A flower image retrieval method based on ROI feature.

PubMed

Hong, An-Xiang; Chen, Gang; Li, Jun-Li; Chi, Zhe-Ru; Zhang, Dan

2004-07-01

Flower image retrieval is a very important step for computer-aided plant species recognition. In this paper, we propose an efficient segmentation method based on color clustering and domain knowledge to extract flower regions from flower images. For flower retrieval, we use the color histogram of a flower region to characterize the color features of flower and two shape-based features sets, Centroid-Contour Distance (CCD) and Angle Code Histogram (ACH), to characterize the shape features of a flower contour. Experimental results showed that our flower region extraction method based on color clustering and domain knowledge can produce accurate flower regions. Flower retrieval results on a database of 885 flower images collected from 14 plant species showed that our Region-of-Interest (ROI) based retrieval approach using both color and shape features can perform better than a method based on the global color histogram proposed by Swain and Ballard (1991) and a method based on domain knowledge-driven segmentation and color names proposed by Das et al.(1999).

Analyzing the impact of sensor characteristics on retrieval methods of solar-induced fluorescence

NASA Astrophysics Data System (ADS)

Ding, Wenjuan; Zhao, Feng; Yang, Lizi

2017-02-01

In this study, we evaluated the influence of retrieval algorithms and sensor characteristics, such as spectral resolution (SR) and signal to noise ratio (SNR), on the retrieval accuracy of fluorescence signal (Fs). Here Fs was retrieved by four commonly used retrieval methods, namely the original Fraunhofer Line Discriminator method (FLD), the 3 bands FLD (3FLD), the improved FLD (iFLD) and the spectral fitting method (SFM). Fs was retrieved in the oxygen A band centered at around 761nm (O2-A). We analyzed the impact of sensor characteristics on four retrieval methods based on simulated data which were generated by the model SCOPE (Soil Canopy Observation, Photochemistry and Energy fluxes), and obtained consistent conclusions when compared with experimental data. Results presented in this study indicate that both retrieval algorithms and sensor characteristics affect the retrieval accuracy of Fs. When applied to the actual measurement, we should choose the instrument with higher performance and adopt appropriate retrieval method according to measuring instruments and conditions.

Phase retrieval using regularization method in intensity correlation imaging

NASA Astrophysics Data System (ADS)

Li, Xiyu; Gao, Xin; Tang, Jia; Lu, Changming; Wang, Jianli; Wang, Bin

2014-11-01

Intensity correlation imaging(ICI) method can obtain high resolution image with ground-based low precision mirrors, in the imaging process, phase retrieval algorithm should be used to reconstituted the object's image. But the algorithm now used(such as hybrid input-output algorithm) is sensitive to noise and easy to stagnate. However the signal-to-noise ratio of intensity interferometry is low especially in imaging astronomical objects. In this paper, we build the mathematical model of phase retrieval and simplified it into a constrained optimization problem of a multi-dimensional function. New error function was designed by noise distribution and prior information using regularization method. The simulation results show that the regularization method can improve the performance of phase retrieval algorithm and get better image especially in low SNR condition

The influence of learning methods on collaboration: prior repeated retrieval enhances retrieval organization, abolishes collaborative inhibition, and promotes post-collaborative memory.

PubMed

Congleton, Adam R; Rajaram, Suparna

2011-11-01

Research on collaborative memory has unveiled the counterintuitive yet robust phenomenon that collaboration impairs group recall. A candidate explanation for this collaborative inhibition effect is the disruption of people's idiosyncratic retrieval strategies during collaboration, and it is hypothesized that employing methods that improve one's organization protects against retrieval disruption. Here it is investigated how one's learning method during the study phase--defined as either repeatedly studying or repeatedly retrieving information--influences retrieval organization and what effects this has on collaborative recall and post-collaborative individual recall. Results show that repeated retrieval consistently eliminated collaborative inhibition. This enabled participants to gain the most from re-exposure to materials recalled by their partners that they themselves did not recall and led to improvements in their individual memory following collaboration. This repeated retrieval advantage stemmed from the preferential manner in which this learning method strengthened retrieval organization. Findings are also discussed that reveal a relationship between retrieval organization and the interaction observed between learning method and short versus long delay seen in the testing effect literature. Finally, results show that the elusive benefits of cross-cuing during collaboration may be best detected with a longer study-test delay. Together, these findings illuminate when and how collaboration can enhance memory.

A new method of content based medical image retrieval and its applications to CT imaging sign retrieval.

PubMed

Ma, Ling; Liu, Xiabi; Gao, Yan; Zhao, Yanfeng; Zhao, Xinming; Zhou, Chunwu

2017-02-01

This paper proposes a new method of content based medical image retrieval through considering fused, context-sensitive similarity. Firstly, we fuse the semantic and visual similarities between the query image and each image in the database as their pairwise similarities. Then, we construct a weighted graph whose nodes represent the images and edges measure their pairwise similarities. By using the shortest path algorithm over the weighted graph, we obtain a new similarity measure, context-sensitive similarity measure, between the query image and each database image to complete the retrieval process. Actually, we use the fused pairwise similarity to narrow down the semantic gap for obtaining a more accurate pairwise similarity measure, and spread it on the intrinsic data manifold to achieve the context-sensitive similarity for a better retrieval performance. The proposed method has been evaluated on the retrieval of the Common CT Imaging Signs of Lung Diseases (CISLs) and achieved not only better retrieval results but also the satisfactory computation efficiency. Copyright © 2017 Elsevier Inc. All rights reserved.

Efficient Methods to Assimilate Satellite Retrievals Based on Information Content. Part 2; Suboptimal Retrieval Assimilation

NASA Technical Reports Server (NTRS)

Joiner, J.; Dee, D. P.

1998-01-01

One of the outstanding problems in data assimilation has been and continues to be how best to utilize satellite data while balancing the tradeoff between accuracy and computational cost. A number of weather prediction centers have recently achieved remarkable success in improving their forecast skill by changing the method by which satellite data are assimilated into the forecast model from the traditional approach of assimilating retrievals to the direct assimilation of radiances in a variational framework. The operational implementation of such a substantial change in methodology involves a great number of technical details, e.g., pertaining to quality control procedures, systematic error correction techniques, and tuning of the statistical parameters in the analysis algorithm. Although there are clear theoretical advantages to the direct radiance assimilation approach, it is not obvious at all to what extent the improvements that have been obtained so far can be attributed to the change in methodology, or to various technical aspects of the implementation. The issue is of interest because retrieval assimilation retains many practical and logistical advantages which may become even more significant in the near future when increasingly high-volume data sources become available. The central question we address here is: how much improvement can we expect from assimilating radiances rather than retrievals, all other things being equal? We compare the two approaches in a simplified one-dimensional theoretical framework, in which problems related to quality control and systematic error correction are conveniently absent. By assuming a perfect radiative transfer model and perfect knowledge of radiance and background error covariances, we are able to formulate a nonlinear local error analysis for each assimilation method. Direct radiance assimilation is optimal in this idealized context, while the traditional method of assimilating retrievals is suboptimal because it

An introduction to the theory of ptychographic phase retrieval methods

NASA Astrophysics Data System (ADS)

Konijnenberg, Sander

2017-12-01

An overview of several ptychographic phase retrieval methods and the theory behind them is presented. By looking into the theory behind more basic single-intensity pattern phase retrieval methods, a theoretical framework is provided for analyzing ptychographic algorithms. Extensions of ptychographic algorithms that deal with issues such as partial coherence, thick samples, or uncertainties of the probe or probe positions are also discussed. This introduction is intended for scientists and students without prior experience in the field of phase retrieval or ptychography to quickly get introduced to the theory, so that they can put the more specialized literature in context more easily.

Phase retrieval with the reverse projection method in the presence of object's scattering

NASA Astrophysics Data System (ADS)

Wang, Zhili; Gao, Kun; Wang, Dajiang

2017-08-01

X-ray grating interferometry can provide substantially increased contrast over traditional attenuation-based techniques in biomedical applications, and therefore novel and complementary information. Recently, special attention has been paid to quantitative phase retrieval in X-ray grating interferometry, which is mandatory to perform phase tomography, to achieve material identification, etc. An innovative approach, dubbed ;Reverse Projection; (RP), has been developed for quantitative phase retrieval. The RP method abandons grating scanning completely, and is thus advantageous in terms of higher efficiency and reduced radiation damage. Therefore, it is expected that this novel method would find its potential in preclinical and clinical implementations. Strictly speaking, the reverse projection method is applicable for objects exhibiting only absorption and refraction. In this contribution, we discuss the phase retrieval with the reverse projection method for general objects with absorption, refraction and scattering simultaneously. Especially, we investigate the influence of the object's scattering on the retrieved refraction signal. Both theoretical analysis and numerical experiments are performed. The results show that the retrieved refraction signal is the product of object's refraction and scattering signals for small values. In the case of a strong scattering, the reverse projection method cannot provide reliable phase retrieval. Those presented results will guide the use of the reverse projection method for future practical applications, and help to explain some possible artifacts in the retrieved images and/or reconstructed slices.

Image Retrieval Method for Multiscale Objects from Optical Colonoscopy Images

PubMed Central

Sakanashi, Hidenori; Takahashi, Eiichi; Murakawa, Masahiro; Aoki, Hiroshi; Takeuchi, Ken; Suzuki, Yasuo

2017-01-01

Optical colonoscopy is the most common approach to diagnosing bowel diseases through direct colon and rectum inspections. Periodic optical colonoscopy examinations are particularly important for detecting cancers at early stages while still treatable. However, diagnostic accuracy is highly dependent on both the experience and knowledge of the medical doctor. Moreover, it is extremely difficult, even for specialist doctors, to detect the early stages of cancer when obscured by inflammations of the colonic mucosa due to intractable inflammatory bowel diseases, such as ulcerative colitis. Thus, to assist the UC diagnosis, it is necessary to develop a new technology that can retrieve similar cases of diagnostic target image from cases in the past that stored the diagnosed images with various symptoms of colonic mucosa. In order to assist diagnoses with optical colonoscopy, this paper proposes a retrieval method for colonoscopy images that can cope with multiscale objects. The proposed method can retrieve similar colonoscopy images despite varying visible sizes of the target objects. Through three experiments conducted with real clinical colonoscopy images, we demonstrate that the method is able to retrieve objects of any visible size and any location at a high level of accuracy. PMID:28255295

Image Retrieval Method for Multiscale Objects from Optical Colonoscopy Images.

PubMed

Nosato, Hirokazu; Sakanashi, Hidenori; Takahashi, Eiichi; Murakawa, Masahiro; Aoki, Hiroshi; Takeuchi, Ken; Suzuki, Yasuo

2017-01-01

Optical colonoscopy is the most common approach to diagnosing bowel diseases through direct colon and rectum inspections. Periodic optical colonoscopy examinations are particularly important for detecting cancers at early stages while still treatable. However, diagnostic accuracy is highly dependent on both the experience and knowledge of the medical doctor. Moreover, it is extremely difficult, even for specialist doctors, to detect the early stages of cancer when obscured by inflammations of the colonic mucosa due to intractable inflammatory bowel diseases, such as ulcerative colitis. Thus, to assist the UC diagnosis, it is necessary to develop a new technology that can retrieve similar cases of diagnostic target image from cases in the past that stored the diagnosed images with various symptoms of colonic mucosa. In order to assist diagnoses with optical colonoscopy, this paper proposes a retrieval method for colonoscopy images that can cope with multiscale objects. The proposed method can retrieve similar colonoscopy images despite varying visible sizes of the target objects. Through three experiments conducted with real clinical colonoscopy images, we demonstrate that the method is able to retrieve objects of any visible size and any location at a high level of accuracy.

Detection of peste des petits ruminants virus antigen using immunofiltration and antigen-competition ELISA methods.

PubMed

Raj, G Dhinakar; Rajanathan, T M C; Kumar, C Senthil; Ramathilagam, G; Hiremath, Geetha; Shaila, M S

2008-06-22

Peste des petits ruminants (PPR) is one of the most economically important diseases affecting sheep and goats in India. An immunofiltration-based test has been developed using either mono-specific serum/monoclonal antibodies (mAb) prepared against a recombinant truncated nucleocapsid protein of rinderpest virus (RPV) cross-reactive with PPR virus. This method consists of coating ocular swab eluate from suspected animals onto a nitrocellulose membrane housed in a plastic module, which is allowed to react with suitable dilutions of a mAb or a mono-specific polyclonal antibody. The antigen-antibody complex formed on the membrane is then detected by protein A-colloidal gold conjugate, which forms a pink colour. In the immunofiltration test, concordant results were obtained using either PPRV mAb or mono-specific serum. Another test, an antigen-competition ELISA which relies on the competition between plate-coated recombinant truncated 'N' protein of RPV and the PPRV 'N' protein present in ocular swab eluates (sample) for binding to the mono-specific antibody against N protein of RPV (in liquid phase) was developed. The cut-off value for this test was established using reverse transcription polymerase chain reaction (RT-PCR) positive and negative oculo-nasal swab samples. Linear correlation between percent inhibition (PI) values in antigen-competition ELISA and virus infectivity titres was 0.992. Comparison of the immunofiltration test with the antigen-competition ELISA yielded a sensitivity of 80% and specificity of 100%. These two tests can serve as a screening (immunofiltration) and confirmatory (antigen-competition ELISA) test, respectively, in the diagnosis of PPR in sheep or goats.

A High-Resolution Aerosol Retrieval Method for Urban Areas Using MISR Data

NASA Astrophysics Data System (ADS)

Moon, T.; Wang, Y.; Liu, Y.; Yu, B.

2012-12-01

Satellite-retrieved Aerosol Optical Depth (AOD) can provide a cost-effective way to monitor particulate air pollution without using expensive ground measurement sensors. One of the current state-of-the-art AOD retrieval method is NASA's Multi-angle Imaging SpectroRadiometer (MISR) operational algorithm, which has the spatial resolution of 17.6 km x 17.6 km. While the MISR baseline scheme already leads to exciting research opportunities to study particle compositions at regional scale, its spatial resolution is too coarse for analyzing urban areas where the AOD level has stronger spatial variations. We develop a novel high-resolution AOD retrieval algorithm that still uses MISR's radiance observations but has the resolution of 4.4km x 4.4km. We achieve the high resolution AOD retrieval by implementing a hierarchical Bayesian model and Monte-Carlo Markov Chain (MCMC) inference method. Our algorithm not only improves the spatial resolution, but also extends the coverage of AOD retrieval and provides with additional composition information of aerosol components that contribute to the AOD. We validate our method using the recent NASA's DISCOVER-AQ mission data, which contains the ground measured AOD values for Washington DC and Baltimore area. The validation result shows that, compared to the operational MISR retrievals, our scheme has 41.1% more AOD retrieval coverage for the DISCOVER-AQ data points and 24.2% improvement in mean-squared error (MSE) with respect to the AERONET ground measurements.

Adjusted Levenberg-Marquardt method application to methene retrieval from IASI/METOP spectra

NASA Astrophysics Data System (ADS)

Khamatnurova, Marina; Gribanov, Konstantin

2016-04-01

Levenberg-Marquardt method [1] with iteratively adjusted parameter and simultaneous evaluation of averaging kernels together with technique of parameters selection are developed and applied to the retrieval of methane vertical profiles in the atmosphere from IASI/METOP spectra. Retrieved methane vertical profiles are then used for calculation of total atmospheric column amount. NCEP/NCAR reanalysis data provided by ESRL (NOAA, Boulder,USA) [2] are taken as initial guess for retrieval algorithm. Surface temperature, temperature and humidity vertical profiles are retrieved before methane vertical profile retrieval for each selected spectrum. Modified software package FIRE-ARMS [3] were used for numerical experiments. To adjust parameters and validate the method we used ECMWF MACC reanalysis data [4]. Methane columnar values retrieved from cloudless IASI spectra demonstrate good agreement with MACC columnar values. Comparison is performed for IASI spectra measured in May of 2012 over Western Siberia. Application of the method for current IASI/METOP measurements are discussed. 1.Ma C., Jiang L. Some Research on Levenberg-Marquardt Method for the Nonlinear Equations // Applied Mathematics and Computation. 2007. V.184. P. 1032-1040 2.http://www.esrl.noaa.gov/psdhttp://www.esrl.noaa.gov/psd 3.Gribanov K.G., Zakharov V.I., Tashkun S.A., Tyuterev Vl.G.. A New Software Tool for Radiative Transfer Calculations and its application to IMG/ADEOS data // JQSRT.2001.V.68.№ 4. P. 435-451. 4.http://www.ecmwf.int/http://www.ecmwf.int

Brain CT image similarity retrieval method based on uncertain location graph.

PubMed

Pan, Haiwei; Li, Pengyuan; Li, Qing; Han, Qilong; Feng, Xiaoning; Gao, Linlin

2014-03-01

A number of brain computed tomography (CT) images stored in hospitals that contain valuable information should be shared to support computer-aided diagnosis systems. Finding the similar brain CT images from the brain CT image database can effectively help doctors diagnose based on the earlier cases. However, the similarity retrieval for brain CT images requires much higher accuracy than the general images. In this paper, a new model of uncertain location graph (ULG) is presented for brain CT image modeling and similarity retrieval. According to the characteristics of brain CT image, we propose a novel method to model brain CT image to ULG based on brain CT image texture. Then, a scheme for ULG similarity retrieval is introduced. Furthermore, an effective index structure is applied to reduce the searching time. Experimental results reveal that our method functions well on brain CT images similarity retrieval with higher accuracy and efficiency.

A joint method to retrieve directional ocean wave spectra from SAR and wave spectrometer data

NASA Astrophysics Data System (ADS)

Ren, Lin; Yang, Jingsong; Zheng, Gang; Wang, Juan

2016-07-01

This paper proposes a joint method to simultaneously retrieve wave spectra at different scales from spaceborne Synthetic Aperture Radar (SAR) and wave spectrometer data. The method combines the output from the two different sensors to overcome retrieval limitations that occur in some sea states. The wave spectrometer sensitivity coefficient is estimated using an effective significant wave height (SWH), which is an average of SAR-derived and wave spectrometer-derived SWH. This averaging extends the area of the sea surface sampled by the nadir beam of the wave spectrometer to improve the accuracy of the estimated sensitivity coefficient in inhomogeneous sea states. Wave spectra are then retrieved from SAR data using wave spectrometer-derived spectra as first guess spectra to complement the short waves lost in SAR data retrieval. In addition, the problem of 180° ambiguity in retrieved spectra is overcome using SAR imaginary cross spectra. Simulated data were used to validate the joint method. The simulations demonstrated that retrieved wave parameters, including SWH, peak wave length (PWL), and peak wave direction (PWD), agree well with reference parameters. Collocated data from ENVISAT advanced SAR (ASAR), the airborne wave spectrometer STORM, the PHAROS buoy, and the European Centre for Medium-Range Weather Forecasting (ECMWF) were then used to verify the proposed method. Wave parameters retrieved from STORM and two ASAR images were compared to buoy and ECMWF wave data. Most of the retrieved parameters were comparable to reference parameters. The results of this study show that the proposed joint retrieval method could be a valuable complement to traditional methods used to retrieve directional ocean wave spectra, particularly in inhomogeneous sea states.

Retrieving Land Surface Temperature from Hyperspectral Thermal Infrared Data Using a Multi-Channel Method

PubMed Central

Zhong, Xinke; Huo, Xing; Ren, Chao; Labed, Jelila; Li, Zhao-Liang

2016-01-01

Land Surface Temperature (LST) is a key parameter in climate systems. The methods for retrieving LST from hyperspectral thermal infrared data either require accurate atmospheric profile data or require thousands of continuous channels. We aim to retrieve LST for natural land surfaces from hyperspectral thermal infrared data using an adapted multi-channel method taking Land Surface Emissivity (LSE) properly into consideration. In the adapted method, LST can be retrieved by a linear function of 36 brightness temperatures at Top of Atmosphere (TOA) using channels where LSE has high values. We evaluated the adapted method using simulation data at nadir and satellite data near nadir. The Root Mean Square Error (RMSE) of the LST retrieved from the simulation data is 0.90 K. Compared with an LST product from the Spinning Enhanced Visible and Infrared Imager (SEVIRI) on Meteosat, the error in the LST retrieved from the Infared Atmospheric Sounding Interferometer (IASI) is approximately 1.6 K. The adapted method can be used for the near-real-time production of an LST product and to provide the physical method to simultaneously retrieve atmospheric profiles, LST, and LSE with a first-guess LST value. The limitations of the adapted method are that it requires the minimum LSE in the spectral interval of 800–950 cm−1 larger than 0.95 and it has not been extended for off-nadir measurements. PMID:27187408

Antigen Masking During Fixation and Embedding, Dissected

PubMed Central

Scalia, Carla Rossana; Boi, Giovanna; Bolognesi, Maddalena Maria; Riva, Lorella; Manzoni, Marco; DeSmedt, Linde; Bosisio, Francesca Maria; Ronchi, Susanna; Leone, Biagio Eugenio; Cattoretti, Giorgio

2016-01-01

Antigen masking in routinely processed tissue is a poorly understood process caused by multiple factors. We sought to dissect the effect on antigenicity of each step of processing by using frozen sections as proxies of the whole tissue. An equivalent extent of antigen masking occurs across variable fixation times at room temperature. Most antigens benefit from longer fixation times (>24 hr) for optimal detection after antigen retrieval (AR; for example, Ki-67, bcl-2, ER). The transfer to a graded alcohol series results in an enhanced staining effect, reproduced by treating the sections with detergents, possibly because of a better access of the polymeric immunohistochemical detection system to tissue structures. A second round of masking occurs upon entering the clearing agent, mostly at the paraffin embedding step. This may depend on the non-freezable water removal. AR fully reverses the masking due both to the fixation time and the paraffin embedding. AR itself destroys some epitopes which do not survive routine processing. Processed frozen sections are a tool to investigate fixation and processing requirements for antigens in routine specimens. PMID:27798289

A Method to Retrieve Rainfall Rate over Land from TRMM Observations

NASA Technical Reports Server (NTRS)

Prabhakara, C.; Iacovazzi, R., Jr.; Yoo, J.-M.

2002-01-01

Tropical Rainfall Measuring Mission (TRMM) Precipitation Radar (PR) observations over mesoscale convective systems (MCSs) reveal that there are localized maxima in the rain rate with a scale of about 10 to 20 km that represent thunderstorms (Cbs). Some of these Cbs are developing or intense, while others are decaying or weak. These Cbs constitute only about 20 % of the rain area of a given MCS. Outside of Cbs, the average rain rate is much weaker than that within Cbs. From an analysis of the PR data, we find that the spatial distribution of rain and its character, convective or stratiform, is highly inhomogeneous. This complex nature of rain exists on a scale comparable to that of a Cb. The 85 GHz brightness temperature, T85, observations of the TRMM Microwave Imager (TMI) radiometer taken over an MCS reflect closely the PR rain rate pattern over land. Local maxima in rain rate shown by PR are observed as local minima in T85. Where there are no minima in T85, PR observations indicate there is light rain. However, the TMI brightness temperature measurements (Tbs) have poor ability to discriminate convective rain from stratiform rain. For this reason, a TMI rain retrieval procedure that depends primarily on the magnitude of Tbs performs poorly. In order to retrieve rain rate from TMI data on land one has to include the spatial distribution information deduced from the T85 data in the retrieval method. Then, quantitative estimation of rain rate can be accomplished. A TMI rain retrieval method developed along these lines can yield estimates of rain rate and its frequency distribution which agree closely with that given by PR. We find the current TRMM project TMI (Version 5) rain retrieval algorithm on land could be improved with the retrieval scheme developed here. To support the conceptual frame work of the rain retrieval method developed here, a theoretical analysis of the TMI brightness temperatures in convective and stratiform regions is presented.

Mathematical, Logical, and Formal Methods in Information Retrieval: An Introduction to the Special Issue.

ERIC Educational Resources Information Center

Crestani, Fabio; Dominich, Sandor; Lalmas, Mounia; van Rijsbergen, Cornelis Joost

2003-01-01

Discusses the importance of research on the use of mathematical, logical, and formal methods in information retrieval to help enhance retrieval effectiveness and clarify underlying concepts of information retrieval. Highlights include logic; probability; spaces; and future research needs. (Author/LRW)

A Method for Retrieving Ground Flash Fraction from Satellite Lightning Imager Data

NASA Technical Reports Server (NTRS)

Koshak, William J.

2009-01-01

A general theory for retrieving the fraction of ground flashes in N lightning observed by a satellite-based lightning imager is provided. An "exponential model" is applied as a physically reasonable constraint to describe the measured optical parameter distributions, and population statistics (i.e., mean, variance) are invoked to add additional constraints to the retrieval process. The retrieval itself is expressed in terms of a Bayesian inference, and the Maximum A Posteriori (MAP) solution is obtained. The approach is tested by performing simulated retrievals, and retrieval error statistics are provided. The ability to retrieve ground flash fraction has important benefits to the atmospheric chemistry community. For example, using the method to partition the existing satellite global lightning climatology into separate ground and cloud flash climatologies will improve estimates of lightning nitrogen oxides (NOx) production; this in turn will improve both regional air quality and global chemistry/climate model predictions.

Quantifying Vegetation Biophysical Variables from Imaging Spectroscopy Data: A Review on Retrieval Methods

NASA Astrophysics Data System (ADS)

Verrelst, Jochem; Malenovský, Zbyněk; Van der Tol, Christiaan; Camps-Valls, Gustau; Gastellu-Etchegorry, Jean-Philippe; Lewis, Philip; North, Peter; Moreno, Jose

2018-06-01

An unprecedented spectroscopic data stream will soon become available with forthcoming Earth-observing satellite missions equipped with imaging spectroradiometers. This data stream will open up a vast array of opportunities to quantify a diversity of biochemical and structural vegetation properties. The processing requirements for such large data streams require reliable retrieval techniques enabling the spatiotemporally explicit quantification of biophysical variables. With the aim of preparing for this new era of Earth observation, this review summarizes the state-of-the-art retrieval methods that have been applied in experimental imaging spectroscopy studies inferring all kinds of vegetation biophysical variables. Identified retrieval methods are categorized into: (1) parametric regression, including vegetation indices, shape indices and spectral transformations; (2) nonparametric regression, including linear and nonlinear machine learning regression algorithms; (3) physically based, including inversion of radiative transfer models (RTMs) using numerical optimization and look-up table approaches; and (4) hybrid regression methods, which combine RTM simulations with machine learning regression methods. For each of these categories, an overview of widely applied methods with application to mapping vegetation properties is given. In view of processing imaging spectroscopy data, a critical aspect involves the challenge of dealing with spectral multicollinearity. The ability to provide robust estimates, retrieval uncertainties and acceptable retrieval processing speed are other important aspects in view of operational processing. Recommendations towards new-generation spectroscopy-based processing chains for operational production of biophysical variables are given.

Advanced Feedback Methods in Information Retrieval.

ERIC Educational Resources Information Center

Salton, G.; And Others

1985-01-01

In this study, automatic feedback techniques are applied to Boolean query statements in online information retrieval to generate improved query statements based on information contained in previously retrieved documents. Feedback operations are carried out using conventional Boolean logic and extended logic. Experimental output is included to…

Evaluation of contents-based image retrieval methods for a database of logos on drug tablets

NASA Astrophysics Data System (ADS)

Geradts, Zeno J.; Hardy, Huub; Poortman, Anneke; Bijhold, Jurrien

2001-02-01

In this research an evaluation has been made of the different ways of contents based image retrieval of logos of drug tablets. On a database of 432 illicitly produced tablets (mostly containing MDMA), we have compared different retrieval methods. Two of these methods were available from commercial packages, QBIC and Imatch, where the implementation of the contents based image retrieval methods are not exactly known. We compared the results for this database with the MPEG-7 shape comparison methods, which are the contour-shape, bounding box and region-based shape methods. In addition, we have tested the log polar method that is available from our own research.

Phase retrieval in annulus sector domain by non-iterative methods

NASA Astrophysics Data System (ADS)

Wang, Xiao; Mao, Heng; Zhao, Da-zun

2008-03-01

Phase retrieval could be achieved by solving the intensity transport equation (ITE) under the paraxial approximation. For the case of uniform illumination, Neumann boundary condition is involved and it makes the solving process more complicated. The primary mirror is usually designed segmented in the telescope with large aperture, and the shape of a segmented piece is often like an annulus sector. Accordingly, It is necessary to analyze the phase retrieval in the annulus sector domain. Two non-iterative methods are considered for recovering the phase. The matrix method is based on the decomposition of the solution into a series of orthogonalized polynomials, while the frequency filtering method depends on the inverse computation process of ITE. By the simulation, it is found that both methods can eliminate the effect of Neumann boundary condition, save a lot of computation time and recover the distorted phase well. The wavefront error (WFE) RMS can be less than 0.05 wavelength, even when some noise is added.

Novel Antigen Identification Method for Discovery of Protective Malaria Antigens by Rapid Testing of DNA Vaccines Encoding Exons from the Parasite Genome

PubMed Central

Haddad, Diana; Bilcikova, Erika; Witney, Adam A.; Carlton, Jane M.; White, Charles E.; Blair, Peter L.; Chattopadhyay, Rana; Russell, Joshua; Abot, Esteban; Charoenvit, Yupin; Aguiar, Joao C.; Carucci, Daniel J.; Weiss, Walter R.

2004-01-01

We describe a novel approach for identifying target antigens for preerythrocytic malaria vaccines. Our strategy is to rapidly test hundreds of DNA vaccines encoding exons from the Plasmodium yoelii yoelii genomic sequence. In this antigen identification method, we measure reduction in parasite burden in the liver after sporozoite challenge in mice. Orthologs of protective P. y. yoelii genes can then be identified in the genomic databases of Plasmodium falciparum and Plasmodium vivax and investigated as candidate antigens for a human vaccine. A pilot study to develop the antigen identification method approach used 192 P. y. yoelii exons from genes expressed during the sporozoite stage of the life cycle. A total of 182 (94%) exons were successfully cloned into a DNA immunization vector with the Gateway cloning technology. To assess immunization strategies, mice were vaccinated with 19 of the new DNA plasmids in addition to the well-characterized protective plasmid encoding P. y. yoelii circumsporozoite protein. Single plasmid immunization by gene gun identified a novel vaccine target antigen which decreased liver parasite burden by 95% and which has orthologs in P. vivax and P. knowlesi but not P. falciparum. Intramuscular injection of DNA plasmids produced a different pattern of protective responses from those seen with gene gun immunization. Intramuscular immunization with plasmid pools could reduce liver parasite burden in mice despite the fact that none of the plasmids was protective when given individually. We conclude that high-throughput cloning of exons into DNA vaccines and their screening is feasible and can rapidly identify new malaria vaccine candidate antigens. PMID:14977966

Comparative exoplanetology with consistent retrieval methods

NASA Astrophysics Data System (ADS)

Barstow, Joanna Katy; Aigrain, Suzanne; Irwin, Patrick Gerard Joseph; Sing, David

2016-10-01

The number of hot Jupiters with broad wavelength spectroscopic data has finally become large enough to make comparative planetology a reasonable proposition. New results presented by Sing et al. (2016) showcase ten hot Jupiters with spectra from the Hubble Space Telescope and photometry from Spitzer, providing insights into the presence of clouds and hazes.Spectral retrieval methods allow interpretation of exoplanet spectra using simple models, with minimal prior assumptions. This is particularly useful for exotic exoplanets, for which we may not yet fully understand the physical processes responsible for their atmospheric characteristics. Consistent spectral retrieval of a range of exoplanets can allow robust comparisons of their derived atmospheric properties.I will present a retrieval analysis using the NEMESIS code (Irwin et al. 2008) of the ten hot Jupiter spectra presented by Sing et al. (2016). The only distinctive aspects of the model for each planet are the mass and radius, and the temperature range explored. All other a priori model parameters are common to all ten objects. We test a range of cloud and haze scenarios, which include: Rayleigh-dominated and grey clouds; different cloud top pressures; and both vertically extended and vertically confined clouds.All ten planets, with the exception of WASP-39b, can be well represented by models with at least some haze or cloud. Our analysis of cloud properties has uncovered trends in cloud top pressure, vertical extent and particle size with planet equilibrium temperature. Taken together, we suggest that these trends indicate condensation and sedimentation of at least two different cloud species across planets of different temperatures, with condensates forming higher up in hotter atmospheres and moving progressively further down in cooler planets.Sing, D. et al. (2016), Nature, 529, 59Irwin, P. G. J. et al. (2008), JQSRT, 109, 1136

Comparison between two lidar methods to retrieve microphysical properties of liquid-water clouds

NASA Astrophysics Data System (ADS)

Jimenez, Cristofer; Ansmann, Albert; Donovan, David; Engelmann, Ronny; Schmidt, Jörg; Wandinger, Ulla

2018-04-01

Since 2010, the Raman dual-FOV lidar system permits the retrieval of microphysical properties of liquid-water clouds during nighttime. A new robust lidar depolarization approach was recently introduced, which permits the retrieval of these properties as well, with high temporal resolution and during daytime. To implement this approach, the lidar system was upgraded, by adding a three channel depolarization receiver. The first preliminary retrieval results and a comparison between both methods is presented.

A content-based image retrieval method for optical colonoscopy images based on image recognition techniques

NASA Astrophysics Data System (ADS)

Nosato, Hirokazu; Sakanashi, Hidenori; Takahashi, Eiichi; Murakawa, Masahiro

2015-03-01

This paper proposes a content-based image retrieval method for optical colonoscopy images that can find images similar to ones being diagnosed. Optical colonoscopy is a method of direct observation for colons and rectums to diagnose bowel diseases. It is the most common procedure for screening, surveillance and treatment. However, diagnostic accuracy for intractable inflammatory bowel diseases, such as ulcerative colitis (UC), is highly dependent on the experience and knowledge of the medical doctor, because there is considerable variety in the appearances of colonic mucosa within inflammations with UC. In order to solve this issue, this paper proposes a content-based image retrieval method based on image recognition techniques. The proposed retrieval method can find similar images from a database of images diagnosed as UC, and can potentially furnish the medical records associated with the retrieved images to assist the UC diagnosis. Within the proposed method, color histogram features and higher order local auto-correlation (HLAC) features are adopted to represent the color information and geometrical information of optical colonoscopy images, respectively. Moreover, considering various characteristics of UC colonoscopy images, such as vascular patterns and the roughness of the colonic mucosa, we also propose an image enhancement method to highlight the appearances of colonic mucosa in UC. In an experiment using 161 UC images from 32 patients, we demonstrate that our method improves the accuracy of retrieving similar UC images.

A similarity measure method combining location feature for mammogram retrieval.

PubMed

Wang, Zhiqiong; Xin, Junchang; Huang, Yukun; Li, Chen; Xu, Ling; Li, Yang; Zhang, Hao; Gu, Huizi; Qian, Wei

2018-05-28

Breast cancer, the most common malignancy among women, has a high mortality rate in clinical practice. Early detection, diagnosis and treatment can reduce the mortalities of breast cancer greatly. The method of mammogram retrieval can help doctors to find the early breast lesions effectively and determine a reasonable feature set for image similarity measure. This will improve the accuracy effectively for mammogram retrieval. This paper proposes a similarity measure method combining location feature for mammogram retrieval. Firstly, the images are pre-processed, the regions of interest are detected and the lesions are segmented in order to get the center point and radius of the lesions. Then, the method, namely Coherent Point Drift, is used for image registration with the pre-defined standard image. The center point and radius of the lesions after registration are obtained and the standard location feature of the image is constructed. This standard location feature can help figure out the location similarity between the image pair from the query image to each dataset image in the database. Next, the content feature of the image is extracted, including the Histogram of Oriented Gradients, the Edge Direction Histogram, the Local Binary Pattern and the Gray Level Histogram, and the image pair content similarity can be calculated using the Earth Mover's Distance. Finally, the location similarity and content similarity are fused to form the image fusion similarity, and the specified number of the most similar images can be returned according to it. In the experiment, 440 mammograms, which are from Chinese women in Northeast China, are used as the database. When fusing 40% lesion location feature similarity and 60% content feature similarity, the results have obvious advantages. At this time, precision is 0.83, recall is 0.76, comprehensive indicator is 0.79, satisfaction is 96.0%, mean is 4.2 and variance is 17.7. The results show that the precision and recall of this

Item-method directed forgetting: Effects at retrieval?

PubMed

Taylor, Tracy L; Cutmore, Laura; Pries, Lotta

2018-02-01

In an item-method directed forgetting paradigm, words are presented one at a time, each followed by an instruction to Remember or Forget; a directed forgetting effect is measured as better subsequent memory for Remember words than Forget words. The dominant view is that the directed forgetting effect arises during encoding due to selective rehearsal of Remember over Forget items. In three experiments we attempted to falsify a strong view that directed forgetting effects in recognition are due only to encoding mechanisms when an item method is used. Across 3 experiments we tested for retrieval-based processes by colour-coding the recognition test items. Black colour provided no information; green colour cued a potential Remember item; and, red colour cued a potential Forget item. Recognition cues were mixed within-blocks in Experiment 1 and between-blocks in Experiments 2 and 3; Experiment 3 added explicit feedback on the accuracy of the recognition decision. Although overall recognition improved with cuing when explicit test performance feedback was added in Experiment 3, in no case was the magnitude of the directed forgetting effect influenced by recognition cueing. Our results argue against a role for retrieval-based strategies that limit recognition of Forget items at test and posit a role for encoding intentions only. Copyright © 2017 Elsevier B.V. All rights reserved.

Research on keyword retrieval method of HBase database based on index structure

NASA Astrophysics Data System (ADS)

Gong, Pijin; Lv, Congmin; Gong, Yongsheng; Ma, Haozhi; Sun, Yang; Wang, Lu

2017-10-01

With the rapid development of manned spaceflight engineering, the scientific experimental data in space application system is increasing rapidly. How to efficiently query the specific data in the mass data volume has become a problem. In this paper, a method of retrieving the object data based on the object attribute as the keyword is proposed. The HBase database is used to store the object data and object attributes, and the secondary index is constructed. The research shows that this method is a good way to retrieve specified data based on object attributes.

Assessing the impact of different satellite retrieval methods on forecast available potential energy

NASA Technical Reports Server (NTRS)

Whittaker, Linda M.; Horn, Lyle H.

1990-01-01

The effects of the inclusion of satellite temperature retrieval data, and of different satellite retrieval methods, on forecasts made with the NASA Goddard Laboratory for Atmospheres (GLA) fourth-order model were investigated using, as the parameter, the available potential energy (APE) in its isentropic form. Calculation of the APE were used to study the differences in the forecast sets both globally and in the Northern Hemisphere during 72-h forecast period. The analysis data sets used for the forecasts included one containing the NESDIS TIROS-N retrievals, the GLA retrievals using the physical inversion method, and a third, which did not contain satellite data, used as a control; two data sets, with and without satellite data, were used for verification. For all three data sets, the Northern Hemisphere values for the total APE showed an increase throughout the forecast period, mostly due to an increase in the zonal component, in contrast to the verification sets, which showed a steady level of total APE.

Double-balloon endoscopy as the primary method for small-bowel video capsule endoscope retrieval.

PubMed

Van Weyenberg, Stijn J B; Van Turenhout, Sietze T; Bouma, Gerd; Van Waesberghe, Jan Hein T M; Van der Peet, Donald L; Mulder, Chris J J; Jacobs, Maarten A J M

2010-03-01

Capsule retention in the small bowel is a known complication of small-bowel video capsule endoscopy. Surgery is the most frequently used method of capsule retrieval. To determine the incidence and causes of capsule retention and to describe double-balloon endoscopy (DBE) as the primary technique used for capsule retrieval. Retrospective analysis of all video capsule studies was performed at our center, and evaluation of the outcome of DBE was the first method used to retrieve entrapped video capsules. Tertiary referral center. A total of 904 patients who underwent small-bowel video capsule endoscopy. Capsule retrieval by DBE. The number of patients in whom capsule retention occurred and the number of patients in whom an entrapped capsule could be retrieved by using DBE. Capsule retention occurred in 8 patients (incidence 0.88%; 95% CI, 0.41%-1.80%) and caused acute small-bowel obstruction in 6 patients. All retained capsules were successfully removed during DBE. Five patients underwent elective surgery to treat the underlying cause of capsule retention. One patient required emergency surgery because of multiple small-bowel perforations. Retrospective design. In our series, the incidence of capsule retention was low. DBE is a reliable method for removing retained capsules and might prevent unnecessary surgery. If surgery is required, preoperative capsule retrieval allows preoperative diagnosis, adequate staging in case of malignancy, and optimal surgical planning. 2010 American Society for Gastrointestinal Endoscopy. Published by Mosby, Inc. All rights reserved.

Retrieve polarization aberration from image degradation: a new measurement method in DUV lithography

NASA Astrophysics Data System (ADS)

Xiang, Zhongbo; Li, Yanqiu

2017-10-01

Detailed knowledge of polarization aberration (PA) of projection lens in higher-NA DUV lithographic imaging is necessary due to its impact to imaging degradations, and precise measurement of PA is conductive to computational lithography techniques such as RET and OPC. Current in situ measurement method of PA thorough the detection of degradations of aerial images need to do linear approximation and apply the assumption of 3-beam/2-beam interference condition. The former approximation neglects the coupling effect of the PA coefficients, which would significantly influence the accuracy of PA retrieving. The latter assumption restricts the feasible pitch of test masks in higher-NA system, conflicts with the Kirhhoff diffraction model of test mask used in retrieving model, and introduces 3D mask effect as a source of retrieving error. In this paper, a new in situ measurement method of PA is proposed. It establishes the analytical quadratic relation between the PA coefficients and the degradations of aerial images of one-dimensional dense lines in coherent illumination through vector aerial imaging, which does not rely on the assumption of 3-beam/2- beam interference and linear approximation. In this case, the retrieval of PA from image degradation can be convert from the nonlinear system of m-quadratic equations to a multi-objective quadratic optimization problem, and finally be solved by nonlinear least square method. Some preliminary simulation results are given to demonstrate the correctness and accuracy of the new PA retrieving model.

The Continuous Monitoring of Desert Dust using an Infrared-based Dust Detection and Retrieval Method

NASA Technical Reports Server (NTRS)

Duda, David P.; Minnis, Patrick; Trepte, Qing; Sun-Mack, Sunny

2006-01-01

Airborne dust and sand are significant aerosol sources that can impact the atmospheric and surface radiation budgets. Because airborne dust affects visibility and air quality, it is desirable to monitor the location and concentrations of this aerosol for transportation and public health. Although aerosol retrievals have been derived for many years using visible and near-infrared reflectance measurements from satellites, the detection and quantification of dust from these channels is problematic over bright surfaces, or when dust concentrations are large. In addition, aerosol retrievals from polar orbiting satellites lack the ability to monitor the progression and sources of dust storms. As a complement to current aerosol dust retrieval algorithms, multi-spectral thermal infrared (8-12 micron) data from the Moderate Resolution Imaging Spectroradiometer (MODIS) and the Meteosat-8 Spinning Enhanced Visible and Infrared Imager (SEVIRI) are used in the development of a prototype dust detection method and dust property retrieval that can monitor the progress of Saharan dust fields continuously, both night and day. The dust detection method is incorporated into the processing of CERES (Clouds and the Earth s Radiant Energy System) aerosol retrievals to produce dust property retrievals. Both MODIS (from Terra and Aqua) and SEVERI data are used to develop the method.

Skill in Retrievals

NASA Technical Reports Server (NTRS)

Aumann, Hartmut H.; Manning, Evan

2008-01-01

Retrieval Skill quantifies the ability of one retrieval from a sounder to be more accurate than the best forecast relative to another with the same of another sounder. This is summarized using a Retrieval Anomaly Skill Score (RASS) which is the cor (retrieved-background, truth-background) * sqrt(f), Where f is defined as the ratio of accepted to the possible retrievals. Charts show various features and comparisons of RASS to other methods of retrieval.

Global retrieval of soil moisture and vegetation properties using data-driven methods

NASA Astrophysics Data System (ADS)

Rodriguez-Fernandez, Nemesio; Richaume, Philippe; Kerr, Yann

2017-04-01

Data-driven methods such as neural networks (NNs) are a powerful tool to retrieve soil moisture from multi-wavelength remote sensing observations at global scale. In this presentation we will review a number of recent results regarding the retrieval of soil moisture with the Soil Moisture and Ocean Salinity (SMOS) satellite, either using SMOS brightness temperatures as input data for the retrieval or using SMOS soil moisture retrievals as reference dataset for the training. The presentation will discuss several possibilities for both the input datasets and the datasets to be used as reference for the supervised learning phase. Regarding the input datasets, it will be shown that NNs take advantage of the synergy of SMOS data and data from other sensors such as the Advanced Scatterometer (ASCAT, active microwaves) and MODIS (visible and infra red). NNs have also been successfully used to construct long time series of soil moisture from the Advanced Microwave Scanning Radiometer - Earth Observing System (AMSR-E) and SMOS. A NN with input data from ASMR-E observations and SMOS soil moisture as reference for the training was used to construct a dataset sharing a similar climatology and without a significant bias with respect to SMOS soil moisture. Regarding the reference data to train the data-driven retrievals, we will show different possibilities depending on the application. Using actual in situ measurements is challenging at global scale due to the scarce distribution of sensors. In contrast, in situ measurements have been successfully used to retrieve SM at continental scale in North America, where the density of in situ measurement stations is high. Using global land surface models to train the NN constitute an interesting alternative to implement new remote sensing surface datasets. In addition, these datasets can be used to perform data assimilation into the model used as reference for the training. This approach has recently been tested at the European Centre

An incremental DPMM-based method for trajectory clustering, modeling, and retrieval.

PubMed

Hu, Weiming; Li, Xi; Tian, Guodong; Maybank, Stephen; Zhang, Zhongfei

2013-05-01

Trajectory analysis is the basis for many applications, such as indexing of motion events in videos, activity recognition, and surveillance. In this paper, the Dirichlet process mixture model (DPMM) is applied to trajectory clustering, modeling, and retrieval. We propose an incremental version of a DPMM-based clustering algorithm and apply it to cluster trajectories. An appropriate number of trajectory clusters is determined automatically. When trajectories belonging to new clusters arrive, the new clusters can be identified online and added to the model without any retraining using the previous data. A time-sensitive Dirichlet process mixture model (tDPMM) is applied to each trajectory cluster for learning the trajectory pattern which represents the time-series characteristics of the trajectories in the cluster. Then, a parameterized index is constructed for each cluster. A novel likelihood estimation algorithm for the tDPMM is proposed, and a trajectory-based video retrieval model is developed. The tDPMM-based probabilistic matching method and the DPMM-based model growing method are combined to make the retrieval model scalable and adaptable. Experimental comparisons with state-of-the-art algorithms demonstrate the effectiveness of our algorithm.

A linear method for the retrieval of sun-induced chlorophyll fluorescence from GOME-2 and SCIAMACHY data

NASA Astrophysics Data System (ADS)

Köhler, P.; Guanter, L.; Joiner, J.

2014-12-01

Global retrievals of near-infrared sun-induced chlorophyll fluorescence (SIF) have been achieved in the last years by means of a number of space-borne atmospheric spectrometers. Here, we present a new retrieval method for medium spectral resolution instruments such as the Global Ozone Monitoring Experiment (GOME-2) and the SCanning Imaging Absorption SpectroMeter for Atmospheric ChartographY (SCIAMACHY). Building upon the previous work by Joiner et al. (2013), our approach solves existing issues in the retrieval such as the non-linearity of the forward model and the arbitrary selection of the number of free parameters. In particular, we use a backward elimination algorithm to optimize the number of coefficients to fit, which reduces also the retrieval noise and selects the number of state vector elements automatically. A sensitivity analysis with simulated spectra has been utilized to evaluate the performance of our retrieval approach. The method has also been applied to estimate SIF from real spectra from GOME-2 and for the first time, from SCIAMACHY. We find a good correspondence of the absolute SIF values and the spatial patterns from the two sensors, which suggests the robustness of the proposed retrieval method. In addition, we examine uncertainties and use our GOME-2 retrievals to show empirically the low sensitivity of the SIF retrieval to cloud contamination.

Hemangiosarcoma in a geriatric Labrador retriever

PubMed Central

Sharma, Diya

2012-01-01

A geriatric Labrador retriever dog was presented for acute collapse. The dog was conscious but lethargic, tachypneic, tachycardic with weak femoral pulses, occasional pulse deficits, and pale mucous membranes. Radiography, ultrasonography, quick assessment tests, and a complete blood (cell) count (CBC)/biochemistry panel indicated internal hemorrhage and potential problems with hemostasis. The dog was euthanized. A necropsy, histopathology, and immunohistochemistry for CD31 and Factor VIII-related antigen cell markers supported a diagnosis of splenic hemangiosarcoma. PMID:23372199

Antigenic analyses of tissues and excretory and secretory products from Strongylus vulgaris.

PubMed

Wynne, E; Slocombe, J O; Wilkie, B N

1981-07-01

Rabbit antisera were prepared against veronal buffered saline extracts of L4 and L5 Strongylus vulgaris, adult S. vulgaris and adult Strongylus equinus retrieved from naturally infected horses. In agar gel diffusion with these antisera, adult S vulgaris and S. equinus each appeared to have at least one unique antigen; larval S. vulgaris appeared to have two species-specific and two stage-specific antigens. There were several common antigens. Excretory and secretory products were collected also from L4 and L5 an maintained over several days in tissue culture fluid. In agar gel diffusion against the above rabbit antisera, a stage-specific antigen was found also in excretory and secretory products. In addition, excretory and secretory products had three antigens in common with adult and larval S. vulgaris, but only one of these was common to adult S. equinus. The excretory and secretory products appear, therefore, to have two species-specific and one stage-specific antigens.

Three-dimensional ordered particulate structures: Method to retrieve characteristics from photonic band gap data

NASA Astrophysics Data System (ADS)

Miskevich, Alexander A.; Loiko, Valery A.

2015-01-01

A method to retrieve characteristics of ordered particulate structures, such as photonic crystals, is proposed. It is based on the solution of the inverse problem using data on the photonic band gap (PBG). The quasicrystalline approximation (QCA) of the theory of multiple scattering of waves and the transfer matrix method (TMM) are used. Retrieval of the refractive index of particles is demonstrated. Refractive indices of the artificial opal particles are estimated using the published experimental data.

Linear information retrieval method in X-ray grating-based phase contrast imaging and its interchangeability with tomographic reconstruction

NASA Astrophysics Data System (ADS)

Wu, Z.; Gao, K.; Wang, Z. L.; Shao, Q. G.; Hu, R. F.; Wei, C. X.; Zan, G. B.; Wali, F.; Luo, R. H.; Zhu, P. P.; Tian, Y. C.

2017-06-01

In X-ray grating-based phase contrast imaging, information retrieval is necessary for quantitative research, especially for phase tomography. However, numerous and repetitive processes have to be performed for tomographic reconstruction. In this paper, we report a novel information retrieval method, which enables retrieving phase and absorption information by means of a linear combination of two mutually conjugate images. Thanks to the distributive law of the multiplication as well as the commutative law and associative law of the addition, the information retrieval can be performed after tomographic reconstruction, thus simplifying the information retrieval procedure dramatically. The theoretical model of this method is established in both parallel beam geometry for Talbot interferometer and fan beam geometry for Talbot-Lau interferometer. Numerical experiments are also performed to confirm the feasibility and validity of the proposed method. In addition, we discuss its possibility in cone beam geometry and its advantages compared with other methods. Moreover, this method can also be employed in other differential phase contrast imaging methods, such as diffraction enhanced imaging, non-interferometric imaging, and edge illumination.

Physical retrieval of precipitation water contents from Special Sensor Microwave/Imager (SSM/I) data. Part 2: Retrieval method and applications (report version)

NASA Technical Reports Server (NTRS)

Olson, William S.

1990-01-01

A physical retrieval method for estimating precipitating water distributions and other geophysical parameters based upon measurements from the DMSP-F8 SSM/I is developed. Three unique features of the retrieval method are (1) sensor antenna patterns are explicitly included to accommodate varying channel resolution; (2) precipitation-brightness temperature relationships are quantified using the cloud ensemble/radiative parameterization; and (3) spatial constraints are imposed for certain background parameters, such as humidity, which vary more slowly in the horizontal than the cloud and precipitation water contents. The general framework of the method will facilitate the incorporation of measurements from the SSMJT, SSM/T-2 and geostationary infrared measurements, as well as information from conventional sources (e.g., radiosondes) or numerical forecast model fields.

High sensitivity phase retrieval method in grating-based x-ray phase contrast imaging

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

Wu, Zhao; Gao, Kun; Chen, Jian

2015-02-15

Purpose: Grating-based x-ray phase contrast imaging is considered as one of the most promising techniques for future medical imaging. Many different methods have been developed to retrieve phase signal, among which the phase stepping (PS) method is widely used. However, further practical implementations are hindered, due to its complex scanning mode and high radiation dose. In contrast, the reverse projection (RP) method is a novel fast and low dose extraction approach. In this contribution, the authors present a quantitative analysis of the noise properties of the refraction signals retrieved by the two methods and compare their sensitivities. Methods: Using themore » error propagation formula, the authors analyze theoretically the signal-to-noise ratios (SNRs) of the refraction images retrieved by the two methods. Then, the sensitivities of the two extraction methods are compared under an identical exposure dose. Numerical experiments are performed to validate the theoretical results and provide some quantitative insight. Results: The SNRs of the two methods are both dependent on the system parameters, but in different ways. Comparison between their sensitivities reveals that for the refraction signal, the RP method possesses a higher sensitivity, especially in the case of high visibility and/or at the edge of the object. Conclusions: Compared with the PS method, the RP method has a superior sensitivity and provides refraction images with a higher SNR. Therefore, one can obtain highly sensitive refraction images in grating-based phase contrast imaging. This is very important for future preclinical and clinical implementations.« less

A new retrieval method for the ice water content of cirrus using data from the CloudSat and CALIPSO

NASA Astrophysics Data System (ADS)

Pan, Honglin; Bu, Lingbing; Kumar, K. Raghavendra; Gao, Haiyang; Huang, Xingyou; Zhang, Wentao

2017-08-01

The CloudSat and CALIPSO (Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observations) are the members of satellite observation system of A-train to achieve the quasi-synchronization observation on the same orbit. With the help of active (CALIOP and CPR) and passive payloads from these two satellites, respectively, unprecedented detailed information of microphysical properties of ice cloud can be retrieved. The ice water content (IWC) is regarded as one of the most important microphysical characteristics of cirrus for its prominent role in cloud radiative forcing. In this paper, we proposed a new joint (Combination) retrieval method using the full advantages of different well established retrieval methods, namely the LIDAR method (for the region Lidar-only), the MWCR method (for the region Radar-only), and Wang method (for the region Lidar-Radar) proposed by Wang et al. (2002). In retrieval of cirrus IWC, empirical formulas of the exponential type were used for both thinner cirrus (detected by Lidar-only), thicker cirrus (detected by radar-only), and the part of cirrus detected by both, respectively. In the present study, the comparison of various methods verified that our proposed new joint method is more comprehensive, rational and reliable. Further, the retrieval information of cirrus is complete and accurate for the region that Lidar cannot penetrate and Radar is insensitive. On the whole, the retrieval results of IWC showed certain differences retrieved from the joint method, Ca&Cl, and ICARE which can be interpreted from the different hypothesis of microphysical characteristics and parameters used in the retrieval method. In addition, our joint method only uses the extinction coefficient and the radar reflectivity factor to calculate the IWC, which is simpler and reduces to some extent the accumulative error. In future studies, we will not only compare the value of IWC but also explore the detailed macrophysical and microphysical characteristics of

A linear method for the retrieval of sun-induced chlorophyll fluorescence from GOME-2 and SCIAMACHY data

NASA Astrophysics Data System (ADS)

Köhler, P.; Guanter, L.; Joiner, J.

2015-06-01

Global retrievals of near-infrared sun-induced chlorophyll fluorescence (SIF) have been achieved in the last few years by means of a number of space-borne atmospheric spectrometers. Here, we present a new retrieval method for medium spectral resolution instruments such as the Global Ozone Monitoring Experiment-2 (GOME-2) and the SCanning Imaging Absorption SpectroMeter for Atmospheric CHartographY (SCIAMACHY). Building upon the previous work by Guanter et al. (2013) and Joiner et al. (2013), our approach provides a solution for the selection of the number of free parameters. In particular, a backward elimination algorithm is applied to optimize the number of coefficients to fit, which reduces also the retrieval noise and selects the number of state vector elements automatically. A sensitivity analysis with simulated spectra has been utilized to evaluate the performance of our retrieval approach. The method has also been applied to estimate SIF at 740 nm from real spectra from GOME-2 and for the first time, from SCIAMACHY. We find a good correspondence of the absolute SIF values and the spatial patterns from the two sensors, which suggests the robustness of the proposed retrieval method. In addition, we compare our results to existing SIF data sets, examine uncertainties and use our GOME-2 retrievals to show empirically the relatively low sensitivity of the SIF retrieval to cloud contamination.

Application of information-retrieval methods to the classification of physical data

NASA Technical Reports Server (NTRS)

Mamotko, Z. N.; Khorolskaya, S. K.; Shatrovskiy, L. I.

1975-01-01

Scientific data received from satellites are characterized as a multi-dimensional time series, whose terms are vector functions of a vector of measurement conditions. Information retrieval methods are used to construct lower dimensional samples on the basis of the condition vector, in order to obtain these data and to construct partial relations. The methods are applied to the joint Soviet-French Arkad project.

Synergistic method for boreal soil moisture and soil freeze retrievals using active and passive microwave instruments

NASA Astrophysics Data System (ADS)

Smolander, Tuomo; Lemmetyinen, Juha; Rautiainen, Kimmo; Schwank, Mike; Pulliainen, Jouni

2017-04-01

Soil moisture and soil freezing are important for diverse hydrological, biogeochemical, and climatological applications. They affect surface energy balance, surface and subsurface water flow, and exchange rates of carbon with the atmosphere. Soil freezing controls important biogeochemical processes, like photosynthetic activity of plants and microbial activity within soils. Permafrost covers approximately 24% of the land surface in the Northern Hemisphere and seasonal freezing occurs on approximately 51% of the area. The retrieval method presented is based on an inversion technique and applies a semiempirical backscattering model that describes the dependence of radar backscattering of forest as a function of stem volume, soil permittivity, the extinction coefficient of forest canopy, surface roughness, incidence angle, and radar frequency. It gives an estimate of soil permittivity using active microwave measurements. Applying a Bayesian assimilation scheme, it is also possible to use other soil permittivity retrievals to regulate this estimate to combine for example low resolution passive observations with high resolution active observations for a synergistic retrieval. This way the higher variance in the active retrieval can be constricted with the passive retrieval when at the same time the spatial resolution of the product is improved compared to the passive-only retrieval. The retrieved soil permittivity estimate can be used to detect soil freeze/thaw state by considering the soil to be frozen when the estimate is below a threshold value. The permittivity retrieval can also be used to estimate the relative moisture of the soil. The method was tested using SAR (Synthetic Aperture Radar) measurements from ENVISAT ASAR instrument for the years 2010-2012 and from Sentinel-1 satellite for the years 2015-2016 in Sodankylä area in Northern Finland. The synergistic method was tested combining the SAR measurements with a SMOS (Soil Moisture Ocean Salinity) radiometer

Guenter Tulip Filter Retrieval Experience: Predictors of Successful Retrieval

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

Turba, Ulku Cenk, E-mail: uct5d@virginia.edu; Arslan, Bulent, E-mail: ba6e@virginia.edu; Meuse, Michael, E-mail: mm5tz@virginia.edu

We report our experience with Guenter Tulip filter placement indications, retrievals, and procedural problems, with emphasis on alternative retrieval techniques. We have identified 92 consecutive patients in whom a Guenter Tulip filter was placed and filter removal attempted. We recorded patient demographic information, filter placement and retrieval indications, procedures, standard and nonstandard filter retrieval techniques, complications, and clinical outcomes. The mean time to retrieval for those who experienced filter strut penetration was statistically significant [F(1,90) = 8.55, p = 0.004]. Filter strut(s) IVC penetration and successful retrieval were found to be statistically significant (p = 0.043). The filter hook-IVC relationshipmore » correlated with successful retrieval. A modified guidewire loop technique was applied in 8 of 10 cases where the hook appeared to penetrate the IVC wall and could not be engaged with a loop snare catheter, providing additional technical success in 6 of 8 (75%). Therefore, the total filter retrieval success increased from 88 to 95%. In conclusion, the Guenter Tulip filter has high successful retrieval rates with low rates of complication. Additional maneuvers such as a guidewire loop method can be used to improve retrieval success rates when the filter hook is endothelialized.« less

Full extraction methods to retrieve effective refractive index and parameters of a bianisotropic metamaterial based on material dispersion models

NASA Astrophysics Data System (ADS)

Hsieh, Feng-Ju; Wang, Wei-Chih

2012-09-01

This paper discusses two improved methods in retrieving effective refractive indices, impedances, and material properties, such as permittivity (ɛ) and permeability (μ), of metamaterials. The first method modified from Kong's retrieval method allows effective constitutive parameters over all frequencies including the anti-resonant band, where imaginary parts of ɛ or μ are negative, to be solved. The second method is based on genetic algorithms and optimization of properly defined goal functions to retrieve parameters of the Drude and Lorentz dispersion models. Equations of effective refractive index and impedance at any reference planes are derived. Split ring resonator-rod based metamaterials operating in terahertz frequencies are designed and investigated with proposed methods. Retrieved material properties and parameters are used to regenerate S-parameters and compared with simulation results generated by cst microwave studio software.

A Multi-Channel Method for Retrieving Surface Temperature for High-Emissivity Surfaces from Hyperspectral Thermal Infrared Images

PubMed Central

Zhong, Xinke; Labed, Jelila; Zhou, Guoqing; Shao, Kun; Li, Zhao-Liang

2015-01-01

The surface temperature (ST) of high-emissivity surfaces is an important parameter in climate systems. The empirical methods for retrieving ST for high-emissivity surfaces from hyperspectral thermal infrared (HypTIR) images require spectrally continuous channel data. This paper aims to develop a multi-channel method for retrieving ST for high-emissivity surfaces from space-borne HypTIR data. With an assumption of land surface emissivity (LSE) of 1, ST is proposed as a function of 10 brightness temperatures measured at the top of atmosphere by a radiometer having a spectral interval of 800–1200 cm−1 and a spectral sampling frequency of 0.25 cm−1. We have analyzed the sensitivity of the proposed method to spectral sampling frequency and instrumental noise, and evaluated the proposed method using satellite data. The results indicated that the parameters in the developed function are dependent on the spectral sampling frequency and that ST of high-emissivity surfaces can be accurately retrieved by the proposed method if appropriate values are used for each spectral sampling frequency. The results also showed that the accuracy of the retrieved ST is of the order of magnitude of the instrumental noise and that the root mean square error (RMSE) of the ST retrieved from satellite data is 0.43 K in comparison with the AVHRR SST product. PMID:26061199

Performance of fluorescence retrieval methods and fluorescence spectrum reconstruction under various sensor spectral configurations

NASA Astrophysics Data System (ADS)

Li, Rong; Zhao, Feng

2015-10-01

Solar-induced chlorophyll fluorescence is closely related to photosynthesis and can serve as an indicator of plant status. Several methods have been proposed to retrieve fluorescence signal (Fs) either at specific spectral bands or within the whole fluorescence emission region. In this study, we investigated the precision of the fluorescence signal obtained through these methods under various sensor spectral characteristics. Simulated datasets generated by the SCOPE (Soil Canopy Observation, Photochemistry and Energy fluxes) model with known `true' Fs as well as an experimental dataset are exploited to investigate four commonly used Fs retrieval methods, namely the original Fraunhofer Line Discriminator method (FLD), the 3 bands FLD (3FLD), the improved FLD (iFLD), and the Spectral Fitting Methods (SFMs). Fluorescence Spectrum Reconstruction (FSR) method is also investigated using simulated datasets. The sensor characteristics of spectral resolution (SR) and signal-to-noise ratio (SNR) are taken into account. According to the results, finer SR and SNR both lead to better accuracy. Lowest precision is obtained for the FLD method with strong overestimation. Some improvements are made by the 3FLD method, but it still tends to overestimate. Generally, the iFLD method and the SFMs provide better accuracy. As to FSR, the shape and magnitude of reconstructed Fs are generally consistent with the `true' Fs distributions when fine SR is exploited. With coarser SR, however, though R2 of the retrieved Fs may be high, large bias is likely to be obtained as well.

The Effectiveness of the Thesaurus Method in Automatic Information Retrieval. Technical Report No. 75-261.

ERIC Educational Resources Information Center

Yu, C. T.; Salton, G.

Formal proofs are given of the effectiveness under well-defined conditions of the thesaurus method in information retrieval. It is shown, in particular, that when certain semantically related terms are added to the information queries originally submitted by the user population, a superior retrieval system is obtained in the sense that for every…

Improve Biomedical Information Retrieval using Modified Learning to Rank Methods.

PubMed

Xu, Bo; Lin, Hongfei; Lin, Yuan; Ma, Yunlong; Yang, Liang; Wang, Jian; Yang, Zhihao

2016-06-14

In these years, the number of biomedical articles has increased exponentially, which becomes a problem for biologists to capture all the needed information manually. Information retrieval technologies, as the core of search engines, can deal with the problem automatically, providing users with the needed information. However, it is a great challenge to apply these technologies directly for biomedical retrieval, because of the abundance of domain specific terminologies. To enhance biomedical retrieval, we propose a novel framework based on learning to rank. Learning to rank is a series of state-of-the-art information retrieval techniques, and has been proved effective in many information retrieval tasks. In the proposed framework, we attempt to tackle the problem of the abundance of terminologies by constructing ranking models, which focus on not only retrieving the most relevant documents, but also diversifying the searching results to increase the completeness of the resulting list for a given query. In the model training, we propose two novel document labeling strategies, and combine several traditional retrieval models as learning features. Besides, we also investigate the usefulness of different learning to rank approaches in our framework. Experimental results on TREC Genomics datasets demonstrate the effectiveness of our framework for biomedical information retrieval.

Connectionist Interaction Information Retrieval.

ERIC Educational Resources Information Center

Dominich, Sandor

2003-01-01

Discussion of connectionist views for adaptive clustering in information retrieval focuses on a connectionist clustering technique and activation spreading-based information retrieval model using the interaction information retrieval method. Presents theoretical as well as simulation results as regards computational complexity and includes…

The prognostic significance of preoperative serum cancer antigen 15-3 levels in endometrial carcinomas

PubMed Central

Tas, Emre E.; Yavuz, Ayse F.

2017-01-01

Objectives: To determine the associations between serum cancer antigen 15-3 levels and prognostic factors in patients with endometrial carcinomas. Additionally, we investigated the clinical utility of serum cancer antigen 15-3 levels in the selection of low-risk patients with endometrioid type, tumor size <2 cm, myometrial invasion ≤50%, and histological grade 1-2. Methods: Ninety-six patients, who were surgically staged at Ankara Yildirim Beyazit University, Ankara, Turkey, between 2007 and 2016, were retrospectively analyzed. Demographic, clinical, and surgical characteristics were retrieved from the patients’ hospital records. A p<0.05 was considered significant. Results: Fifteen patients had advanced (≥Stage II) disease, 14 patients had Type 2 histology, 20 patients had Grade 3 tumors, 23 patients had lymphovascular space invasion, and 10 patients had positive lymph node involvement. Serum cancer antigen 15-3 levels were significantly higher in patients with advanced (≥Stage II) disease, Type 2 histology, Grade 3 tumors, lymp°hovascular space invasion, and positive lymph node involvement (p<0.05). Serum cancer antigen 15-3 levels were also significantly correlated with tumor size (p=0.006). Serum cancer antigen 15-3 levels were significantly lower (95% confidence interval: 0.57−0.79; p=0.03) in low-risk patients compared to other endometrial carcinoma patients. A cutoff of 25.0 IU/mL was used to identify high-risk patients with a specificity of 100%. Conclusion: Serum cancer antigen 15-3 levels significantly correlated with prognostic factors and were a useful diagnostic tool for endometrial carcinomas. PMID:29114696

Hepatitis B Core Antigen in Hepatocytes of Chronic Hepatitis B: Comparison between Indirect Immunofluorescence and Immunoperoxidase Method

PubMed Central

Tabassum, Shahina; Al-Mahtab, Mamun; Nessa, Afzalun; Jahan, Munira; Shamim Kabir, Chowdhury Mohammad; Kamal, Mohammad; Cesar Aguilar, Julio

2015-01-01

Background Hepatitis B virus (HBV) infection has many faces. Precore and core promoter mutants resemble inactive carrier status. The identification of hepatitis B core antigen (HBcAg) in hepatocytes may have variable clinical significance. The present study was undertaken to detect HBcAg in chronic hepatitis B (CHB) patients and to assess the efficacy of detection system by indirect immunofluorescence (IIF) and indirect immunoperoxidase (IIP). Materials and methods The study was done in 70 chronic HBV-infected patients. Out of 70 patients, eight (11.4%) were hepatitis B e antigen (HBeAg) positive and 62 (88.57%) were HBeAg negative. Hepatitis B core antigen was detected by indirect immunofluorescence (IIF) and indirect immunoperoxidase (IIP) methods in liver tissue. Results All HBeAg positive patients expressed HBcAg by both IIF and IIP methods. Out of 62 patients with HBeAg-negative CHB, HBcAg was detected by IIF in 55 (88.7%) patients and by IIP in 51 (82.26%) patients. A positive relation among viral load and HBcAg detection was also found. This was more evident in the case of HBeAg negative patients and showed a positive relation with HBV DNA levels. Conclusion Hepatitis B core antigen can be detected using the IIF from formalin fixed paraffin block preparation and also by IIP method. This seems to reflect the magnitudes of HBV replication in CHB. How to cite this article Raihan R, Tabassum S, Al-Mahtab M, Nessa A, Jahan M, Kabir CMS, Kamal M, Aguilar JC. Hepatitis B Core Antigen in Hepatocytes of Chronic Hepatitis B: Comparison between Indirect Immunofluorescence and Immunoperoxidase Method. Euroasian J Hepato-Gastroenterol 2015;5(1):7-10. PMID:29201677

Retrievable Inferior Vena Cava Filters: Factors that Affect Retrieval Success

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

Geisbuesch, Philipp, E-mail: philippgeisbuesch@gmx.de; Benenati, James F.; Pena, Constantino S.

Purpose: To report and analyze the indications, procedural success, and complications of retrievable inferior vena cava filters (rIVCF) placement and to identify parameters that influence retrieval attempt and failure. Methods: Between January 2005 and December 2010, a total of 200 patients (80 men, median age 67 years, range 11-95 years) received a rIVCF with the clinical possibility that it could be removed. All patients with rIVCF were prospectively entered into a database and followed until retrieval or a decision not to retrieve the filter was made. A retrospective analysis of this database was performed. Results: Sixty-one percent of patients hadmore » an accepted indication for filter placement; 39% of patients had a relative indication. There was a tendency toward a higher retrieval rate in patients with relative indications (40% vs. 55%, P = 0.076). Filter placement was technically successful in all patients, with no procedure-related mortality. The retrieval rate was 53%. Patient age of >80 years (odds ratio [OR] 0.056, P > 0.0001) and presence of malignancy (OR 0.303, P = 0.003) was associated with a significantly reduced probability for attempted retrieval. Retrieval failure occurred in 7% (6 of 91) of all retrieval attempts. A time interval of > 90 days between implantation and attempted retrieval was associated with retrieval failure (OR 19.8, P = 0.009). Conclusions: Patient age >80 years and a history of malignancy are predictors of a reduced probability for retrieval attempt. The rate of retrieval failure is low and seems to be associated with a time interval of >90 days between filter placement and retrieval.« less

Application of an enzyme-labeled antigen method for visualizing plasma cells producing antibodies against Strep A, a carbohydrate antigen of Streptococcus pyogenes, in recurrent tonsillitis.

PubMed

Onouchi, Takanori; Mizutani, Yasuyoshi; Shiogama, Kazuya; Inada, Ken-ichi; Okada, Tatsuyoshi; Naito, Kensei; Tsutsumi, Yutaka

2015-01-01

Streptococcus pyogenes is the main causative pathogen of recurrent tonsillitis. Histologically, lesions of recurrent tonsillitis contain numerous plasma cells. Strep A is an antigenic carbohydrate molecule on the cell wall of S. pyogenes. As expected, plasma cells in subjects with recurrent tonsillitis secrete antibodies against Strep A. The enzyme-labeled antigen method is a novel histochemical technique that visualizes specific antibody-producing cells in tissue sections by employing a biotin-labeled antigen as a probe. The purpose of the present study was to visualize plasma cells producing antibodies reactive with Strep A in recurrent tonsillitis. Firstly, the lymph nodes of rats immunized with boiled S. pyogenes were paraformaldehyde-fixed and specific plasma cells localized in frozen sections with biotinylated Strep A. Secondly, an enzyme-labeled antigen method was used on human tonsil surgically removed from 12 patients with recurrent tonsillitis. S. pyogenes genomes were PCR-detected in all 12 specimens. The emm genotypes belonged to emm12 in nine specimens and emm1 in three. Plasma cells producing anti-Strep A antibodies were demonstrated in prefixed frozen sections of rat lymph nodes, 8/12 human specimens from patients with recurrent tonsillitis but not in two control tonsils. In human tonsils, Strep A-reactive plasma cells were observed within the reticular squamous mucosa and just below the mucosa, and the specific antibodies belonged to either IgA or IgG classes. Our technique is effective in visualizing immunocytes producing specific antibodies against the bacterial carbohydrate antigen, and is thus a novel histochemical tool for analyzing immune reactions in infectious disorders. © 2014 The Authors. Microbiology and Immunology Published by The Societies and Wiley Publishing Asia Pty Ltd.

Probabilistic and machine learning-based retrieval approaches for biomedical dataset retrieval

PubMed Central

Karisani, Payam; Qin, Zhaohui S; Agichtein, Eugene

2018-01-01

Abstract The bioCADDIE dataset retrieval challenge brought together different approaches to retrieval of biomedical datasets relevant to a user’s query, expressed as a text description of a needed dataset. We describe experiments in applying a data-driven, machine learning-based approach to biomedical dataset retrieval as part of this challenge. We report on a series of experiments carried out to evaluate the performance of both probabilistic and machine learning-driven techniques from information retrieval, as applied to this challenge. Our experiments with probabilistic information retrieval methods, such as query term weight optimization, automatic query expansion and simulated user relevance feedback, demonstrate that automatically boosting the weights of important keywords in a verbose query is more effective than other methods. We also show that although there is a rich space of potential representations and features available in this domain, machine learning-based re-ranking models are not able to improve on probabilistic information retrieval techniques with the currently available training data. The models and algorithms presented in this paper can serve as a viable implementation of a search engine to provide access to biomedical datasets. The retrieval performance is expected to be further improved by using additional training data that is created by expert annotation, or gathered through usage logs, clicks and other processes during natural operation of the system. Database URL: https://github.com/emory-irlab/biocaddie PMID:29688379

System and method for phase retrieval for radio telescope and antenna control

NASA Technical Reports Server (NTRS)

Dean, Bruce H. (Inventor)

2013-01-01

Disclosed herein are systems, methods, and non-transitory computer-readable storage media for radio phase retrieval. A system practicing the method gathers first data from radio waves associated with an object observed via a first aperture, gathers second data from radio waves associated with the object observed via an introduced second aperture associated with the first aperture, generates reduced noise data by incoherently subtracting the second data from the first data, and performs phase retrieval for the radio waves by modeling the reduced noise data using a single Fourier transform. The first and second apertures are at different positions, such as side by side. This approach can include determining a value Q which represents a ratio of wavelength times a focal ratio divided by pixel spacing. This information can be used to accurately measure and correct alignment errors or other optical system flaws in the apertures.

The Influence of Learning Methods on Collaboration: Prior Repeated Retrieval Enhances Retrieval Organization, Abolishes Collaborative Inhibition, and Promotes Post-Collaborative Memory

ERIC Educational Resources Information Center

Congleton, Adam R.; Rajaram, Suparna

2011-01-01

Research on collaborative memory has unveiled the counterintuitive yet robust phenomenon that collaboration impairs group recall. A candidate explanation for this "collaborative inhibition" effect is the disruption of people's idiosyncratic retrieval strategies during collaboration, and it is hypothesized that employing methods that improve one's…

Time-Quality Tradeoff of Waiting Strategies for Tutors to Retrieve Relevant Teaching Methods

ERIC Educational Resources Information Center

Shih, Wen-Chung; Tseng, Shian-Shyong; Yang, Che-Ching; Liang, Tyne

2011-01-01

As more and more undergraduate students act as voluntary tutors to rural pupils after school, there is a growing need for a supporting environment to facilitate adaptive instruction. Among others, a teaching method retrieval system is intended to help tutors find relevant teaching methods for teaching a particular concept. However, teaching…

Homogenized description and retrieval method of nonlinear metasurfaces

NASA Astrophysics Data System (ADS)

Liu, Xiaojun; Larouche, Stéphane; Smith, David R.

2018-03-01

A patterned, plasmonic metasurface can strongly scatter incident light, functioning as an extremely low-profile lens, filter, reflector or other optical device. When the metasurface is patterned uniformly, its linear optical properties can be expressed using effective surface electric and magnetic polarizabilities obtained through a homogenization procedure. The homogenized description of a nonlinear metasurface, however, presents challenges both because of the inherent anisotropy of the medium as well as the much larger set of potential wave interactions available, making it challenging to assign effective nonlinear parameters to the otherwise inhomogeneous layer of metamaterial elements. Here we show that a homogenization procedure can be developed to describe nonlinear metasurfaces, which derive their nonlinear response from the enhanced local fields arising within the structured plasmonic elements. With the proposed homogenization procedure, we are able to assign effective nonlinear surface polarization densities to a nonlinear metasurface, and link these densities to the effective nonlinear surface susceptibilities and averaged macroscopic pumping fields across the metasurface. These effective nonlinear surface polarization densities are further linked to macroscopic nonlinear fields through the generalized sheet transition conditions (GSTCs). By inverting the GSTCs, the effective nonlinear surface susceptibilities of the metasurfaces can be solved for, leading to a generalized retrieval method for nonlinear metasurfaces. The application of the homogenization procedure and the GSTCs are demonstrated by retrieving the nonlinear susceptibilities of a SiO2 nonlinear slab. As an example, we investigate a nonlinear metasurface which presents nonlinear magnetoelectric coupling in near infrared regime. The method is expected to apply to any patterned metasurface whose thickness is much smaller than the wavelengths of operation, with inclusions of arbitrary geometry

Conjugate gradient method for phase retrieval based on the Wirtinger derivative.

PubMed

Wei, Zhun; Chen, Wen; Qiu, Cheng-Wei; Chen, Xudong

2017-05-01

A conjugate gradient Wirtinger flow (CG-WF) algorithm for phase retrieval is proposed in this paper. It is shown that, compared with recently reported Wirtinger flow and its modified methods, the proposed CG-WF algorithm is able to dramatically accelerate the convergence rate while keeping the dominant computational cost of each iteration unchanged. We numerically illustrate the effectiveness of our method in recovering 1D Gaussian signals and 2D natural color images under both Gaussian and coded diffraction pattern models.

Antigenic evaluation of a recombinant baculovirus-expressed Sarcocystis neurona SAG1 antigen.

PubMed

Gupta, G D; Lakritz, J; Saville, W J; Livingston, R S; Dubey, J P; Middleton, J R; Marsh, A E

2004-10-01

Sarcocystis neurona is the primary parasite associated with equine protozoal myeloencephalitis (EPM). This is a commonly diagnosed neurological disorder in the Americas that infects the central nervous system of horses. Current serologic assays utilize culture-derived parasites as antigen. This method requires large numbers of parasites to be grown in culture, which is labor intensive and time consuming. Also, a culture-derived whole-parasite preparation contains conserved antigens that could cross-react with antibodies against other Sarcocystis species and members of Sarcocystidae such as Neospora spp., Hammondia spp., and Toxoplasma gondii. Therefore, there is a need to develop an improved method for the detection of S. neurona-specific antibodies. The sera of infected horses react strongly to surface antigen 1 (SnSAG1), an approximately 29-kDa protein, in immunoblot analysis, suggesting that it is an immunodominant antigen. The SnSAG1 gene of S. neurona was cloned, and recombinant S. neurona SAG1 protein (rSnSAG1-Bac) was expressed with the use of a baculovirus system. By immunoblot analysis, the rSnSAG1-Bac antigen detected antibodies to S. neurona from naturally infected and experimentally inoculated equids, cats, rabbit, mice, and skunk. This is the first report of a baculovirus-expressed recombinant S. neurona antigen being used to detect anti-S. neurona antibodies in a variety of host species.

A minimum albedo aerosol retrieval method for the new-generation geostationary meteorological satellite Himawari-8

NASA Astrophysics Data System (ADS)

Yan, Xing; Li, Zhanqing; Luo, Nana; Shi, Wenzhong; Zhao, Wenji; Yang, Xingchuan; Jin, Jiannan

2018-07-01

Aerosol properties, including aerosol optical thickness (AOT) and fine-mode fraction (FMF), are important physical data and are fundamental for climate studies. A minimum albedo aerosol retrieval method (MAARM) was developed for the retrieval of aerosol properties based on the new-generation geostationary meteorological satellite Himawari-8. This method is based on the albedo data which is directly obtained from the Himawari-8 and can successfully output AOT, FMF, and the Ångström exponent (AE) directly. As part of the MAARM, a modified radiative transfer equation was proposed that considers the impact of aerosol multiple scattering. Through comparisons with output from the Second Simulation of a Satellite Signal in the Solar Spectrum (6S) radiative transfer code, the modified radiative transfer equation achieved a high accuracy for the aerosol reflectance calculation ( 5%). Aerosol Robotic Network (AERONET) data from three sites in Beijing and its surrounding area for the year 2016 were used to validate MAARM aerosol retrievals. Fifty-seven percent, 57%, and 56% of derived AOT values fell within the estimated error envelope at the Beijing, the Chinese Academy of Meteorological Sciences (CAMS), and Xianghe AERONET stations, respectively. In addition, 36% (58%) of MAARM-derived FMF values fell within the ±10%AERONET FMF envelope (the ±25%AERONET FMF envelope). Overall, an improvement was achieved by the MAARM in retrieving AOT, FMF, and AE compared with Himawari-8 standard aerosol property retrievals; however, there remains a distinct lack of skills in determining FMF and AE and their use from the MAARM retrieval is not recommended at this time. Given that the Himawari-8 satellite provides observations at 10-min intervals, the MAARM is capable of monitoring the spatial distribution of and variation in AOT with a high temporal resolution.

A method for retrieving vertical ozone profiles from limb scattered measurements

NASA Astrophysics Data System (ADS)

Wang, Zijun; Chen, Shengbo; Yang, Chunyan; Jin, Lihua

2011-10-01

A two-step method is employed in this study to retrieve vertical ozone profiles using scattered measurements from the limb of the atmosphere. The combination of the Differential Optical Absorption Spectroscopy (DOAS) and the Multiplicative Algebraic Reconstruction Technique (MART) is proposed. First, the limb radiance, measured over a range of tangent heights, is processed using the DOAS technique to recover the effective column densities of atmospheric ozone. Second, these effective column densities along the lines of sight (LOSs) are inverted using the MART coupled with a forward model SCIATRAN (radiative transfer model for SCIAMACHY) to derive the ozone profiles. This method is applied to Optical Spectrograph and Infra Red Imager System (OSIRIS) radiance, using the wavelength windows 571-617 nm. Vertical ozone profiles between 10 and 48 km are derived with a vertical resolution of 1 km. The results illustrate a good agreement with the cloud-free coincident SCanning Imaging Absorption spectroMeter for Atmospheric CHartographY (SCIAMACHY) ozone measurements, with deviations less than ±10% (±5% for altitudes from 17 to 47 km). Furthermore, sensitivities of retrieved ozone to aerosol, cloud parameters and NO2 concentration are also investigated.

Antigenic analyses of tissues and excretory and secretory products from Strongylus vulgaris.

PubMed Central

Wynne, E; Slocombe, J O; Wilkie, B N

1981-01-01

Rabbit antisera were prepared against veronal buffered saline extracts of L4 and L5 Strongylus vulgaris, adult S. vulgaris and adult Strongylus equinus retrieved from naturally infected horses. In agar gel diffusion with these antisera, adult S vulgaris and S. equinus each appeared to have at least one unique antigen; larval S. vulgaris appeared to have two species-specific and two stage-specific antigens. There were several common antigens. Excretory and secretory products were collected also from L4 and L5 an maintained over several days in tissue culture fluid. In agar gel diffusion against the above rabbit antisera, a stage-specific antigen was found also in excretory and secretory products. In addition, excretory and secretory products had three antigens in common with adult and larval S. vulgaris, but only one of these was common to adult S. equinus. The excretory and secretory products appear, therefore, to have two species-specific and one stage-specific antigens. Images Fig. 1 a and b. Fig. 2 a and b. Fig. 3 a and b. Fig. 4 a and b. Fig. 5 a and b. Fig. 6 a and b. Fig. 7 a and b. Fig. 8 a and b. PMID:6804070

Comparison of methods for measurement and retrieval of SIF with tower based sensors

NASA Astrophysics Data System (ADS)

Kornfeld, A.; Berry, J. A.

2017-12-01

As the popularity of solar induced fluorescence (SIF) measurement increases, the number of ways to measure and process the data has also increased, leaving a bewildering array of choices for the practitioner. To help clarify the advantages and disadvantages of several methods, we modified our foreoptic, Rotaprism, to measure spectra using either bi-hemispheric (cosine correcting diffusers on both upward and downward views) or hemispherical-conical views (only the upward view is cosine corrected). To test spatial sensitivity of each optic, we recorded data after moving the device relatively short distances - 1-2x the sensor's height above the canopy. When using conical measurements, measured SIF varied by as much as 100% across locations, whereas bi-hemispherical measurements were nearly unaffected by the moves. Reflectance indexes such as NDVI, PRI, NIRv were also spatially sensitive for the conical measurements. We also compared retrievals using either the O2A band or the adjacent Fraunhofer band to examine the relative advantages of each retrieval band for full-day retrievals. Finally, we investigated how choice of retrieval algorithm (SVD, FLD, SFM) affects the computed results. The primary site for this experiment was a California bunchgrass/tallgrass field. Additional data from the Brazilian Amazon will also be used, where appropriate, to support our conclusions.

Exploiting salient semantic analysis for information retrieval

NASA Astrophysics Data System (ADS)

Luo, Jing; Meng, Bo; Quan, Changqin; Tu, Xinhui

2016-11-01

Recently, many Wikipedia-based methods have been proposed to improve the performance of different natural language processing (NLP) tasks, such as semantic relatedness computation, text classification and information retrieval. Among these methods, salient semantic analysis (SSA) has been proven to be an effective way to generate conceptual representation for words or documents. However, its feasibility and effectiveness in information retrieval is mostly unknown. In this paper, we study how to efficiently use SSA to improve the information retrieval performance, and propose a SSA-based retrieval method under the language model framework. First, SSA model is adopted to build conceptual representations for documents and queries. Then, these conceptual representations and the bag-of-words (BOW) representations can be used in combination to estimate the language models of queries and documents. The proposed method is evaluated on several standard text retrieval conference (TREC) collections. Experiment results on standard TREC collections show the proposed models consistently outperform the existing Wikipedia-based retrieval methods.

Three methods to retrieve slant total electron content measurements from ground-based GPS receivers and performance assessment

NASA Astrophysics Data System (ADS)

Zhang, Baocheng

2016-07-01

The high sampling rate along with the global coverage of ground-based receivers makes Global Positioning System (GPS) data particularly ideal for sensing the Earth's ionosphere. Retrieval of slant total electron content measurements (TECMs) constitutes a key first step toward extracting various ionospheric parameters from GPS data. Within the ionospheric community, the interpretation of TECM is widely recognized as the slant total electron content along the satellite receiver line of sight, biased by satellite and receiver differential code biases (DCBs). The Carrier-to-Code Leveling (CCL) has long been used as a geometry-free method for retrieving TECM, mainly because of its simplicity and effectiveness. In fact, however, the CCL has proven inaccurate as it may give rise to TECM very susceptible to so-called leveling errors. With the goal of attaining more accurate TECM retrieval, we report in this contribution two other methods than the CCL, namely, the Precise Point Positioning (PPP) and the Array-aided PPP (A-PPP). The PPP further exploits the International GPS Service (IGS) orbit and clock products and turns out to be a geometry-based method. The A-PPP is designed to retrieve TECM from an array of colocated receivers, taking advantage of the broadcast orbit and clock products. Moreover, A-PPP also takes into account the fact that the ionospheric effects measured from one satellite to all colocated receivers ought to be the same, thus leading to the estimability of interreceiver DCB. We perform a comparative study of the formal precision and the empirical accuracy of the TECM that are retrieved, respectively, by three methods from the same set of GPS data. Results of such a study can be used to assess the actual performance of the three methods. In addition, we check the temporal stability in A-PPP-derived interreceiver DCB estimates over time periods ranging from 1 to 3 days.

Soluble Antigen Fluorescent-Antibody Technique

PubMed Central

Toussaint, Andre J.; Anderson, Robert I.

1965-01-01

An indirect fluorescent-antibody (FA) procedure employing soluble antigen fixed onto an artificial matrix was developed, and a mechanical means for reading of test results was devised. The method employs two small cellulose acetate paper discs for each test. One disc contains soluble antigen diluted in 1% bovine serum albumin (BSA); the other contains only 1% BSA and serves as a control. After testing by the indirect FA procedure, the results of the tests are read on a fluorometer fitted with a paper chromatogram door. The instrument is set at zero with the control disc as a blank, and the specific fluorescence of the antigen disc is determined. Findings obtained with homologous and heterologous antisera indicated that the method yields excellent results. The soluble antigen fluorescent-antibody technique has definite advantages over the conventional indirect FA procedures. (i) The investigator may objectively select the antigen to be employed. (ii) It is possible to obtain objective mechanical reading of test results rather than the highly subjective readings required by conventional methods. (iii) The system compensates for any nonspecific fluorescence contributed either by the serum (e.g., drugs) or by free fluorescein in the conjugated antiserum. Images Fig. 1 PMID:14339261

Concepts and applications for influenza antigenic cartography

PubMed Central

Cai, Zhipeng; Zhang, Tong; Wan, Xiu-Feng

2011-01-01

Influenza antigenic cartography projects influenza antigens into a two or three dimensional map based on immunological datasets, such as hemagglutination inhibition and microneutralization assays. A robust antigenic cartography can facilitate influenza vaccine strain selection since the antigenic map can simplify data interpretation through intuitive antigenic map. However, antigenic cartography construction is not trivial due to the challenging features embedded in the immunological data, such as data incompleteness, high noises, and low reactors. To overcome these challenges, we developed a computational method, temporal Matrix Completion-Multidimensional Scaling (MC-MDS), by adapting the low rank MC concept from the movie recommendation system in Netflix and the MDS method from geographic cartography construction. The application on H3N2 and 2009 pandemic H1N1 influenza A viruses demonstrates that temporal MC-MDS is effective and efficient in constructing influenza antigenic cartography. The web sever is available at http://sysbio.cvm.msstate.edu/AntigenMap. PMID:21761589

Performance Evaluation of Machine Learning Methods for Leaf Area Index Retrieval from Time-Series MODIS Reflectance Data

PubMed Central

Wang, Tongtong; Xiao, Zhiqiang; Liu, Zhigang

2017-01-01

Leaf area index (LAI) is an important biophysical parameter and the retrieval of LAI from remote sensing data is the only feasible method for generating LAI products at regional and global scales. However, most LAI retrieval methods use satellite observations at a specific time to retrieve LAI. Because of the impacts of clouds and aerosols, the LAI products generated by these methods are spatially incomplete and temporally discontinuous, and thus they cannot meet the needs of practical applications. To generate high-quality LAI products, four machine learning algorithms, including back-propagation neutral network (BPNN), radial basis function networks (RBFNs), general regression neutral networks (GRNNs), and multi-output support vector regression (MSVR) are proposed to retrieve LAI from time-series Moderate Resolution Imaging Spectroradiometer (MODIS) reflectance data in this study and performance of these machine learning algorithms is evaluated. The results demonstrated that GRNNs, RBFNs, and MSVR exhibited low sensitivity to training sample size, whereas BPNN had high sensitivity. The four algorithms performed slightly better with red, near infrared (NIR), and short wave infrared (SWIR) bands than red and NIR bands, and the results were significantly better than those obtained using single band reflectance data (red or NIR). Regardless of band composition, GRNNs performed better than the other three methods. Among the four algorithms, BPNN required the least training time, whereas MSVR needed the most for any sample size. PMID:28045443

Performance Evaluation of Machine Learning Methods for Leaf Area Index Retrieval from Time-Series MODIS Reflectance Data.

PubMed

Wang, Tongtong; Xiao, Zhiqiang; Liu, Zhigang

2017-01-01

Leaf area index (LAI) is an important biophysical parameter and the retrieval of LAI from remote sensing data is the only feasible method for generating LAI products at regional and global scales. However, most LAI retrieval methods use satellite observations at a specific time to retrieve LAI. Because of the impacts of clouds and aerosols, the LAI products generated by these methods are spatially incomplete and temporally discontinuous, and thus they cannot meet the needs of practical applications. To generate high-quality LAI products, four machine learning algorithms, including back-propagation neutral network (BPNN), radial basis function networks (RBFNs), general regression neutral networks (GRNNs), and multi-output support vector regression (MSVR) are proposed to retrieve LAI from time-series Moderate Resolution Imaging Spectroradiometer (MODIS) reflectance data in this study and performance of these machine learning algorithms is evaluated. The results demonstrated that GRNNs, RBFNs, and MSVR exhibited low sensitivity to training sample size, whereas BPNN had high sensitivity. The four algorithms performed slightly better with red, near infrared (NIR), and short wave infrared (SWIR) bands than red and NIR bands, and the results were significantly better than those obtained using single band reflectance data (red or NIR). Regardless of band composition, GRNNs performed better than the other three methods. Among the four algorithms, BPNN required the least training time, whereas MSVR needed the most for any sample size.

Serological purification of polysaccharide antigens from Streptococcus mutans serotypes a and d: characterization of multiple antigenic determinants.

PubMed

Linzer, R; Mukasa, H; Slade, H D

1975-10-01

The polysaccharide antigen preparations from serotype a and serotype d strains of Streptococcus mutans contained both a serotype-specific antigenic determinant and a common a-d antigenic determinant, as demonstrated by agar gel diffusion studies and a quantitative cross-precipitin assay. The chromatographically purified antigens were isolated by a method which depended on their serological specificity to determine if these two antigenic determinants were located on the same molecule. The a and d polysaccharides were recovered from specific antigen-antibody complexes and characterized with respect to their immunological specificity and chemical composition. Agar gel diffusion tests demonstrated that, in both the a and d preparations, the serotype-specific antigenic determinant and the common a-d antigenic determinant were present in one molecule.

Determining similarity in histological images using graph-theoretic description and matching methods for content-based image retrieval in medical diagnostics

PubMed Central

2012-01-01

Background Computer-based analysis of digitalized histological images has been gaining increasing attention, due to their extensive use in research and routine practice. The article aims to contribute towards the description and retrieval of histological images by employing a structural method using graphs. Due to their expressive ability, graphs are considered as a powerful and versatile representation formalism and have obtained a growing consideration especially by the image processing and computer vision community. Methods The article describes a novel method for determining similarity between histological images through graph-theoretic description and matching, for the purpose of content-based retrieval. A higher order (region-based) graph-based representation of breast biopsy images has been attained and a tree-search based inexact graph matching technique has been employed that facilitates the automatic retrieval of images structurally similar to a given image from large databases. Results The results obtained and evaluation performed demonstrate the effectiveness and superiority of graph-based image retrieval over a common histogram-based technique. The employed graph matching complexity has been reduced compared to the state-of-the-art optimal inexact matching methods by applying a pre-requisite criterion for matching of nodes and a sophisticated design of the estimation function, especially the prognosis function. Conclusion The proposed method is suitable for the retrieval of similar histological images, as suggested by the experimental and evaluation results obtained in the study. It is intended for the use in Content Based Image Retrieval (CBIR)-requiring applications in the areas of medical diagnostics and research, and can also be generalized for retrieval of different types of complex images. Virtual Slides The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1224798882787923. PMID:23035717

Talbot-Lau x-ray deflectometry phase-retrieval methods for electron density diagnostics in high-energy density experiments.

PubMed

Valdivia, Maria Pia; Stutman, Dan; Stoeckl, Christian; Mileham, Chad; Begishev, Ildar A; Bromage, Jake; Regan, Sean P

2018-01-10

Talbot-Lau x-ray interferometry uses incoherent x-ray sources to measure refraction index changes in matter. These measurements can provide accurate electron density mapping through phase retrieval. An adaptation of the interferometer has been developed in order to meet the specific requirements of high-energy density experiments. This adaptation is known as a moiré deflectometer, which allows for single-shot capabilities in the form of interferometric fringe patterns. The moiré x-ray deflectometry technique requires a set of object and reference images in order to provide electron density maps, which can be costly in the high-energy density environment. In particular, synthetic reference phase images obtained ex situ through a phase-scan procedure, can provide a feasible solution. To test this procedure, an object phase map was retrieved from a single-shot moiré image obtained from a plasma-produced x-ray source. A reference phase map was then obtained from phase-stepping measurements using a continuous x-ray tube source in a small laboratory setting. The two phase maps were used to retrieve an electron density map. A comparison of the moiré and phase-stepping phase-retrieval methods was performed to evaluate single-exposure plasma electron density mapping for high-energy density and other transient plasma experiments. It was found that a combination of phase-retrieval methods can deliver accurate refraction angle mapping. Once x-ray backlighter quality is optimized, the ex situ method is expected to deliver electron density mapping with improved resolution. The steps necessary for improved diagnostic performance are discussed.

Application of Rough Sets to Information Retrieval.

ERIC Educational Resources Information Center

Miyamoto, Sadaaki

1998-01-01

Develops a method of rough retrieval, an application of the rough set theory to information retrieval. The aim is to: (1) show that rough sets are naturally applied to information retrieval in which categorized information structure is used; and (2) show that a fuzzy retrieval scheme is induced from the rough retrieval. (AEF)

A method of solving tilt illumination for multiple distance phase retrieval

NASA Astrophysics Data System (ADS)

Guo, Cheng; Li, Qiang; Tan, Jiubin; Liu, Shutian; Liu, Zhengjun

2018-07-01

Multiple distance phase retrieval is a technique of using a series of intensity patterns to reconstruct a complex-valued image of object. However, tilt illumination originating from the off-axis displacement of incident light significantly impairs its imaging quality. To eliminate this affection, we use cross-correlation calibration to estimate oblique angle of incident light and a Fourier-based strategy to correct tilted illumination effect. Compared to other methods, binary and biological object are both stably reconstructed in simulation and experiment. This work provides a simple but beneficial method to solve the problem of tilt illumination for lens-free multi-distance system.

A scalable method for O-antigen purification applied to various Salmonella serovars

PubMed Central

Micoli, F.; Rondini, S.; Gavini, M.; Pisoni, I.; Lanzilao, L.; Colucci, A.M.; Giannelli, C.; Pippi, F.; Sollai, L.; Pinto, V.; Berti, F.; MacLennan, C.A.; Martin, L.B.; Saul, A.

2014-01-01

The surface lipopolysaccharide of gram-negative bacteria is both a virulence factor and a B cell antigen. Antibodies against O-antigen of lipopolysaccharide may confer protection against infection, and O-antigen conjugates have been designed against multiple pathogens. Here, we describe a simplified methodology for extraction and purification of the O-antigen core portion of Salmonella lipopolysaccharide, suitable for large-scale production. Lipopolysaccharide extraction and delipidation are performed by acetic acid hydrolysis of whole bacterial culture and can take place directly in a bioreactor, without previous isolation and inactivation of bacteria. Further O-antigen core purification consists of rapid filtration and precipitation steps, without using enzymes or hazardous chemicals. The process was successfully applied to various Salmonella enterica serovars (Paratyphi A, Typhimurium, and Enteritidis), obtaining good yields of high-quality material, suitable for conjugate vaccine preparations. PMID:23142430

A Comparison of Two Methods for Retrieving ICD-9-CM data: The Effect of Using an Ontology-based Method for Handling Terminology Changes

PubMed Central

Yu, Alexander C.; Cimino, James J.

2012-01-01

Objective Most existing controlled terminologies can be characterized as collections of terms, wherein the terms are arranged in a simple list or organized in a hierarchy. These kinds of terminologies are considered useful for standardizing terms and encoding data and are currently used in many existing information systems. However, they suffer from a number of limitations that make data reuse difficult. Relatively recently, it has been proposed that formal ontological methods can be applied to some of the problems of terminological design. Biomedical ontologies organize concepts (embodiments of knowledge about biomedical reality) whereas terminologies organize terms (what is used to code patient data at a certain point in time, based on the particular terminology version). However, the application of these methods to existing terminologies is not straightforward. The use of these terminologies is firmly entrenched in many systems, and what might seem to be a simple option of replacing these terminologies is not possible. Moreover, these terminologies evolve over time in order to suit the needs of users. Any methodology must therefore take these constraints into consideration, hence the need for formal methods of managing changes. Along these lines, we have developed a formal representation of the concept-term relation, around which we have also developed a methodology for management of terminology changes. The objective of this study was to determine whether our methodology would result in improved retrieval of data. Design Comparison of two methods for retrieving data encoded with terms from the International Classification of Diseases (ICD-9-CM), based on their recall when retrieving data for ICD-9-CM terms whose codes had changed but which had retained their original meaning (code change). Measurements Recall and interclass correlation coefficient. Results Statistically significant differences were detected (p<0.05) with the McNemar test for two terms whose

A novel content-based medical image retrieval method based on query topic dependent image features (QTDIF)

NASA Astrophysics Data System (ADS)

Xiong, Wei; Qiu, Bo; Tian, Qi; Mueller, Henning; Xu, Changsheng

2005-04-01

Medical image retrieval is still mainly a research domain with a large variety of applications and techniques. With the ImageCLEF 2004 benchmark, an evaluation framework has been created that includes a database, query topics and ground truth data. Eleven systems (with a total of more than 50 runs) compared their performance in various configurations. The results show that there is not any one feature that performs well on all query tasks. Key to successful retrieval is rather the selection of features and feature weights based on a specific set of input features, thus on the query task. In this paper we propose a novel method based on query topic dependent image features (QTDIF) for content-based medical image retrieval. These feature sets are designed to capture both inter-category and intra-category statistical variations to achieve good retrieval performance in terms of recall and precision. We have used Gaussian Mixture Models (GMM) and blob representation to model medical images and construct the proposed novel QTDIF for CBIR. Finally, trained multi-class support vector machines (SVM) are used for image similarity ranking. The proposed methods have been tested over the Casimage database with around 9000 images, for the given 26 image topics, used for imageCLEF 2004. The retrieval performance has been compared with the medGIFT system, which is based on the GNU Image Finding Tool (GIFT). The experimental results show that the proposed QTDIF-based CBIR can provide significantly better performance than systems based general features only.

A linear method for the retrieval of sun-induced chlorophyll fluorescence from GOME-2 and SCIAMACHY data

NASA Astrophysics Data System (ADS)

Köhler, Philipp; Guanter, Luis; Joiner, Joanna

2015-04-01

Global retrievals of near-infrared sun-induced chlorophyll fluorescence (SIF) have been achieved in the last several years by means of space-borne atmospheric spectrometers. SIF is an electromagnetic signal emitted by the chlorophyll-a of photosynthetically active vegetation in the 650-850 nm spectral range. It represents a part of the excess energy during the process of photosynthesis and provides a measure of photosynthetic activity. The key challenge to retrieve SIF from space is to isolate the signal from the about 100 times more intense reflected solar radiation in the measured top of atmosphere (TOA) radiance spectrum. Nevertheless, it has been demonstrated that a number of satellite sensors provide the necessary spectral and radiometric performance to evaluate the in-filling of solar Fraunhofer lines and/or atmospheric absorption features by SIF. We will present recent developments for the retrieval of SIF from medium spectral resolution space-borne spectrometers such as the Global Ozone Monitoring Experiment (GOME-2) and the Scanning Imaging Absorption SpectroMeter for Atmospheric ChartographY (SCIAMACHY). Building upon the previous work by Joiner et al. 2013, our approach solves existing issues in the retrieval such as the non-linearity of the forward model and the arbitrary selection of the number of free parameters. In particular, we use a backward elimination algorithm to optimize the number of coefficients to fit, which reduces also the retrieval noise and selects the number of state vector elements automatically. A sensitivity analysis with simulated spectra has been utilized to evaluate the performance of our retrieval approach. The method has also been applied to estimate SIF from real spectra from GOME-2 and for the first time, from SCIAMACHY. We are able to present a time series of GOME-2 SIF results covering the 2007-2011 time period and SCIAMACHY SIF results between 2003-2011. This represents an almost one decade long record of global SIF. We

Determining similarity in histological images using graph-theoretic description and matching methods for content-based image retrieval in medical diagnostics.

PubMed

Sharma, Harshita; Alekseychuk, Alexander; Leskovsky, Peter; Hellwich, Olaf; Anand, R S; Zerbe, Norman; Hufnagl, Peter

2012-10-04

Computer-based analysis of digitalized histological images has been gaining increasing attention, due to their extensive use in research and routine practice. The article aims to contribute towards the description and retrieval of histological images by employing a structural method using graphs. Due to their expressive ability, graphs are considered as a powerful and versatile representation formalism and have obtained a growing consideration especially by the image processing and computer vision community. The article describes a novel method for determining similarity between histological images through graph-theoretic description and matching, for the purpose of content-based retrieval. A higher order (region-based) graph-based representation of breast biopsy images has been attained and a tree-search based inexact graph matching technique has been employed that facilitates the automatic retrieval of images structurally similar to a given image from large databases. The results obtained and evaluation performed demonstrate the effectiveness and superiority of graph-based image retrieval over a common histogram-based technique. The employed graph matching complexity has been reduced compared to the state-of-the-art optimal inexact matching methods by applying a pre-requisite criterion for matching of nodes and a sophisticated design of the estimation function, especially the prognosis function. The proposed method is suitable for the retrieval of similar histological images, as suggested by the experimental and evaluation results obtained in the study. It is intended for the use in Content Based Image Retrieval (CBIR)-requiring applications in the areas of medical diagnostics and research, and can also be generalized for retrieval of different types of complex images. The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1224798882787923.

Care episode retrieval: distributional semantic models for information retrieval in the clinical domain.

PubMed

Moen, Hans; Ginter, Filip; Marsi, Erwin; Peltonen, Laura-Maria; Salakoski, Tapio; Salanterä, Sanna

2015-01-01

Patients' health related information is stored in electronic health records (EHRs) by health service providers. These records include sequential documentation of care episodes in the form of clinical notes. EHRs are used throughout the health care sector by professionals, administrators and patients, primarily for clinical purposes, but also for secondary purposes such as decision support and research. The vast amounts of information in EHR systems complicate information management and increase the risk of information overload. Therefore, clinicians and researchers need new tools to manage the information stored in the EHRs. A common use case is, given a--possibly unfinished--care episode, to retrieve the most similar care episodes among the records. This paper presents several methods for information retrieval, focusing on care episode retrieval, based on textual similarity, where similarity is measured through domain-specific modelling of the distributional semantics of words. Models include variants of random indexing and the semantic neural network model word2vec. Two novel methods are introduced that utilize the ICD-10 codes attached to care episodes to better induce domain-specificity in the semantic model. We report on experimental evaluation of care episode retrieval that circumvents the lack of human judgements regarding episode relevance. Results suggest that several of the methods proposed outperform a state-of-the art search engine (Lucene) on the retrieval task.

Care episode retrieval: distributional semantic models for information retrieval in the clinical domain

PubMed Central

2015-01-01

Patients' health related information is stored in electronic health records (EHRs) by health service providers. These records include sequential documentation of care episodes in the form of clinical notes. EHRs are used throughout the health care sector by professionals, administrators and patients, primarily for clinical purposes, but also for secondary purposes such as decision support and research. The vast amounts of information in EHR systems complicate information management and increase the risk of information overload. Therefore, clinicians and researchers need new tools to manage the information stored in the EHRs. A common use case is, given a - possibly unfinished - care episode, to retrieve the most similar care episodes among the records. This paper presents several methods for information retrieval, focusing on care episode retrieval, based on textual similarity, where similarity is measured through domain-specific modelling of the distributional semantics of words. Models include variants of random indexing and the semantic neural network model word2vec. Two novel methods are introduced that utilize the ICD-10 codes attached to care episodes to better induce domain-specificity in the semantic model. We report on experimental evaluation of care episode retrieval that circumvents the lack of human judgements regarding episode relevance. Results suggest that several of the methods proposed outperform a state-of-the art search engine (Lucene) on the retrieval task. PMID:26099735

A two-step method for retrieving the longitudinal profile of an electron bunch from its coherent radiation

NASA Astrophysics Data System (ADS)

Pelliccia, Daniele; Sen, Tanaji

2014-11-01

The coherent radiation emitted by an electron bunch provides a diagnostic signal that can be used to estimate its longitudinal distribution. Commonly only the amplitude of the intensity spectrum can be measured and the associated phase must be calculated to obtain the bunch profile. Very recently an iterative method was proposed to retrieve this phase. However ambiguities associated with non-uniqueness of the solution are always present in the phase retrieval procedure. Here we present a method to overcome the ambiguity problem by first performing multiple independent runs of the phase retrieval procedure and then second, sorting the good solutions by means of cross-correlation analysis. Results obtained with simulated bunches of various shapes and experimental measured spectra are presented, discussed and compared with the established Kramers-Kronig method. It is shown that even when the effect of the ambiguities is strong, as is the case for a double peak in the profile, the cross-correlation post-processing is able to filter out unwanted solutions. We show that, unlike the Kramers-Kronig method, the combined approach presented is able to faithfully reconstruct complicated bunch profiles.

Development of the CODER System: A Testbed for Artificial Intelligence Methods in Information Retrieval.

ERIC Educational Resources Information Center

Fox, Edward A.

1987-01-01

Discusses the CODER system, which was developed to investigate the application of artificial intelligence methods to increase the effectiveness of information retrieval systems, particularly those involving heterogeneous documents. Highlights include the use of PROLOG programing, blackboard-based designs, knowledge engineering, lexicological…

Use of information-retrieval languages in automated retrieval of experimental data from long-term storage

NASA Technical Reports Server (NTRS)

Khovanskiy, Y. D.; Kremneva, N. I.

1975-01-01

Problems and methods are discussed of automating information retrieval operations in a data bank used for long term storage and retrieval of data from scientific experiments. Existing information retrieval languages are analyzed along with those being developed. The results of studies discussing the application of the descriptive 'Kristall' language used in the 'ASIOR' automated information retrieval system are presented. The development and use of a specialized language of the classification-descriptive type, using universal decimal classification indices as the main descriptors, is described.

Cell membrane antigen-antibody complex dissociation by the widely used glycine-HCL method: an unreliable procedure for studying antibody internalization.

PubMed

Tsaltas, G; Ford, C H

1993-02-01

Methods following the process of binding and internalization of antibodies to cell surface antigens have often employed low pH isoosmolar buffers in order to dissociate surface antigen-antibody complexes. One of the most widely used buffers is a 0.05 M glycine-HCL buffer pH 2.8. Since the efficacy of action of this buffer was critical to a series of internalization experiments employing monoclonal antibodies (Mabs) to carcinoembryonic antigen (CEA) expressing cancer cell lines in this laboratory, we tested its performance in a number of different assays. Our results indicate that this buffer only partially dissociates antigen-antibody bonds and therefore can introduce major inaccuracies in internalization experiments.

Multiple Diphtheria Antigen-Antibody Systems Investigated by Passive Haemagglutination Techniques and Other Methods

PubMed Central

Fulthorpe, A. J.

1962-01-01

A fair degree of correlation has been found between the in vivo antitoxin content of sera from horses immunized with crude Corynebacterium diphtheriae culture filtrates and the direct agglutinin titre of the sera when tested with sheep cells sensitized with diphtheria toxoid. Haemagglutination inhibition tests at the LA level of test with the same sera showed some rather large discrepancies from the in vivo and further tests with special agglutinin inhibiting toxins suggested that specific antitoxin free from other accessory antibodies might be non-agglutinating, and therefore not titratable by haemagglutination inhibition. The phosphate-stable, pepsin-stable and trypsin-stable antigens isolated from culture filtrates of C. diphtheriae were found to contain extremely small quantities of specific toxoid, and cross titration of each of the three antigen preparations showed that there was very little contamination by other antigens within the group. Absorption of diphtheria antiserum with red cells sensitized with each of the three accessory antigens individually, showed that the antibodies were highly specific and distinct. Absorption of diphtheria antiserum with a mixture of red cells sensitized with the three different antigens removed all demonstrable accessory antibodies, and the absorbed serum would no longer agglutinate cells sensitized with complete diphtheria toxoid. The absorbed serum, however, retained a large proportion of its neutralizing capacity for diphtheria toxin, when titrated in vivo. Titration of each of the accessory antibodies in a number of horse sera by haemagglutination inhibition demonstrated a correlation between the values for the accessory antibodies to the phosphate-stable and pepsin-stable antigens, but no correlation with the values for the antibody to the trypsin-stable antigen, when compared with results of the flocculation test. The relative proportions of diphtheria toxin and of the phosphate-stable and pepsin-stable antigens

Content-Based Medical Image Retrieval

NASA Astrophysics Data System (ADS)

Müller, Henning; Deserno, Thomas M.

This chapter details the necessity for alternative access concepts to the currently mainly text-based methods in medical information retrieval. This need is partly due to the large amount of visual data produced, the increasing variety of medical imaging data and changing user patterns. The stored visual data contain large amounts of unused information that, if well exploited, can help diagnosis, teaching and research. The chapter briefly reviews the history of image retrieval and its general methods before technologies that have been developed in the medical domain are focussed. We also discuss evaluation of medical content-based image retrieval (CBIR) systems and conclude with pointing out their strengths, gaps, and further developments. As examples, the MedGIFT project and the Image Retrieval in Medical Applications (IRMA) framework are presented.

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.

AntigenMap 3D: an online antigenic cartography resource.

PubMed

Barnett, J Lamar; Yang, Jialiang; Cai, Zhipeng; Zhang, Tong; Wan, Xiu-Feng

2012-05-01

Antigenic cartography is a useful technique to visualize and minimize errors in immunological data by projecting antigens to 2D or 3D cartography. However, a 2D cartography may not be sufficient to capture the antigenic relationship from high-dimensional immunological data. AntigenMap 3D presents an online, interactive, and robust 3D antigenic cartography construction and visualization resource. AntigenMap 3D can be applied to identify antigenic variants and vaccine strain candidates for pathogens with rapid antigenic variations, such as influenza A virus. http://sysbio.cvm.msstate.edu/AntigenMap3D

Generating Concise Rules for Human Motion Retrieval

NASA Astrophysics Data System (ADS)

Mukai, Tomohiko; Wakisaka, Ken-Ichi; Kuriyama, Shigeru

This paper proposes a method for retrieving human motion data with concise retrieval rules based on the spatio-temporal features of motion appearance. Our method first converts motion clip into a form of clausal language that represents geometrical relations between body parts and their temporal relationship. A retrieval rule is then learned from the set of manually classified examples using inductive logic programming (ILP). ILP automatically discovers the essential rule in the same clausal form with a user-defined hypothesis-testing procedure. All motions are indexed using this clausal language, and the desired clips are retrieved by subsequence matching using the rule. Such rule-based retrieval offers reasonable performance and the rule can be intuitively edited in the same language form. Consequently, our method enables efficient and flexible search from a large dataset with simple query language.

An Abstraction-Based Data Model for Information Retrieval

NASA Astrophysics Data System (ADS)

McAllister, Richard A.; Angryk, Rafal A.

Language ontologies provide an avenue for automated lexical analysis that may be used to supplement existing information retrieval methods. This paper presents a method of information retrieval that takes advantage of WordNet, a lexical database, to generate paths of abstraction, and uses them as the basis for an inverted index structure to be used in the retrieval of documents from an indexed corpus. We present this method as a entree to a line of research on using ontologies to perform word-sense disambiguation and improve the precision of existing information retrieval techniques.

A comparison of two methods for retrieving ICD-9-CM data: the effect of using an ontology-based method for handling terminology changes.

PubMed

Yu, Alexander C; Cimino, James J

2011-04-01

Most existing controlled terminologies can be characterized as collections of terms, wherein the terms are arranged in a simple list or organized in a hierarchy. These kinds of terminologies are considered useful for standardizing terms and encoding data and are currently used in many existing information systems. However, they suffer from a number of limitations that make data reuse difficult. Relatively recently, it has been proposed that formal ontological methods can be applied to some of the problems of terminological design. Biomedical ontologies organize concepts (embodiments of knowledge about biomedical reality) whereas terminologies organize terms (what is used to code patient data at a certain point in time, based on the particular terminology version). However, the application of these methods to existing terminologies is not straightforward. The use of these terminologies is firmly entrenched in many systems, and what might seem to be a simple option of replacing these terminologies is not possible. Moreover, these terminologies evolve over time in order to suit the needs of users. Any methodology must therefore take these constraints into consideration, hence the need for formal methods of managing changes. Along these lines, we have developed a formal representation of the concept-term relation, around which we have also developed a methodology for management of terminology changes. The objective of this study was to determine whether our methodology would result in improved retrieval of data. Comparison of two methods for retrieving data encoded with terms from the International Classification of Diseases (ICD-9-CM), based on their recall when retrieving data for ICD-9-CM terms whose codes had changed but which had retained their original meaning (code change). Recall and interclass correlation coefficient. Statistically significant differences were detected (p<0.05) with the McNemar test for two terms whose codes had changed. Furthermore, when all

Antigen recovery and preservation using the microwave irradiation of biological samples for transmission electron microscopy analysis.

PubMed

Aïoun, Josiane; Chat, Sophie; Bordat, Christian; Péchoux, Christine

2013-01-01

Most studies using microwave irradiation (MWI) for the preparation of tissue samples have reported an improvement in structural integrity. However, there have been few studies on the effect of microwave (MW) on antigen preservation during sample preparation prior to immunolocalization. This report documents our experience of specimen preparation using an automatic microwave apparatus to obtain antigen preservation and retrieval. We tested the effects of MW processing vs. conventional procedures on the morphology and antigenicity of two different tissues: the brain and mammary gland, whose chemical composition and anatomical organization are quite different. We chose to locate the transcription factor PPARβ/δ using immunocytochemistry on brain tissue sections from hamsters. Antigen retrieval protocols involving MWI were used to restore immunoreactivity. We also studied the efficiency of the ultrastructural immunolocalization of both PPARγ and caveolin-1 following MWI vs. conventional treatment, on mammary gland tissue from mice at 10 days of lactation. Our findings showed that the treatment of tissue samples with MWI, in the context of a process lasting just a few hours from fixation to immunolocalization, enabled similar, or even better, results than conventional protocols. The quantification of immunolabeling for cav-1 indicated an increase in density of up to three-fold in tissues processed in the microwave oven. Furthermore, MW treatment permitted the localization of PPARβ/δ in glutaraldehyde-fixed specimens, which was impossible in the absence of MWI. This study thus showed that techniques involving the use of microwaves could largely improve both ultrastructure and immunodetection. Copyright © 2013 Elsevier Ltd. All rights reserved.

Bayesian nonparametric clustering in phylogenetics: modeling antigenic evolution in influenza.

PubMed

Cybis, Gabriela B; Sinsheimer, Janet S; Bedford, Trevor; Rambaut, Andrew; Lemey, Philippe; Suchard, Marc A

2018-01-30

Influenza is responsible for up to 500,000 deaths every year, and antigenic variability represents much of its epidemiological burden. To visualize antigenic differences across many viral strains, antigenic cartography methods use multidimensional scaling on binding assay data to map influenza antigenicity onto a low-dimensional space. Analysis of such assay data ideally leads to natural clustering of influenza strains of similar antigenicity that correlate with sequence evolution. To understand the dynamics of these antigenic groups, we present a framework that jointly models genetic and antigenic evolution by combining multidimensional scaling of binding assay data, Bayesian phylogenetic machinery and nonparametric clustering methods. We propose a phylogenetic Chinese restaurant process that extends the current process to incorporate the phylogenetic dependency structure between strains in the modeling of antigenic clusters. With this method, we are able to use the genetic information to better understand the evolution of antigenicity throughout epidemics, as shown in applications of this model to H1N1 influenza. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Initial retrieval shields against retrieval-induced forgetting

PubMed Central

Racsmány, Mihály; Keresztes, Attila

2015-01-01

Testing, as a form of retrieval, can enhance learning but it can also induce forgetting of related memories, a phenomenon known as retrieval-induced forgetting (RIF). In four experiments we explored whether selective retrieval and selective restudy of target memories induce forgetting of related memories with or without initial retrieval of the entire learning set. In Experiment 1, subjects studied category-exemplar associations, some of which were then either restudied or retrieved. RIF occurred on a delayed final test only when memories were retrieved and not when they were restudied. In Experiment 2, following the study phase of category-exemplar associations, subjects attempted to recall all category-exemplar associations, then they selectively retrieved or restudied some of the exemplars. We found that, despite the huge impact on practiced items, selective retrieval/restudy caused no decrease in final recall of related items. In Experiment 3, we replicated the main result of Experiment 2 by manipulating initial retrieval as a within-subject variable. In Experiment 4 we replicated the main results of the previous experiments with non-practiced (Nrp) baseline items. These findings suggest that initial retrieval of the learning set shields against the forgetting effect of later selective retrieval. Together, our results support the context shift theory of RIF. PMID:26052293

Initial retrieval shields against retrieval-induced forgetting.

PubMed

Racsmány, Mihály; Keresztes, Attila

2015-01-01

Testing, as a form of retrieval, can enhance learning but it can also induce forgetting of related memories, a phenomenon known as retrieval-induced forgetting (RIF). In four experiments we explored whether selective retrieval and selective restudy of target memories induce forgetting of related memories with or without initial retrieval of the entire learning set. In Experiment 1, subjects studied category-exemplar associations, some of which were then either restudied or retrieved. RIF occurred on a delayed final test only when memories were retrieved and not when they were restudied. In Experiment 2, following the study phase of category-exemplar associations, subjects attempted to recall all category-exemplar associations, then they selectively retrieved or restudied some of the exemplars. We found that, despite the huge impact on practiced items, selective retrieval/restudy caused no decrease in final recall of related items. In Experiment 3, we replicated the main result of Experiment 2 by manipulating initial retrieval as a within-subject variable. In Experiment 4 we replicated the main results of the previous experiments with non-practiced (Nrp) baseline items. These findings suggest that initial retrieval of the learning set shields against the forgetting effect of later selective retrieval. Together, our results support the context shift theory of RIF.

A fully automatic end-to-end method for content-based image retrieval of CT scans with similar liver lesion annotations.

PubMed

Spanier, A B; Caplan, N; Sosna, J; Acar, B; Joskowicz, L

2018-01-01

The goal of medical content-based image retrieval (M-CBIR) is to assist radiologists in the decision-making process by retrieving medical cases similar to a given image. One of the key interests of radiologists is lesions and their annotations, since the patient treatment depends on the lesion diagnosis. Therefore, a key feature of M-CBIR systems is the retrieval of scans with the most similar lesion annotations. To be of value, M-CBIR systems should be fully automatic to handle large case databases. We present a fully automatic end-to-end method for the retrieval of CT scans with similar liver lesion annotations. The input is a database of abdominal CT scans labeled with liver lesions, a query CT scan, and optionally one radiologist-specified lesion annotation of interest. The output is an ordered list of the database CT scans with the most similar liver lesion annotations. The method starts by automatically segmenting the liver in the scan. It then extracts a histogram-based features vector from the segmented region, learns the features' relative importance, and ranks the database scans according to the relative importance measure. The main advantages of our method are that it fully automates the end-to-end querying process, that it uses simple and efficient techniques that are scalable to large datasets, and that it produces quality retrieval results using an unannotated CT scan. Our experimental results on 9 CT queries on a dataset of 41 volumetric CT scans from the 2014 Image CLEF Liver Annotation Task yield an average retrieval accuracy (Normalized Discounted Cumulative Gain index) of 0.77 and 0.84 without/with annotation, respectively. Fully automatic end-to-end retrieval of similar cases based on image information alone, rather that on disease diagnosis, may help radiologists to better diagnose liver lesions.

Gunther Tulip Retrievable Inferior Vena Caval Filters: Indications, Efficacy, Retrieval, and Complications

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

Looby, S.; Given, M.F.; Geoghegan, T.

Purpose. We evaluated the Gunther Tulip (GT) retrievable inferior vena cava (IVC) filter with regard to indications, filtration efficacy, complications, retrieval window, and use of anticoagulation. Method. A retrospective study was performed of 147 patients (64 men, 83 women; mean age 58.8 years) who underwent retrievable GT filter insertion between 2001 and 2005. The indications for placement included a diagnosis of pulmonary embolism or deep venous thrombosis with a contraindication to anticoagulation (n = 68), pulmonary embolism or deep venous thrombosis while on anticoagulation (n = 49), prophylactic filter placement for high-risk surgical patients with a past history of pulmonarymore » embolism or deep venous thrombosis (n = 20), and a high risk of pulmonary embolism or deep venous thrombosis (n = 10). Forty-nine of the 147 patients did not receive anticoagulation (33.7%) while 96 of 147 patients did, 82 of these receiving warfarin (56.5%), 11 receiving low-molecular weight heparins (7.58%), and 3 receiving antiplatelet agents alone (2.06%). Results. Filter placement was successful in 147 patients (100%). Two patients had two filters inserted. Of the 147 patients, filter deployment was on a permanent basis in 102 and with an intention to retrieve in 45 patients. There were 36 (80%) successful retrievals and 9 (20%) failed retrievals. The mean time to retrieval was 33.6 days. The reasons for failed retrieval included filter struts tightly adherent to the IVC wall (5/9), extreme filter tilt (2/9), and extensive filter thrombus (2/9). Complications included pneumothorax (n = 4), failure of filter expansion (n = 1), and breakthrough pulmonary embolism (n = 1). No IVC thrombotic episodes were recorded. Discussion. The Gunther Tulip retrievable filter can be used as a permanent or a retrievable filter. It is safe and efficacious. GT filters can be safely retrieved at a mean time interval of 33.6 days. The newly developed Celect filter may extend the retrieval

Evaluation of retrieval methods of daytime convective boundary layer height based on lidar data

NASA Astrophysics Data System (ADS)

Li, Hong; Yang, Yi; Hu, Xiao-Ming; Huang, Zhongwei; Wang, Guoyin; Zhang, Beidou; Zhang, Tiejun

2017-04-01

The atmospheric boundary layer height is a basic parameter in describing the structure of the lower atmosphere. Because of their high temporal resolution, ground-based lidar data are widely used to determine the daytime convective boundary layer height (CBLH), but the currently available retrieval methods have their advantages and drawbacks. In this paper, four methods of retrieving the CBLH (i.e., the gradient method, the idealized backscatter method, and two forms of the wavelet covariance transform method) from lidar normalized relative backscatter are evaluated, using two artificial cases (an idealized profile and a case similar to real profile), to test their stability and accuracy. The results show that the gradient method is suitable for high signal-to-noise ratio conditions. The idealized backscatter method is less sensitive to the first estimate of the CBLH; however, it is computationally expensive. The results obtained from the two forms of the wavelet covariance transform method are influenced by the selection of the initial input value of the wavelet amplitude. Further sensitivity analysis using real profiles under different orders of magnitude of background counts show that when different initial input values are set, the idealized backscatter method always obtains consistent CBLH. For two wavelet methods, the different CBLH are always obtained with the increase in the wavelet amplitude when noise is significant. Finally, the CBLHs as measured by three lidar-based methods are evaluated by as measured from L-band soundings. The boundary layer heights from two instruments coincide with ±200 m in most situations.

Concept-Based Retrieval from Critical Incident Reports.

PubMed

Denecke, Kerstin

2017-01-01

Critical incident reporting systems (CIRS) are used as a means to collect anonymously entered information of incidents that occurred for example in a hospital. Analyzing this information helps to identify among others problems in the workflow, in the infrastructure or in processes. The entire potential of these sources of experiential knowledge remains often unconsidered since retrieval of relevant reports and their analysis is difficult and time-consuming, and the reporting systems often do not provide support for these tasks. The objective of this work is to develop a method for retrieving reports from the CIRS related to a specific user query. atural language processing (NLP) and information retrieval (IR) methods are exploited for realizing the retrieval. We compare standard retrieval methods that rely upon frequency of words with an approach that includes a semantic mapping of natural language to concepts of a medical ontology. By an evaluation, we demonstrate the feasibility of semantic document enrichment to improve recall in incident reporting retrieval. It is shown that a combination of standard keyword-based retrieval with semantic search results in highly satisfactory recall values. In future work, the evaluation should be repeated on a larger data set and real-time user evaluation need to be performed to assess user satisfactory with the system and results.

A Novel Method of Case Representation and Retrieval in CBR for E-Learning

ERIC Educational Resources Information Center

Khamparia, Aditya; Pandey, Babita

2017-01-01

In this paper we have discussed a novel method which has been developed for representation and retrieval of cases in case based reasoning (CBR) as a part of e-learning system which is based on various student features. In this approach we have integrated Artificial Neural Network (ANN) with Data mining (DM) and CBR. ANN is used to find the…

Clustering Methods; Part IV of Scientific Report No. ISR-18, Information Storage and Retrieval...

ERIC Educational Resources Information Center

Cornell Univ., Ithaca, NY. Dept. of Computer Science.

Two papers are included as Part Four of this report on Salton's Magical Automatic Retriever of Texts (SMART) project report. The first paper: "A Controlled Single Pass Classification Algorithm with Application to Multilevel Clustering" by D. B. Johnson and J. M. Laferente presents a single pass clustering method which compares favorably…

Data Compression in Full-Text Retrieval Systems.

ERIC Educational Resources Information Center

Bell, Timothy C.; And Others

1993-01-01

Describes compression methods for components of full-text systems such as text databases on CD-ROM. Topics discussed include storage media; structures for full-text retrieval, including indexes, inverted files, and bitmaps; compression tools; memory requirements during retrieval; and ranking and information retrieval. (Contains 53 references.)…

Can We Retrieve the Information Which Was Intentionally Forgotten? Electrophysiological Correlates of Strategic Retrieval in Directed Forgetting.

PubMed

Mao, Xinrui; Tian, Mengxi; Liu, Yi; Li, Bingcan; Jin, Yan; Wu, Yanhong; Guo, Chunyan

2017-01-01

Retrieval inhibition hypothesis of directed forgetting effects assumed TBF (to-be-forgotten) items were not retrieved intentionally, while selective rehearsal hypothesis assumed the memory representation of retrieved TBF (to-be-forgotten) items was weaker than TBR (to-be-remembered) items. Previous studies indicated that directed forgetting effects of item-cueing method resulted from selective rehearsal at encoding, but the mechanism of retrieval inhibition that affected directed forgetting of TBF (to-be-forgotten) items was not clear. Strategic retrieval is a control process allowing the selective retrieval of target information, which includes retrieval orientation and strategic recollection. Retrieval orientation via the comparison of tasks refers to the specific form of processing resulted by retrieval efforts. Strategic recollection is the type of strategies to recollect studied items for the retrieval success of targets. Using a "directed forgetting" paradigm combined with a memory exclusion task, our investigation of strategic retrieval in directed forgetting assisted to explore how retrieval inhibition played a role on directed forgetting effects. When TBF items were targeted, retrieval orientation showed more positive ERPs to new items, indicating that TBF items demanded more retrieval efforts. The results of strategic recollection indicated that: (a) when TBR items were retrieval targets, late parietal old/new effects were only evoked by TBR items but not TBF items, indicating the retrieval inhibition of TBF items; (b) when TBF items were retrieval targets, the late parietal old/new effect were evoked by both TBR items and TBF items, indicating that strategic retrieval could overcome retrieval inhibition of TBF items. These findings suggested the modulation of strategic retrieval on retrieval inhibition of directed forgetting, supporting that directed forgetting effects were not only caused by selective rehearsal, but also retrieval inhibition.

Can We Retrieve the Information Which Was Intentionally Forgotten? Electrophysiological Correlates of Strategic Retrieval in Directed Forgetting

PubMed Central

Mao, Xinrui; Tian, Mengxi; Liu, Yi; Li, Bingcan; Jin, Yan; Wu, Yanhong; Guo, Chunyan

2017-01-01

Retrieval inhibition hypothesis of directed forgetting effects assumed TBF (to-be-forgotten) items were not retrieved intentionally, while selective rehearsal hypothesis assumed the memory representation of retrieved TBF (to-be-forgotten) items was weaker than TBR (to-be-remembered) items. Previous studies indicated that directed forgetting effects of item-cueing method resulted from selective rehearsal at encoding, but the mechanism of retrieval inhibition that affected directed forgetting of TBF (to-be-forgotten) items was not clear. Strategic retrieval is a control process allowing the selective retrieval of target information, which includes retrieval orientation and strategic recollection. Retrieval orientation via the comparison of tasks refers to the specific form of processing resulted by retrieval efforts. Strategic recollection is the type of strategies to recollect studied items for the retrieval success of targets. Using a “directed forgetting” paradigm combined with a memory exclusion task, our investigation of strategic retrieval in directed forgetting assisted to explore how retrieval inhibition played a role on directed forgetting effects. When TBF items were targeted, retrieval orientation showed more positive ERPs to new items, indicating that TBF items demanded more retrieval efforts. The results of strategic recollection indicated that: (a) when TBR items were retrieval targets, late parietal old/new effects were only evoked by TBR items but not TBF items, indicating the retrieval inhibition of TBF items; (b) when TBF items were retrieval targets, the late parietal old/new effect were evoked by both TBR items and TBF items, indicating that strategic retrieval could overcome retrieval inhibition of TBF items. These findings suggested the modulation of strategic retrieval on retrieval inhibition of directed forgetting, supporting that directed forgetting effects were not only caused by selective rehearsal, but also retrieval inhibition. PMID

Noise robustness of a combined phase retrieval and reconstruction method for phase-contrast tomography.

PubMed

Kongskov, Rasmus Dalgas; Jørgensen, Jakob Sauer; Poulsen, Henning Friis; Hansen, Per Christian

2016-04-01

Classical reconstruction methods for phase-contrast tomography consist of two stages: phase retrieval and tomographic reconstruction. A novel algebraic method combining the two was suggested by Kostenko et al. [Opt. Express21, 12185 (2013)OPEXFF1094-408710.1364/OE.21.012185], and preliminary results demonstrated improved reconstruction compared with a given two-stage method. Using simulated free-space propagation experiments with a single sample-detector distance, we thoroughly compare the novel method with the two-stage method to address limitations of the preliminary results. We demonstrate that the novel method is substantially more robust toward noise; our simulations point to a possible reduction in counting times by an order of magnitude.

Ecobody technology: rapid monoclonal antibody screening method from single B cells using cell-free protein synthesis for antigen-binding fragment formation.

PubMed

Ojima-Kato, Teruyo; Nagai, Satomi; Nakano, Hideo

2017-10-25

We report a rapid and cost-effective monoclonal antibody screening method from single animal B cells using reverse transcription (RT)-PCR and Escherichia coli cell-free protein synthesis (CFPS), which allows evaluation of antibodies within 2 working days. This process is named "Ecobody technology". The method includes strategies to isolate B cells that specifically bind an antigen from the peripheral blood of immunised animals, and single-cell RT-PCR to generate DNA fragments of the V H and V L genes, followed by CFPS for production of fragments of antigen binding (Fab). In the CFPS step, we employed our techniques: 1) 'Zipbody' as a method for producing Fab, in which the association of heavy and light chains is facilitated by adhesive leucine zipper peptides fused at the C-termini of the Fab; and 2) an N-terminal SKIK peptide tag that can increase protein expression levels. Using Ecobody technology, we obtained highly-specific monoclonal antibodies for the antigens Vibrio parahaemolyticus and E. coli O26. The anti-V. parahaemolyticus Zipbody mAb was further produced in E. coli strain SHuffle T7 Express in inclusion bodies and refolded by a conventional method, resulting in significant antigen-binding activity (K D  = 469 pM) and productivity of 8.5 mg purified antibody/L-culture.

Surfing for suicide methods and help: content analysis of websites retrieved with search engines in Austria and the United States.

PubMed

Till, Benedikt; Niederkrotenthaler, Thomas

2014-08-01

The Internet provides a variety of resources for individuals searching for suicide-related information. Structured content-analytic approaches to assess intercultural differences in web contents retrieved with method-related and help-related searches are scarce. We used the 2 most popular search engines (Google and Yahoo/Bing) to retrieve US-American and Austrian search results for the term suicide, method-related search terms (e.g., suicide methods, how to kill yourself, painless suicide, how to hang yourself), and help-related terms (e.g., suicidal thoughts, suicide help) on February 11, 2013. In total, 396 websites retrieved with US search engines and 335 websites from Austrian searches were analyzed with content analysis on the basis of current media guidelines for suicide reporting. We assessed the quality of websites and compared findings across search terms and between the United States and Austria. In both countries, protective outweighed harmful website characteristics by approximately 2:1. Websites retrieved with method-related search terms (e.g., how to hang yourself) contained more harmful (United States: P < .001, Austria: P < .05) and fewer protective characteristics (United States: P < .001, Austria: P < .001) compared to the term suicide. Help-related search terms (e.g., suicidal thoughts) yielded more websites with protective characteristics (United States: P = .07, Austria: P < .01). Websites retrieved with U.S. search engines generally had more protective characteristics (P < .001) than searches with Austrian search engines. Resources with harmful characteristics were better ranked than those with protective characteristics (United States: P < .01, Austria: P < .05). The quality of suicide-related websites obtained depends on the search terms used. Preventive efforts to improve the ranking of preventive web content, particularly regarding method-related search terms, seem necessary. © Copyright 2014 Physicians Postgraduate Press, Inc.

Do FY antigens act as minor histocompatibility antigens in the graft-versus-host disease paradigm after human leukocyte antigen-identical sibling hematopoietic stem cell transplantation?

PubMed

Sellami, Mohamed Hichem; Chaabane, Manel; Kaabi, Houda; Torjemane, Lamia; Ladeb, Saloua; Ben Othmane, Tarek; Hmida, Slama

2012-03-01

FY antigens are candidate minor histocompatibility antigens relevant to renal allograft rejection, but no data have been reported about their role in graft-versus-host disease (GVHD) incidence after human leukocyte antigen (HLA)-identical siblings hematopoietic stem cell transplantation (HSCT). The aim of this study was to examine the effect of donor/recipient disparity at FY antigens on the incidence of GVHD in Tunisian patients receiving an HLA-identical HSCT. This work enrolled 105 Tunisian pairs of recipients and their HLA-identical sibling donors of HSCs. FY genotyping was performed with the polymerase chain reaction-sequence-specific primer method and donor/recipient disparity for these antigens was analyzed at two levels: incompatibility and nonidentity. The case-control analyses showed no significant correlation between FY disparity and the incidence of either acute or chronic GVHD. Sample size calculation showed that 572 cases and 1716 controls would be necessary to be able to detect a significant association with 80% power and two-sided type I error level of 5% (α=0.05). The lack of association in the studied cohort may be explained by the low immunogenicity of FY antigens in HSCT context, compared with other antigens such as HA-1 and CD31.

Retrievals of heavy ozone with MIPAS

NASA Astrophysics Data System (ADS)

Jonkheid, Bastiaan; Röckmann, Thomas; Glatthor, Norbert; Janssen, Christof; Stiller, Gabriele; von Clarmann, Thomas

2016-12-01

A method for retrieval of 18O-substituted isotopomers of O3 in the stratosphere with the Michelson Interferometer for Passive Atmospheric Sounding (MIPAS) is presented. Using a smoothing regularisation constraint, volume mixing ratio profiles are retrieved for the main isotopologue and the symmetric and asymmetric isotopomers of singly substituted O3. For the retrieval of the heavy isotopologues, two microwindows in the MIPAS A band (685-970 cm-1) and six in the AB band (1020-1170 cm-1) are used. As the retrievals are performed as perturbations on the previously retrieved a priori profiles, the vertical resolution of the individual isotopomer profiles is very similar, which is important when calculating the ratio between two isotopomers. The performance of the method is evaluated using 1044 vertical profiles recorded with MIPAS on 1 July 2003. The mean values are separated by latitude bands, along with estimates of their uncertainties. The asymmetric isotopomer shows a mean enrichment of ˜ 8 %, with a vertical profile that increases up to 33 km and decreases at higher altitudes. This decrease with altitude is a robust result that does not depend on retrieval settings, and it has not been reported clearly in previously published datasets. The symmetric isotopomer is considerably less enriched, with mean values around 3 % and with a large spread. In individual retrievals the uncertainty of the enrichment is dominated by the measurement noise (2-4 %), which can be reduced by averaging multiple retrievals; systematic uncertainties linked to the retrieval are generally small at ˜ 0.5 %, but this is likely underestimated because the uncertainties in key spectroscopic parameters are unknown. The variabilities in the retrieval results are largest for the Southern Hemisphere.

A Bayesian approach to microwave precipitation profile retrieval

NASA Technical Reports Server (NTRS)

Evans, K. Franklin; Turk, Joseph; Wong, Takmeng; Stephens, Graeme L.

1995-01-01

A multichannel passive microwave precipitation retrieval algorithm is developed. Bayes theorem is used to combine statistical information from numerical cloud models with forward radiative transfer modeling. A multivariate lognormal prior probability distribution contains the covariance information about hydrometeor distribution that resolves the nonuniqueness inherent in the inversion process. Hydrometeor profiles are retrieved by maximizing the posterior probability density for each vector of observations. The hydrometeor profile retrieval method is tested with data from the Advanced Microwave Precipitation Radiometer (10, 19, 37, and 85 GHz) of convection over ocean and land in Florida. The CP-2 multiparameter radar data are used to verify the retrieved profiles. The results show that the method can retrieve approximate hydrometeor profiles, with larger errors over land than water. There is considerably greater accuracy in the retrieval of integrated hydrometeor contents than of profiles. Many of the retrieval errors are traced to problems with the cloud model microphysical information, and future improvements to the algorithm are suggested.

Challenges and opportunities of using liquid chromatography and mass spectrometry methods to develop complex vaccine antigens as pharmaceutical dosage forms.

PubMed

Hickey, John M; Sahni, Neha; Toth, Ronald T; Kumru, Ozan S; Joshi, Sangeeta B; Middaugh, C Russell; Volkin, David B

2016-10-01

Liquid chromatographic methods, combined with mass spectrometry, offer exciting and important opportunities to better characterize complex vaccine antigens including recombinant proteins, virus-like particles, inactivated viruses, polysaccharides, and protein-polysaccharide conjugates. The current abilities and limitations of these physicochemical methods to complement traditional in vitro and in vivo vaccine potency assays are explored in this review through the use of illustrative case studies. Various applications of these state-of-the art techniques are illustrated that include the analysis of influenza vaccines (inactivated whole virus and recombinant hemagglutinin), virus-like particle vaccines (human papillomavirus and hepatitis B), and polysaccharide linked to protein carrier vaccines (pneumococcal). Examples of utilizing these analytical methods to characterize vaccine antigens in the presence of adjuvants, which are often included to boost immune responses as part of the final vaccine dosage form, are also presented. Some of the challenges of using chromatographic and LC-MS as physicochemical assays to routinely test complex vaccine antigens are also discussed. Copyright © 2016 Elsevier B.V. All rights reserved.

Retrieval feedback in MEDLINE.

PubMed Central

Srinivasan, P

1996-01-01

OBJECTIVE: To investigate a new approach for query expansion based on retrieval feedback. The first objective in this study was to examine alternative query-expansion methods within the same retrieval-feedback framework. The three alternatives proposed are: expansion on the MeSH query field alone, expansion on the free-text field alone, and expansion on both the MeSH and the free-text fields. The second objective was to gain further understanding of retrieval feedback by examining possible dependencies on relevant documents during the feedback cycle. DESIGN: Comparative study of retrieval effectiveness using the original unexpanded and the alternative expanded user queries on a MEDLINE test collection of 75 queries and 2,334 MEDLINE citations. MEASUREMENTS: Retrieval effectivenesses of the original unexpanded and the alternative expanded queries were compared using 11-point-average precision scores (11-AvgP). These are averages of precision scores obtained at 11 standard recall points. RESULTS: All three expansion strategies significantly improved the original queries in terms of retrieval effectiveness. Expansion on MeSH alone was equivalent to expansion on both MeSH and the free-text fields. Expansion on the free-text field alone improved the queries significantly less than did the other two strategies. The second part of the study indicated that retrieval-feedback-based expansion yields significant performance improvements independent of the availability of relevant documents for feedback information. CONCLUSIONS: Retrieval feedback offers a robust procedure for query expansion that is most effective for MEDLINE when applied to the MeSH field. PMID:8653452

A differential optical absorption spectroscopy method for retrieval from ground-based Fourier transform spectrometers measurements of the direct solar beam

NASA Astrophysics Data System (ADS)

Huo, Yanfeng; Duan, Minzheng; Tian, Wenshou; Min, Qilong

2015-08-01

A differential optical absorption spectroscopy (DOAS)-like algorithm is developed to retrieve the column-averaged dryair mole fraction of carbon dioxide from ground-based hyper-spectral measurements of the direct solar beam. Different to the spectral fitting method, which minimizes the difference between the observed and simulated spectra, the ratios of multiple channel-pairs—one weak and one strong absorption channel—are used to retrieve from measurements of the shortwave infrared (SWIR) band. Based on sensitivity tests, a super channel-pair is carefully selected to reduce the effects of solar lines, water vapor, air temperature, pressure, instrument noise, and frequency shift on retrieval errors. The new algorithm reduces computational cost and the retrievals are less sensitive to temperature and H2O uncertainty than the spectral fitting method. Multi-day Total Carbon Column Observing Network (TCCON) measurements under clear-sky conditions at two sites (Tsukuba and Bremen) are used to derive xxxx for the algorithm evaluation and validation. The DOAS-like results agree very well with those of the TCCON algorithm after correction of an airmass-dependent bias.

Sensitivity Analysis for Atmospheric Infrared Sounder (AIRS) CO2 Retrieval

NASA Technical Reports Server (NTRS)

Gat, Ilana

2012-01-01

The Atmospheric Infrared Sounder (AIRS) is a thermal infrared sensor able to retrieve the daily atmospheric state globally for clear as well as partially cloudy field-of-views. The AIRS spectrometer has 2378 channels sensing from 15.4 micrometers to 3.7 micrometers, of which a small subset in the 15 micrometers region has been selected, to date, for CO2 retrieval. To improve upon the current retrieval method, we extended the retrieval calculations to include a prior estimate component and developed a channel ranking system to optimize the channels and number of channels used. The channel ranking system uses a mathematical formalism to rapidly process and assess the retrieval potential of large numbers of channels. Implementing this system, we identifed a larger optimized subset of AIRS channels that can decrease retrieval errors and minimize the overall sensitivity to other iridescent contributors, such as water vapor, ozone, and atmospheric temperature. This methodology selects channels globally by accounting for the latitudinal, longitudinal, and seasonal dependencies of the subset. The new methodology increases accuracy in AIRS CO2 as well as other retrievals and enables the extension of retrieved CO2 vertical profiles to altitudes ranging from the lower troposphere to upper stratosphere. The extended retrieval method for CO2 vertical profile estimation using a maximum-likelihood estimation method. We use model data to demonstrate the beneficial impact of the extended retrieval method using the new channel ranking system on CO2 retrieval.

An automatic method for retrieving and indexing catalogues of biomedical courses.

PubMed

Maojo, Victor; de la Calle, Guillermo; García-Remesal, Miguel; Bankauskaite, Vaida; Crespo, Jose

2008-11-06

Although there is wide information about Biomedical Informatics education and courses in different Websites, information is usually not exhaustive and difficult to update. We propose a new methodology based on information retrieval techniques for extracting, indexing and retrieving automatically information about educational offers. A web application has been developed to make available such information in an inventory of courses and educational offers.

Patent information retrieval: approaching a method and analysing nanotechnology patent collaborations.

PubMed

Ozcan, Sercan; Islam, Nazrul

2017-01-01

Many challenges still remain in the processing of explicit technological knowledge documents such as patents. Given the limitations and drawbacks of the existing approaches, this research sets out to develop an improved method for searching patent databases and extracting patent information to increase the efficiency and reliability of nanotechnology patent information retrieval process and to empirically analyse patent collaboration. A tech-mining method was applied and the subsequent analysis was performed using Thomson data analyser software. The findings show that nations such as Korea and Japan are highly collaborative in sharing technological knowledge across academic and corporate organisations within their national boundaries, and China presents, in some cases, a great illustration of effective patent collaboration and co-inventorship. This study also analyses key patent strengths by country, organisation and technology.

Multi-sensor data processing method for improved satellite retrievals

NASA Astrophysics Data System (ADS)

Fan, Xingwang

2017-04-01

Satellite remote sensing has provided massive data that improve the overall accuracy and extend the time series of environmental studies. In reflective solar bands, satellite data are related to land surface properties via radiative transfer (RT) equations. These equations generally include sensor-related (calibration coefficients), atmosphere-related (aerosol optical thickness) and surface-related (surface reflectance) parameters. It is an ill-posed problem to solve three parameters with only one RT equation. Even if there are two RT equations (dual-sensor data), the problem is still unsolvable. However, a robust solution can be obtained when any two parameters are known. If surface and atmosphere are known, sensor intercalibration can be performed. For example, the Advanced Very High Resolution Radiometer (AVHRR) was calibrated to the MODerate-resolution Imaging Spectroradiometer (MODIS) in Fan and Liu (2014) [Fan, X., and Liu, Y. (2014). Quantifying the relationship between intersensor images in solar reflective bands: Implications for intercalibration. IEEE Transactions on Geoscience and Remote Sensing, 52(12), 7727-7737.]. If sensor and surface are known, atmospheric data can be retrieved. For example, aerosol data were retrieved using tandem TERRA and AQUA MODIS images in Fan and Liu (2016a) [Fan, X., and Liu, Y. (2016a). Exploiting TERRA-AQUA MODIS relationship in the reflective solar bands for aerosol retrieval. Remote Sensing, 8(12), 996.]. If sensor and atmosphere are known, data consistency can be obtained. For example, Normalized Difference Vegetation Index (NDVI) data were intercalibrated among coarse-resolution sensors in Fan and Liu (2016b) [Fan, X., and Liu, Y. (2016b). A global study of NDVI difference among moderate-resolution satellite sensors. ISPRS Journal of Photogrammetry and Remote Sensing, 121, 177-191.], and among fine-resolution sensors in Fan and Liu (2017) [Fan, X., and Liu, Y. (2017). A generalized model for intersensor NDVI

Immunohistochemical detection and correlation between MHC antigen and cell-mediated immune system in recurrent glioma by APAAP method.

PubMed

Miyagi, K; Ingram, M; Techy, G B; Jacques, D B; Freshwater, D B; Sheldon, H

1990-09-01

As part of an on-going clinical trial of immunotherapy for recurrent malignant gliomas, using alkaline phosphatase-anti-alkaline phosphatase method with monoclonal antibodies, we investigated the correlation between expression of the major histocompatibility complex (MHC) and the subpopulation of tumor-infiltrating lymphocytes (TILs) in 38 glioma specimens (20 grade IV, 11 grade III, and 7 grade II) from 33 patients. Thirty specimens (78.9%) were positive to class I MHC antigen and 20 (52.6%) were positive to class II MHC antigen. The correlations between class I MHC antigen expression and the number of infiltrating T8 (p less than 0.01), and also between class II MHC antigen expression and the number of infiltrating T4 (p less than 0.05) were significant. We conclude that TILs are the result of immunoreaction (host-defense mechanism). 31.6% of specimens had perivascular infiltration of T cells. The main infiltrating lymphocyte subset in moderate to marked perivascular cuffing was T4. Our results may indicate that lack of MHC antigen on the glioma cell surface has a share in the poor immunogenicity in glioma-bearing patients. In addition, considering the effector/target ratio, the number of infiltrating lymphocytes against glioma cells was too small, so the immunological intervention seems to be essential in glioma therapy. Previous radiation therapy and chemotherapy, including steroid therapy, did not influence lymphocyte and macrophage infiltration.

Retrieving handwriting by combining word spotting and manifold ranking

NASA Astrophysics Data System (ADS)

Peña Saldarriaga, Sebastián; Morin, Emmanuel; Viard-Gaudin, Christian

2012-01-01

Online handwritten data, produced with Tablet PCs or digital pens, consists in a sequence of points (x, y). As the amount of data available in this form increases, algorithms for retrieval of online data are needed. Word spotting is a common approach used for the retrieval of handwriting. However, from an information retrieval (IR) perspective, word spotting is a primitive keyword based matching and retrieval strategy. We propose a framework for handwriting retrieval where an arbitrary word spotting method is used, and then a manifold ranking algorithm is applied on the initial retrieval scores. Experimental results on a database of more than 2,000 handwritten newswires show that our method can improve the performances of a state-of-the-art word spotting system by more than 10%.

Effective material parameter retrieval of anisotropic elastic metamaterials with inherent nonlocality

NASA Astrophysics Data System (ADS)

Lee, Hyung Jin; Lee, Heung Son; Ma, Pyung Sik; Kim, Yoon Young

2016-09-01

In this paper, the scattering (S-) parameter retrieval method is presented specifically for anisotropic elastic metamaterials; so far, no retrieval has been accomplished when elastic metamaterials exhibit fully anisotropic behavior. Complex constitutive property and intrinsic scattering behavior of elastic metamaterials make their characterization far more complicated than that for acoustic and electromagnetic metamaterials. In particular, elastic metamaterials generally exhibit anisotropic scattering behavior due to higher scattering modes associated with shear deformation. They also exhibit nonlocal responses to some degrees, which originate from strong multiple scattering interactions even in the long wavelength limit. Accordingly, the conventional S-parameter retrieval methods cannot be directly used for elastic metamaterials, because they determine only the diagonal components in effective tensor property. Also, the conventional methods simply use the analytic inversion formulae for the material characterization so that inherent nonlocality cannot be taken into account. To establish a retrieval method applicable to anisotropic elastic metamaterials, we propose an alternative S-parameter method to deal with full anisotropy of elastic metamaterials. To retrieve the whole effective anisotropic parameter, we utilize not only normal but also oblique wave incidences. For the retrieval, we first retrieve the ratio of the effective stiffness tensor to effective density and then determine the effective density. The proposed retrieval method is validated by characterizing the effective material parameters of various types of non-resonant anisotropic metamaterials. It is found that the whole effective parameters are retrieved consistently regardless of used retrieval conditions in spite of inherent nonlocality.

Analyzing Document Retrievability in Patent Retrieval Settings

NASA Astrophysics Data System (ADS)

Bashir, Shariq; Rauber, Andreas

Most information retrieval settings, such as web search, are typically precision-oriented, i.e. they focus on retrieving a small number of highly relevant documents. However, in specific domains, such as patent retrieval or law, recall becomes more relevant than precision: in these cases the goal is to find all relevant documents, requiring algorithms to be tuned more towards recall at the cost of precision. This raises important questions with respect to retrievability and search engine bias: depending on how the similarity between a query and documents is measured, certain documents may be more or less retrievable in certain systems, up to some documents not being retrievable at all within common threshold settings. Biases may be oriented towards popularity of documents (increasing weight of references), towards length of documents, favour the use of rare or common words; rely on structural information such as metadata or headings, etc. Existing accessibility measurement techniques are limited as they measure retrievability with respect to all possible queries. In this paper, we improve accessibility measurement by considering sets of relevant and irrelevant queries for each document. This simulates how recall oriented users create their queries when searching for relevant information. We evaluate retrievability scores using a corpus of patents from US Patent and Trademark Office.

Analysis of mixing-layer height retrieval methods using backscatter lidar returns and microwave-radiometer temperature observations in the context of synergy

NASA Astrophysics Data System (ADS)

Saeed, Umar; Rocadenbosch, Francesc

2017-04-01

Mixing Layer Height (MLH) is an important parameter in many different atmospheric and meteorological applications. However, there does not exist a single instrument or method which provides accurate and physically consistent estimates of MLH. Instead, there are several methods for MLH estimation based on the measurements of different atmospheric tracers using different instruments [1, 2]. In this work, MLH retrieval methods using backscattered lidar signals and Microwave Radiometer (MWR)-retrieved potential-temperature profiles are compared in terms of their associated uncertainties. The Extended Kalman Filter (EKF) is used for MLH retrieval from backscattered lidar signals [3] and parcel method [4] is used for MLH retrieval from MWR-retrieved potential-temperature profiles. Measurement and retrieval errors are revisited and incorporated into the MLH estimation methods used. Uncertainties on MLH estimates from the two methods are compared along with a combined MLH-retrieval discussion case. The uncertainty analysis is validated using long-term lidar and MWR measurement data, under different atmospheric conditions, from the HD(CP)2 Observational Prototype Experiment (HOPE) campaign at Jülich, Germany [5]. MLH estimates from a Doppler wind lidar and radiosondes are used as reference. This work has received funding from the European Union Seventh Framework Programme, FP7 People, ITN Marie Curie Actions Programme (2012-2016) in the frame of ITaRS project (GA 289923), H2020 programme under ACTRIS-2 project (GA 654109), the Spanish Ministry of Economy and Competitiveness - European Regional Development Funds under TEC2015-63832-P project, and from the Generalitat de Catalunya (Grup de Recerca Consolidat) 2014-SGR-583. [1] S. Emeis, Surface-based Remote Sensing of the Atmospheric Boundary Layer. 978-90-481-9339-4, Springer, 2010. [2] P. Seibert, F. Beyrich, S.-E. Gryning, S. Joffre, A. Rasmussen, and P. Tercier, "Review and intercomparison of operational methods for the

A new method for the automatic retrieval of medical cases based on the RadLex ontology.

PubMed

Spanier, A B; Cohen, D; Joskowicz, L

2017-03-01

The goal of medical case-based image retrieval (M-CBIR) is to assist radiologists in the clinical decision-making process by finding medical cases in large archives that most resemble a given case. Cases are described by radiology reports comprised of radiological images and textual information on the anatomy and pathology findings. The textual information, when available in standardized terminology, e.g., the RadLex ontology, and used in conjunction with the radiological images, provides a substantial advantage for M-CBIR systems. We present a new method for incorporating textual radiological findings from medical case reports in M-CBIR. The input is a database of medical cases, a query case, and the number of desired relevant cases. The output is an ordered list of the most relevant cases in the database. The method is based on a new case formulation, the Augmented RadLex Graph and an Anatomy-Pathology List. It uses a new case relatedness metric [Formula: see text] that prioritizes more specific medical terms in the RadLex tree over less specific ones and that incorporates the length of the query case. An experimental study on 8 CT queries from the 2015 VISCERAL 3D Case Retrieval Challenge database consisting of 1497 volumetric CT scans shows that our method has accuracy rates of 82 and 70% on the first 10 and 30 most relevant cases, respectively, thereby outperforming six other methods. The increasing amount of medical imaging data acquired in clinical practice constitutes a vast database of untapped diagnostically relevant information. This paper presents a new hybrid approach to retrieving the most relevant medical cases based on textual and image information.

Antigenic Structure of Rabbit γ Globulin

PubMed Central

Dubiski, S.; Dubiska, Anna; Skalba, Danuta; Kelus, A.

1961-01-01

By iso-immunization, antisera to five rabbit γ globulin antigens were obtained. They are called A (former Da), B, C, D and E. Individual sera of 670 rabbits belonging to six separate populations were tested by precipitation methods. The distribution of the iso-antigens and their combinations into serum groups were studied. Each particular γ globulin iso-antigen was found to be of hereditary character; they seem to form three genetic systems: A, C and BDE, statistically independent. Various antisera from England, Poland and U.S.A were compared. PMID:13724581

Scalable ranked retrieval using document images

NASA Astrophysics Data System (ADS)

Jain, Rajiv; Oard, Douglas W.; Doermann, David

2013-12-01

Despite the explosion of text on the Internet, hard copy documents that have been scanned as images still play a significant role for some tasks. The best method to perform ranked retrieval on a large corpus of document images, however, remains an open research question. The most common approach has been to perform text retrieval using terms generated by optical character recognition. This paper, by contrast, examines whether a scalable segmentation-free image retrieval algorithm, which matches sub-images containing text or graphical objects, can provide additional benefit in satisfying a user's information needs on a large, real world dataset. Results on 7 million scanned pages from the CDIP v1.0 test collection show that content based image retrieval finds a substantial number of documents that text retrieval misses, and that when used as a basis for relevance feedback can yield improvements in retrieval effectiveness.

Immunity to tumour antigens.

PubMed

Li, Geng; Ali, Selman A; McArdle, Stephanie E B; Mian, Shahid; Ahmad, Murrium; Miles, Amanda; Rees, Robert C

2005-01-01

During the last decade, a large number of human tumour antigens have been identified. These antigens are classified as tumour-specific shared antigens, tissue-specific differentiation antigens, overexpressed antigens, tumour antigens resulting from mutations, viral antigens and fusion proteins. Antigens recognised by effectors of immune system are potential targets for antigen-specific cancer immunotherapy. However, most tumour antigens are self-proteins and are generally of low immunogenicity and the immune response elicited towards these tumour antigens is not always effective. Strategies to induce and enhance the tumour antigen-specific response are needed. This review will summarise the approaches to discovery of tumour antigens, the current status of tumour antigens, and their potential application to cancer treatment.

JAL (RH48) blood group antigen: serologic observations

PubMed Central

Lomas-Francis, Christine; Alcantara, Denden; Westhoff, Connie; Uehlinger, Joan; Valvasori, Marilia; Castilho, Lillian; Reid, Marion E.

2009-01-01

BACKGROUND JAL (RH48) is a low-prevalence antigen in the Rh blood group system and anti-JAL has caused hemolytic disease of the newborn. JAL is associated with either a haplotype carrying depressed C and e antigens or one carrying depressed c and e antigens. Blood samples from JAL+ people were tested, published serologic findings were confirmed, serologic studies were extended to include expression of other Rh antigens, and the antibody specificities produced by three sensitized JAL+ probands are reported. STUDY DESIGN AND METHODS Red blood cell (RBC) samples from 17 (12 probands) JAL+ persons were tested by hemagglutination using standard methods. RESULTS RBCs from both the Caucasian JAL+ probands had the (C)(e) haplotype and weakened C, e, hrB, and hrS antigens. JAL+ samples from black persons had the (c)(e) haplotype and expressed weakened c, e, f, V, VS, hrB, and hrS antigens. Plasma from three sensitized c+e+ JAL+ probands contained alloanti-c, alloanti-e, or alloantibody of apparent anti-Rh17 specificity. This study shows that this alloanti-Rh17–like antibody recognizes the high-prevalence antigen antithetical to JAL that has been named CEST. CONCLUSIONS The presence of the JAL antigen has a quantitative (weakening) effect on the expression of C, e, hrB, and hrS antigens in Caucasian persons and of c, e, f, V, VS, hrB, and hrS antigens in people of black African ancestry. A qualitative effect also was demonstrated by the presence of alloanti-c or alloanti-e in the plasma of two transfused c+e+ patients and by an antibody (anti-CEST) that recognizes the high-prevalence antigen antithetical to JAL. PMID:19192256

Semantic-based surveillance video retrieval.

PubMed

Hu, Weiming; Xie, Dan; Fu, Zhouyu; Zeng, Wenrong; Maybank, Steve

2007-04-01

Visual surveillance produces large amounts of video data. Effective indexing and retrieval from surveillance video databases are very important. Although there are many ways to represent the content of video clips in current video retrieval algorithms, there still exists a semantic gap between users and retrieval systems. Visual surveillance systems supply a platform for investigating semantic-based video retrieval. In this paper, a semantic-based video retrieval framework for visual surveillance is proposed. A cluster-based tracking algorithm is developed to acquire motion trajectories. The trajectories are then clustered hierarchically using the spatial and temporal information, to learn activity models. A hierarchical structure of semantic indexing and retrieval of object activities, where each individual activity automatically inherits all the semantic descriptions of the activity model to which it belongs, is proposed for accessing video clips and individual objects at the semantic level. The proposed retrieval framework supports various queries including queries by keywords, multiple object queries, and queries by sketch. For multiple object queries, succession and simultaneity restrictions, together with depth and breadth first orders, are considered. For sketch-based queries, a method for matching trajectories drawn by users to spatial trajectories is proposed. The effectiveness and efficiency of our framework are tested in a crowded traffic scene.

Automatic Evidence Retrieval for Systematic Reviews

PubMed Central

Choong, Miew Keen; Galgani, Filippo; Dunn, Adam G

2014-01-01

Background Snowballing involves recursively pursuing relevant references cited in the retrieved literature and adding them to the search results. Snowballing is an alternative approach to discover additional evidence that was not retrieved through conventional search. Snowballing’s effectiveness makes it best practice in systematic reviews despite being time-consuming and tedious. Objective Our goal was to evaluate an automatic method for citation snowballing’s capacity to identify and retrieve the full text and/or abstracts of cited articles. Methods Using 20 review articles that contained 949 citations to journal or conference articles, we manually searched Microsoft Academic Search (MAS) and identified 78.0% (740/949) of the cited articles that were present in the database. We compared the performance of the automatic citation snowballing method against the results of this manual search, measuring precision, recall, and F1 score. Results The automatic method was able to correctly identify 633 (as proportion of included citations: recall=66.7%, F1 score=79.3%; as proportion of citations in MAS: recall=85.5%, F1 score=91.2%) of citations with high precision (97.7%), and retrieved the full text or abstract for 490 (recall=82.9%, precision=92.1%, F1 score=87.3%) of the 633 correctly retrieved citations. Conclusions The proposed method for automatic citation snowballing is accurate and is capable of obtaining the full texts or abstracts for a substantial proportion of the scholarly citations in review articles. By automating the process of citation snowballing, it may be possible to reduce the time and effort of common evidence surveillance tasks such as keeping trial registries up to date and conducting systematic reviews. PMID:25274020

A method for retrieving endodontic or atypical nonendodontic separated instruments from the root canal: a report of two cases.

PubMed

Monteiro, Jardel Camilo do Carmo; Kuga, Milton Carlos; Dantas, Andrea Abi Rached; Jordão-Basso, Keren Cristina Fagundes; Keine, Katia Cristina; Ruchaya, Prashant Jay; Faria, Gisele; Leonardo, Renato de Toledo

2014-11-01

This clinical report presents a new method for retrieving separated instruments from the root canal with minimally invasive procedures. The presence of separated instrument in root canal may interfere in the endodontic treatment prognosis. There are several recommended methods to retrieve separated instruments, but some are difficult in clinically practice. This study describes two cases of separated instrument removal from the root canal using a stainless-steel prepared needle associated with a K-file. Case 1 presented a fractured gutta-percha condenser within the mandibular second premolar, it was separated during incorrect intracanal medication calcium hydroxide placement. Case 2 had a fractured sewing needle within the upper central incisor that the patient used to remove food debris from the root canal. After cervical preparation, the fractured instruments were fitted inside a prepared needle and then an endodontic instrument (#25 K-file) was adapted with clockwise turning motion between the needle inner wall and the fragment. The endodontic or atypical nonendodontic separated instrument may be easily pull on of the root canal using a single and low cost device. The methods for retrieving separated instruments from root canal are difficult and destructive procedures. The present case describes a simple method to solve this problem.

Characterization of freshly retrieved preantral follicles using a low-invasive, mechanical isolation method extended to different ruminant species.

PubMed

Langbeen, A; Jorssen, E P A; Fransen, E; Rodriguez, A P A; García, M Chong; Leroy, J L M R; Bols, P E J

2015-10-01

Due to the increased interest in preantral follicular physiology, non-invasive retrieval and morphological classification are crucial. Therefore, this study aimed: (1) to standardize a minimally invasive isolation protocol, applicable to three ruminant species; (2) to morphologically classify preantral follicles upon retrieval; and (3) to describe morphological features of freshly retrieved follicles compared with follicle characteristics using invasive methods. Bovine, caprine and ovine ovarian cortex strips were retrieved from slaughterhouse ovaries and dispersed. This suspension was filtered, centrifuged, re-suspended and transferred to a Petri dish, to which 0.025 mg/ml neutral red (NR) was added to assess the viability of the isolated follicles. Between 59 and 191 follicles per follicle class and per species were collected and classified by light microscopy, based on follicular cell morphology. Subsequently, follicle diameters were measured. The proposed isolation protocol was applicable to all three species and showed a significant, expected increase in diameter with developmental stage. With an average diameter of 37 ± 5 μm for primordial follicles, 47 ± 6.3 μm for primary follicles and 67.1 ± 13.1 μm for secondary follicles, no significant difference in diameter among the three species was observed. Bovine, caprine and ovine follicles (63, 59 and 50% respectively) were graded as viable upon retrieval. Using the same morphological characteristics as determined by invasive techniques [e.g. haematoxylin-eosin (HE) sections], cumulus cell morphology and follicle diameter could be used routinely to classify freshly retrieved follicles. Finally, we applied a mechanical, minimally invasive, follicle isolation protocol and extended it to three ruminant species, yielding viable preantral follicles without compromising further in vitro processing and allowing routine follicle characterization upon retrieval.

Extraction of Cell-Wall Polysaccharide Antigen from Streptococci

PubMed Central

Slade, Hutton D.

1965-01-01

Slade, Hutton D. (Northwestern University Medical School, Chicago, Ill., and Max-Planck Institut für Immunbiologie, Freiburg, Germany). Extraction of cell-wall polysaccharide antigen from streptococci. J. Bacteriol. 90:667–672. 1965.—The carbohydrate grouping antigens in the cell walls of streptococci belonging to groups A, E, G, L, and T were extracted with 5% trichloroacetic acid at 90 C. The antigens were removed also from dry whole cells by extraction with trichloroacetic acid followed by treatment with phenol-water. Details of the methods are presented. The antigens obtained by use of either of these procedures were suitable for studies on immunological specificity and chemical structure. Quantitative enzymatic and chemical analyses of two group E antigens and one group T preparation showed the presence of l-rhamnose (22 to 44%), d-glucose (7 to 22%), d-galactose (T antigen only, 26%), glucosamine (2 to 16%), and galactosamine (T antigen only, 3%). In addition, analyses of A and G antigen preparations are presented. The protein and phosphate content of the A and E antigens were about 1% each. Quantitative precipitin curves of these antigens are presented. PMID:16562065

Automatic medical image annotation and keyword-based image retrieval using relevance feedback.

PubMed

Ko, Byoung Chul; Lee, JiHyeon; Nam, Jae-Yeal

2012-08-01

This paper presents novel multiple keywords annotation for medical images, keyword-based medical image retrieval, and relevance feedback method for image retrieval for enhancing image retrieval performance. For semantic keyword annotation, this study proposes a novel medical image classification method combining local wavelet-based center symmetric-local binary patterns with random forests. For keyword-based image retrieval, our retrieval system use the confidence score that is assigned to each annotated keyword by combining probabilities of random forests with predefined body relation graph. To overcome the limitation of keyword-based image retrieval, we combine our image retrieval system with relevance feedback mechanism based on visual feature and pattern classifier. Compared with other annotation and relevance feedback algorithms, the proposed method shows both improved annotation performance and accurate retrieval results.

Towards a true aerosol-and-cloud retrieval scheme

NASA Astrophysics Data System (ADS)

Thomas, Gareth; Poulsen, Caroline; Povey, Adam; McGarragh, Greg; Jerg, Matthias; Siddans, Richard; Grainger, Don

2014-05-01

The Optimal Retrieval of Aerosol and Cloud (ORAC) - formally the Oxford-RAL Aerosol and Cloud retrieval - offers a framework that can provide consistent and well characterised properties of both aerosols and clouds from a range of imaging satellite instruments. Several practical issues stand in the way of achieving the potential of this combined scheme however; in particular the sometimes conflicting priorities and requirements of aerosol and cloud retrieval problems, and the question of the unambiguous identification of aerosol and cloud pixels. This presentation will present recent developments made to the ORAC scheme for both aerosol and cloud, and detail how these are being integrated into a single retrieval framework. The implementation of a probabilistic method for pixel identification will also be presented, for both cloud detection and aerosol/cloud type selection. The method is based on Bayesian methods applied the optimal estimation retrieval output of ORAC and is particularly aimed at providing additional information in the so-called "twilight zone", where pixels can't be unambiguously identified as either aerosol or cloud and traditional cloud or aerosol products do not provide results.

EM-21 Retrieval Knowledge Center: Waste Retrieval Challenges

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

Fellinger, Andrew P.; Rinker, Michael W.; Berglin, Eric J.

EM-21 is the Waste Processing Division of the Office of Engineering and Technology, within the U.S. Department of Energy’s (DOE) Office of Environmental Management (EM). In August of 2008, EM-21 began an initiative to develop a Retrieval Knowledge Center (RKC) to provide the DOE, high level waste retrieval operators, and technology developers with centralized and focused location to share knowledge and expertise that will be used to address retrieval challenges across the DOE complex. The RKC is also designed to facilitate information sharing across the DOE Waste Site Complex through workshops, and a searchable database of waste retrieval technology information.more » The database may be used to research effective technology approaches for specific retrieval tasks and to take advantage of the lessons learned from previous operations. It is also expected to be effective for remaining current with state-of-the-art of retrieval technologies and ongoing development within the DOE Complex. To encourage collaboration of DOE sites with waste retrieval issues, the RKC team is co-led by the Savannah River National Laboratory (SRNL) and the Pacific Northwest National Laboratory (PNNL). Two RKC workshops were held in the Fall of 2008. The purpose of these workshops was to define top level waste retrieval functional areas, exchange lessons learned, and develop a path forward to support a strategic business plan focused on technology needs for retrieval. The primary participants involved in these workshops included retrieval personnel and laboratory staff that are associated with Hanford and Savannah River Sites since the majority of remaining DOE waste tanks are located at these sites. This report summarizes and documents the results of the initial RKC workshops. Technology challenges identified from these workshops and presented here are expected to be a key component to defining future RKC-directed tasks designed to facilitate tank waste retrieval solutions.« less

Cloud Property Retrieval Products for Graciosa Island, Azores

DOE Data Explorer

Dong, Xiquan

2014-05-05

The motivation for developing this product was to use the Dong et al. 1998 method to retrieve cloud microphysical properties, such as cloud droplet effective radius, cloud droplets number concentration, and optical thickness. These retrieved properties have been used to validate the satellite retrieval, and evaluate the climate simulations and reanalyses. We had been using this method to retrieve cloud microphysical properties over ARM SGP and NSA sites. We also modified the method for the AMF at Shouxian, China and some IOPs, e.g. ARM IOP at SGP in March, 2000. The ARSCL data from ARM data archive over the SGP and NSA have been used to determine the cloud boundary and cloud phase. For these ARM permanent sites, the ARSCL data was developed based on MMCR measurements, however, there were no data available at the Azores field campaign. We followed the steps to generate this derived product and also include the MPLCMASK cloud retrievals to determine the most accurate cloud boundaries, including the thin cirrus clouds that WACR may under-detect. We use these as input to retrieve the cloud microphysical properties. Due to the different temporal resolutions of the derived cloud boundary heights product and the cloud properties product, we submit them as two separate netcdf files.

A Method to Retrieve Rainfall Rate Over Land from TRMM Microwave Imager Observations

NASA Technical Reports Server (NTRS)

Prabhakara, C.; Iacovazzi, R., Jr.; Yoo, J.-M.; Lau, William K. M. (Technical Monitor)

2002-01-01

Over tropical land regions, rain rate maxima in mesoscale convective systems revealed by the Precipitation Radar (PR) flown on the Tropical Rainfall Measuring Mission (TRMM) satellite are found to correspond to thunderstorms, i.e., Cbs. These Cbs are reflected as minima in the 85 GHz brightness temperature, T85, observed by the TRMM Microwave Imager (TMI) radiometer. Because the magnitude of TMI observations do not discriminate satisfactorily convective and stratiform rain, we developed here a different TMI discrimination method. In this method, two types of Cbs, strong and weak, are inferred from the Laplacian of T85 at minima. Then, to retrieve rain rate, where T85 is less than 270 K, a weak (background) rain rate is deduced using T85 observations. Furthermore, over a circular area of 10 km radius centered at the location of each T85 minimum, an additional Cb component of rain rate is added to the background rain rate. This Cb component of rain rate is estimated with the help of (T19-T37) and T85 observations. Initially, our algorithm is calibrated with the PR rain rate measurements from 20 MCS rain events. After calibration, this method is applied to TMI data taken from several tropical land regions. With the help of the PR observations, we show that the spatial distribution and intensity of rain rate over land estimated from our algorithm are better than those given by the current TMI-Version-5 Algorithm. For this reason, our algorithm may be used to improve the current state of rain retrievals on land.

3D model retrieval method based on mesh segmentation

NASA Astrophysics Data System (ADS)

Gan, Yuanchao; Tang, Yan; Zhang, Qingchen

2012-04-01

In the process of feature description and extraction, current 3D model retrieval algorithms focus on the global features of 3D models but ignore the combination of global and local features of the model. For this reason, they show less effective performance to the models with similar global shape and different local shape. This paper proposes a novel algorithm for 3D model retrieval based on mesh segmentation. The key idea is to exact the structure feature and the local shape feature of 3D models, and then to compares the similarities of the two characteristics and the total similarity between the models. A system that realizes this approach was built and tested on a database of 200 objects and achieves expected results. The results show that the proposed algorithm improves the precision and the recall rate effectively.

Comparison of antigen-capture ELISA to stool-culture methods for the detection of asymptomatic Entamoeba species infection in Kafer Daoud, Egypt.

PubMed

Abd-Alla, M D; Wahib, A A; Ravdin, J I

2000-05-01

We performed a prospective field study in the village of Kafer Daoud in Menofia, Egypt to compare the fecal culture method with enzyme linked immuno assay (ELISA) for detection of 170 kDa lectin antigen in feces for diagnosis of asymptomatic Entamoeba histolytica and Entamoeba dispar infection. All subjects with E. histolytica or E. dispar infection detected by culture also had positive ELISA for amebic antigen in their feces and an additional 57 Entameoba infections missed by culture were detected by ELISA (P < 0.001 compared to culture). The presence of fecal anti-lectin IgA antibodies and serum anti-LC3 (recombinant cysteine-rich lectin protein) IgG antibodies were positive predictors for E. histolytica infection (P < 0.03). Of interest, infection with Trichomonas hominis but not Blastocystis hominis was positively associated with E. histolytica infection (P < 0.05). In conclusion, ELISA for detection of fecal lectin antigen is a more sensitive method than fecal culture for detecting asymptomatic E. histolytica infection.

SIFT Meets CNN: A Decade Survey of Instance Retrieval.

PubMed

Zheng, Liang; Yang, Yi; Tian, Qi

2018-05-01

In the early days, content-based image retrieval (CBIR) was studied with global features. Since 2003, image retrieval based on local descriptors (de facto SIFT) has been extensively studied for over a decade due to the advantage of SIFT in dealing with image transformations. Recently, image representations based on the convolutional neural network (CNN) have attracted increasing interest in the community and demonstrated impressive performance. Given this time of rapid evolution, this article provides a comprehensive survey of instance retrieval over the last decade. Two broad categories, SIFT-based and CNN-based methods, are presented. For the former, according to the codebook size, we organize the literature into using large/medium-sized/small codebooks. For the latter, we discuss three lines of methods, i.e., using pre-trained or fine-tuned CNN models, and hybrid methods. The first two perform a single-pass of an image to the network, while the last category employs a patch-based feature extraction scheme. This survey presents milestones in modern instance retrieval, reviews a broad selection of previous works in different categories, and provides insights on the connection between SIFT and CNN-based methods. After analyzing and comparing retrieval performance of different categories on several datasets, we discuss promising directions towards generic and specialized instance retrieval.

Quantitative immunohistochemistry of factor VIII-related antigen in breast carcinoma: a comparison of computer-assisted image analysis with established counting methods.

PubMed

Kohlberger, P D; Obermair, A; Sliutz, G; Heinzl, H; Koelbl, H; Breitenecker, G; Gitsch, G; Kainz, C

1996-06-01

Microvessel density in the area of the most intense neovascularization in invasive breast carcinoma is reported to be an independent prognostic factor. The established method of enumeration of microvessel density is to count the vessels using an ocular raster (counted microvessel density [CMVD]). The vessels were detected by staining endothelial cells using Factor VIII-related antigen. The aim of the study was to compare the CMVD results with the percentage of factor VIII-related antigen-stained area using computer-assisted image analysis. A true color red-green-blue (RGB) image analyzer based on a morphologically reduced instruction set computer processor was used to evaluate the area of stained endothelial cells. Sixty invasive breast carcinomas were included in the analysis. There was no significant correlation between the CMVD and the percentage of factor VIII-related antigen-stained area (Spearman correlation coefficient = 0.24, confidence interval = 0.02-0.46). Although high CMVD was significantly correlated with poorer recurrence free survival (P = .024), percentage of factor VIII-related antigen-stained area showed no prognostic value. Counted microvessel density and percentage of factor VIII-related antigen-stained area showed a highly significant correlation with vessel invasion (P = .0001 and P = .02, respectively). There was no correlation between CMVD and percentage of factor VIII-related antigen-stained area with other prognostic factors. In contrast to the CMVD within malignant tissue, the percentage of factor VIII-related antigen-stained area is not suitable as an indicator of prognosis in breast cancer patients.

Automatic evidence retrieval for systematic reviews.

PubMed

Choong, Miew Keen; Galgani, Filippo; Dunn, Adam G; Tsafnat, Guy

2014-10-01

Snowballing involves recursively pursuing relevant references cited in the retrieved literature and adding them to the search results. Snowballing is an alternative approach to discover additional evidence that was not retrieved through conventional search. Snowballing's effectiveness makes it best practice in systematic reviews despite being time-consuming and tedious. Our goal was to evaluate an automatic method for citation snowballing's capacity to identify and retrieve the full text and/or abstracts of cited articles. Using 20 review articles that contained 949 citations to journal or conference articles, we manually searched Microsoft Academic Search (MAS) and identified 78.0% (740/949) of the cited articles that were present in the database. We compared the performance of the automatic citation snowballing method against the results of this manual search, measuring precision, recall, and F1 score. The automatic method was able to correctly identify 633 (as proportion of included citations: recall=66.7%, F1 score=79.3%; as proportion of citations in MAS: recall=85.5%, F1 score=91.2%) of citations with high precision (97.7%), and retrieved the full text or abstract for 490 (recall=82.9%, precision=92.1%, F1 score=87.3%) of the 633 correctly retrieved citations. The proposed method for automatic citation snowballing is accurate and is capable of obtaining the full texts or abstracts for a substantial proportion of the scholarly citations in review articles. By automating the process of citation snowballing, it may be possible to reduce the time and effort of common evidence surveillance tasks such as keeping trial registries up to date and conducting systematic reviews.

Ovarian tumor antigens.

PubMed

Bhattacharya, M; Barlow, J J

1978-09-01

Evidence has been reported for at least two common tumor-associated antigens, or antigenic determinants, in human cystadenocarcinomas of the ovary that are apparently absent in tissues of normal reproductive organs. These antigenic determinants are immunologically distinct from carcinoembryonic antigen, alpha-fetoprotein, ferritins and histocompatibility antigens. One of these two ovarian cystadenocarcinoma-associated antigens (OCAA) is not detectable in any ovarian carcinomas except serous or mucinous types, other gynecologic or nongynecologic malignancies thus far tested, while the second antigen is present in about 90% of all gynecologic tumors and occasionally in breast and colon tumors. OCAA has been purified and partially characterized. It is a high molecular weight glycoprotein which carries the unique ovarian tumor-specific antigenic determinant along with some normal cross-reacting determinants. High levels of this glycoprotein antigen have been detected in the sera of ovarian cancer patients with advanced disease by the radioimmunoassay inhibition technique. The serial determination of circulating OCAA appeared to correlate with tumor volume as well as the clinical status of the patients.

Retrieval of constituent mixing ratios from limb thermal emission spectra

NASA Technical Reports Server (NTRS)

Shaffer, William A.; Kunde, Virgil G.; Conrath, Barney J.

1988-01-01

An onion-peeling iterative, least-squares relaxation method to retrieve mixing ratio profiles from limb thermal emission spectra is presented. The method has been tested on synthetic data, containing various amounts of added random noise for O3, HNO3, and N2O. The retrieval method is used to obtain O3 and HNO3 mixing ratio profiles from high-resolution thermal emission spectra. Results of the retrievals compare favorably with those obtained previously.

Retrieval of the scattering and microphysical properties of aerosols from ground-based optical measurements including polarization. I. Method.

PubMed

Vermeulen, A; Devaux, C; Herman, M

2000-11-20

A method has been developed for retrieving the scattering and microphysical properties of atmospheric aerosol from measurements of solar transmission, aureole, and angular distribution of the scattered and polarized sky light in the solar principal plane. Numerical simulations of measurements have been used to investigate the feasibility of the method and to test the algorithm's performance. It is shown that the absorption and scattering properties of an aerosol, i.e., the single-scattering albedo, the phase function, and the polarization for single scattering of incident unpolarized light, can be obtained by use of radiative transfer calculations to correct the values of scattered radiance and polarized radiance for multiple scattering, Rayleigh scattering, and the influence of ground. The method requires only measurement of the aerosol's optical thickness and an estimate of the ground's reflectance and does not need any specific assumption about properties of the aerosol. The accuracy of the retrieved phase function and polarization of the aerosols is examined at near-infrared wavelengths (e.g., 0.870 mum). The aerosol's microphysical properties (size distribution and complex refractive index) are derived in a second step. The real part of the refractive index is a strong function of the polarization, whereas the imaginary part is strongly dependent on the sky's radiance and the retrieved single-scattering albedo. It is demonstrated that inclusion of polarization data yields the real part of the refractive index.

3D object retrieval using salient views

PubMed Central

Shapiro, Linda G.

2013-01-01

This paper presents a method for selecting salient 2D views to describe 3D objects for the purpose of retrieval. The views are obtained by first identifying salient points via a learning approach that uses shape characteristics of the 3D points (Atmosukarto and Shapiro in International workshop on structural, syntactic, and statistical pattern recognition, 2008; Atmosukarto and Shapiro in ACM multimedia information retrieval, 2008). The salient views are selected by choosing views with multiple salient points on the silhouette of the object. Silhouette-based similarity measures from Chen et al. (Comput Graph Forum 22(3):223–232, 2003) are then used to calculate the similarity between two 3D objects. Retrieval experiments were performed on three datasets: the Heads dataset, the SHREC2008 dataset, and the Princeton dataset. Experimental results show that the retrieval results using the salient views are comparable to the existing light field descriptor method (Chen et al. in Comput Graph Forum 22(3):223–232, 2003), and our method achieves a 15-fold speedup in the feature extraction computation time. PMID:23833704

A simplified immunoprecipitation method for quantitatively measuring antibody responses in clinical sera samples by using mammalian-produced Renilla luciferase-antigen fusion proteins.

PubMed

Burbelo, Peter D; Goldman, Radoslav; Mattson, Thomas L

2005-08-18

Assays detecting human antigen-specific antibodies are medically useful. However, the usefulness of existing simple immunoassay formats is limited by technical considerations such as sera antibodies to contaminants in insufficiently pure antigen, a problem likely exacerbated when antigen panels are screened to obtain clinically useful data. We developed a novel and simple immunoprecipitation technology for identifying clinical sera containing antigen-specific antibodies and for generating quantitative antibody response profiles. This method is based on fusing protein antigens to an enzyme reporter, Renilla luciferase (Ruc), and expressing these fusions in mammalian cells, where mammalian-specific post-translational modifications can be added. After mixing crude extracts, sera and protein A/G beads together and incubating, during which the Ruc-antigen fusion become immobilized on the A/G beads, antigen-specific antibody is quantitated by washing the beads and adding coelenterazine substrate and measuring light production. We have characterized this technology with sera from patients having three different types of cancers. We show that 20-85% of these sera contain significant titers of antibodies against at least one of five frequently mutated and/or overexpressed tumor-associated proteins. Five of six colon cancer sera tested gave responses that were statistically significantly greater than the average plus three standard deviations of 10 control sera. The results of competition experiments, preincubating positive sera with unmodified E. coli-produced antigens, varied dramatically. This technology has several advantages over current quantitative immunoassays including its relative simplicity, its avoidance of problems associated with E. coli-produced antigens and its use of antigens that can carry mammalian or disease-specific post-translational modifications. This assay should be generally useful for analyzing sera for antibodies recognizing any protein or its

A simplified immunoprecipitation method for quantitatively measuring antibody responses in clinical sera samples by using mammalian-produced Renilla luciferase-antigen fusion proteins

PubMed Central

Burbelo, Peter D; Goldman, Radoslav; Mattson, Thomas L

2005-01-01

Background Assays detecting human antigen-specific antibodies are medically useful. However, the usefulness of existing simple immunoassay formats is limited by technical considerations such as sera antibodies to contaminants in insufficiently pure antigen, a problem likely exacerbated when antigen panels are screened to obtain clinically useful data. Results We developed a novel and simple immunoprecipitation technology for identifying clinical sera containing antigen-specific antibodies and for generating quantitative antibody response profiles. This method is based on fusing protein antigens to an enzyme reporter, Renilla luciferase (Ruc), and expressing these fusions in mammalian cells, where mammalian-specific post-translational modifications can be added. After mixing crude extracts, sera and protein A/G beads together and incubating, during which the Ruc-antigen fusion become immobilized on the A/G beads, antigen-specific antibody is quantitated by washing the beads and adding coelenterazine substrate and measuring light production. We have characterized this technology with sera from patients having three different types of cancers. We show that 20–85% of these sera contain significant titers of antibodies against at least one of five frequently mutated and/or overexpressed tumor-associated proteins. Five of six colon cancer sera tested gave responses that were statistically significantly greater than the average plus three standard deviations of 10 control sera. The results of competition experiments, preincubating positive sera with unmodified E. coli-produced antigens, varied dramatically. Conclusion This technology has several advantages over current quantitative immunoassays including its relative simplicity, its avoidance of problems associated with E. coli-produced antigens and its use of antigens that can carry mammalian or disease-specific post-translational modifications. This assay should be generally useful for analyzing sera for antibodies

Retrieval practice is an efficient method of enhancing the retention of anatomy and physiology information.

PubMed

Dobson, John L

2013-06-01

Although a great deal of empirical evidence has indicated that retrieval practice is an effective means of promoting learning and memory, very few studies have investigated the strategy in the context of an actual class. The primary purpose of this study was to determine if a series of very brief retrieval quizzes could significantly improve the retention of previously tested information throughout an anatomy and physiology course. A second purpose was to determine if there were any significant differences between expanding and uniform patterns of retrieval that followed a standardized initial retrieval delay. Anatomy and physiology students were assigned to either a control group or groups that were repeatedly prompted to retrieve a subset of previously tested course information via a series of quizzes that were administered on either an expanding or a uniform schedule. Each retrieval group completed a total of 10 retrieval quizzes, and the series of quizzes required (only) a total of 2 h to complete. Final retention of the exam subset material was assessed during the last week of the semester. There were no significant differences between the expanding and uniform retrieval groups, but both retained an average of 41% more of the subset material than did the control group (ANOVA, F = 129.8, P = 0.00, ηp(2) = 0.36). In conclusion, retrieval practice is a highly efficient and effective strategy for enhancing the retention of anatomy and physiology material.

Phase retrieval by coherent modulation imaging

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

Zhang, Fucai; Chen, Bo; Morrison, Graeme R.

Phase retrieval is a long-standing problem in imaging when only the intensity of the wavefield can be recorded. Coherent diffraction imaging (CDI) is a lensless technique that uses iterative algorithms to recover amplitude and phase contrast images from diffraction intensity data. For general samples, phase retrieval from a single diffraction pattern has been an algorithmic and experimental challenge. Here we report a method of phase retrieval that uses a known modulation of the sample exit-wave. This coherent modulation imaging (CMI) method removes inherent ambiguities of CDI and uses a reliable, rapidly converging iterative algorithm involving three planes. It works formore » extended samples, does not require tight support for convergence, and relaxes dynamic range requirements on the detector. CMI provides a robust method for imaging in materials and biological science, while its single-shot capability will benefit the investigation of dynamical processes with pulsed sources, such as X-ray free electron laser.« less

Phase retrieval by coherent modulation imaging

DOE PAGES

Zhang, Fucai; Chen, Bo; Morrison, Graeme R.; ...

2016-11-18

Phase retrieval is a long-standing problem in imaging when only the intensity of the wavefield can be recorded. Coherent diffraction imaging (CDI) is a lensless technique that uses iterative algorithms to recover amplitude and phase contrast images from diffraction intensity data. For general samples, phase retrieval from a single diffraction pattern has been an algorithmic and experimental challenge. Here we report a method of phase retrieval that uses a known modulation of the sample exit-wave. This coherent modulation imaging (CMI) method removes inherent ambiguities of CDI and uses a reliable, rapidly converging iterative algorithm involving three planes. It works formore » extended samples, does not require tight support for convergence, and relaxes dynamic range requirements on the detector. CMI provides a robust method for imaging in materials and biological science, while its single-shot capability will benefit the investigation of dynamical processes with pulsed sources, such as X-ray free electron laser.« less

Phase retrieval by coherent modulation imaging.

PubMed

Zhang, Fucai; Chen, Bo; Morrison, Graeme R; Vila-Comamala, Joan; Guizar-Sicairos, Manuel; Robinson, Ian K

2016-11-18

Phase retrieval is a long-standing problem in imaging when only the intensity of the wavefield can be recorded. Coherent diffraction imaging is a lensless technique that uses iterative algorithms to recover amplitude and phase contrast images from diffraction intensity data. For general samples, phase retrieval from a single-diffraction pattern has been an algorithmic and experimental challenge. Here we report a method of phase retrieval that uses a known modulation of the sample exit wave. This coherent modulation imaging method removes inherent ambiguities of coherent diffraction imaging and uses a reliable, rapidly converging iterative algorithm involving three planes. It works for extended samples, does not require tight support for convergence and relaxes dynamic range requirements on the detector. Coherent modulation imaging provides a robust method for imaging in materials and biological science, while its single-shot capability will benefit the investigation of dynamical processes with pulsed sources, such as X-ray free-electron lasers.

Functional-anatomic study of episodic retrieval using fMRI. I. Retrieval effort versus retrieval success.

PubMed

Buckner, R L; Koutstaal, W; Schacter, D L; Wagner, A D; Rosen, B R

1998-04-01

A number of recent functional imaging studies have identified brain areas activated during tasks involving episodic memory retrieval. The identification of such areas provides a foundation for targeted hypotheses regarding the more specific contributions that these areas make to episodic retrieval. As a beginning effort toward such an endeavor, whole-brain functional magnetic resonance imaging (fMRI) was used to examine 14 subjects during episodic word recognition in a block-designed fMRI experiment. Study conditions were manipulated by presenting either shallow or deep encoding tasks. This manipulation yielded two recognition conditions that differed with regard to retrieval effort and retrieval success: shallow encoding yielded low levels of recognition success with high levels of retrieval effort, and deep encoding yielded high levels of recognition success with low levels of effort. Many brain areas were activated in common by these two recognition conditions compared to a low-level fixation condition, including left and right prefrontal regions often detected during PET episodic retrieval paradigms (e.g., R. L. Buckner et al., 1996, J. Neurosci. 16, 6219-6235) thereby generalizing these findings to fMRI. Characterization of the activated regions in relation to the separate recognition conditions showed (1) bilateral anterior insular regions and a left dorsal prefrontal region were more active after shallow encoding, when retrieval demanded greatest effort, and (2) right anterior prefrontal cortex, which has been implicated in episodic retrieval, was most active during successful retrieval after deep encoding. We discuss these findings in relation to component processes involved in episodic retrieval and in the context of a companion study using event-related fMRI.

Method for utilizing properties of the sinc(x) function for phase retrieval on nyquist-under-sampled data

NASA Technical Reports Server (NTRS)

Dean, Bruce H. (Inventor); Smith, Jeffrey Scott (Inventor); Aronstein, David L. (Inventor)

2012-01-01

Disclosed herein are systems, methods, and non-transitory computer-readable storage media for simulating propagation of an electromagnetic field, performing phase retrieval, or sampling a band-limited function. A system practicing the method generates transformed data using a discrete Fourier transform which samples a band-limited function f(x) without interpolating or modifying received data associated with the function f(x), wherein an interval between repeated copies in a periodic extension of the function f(x) obtained from the discrete Fourier transform is associated with a sampling ratio Q, defined as a ratio of a sampling frequency to a band-limited frequency, and wherein Q is assigned a value between 1 and 2 such that substantially no aliasing occurs in the transformed data, and retrieves a phase in the received data based on the transformed data, wherein the phase is used as feedback to an optical system.

Chemoselective ligation and antigen vectorization.

PubMed

Gras-Masse, H

2001-01-01

The interest in cocktail-lipopeptide vaccines has now been confirmed by phase I clinical trials: highly diversified B-, T-helper or cytotoxic T-cell epitopes can be combined with a lipophilic vector for the induction of B- and T-cell responses of predetermined specificity. With the goal of producing an improved vaccine that should ideally induce a multispecific response in non-selected populations, increasing the diversity of the immunizing mixture represents one of the most obvious strategies.The selective delivery of antigens to professional antigen-presenting cells represents another promising approach for the improvement of vaccine efficacy. In this context, the mannose-receptor represents an attractive entry point for the targeting to dendritic cells of antigens linked to clustered glycosides or glycomimetics. In all cases, highly complex but fully characterized molecules must be produced. To develop a modular and flexible strategy which could be generally applicable to a large set of peptide antigens, we elected to explore the potentialities of chemoselective ligation methods. The hydrazone bond was found particularly reliable and fully compatible with sulphide ligation. Hydrazone/thioether orthogonal ligation systems could be developed to account for the nature of the antigens and the solubility of the vector systems. Copyright 2001 The International Association for Biologicals.

Development of the ECODAB into a relational database for Escherichia coli O-antigens and other bacterial polysaccharides.

PubMed

Rojas-Macias, Miguel A; Ståhle, Jonas; Lütteke, Thomas; Widmalm, Göran

2015-03-01

Escherichia coli O-antigen database (ECODAB) is a web-based application to support the collection of E. coli O-antigen structures, polymerase and flippase amino acid sequences, NMR chemical shift data of O-antigens as well as information on glycosyltransferases (GTs) involved in the assembly of O-antigen polysaccharides. The database content has been compiled from scientific literature. Furthermore, the system has evolved from being a repository to one that can be used for generating novel data on its own. GT specificity is suggested through sequence comparison with GTs whose function is known. The migration of ECODAB to a relational database has allowed the automation of all processes to update, retrieve and present information, thereby, endowing the system with greater flexibility and improved overall performance. ECODAB is freely available at http://www.casper.organ.su.se/ECODAB/. Currently, data on 169 E. coli unique O-antigen entries and 338 GTs is covered. Moreover, the scope of the database has been extended so that polysaccharide structure and related information from other bacteria subsequently can be added, for example, from Streptococcus pneumoniae. © The Author 2014. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

A humming retrieval system based on music fingerprint

NASA Astrophysics Data System (ADS)

Han, Xingkai; Cao, Baiyu

2011-10-01

In this paper, we proposed an improved music information retrieval method utilizing the music fingerprint. The goal of this method is to represent the music with compressed musical information. Based on the selected MIDI files, which are generated automatically as our music target database, we evaluate the accuracy, effectiveness, and efficiency of this method. In this research we not only extract the feature sequence, which can represent the file effectively, from the query and melody database, but also make it possible for retrieving the results in an innovative way. We investigate on the influence of noise to the performance of our system. As experimental result shows, the retrieval accuracy arriving at up to91% without noise is pretty well

Generating region proposals for histopathological whole slide image retrieval.

PubMed

Ma, Yibing; Jiang, Zhiguo; Zhang, Haopeng; Xie, Fengying; Zheng, Yushan; Shi, Huaqiang; Zhao, Yu; Shi, Jun

2018-06-01

Content-based image retrieval is an effective method for histopathological image analysis. However, given a database of huge whole slide images (WSIs), acquiring appropriate region-of-interests (ROIs) for training is significant and difficult. Moreover, histopathological images can only be annotated by pathologists, resulting in the lack of labeling information. Therefore, it is an important and challenging task to generate ROIs from WSI and retrieve image with few labels. This paper presents a novel unsupervised region proposing method for histopathological WSI based on Selective Search. Specifically, the WSI is over-segmented into regions which are hierarchically merged until the WSI becomes a single region. Nucleus-oriented similarity measures for region mergence and Nucleus-Cytoplasm color space for histopathological image are specially defined to generate accurate region proposals. Additionally, we propose a new semi-supervised hashing method for image retrieval. The semantic features of images are extracted with Latent Dirichlet Allocation and transformed into binary hashing codes with Supervised Hashing. The methods are tested on a large-scale multi-class database of breast histopathological WSIs. The results demonstrate that for one WSI, our region proposing method can generate 7.3 thousand contoured regions which fit well with 95.8% of the ROIs annotated by pathologists. The proposed hashing method can retrieve a query image among 136 thousand images in 0.29 s and reach precision of 91% with only 10% of images labeled. The unsupervised region proposing method can generate regions as predictions of lesions in histopathological WSI. The region proposals can also serve as the training samples to train machine-learning models for image retrieval. The proposed hashing method can achieve fast and precise image retrieval with small amount of labels. Furthermore, the proposed methods can be potentially applied in online computer-aided-diagnosis systems. Copyright

A Ground Flash Fraction Retrieval Algorithm for GLM

NASA Technical Reports Server (NTRS)

Koshak, William J.

2010-01-01

A Bayesian inversion method is introduced for retrieving the fraction of ground flashes in a set of N lightning observed by a satellite lightning imager (such as the Geostationary Lightning Mapper, GLM). An exponential model is applied as a physically reasonable constraint to describe the measured lightning optical parameter distributions. Population statistics (i.e., the mean and variance) are invoked to add additional constraints to the retrieval process. The Maximum A Posteriori (MAP) solution is employed. The approach is tested by performing simulated retrievals, and retrieval error statistics are provided. The approach is feasible for N greater than 2000, and retrieval errors decrease as N is increased.

Compact binary hashing for music retrieval

NASA Astrophysics Data System (ADS)

Seo, Jin S.

2014-03-01

With the huge volume of music clips available for protection, browsing, and indexing, there is an increased attention to retrieve the information contents of the music archives. Music-similarity computation is an essential building block for browsing, retrieval, and indexing of digital music archives. In practice, as the number of songs available for searching and indexing is increased, so the storage cost in retrieval systems is becoming a serious problem. This paper deals with the storage problem by extending the supervector concept with the binary hashing. We utilize the similarity-preserving binary embedding in generating a hash code from the supervector of each music clip. Especially we compare the performance of the various binary hashing methods for music retrieval tasks on the widely-used genre dataset and the in-house singer dataset. Through the evaluation, we find an effective way of generating hash codes for music similarity estimation which improves the retrieval performance.

Prediction of site-specific interactions in antibody-antigen complexes: the proABC method and server.

PubMed

Olimpieri, Pier Paolo; Chailyan, Anna; Tramontano, Anna; Marcatili, Paolo

2013-09-15

Antibodies or immunoglobulins are proteins of paramount importance in the immune system. They are extremely relevant as diagnostic, biotechnological and therapeutic tools. Their modular structure makes it easy to re-engineer them for specific purposes. Short of undergoing a trial and error process, these experiments, as well as others, need to rely on an understanding of the specific determinants of the antibody binding mode. In this article, we present a method to identify, on the basis of the antibody sequence alone, which residues of an antibody directly interact with its cognate antigen. The method, based on the random forest automatic learning techniques, reaches a recall and specificity as high as 80% and is implemented as a free and easy-to-use server, named prediction of Antibody Contacts. We believe that it can be of great help in re-design experiments as well as a guide for molecular docking experiments. The results that we obtained also allowed us to dissect which features of the antibody sequence contribute most to the involvement of specific residues in binding to the antigen. http://www.biocomputing.it/proABC. anna.tramontano@uniroma1.it or paolo.marcatili@gmail.com Supplementary data are available at Bioinformatics online.

Are retrievable vena cava filters placed in trauma patients really retrievable?

PubMed

Leeper, W R; Murphy, P B; Vogt, K N; Leeper, T J; Kribs, S W; Gray, D K; Parry, N G

2016-08-01

Concerns have arisen regarding the use of retrievable inferior vena cava filters (rIVCFs) in trauma patients due to increasing reports of low retrieval rates. We hypothesized that complete follow-up with a dedicated trauma nurse practitioner would be associated with a higher rate of retrievability. This study was undertaken to determine the rate of retrievability of rIVCFs placed in a Canadian Lead Trauma Centre, and to compare the rate of retrievability in our trauma population to our non-trauma patients. We performed a retrospective cohort study of all patients with rIVCF placed between Jan 1 2000 and June 30 2014. Data were collected on demographics, indication for filter placement, retrieval status, and reasons for non-retrieval. Comparison was made between trauma patients and non-trauma patients. A total of 374 rIVCFs were placed (61 in trauma patients and 313 in non-trauma patients) and follow-up was complete for the entire cohort. Filter retrieval was achieved in 86.9 % of trauma patients. Reasons for non-retrieval were technical in two patients, and death before retrieval in six patients. Retrieval was successful in 48.9 % of non-trauma patients. This study demonstrates that rIVCFs can be successfully retrieved amongst trauma patients. We demonstrated a higher rate of successful retrieval amongst trauma patients than non-trauma patients in our institution. Careful patient follow-up may play a role in successful retrieval of rIVCFs.

Mapping epitopes and antigenicity by site-directed masking

NASA Astrophysics Data System (ADS)

Paus, Didrik; Winter, Greg

2006-06-01

Here we describe a method for mapping the binding of antibodies to the surface of a folded antigen. We first created a panel of mutant antigens (-lactamase) in which single surface-exposed residues were mutated to cysteine. We then chemically tethered the cysteine residues to a solid phase, thereby masking a surface patch centered on each cysteine residue and blocking the binding of antibodies to this region of the surface. By these means we mapped the epitopes of several mAbs directed to -lactamase. Furthermore, by depleting samples of polyclonal antisera to the masked antigens and measuring the binding of each depleted sample of antisera to unmasked antigen, we mapped the antigenicity of 23 different epitopes. After immunization of mice and rabbits with -lactamase in Freund's adjuvant, we found that the antisera reacted with both native and denatured antigen and that the antibody response was mainly directed to an exposed and flexible loop region of the native antigen. By contrast, after immunization in PBS, we found that the antisera reacted only weakly with denatured antigen and that the antibody response was more evenly distributed over the antigenic surface. We suggest that denatured antigen (created during emulsification in Freund's adjuvant) elicits antibodies that bind mainly to the flexible regions of the native protein and that this explains the correlation between antigenicity and backbone flexibility. Denaturation of antigen during vaccination or natural infections would therefore be expected to focus the antibody response to the flexible loops. backbone flexibility | Freund's adjuvant | conformational epitope | antisera

Impact of antigenic exposures and role of molecular blood grouping in enhancing transfusion safety in chronically transfused thalassemics.

PubMed

Makroo, Raj Nath; Agrawal, Soma; Bhatia, Aakanksha; Chowdhry, Mohit; Thakur, Uday Kumar

2016-01-01

Red cell alloimmunization is an acknowledged complication of blood transfusion. Current transfusion practices for thalassemia do not cater to this risk. Serological phenotyping is usually not reliable in these cases unless performed before the first transfusion. Under such circumstances, molecular blood grouping is an effective alternative. To perform molecular blood group genotyping in chronically transfused thalassemia patients and assess the risk of antigenic exposure and incidence of alloimmunization with current transfusion protocols. Molecular blood group genotyping was performed for 47 chronically transfused thalassemia patients. Their 1-year transfusion records were retrieved to assess the antigenic exposure and the frequency thereof. Of 47 patients, 6 were already alloimmunized (3 with anti-E and 3 with anti-K) and were receiving the corresponding antigen negative units. We observed that random selection of ABO and Rh D matched units resulted in 57.7% ±8.26% chance of Rh and Kell phenotype matching also. Forty-four patients had received one or more antigenic exposures at least once. The 6 already alloimmunized patients were further exposed to antigens other than the ones they were immunized to. During the study period, only one patient developed an alloantibody, anti-E with exposure to antigens C (92%) and/or E (32%) at each transfusion. Several factors apart from mere antigen exposure may influence the development of alloimmunization as most of our patients received antigenic exposures but not alloimmunized. Our data provide an impetus for future large-scale studies to understand the development of alloimmunization in such patients.

Selective memory retrieval can impair and improve retrieval of other memories.

PubMed

Bäuml, Karl-Heinz T; Samenieh, Anuscheh

2012-03-01

Research from the past decades has shown that retrieval of a specific memory (e.g., retrieving part of a previous vacation) typically attenuates retrieval of other memories (e.g., memories for other details of the event), causing retrieval-induced forgetting. More recently, however, it has been shown that retrieval can both attenuate and aid recall of other memories (K.-H. T. Bäuml & A. Samenieh, 2010). To identify the circumstances under which retrieval aids recall, the authors examined retrieval dynamics in listwise directed forgetting, context-dependent forgetting, proactive interference, and in the absence of any induced memory impairment. They found beneficial effects of selective retrieval in listwise directed forgetting and context-dependent forgetting but detrimental effects in all the other conditions. Because context-dependent forgetting and listwise directed forgetting arguably reflect impaired context access, the results suggest that memory retrieval aids recall of memories that are subject to impaired context access but attenuates recall in the absence of such circumstances. The findings are consistent with a 2-factor account of memory retrieval and suggest the existence of 2 faces of memory retrieval. 2012 APA, all rights reserved

Frequency of DEA 1 antigen in 1037 mongrel and PUREBREED dogs in ITALY.

PubMed

Carli, E; Carminato, A; Ravagnan, S; Capello, K; Antognoni, M T; Miglio, A; Furlanello, T; Proverbio, D; Spada, E; Stefani, A; Mutinelli, F; Vascellari, M

2017-11-29

The prevalence of dog erythrocyte antigen (DEA 1) in canine population is approximately 40-60%. Often data are limited to a small number of breeds and/or dogs. The aims of this study were to evaluate frequency of DEA 1 in a large population of purebred and mongrel dogs including Italian native breeds and to recognize a possible association between DEA 1 and breed, sex, and genetic and phenotypical/functional classifications of breeds. Frequencies of DEA 1 blood group collected from screened/enrolled blood donors and from healthy and sick dogs were retrospectively evaluated. The breed and the sex were recorded when available. DEA 1 blood typing was assessed by immunocromatographic test on K3EDTA blood samples. The prevalence of DEA 1 antigen was statistically related to breed, gender, Fédération Cynologique Internationale (FCI) and genotypic grouping. Sixty-two per cent dogs resulted DEA 1+ and 38% DEA 1-. DEA 1- was statistically associated with Dogo Argentino, Dobermann, German Shepherd, Boxer, Corso dogs, the molossian dogs, the FCI group 1, 2 and 3 and the genetic groups "working dogs" and "mastiff". DEA 1+ was statistically associated with Rottweiler, Briquet Griffon Vendéen, Bernese mountain dog, Golden Retriever, the hunting breeds, the FCI group 4, 6, 7 and 8 and the genetic groups "scent hounds" and "retrievers". No gender association was observed. Data obtained by this work may be clinically useful to drive blood donor enrollment and selection among different breeds.

Robust phase retrieval of complex-valued object in phase modulation by hybrid Wirtinger flow method

NASA Astrophysics Data System (ADS)

Wei, Zhun; Chen, Wen; Yin, Tiantian; Chen, Xudong

2017-09-01

This paper presents a robust iterative algorithm, known as hybrid Wirtinger flow (HWF), for phase retrieval (PR) of complex objects from noisy diffraction intensities. Numerical simulations indicate that the HWF method consistently outperforms conventional PR methods in terms of both accuracy and convergence rate in multiple phase modulations. The proposed algorithm is also more robust to low oversampling ratios, loose constraints, and noisy environments. Furthermore, compared with traditional Wirtinger flow, sample complexity is largely reduced. It is expected that the proposed HWF method will find applications in the rapidly growing coherent diffractive imaging field for high-quality image reconstruction with multiple modulations, as well as other disciplines where PR is needed.

Combination of DNA-based and conventional methods to detect human leukocyte antigen polymorphism and its use for paternity testing.

PubMed

Kereszturya, László; Rajczya, Katalin; Lászikb, András; Gyódia, Eva; Pénzes, Mária; Falus, András; Petrányia, Gyõzõ G

2002-03-01

In cases of disputed paternity, the scientific goal is to promote either the exclusion of a falsely accused man or the affiliation of the alleged father. Until now, in addition to anthropologic characteristics, the determination of genetic markers included human leukocyte antigen gene variants; erythrocyte antigens and serum proteins were used for that reason. Recombinant DNA techniques provided a new set of highly variable genetic markers based on DNA nucleotide sequence polymorphism. From the practical standpoint, the application of these techniques to paternity testing provides greater versatility than do conventional genetic marker systems. The use of methods to detect the polymorphism of human leukocyte antigen loci significantly increases the chance of validation of ambiguous results in paternity testing. The outcome of 2384 paternity cases investigated by serologic and/or DNA-based human leukocyte antigen typing was statistically analyzed. Different cases solved by DNA typing are presented involving cases with one or two accused men, exclusions and nonexclusions, and tests of the paternity of a deceased man. The results provide evidence for the advantage of the combined application of various techniques in forensic diagnostics and emphasizes the outstanding possibilities of DNA-based assays. Representative examples demonstrate the strength of combined techniques in paternity testing.

A framework for quantifying the impacts of sub-pixel reflectance variance and covariance on cloud optical thickness and effective radius retrievals based on the bi-spectral method

NASA Astrophysics Data System (ADS)

Zhang, Z.; Werner, F.; Cho, H.-M.; Wind, G.; Platnick, S.; Ackerman, A. S.; Di Girolamo, L.; Marshak, A.; Meyer, Kerry

2017-02-01

The so-called bi-spectral method retrieves cloud optical thickness (τ) and cloud droplet effective radius (re) simultaneously from a pair of cloud reflectance observations, one in a visible or near infrared (VIS/NIR) band and the other in a shortwave-infrared (SWIR) band. A cloudy pixel is usually assumed to be horizontally homogeneous in the retrieval. Ignoring sub-pixel variations of cloud reflectances can lead to a significant bias in the retrieved τ and re. In this study, we use the Taylor expansion of a two-variable function to understand and quantify the impacts of sub-pixel variances of VIS/NIR and SWIR cloud reflectances and their covariance on the τ and re retrievals. This framework takes into account the fact that the retrievals are determined by both VIS/NIR and SWIR band observations in a mutually dependent way. In comparison with previous studies, it provides a more comprehensive understanding of how sub-pixel cloud reflectance variations impact the τ and re retrievals based on the bi-spectral method. In particular, our framework provides a mathematical explanation of how the sub-pixel variation in VIS/NIR band influences the re retrieval and why it can sometimes outweigh the influence of variations in the SWIR band and dominate the error in re retrievals, leading to a potential contribution of positive bias to the re retrieval.

A Framework for Quantifying the Impacts of Sub-Pixel Reflectance Variance and Covariance on Cloud Optical Thickness and Effective Radius Retrievals Based on the Bi-Spectral Method.

NASA Technical Reports Server (NTRS)

Zhang, Z; Werner, F.; Cho, H. -M.; Wind, Galina; Platnick, S.; Ackerman, A. S.; Di Girolamo, L.; Marshak, A.; Meyer, Kerry

2017-01-01

The so-called bi-spectral method retrieves cloud optical thickness (t) and cloud droplet effective radius (re) simultaneously from a pair of cloud reflectance observations, one in a visible or near infrared (VIS/NIR) band and the other in a shortwave-infrared (SWIR) band. A cloudy pixel is usually assumed to be horizontally homogeneous in the retrieval. Ignoring sub-pixel variations of cloud reflectances can lead to a significant bias in the retrieved t and re. In this study, we use the Taylor expansion of a two-variable function to understand and quantify the impacts of sub-pixel variances of VIS/NIR and SWIR cloud reflectances and their covariance on the t and re retrievals. This framework takes into account the fact that the retrievals are determined by both VIS/NIR and SWIR band observations in a mutually dependent way. In comparison with previous studies, it provides a more comprehensive understanding of how sub-pixel cloud reflectance variations impact the t and re retrievals based on the bi-spectral method. In particular, our framework provides a mathematical explanation of how the sub-pixel variation in VIS/NIR band influences the re retrieval and why it can sometimes outweigh the influence of variations in the SWIR band and dominate the error in re retrievals, leading to a potential contribution of positive bias to the re retrieval.

Broadband Phase Retrieval for Image-Based Wavefront Sensing

NASA Technical Reports Server (NTRS)

Dean, Bruce H.

2007-01-01

A focus-diverse phase-retrieval algorithm has been shown to perform adequately for the purpose of image-based wavefront sensing when (1) broadband light (typically spanning the visible spectrum) is used in forming the images by use of an optical system under test and (2) the assumption of monochromaticity is applied to the broadband image data. Heretofore, it had been assumed that in order to obtain adequate performance, it is necessary to use narrowband or monochromatic light. Some background information, including definitions of terms and a brief description of pertinent aspects of image-based phase retrieval, is prerequisite to a meaningful summary of the present development. Phase retrieval is a general term used in optics to denote estimation of optical imperfections or aberrations of an optical system under test. The term image-based wavefront sensing refers to a general class of algorithms that recover optical phase information, and phase-retrieval algorithms constitute a subset of this class. In phase retrieval, one utilizes the measured response of the optical system under test to produce a phase estimate. The optical response of the system is defined as the image of a point-source object, which could be a star or a laboratory point source. The phase-retrieval problem is characterized as image-based in the sense that a charge-coupled-device camera, preferably of scientific imaging quality, is used to collect image data where the optical system would normally form an image. In a variant of phase retrieval, denoted phase-diverse phase retrieval [which can include focus-diverse phase retrieval (in which various defocus planes are used)], an additional known aberration (or an equivalent diversity function) is superimposed as an aid in estimating unknown aberrations by use of an image-based wavefront-sensing algorithm. Image-based phase-retrieval differs from such other wavefront-sensing methods, such as interferometry, shearing interferometry, curvature

Nonstationary signal analysis in episodic memory retrieval

NASA Astrophysics Data System (ADS)

Ku, Y. G.; Kawasumi, Masashi; Saito, Masao

2004-04-01

The problem of blind source separation from a mixture that has nonstationarity can be seen in signal processing, speech processing, spectral analysis and so on. This study analyzed EEG signal during episodic memory retrieval using ICA and TVAR. This paper proposes a method which combines ICA and TVAR. The signal from the brain not only exhibits the nonstationary behavior, but also contain artifacts. EEG data at the frontal lobe (F3) from the scalp is collected during the episodic memory retrieval task. The method is applied to EEG data for analysis. The artifact (eye movement) is removed by ICA, and a single burst (around 6Hz) is obtained by TVAR, suggesting that the single burst is related to the brain activity during the episodic memory retrieval.

The role of retrieval mode and retrieval orientation in retrieval practice: insights from comparing recognition memory testing formats and restudying.

PubMed

Gao, Chuanji; Rosburg, Timm; Hou, Mingzhu; Li, Bingbing; Xiao, Xin; Guo, Chunyan

2016-12-01

The effectiveness of retrieval practice for aiding long-term memory, referred to as the testing effect, has been widely demonstrated. However, the specific neurocognitive mechanisms underlying this phenomenon remain unclear. In the present study, we sought to explore the role of pre-retrieval processes at initial testing on later recognition performance by using event-related potentials (ERPs). Subjects studied two lists of words (Chinese characters) and then performed a recognition task or a source memory task, or restudied the word lists. At the end of the experiment, subjects received a final recognition test based on the remember-know paradigm. Behaviorally, initial testing (active retrieval) enhanced memory retention relative to restudying (passive retrieval). The retrieval mode at initial testing was indexed by more positive-going ERPs for unstudied items in the active-retrieval tasks than in passive retrieval from 300 to 900 ms. Follow-up analyses showed that the magnitude of the early ERP retrieval mode effect (300-500 ms) was predictive of the behavioral testing effect later on. In addition, the ERPs for correctly rejected new items during initial testing differed between the two active-retrieval tasks from 500 to 900 ms, and this ERP retrieval orientation effect predicted differential behavioral testing gains between the two active-retrieval conditions. Our findings confirm that initial testing promotes later retrieval relative to restudying, and they further suggest that adopting pre-retrieval processing in the forms of retrieval mode and retrieval orientation might contribute to these memory enhancements.

A cloud-based framework for large-scale traditional Chinese medical record retrieval.

PubMed

Liu, Lijun; Liu, Li; Fu, Xiaodong; Huang, Qingsong; Zhang, Xianwen; Zhang, Yin

2018-01-01

Electronic medical records are increasingly common in medical practice. The secondary use of medical records has become increasingly important. It relies on the ability to retrieve the complete information about desired patient populations. How to effectively and accurately retrieve relevant medical records from large- scale medical big data is becoming a big challenge. Therefore, we propose an efficient and robust framework based on cloud for large-scale Traditional Chinese Medical Records (TCMRs) retrieval. We propose a parallel index building method and build a distributed search cluster, the former is used to improve the performance of index building, and the latter is used to provide high concurrent online TCMRs retrieval. Then, a real-time multi-indexing model is proposed to ensure the latest relevant TCMRs are indexed and retrieved in real-time, and a semantics-based query expansion method and a multi- factor ranking model are proposed to improve retrieval quality. Third, we implement a template-based visualization method for displaying medical reports. The proposed parallel indexing method and distributed search cluster can improve the performance of index building and provide high concurrent online TCMRs retrieval. The multi-indexing model can ensure the latest relevant TCMRs are indexed and retrieved in real-time. The semantics expansion method and the multi-factor ranking model can enhance retrieval quality. The template-based visualization method can enhance the availability and universality, where the medical reports are displayed via friendly web interface. In conclusion, compared with the current medical record retrieval systems, our system provides some advantages that are useful in improving the secondary use of large-scale traditional Chinese medical records in cloud environment. The proposed system is more easily integrated with existing clinical systems and be used in various scenarios. Copyright © 2017. Published by Elsevier Inc.

BIBLIO: A Computerized Retrieval System for Communication Education.

ERIC Educational Resources Information Center

Williams, M. Lee; Edwards, Renee

1983-01-01

Describes BIBLIO, a computer program created for the storage and retrieval of articles in the 1970-80 issues of "Communication Education." Tells how articles were coded, method used to retrieve information, and advantages and uses of the system. (PD)

STUDIES ON THE ANTIGENIC STRUCTURE OF SOME MAMMALIAN SPERMATOZOA

PubMed Central

Henle, Werner; Henle, Gertrude; Chambers, Leslie A.

1938-01-01

1. A method has been described for separation of heads and tails of mammalian spermatozoa. 2. By means of absorption technique applied to homologous spermatozoal sera, head-specific and tail-specific antigens could be demonstrated. Both are heat-labile. 3. A heat-stable antigen was found to be common to both heads and tails. This substance is species-specific. 4. Antibodies against the head- and tail-specific antigens led to two different types of agglutination as shown by the slide method. 5. Using heterologous antisera against spermatozoa three different cross-reacting antigens could be observed, two in the heads, one in the tails. 6. One of the head-antigens is not active in the native cell; it comes to action only after breaking the cell. Antibodies against this substance were not found in antisera against native bull spermatozoa but were formed when vibrated spermatozoa or heads were injected into rabbits. 7. The cross-reactions can be removed from an antiserum leaving the head- as well as the tail-specific reaction intact. PMID:19870792

Multilayered Clouds Identification and Retrieval for CERES Using MODIS

NASA Technical Reports Server (NTRS)

Sun-Mack, Sunny; Minnis, Patrick; Chen, Yan; Yi, Yuhong; Huang, Jainping; Lin, Bin; Fan, Alice; Gibson, Sharon; Chang, Fu-Lung

2006-01-01

Traditionally, analyses of satellite data have been limited to interpreting the radiances in terms of single layer clouds. Generally, this results in significant errors in the retrieved properties for multilayered cloud systems. Two techniques for detecting overlapped clouds and retrieving the cloud properties using satellite data are explored to help address the need for better quantification of cloud vertical structure. The first technique was developed using multispectral imager data with secondary imager products (infrared brightness temperature differences, BTD). The other method uses microwave (MWR) data. The use of BTD, the 11-12 micrometer brightness temperature difference, in conjunction with tau, the retrieved visible optical depth, was suggested by Kawamoto et al. (2001) and used by Pavlonis et al. (2004) as a means to detect multilayered clouds. Combining visible (VIS; 0.65 micrometer) and infrared (IR) retrievals of cloud properties with microwave (MW) retrievals of cloud water temperature Tw and liquid water path LWP retrieved from satellite microwave imagers appears to be a fruitful approach for detecting and retrieving overlapped clouds (Lin et al., 1998, Ho et al., 2003, Huang et al., 2005). The BTD method is limited to optically thin cirrus over low clouds, while the MWR method is limited to ocean areas only. With the availability of VIS and IR data from the Moderate Resolution Imaging Spectroradiometer (MODIS) and MW data from the Advanced Microwave Scanning Radiometer EOS (AMSR-E), both on Aqua, it is now possible to examine both approaches simultaneously. This paper explores the use of the BTD method as applied to MODIS and AMSR-E data taken from the Aqua satellite over non-polar ocean surfaces.

Retrieval of reflections from ambient noise using illumination diagnosis

NASA Astrophysics Data System (ADS)

Vidal, C. Almagro; Draganov, D.; van der Neut, J.; Drijkoningen, G.; Wapenaar, K.

2014-09-01

Seismic interferometry (SI) enables the retrieval of virtual sources at the location of receivers. In the case of passive SI, no active sources are used for the retrieval of the reflection response of the subsurface, but ambient-noise recordings only. The resulting retrieved response is determined by the illumination characteristics of the recorded ambient noise. Characteristics like geometrical distribution and signature of the noise sources, together with the complexity of the medium and the length of the noise records, determine the quality of the retrieved virtual-shot events. To retrieve body wave reflections, one needs to correlate body-wave noise. A source of such noise might be regional seismicity. In regions with notable human presence, the dominant noise sources are generally located at or close to the surface. In the latter case, the noise will be dominated by surface waves and consequently also the retrieved virtual common-source panels will contain dominant retrieved surface waves, drowning out possible retrieved reflections. In order to retrieve reflection events, suppression of the surface waves becomes the most important pre-processing goal. Because of the reasons mentioned above, we propose a fast method to evaluate the illumination characteristics of ambient noise using the correlation results from ambient-noise records. The method is based on the analysis of the so-called source function of the retrieved virtual-shot panel, and evaluates the apparent slowness of arrivals in the correlation results that pass through the position of the virtual source and at zero time. The results of the diagnosis are used to suppress the retrieval of surface waves and therefore to improve the quality of the retrieved reflection response. We explain the approach using modelled data from transient and continuous noise sources and an example from a passive field data set recorded at Annerveen, Northern Netherlands.

Retrieval attempts enhance learning, but retrieval success (versus failure) does not matter.

PubMed

Kornell, Nate; Klein, Patricia Jacobs; Rawson, Katherine A

2015-01-01

Retrieving information from memory enhances learning. We propose a 2-stage framework to explain the benefits of retrieval. Stage 1 takes place as one attempts to retrieve an answer, which activates knowledge related to the retrieval cue. Stage 2 begins when the answer becomes available, at which point appropriate connections are strengthened and inappropriate connections may be weakened. This framework raises a basic question: Does it matter whether Stage 2 is initiated via successful retrieval or via an external presentation of the answer? To test this question, we asked participants to attempt retrieval and then randomly assigned items (which were equivalent otherwise) to be retrieved successfully or to be copied (i.e., not retrieved). Experiments 1, 2, 4, and 5 tested assumptions necessary for interpreting Experiments 3a, 3b, and 6. Experiments 3a, 3b, and 6 did not support the hypothesis that retrieval success produces more learning than does retrieval failure followed by feedback. It appears that retrieval attempts promote learning but retrieval success per se does not. PsycINFO Database Record (c) 2015 APA, all rights reserved.

Glioma antigen.

PubMed

Toda, Masahiro

2012-01-01

Because several antigenic peptides of human tumors that are recognized by T-lymphocytes have been identified, immune responses against cancer can now be artificially manipulated. Furthermore, since T-lymphocytes have been found to play an important role in the rejection of tumors by the host and also to have antigen-specific proliferative potentials and memory mechanisms, T-lymphocytes are thought to play a central role in cancer vaccination. Although multidisciplinary therapies have been attempted for the treatment of gliomas, the results remain unsatisfactory. For the development of new therapies against gliomas, it is required to identify tumor antigens as targets for specific immunotherapy. In this chapter, recent progress in research on glioma antigens is described.

Development of a Global Multilayered Cloud Retrieval System

NASA Technical Reports Server (NTRS)

Huang, J.; Minnis, P.; Lin, B.; Yi, Y.; Ayers, J. K.; Khaiyer, M. M.; Arduini, R.; Fan, T.-F

2004-01-01

A more rigorous multilayered cloud retrieval system has been developed to improve the determination of high cloud properties in multilayered clouds. The MCRS attempts a more realistic interpretation of the radiance field than earlier methods because it explicitly resolves the radiative transfer that would produce the observed radiances. A two-layer cloud model was used to simulate multilayered cloud radiative characteristics. Despite the use of a simplified two-layer cloud reflectance parameterization, the MCRS clearly produced a more accurate retrieval of ice water path than simple differencing techniques used in the past. More satellite data and ground observation have to be used to test the MCRS. The MCRS methods are quite appropriate for interpreting the radiances when the high cloud has a relatively large optical depth (tau(sub I) greater than 2). For thinner ice clouds, a more accurate retrieval might be possible using infrared methods. Selection of an ice cloud retrieval and a variety of other issues must be explored before a complete global application of this technique can be implemented. Nevertheless, the initial results look promising.

Content-based video retrieval by example video clip

NASA Astrophysics Data System (ADS)

Dimitrova, Nevenka; Abdel-Mottaleb, Mohamed

1997-01-01

This paper presents a novel approach for video retrieval from a large archive of MPEG or Motion JPEG compressed video clips. We introduce a retrieval algorithm that takes a video clip as a query and searches the database for clips with similar contents. Video clips are characterized by a sequence of representative frame signatures, which are constructed from DC coefficients and motion information (`DC+M' signatures). The similarity between two video clips is determined by using their respective signatures. This method facilitates retrieval of clips for the purpose of video editing, broadcast news retrieval, or copyright violation detection.

A content-based news video retrieval system: NVRS

NASA Astrophysics Data System (ADS)

Liu, Huayong; He, Tingting

2009-10-01

This paper focus on TV news programs and design a content-based news video browsing and retrieval system, NVRS, which is convenient for users to fast browsing and retrieving news video by different categories such as political, finance, amusement, etc. Combining audiovisual features and caption text information, the system automatically segments a complete news program into separate news stories. NVRS supports keyword-based news story retrieval, category-based news story browsing and generates key-frame-based video abstract for each story. Experiments show that the method of story segmentation is effective and the retrieval is also efficient.

Tank Waste Retrieval Lessons Learned at the Hanford Site

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

Dodd, R.A.

EPA approval of an exception to the waste retrieval criteria for a specific tank. Tank waste retrieval has been conducted at the Hanford Site over the last few decades using a method referred to as Past Practice Hydraulic Sluicing. Past Practice Hydraulic Sluicing employs large volumes of DST supernatant and water to dislodge, dissolve, mobilize, and retrieve tank waste. Concern over the leak integrity of SSTs resulted in the need for tank waste retrieval methods capable of using smaller volumes of liquid in a more controlled manner. Retrieval of SST waste in accordance with HFFACO requirements was initiated at the Hanford Site in April 2003. New and innovative tank waste retrieval methods that minimize and control the use of liquids are being implemented for the first time. These tank waste retrieval methods replace Past Practice Hydraulic Sluicing and employ modified sluicing, vacuum retrieval, and in-tank vehicle techniques. Waste retrieval has been completed in seven Hanford Site SSTs (C-106, C-103, C-201, C-202, C-203, C-204, and S-112) in accordance with HFFACO requirements. Three additional tanks are currently in the process of being retrieved (C-108, C-109 and S-102) Preparation for retrieval of two additional SSTs (C-104 and C-110) is ongoing with retrieval operations forecasted to start in calendar year 2008. Tank C-106 was retrieved to a residual waste volume of 470 ft{sup 3} using oxalic acid dissolution and modified sluicing. An Appendix H exception request for Tank C-106 is undergoing review. Tank C-103 was retrieved to a residual volume of 351 ft{sup 3} using a modified sluicing technology. This approach was successful at reaching the TPA limits for this tank of less than 360 ft{sup 3}and the limits of the technology. Tanks C-201, C-202, C-203, and C-204 are smaller (55,000 gallon) tanks and waste removal was completed in accordance with HFFACO requirements using a vacuum retrieval system. Residual waste volumes in each of these four tanks were less

Induction of human antigen-specific suppressor factors in vitro.

PubMed Central

Kontiainen, S; Woody, J N; Rees, A; Feldmann, M

1981-01-01

Based on methods used for the in vitro induction of antigen-specific suppressor cells in the mouse, we have cultured Ficoll-Isopaque-separated human blood cells with high dose of antigen (100 microgram/ml) in Marbrook culture vessels for 4 days. The resulting cells, when further recultured for 24 hr with a low dose of antigen (1 microgram/ml), released into the supernatant material, termed 'suppressor factor', which inhibited, in an antigen-specific manner, the antibody response of mouse spleen cells in culture. The suppressor factor was analysed using immunoabsorbents, and was bound to and eluted from specific antigen, concanavalin A and lentil lectin, anti-human Ia antibodies, and anti-mouse suppressor factor antibodies, but was not bound to antibodies against human IgG. PMID:6169475

Method for indexing and retrieving manufacturing-specific digital imagery based on image content

DOEpatents

Ferrell, Regina K.; Karnowski, Thomas P.; Tobin, Jr., Kenneth W.

2004-06-15

A method for indexing and retrieving manufacturing-specific digital images based on image content comprises three steps. First, at least one feature vector can be extracted from a manufacturing-specific digital image stored in an image database. In particular, each extracted feature vector corresponds to a particular characteristic of the manufacturing-specific digital image, for instance, a digital image modality and overall characteristic, a substrate/background characteristic, and an anomaly/defect characteristic. Notably, the extracting step includes generating a defect mask using a detection process. Second, using an unsupervised clustering method, each extracted feature vector can be indexed in a hierarchical search tree. Third, a manufacturing-specific digital image associated with a feature vector stored in the hierarchicial search tree can be retrieved, wherein the manufacturing-specific digital image has image content comparably related to the image content of the query image. More particularly, can include two data reductions, the first performed based upon a query vector extracted from a query image. Subsequently, a user can select relevant images resulting from the first data reduction. From the selection, a prototype vector can be calculated, from which a second-level data reduction can be performed. The second-level data reduction can result in a subset of feature vectors comparable to the prototype vector, and further comparable to the query vector. An additional fourth step can include managing the hierarchical search tree by substituting a vector average for several redundant feature vectors encapsulated by nodes in the hierarchical search tree.

Comparison of different methods to retrieve optical-equivalent snow grain size in central Antarctica

NASA Astrophysics Data System (ADS)

Carlsen, Tim; Birnbaum, Gerit; Ehrlich, André; Freitag, Johannes; Heygster, Georg; Istomina, Larysa; Kipfstuhl, Sepp; Orsi, Anaïs; Schäfer, Michael; Wendisch, Manfred

2017-11-01

The optical-equivalent snow grain size affects the reflectivity of snow surfaces and, thus, the local surface energy budget in particular in polar regions. Therefore, the specific surface area (SSA), from which the optical snow grain size is derived, was observed for a 2-month period in central Antarctica (Kohnen research station) during austral summer 2013/14. The data were retrieved on the basis of ground-based spectral surface albedo measurements collected by the COmpact RAdiation measurement System (CORAS) and airborne observations with the Spectral Modular Airborne Radiation measurement sysTem (SMART). The snow grain size and pollution amount (SGSP) algorithm, originally developed to analyze spaceborne reflectance measurements by the MODerate Resolution Imaging Spectroradiometer (MODIS), was modified in order to reduce the impact of the solar zenith angle on the retrieval results and to cover measurements in overcast conditions. Spectral ratios of surface albedo at 1280 and 1100 nm wavelength were used to reduce the retrieval uncertainty. The retrieval was applied to the ground-based and airborne observations and validated against optical in situ observations of SSA utilizing an IceCube device. The SSA retrieved from CORAS observations varied between 27 and 89 m2 kg-1. Snowfall events caused distinct relative maxima of the SSA which were followed by a gradual decrease in SSA due to snow metamorphism and wind-induced transport of freshly fallen ice crystals. The ability of the modified algorithm to include measurements in overcast conditions improved the data coverage, in particular at times when precipitation events occurred and the SSA changed quickly. SSA retrieved from measurements with CORAS and MODIS agree with the in situ observations within the ranges given by the measurement uncertainties. However, SSA retrieved from the airborne SMART data slightly underestimated the ground-based results.

Cirrus Heterogeneity Effects on Cloud Optical Properties Retrieved with an Optimal Estimation Method from MODIS VIS to TIR Channels.

NASA Technical Reports Server (NTRS)

Fauchez, T.; Platnick, S.; Meyer, K.; Sourdeval, O.; Cornet, C.; Zhang, Z.; Szczap, F.

2016-01-01

This study presents preliminary results on the effect of cirrus heterogeneities on top-of-atmosphere (TOA) simulated radiances or reflectances for MODIS channels centered at 0.86, 2.21, 8.56, 11.01 and 12.03 micrometers , and on cloud optical properties retrieved with a research-level optimal estimation method (OEM). Synthetic cirrus cloud fields are generated using a 3D cloud generator (3DCLOUD) and radiances/reflectances are simulated using a 3D radiative transfer code (3DMCPOL). We find significant differences between the heterogeneity effects on either visible and near-infrared (VNIR) or thermal infrared (TIR) radiances. However, when both wavelength ranges are combined, heterogeneity effects are dominated by the VNIR horizontal radiative transport effect. As a result, small optical thicknesses are overestimated and large ones are underestimated. Retrieved effective diameter are found to be slightly affected, contrarily to retrievals using TIR channels only.

Combining approaches to on-line handwriting information retrieval

NASA Astrophysics Data System (ADS)

Peña Saldarriaga, Sebastián; Viard-Gaudin, Christian; Morin, Emmanuel

2010-01-01

In this work, we propose to combine two quite different approaches for retrieving handwritten documents. Our hypothesis is that different retrieval algorithms should retrieve different sets of documents for the same query. Therefore, significant improvements in retrieval performances can be expected. The first approach is based on information retrieval techniques carried out on the noisy texts obtained through handwriting recognition, while the second approach is recognition-free using a word spotting algorithm. Results shows that for texts having a word error rate (WER) lower than 23%, the performances obtained with the combined system are close to the performances obtained on clean digital texts. In addition, for poorly recognized texts (WER > 52%), an improvement of nearly 17% can be observed with respect to the best available baseline method.

Breast Histopathological Image Retrieval Based on Latent Dirichlet Allocation.

PubMed

Ma, Yibing; Jiang, Zhiguo; Zhang, Haopeng; Xie, Fengying; Zheng, Yushan; Shi, Huaqiang; Zhao, Yu

2017-07-01

In the field of pathology, whole slide image (WSI) has become the major carrier of visual and diagnostic information. Content-based image retrieval among WSIs can aid the diagnosis of an unknown pathological image by finding its similar regions in WSIs with diagnostic information. However, the huge size and complex content of WSI pose several challenges for retrieval. In this paper, we propose an unsupervised, accurate, and fast retrieval method for a breast histopathological image. Specifically, the method presents a local statistical feature of nuclei for morphology and distribution of nuclei, and employs the Gabor feature to describe the texture information. The latent Dirichlet allocation model is utilized for high-level semantic mining. Locality-sensitive hashing is used to speed up the search. Experiments on a WSI database with more than 8000 images from 15 types of breast histopathology demonstrate that our method achieves about 0.9 retrieval precision as well as promising efficiency. Based on the proposed framework, we are developing a search engine for an online digital slide browsing and retrieval platform, which can be applied in computer-aided diagnosis, pathology education, and WSI archiving and management.

Mutual information based feature selection for medical image retrieval

NASA Astrophysics Data System (ADS)

Zhi, Lijia; Zhang, Shaomin; Li, Yan

2018-04-01

In this paper, authors propose a mutual information based method for lung CT image retrieval. This method is designed to adapt to different datasets and different retrieval task. For practical applying consideration, this method avoids using a large amount of training data. Instead, with a well-designed training process and robust fundamental features and measurements, the method in this paper can get promising performance and maintain economic training computation. Experimental results show that the method has potential practical values for clinical routine application.

Immunization Elicits Antigen-Specific Antibody Sequestration in Dorsal Root Ganglia Sensory Neurons

PubMed Central

Gunasekaran, Manojkumar; Chatterjee, Prodyot K.; Shih, Andrew; Imperato, Gavin H.; Addorisio, Meghan; Kumar, Gopal; Lee, Annette; Graf, John F.; Meyer, Dan; Marino, Michael; Puleo, Christopher; Ashe, Jeffrey; Cox, Maureen A.; Mak, Tak W.; Bouton, Chad; Sherry, Barbara; Diamond, Betty; Andersson, Ulf; Coleman, Thomas R.; Metz, Christine N.; Tracey, Kevin J.; Chavan, Sangeeta S.

2018-01-01

The immune and nervous systems are two major organ systems responsible for host defense and memory. Both systems achieve memory and learning that can be retained, retrieved, and utilized for decades. Here, we report the surprising discovery that peripheral sensory neurons of the dorsal root ganglia (DRGs) of immunized mice contain antigen-specific antibodies. Using a combination of rigorous molecular genetic analyses, transgenic mice, and adoptive transfer experiments, we demonstrate that DRGs do not synthesize these antigen-specific antibodies, but rather sequester primarily IgG1 subtype antibodies. As revealed by RNA-seq and targeted quantitative PCR (qPCR), dorsal root ganglion (DRG) sensory neurons harvested from either naïve or immunized mice lack enzymes (i.e., RAG1, RAG2, AID, or UNG) required for generating antibody diversity and, therefore, cannot make antibodies. Additionally, transgenic mice that express a reporter fluorescent protein under the control of Igγ1 constant region fail to express Ighg1 transcripts in DRG sensory neurons. Furthermore, neural sequestration of antibodies occurs in mice rendered deficient in neuronal Rag2, but antibody sequestration is not observed in DRG sensory neurons isolated from mice that lack mature B cells [e.g., Rag1 knock out (KO) or μMT mice]. Finally, adoptive transfer of Rag1-deficient bone marrow (BM) into wild-type (WT) mice or WT BM into Rag1 KO mice revealed that antibody sequestration was observed in DRG sensory neurons of chimeric mice with WT BM but not with Rag1-deficient BM. Together, these results indicate that DRG sensory neurons sequester and retain antigen-specific antibodies released by antibody-secreting plasma cells. Coupling this work with previous studies implicating DRG sensory neurons in regulating antigen trafficking during immunization raises the interesting possibility that the nervous system collaborates with the immune system to regulate antigen-mediated responses. PMID:29755449

Prostate-specific antigen velocity is not better than total prostate-specific antigen in predicting prostate biopsy diagnosis.

PubMed

Gorday, William; Sadrzadeh, Hossein; de Koning, Lawrence; Naugler, Christopher T

2015-12-01

1.) Identify whether prostate-specific antigen velocity improves the ability to predict prostate biopsy diagnosis. 2.) Test whether there is an increase in the predictive capability of models when Gleason 7 prostate cancers are separated into a 3+4 and a 4+3 group. Calgary Laboratory Services' Clinical Laboratory Information System was searched for prostate biopsies reported between January 1, 2009 and December 31, 2013. Total prostate-specific antigen tests were recorded for each patient from January 1, 2007 to the most recent test before their recorded prostate biopsy. The data set was divided into the following three groups for comparison; benign, all prostate cancer and Gleason 7-10. The Gleason grade 7-10 group was further divided into 4+3 and 3+4 Gleason 7 prostate cancers. Prostate-specific antigen velocity was calculated using four different methods found in the literature. Receiver operator curves were used to assess operational characteristics of the tests. 4622 men between the ages of 40-89 with a prostate biopsy were included for analysis. Combining prostate-specific antigen velocity with total prostate-specific antigen (AUC=0.570-0.712) resulted in small non-statistically significant changes to the area under the curve compared to the area under the curve of total prostate-specific antigen alone (AUC=0.572-0.699). There were marked increases in the area under curves when 3+4 and 4+3 Gleason 7 cancers were separated. Prostate-specific antigen velocity does not add predictive value for prostate biopsy diagnosis. The clinical significance of the prostate specific antigen test can be improved by separating Gleason 7 prostate cancers into a 3+4 and 4+3 group. Copyright © 2015 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Heritability of levels of autoantibodies to thyroid antigens using the method of plotting regression of offspring on midparent (ROMP).

PubMed

Outschoorn, Ingrid M; Hoffman, William H; Rose, Noel R; Burek, C Lynne

2007-07-01

Only a few methods can be applied in a simple manner to estimate the genetic control of autoimmunity in humans. Here we examined the heritability of autoantibodies to two thyroid antigens; thyroglobulin (Tg) and thyroperoxidase (TPO, formerly known as thyroid microsomal antigen), using methods of regression of offspring on mid-parental values (ROMP). With the data sets available, affected and unaffected siblings were compared by this rapid screening method using results determined by hemagglutination (HA). The presence of both types of autoantibodies showed positive heritability in patients with Graves' thyrotoxicosis (TT), but it was not observed in chronic lymphocytic or Hashimoto's thyroiditis (CLT) patients. Since these assays have been extensively used over the years by most diagnostic and research laboratories, they should provide some insight as to which quantifiable parameters may be usefully accumulated to help select groups of patients and their families for further genetic study. ROMP may also be useful to determine the sequential appearance of different types of antibody in predicting disease onset in other family members, and in distinguishing maternal and paternal effects on imprinting. The method may be extended to study epitope spreading and other measures of disease progression.

Content-based cell pathology image retrieval by combining different features

NASA Astrophysics Data System (ADS)

Zhou, Guangquan; Jiang, Lu; Luo, Limin; Bao, Xudong; Shu, Huazhong

2004-04-01

Content Based Color Cell Pathology Image Retrieval is one of the newest computer image processing applications in medicine. Recently, some algorithms have been developed to achieve this goal. Because of the particularity of cell pathology images, the result of the image retrieval based on single characteristic is not satisfactory. A new method for pathology image retrieval by combining color, texture and morphologic features to search cell images is proposed. Firstly, nucleus regions of leukocytes in images are automatically segmented by K-mean clustering method. Then single leukocyte region is detected by utilizing thresholding algorithm segmentation and mathematics morphology. The features that include color, texture and morphologic features are extracted from single leukocyte to represent main attribute in the search query. The features are then normalized because the numerical value range and physical meaning of extracted features are different. Finally, the relevance feedback system is introduced. So that the system can automatically adjust the weights of different features and improve the results of retrieval system according to the feedback information. Retrieval results using the proposed method fit closely with human perception and are better than those obtained with the methods based on single feature.

DOLPHIn—Dictionary Learning for Phase Retrieval

NASA Astrophysics Data System (ADS)

Tillmann, Andreas M.; Eldar, Yonina C.; Mairal, Julien

2016-12-01

We propose a new algorithm to learn a dictionary for reconstructing and sparsely encoding signals from measurements without phase. Specifically, we consider the task of estimating a two-dimensional image from squared-magnitude measurements of a complex-valued linear transformation of the original image. Several recent phase retrieval algorithms exploit underlying sparsity of the unknown signal in order to improve recovery performance. In this work, we consider such a sparse signal prior in the context of phase retrieval, when the sparsifying dictionary is not known in advance. Our algorithm jointly reconstructs the unknown signal - possibly corrupted by noise - and learns a dictionary such that each patch of the estimated image can be sparsely represented. Numerical experiments demonstrate that our approach can obtain significantly better reconstructions for phase retrieval problems with noise than methods that cannot exploit such "hidden" sparsity. Moreover, on the theoretical side, we provide a convergence result for our method.

Retrieval attempts enhance learning regardless of time spent trying to retrieve.

PubMed

Vaughn, Kalif E; Hausman, Hannah; Kornell, Nate

2017-03-01

Attempting to retrieve information from memory is an engaging cognitive activity. We predicted that people would learn more when they had spent more time attempting to retrieve. In experiments 1a and 1b, participants were shown trivia questions for 0, 5, 10, or 30 seconds and then the answer was revealed. They took a final test immediately or after 48 hours. Retrieval enhanced learning, but the length of the retrieval attempt had no effect (i.e., final test performance was equivalent in the 5-, 10-, and 30-second conditions and worse in the 0-second condition). During the initial retrieval attempt, more time did increase recall, suggesting that participants continued to engage in productive retrieval activities when given more time. Showing the answer for longer (7 versus 2 seconds) increased learning in Experiments 2a and 2b. Experiment 3 examined the effect of retrieval success and Experiment 4 replicated the results using different materials. These results have direct implications for current theories of retrieval.

A Deep Learning-Based Method for Similar Patient Question Retrieval in Chinese.

PubMed

Tang, Guo Yu; Ni, Yuan; Xie, Guo Tong; Fan, Xin Li; Shi, Yan Ling

2017-01-01

The online patient question and answering (Q&A) system, either as a website or a mobile application, attracts an increasing number of users in China. Patients will post their questions and the registered doctors then provide the corresponding answers. A large amount of questions with answers from doctors are accumulated. Instead of awaiting the response from a doctor, the newly posted question could be quickly answered by finding a semantically equivalent question from the Q&A achive. In this study, we investigated a novel deep learning based method to retrieve the similar patient question in Chinese. An unsupervised learning algorithm using deep neural network is performed on the corpus to generate the word embedding. The word embedding was then used as the input to a supervised learning algorithm using a designed deep neural network, i.e. the supervised neural attention model (SNA), to predict the similarity between two questions. The experimental results showed that our SNA method achieved P@1 = 77% and P@5 = 84%, which outperformed all other compared methods.

Rods and cones contain antigenically distinctive S-antigens.

PubMed

Nork, T M; Mangini, N J; Millecchia, L L

1993-09-01

S-antigen (48 kDa protein or arrestin) is known to be present in rod photoreceptors. Its localization in cones is less clear with several conflicting reports among various species examined. This study employed three different anti-S-antigen antibodies (a48K, a polyclonal antiserum and two monoclonal antibodies, MAb A9-C6 and MAb 5c6.47) and examined their localization in rods and cones of human and cat retinas. To identify the respective cone types, an enzyme histochemical technique for carbonic anhydrase (CA) was employed to distinguish blue cones (CA-negative) from red or green cones (CA-positive). S-antigen localization was then examined by immunocytochemical staining of adjacent sections. In human retinas, a similar labeling pattern was seen with both a48K and MAb A9-C6, i.e., the rods and blue-sensitive cones were strongly positive, whereas the red- or green-sensitive cones showed little immunoreactivity. All human photoreceptors showed reactivity to MAb 5c6.47. In the cat retina, only CA-positive cones could be found. As in the human retina, both rods and cones of the cat were positive for MAb 5c6.47. A difference from the labeling pattern in human retina was noted for the other S-antigen antibodies; a48K labeled rods and all of the cones, whereas MAb A9-C6 reacted strongly with the rods but showed no cone staining. These results suggest that both rods and cones contain S-antigen but that they are antigenically distinctive.

Utility of PCR, Culture, and Antigen Detection Methods for Diagnosis of Legionellosis.

PubMed

Chen, Derrick J; Procop, Gary W; Vogel, Sherilynn; Yen-Lieberman, Belinda; Richter, Sandra S

2015-11-01

The goal of this retrospective study was to evaluate the performance of different diagnostic tests for Legionnaires' disease in a clinical setting where Legionella pneumophila PCR had been introduced. Electronic medical records at the Cleveland Clinic were searched for Legionella urinary antigen (UAG), culture, and PCR tests ordered from March 2010 through December 2013. For cases where two or more test methods were performed and at least one was positive, the medical record was reviewed for relevant clinical and epidemiologic factors. Excluding repeat testing on a given patient, 19,912 tests were ordered (12,569 UAG, 3,747 cultures, and 3,596 PCR) with 378 positive results. The positivity rate for each method was 0.4% for culture, 0.8% for PCR, and 2.7% for UAG. For 37 patients, at least two test methods were performed with at least one positive result: 10 (27%) cases were positive by all three methods, 16 (43%) were positive by two methods, and 11 (30%) were positive by one method only. For the 32 patients with medical records available, clinical presentation was consistent with proven or probable Legionella infection in 84% of the cases. For those cases, the sensitivities of culture, PCR, and UAG were 50%, 92%, and 96%, respectively. The specificities were 100% for culture and 99.9% for PCR and UAG. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Utility of PCR, Culture, and Antigen Detection Methods for Diagnosis of Legionellosis

PubMed Central

Chen, Derrick J.; Procop, Gary W.; Vogel, Sherilynn; Yen-Lieberman, Belinda

2015-01-01

The goal of this retrospective study was to evaluate the performance of different diagnostic tests for Legionnaires' disease in a clinical setting where Legionella pneumophila PCR had been introduced. Electronic medical records at the Cleveland Clinic were searched for Legionella urinary antigen (UAG), culture, and PCR tests ordered from March 2010 through December 2013. For cases where two or more test methods were performed and at least one was positive, the medical record was reviewed for relevant clinical and epidemiologic factors. Excluding repeat testing on a given patient, 19,912 tests were ordered (12,569 UAG, 3,747 cultures, and 3,596 PCR) with 378 positive results. The positivity rate for each method was 0.4% for culture, 0.8% for PCR, and 2.7% for UAG. For 37 patients, at least two test methods were performed with at least one positive result: 10 (27%) cases were positive by all three methods, 16 (43%) were positive by two methods, and 11 (30%) were positive by one method only. For the 32 patients with medical records available, clinical presentation was consistent with proven or probable Legionella infection in 84% of the cases. For those cases, the sensitivities of culture, PCR, and UAG were 50%, 92%, and 96%, respectively. The specificities were 100% for culture and 99.9% for PCR and UAG. PMID:26292304

Learning semantic and visual similarity for endomicroscopy video retrieval.

PubMed

Andre, Barbara; Vercauteren, Tom; Buchner, Anna M; Wallace, Michael B; Ayache, Nicholas

2012-06-01

Content-based image retrieval (CBIR) is a valuable computer vision technique which is increasingly being applied in the medical community for diagnosis support. However, traditional CBIR systems only deliver visual outputs, i.e., images having a similar appearance to the query, which is not directly interpretable by the physicians. Our objective is to provide a system for endomicroscopy video retrieval which delivers both visual and semantic outputs that are consistent with each other. In a previous study, we developed an adapted bag-of-visual-words method for endomicroscopy retrieval, called "Dense-Sift," that computes a visual signature for each video. In this paper, we present a novel approach to complement visual similarity learning with semantic knowledge extraction, in the field of in vivo endomicroscopy. We first leverage a semantic ground truth based on eight binary concepts, in order to transform these visual signatures into semantic signatures that reflect how much the presence of each semantic concept is expressed by the visual words describing the videos. Using cross-validation, we demonstrate that, in terms of semantic detection, our intuitive Fisher-based method transforming visual-word histograms into semantic estimations outperforms support vector machine (SVM) methods with statistical significance. In a second step, we propose to improve retrieval relevance by learning an adjusted similarity distance from a perceived similarity ground truth. As a result, our distance learning method allows to statistically improve the correlation with the perceived similarity. We also demonstrate that, in terms of perceived similarity, the recall performance of the semantic signatures is close to that of visual signatures and significantly better than those of several state-of-the-art CBIR methods. The semantic signatures are thus able to communicate high-level medical knowledge while being consistent with the low-level visual signatures and much shorter than them

Texture-specific bag of visual words model and spatial cone matching-based method for the retrieval of focal liver lesions using multiphase contrast-enhanced CT images.

PubMed

Xu, Yingying; Lin, Lanfen; Hu, Hongjie; Wang, Dan; Zhu, Wenchao; Wang, Jian; Han, Xian-Hua; Chen, Yen-Wei

2018-01-01

The bag of visual words (BoVW) model is a powerful tool for feature representation that can integrate various handcrafted features like intensity, texture, and spatial information. In this paper, we propose a novel BoVW-based method that incorporates texture and spatial information for the content-based image retrieval to assist radiologists in clinical diagnosis. This paper presents a texture-specific BoVW method to represent focal liver lesions (FLLs). Pixels in the region of interest (ROI) are classified into nine texture categories using the rotation-invariant uniform local binary pattern method. The BoVW-based features are calculated for each texture category. In addition, a spatial cone matching (SCM)-based representation strategy is proposed to describe the spatial information of the visual words in the ROI. In a pilot study, eight radiologists with different clinical experience performed diagnoses for 20 cases with and without the top six retrieved results. A total of 132 multiphase computed tomography volumes including five pathological types were collected. The texture-specific BoVW was compared to other BoVW-based methods using the constructed dataset of FLLs. The results show that our proposed model outperforms the other three BoVW methods in discriminating different lesions. The SCM method, which adds spatial information to the orderless BoVW model, impacted the retrieval performance. In the pilot trial, the average diagnosis accuracy of the radiologists was improved from 66 to 80% using the retrieval system. The preliminary results indicate that the texture-specific features and the SCM-based BoVW features can effectively characterize various liver lesions. The retrieval system has the potential to improve the diagnostic accuracy and the confidence of the radiologists.

On the VHF Source Retrieval Errors Associated with Lightning Mapping Arrays (LMAs)

NASA Technical Reports Server (NTRS)

Koshak, W.

2016-01-01

This presentation examines in detail the standard retrieval method: that of retrieving the (x, y, z, t) parameters of a lightning VHF point source from multiple ground-based Lightning Mapping Array (LMA) time-of-arrival (TOA) observations. The solution is found by minimizing a chi-squared function via the Levenberg-Marquardt algorithm. The associated forward problem is examined to illustrate the importance of signal-to-noise ratio (SNR). Monte Carlo simulated retrievals are used to assess the benefits of changing various LMA network properties. A generalized retrieval method is also introduced that, in addition to TOA data, uses LMA electric field amplitude measurements to retrieve a transient VHF dipole moment source.

Monoclonal antibodies against simian virus 40 T antigens: evidence for distinct sublcasses of large T antigen and for similarities among nonviral T antigens.

PubMed Central

Gurney, E G; Harrison, R O; Fenno, J

1980-01-01

We have isolated three clones of hybrid cells which synthesize antibodies specific for determinants on simian virus 40 (SV40) T antigens. Mouse myeloma NS1 cells were fused with spleen cells from mice that had been immunized with SV40-transformed mouse cells. Hybrid cells were selected in HAT medium and cloned in soft agar. We used an enzyme-linked immunosorbent assay for detection and quantification of mouse antibodies against SV40 T antigens. Monoclonal antibodies from 3 of the 24 clones that scored as positive in the enzyme-linked immunosorbent assay were verified by immunoprecipitation to be specific for SV40 T antigens. Two clones (7 and 412) produced antibodies that recognized denaturation-sensitive antigenic determinants unique to large T antigen. Antibodies from clone 7 appeared to have a low affinity for large T antigen. Antibodies from clone 412 had a higher affinity for large T antigen but did not recognize a subclass of large T antigen that was recognized by tumor serum. Antibodies of the third clone, clone 122, recognized a denaturation-stable antigenic determinant of the 53,000-dalton mouse nonviral T antigen in SV40-transformed cells. Antibodies from clone 122 also recognized similar (51,000- to 56,000-dalton) nonviral T antigens in SV40-transormed or lytically infected cells from five mammalian species and in four uninfected mouse lines. From these observations, we have concluded that (i) the 94,000-dalton SV40 large T antigen may exist as immunologically distinguishable subclasses, and (ii) the nonviral T antigens of five mammalian species share at least one antigenic determinant. Images PMID:6155477

Bayesian aerosol retrieval algorithm for MODIS AOD retrieval over land

NASA Astrophysics Data System (ADS)

Lipponen, Antti; Mielonen, Tero; Pitkänen, Mikko R. A.; Levy, Robert C.; Sawyer, Virginia R.; Romakkaniemi, Sami; Kolehmainen, Ville; Arola, Antti

2018-03-01

We have developed a Bayesian aerosol retrieval (BAR) algorithm for the retrieval of aerosol optical depth (AOD) over land from the Moderate Resolution Imaging Spectroradiometer (MODIS). In the BAR algorithm, we simultaneously retrieve all dark land pixels in a granule, utilize spatial correlation models for the unknown aerosol parameters, use a statistical prior model for the surface reflectance, and take into account the uncertainties due to fixed aerosol models. The retrieved parameters are total AOD at 0.55 µm, fine-mode fraction (FMF), and surface reflectances at four different wavelengths (0.47, 0.55, 0.64, and 2.1 µm). The accuracy of the new algorithm is evaluated by comparing the AOD retrievals to Aerosol Robotic Network (AERONET) AOD. The results show that the BAR significantly improves the accuracy of AOD retrievals over the operational Dark Target (DT) algorithm. A reduction of about 29 % in the AOD root mean square error and decrease of about 80 % in the median bias of AOD were found globally when the BAR was used instead of the DT algorithm. Furthermore, the fraction of AOD retrievals inside the ±(0.05+15 %) expected error envelope increased from 55 to 76 %. In addition to retrieving the values of AOD, FMF, and surface reflectance, the BAR also gives pixel-level posterior uncertainty estimates for the retrieved parameters. The BAR algorithm always results in physical, non-negative AOD values, and the average computation time for a single granule was less than a minute on a modern personal computer.

Kinetics of T-cell receptor-dependent antigen recognition determined in vivo by multi-spectral normalized epifluorescence laser scanning

NASA Astrophysics Data System (ADS)

Favicchio, Rosy; Zacharakis, Giannis; Oikonomaki, Katerina; Zacharopoulos, Athanasios; Mamalaki, Clio; Ripoll, Jorge

2012-07-01

Detection of multiple fluorophores in conditions of low signal represents a limiting factor for the application of in vivo optical imaging techniques in immunology where fluorescent labels report for different functional characteristics. A noninvasive in vivo Multi-Spectral Normalized Epifluorescence Laser scanning (M-SNELS) method was developed for the simultaneous and quantitative detection of multiple fluorophores in low signal to noise ratios and used to follow T-cell activation and clonal expansion. Colocalized DsRed- and GFP-labeled T cells were followed in tandem during the mounting of an immune response. Spectral unmixing was used to distinguish the overlapping fluorescent emissions representative of the two distinct cell populations and longitudinal data reported the discrete pattern of antigen-driven proliferation. Retrieved values were validated both in vitro and in vivo with flow cytometry and significant correlation between all methodologies was achieved. Noninvasive M-SNELS successfully quantified two colocalized fluorescent populations and provides a valid alternative imaging approach to traditional invasive methods for detecting T cell dynamics.

Memory Retrieval in Mice and Men

PubMed Central

Ben-Yakov, Aya; Dudai, Yadin; Mayford, Mark R.

2015-01-01

Retrieval, the use of learned information, was until recently mostly terra incognita in the neurobiology of memory, owing to shortage of research methods with the spatiotemporal resolution required to identify and dissect fast reactivation or reconstruction of complex memories in the mammalian brain. The development of novel paradigms, model systems, and new tools in molecular genetics, electrophysiology, optogenetics, in situ microscopy, and functional imaging, have contributed markedly in recent years to our ability to investigate brain mechanisms of retrieval. We review selected developments in the study of explicit retrieval in the rodent and human brain. The picture that emerges is that retrieval involves coordinated fast interplay of sparse and distributed corticohippocampal and neocortical networks that may permit permutational binding of representational elements to yield specific representations. These representations are driven largely by the activity patterns shaped during encoding, but are malleable, subject to the influence of time and interaction of the existing memory with novel information. PMID:26438596

Diversification of visual media retrieval results using saliency detection

NASA Astrophysics Data System (ADS)

Muratov, Oleg; Boato, Giulia; De Natale, Franesco G. B.

2013-03-01

Diversification of retrieval results allows for better and faster search. Recently there has been proposed different methods for diversification of image retrieval results mainly utilizing text information and techniques imported from natural language processing domain. However, images contain visual information that is impossible to describe in text and the use of visual features is inevitable. Visual saliency is information about the main object of an image implicitly included by humans while creating visual content. For this reason it is naturally to exploit this information for the task of diversification of the content. In this work we study whether visual saliency can be used for the task of diversification and propose a method for re-ranking image retrieval results using saliency. The evaluation has shown that the use of saliency information results in higher diversity of retrieval results.

Medical image retrieval system using multiple features from 3D ROIs

NASA Astrophysics Data System (ADS)

Lu, Hongbing; Wang, Weiwei; Liao, Qimei; Zhang, Guopeng; Zhou, Zhiming

2012-02-01

Compared to a retrieval using global image features, features extracted from regions of interest (ROIs) that reflect distribution patterns of abnormalities would benefit more for content-based medical image retrieval (CBMIR) systems. Currently, most CBMIR systems have been designed for 2D ROIs, which cannot reflect 3D anatomical features and region distribution of lesions comprehensively. To further improve the accuracy of image retrieval, we proposed a retrieval method with 3D features including both geometric features such as Shape Index (SI) and Curvedness (CV) and texture features derived from 3D Gray Level Co-occurrence Matrix, which were extracted from 3D ROIs, based on our previous 2D medical images retrieval system. The system was evaluated with 20 volume CT datasets for colon polyp detection. Preliminary experiments indicated that the integration of morphological features with texture features could improve retrieval performance greatly. The retrieval result using features extracted from 3D ROIs accorded better with the diagnosis from optical colonoscopy than that based on features from 2D ROIs. With the test database of images, the average accuracy rate for 3D retrieval method was 76.6%, indicating its potential value in clinical application.

Expression of the Thomsen-Friedenreich (TF) tumor antigen in human abort placentas.

PubMed

Richter, D U; Jeschke, U; Bergemann, C; Makovitzky, J; Lüthen, F; Karsten, U; Briese, V

2005-01-01

The Thomsen-Friedenreich antigen (TF), or more precisely epitope, has been known as a pancarcinoma antigen. It consists of galactose-beta1-3-N-acetylgalactose. We have already described the expression of TF in the normal placenta. TF is expressed by the syncytium and by extravillous trophoblast cells. In this study, we investigated the expression of TF in the abort placenta. Frozen samples of human abort placentas (12 placentas), obtained from the first and second trimesters of pregnancy and, for comparison, samples of normal placentas (17 placentas) from the first, second and third trimesters of pregnancy, were used. Expression of TF was investigated by immunohistochemical methods. For identification of TF-positive cells in abort placentas, immunofluorescence methods were used. Evaluation of simple and double immunofluorescence was performed on a laser scanning microscope. Furthermore, we isolated trophoblast cells from first and third trimester placentas and evaluated cytokeratin 7 and Muc1 expression by immunofluorescence methods. We observed expression of TF antigen in the syncytiotrophoblasts layer of the placenta in all three trimesters of pregnancy in normal and abort placentas evaluated by immunohistochemical methods. There was no expression of TF antigen in the decidua of abort placentas. Immunofluorescence double staining of TF antigen and cytokeratin 7 showed reduced expression of both antigens in the abort decidua and co-expression of both antigens in the syncytiotrophoblast layer of normal and abort placentas. TF expression in the syncytiotrophoblast was reduced in abort placentas. In the isolated trophoblast cells, no TF expression was found, however, Muc1 expression was visualized. Expression of TF antigen was reduced in the first and second trimester abort decidua compared to the normal decidua during the same time of pregnancy. TF antigen was restricted to the syncytiotrophoblast and extravillous trophoblast cells in the decidua. Abort placentas

Retrieval of all effective susceptibilities in nonlinear metamaterials

NASA Astrophysics Data System (ADS)

Larouche, Stéphane; Radisic, Vesna

2018-04-01

Electromagnetic metamaterials offer a great avenue to engineer and amplify the nonlinear response of materials. Their electric, magnetic, and magnetoelectric linear and nonlinear response are related to their structure, providing unprecedented liberty to control those properties. Both the linear and the nonlinear properties of metamaterials are typically anisotropic. While the methods to retrieve the effective linear properties are well established, existing nonlinear retrieval methods have serious limitations. In this work, we generalize a nonlinear transfer matrix approach to account for all nonlinear susceptibility terms and show how to use this approach to retrieve all effective nonlinear susceptibilities of metamaterial elements. The approach is demonstrated using sum frequency generation, but can be applied to other second-order or higher-order processes.

Studies and Application of Remote Sensing Retrieval Method of Soil Moisture Content in Land Parcel Units in Irrigation Area

NASA Astrophysics Data System (ADS)

Zhu, H.; Zhao, H. L.; Jiang, Y. Z.; Zang, W. B.

2018-05-01

Soil moisture is one of the important hydrological elements. Obtaining soil moisture accurately and effectively is of great significance for water resource management in irrigation area. During the process of soil moisture content retrieval with multiremote sensing data, multi- remote sensing data always brings multi-spatial scale problems which results in inconformity of soil moisture content retrieved by remote sensing in different spatial scale. In addition, agricultural water use management has suitable spatial scale of soil moisture information so as to satisfy the demands of dynamic management of water use and water demand in certain unit. We have proposed to use land parcel unit as the minimum unit to do soil moisture content research in agricultural water using area, according to soil characteristics, vegetation coverage characteristics in underlying layer, and hydrological characteristic into the basis of study unit division. We have proposed division method of land parcel units. Based on multi thermal infrared and near infrared remote sensing data, we calculate the ndvi and tvdi index and make a statistical model between the tvdi index and soil moisture of ground monitoring station. Then we move forward to study soil moisture remote sensing retrieval method on land parcel unit scale. And the method has been applied in Hetao irrigation area. Results show that compared with pixel scale the soil moisture content in land parcel unit scale has displayed stronger correlation with true value. Hence, remote sensing retrieval method of soil moisture content in land parcel unit scale has shown good applicability in Hetao irrigation area. We converted the research unit into the scale of land parcel unit. Using the land parcel units with unified crops and soil attributes as the research units more complies with the characteristics of agricultural water areas, avoids the problems such as decomposition of mixed pixels and excessive dependence on high-resolution data

Latent Semantic Analysis as a Method of Content-Based Image Retrieval in Medical Applications

ERIC Educational Resources Information Center

Makovoz, Gennadiy

2010-01-01

The research investigated whether a Latent Semantic Analysis (LSA)-based approach to image retrieval can map pixel intensity into a smaller concept space with good accuracy and reasonable computational cost. From a large set of M computed tomography (CT) images, a retrieval query found all images for a particular patient based on semantic…

Multiview Locally Linear Embedding for Effective Medical Image Retrieval

PubMed Central

Shen, Hualei; Tao, Dacheng; Ma, Dianfu

2013-01-01

Content-based medical image retrieval continues to gain attention for its potential to assist radiological image interpretation and decision making. Many approaches have been proposed to improve the performance of medical image retrieval system, among which visual features such as SIFT, LBP, and intensity histogram play a critical role. Typically, these features are concatenated into a long vector to represent medical images, and thus traditional dimension reduction techniques such as locally linear embedding (LLE), principal component analysis (PCA), or laplacian eigenmaps (LE) can be employed to reduce the “curse of dimensionality”. Though these approaches show promising performance for medical image retrieval, the feature-concatenating method ignores the fact that different features have distinct physical meanings. In this paper, we propose a new method called multiview locally linear embedding (MLLE) for medical image retrieval. Following the patch alignment framework, MLLE preserves the geometric structure of the local patch in each feature space according to the LLE criterion. To explore complementary properties among a range of features, MLLE assigns different weights to local patches from different feature spaces. Finally, MLLE employs global coordinate alignment and alternating optimization techniques to learn a smooth low-dimensional embedding from different features. To justify the effectiveness of MLLE for medical image retrieval, we compare it with conventional spectral embedding methods. We conduct experiments on a subset of the IRMA medical image data set. Evaluation results show that MLLE outperforms state-of-the-art dimension reduction methods. PMID:24349277

Method of retrieving a liquid sample, a suction lysimeter, a portable suction lysimeter, a lysimeter system, and a deep lysimeter

DOEpatents

Hubbell, Joel M.; Sisson, James B.

2003-08-26

A method of retrieving a liquid sample comprises providing a portable lysimeter including a semi-permeable membrane and a chamber in fluid communication with the semi-permeable membrane; making a hole at a site from which a liquid sample is desired; evacuating the chamber by applying a vacuum to the chamber; lowering the portable lysimeter into the hole; obtaining a sample in the chamber; and retrieving the lysimeter from the bore; wherein it is not necessary to backfill the bore. A portable lysimeter includes a semi-permeable member and a chamber in fluid communication with the semi-permeable membrane.

A novel method to improve MODIS AOD retrievals in cloudy pixels using an analog ensemble approach

NASA Astrophysics Data System (ADS)

Kumar, R.; Raman, A.; Delle Monache, L.; Alessandrini, S.; Cheng, W. Y. Y.; Gaubert, B.; Arellano, A. F.

2016-12-01

Particulate matter (PM) concentrations are one of the fundamental indicators of air quality. Earth orbiting satellite platforms acquire column aerosol abundance that can in turn provide information about the PM concentrations. One of the serious limitations of column aerosol retrievals from low earth orbiting satellites is that these algorithms are based on clear sky assumptions. They do not retrieve AOD in cloudy pixels. After filtering cloudy pixels, these algorithms also arbitrarily remove brightest and darkest 25% of remaining pixels over ocean and brightest and darkest 50% pixels over land to filter any residual contamination from clouds. This becomes a critical issue especially in regions that experience monsoon, like Asia and North America. In case of North America, monsoon season experiences wide variety of extreme air quality events such as fires in California and dust storms in Arizona. Assessment of these episodic events warrants frequent monitoring of aerosol observations from remote sensing retrievals. In this study, we demonstrate a method to fill in cloudy pixels in Moderate Imaging Resolution Spectroradiometer (MODIS) AOD retrievals based on ensembles generated using an analog-based approach (AnEn). It provides a probabilistic distribution of AOD in cloudy pixels using historical records of model simulations of meteorological predictors such as AOD, relative humidity, and wind speed, and past observational records of MODIS AOD at a given target site. We use simulations from a coupled community weather forecasting model with chemistry (WRF-Chem) run at a resolution comparable to MODIS AOD. Analogs selected from summer months (June, July) of 2011-2013 from model and corresponding observations are used as a training dataset. Then, missing AOD retrievals in cloudy pixels in the last 31 days of the selected period are estimated. Here, we use AERONET stations as target sites to facilitate comparison against in-situ measurements. We use two approaches to

Lower Tropospheric Ozone Retrievals from Infrared Satellite Observations Using a Self-Adapting Regularization Method

NASA Astrophysics Data System (ADS)

Eremenko, M.; Sgheri, L.; Ridolfi, M.; Dufour, G.; Cuesta, J.

2017-12-01

Lower tropospheric ozone (O3) retrievals from nadir sounders is challenging due to the lack of vertical sensitivity of the measurements and towards the lowest layers. If improvements have been made during the last decade, it is still important to explore possibilities to improve the retrieval algorithms themselves. O3 retrieval from nadir satellite observations is an ill-conditioned problem, which requires regularization using constraint matrices. Up to now, most of the retrieval algorithms rely on a fixed constraint. The constraint is determined and fixed beforehand, on the basis of sensitivity tests. This does not allow ones to take advantage of the entire capabilities of the satellite measurements, which vary with the thermal conditions of the observed scenes. To overcome this limitation, we developed a self-adapting and altitude-dependent regularization scheme. A crucial step is the choice of the strength of the constraint. This choice is done during an iterative process and depends on the measurement errors and on the sensitivity of the measurements to the target parameters at the different altitudes. The challenge is to limit the use of a priori constraints to the minimal amount needed to perform the inversion. The algorithm has been tested on synthetic observations matching the future IASI-NG satellite instrument. IASI-NG measurements are simulated on the basis of O3 concentrations taken from an atmospheric model and retrieved using two retrieval schemes (the standard and self-adapting ones). Comparison of the results shows that the sensitivity of the observations to the O3 amount in the lowest layers (given by the degrees of freedom for the solution) is increased, which allows a better description of the ozone distribution, especially in the case of large ozone plumes. Biases are reduced and the spatial correlation is improved. Tentative of application to real observations from IASI, currently onboard the Metop satellite will also be presented.

Defining the Genetic Features of O-Antigen Biosynthesis Gene Cluster and Performance of an O-Antigen Serotyping Scheme for Escherichia albertii.

PubMed

Wang, Hong; Zheng, Han; Li, Qun; Xu, Yanmei; Wang, Jianping; Du, Pengcheng; Li, Xinqiong; Liu, Xiang; Zhang, Ling; Zou, Nianli; Yan, Guodong; Zhang, Zhengdong; Jing, Huaiqi; Xu, Jianguo; Xiong, Yanwen

2017-01-01

Escherichia albertii is a newly described and emerging diarrheagenic pathogen responsible for outbreaks of gastroenteritis. Serotyping plays an important role in diagnosis and epidemiological studies for pathogens of public health importance. The diversity of O-antigen biosynthesis gene clusters (O-AGCs) provides the primary basis for serotyping. However, little is known about the distribution and diversity of O-AGCs of E. albertii strains. Here, we presented a complete sequence set for the O-AGCs from 52 E. albertii strains and identified seven distinct O-AGCs. Six of these were also found in 15 genomes of E. albertii strains deposited in the public database. Possession of wzy / wzx genes in each O-AGC strongly suggest that O-antigens of E. albertii were synthesized by the Wzx/Wzy-dependent pathway. Furthermore, we performed an O-antigen serotyping scheme for E. albertii based on specific antisera against seven O-antigens and a high throughput xTAG Luminex assay to simultaneously detect seven O-AGCs. Both methods accurately identified serotypes of 64 tested E. albertii strains. Our data revealed the high-level diversity of O-AGCs in E. albertii . We also provide valuable methods to reliably identify and serotype this bacterium.

Improving Retrieval Performance by Relevance Feedback.

ERIC Educational Resources Information Center

Salton, Gerard; Buckley, Chris

1990-01-01

Briefly describes the principal relevance feedback methods that have been introduced over the years and evaluates the effectiveness of the methods in producing improved query formulations. Prescriptions are given for conducting text retrieval operations iteratively using relevance feedback. (24 references) (Author/CLB)

North Alabama Lightning Mapping Array (LMA): VHF Source Retrieval Algorithm and Error Analyses

NASA Technical Reports Server (NTRS)

Koshak, W. J.; Solakiewicz, R. J.; Blakeslee, R. J.; Goodman, S. J.; Christian, H. J.; Hall, J.; Bailey, J.; Krider, E. P.; Bateman, M. G.; Boccippio, D.

2003-01-01

Two approaches are used to characterize how accurately the North Alabama Lightning Mapping Array (LMA) is able to locate lightning VHF sources in space and in time. The first method uses a Monte Carlo computer simulation to estimate source retrieval errors. The simulation applies a VHF source retrieval algorithm that was recently developed at the NASA Marshall Space Flight Center (MSFC) and that is similar, but not identical to, the standard New Mexico Tech retrieval algorithm. The second method uses a purely theoretical technique (i.e., chi-squared Curvature Matrix Theory) to estimate retrieval errors. Both methods assume that the LMA system has an overall rms timing error of 50 ns, but all other possible errors (e.g., multiple sources per retrieval attempt) are neglected. The detailed spatial distributions of retrieval errors are provided. Given that the two methods are completely independent of one another, it is shown that they provide remarkably similar results. However, for many source locations, the Curvature Matrix Theory produces larger altitude error estimates than the (more realistic) Monte Carlo simulation.

Water vapour retrieval using the Precision Solar Spectroradiometer

NASA Astrophysics Data System (ADS)

Raptis, Panagiotis-Ioannis; Kazadzis, Stelios; Gröbner, Julian; Kouremeti, Natalia; Doppler, Lionel; Becker, Ralf; Helmis, Constantinos

2018-02-01

The Precision Solar Spectroradiometer (PSR) is a new spectroradiometer developed at Physikalisch-Meteorologisches Observatorium Davos - World Radiation Center (PMOD-WRC), Davos, measuring direct solar irradiance at the surface, in the 300-1020 nm spectral range and at high temporal resolution. The purpose of this work is to investigate the instrument's potential to retrieve integrated water vapour (IWV) using its spectral measurements. Two different approaches were developed in order to retrieve IWV: the first one uses single-channel and wavelength measurements, following a theoretical water vapour high absorption wavelength, and the second one uses direct sun irradiance integrated at a certain spectral region. IWV results have been validated using a 2-year data set, consisting of an AERONET sun-photometer Cimel CE318, a Global Positioning System (GPS), a microwave radiometer profiler (MWP) and radiosonde retrievals recorded at Meteorological Observatorium Lindenberg, Germany. For the monochromatic approach, better agreement with retrievals from other methods and instruments was achieved using the 946 nm channel, while for the spectral approach the 934-948 nm window was used. Compared to other instruments' retrievals, the monochromatic approach leads to mean relative differences up to 3.3 % with the coefficient of determination (R2) being in the region of 0.87-0.95, while for the spectral approach mean relative differences up to 0.7 % were recorded with R2 in the region of 0.96-0.98. Uncertainties related to IWV retrieval methods were investigated and found to be less than 0.28 cm for both methods. Absolute IWV deviations of differences between PSR and other instruments were determined the range of 0.08-0.30 cm and only in extreme cases would reach up to 15 %.

A publicly available benchmark for biomedical dataset retrieval: the reference standard for the 2016 bioCADDIE dataset retrieval challenge

PubMed Central

Gururaj, Anupama E.; Chen, Xiaoling; Pournejati, Saeid; Alter, George; Hersh, William R.; Demner-Fushman, Dina; Ohno-Machado, Lucila

2017-01-01

Abstract The rapid proliferation of publicly available biomedical datasets has provided abundant resources that are potentially of value as a means to reproduce prior experiments, and to generate and explore novel hypotheses. However, there are a number of barriers to the re-use of such datasets, which are distributed across a broad array of dataset repositories, focusing on different data types and indexed using different terminologies. New methods are needed to enable biomedical researchers to locate datasets of interest within this rapidly expanding information ecosystem, and new resources are needed for the formal evaluation of these methods as they emerge. In this paper, we describe the design and generation of a benchmark for information retrieval of biomedical datasets, which was developed and used for the 2016 bioCADDIE Dataset Retrieval Challenge. In the tradition of the seminal Cranfield experiments, and as exemplified by the Text Retrieval Conference (TREC), this benchmark includes a corpus (biomedical datasets), a set of queries, and relevance judgments relating these queries to elements of the corpus. This paper describes the process through which each of these elements was derived, with a focus on those aspects that distinguish this benchmark from typical information retrieval reference sets. Specifically, we discuss the origin of our queries in the context of a larger collaborative effort, the biomedical and healthCAre Data Discovery Index Ecosystem (bioCADDIE) consortium, and the distinguishing features of biomedical dataset retrieval as a task. The resulting benchmark set has been made publicly available to advance research in the area of biomedical dataset retrieval. Database URL: https://biocaddie.org/benchmark-data PMID:29220453

Enzyme-linked immunosorbent assay for detection of antibodies to Epstein-Barr virus antigens.

PubMed

Voevodin, A F; Pácsa, A S

1983-01-01

Enzyme-Linked Immunosorbent Assay (ELISA) was standardized for measurement of antibody activity of reference human and baboon (Papio hamadryas) sera to soluble Epstein-Barr virus (EBV) antigens. A comparison with the immunofluorescent (IF) method showed that ELISA detects antibody specifically and sensitivity. In ELISA, Herpesvirus Papio (HVP) nuclear antigen (HUPNA) positive baboon serum reacted with EBV nuclear antigen (EBNA), as a further indication of the antigenic similarity between HVP and EBV. Forty-two baboon sera were tested with EBV antigens in both ELISA and IF test. The results showed an agreement between the two methods and also that by the use of EBV antigens, ELISA measures anti-HVP activity of baboon sera. ELISA did not reveal significant difference in antibody activity of 23 baboons with lymphoma and that of 24 healthy baboons. Results provide further data that ELISA can be used effectively in the field of EBV serology.

Antigen processing and remodeling of the endosomal pathway: requirements for antigen cross-presentation.

PubMed

Compeer, Ewoud Bernardus; Flinsenberg, Thijs Willem Hendrik; van der Grein, Susanna Geertje; Boes, Marianne

2012-01-01

Cross-presentation of endocytosed antigen as peptide/class I major histocompatibility complex complexes plays a central role in the elicitation of CD8(+) T cell clones that mediate anti-viral and anti-tumor immune responses. While it has been clear that there are specific subsets of professional antigen presenting cells capable of antigen cross-presentation, identification of mechanisms involved is still ongoing. Especially amongst dendritic cells (DC), there are specialized subsets that are highly proficient at antigen cross-presentation. We here present a focused survey on the cell biological processes in the endosomal pathway that support antigen cross-presentation. This review highlights DC-intrinsic mechanisms that facilitate the cross-presentation of endocytosed antigen, including receptor-mediated uptake, maturation-induced endosomal sorting of membrane proteins, dynamic remodeling of endosomal structures and cell surface-directed endosomal trafficking. We will conclude with the description of pathogen-induced deviation of endosomal processing, and discuss how immune evasion strategies pertaining endosomal trafficking may preclude antigen cross-presentation.

Retrieval Attempts Enhance Learning, but Retrieval Success (versus Failure) Does Not Matter

ERIC Educational Resources Information Center

Kornell, Nate; Klein, Patricia Jacobs; Rawson, Katherine A.

2015-01-01

Retrieving information from memory enhances learning. We propose a 2-stage framework to explain the benefits of retrieval. Stage 1 takes place as one attempts to retrieve an answer, which activates knowledge related to the retrieval cue. Stage 2 begins when the answer becomes available, at which point appropriate connections are strengthened and…

An integrated content and metadata based retrieval system for art.

PubMed

Lewis, Paul H; Martinez, Kirk; Abas, Fazly Salleh; Fauzi, Mohammad Faizal Ahmad; Chan, Stephen C Y; Addis, Matthew J; Boniface, Mike J; Grimwood, Paul; Stevenson, Alison; Lahanier, Christian; Stevenson, James

2004-03-01

A new approach to image retrieval is presented in the domain of museum and gallery image collections. Specialist algorithms, developed to address specific retrieval tasks, are combined with more conventional content and metadata retrieval approaches, and implemented within a distributed architecture to provide cross-collection searching and navigation in a seamless way. External systems can access the different collections using interoperability protocols and open standards, which were extended to accommodate content based as well as text based retrieval paradigms. After a brief overview of the complete system, we describe the novel design and evaluation of some of the specialist image analysis algorithms including a method for image retrieval based on sub-image queries, retrievals based on very low quality images and retrieval using canvas crack patterns. We show how effective retrieval results can be achieved by real end-users consisting of major museums and galleries, accessing the distributed but integrated digital collections.

Methods for heel retrieval for tanks C-101, C-102, and C-111 at the Hanford Site

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

Sams, Terry L.; Kirch, N. W.; Reynolds, Jacob G.

The purpose of this paper is to evaluate the prospects of using bulk waste characteristics to determine the most appropriate heel retrieval technology. If the properties of hard to remove heels can be determined before bulk retrieval, then a heel retrieval technology can be selected before bulk retrieval is complete. This would save substantially on sampling costs and would allow the deployment of the heel retrieval technology immediately after bulk retrieval. The latter would also accelerate the heel removal schedule. A number of C-farm retrievals have been fully or partially completed at the time of this writing. Thus, there ismore » already substantial information on the success of different technologies and the composition of the heels. There is also substantial information on the waste types in each tank based on historical records. Therefore, this study will correlate the performance of technologies used so far and compare them to the known waste types in the tanks. This will be used to estimate the performance of future C Farm heel retrievals. An initial decision tree is developed and employed on tanks C-101, C-102, and C 111. An assumption of this study is that no additional characterization information would be available, before or after retrieval. Note that collecting additional information would substantially increase the probability of success. Deploying some in-situ testing technologies, such as a water lance or an in-situ Raman probe, might substantially increase the probability of successfully selecting the process conditions without having to take samples from the tanks for laboratory analysis.« less

Costs and benefits in item-method directed forgetting: differential effects of encoding and retrieval.

PubMed

Lee, Yuh-Shiow

2013-01-01

This study examined how encoding and retrieval factors affected directed forgetting costs and benefits in an item-method procedure. Experiment 1 used a typical item-method procedure and revealed a levels-of-processing effect in overall recall. However, the deep encoding condition showed a smaller directed forgetting effect than the shallow encoding conditions. More importantly, "remember" (R) words were selectively rehearsed as indicated by greater recall from the primacy portion of the list and more apt to be recalled before "forget" (F) words. Experiment 2 showed that a deep encoding operation reduced directed forgetting costs and that directed forgetting benefits occurred only when R words were recalled before F words. These findings supported the hypotheses that encoding manipulation affected directed forgetting costs and that directed forgetting benefits were associated with output order bias. Results were discussed in terms of mechanisms that produce item-method directed forgetting.

Natural texture retrieval based on perceptual similarity measurement

NASA Astrophysics Data System (ADS)

Gao, Ying; Dong, Junyu; Lou, Jianwen; Qi, Lin; Liu, Jun

2018-04-01

A typical texture retrieval system performs feature comparison and might not be able to make human-like judgments of image similarity. Meanwhile, it is commonly known that perceptual texture similarity is difficult to be described by traditional image features. In this paper, we propose a new texture retrieval scheme based on texture perceptual similarity. The key of the proposed scheme is that prediction of perceptual similarity is performed by learning a non-linear mapping from image features space to perceptual texture space by using Random Forest. We test the method on natural texture dataset and apply it on a new wallpapers dataset. Experimental results demonstrate that the proposed texture retrieval scheme with perceptual similarity improves the retrieval performance over traditional image features.

Pulse retrieval algorithm for interferometric frequency-resolved optical gating based on differential evolution.

PubMed

Hyyti, Janne; Escoto, Esmerando; Steinmeyer, Günter

2017-10-01

A novel algorithm for the ultrashort laser pulse characterization method of interferometric frequency-resolved optical gating (iFROG) is presented. Based on a genetic method, namely, differential evolution, the algorithm can exploit all available information of an iFROG measurement to retrieve the complex electric field of a pulse. The retrieval is subjected to a series of numerical tests to prove the robustness of the algorithm against experimental artifacts and noise. These tests show that the integrated error-correction mechanisms of the iFROG method can be successfully used to remove the effect from timing errors and spectrally varying efficiency in the detection. Moreover, the accuracy and noise resilience of the new algorithm are shown to outperform retrieval based on the generalized projections algorithm, which is widely used as the standard method in FROG retrieval. The differential evolution algorithm is further validated with experimental data, measured with unamplified three-cycle pulses from a mode-locked Ti:sapphire laser. Additionally introducing group delay dispersion in the beam path, the retrieval results show excellent agreement with independent measurements with a commercial pulse measurement device based on spectral phase interferometry for direct electric-field retrieval. Further experimental tests with strongly attenuated pulses indicate resilience of differential-evolution-based retrieval against massive measurement noise.

A Method to Retrieve the Multi-Receiver Moho Reflection Response from SH-Wave Scattering Coda in the Radiative Transfer Regime

NASA Astrophysics Data System (ADS)

Hartstra, I.; Wapenaar, C. P. A.

2015-12-01

We discuss a method to retrieve the multi-receiver Moho reflection response by interferometry from SH-wave coda in the 0.5-3 Hz frequency range. An image derived from a reflection response with a well defined virtual source would provide deterministic impedance contrasts, which can complement transmission tomography. For an accurate retrieval, cross-correlation interferometry requires the coda wave field to sample the imaging target and isotropically illuminate the receiver array. When these illumination requirements are not or only partially met, the stationary phase cannot be fully captured and artifacts will contaminate the retrieved reflection response. Here we conduct numerical scalar 2D finite difference simulations to investigate the challenging situation in which only shallow crustal earthquake sources illuminate the Moho and the response is recorded by a 2D linear array. We quantify to what extent the prevalence of scatterers in the crust can improve the illumination conditions and thus the retrieval of the Moho reflection. The accuracy of the retrieved reflection is evaluated for two physically different scattering regimes: the Rayleigh and Mie regime. We only use the earlier part of the scattering coda, because we have found that the later diffusive part does not significantly improve the retrieval. The density of the spherical scatterers is varied in order to change the scattering mean free path. This characteristic length scale is calculated for each model with the 2D radiative transfer equation, which is the governing equation in the earlier part of the scattering coda. The experiment is repeated for models of different geological settings derived from existing S-wave tomographies, which vary in Moho depth and reflectivity. The scattering mean free path can be approximated for real data if intrinsic attenuation is known, because the wavenumber-dependent scattering attenuation of the coherent wave amplitude is dependent on the scattering mean free path

Retrieval of Absorbing Aerosols Above Clouds retrieval over the South East Atlantic Ocean from MSG/SEVIRI

NASA Astrophysics Data System (ADS)

Peers, F.; Haywood, J. M.; Francis, P. N.; Meyer, K.; Platnick, S. E.

2017-12-01

Over the South East Atlantic Ocean, biomass burning aerosols from Southern Africa are frequently observed above clouds during fire season. However, the quantification of their interactions with both radiations and clouds remains uncertain because of a lack of information on aerosol properties and on their interaction process. In the last decade, methods have been developed to retrieve aerosol optical properties above clouds from satellite measurements, especially over the South East Atlantic Ocean. Most of these methods have been applied to polar orbiting instruments which prevent the analysis of aerosols and clouds at a sub-daily scale. With its wide spatial coverage and its high temporal resolution, the geostationary instrument SEVIRI, on board the MSG platform, offers a unique opportunity to monitor aerosols in this region and to evaluate their impact on clouds and their radiative effects. In this study, we will investigate the possibility of retrieving simultaneously aerosol and cloud properties (i.e. aerosol and cloud optical thicknesses and cloud droplet effective radius) when aerosols are located above clouds. The retrieved properties will then be compared with the ones obtained from MODIS [Meyer et al., 2015] as well as observations from the CLARIFY-2017 field campaign.

ABO, Rhesus, and Kell Antigens, Alleles, and Haplotypes in West Bengal, India

PubMed Central

Basu, Debapriya; Datta, Suvro Sankha; Montemayor, Celina; Bhattacharya, Prasun; Mukherjee, Krishnendu; Flegel, Willy A.

2018-01-01

Background Few studies have documented the blood group antigens in the population of eastern India. Frequencies of some common alleles and haplotypes were unknown. We describe phenotype, allele, and haplotype frequencies in the state of West Bengal, India. Methods We tested 1,528 blood donors at the Medical College Hospital, Kolkata. The common antigens of the ABO, Rhesus, and Kell blood group systems were determined by standard serologic methods in tubes. Allele and haplotype frequencies were calculated with an iterative method that yielded maximum-likelihood estimates under the assumption of a Hardy-Weinberg equilibrium. Results The prevalence of ABO antigens were B (34%), O (32%), A (25%), and AB (9%) with ABO allele frequencies for O = 0.567, A = 0.189, and B = 0.244. The D antigen (RH1) was observed in 96.6% of the blood donors with RH haplotype frequencies, such as for CDe = 0.688809, cde = 0.16983 and CdE = 0.000654. The K antigen (K1) was observed in 12 donors (0.79%) with KEL allele frequencies for K = 0.004 and k = 0.996. Conclusions: For the Bengali population living in the south of West Bengal, we established the frequencies of the major clinically relevant antigens in the ABO, Rhesus, and Kell blood group systems and derived estimates for the underlying ABO and KEL alleles and RH haplotypes. Such blood donor screening will improve the availability of compatible red cell units for transfusion. Our approach using widely available routine methods can readily be applied in other regions, where the sufficient supply of blood typed for the Rh and K antigens is lacking. PMID:29593462

Less we forget: retrieval cues and release from retrieval-induced forgetting.

PubMed

Jonker, Tanya R; Seli, Paul; Macleod, Colin M

2012-11-01

Retrieving some items from memory can impair the subsequent recall of other related but not retrieved items, a phenomenon called retrieval-induced forgetting (RIF). The dominant explanation of RIF-the inhibition account-asserts that forgetting occurs because related items are suppressed during retrieval practice to reduce retrieval competition. This item inhibition persists, making it more difficult to recall the related items on a later test. In our set of experiments, each category was designed such that each exemplar belonged to one of two subcategories (e.g., each BIRD exemplar was either a bird of prey or a pet bird), but this subcategory information was not made explicit during study or retrieval practice. Practicing retrieval of items from only one subcategory led to RIF for items from the other subcategory when cued only with the overall category label (BIRD) at test. However, adapting the technique of Gardiner, Craik, and Birtwistle (Journal of Learning and Verbal Behavior 11:778-783, 1972), providing subcategory cues during the final test eliminated RIF. The results challenge the inhibition account's fundamental assumption of cue independence but are consistent with a cue-based interference account.

Comparative evaluation of polarimetric and bi-spectral cloud microphysics retrievals: Retrieval closure experiments and comparisons based on idealized and LES case studies

NASA Astrophysics Data System (ADS)

Miller, D. J.; Zhang, Z.; Ackerman, A. S.; Platnick, S. E.; Cornet, C.

2016-12-01

A remote sensing cloud retrieval simulator, created by coupling an LES cloud model with vector radiative transfer (RT) models is the ideal framework for assessing cloud remote sensing techniques. This simulator serves as a tool for understanding bi-spectral and polarimetric retrievals by comparing them directly to LES cloud properties (retrieval closure comparison) and for comparing the retrieval techniques to one another. Our simulator utilizes the DHARMA LES [Ackerman et al., 2004] with cloud properties based on marine boundary layer (MBL) clouds observed during the DYCOMS-II and ATEX field campaigns. The cloud reflectances are produced by the vectorized RT models based on polarized doubling adding and monte carlo techniques (PDA, MCPOL). Retrievals are performed utilizing techniques as similar as possible to those implemented on their corresponding well known instruments; polarimetric retrievals are based on techniques implemented for polarimeters (POLDER, AirMSPI, and RSP) and bi-spectral retrievals are performed using the Nakajima-King LUT method utilized on a number of spectral instruments (MODIS and VIIRS). Retrieval comparisons focus on cloud droplet effective radius (re), effective variance (ve), and cloud optical thickness (τ). This work explores the sensitivities of these two retrieval techniques to various observation limitations, such as spatial resolution/cloud inhomogeneity, impact of 3D radiative effects, and angular resolution requirements. With future remote sensing missions like NASA's Aerosols/Clouds/Ecosystems (ACE) planning to feature advanced polarimetric instruments it is important to understand how these retrieval techniques compare to one another. The cloud retrieval simulator we've developed allows us to probe these important questions in a realistically relevant test bed.

Downscaling Thermal Infrared Radiance for Subpixel Land Surface Temperature Retrieval

PubMed Central

Liu, Desheng; Pu, Ruiliang

2008-01-01

Land surface temperature (LST) retrieved from satellite thermal sensors often consists of mixed temperature components. Retrieving subpixel LST is therefore needed in various environmental and ecological studies. In this paper, we developed two methods for downscaling coarse resolution thermal infrared (TIR) radiance for the purpose of subpixel temperature retrieval. The first method was developed on the basis of a scale-invariant physical model on TIR radiance. The second method was based on a statistical relationship between TIR radiance and land cover fraction at high spatial resolution. The two methods were applied to downscale simulated 990-m ASTER TIR data to 90-m resolution. When validated against the original 90-m ASTER TIR data, the results revealed that both downscaling methods were successful in capturing the general patterns of the original data and resolving considerable spatial details. Further quantitative assessments indicated a strong agreement between the true values and the estimated values by both methods. PMID:27879844

Downscaling Thermal Infrared Radiance for Subpixel Land Surface Temperature Retrieval.

PubMed

Liu, Desheng; Pu, Ruiliang

2008-04-06

Land surface temperature (LST) retrieved from satellite thermal sensors often consists of mixed temperature components. Retrieving subpixel LST is therefore needed in various environmental and ecological studies. In this paper, we developed two methods for downscaling coarse resolution thermal infrared (TIR) radiance for the purpose of subpixel temperature retrieval. The first method was developed on the basis of a scale-invariant physical model on TIR radiance. The second method was based on a statistical relationship between TIR radiance and land cover fraction at high spatial resolution. The two methods were applied to downscale simulated 990-m ASTER TIR data to 90-m resolution. When validated against the original 90-m ASTER TIR data, the results revealed that both downscaling methods were successful in capturing the general patterns of the original data and resolving considerable spatial details. Further quantitative assessments indicated a strong agreement between the true values and the estimated values by both methods.

Cancer vaccine--Antigenics.

PubMed

2002-01-01

Antigenics is developing a therapeutic cancer vaccine based on heat-shock proteins (HSPs). The vaccine [HSPPC-96, Oncophage] is in a pivotal phase III clinical trial for renal cancer at 80 clinical sites worldwide. The trial is enrolling at least 500 patients who are randomised to receive surgical removal of the primary tumour followed by out-patient treatment with Oncophage((R)) or surgery only. This study was initiated on the basis of results from a pilot phase I/II study and preliminary results from a phase II study in patients with renal cell cancer. In October 2001, Oncophage was designated as a fast-track product by the Food and Drug Administration in the US for the treatment of renal cell carcinoma. Oncophage is in phase I/II trials in Italy for colorectal cancer (30 patients) and melanoma. The trials in Italy are being conducted at the Istituto dei Tumouri, Milan (in association with Sigma-Tau). Preliminary data from the phase II trial for melanoma was presented at the AACR-NCI-EORTC International Conference in Florida, USA, in October 2001. Oncophage is also in a phase I/II (42 patients) and a phase II trial (84 patients) in the US for renal cell cancer, a phase II trial in the US for non-Hodgkin's lymphoma (35 patients), a phase II trial in the US for sarcoma (20-35 patients), a phase I/II trial in the US for melanoma (36 patients), and phase I/II trials in Germany for gastric (30 patients) and pancreatic cancers. A pilot phase I trial in patients with pancreatic cancer began in the US in 1997 with 5 patients enrolled. In November 2000, Antigenics announced that this trial had been expanded to a phase I/II study which would now include survival as an endpoint and would enroll 5 additional patients. The US trials are being performed at Memorial Sloan-Kettering Cancer Center and the M.D. Anderson Cancer Center. The trials in Germany are being carried out at Johannes Gutenberg-University Hospital, Mainz. Oncophage is an autologous vaccine consisting of

Retrieving Leaf Area Index (LAI) Using Remote Sensing: Theories, Methods and Sensors

PubMed Central

Zheng, Guang; Moskal, L. Monika

2009-01-01

The ability to accurately and rapidly acquire leaf area index (LAI) is an indispensable component of process-based ecological research facilitating the understanding of gas-vegetation exchange phenomenon at an array of spatial scales from the leaf to the landscape. However, LAI is difficult to directly acquire for large spatial extents due to its time consuming and work intensive nature. Such efforts have been significantly improved by the emergence of optical and active remote sensing techniques. This paper reviews the definitions and theories of LAI measurement with respect to direct and indirect methods. Then, the methodologies for LAI retrieval with regard to the characteristics of a range of remotely sensed datasets are discussed. Remote sensing indirect methods are subdivided into two categories of passive and active remote sensing, which are further categorized as terrestrial, aerial and satellite-born platforms. Due to a wide variety in spatial resolution of remotely sensed data and the requirements of ecological modeling, the scaling issue of LAI is discussed and special consideration is given to extrapolation of measurement to landscape and regional levels. PMID:22574042

Retrieving Leaf Area Index (LAI) Using Remote Sensing: Theories, Methods and Sensors.

PubMed

Zheng, Guang; Moskal, L Monika

2009-01-01

The ability to accurately and rapidly acquire leaf area index (LAI) is an indispensable component of process-based ecological research facilitating the understanding of gas-vegetation exchange phenomenon at an array of spatial scales from the leaf to the landscape. However, LAI is difficult to directly acquire for large spatial extents due to its time consuming and work intensive nature. Such efforts have been significantly improved by the emergence of optical and active remote sensing techniques. This paper reviews the definitions and theories of LAI measurement with respect to direct and indirect methods. Then, the methodologies for LAI retrieval with regard to the characteristics of a range of remotely sensed datasets are discussed. Remote sensing indirect methods are subdivided into two categories of passive and active remote sensing, which are further categorized as terrestrial, aerial and satellite-born platforms. Due to a wide variety in spatial resolution of remotely sensed data and the requirements of ecological modeling, the scaling issue of LAI is discussed and special consideration is given to extrapolation of measurement to landscape and regional levels.

Retrieval of tropospheric carbon monoxide for the MOPITT experiment

NASA Astrophysics Data System (ADS)

Pan, Liwen; Gille, John C.; Edwards, David P.; Bailey, Paul L.; Rodgers, Clive D.

1998-12-01

A retrieval method for deriving the tropospheric carbon monoxide (CO) profile and column amount under clear sky conditions has been developed for the Measurements of Pollution In The Troposphere (MOPITT) instrument, scheduled for launch in 1998 onboard the EOS-AM1 satellite. This paper presents a description of the method along with analyses of retrieval information content. These analyses characterize the forward measurement sensitivity, the contribution of a priori information, and the retrieval vertical resolution. Ensembles of tropospheric CO profiles were compiled both from aircraft in situ measurements and from chemical model results and were used in retrieval experiments to characterize the method and to study the sensitivity to different parameters. Linear error analyses were carried out in parallel with the ensemble experiments. Results of these experiments and analyses indicate that MOPITT CO column measurements will have better than 10% precision, and CO profile measurement will have approximately three pieces of independent information that will resolve 3-5 tropospheric layers to approximately 10% precision. These analyses are important for understanding MOPITT data, both for application of data in tropospheric chemistry studies and for comparison with in situ measurements.

Frequency and reactivity of antigen-specific T cells were concurrently measured through the combination of artificial antigen-presenting cell, MACS and ELISPOT.

PubMed

Shen, Chuanlai; Xu, Tao; Wu, You; Li, Xiaoe; Xia, Lingzhi; Wang, Wei; Shahzad, Khawar Ali; Zhang, Lei; Wan, Xin; Qiu, Jie

2017-11-27

Conventional peptide-major histocompatibility complex (pMHC) multimer staining, intracellular cytokine staining, and enzyme-linked immunospot (ELISPOT) assay cannot concurrently determine the frequency and reactivity of antigen-specific T cells (AST) in a single assay. In this report, pMHC multimer, magnetic-activated cell sorting (MACS), and ELISPOT techniques have been integrated into a micro well by coupling pMHC multimers onto cell-sized magnetic beads to characterize AST cell populations in a 96-well microplate which pre-coated with cytokine-capture antibodies. This method, termed AAPC-microplate, allows the enumeration and local cytokine production of AST cells in a single assay without using flow cytometry or fluorescence intensity scanning, thus will be widely applicable. Here, ovalbumin 257-264 -specific CD8 + T cells from OT-1 T cell receptor (TCR) transgenic mice were measured. The methodological accuracy, specificity, reproducibility, and sensitivity in enumerating AST cells compared well with conventional pMHC multimer staining. Furthermore, the AAPC-microplate was applied to detect the frequency and reactivity of Hepatitis B virus (HBV) core antigen 18-27 - and surface antigen 183-191 -specific CD8 + T cells for the patients, and was compared with conventional method. This method without the need of high-end instruments may facilitate the routine analysis of patient-specific cellular immune response pattern to a given antigen in translational studies.

Computer Information Retrieval for Journalists.

ERIC Educational Resources Information Center

Rodewald, Pam

1989-01-01

Discusses the use of computer information retrieval (on-line electronic search methods). Examines advantages and disadvantages of on-line searching versus manual searching. Offers questions to help in the decision to purchase and use on-line searching with students. (MS)

Efficient view based 3-D object retrieval using Hidden Markov Model

NASA Astrophysics Data System (ADS)

Jain, Yogendra Kumar; Singh, Roshan Kumar

2013-12-01

Recent research effort has been dedicated to view based 3-D object retrieval, because of highly discriminative property of 3-D object and has multi view representation. The state-of-art method is highly depending on their own camera array setting for capturing views of 3-D object and use complex Zernike descriptor, HAC for representative view selection which limit their practical application and make it inefficient for retrieval. Therefore, an efficient and effective algorithm is required for 3-D Object Retrieval. In order to move toward a general framework for efficient 3-D object retrieval which is independent of camera array setting and avoidance of representative view selection, we propose an Efficient View Based 3-D Object Retrieval (EVBOR) method using Hidden Markov Model (HMM). In this framework, each object is represented by independent set of view, which means views are captured from any direction without any camera array restriction. In this, views are clustered (including query view) to generate the view cluster, which is then used to build the query model with HMM. In our proposed method, HMM is used in twofold: in the training (i.e. HMM estimate) and in the retrieval (i.e. HMM decode). The query model is trained by using these view clusters. The EVBOR query model is worked on the basis of query model combining with HMM. The proposed approach remove statically camera array setting for view capturing and can be apply for any 3-D object database to retrieve 3-D object efficiently and effectively. Experimental results demonstrate that the proposed scheme has shown better performance than existing methods. [Figure not available: see fulltext.

Antigen clasping by two antigen-binding sites of an exceptionally specific antibody for histone methylation

DOE PAGES

Hattori, Takamitsu; Lai, Darson; Dementieva, Irina S.; ...

2016-02-09

Antibodies have a well-established modular architecture wherein the antigen-binding site residing in the antigen-binding fragment (Fab or Fv) is an autonomous and complete unit for antigen recognition. Here, we describe antibodies departing from this paradigm. We developed recombinant antibodies to trimethylated lysine residues on histone H3, important epigenetic marks and challenging targets for molecular recognition. Quantitative characterization demonstrated their exquisite specificity and high affinity, and they performed well in common epigenetics applications. Surprisingly, crystal structures and biophysical analyses revealed that two antigen-binding sites of these antibodies form a head-to-head dimer and cooperatively recognize the antigen in the dimer interface. Thismore » “antigen clasping” produced an expansive interface where trimethylated Lys bound to an unusually extensive aromatic cage in one Fab and the histone N terminus to a pocket in the other, thereby rationalizing the high specificity. A long-neck antibody format with a long linker between the antigen-binding module and the Fc region facilitated antigen clasping and achieved both high specificity and high potency. Antigen clasping substantially expands the paradigm of antibody–antigen recognition and suggests a strategy for developing extremely specific antibodies.« less

Antigen clasping by two antigen-binding sites of an exceptionally specific antibody for histone methylation

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

Hattori, Takamitsu; Lai, Darson; Dementieva, Irina S.

Antibodies have a well-established modular architecture wherein the antigen-binding site residing in the antigen-binding fragment (Fab or Fv) is an autonomous and complete unit for antigen recognition. Here, we describe antibodies departing from this paradigm. We developed recombinant antibodies to trimethylated lysine residues on histone H3, important epigenetic marks and challenging targets for molecular recognition. Quantitative characterization demonstrated their exquisite specificity and high affinity, and they performed well in common epigenetics applications. Surprisingly, crystal structures and biophysical analyses revealed that two antigen-binding sites of these antibodies form a head-to-head dimer and cooperatively recognize the antigen in the dimer interface. Thismore » “antigen clasping” produced an expansive interface where trimethylated Lys bound to an unusually extensive aromatic cage in one Fab and the histone N terminus to a pocket in the other, thereby rationalizing the high specificity. A long-neck antibody format with a long linker between the antigen-binding module and the Fc region facilitated antigen clasping and achieved both high specificity and high potency. Antigen clasping substantially expands the paradigm of antibody–antigen recognition and suggests a strategy for developing extremely specific antibodies.« less

Intelligent retrieval of medical images from the Internet

NASA Astrophysics Data System (ADS)

Tang, Yau-Kuo; Chiang, Ted T.

1996-05-01

The object of this study is using Internet resources to provide a cost-effective, user-friendly method to access the medical image archive system and to provide an easy method for the user to identify the images required. This paper describes the prototype system architecture, the implementation, and results. In the study, we prototype the Intelligent Medical Image Retrieval (IMIR) system as a Hypertext Transport Prototype server and provide Hypertext Markup Language forms for user, as an Internet client, using browser to enter image retrieval criteria for review. We are developing the intelligent retrieval engine, with the capability to map the free text search criteria to the standard terminology used for medical image identification. We evaluate retrieved records based on the number of the free text entries matched and their relevance level to the standard terminology. We are in the integration and testing phase. We have collected only a few different types of images for testing and have trained a few phrases to map the free text to the standard medical terminology. Nevertheless, we are able to demonstrate the IMIR's ability to search, retrieve, and review medical images from the archives using general Internet browser. The prototype also uncovered potential problems in performance, security, and accuracy. Additional studies and enhancements will make the system clinically operational.

Detection of influenza antigenic variants directly from clinical samples using polyclonal antibody based proximity ligation assays

PubMed Central

Martin, Brigitte E.; Jia, Kun; Sun, Hailiang; Ye, Jianqiang; Hall, Crystal; Ware, Daphne; Wan, Xiu-Feng

2016-01-01

Identification of antigenic variants is the key to a successful influenza vaccination program. The empirical serological methods to determine influenza antigenic properties require viral propagation. Here a novel quantitative PCR-based antigenic characterization method using polyclonal antibody and proximity ligation assays, or so-called polyPLA, was developed and validated. This method can detect a viral titer that is less than 1000 TCID50/mL. Not only can this method differentiate between different HA subtypes of influenza viruses but also effectively identify antigenic drift events within the same HA subtype of influenza viruses. Applications in H3N2 seasonal influenza data showed that the results from this novel method are consistent with those from the conventional serological assays. This method is not limited to the detection of antigenic variants in influenza but also other pathogens. It has the potential to be applied through a large-scale platform in disease surveillance requiring minimal biosafety and directly using clinical samples. PMID:25546251

Assessment of Snared-Loop Technique When Standard Retrieval of Inferior Vena Cava Filters Fails

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

Doody, Orla, E-mail: orla_doody@hotmail.com; Noe, Geertje; Given, Mark F.

Purpose To identify the success and complications related to a variant technique used to retrieve inferior vena cava filters when simple snare approach has failed. Methods A retrospective review of all Cook Guenther Tulip filters and Cook Celect filters retrieved between July 2006 and February 2008 was performed. During this period, 130 filter retrievals were attempted. In 33 cases, the standard retrieval technique failed. Retrieval was subsequently attempted with our modified retrieval technique. Results The retrieval was successful in 23 cases (mean dwell time, 171.84 days; range, 5-505 days) and unsuccessful in 10 cases (mean dwell time, 162.2 days; range,more » 94-360 days). Our filter retrievability rates increased from 74.6% with the standard retrieval method to 92.3% when the snared-loop technique was used. Unsuccessful retrieval was due to significant endothelialization (n = 9) and caval penetration by the filter (n = 1). A single complication occurred in the group, in a patient developing pulmonary emboli after attempted retrieval. Conclusion The technique we describe increased the retrievability of the two filters studied. Hook endothelialization is the main factor resulting in failed retrieval and continues to be a limitation with these filters.« less

Measurement of plasminogen activator inhibitor type 1 antigen: comparison of Tintelize and Imubind methods.

PubMed

Stroop, D M; Glueck, C J; Tracy, T M; Schumacher, H R

1994-12-01

Our specific aim was to compare three plasminogen activator-inhibitor type 1 (PAI-1) antigen ELISA kit assays (the Biopool AB, Ltd, TintElize PAI-1 Strip-Well Format; the American Diagnostica, Inc., Imubind 822/1; and the second generation Imubind 822/1S). Within-run coefficients of variation (n = 6) for the TintElize, Imubind 822/1 and Imubind 822/1S methods were 5.5%, 5.9% and 6.8%, respectively. Between-run coefficients of variation for six aliquots per run were 2.9% for TintElize, 3.8% for Imubind 822/1, and 3.5% for Imubind 822/1S. Comparison of the average of duplicate aliquots from hyperlipidaemic patients demonstrated intraclass correlations of 0.75, 0.79 and 0.95 for TintElize vs Imubind 822/1 (n = 39), TintElize vs Imubind 822/1S (n = 39), and Imubind 822/1 vs 822/1S (n = 84), respectively. Lower 95% confidence interval limits of the intraclass correlation were 0.55, 0.48 and 0.93, respectively. Mean PAI-1 antigen values (n = 39) were 12.1, 15.8, 15.8 and 16.0 ng/ml, respectively, for TintElize, TintElize without using the quenching well, Imubind 822/1, and Imubind 822/1S. All three methods were easily performed and exhibited high correlation and reproducibility. A significant systematic bias (P < 0.006) existed between TintElize and TintElize without using the quenching well, Imubind 822/1, and Imubind 822/1S. However, there was no significant bias when TintElize without using the quenching well is compared with Imubind 822/1 (P > 0.8) and to 822/1S (P > 0.8) nor is there significant systematic bias between Imubind 822/1 and 822/1S (P > 0.3). By convention, interchangeability between assay methods suggests that the lower limit of the 95% intraclass correlation confidence interval be greater than 0.75.(ABSTRACT TRUNCATED AT 250 WORDS)

Probing the Energetics of Antigen-Antibody Recognition by Titration Microcalorimetry

PubMed

Jelesarov; Leder; Bosshard

1996-06-01

Our understanding of the energetics that govern antigen-antibody recognition lags behind the increasingly rapid accumulation of structural information on antigen-antibody complexes. Thanks to the development of highly sensitive microcalorimeters, the thermodynamic parameters of antigen-antibody interactions can now be measured with precision and using only nanomole quantities of protein. The method of choice is isothermal titration calorimetry, in which a solution of the antibody (or antigen) is titrated with small aliquots of the antigen (or antibody) and the heat change accompanying the formation of the antigen-antibody complex is measured with a sensitivity as high as 0.1 μcal s-1. The free energy of binding (DeltaG), the binding enthalpy (DeltaH), and the binding entropy (DeltaS) are usually obtained from a single experiment, and no spectroscopic or radioactive label must be introduced into the antigen or antibody. The often large and negative change in heat capacity (DeltaCp) accompanying the formation of an antigen-antibody complex is obtained from DeltaH measured at different temperatures. The basic theory and the principle of the measurements are reviewed and illustrated by examples. The thermodynamic parameters relate to the dynamic physical forces that govern the association of the freely moving antigen and antibody into a well-structured and unique complex. This information complements the static picture of the antigen-antibody complex that results from X-ray diffraction analysis. Attempts to correlate dynamic and static aspects are discussed briefly.

Phase retrieval using a modified Shack-Hartmann wavefront sensor with defocus.

PubMed

Li, Changwei; Li, Bangming; Zhang, Sijiong

2014-02-01

This paper proposes a modified Shack-Hartmann wavefront sensor for phase retrieval. The sensor is revamped by placing a detector at a defocused plane before the focal plane of the lenslet array of the Shack-Hartmann sensor. The algorithm for phase retrieval is an optimization with initial Zernike coefficients calculated by the conventional phase reconstruction of the Shack-Hartmann sensor. Numerical simulations show that the proposed sensor permits sensitive, accurate phase retrieval. Furthermore, experiments tested the feasibility of phase retrieval using the proposed sensor. The surface irregularity for a flat mirror was measured by the proposed method and a Veeco interferometer, respectively. The irregularity for the mirror measured by the proposed method is in very good agreement with that measured using the Veeco interferometer.

Complex amplitude reconstruction by iterative amplitude-phase retrieval algorithm with reference

NASA Astrophysics Data System (ADS)

Shen, Cheng; Guo, Cheng; Tan, Jiubin; Liu, Shutian; Liu, Zhengjun

2018-06-01

Multi-image iterative phase retrieval methods have been successfully applied in plenty of research fields due to their simple but efficient implementation. However, there is a mismatch between the measurement of the first long imaging distance and the sequential interval. In this paper, an amplitude-phase retrieval algorithm with reference is put forward without additional measurements or priori knowledge. It gets rid of measuring the first imaging distance. With a designed update formula, it significantly raises the convergence speed and the reconstruction fidelity, especially in phase retrieval. Its superiority over the original amplitude-phase retrieval (APR) method is validated by numerical analysis and experiments. Furthermore, it provides a conceptual design of a compact holographic image sensor, which can achieve numerical refocusing easily.

A Minimally Invasive Method for Retrieving Single Adherent Cells of Different Types from Cultures

PubMed Central

Zeng, Jia; Mohammadreza, Aida; Gao, Weimin; Merza, Saeed; Smith, Dean; Kelbauskas, Laimonas; Meldrum, Deirdre R.

2014-01-01

The field of single-cell analysis has gained a significant momentum over the last decade. Separation and isolation of individual cells is an indispensable step in almost all currently available single-cell analysis technologies. However, stress levels introduced by such manipulations remain largely unstudied. We present a method for minimally invasive retrieval of selected individual adherent cells of different types from cell cultures. The method is based on a combination of mechanical (shear flow) force and biochemical (trypsin digestion) treatment. We quantified alterations in the transcription levels of stress response genes in individual cells exposed to varying levels of shear flow and trypsinization. We report optimal temperature, RNA preservation reagents, shear force and trypsinization conditions necessary to minimize changes in the stress-related gene expression levels. The method and experimental findings are broadly applicable and can be used by a broad research community working in the field of single cell analysis. PMID:24957932

Retrieval of cloud properties from POLDER-3 data using the neural network approach

NASA Astrophysics Data System (ADS)

Di Noia, A.; Hasekamp, O. P.

2017-12-01

Satellite multi-angle spectroplarimetry is a useful technique for observing the microphysical properties of clouds and aerosols. Most of the algorithms for the retrieval of cloud and aerosol properties from satellite measurements require multiple calls to radiative transfer models, which make the retrieval computationally expensive. A traditional alternative to these schemes is represented by lookup-tables (LUTs), where the retrieval is performed by choosing, within a predefined database of combinations of clouds or aerosol properties, the combination that best fits the measurements. LUT retrievals are quicker than full-physics, iterative retrievals, but their accuracy is limited by the number of entries stored in the LUT. Another retrieval method capable of producing very quick retrievals without a big sacrifice in accuracy is the neural network method. Neural network methods are routinely applied to several types of satellite measurements, but their application to multi-angle spectropolarimetric data is still in its early stage, because of the difficulty of accounting for the angular variability of the measurements in the training process. We have recently developed a neural network scheme for the retrieval of cloud properties from POLDER-3 data. The neural network retrieval is trained using synthetic measurements performed for realistic combinations of cloud properties and measurement angles, and is able to process an entire orbit in about 20 seconds. Comparisons of the retrieved cloud properties with Moderate Resolution Imaging Spectroradiometer (MODIS) gridded products during one year show encouraging retrieval performance for cloud optical thickness and effective radius. A discussion of the setup of the neural network and of the validation results will be the main topic of our presentation.

Imaging of blood antigen distribution on blood cells by thermal lens microscopy

NASA Astrophysics Data System (ADS)

Kimura, Hiroko; Sekiguchi, Kazuya; Nagao, Fumiko; Mukaida, Masahiro; Kitamori, Takehiko; Sawada, Tsuguo

2000-05-01

Blood group antigens on a cell were measured by a new microscopic method, i.e. thermal lens microscopy which involves spectrometry using a laser-induced thermal-lens effect. The blood group antigen was immunologically stained using antibody labeled with colloidal gold. Human leukocyte antigens (HLA) on lymphocytes and mononuclear leukocytes were observed by the thermal lens microscope, and Lewis blood group antigens on erythrocytes and polymorphonuclear leukocytes were also observed. The antigen distribution on each cell-surface was imaged using this technique. In spite of convex surface of living cells, colloidal gold was correctly quantified by adjusting the deviation of the focal point of the probe laser by the phase of the signal. In the measurement of leukocyte antigens, antigens of HLA-A, -B, -C loci on the lymphocytes were identified and quantitated by using a single cell. The image of HLA-A, -B, -C antigen distribution on a mononuclear leukocyte was obtained. In the measurement of erythrocyte antigens, a small quantity of Lewis antigens was detected on the cord erythrocytes. Localized small quantities of membrane antigens are better quantitated without extraction or cytolysis. Our thermal lens microscope is a powerful and highly sensitive analytical tool for detecting and quantitating localized antigens in single cells and/or cell-surface-associated molecules.

Propagation based phase retrieval of simulated intensity measurements using artificial neural networks

NASA Astrophysics Data System (ADS)

Kemp, Z. D. C.

2018-04-01

Determining the phase of a wave from intensity measurements has many applications in fields such as electron microscopy, visible light optics, and medical imaging. Propagation based phase retrieval, where the phase is obtained from defocused images, has shown significant promise. There are, however, limitations in the accuracy of the retrieved phase arising from such methods. Sources of error include shot noise, image misalignment, and diffraction artifacts. We explore the use of artificial neural networks (ANNs) to improve the accuracy of propagation based phase retrieval algorithms applied to simulated intensity measurements. We employ a phase retrieval algorithm based on the transport-of-intensity equation to obtain the phase from simulated micrographs of procedurally generated specimens. We then train an ANN with pairs of retrieved and exact phases, and use the trained ANN to process a test set of retrieved phase maps. The total error in the phase is significantly reduced using this method. We also discuss a variety of potential extensions to this work.

Comparisons of Upper Tropospheric Humidity Retrievals from TOVS and METEOSAT

NASA Technical Reports Server (NTRS)

Escoffier, C.; Bates, J.; Chedin, A.; Rossow, W. B.; Schmetz, J.

1999-01-01

Two different methods for retrieving Upper Tropospheric Humidities (UTH) from the TOVS (TIROS Operational Vertical Sounder) instruments aboard NOAA polar orbiting satellites are presented and compared. The first one, from the Environmental Technology Laboratory, computed by J. Bates and D. Jackson (hereafter BJ method), estimates UTH from a simplified radiative transfer analysis of the upper tropospheric infrared water vapor channel at wavelength measured by HIRS (6.3 micrometer). The second one results from a neural network analysis of the TOVS (HIRS and MSU) data developed at, the Laboratoire de Meteorologie Dynamique (hereafter the 3I (Improved Initialization Inversion) method). Although the two methods give very similar retrievals in temperate regions (30-60 N and S), an absolute bias up to 16% appears in the convective zone of the tropics. The two datasets have also been compared with UTH retrievals from infrared radiance measurements in the 6.3 micrometer channel from the geostationary satellite METEOSAT (hereafter MET method). The METEOSAT retrievals are systematically drier than the TOVS-based results by an absolute bias between 5 and 25%. Despite the biases, the spatial and temporal correlations are very good. The purpose of this study is to explain the deviations observed between the three datasets. The sensitivity of UTH to air temperature and humidity profiles is analysed as are the clouds effects. Overall, the comparison of the three retrievals gives an assessment of the current uncertainties in water vapor amounts in the upper troposphere as determined from NOAA and METEOSAT satellites.

Cloud-top height retrieval from polarizing remote sensor POLDER

NASA Astrophysics Data System (ADS)

He, Xianqiang; Pan, Delu; Yan, Bai; Mao, Zhihua

2006-10-01

A new cloud-top height retrieval method is proposed by using polarizing remote sensing. In cloudy conditions, it shows that, in purple and blue bands, linear polarizing radiance at the top-of-atmosphere (TOA) is mainly contributed by Rayleigh scattering of the atmosphere's molecules above cloud, and the contribution by cloud reflection and aerosol scattering can be neglected. With such characteristics, the basis principle and method of cloud-top height retrieval using polarizing remote sensing are presented in detail, and tested by the polarizing remote sensing data of POLDER. The satellite-derived cloud-top height product can not only show the distribution of global cloud-top height, but also obtain the cloud-top height distribution of moderate-scale meteorological phenomena like hurricanes and typhoons. This new method is promising to become the operational algorithm for cloud-top height retrieval for POLDER and the future polarizing remote sensing satellites.

A fast image retrieval method based on SVM and imbalanced samples in filtering multimedia message spam

NASA Astrophysics Data System (ADS)

Chen, Zhang; Peng, Zhenming; Peng, Lingbing; Liao, Dongyi; He, Xin

2011-11-01

With the swift and violent development of the Multimedia Messaging Service (MMS), it becomes an urgent task to filter the Multimedia Message (MM) spam effectively in real-time. For the fact that most MMs contain images or videos, a method based on retrieving images is given in this paper for filtering MM spam. The detection method used in this paper is a combination of skin-color detection, texture detection, and face detection, and the classifier for this imbalanced problem is a very fast multi-classification combining Support vector machine (SVM) with unilateral binary decision tree. The experiments on 3 test sets show that the proposed method is effective, with the interception rate up to 60% and the average detection time for each image less than 1 second.

Retrieving vertical ozone profiles from measurements of global spectral irradiance

NASA Astrophysics Data System (ADS)

Bernhard, Germar; Petropavlovskikh, Irina; Mayer, Bernhard

2017-12-01

A new method is presented to determine vertical ozone profiles from measurements of spectral global (direct Sun plus upper hemisphere) irradiance in the ultraviolet. The method is similar to the widely used Umkehr technique, which inverts measurements of zenith sky radiance. The procedure was applied to measurements of a high-resolution spectroradiometer installed near the centre of the Greenland ice sheet. Retrieved profiles were validated with balloon-sonde observations and ozone profiles from the space-borne Microwave Limb Sounder (MLS). Depending on altitude, the bias between retrieval results presented in this paper and MLS observations ranges between -5 and +3 %. The magnitude of this bias is comparable, if not smaller, to values reported in the literature for the standard Dobson Umkehr method. Total ozone columns (TOCs) calculated from the retrieved profiles agree to within 0.7±2.0 % (±1σ) with TOCs measured by the Ozone Monitoring Instrument on board the Aura satellite. The new method is called the Global-Umkehr method.

Manufacture of Clinical-Grade CD19-Specific T Cells Stably Expressing Chimeric Antigen Receptor Using Sleeping Beauty System and Artificial Antigen Presenting Cells

PubMed Central

Singh, Harjeet; Figliola, Matthew J.; Dawson, Margaret J.; Olivares, Simon; Zhang, Ling; Yang, Ge; Maiti, Sourindra; Manuri, Pallavi; Senyukov, Vladimir; Jena, Bipulendu; Kebriaei, Partow; Champlin, Richard E.; Huls, Helen; Cooper, Laurence J. N.

2013-01-01

Adoptive transfer of T cells expressing a CD19-specific chimeric antigen receptor (CAR) is being evaluated in multiple clinical trials. Our current approach to adoptive immunotherapy is based on a second generation CAR (designated CD19RCD28) that signals through a CD28 and CD3-ζ endodomain. T cells are electroporated with DNA plasmids from the Sleeping Beauty (SB) transposon/transposase system to express this CAR. Stable integrants of genetically modified T cells can then be retrieved when co-cultured with designer artificial antigen presenting cells (aAPC) in the presence of interleukin (IL)-2 and 21. Here, we reveal how the platform technologies of SB-mediated transposition and CAR-dependent propagation on aAPC were adapted for human application. Indeed, we have initiated clinical trials in patients with high-risk B-lineage malignancies undergoing autologous and allogeneic hematopoietic stem-cell transplantation (HSCT). We describe the process to manufacture clinical grade CD19-specific T cells derived from healthy donors. Three validation runs were completed in compliance with current good manufacturing practice for Phase I/II trials demonstrating that by 28 days of co-culture on γ-irradiated aAPC ∼1010 T cells were produced of which >95% expressed CAR. These genetically modified and propagated T cells met all quality control testing and release criteria in support of infusion. PMID:23741305

Calcium-dependent antigen binding as a novel modality for antibody recycling by endosomal antigen dissociation

PubMed Central

Hironiwa, N; Ishii, S; Kadono, S; Iwayanagi, Y; Mimoto, F; Habu, K; Igawa, T; Hattori, K

2016-01-01

The pH-dependent antigen binding antibody, termed a recycling antibody, has recently been reported as an attractive type of second-generation engineered therapeutic antibody. A recycling antibody can dissociate antigen in the acidic endosome, and thus bind to its antigen multiple times. As a consequence, a recycling antibody can neutralize large amounts of antigen in plasma. Because this approach relies on histidine residues to achieve pH-dependent antigen binding, which could limit the epitopes that can be targeted and affect the rate of antigen dissociation in the endosome, we explored an alternative approach for generating recycling antibodies. Since calcium ion concentration is known to be lower in endosome than in plasma, we hypothesized that an antibody with antigen-binding properties that are calcium-dependent could be used as recycling antibody. Here, we report a novel anti-interleukin-6 receptor (IL-6R) antibody, identified from a phage library that binds to IL-6R only in the presence of a calcium ion. Thermal dynamics and a crystal structure study revealed that the calcium ion binds to the heavy chain CDR3 region (HCDR3), which changes and possibly stabilizes the structure of HCDR3 to make it bind to antigen calcium dependently (PDB 5AZE). In vitro and in vivo studies confirmed that this calcium-dependent antigen-binding antibody can dissociate its antigen in the endosome and accelerate antigen clearance from plasma, making it a novel approach for generating recycling antibody. PMID:26496237

Chlorphenesin: an Antigen-Associated Immunosuppressant

PubMed Central

Whang, H. Y.; Neter, E.

1970-01-01

Chlorphenesin (3-p-chlorophenoxy-1,2-propanediol), when injected intravenously together with either of two common bacterial antigens, inhibits the antibody response of the rabbit. The antigens studied are those common to Enterobacteriaceae and to gram-positive bacteria. The immunosuppression is contingent upon incubation of chlorphenesin and antigen in vitro prior to administration, since separate injection of antigen and inhibitor or of mixtures without prior incubation yields undiminished antibody response. Chlorphenesin, as shown by hemagglutination-inhibition tests, does not alter the antigenic determinants, because antibody neutralization occurs in the presence or absence of the drug. The immunosuppressive effect is reversible, since precipitation of chlorphenesin at 4 C substantially restores immunogenicity. Animals immunized with antigen-drug mixtures, which fail to respond with significant antibody production, nonetheless are immunologically primed. It is concluded that chlorphenesin represents another example of antigen-associated immunosuppressants. PMID:16557800

Chlorphenesin: an antigen-associated immunosuppressant.

PubMed

Whang, H Y; Neter, E

1970-07-01

Chlorphenesin (3-p-chlorophenoxy-1,2-propanediol), when injected intravenously together with either of two common bacterial antigens, inhibits the antibody response of the rabbit. The antigens studied are those common to Enterobacteriaceae and to gram-positive bacteria. The immunosuppression is contingent upon incubation of chlorphenesin and antigen in vitro prior to administration, since separate injection of antigen and inhibitor or of mixtures without prior incubation yields undiminished antibody response. Chlorphenesin, as shown by hemagglutination-inhibition tests, does not alter the antigenic determinants, because antibody neutralization occurs in the presence or absence of the drug. The immunosuppressive effect is reversible, since precipitation of chlorphenesin at 4 C substantially restores immunogenicity. Animals immunized with antigen-drug mixtures, which fail to respond with significant antibody production, nonetheless are immunologically primed. It is concluded that chlorphenesin represents another example of antigen-associated immunosuppressants.

Multi-field query expansion is effective for biomedical dataset retrieval

PubMed Central

2017-01-01

Abstract In the context of the bioCADDIE challenge addressing information retrieval of biomedical datasets, we propose a method for retrieval of biomedical data sets with heterogenous schemas through query reformulation. In particular, the method proposed transforms the initial query into a multi-field query that is then enriched with terms that are likely to occur in the relevant datasets. We compare and evaluate two query expansion strategies, one based on the Rocchio method and another based on a biomedical lexicon. We then perform a comprehensive comparative evaluation of our method on the bioCADDIE dataset collection for biomedical retrieval. We demonstrate the effectiveness of our multi-field query method compared to two baselines, with MAP improved from 0.2171 and 0.2669 to 0.2996. We also show the benefits of query expansion, where the Rocchio expanstion method improves the MAP for our two baselines from 0.2171 and 0.2669 to 0.335. We show that the Rocchio query expansion method slightly outperforms the one based on the biomedical lexicon as a source of terms, with an improvement of roughly 3% for MAP. However, the query expansion method based on the biomedical lexicon is much less resource intensive since it does not require computation of any relevance feedback set or any initial execution of the query. Hence, in term of trade-off between efficiency, execution time and retrieval accuracy, we argue that the query expansion method based on the biomedical lexicon offers the best performance for a prototype biomedical data search engine intended to be used at a large scale. In the official bioCADDIE challenge results, although our approach is ranked seventh in terms of the infNDCG evaluation metric, it ranks second in term of P@10 and NDCG. Hence, the method proposed here provides overall good retrieval performance in relation to the approaches of other competitors. Consequently, the observations made in this paper should benefit the development of a Data

Web-based multimedia information retrieval for clinical application research

NASA Astrophysics Data System (ADS)

Cao, Xinhua; Hoo, Kent S., Jr.; Zhang, Hong; Ching, Wan; Zhang, Ming; Wong, Stephen T. C.

2001-08-01

We described a web-based data warehousing method for retrieving and analyzing neurological multimedia information. The web-based method supports convenient access, effective search and retrieval of clinical textual and image data, and on-line analysis. To improve the flexibility and efficiency of multimedia information query and analysis, a three-tier, multimedia data warehouse for epilepsy research has been built. The data warehouse integrates clinical multimedia data related to epilepsy from disparate sources and archives them into a well-defined data model.

Aerosol-type retrieval and uncertainty quantification from OMI data

NASA Astrophysics Data System (ADS)

Kauppi, Anu; Kolmonen, Pekka; Laine, Marko; Tamminen, Johanna

2017-11-01

We discuss uncertainty quantification for aerosol-type selection in satellite-based atmospheric aerosol retrieval. The retrieval procedure uses precalculated aerosol microphysical models stored in look-up tables (LUTs) and top-of-atmosphere (TOA) spectral reflectance measurements to solve the aerosol characteristics. The forward model approximations cause systematic differences between the modelled and observed reflectance. Acknowledging this model discrepancy as a source of uncertainty allows us to produce more realistic uncertainty estimates and assists the selection of the most appropriate LUTs for each individual retrieval.This paper focuses on the aerosol microphysical model selection and characterisation of uncertainty in the retrieved aerosol type and aerosol optical depth (AOD). The concept of model evidence is used as a tool for model comparison. The method is based on Bayesian inference approach, in which all uncertainties are described as a posterior probability distribution. When there is no single best-matching aerosol microphysical model, we use a statistical technique based on Bayesian model averaging to combine AOD posterior probability densities of the best-fitting models to obtain an averaged AOD estimate. We also determine the shared evidence of the best-matching models of a certain main aerosol type in order to quantify how plausible it is that it represents the underlying atmospheric aerosol conditions.The developed method is applied to Ozone Monitoring Instrument (OMI) measurements using a multiwavelength approach for retrieving the aerosol type and AOD estimate with uncertainty quantification for cloud-free over-land pixels. Several larger pixel set areas were studied in order to investigate the robustness of the developed method. We evaluated the retrieved AOD by comparison with ground-based measurements at example sites. We found that the uncertainty of AOD expressed by posterior probability distribution reflects the difficulty in model

Keratin, luminal epithelial antigen and carcinoembryonic antigen in human urinary bladder carcinomas. An immunohistochemical study.

PubMed

Nathrath, W B; Arnholdt, H; Wilson, P D

1982-01-01

14 urinary bladder carcinomas of all main types were investigated with antisera to "broad spectrum keratin" (aK), "luminal epithelial antigen" (aLEA) and carcinoembryonic antigen (aCEA), using an indirect immunoperoxidase method on formalin fixed paraffin embedded sections. Keratin and LEA were both present in normal transitional epithelium, papilloma and carcinoma in situ whereas CEA was absent. Transitional cell carcinomas reacted with both aK and aLEA whereas CEA was seen only in a few foci. In squamous metaplasia and squamous carcinoma reaction with aK was particularly strong, while LEA was almost lacking and CEA was present in necrotic centres. In adenocarcinomas aK and aLEA reacted equally while aCEA reacted only on the surface.

Implementation of Cloud Retrievals for Tropospheric Emission Spectrometer (TES) Atmospheric Retrievals: Part 1. Description and Characterization of Errors on Trace Gas Retrievals

NASA Technical Reports Server (NTRS)

Kulawik, Susan S.; Worden, John; Eldering, Annmarie; Bowman, Kevin; Gunson, Michael; Osterman, Gregory B.; Zhang, Lin; Clough, Shepard A.; Shephard, Mark W.; Beer, Reinhard

2006-01-01

We develop an approach to estimate and characterize trace gas retrievals in the presence of clouds in high spectral measurements of upwelling radiance in the infrared spectral region (650-2260/cm). The radiance contribution of clouds is parameterized in terms of a set of frequency-dependent nonscattering optical depths and a cloud height. These cloud parameters are retrieved jointly with surface temperature, emissivity, atmospheric temperature, and trace gases such as ozone from spectral data. We demonstrate the application of this approach using data from the Tropospheric Emission Spectrometer (TES) and test data simulated with a scattering radiative transfer model. We show the value of this approach in that it results in accurate estimates of errors for trace gas retrievals, and the retrieved values improve over the initial guess for a wide range of cloud conditions. Comparisons are made between TES retrievals of ozone, temperature, and water to model fields from the Global Modeling and Assimilation Office (GMAO), temperature retrievals from the Atmospheric Infrared Sounder (AIRS), tropospheric ozone columns from the Goddard Earth Observing System (GEOS) GEOS-Chem, and ozone retrievals from the Total Ozone Mapping Spectrometer (TOMS). In each of these cases, this cloud retrieval approach does not introduce observable biases into TES retrievals.

Application of an Optimal Estimation Method to the Retrieval of Aerosol Properties Using Multispectral, Multiangle Polarimetric Measurements From the Research Scanning Polarimeter.

NASA Astrophysics Data System (ADS)

Waquet, F.; Cairns, B.; Chowdhary, J.; Knobelspiesse, K.; Mishchenko, M. I.; Travis, L. D.

2006-12-01

Aerosols affect the climate directly by means of reflecting and absorbing sunlight, and indirectly by means of changing the formation and evolution of clouds. The uncertainties associated with these forcing are however highly uncertain, and may add up to be equal in magnitude but opposite in sign to the climate forcing caused by greenhouse gasses. To reduce these uncertainties, accurate retrievals of the effective size of the particles, their complex refractive index and the column number density are required. Intensity-based techniques for aerosol remote sensing from space only partially meet these requirements because they provide reasonable estimates of only the aerosol size distribution and optical thickness, and only over ocean. Laboratory and theoretical studies, on the other hand, show that the multi-angle, multi-spectral behavior of polarization of light scattered by aerosol particles contains sufficient information to provide all the relevant properties of these particles. The Research Scanning Polarimeter (RSP) instrument provides an opportunity to extend such studies to the polarimetric retrieval of aerosol properties from actual remote sensing data. This instrument provides photo-polarimetric measurements of a scene in 152 viewing angles covering an angular range of 120 degrees, and in 9 spectral bands covering a spectral range of 0.41 to 2.25 micrometers. It was recently deployed in the ALIVE field experiment in Oklahoma and the MILAGRO field experiment near Mexico City, in conjunction with many other space-, air-, and ground-based sensors, to study aerosols over land and ocean. The purpose of this study is to use data acquired during these field experiments by the RSP instrument and various other sensors to evaluate a new method for aerosol polarimetry over land. Our approach follows one of the so-called optimal methods described by Rodger (2004) with a few modifications. We describe the optimal method selected and modified for RSP-type data sets, and

Monetary rewards influence retrieval orientations.

PubMed

Halsband, Teresa M; Ferdinand, Nicola K; Bridger, Emma K; Mecklinger, Axel

2012-09-01

Reward anticipation during learning is known to support memory formation, but its role in retrieval processes is so far unclear. Retrieval orientations, as a reflection of controlled retrieval processing, are one aspect of retrieval that might be modulated by reward. These processes can be measured using the event-related potentials (ERPs) elicited by retrieval cues from tasks with different retrieval requirements, such as via changes in the class of targeted memory information. To determine whether retrieval orientations of this kind are modulated by reward during learning, we investigated the effects of high and low reward expectancy on the ERP correlates of retrieval orientation in two separate experiments. The reward manipulation at study in Experiment 1 was associated with later memory performance, whereas in Experiment 2, reward was directly linked to accuracy in the study task. In both studies, the participants encoded mixed lists of pictures and words preceded by high- or low-reward cues. After 24 h, they performed a recognition memory exclusion task, with words as the test items. In addition to a previously reported material-specific effect of retrieval orientation, a frontally distributed, reward-associated retrieval orientation effect was found in both experiments. These findings suggest that reward motivation during learning leads to the adoption of a reward-associated retrieval orientation to support the retrieval of highly motivational information. Thus, ERP retrieval orientation effects not only reflect retrieval processes related to the sought-for materials, but also relate to the reward conditions with which items were combined during encoding.

Fluorescence correlation spectroscopy as a method for assessment of interactions between phage displaying antibodies and soluble antigen

PubMed Central

Lagerkvist, Ann Catrin; Földes-Papp, Zeno; Persson, Mats A.A.; Rigler, Rudolf

2001-01-01

Phage display is widely used for expression of combinatorial libraries, not least for protein engineering purposes. Precise selection at the single molecule level will provide an improved tool for generating proteins with complex and distinct properties from large molecular libraries. To establish such an improved selection system, we here report the detection of specific interactions between phage with displayed antibody fragments and fluorescently labeled soluble antigen based on Fluorescence Correlation Spectroscopy (FCS). Our novel strategy comprises the use of two separate fluorochromes for detection of the phage–antigen complex, either with labeled antiphage antibody or using a labeled antigen. As a model system, we studied a human monoclonal antibody to the hepatitis-C virus (HCV) envelope protein E2 and its cognate antigen (rE2 or rE1/E2). We could thus assess the specific interactions and determine the fraction of specific versus background phage (26% specific phage). Aggregation of these particular antigens made it difficult to reliably utilize the full potential of cross-correlation studies using the two labels simultaneously. However, with true monomeric proteins, this will certainly be possible, offering a great advantage in a safer and highly specific detection system. PMID:11468349

Methods for Heel Retrieval for Tanks C-101, C-102, and C-111 at the Hanford Site - 13064

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

Sams, T.L.; Kirch, N.W.; Reynolds, J.H.

The purpose of this paper is to evaluate the prospects of using bulk waste characteristics to determine the most appropriate heel retrieval technology. If the properties of hard to remove heels can be determined before bulk retrieval, then a heel retrieval technology can be selected before bulk retrieval is complete. This would save substantially on sampling costs and would allow the deployment of the heel retrieval technology immediately after bulk retrieval. The latter would also accelerate the heel removal schedule. A number of C-farm retrievals have been fully or partially completed at the time of this writing. Thus, there ismore » already substantial information on the success of different technologies and the composition of the heels. There is also substantial information on the waste types in each tank based on historical records. Therefore, this study will correlate the performance of technologies used so far and compare them to the known waste types in the tanks. This will be used to estimate the performance of future C Farm heel retrievals. An initial decision tree is developed and employed on tanks C-101, C-102, and C 111. An assumption of this study is that no additional characterization information would be available, before or after retrieval. Note that collecting additional information would substantially increase the probability of success. Deploying some in-situ testing technologies, such as a water lance or an in-situ Raman probe, might substantially increase the probability of successfully selecting the process conditions without having to take samples from the tanks for laboratory analysis. (authors)« less

Errorless learning and spaced retrieval: how do these methods fare in healthy and clinical populations?

PubMed

Haslam, Catherine; Hodder, Kathryn I; Yates, Philip J

2011-04-01

While errorless learning and spaced retrieval have both proved effective in helping many patients with acquired brain injury (ABI) and dementia learn novel information, it is not clear which of these principles we should apply to target treatment most effectively. To address this issue we conducted a systematic comparison of these principles in three experiments, comparing their effectiveness in healthy controls (N = 60), patients with ABI (N = 30), and patients with dementia (N = 15). Participants were asked to learn face-name associations, and the relative effectiveness of the principles over and above trial-and-error learning was investigated. The results were remarkably consistent across experiments: Both errorless learning and spaced retrieval produced greater accuracy in name recall than did trial-and-error learning, but recall under conditions of spaced retrieval was significantly better than that under errorless learning. We discuss the implications of these findings and suggest that spaced retrieval may be the stronger memory rehabilitation principle when it comes to learning face-name associations in people with mild to moderate memory impairment.

A graph-based approach for the retrieval of multi-modality medical images.

PubMed

Kumar, Ashnil; Kim, Jinman; Wen, Lingfeng; Fulham, Michael; Feng, Dagan

2014-02-01

In this paper, we address the retrieval of multi-modality medical volumes, which consist of two different imaging modalities, acquired sequentially, from the same scanner. One such example, positron emission tomography and computed tomography (PET-CT), provides physicians with complementary functional and anatomical features as well as spatial relationships and has led to improved cancer diagnosis, localisation, and staging. The challenge of multi-modality volume retrieval for cancer patients lies in representing the complementary geometric and topologic attributes between tumours and organs. These attributes and relationships, which are used for tumour staging and classification, can be formulated as a graph. It has been demonstrated that graph-based methods have high accuracy for retrieval by spatial similarity. However, naïvely representing all relationships on a complete graph obscures the structure of the tumour-anatomy relationships. We propose a new graph structure derived from complete graphs that structurally constrains the edges connected to tumour vertices based upon the spatial proximity of tumours and organs. This enables retrieval on the basis of tumour localisation. We also present a similarity matching algorithm that accounts for different feature sets for graph elements from different imaging modalities. Our method emphasises the relationships between a tumour and related organs, while still modelling patient-specific anatomical variations. Constraining tumours to related anatomical structures improves the discrimination potential of graphs, making it easier to retrieve similar images based on tumour location. We evaluated our retrieval methodology on a dataset of clinical PET-CT volumes. Our results showed that our method enabled the retrieval of multi-modality images using spatial features. Our graph-based retrieval algorithm achieved a higher precision than several other retrieval techniques: gray-level histograms as well as state

A safe and efficient method to retrieve mesenchymal stem cells from three-dimensional fibrin gels.

PubMed

Carrion, Bita; Janson, Isaac A; Kong, Yen P; Putnam, Andrew J

2014-03-01

Mesenchymal stem cells (MSCs) display multipotent characteristics that make them ideal for potential therapeutic applications. MSCs are typically cultured as monolayers on tissue culture plastic, but there is increasing evidence suggesting that they may lose their multipotency over time in vitro and eventually cease to retain any resemblance to in vivo resident MSCs. Three-dimensional (3D) culture systems that more closely recapitulate the physiological environment of MSCs and other cell types are increasingly explored for their capacity to support and maintain the cell phenotypes. In much of our own work, we have utilized fibrin, a natural protein-based material that serves as the provisional extracellular matrix during wound healing. Fibrin has proven to be useful in numerous tissue engineering applications and has been used clinically as a hemostatic material. Its rapid self-assembly driven by thrombin-mediated alteration of fibrinogen makes fibrin an attractive 3D substrate, in which cells can adhere, spread, proliferate, and undergo complex morphogenetic programs. However, there is a significant need for simple cost-effective methods to safely retrieve cells encapsulated within fibrin hydrogels to perform additional analyses or use the cells for therapy. Here, we present a safe and efficient protocol for the isolation of MSCs from 3D fibrin gels. The key ingredient of our successful extraction method is nattokinase, a serine protease of the subtilisin family that has a strong fibrinolytic activity. Our data show that MSCs recovered from 3D fibrin gels using nattokinase are not only viable but also retain their proliferative and multilineage potentials. Demonstrated for MSCs, this method can be readily adapted to retrieve any other cell type from 3D fibrin gel constructs for various applications, including expansion, bioassays, and in vivo implantation.

A Safe and Efficient Method to Retrieve Mesenchymal Stem Cells from Three-Dimensional Fibrin Gels

PubMed Central

Carrion, Bita; Janson, Isaac A.; Kong, Yen P.

2014-01-01

Mesenchymal stem cells (MSCs) display multipotent characteristics that make them ideal for potential therapeutic applications. MSCs are typically cultured as monolayers on tissue culture plastic, but there is increasing evidence suggesting that they may lose their multipotency over time in vitro and eventually cease to retain any resemblance to in vivo resident MSCs. Three-dimensional (3D) culture systems that more closely recapitulate the physiological environment of MSCs and other cell types are increasingly explored for their capacity to support and maintain the cell phenotypes. In much of our own work, we have utilized fibrin, a natural protein-based material that serves as the provisional extracellular matrix during wound healing. Fibrin has proven to be useful in numerous tissue engineering applications and has been used clinically as a hemostatic material. Its rapid self-assembly driven by thrombin-mediated alteration of fibrinogen makes fibrin an attractive 3D substrate, in which cells can adhere, spread, proliferate, and undergo complex morphogenetic programs. However, there is a significant need for simple cost-effective methods to safely retrieve cells encapsulated within fibrin hydrogels to perform additional analyses or use the cells for therapy. Here, we present a safe and efficient protocol for the isolation of MSCs from 3D fibrin gels. The key ingredient of our successful extraction method is nattokinase, a serine protease of the subtilisin family that has a strong fibrinolytic activity. Our data show that MSCs recovered from 3D fibrin gels using nattokinase are not only viable but also retain their proliferative and multilineage potentials. Demonstrated for MSCs, this method can be readily adapted to retrieve any other cell type from 3D fibrin gel constructs for various applications, including expansion, bioassays, and in vivo implantation. PMID:23808842

Th1/Th2 balance and humoral immune response to potential antigens as early diagnostic method of equine Strongylus nematode infection

PubMed Central

Abo-Aziza, Faten A. M.; Hendawy, Seham H. M.; Namaky, Amira H. El; Ashry, Heba M.

2017-01-01

Aim:: The aim of this study was to investigate the early diagnosis of strongyle infection based on early changes in Th1 and Th2 cytokines beside the diagnostic accuracy values and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and western blotting profiles using prepared strongyles antigens. Materials and Methods:: A total of 73 donkeys had a mean age of 4-32 years old were parasitologically examined for strongyle infection. The early changes in Th1 and Th2 cytokines were determined, and the diagnostic accuracy values and SDS-PAGE and western blotting profiles were performed using prepared strongyles antigens; crude somatic Strongylus vulgaris (CSS), excretory-secretory S. vulgaris (ESS), crude somatic Cyathostomins (CSC), and excretory-secretory Cyathostomins (ESC). Results:: The results revealed highest 437.04% and lowest 37.81% immunoglobulin G (IgG) in high and low egg shedder groups when using ESC and CSS antigens, respectively. Antibodies index for ESS and CSC were significantly higher in moderate egg shedder group while that for ESS and CSC, ESC was significantly higher in high egg shedder group. Tumor necrosis factor alpha (TNF-α)/interleukin-4 (IL-4) balance in S. vulgaris infected donkeys was approximately equal in apparently healthy, low and high egg shedder groups while TNF-α < IL-4 in moderate egg shedder. In Cyathostomins infected animals, TNF-α/IL-4 balance was approximately equal in apparently healthy group while it was low in moderate and high egg shedder groups. The diagnostic accuracy showed that the higher specificity (46.6%) and prevalence (95.40%) were recorded by CSS and ESC antigens, respectively. However, SDS-PAGE and western blotting profiling proved that the band at molecular weight 25 kDa is exhibited by CSS antigen. Conclusion:: Combination of detecting level of TNF-α/IL-4 balance, CSS antigen and IgG concentration is good tool for appropriate diagnosis of such infection. More advancement research must be done

Phase-step retrieval for tunable phase-shifting algorithms

NASA Astrophysics Data System (ADS)

Ayubi, Gastón A.; Duarte, Ignacio; Perciante, César D.; Flores, Jorge L.; Ferrari, José A.

2017-12-01

Phase-shifting (PS) is a well-known technique for phase retrieval in interferometry, with applications in deflectometry and 3D-profiling, which requires a series of intensity measurements with certain phase-steps. Usually the phase-steps are evenly spaced, and its knowledge is crucial for the phase retrieval. In this work we present a method to extract the phase-step between consecutive interferograms. We test the proposed technique with images corrupted by additive noise. The results were compared with other known methods. We also present experimental results showing the performance of the method when spatial filters are applied to the interferograms and the effect that they have on their relative phase-steps.

Retrieval of Emotional Memories

PubMed Central

Buchanan, Tony W.

2008-01-01

Long-term memories are influenced by the emotion experienced during learning as well as by the emotion experienced during memory retrieval. The present article reviews the literature addressing the effects of emotion on retrieval, focusing on the cognitive and neurological mechanisms that have been revealed. The reviewed research suggests that the amygdala, in combination with the hippocampus and prefrontal cortex, plays an important role in the retrieval of memories for emotional events. The neural regions necessary for online emotional processing also influence emotional memory retrieval, perhaps through the reexperience of emotion during the retrieval process. PMID:17723029

A 3D model retrieval approach based on Bayesian networks lightfield descriptor

NASA Astrophysics Data System (ADS)

Xiao, Qinhan; Li, Yanjun

2009-12-01

A new 3D model retrieval methodology is proposed by exploiting a novel Bayesian networks lightfield descriptor (BNLD). There are two key novelties in our approach: (1) a BN-based method for building lightfield descriptor; and (2) a 3D model retrieval scheme based on the proposed BNLD. To overcome the disadvantages of the existing 3D model retrieval methods, we explore BN for building a new lightfield descriptor. Firstly, 3D model is put into lightfield, about 300 binary-views can be obtained along a sphere, then Fourier descriptors and Zernike moments descriptors can be calculated out from binaryviews. Then shape feature sequence would be learned into a BN model based on BN learning algorithm; Secondly, we propose a new 3D model retrieval method by calculating Kullback-Leibler Divergence (KLD) between BNLDs. Beneficial from the statistical learning, our BNLD is noise robustness as compared to the existing methods. The comparison between our method and the lightfield descriptor-based approach is conducted to demonstrate the effectiveness of our proposed methodology.

A framework based on 2-D Taylor expansion for quantifying the impacts of subpixel reflectance variance and covariance on cloud optical thickness and effective radius retrievals based on the bispectral method

NASA Astrophysics Data System (ADS)

Zhang, Z.; Werner, F.; Cho, H.-M.; Wind, G.; Platnick, S.; Ackerman, A. S.; Di Girolamo, L.; Marshak, A.; Meyer, K.

2016-06-01

The bispectral method retrieves cloud optical thickness (τ) and cloud droplet effective radius (re) simultaneously from a pair of cloud reflectance observations, one in a visible or near-infrared (VIS/NIR) band and the other in a shortwave infrared (SWIR) band. A cloudy pixel is usually assumed to be horizontally homogeneous in the retrieval. Ignoring subpixel variations of cloud reflectances can lead to a significant bias in the retrieved τ and re. In the literature, the retrievals of τ and re are often assumed to be independent and considered separately when investigating the impact of subpixel cloud reflectance variations on the bispectral method. As a result, the impact on τ is contributed only by the subpixel variation of VIS/NIR band reflectance and the impact on re only by the subpixel variation of SWIR band reflectance. In our new framework, we use the Taylor expansion of a two-variable function to understand and quantify the impacts of subpixel variances of VIS/NIR and SWIR cloud reflectances and their covariance on the τ and re retrievals. This framework takes into account the fact that the retrievals are determined by both VIS/NIR and SWIR band observations in a mutually dependent way. In comparison with previous studies, it provides a more comprehensive understanding of how subpixel cloud reflectance variations impact the τ and re retrievals based on the bispectral method. In particular, our framework provides a mathematical explanation of how the subpixel variation in VIS/NIR band influences the re retrieval and why it can sometimes outweigh the influence of variations in the SWIR band and dominate the error in re retrievals, leading to a potential contribution of positive bias to the re retrieval. We test our framework using synthetic cloud fields from a large-eddy simulation and real observations from Moderate Resolution Imaging Spectroradiometer. The predicted results based on our framework agree very well with the numerical simulations. Our

A Framework Based on 2-D Taylor Expansion for Quantifying the Impacts of Subpixel Reflectance Variance and Covariance on Cloud Optical Thickness and Effective Radius Retrievals Based on the Bispectral Method

NASA Technical Reports Server (NTRS)

Zhang, Z.; Werner, F.; Cho, H.-M.; Wind, G.; Platnick, S.; Ackerman, A. S.; Di Girolamo, L.; Marshak, A.; Meyer, K.

2016-01-01

The bispectral method retrieves cloud optical thickness (t) and cloud droplet effective radius (re) simultaneously from a pair of cloud reflectance observations, one in a visible or near-infrared (VIS/NIR) band and the other in a shortwave infrared (SWIR) band. A cloudy pixel is usually assumed to be horizontally homogeneous in the retrieval. Ignoring subpixel variations of cloud reflectances can lead to a significant bias in the retrieved t and re. In the literature, the retrievals of t and re are often assumed to be independent and considered separately when investigating the impact of subpixel cloud reflectance variations on the bispectral method. As a result, the impact on t is contributed only by the subpixel variation of VIS/NIR band reflectance and the impact on re only by the subpixel variation of SWIR band reflectance. In our new framework, we use the Taylor expansion of a two-variable function to understand and quantify the impacts of subpixel variances of VIS/NIR and SWIR cloud reflectances and their covariance on the t and re retrievals. This framework takes into account the fact that the retrievals are determined by both VIS/NIR and SWIR band observations in a mutually dependent way. In comparison with previous studies, it provides a more comprehensive understanding of how subpixel cloud reflectance variations impact the t and re retrievals based on the bispectral method. In particular, our framework provides a mathematical explanation of how the subpixel variation in VIS/NIR band influences the re retrieval and why it can sometimes outweigh the influence of variations in the SWIR band and dominate the error in re retrievals, leading to a potential contribution of positive bias to the re retrieval. We test our framework using synthetic cloud fields from a large-eddy simulation and real observations from Moderate Resolution Imaging Spectroradiometer. The predicted results based on our framework agree very well with the numerical simulations. Our

Competitive retrieval is not a prerequisite for forgetting in the retrieval practice paradigm.

PubMed

Camp, Gino; Dalm, Sander

2016-09-01

Retrieving information from memory can lead to forgetting of other, related information. The inhibition account of this retrieval-induced forgetting effect predicts that this form of forgetting occurs when competition arises between the practiced information and the related information, leading to inhibition of the related information. In the standard retrieval practice paradigm, a retrieval practice task is used in which participants retrieve the items based on a category-plus-stem cue (e.g., FRUIT-or___). In the current experiment, participants instead generated the target based on a cue in which the first 2 letters of the target were transposed (e.g., FRUIT-roange). This noncompetitive task also induced forgetting of unpracticed items from practiced categories. This finding is inconsistent with the inhibition account, which asserts that the forgetting effect depends on competitive retrieval. We argue that interference-based accounts of forgetting and the context-based account of retrieval-induced forgetting can account for this result. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Retrieval-practice task affects relationship between working memory capacity and retrieval-induced forgetting.

PubMed

Storm, Benjamin C; Bui, Dung C

2016-11-01

Retrieving a subset of items from memory can cause forgetting of other items in memory, a phenomenon referred to as retrieval-induced forgetting (RIF). Individuals who exhibit greater amounts of RIF have been shown to also exhibit superior working memory capacity (WMC) and faster stop-signal reaction times (SSRTs), results which have been interpreted as suggesting that RIF reflects an inhibitory process that is mediated by the processes of executive control. Across four experiments, we sought to further elucidate this issue by manipulating the way in which participants retrieved items during retrieval practice and examining how the resulting effects of forgetting correlated with WMC (Experiments 1-3) and SSRT (Experiment 4). Significant correlations were observed when participants retrieved items from an earlier study phase (within-list retrieval practice), but not when participants generated items from semantic memory (extra-list retrieval practice). These results provide important new insight into the role of executive-control processes in RIF.

Retrieval Practice Is an Efficient Method of Enhancing the Retention of Anatomy and Physiology Information

ERIC Educational Resources Information Center

Dobson, John L.

2013-01-01

Although a great deal of empirical evidence has indicated that retrieval practice is an effective means of promoting learning and memory, very few studies have investigated the strategy in the context of an actual class. The primary purpose of this study was to determine if a series of very brief retrieval quizzes could significantly improve the…

Validating Satellite-Retrieved Cloud Properties for Weather and Climate Applications

NASA Astrophysics Data System (ADS)

Minnis, P.; Bedka, K. M.; Smith, W., Jr.; Yost, C. R.; Bedka, S. T.; Palikonda, R.; Spangenberg, D.; Sun-Mack, S.; Trepte, Q.; Dong, X.; Xi, B.

2014-12-01

Cloud properties determined from satellite imager radiances are increasingly used in weather and climate applications, particularly in nowcasting, model assimilation and validation, trend monitoring, and precipitation and radiation analyses. The value of using the satellite-derived cloud parameters is determined by the accuracy of the particular parameter for a given set of conditions, such as viewing and illumination angles, surface background, and cloud type and structure. Because of the great variety of those conditions and of the sensors used to monitor clouds, determining the accuracy or uncertainties in the retrieved cloud parameters is a daunting task. Sensitivity studies of the retrieved parameters to the various inputs for a particular cloud type are helpful for understanding the errors associated with the retrieval algorithm relative to the plane-parallel world assumed in most of the model clouds that serve as the basis for the retrievals. Real world clouds, however, rarely fit the plane-parallel mold and generate radiances that likely produce much greater errors in the retrieved parameter than can be inferred from sensitivity analyses. Thus, independent, empirical methods are used to provide a more reliable uncertainty analysis. At NASA Langley, cloud properties are being retrieved from both geostationary (GEO) and low-earth orbiting (LEO) satellite imagers for climate monitoring and model validation as part of the NASA CERES project since 2000 and from AVHRR data since 1978 as part of the NOAA CDR program. Cloud properties are also being retrieved in near-real time globally from both GEO and LEO satellites for weather model assimilation and nowcasting for hazards such as aircraft icing. This paper discusses the various independent datasets and approaches that are used to assessing the imager-based satellite cloud retrievals. These include, but are not limited to data from ARM sites, CloudSat, and CALIPSO. This paper discusses the use of the various

Group differences in adult simple arithmetic: good retrievers, not-so-good retrievers, and perfectionists.

PubMed

Hecht, Steven A

2006-01-01

We used the choice/no-choice methodology in two experiments to examine patterns of strategy selection and execution in groups of undergraduates. Comparisons between choice and no-choice trials revealed three groups. Some participants good retrievers) were consistently able to use retrieval to solve almost all arithmetic problems. Other participants (perfectionists) successfully used retrieval substantially less often in choice-allowed trials than when strategy choices were prohibited. Not-so-good retrievers retrieved correct answers less often than the other participants in both the choice-allowed and no-choice conditions. No group differences emerged with respect to time needed to search and access answers from long-term memory; however, not-so-good retrievers were consistently slower than the other subgroups at executing fact-retrieval processes that are peripheral to memory search and access. Theoretical models of simple arithmetic, such as the Strategy Choice and Discovery Simulation (Shrager & Siegler, 1998), should be updated to include the existence of both perfectionist and not-so-good retriever adults.

Cross-Modal Retrieval With CNN Visual Features: A New Baseline.

PubMed

Wei, Yunchao; Zhao, Yao; Lu, Canyi; Wei, Shikui; Liu, Luoqi; Zhu, Zhenfeng; Yan, Shuicheng

2017-02-01

Recently, convolutional neural network (CNN) visual features have demonstrated their powerful ability as a universal representation for various recognition tasks. In this paper, cross-modal retrieval with CNN visual features is implemented with several classic methods. Specifically, off-the-shelf CNN visual features are extracted from the CNN model, which is pretrained on ImageNet with more than one million images from 1000 object categories, as a generic image representation to tackle cross-modal retrieval. To further enhance the representational ability of CNN visual features, based on the pretrained CNN model on ImageNet, a fine-tuning step is performed by using the open source Caffe CNN library for each target data set. Besides, we propose a deep semantic matching method to address the cross-modal retrieval problem with respect to samples which are annotated with one or multiple labels. Extensive experiments on five popular publicly available data sets well demonstrate the superiority of CNN visual features for cross-modal retrieval.

Uncertainty Assessment of Space-Borne Passive Soil Moisture Retrievals

NASA Technical Reports Server (NTRS)

Quets, Jan; De Lannoy, Gabrielle; Reichle, Rolf; Cosh, Michael; van der Schalie, Robin; Wigneron, Jean-Pierre

2017-01-01

The uncertainty associated with passive soil moisture retrieval is hard to quantify, and known to be underlain by various, diverse, and complex causes. Factors affecting space-borne retrieved soil moisture estimation include: (i) the optimization or inversion method applied to the radiative transfer model (RTM), such as e.g. the Single Channel Algorithm (SCA), or the Land Parameter Retrieval Model (LPRM), (ii) the selection of the observed brightness temperatures (Tbs), e.g. polarization and incidence angle, (iii) the definition of the cost function and the impact of prior information in it, and (iv) the RTM parameterization (e.g. parameterizations officially used by the SMOS L2 and SMAP L2 retrieval products, ECMWF-based SMOS assimilation product, SMAP L4 assimilation product, and perturbations from those configurations). This study aims at disentangling the relative importance of the above-mentioned sources of uncertainty, by carrying out soil moisture retrieval experiments, using SMOS Tb observations in different settings, of which some are mentioned above. The ensemble uncertainties are evaluated at 11 reference CalVal sites, over a time period of more than 5 years. These experimental retrievals were inter-compared, and further confronted with in situ soil moisture measurements and operational SMOS L2 retrievals, using commonly used skill metrics to quantify the temporal uncertainty in the retrievals.

Content based Image Retrieval based on Different Global and Local Color Histogram Methods: A Survey

NASA Astrophysics Data System (ADS)

Suhasini, Pallikonda Sarah; Sri Rama Krishna, K.; Murali Krishna, I. V.

2017-02-01

Different global and local color histogram methods for content based image retrieval (CBIR) are investigated in this paper. Color histogram is a widely used descriptor for CBIR. Conventional method of extracting color histogram is global, which misses the spatial content, is less invariant to deformation and viewpoint changes, and results in a very large three dimensional histogram corresponding to the color space used. To address the above deficiencies, different global and local histogram methods are proposed in recent research. Different ways of extracting local histograms to have spatial correspondence, invariant colour histogram to add deformation and viewpoint invariance and fuzzy linking method to reduce the size of the histogram are found in recent papers. The color space and the distance metric used are vital in obtaining color histogram. In this paper the performance of CBIR based on different global and local color histograms in three different color spaces, namely, RGB, HSV, L*a*b* and also with three distance measures Euclidean, Quadratic and Histogram intersection are surveyed, to choose appropriate method for future research.

Toward an Episodic Context Account of Retrieval-Based Learning: Dissociating Retrieval Practice and Elaboration

ERIC Educational Resources Information Center

Lehman, Melissa; Smith, Megan A.; Karpicke, Jeffrey D.

2014-01-01

We tested the predictions of 2 explanations for retrieval-based learning; while the elaborative retrieval hypothesis assumes that the retrieval of studied information promotes the generation of semantically related information, which aids in later retrieval (Carpenter, 2009), the episodic context account proposed by Karpicke, Lehman, and Aue (in…

A Novel Method Linking Antigen Presentation by Human Monocyte-Derived Macrophages to CD8+ T Cell Polyfunctionality

PubMed Central

Short, Kirsty R.; Grant, Emma J.; Vissers, Marloes; Reading, Patrick C.; Diavatopoulos, Dimitri A.; Kedzierska, Katherine

2013-01-01

To understand the interactions between innate and adaptive immunity, and specifically how virally infected macrophages impact T cell function, novel assays examining the ability of macrophages to present antigen to CD8+ T cells are needed. In the present study, we have developed a robust in vitro assay to measure how antigen presentation by human monocyte-derived macrophages (MDMs) affects the functional capacity of autologous CD8+ T cells. The assay is based on the polyfunctional characteristics of antigen-specific CD8+ T cells, and is thus called a Mac-CD8 Polyfunctionality Assay. Following purification of monocytes and their maturation to MDMs, MDMs were pulsed with an antigenic peptide to be presented to CD8+ T cells. Peptide-pulsed MDMs were then incubated with antigen-specific CD8+ T cells in order to assess the efficacy of antigen presentation to T cells. CD8+ T cell polyfunctionality was assessed by staining with mAbs to IFN-γ, TNF-α, and CD107a in a multi-color intracellular cytokine staining assay. To highlight the utility of the Mac-CD8 Polyfunctionality Assay, we assessed the effects of influenza infection on the ability of human macrophages to present antigen to CD8+ T cells. We found that influenza infection of human MDMs can alter the effector efficacy of MDMs to activate more CD8+ T cells with cytotoxic capacity. This has important implications for understanding how the virus-infected macrophages affect adaptive immunity at the site of infection. PMID:24312096

Practical quantum retrieval games

NASA Astrophysics Data System (ADS)

Arrazola, Juan Miguel; Karasamanis, Markos; Lütkenhaus, Norbert

2016-06-01

Complex cryptographic protocols are often constructed from simpler building blocks. In order to advance quantum cryptography, it is important to study practical building blocks that can be used to develop new protocols. An example is quantum retrieval games (QRGs), which have broad applicability and have already been used to construct quantum money schemes. In this work, we introduce a general construction of quantum retrieval games based on the hidden matching problem and show how they can be implemented in practice using available technology. More precisely, we provide a general method to construct (1-out-of-k ) QRGs, proving that their cheating probabilities decrease exponentially in k . In particular, we define QRGs based on coherent states of light, which can be implemented even in the presence of experimental imperfections. Our results constitute a tool in the arsenal of the practical quantum cryptographer.

Which is the best method to trace group A streptococci in sore throat patients: culture or GAS antigen test?

PubMed

Lindbaek, Morten; Høiby, Ernst Arne; Lermark, Gro; Steinsholt, Inger Marie; Hjortdahl, Per

2004-12-01

To compare an antigen detection test (GAS antigen test) with the results from combinations of two various bacteriological test media in general practice patients with sore throat. Furthermore to assess the diagnostic properties of the chosen GAS antigen test and to compare semi-quantitative results of this test with the bacterial load found in the throat culture. Two Norwegian general practices in Stokke and Kongsberg communities. 306 patients with sore throat lasting less than 7 days; 244 were adults, 62 were children under 10 years old, mean age 23.9 years (SD 15.0), 40% were men. Results from GAS antigen test, and distribution of bacteriological findings in throat cultures, compared with the results of our GAS antigen test; semi-quantitative results of the GAS antigen test compared with the bacterial load by culture. In the primary culture 110 patients harboured group A streptococci (GAS) infection, while the second culture identified another 17, giving a total of 127 patients. Some 33 patients harboured large-colony groups C and G. The GAS antigen test used had a sensitivity of 97% and specificity of 95% regarding GAS when compared with the two cultures. We found a significant correlation between the bacterial loads by culture and the semi-quantitative results of the GAS antigen test. By using a second, different set of bacteriological media, we identified an additional 17 patients with GAS infections. This raises the question of validity of frequently used reference standards in studies related to streptococcal infections. Compared with the combined results of the two throat cultures, the GAS antigen test used showed high sensitivity and specificity. Semi-quantitative evaluations of the rapid immunological test may also be of clinical value.

Retrieval of daytime [O3] altitude profile from measurements of 1.27 μm O2 emission in the mesosphere: a comparison of methods

NASA Astrophysics Data System (ADS)

Yankovsky, Valentine A.; Manuilova, Rada O.

2017-11-01

The altitude profiles of ozone concentration are retrieved from measurements of the volume emission rate in the 1.27 μm oxygen band in the TIMED-SABER experiment. In this study we compare the methods of retrieval of daytime [O3] altitude profile in the framework of two models: electronic-vibrational kinetics and a purely electronic kinetics of excited products of ozone and oxygen photolysis. In order to retrieve the [O3] altitude profile from the measurements of the intensity of the O2 band in the region of 1.27 μm correctly, it is necessary to use the photochemical model of the electronic-vibrational kinetics of excited products of ozone and oxygen photolysis in the mesosphere and lower thermosphere.

Prediction of destination entry and retrieval times using keystroke-level models

DOT National Transportation Integrated Search

1998-04-01

Thirty-six drivers entered and retrieved destinations using an Ali-Scout navigation computer. Retrieval involved keying in part of the destination name, scrolling through a list of names, or a combination of those methods. Entry required keying in th...

A Solar Reflectance Method for Retrieving Cloud Optical Thickness and Droplet Size Over Snow and Ice Surfaces

NASA Technical Reports Server (NTRS)

Platnick, S.; Li, J. Y.; King, M. D.; Gerber, H.; Hobbs, P. V.

1999-01-01

Cloud optical thickness and effective radius retrievals from solar reflectance measurements are traditionally implemented using a combination of spectral channels that are absorbing and non-absorbing for water particles. Reflectances in non-absorbing channels (e.g., 0.67, 0.86, 1.2 micron spectral window bands) are largely dependent on cloud optical thickness, while longer wavelength absorbing channels (1.6, 2. 1, and 3.7 micron window bands) provide cloud particle size information. Cloud retrievals over ice and snow surfaces present serious difficulties. At the shorter wavelengths, ice is bright and highly variable, both characteristics acting to significantly increase cloud retrieval uncertainty. In contrast, reflectances at the longer wavelengths are relatively small and may be comparable to that of dark open water. A modification to the traditional cloud retrieval technique is devised. The new algorithm uses only a combination of absorbing spectral channels for which the snow/ice albedo is relatively small. Using this approach, retrievals have been made with the MODIS Airborne Simulator (MAS) imager flown aboard the NASA ER-2 from May - June 1998 during the Arctic FIRE-ACE field deployment. Data from several coordinated ER-2 and University of Washington CV-580 in situ aircraft observations of liquid water stratus clouds are examined. MAS retrievals of optical thickness, droplet effective radius, and liquid water path are shown to be in good agreement with the in situ measurements. The initial success of the technique has implications for future operational satellite cloud retrieval algorithms in polar and wintertime regions.

Selective Convolutional Descriptor Aggregation for Fine-Grained Image Retrieval.

PubMed

Wei, Xiu-Shen; Luo, Jian-Hao; Wu, Jianxin; Zhou, Zhi-Hua

2017-06-01

Deep convolutional neural network models pre-trained for the ImageNet classification task have been successfully adopted to tasks in other domains, such as texture description and object proposal generation, but these tasks require annotations for images in the new domain. In this paper, we focus on a novel and challenging task in the pure unsupervised setting: fine-grained image retrieval. Even with image labels, fine-grained images are difficult to classify, letting alone the unsupervised retrieval task. We propose the selective convolutional descriptor aggregation (SCDA) method. The SCDA first localizes the main object in fine-grained images, a step that discards the noisy background and keeps useful deep descriptors. The selected descriptors are then aggregated and the dimensionality is reduced into a short feature vector using the best practices we found. The SCDA is unsupervised, using no image label or bounding box annotation. Experiments on six fine-grained data sets confirm the effectiveness of the SCDA for fine-grained image retrieval. Besides, visualization of the SCDA features shows that they correspond to visual attributes (even subtle ones), which might explain SCDA's high-mean average precision in fine-grained retrieval. Moreover, on general image retrieval data sets, the SCDA achieves comparable retrieval results with the state-of-the-art general image retrieval approaches.

Noncompetitive retrieval practice causes retrieval-induced forgetting in cued recall but not in recognition.

PubMed

Grundgeiger, Tobias

2014-04-01

Retrieving a subset of learned items can lead to the forgetting of related items. Such retrieval-induced forgetting (RIF) can be explained by the inhibition of irrelevant items in order to overcome retrieval competition when the target item is retrieved. According to the retrieval inhibition account, such retrieval competition is a necessary condition for RIF. However, research has indicated that noncompetitive retrieval practice can also cause RIF by strengthening cue-item associations. According to the strength-dependent competition account, the strengthened items interfere with the retrieval of weaker items, resulting in impaired recall of weaker items in the final memory test. The aim of this study was to replicate RIF caused by noncompetitive retrieval practice and to determine whether this forgetting is also observed in recognition tests. In the context of RIF, it has been assumed that recognition tests circumvent interference and, therefore, should not be sensitive to forgetting due to strength-dependent competition. However, this has not been empirically tested, and it has been suggested that participants may reinstate learned cues as retrieval aids during the final test. In the present experiments, competitive practice or noncompetitive practice was followed by either final cued-recall tests or recognition tests. In cued-recall tests, RIF was observed in both competitive and noncompetitive conditions. However, in recognition tests, RIF was observed only in the competitive condition and was absent in the noncompetitive condition. The result underscores the contribution of strength-dependent competition to RIF. However, recognition tests seem to be a reliable way of distinguishing between RIF due to retrieval inhibition or strength-dependent competition.

[Results of a study of the diagnostic qualities of brucellosis and tularemic antigenic erythrocytic diagnostica].

PubMed

Tsybin, B P; Taran, I F; Tinker, A I

1975-09-01

The authors elaborated methods of preparation of brucella and tularemia antigenic erythrocytic diagnostic agents which were characterized as highly specific, specific and stable preparations in mass examination of humans and animals at various stages of the vaccinal and infectous processes. The simplicity of obtaining specific antigens intended for the sensitization of formalinized erythrocytes and stability of the results of results of reproduction of the methods of preparation of the antigenic erythrocytic diagnostic agents offered a possibility of recommending the mentioned methods of industrial preparation of the diagnostic agents.

Skin image retrieval using Gabor wavelet texture feature.

PubMed

Ou, X; Pan, W; Zhang, X; Xiao, P

2016-12-01

Skin imaging plays a key role in many clinical studies. We have used many skin imaging techniques, including the recently developed capacitive contact skin imaging based on fingerprint sensors. The aim of this study was to develop an effective skin image retrieval technique using Gabor wavelet transform, which can be used on different types of skin images, but with a special focus on skin capacitive contact images. Content-based image retrieval (CBIR) is a useful technology to retrieve stored images from database by supplying query images. In a typical CBIR, images are retrieved based on colour, shape, texture, etc. In this study, texture feature is used for retrieving skin images, and Gabor wavelet transform is used for texture feature description and extraction. The results show that the Gabor wavelet texture features can work efficiently on different types of skin images. Although Gabor wavelet transform is slower compared with other image retrieval techniques, such as principal component analysis (PCA) and grey-level co-occurrence matrix (GLCM), Gabor wavelet transform is the best for retrieving skin capacitive contact images and facial images with different orientations. Gabor wavelet transform can also work well on facial images with different expressions and skin cancer/disease images. We have developed an effective skin image retrieval method based on Gabor wavelet transform, that it is useful for retrieving different types of images, namely digital colour face images, digital colour skin cancer and skin disease images, and particularly greyscale skin capacitive contact images. Gabor wavelet transform can also be potentially useful for face recognition (with different orientation and expressions) and skin cancer/disease diagnosis. © 2016 Society of Cosmetic Scientists and the Société Française de Cosmétologie.

BEST: Improved Prediction of B-Cell Epitopes from Antigen Sequences

PubMed Central

Gao, Jianzhao; Faraggi, Eshel; Zhou, Yaoqi; Ruan, Jishou; Kurgan, Lukasz

2012-01-01

Accurate identification of immunogenic regions in a given antigen chain is a difficult and actively pursued problem. Although accurate predictors for T-cell epitopes are already in place, the prediction of the B-cell epitopes requires further research. We overview the available approaches for the prediction of B-cell epitopes and propose a novel and accurate sequence-based solution. Our BEST (B-cell Epitope prediction using Support vector machine Tool) method predicts epitopes from antigen sequences, in contrast to some method that predict only from short sequence fragments, using a new architecture based on averaging selected scores generated from sliding 20-mers by a Support Vector Machine (SVM). The SVM predictor utilizes a comprehensive and custom designed set of inputs generated by combining information derived from the chain, sequence conservation, similarity to known (training) epitopes, and predicted secondary structure and relative solvent accessibility. Empirical evaluation on benchmark datasets demonstrates that BEST outperforms several modern sequence-based B-cell epitope predictors including ABCPred, method by Chen et al. (2007), BCPred, COBEpro, BayesB, and CBTOPE, when considering the predictions from antigen chains and from the chain fragments. Our method obtains a cross-validated area under the receiver operating characteristic curve (AUC) for the fragment-based prediction at 0.81 and 0.85, depending on the dataset. The AUCs of BEST on the benchmark sets of full antigen chains equal 0.57 and 0.6, which is significantly and slightly better than the next best method we tested. We also present case studies to contrast the propensity profiles generated by BEST and several other methods. PMID:22761950

[Competition-dependence on retrieval-induced forgetting: the influence of the amount of retrieval cues].

PubMed

Yamada, Yohei; Tsukimoto, Takashi; Hirano, Tetsuji

2010-02-01

Remembering some of the studied (target) items impairs subsequent remembrance of relevant (non-target) items. This phenomenon, retrieval-induced forgetting (RIF), occurs when non-targets actively compete with the retrieval of a target. Researchers suggest that suppression mechanisms reduce interference from relevant items to facilitate the retrieval of target items (Anderson, 2003). Competition-dependence is one of the properties that support the suppression hypothesis (Anderson, Bjork, & Bjork, 1994). In the present study, we manipulated the type of retrieval practice (normal, last-letter, or category-name) in order to vary the degree of competition between the target and the non-targets. For the high-scoring retrieval practice group, RIF occurred in the normal retrieval condition, but not in the last-letter or in the category-name conditions. For the low-scoring retrieval practice group, RIF did not occur in any of the conditions. These findings provide new evidence that the occurrence of RIF depends on the degree of competition between a target item and related non-target items during retrieval practice.

Feature hashing for fast image retrieval

NASA Astrophysics Data System (ADS)

Yan, Lingyu; Fu, Jiarun; Zhang, Hongxin; Yuan, Lu; Xu, Hui

2018-03-01

Currently, researches on content based image retrieval mainly focus on robust feature extraction. However, due to the exponential growth of online images, it is necessary to consider searching among large scale images, which is very timeconsuming and unscalable. Hence, we need to pay much attention to the efficiency of image retrieval. In this paper, we propose a feature hashing method for image retrieval which not only generates compact fingerprint for image representation, but also prevents huge semantic loss during the process of hashing. To generate the fingerprint, an objective function of semantic loss is constructed and minimized, which combine the influence of both the neighborhood structure of feature data and mapping error. Since the machine learning based hashing effectively preserves neighborhood structure of data, it yields visual words with strong discriminability. Furthermore, the generated binary codes leads image representation building to be of low-complexity, making it efficient and scalable to large scale databases. Experimental results show good performance of our approach.

Mathematics and Information Retrieval.

ERIC Educational Resources Information Center

Salton, Gerald

1979-01-01

Examines the main mathematical approaches to information retrieval, including both algebraic and probabilistic models, and describes difficulties which impede formalization of information retrieval processes. A number of developments are covered where new theoretical understandings have directly led to improved retrieval techniques and operations.…

The present status and problems in document retrieval system : document input type retrieval system

NASA Astrophysics Data System (ADS)

Inagaki, Hirohito

The office-automation (OA) made many changes. Many documents were begun to maintained in an electronic filing system. Therefore, it is needed to establish efficient document retrieval system to extract useful information. Current document retrieval systems are using simple word-matching, syntactic-matching, semantic-matching to obtain high retrieval efficiency. On the other hand, the document retrieval systems using special hardware devices, such as ISSP, were developed for aiming high speed retrieval. Since these systems can accept a single sentence or keywords as input, it is difficult to explain searcher's request. We demonstrated document input type retrieval system, which can directly accept document as an input, and can search similar documents from document data-base.

Development of an algorithm for production of inactivated arbovirus antigens in cell culture

PubMed Central

Goodman, C.H.; Russell, B.J.; Velez, J.O.; Laven, J.J.; Nicholson, W.L; Bagarozzi, D.A.; Moon, J.L.; Bedi, K.; Johnson, B.W.

2015-01-01

Arboviruses are medically important pathogens that cause human disease ranging from a mild fever to encephalitis. Laboratory diagnosis is essential to differentiate arbovirus infections from other pathogens with similar clinical manifestations. The Arboviral Diseases Branch (ADB) reference laboratory at the CDC Division of Vector-Borne Diseases (DVBD) produces reference antigens used in serological assays such as the virus-specific immunoglobulin M antibody-capture enzyme-linked immunosorbent assay (MAC-ELISA). Antigen production in cell culture has largely replaced the use of suckling mice; however, the methods are not directly transferable. The development of a cell culture antigen production algorithm for nine arboviruses from the three main arbovirus families, Flaviviridae, Togaviridae, and Bunyaviridae, is described here. Virus cell culture growth and harvest conditions were optimized, inactivation methods were evaluated, and concentration procedures were compared for each virus. Antigen performance was evaluated by the MAC-ELISA at each step of the procedure. The antigen production algorithm is a framework for standardization of methodology and quality control; however, a single antigen production protocol was not applicable to all arboviruses and needed to be optimized for each virus. PMID:25102428

INFORMATION STORAGE AND RETRIEVAL, REPORTS ON EVALUATION, CLUSTERING, AND FEEDBACK.

ERIC Educational Resources Information Center

SALTON, GERALD

THE TWELFTH IN A SERIES COVERING RESEARCH IN AUTOMATIC STORAGE AND RETRIEVAL, THIS REPORT IS DIVIDED INTO THREE PARTS TITLED EVALUATION, CLUSTER SEARCHING, AND USER FEEDBACK METHODS, RESPECTIVELY. THE FIRST PART, EVALUATION, CONTAINS A COMPLETE SUMMARY OF THE RETRIEVAL RESULTS DERIVED FROM SOME SIXTY DIFFERENT TEXT ANALYSIS EXPERIMENTS. IN EACH…

The Ecosystem of Information Retrieval

ERIC Educational Resources Information Center

Rodriguez-Munoz, Jose-Vicente; Martinez-Mendez, Francisco-Javier; Pastor-Sanchez, Juan-Antonio

2012-01-01

Introduction: This paper presents an initial proposal for a formal framework that, by studying the metric variables involved in information retrieval, can establish the sequence of events involved and how to perform it. Method: A systematic approach from the equations of Shannon and Weaver to establish the decidability of information retrieval…

Retrieval of Mid-tropospheric CO2 Directly from AIRS Measurements

NASA Technical Reports Server (NTRS)

Olsen, Edward T.; Chahine, Moustafa T.; Chen, Luke L.; Pagano, Thomas S.

2008-01-01

We apply the method of Vanishing Partial Derivatives (VPD) to AIRS spectra to retrieve daily the global distribution of CO2 at a nadir geospatial resolution of 90 km x 90 km without requiring a first-guess input beyond the global average. Our retrievals utilize the 15 (micro)m band radiances, a complex spectral region. This method may be of value in other applications, in which spectral signatures of multiple species are not well isolated spectrally from one another.

Trace gas retrieval for limb DOAS under changing atmospheric conditions: The X-gas scaling method vs optimal estimation

NASA Astrophysics Data System (ADS)

Hueneke, Tilman; Grossmann, Katja; Knecht, Matthias; Raecke, Rasmus; Stutz, Jochen; Werner, Bodo; Pfeilsticker, Klaus

2016-04-01

Changing atmospheric conditions during DOAS measurements from fast moving aircraft platforms pose a challenge for trace gas retrievals. Traditional inversion techniques to retrieve trace gas concentrations from limb scattered UV/vis spectroscopy, like optimal estimation, require a-priori information on Mie extinction (e.g., aerosol concentration and cloud cover) and albedo, which determine the atmospheric radiative transfer. In contrast to satellite applications, cloud filters can not be applied because they would strongly reduce the usable amount of expensively gathered measurement data. In contrast to ground-based MAX-DOAS applications, an aerosol retrieval based on O4 is not able to constrain the radiative transfer in air-borne applications due to the rapidly decreasing amount of O4 with altitude. Furthermore, the assumption of a constant cloud cover is not valid for fast moving aircrafts, thus requiring 2D or even 3D treatment of the radiative transfer. Therefore, traditional techniques are not applicable for most of the data gathered by fast moving aircraft platforms. In order to circumvent these limitations, we have been developing the so-called X-gas scaling method. By utilising a proxy gas X (e.g. O3, O4, …), whose concentration is either a priori known or simultaneously in-situ measured as well as remotely measured, an effective absorption length for the target gas is inferred. In this presentation, we discuss the strengths and weaknesses of the novel approach along with some sample cases. A particular strength of the X-gas scaling method is its insensitivity towards the aerosol abundance and cloud cover as well as wavelength dependent effects, whereas its sensitivity towards the profiles of both gases requires a priori information on their shapes.

EVA Retriever Demonstration

NASA Technical Reports Server (NTRS)

1988-01-01

The EVA retriever is demonstrated in the Manipulator Development Facility (MDF). The retriever moves on the air bearing table 'searching' for its target, in this case tools 'dropped' by astronauts on orbit.

Cross-Domain Multi-View Object Retrieval via Multi-Scale Topic Models.

PubMed

Hong, Richang; Hu, Zhenzhen; Wang, Ruxin; Wang, Meng; Tao, Dacheng

2016-09-27

The increasing number of 3D objects in various applications has increased the requirement for effective and efficient 3D object retrieval methods, which attracted extensive research efforts in recent years. Existing works mainly focus on how to extract features and conduct object matching. With the increasing applications, 3D objects come from different areas. In such circumstances, how to conduct object retrieval becomes more important. To address this issue, we propose a multi-view object retrieval method using multi-scale topic models in this paper. In our method, multiple views are first extracted from each object, and then the dense visual features are extracted to represent each view. To represent the 3D object, multi-scale topic models are employed to extract the hidden relationship among these features with respected to varied topic numbers in the topic model. In this way, each object can be represented by a set of bag of topics. To compare the objects, we first conduct topic clustering for the basic topics from two datasets, and then generate the common topic dictionary for new representation. Then, the two objects can be aligned to the same common feature space for comparison. To evaluate the performance of the proposed method, experiments are conducted on two datasets. The 3D object retrieval experimental results and comparison with existing methods demonstrate the effectiveness of the proposed method.

JURASSIC Retrieval Processing

NASA Astrophysics Data System (ADS)

Blank, J.; Ungermann, J.; Guggenmoser, T.; Kaufmann, M.; Riese, M.

2012-04-01

The Gimballed Limb Observer for Radiance Imaging in the Atmosphere (GLORIA) is an aircraft based infrared limb-sounder. This presentation will give an overview of the retrieval techniques used for the analysis of data produced by the GLORIA instrument. For data processing, the JUelich RApid Spectral SImulation Code 2 (JURASSIC2) was developed. It consists of a set of programs to retrieve atmospheric profiles from GLORIA measurements. The GLORIA Michelson interferometer can run with a wide range of parameters. In the dynamics mode, spectra are generate with a medium spectral and a very high temporal and spatial resolution. Each sample can contain thousands of spectral lines for each contributing trace gas. In the JURASSIC retrieval code this is handled by using a radiative transport model based on the Emissivity Growth Approximation. Deciding which samples should be included in the retrieval is a non-trivial task and requires specific domain knowledge. To ease this problem we developed an automatic selection program by analysing the Shannon information content. By taking into account data for all relevant trace gases and instrument effects, optimal integrated spectral windows are computed. This includes considerations for cross-influence of trace gases, which has non-obvious consequence for the contribution of spectral samples. We developed methods to assess the influence of spectral windows on the retrieval. While we can not exhaustively search the whole range of possible spectral sample combinations, it is possible to optimize information content using a genetic algorithm. The GLORIA instrument is mounted with a viewing direction perpendicular to the flight direction. A gimbal frame makes it possible to move the instrument 45° to both direction. By flying on a circular path, it is possible to generate images of an area of interest from a wide range of angles. These can be analyzed in a 3D-tomographic fashion, which yields superior spatial resolution along line of

Immunofluorescent staining of nuclear antigen in lymphoid cells transformed by Herpesvirus papio (HVP).

PubMed

Schmitz, H

1981-01-01

An improved fixation method for antigen detection in lymphoblastoid cells is described. Herpesvirus papio nuclear antigen (HUPNA) could be stained in several transformed lymphoid cell lines by anti-complement immunofluorescence (ACIF). Antibody to HUPNA was detected in many human sera containing antibodies to Epstein-Barr virus capsid and nuclear antigen (EBNA). Rheumatoid arthritis sera showed a high incidence of both anti-EBNA and anti-HUPNA antibodies.

In vitro antigen-induced, antigen-specific antibody production in man. Specific and polyclonal components, kinetics, and cellular requirements

PubMed Central

1981-01-01

A highly specific and reproducible antigen-induced, antigen-specific culture and assay system for antibody production by human peripheral blood B lymphocytes has been developed. The system is clearly T cell and monocyte dependent and is independent of exogenous mitogens. The major factors in our ability to trigger specific antibody production with antigen alone have been the use of extremely low concentrations of antigen in vitro (doses several orders of magnitude below those inducing a peak blastogenic response), careful attention to in vitro cell density and culture vessel geometry, and appreciation of the kinetics of the circulating antigen-inducible B cell repertoire. A dichotomy and overlap between antigen-induced, antigen-specific and antigen-induced, polyclonal responses was observed in the study of doubly immunized individuals. Whereas antibody responses highly specific for the antigen in culture were observed under one set of culture conditions (flat-bottomed vessels, 1.5 x 10(6) cells), switching to another culture system (round-bottomed vessels, 5 x 10(5) cells) resulted in polyclonal responses to antigen. Despite these culture condition-related differences in the induction of antibody synthesis, the suppression of specific antibody production that occurred at high concentrations of antigen was specific only for the antigen in culture. The capability to easily and reproducibly look at truly antigen-induced, antigen specific antibody production should be a major tool in furthering the understanding of human B cell activation and immunoregulation. PMID:6169778

Improved image retrieval based on fuzzy colour feature vector

NASA Astrophysics Data System (ADS)

Ben-Ahmeida, Ahlam M.; Ben Sasi, Ahmed Y.

2013-03-01

One of Image indexing techniques is the Content-Based Image Retrieval which is an efficient way for retrieving images from the image database automatically based on their visual contents such as colour, texture, and shape. In this paper will be discuss how using content-based image retrieval (CBIR) method by colour feature extraction and similarity checking. By dividing the query image and all images in the database into pieces and extract the features of each part separately and comparing the corresponding portions in order to increase the accuracy in the retrieval. The proposed approach is based on the use of fuzzy sets, to overcome the problem of curse of dimensionality. The contribution of colour of each pixel is associated to all the bins in the histogram using fuzzy-set membership functions. As a result, the Fuzzy Colour Histogram (FCH), outperformed the Conventional Colour Histogram (CCH) in image retrieving, due to its speedy results, where were images represented as signatures that took less size of memory, depending on the number of divisions. The results also showed that FCH is less sensitive and more robust to brightness changes than the CCH with better retrieval recall values.

Retrieving self-vocalized information: An event-related potential (ERP) study on the effect of retrieval orientation.

PubMed

Rosburg, Timm; Johansson, Mikael; Sprondel, Volker; Mecklinger, Axel

2014-11-18

Retrieval orientation refers to a pre-retrieval process and conceptualizes the specific form of processing that is applied to a retrieval cue. In the current event-related potential (ERP) study, we sought to find evidence for an involvement of the auditory cortex when subjects attempt to retrieve vocalized information, and hypothesized that adopting retrieval orientation would be beneficial for retrieval accuracy. During study, participants saw object words that they subsequently vocalized or visually imagined. At test, participants had to identify object names of one study condition as targets and to reject object names of the second condition together with new items. Target category switched after half of the test trials. Behaviorally, participants responded less accurately and more slowly to targets of the vocalize condition than to targets of the imagine condition. ERPs to new items varied at a single left electrode (T7) between 500 and 800ms, indicating a moderate retrieval orientation effect in the subject group as a whole. However, whereas the effect was strongly pronounced in participants with high retrieval accuracy, it was absent in participants with low retrieval accuracy. A current source density (CSD) mapping of the retrieval orientation effect indicated a source over left temporal regions. Independently from retrieval accuracy, the ERP retrieval orientation effect was surprisingly also modulated by test order. Findings are suggestive for an involvement of the auditory cortex in retrieval attempts of vocalized information and confirm that adopting retrieval orientation is potentially beneficial for retrieval accuracy. The effects of test order on retrieval-related processes might reflect a stronger focus on the newness of items in the more difficult test condition when participants started with this condition. Copyright © 2014 Elsevier Inc. All rights reserved.

Multi-field query expansion is effective for biomedical dataset retrieval.

PubMed

Bouadjenek, Mohamed Reda; Verspoor, Karin

2017-01-01

In the context of the bioCADDIE challenge addressing information retrieval of biomedical datasets, we propose a method for retrieval of biomedical data sets with heterogenous schemas through query reformulation. In particular, the method proposed transforms the initial query into a multi-field query that is then enriched with terms that are likely to occur in the relevant datasets. We compare and evaluate two query expansion strategies, one based on the Rocchio method and another based on a biomedical lexicon. We then perform a comprehensive comparative evaluation of our method on the bioCADDIE dataset collection for biomedical retrieval. We demonstrate the effectiveness of our multi-field query method compared to two baselines, with MAP improved from 0.2171 and 0.2669 to 0.2996. We also show the benefits of query expansion, where the Rocchio expanstion method improves the MAP for our two baselines from 0.2171 and 0.2669 to 0.335. We show that the Rocchio query expansion method slightly outperforms the one based on the biomedical lexicon as a source of terms, with an improvement of roughly 3% for MAP. However, the query expansion method based on the biomedical lexicon is much less resource intensive since it does not require computation of any relevance feedback set or any initial execution of the query. Hence, in term of trade-off between efficiency, execution time and retrieval accuracy, we argue that the query expansion method based on the biomedical lexicon offers the best performance for a prototype biomedical data search engine intended to be used at a large scale. In the official bioCADDIE challenge results, although our approach is ranked seventh in terms of the infNDCG evaluation metric, it ranks second in term of P@10 and NDCG. Hence, the method proposed here provides overall good retrieval performance in relation to the approaches of other competitors. Consequently, the observations made in this paper should benefit the development of a Data Discovery

X-ray absorption fine structure of artificial antigens for cadmium

NASA Astrophysics Data System (ADS)

Lu, Liang; Liu, Aiping; Chen, Fusheng; Wang, Xiaohong

2011-11-01

Immunoassay technology as a quick and large-scale screening method to detect metal ions in foods and environmental samples has rapidly been developed due to several advantages over conventional instrument-intensive methods. Unlike biomacromolecule, metal ions are haptens without immunogenicity, so successful preparation of artificial antigens is the first critical step for establishing immunoassay methods for them. In the current paper, cadmium ions were conjugated to BSA and OVA, respectively, using bifunctional chelator, p-SCN-Bn-DTPA. The ultraviolet analysis indicated that the maximum absorption peak of Cd-p-SCN-DTPA-BSA and Cd-p-SCN-DTPA-OVA had a small peak shift and an apparent absorbance increase compared to that of BSA and OVA, and the extents of substitution of ɛ-amino in both conjugates were 51.2% and 58.6%, respectively. In addition, the EXAFS of conjugates implied that Cd 2+ coordinated with N and O atoms of DTPA in artificial antigens, the coordination type and number of Cd-DTPA, Cd-p-SCN-Bn-DTPA-BSA, Cd-p-SCN-Bn-DTPA-OVA were the same. XANES region and geometries of the three compounds were also same. These results implied that the three antigens had the similar local structure and atomic geometry. This was the first time that the XAFS was attempted for the identification of artificial heavy metal ion antigens.

Feedback increases benefits but not costs of retrieval practice: Retrieval-induced forgetting is strength independent.

PubMed

Tempel, Tobias; Frings, Christian

2018-04-01

We examined how the provision of feedback affected two separate effects of retrieval practice: strengthening of practiced information and forgetting of related, unpracticed information. Feedback substantially increased recall of retrieval-practiced items. This unsurprising result shows once again that restudy opportunities boost the benefits of testing. In contrast, retrieval-induced forgetting was unaffected by the manipulation and occurred in equal size with or without feedback. These findings demonstrate strength independence of retrieval-induced forgetting and thus support a theoretical account assuming that an inhibitory mechanism causes retrieval-induced forgetting. According to this theory, inhibition resolves competition that arises during retrieval attempts but is unrelated to the consequences of retrieval practice concerning practiced items. The present results match these assumptions and contradict the theoretical alternative that blocking by strengthened information might explain retrieval-induced forgetting. We discuss our findings against the background of previous studies.

Development and application of a probability distribution retrieval scheme to the remote sensing of clouds and precipitation

NASA Astrophysics Data System (ADS)

McKague, Darren Shawn

2001-12-01

The statistical properties of clouds and precipitation on a global scale are important to our understanding of climate. Inversion methods exist to retrieve the needed cloud and precipitation properties from satellite data pixel-by-pixel that can then be summarized over large data sets to obtain the desired statistics. These methods can be quite computationally expensive, and typically don't provide errors on the statistics. A new method is developed to directly retrieve probability distributions of parameters from the distribution of measured radiances. The method also provides estimates of the errors on the retrieved distributions. The method can retrieve joint distributions of parameters that allows for the study of the connection between parameters. A forward radiative transfer model creates a mapping from retrieval parameter space to radiance space. A Monte Carlo procedure uses the mapping to transform probability density from the observed radiance histogram to a two- dimensional retrieval property probability distribution function (PDF). An estimate of the uncertainty in the retrieved PDF is calculated from random realizations of the radiance to retrieval parameter PDF transformation given the uncertainty of the observed radiances, the radiance PDF, the forward radiative transfer, the finite number of prior state vectors, and the non-unique mapping to retrieval parameter space. The retrieval method is also applied to the remote sensing of precipitation from SSM/I microwave data. A method of stochastically generating hydrometeor fields based on the fields from a numerical cloud model is used to create the precipitation parameter radiance space transformation. The impact of vertical and horizontal variability within the hydrometeor fields has a significant impact on algorithm performance. Beamfilling factors are computed from the simulated hydrometeor fields. The beamfilling factors vary quite a bit depending upon the horizontal structure of the rain. The

Identification of novel tumor antigens with patient-derived immune-selected antibodies

PubMed Central

Rodriguez-Pinto, Daniel; Sparkowski, Jason; Keough, Martin P.; Phoenix, Kathryn N.; Vumbaca, Frank; Han, David K.; Gundelfinger, Eckart D.; Beesley, Philip

2010-01-01

The identification of tumor antigens capable of eliciting an immune response in vivo may be an effective method to identify therapeutic cancer targets. We have developed a method to identify such antigens using frozen tumor-draining lymph node samples from breast cancer patients. Immune responses in tumor-draining lymph nodes were identified by immunostaining lymph node sections for B-cell markers (CD20&CD23) and Ki67 which revealed cell proliferation in germinal center zones. Antigen-dependent somatic hypermutation (SH) and clonal expansion (CE) were present in heavy chain variable (VH) domain cDNA clones obtained from these germinal centers, but not from Ki67 negative germinal centers. Recombinant VH single-domain antibodies were used to screen tumor proteins and affinity select potential tumor antigens. Neuroplastin (NPTN) was identified as a candidate breast tumor antigen using proteomic identification of affinity selected tumor proteins with a recombinant VH single chain antibody. NPTN was found to be highly expressed in approximately 20% of invasive breast carcinomas and 50% of breast carcinomas with distal metastasis using a breast cancer tissue array. Additionally, NPTN over-expression in a breast cancer cell line resulted in a significant increase in tumor growth and angiogenesis in vivo which was related to increased VEGF production in the transfected cells. These results validate NPTN as a tumor-associated antigen which could promote breast tumor growth and metastasis if aberrantly expressed. These studies also demonstrate that humoral immune responses in tumor-draining lymph nodes can provide antibody reagents useful in identifying tumor antigens with applications for biomarker screening, diagnostics and therapeutic interventions. PMID:18568347

Automated typing of red blood cell and platelet antigens: a whole-genome sequencing study.

PubMed

Lane, William J; Westhoff, Connie M; Gleadall, Nicholas S; Aguad, Maria; Smeland-Wagman, Robin; Vege, Sunitha; Simmons, Daimon P; Mah, Helen H; Lebo, Matthew S; Walter, Klaudia; Soranzo, Nicole; Di Angelantonio, Emanuele; Danesh, John; Roberts, David J; Watkins, Nick A; Ouwehand, Willem H; Butterworth, Adam S; Kaufman, Richard M; Rehm, Heidi L; Silberstein, Leslie E; Green, Robert C

2018-06-01

There are more than 300 known red blood cell (RBC) antigens and 33 platelet antigens that differ between individuals. Sensitisation to antigens is a serious complication that can occur in prenatal medicine and after blood transfusion, particularly for patients who require multiple transfusions. Although pre-transfusion compatibility testing largely relies on serological methods, reagents are not available for many antigens. Methods based on single-nucleotide polymorphism (SNP) arrays have been used, but typing for ABO and Rh-the most important blood groups-cannot be done with SNP typing alone. We aimed to develop a novel method based on whole-genome sequencing to identify RBC and platelet antigens. This whole-genome sequencing study is a subanalysis of data from patients in the whole-genome sequencing arm of the MedSeq Project randomised controlled trial (NCT01736566) with no measured patient outcomes. We created a database of molecular changes in RBC and platelet antigens and developed an automated antigen-typing algorithm based on whole-genome sequencing (bloodTyper). This algorithm was iteratively improved to address cis-trans haplotype ambiguities and homologous gene alignments. Whole-genome sequencing data from 110 MedSeq participants (30 × depth) were used to initially validate bloodTyper through comparison with conventional serology and SNP methods for typing of 38 RBC antigens in 12 blood-group systems and 22 human platelet antigens. bloodTyper was further validated with whole-genome sequencing data from 200 INTERVAL trial participants (15 × depth) with serological comparisons. We iteratively improved bloodTyper by comparing its typing results with conventional serological and SNP typing in three rounds of testing. The initial whole-genome sequencing typing algorithm was 99·5% concordant across the first 20 MedSeq genomes. Addressing discordances led to development of an improved algorithm that was 99·8% concordant for the remaining 90 Med

Dictionary Pruning with Visual Word Significance for Medical Image Retrieval

PubMed Central

Zhang, Fan; Song, Yang; Cai, Weidong; Hauptmann, Alexander G.; Liu, Sidong; Pujol, Sonia; Kikinis, Ron; Fulham, Michael J; Feng, David Dagan; Chen, Mei

2016-01-01

Content-based medical image retrieval (CBMIR) is an active research area for disease diagnosis and treatment but it can be problematic given the small visual variations between anatomical structures. We propose a retrieval method based on a bag-of-visual-words (BoVW) to identify discriminative characteristics between different medical images with Pruned Dictionary based on Latent Semantic Topic description. We refer to this as the PD-LST retrieval. Our method has two main components. First, we calculate a topic-word significance value for each visual word given a certain latent topic to evaluate how the word is connected to this latent topic. The latent topics are learnt, based on the relationship between the images and words, and are employed to bridge the gap between low-level visual features and high-level semantics. These latent topics describe the images and words semantically and can thus facilitate more meaningful comparisons between the words. Second, we compute an overall-word significance value to evaluate the significance of a visual word within the entire dictionary. We designed an iterative ranking method to measure overall-word significance by considering the relationship between all latent topics and words. The words with higher values are considered meaningful with more significant discriminative power in differentiating medical images. We evaluated our method on two public medical imaging datasets and it showed improved retrieval accuracy and efficiency. PMID:27688597

Dictionary Pruning with Visual Word Significance for Medical Image Retrieval.

PubMed

Zhang, Fan; Song, Yang; Cai, Weidong; Hauptmann, Alexander G; Liu, Sidong; Pujol, Sonia; Kikinis, Ron; Fulham, Michael J; Feng, David Dagan; Chen, Mei

2016-02-12

Content-based medical image retrieval (CBMIR) is an active research area for disease diagnosis and treatment but it can be problematic given the small visual variations between anatomical structures. We propose a retrieval method based on a bag-of-visual-words (BoVW) to identify discriminative characteristics between different medical images with Pruned Dictionary based on Latent Semantic Topic description. We refer to this as the PD-LST retrieval. Our method has two main components. First, we calculate a topic-word significance value for each visual word given a certain latent topic to evaluate how the word is connected to this latent topic. The latent topics are learnt, based on the relationship between the images and words, and are employed to bridge the gap between low-level visual features and high-level semantics. These latent topics describe the images and words semantically and can thus facilitate more meaningful comparisons between the words. Second, we compute an overall-word significance value to evaluate the significance of a visual word within the entire dictionary. We designed an iterative ranking method to measure overall-word significance by considering the relationship between all latent topics and words. The words with higher values are considered meaningful with more significant discriminative power in differentiating medical images. We evaluated our method on two public medical imaging datasets and it showed improved retrieval accuracy and efficiency.

Words, concepts, or both: optimal indexing units for automated information retrieval.

PubMed Central

Hersh, W. R.; Hickam, D. H.; Leone, T. J.

1992-01-01

What is the best way to represent the content of documents in an information retrieval system? This study compares the retrieval effectiveness of five different methods for automated (machine-assigned) indexing using three test collections. The consistently best methods are those that use indexing based on the words that occur in the available text of each document. Methods used to map text into concepts from a controlled vocabulary showed no advantage over the word-based methods. This study also looked at an approach to relevance feedback which showed benefit for both word-based and concept-based methods. PMID:1482951

ANTIGENIC MODULATION

PubMed Central

Old, Lloyd J.; Stockert, Elisabeth; Boyse, Edward A.; Kim, Jae Ho

1968-01-01

Antigenic modulation (the loss of TL antigens from TL+ cells exposed to TL antibody in the absence of lytic complement) has been demonstrated in vitro. An ascites leukemia, phenotype TL.1,2,3, which modulates rapidly and completely when incubated with TL antiserum in vitro, was selected for further study of the phenomenon. Over a wide range of TL antibody concentrations modulation at 37°C was detectable within 10 min and was complete within approximately 1 hr. The cells were initially sensitized to C' by their contact with antibody, thereafter losing this sensitivity to C' lysis together with their sensitivity to TL antibody and C' in the cytotoxic test. The capacity of the cells to undergo modulation was abolished by actinomycin D and by iodoacetamide, and by reducing the temperature of incubation to 0°C. Thus modulation apparently is an active cellular process. Antigens TL. 1,2, and 3 are all modulated by anti-TL.1,3 serum and by anti-TL.3 serum. This modulation affects all three TL components together, even when antibody to one or two of them is lacking. aAnti-TL.2 serum does not induce modulation and in fact impairs modulation by the other TL antibodies. The influence of the TL phenotype of cells upon the demonstrable content of H-2 (D region) isoantigen, first shown in cells modulated in vivo, has been observed with cells modulated in vitro. Cells undergoing modulation show a progressive increase in H-2 (D region) antigen over a period of 4 hr, with no change in H-2 antigens of the K region. Restoration of the TL+ phenotype of modulated cells after removal of antibody is less rapid than TL+ → TL- modulation and may require several cell divisions. PMID:5636556

The genetic origin of minor histocompatibility antigens.

PubMed

Roopenian, D C; Christianson, G J; Davis, A P; Zuberi, A R; Mobraaten, L E

1993-01-01

The purpose of this study was to elucidate the genetic origin of minor histocompatibility (H) antigens. Toward this end common inbred mouse strains, distinct subspecies, and species of the subgenus Mus were examined for expression of various minor H antigens. These antigens were encoded by the classical minor H loci H-3 and H-4 or by newly identified minor H antigens detected as a consequence of mutation. Both minor H antigens that stimulate MHC class I-restricted cytotoxic T cells (Tc) and antigens that stimulate MHC class II-restricted helper T cells (Th) were monitored. The results suggested that strains of distinct ancestry commonly express identical or cross-reactive antigens. Moreover, a correlation between the lack of expression of minor H antigens and ancestral heritage was observed. To address whether the antigens found on unrelated strains were allelic with the sensitizing minor H antigens or a consequence of antigen cross-reactivity, classical genetic segregation analysis was carried out. Even in distinct subspecies and species, the minor H antigens always mapped to the site of the appropriate minor H locus. Together the results suggest: 1) minor H antigen sequences are evolutionarily stable in that their pace of antigenic change is slow enough to predate subspeciation and speciation; 2) the minor H antigens originated in the inbred strains as a consequence of a rare polymorphism or loss mutation carried in a founder mouse stock that caused the mouse to perceive the wild-type protein as foreign; 3) there is a remarkable lack of antigenic cross-reactivity between the defined minor H antigens and other gene products.

Evaluation of Gastrothylax crumenifer antigenic preparation in serodiagnosis of paramphistomiasis in sheep.

PubMed

Ahmad, Tariq; Reshi, Mohammad Latif; Cheshti, M Z; Tanveer, Syed; Shah, Zaffar Amin; Fomada, Bashir Ahmad; Raina, O K

2014-04-01

An evaluation of Gastrothylax crumenifer crude antigen preparation viz., Somatic Antigen (SAg), Excretory Secretory Antigen (ESAg) and Egg Antigen (EAg) in serodiagnosis of disease was undertaken. Test sera samples were obtained from 30 Paramphistomiasis Positive and 30 Gastrothylax free sheep slaughtered at Hazratbal Kashmir. The referral antigenic preparation were evaluated against Paramphistomiasis positive sera, via., control negative sera, using double immunodiffusion test (DID), (IEP) Immunoelectrophoretic assay and ELISA. The performance of referral antigens, as assessed from percent sensitivity and specificity, revealed an increasing trend from DID (Double immunodiffusion-An immunological technique used in the detection, identification and quantification of antibodies and antigens) to IEP (immunoelectrophoresis-A general name for a number of biochemical methods for separation and characterization of proteins based on electrophoresis and reaction with antibodies), followed by ELISA, detecting higher number of sheep positive for paramphistomiasis. In ELISA the ESAg and SAg were evaluated as most reactive antigens with no significant difference and EAg was the least antigenic. In IEP, EAg had the higher sensitivity (60%) and analogous specificity of SAg and ESAg. The formation of the preceptin lines in the proximity to EAg containing wells (cathode end) in IEP was suggestive of higher molecular weight of G. crumenifer specific protein molecules with slower rate of migration. Purification and characterization of G. crumenifer and identification of specific antigenic molecules, particularly in EAg has been suggested for qualitative improvement of diagnostic value of the antigens in the tests used here in.

The Community Cloud retrieval for CLimate (CC4CL) - Part 2: The optimal estimation approach

NASA Astrophysics Data System (ADS)

McGarragh, Gregory R.; Poulsen, Caroline A.; Thomas, Gareth E.; Povey, Adam C.; Sus, Oliver; Stapelberg, Stefan; Schlundt, Cornelia; Proud, Simon; Christensen, Matthew W.; Stengel, Martin; Hollmann, Rainer; Grainger, Roy G.

2018-06-01

The Community Cloud retrieval for Climate (CC4CL) is a cloud property retrieval system for satellite-based multispectral imagers and is an important component of the Cloud Climate Change Initiative (Cloud_cci) project. In this paper we discuss the optimal estimation retrieval of cloud optical thickness, effective radius and cloud top pressure based on the Optimal Retrieval of Aerosol and Cloud (ORAC) algorithm. Key to this method is the forward model, which includes the clear-sky model, the liquid water and ice cloud models, the surface model including a bidirectional reflectance distribution function (BRDF), and the "fast" radiative transfer solution (which includes a multiple scattering treatment). All of these components and their assumptions and limitations will be discussed in detail. The forward model provides the accuracy appropriate for our retrieval method. The errors are comparable to the instrument noise for cloud optical thicknesses greater than 10. At optical thicknesses less than 10 modeling errors become more significant. The retrieval method is then presented describing optimal estimation in general, the nonlinear inversion method employed, measurement and a priori inputs, the propagation of input uncertainties and the calculation of subsidiary quantities that are derived from the retrieval results. An evaluation of the retrieval was performed using measurements simulated with noise levels appropriate for the MODIS instrument. Results show errors less than 10 % for cloud optical thicknesses greater than 10. Results for clouds of optical thicknesses less than 10 have errors up to 20 %.

Experiments on sparsity assisted phase retrieval of phase objects

NASA Astrophysics Data System (ADS)

Gaur, Charu; Lochab, Priyanka; Khare, Kedar

2017-05-01

Iterative phase retrieval algorithms such as the Gerchberg-Saxton method and the Fienup hybrid input-output method are known to suffer from the twin image stagnation problem, particularly when the solution to be recovered is complex valued and has centrosymmetric support. Recently we showed that the twin image stagnation problem can be addressed using image sparsity ideas (Gaur et al 2015 J. Opt. Soc. Am. A 32 1922). In this work we test this sparsity assisted phase retrieval method with experimental single shot Fourier transform intensity data frames corresponding to phase objects displayed on a spatial light modulator. The standard iterative phase retrieval algorithms are combined with an image sparsity based penalty in an adaptive manner. Illustrations for both binary and continuous phase objects are provided. It is observed that image sparsity constraint has an important role to play in obtaining meaningful phase recovery without encountering the well-known stagnation problems. The results are valuable for enabling single shot coherent diffraction imaging of phase objects for applications involving illumination wavelengths over a wide range of electromagnetic spectrum.

Changes in structural and antigenic properties of proteins by radiation

NASA Astrophysics Data System (ADS)

Kume, Tamikazu; Matsuda, Tsukasa

1995-08-01

Radiation effect on structural and antigenic properties of proteins (0.2% in 0.01 M phosphate buffer, pH 7.4) were investigated using ovalbumin (OVA) and bovine serum albumin (BSA). Aggregation of OVA and BSA was induced by radiation and the molecular mass increased significantly in N 2. Significant changes in surface hydrophobicity and [ θ] 222 nm of CD were also observed by radiation showing the destruction of secondary structure of proteins. Antigenicity of irradiated OVA measured by the method of immunodiffusion was decreased by radiation, and the reactivity to anti-OVA antibody was almost diminished at 8 kGy in N 2 and 4 kGy in O 2, respectively. The reactivity of BSA was diminished at 4 kGy both in N 2 and O 2. Changes in hydrophobicity of OVA did not correspond to the decrease in antigenicity, whereas the changes in [ θ] 222 nm relatively well corresponded to the antigenicity. The SDS-PAGE and immunoblotting analysis showed that radiation at higher doses induced the production of protein aggregates and degraded fragments with reactivity to the specific antibodies. These results suggest that the main part of conformation-dependent antigenic structure (conformational epitope) is easily lost by radiation, but some antigenicity, which is mostly due to the amino acid sequence-dependent antigenic structures (sequential epitopes), remains even at higher dose.

Music Retrieval Based on the Relation between Color Association and Lyrics

NASA Astrophysics Data System (ADS)

Nakamur, Tetsuaki; Utsumi, Akira; Sakamoto, Maki

Various methods for music retrieval have been proposed. Recently, many researchers are tackling developing methods based on the relationship between music and feelings. In our previous psychological study, we found that there was a significant correlation between colors evoked from songs and colors evoked only from lyrics, and showed that the music retrieval system using lyrics could be developed. In this paper, we focus on the relationship among music, lyrics and colors, and propose a music retrieval method using colors as queries and analyzing lyrics. This method estimates colors evoked from songs by analyzing lyrics of the songs. On the first step of our method, words associated with colors are extracted from lyrics. We assumed two types of methods to extract words associated with colors. In the one of two methods, the words are extracted based on the result of a psychological experiment. In the other method, in addition to the words extracted based on the result of the psychological experiment, the words from corpora for the Latent Semantic Analysis are extracted. On the second step, colors evoked from the extracted words are compounded, and the compounded colors are regarded as those evoked from the song. On the last step, colors as queries are compared with colors estimated from lyrics, and the list of songs is presented based on similarities. We evaluated the two methods described above and found that the method based on the psychological experiment and corpora performed better than the method only based on the psychological experiment. As a result, we showed that the method using colors as queries and analyzing lyrics is effective for music retrieval.

Case retrieval in medical databases by fusing heterogeneous information.

PubMed

Quellec, Gwénolé; Lamard, Mathieu; Cazuguel, Guy; Roux, Christian; Cochener, Béatrice

2011-01-01

A novel content-based heterogeneous information retrieval framework, particularly well suited to browse medical databases and support new generation computer aided diagnosis (CADx) systems, is presented in this paper. It was designed to retrieve possibly incomplete documents, consisting of several images and semantic information, from a database; more complex data types such as videos can also be included in the framework. The proposed retrieval method relies on image processing, in order to characterize each individual image in a document by their digital content, and information fusion. Once the available images in a query document are characterized, a degree of match, between the query document and each reference document stored in the database, is defined for each attribute (an image feature or a metadata). A Bayesian network is used to recover missing information if need be. Finally, two novel information fusion methods are proposed to combine these degrees of match, in order to rank the reference documents by decreasing relevance for the query. In the first method, the degrees of match are fused by the Bayesian network itself. In the second method, they are fused by the Dezert-Smarandache theory: the second approach lets us model our confidence in each source of information (i.e., each attribute) and take it into account in the fusion process for a better retrieval performance. The proposed methods were applied to two heterogeneous medical databases, a diabetic retinopathy database and a mammography screening database, for computer aided diagnosis. Precisions at five of 0.809 ± 0.158 and 0.821 ± 0.177, respectively, were obtained for these two databases, which is very promising.

Synergistic atmospheric retrievals: Using OMEGA and PFS to retrieve martian CO

NASA Astrophysics Data System (ADS)

Robert, S.; Aoki, S.; Piccialli, A.; Audouard, J.; Montmessin, F.; Ferron, S.; Altieri, F.; Bellucci, G.; Geminale, A.; Giuranna, M.; Sindoni, G.; Vandaele, A. C.

2017-09-01

Recently, a theoretical study was published showing how science return can benefit from synergistic retrievals [Robert et al., 2017]. The same approach is here applied to experimental data. OMEGA and PFS instruments, both on Mars Express spacecraft, have collected high-quality data enabling us to retrieve CO volume mixing ratio, among others. The synergy between OMEGA and PFS channels will be presented and the benefits of the synergy will be described by comparing synergistic spectral retrievals and non-synergistic ones.

Testing the MODIS Satellite Retrieval of Aerosol Fine-Mode Fraction

NASA Technical Reports Server (NTRS)

Anderson, Theodore L.; Wu, Yonghua; Chu, D. Allen; Schmid, Beat; Redemann, Jens; Dubovik, Oleg

2005-01-01

Satellite retrievals of the fine-mode fraction (FMF) of midvisible aerosol optical depth, tau, are potentially valuable for constraining chemical transport models and for assessing the global distribution of anthropogenic aerosols. Here we compare satellite retrievals of FMF from the Moderate Resolution Imaging Spectroradiometer (MODIS) to suborbital data on the submicrometer fraction (SMF) of tau. SMF is a closely related parameter that is directly measurable by in situ techniques. The primary suborbital method uses in situ profiling of SMF combined with airborne Sun photometry both to validate the in situ estimate of ambient extinction and to take into account the aerosol above the highest flight level. This method is independent of the satellite retrieval and has well-known accuracy but entails considerable logistical and technical difficulties. An alternate method uses Sun photometer measurements near the surface and an empirical relation between SMF and the Angstrom exponent, A, a measure of the wavelength dependence of optical depth or extinction. Eleven primary and fifteen alternate comparisons are examined involving varying mixtures of dust, sea salt, and pollution in the vicinity of Korea and Japan. MODIS ocean retrievals of FMF are shown to be systematically higher than suborbital estimates of SMF by about 0.2. The most significant cause of this discrepancy involves the relationship between 5 and fine-mode partitioning; in situ measurements indicate a systematically different relationship from what is assumed in the satellite retrievals. Based on these findings, we recommend: (1) satellite programs should concentrate on retrieving and validating since an excellent validation program is in place for doing this, and (2) suborbital measurements should be used to derive relationships between A and fine-mode partitioning to allow interpretation of the satellite data in terms of fine-mode aerosol optical depth.

Central Tolerance to Tissue-specific Antigens Mediated by Direct and Indirect Antigen Presentation

PubMed Central

Gallegos, Alena M.; Bevan, Michael J.

2004-01-01

Intrathymic expression of tissue-specific antigens (TSAs) by medullary thymic epithelial cells (Mtecs) leads to deletion of autoreactive T cells. However, because Mtecs are known to be poor antigen-presenting cells (APCs) for tolerance to ubiquitous antigens, and very few Mtecs express a given TSA, it was unclear if central tolerance to TSA was induced directly by Mtec antigen presentation or indirectly by thymic bone marrow (BM)-derived cells via cross-presentation. We show that professional BM-derived APCs acquire TSAs from Mtecs and delete autoreactive CD8 and CD4 T cells. Although direct antigen presentation by Mtecs did not delete the CD4 T cell population tested in this study, Mtec presentation efficiently deleted both monoclonal and polyclonal populations of CD8 T cells. For developing CD8 T cells, deletion by BM-derived APC and by Mtec presentation occurred abruptly at the transitional, CD4high CD8low TCRintermediate stage, presumably as the cells transit from the cortex to the medulla. These studies reveal a cooperative relationship between Mtecs and BM-derived cells in thymic elimination of autoreactive T cells. Although Mtecs synthesize TSAs and delete a subset of autoreactive T cells, BM-derived cells extend the range of clonal deletion by cross-presenting antigen captured from Mtecs. PMID:15492126

Cellular Pathway(S) of Antigen Processing and Presentation in Fish APC: Endosomal Involvement and Cell-Free Antigen Presentation

PubMed Central

Vallejo, Abbe N.; Miller, Norman W.; Harvey, Nancy E.; Cuchens, Marvin A.; Warr, Gregory W.

1992-01-01

Studies were conducted to address further the role(s) of antigen processing and presentation in the induction of immune responses in a phylogenetically lower vertebrate, specifically a teleost, the channel catfish. In particular, studies were aimed at determining the subcellular compartments involved in antigen degradation by channel catfish antigen-presenting cells (APC) as well as ascertaining the reexpression of immunogenic peptides on the surfaces of APC. The results showed that exogenous protein antigens were actively endocytosed by APC as detected by flow cytometry. Use of radiolabeled antigen and subcellular fractionation protocols also showed that antigen localized in endosomes/lysosomes. Furthermore, there was an apparent redistribution of antigen between these organelles and the plasma membrane during the course of antigen pulsing. Functional assays for the induction of in vitro antigen-specific proliferation of immune catfish peripheral blood leukocytes (PBL) showed that membrane preparations from antigen-pulsed autologous APC were highly stimulatory. The magnitude of responses elicited with such membrane preparations was very similar to that of PBL cultures stimulated with native antigen-pulsed and fixed intact APC or prefixed intact APC incubated with a peptide fragment of the nominal antigen. Current data further corroborate our previous findings that steps akin to antigen processing and presentation are clearly important in the induction of immune responses in lower vertebrates like fish, in a manner similar to that seen in mammalian systems. Consequently, it would appear that many immune functions among the diverse taxa of vertebrates are remarkably conserved. PMID:1343103

Antigenic mapping of an H9N2 avian influenza virus reveals two discrete antigenic sites and a novel mechanism of immune escape.

PubMed

Peacock, Thomas; Reddy, Kolli; James, Joe; Adamiak, Beata; Barclay, Wendy; Shelton, Holly; Iqbal, Munir

2016-01-07

H9N2 avian influenza virus is a major cause of poultry production loss across Asia leading to the wide use of vaccines. Efficacy of vaccines is often compromised due to the rapid emergence of antigenic variants. To improve the effectiveness of vaccines in the field, a better understanding of the antigenic epitopes of the major antigen, hemagglutinin, is required. To address this, a panel of nine monoclonal antibodies were generated against a contemporary Pakistani H9N2 isolate, which represents a major Asian H9N2 viral lineage. Antibodies were characterized in detail and used to select a total of 26 unique 'escape' mutants with substitutions across nine different amino acid residues in hemagglutinin including seven that have not been described as antigenic determinants for H9N2 viruses before. Competition assays and structural mapping revealed two novel, discrete antigenic sites "H9-A" and "H9-B". Additionally, a second subset of escape mutants contained amino acid deletions within the hemagglutinin receptor binding site. This constitutes a novel method of escape for group 1 hemagglutinins and could represent an alternative means for H9N2 viruses to overcome vaccine induced immunity. These results will guide surveillance efforts for arising antigenic variants as well as evidence based vaccine seed selection and vaccine design.

Antigenic mapping of an H9N2 avian influenza virus reveals two discrete antigenic sites and a novel mechanism of immune escape

PubMed Central

Peacock, Thomas; Reddy, Kolli; James, Joe; Adamiak, Beata; Barclay, Wendy; Shelton, Holly; Iqbal, Munir

2016-01-01

H9N2 avian influenza virus is a major cause of poultry production loss across Asia leading to the wide use of vaccines. Efficacy of vaccines is often compromised due to the rapid emergence of antigenic variants. To improve the effectiveness of vaccines in the field, a better understanding of the antigenic epitopes of the major antigen, hemagglutinin, is required. To address this, a panel of nine monoclonal antibodies were generated against a contemporary Pakistani H9N2 isolate, which represents a major Asian H9N2 viral lineage. Antibodies were characterized in detail and used to select a total of 26 unique ‘escape’ mutants with substitutions across nine different amino acid residues in hemagglutinin including seven that have not been described as antigenic determinants for H9N2 viruses before. Competition assays and structural mapping revealed two novel, discrete antigenic sites “H9-A” and “H9-B”. Additionally, a second subset of escape mutants contained amino acid deletions within the hemagglutinin receptor binding site. This constitutes a novel method of escape for group 1 hemagglutinins and could represent an alternative means for H9N2 viruses to overcome vaccine induced immunity. These results will guide surveillance efforts for arising antigenic variants as well as evidence based vaccine seed selection and vaccine design. PMID:26738561

Mapping Antigenic Motifs in the Trypomastigote Small Surface Antigen from Trypanosoma cruzi

PubMed Central

Balouz, Virginia; Cámara, María de los Milagros; Cánepa, Gaspar E.; Carmona, Santiago J.; Volcovich, Romina; Gonzalez, Nicolás; Altcheh, Jaime; Agüero, Fernán

2015-01-01

The trypomastigote small surface antigen (TSSA) is a mucin-like molecule from Trypanosoma cruzi, the etiological agent of Chagas disease, which displays amino acid polymorphisms in parasite isolates. TSSA expression is restricted to the surface of infective cell-derived trypomastigotes, where it functions as an adhesin and engages surface receptors on the host cell as a prerequisite for parasite internalization. Previous results have established TSSA-CL, the isoform encoded by the CL Brener clone, as an appealing candidate for use in serology-based diagnostics for Chagas disease. Here, we used a combination of peptide- and recombinant protein-based tools to map the antigenic structure of TSSA-CL at maximal resolution. Our results indicate the presence of different partially overlapping B-cell epitopes clustering in the central portion of TSSA-CL, which contains most of the polymorphisms found in parasite isolates. Based on these results, we assessed the serodiagnostic performance of a 21-amino-acid-long peptide that spans TSSA-CL major antigenic determinants, which was similar to the performance of the previously validated glutathione S-transferase (GST)-TSSA-CL fusion molecule. Furthermore, the tools developed for the antigenic characterization of the TSSA antigen were also used to explore other potential diagnostic applications of the anti-TSSA humoral response in Chagasic patients. Overall, our present results provide additional insights into the antigenic structure of TSSA-CL and support this molecule as an excellent target for molecular intervention in Chagas disease. PMID:25589551

Learning Short Binary Codes for Large-scale Image Retrieval.

PubMed

Liu, Li; Yu, Mengyang; Shao, Ling

2017-03-01

Large-scale visual information retrieval has become an active research area in this big data era. Recently, hashing/binary coding algorithms prove to be effective for scalable retrieval applications. Most existing hashing methods require relatively long binary codes (i.e., over hundreds of bits, sometimes even thousands of bits) to achieve reasonable retrieval accuracies. However, for some realistic and unique applications, such as on wearable or mobile devices, only short binary codes can be used for efficient image retrieval due to the limitation of computational resources or bandwidth on these devices. In this paper, we propose a novel unsupervised hashing approach called min-cost ranking (MCR) specifically for learning powerful short binary codes (i.e., usually the code length shorter than 100 b) for scalable image retrieval tasks. By exploring the discriminative ability of each dimension of data, MCR can generate one bit binary code for each dimension and simultaneously rank the discriminative separability of each bit according to the proposed cost function. Only top-ranked bits with minimum cost-values are then selected and grouped together to compose the final salient binary codes. Extensive experimental results on large-scale retrieval demonstrate that MCR can achieve comparative performance as the state-of-the-art hashing algorithms but with significantly shorter codes, leading to much faster large-scale retrieval.

Theory of retrieving orientation-resolved molecular information using time-domain rotational coherence spectroscopy

NASA Astrophysics Data System (ADS)

Wang, Xu; Le, Anh-Thu; Zhou, Zhaoyan; Wei, Hui; Lin, C. D.

2017-08-01

We provide a unified theoretical framework for recently emerging experiments that retrieve fixed-in-space molecular information through time-domain rotational coherence spectroscopy. Unlike a previous approach by Makhija et al. (V. Makhija et al., arXiv:1611.06476), our method can be applied to the retrieval of both real-valued (e.g., ionization yield) and complex-valued (e.g., induced dipole moment) molecular response information. It is also a direct retrieval method without using iterations. We also demonstrate that experimental parameters, such as the fluence of the aligning laser pulse and the rotational temperature of the molecular ensemble, can be quite accurately determined using a statistical method.

Digital micromirror device as amplitude diffuser for multiple-plane phase retrieval

NASA Astrophysics Data System (ADS)

Abregana, Timothy Joseph T.; Hermosa, Nathaniel P.; Almoro, Percival F.

2017-06-01

Previous implementations of the phase diffuser used in the multiple-plane phase retrieval method included a diffuser glass plate with fixed optical properties or a programmable yet expensive spatial light modulator. Here a model for phase retrieval based on a digital micromirror device as amplitude diffuser is presented. The technique offers programmable, convenient and low-cost amplitude diffuser for a non-stagnating iterative phase retrieval. The technique is demonstrated in the reconstructions of smooth object wavefronts.

Aerosol Optical Retrieval and Surface Reflectance from Airborne Remote Sensing Data over Land

PubMed Central

Bassani, Cristiana; Cavalli, Rosa Maria; Pignatti, Stefano

2010-01-01

Quantitative analysis of atmospheric optical properties and surface reflectance can be performed by applying radiative transfer theory in the Atmosphere-Earth coupled system, for the atmospheric correction of hyperspectral remote sensing data. This paper describes a new physically-based algorithm to retrieve the aerosol optical thickness at 550nm (τ550) and the surface reflectance (ρ) from airborne acquired data in the atmospheric window of the Visible and Near-Infrared (VNIR) range. The algorithm is realized in two modules. Module A retrieves τ550 with a minimization algorithm, then Module B retrieves the surface reflectance ρ for each pixel of the image. The method was tested on five remote sensing images acquired by an airborne sensor under different geometric conditions to evaluate the reliability of the method. The results, τ550 and ρ, retrieved from each image were validated with field data contemporaneously acquired by a sun-sky radiometer and a spectroradiometer, respectively. Good correlation index, r, and low root mean square deviations, RMSD, were obtained for the τ550 retrieved by Module A (r2 = 0.75, RMSD = 0.08) and the ρ retrieved by Module B (r2 ≤ 0.9, RMSD ≤ 0.003). Overall, the results are encouraging, indicating that the method is reliable for optical atmospheric studies and the atmospheric correction of airborne hyperspectral images. The method does not require additional at-ground measurements about at-ground reflectance of the reference pixel and aerosol optical thickness. PMID:22163558

Automatic query formulations in information retrieval.

PubMed

Salton, G; Buckley, C; Fox, E A

1983-07-01

Modern information retrieval systems are designed to supply relevant information in response to requests received from the user population. In most retrieval environments the search requests consist of keywords, or index terms, interrelated by appropriate Boolean operators. Since it is difficult for untrained users to generate effective Boolean search requests, trained search intermediaries are normally used to translate original statements of user need into useful Boolean search formulations. Methods are introduced in this study which reduce the role of the search intermediaries by making it possible to generate Boolean search formulations completely automatically from natural language statements provided by the system patrons. Frequency considerations are used automatically to generate appropriate term combinations as well as Boolean connectives relating the terms. Methods are covered to produce automatic query formulations both in a standard Boolean logic system, as well as in an extended Boolean system in which the strict interpretation of the connectives is relaxed. Experimental results are supplied to evaluate the effectiveness of the automatic query formulation process, and methods are described for applying the automatic query formulation process in practice.

Retrieval evaluation and distance learning from perceived similarity between endomicroscopy videos.

PubMed

André, Barbara; Vercauteren, Tom; Buchner, Anna M; Wallace, Michael B; Ayache, Nicholas

2011-01-01

Evaluating content-based retrieval (CBR) is challenging because it requires an adequate ground-truth. When the available groundtruth is limited to textual metadata such as pathological classes, retrieval results can only be evaluated indirectly, for example in terms of classification performance. In this study we first present a tool to generate perceived similarity ground-truth that enables direct evaluation of endomicroscopic video retrieval. This tool uses a four-points Likert scale and collects subjective pairwise similarities perceived by multiple expert observers. We then evaluate against the generated ground-truth a previously developed dense bag-of-visual-words method for endomicroscopic video retrieval. Confirming the results of previous indirect evaluation based on classification, our direct evaluation shows that this method significantly outperforms several other state-of-the-art CBR methods. In a second step, we propose to improve the CBR method by learning an adjusted similarity metric from the perceived similarity ground-truth. By minimizing a margin-based cost function that differentiates similar and dissimilar video pairs, we learn a weight vector applied to the visual word signatures of videos. Using cross-validation, we demonstrate that the learned similarity distance is significantly better correlated with the perceived similarity than the original visual-word-based distance.

A Framework Based on 2-D Taylor Expansion for Quantifying the Impacts of Sub-Pixel Reflectance Variance and Covariance on Cloud Optical Thickness and Effective Radius Retrievals Based on the Bi-Spectral Method

NASA Technical Reports Server (NTRS)

Zhang, Z.; Werner, F.; Cho, H. -M.; Wind, G.; Platnick, S.; Ackerman, A. S.; Di Girolamo, L.; Marshak, A.; Meyer, Kerry

2016-01-01

The bi-spectral method retrieves cloud optical thickness and cloud droplet effective radius simultaneously from a pair of cloud reflectance observations, one in a visible or near-infrared (VISNIR) band and the other in a shortwave infrared (SWIR) band. A cloudy pixel is usually assumed to be horizontally homogeneous in the retrieval. Ignoring sub-pixel variations of cloud reflectances can lead to a significant bias in the retrieved and re. In the literature, the retrievals of and re are often assumed to be independent and considered separately when investigating the impact of sub-pixel cloud reflectance variations on the bi-spectral method. As a result, the impact on is contributed only by the sub-pixel variation of VISNIR band reflectance and the impact on re only by the sub-pixel variation of SWIR band reflectance. In our new framework, we use the Taylor expansion of a two-variable function to understand and quantify the impacts of sub-pixel variances of VISNIR and SWIR cloud reflectances and their covariance on the and re retrievals. This framework takes into account the fact that the retrievals are determined by both VISNIR and SWIR band observations in a mutually dependent way. In comparison with previous studies, it provides a more comprehensive understanding of how sub-pixel cloud reflectance variations impact the and re retrievals based on the bi-spectral method. In particular, our framework provides a mathematical explanation of how the sub-pixel variation in VISNIR band influences the re retrieval and why it can sometimes outweigh the influence of variations in the SWIR band and dominate the error in re retrievals, leading to a potential contribution of positive bias to the re retrieval. We test our framework using synthetic cloud fields from a large-eddy simulation and real observations from Moderate Resolution Imaging Spectroradiometer. The predicted results based on our framework agree very well with the numerical simulations. Our framework can be used

Photogrammetric Retrieval of Etna's Plume Height from SEVIRI and MODIS

NASA Astrophysics Data System (ADS)

Zaksek, K.; Ganci, G.; Hort, M. K.

2013-12-01

Even remote volcanoes can impact the modern society due to volcanic ash dispersion in the atmosphere. A lot of research is currently dedicated to minimizing the impact of volcanic ash on air traffic. But the ash transport in the atmosphere and its deposition on land and in the oceans may also significantly influence the climate through modifications of atmospheric CO2. The emphasis of this contribution is the retrieval of volcanic ash plume height. This is important information for air traffic, to predict ash transport and to estimate the mass flux of the ejected material. The best way to monitor volcanic ash cloud top height (ACTH) on the global level is using satellite remote sensing. The most commonly used method for satellite ACTH compares brightness temperature of the cloud with the atmospheric temperature profile. Because of well-known uncertainties of this method we propose photogrammetric methods based on the parallax between data retrieved from geostationary (SEVIRI, HRV band; 1000 m spatial resolution) and polar orbiting satellites (MODIS, band 1; 250 m spatial resolution). The procedure works well if the data from both satellites are retrieved nearly simultaneously butMODIS does not retrieve the data at exactly the same time as SEVIRI. To compensate for advection in the atmosphere we use two sequential SEVIRI images (one before and one after the MODIS retrieval) and interpolate the cloud position from SEVIRI data to the time of MODIS retrieval. ACTH is then estimated by intersection of corresponding lines-of-view from MODIS and interpolated SEVIRI data. The proposed method has already been tested for the case of the Eyjafjallajökull eruption in April 2010. This case study had almost perfect conditions as the plume was vast and stretching over a homogeneous background - ocean. Here we show results of ACTH estimation during lava fountaining activity of Mount Etna in years 2011-2013. This activity resulted in volcanic ash plumes that are much smaller than

Radioimmunoassays of hidden viral antigens

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

Neurath, A.R.; Strick, N.; Baker, L.

1982-07-01

Antigens corresponding to infectious agents may be present in biological specimens only in a cryptic form bound to antibodies and, thus, may elude detection. We describe a solid-phase technique for separation of antigens from antibodies. Immune complexes are precipitated from serum by polyethylene glycol, dissociated with NaSCN, and adsorbed onto nitrocellulose or polystyrene supports. Antigens remain topographically separated from antibodies after removal of NaSCN and can be detected with radiolabeled antibodies. Genomes from viruses immobilized on nitrocellulose can be identified by nucleic acid hybridization. Nanogram quantities of sequestered hepatitis B surface and core antigens and picogram amounts of hepatitis Bmore » virus DNA were detected. Antibody-bound adenovirus, herpesvirus, and measles virus antigens were discerned by the procedure.« less

Quantitative analysis of antigen for the induction of tolerance in carcinoembryonic antigen transgenic mice.

PubMed Central

Hasegawa, T; Isobe, K; Nakashima, I; Shimokata, K

1992-01-01

In order to analyse the amounts of antigen in the thymus for the induction of tolerance, several carcinoembryonic antigen (CEA) transgenic lines were established which expressed human CEA antigen with different amounts. The chimeric KSN nude mice transplanted with the thymus of the B601 line (in which CEA mRNA and CEA protein could be detected in various tissues) to kidney capsule showed tolerance to human CEA. On the other hand, the chimeric KSN nude mice transplanted with the thymus of the B602 or BC60 line (in which neither CEA mRNA nor CEA protein could be detected by Northern blot analysis and flow cytometry analysis) or normal C57BL/6 (B6) did not develop the tolerance to human CEA. However, the chimeric KSN nude mice transplanted simultaneously with thymus of the B6 and spleen of the B601 line became tolerant to human CEA antigen. In the case of systemic immunization with cells which had CEA antigen, the B601 line was tolerant to human CEA. Surprisingly, the B602 and BC60 lines were also tolerant to CEA molecule. These results indicate that not only the antigen present in the thymus but also the antigen which flows from the peripheral organs to the thymus may be necessary for the induction of CEA tolerance. Images Figure 1 PMID:1493931

Using Conceptual Categories of Questions To Measure Differences in Retrieval Performance.

ERIC Educational Resources Information Center

Keyes, John G.

1996-01-01

To investigate the relationship between the retrieval mechanism and the level of question elaboration, this study divided 100 questions from the cystic fibrosis database into five conceptual categories based on their semantic representations. Two retrieval methods were chosen to investigate potential differences in outcomes across conceptual…

Scalable Integrated Region-Based Image Retrieval Using IRM and Statistical Clustering.

ERIC Educational Resources Information Center

Wang, James Z.; Du, Yanping

Statistical clustering is critical in designing scalable image retrieval systems. This paper presents a scalable algorithm for indexing and retrieving images based on region segmentation. The method uses statistical clustering on region features and IRM (Integrated Region Matching), a measure developed to evaluate overall similarity between images…

Retrieving Liquid Water Path and Precipitable Water Vapor from the Atmospheric Radiation Measurement (ARM) Microwave Radiometers

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

Turner, David D.; Clough, Shepard A.; Liljegren, James C.

2007-11-01

Ground-based two-channel microwave radiometers have been used for over 15 years by the Atmospheric Radiation Measurement (ARM) program to provide observations of downwelling emitted radiance from which precipitable water vapor (PWV) and liquid water path (LWP) – twp geophysical parameters critical for many areas of atmospheric research – are retrieved. An algorithm that utilizes two advanced retrieval techniques, a computationally expensive physical-iterative approach and an efficient statistical method, has been developed to retrieve these parameters. An important component of this Microwave Retrieval (MWRRET) algorithm is the determination of small (< 1K) offsets that are subtracted from the observed brightness temperaturesmore » before the retrievals are performed. Accounting for these offsets removes systematic biases from the observations and/or the model spectroscopy necessary for the retrieval, significantly reducing the systematic biases in the retrieved LWP. The MWRRET algorithm provides significantly more accurate retrievals than the original ARM statistical retrieval which uses monthly retrieval coefficients. By combining the two retrieval methods with the application of brightness temperature offsets to reduce the spurious LWP bias in clear skies, the MWRRET algorithm provides significantly better retrievals of PWV and LWP from the ARM 2-channel microwave radiometers compared to the original ARM product.« less

Trial-to-trial dynamics of selective long-term-memory retrieval with continuously changing retrieval targets.

PubMed

Kizilirmak, Jasmin M; Rösler, Frank; Khader, Patrick H

2014-10-01

How do we control the successive retrieval of behaviorally relevant information from long-term memory (LTM) without being distracted by other potential retrieval targets associated to the same retrieval cues? Here, we approach this question by investigating the nature of trial-by-trial dynamics of selective LTM retrieval, i.e., in how far retrieval in one trial has detrimental or facilitatory effects on selective retrieval in the following trial. Participants first learned associations between retrieval cues and targets, with one cue always being linked to three targets, forming small associative networks. In successive trials, participants had to access either the same or a different target belonging to either the same or a different cue. We found that retrieval times were faster for targets that had already been relevant in the previous trial, with this facilitatory effect being substantially weaker when the associative network changed in which the targets were embedded. Moreover, staying within the same network still had a facilitatory effect even if the target changed, which became evident in a relatively higher memory performance in comparison to a network change. Furthermore, event-related brain potentials (ERPs) showed topographically and temporally dissociable correlates of these effects, suggesting that they result from combined influences of distinct processes that aid memory retrieval when relevant and irrelevant targets change their status from trial to trial. Taken together, the present study provides insight into the different processing stages of memory retrieval when fast switches between retrieval targets are required. Copyright © 2014 Elsevier Inc. All rights reserved.

Detection of soluble antigens of Toxoplasma gondii by a four-layer modification of an enzyme immunoassay.

PubMed Central

Turunen, H J

1983-01-01

A sensitive four-layer modification of an enzyme immunoassay for the detection of soluble antigens of Toxoplasma gondii is described. Microtiter plates were sensitized with rabbit anti-toxoplasma immunoglobulins (6 micrograms/ml) used as the primary antibodies; guinea pig anti-toxoplasma immunoglobulins (6 micrograms/ml) were used as the secondary trapping antibodies. Horseradish peroxidase-conjugated anti-guinea pig immunoglobulins were used as the indicator antibodies. The specificity of the antigen assay was confirmed by using guinea pig immunoglobulins from preimmunization sera. The sensitivity of the antigen assay was found to be at least 10 ng of antigen protein per ml. The suitability of the method for detecting antigens of T. gondii in different specimens was studied by experimental toxoplasma infection in mice. Antigenic components of T. gondii could be detected in different tissue specimens from infected animals from the first day after infection onwards. Toxoplasma antigen in serum and urine samples from infected mice reached detectable levels on day 2 after infection followed by a linear increase in antigen concentration in succeeding samples. This method might offer a valuable aid for a rapid etiological diagnosis also in human cases of acute toxoplasmosis. PMID:6345574

[Regression analysis to select native-like structures from decoys of antigen-antibody docking].

PubMed

Chen, Zhengshan; Chi, Xiangyang; Fan, Pengfei; Zhang, Guanying; Wang, Meirong; Yu, Changming; Chen, Wei

2018-06-25

Given the increasing exploitation of antibodies in different contexts such as molecular diagnostics and therapeutics, it would be beneficial to unravel properties of antigen-antibody interaction with modeling of computational protein-protein docking, especially, in the absence of a cocrystal structure. However, obtaining a native-like antigen-antibody structure remains challenging due in part to failing to reliably discriminate accurate from inaccurate structures among tens of thousands of decoys after computational docking with existing scoring function. We hypothesized that some important physicochemical and energetic features could be used to describe antigen-antibody interfaces and identify native-like antigen-antibody structure. We prepared a dataset, a subset of Protein-Protein Docking Benchmark Version 4.0, comprising 37 nonredundant 3D structures of antigen-antibody complexes, and used it to train and test multivariate logistic regression equation which took several important physicochemical and energetic features of decoys as dependent variables. Our results indicate that the ability to identify native-like structures of our method is superior to ZRANK and ZDOCK score for the subset of antigen-antibody complexes. And then, we use our method in workflow of predicting epitope of anti-Ebola glycoprotein monoclonal antibody-4G7 and identify three accurate residues in its epitope.

Web image retrieval using an effective topic and content-based technique

NASA Astrophysics Data System (ADS)

Lee, Ching-Cheng; Prabhakara, Rashmi

2005-03-01

There has been an exponential growth in the amount of image data that is available on the World Wide Web since the early development of Internet. With such a large amount of information and image available and its usefulness, an effective image retrieval system is thus greatly needed. In this paper, we present an effective approach with both image matching and indexing techniques that improvise on existing integrated image retrieval methods. This technique follows a two-phase approach, integrating query by topic and query by example specification methods. In the first phase, The topic-based image retrieval is performed by using an improved text information retrieval (IR) technique that makes use of the structured format of HTML documents. This technique consists of a focused crawler that not only provides for the user to enter the keyword for the topic-based search but also, the scope in which the user wants to find the images. In the second phase, we use query by example specification to perform a low-level content-based image match in order to retrieve smaller and relatively closer results of the example image. From this, information related to the image feature is automatically extracted from the query image. The main objective of our approach is to develop a functional image search and indexing technique and to demonstrate that better retrieval results can be achieved.

Uniform Atmospheric Retrievals of Ultracool Late-T and Early-Y dwarfs

NASA Astrophysics Data System (ADS)