saliency detection is an important procedure for machines to understand visual world as humans do. In this paper, we consider a specific saliency detection problem of predicting human eye fixations when they freely view natural images, and propose a novel dual low-rank pursuit (DLRP) method. DLRP learns saliency-aware feature transformations by utilizing available supervision information and constructs discriminative bases for effectively detecting human fixation points under the popular low-rank and sparsity-pursuit framework. Benefiting from the embedded high-level information in the supervised learning process, DLRP is able to predict fixations accurately without performing the expensive object segmentation as in the previous works. Comprehensive experiments clearly show the superiority of the proposed DLRP method over the established state-of-the-art methods. We also empirically demonstrate that DLRP provides stronger generalization performance across different data sets and inherits the advantages of both the bottom-up- and top-down-based saliency detection methods.

Detecting presence of cardiovascular disease through mitochondria respiration as depicted through biophotonic emission.

PubMed

Rizzo, Nancy R; Hank, Nicole C; Zhang, Jian

2016-08-01

Increased production of reactive oxygen species (ROS) in mitochondria, play an important role in the cardiovascular system. Furthermore, oxidative metabolism of mitochondria comprised of biophoton emissions, are linked to ROS and oxidative stress. In this review we investigated the association between the ability of ClearViewTM system (ClearView) to indicate the presence or absence of cardiovascular disease through mitochondria respiration as depicted through biophotonic emission. One hundred and ninety-five out of the three hundred and fifty-three human subjects enrolled in this prospective, single site study had at least one cardiovascular related diagnosis. Measurements with ClearView consisted of scanning all 10 fingers twice. Images were captured through the ClearView software and analyzed to produce a scale that indicates the presence or absence of cardiovascular disease. The association of ClearView's ability to indicate the presence or absence of cardiovascular disease with a physician's diagnosis was assessed using odds ratios (OR) and area under ROC curve (AUC). Adjusting for age, OR of ClearView measurements conducted with capacitive barrier was 3.44 (95%CI: 2.13, 5.55) and the OR without the capacitive barrier was 2.15 (95%CI: 1.42, 3.23). The OR in men were 5.91 (95%CI: 2.35, 14.85) and 2.88 (95%CI: 1.38, 6.01), adjusting for age and corresponding to with and without capacitive barrier. The OR in women were 3.50 (95%CI: 1.86, 6.59) and 2.09 (95%CI: 1.20, 3.64) with and without capacitive barrier. AUCs for measurements with capacitive barrier were >0.90. ClearView detected the presence or absence of cardiovascular disease independent of other conditions. Published by Elsevier B.V.

Method for rapid base sequencing in DNA and RNA with two base labeling

DOEpatents

Jett, J.H.; Keller, R.A.; Martin, J.C.; Posner, R.G.; Marrone, B.L.; Hammond, M.L.; Simpson, D.J.

1995-04-11

A method is described for rapid-base sequencing in DNA and RNA with two-base labeling and employing fluorescent detection of single molecules at two wavelengths. Bases modified to accept fluorescent labels are used to replicate a single DNA or RNA strand to be sequenced. The bases are then sequentially cleaved from the replicated strand, excited with a chosen spectrum of electromagnetic radiation, and the fluorescence from individual, tagged bases detected in the order of cleavage from the strand. 4 figures.

Method for rapid base sequencing in DNA and RNA with two base labeling

DOEpatents

Jett, James H.; Keller, Richard A.; Martin, John C.; Posner, Richard G.; Marrone, Babetta L.; Hammond, Mark L.; Simpson, Daniel J.

1995-01-01

Method for rapid-base sequencing in DNA and RNA with two-base labeling and employing fluorescent detection of single molecules at two wavelengths. Bases modified to accept fluorescent labels are used to replicate a single DNA or RNA strand to be sequenced. The bases are then sequentially cleaved from the replicated strand, excited with a chosen spectrum of electromagnetic radiation, and the fluorescence from individual, tagged bases detected in the order of cleavage from the strand.

Combined FLIM and reflectance confocal microscopy for epithelial imaging

NASA Astrophysics Data System (ADS)

Jabbour, Joey M.; Cheng, Shuna; Shrestha, Sebina; Malik, Bilal; Jo, Javier A.; Applegate, Brian; Maitland, Kristen C.

2012-03-01

Current methods for detection of oral cancer lack the ability to delineate between normal and precancerous tissue with adequate sensitivity and specificity. The usual diagnostic mechanism involves visual inspection and palpation followed by tissue biopsy and histopathology, a process both invasive and time-intensive. A more sensitive and objective screening method can greatly facilitate the overall process of detection of early cancer. To this end, we present a multimodal imaging system with fluorescence lifetime imaging (FLIM) for wide field of view guidance and reflectance confocal microscopy for sub-cellular resolution imaging of epithelial tissue. Moving from a 12 x 12 mm2 field of view with 157 ìm lateral resolution using FLIM to 275 x 200 μm2 with lateral resolution of 2.2 μm using confocal microscopy, hamster cheek pouch model is imaged both in vivo and ex vivo. The results indicate that our dual modality imaging system can identify and distinguish between different tissue features, and, therefore, can potentially serve as a guide in early oral cancer detection..

Wave study of compound eyes for efficient infrared detection

NASA Astrophysics Data System (ADS)

Kilinc, Takiyettin Oytun; Hayran, Zeki; Kocer, Hasan; Kurt, Hamza

2017-08-01

Improving sensitivity in the infrared spectrum is a challenging task. Detecting infrared light over a wide bandwidth and at low power consumption is very important. Novel solutions can be acquired by mimicking biological eyes such as compound eye with many individual lenses inspired from the nature. The nature provides many ingenious approaches of sensing and detecting the surrounding environment. Even though compound eye consists of small optical units, it can detect wide-angle electromagnetic waves and it has high transmission and low reflection loss. Insects have eyes that are superior compared to human eyes (single-aperture eyes) in terms of compactness, robustness, wider field of view, higher sensitivity of light intensity and being cheap vision systems. All these desired properties are accompanied by an important drawback: lower spatial resolution. The first step to investigate the feasibility of bio-inspired optics in photodetectors is to perform light interaction with the optical system that gather light and detect it. The most common method used in natural vision systems is the ray analysis. Light wave characteristics are not taken into consideration in such analyses, such as the amount of energy at the focal point or photoreceptor site, the losses caused by reflection at the interfaces and absorption cannot be investigated. In this study, we present a bio-inspired optical detection system investigated by wave analysis. We numerically model the wave analysis based on Maxwell equations from the viewpoint of efficient light detection and revealing the light propagation after intercepting the first interface of the eye towards the photoreceptor site.

Integrated Micro-Optics for Microfluidic Detection.

PubMed

Kazama, Yuto; Hibara, Akihide

2016-01-01

A method of embedding micro-optics into a microfluidic device was proposed and demonstrated. First, the usefulness of embedded right-angle prisms was demonstrated in microscope observation. Lateral-view microscopic observation of an aqueous dye flow in a 100-μm-sized microchannel was demonstrated. Then, the embedded right-angle prisms were utilized for multi-beam laser spectroscopy. Here, crossed-beam thermal lens detection of a liquid sample was applied to glucose detection.

SCOUP: a probabilistic model based on the Ornstein-Uhlenbeck process to analyze single-cell expression data during differentiation.

PubMed

Matsumoto, Hirotaka; Kiryu, Hisanori

2016-06-08

Single-cell technologies make it possible to quantify the comprehensive states of individual cells, and have the power to shed light on cellular differentiation in particular. Although several methods have been developed to fully analyze the single-cell expression data, there is still room for improvement in the analysis of differentiation. In this paper, we propose a novel method SCOUP to elucidate differentiation process. Unlike previous dimension reduction-based approaches, SCOUP describes the dynamics of gene expression throughout differentiation directly, including the degree of differentiation of a cell (in pseudo-time) and cell fate. SCOUP is superior to previous methods with respect to pseudo-time estimation, especially for single-cell RNA-seq. SCOUP also successfully estimates cell lineage more accurately than previous method, especially for cells at an early stage of bifurcation. In addition, SCOUP can be applied to various downstream analyses. As an example, we propose a novel correlation calculation method for elucidating regulatory relationships among genes. We apply this method to a single-cell RNA-seq data and detect a candidate of key regulator for differentiation and clusters in a correlation network which are not detected with conventional correlation analysis. We develop a stochastic process-based method SCOUP to analyze single-cell expression data throughout differentiation. SCOUP can estimate pseudo-time and cell lineage more accurately than previous methods. We also propose a novel correlation calculation method based on SCOUP. SCOUP is a promising approach for further single-cell analysis and available at https://github.com/hmatsu1226/SCOUP.

Single-Cell Sequencing for Precise Cancer Research: Progress and Prospects.

PubMed

Zhang, Xiaoyan; Marjani, Sadie L; Hu, Zhaoyang; Weissman, Sherman M; Pan, Xinghua; Wu, Shixiu

2016-03-15

Advances in genomic technology have enabled the faithful detection and measurement of mutations and the gene expression profile of cancer cells at the single-cell level. Recently, several single-cell sequencing methods have been developed that permit the comprehensive and precise analysis of the cancer-cell genome, transcriptome, and epigenome. The use of these methods to analyze cancer cells has led to a series of unanticipated discoveries, such as the high heterogeneity and stochastic changes in cancer-cell populations, the new driver mutations and the complicated clonal evolution mechanisms, and the novel identification of biomarkers of variant tumors. These methods and the knowledge gained from their utilization could potentially improve the early detection and monitoring of rare cancer cells, such as circulating tumor cells and disseminated tumor cells, and promote the development of personalized and highly precise cancer therapy. Here, we discuss the current methods for single cancer-cell sequencing, with a strong focus on those practically used or potentially valuable in cancer research, including single-cell isolation, whole genome and transcriptome amplification, epigenome profiling, multi-dimensional sequencing, and next-generation sequencing and analysis. We also examine the current applications, challenges, and prospects of single cancer-cell sequencing. ©2016 American Association for Cancer Research.

New Surface-Enhanced Raman Sensing Chip Designed for On-Site Detection of Active Ricin in Complex Matrices Based on Specific Depurination.

PubMed

Tang, Ji-Jun; Sun, Jie-Fang; Lui, Rui; Zhang, Zong-Mian; Liu, Jing-Fu; Xie, Jian-Wei

2016-01-27

Quick and accurate on-site detection of active ricin has very important realistic significance in view of national security and defense. In this paper, optimized single-stranded oligodeoxynucleotides named poly(21dA), which function as a depurination substrate of active ricin, were screened and chemically attached on gold nanoparticles (AuNPs, ∼100 nm) via the Au-S bond [poly(21dA)-AuNPs]. Subsequently, poly(21dA)-AuNPs were assembled on a dihydrogen lipoic-acid-modified Si wafer (SH-Si), thus forming the specific surface-enhanced Raman spectroscopy (SERS) chip [poly(21dA)-AuNPs@SH-Si] for depurination of active ricin. Under optimized conditions, active ricin could specifically hydrolyze multiple adenines from poly(21dA) on the chip. This depurination-induced composition change could be conveniently monitored by measuring the distinct attenuation of the SERS signature corresponding to adenine. To improve sensitivity of this method, a silver nanoshell was deposited on post-reacted poly(21dA)-AuNPs, which lowered the limit of detection to 8.9 ng mL(-1). The utility of this well-controlled SERS chip was successfully demonstrated in food and biological matrices spiked with different concentrations of active ricin, thus showing to be very promising assay for reliable and rapid on-site detection of active ricin.

EINVis: a visualization tool for analyzing and exploring genetic interactions in large-scale association studies.

PubMed

Wu, Yubao; Zhu, Xiaofeng; Chen, Jian; Zhang, Xiang

2013-11-01

Epistasis (gene-gene interaction) detection in large-scale genetic association studies has recently drawn extensive research interests as many complex traits are likely caused by the joint effect of multiple genetic factors. The large number of possible interactions poses both statistical and computational challenges. A variety of approaches have been developed to address the analytical challenges in epistatic interaction detection. These methods usually output the identified genetic interactions and store them in flat file formats. It is highly desirable to develop an effective visualization tool to further investigate the detected interactions and unravel hidden interaction patterns. We have developed EINVis, a novel visualization tool that is specifically designed to analyze and explore genetic interactions. EINVis displays interactions among genetic markers as a network. It utilizes a circular layout (specially, a tree ring view) to simultaneously visualize the hierarchical interactions between single nucleotide polymorphisms (SNPs), genes, and chromosomes, and the network structure formed by these interactions. Using EINVis, the user can distinguish marginal effects from interactions, track interactions involving more than two markers, visualize interactions at different levels, and detect proxy SNPs based on linkage disequilibrium. EINVis is an effective and user-friendly free visualization tool for analyzing and exploring genetic interactions. It is publicly available with detailed documentation and online tutorial on the web at http://filer.case.edu/yxw407/einvis/. © 2013 WILEY PERIODICALS, INC.

Global cloud top height retrieval using SCIAMACHY limb spectra: model studies and first results

NASA Astrophysics Data System (ADS)

Eichmann, Kai-Uwe; Lelli, Luca; von Savigny, Christian; Sembhi, Harjinder; Burrows, John P.

2016-03-01

Cloud top heights (CTHs) are retrieved for the period 1 January 2003 to 7 April 2012 using height-resolved limb spectra measured with the SCanning Imaging Absorption SpectroMeter for Atmospheric CHartographY (SCIAMACHY) on board ENVISAT (ENVIronmental SATellite). In this study, we present the retrieval code SCODA (SCIAMACHY cloud detection algorithm) based on a colour index method and test the accuracy of the retrieved CTHs in comparison to other methods. Sensitivity studies using the radiative transfer model SCIATRAN show that the method is capable of detecting cloud tops down to about 5 km and very thin cirrus clouds up to the tropopause. Volcanic particles can be detected that occasionally reach the lower stratosphere. Upper tropospheric ice clouds are observable for a nadir cloud optical thickness (COT) ≥ 0.01, which is in the subvisual range. This detection sensitivity decreases towards the lowermost troposphere. The COT detection limit for a water cloud top height of 5 km is roughly 0.1. This value is much lower than thresholds reported for passive cloud detection methods in nadir-viewing direction. Low clouds at 2 to 3 km can only be retrieved under very clean atmospheric conditions, as light scattering of aerosol particles interferes with the cloud particle scattering. We compare co-located SCIAMACHY limb and nadir cloud parameters that are retrieved with the Semi-Analytical CloUd Retrieval Algorithm (SACURA). Only opaque clouds (τN,c > 5) are detected with the nadir passive retrieval technique in the UV-visible and infrared wavelength ranges. Thus, due to the frequent occurrence of thin clouds and subvisual cirrus clouds in the tropics, larger CTH deviations are detected between both viewing geometries. Zonal mean CTH differences can be as high as 4 km in the tropics. The agreement in global cloud fields is sufficiently good. However, the land-sea contrast, as seen in nadir cloud occurrence frequency distributions, is not observed in limb geometry. Co-located cloud top height measurements of the limb-viewing Michelson Interferometer for Passive Atmospheric Sounding (MIPAS) on ENVISAT are compared for the period from January 2008 to March 2012. The global CTH agreement of about 1 km is observed, which is smaller than the vertical field of view of both instruments. Lower stratospheric aerosols from volcanic eruptions occasionally interfere with the cloud retrieval and inhibit the detection of tropospheric clouds. The aerosol impact on cloud retrievals was studied for the volcanoes Kasatochi (August 2008), Sarychev Peak (June 2009), and Nabro (June 2011). Long-lasting aerosol scattering is detected after these events in the Northern Hemisphere for heights above 12.5 km in tropical and polar latitudes. Aerosol top heights up to about 22 km are found in 2009 and the enhanced lower stratospheric aerosol layer persisted for about 7 months. In August 2009 about 82 % of the lower stratosphere between 30 and 70° N was filled with scattering particles and nearly 50 % in October 2008.

Multiplexed Single Intact Cell Droplet Digital PCR (MuSIC ddPCR) Method for Specific Detection of Enterohemorrhagic E. coli (EHEC) in Food Enrichment Cultures

PubMed Central

McMahon, Tanis C.; Blais, Burton W.; Wong, Alex; Carrillo, Catherine D.

2017-01-01

Foodborne illness attributed to enterohemorrhagic E. coli (EHEC), a highly pathogenic subset of Shiga toxin-producing E. coli (STEC), is increasingly recognized as a significant public health issue. Current microbiological methods for identification of EHEC in foods often use PCR-based approaches to screen enrichment broth cultures for characteristic gene markers [i.e., Shiga toxin (stx) and intimin (eae)]. However, false positives arise when complex food matrices, such as beef, contain mixtures of eae-negative STEC and eae-positive E. coli, but no EHEC with both markers in a single cell. To reduce false-positive detection of EHEC in food enrichment samples, a Multiplexed, Single Intact Cell droplet digital PCR (MuSIC ddPCR) assay capable of detecting the co-occurrence of the stx and eae genes in a single bacterial cell was developed. This method requires: (1) dispersal of intact bacteria into droplets; (2) release of genomic DNA (gDNA) by heat lysis; and (3) amplification and detection of genetic targets (stx and eae) using standard TaqMan chemistries with ddPCR. Performance of the method was tested with panels of EHEC and non-target E. coli. By determining the linkage (i.e., the proportion of droplets in which stx and eae targets were both amplified), samples containing EHEC (typically greater than 20% linkage) could be distinguished from samples containing mixtures of eae-negative STEC and eae-positive E. coli (0–2% linkage). The use of intact cells was necessary as this linkage was not observed with gDNA extracts. EHEC could be accurately identified in enrichment broth cultures containing excess amounts of background E. coli and in enrichment cultures derived from ground beef/pork and leafy-green produce samples. To our knowledge, this is the first report of dual-target detection in single bacterial cells using ddPCR. The application of MuSIC ddPCR to enrichment-culture screening would reduce false-positives, thereby improving the cost, speed, and accuracy of current methods for EHEC detection in foods. PMID:28303131

Multiplexed Single Intact Cell Droplet Digital PCR (MuSIC ddPCR) Method for Specific Detection of Enterohemorrhagic E. coli (EHEC) in Food Enrichment Cultures.

PubMed

McMahon, Tanis C; Blais, Burton W; Wong, Alex; Carrillo, Catherine D

2017-01-01

Foodborne illness attributed to enterohemorrhagic E. coli (EHEC), a highly pathogenic subset of Shiga toxin-producing E. coli (STEC), is increasingly recognized as a significant public health issue. Current microbiological methods for identification of EHEC in foods often use PCR-based approaches to screen enrichment broth cultures for characteristic gene markers [i.e., Shiga toxin ( stx ) and intimin ( eae )]. However, false positives arise when complex food matrices, such as beef, contain mixtures of eae -negative STEC and eae -positive E. coli , but no EHEC with both markers in a single cell. To reduce false-positive detection of EHEC in food enrichment samples, a Multiplexed, Single Intact Cell droplet digital PCR (MuSIC ddPCR) assay capable of detecting the co-occurrence of the stx and eae genes in a single bacterial cell was developed. This method requires: (1) dispersal of intact bacteria into droplets; (2) release of genomic DNA (gDNA) by heat lysis; and (3) amplification and detection of genetic targets ( stx and eae ) using standard TaqMan chemistries with ddPCR. Performance of the method was tested with panels of EHEC and non-target E. coli . By determining the linkage (i.e., the proportion of droplets in which stx and eae targets were both amplified), samples containing EHEC (typically greater than 20% linkage) could be distinguished from samples containing mixtures of eae -negative STEC and eae -positive E. coli (0-2% linkage). The use of intact cells was necessary as this linkage was not observed with gDNA extracts. EHEC could be accurately identified in enrichment broth cultures containing excess amounts of background E. coli and in enrichment cultures derived from ground beef/pork and leafy-green produce samples. To our knowledge, this is the first report of dual-target detection in single bacterial cells using ddPCR. The application of MuSIC ddPCR to enrichment-culture screening would reduce false-positives, thereby improving the cost, speed, and accuracy of current methods for EHEC detection in foods.

A Prospective Study of the Use of Fetal Intelligent Navigation Echocardiography (FINE) to Obtain Standard Fetal Echocardiography Views

PubMed Central

Veronese, Paola; Bogana, Gianna; Cerutti, Alessia; Yeo, Lami; Romero, Roberto; Gervasi, Maria Teresa

2016-01-01

Objective To evaluate the performance of Fetal Intelligent Navigation Echocardiography (FINE) applied to spatiotemporal image correlation (STIC) volume datasets of the normal fetal heart in generating standard fetal echocardiography views. Methods In this prospective cohort study of patients with normal fetal hearts (19-30 gestational weeks), one or more STIC volume datasets were obtained of the apical four-chamber view. Each STIC volume successfully obtained was evaluated by STICLoop™ to determine its appropriateness before applying the FINE method. Visualization rates for standard fetal echocardiography views using diagnostic planes and/or Virtual Intelligent Sonographer Assistance (VIS-Assistance®) were calculated. Results One or more STIC volumes (n=463 total) were obtained in 246 patients. A single STIC volume per patient was analyzed using the FINE method. In normal cases, FINE was able to generate nine fetal echocardiography views using: 1) diagnostic planes in 76-100% of cases; 2) VIS-Assistance® in 96-100% of cases; and 3) a combination of diagnostic planes and/or VIS-Assistance® in 96-100% of cases. Conclusion FINE applied to STIC volumes can successfully generate nine standard fetal echocardiography views in 96-100% of cases in the second and third trimesters. This suggests that the technology can be used as a method to screen for congenital heart disease. PMID:27309391

Comparison of a single-view and a double-view aerosol optical depth retrieval algorithm

NASA Astrophysics Data System (ADS)

Henderson, Bradley G.; Chylek, Petr

2003-11-01

We compare the results of a single-view and a double-view aerosol optical depth (AOD) retrieval algorithm applied to image pairs acquired over NASA Stennis Space Center, Mississippi. The image data were acquired by the Department of Energy's (DOE) Multispectral Thermal Imager (MTI), a pushbroom satellite imager with 15 bands from the visible to the thermal infrared. MTI has the ability to acquire imagery in pairs in which the first image is a near-nadir view and the second image is off-nadir with a zenith angle of approximately 60°. A total of 15 image pairs were used in the analysis. For a given image pair, AOD retrieval is performed twice---once using a single-view algorithm applied to the near-nadir image, then again using a double-view algorithm. Errors for both retrievals are computed by comparing the results to AERONET AOD measurements obtained at the same time and place. The single-view algorithm showed an RMS error about the mean of 0.076 in AOD units, whereas the double-view algorithm showed a modest improvement with an RMS error of 0.06. The single-view errors show a positive bias which is presumed to be a result of the empirical relationship used to determine ground reflectance in the visible. A plot of AOD error of the double-view algorithm versus time shows a noticeable trend which is interpreted to be a calibration drift. When this trend is removed, the RMS error of the double-view algorithm drops to 0.030. The single-view algorithm qualitatively appears to perform better during the spring and summer whereas the double-view algorithm seems to be less sensitive to season.

Chip-based wide field-of-view nanoscopy

NASA Astrophysics Data System (ADS)

Diekmann, Robin; Helle, Øystein I.; Øie, Cristina I.; McCourt, Peter; Huser, Thomas R.; Schüttpelz, Mark; Ahluwalia, Balpreet S.

2017-04-01

Present optical nanoscopy techniques use a complex microscope for imaging and a simple glass slide to hold the sample. Here, we demonstrate the inverse: the use of a complex, but mass-producible optical chip, which hosts the sample and provides a waveguide for the illumination source, and a standard low-cost microscope to acquire super-resolved images via two different approaches. Waveguides composed of a material with high refractive-index contrast provide a strong evanescent field that is used for single-molecule switching and fluorescence excitation, thus enabling chip-based single-molecule localization microscopy. Additionally, multimode interference patterns induce spatial fluorescence intensity variations that enable fluctuation-based super-resolution imaging. As chip-based nanoscopy separates the illumination and detection light paths, total-internal-reflection fluorescence excitation is possible over a large field of view, with up to 0.5 mm × 0.5 mm being demonstrated. Using multicolour chip-based nanoscopy, we visualize fenestrations in liver sinusoidal endothelial cells.

A miniaturized NQR spectrometer for a multi-channel NQR-based detection device.

PubMed

Beguš, Samo; Jazbinšek, Vojko; Pirnat, Janez; Trontelj, Zvonko

2014-10-01

A low frequency (0.5-5 MHz) battery operated sensitive pulsed NQR spectrometer with a transmitter power up to 5 W and a total mass of about 3 kg aimed at detecting (14)N NQR signals, predominantly of illicit materials, was designed and assembled. This spectrometer uses a standard software defined radio (SDR) platform for the data acquisition unit. Signal processing is done with the LabView Virtual instrument on a personal computer. We successfully tested the spectrometer by measuring (14)N NQR signals from aminotetrazole monohydrate (ATMH), potassium nitrate (PN), paracetamol (PCM) and trinitrotoluene (TNT). Such a spectrometer is a feasible component of a portable single or multichannel (14)N NQR based detection device. Copyright © 2014 Elsevier Inc. All rights reserved.

Preliminary study on detection technology of the cladding weld of spent fuel storage pool

NASA Astrophysics Data System (ADS)

Qi, Pan; Cui, Hongyan; Feng, Meiming; Shao, Wenbin; Liao, Shusheng; Li, Wei

2018-04-01

As the first barrier of the Spent fuel storage pool, the steel cladding using different sizes (length×width) of 304L stainless steel with 3˜6mm thickness plate argon arc welded together which is direct contacted with boric acid water. Environmental humidity between the back of steel cladding and concrete, makes phosphate, chloride ion overflowed from the concrete that corroded on the weld zone with different mechanism. Part of the corrosion defects can penetrate leaded to leakage of boric acid water in penetration position accelerated crack propagation. In view of the above situation and combined with the actual needs of the power plant, the development of effective underwater nondestructive testing means of the weld area for periodic inspection and monitoring is necessary. A single method may lead to the missing of defects detection due to weld reinforcement unpolished. In this paper, eddy current array (ARRAY) and Alternating Current Field Measurement (ACFM) are adapted to test the limit sensitivity and resolution through by the specimens with artificial defects which make their detection abilities close to satisfy engineering requirements. The preliminary study found that Φ0.5mm through-wall hole and with 2mm length and 0.3mm width through-wall crack in the weld can be good inspected.

Ultrasound Techniques for Space Applications

NASA Technical Reports Server (NTRS)

Rooney, James A.

1985-01-01

Ultrasound has proven to be a safe non-invasive technique for imaging organs and measuring cardiovascular function. It has unique advantages for application to problems with man in space including evaluation of cardiovascular function both in serial studies and during critical operations. In addition, specialized instrumentation may be capable of detecting the onset of decompression sickness during EVA activities. A spatial location and three-dimensional reconstruction system is being developed to improve the accuracy and reproducibility for serial comparative ultrasound studies of cardiovascular function. The three-dimensional method permits the acquisition of ultrasonic images from many views that can be recombined into a single reconstruction of the heart or vasculature. In addition to conventional imaging and monitoring systems, it is sometimes necessary or desirable to develop instrumentation for special purposes. One example of this type of development is the design of a pulsed-Doppler system to monitor cerebral blood flow during critical operations such as re-entry. A second example is the design of a swept-frequency ultrasound system for the detection of bubbles in the circulatory system and/or soft tissues as an early indication of the onset of decompression sickness during EVA activities. This system exploits the resonant properties of bubbles and can detect both fundamental and second harmonic emissions from the insonified region.

Reversible gating of smart plasmonic molecular traps using thermoresponsive polymers for single-molecule detection

PubMed Central

Zheng, Yuanhui; Soeriyadi, Alexander H.; Rosa, Lorenzo; Ng, Soon Hock; Bach, Udo; Justin Gooding, J.

2015-01-01

Single-molecule surface-enhanced Raman spectroscopy (SERS) has attracted increasing interest for chemical and biochemical sensing. Many conventional substrates have a broad distribution of SERS enhancements, which compromise reproducibility and result in slow response times for single-molecule detection. Here we report a smart plasmonic sensor that can reversibly trap a single molecule at hotspots for rapid single-molecule detection. The sensor was fabricated through electrostatic self-assembly of gold nanoparticles onto a gold/silica-coated silicon substrate, producing a high yield of uniformly distributed hotspots on the surface. The hotspots were isolated with a monolayer of a thermoresponsive polymer (poly(N-isopropylacrylamide)), which act as gates for molecular trapping at the hotspots. The sensor shows not only a good SERS reproducibility but also a capability to repetitively trap and release molecules for single-molecular sensing. The single-molecule sensitivity is experimentally verified using SERS spectral blinking and bianalyte methods. PMID:26549539

Methods for Integrated Air Sampling and DNA Analysis for Detection of Airborne Fungal Spores

PubMed Central

Williams, Roger H.; Ward, Elaine; McCartney, H. Alastair

2001-01-01

Integrated air sampling and PCR-based methods for detecting airborne fungal spores, using Penicillium roqueforti as a model fungus, are described. P. roqueforti spores were collected directly into Eppendorf tubes using a miniature cyclone-type air sampler. They were then suspended in 0.1% Nonidet P-40, and counted using microscopy. Serial dilutions of the spores were made. Three methods were used to produce DNA for PCR tests: adding untreated spores to PCRs, disrupting spores (fracturing of spore walls to release the contents) using Ballotini beads, and disrupting spores followed by DNA purification. Three P. roqueforti-specific assays were tested: single-step PCR, nested PCR, and PCR followed by Southern blotting and probing. Disrupting the spores was found to be essential for achieving maximum sensitivity of the assay. Adding untreated spores to the PCR did allow the detection of P. roqueforti, but this was never achieved when fewer than 1,000 spores were added to the PCR. By disrupting the spores, with or without subsequent DNA purification, it was possible to detect DNA from a single spore. When known quantities of P. roqueforti spores were added to air samples consisting of high concentrations of unidentified fungal spores, pollen, and dust, detection sensitivity was reduced. P. roqueforti DNA could not be detected using untreated or disrupted spore suspensions added to the PCRs. However, using purified DNA, it was possible to detect 10 P. roqueforti spores in a background of 4,500 other spores. For all DNA extraction methods, nested PCR was more sensitive than single-step PCR or PCR followed by Southern blotting. PMID:11375150

Multiple kernel SVR based on the MRE for remote sensing water depth fusion detection

NASA Astrophysics Data System (ADS)

Wang, Jinjin; Ma, Yi; Zhang, Jingyu

2018-03-01

Remote sensing has an important means of water depth detection in coastal shallow waters and reefs. Support vector regression (SVR) is a machine learning method which is widely used in data regression. In this paper, SVR is used to remote sensing multispectral bathymetry. Aiming at the problem that the single-kernel SVR method has a large error in shallow water depth inversion, the mean relative error (MRE) of different water depth is retrieved as a decision fusion factor with single kernel SVR method, a multi kernel SVR fusion method based on the MRE is put forward. And taking the North Island of the Xisha Islands in China as an experimentation area, the comparison experiments with the single kernel SVR method and the traditional multi-bands bathymetric method are carried out. The results show that: 1) In range of 0 to 25 meters, the mean absolute error(MAE)of the multi kernel SVR fusion method is 1.5m,the MRE is 13.2%; 2) Compared to the 4 single kernel SVR method, the MRE of the fusion method reduced 1.2% (1.9%) 3.4% (1.8%), and compared to traditional multi-bands method, the MRE reduced 1.9%; 3) In 0-5m depth section, compared to the single kernel method and the multi-bands method, the MRE of fusion method reduced 13.5% to 44.4%, and the distribution of points is more concentrated relative to y=x.

Development of a Highly Sensitive Nested-PCR Procedure Using a Single Closed Tube for Detection of Erwinia amylovora in Asymptomatic Plant Material

PubMed Central

Llop, Pablo; Bonaterra, Anna; Peñalver, Javier; López, María M.

2000-01-01

A novel method, which involves a nested PCR in a single closed tube, was developed for the sensitive detection of Erwinia amylovora in plant material. The external and internal primer pairs used had different annealing temperatures and directed the amplification of a specific DNA fragment from plasmid pEA29. The procedure involved two consecutive PCRs, the first of which was performed at a higher annealing temperature that allowed amplification only by the external primer pair. Using pure cultures of E. amylovora, the sensitivity of the nested PCR in one tube was similar to that of a standard nested PCR in two tubes. The specificity and sensitivity were greater than those of standard PCR procedures that used a single primer pair. The presence of inhibitors in plant material, very common in E. amylovora hosts, is overcome with this system in combination with a simple DNA extraction protocol because it eliminates many of the inhibitory compounds. In addition, it needs a very small sample volume (1 μl of DNA extracted). With 83 samples of naturally infected material, this method achieved better results than any other PCR technique: standard PCR detected 55% of positive samples, two-tube nested PCR detected 71% of positive samples, and nested PCR in a single closed tube detected 78% of positive samples. When analyzing asymptomatic plant material, the number of positive samples detected by the developed nested PCR was also the highest, compared with the PCR protocols indicated previously (17, 20, and 25% of 251 samples analyzed, respectively). This method is proposed for the detection of endophytic and epiphytic populations of E. amylovora in epidemiological studies and for routine use in quarantine surveys, due to its high sensitivity, specificity, speed, and simplicity. PMID:10788384

Fast Detection of Airports on Remote Sensing Images with Single Shot MultiBox Detector

NASA Astrophysics Data System (ADS)

Xia, Fei; Li, HuiZhou

2018-01-01

This paper introduces a method for fast airport detection on remote sensing images (RSIs) using Single Shot MultiBox Detector (SSD). To our knowledge, this could be the first study which introduces an end-to-end detection model into airport detection on RSIs. Based on the common low-level features between natural images and RSIs, a convolution neural network trained on large amounts of natural images was transferred to tackle the airport detection problem with limited annotated data. To deal with the specific characteristics of RSIs, some related parameters in the SSD, such as the scales and layers, were modified for more accurate and rapider detection. The experiments show that the proposed method could achieve 83.5% Average Recall at 8 FPS on RSIs with the size of 1024*1024. In contrast to Faster R-CNN, an improvement on AP and speed could be obtained.

L-RCA (ligation-rolling circle amplification): a general method for genotyping of single nucleotide polymorphisms (SNPs)

PubMed Central

Qi, Xiaoquan; Bakht, Saleha; Devos, Katrien M.; Gale, Mike D.; Osbourn, Anne

2001-01-01

A flexible, non-gel-based single nucleotide polymorphism (SNP) detection method is described. The method adopts thermostable ligation for allele discrimination and rolling circle amplification (RCA) for signal enhancement. Clear allelic discrimination was achieved after staining of the final reaction mixtures with Cybr-Gold and visualisation by UV illumination. The use of a compatible buffer system for all enzymes allows the reaction to be initiated and detected in the same tube or microplate well, so that the experiment can be scaled up easily for high-throughput detection. Only a small amount of DNA (i.e. 50 ng) is required per assay, and use of carefully designed short padlock probes coupled with generic primers and probes make the SNP detection cost effective. Biallelic assay by hybridisation of the RCA products with fluorescence dye-labelled probes is demonstrated, indicating that ligation-RCA (L-RCA) has potential for multiplexed assays. PMID:11713336

Colorimetric detection of UV light-induced single-strand DNA breaks using gold nanoparticles.

PubMed

Kim, Joong Hyun; Chung, Chan Ho; Chung, Bong Hyun

2013-02-21

We developed a colorimetric method to specifically detect single-strand DNA breaks using gold nanoparticles. In our assay, broken DNA cannot stabilize gold nanoparticles to prevent salt-induced aggregation as good as intact DNA can, and this effect can be easily observed with the naked eye as a red-to-purple color change.

Earth analysis methods, subsurface feature detection methods, earth analysis devices, and articles of manufacture

DOEpatents

West, Phillip B [Idaho Falls, ID; Novascone, Stephen R [Idaho Falls, ID; Wright, Jerry P [Idaho Falls, ID

2012-05-29

Earth analysis methods, subsurface feature detection methods, earth analysis devices, and articles of manufacture are described. According to one embodiment, an earth analysis method includes engaging a device with the earth, analyzing the earth in a single substantially lineal direction using the device during the engaging, and providing information regarding a subsurface feature of the earth using the analysis.

Earth analysis methods, subsurface feature detection methods, earth analysis devices, and articles of manufacture

DOEpatents

West, Phillip B [Idaho Falls, ID; Novascone, Stephen R [Idaho Falls, ID; Wright, Jerry P [Idaho Falls, ID

2011-09-27

Earth analysis methods, subsurface feature detection methods, earth analysis devices, and articles of manufacture are described. According to one embodiment, an earth analysis method includes engaging a device with the earth, analyzing the earth in a single substantially lineal direction using the device during the engaging, and providing information regarding a subsurface feature of the earth using the analysis.

Single Laboratory Validated Method for Determination of Cylindrospermopsin and Anatoxin-a in Ambient Freshwaters by Liquid Chromatography/Tandem Mass Spectrometry (LC/MS/MS)

EPA Pesticide Factsheets

This document is a standardized single laboratory validated liquid chromatography/tandem mass spectrometry (LC/MS/MS) method for the detection and quantification of cyanotoxins (combined intracellular and extracellular) in ambient freshwaters.

A rapid, ratiometric, enzyme-free, and sensitive single-step miRNA detection using three-way junction based FRET probes

NASA Astrophysics Data System (ADS)

Luo, Qingying; Liu, Lin; Yang, Cai; Yuan, Jing; Feng, Hongtao; Chen, Yan; Zhao, Peng; Yu, Zhiqiang; Jin, Zongwen

2018-03-01

MicroRNAs (miRNAs) are single stranded endogenous molecules composed of only 18-24 nucleotides which are critical for gene expression regulating the translation of messenger RNAs. Conventional methods based on enzyme-assisted nucleic acid amplification techniques have many problems, such as easy contamination, high cost, susceptibility to false amplification, and tendency to have sequence mismatches. Here we report a rapid, ratiometric, enzyme-free, sensitive, and highly selective single-step miRNA detection using three-way junction assembled (or self-assembled) FRET probes. The developed strategy can be operated within the linear range from subnanomolar to hundred nanomolar concentrations of miRNAs. In comparison with the traditional approaches, our method showed high sensitivity for the miRNA detection and extreme selectivity for the efficient discrimination of single-base mismatches. The results reveal that the strategy paved a new avenue for the design of novel highly specific probes applicable in diagnostics and potentially in microscopic imaging of miRNAs in real biological environments.

Nanopore sensing at ultra-low concentrations using single-molecule dielectrophoretic trapping

PubMed Central

Freedman, Kevin J.; Otto, Lauren M.; Ivanov, Aleksandar P.; Barik, Avijit; Oh, Sang-Hyun; Edel, Joshua B.

2016-01-01

Single-molecule techniques are being developed with the exciting prospect of revolutionizing the healthcare industry by generating vast amounts of genetic and proteomic data. One exceptionally promising route is in the use of nanopore sensors. However, a well-known complexity is that detection and capture is predominantly diffusion limited. This problem is compounded when taking into account the capture volume of a nanopore, typically 108–1010 times smaller than the sample volume. To rectify this disproportionate ratio, we demonstrate a simple, yet powerful, method based on coupling single-molecule dielectrophoretic trapping to nanopore sensing. We show that DNA can be captured from a controllable, but typically much larger, volume and concentrated at the tip of a metallic nanopore. This enables the detection of single molecules at concentrations as low as 5 fM, which is approximately a 103 reduction in the limit of detection compared with existing methods, while still maintaining efficient throughput. PMID:26732171

Rapid single cell detection of Staphylococcus aureus by aptamer-conjugated gold nanoparticles

PubMed Central

Chang, Yi-Chung; Yang, Chia-Ying; Sun, Ruei-Lin; Cheng, Yi-Feng; Kao, Wei-Chen; Yang, Pan-Chyr

2013-01-01

Staphylococcus aureus is one of the most important human pathogens, causing more than 500,000 infections in the United States each year. Traditional methods for bacterial culture and identification take several days, wasting precious time for patients who are suffering severe bacterial infections. Numerous nucleic acid-based detection methods have been introduced to address this deficiency; however, the costs and requirement for expensive equipment may limit the widespread use of such technologies. Thus, there is an unmet demand of new platform technology to improve the bacterial detection and identification in clinical practice. In this study, we developed a rapid, ultra-sensitive, low cost, and non-polymerase chain reaction (PCR)-based method for bacterial identification. Using this method, which measures the resonance light-scattering signal of aptamer-conjugated gold nanoparticles, we successfully detected single S. aureus cell within 1.5 hours. This new platform technology may have potential to develop a rapid and sensitive bacterial testing at point-of-care. PMID:23689505

Rapid single cell detection of Staphylococcus aureus by aptamer-conjugated gold nanoparticles.

PubMed

Chang, Yi-Chung; Yang, Chia-Ying; Sun, Ruei-Lin; Cheng, Yi-Feng; Kao, Wei-Chen; Yang, Pan-Chyr

2013-01-01

Staphylococcus aureus is one of the most important human pathogens, causing more than 500,000 infections in the United States each year. Traditional methods for bacterial culture and identification take several days, wasting precious time for patients who are suffering severe bacterial infections. Numerous nucleic acid-based detection methods have been introduced to address this deficiency; however, the costs and requirement for expensive equipment may limit the widespread use of such technologies. Thus, there is an unmet demand of new platform technology to improve the bacterial detection and identification in clinical practice. In this study, we developed a rapid, ultra-sensitive, low cost, and non-polymerase chain reaction (PCR)-based method for bacterial identification. Using this method, which measures the resonance light-scattering signal of aptamer-conjugated gold nanoparticles, we successfully detected single S. aureus cell within 1.5 hours. This new platform technology may have potential to develop a rapid and sensitive bacterial testing at point-of-care.

Display of travelling 3D scenes from single integral-imaging capture

NASA Astrophysics Data System (ADS)

Martinez-Corral, Manuel; Dorado, Adrian; Hong, Seok-Min; Sola-Pikabea, Jorge; Saavedra, Genaro

2016-06-01

Integral imaging (InI) is a 3D auto-stereoscopic technique that captures and displays 3D images. We present a method for easily projecting the information recorded with this technique by transforming the integral image into a plenoptic image, as well as choosing, at will, the field of view (FOV) and the focused plane of the displayed plenoptic image. Furthermore, with this method we can generate a sequence of images that simulates a camera travelling through the scene from a single integral image. The application of this method permits to improve the quality of 3D display images and videos.

Solid-phase microfibers based on polyethylene glycol modified single-walled carbon nanotubes for the determination of chlorinated organic carriers in textiles.

PubMed

Zhang, Wei-Ya; Sun, Yin; Wang, Cheng-Ming; Wu, Cai-Ying

2011-09-01

Based on polyethylene glycol modified single-walled carbon nanotubes, a novel sol-gel fiber coating was prepared and applied to the headspace microextraction of chlorinated organic carriers (COCs) in textiles by gas chromatography-electron capture detection. The preparation of polyethylene glycol modified single-walled carbon nanotubes and the sol-gel fiber coating process was stated and confirmed by infrared spectra, Raman spectroscopy, and scanning electron microscopy. Several parameters affecting headspace microextraction, including extraction temperature, extraction time, salting-out effect, and desorption time, were optimized by detecting 11 COCs in simulative sweat samples. Compared with the commercial solid-phase microextraction fibers, the sol-gel polyethylene glycol modified single-walled carbon nanotubes fiber showed higher extraction efficiency, better thermal stability, and longer life span. The method detection limits for COCs were in the range from 0.02 to 7.5 ng L(-1) (S/N = 3). The linearity of the developed method varied from 0.001 to 50 μg L(-1) for all analytes, with coefficients of correlation greater than 0.974. The developed method was successfully applied to the analysis of trace COCs in textiles, the recoveries of the analytes indicated that the developed method was considerably useful for the determination of COCs in ecological textile samples.

Accelerated SPECT Monte Carlo Simulation Using Multiple Projection Sampling and Convolution-Based Forced Detection

NASA Astrophysics Data System (ADS)

Liu, Shaoying; King, Michael A.; Brill, Aaron B.; Stabin, Michael G.; Farncombe, Troy H.

2008-02-01

Monte Carlo (MC) is a well-utilized tool for simulating photon transport in single photon emission computed tomography (SPECT) due to its ability to accurately model physical processes of photon transport. As a consequence of this accuracy, it suffers from a relatively low detection efficiency and long computation time. One technique used to improve the speed of MC modeling is the effective and well-established variance reduction technique (VRT) known as forced detection (FD). With this method, photons are followed as they traverse the object under study but are then forced to travel in the direction of the detector surface, whereby they are detected at a single detector location. Another method, called convolution-based forced detection (CFD), is based on the fundamental idea of FD with the exception that detected photons are detected at multiple detector locations and determined with a distance-dependent blurring kernel. In order to further increase the speed of MC, a method named multiple projection convolution-based forced detection (MP-CFD) is presented. Rather than forcing photons to hit a single detector, the MP-CFD method follows the photon transport through the object but then, at each scatter site, forces the photon to interact with a number of detectors at a variety of angles surrounding the object. This way, it is possible to simulate all the projection images of a SPECT simulation in parallel, rather than as independent projections. The result of this is vastly improved simulation time as much of the computation load of simulating photon transport through the object is done only once for all projection angles. The results of the proposed MP-CFD method agrees well with the experimental data in measurements of point spread function (PSF), producing a correlation coefficient (r2) of 0.99 compared to experimental data. The speed of MP-CFD is shown to be about 60 times faster than a regular forced detection MC program with similar results.

Supercontinuum Fourier transform spectrometry with balanced detection on a single photodiode

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goncharov, Vasily; Hall, Gregory

Here, we have developed phase-sensitive signal detection and processing algorithms for Fourier transform spectrometers fitted with supercontinuum sources for applications requiring ultimate sensitivity. Similar to well-established approach of source noise cancellation through balanced detection of monochromatic light, our method is capable of reducing the relative intensity noise of polychromatic light by 40 dB. Unlike conventional balanced detection, which relies on differential absorption measured with a well matched pair of photo-detectors, our algorithm utilizes phase-sensitive differential detection on a single photodiode and is capable of the real-time correction for instabilities in supercontinuum spectral structure over a broad range of wavelengths. Inmore » the resulting method is universal in terms of applicable wavelengths and compatible with commercial spectrometers. We present a proof-of-principle experimental« less

Supercontinuum Fourier transform spectrometry with balanced detection on a single photodiode

DOE PAGES

Goncharov, Vasily; Hall, Gregory

2016-08-25

Here, we have developed phase-sensitive signal detection and processing algorithms for Fourier transform spectrometers fitted with supercontinuum sources for applications requiring ultimate sensitivity. Similar to well-established approach of source noise cancellation through balanced detection of monochromatic light, our method is capable of reducing the relative intensity noise of polychromatic light by 40 dB. Unlike conventional balanced detection, which relies on differential absorption measured with a well matched pair of photo-detectors, our algorithm utilizes phase-sensitive differential detection on a single photodiode and is capable of the real-time correction for instabilities in supercontinuum spectral structure over a broad range of wavelengths. Inmore » the resulting method is universal in terms of applicable wavelengths and compatible with commercial spectrometers. We present a proof-of-principle experimental« less

Dual role of allylsamarium bromide as a Grignard reagent and a single electron transfer reagent in the one-pot synthesis of terminal olefins.

PubMed

Li, Ying; Hu, Yuan-Yuan; Zhang, Song-Lin

2013-11-21

The utility of allylsamarium bromide, both as a nucleophilic reagent and a single-electron transfer reagent, in the reaction of carbonyl compounds with allylsamarium bromide in the presence of diethyl phosphate is reported in this communication. From a synthetic point of view, a simple one-pot method for the preparation of terminal olefins is developed.

Switchable DNA interfaces for the highly sensitive detection of label-free DNA targets.

PubMed

Rant, Ulrich; Arinaga, Kenji; Scherer, Simon; Pringsheim, Erika; Fujita, Shozo; Yokoyama, Naoki; Tornow, Marc; Abstreiter, Gerhard

2007-10-30

We report a method to detect label-free oligonucleotide targets. The conformation of surface-tethered probe nucleic acids is modulated by alternating electric fields, which cause the molecules to extend away from or fold onto the biased surface. Binding (hybridization) of targets to the single-stranded probes results in a pronounced enhancement of the layer-height modulation amplitude, monitored optically in real time. The method features an exceptional detection limit of <3 x 10(8) bound targets per cm(2) sensor area. Single base-pair mismatches in the sequences of DNA complements may readily be identified; moreover, binding kinetics and binding affinities can be determined with high accuracy. When driving the DNA to oscillate at frequencies in the kHz regime, distinct switching kinetics are revealed for single- and double-stranded DNA. Molecular dynamics are used to identify the binding state of molecules according to their characteristic kinetic fingerprints by using a chip-compatible detection format.

Switchable DNA interfaces for the highly sensitive detection of label-free DNA targets

PubMed Central

Rant, Ulrich; Arinaga, Kenji; Scherer, Simon; Pringsheim, Erika; Fujita, Shozo; Yokoyama, Naoki; Tornow, Marc; Abstreiter, Gerhard

2007-01-01

We report a method to detect label-free oligonucleotide targets. The conformation of surface-tethered probe nucleic acids is modulated by alternating electric fields, which cause the molecules to extend away from or fold onto the biased surface. Binding (hybridization) of targets to the single-stranded probes results in a pronounced enhancement of the layer-height modulation amplitude, monitored optically in real time. The method features an exceptional detection limit of <3 × 108 bound targets per cm2 sensor area. Single base-pair mismatches in the sequences of DNA complements may readily be identified; moreover, binding kinetics and binding affinities can be determined with high accuracy. When driving the DNA to oscillate at frequencies in the kHz regime, distinct switching kinetics are revealed for single- and double-stranded DNA. Molecular dynamics are used to identify the binding state of molecules according to their characteristic kinetic fingerprints by using a chip-compatible detection format. PMID:17951434

A PCR method for the detection and differentiation of Lentinus edodes and Trametes versicolor in defined-mixed cultures used for wastewater treatment.

PubMed

García-Mena, Jaime; Cano-Ramirez, Claudia; Garibay-Orijel, Claudio; Ramirez-Canseco, Sergio; Poggi-Varaldo, Héctor M

2005-06-01

A PCR-based method for the quantitative detection of Lentinus edodes and Trametes versicolor, two ligninolytic fungi applied for wastewater treatment and bioremediation, was developed. Genomic DNA was used to optimize a PCR method targeting the conserved copper-binding sequence of laccase genes. The method allowed the quantitative detection and differentiation of these fungi in single and defined-mixed cultures after fractionation of the PCR products by electrophoresis in agarose gels. Amplified products of about 150 bp for L. edodes, and about 200 bp for T. versicolor were purified and cloned. The PCR method showed a linear detection response in the 1.0 microg-1 ng range. The same method was tested with genomic DNA from a third fungus (Phanerochaete chrysosporium), yielding a fragment of about 400 bp. Southern-blot and DNA sequence analysis indicated that a specific PCR product was amplified from each genome, and that these corresponded to sequences of laccase genes. This PCR protocol permits the detection and differentiation of three ligninolytic fungi by amplifying DNA fragments of different sizes using a single pair of primers, without further enzymatic restriction of the PCR products. This method has potential use in the monitoring, evaluation, and improvement of fungal cultures used in wastewater treatment processes.

Algorithm for parametric community detection in networks.

PubMed

Bettinelli, Andrea; Hansen, Pierre; Liberti, Leo

2012-07-01

Modularity maximization is extensively used to detect communities in complex networks. It has been shown, however, that this method suffers from a resolution limit: Small communities may be undetectable in the presence of larger ones even if they are very dense. To alleviate this defect, various modifications of the modularity function have been proposed as well as multiresolution methods. In this paper we systematically study a simple model (proposed by Pons and Latapy [Theor. Comput. Sci. 412, 892 (2011)] and similar to the parametric model of Reichardt and Bornholdt [Phys. Rev. E 74, 016110 (2006)]) with a single parameter α that balances the fraction of within community edges and the expected fraction of edges according to the configuration model. An exact algorithm is proposed to find optimal solutions for all values of α as well as the corresponding successive intervals of α values for which they are optimal. This algorithm relies upon a routine for exact modularity maximization and is limited to moderate size instances. An agglomerative hierarchical heuristic is therefore proposed to address parametric modularity detection in large networks. At each iteration the smallest value of α for which it is worthwhile to merge two communities of the current partition is found. Then merging is performed and the data are updated accordingly. An implementation is proposed with the same time and space complexity as the well-known Clauset-Newman-Moore (CNM) heuristic [Phys. Rev. E 70, 066111 (2004)]. Experimental results on artificial and real world problems show that (i) communities are detected by both exact and heuristic methods for all values of the parameter α; (ii) the dendrogram summarizing the results of the heuristic method provides a useful tool for substantive analysis, as illustrated particularly on a Les Misérables data set; (iii) the difference between the parametric modularity values given by the exact method and those given by the heuristic is moderate; (iv) the heuristic version of the proposed parametric method, viewed as a modularity maximization tool, gives better results than the CNM heuristic for large instances.

Development and test of photon counting lidar

NASA Astrophysics Data System (ADS)

Wang, Chun-hui; Wang, Ao-you; Tao, Yu-liang; Li, Xu; Peng, Huan; Meng, Pei-bei

2018-02-01

In order to satisfy the application requirements of spaceborne three dimensional imaging lidar , a prototype of nonscanning multi-channel lidar based on receiver field of view segmentation was designed and developed. High repetition frequency micro-pulse lasers, optics fiber array and Geiger-mode APD, combination with time-correlated single photon counting technology, were adopted to achieve multi-channel detection. Ranging experiments were carried out outdoors. In low echo photon condition, target photon counting showed time correlated and noise photon counting were random. Detection probability and range precision versus threshold were described and range precision increased from 0.44 to 0.11 when threshold increased from 4 to 8.

Detecting earthquakes over a seismic network using single-station similarity measures

NASA Astrophysics Data System (ADS)

Bergen, Karianne J.; Beroza, Gregory C.

2018-06-01

New blind waveform-similarity-based detection methods, such as Fingerprint and Similarity Thresholding (FAST), have shown promise for detecting weak signals in long-duration, continuous waveform data. While blind detectors are capable of identifying similar or repeating waveforms without templates, they can also be susceptible to false detections due to local correlated noise. In this work, we present a set of three new methods that allow us to extend single-station similarity-based detection over a seismic network; event-pair extraction, pairwise pseudo-association, and event resolution complete a post-processing pipeline that combines single-station similarity measures (e.g. FAST sparse similarity matrix) from each station in a network into a list of candidate events. The core technique, pairwise pseudo-association, leverages the pairwise structure of event detections in its network detection model, which allows it to identify events observed at multiple stations in the network without modeling the expected moveout. Though our approach is general, we apply it to extend FAST over a sparse seismic network. We demonstrate that our network-based extension of FAST is both sensitive and maintains a low false detection rate. As a test case, we apply our approach to 2 weeks of continuous waveform data from five stations during the foreshock sequence prior to the 2014 Mw 8.2 Iquique earthquake. Our method identifies nearly five times as many events as the local seismicity catalogue (including 95 per cent of the catalogue events), and less than 1 per cent of these candidate events are false detections.

Gastric cancer screening of a high-risk population in Japan using serum pepsinogen and barium digital radiography.

PubMed

Ohata, Hiroshi; Oka, Masashi; Yanaoka, Kimihiko; Shimizu, Yasuhito; Mukoubayashi, Chizu; Mugitani, Kouichi; Iwane, Masataka; Nakamura, Hideya; Tamai, Hideyuki; Arii, Kenji; Nakata, Hiroya; Yoshimura, Noriko; Takeshita, Tetsuya; Miki, Kazumasa; Mohara, Osamu; Ichinose, Masao

2005-10-01

With the aim of developing more efficient gastric cancer screening programs for use in Japan, we studied a new screening program that combines serum pepsinogen (PG) testing and barium digital radiography (DR). A total of 17 647 middle-aged male subjects underwent workplace screening over a 7-year period using a combination of PG testing and DR. This program's effectiveness, as well as other characteristics of the program, was analyzed. Forty-nine cases of gastric cancer were detected (comprising 88% early cancer cases). The detection rate was 0.28%, and the positive predictive value was 0.85%. The PG test detected 63.3% of cases, DR detected 69.4% of cases, and both tests were positive in 32.7% of cancer cases. The two methods were almost equally effective, and were considerably more effective than conventional screening using photofluorography. Each screening method detected a distinct gastric cancer subgroup; the PG test efficiently detected asymptomatic small early cancer with intestinal type histology, while DR was efficient at detecting cancers with depressed or ulcerated morphology and diffuse type histology. The cost for the detection of a single cancer was much less than that for conventional screening. In fact, it is possible to further reduce the cost of detecting a single cancer to a cost comparable to that of surgically resecting a single gastric cancer. Thus, it is probable that a highly efficient gastric cancer screening system can be implemented by combining the two screening methods. Such a screening program would be beneficial in a population at high risk for gastric cancer.

Detection and identification of genetically modified EE-1 brinjal (Solanum melongena) by single, multiplex and SYBR® real-time PCR.

PubMed

Ballari, Rajashekhar V; Martin, Asha; Gowda, Lalitha R

2013-01-01

Brinjal is an important vegetable crop. Major crop loss of brinjal is due to insect attack. Insect-resistant EE-1 brinjal has been developed and is awaiting approval for commercial release. Consumer health concerns and implementation of international labelling legislation demand reliable analytical detection methods for genetically modified (GM) varieties. End-point and real-time polymerase chain reaction (PCR) methods were used to detect EE-1 brinjal. In end-point PCR, primer pairs specific to 35S CaMV promoter, NOS terminator and nptII gene common to other GM crops were used. Based on the revealed 3' transgene integration sequence, primers specific for the event EE-1 brinjal were designed. These primers were used for end-point single, multiplex and SYBR-based real-time PCR. End-point single PCR showed that the designed primers were highly specific to event EE-1 with a sensitivity of 20 pg of genomic DNA, corresponding to 20 copies of haploid EE-1 brinjal genomic DNA. The limits of detection and quantification for SYBR-based real-time PCR assay were 10 and 100 copies respectively. The prior development of detection methods for this important vegetable crop will facilitate compliance with any forthcoming labelling regulations. Copyright © 2012 Society of Chemical Industry.

Single Upconversion Nanoparticle-Bacterium Cotrapping for Single-Bacterium Labeling and Analysis.

PubMed

Xin, Hongbao; Li, Yuchao; Xu, Dekang; Zhang, Yueli; Chen, Chia-Hung; Li, Baojun

2017-04-01

Detecting and analyzing pathogenic bacteria in an effective and reliable manner is crucial for the diagnosis of acute bacterial infection and initial antibiotic therapy. However, the precise labeling and analysis of bacteria at the single-bacterium level are a technical challenge but very important to reveal important details about the heterogeneity of cells and responds to environment. This study demonstrates an optical strategy for single-bacterium labeling and analysis by the cotrapping of single upconversion nanoparticles (UCNPs) and bacteria together. A single UCNP with an average size of ≈120 nm is first optically trapped. Both ends of a single bacterium are then trapped and labeled with single UCNPs emitting green light. The labeled bacterium can be flexibly moved to designated locations for further analysis. Signals from bacteria of different sizes are detected in real time for single-bacterium analysis. This cotrapping method provides a new approach for single-pathogenic-bacterium labeling, detection, and real-time analysis at the single-particle and single-bacterium level. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Blood detection in wireless capsule endoscopy using expectation maximization clustering

NASA Astrophysics Data System (ADS)

Hwang, Sae; Oh, JungHwan; Cox, Jay; Tang, Shou Jiang; Tibbals, Harry F.

2006-03-01

Wireless Capsule Endoscopy (WCE) is a relatively new technology (FDA approved in 2002) allowing doctors to view most of the small intestine. Other endoscopies such as colonoscopy, upper gastrointestinal endoscopy, push enteroscopy, and intraoperative enteroscopy could be used to visualize up to the stomach, duodenum, colon, and terminal ileum, but there existed no method to view most of the small intestine without surgery. With the miniaturization of wireless and camera technologies came the ability to view the entire gestational track with little effort. A tiny disposable video capsule is swallowed, transmitting two images per second to a small data receiver worn by the patient on a belt. During an approximately 8-hour course, over 55,000 images are recorded to a worn device and then downloaded to a computer for later examination. Typically, a medical clinician spends more than two hours to analyze a WCE video. Research has been attempted to automatically find abnormal regions (especially bleeding) to reduce the time needed to analyze the videos. The manufacturers also provide the software tool to detect the bleeding called Suspected Blood Indicator (SBI), but its accuracy is not high enough to replace human examination. It was reported that the sensitivity and the specificity of SBI were about 72% and 85%, respectively. To address this problem, we propose a technique to detect the bleeding regions automatically utilizing the Expectation Maximization (EM) clustering algorithm. Our experimental results indicate that the proposed bleeding detection method achieves 92% and 98% of sensitivity and specificity, respectively.

Labeled RFS-Based Track-Before-Detect for Multiple Maneuvering Targets in the Infrared Focal Plane Array.

PubMed

Li, Miao; Li, Jun; Zhou, Yiyu

2015-12-08

The problem of jointly detecting and tracking multiple targets from the raw observations of an infrared focal plane array is a challenging task, especially for the case with uncertain target dynamics. In this paper a multi-model labeled multi-Bernoulli (MM-LMB) track-before-detect method is proposed within the labeled random finite sets (RFS) framework. The proposed track-before-detect method consists of two parts-MM-LMB filter and MM-LMB smoother. For the MM-LMB filter, original LMB filter is applied to track-before-detect based on target and measurement models, and is integrated with the interacting multiple models (IMM) approach to accommodate the uncertainty of target dynamics. For the MM-LMB smoother, taking advantage of the track labels and posterior model transition probability, the single-model single-target smoother is extended to a multi-model multi-target smoother. A Sequential Monte Carlo approach is also presented to implement the proposed method. Simulation results show the proposed method can effectively achieve tracking continuity for multiple maneuvering targets. In addition, compared with the forward filtering alone, our method is more robust due to its combination of forward filtering and backward smoothing.

Labeled RFS-Based Track-Before-Detect for Multiple Maneuvering Targets in the Infrared Focal Plane Array

PubMed Central

Li, Miao; Li, Jun; Zhou, Yiyu

2015-01-01

The problem of jointly detecting and tracking multiple targets from the raw observations of an infrared focal plane array is a challenging task, especially for the case with uncertain target dynamics. In this paper a multi-model labeled multi-Bernoulli (MM-LMB) track-before-detect method is proposed within the labeled random finite sets (RFS) framework. The proposed track-before-detect method consists of two parts—MM-LMB filter and MM-LMB smoother. For the MM-LMB filter, original LMB filter is applied to track-before-detect based on target and measurement models, and is integrated with the interacting multiple models (IMM) approach to accommodate the uncertainty of target dynamics. For the MM-LMB smoother, taking advantage of the track labels and posterior model transition probability, the single-model single-target smoother is extended to a multi-model multi-target smoother. A Sequential Monte Carlo approach is also presented to implement the proposed method. Simulation results show the proposed method can effectively achieve tracking continuity for multiple maneuvering targets. In addition, compared with the forward filtering alone, our method is more robust due to its combination of forward filtering and backward smoothing. PMID:26670234

Source Detection with Bayesian Inference on ROSAT All-Sky Survey Data Sample

NASA Astrophysics Data System (ADS)

Guglielmetti, F.; Voges, W.; Fischer, R.; Boese, G.; Dose, V.

2004-07-01

We employ Bayesian inference for the joint estimation of sources and background on ROSAT All-Sky Survey (RASS) data. The probabilistic method allows for detection improvement of faint extended celestial sources compared to the Standard Analysis Software System (SASS). Background maps were estimated in a single step together with the detection of sources without pixel censoring. Consistent uncertainties of background and sources are provided. The source probability is evaluated for single pixels as well as for pixel domains to enhance source detection of weak and extended sources.

THE SCREENING AND RANKING ALGORITHM FOR CHANGE-POINTS DETECTION IN MULTIPLE SAMPLES

PubMed Central

Song, Chi; Min, Xiaoyi; Zhang, Heping

2016-01-01

The chromosome copy number variation (CNV) is the deviation of genomic regions from their normal copy number states, which may associate with many human diseases. Current genetic studies usually collect hundreds to thousands of samples to study the association between CNV and diseases. CNVs can be called by detecting the change-points in mean for sequences of array-based intensity measurements. Although multiple samples are of interest, the majority of the available CNV calling methods are single sample based. Only a few multiple sample methods have been proposed using scan statistics that are computationally intensive and designed toward either common or rare change-points detection. In this paper, we propose a novel multiple sample method by adaptively combining the scan statistic of the screening and ranking algorithm (SaRa), which is computationally efficient and is able to detect both common and rare change-points. We prove that asymptotically this method can find the true change-points with almost certainty and show in theory that multiple sample methods are superior to single sample methods when shared change-points are of interest. Additionally, we report extensive simulation studies to examine the performance of our proposed method. Finally, using our proposed method as well as two competing approaches, we attempt to detect CNVs in the data from the Primary Open-Angle Glaucoma Genes and Environment study, and conclude that our method is faster and requires less information while our ability to detect the CNVs is comparable or better. PMID:28090239

Flexible, multi-measurement guided wave damage detection under varying temperatures

NASA Astrophysics Data System (ADS)

Douglass, Alexander C. S.; Harley, Joel B.

2018-04-01

Temperature compensation in structural health monitoring helps identify damage in a structure by removing data variations due to environmental conditions, such as temperature. Stretch-based methods are one of the most commonly used temperature compensation methods. To account for variations in temperature, stretch-based methods optimally stretch signals in time to optimally match a measurement to a baseline. All of the data is then compared with the single baseline to determine the presence of damage. Yet, for these methods to be effective, the measurement and the baseline must satisfy the inherent assumptions of the temperature compensation method. In many scenarios, these assumptions are wrong, the methods generate error, and damage detection fails. To improve damage detection, a multi-measurement damage detection method is introduced. By using each measurement in the dataset as a baseline, error caused by imperfect temperature compensation is reduced. The multi-measurement method increases the detection effectiveness of our damage metric, or damage indicator, over time and reduces the presence of additional peaks caused by temperature that could be mistaken for damage. By using many baselines, the variance of the damage indicator is reduced and the effects from damage are amplified. Notably, the multi-measurement improves damage detection over single-measurement methods. This is demonstrated through an increase in the maximum of our damage signature from 0.55 to 0.95 (where large values, up to a maximum of one, represent a statistically significant change in the data due to damage).

Robust estimation of mammographic breast density: a patient-based approach

NASA Astrophysics Data System (ADS)

Heese, Harald S.; Erhard, Klaus; Gooßen, Andre; Bulow, Thomas

2012-02-01

Breast density has become an established risk indicator for developing breast cancer. Current clinical practice reflects this by grading mammograms patient-wise as entirely fat, scattered fibroglandular, heterogeneously dense, or extremely dense based on visual perception. Existing (semi-) automated methods work on a per-image basis and mimic clinical practice by calculating an area fraction of fibroglandular tissue (mammographic percent density). We suggest a method that follows clinical practice more strictly by segmenting the fibroglandular tissue portion directly from the joint data of all four available mammographic views (cranio-caudal and medio-lateral oblique, left and right), and by subsequently calculating a consistently patient-based mammographic percent density estimate. In particular, each mammographic view is first processed separately to determine a region of interest (ROI) for segmentation into fibroglandular and adipose tissue. ROI determination includes breast outline detection via edge-based methods, peripheral tissue suppression via geometric breast height modeling, and - for medio-lateral oblique views only - pectoral muscle outline detection based on optimizing a three-parameter analytic curve with respect to local appearance. Intensity harmonization based on separately acquired calibration data is performed with respect to compression height and tube voltage to facilitate joint segmentation of available mammographic views. A Gaussian mixture model (GMM) on the joint histogram data with a posteriori calibration guided plausibility correction is finally employed for tissue separation. The proposed method was tested on patient data from 82 subjects. Results show excellent correlation (r = 0.86) to radiologist's grading with deviations ranging between -28%, (q = 0.025) and +16%, (q = 0.975).

Probing cellular heterogeneity in cytokine-secreting immune cells using droplet-based microfluidics.

PubMed

Chokkalingam, Venkatachalam; Tel, Jurjen; Wimmers, Florian; Liu, Xin; Semenov, Sergey; Thiele, Julian; Figdor, Carl G; Huck, Wilhelm T S

2013-12-21

Here, we present a platform to detect cytokine (IL-2, IFN-γ, TNF-α) secretion of single, activated T-cells in droplets over time. We use a novel droplet-based microfluidic approach to encapsulate cells in monodisperse agarose droplets together with functionalized cytokine-capture beads for subsequent binding and detection of secreted cytokines from single cells. This method allows high-throughput detection of cellular heterogeneity and maps subsets within cell populations with specific functions.

The MetaTelescope, a System for the Detection of Objects in Low and Higher Earth Orbits

NASA Astrophysics Data System (ADS)

Boer, M.

We present an original design involving several telescopes for the detection of mobiles in space over a very wide field of view. The system uses relatively simple and cheap telescopes associated with commercial CCD cameras that can be placed either in a single location or in relatively close (100m - 10km) locations. This last set-up opens the possibility of detecting parallaxes, but sky conditions should remain almost identical. Areas on the order of 800 square degrees can be surveyed. The system is versatile, i.e. it can detect and follow up objects either in the LEO or higher orbits. We will present the system, how it can be operated in order to have a more efficient setup while using even less telescopes, and possible implementations for space surveillance activities.

Single Laboratory Validated Method for Determination of Microcystins and Nodularin in Ambient Freshwaters by Solid Phase Extraction and Liquid Chromatography/ Tandem Mass Spectrometry (LC/MS/MS)

EPA Pesticide Factsheets

This document is a standardized, single laboratory validated liquid chromatography/tandem mass spectrometry (LC/MS/MS) method for the detection of cyanotoxins—microsystins and nodularin (combined intracellular and extracellular)—in ambient freshwaters.

Single phase computed tomography is equivalent to dual phase method for localizing hyperfunctioning parathyroid glands in patients with primary hyperparathyroidism: a retrospective review

PubMed Central

Morón, Fanny; Delumpa, Alfred; Guffey, Danielle; Dunaway, David

2017-01-01

Objective This study aims to compare the sensitivity of dual phase (non-contrast and arterial) versus single phase (arterial) CT for detection of hyper-functioning parathyroid glands in patients with primary hyperparathyroidism. Methods The CT scans of thirty-two patients who have biochemical evidence of primary hyperparathyroidism, pathologically proven parathyroid adenomas, and pre-operative multiphase parathyroid imaging were evaluated retrospectively in order to compare the adequacy of single phase vs. dual phase CT scans for the detection of parathyroid adenomas. Results The parathyroid adenomas were localized in 83% of cases on single arterial phase CT and 80% of cases on dual phase CT. The specificity for localization of parathyroid tumor was 96% for single phase CT and 97% for dual phase CT. The results were not significantly different (p = 0.695). These results are similar to those found in the literature for multiphase CT of 55–94%. Conclusions Our study supports the use of a single arterial phase CT for the detection of hyperfunctioning parathyroid adenomas. Advances in knowledge: a single arterial phase CT has similar sensitivity for localizing parathyroid adenomas as dual phase CT and significantly reduces radiation dose to the patient. PMID:28828238

Highly specific and cost-efficient detection of Salmonella Paratyphi A combining aptamers with single-walled carbon nanotubes.

PubMed

Yang, Ming; Peng, Zhihui; Ning, Yi; Chen, Yongzhe; Zhou, Qin; Deng, Le

2013-05-22

In this paper, a panel of single-stranded DNA aptamers with high affinity and specificity against Salmonella Paratyphi A was selected from an enriched oligonucleotide pool by a whole-cell-Systematic Evolution of Ligands by Exponential Enrichment (SELEX) procedure, during which four other Salmonella serovars were used as counter-selection targets. It was determined through a fluorescence assay that the selected aptamers had high binding ability and specificity to this pathogen. The dissociation constant of these aptamers were up to nanomolar range, and aptamer Apt22 with the lowest Kd (47 ± 3 nM) was used in cell imaging experiments. To detect this bacteria with high specificity and cost-efficiently, a novel useful detection method was also constructed based on the noncovalent self-assembly of single-walled carbon nanotubes (SWNTs) and DNAzyme-labeled aptamer detection probes. The amounts of target bacteria could be quantified by exploiting chemoluminescence intensity changes at 420 nm and the detection limit of the method was 103 cfu/mL. This study demonstrated the applicability of Salmonella specific aptamers and their potential for use in the detection of Salmonella in food, clinical and environmental samples.

Approaching the Limit in Atomic Spectrochemical Analysis.

ERIC Educational Resources Information Center

Hieftje, Gary M.

1982-01-01

To assess the ability of current analytical methods to approach the single-atom detection level, theoretical and experimentally determined detection levels are presented for several chemical elements. A comparison of these methods shows that the most sensitive atomic spectrochemical technique currently available is based on emission from…

Diagnostic Accuracy and Cost-Effectiveness of Alternative Methods for Detection of Soil-Transmitted Helminths in a Post-Treatment Setting in Western Kenya

PubMed Central

Kepha, Stella; Kihara, Jimmy H.; Njenga, Sammy M.; Pullan, Rachel L.; Brooker, Simon J.

2014-01-01

Objectives This study evaluates the diagnostic accuracy and cost-effectiveness of the Kato-Katz and Mini-FLOTAC methods for detection of soil-transmitted helminths (STH) in a post-treatment setting in western Kenya. A cost analysis also explores the cost implications of collecting samples during school surveys when compared to household surveys. Methods Stool samples were collected from children (n = 652) attending 18 schools in Bungoma County and diagnosed by the Kato-Katz and Mini-FLOTAC coprological methods. Sensitivity and additional diagnostic performance measures were analyzed using Bayesian latent class modeling. Financial and economic costs were calculated for all survey and diagnostic activities, and cost per child tested, cost per case detected and cost per STH infection correctly classified were estimated. A sensitivity analysis was conducted to assess the impact of various survey parameters on cost estimates. Results Both diagnostic methods exhibited comparable sensitivity for detection of any STH species over single and consecutive day sampling: 52.0% for single day Kato-Katz; 49.1% for single-day Mini-FLOTAC; 76.9% for consecutive day Kato-Katz; and 74.1% for consecutive day Mini-FLOTAC. Diagnostic performance did not differ significantly between methods for the different STH species. Use of Kato-Katz with school-based sampling was the lowest cost scenario for cost per child tested ($10.14) and cost per case correctly classified ($12.84). Cost per case detected was lowest for Kato-Katz used in community-based sampling ($128.24). Sensitivity analysis revealed the cost of case detection for any STH decreased non-linearly as prevalence rates increased and was influenced by the number of samples collected. Conclusions The Kato-Katz method was comparable in diagnostic sensitivity to the Mini-FLOTAC method, but afforded greater cost-effectiveness. Future work is required to evaluate the cost-effectiveness of STH surveillance in different settings. PMID:24810593

Research on distributed optical fiber sensing data processing method based on LabVIEW

NASA Astrophysics Data System (ADS)

Li, Zhonghu; Yang, Meifang; Wang, Luling; Wang, Jinming; Yan, Junhong; Zuo, Jing

2018-01-01

The pipeline leak detection and leak location problem have gotten extensive attention in the industry. In this paper, the distributed optical fiber sensing system is designed based on the heat supply pipeline. The data processing method of distributed optical fiber sensing based on LabVIEW is studied emphatically. The hardware system includes laser, sensing optical fiber, wavelength division multiplexer, photoelectric detector, data acquisition card and computer etc. The software system is developed using LabVIEW. The software system adopts wavelet denoising method to deal with the temperature information, which improved the SNR. By extracting the characteristic value of the fiber temperature information, the system can realize the functions of temperature measurement, leak location and measurement signal storage and inquiry etc. Compared with traditional negative pressure wave method or acoustic signal method, the distributed optical fiber temperature measuring system can measure several temperatures in one measurement and locate the leak point accurately. It has a broad application prospect.

Finger tips detection for two handed gesture recognition

NASA Astrophysics Data System (ADS)

Bhuyan, M. K.; Kar, Mithun Kumar; Neog, Debanga Raj

2011-10-01

In this paper, a novel algorithm is proposed for fingertips detection in view of two-handed static hand pose recognition. In our method, finger tips of both hands are detected after detecting hand regions by skin color-based segmentation. At first, the face is removed in the image by using Haar classifier and subsequently, the regions corresponding to the gesturing hands are isolated by a region labeling technique. Next, the key geometric features characterizing gesturing hands are extracted for two hands. Finally, for all possible/allowable finger movements, a probabilistic model is developed for pose recognition. Proposed method can be employed in a variety of applications like sign language recognition and human-robot-interactions etc.

Sulfide chemiluminescence detection

DOEpatents

Spurlin, Stanford R.; Yeung, Edward S.

1985-01-01

A method of chemiluminescently determining a sulfide which is either hydrogen sulfide or methyl mercaptan by reacting the sulfide with chlorine dioxide at low pressure and under conditions which allow a longer reaction time in emission of a single photon for every two sulfide containing species, and thereafter, chemiluminescently detecting and determining the sulfide. The invention also relates not only to the detection method, but the novel chemical reaction and a specifically designed chemiluminescence detection cell for the reaction.

Spectroelectrochemical detection of microRNA-155 based on functional RNA immobilization onto ITO/GNP nanopattern.

PubMed

Mohammadniaei, Mohsen; Yoon, Jinho; Lee, Taek; Choi, Jeong-Woo

2018-05-20

We fabricated a microRNA biosensor using the combination of surface enhanced Raman spectroscopy (SERS) and electrochemical (EC) techniques. For the first time, the weaknesses of each techniques for microRNA detection was compensated by the other ones to give rise to the specific and wide-range detection of miR-155. A single stranded 3' methylene blue (MB) and 5' thiol-modified RNA (MB-ssRNA-SH) was designed to detect the target miR-155 and immobilized onto the gold nanoparticle-modified ITO (ITO/GNP). Upon the invasion of target strand, the double-stranded RNA transformed rapidly to an upright structure resulting in a notable decrease in SERS and redox signals of the MB. For the first time, by combination of SERS and EC techniques in a single platform we extended the dynamic range of both techniques from 10 pM to 450 nM (SERS: 10 pM-5 nM and EC: 5 nM-450 nM). As well, the SERS technique improved the detection limit of the EC method from 100 pM to 100 fM, while the EC method covered single-mismatch detection which was the SERS deficiency. The fabricated single-step biosensor possessing a good capability of miRNA detection in human serum, could be employed throughout the broad ranges of biomedical and bioelectronics applications. Copyright © 2018 Elsevier B.V. All rights reserved.

Aspects of detection and tracking of ground targets from an airborne EO/IR sensor

NASA Astrophysics Data System (ADS)

Balaji, Bhashyam; Sithiravel, Rajiv; Daya, Zahir; Kirubarajan, Thiagalingam

2015-05-01

An airborne EO/IR (electro-optical/infrared) camera system comprises of a suite of sensors, such as a narrow and wide field of view (FOV) EO and mid-wave IR sensors. EO/IR camera systems are regularly employed on military and search and rescue aircrafts. The EO/IR system can be used to detect and identify objects rapidly in daylight and at night, often with superior performance in challenging conditions such as fog. There exist several algorithms for detecting potential targets in the bearing elevation grid. The nonlinear filtering problem is one of estimation of the kinematic parameters from bearing and elevation measurements from a moving platform. In this paper, we developed a complete model for the state of a target as detected by an airborne EO/IR system and simulated a typical scenario with single target with 1 or 2 airborne sensors. We have demonstrated the ability to track the target with `high precision' and noted the improvement from using two sensors on a single platform or on separate platforms. The performance of the Extended Kalman filter (EKF) is investigated on simulated data. Image/video data collected from an IR sensor on an airborne platform are processed using an image tracking by detection algorithm.

Rapid and sensitive multiplex single-tube nested PCR for the identification of five human Plasmodium species.

PubMed

Saito, Takahiro; Kikuchi, Aoi; Kaneko, Akira; Isozumi, Rie; Teramoto, Isao; Kimura, Masatsugu; Hirasawa, Noriyasu; Hiratsuka, Masahiro

2018-06-01

Malaria is caused by five species of Plasmodium in humans. Microscopy is currently used for pathogen detection, requiring considerable training and technical expertise as the parasites are often difficult to differentiate morphologically. Rapid diagnostic tests are as reliable as microscopy and offer faster diagnoses but possess lower detection limits and are incapable of distinguishing among the parasitic species. To improve global health efforts towards malaria control, a rapid, sensitive, species-specific, and economically viable diagnostic method is needed. In this study, we designed a malaria diagnostic method involving a multiplex single-tube nested PCR targeting Plasmodium mitochondrial cytochrome c oxidase III and single-stranded tag hybridization chromatographic printed-array strip. The detection sensitivity was found to be at least 40 times higher than that of agarose gel electrophoresis with ethidium bromide. This system also enables the identification of both single- and mixed-species malaria infections. The assay was validated with 152 Kenyan samples; using nested PCR as the standard, the assay's sensitivity and specificity were 88.7% and 100.0%, respectively. The turnaround time required, from PCR preparation to signal detection, is 90min. Our method should improve the diagnostic speed, treatment efficacy, and control of malaria, in addition to facilitating surveillance within global malaria eradication programs. Copyright © 2018 Elsevier B.V. All rights reserved.

IBIC characterisation of novel detectors for single atom doping of quantum computer devices

NASA Astrophysics Data System (ADS)

Yang, Changyi; Jamieson, David N.; Pakes, Chris I.; George, Damien P.; Hearne, Sean M.; Dzurak, Andrew S.; Gauja, Eric; Stanley, F.; Clark, R. G.

2003-09-01

Single ion implantation and online detection is highly desirable for the emerging application, in which single 31P ions need to be inserted in prefabricated silicon cells to construct solid-state quantum bits (qubits). In order to fabricate qubit arrays, we have developed novel detectors that employ detector electrodes adjacent to the prefabricated cells that can detect single keV ion strikes appropriate for the fabrication of shallow phosphorus arrays. The method utilises a high purity silicon substrate with very high resistivity, a thin SiO 2 surface layer, nanometer masks for the lateral positioning single phosphorus implantation, biased electrodes applied to the surface of the silicon and sensitive electronics that can detect the charge transient from single keV ion strikes. A TCAD (Technology Computer Aided Design) software package was applied in the optimisation of the device design and simulation of the detector performance. Here we show the characterisation of these detectors using ion beam induced charge (IBIC) with a focused 2 MeV He ions in a nuclear microprobe. The IBIC imaging method in a nuclear microprobe allowed us to measure the dead-layer thickness of the detector structure (required to be very thin for successful detection of keV ions), and the spatial distribution of the charge collection efficiency around the entire region of the detector. We show that our detectors have near 100% charge collection efficiency for MeV ions, extremely thin dead-layer thickness (about 7 nm) and a wide active region extending laterally from the electrodes (10-20 μm) where qubit arrays can be constructed. We demonstrate that the device can be successfully applied in the detection of keV ionisation energy from single events of keV X-rays and keV 31P ions.

Development of a compact laser-based single photon ionization time-of-flight mass spectrometer

NASA Astrophysics Data System (ADS)

Tonokura, Kenichi; Kanno, Nozomu; Yamamoto, Yukio; Yamada, Hiroyuki

2010-02-01

We have developed a compact, laser-based, single photon ionization time-of-flight mass spectrometer (SPI-TOF-MS) for on-line monitoring of trace organic species. To obtain the mass spectrum, we use a nearly fragmentation-free SPI technique with 10.5 eV (118 nm) vacuum ultraviolet laser pulses generated by frequency tripling of the third harmonic of an Nd:YAG laser. The instrument can be operated in a linear TOF-MS mode or a reflectron TOF-MS mode in the coaxial design. We designed ion optics to optimize detection sensitivity and mass resolution. For data acquisition, the instrument is controlled using LabVIEW control software. The total power requirement for the vacuum unit, control electronics unit, ion optics, and detection system is approximately 100 W. We achieve a detection limit of parts per billion by volume (ppbv) for on-line trace analysis of several organic compounds. A mass resolution of 800 at about 100 amu is obtained for reflectron TOF-MS mode in a 0.35 m long instrument. The application of on-line monitoring of diesel engine exhaust was demonstrated.

A single field of view method for retrieving tropospheric temperature profiles from cloud-contaminated radiance data

NASA Technical Reports Server (NTRS)

Hodges, D. B.

1976-01-01

An iterative method is presented to retrieve single field of view (FOV) tropospheric temperature profiles directly from cloud-contaminated radiance data. A well-defined temperature profile may be calculated from the radiative transfer equation (RTE) for a partly cloudy atmosphere when the average fractional cloud amount and cloud-top height for the FOV are known. A cloud model is formulated to calculate the fractional cloud amount from an estimated cloud-top height. The method is then examined through use of simulated radiance data calculated through vertical integration of the RTE for a partly cloudy atmosphere using known values of cloud-top height(s) and fractional cloud amount(s). Temperature profiles are retrieved from the simulated data assuming various errors in the cloud parameters. Temperature profiles are retrieved from NOAA-4 satellite-measured radiance data obtained over an area dominated by an active cold front and with considerable cloud cover and compared with radiosonde data. The effects of using various guessed profiles and the number of iterations are considered.

A distributed database view of network tracking systems

NASA Astrophysics Data System (ADS)

Yosinski, Jason; Paffenroth, Randy

2008-04-01

In distributed tracking systems, multiple non-collocated trackers cooperate to fuse local sensor data into a global track picture. Generating this global track picture at a central location is fairly straightforward, but the single point of failure and excessive bandwidth requirements introduced by centralized processing motivate the development of decentralized methods. In many decentralized tracking systems, trackers communicate with their peers via a lossy, bandwidth-limited network in which dropped, delayed, and out of order packets are typical. Oftentimes the decentralized tracking problem is viewed as a local tracking problem with a networking twist; we believe this view can underestimate the network complexities to be overcome. Indeed, a subsequent 'oversight' layer is often introduced to detect and handle track inconsistencies arising from a lack of robustness to network conditions. We instead pose the decentralized tracking problem as a distributed database problem, enabling us to draw inspiration from the vast extant literature on distributed databases. Using the two-phase commit algorithm, a well known technique for resolving transactions across a lossy network, we describe several ways in which one may build a distributed multiple hypothesis tracking system from the ground up to be robust to typical network intricacies. We pay particular attention to the dissimilar challenges presented by network track initiation vs. maintenance and suggest a hybrid system that balances speed and robustness by utilizing two-phase commit for only track initiation transactions. Finally, we present simulation results contrasting the performance of such a system with that of more traditional decentralized tracking implementations.

Deconvolution single shot multibox detector for supermarket commodity detection and classification

NASA Astrophysics Data System (ADS)

Li, Dejian; Li, Jian; Nie, Binling; Sun, Shouqian

2017-07-01

This paper proposes an image detection model to detect and classify supermarkets shelves' commodity. Based on the principle of the features directly affects the accuracy of the final classification, feature maps are performed to combine high level features with bottom level features. Then set some fixed anchors on those feature maps, finally the label and the position of commodity is generated by doing a box regression and classification. In this work, we proposed a model named Deconvolutiuon Single Shot MultiBox Detector, we evaluated the model using 300 images photographed from real supermarket shelves. Followed the same protocol in other recent methods, the results showed that our model outperformed other baseline methods.

Quaternion-valued single-phase model for three-phase power system

NASA Astrophysics Data System (ADS)

Gou, Xiaoming; Liu, Zhiwen; Liu, Wei; Xu, Yougen; Wang, Jiabin

2018-03-01

In this work, a quaternion-valued model is proposed in lieu of the Clarke's α, β transformation to convert three-phase quantities to a hypercomplex single-phase signal. The concatenated signal can be used for harmonic distortion detection in three-phase power systems. In particular, the proposed model maps all the harmonic frequencies into frequencies in the quaternion domain, while the Clarke's transformation-based methods will fail to detect the zero sequence voltages. Based on the quaternion-valued model, the Fourier transform, the minimum variance distortionless response (MVDR) algorithm and the multiple signal classification (MUSIC) algorithm are presented as examples to detect harmonic distortion. Simulations are provided to demonstrate the potentials of this new modeling method.

Mapping yeast origins of replication via single-stranded DNA detection.

PubMed

Feng, Wenyi; Raghuraman, M K; Brewer, Bonita J

2007-02-01

Studies in th Saccharomyces cerevisiae have provided a framework for understanding how eukaryotic cells replicate their chromosomal DNA to ensure faithful transmission of genetic information to their daughter cells. In particular, S. cerevisiae is the first eukaryote to have its origins of replication mapped on a genomic scale, by three independent groups using three different microarray-based approaches. Here we describe a new technique of origin mapping via detection of single-stranded DNA in yeast. This method not only identified the majority of previously discovered origins, but also detected new ones. We have also shown that this technique can identify origins in Schizosaccharomyces pombe, illustrating the utility of this method for origin mapping in other eukaryotes.

Direct experimental observation of nonclassicality in ensembles of single-photon emitters

NASA Astrophysics Data System (ADS)

Moreva, E.; Traina, P.; Forneris, J.; Degiovanni, I. P.; Ditalia Tchernij, S.; Picollo, F.; Brida, G.; Olivero, P.; Genovese, M.

2017-11-01

In this work we experimentally demonstrate a recently proposed criterion addressed to detect nonclassical behavior in the fluorescence emission of ensembles of single-photon emitters. In particular, we apply the method to study clusters of nitrogen-vacancy centers in diamond characterized with single-photon-sensitive confocal microscopy. Theoretical considerations on the behavior of the parameter at any arbitrary order in the presence of Poissonian noise are presented and, finally, the opportunity of detecting manifold coincidences is discussed.

Use of local noise power spectrum and wavelet analysis in quantitative image quality assurance for EPIDs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Soyoung

Purpose: To investigate the use of local noise power spectrum (NPS) to characterize image noise and wavelet analysis to isolate defective pixels and inter-subpanel flat-fielding artifacts for quantitative quality assurance (QA) of electronic portal imaging devices (EPIDs). Methods: A total of 93 image sets including custom-made bar-pattern images and open exposure images were collected from four iViewGT a-Si EPID systems over three years. Global quantitative metrics such as modulation transform function (MTF), NPS, and detective quantum efficiency (DQE) were computed for each image set. Local NPS was also calculated for individual subpanels by sampling region of interests within each subpanelmore » of the EPID. The 1D NPS, obtained by radially averaging the 2D NPS, was fitted to a power-law function. The r-square value of the linear regression analysis was used as a singular metric to characterize the noise properties of individual subpanels of the EPID. The sensitivity of the local NPS was first compared with the global quantitative metrics using historical image sets. It was then compared with two commonly used commercial QA systems with images collected after applying two different EPID calibration methods (single-level gain and multilevel gain). To detect isolated defective pixels and inter-subpanel flat-fielding artifacts, Haar wavelet transform was applied on the images. Results: Global quantitative metrics including MTF, NPS, and DQE showed little change over the period of data collection. On the contrary, a strong correlation between the local NPS (r-square values) and the variation of the EPID noise condition was observed. The local NPS analysis indicated image quality improvement with the r-square values increased from 0.80 ± 0.03 (before calibration) to 0.85 ± 0.03 (after single-level gain calibration) and to 0.96 ± 0.03 (after multilevel gain calibration), while the commercial QA systems failed to distinguish the image quality improvement between the two calibration methods. With wavelet analysis, defective pixels and inter-subpanel flat-fielding artifacts were clearly identified as spikes after thresholding the inversely transformed images. Conclusions: The proposed local NPS (r-square values) showed superior sensitivity to the noise level variations of individual subpanels compared with global quantitative metrics such as MTF, NPS, and DQE. Wavelet analysis was effective in detecting isolated defective pixels and inter-subpanel flat-fielding artifacts. The proposed methods are promising for the early detection of imaging artifacts of EPIDs.« less

Storing quantum information in spins and high-sensitivity ESR

NASA Astrophysics Data System (ADS)

Morton, John J. L.; Bertet, Patrice

2018-02-01

Quantum information, encoded within the states of quantum systems, represents a novel and rich form of information which has inspired new types of computers and communications systems. Many diverse electron spin systems have been studied with a view to storing quantum information, including molecular radicals, point defects and impurities in inorganic systems, and quantum dots in semiconductor devices. In these systems, spin coherence times can exceed seconds, single spins can be addressed through electrical and optical methods, and new spin systems with advantageous properties continue to be identified. Spin ensembles strongly coupled to microwave resonators can, in principle, be used to store the coherent states of single microwave photons, enabling so-called microwave quantum memories. We discuss key requirements in realising such memories, including considerations for superconducting resonators whose frequency can be tuned onto resonance with the spins. Finally, progress towards microwave quantum memories and other developments in the field of superconducting quantum devices are being used to push the limits of sensitivity of inductively-detected electron spin resonance. The state-of-the-art currently stands at around 65 spins per √{ Hz } , with prospects to scale down to even fewer spins.

Storing quantum information in spins and high-sensitivity ESR.

PubMed

Morton, John J L; Bertet, Patrice

2018-02-01

Quantum information, encoded within the states of quantum systems, represents a novel and rich form of information which has inspired new types of computers and communications systems. Many diverse electron spin systems have been studied with a view to storing quantum information, including molecular radicals, point defects and impurities in inorganic systems, and quantum dots in semiconductor devices. In these systems, spin coherence times can exceed seconds, single spins can be addressed through electrical and optical methods, and new spin systems with advantageous properties continue to be identified. Spin ensembles strongly coupled to microwave resonators can, in principle, be used to store the coherent states of single microwave photons, enabling so-called microwave quantum memories. We discuss key requirements in realising such memories, including considerations for superconducting resonators whose frequency can be tuned onto resonance with the spins. Finally, progress towards microwave quantum memories and other developments in the field of superconducting quantum devices are being used to push the limits of sensitivity of inductively-detected electron spin resonance. The state-of-the-art currently stands at around 65 spins per Hz, with prospects to scale down to even fewer spins. Copyright © 2017. Published by Elsevier Inc.

Single Laboratory Comparison of Quantitative Real-Time PCR Assays for the Detection of Human Fecal Pollution

EPA Science Inventory

There are numerous quantitative real-time PCR (qPCR) methods available to detect and enumerate human fecal pollution in ambient waters. Each assay employs distinct primers and/or probes and many target different genes and microorganisms leading to potential variations in method ...

Image analysis driven single-cell analytics for systems microbiology.

PubMed

Balomenos, Athanasios D; Tsakanikas, Panagiotis; Aspridou, Zafiro; Tampakaki, Anastasia P; Koutsoumanis, Konstantinos P; Manolakos, Elias S

2017-04-04

Time-lapse microscopy is an essential tool for capturing and correlating bacterial morphology and gene expression dynamics at single-cell resolution. However state-of-the-art computational methods are limited in terms of the complexity of cell movies that they can analyze and lack of automation. The proposed Bacterial image analysis driven Single Cell Analytics (BaSCA) computational pipeline addresses these limitations thus enabling high throughput systems microbiology. BaSCA can segment and track multiple bacterial colonies and single-cells, as they grow and divide over time (cell segmentation and lineage tree construction) to give rise to dense communities with thousands of interacting cells in the field of view. It combines advanced image processing and machine learning methods to deliver very accurate bacterial cell segmentation and tracking (F-measure over 95%) even when processing images of imperfect quality with several overcrowded colonies in the field of view. In addition, BaSCA extracts on the fly a plethora of single-cell properties, which get organized into a database summarizing the analysis of the cell movie. We present alternative ways to analyze and visually explore the spatiotemporal evolution of single-cell properties in order to understand trends and epigenetic effects across cell generations. The robustness of BaSCA is demonstrated across different imaging modalities and microscopy types. BaSCA can be used to analyze accurately and efficiently cell movies both at a high resolution (single-cell level) and at a large scale (communities with many dense colonies) as needed to shed light on e.g. how bacterial community effects and epigenetic information transfer play a role on important phenomena for human health, such as biofilm formation, persisters' emergence etc. Moreover, it enables studying the role of single-cell stochasticity without losing sight of community effects that may drive it.

Blur Detection is Unaffected by Cognitive Load.

PubMed

Loschky, Lester C; Ringer, Ryan V; Johnson, Aaron P; Larson, Adam M; Neider, Mark; Kramer, Arthur F

2014-03-01

Blur detection is affected by retinal eccentricity, but is it also affected by attentional resources? Research showing effects of selective attention on acuity and contrast sensitivity suggests that allocating attention should increase blur detection. However, research showing that blur affects selection of saccade targets suggests that blur detection may be pre-attentive. To investigate this question, we carried out experiments in which viewers detected blur in real-world scenes under varying levels of cognitive load manipulated by the N -back task. We used adaptive threshold estimation to measure blur detection thresholds at 0°, 3°, 6°, and 9° eccentricity. Participants carried out blur detection as a single task, a single task with to-be-ignored letters, or an N-back task with four levels of cognitive load (0, 1, 2, or 3-back). In Experiment 1, blur was presented gaze-contingently for occasional single eye fixations while participants viewed scenes in preparation for an easy picture recognition memory task, and the N -back stimuli were presented auditorily. The results for three participants showed a large effect of retinal eccentricity on blur thresholds, significant effects of N -back level on N -back performance, scene recognition memory, and gaze dispersion, but no effect of N -back level on blur thresholds. In Experiment 2, we replicated Experiment 1 but presented the images tachistoscopically for 200 ms (half with, half without blur), to determine whether gaze-contingent blur presentation in Experiment 1 had produced attentional capture by blur onset during a fixation, thus eliminating any effect of cognitive load on blur detection. The results with three new participants replicated those of Experiment 1, indicating that the use of gaze-contingent blur presentation could not explain the lack of effect of cognitive load on blur detection. Thus, apparently blur detection in real-world scene images is unaffected by attentional resources, as manipulated by the cognitive load produced by the N -back task.

Linear and Non-Linear Optical Imaging of Cancer Cells with Silicon Nanoparticles

PubMed Central

Tolstik, Elen; Osminkina, Liubov A.; Akimov, Denis; Gongalsky, Maksim B.; Kudryavtsev, Andrew A.; Timoshenko, Victor Yu.; Heintzmann, Rainer; Sivakov, Vladimir; Popp, Jürgen

2016-01-01

New approaches for visualisation of silicon nanoparticles (SiNPs) in cancer cells are realised by means of the linear and nonlinear optics in vitro. Aqueous colloidal solutions of SiNPs with sizes of about 10–40 nm obtained by ultrasound grinding of silicon nanowires were introduced into breast cancer cells (MCF-7 cell line). Further, the time-varying nanoparticles enclosed in cell structures were visualised by high-resolution structured illumination microscopy (HR-SIM) and micro-Raman spectroscopy. Additionally, the nonlinear optical methods of two-photon excited fluorescence (TPEF) and coherent anti-Stokes Raman scattering (CARS) with infrared laser excitation were applied to study the localisation of SiNPs in cells. Advantages of the nonlinear methods, such as rapid imaging, which prevents cells from overheating and larger penetration depth compared to the single-photon excited HR-SIM, are discussed. The obtained results reveal new perspectives of the multimodal visualisation and precise detection of the uptake of biodegradable non-toxic SiNPs by cancer cells and they are discussed in view of future applications for the optical diagnostics of cancer tumours. PMID:27626408

A Note on Testing Mediated Effects in Structural Equation Models: Reconciling Past and Current Research on the Performance of the Test of Joint Significance

ERIC Educational Resources Information Center

Valente, Matthew J.; Gonzalez, Oscar; Miocevic, Milica; MacKinnon, David P.

2016-01-01

Methods to assess the significance of mediated effects in education and the social sciences are well studied and fall into two categories: single sample methods and computer-intensive methods. A popular single sample method to detect the significance of the mediated effect is the test of joint significance, and a popular computer-intensive method…

Quantum Noise of Electron-Phonon Heat Current

NASA Astrophysics Data System (ADS)

Pekola, Jukka P.; Karimi, Bayan

2018-06-01

We analyze heat current fluctuations between electrons and phonons in a metal. In equilibrium we recover the standard result consistent with the fluctuation-dissipation theorem. Here we show that heat current noise at finite frequencies remains non-vanishing down to zero temperature. From the experimental point of view, it is a small effect and up to now elusive. We briefly discuss the impact of electron-phonon heat current fluctuations on calorimetry, particularly in the regime of single microwave-photon detection.

Sensitivity Simulation of Compressed Sensing Based Electronic Warfare Receiver Using Orthogonal Matching Pursuit Algorithm

DTIC Science & Technology

2016-02-01

algorithm is used to process CS data. The insufficient nature of the sparcity of the signal adversely affects the signal detection probability for...with equal probability. The scheme was proposed [2] for image processing using single pixel camera, where the field of view was masked by a grid...modulation. The orthogonal matching pursuit (OMP) algorithm is used to process CS data. The insufficient nature of the sparcity of the signal

Peripheral Prism Glasses: Effects of Moving and Stationary Backgrounds

PubMed Central

Shen, Jieming; Peli, Eli; Bowers, Alex R.

2015-01-01

Purpose Unilateral peripheral prisms for homonymous hemianopia (HH) expand the visual field through peripheral binocular visual confusion, a stimulus for binocular rivalry that could lead to reduced predominance (partial local suppression) of the prism image and limit device functionality. Using natural-scene images and motion videos, we evaluated whether detection was reduced in binocular compared to monocular viewing. Methods Detection rates of nine participants with HH or quadranopia and normal binocularity wearing peripheral prisms were determined for static checkerboard perimetry targets briefly presented in the prism expansion area and the seeing hemifield. Perimetry was conducted under monocular and binocular viewing with targets presented over videos of real-world driving scenes and still frame images derived from those videos. Results With unilateral prisms, detection rates in the prism expansion area were significantly lower in binocular than monocular (prism eye) viewing on the motion background (medians 13% and 58%, respectively, p = 0.008), but not the still frame background (63% and 68%, p = 0.123). When the stimulus for binocular rivalry was reduced by fitting prisms bilaterally in 1 HH and 1 normally-sighted subject with simulated HH, prism-area detection rates on the motion background were not significantly different (p > 0.6) in binocular and monocular viewing. Conclusions Conflicting binocular motion appears to be a stimulus for reduced predominance of the prism image in binocular viewing when using unilateral peripheral prisms. However, the effect was only found for relatively small targets. Further testing is needed to determine the extent to which this phenomenon might affect the functionality of unilateral peripheral prisms in more real-world situations. PMID:25785533

Antibody-Mediated Small Molecule Detection Using Programmable DNA-Switches.

PubMed

Rossetti, Marianna; Ippodrino, Rudy; Marini, Bruna; Palleschi, Giuseppe; Porchetta, Alessandro

2018-06-13

The development of rapid, cost-effective, and single-step methods for the detection of small molecules is crucial for improving the quality and efficiency of many applications ranging from life science to environmental analysis. Unfortunately, current methodologies still require multiple complex, time-consuming washing and incubation steps, which limit their applicability. In this work we present a competitive DNA-based platform that makes use of both programmable DNA-switches and antibodies to detect small target molecules. The strategy exploits both the advantages of proximity-based methods and structure-switching DNA-probes. The platform is modular and versatile and it can potentially be applied for the detection of any small target molecule that can be conjugated to a nucleic acid sequence. Here the rational design of programmable DNA-switches is discussed, and the sensitive, rapid, and single-step detection of different environmentally relevant small target molecules is demonstrated.

Adaboost multi-view face detection based on YCgCr skin color model

NASA Astrophysics Data System (ADS)

Lan, Qi; Xu, Zhiyong

2016-09-01

Traditional Adaboost face detection algorithm uses Haar-like features training face classifiers, whose detection error rate is low in the face region. While under the complex background, the classifiers will make wrong detection easily to the background regions with the similar faces gray level distribution, which leads to the error detection rate of traditional Adaboost algorithm is high. As one of the most important features of a face, skin in YCgCr color space has good clustering. We can fast exclude the non-face areas through the skin color model. Therefore, combining with the advantages of the Adaboost algorithm and skin color detection algorithm, this paper proposes Adaboost face detection algorithm method that bases on YCgCr skin color model. Experiments show that, compared with traditional algorithm, the method we proposed has improved significantly in the detection accuracy and errors.

Improvement of resolution in full-view linear-array photoacoustic computed tomography using a novel adaptive weighting method

NASA Astrophysics Data System (ADS)

Omidi, Parsa; Diop, Mamadou; Carson, Jeffrey; Nasiriavanaki, Mohammadreza

2017-03-01

Linear-array-based photoacoustic computed tomography is a popular methodology for deep and high resolution imaging. However, issues such as phase aberration, side-lobe effects, and propagation limitations deteriorate the resolution. The effect of phase aberration due to acoustic attenuation and constant assumption of the speed of sound (SoS) can be reduced by applying an adaptive weighting method such as the coherence factor (CF). Utilizing an adaptive beamforming algorithm such as the minimum variance (MV) can improve the resolution at the focal point by eliminating the side-lobes. Moreover, invisibility of directional objects emitting parallel to the detection plane, such as vessels and other absorbing structures stretched in the direction perpendicular to the detection plane can degrade resolution. In this study, we propose a full-view array level weighting algorithm in which different weighs are assigned to different positions of the linear array based on an orientation algorithm which uses the histogram of oriented gradient (HOG). Simulation results obtained from a synthetic phantom show the superior performance of the proposed method over the existing reconstruction methods.

Single-protein detection in crowded molecular environments in cryo-EM images

PubMed Central

Rickgauer, J Peter; Grigorieff, Nikolaus; Denk, Winfried

2017-01-01

We present an approach to study macromolecular assemblies by detecting component proteins’ characteristic high-resolution projection patterns, calculated from their known 3D structures, in single electron cryo-micrographs. Our method detects single apoferritin molecules in vitreous ice with high specificity and determines their orientation and location precisely. Simulations show that high spatial-frequency information and—in the presence of protein background—a whitening filter are essential for optimal detection, in particular for images taken far from focus. Experimentally, we could detect small viral RNA polymerase molecules, distributed randomly among binding locations, inside rotavirus particles. Based on the currently attainable image quality, we estimate a threshold for detection that is 150 kDa in ice and 300 kDa in 100 nm thick samples of dense biological material. DOI: http://dx.doi.org/10.7554/eLife.25648.001 PMID:28467302

A multimodal detection model of dolphins to estimate abundance validated by field experiments.

PubMed

Akamatsu, Tomonari; Ura, Tamaki; Sugimatsu, Harumi; Bahl, Rajendar; Behera, Sandeep; Panda, Sudarsan; Khan, Muntaz; Kar, S K; Kar, C S; Kimura, Satoko; Sasaki-Yamamoto, Yukiko

2013-09-01

Abundance estimation of marine mammals requires matching of detection of an animal or a group of animal by two independent means. A multimodal detection model using visual and acoustic cues (surfacing and phonation) that enables abundance estimation of dolphins is proposed. The method does not require a specific time window to match the cues of both means for applying mark-recapture method. The proposed model was evaluated using data obtained in field observations of Ganges River dolphins and Irrawaddy dolphins, as examples of dispersed and condensed distributions of animals, respectively. The acoustic detection probability was approximately 80%, 20% higher than that of visual detection for both species, regardless of the distribution of the animals in present study sites. The abundance estimates of Ganges River dolphins and Irrawaddy dolphins fairly agreed with the numbers reported in previous monitoring studies. The single animal detection probability was smaller than that of larger cluster size, as predicted by the model and confirmed by field data. However, dense groups of Irrawaddy dolphins showed difference in cluster sizes observed by visual and acoustic methods. Lower detection probability of single clusters of this species seemed to be caused by the clumped distribution of this species.

Limited view angle iterative CT reconstruction

NASA Astrophysics Data System (ADS)

Kisner, Sherman J.; Haneda, Eri; Bouman, Charles A.; Skatter, Sondre; Kourinny, Mikhail; Bedford, Simon

2012-03-01

Computed Tomography (CT) is widely used for transportation security to screen baggage for potential threats. For example, many airports use X-ray CT to scan the checked baggage of airline passengers. The resulting reconstructions are then used for both automated and human detection of threats. Recently, there has been growing interest in the use of model-based reconstruction techniques for application in CT security systems. Model-based reconstruction offers a number of potential advantages over more traditional direct reconstruction such as filtered backprojection (FBP). Perhaps one of the greatest advantages is the potential to reduce reconstruction artifacts when non-traditional scan geometries are used. For example, FBP tends to produce very severe streaking artifacts when applied to limited view data, which can adversely affect subsequent processing such as segmentation and detection. In this paper, we investigate the use of model-based reconstruction in conjunction with limited-view scanning architectures, and we illustrate the value of these methods using transportation security examples. The advantage of limited view architectures is that it has the potential to reduce the cost and complexity of a scanning system, but its disadvantage is that limited-view data can result in structured artifacts in reconstructed images. Our method of reconstruction depends on the formulation of both a forward projection model for the system, and a prior model that accounts for the contents and densities of typical baggage. In order to evaluate our new method, we use realistic models of baggage with randomly inserted simple simulated objects. Using this approach, we show that model-based reconstruction can substantially reduce artifacts and improve important metrics of image quality such as the accuracy of the estimated CT numbers.

Classification Accuracy Increase Using Multisensor Data Fusion

NASA Astrophysics Data System (ADS)

Makarau, A.; Palubinskas, G.; Reinartz, P.

2011-09-01

The practical use of very high resolution visible and near-infrared (VNIR) data is still growing (IKONOS, Quickbird, GeoEye-1, etc.) but for classification purposes the number of bands is limited in comparison to full spectral imaging. These limitations may lead to the confusion of materials such as different roofs, pavements, roads, etc. and therefore may provide wrong interpretation and use of classification products. Employment of hyperspectral data is another solution, but their low spatial resolution (comparing to multispectral data) restrict their usage for many applications. Another improvement can be achieved by fusion approaches of multisensory data since this may increase the quality of scene classification. Integration of Synthetic Aperture Radar (SAR) and optical data is widely performed for automatic classification, interpretation, and change detection. In this paper we present an approach for very high resolution SAR and multispectral data fusion for automatic classification in urban areas. Single polarization TerraSAR-X (SpotLight mode) and multispectral data are integrated using the INFOFUSE framework, consisting of feature extraction (information fission), unsupervised clustering (data representation on a finite domain and dimensionality reduction), and data aggregation (Bayesian or neural network). This framework allows a relevant way of multisource data combination following consensus theory. The classification is not influenced by the limitations of dimensionality, and the calculation complexity primarily depends on the step of dimensionality reduction. Fusion of single polarization TerraSAR-X, WorldView-2 (VNIR or full set), and Digital Surface Model (DSM) data allow for different types of urban objects to be classified into predefined classes of interest with increased accuracy. The comparison to classification results of WorldView-2 multispectral data (8 spectral bands) is provided and the numerical evaluation of the method in comparison to other established methods illustrates the advantage in the classification accuracy for many classes such as buildings, low vegetation, sport objects, forest, roads, rail roads, etc.

Diagnostic accuracy and cost-effectiveness of alternative methods for detection of soil-transmitted helminths in a post-treatment setting in western Kenya.

PubMed

Assefa, Liya M; Crellen, Thomas; Kepha, Stella; Kihara, Jimmy H; Njenga, Sammy M; Pullan, Rachel L; Brooker, Simon J

2014-05-01

This study evaluates the diagnostic accuracy and cost-effectiveness of the Kato-Katz and Mini-FLOTAC methods for detection of soil-transmitted helminths (STH) in a post-treatment setting in western Kenya. A cost analysis also explores the cost implications of collecting samples during school surveys when compared to household surveys. Stool samples were collected from children (n = 652) attending 18 schools in Bungoma County and diagnosed by the Kato-Katz and Mini-FLOTAC coprological methods. Sensitivity and additional diagnostic performance measures were analyzed using Bayesian latent class modeling. Financial and economic costs were calculated for all survey and diagnostic activities, and cost per child tested, cost per case detected and cost per STH infection correctly classified were estimated. A sensitivity analysis was conducted to assess the impact of various survey parameters on cost estimates. Both diagnostic methods exhibited comparable sensitivity for detection of any STH species over single and consecutive day sampling: 52.0% for single day Kato-Katz; 49.1% for single-day Mini-FLOTAC; 76.9% for consecutive day Kato-Katz; and 74.1% for consecutive day Mini-FLOTAC. Diagnostic performance did not differ significantly between methods for the different STH species. Use of Kato-Katz with school-based sampling was the lowest cost scenario for cost per child tested ($10.14) and cost per case correctly classified ($12.84). Cost per case detected was lowest for Kato-Katz used in community-based sampling ($128.24). Sensitivity analysis revealed the cost of case detection for any STH decreased non-linearly as prevalence rates increased and was influenced by the number of samples collected. The Kato-Katz method was comparable in diagnostic sensitivity to the Mini-FLOTAC method, but afforded greater cost-effectiveness. Future work is required to evaluate the cost-effectiveness of STH surveillance in different settings.

The use of biochemical methods in extraterrestrial life detection

NASA Astrophysics Data System (ADS)

McDonald, Gene

2006-08-01

Instrument development for in situ extraterrestrial life detection focuses primarily on the ability to distinguish between biological and non-biological material, mostly through chemical analysis for potential biosignatures (e.g., biogenic minerals, enantiomeric excesses). In constrast, biochemical analysis techniques commonly applied to Earth life focus primarily on the exploration of cellular and molecular processes, not on the classification of a given system as biological or non-biological. This focus has developed because of the relatively large functional gap between life and non-life on Earth today. Life on Earth is very diverse from an environmental and physiological point of view, but is highly conserved from a molecular point of view. Biochemical analysis techniques take advantage of this similarity of all terrestrial life at the molecular level, particularly through the use of biologically-derived reagents (e.g., DNA polymerases, antibodies), to enable analytical methods with enormous sensitivity and selectivity. These capabilities encourage consideration of such reagents and methods for use in extraterrestrial life detection instruments. The utility of this approach depends in large part on the (unknown at this time) degree of molecular compositional differences between extraterrestrial and terrestrial life. The greater these differences, the less useful laboratory biochemical techniques will be without significant modification. Biochemistry and molecular biology methods may need to be "de-focused" in order to produce instruments capable of unambiguously detecting a sufficiently wide range of extraterrestrial biochemical systems. Modern biotechnology tools may make that possible in some cases.

Method to determine and adjust the alignment of the transmitter and receiver fields of view of a LIDAR system

DOEpatents

Schmitt, Randal L [Tijeras, NM; Henson, Tammy D [Albuquerque, NM; Krumel, Leslie J [Cedar Crest, NM; Hargis, Jr., Philip J.

2006-06-20

A method to determine the alignment of the transmitter and receiver fields of view of a light detection and ranging (LIDAR) system. This method can be employed to determine the far-field intensity distribution of the transmitter beam, as well as the variations in transmitted laser beam pointing as a function of time, temperature, or other environmental variables that may affect the co-alignment of the LIDAR system components. In order to achieve proper alignment of the transmitter and receiver optical systems when a LIDAR system is being used in the field, this method employs a laser-beam-position-sensing detector as an integral part of the receiver optics of the LIDAR system.

Visualizing frequent patterns in large multivariate time series

NASA Astrophysics Data System (ADS)

Hao, M.; Marwah, M.; Janetzko, H.; Sharma, R.; Keim, D. A.; Dayal, U.; Patnaik, D.; Ramakrishnan, N.

2011-01-01

The detection of previously unknown, frequently occurring patterns in time series, often called motifs, has been recognized as an important task. However, it is difficult to discover and visualize these motifs as their numbers increase, especially in large multivariate time series. To find frequent motifs, we use several temporal data mining and event encoding techniques to cluster and convert a multivariate time series to a sequence of events. Then we quantify the efficiency of the discovered motifs by linking them with a performance metric. To visualize frequent patterns in a large time series with potentially hundreds of nested motifs on a single display, we introduce three novel visual analytics methods: (1) motif layout, using colored rectangles for visualizing the occurrences and hierarchical relationships of motifs in a multivariate time series, (2) motif distortion, for enlarging or shrinking motifs as appropriate for easy analysis and (3) motif merging, to combine a number of identical adjacent motif instances without cluttering the display. Analysts can interactively optimize the degree of distortion and merging to get the best possible view. A specific motif (e.g., the most efficient or least efficient motif) can be quickly detected from a large time series for further investigation. We have applied these methods to two real-world data sets: data center cooling and oil well production. The results provide important new insights into the recurring patterns.

Sequential determination of multi-nutrient elements in natural water samples with a reverse flow injection system.

PubMed

Lin, Kunning; Ma, Jian; Yuan, Dongxing; Feng, Sichao; Su, Haitao; Huang, Yongming; Shangguan, Qipei

2017-05-15

An integrated system was developed for automatic and sequential determination of NO 2 - , NO 3 - , PO 4 3- , Fe 2+ , Fe 3+ and Mn 2+ in natural waters based on reverse flow injection analysis combined with spectrophotometric detection. The system operation was controlled by a single chip microcomputer and laboratory-programmed software written in LabVIEW. The experimental parameters for each nutrient element analysis were optimized based on a univariate experimental design, and interferences from common ions were evaluated. The upper limits of the linear range (along with detection limit, µmolL -1 ) of the proposed method was 20 (0.03), 200 (0.7), 12 (0.3), 5 (0.03), 5 (0.03), 9 (0.2) µmolL -1 , for NO 2 - , NO 3 - , PO 4 3- , Fe 2+ , Fe 3+ and Mn 2+ , respectively. The relative standard deviations were below 5% (n=9-13) and the recoveries varied from 88.0±1.0% to 104.5±1.0% for spiked water samples. The sample throughput was about 20h -1 . This system has been successfully applied for the determination of multi-nutrient elements in different kinds of water samples and showed good agreement with reference methods (slope 1.0260±0.0043, R 2 =0.9991, n=50). Copyright © 2017 Elsevier B.V. All rights reserved.

Whales from space: counting southern right whales by satellite.

PubMed

Fretwell, Peter T; Staniland, Iain J; Forcada, Jaume

2014-01-01

We describe a method of identifying and counting whales using very high resolution satellite imagery through the example of southern right whales breeding in part of the Golfo Nuevo, Península Valdés in Argentina. Southern right whales have been extensively hunted over the last 300 years and although numbers have recovered from near extinction in the early 20(th) century, current populations are fragmented and are estimated at only a small fraction of pre-hunting total. Recent extreme right whale calf mortality events at Península Valdés, which constitutes the largest single population, have raised fresh concern for the future of the species. The WorldView2 satellite has a maximum 50 cm resolution and a water penetrating coastal band in the far-blue part of the spectrum that allows it to see deeper into the water column. Using an image covering 113 km², we identified 55 probable whales and 23 other features that are possibly whales, with a further 13 objects that are only detected by the coastal band. Comparison of a number of classification techniques, to automatically detect whale-like objects, showed that a simple thresholding technique of the panchromatic and coastal band delivered the best results. This is the first successful study using satellite imagery to count whales; a pragmatic, transferable method using this rapidly advancing technology that has major implications for future surveys of cetacean populations.

Novel Method to Detect and Characterize 18F-FDG Infiltration at the Injection Site: A Single-Institution Experience.

PubMed

Muzaffar, Razi; Frye, Sarah A; McMunn, Anna; Ryan, Kelley; Lattanze, Ron; Osman, Medhat M

2017-12-01

A novel quality control and quality assurance device provides time-activity curves that can identify and characterize PET/CT radiotracer infiltration at the injection site during the uptake phase. The purpose of this study was to compare rates of infiltration detected by the device with rates detected by physicians. We also assessed the value of using the device to improve injection results in our center. Methods: 109 subjects consented to the study. All had passive device sensors applied to their skin near the injection site and mirrored on the contralateral arm during the entire uptake period. Nuclear medicine physicians reviewed standard images for the presence of dose infiltration. Sensor-generated time-activity curves were independently examined and then compared with the physician reports. Injection data captured by the software were analyzed, and the results were provided to the technologists. Improvement measures were implemented, and rates were remeasured. Results: Physician review of the initial 40 head-to-toe field-of-view images identified 15 cases (38%) of dose infiltration (9 minor, 5 moderate, and 1 significant). Sensor time-activity curves on these 40 cases independently identified 22 cases (55%) of dose infiltration (16 minor, 5 moderate, and 1 significant). After the time-activity curve results and the contributing factor analysis were shared with technologists, injection techniques were modified and an additional 69 cases were studied. Of these, physician review identified 17 cases (25%) of infiltration (13 minor, 3 moderate, and 1 significant), a 34% decline. Sensor time-activity curves identified 4 cases (6%) of infiltration (2 minor and 2 moderate), an 89% decline. Conclusion: The device provides valuable quality control information for each subject. Time-activity curves can further characterize visible infiltration. Even when the injection site was out of the field of view, the time-activity curves could still detect and characterize infiltration. Our initial experience showed that the quality assurance information obtained from the device helped reduce the rate and severity of infiltration. The device revealed site-specific contributing factors that helped nuclear medicine physicians and technologists customize their quality improvement efforts to these site-specific issues. Reducing infiltration can improve image quality and SUV quantification, as well as the ability to minimize variability in a site's PET/CT results. © 2017 by the Society of Nuclear Medicine and Molecular Imaging.

Detection of singly- and doubly-charged quaternary ammonium drugs in equine urine by liquid chromatography/tandem mass spectrometry.

PubMed

Ho, Emmie N M; Kwok, W H; Wong, April S Y; Wan, Terence S M

2012-01-13

Quaternary ammonium drugs (QADs) are anticholinergic agents some of which are known to have been abused or misused in equine sports. A recent review of literature shows that the screening methods reported thus far for QADs mainly cover singly-charged QADs. Doubly-charged QADs are extremely polar substances which are difficult to be extracted and poorly retained on reversed-phase columns. It would be ideal if a comprehensive method can be developed which can detect both singly- and doubly-charged QADs. This paper describes an efficient liquid chromatography/tandem mass spectrometry (LC/MS/MS) method for the simultaneous detection and confirmation of 38 singly- and doubly-charged QADs at sub-parts-per-billion (ppb) to low-ppb levels in equine urine after solid-phase extraction. Quaternary ammonium drugs were extracted from equine urine by solid-phase extraction (SPE) using an ISOLUTE(®) CBA SPE column and analysed by LC/MS/MS in the positive electrospray ionisation mode. Separation of the 38 QADs was achieved on a polar group embedded C18 LC column with a mixture of aqueous ammonium formate (pH 3.0, 10 mM) and acetonitrile as the mobile phase. Detection and confirmation of the 38 QADs at sub-ppb to low-ppb levels in equine urine could be achieved within 16 min using selected reaction monitoring (SRM). Matrix interference of the target transitions at the expected retention times was not observed. Other method validation data, including precision and recovery, were acceptable. The method was successfully applied to the analyses of drug-administration samples. Copyright © 2011 Elsevier B.V. All rights reserved.

Single quantum dot analysis enables multiplexed point mutation detection by gap ligase chain reaction.

PubMed

Song, Yunke; Zhang, Yi; Wang, Tza-Huei

2013-04-08

Gene point mutations present important biomarkers for genetic diseases. However, existing point mutation detection methods suffer from low sensitivity, specificity, and a tedious assay processes. In this report, an assay technology is proposed which combines the outstanding specificity of gap ligase chain reaction (Gap-LCR), the high sensitivity of single-molecule coincidence detection, and the superior optical properties of quantum dots (QDs) for multiplexed detection of point mutations in genomic DNA. Mutant-specific ligation products are generated by Gap-LCR and subsequently captured by QDs to form DNA-QD nanocomplexes that are detected by single-molecule spectroscopy (SMS) through multi-color fluorescence burst coincidence analysis, allowing for multiplexed mutation detection in a separation-free format. The proposed assay is capable of detecting zeptomoles of KRAS codon 12 mutation variants with near 100% specificity. Its high sensitivity allows direct detection of KRAS mutation in crude genomic DNA without PCR pre-amplification. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular Analysis of Single Tumor Glands Using the Crypt Isolation Method in Endometrial Carcinomas.

PubMed

Nagasawa, Takayuki; Sugai, Tamotsu; Shoji, Tadahiro; Habano, Wataru; Sugiyama, Toru

2016-11-01

Endometrial adenocarcinomas are characterized by the presence of many single tumor glands in which multiple genetic changes have accumulated. To elucidate the differences in molecular abnormalities among single tumor glands, individual tumor glands were analyzed and microsatellite alterations (loss of heterozygosity (LOH) and microsatellite instability [MSI]) were examined using the crypt isolation method in glands from each tumor from patients with endometrial carcinoma. Twenty-five patients with endometrial adenocarcinoma who underwent surgery were included in this study. We obtained cancerous individual isolated tumor glands from each patient using the crypt isolation method. For LOH and MSI analyses, we used 15 microsatellite markers (3p, 5q, 10q, 13q, 17p, 18q, BAT25, and BAT26) and the promoter regions of 6 genes (transforming growth factor beta receptor II, BAX, insulin-like growth factor II receptor, E2F4, MutS homolog 3, and MSH6). Loss of heterozygosity was detected in 8 (32%) of 25 patients, and MSI was detected in 9 (36%) of 25 patients. Some MSI-positive carcinomas had LOH in single tumor gland samples, and the coexistence of LOH and MSI was confirmed. In 16 (64%) of 25 cases, intratumoral genetic heterogeneity among single tumor gland samples was detected. By analyzing multiple single tumor glands within the same tumor, we found that endometrial adenocarcinoma was composed of various tumor glands with different molecular abnormalities, even in a limited region within the same tumor.

Quantifying clutter: A comparison of four methods and their relationship to bat detection

Treesearch

Joy M. O’Keefe; Susan C. Loeb; Hoke S. Hill Jr.; J. Drew Lanham

2014-01-01

The degree of spatial complexity in the environment, or clutter, affects the quality of foraging habitats for bats and their detection with acoustic systems. Clutter has been assessed in a variety of ways but there are no standardized methods for measuring clutter. We compared four methods (Visual Clutter, Cluster, Single Variable, and Clutter Index) and related these...

Single photon detection and signal analysis for high sensitivity dosimetry based on optically stimulated luminescence with beryllium oxide

NASA Astrophysics Data System (ADS)

Radtke, J.; Sponner, J.; Jakobi, C.; Schneider, J.; Sommer, M.; Teichmann, T.; Ullrich, W.; Henniger, J.; Kormoll, T.

2018-01-01

Single photon detection applied to optically stimulated luminescence (OSL) dosimetry is a promising approach due to the low level of luminescence light and the known statistical behavior of single photon events. Time resolved detection allows to apply a variety of different and independent data analysis methods. Furthermore, using amplitude modulated stimulation impresses time- and frequency information into the OSL light and therefore allows for additional means of analysis. Considering the impressed frequency information, data analysis by using Fourier transform algorithms or other digital filters can be used for separating the OSL signal from unwanted light or events generated by other phenomena. This potentially lowers the detection limits of low dose measurements and might improve the reproducibility and stability of obtained data. In this work, an OSL system based on a single photon detector, a fast and accurate stimulation unit and an FPGA is presented. Different analysis algorithms which are applied to the single photon data are discussed.

Sulfide chemiluminescence detection

DOEpatents

Spurlin, S.R.; Yeung, E.S.

1985-11-26

A method is described for chemiluminescently determining a sulfide which is either hydrogen sulfide or methyl mercaptan by reacting the sulfide with chlorine dioxide at low pressure and under conditions which allow a longer reaction time in emission of a single photon for every two sulfide containing species, and thereafter, chemiluminescently detecting and determining the sulfide. The invention also relates not only to the detection method, but the novel chemical reaction and a specifically designed chemiluminescence detection cell for the reaction. 4 figs.

Apparatus for use in sulfide chemiluminescence detection

DOEpatents

Spurlin, Stanford R.; Yeung, Edward S.

1987-01-01

A method of chemiluminescently determining a sulfide which is either hydrogen sulfide or methyl mercaptan by reacting the sulfide with chlorine dioxide at low pressure and under conditions which allow a longer reaction time in emission of a single photon for every two sulfide containing species, and thereafter, chemiluminescently detecting and determining the sulfide. The invention also relates not only to the detection method, but the novel chemical reaction and a specifically designed chemiluminescence detection cell for the reaction.

Simultaneous multiview capture and fusion improves spatial resolution in wide-field and light-sheet microscopy

PubMed Central

Wu, Yicong; Chandris, Panagiotis; Winter, Peter W.; Kim, Edward Y.; Jaumouillé, Valentin; Kumar, Abhishek; Guo, Min; Leung, Jacqueline M.; Smith, Corey; Rey-Suarez, Ivan; Liu, Huafeng; Waterman, Clare M.; Ramamurthi, Kumaran S.; La Riviere, Patrick J.; Shroff, Hari

2016-01-01

Most fluorescence microscopes are inefficient, collecting only a small fraction of the emitted light at any instant. Besides wasting valuable signal, this inefficiency also reduces spatial resolution and causes imaging volumes to exhibit significant resolution anisotropy. We describe microscopic and computational techniques that address these problems by simultaneously capturing and subsequently fusing and deconvolving multiple specimen views. Unlike previous methods that serially capture multiple views, our approach improves spatial resolution without introducing any additional illumination dose or compromising temporal resolution relative to conventional imaging. When applying our methods to single-view wide-field or dual-view light-sheet microscopy, we achieve a twofold improvement in volumetric resolution (~235 nm × 235 nm × 340 nm) as demonstrated on a variety of samples including microtubules in Toxoplasma gondii, SpoVM in sporulating Bacillus subtilis, and multiple protein distributions and organelles in eukaryotic cells. In every case, spatial resolution is improved with no drawback by harnessing previously unused fluorescence. PMID:27761486

Velocity measurements by laser resonance fluorescence. [single atom diffusional motion

NASA Technical Reports Server (NTRS)

She, C. Y.; Fairbank, W. M., Jr.

1980-01-01

The photonburst correlation method was used to detect single atoms in a buffer gas. Real time flow velocity measurements with laser induced resonance fluorescence from single or multiple atoms was demonstrated and this method was investigated as a tool for wind tunnel flow measurement. Investigations show that single atoms and their real time diffusional motion on a buffer gas can be measured by resonance fluorescence. By averaging over many atoms, flow velocities up to 88 m/s were measured in a time of 0.5 sec. It is expected that higher flow speeds can be measured and that the measurement time can be reduced by a factor of 10 or more by careful experimental design. The method is clearly not ready for incorporation in high speed wind tunnels because it is not yet known whether the stray light level will be higher or lower, and it is not known what detection efficiency can be obtained in a wind tunnel situation.

Transmission and full-band coherent detection of polarization-multiplexed all-optical Nyquist signals generated by Sinc-shaped Nyquist pulses

PubMed Central

Zhang, Junwen; Yu, Jianjun; Chi, Nan

2015-01-01

All optical method is considered as a promising technique for high symbol rate Nyquist signal generation, which has attracted a lot of research interests for high spectral-efficiency and high-capacity optical communication system. In this paper, we extend our previous work and report the fully experimental demonstration of polarization-division multiplexed (PDM) all-optical Nyquist signal generation based on Sinc-shaped Nyquist pulse with advanced modulation formats, fiber-transmission and single-receiver full-band coherent detection. Using this scheme, we have successfully demonstrated the generation, fiber transmission and single-receiver full-band coherent detection of all-optical Nyquist PDM-QPSK and PDM-16QAM signals up to 125-GBaud. 1-Tb/s single-carrier PDM-16QAM signal generation and full-band coherent detection is realized, which shows the advantage and feasibility of the single-carrier all-optical Nyquist signals. PMID:26323238

Detection limit of intragenic deletions with targeted array comparative genomic hybridization

PubMed Central

2013-01-01

Background Pathogenic mutations range from single nucleotide changes to deletions or duplications that encompass a single exon to several genes. The use of gene-centric high-density array comparative genomic hybridization (aCGH) has revolutionized the detection of intragenic copy number variations. We implemented an exon-centric design of high-resolution aCGH to detect single- and multi-exon deletions and duplications in a large set of genes using the OGT 60 K and 180 K arrays. Here we describe the molecular characterization and breakpoint mapping of deletions at the smaller end of the detectable range in several genes using aCGH. Results The method initially implemented to detect single to multiple exon deletions, was able to detect deletions much smaller than anticipated. The selected deletions we describe vary in size, ranging from over 2 kb to as small as 12 base pairs. The smallest of these deletions are only detectable after careful manual review during data analysis. Suspected deletions smaller than the detection size for which the method was optimized, were rigorously followed up and confirmed with PCR-based investigations to uncover the true detection size limit of intragenic deletions with this technology. False-positive deletion calls often demonstrated single nucleotide changes or an insertion causing lower hybridization of probes demonstrating the sensitivity of aCGH. Conclusions With optimizing aCGH design and careful review process, aCGH can uncover intragenic deletions as small as dozen bases. These data provide insight that will help optimize probe coverage in array design and illustrate the true assay sensitivity. Mapping of the breakpoints confirms smaller deletions and contributes to the understanding of the mechanism behind these events. Our knowledge of the mutation spectra of several genes can be expected to change as previously unrecognized intragenic deletions are uncovered. PMID:24304607

Design of a Multi-Sensor Cooperation Travel Environment Perception System for Autonomous Vehicle

PubMed Central

Chen, Long; Li, Qingquan; Li, Ming; Zhang, Liang; Mao, Qingzhou

2012-01-01

This paper describes the environment perception system designed for intelligent vehicle SmartV-II, which won the 2010 Future Challenge. This system utilizes the cooperation of multiple lasers and cameras to realize several necessary functions of autonomous navigation: road curb detection, lane detection and traffic sign recognition. Multiple single scan lasers are integrated to detect the road curb based on Z-variance method. Vision based lane detection is realized by two scans method combining with image model. Haar-like feature based method is applied for traffic sign detection and SURF matching method is used for sign classification. The results of experiments validate the effectiveness of the proposed algorithms and the whole system.

Single-beam, dual-view digital holographic interferometry for biomechanical strain measurements of biological objects

NASA Astrophysics Data System (ADS)

Pantelić, Dejan V.; Grujić, Dušan Ž.; Vasiljević, Darko M.

2014-12-01

We describe a method for dual-view biomechanical strain measurements of highly asymmetrical biological objects, like teeth or bones. By using a spherical mirror, we were able to simultaneously record a digital hologram of the object itself and the mirror image of its (otherwise invisible) rear side. A single laser beam was sufficient to illuminate both sides of the object, and to provide a reference beam. As a result, the system was mechanically very stable, enabling long exposure times (up to 2 min) without the need for vibration isolation. The setup is simple to construct and adjust, and can be used to interferometrically observe any object that is smaller than the mirror diameter. Parallel data processing on a CUDA-enabled (compute unified device architecture) graphics card was used to reconstruct digital holograms and to further correct image distortion. We used the setup to measure the deformation of a tooth due to mastication forces. The finite-element method was used to compare experimental results and theoretical predictions.

Single-beam, dual-view digital holographic interferometry for biomechanical strain measurements of biological objects.

PubMed

Pantelić, Dejan V; Grujić, Dušan Ž; Vasiljević, Darko M

2014-12-01

We describe a method for dual-view biomechanical strain measurements of highly asymmetrical biological objects, like teeth or bones. By using a spherical mirror, we were able to simultaneously record a digital hologram of the object itself and the mirror image of its (otherwise invisible) rear side. A single laser beam was sufficient to illuminate both sides of the object, and to provide a reference beam. As a result, the system was mechanically very stable, enabling long exposure times (up to 2 min) without the need for vibration isolation. The setup is simple to construct and adjust, and can be used to interferometrically observe any object that is smaller than the mirror diameter. Parallel data processing on a CUDA-enabled (compute unified device architecture) graphics card was used to reconstruct digital holograms and to further correct image distortion. We used the setup to measure the deformation of a tooth due to mastication forces. The finite-element method was used to compare experimental results and theoretical predictions.

Detection of Golden apples' climacteric peak by laser biospeckle measurements.

PubMed

Nassif, Rana; Nader, Christelle Abou; Afif, Charbel; Pellen, Fabrice; Le Brun, Guy; Le Jeune, Bernard; Abboud, Marie

2014-12-10

In this paper, we report a study in which a laser biospeckle technique is used to detect the climacteric peak indicating the optimal ripeness of fruits. We monitor two batches of harvested Golden apples going through the ripening phase in low- and room-temperature environments, determine speckle parameters, and measure the emitted ethylene concentration using gas chromatography as reference method. Speckle results are then correlated to the emitted ethylene concentration by a principal component analysis. From a practical point of view, this approach allows us to validate biospeckle as a noninvasive and alternative method to respiration rate and ethylene production for climacteric peak detection as a ripening index.

[Automated analyzer of enzyme immunoassay].

PubMed

Osawa, S

1995-09-01

Automated analyzers for enzyme immunoassay can be classified by several points of view: the kind of labeled antibodies or enzymes, detection methods, the number of tests per unit time, analytical time and speed per run. In practice, it is important for us consider the several points such as detection limits, the number of tests per unit time, analytical range, and precision. Most of the automated analyzers on the market can randomly access and measure samples. I will describe the recent advance of automated analyzers reviewing their labeling antibodies and enzymes, the detection methods, the number of test per unit time and analytical time and speed per test.

Vision-based obstacle avoidance

DOEpatents

Galbraith, John [Los Alamos, NM

2006-07-18

A method for allowing a robot to avoid objects along a programmed path: first, a field of view for an electronic imager of the robot is established along a path where the electronic imager obtains the object location information within the field of view; second, a population coded control signal is then derived from the object location information and is transmitted to the robot; finally, the robot then responds to the control signal and avoids the detected object.

Text Line Detection from Rectangle Traffic Panels of Natural Scene

NASA Astrophysics Data System (ADS)

Wang, Shiyuan; Huang, Linlin; Hu, Jian

2018-01-01

Traffic sign detection and recognition is very important for Intelligent Transportation. Among traffic signs, traffic panel contains rich information. However, due to low resolution and blur in the rectangular traffic panel, it is difficult to extract the character and symbols. In this paper, we propose a coarse-to-fine method to detect the Chinese character on traffic panels from natural scenes. Given a traffic panel Color Quantization is applied to extract candidate regions of Chinese characters. Second, a multi-stage filter based on learning is applied to discard the non-character regions. Third, we aggregate the characters for text lines by Distance Metric Learning method. Experimental results on real traffic images from Baidu Street View demonstrate the effectiveness of the proposed method.

Single-Cell RNA-Sequencing in Glioma.

PubMed

Johnson, Eli; Dickerson, Katherine L; Connolly, Ian D; Hayden Gephart, Melanie

2018-04-10

In this review, we seek to summarize the literature concerning the use of single-cell RNA-sequencing for CNS gliomas. Single-cell analysis has revealed complex tumor heterogeneity, subpopulations of proliferating stem-like cells and expanded our view of tumor microenvironment influence in the disease process. Although bulk RNA-sequencing has guided our initial understanding of glioma genetics, this method does not accurately define the heterogeneous subpopulations found within these tumors. Single-cell techniques have appealing applications in cancer research, as diverse cell types and the tumor microenvironment have important implications in therapy. High cost and difficult protocols prevent widespread use of single-cell RNA-sequencing; however, continued innovation will improve accessibility and expand our of knowledge gliomas.

Remote sounding of cloudy atmospheres. I - The single cloud layer

NASA Technical Reports Server (NTRS)

Chahine, M. T.

1974-01-01

The relaxation method for the inverse solution of the radiative transfer equation is applied in a dual-frequency scheme for the determination of complete vertical temperature profiles in cloudy atmospheres from radiance observations alone, without any additional information related to the expected solutions. The dual-frequency principle employs to advantage a property in the Planck function of the dependence of intensity on frequency. This property leads to the formulation of a new convergence criterion for the selection of cloud-sounding frequencies to be used for reconstructing the clear column radiance from observations made in the presence of a broken cloud layer in all fields of view. The principle is applied to the case of observations in two adjacent or partially overlapping fields of view and to the case of observations in a single field of view. The solutions are illustrated by numerical examples in the dual-frequency ranges of the 4.3 and 15-micron CO2 bands of the terrestrial atmosphere.

The clinical performance evaluation of novel protein chips for eleven biomarkers detection and the diagnostic model study.

PubMed

Luo, Yuan; Zhu, Xu; Zhang, Pengjun; Shen, Qian; Wang, Zi; Wen, Xinyu; Wang, Ling; Gao, Jing; Dong, Jin; Yang, Caie; Wu, Tangming; Zhu, Zheng; Tian, Yaping

2015-01-01

We aimed to develop and validate two novel protein chips, which are based on microarray chemiluminescence immunoassay and can simultaneously detected 11 biomarkers, and then to evaluate their clinical diagnostic value by comparing with the traditional methods. Protein chips were evaluated for limit of detection, specificity, common interferences, linearity, precision and accuracy. 11 biomarkers were simultaneously detected by traditional methods and protein chips in 3683 samples, which included 1723 cancer patients, 1798 benign diseases patients and 162 healthy controls. After assay validation, protein chips demonstrated high sensitivity, high specificity, good linearity, low imprecision and were free of common interferences. Compared with the traditional methods, protein chips have good correlation in the detection of all the 13 kinds of biomarkers (r≥0.935, P<0.001). For specific cancer detection, there were no statistically significant differences between the traditional method and novel protein chips, except that male protein chip showed significantly better diagnostic value on NSE detection (P=0.004) but significantly worse value on pro-GRP detection (P=0.012), female chip showed significantly better diagnostic value on pro-GRP detection (P=0.005). Furthermore, both male and female multivariate diagnostic models had significantly better diagnostic value than single detection of PGI, PG II, pro-GRP, NSE and CA125 (P<0.05). In addition, male models had significantly better diagnostic value than single CA199 and free-PSA (P<0.05), while female models observed significantly better diagnostic value than single CA724 and β-HCG (P<0.05). For total disease or cancer detection, the AUC of multivariate logistic regression for the male and female disease detection was 0.981 (95% CI: 0.975-0.987) and 0.836 (95% CI: 0.798-0.874), respectively. While, that for total cancer detection was 0.691 (95% CI: 0.666-0.717) and 0.753 (95% CI: 0.731-0.775), respectively. The new designed protein chips are simple, multiplex and reliable clinical assays and the multi-parameter diagnostic models based on them could significantly improve their clinical performance.

The clinical performance evaluation of novel protein chips for eleven biomarkers detection and the diagnostic model study

PubMed Central

Luo, Yuan; Zhu, Xu; Zhang, Pengjun; Shen, Qian; Wang, Zi; Wen, Xinyu; Wang, Ling; Gao, Jing; Dong, Jin; Yang, Caie; Wu, Tangming; Zhu, Zheng; Tian, Yaping

2015-01-01

We aimed to develop and validate two novel protein chips, which are based on microarray chemiluminescence immunoassay and can simultaneously detected 11 biomarkers, and then to evaluate their clinical diagnostic value by comparing with the traditional methods. Protein chips were evaluated for limit of detection, specificity, common interferences, linearity, precision and accuracy. 11 biomarkers were simultaneously detected by traditional methods and protein chips in 3683 samples, which included 1723 cancer patients, 1798 benign diseases patients and 162 healthy controls. After assay validation, protein chips demonstrated high sensitivity, high specificity, good linearity, low imprecision and were free of common interferences. Compared with the traditional methods, protein chips have good correlation in the detection of all the 13 kinds of biomarkers (r≥0.935, P<0.001). For specific cancer detection, there were no statistically significant differences between the traditional method and novel protein chips, except that male protein chip showed significantly better diagnostic value on NSE detection (P=0.004) but significantly worse value on pro-GRP detection (P=0.012), female chip showed significantly better diagnostic value on pro-GRP detection (P=0.005). Furthermore, both male and female multivariate diagnostic models had significantly better diagnostic value than single detection of PGI, PG II, pro-GRP, NSE and CA125 (P<0.05). In addition, male models had significantly better diagnostic value than single CA199 and free-PSA (P<0.05), while female models observed significantly better diagnostic value than single CA724 and β-HCG (P<0.05). For total disease or cancer detection, the AUC of multivariate logistic regression for the male and female disease detection was 0.981 (95% CI: 0.975-0.987) and 0.836 (95% CI: 0.798-0.874), respectively. While, that for total cancer detection was 0.691 (95% CI: 0.666-0.717) and 0.753 (95% CI: 0.731-0.775), respectively. The new designed protein chips are simple, multiplex and reliable clinical assays and the multi-parameter diagnostic models based on them could significantly improve their clinical performance. PMID:26884957

An extension of the Coconut Cream Agar method to screen Penicillium citrinum isolates for citrinin production.

PubMed

Mohamed, S; Flint, S; Palmer, J; Fletcher, G C; Pitt, J I

2013-09-01

A simple and rapid screening method was developed for the detection of citrinin in fungal cultures using Coconut Cream Agar (CCA) described previously for detecting aflatoxin and ochratoxin A. Fifteen isolates of Penicillium citrinum were inoculated onto CCA and incubated at 25 and 30°C for 10 days. All isolates produced a distinct yellow green fluorescence on CCA when the reverse side of the agar plates were viewed under long wavelength UV light. Detection was optimal at 25°C after four to 5 days of incubation. Isolates positive by the CCA method also tested positive for citrinin production by the TLC agar plug method after growth on CCA, Czapek yeast extract agar and yeast extract sucrose agar. Control cultures were negative by both methods, indicating that the CCA Petri dish method was suitable for screening cultures for citrinin production. © 2013 The Society for Applied Microbiology.

Radiographical definition of the proximal tibiofibular joint - A cross-sectional study of 2984 knees and literature review.

PubMed

Hey, Hwee Weng Dennis; Ng, Li Wen Nathaniel; Ng, Yau Hong; Sng, Wei Zhong Jonathan; Manohara, Ruben; Thambiah, Joseph Shanthakumar

2016-06-01

Proximal tibiofibular joint (PTFJ) injuries are not uncommon but relatively understudied. This study evaluates the effectiveness of 2 radiographic methods in assessing the integrity of the PTFJ. This is a cross-sectional study of 2984 consecutive patients with knee X-rays done in a single institution over a 4-month period. A total of 5968 knee X-rays were assessed using 2 methods-[1] The direction in which the fibula points to in relation to the lateral femoral epicondyle on anteroposterior view and Blumensaat line on lateral view. [2] The degree of tibiofibular overlap as percentage of widest portion of the fibula head. Sensitivity and specificity of these methods in diagnosing a disrupted PTFJ are calculated. Variables including quality of X-rays, weight-bearing status of AP views and degree of knee flexion on lateral views are also recorded. Univariate analysis was carried out to investigate the association between variables using chi-square test for nominal data and student t-test for continuous data. The fibular points towards the lateral femoral epicondyle on AP view in 94.4% of the patients and points towards the posterior half of the Blumensaat line on lateral view in 98.1% of the patients. Using this method, weight-bearing X-rays are significantly associated with the direction the fibula is pointing (p<0.01) on the AP view and the degree of knee flexion is associated with the direction the fibula is pointing (p<0.01) on the lateral view. The AP tibiofibular overlap ranges from >0% to <75% in 94.1% of the patients and the lateral tibiofibular overlap ranges from >0% to <75% in 84.5% of the patients. This method is associated with whether true orthogonal X-rays of the knees are taken (p=0.048). The direction in which the fibula is pointing and the percentage of tibiofibular overlap are highly specific radiographic methods useful in defining the PTFJ. The first method requires a weight-bearing view on AP assessment and >20 degrees of flexion on lateral assessment. True orthogonal AP and lateral views are required for the second method to be used. Copyright © 2016 Elsevier Ltd. All rights reserved.

Method of generating chemiluminescent light

DOEpatents

Spurlin, S.R.; Yeung, E.S.

1986-03-11

A method of chemiluminescently determining a sulfide which is either hydrogen sulfide or methyl mercaptan by reacting the sulfide with chlorine dioxide at low pressure and under conditions which allow a longer reaction time in emission of a single photon for every two sulfide containing species, and thereafter, chemiluminescently detecting and determining the sulfide. The invention also relates not only to the detection method, but the novel chemical reaction that generates chemiluminescent light and a specifically designed chemiluminescence detection cell for the reaction. 4 figs.

Method of generating chemiluminescent light

DOEpatents

Spurlin, Stanford R.; Yeung, Edward S.

1986-01-01

A method of chemiluminescently determining a sulfide which is either hydrogen sulfide or methyl mercaptan by reacting the sulfide with chlorine dioxide at low pressure and under conditions which allow a longer reaction time in emission of a single photon for every two sulfide containing species, and thereafter, chemiluminescently detecting and determining the sulfide. The invention also relates not only to the detection method, but the novel chemical reaction that generates chemiluminescent light and a specifically designed chemiluminescence detection cell for the reaction.

Accuracy and consistency of radiographic interpretation among clinical instructors using two viewing systems.

PubMed

Lanning, Sharon K; Best, Al M; Temple, Henry J; Richards, Philip S; Carey, Allison; McCauley, Laurie K

2006-02-01

Accurate and consistent radiographic interpretation among clinical instructors is needed for assessment of teaching, student performance, and patient care. The purpose of this investigation was to determine if the method of radiographic viewing affects accuracy and consistency of instructors' determinations of bone loss. Forty-one clinicians who provide instruction in a dental school clinical teaching program (including periodontists, general dentists, periodontal graduate students, and dental hygienists) quantified bone loss for up to twenty-five teeth into four descriptive categories using a view box for plain film viewing or a projection system for digitized image viewing. Ratings were compared to the correct category as determined by direct measurement using the Schei ruler. Agreement with the correct choice for the view box and projection system was 70.2 percent and 64.5 percent, respectively. The mean difference was better for a projection system due to small rater error by graduate students. Projection system ratings were slightly less consistent than view box ratings. Dental hygiene faculty ratings were the most consistent but least accurate. Although the projection system resulted in slightly reduced accuracy and consistency among instructors, training sessions utilizing a single method for projecting digitized radiographic images have their advantages and may positively influence dental education and patient care by enhancing accuracy and consistency of radiographic interpretation among instructors.

Detection of Stimulants and Narcotics by Liquid Chromatography-Tandem Mass Spectrometry and Gas Chromatography-Mass Spectrometry for Sports Doping Control.

PubMed

Ahrens, Brian D; Kucherova, Yulia; Butch, Anthony W

2016-01-01

Sports drug testing laboratories are required to detect several classes of compounds that are prohibited at all times, which include anabolic agents, peptide hormones, growth factors, beta-2 agonists, hormones and metabolic modulators, and diuretics/masking agents. Other classes of compounds such as stimulants, narcotics, cannabinoids, and glucocorticoids are also prohibited, but only when an athlete is in competition. A single class of compounds can contain a large number of prohibited substances and all of the compounds should be detected by the testing procedure. Since there are almost 70 stimulants on the prohibited list it can be a challenge to develop a single screening method that will optimally detect all the compounds. We describe a combined liquid chromatography-tandem mass spectrometry (LC-MS/MS) and gas chromatography-mass spectrometry (GC-MS) testing method for detection of all the stimulants and narcotics on the World Anti-Doping Agency prohibited list. Urine for LC-MS/MS testing does not require sample pretreatment and is a direct dilute and shoot method. Urine samples for the GC-MS method require a liquid-liquid extraction followed by derivatization with trifluoroacetic anhydride.

AATSR Based Volcanic Ash Plume Top Height Estimation

NASA Astrophysics Data System (ADS)

Virtanen, Timo H.; Kolmonen, Pekka; Sogacheva, Larisa; Sundstrom, Anu-Maija; Rodriguez, Edith; de Leeuw, Gerrit

2015-11-01

The AATSR Correlation Method (ACM) height estimation algorithm is presented. The algorithm uses Advanced Along Track Scanning Radiometer (AATSR) satellite data to detect volcanic ash plumes and to estimate the plume top height. The height estimate is based on the stereo-viewing capability of the AATSR instrument, which allows to determine the parallax between the satellite's nadir and 55◦ forward views, and thus the corresponding height. AATSR provides an advantage compared to other stereo-view satellite instruments: with AATSR it is possible to detect ash plumes using brightness temperature difference between thermal infrared (TIR) channels centered at 11 and 12 μm. The automatic ash detection makes the algorithm efficient in processing large quantities of data: the height estimate is calculated only for the ash-flagged pixels. Besides ash plumes, the algorithm can be applied to any elevated feature with sufficient contrast to the background, such as smoke and dust plumes and clouds. The ACM algorithm can be applied to the Sea and Land Surface Temperature Radiometer (SLSTR), scheduled for launch at the end of 2015.

SDTCP: Towards Datacenter TCP Congestion Control with SDN for IoT Applications.

PubMed

Lu, Yifei; Ling, Zhen; Zhu, Shuhong; Tang, Ling

2017-01-08

The Internet of Things (IoT) has gained popularity in recent years. Today's IoT applications are now increasingly deployed in cloud platforms to perform Big Data analytics. In cloud data center networks (DCN), TCP incast usually happens when multiple senders simultaneously communicate with a single receiver. However, when TCP incast happens, DCN may suffer from both throughput collapse for TCP burst flows and temporary starvation for TCP background flows. In this paper, we propose a software defined network (SDN)-based TCP congestion control mechanism, referred to as SDTCP, to leverage the features, e.g., centralized control methods and the global view of the network, in order to solve the TCP incast problems. When we detect network congestion on an OpenFlow switch, our controller can select the background flows and reduce their bandwidth by adjusting the advertised window of TCP ACK packets of the corresponding background flows so as to reserve more bandwidth for burst flows. SDTCP is transparent to the end systems and can accurately decelerate the rate of background flows by leveraging the global view of the network gained via SDN. The experiments demonstrate that our SDTCP can provide high tolerance for burst flows and achieve better flow completion time for short flows. Therefore, SDTCP is an effective and scalable solution for the TCP incast problem.

Light-sheet enhanced resolution of light field microscopy for rapid imaging of large volumes

NASA Astrophysics Data System (ADS)

Madrid Wolff, Jorge; Castro, Diego; Arbeláez, Pablo; Forero-Shelton, Manu

2018-02-01

Whole-brain imaging is challenging because it demands microscopes with high temporal and spatial resolution, which are often at odds, especially in the context of large fields of view. We have designed and built a light-sheet microscope with digital micromirror illumination and light-field detection. On the one hand, light sheets provide high resolution optical sectioning on live samples without compromising their viability. On the other hand, light field imaging makes it possible to reconstruct full volumes of relatively large fields of view from a single camera exposure; however, its enhanced temporal resolution comes at the expense of spatial resolution, limiting its applicability. We present an approach to increase the resolution of light field images using DMD-based light sheet illumination. To that end, we develop a method to produce synthetic resolution targets for light field microscopy and a procedure to correct the depth at which planes are refocused with rendering software. We measured the axial resolution as a function of depth and show a three-fold potential improvement with structured illumination, albeit by sacrificing some temporal resolution, also three-fold. This results in an imaging system that may be adjusted to specific needs without having to reassemble and realign it. This approach could be used to image relatively large samples at high rates.

Can a Single Sagittal Magnetic Resonance Imaging Slice Represent Whole Fatty Infiltration in Chronic Rotator Cuff Tears at the Supraspinatus?

PubMed Central

Lee, Yong-Beom; Yang, Cheol-Jung; Li, Cheng Zhen; Zhuan, Zhong; Kwon, Seung-Cheol

2018-01-01

Background This study aimed to investigate whether fatty infiltration (FI) measured on a single sagittal magnetic resonance imaging (MRI) slice can represent FI of the whole supraspinatus muscle. Methods This study retrospectively reviewed the MRIs of 106 patients (age 50–79 years) divided into three rotator cuff tear-size groups: medium, large, and massive. Fat mass and muscle mass on all T1-weighted sagittal MRI scans (FA and MA) were measured. Of the total MRI scans, the Y-view was defined as the most lateral image of the junction of the scapular spine with the scapular body on the oblique sagittal T1-weighted image. Fat mass and muscle mass seen on this Y-view single slice were recorded as F1 and M1, respectively. Fat mass and muscle mass were also assessed on MRI scans lateral and medial to the Y-view. The means of fat mass and muscle mass on these three slices were recorded as F3 and M3, respectively. Average FI ratios (fat mass/muscle mass) of the three assessment methods (F1/M1, FA/MA, and F3/M3) were compared. Intraclass correlation coefficients (ICCs) were calculated for inter- and intraobserver reliability. Results ICCs showed higher reliability (> 0.8) for all measurements. F1/M1 values were not statistically different from FA/MA and F3/M3 values (p > 0.05), except in males with medium and large tears. F3/M3 and FA/MA were not statistically different. The difference between F1/M1 and FA/MA did not exceed 2%. Conclusions A single sagittal MRI slice can represent the whole FI in chronic rotator cuff tears, except in some patient groups. We recommend measurement of FI using a single sagittal MRI slice, given the effort required for repeated measurements. PMID:29564048

Method and apparatus for determining viscosity

DOEpatents

Chu, Benjamin; Dhadwal, Harbans S.

1990-01-01

A capillary viscometer is provided which includes a fiber-optic probe and a phototransistor which produces an output signal as a liquid meniscus falls through the field of view of a detecting fiber bundle. An analog circuit is employed for receiving the signal and starting or stopping a digital counter in response thereto. The circuit includes first and second differentiators and a zero detection portion for detecting zero value outputs from the second differentiator. The counter is started or stopped upon the generation of a triggering pulse at the time such zero value is detected.

Acoustic and satellite remote sensing of shallow nearshore marine habitats in the Gwaii Haanas National Marine Conservation Area

NASA Astrophysics Data System (ADS)

Reshitnyk, Luba Yvanka

The ability to map nearshore habitat (i.e. submerged aquatic vegetation) is an integral component of marine conservation. The main goal of this thesis was to examine the ability of high resolution, multispectral satellite imagery and a single-beam acoustic ground discrimination system to map the location of marine habitats in Bag Harbour, found in the Gwaii Haanas National Marine Conservation Area Reserve. To meet this goal, two objectives were addressed: (1) Using the QTC View V sing-beam acoustic ground discrimination system, identify which frequency (50 kHz or 200 kHz) is best suited for mapping marine habitat; (2) evaluate the ability to map nearshore marine habitat using WorldView-2 high resolution, multispectral satellite imagery and compare the results of marine habitat maps derived from the acoustic and satellite datasets. Ground-truth data for both acoustic and satellite data were collected via towed underwater video camera on June 3rd and 4th, 2012. Acoustic data (50 and 200 kHz) were collected on June 23rd and 24 th, 2012, respectively. The results of this study are organized into two papers. The first paper focuses on objective 1 where the QTC View V single-beam acoustic ground discrimination system was used to map nearshore habitat at a site within the Gwaii Haanas National Marine Conservation Area using two survey frequencies -- 50 kHz and 200 kHz. The results show that the 200 kHz data outperformed the 50 kHz data set in both thematic and spatial accuracy. The 200 kHz dataset was able to identify two species of submerged aquatic vegetation, eelgrass ( Zostera marina) and a red algae (Chondrocanthus exasperatus ) while the 50 kHz dataset was only able to detect the distribution of eelgrass. The best overall accuracy achieved with the 200 kHz dataset was 86% for a habitat map with three classes (dense eelgrass, dense red algae and unvegetated substrate) compared to the 50 kHz habitat classification with two classes (dense eelgrass and unvegetated substrate) that had an overall accuracy of 70%. Neither dataset was capable if discerning the distribution of green algae (Ulva spp.) or brown algae (Fucus spp.), also present at the site. The second paper examines the benthic habitat maps created using WorldView-2 satellite imagery and the QTC View V single-beam acoustic ground discrimination system (AGDS) at 200 kHz (objective 2). Optical and acoustic remote sensing technologies both present unique capabilities of mapping nearshore habitat. Acoustic systems are able to map habitat in subtidal regions outside of the range of optical sensors while optical sensors such as WorldView-2 provide higher spatial and spectral resolution. The results of this study found that the WorldView-2 achieved the highest overall accuracy (75%) for mapping shallow (<3 m) benthic classes (green algae, brown algae, eelgrass and unvegetated substrate). The 200 kHz data were found to perform best in deeper (>3 m) regions and were able to detect the distribution of eelgrass, red algae and unvegetated substrate. A final habitat map was produced composed of these outputs to create a final, comprehensive habitat map of Bag Harbour. These results highlight the benefits and limitations of each remote sensing technology from a conservation management perspective. The main benefits of the WorldView-2 imagery stem from the high resolution (2 x 2 m) pixel resolution, with a single image covering many kilometers of coastline, and ability to discern habitats in the intertidal region that were undetectable by AGDS. However, the main limitation of this technology is the ability to acquire imagery under ideal conditions (low tide and calm seas). In contrast, the QTC View V system requires more hours spent collecting acoustic data in the field, is limited in the number of habitats it is able to detect and creates maps based on interpolated point data (compared to the continuous raster data of the WorldView-2 imagery). If, however, the objectives of the conservation management to create high resolution benthic habitat maps of subtidal habitats (e.g. eelgrass and benthic red algae) at a handful of sites (in contrast to continuous coastal coverage), the QTC View V system is more suitable. Whichever system is used ground-truth data are required to train and validate each dataset.

Research on infrared ship detection method in sea-sky background

NASA Astrophysics Data System (ADS)

Tang, Da; Sun, Gang; Wang, Ding-he; Niu, Zhao-dong; Chen, Zeng-ping

2013-09-01

An approach to infrared ship detection based on sea-sky-line(SSL) detection, ROI extraction and feature recognition is proposed in this paper. Firstly, considering that far ships are expected to be adjacent to the SSL, SSL is detected to find potential target areas. Radon transform is performed on gradient image to choose candidate SSLs, and detection result is given by fuzzy synthetic evaluation values. Secondly, in view of recognizable condition that there should be enough differences between target and background in infrared image, two gradient masks have been created and improved as practical guidelines in eliminating false alarm. Thirdly, extract ROI near the SSL by using multi-grade segmentation and fusion method after image sharpening, and unsuitable candidates are screened out according to the gradient masks and ROI shape. Finally, we segment the rest of ROIs by two-stage modified OTSU, and calculate target confidence as a standard measuring the facticity of target. Compared with other ship detection methods, proposed method is suitable for bipolar targets, which offers a good practicability and accuracy, and achieves a satisfying detection speed. Detection experiments with 200 thousand frames show that the proposed method is widely applicable, powerful in resistance to interferences and noises with a detection rate of above 95%, which satisfies the engineering needs commendably.

The Kepler Mission: A Photometric Search for Earthlike Planets

NASA Technical Reports Server (NTRS)

Lissauer, Jack J.; Borucki, William; Koch, David; Young, Richard E. (Technical Monitor)

1998-01-01

If Earth lies in or near the orbital plane of an extrasolar planet, that planet passes in front of the disk of its star once each orbit as viewed from Earth. Precise photometry can reveal such transits, which can be distinguished from rotationally-modulated starspots and intrinsic stellar variability by their periodicity, square-well shapes and relative spectral neutrality. Transit observations would provide the size and orbital period of the detected planet. Although geometrical considerations limit the fraction of planets detectable by this technique, many stars can be surveyed within the field of view of one telescope, so transit photometry is quite efficient. Scintillation in and variability of Earth's atmosphere limit photometric precision to roughly one-thousandth of a magnitude, allowing detection of transits by Jupiter-sized planets but not by Earth-sized planets from the ground. The COROT spacecraft will be able to detect Uranus-sized planets orbiting near stars. The Kepler Mission, which is being proposed to NASA's Discovery Program this year, will have a photometer with a larger aperture (1 meter) than will COROT, so it will be able to detect transits by planets as small as Earth. Moreover, the Kepler mission will examine the same star field for four years, allowing confirmation of planets with orbital periods of a year. If the Sun's planetary system is typical for single stars, Kepler should detect approximately 480 terrestrial planets. Assuming the statistics from radial velocity surveys are typical, Kepler should also detect transits of 150 inner giant planets and reflected light variations of 1400 giant planets with orbital periods of less than one week.

Real-time detection and monitoring of the drug resistance of single myeloid leukemia cells by diffused total internal reflection.

PubMed

Liang, L; Jin, Y X; Zhu, X Q; Zhou, F L; Yang, Y

2018-05-15

Real-time detection and monitoring of the drug resistance of single cells have important significance in clinical diagnosis and therapy. Traditional methods operate a number of times for each individual concentration, and innovation is required for the design of more simple and efficient manipulation platforms with necessary higher sensitivity. Here, we have developed a novel diffused total internal reflection (TIR) method to perform drug metabolism and cytotoxicity analysis of trapped myeloid leukemia cells. Molm-13 cells, a type of acute myeloid leukemia cell, were chosen and injected into the device and fittingly captured by cell traps. Differing from previous studies, a series of different concentrations of azelaic acid (AZA) drug could be used from 0 mM to 50 mM through convection and diffusion processes in a single chip, with each concentration region featuring 50 cells, with a total of 549 cell trapping units. Thanks to the high sensitivity of the TIR method, only cells with the same drug concentration could be illuminated in the detection process. By adjusting the incident angle, we could exactly detect and monitor the drug resistance of the cells using different drug concentrations and the experimental resolution of the drug concentration was as small as 5 mM. Images of the membrane integrity and morphology of the cells in the bright field were measured and we also monitored the cell viabilities in the dark field over 2 hours. The effects of AZA on the Molm-13 cells were explored in different concentrations at the single cell level. Compared with the results of the traditional MTT assay method, the experimental results are more simple and accurate. A cell death of 5% at an AZA concentration of 5 mM was observed after 30 minutes, while a concentration of 40 mM corresponded to a 98% cell death. The designed method in this study provides a novel toolkit to control and monitor drug resistance at the single cell level more easily with higher sensitivity and we believe it has significant potential application in single cell quality assessment and medicine analysis in clinical practice.

Thin wetting film lensless imaging

NASA Astrophysics Data System (ADS)

Allier, C. P.; Poher, V.; Coutard, J. G.; Hiernard, G.; Dinten, J. M.

2011-03-01

Lensless imaging has recently attracted a lot of attention as a compact, easy-to-use method to image or detect biological objects like cells, but failed at detecting micron size objects like bacteria that often do not scatter enough light. In order to detect single bacterium, we have developed a method based on a thin wetting film that produces a micro-lens effect. Compared with previously reported results, a large improvement in signal to noise ratio is obtained due to the presence of a micro-lens on top of each bacterium. In these conditions, standard CMOS sensors are able to detect single bacterium, e.g. E.coli, Bacillus subtilis and Bacillus thuringiensis, with a large signal to noise ratio. This paper presents our sensor optimization to enhance the SNR; improve the detection of sub-micron objects; and increase the imaging FOV, from 4.3 mm2 to 12 mm2 to 24 mm2, which allows the detection of bacteria contained in 0.5μl to 4μl to 10μl, respectively.

Single Laboratory Comparison of Quantitative Real-Time PCR Assays for the Detection of Human Fecal Pollution - Poster

EPA Science Inventory

There are numerous quantitative real-time PCR (qPCR) methods available to detect and enumerate human fecal pollution in ambient waters. Each assay employs distinct primers and/or probes and many target different genes and microorganisms leading to potential variations in method p...

Analysis of glycosaminoglycan-derived disaccharides by capillary electrophoresis using laser-induced fluorescence detection

PubMed Central

Chang, Yuqing; Yang, Bo; Zhao, Xue; Linhardt, Robert J.

2012-01-01

A quantitative and highly sensitive method for the analysis of glycosaminoglycan (GAG)-derived disaccharides is presented that relies on capillary electrophoresis (CE) with laser-induced fluorescence (LIF) detection. This method enables complete separation of seventeen GAG-derived disaccharides in a single run. Unsaturated disaccharides were derivatized with 2-aminoacridone (AMAC) to improve sensitivity. The limit of detection was at the attomole level and about 100-fold more sensitive than traditional CE-ultraviolet detection. A CE separation timetable was developed to achieve complete resolution and shorten analysis time. The RSD of migration time and peak areas at both low and high concentrations of unsaturated disaccharides are all less than 2.7% and 3.2%, respectively, demonstrating that this is a reproducible method. This analysis was successfully applied to cultured Chinese hamster ovary cell samples for determination of GAG disaccharides. The current method simplifies GAG extraction steps, and reduces inaccuracy in calculating ratios of heparin/heparan sulfate to chondroitin sulfate/dermatan sulfate, resulting from the separate analyses of a single sample. PMID:22609076

Development and validation of a FISH-based method for the detection and quantification of E. coli and coliform bacteria in water samples.

PubMed

Hügler, Michael; Böckle, Karin; Eberhagen, Ingrid; Thelen, Karin; Beimfohr, Claudia; Hambsch, Beate

2011-01-01

Monitoring of microbiological contaminants in water supplies requires fast and sensitive methods for the specific detection of indicator organisms or pathogens. We developed a protocol for the simultaneous detection of E. coli and coliform bacteria based on the Fluorescence in situ Hybridization (FISH) technology. This protocol consists of two approaches. The first allows the direct detection of single E. coli and coliform bacterial cells on the filter membranes. The second approach includes incubation of the filter membranes on a nutrient agar plate and subsequent detection of the grown micro-colonies. Both approaches were validated using drinking water samples spiked with pure cultures and naturally contaminated water samples. The effects of heat, chlorine and UV disinfection were also investigated. The micro-colony approach yielded very good results for all samples and conditions tested, and thus can be thoroughly recommended for usage as an alternative method to detect E. coli and coliform bacteria in water samples. However, during this study, some limitations became visible for the single cell approach. The method cannot be applied for water samples which have been disinfected by UV irradiation. In addition, our results indicated that green fluorescent dyes are not suitable to be used with chlorine disinfected samples.

Visualization and automatic detection of defect distribution in GaN atomic structure from sampling Moiré phase.

PubMed

Wang, Qinghua; Ri, Shien; Tsuda, Hiroshi; Kodera, Masako; Suguro, Kyoichi; Miyashita, Naoto

2017-09-19

Quantitative detection of defects in atomic structures is of great significance to evaluating product quality and exploring quality improvement process. In this study, a Fourier transform filtered sampling Moire technique was proposed to visualize and detect defects in atomic arrays in a large field of view. Defect distributions, defect numbers and defect densities could be visually and quantitatively determined from a single atomic structure image at low cost. The effectiveness of the proposed technique was verified from numerical simulations. As an application, the dislocation distributions in a GaN/AlGaN atomic structure in two directions were magnified and displayed in Moire phase maps, and defect locations and densities were detected automatically. The proposed technique is able to provide valuable references to material scientists and engineers by checking the effect of various treatments for defect reduction. © 2017 IOP Publishing Ltd.

Characterization of circulating tumor cell aggregates identified in patients with epithelial tumors

NASA Astrophysics Data System (ADS)

Cho, Edward H.; Wendel, Marco; Luttgen, Madelyn; Yoshioka, Craig; Marrinucci, Dena; Lazar, Daniel; Schram, Ethan; Nieva, Jorge; Bazhenova, Lyudmila; Morgan, Alison; Ko, Andrew H.; Korn, W. Michael; Kolatkar, Anand; Bethel, Kelly; Kuhn, Peter

2012-02-01

Circulating tumor cells (CTCs) have been implicated as a population of cells that may seed metastasis and venous thromboembolism (VTE), two major causes of mortality in cancer patients. Thus far, existing CTC detection technologies have been unable to reproducibly detect CTC aggregates in order to address what contribution CTC aggregates may make to metastasis or VTE. We report here an enrichment-free immunofluorescence detection method that can reproducibly detect and enumerate homotypic CTC aggregates in patient samples. We identified CTC aggregates in 43% of 86 patient samples. The fraction of CTC aggregation was investigated in blood draws from 24 breast, 14 non-small cell lung, 18 pancreatic, 15 prostate stage IV cancer patients and 15 normal blood donors. Both single CTCs and CTC aggregates were measured to determine whether differences exist in the physical characteristics of these two populations. Cells contained in CTC aggregates had less area and length, on average, than single CTCs. Nuclear to cytoplasmic ratios between single CTCs and CTC aggregates were similar. This detection method may assist future studies in determining which population of cells is more physically likely to contribute to metastasis and VTE.

[Detection of KRAS mutation in colorectal cancer patients' cfDNA with droplet digital PCR].

PubMed

Luo, Yuwen; Li, Yao

2018-03-25

This study aims to develop a new method for the detection of KRAS mutations related to colorectal cancer in cfDNA, and to evaluate the sensitivity and accuracy of the detection. We designed a method of cfDNA based KRAS detection by droplets digital PCR (ddPCR). The theoretical performance of the method is evaluated by reference standard and compared to the ARMS PCR method. Two methods, ddPCR and qPCR, were successfully established to detect KRAS wild type and 7 mutants. Both methods were validated using plasmid standards and actual samples. The results were evaluated by false positive rate, linearity, and limit of detection. Finally, 52 plasma cfDNA samples from patients and 20 samples from healthy people were tested, the clinical sensitivity is 97.64%, clinical specificity is 81.43%. ddPCR method shows higher performance than qPCR. The LOD of ddPCR method reached single digits of cfDNA copies, it can detect as low as 0.01% to 0.04% mutation abundance.

Vision based speed breaker detection for autonomous vehicle

NASA Astrophysics Data System (ADS)

C. S., Arvind; Mishra, Ritesh; Vishal, Kumar; Gundimeda, Venugopal

2018-04-01

In this paper, we are presenting a robust and real-time, vision-based approach to detect speed breaker in urban environments for autonomous vehicle. Our method is designed to detect the speed breaker using visual inputs obtained from a camera mounted on top of a vehicle. The method performs inverse perspective mapping to generate top view of the road and segment out region of interest based on difference of Gaussian and median filter images. Furthermore, the algorithm performs RANSAC line fitting to identify the possible speed breaker candidate region. This initial guessed region via RANSAC, is validated using support vector machine. Our algorithm can detect different categories of speed breakers on cement, asphalt and interlock roads at various conditions and have achieved a recall of 0.98.

[Place of indocyanine green coupled with fluorescence imaging in research of breast cancer sentinel node].

PubMed

Vermersch, Charlotte; Raia Barjat, Tiphaine; Perrot, Marianne; Lima, Suzanne; Chauleur, Céline

2016-04-01

The sentinel node has a fundamental role in the management of early breast cancer. Currently, the double detection of blue and radioisotope is recommended. But in common practice, many centers use a single method. However, with a single detection, the risk of false negatives and the identification failure rate increase to a significant extent and the number of sentinel lymph node detected and removed is not enough. Furthermore, the tracers used until now show inconveniences. The purpose of this work is to present a new method of detection, using the green of indocyanine coupled with fluorescence imaging, and to compare it with the already existing methods. The method combined by fluorescence and isotopic is reliable, sure, of fast learning and could constitute a good strategy of detection. The major interest is to obtain a satisfactory number of sentinel nodes. The profit could be even more important for overweight patients. The fluorescence used alone is at the moment not possible. Wide ranging studies are necessary. The FLUOTECH, randomized study of 100 patients, comparing the isotopic method of double isotope technique and fluorescence, is underway to confirm these data. Copyright © 2016 Société Française du Cancer. Published by Elsevier Masson SAS. All rights reserved.

Single Cell Spectroscopy: Noninvasive Measures of Small-Scale Structure and Function

PubMed Central

Mousoulis, Charilaos; Xu, Xin; Reiter, David A.; Neu, Corey P.

2013-01-01

The advancement of spectroscopy methods attained through increases in sensitivity, and often with the coupling of complementary techniques, has enabled real-time structure and function measurements of single cells. The purpose of this review is to illustrate, in light of advances, the strengths and the weaknesses of these methods. Included also is an assessment of the impact of the experimental setup and conditions of each method on cellular function and integrity. A particular emphasis is placed on noninvasive and nondestructive techniques for achieving single cell detection, including nuclear magnetic resonance, in addition to physical, optical, and vibrational methods. PMID:23886910

Multichordal charge exchange recombination spectroscopy on Doublet III (abstract)

NASA Astrophysics Data System (ADS)

Seraydarian, R. P.; Burrell, K. H.; Kahn, C.

1985-05-01

Single shot, multipoint ion temperature and plasma rotation profiles have been routinely obtained on the Doublet III tokamak for 32 consecutive time slices with 20-ms resolution. A six-chord tangentially viewing spectroscopic diagnostic has been built to look at radiation emitted by fully stripped low-Z impurity ions (He, C, O) that have undergone charge exchange recombination with hydrogen atoms from a 3-MW heating beam. The main components of the instrument are a single monochromator for wavelength dispersion, a single image intensifier tube for photon gain, and a pair of 1024-element linear photodiode arrays for detection. A special arrangement of fiber optics allows simultaneous data acquisition from all chords without the use of scanning mirrors or other moving parts. Ion temperature profiles taken under a variety of plasma conditions will be presented.

Optimization of Self-Directed Target Coverage in Wireless Multimedia Sensor Network

PubMed Central

Yang, Yang; Wang, Yufei; Pi, Dechang; Wang, Ruchuan

2014-01-01

Video and image sensors in wireless multimedia sensor networks (WMSNs) have directed view and limited sensing angle. So the methods to solve target coverage problem for traditional sensor networks, which use circle sensing model, are not suitable for WMSNs. Based on the FoV (field of view) sensing model and FoV disk model proposed, how expected multimedia sensor covers the target is defined by the deflection angle between target and the sensor's current orientation and the distance between target and the sensor. Then target coverage optimization algorithms based on expected coverage value are presented for single-sensor single-target, multisensor single-target, and single-sensor multitargets problems distinguishingly. Selecting the orientation that sensor rotated to cover every target falling in the FoV disk of that sensor for candidate orientations and using genetic algorithm to multisensor multitargets problem, which has NP-complete complexity, then result in the approximated minimum subset of sensors which covers all the targets in networks. Simulation results show the algorithm's performance and the effect of number of targets on the resulting subset. PMID:25136667

Viewing Ice Crystals Using Polarized Light.

ERIC Educational Resources Information Center

Kinsman, E. M.

1992-01-01

Describes a method for identifying and examining single ice crystals by photographing a thin sheet of ice placed between two inexpensive polarizing filters. Suggests various natural and prepared sources for ice that promote students' insight into crystal structures, and yield colorful optical displays. Includes directions, precautions, and sample…

Apparatus for use in sulfide chemiluminescence detection

DOEpatents

Spurlin, S.R.; Yeung, E.S.

1987-01-06

A method is described for chemiluminescently determining a sulfide which is either hydrogen sulfide or methyl mercaptan by reacting the sulfide with chlorine dioxide at low pressure and under conditions which allow a longer reaction time in emission of a single photon for every two sulfide containing species, and thereafter, chemiluminescently detecting and determining the sulfide. The invention also relates not only to the detection method, but the novel chemical reaction and a specifically designed chemiluminescence detection cell for the reaction. 4 figs.