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Sample records for antigen retrieval methods

  1. How does antigen retrieval work?

    PubMed

    Leong, Trishe Y-M; Leong, Anthony S-Y

    2007-03-01

    The introduction of antigen retrieval has enabled immunohistology to become an integral component of morphologic diagnosis, routinely employed in cancer diagnosis, and for the identification of therapeutic and prognostic markers. The mechanism of antigen retrieval, however, remains speculative with the key to our understanding embedded in the actions of formaldehyde on proteins. One commonly held concept is that heat primarily breaks down protein cross-linkages that occur with aldehyde fixation, thus "unmasking" protein epitopes of interest. Enzymatic pretreatment is also thought to have a similar action whereas such "breakages" are the result of extremely rapid molecular movement induced by microwaves and ultrasound. The formation of rigid cagelike calcium complexes during formaldehyde fixation is another suggested mechanism of antigen masking requiring chelating agents for reversal. A more recent suggestion for the antigen retrieval phenomenon has evoked the Mannich reaction, which occurs with the cross-linking of some proteins. Such cross-linkages can be hydrolyzed by heat or alkalis so that the process of antigen retrieval may be the simple removal of such cross-linked proteins that are sterically interfering with the binding of antibodies to linear protein epitopes in the tissue section. We are clearly not yet in possession of all the answers to the problem.

  2. Antigen Retrieval Causes Protein Unfolding

    PubMed Central

    Fowler, Carol B.; Evers, David L.; O’Leary, Timothy J.; Mason, Jeffrey T.

    2011-01-01

    Antigen retrieval (AR), in which formalin-fixed paraffin-embedded tissue sections are briefly heated in buffers at high temperature, often greatly improves immunohistochemical staining. An important unresolved question regarding AR is how formalin treatment affects the conformation of protein epitopes and how heating unmasks these epitopes for subsequent antibody binding. The objective of the current study was to use model proteins to determine the effect of formalin treatment on protein conformation and thermal stability in relation to the mechanism of AR. Sodium dodecyl sulfate polyacrylamide gel electrophoresis was used to identify the presence of protein formaldehyde cross-links, and circular dichroism spectropolarimetry was used to determine the effect of formalin treatment and high-temperature incubation on the secondary and tertiary structure of the model proteins. Results revealed that for some proteins, formalin treatment left the native protein conformation unaltered, whereas for others, formalin denatured tertiary structure, yielding a molten globule protein. In either case, heating to temperatures used in AR methods led to irreversible protein unfolding, which supports a linear epitope model of recovered protein immunoreactivity. Consequently, the core mechanism of AR likely centers on the restoration of normal protein chemical composition coupled with improved accessibility to linear epitopes through protein unfolding. PMID:21411808

  3. Utility of CD15, CD30 & CD45 in the immunohistochemical diagnosis of Hodgkin's disease by antigen retrieval method.

    PubMed

    Arici, D S; Aker, H; Güngör, M

    1999-01-01

    The utility of staining Reed-Sternberg (RS) cells with CD30, CD15 and CD45 as a diagnostic aid in Hodgkin's disease (HD) and the value of microwave citrate antigen retrieval (AR) method in improving the results of immunohistochemical (IHC) studies were evaluated. Histological and immunohistological studies were carried out on 21 patients with HD seen from January 1987 to December 1996 in the Pathology Department of the Cumhuriyet University, School of Medicine. Avidin biotin peroxidase complex (ABC) was used in IHC study as a method for detection of RS cells. Monoclonal antibodies CD30, CD15 and CD45 were applied on formalin fixed paraffin embedded tissue sections. In order to enhance the immunoreactivity, microwave citrate AR method and proteolytic pretreatment were used. The reactivity of RS cells and staining patterns were determined. In 14 (70%) of the 20 patients, RS cells stained positively with CD30, in 16 (80%) CD15 staining was positive and only 1 (5%) was positively stained with CD45. A combination of cytoplasmic with cell surface staining was common with CD30, while paranuclear deposit with cell surface and cytoplasmic staining was common with CD15. In conclusion, to facilitate the detection of RS cells in formalin fixed paraffin embedded tissues, the application of a panel of markers appears to be necessary. Also AR method seems to be helpful in obtaining optimal results on formalin fixed paraffin embedded tissue.

  4. Enhanced Antigen Retrieval of Amyloid β Immunohistochemistry

    PubMed Central

    Kai, Hideaki; Ogino, Koichi; Hatsuta, Hiroyuki; Murayama, Shigeo; Kitamoto, Tetsuyuki

    2012-01-01

    Senile plaques, extracellular deposits of amyloid β peptide (Aβ), are one of the pathological hallmarks of Alzheimer disease (AD). As the standard immunohistochemical detection method for Aβ deposits, anti-Aβ immunohistochemistry combined with antigen retrieval (AR) by formic acid (FA) has been generally used. Here, we present a more efficient AR for Aβ antigen. On brain sections of AD and its mouse model, a double combination of either autoclave heating in EDTA buffer or digestion with proteinase K plus FA treatment reinforced Aβ immunoreactivity. A further triple combination of digestion with proteinase K (P), autoclave heating in EDTA buffer (A), and FA treatment (F), when employed in this order, gave a more enhanced immunoreactivity. Our PAF method prominently visualized various forms of Aβ deposits in AD that have not been clearly detected previously and revealed numerous minute-sized plaques both in AD and the mouse model. Quantification of Aβ loads showed that the AR effect by the PAF method was 1.86-fold (in the aged human brain) and 4.64-fold (in the mouse brain) higher than that by the FA method. Thus, the PAF method could have the potential to be the most sensitive tool so far to study Aβ pathology in AD and its mouse model. PMID:22821668

  5. Formaldehyde scavengers function as novel antigen retrieval agents

    PubMed Central

    Vollert, Craig T.; Moree, Wilna J.; Gregory, Steven; Bark, Steven J.; Eriksen, Jason L.

    2015-01-01

    Antigen retrieval agents improve the detection of formaldehyde-fixed proteins, but how they work is not well understood. We demonstrate that formaldehyde scavenging represents a key characteristic associated with effective antigen retrieval; under controlled temperature and pH conditions, scavenging improves the typical antigen retrieval process through reversal of formaldehyde-protein adduct formation. This approach provides a rational framework for the identification and development of more effective antigen retrieval agents. PMID:26612041

  6. A New Antigen Retrieval Technique for Human Brain Tissue

    PubMed Central

    Byne, William; Haroutunian, Vahram; García-Villanueva, Mercedes; Rábano, Alberto; García-Amado, María; Prensa, Lucía; Giménez-Amaya, José Manuel

    2008-01-01

    Immunohistochemical staining of tissues is a powerful tool used to delineate the presence or absence of an antigen. During the last 30 years, antigen visualization in human brain tissue has been significantly limited by the masking effect of fixatives. In the present study, we have used a new method for antigen retrieval in formalin-fixed human brain tissue and examined the effectiveness of this protocol to reveal masked antigens in tissues with both short and long formalin fixation times. This new method, which is based on the use of citraconic acid, has not been previously utilized in brain tissue although it has been employed in various other tissues such as tonsil, ovary, skin, lymph node, stomach, breast, colon, lung and thymus. Thus, we reported here a novel method to carry out immunohistochemical studies in free-floating human brain sections. Since fixation of brain tissue specimens in formaldehyde is a commonly method used in brain banks, this new antigen retrieval method could facilitate immunohistochemical studies of brains with prolonged formalin fixation times. PMID:18852880

  7. Comparative analysis of two immunohistochemical methods for antigen retrieval in the optical lobe of the honeybee Apis mellifera: myosin-V assay.

    PubMed

    Calábria, Luciana Karen; Teixeira, Renata Roland; Coelho Gonçalves, Sybelli Magda; Passos Lima, Andreia Barcelos; Santos, Ana Alice Diniz Dos; Martins, Antônio Roberto; Espindola, Foued Salmen

    2010-01-01

    The present study compared two heating methods currently used for antigen retrieval (AR) immunostaining: the microwave oven and the steam cooker. Myosin-V, a molecular motor involved in vesicle transport, was used as a neuronal marker in honeybee Apis mellifera brains fixed in formalin. Overall, the steam cooker showed the most satisfactory AR results. At 100 ºC, tissue morphology was maintained and revealed epitope recovery, while evaporation of the AR solution was markedly reduced; this is important for stabilizing the sodium citrate molarity of the AR buffer and reducing background effects. Standardization of heat-mediated AR of formalin-fixed and paraffin-embedded tissue sections results in more reliable immunostaining of the honeybee brain.

  8. EFFECTIVENESS OF INFORMATION RETRIEVAL METHODS.

    ERIC Educational Resources Information Center

    SWETS, JOHN A.

    RESULTS OF FIFTY DIFFERENT RETRIEVAL METHODS AS APPLIED IN THREE EXPERIMENTAL RETRIEVAL SYSTEMS WERE SUBJECTED TO AN ANALYSIS SUGGESTED BY STATISTICAL DECISION THEORY. THE ANALYSIS USES A PREVIOUSLY-PROPOSED MEASURE OF EFFECTIVENESS AND DEMONSTRATES ITS SEVERAL PROPERTIES. SOME OF THESE PROPERTIES ARE--(1) IT ENABLES THE RETRIEVAL SYSTEM TO…

  9. Instability of induction cooker (electromagnetic stove) antigen retrieval in immunohistochemistry.

    PubMed

    Ding, Wei; Zheng, Xiang-Yi

    2012-03-01

    An induction cooker is a modern electric cooker that takes electromagnetic induction principle to heat. As it has high efficiency, no open flame, and is safe and convenient, more and more laboratories use it as an antigen retrieval heating tool in immunohistochemistry. We found that there was still some instability with the induction cooker, because with certain antigens the power change influenced the results of immunohistochemistry staining, showing weaker staining intensity or decreased number of positive cells, but which were not entirely negative. For some antigens, it had no influence on results. The instability of this heating tool for antigen retrieval was caused partly by negligent operators, and which may influence the experimental results and the pathologic diagnosis.

  10. High temperature antigen retrieval and loss of nuclear morphology: a comparison of microwave and autoclave techniques.

    PubMed Central

    Hunt, N C; Attanoos, R; Jasani, B

    1996-01-01

    The use of high temperature antigen retrieval methods has been of major importance in increasing the diagnostic utility of immunocytochemistry. However, these techniques are not without their problems and in this report attention is drawn to a loss of nuclear morphological detail, including mitotic figures, following microwave antigen retrieval. This was not seen with an equivalent autoclave technique. This phenomenon was quantified using image analysis in a group of B cell lymphomas stained with the antibody L26. Loss of nuclear morphological detail may lead to difficulty in identifying cells accurately, which is important in the diagnostic setting-for example, when trying to distinguish a malignant lymphoid infiltrate within a mixed cell population. In such cases it would clearly be wise to consider the use of alternative high temperature retrieval methods and accept their slightly lower staining enhancement capability compared with the microwave technique. Images PMID:9038766

  11. Immunohistochemical detection of disease-associated prion protein in the intestine of cattle naturally affected with bovine spongiform encephalopathy by using an alkaline-based chemical antigen retrieval method.

    PubMed

    Okada, Hiroyuki; Iwamaru, Yoshihumi; Imamura, Morikazu; Masujin, Kentaro; Yokoyama, Takashi; Mohri, Shirou

    2010-11-01

    An alkaline-based chemical antigen retrieval pretreatment step was used to enhance immunolabeling of disease-associated prion protein (PrP(Sc)) in formalin-fixed and paraffin-embedded tissue sections from cattle naturally affected with bovine spongiform encephalopathy (BSE). The modified chemical method used in this study amplified the PrP(Sc) signal by unmasking PrP(Sc) compared with the normal cellular prion protein. In addition, this method reduced nonspecific background immunolabeling that resulted from the destruction of the residual normal cellular form of prion protein, and reduced the treatment time compared with the usual autoclave pretreatment step. Immunolabeled PrP(Sc) was thereby clearly detected in the myenteric plexus of the ileum in naturally occurring BSE cattle.

  12. Immunohistochemical diagnosis of Alport's syndrome in paraffin-embedded renal sections: antigen retrieval with autoclave heating.

    PubMed

    Naito, Ichiro; Ninomiya, Yoshifumi; Nomura, Shinsuke

    2003-03-01

    Alport's syndrome (AS) is a hereditary renal disease caused by mutations in the genes encoding collagen type IV. Immunohistochemical analysis of the alpha chains of collagen type IV has been found to be useful for the diagnosis of this disease. The monoclonal antibodies (mAbs) generated by us recognize alpha 1(IV) through alpha 6(IV) chains of collagen type IV on fresh-frozen sections but not on paraffin-embedded sections. Antigen retrieval by autoclave heating has been found to restore the epitopes recognized by the mAbs; however the heating conditions had not been well established. In this study, the heating conditions were carefully examined using renal sections obtained from AS and non-AS patients. The heating was performed in an autoclave, at 105 degrees -127 degrees C for 6-8 min. During the heating, the sections were immersed in 0.2 N HCl solution (pH 0.9). Then, the mAbs were applied for 30 min, and the bound mAbs were detected using the LSAB kit. The optimal temperature for the antigen retrieval varied among specimens, and was dependent on the type of basement membrane examined. Thus, it was considered that heating at two or three different temperatures could be helpful for the precise diagnosis of AS. Adopting the antigen retrieval method could extend the possibility of immunohistochemical diagnosis of AS to cases without using fresh-frozen sections.

  13. Combining immunodetection with histochemical techniques: the effect of heat-induced antigen retrieval on picro-Sirius red staining.

    PubMed

    Gadd, Victoria L

    2014-12-01

    Picro-Sirius red is a routine diagnostic stain intended for the histological visualization of collagen fibers (fibrosis) in tissue. Multi-label immunohistochemistry is a powerful tool used by researchers to visualize different cell types and their location within a tissue specimen, and to observe co-localization of antigens. Combining the specificity of immunodetection with the simplicity of Sirius red staining will allow researchers to visualize multi-antigen detection in relation to fibrosis, a common histological feature of injury in many chronic diseases. Pre-treatment of formalin-fixed, paraffin-embedded tissue (FFPE) specimens with antigen retrieval is essential for the work-up of most commercially available antibodies. The most common form of antigen retrieval involves boiling tissue specimens in buffer to break the cross-linkages caused by formalin fixation. However, this method causes tissue modification and collagen fiber shrinkage leading to suboptimal results when counterstaining for Sirius red. Reduced heat and enzymatic digestion are antigen retrieval methods compatible with Sirius red counterstaining. This paper will discuss the difficulties faced when combining these two staining methods, and provide a detailed method for the simultaneous detection of antigen and Sirius red in FFPE tissues. © The Author(s) 2014.

  14. Electrochemical antigen-retrieval of formaldehyde fixed and paraffin-embedded archived leprosy skin biopsies.

    PubMed

    Sergio, Navarro-Fierros; Cecilia, Guillen-Vargas; Sonia, Luquin; la Mora Pedro, Garzon-De; Joaquin, Garcia-Estrada; Mary, Fafutis-Morris

    2004-06-01

    While formaldehyde fixation preserves tissue morphology, it often hinders immunodetection of antigens in paraffin-embedded tissue because the antigens are masked. Antigen unmasking can be achieved with treatments such as microwave irradiation but they often lead to excessive tissue damage. Therefore, an electrochemical antigen-retrieval method (EAR) was devised in which an alternating electric current is passed through the tissue in a chamber containing an electrolyte buffer. The results obtained with this method were compared to those after microwave irradiation using archived samples of formaldehyde-fixed and paraffin-embedded lepromatous leprosy skin. The efficacy of the two unmasking procedures was assessed by the immunodetectability of several marker antigens using 24 antibodies. Fifteen antibodies that were directed against transmembrane proteins (CD), and the remaining 9 against cytokeratins 18.6 and 19, laminin, vimentin, S100a, BCG, Ulex europaeus lectin, PCNA, and P21ras. Simple and double immunohistochemistry was performed using the universal ENVISION and LSAB + AP detection systems. After unmasking with the EAR method, immunoreactivity was clearly detected with 22 of the 24 antibodies in single labeling reactions. They include the critical antigens CD3 and CD4 for identifying the T lymphocyte lineages. In contrast, only 20 of the antibodies reacted after microwave irradiation. After double immunolabeling, immunoreactivity was quantitatively similar with both methods. However, the EAR unmasking produced a stronger labeling reaction. Thus, with double labeling immunohistochemistry, EAR made it possible to use higher antibody dilutions and shorter incubation times. Heat damage was also prevented. In conclusion, EAR treatment produces better staining results than microwave irradiation treatment.

  15. Post-embedding Mammalian Tissue for Immunoelectron Microscopy: A Standardized Procedure Based on Heat-Induced Antigen Retrieval.

    PubMed

    Yamashita, Shuji

    2016-01-01

    We describe a standardized method of fixation, antigen retrieval, and image contrasting for post-embedding immunoelectron microscopy. Tissues are fixed with formaldehyde solutions containing Ca(2+) and Mg(2+) ions at pH 7.4 and then at pH 8.5. After dehydration with dimethylformamide, the specimens are embedded in LR-White resin. For antigen retrieval, ultrathin sections are heated in 0.5 M Tris-HCl, pH 9.0, for 1-2 h at 95 °C. After immunogold labeling, the sections are treated with a mixture of tannic acid and glutaraldehyde, with OsO4 solution, and then double-stained with uranyl acetate and lead citrate. The standardized method yields strong and reproducible immunoreactions for many antigens showing excellent image contrast without destruction of fine structures.

  16. Robust keyword retrieval method for OCRed text

    NASA Astrophysics Data System (ADS)

    Fujii, Yusaku; Takebe, Hiroaki; Tanaka, Hiroshi; Hotta, Yoshinobu

    2011-01-01

    Document management systems have become important because of the growing popularity of electronic filing of documents and scanning of books, magazines, manuals, etc., through a scanner or a digital camera, for storage or reading on a PC or an electronic book. Text information acquired by optical character recognition (OCR) is usually added to the electronic documents for document retrieval. Since texts generated by OCR generally include character recognition errors, robust retrieval methods have been introduced to overcome this problem. In this paper, we propose a retrieval method that is robust against both character segmentation and recognition errors. In the proposed method, the insertion of noise characters and dropping of characters in the keyword retrieval enables robustness against character segmentation errors, and character substitution in the keyword of the recognition candidate for each character in OCR or any other character enables robustness against character recognition errors. The recall rate of the proposed method was 15% higher than that of the conventional method. However, the precision rate was 64% lower.

  17. Evolutionary Computing Methods for Spectral Retrieval

    NASA Technical Reports Server (NTRS)

    Terrile, Richard; Fink, Wolfgang; Huntsberger, Terrance; Lee, Seugwon; Tisdale, Edwin; VonAllmen, Paul; Tinetti, Geivanna

    2009-01-01

    A methodology for processing spectral images to retrieve information on underlying physical, chemical, and/or biological phenomena is based on evolutionary and related computational methods implemented in software. In a typical case, the solution (the information that one seeks to retrieve) consists of parameters of a mathematical model that represents one or more of the phenomena of interest. The methodology was developed for the initial purpose of retrieving the desired information from spectral image data acquired by remote-sensing instruments aimed at planets (including the Earth). Examples of information desired in such applications include trace gas concentrations, temperature profiles, surface types, day/night fractions, cloud/aerosol fractions, seasons, and viewing angles. The methodology is also potentially useful for retrieving information on chemical and/or biological hazards in terrestrial settings. In this methodology, one utilizes an iterative process that minimizes a fitness function indicative of the degree of dissimilarity between observed and synthetic spectral and angular data. The evolutionary computing methods that lie at the heart of this process yield a population of solutions (sets of the desired parameters) within an accuracy represented by a fitness-function value specified by the user. The evolutionary computing methods (ECM) used in this methodology are Genetic Algorithms and Simulated Annealing, both of which are well-established optimization techniques and have also been described in previous NASA Tech Briefs articles. These are embedded in a conceptual framework, represented in the architecture of the implementing software, that enables automatic retrieval of spectral and angular data and analysis of the retrieved solutions for uniqueness.

  18. Antigen retrieval causes protein unfolding: evidence for a linear epitope model of recovered immunoreactivity.

    PubMed

    Fowler, Carol B; Evers, David L; O'Leary, Timothy J; Mason, Jeffrey T

    2011-04-01

    Antigen retrieval (AR), in which formalin-fixed paraffin-embedded tissue sections are briefly heated in buffers at high temperature, often greatly improves immunohistochemical staining. An important unresolved question regarding AR is how formalin treatment affects the conformation of protein epitopes and how heating unmasks these epitopes for subsequent antibody binding. The objective of the current study was to use model proteins to determine the effect of formalin treatment on protein conformation and thermal stability in relation to the mechanism of AR. Sodium dodecyl sulfate polyacrylamide gel electrophoresis was used to identify the presence of protein formaldehyde cross-links, and circular dichroism spectropolarimetry was used to determine the effect of formalin treatment and high-temperature incubation on the secondary and tertiary structure of the model proteins. Results revealed that for some proteins, formalin treatment left the native protein conformation unaltered, whereas for others, formalin denatured tertiary structure, yielding a molten globule protein. In either case, heating to temperatures used in AR methods led to irreversible protein unfolding, which supports a linear epitope model of recovered protein immunoreactivity. Consequently, the core mechanism of AR likely centers on the restoration of normal protein chemical composition coupled with improved accessibility to linear epitopes through protein unfolding.

  19. [Radiocompetitive method of H antigen determination].

    PubMed

    Semenova, G B; Sokolov, Ia A; Liashenko, V A

    1978-06-01

    The authors describe a radiocompetitive method of H-d-monomere determination with the sensitivity of 2 ng/ml in double antibodies modification; this method was used for comparing the immunological affinity of the affiliated H-antigens. A difference between the immunological affinity to the antibodies in a monomere, polymere and the flagellum was shown.

  20. Cardiovascular demands of deer retrieval methods.

    PubMed

    Fountaine, Charles J; Evenson, Mitchell J

    2015-06-01

    The purpose of this study was to compare the cardiovascular (CV) demands of 2 deer retrieval methods. Twelve male participants (weight 86±24 kg, age 21±1 years) performed a maximum treadmill test on day 1 to determine baseline fitness levels. On day 2, all participants first towed, then dragged a 45-kg simulated deer carcass for 457 m at a self-selected pace. The tow condition utilized a shoulder harness system with a 2-m strap connecting the harness to the carcass, allowing the participant to walk upright as he towed the load. The dragging condition required the participants to flex their trunk, grasp the legs of the deer with both hands, and drag the carcass the length of the course. Heart rate and oxygen consumption (VO2) from each trial were measured by indirect calorimetry. The CV responses of towing were significantly less compared with those of dragging for VO2 peak (P=.001), peak heart rate (P=.003), average heart rate (P=.028), and rating of perceived exertion (P<.001). No significant differences were observed for average VO2 (P=.91) or time to completion (P=.27). The results of this study suggest towing a deer with a shoulder harness results in significant reductions in CV demand and lower perceived exertion compared with traditional deer dragging techniques. Deer hunters who are deconditioned or have CV risk factors are strongly encouraged to consider deer retrieval methods utilizing a shoulder harness and tow rope to mitigate the increased demands commonly found with traditional retrieval methods. Copyright © 2015 Wilderness Medical Society. Published by Elsevier Inc. All rights reserved.

  1. Rapid Immunocytochemistry with Simple Heat-Induced Antigen Retrieval Technique for Improvement in the Quality of Cytological Diagnosis

    PubMed Central

    Kamoshida, Shingo; Kawamura, Jumpei; Harada, Kunihiko; Kawai, Kenji; Kuwao, Sadahito; Sawabe, Motoji

    2013-01-01

    Rapid immunocytochemistry (ICC) can improve the accuracy of intraoperative cytological diagnoses; however, it is usually applied without heat-induced antigen retrieval (HIAR). We established a HIAR method for rapid ICC and evaluated its efficacy and reliability. Rapidly fixed smear samples were immunostained using 35 antibodies. We compared the results of HIAR by boiling in a pot or heating in an electric kettle. The smears were incubated for 3 min with each primary antibody and immuno-enzyme polymer reagent, and for 1 min with diaminobenzidine solution. HIAR for 1 min using the kettle method yielded the best cellular integrity. For 32 out of the 35 antibodies, results achieved using rapid ICC within 11 min were comparable to that achieved using standard ICC. HIAR was essential for 13 antibodies. For two of the antibodies, HIAR was not required when standard ICC was applied, but consistent staining with rapid ICC was obtained only with HIAR. In conclusion, we established a rapid ICC procedure using a simple HIAR method, which allowed efficient immunostaining of a panel of antigens, including nuclear antigens, within only 11 min. The combined use of this rapid ICC technique with other staining techniques could be useful for improving intraoperative cytological diagnoses. PMID:24004858

  2. 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

  3. Atraumatic Flexor tendon retrieval- a simple method

    PubMed Central

    2013-01-01

    Background Zone 2 flexor tendon injuries still represent a challenging problem to hand surgeons despite the well developed surgical techniques and suture materials. Meticulous surgical repair with atraumatic handling of the severed tendon stumps and minimal damage to the tendon sheath are particularly important to prevent postoperative adhesions and ruptures in this area. In zone 2 flexor tendon injuries proximal to the vinculas, the cut ends of the flexor tendons retract to the palm with muscle contraction. To retrieve the severed proximal flexor tendon under tendon sheath and pulley system is very difficult without damaging these structures. Many techniques are described in the literature for the delivery of the retracted proximal tendon stump to the repair site. Methods In this report we would like to present a simple and relatively atraumatic technique that facilitates passing of the retracted flexor tendon through the pulleys in zone 2. We sutured the proximal tendon stump at the distal palmar crease with 3–0 polypropylene suture and used a 14 gauge plastic feeding tube, acting like a conduit for the passage of straightened needle to the finger. Results We have used this technique 21 times without any complication in our clinic. We have not seen any suture breakage during the passage or needle breakage due to the bending of the needle. Conclusions We have found this technique is very simple and very effective in retrieving the retracted tendon stump without causing undue damage to the tendon stump or tendon sheath. PMID:24040913

  4. p53 gene product expression in resected non-small cell carcinoma of the lung, with studies of concurrent cytological preparations and microwave antigen retrieval.

    PubMed Central

    Binks, S; Clelland, C A; Ronan, J; Bell, J

    1997-01-01

    AIM: To document the frequency and extent of p53 gene product expression in paraffin sections of resected non-small cell carcinoma of the lung and in cytological preparations of the same tumours; to determine the effect of microwave antigen retrieval on antigen detection. METHODS: Representative paraffin sections of 50 non-small cell carcinomas were stained with an antibody to p53 gene product (DO-7) both with and without prior microwave antigen retrieval. Cytoblocks and cell smears obtained from 19 cases were similarly stained. RESULTS: Using a histochemical scoring system (0-300) which takes into account staining intensity and extent, 78% (n = 39) of microwave pretreated paraffin sections and 52% (n = 26) of non-pretreated sections scored between 5 and 300; p = 0.001; 56% (n = 28) of microwave pretreated sections and only 2% (n = 1) of non-pretreated sections scored between 100 and 300 (p = 0.0001); 75% of direct smears of tumours and 80% of cytoblocks stained similarly to the paraffin sections of the resected specimens. No smears or cytoblocks stained positively when the sections of the resected specimen were negative. CONCLUSIONS: As up to 78% of non-small cell lung carcinomas overexpress p53 gene product, this may prove to be a valuable diagnostic method in biopsy or cytological material when the morphological diagnosis is uncertain. Microwave antigen retrieval is effective on formalin fixed tissue. Images PMID:9215149

  5. 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…

  6. Microwave-Assisted Tissue Preparation for Rapid Fixation, Decalcification, Antigen Retrieval, Cryosectioning, and Immunostaining

    PubMed Central

    2016-01-01

    Microwave irradiation of tissue during fixation and subsequent histochemical staining procedures significantly reduces the time required for incubation in fixation and staining solutions. Minimizing the incubation time in fixative reduces disruption of tissue morphology, and reducing the incubation time in staining solution or antibody solution decreases nonspecific labeling. Reduction of incubation time in staining solution also decreases the level of background noise. Microwave-assisted tissue preparation is applicable for tissue fixation, decalcification of bone tissues, treatment of adipose tissues, antigen retrieval, and other special staining of tissues. Microwave-assisted tissue fixation and staining are useful tools for histological analyses. This review describes the protocols using microwave irradiation for several essential procedures in histochemical studies, and these techniques are applicable to other protocols for tissue fixation and immunostaining in the field of cell biology. PMID:27840640

  7. Antigen retrieval reveals widespread basolateral expression of syntaxin 3 in renal epithelia.

    PubMed

    Breton, Sylvie; Inoue, Takeaki; Knepper, Mark A; Brown, Dennis

    2002-03-01

    Soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins play a key role in docking and fusion of intracellular transport vesicles and may regulate apical and basolateral membrane protein delivery in epithelial cells. In a previous study, syntaxin 3 (a target SNARE) protein was detectable in the kidney only in intercalated cells. We now report a more widespread distribution of syntaxin 3 in a variety of renal epithelial cells after antigen retrieval. Sections of rat kidney were treated with SDS and incubated with antisyntaxin 3 antibodies. Strong basolateral membrane staining was seen in descending and ascending thin limbs of Henle, thick ascending limbs of Henle, the macula densa, distal and connecting tubules, and all cells of the collecting duct including A- and B-intercalated cells. The papillary surface epithelium and the transitional epithelium of the ureter were also stained, but proximal tubules were negative. Western blotting revealed a strong signal at 37 kDa in all regions, and the antigen was restricted to membrane fractions. SDS treatment was not necessary to reveal syntaxin 3 in intercalated cells. These data show that syntaxin 3 might be involved in basolateral trafficking pathways in most renal epithelial cell types. The exclusive basolateral location of syntaxin 3 in situ, however, contrasts with the apical location of this SNARE protein in some kidney epithelial cells in culture.

  8. Method for comparing content based image retrieval methods

    NASA Astrophysics Data System (ADS)

    Barnard, Kobus; Shirahatti, Nikhil V.

    2003-01-01

    We assume that the goal of content based image retrieval is to find images which are both semantically and visually relevant to users based on image descriptors. These descriptors are often provided by an example image--the query by example paradigm. In this work we develop a very simple method for evaluating such systems based on large collections of images with associated text. Examples of such collections include the Corel image collection, annotated museum collections, news photos with captions, and web images with associated text based on heuristic reasoning on the structure of typical web pages (such as used by Google(tm)). The advantage of using such data is that it is plentiful, and the method we propose can be automatically applied to hundreds of thousands of queries. However, it is critical that such a method be verified against human usage, and to do this we evaluate over 6000 query/result pairs. Our results strongly suggest that at least in the case of the Corel image collection, the automated measure is a good proxy for human evaluation. Importantly, our human evaluation data can be reused for the evaluation of any content based image retrieval system and/or the verification of additional proxy measures.

  9. Using optimal estimation method for upper atmospheric Lidar temperature retrieval

    NASA Astrophysics Data System (ADS)

    Zou, Rongshi; Pan, Weilin; Qiao, Shuai

    2016-07-01

    Conventional ground based Rayleigh lidar temperature retrieval use integrate technique, which has limitations that necessitate abandoning temperatures retrieved at the greatest heights due to the assumption of a seeding value required to initialize the integration at the highest altitude. Here we suggests the use of a method that can incorporate information from various sources to improve the quality of the retrieval result. This approach inverts lidar equation via optimal estimation method(OEM) based on Bayesian theory together with Gaussian statistical model. It presents many advantages over the conventional ones: 1) the possibility of incorporating information from multiple heterogeneous sources; 2) provides diagnostic information about retrieval qualities; 3) ability of determining vertical resolution and maximum height to which the retrieval is mostly independent of the a priori profile. This paper compares one-hour temperature profiles retrieved using conventional and optimal estimation methods at Golmud, Qinghai province, China. Results show that OEM results show a better agreement with SABER profile compared with conventional one, in some region it is much lower than SABER profile, which is a very different results compared with previous studies, further studies are needed to explain this phenomenon. The success of applying OEM on temperature retrieval is a validation for using as retrieval framework in large synthetic observation systems including various active remote sensing instruments by incorporating all available measurement information into the model and analyze groups of measurements simultaneously to improve the results.

  10. Group-Based Image Retrieval Method for Video Image Annotation

    NASA Astrophysics Data System (ADS)

    Murabayashi, Noboru; Kurahashi, Setsuya; Yoshida, Kenichi

    This paper proposes a group-based image retrieval method for video image annotation systems. Although the wide spread use of video camera recorders has increased the demand for an automated annotation system for personal videos, conventional image retrieval methods cannot achieve enough accuracy to be used as an annotation engine. Recording conditions, such as change of the brightness by weather condition, shadow by the surroundings, and etc, affect the qualities of images recorded by the personal video camera recorders. The degraded image of personal video makes the retrieval task difficult. Furthermore, it is difficult to discriminate similar images without any auxiliary information. To cope with these difficulties, this paper proposes a group-based image retrieval method. Its characteristics are 1) the use of image similarity based on the wavelet transformation based features and the scale invariant feature transform based features, and 2) the pre-grouping of related images and screening using group information. Experimental results show that the proposed method can improve image retrieval accuracy to 90% up from the conventional method of 40%.

  11. Comparison of heat induced antigen retrieval techniques for immune-histochemical estrogen receptor expression in ductal carcinoma of breast in females.

    PubMed

    Qadir, Abdul; Mushtaq, Sajid; Sharif, Muhammad Ashraf; Mamoon, Nadira; Khadim, Muhammad Tahir

    2010-08-01

    To compare immunohistochemical estrogen receptor expression on formalin-fixed, paraffin-embedded breast carcinoma tissue sections by using regular, extended microwave heating and pressure cooker technique for heat induced antigen retrieval. Quasi experimental study. Department of Histopathology, Armed Forces Institute of Pathology, Rawalpindi, from August 2006 to July 2007. The study was conducted on 40 cases of breast carcinoma diagnosed on histopathology and selected by convenience sampling. One section each of the tumour was separately subjected to regular microwave heating (10 minutes), extended microwave heating (20 minutes) and pressure cooker (heating for 2 minutes after reaching full pressure). A nuclear staining of >10% cells with moderate intensity was considered positive and frequency of ER expression by each technique was compared statistically. Sensitivity and specificity of the techniques was determined using pressure cooker technique as the gold standard for this study. Out of 40 cases, ER expression in 24 (60%) cases was seen by microwave regular heating (MRH) and in 30 (75%) cases by microwave extending heating (MEH) technique. Pressure cooker (PC) technique for antigen retrieval demonstrated 34 (85%) cases with ER expression. Out of 16 which were negative by MRH technique, 6 became positive by MEH while 10 became positive by PC. Statistically significant difference in ER expression by PC and MEH technique was seen in comparison to MRH with a p-value of <0.05. Moreover, 4 cases which were negative by MEH technique turned positive for ER expression by PC. MRH and MEH had 100% specificity but sensitivity was 70.6% and 88.2% respectively taking PC technique as gold standard with diagnostic accuracy of MEH as 90% and MRH as 75%. Pressure cooker antigen retrieval technique is a better method than microwave heating. The increase in duration of heating improves the percentage of positive cells as well as intensity of ER immuno-staining which entitles

  12. 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

  13. Retrieval practice can eliminate list method directed forgetting.

    PubMed

    Abel, Magdalena; Bäuml, Karl-Heinz T

    2016-01-01

    It has recently been shown that retrieval practice can reduce memories' susceptibility to interference, like retroactive and proactive interference. In this study, we therefore examined whether retrieval practice can also reduce list method directed forgetting, a form of intentional forgetting that presupposes interference. In each of two experiments, subjects successively studied two lists of items. After studying each single list, subjects restudied the list items to enhance learning, or they were asked to recall the items. Following restudy or retrieval practice of list 1 items, subjects were cued to either forget the list or remember it for an upcoming final test. Experiment 1 employed a free-recall and Experiment 1 a cued-recall procedure on the final memory test. In both experiments, directed forgetting was present in the restudy condition but was absent in the retrieval-practice condition, indicating that retrieval practice can reduce or even eliminate this form of forgetting. The results are consistent with the view that retrieval practice enhances list segregation processes. Such processes may reduce interference between lists and thus reduce directed forgetting.

  14. Phase retrieval methods for surface crystallography

    NASA Astrophysics Data System (ADS)

    Harder, Ross John

    The key to understanding, and perhaps more importantly predicting, the detailed properties of materials and surfaces is an accurate model of the atomic structure of the surface. Everything from the flow of current through a transistor in an integrated circuit, to the function of the catalyst in a car's catalytic converter depends on the atomic structure of the surface under consideration. Determination of the structures of surfaces on an atomic scale is carried out through several experimental methods. In the case of crystal surfaces, diffraction methods are frequently employed. These methods exploit the long-range periodicity of a crystal and the predictable interference of scattered waves due to this periodicity to detect the atomic structure of the material. In these techniques the intensities of the scattered radiation (electromagnetic or particle) are measured although it is in the relative phases of the scattered waves where much of the structural information is contained. Unfortunately the loss of the mostly immeasurable phases leads to time consuming and tedious methods for analysis of diffraction data which depend on models proposed by the investigator. The work presented here is a method by which this phase information can be recovered given just the measured intensities and the presumed known, bulk crystalline structure to enable the model-independent determination of the atomic-scale structure of the surface. This work has been carried out for two different diffraction methods with surface sensitivity. The first is surface x-ray diffraction (SXRD) for which the method will be described in detail. The second is the case of low energy electron diffraction (LEED) to which the method developed in the first case will be applied through identification of justifiable analogies between the two techniques. Results from simulated data are presented from several different classes of surface structures.

  15. Graphical Retrieval Method for Orthorhombic Anisotropic Materials

    DTIC Science & Technology

    2010-07-01

    or nanostructures. We limit our discussion in nonchiral materials. To illustrate the key point we adopt multilayer method that has been used to model...every general multilayer is equivalent to a two-homogeneous-layer system and every symmetric multilayer is equivalent to a single homogeneous layer...characterized by an equivalent index and equivalent thickness[15]. In metamaterials, a single unit-cell layer can be considered as a multilayer system

  16. Energy filtering transmission electron microscopy immunocytochemistry and antigen retrieval of surface layer proteins from Tannerella forsythensis using microwave or autoclave heating with citraconic anhydride

    PubMed Central

    2012-01-01

    Tannerella forsythensis (Bacteroides forsythus), an anaerobic Gram-negative species of bacteria that plays a role in the progression of periodontal disease, has a unique bacterial protein profile. It is characterized by two unique protein bands with molecular weights of more than 200 kDa. It also is known to have a typical surface layer (S-layer) consisting of regularly arrayed subunits outside the outer membrane. We examined the relationship between high molecular weight proteins and the S-layer using electron microscopic immunolabeling with chemical fixation and an antigen retrieval procedure consisting of heating in a microwave oven or autoclave with citraconic anhydride. Immunogold particles were localized clearly at the outermost cell surface. We also used energy-filtering transmission electron microscopy (EFTEM) to visualize 3, 3′-diaminobenzidine tetrahydrochloride (DAB) reaction products after microwave antigen retrieval with 1% citraconic anhydride. The three-window method for electron spectroscopic images (ESI) of nitrogen by the EFTEM reflected the presence of moieties demonstrated by the DAB reaction with horseradish peroxidase (HRP)-conjugated secondary antibodies instead of immunogold particles. The mapping patterns of net nitrogen were restricted to the outermost cell surface. PMID:22984898

  17. Energy filtering transmission electron microscopy immunocytochemistry and antigen retrieval of surface layer proteins from Tannerella forsythensis using microwave or autoclave heating with citraconic anhydride.

    PubMed

    Moriguchi, K; Mitamura, Y; Iwami, J; Hasegawa, Y; Higuchi, N; Murakami, Y; Maeda, H; Yoshimura, F; Nakamura, H; Ohno, N

    2012-11-01

    Tannerella forsythensis (Bacteroides forsythus), an anaerobic Gram-negative species of bacteria that plays a role in the progression of periodontal disease, has a unique bacterial protein profile. It is characterized by two unique protein bands with molecular weights of more than 200 kDa. It also is known to have a typical surface layer (S-layer) consisting of regularly arrayed subunits outside the outer membrane. We examined the relationship between high molecular weight proteins and the S-layer using electron microscopic immunolabeling with chemical fixation and an antigen retrieval procedure consisting of heating in a microwave oven or autoclave with citraconic anhydride. Immunogold particles were localized clearly at the outermost cell surface. We also used energy-filtering transmission electron microscopy (EFTEM) to visualize 3, 3'-diaminobenzidine tetrahydrochloride (DAB) reaction products after microwave antigen retrieval with 1% citraconic anhydride. The three-window method for electron spectroscopic images (ESI) of nitrogen by the EFTEM reflected the presence of moieties demonstrated by the DAB reaction with horseradish peroxidase (HRP)-conjugated secondary antibodies instead of immunogold particles. The mapping patterns of net nitrogen were restricted to the outermost cell surface.

  18. Hybrid projection-reflection method for phase retrieval

    NASA Astrophysics Data System (ADS)

    Bauschke, Heinz H.; Combettes, Patrick L.; Luke, D. Russell

    2003-06-01

    The phase-retrieval problem, fundamental in applied physics and engineering, addresses the question of how to determine the phase of a complex-valued function from modulus data and additional a priori information. Recently we identified two important methods for phase retrieval, namely, Fienup's basic input-output and hybrid input-output (HIO) algorithms, with classical convex projection methods and suggested that further connections between convex optimization and phase retrieval should be explored. Following up on this work, we introduce a new projection-based method, termed the hybrid projection-reflection (HPR) algorithm, for solving phase-retrieval problems featuring nonnegativity constraints in the object domain. Motivated by properties of the HPR algorithm for convex constraints, we recommend an error measure studied by Fienup more than 20 years ago. This error measure, which has received little attention in the literature, lends itself to an easily implementable stopping criterion. In numerical experiments we found the HPR algorithm to be a competitive alternative to the HIO algorithm and the stopping criterion to be reliable and robust.

  19. 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

  20. Generalized method for retrieving effective parameters of anisotropic metamaterials.

    PubMed

    Castanié, A; Mercier, J-F; Félix, S; Maurel, A

    2014-12-01

    Electromagnetic or acoustic metamaterials can be described in terms of equivalent effective, in general anisotropic, media and several techniques exist to determine the effective permeability and permittivity (or effective mass density and bulk modulus in the context of acoustics). Among these techniques, retrieval methods use the measured reflection and transmission coefficients (or scattering coefficients) for waves incident on a metamaterial slab containing few unit cells. Until now, anisotropic effective slabs have been considered in the literature but they are limited to the case where one of the axes of anisotropy is aligned with the slab interface. We propose an extension to arbitrary orientations of the principal axes of anisotropy and oblique incidence. The retrieval method is illustrated in the electromagnetic case for layered media, and in the acoustic case for array of tilted elliptical particles.

  1. Evaluation methods for retrieving information from interferograms of biomedical objects

    NASA Astrophysics Data System (ADS)

    Podbielska, Halina; Rottenkolber, Matthias

    1996-04-01

    Interferograms in the form of fringe patterns can be produced in two-beam interferometers, holographic or speckle interferometers, in setups realizing moire techniques or in deflectometers. Optical metrology based on the principle of interference can be applied as a testing tool in biomedical research. By analyzing of the fringe pattern images, information about the shape or mechanical behavior of the object under study can be retrieved. Here, some of the techniques for creating fringe pattern images were presented along with methods of analysis. Intensity based analysis as well as methods of phase measurements, are mentioned. Applications of inteferometric methods, especially in the field of experimental orthopedics, endoscopy and ophthalmology are pointed out.

  2. Selection of buffer pH by the isoelectric point of the antigen for the efficient heat-induced epitope retrieval: re-appraisal for nuclear protein pathobiology.

    PubMed

    Kajiya, Hanako; Takekoshi, Susumu; Takei, Mao; Egashira, Noboru; Miyakoshi, Takashi; Serizawa, Akihito; Teramoto, Akira; Osamura, Robert Y

    2009-12-01

    Epitope retrieval (ER) using heating causes a dramatic improvement in the sensitivity of immunohistochemistry for formalin-fixed paraffin-embedded (FFPE) tissue sections. Here, the relationship between the pH of the retrieval buffer used for heat-induced epitope retrieval (HIER) and the isoelectric points (pI) of the antigen recognized by antibodies against nuclear proteins (mainly human pituitary transcription factors in this study) was investigated using FFPE tissue sections. A universal buffer, with a buffering capacity over a wide pH range from 2.0 to 12.0, was used for HIER. We found that the intensity of staining for most nuclear proteins after HIER depended simply on the pH of the buffer. Importantly, for efficient HIER, antigens with acidic pI required basic pH buffer conditions, while antigens with alkaline pI required acidic conditions. This implies that the electrostatic charge of the antigens contributed significantly to the efficiency of HIER. We conclude that appropriate selection of the pH of the buffer based on the pI of the individual antigens is of great importance for efficient ER. It is concluded that the mechanism of HEIR may, therefore, depend to a large extent on the pI of the antigen under investigation.

  3. A passage retrieval method based on probabilistic information retrieval model and UMLS concepts in biomedical question answering.

    PubMed

    Sarrouti, Mourad; Ouatik El Alaoui, Said

    2017-04-01

    Passage retrieval, the identification of top-ranked passages that may contain the answer for a given biomedical question, is a crucial component for any biomedical question answering (QA) system. Passage retrieval in open-domain QA is a longstanding challenge widely studied over the last decades. However, it still requires further efforts in biomedical QA. In this paper, we present a new biomedical passage retrieval method based on Stanford CoreNLP sentence/passage length, probabilistic information retrieval (IR) model and UMLS concepts. In the proposed method, we first use our document retrieval system based on PubMed search engine and UMLS similarity to retrieve relevant documents to a given biomedical question. We then take the abstracts from the retrieved documents and use Stanford CoreNLP for sentence splitter to make a set of sentences, i.e., candidate passages. Using stemmed words and UMLS concepts as features for the BM25 model, we finally compute the similarity scores between the biomedical question and each of the candidate passages and keep the N top-ranked ones. Experimental evaluations performed on large standard datasets, provided by the BioASQ challenge, show that the proposed method achieves good performances compared with the current state-of-the-art methods. The proposed method significantly outperforms the current state-of-the-art methods by an average of 6.84% in terms of mean average precision (MAP). We have proposed an efficient passage retrieval method which can be used to retrieve relevant passages in biomedical QA systems with high mean average precision. Copyright © 2017 Elsevier Inc. All rights reserved.

  4. 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.

  5. A damped Newton variational inversion method for SAR wind retrieval

    NASA Astrophysics Data System (ADS)

    Jiang, Zhuhui; Li, Yuanxiang; Yu, Fangjie; Chen, Ge; Yu, Wenxian

    2017-01-01

    The variational inversion for synthetic aperture radar (SAR) wind retrieval can take all sources' errors into account, but its iterative computation is very time consuming. For the wind vectors, (u, v) components are commonly used for variational inversion, but they are not intuitive for practical applications. In this paper, we modify the decomposition of wind vectors in the cost function into wind speed and wind direction and adopt the damped Newton method (DNVAR) to solve the cost function. Experimental results on simulated data show that DNVAR can effectively reduce background wind vector errors. Additionally, the average number of iterations is reduced drastically compared to prior arts. Furthermore, a detailed comparison between direct SAR wind retrieval (DIRECT) and DNVAR is performed. Simulations reveal that the DNVAR errors are smaller than the background wind vector errors in all considered cases. Thus, DNVAR could be employed to retrieve SAR sea surface wind. For practical applications, when the background wind speed is within moderate and high wind speed range, DNVAR has higher accuracy and is thus preferred. Otherwise, both DNVAR and DIRECT are feasible, considering the unknown actual errors of both background wind vectors and geophysical model function. Experimental results on Envisat/advanced synthetic aperture radar data show that the wind speed accuracy of DIRECT is largely affected by the background wind direction errors, but DNVAR can reduce the wind direction errors with minor effect on the wind speed errors in comparison with the background wind errors.

  6. Improved retrievals of the optical properties of cirrus clouds by a combination of lidar methods.

    PubMed

    Cadet, Bertrand; Giraud, Vincent; Haeffelin, Martial; Keckhut, Philippe; Rechou, Anne; Baldy, Serge

    2005-03-20

    We focus on improvement of the retrieval of optical properties of cirrus clouds by combining two lidar methods. We retrieve the cloud's optical depth by using independently the molecular backscattering profile below and above the cloud [molecular integration (MI) method] and the backscattering profile inside the cloud with an a priori effective lidar ratio [particle integration (PI) method]. When the MI method is reliable, the combined MI-PI method allows us to retrieve the optimal effective lidar ratio. We compare these results with Raman lidar retrievals. We then use the derived optimal effective lidar ratio for retrieval with the PI method for situations in which the MI method cannot be applied.

  7. Contrast of doppler radar wind field retrieval methods between VVP and advanced simple adjoint model

    NASA Astrophysics Data System (ADS)

    Kang, Hao; Wei, Ming; Tang, Liping

    2007-12-01

    The wind retrieval of single Doppler radar data is important for severe weather forecasting. The contrast of wind retrieve methods between VVP and advanced simple adjoint model has been made. The typhoon and rainstorm wind retrieval results indicate two methods have their own advantage and disadvantage because the assume conditions and processing ways are different, this work is valuable for the retrieval wind field application in research and operation.

  8. Radial immunodiffusion: a simple and rapid method for detection of Marek's disease antigen(s).

    PubMed

    Marquardt, W W

    1972-05-01

    A qualitative radial immunodiffusion technique is described which detects antigen(s) in feathers from live or dead chickens infected with Marek's disease herpesvirus. Antiserum, which is incorporated into a support medium, reacts with antigen(s) in the feather tip producing a radial precipitin ring. Antigen(s) was detected in 93.3% of experimentally inoculated chickens 21 days postinoculation and in 100% of infected birds subsequently tested through 6 weeks. No antigen was detectable in the feathers of uninoculated control chickens. The technique is simple and rapid to perform. Positive tests could be detected after 1 to 2 hours of incubation. Antigen detection by the radial immunodiffusion test correlated well with other criteria of infection. This technique should have application as a laboratory research tool and as an adjunct for a rapid flock diagnosis of Marek's disease.

  9. 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)

  10. 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)

  11. Robustness of phase retrieval methods in x-ray phase contrast imaging: A comparison

    PubMed Central

    Yan, Aimin; Wu, Xizeng; Liu, Hong

    2011-01-01

    Purpose: The robustness of the phase retrieval methods is of critical importance for limiting and reducing radiation doses involved in x-ray phase contrast imaging. This work is to compare the robustness of two phase retrieval methods by analyzing the phase maps retrieved from the experimental images of a phantom. Methods: Two phase retrieval methods were compared. One method is based on the transport of intensity equation (TIE) for phase contrast projections, and the TIE-based method is the most commonly used method for phase retrieval in the literature. The other is the recently developed attenuation-partition based (AP-based) phase retrieval method. The authors applied these two methods to experimental projection images of an air-bubble wrap phantom for retrieving the phase map of the bubble wrap. The retrieved phase maps obtained by using the two methods are compared. Results: In the wrap’s phase map retrieved by using the TIE-based method, no bubble is recognizable, hence, this method failed completely for phase retrieval from these bubble wrap images. Even with the help of the Tikhonov regularization, the bubbles are still hardly visible and buried in the cluttered background in the retrieved phase map. The retrieved phase values with this method are grossly erroneous. In contrast, in the wrap’s phase map retrieved by using the AP-based method, the bubbles are clearly recovered. The retrieved phase values with the AP-based method are reasonably close to the estimate based on the thickness-based measurement. The authors traced these stark performance differences of the two methods to their different techniques employed to deal with the singularity problem involved in the phase retrievals. Conclusions: This comparison shows that the conventional TIE-based phase retrieval method, regardless if Tikhonov regularization is used or not, is unstable against the noise in the wrap’s projection images, while the AP-based phase retrieval method is shown in these

  12. Robustness of phase retrieval methods in x-ray phase contrast imaging: A comparison

    SciTech Connect

    Yan, Aimin; Wu, Xizeng; Liu, Hong

    2011-09-15

    Purpose: The robustness of the phase retrieval methods is of critical importance for limiting and reducing radiation doses involved in x-ray phase contrast imaging. This work is to compare the robustness of two phase retrieval methods by analyzing the phase maps retrieved from the experimental images of a phantom. Methods: Two phase retrieval methods were compared. One method is based on the transport of intensity equation (TIE) for phase contrast projections, and the TIE-based method is the most commonly used method for phase retrieval in the literature. The other is the recently developed attenuation-partition based (AP-based) phase retrieval method. The authors applied these two methods to experimental projection images of an air-bubble wrap phantom for retrieving the phase map of the bubble wrap. The retrieved phase maps obtained by using the two methods are compared. Results: In the wrap's phase map retrieved by using the TIE-based method, no bubble is recognizable, hence, this method failed completely for phase retrieval from these bubble wrap images. Even with the help of the Tikhonov regularization, the bubbles are still hardly visible and buried in the cluttered background in the retrieved phase map. The retrieved phase values with this method are grossly erroneous. In contrast, in the wrap's phase map retrieved by using the AP-based method, the bubbles are clearly recovered. The retrieved phase values with the AP-based method are reasonably close to the estimate based on the thickness-based measurement. The authors traced these stark performance differences of the two methods to their different techniques employed to deal with the singularity problem involved in the phase retrievals. Conclusions: This comparison shows that the conventional TIE-based phase retrieval method, regardless if Tikhonov regularization is used or not, is unstable against the noise in the wrap's projection images, while the AP-based phase retrieval method is shown in these

  13. Serological versus antigen detection methods for Giardia duodenalis diagnosis.

    PubMed

    Bashir, M; Farid, A; Rabia, I; Mostafa, B; El Amir, A

    2014-12-01

    Giardiasis constitutes an important public health problem in the world. Contamination of the water with fecal materials including viruses and pathogenic protozoa still represents an environmental health hazard, especially in rural areas. The survey study evaluated the relation between seropositivity and some risk factors. Moreover, the study compared between the serological IgG and IgM level and antigen detection methods for the diagnosis of giardiasis. The results indicate that sex distribution and age were the mean risk factors for seroprevelence. In this study, sera samples were employed in sandwich ELISA assay, to detect circulating Giardia antigens. None of the negative control serum samples gave a positive reaction, but cross reaction was encountered with 3 case of Cryptosporidium. The specificity of the assay was 94.830/a. On the other hand, the sensitivity of the Giardia patient's sera was 94.12% which was higher than that of IgG (86.25%) and IgM (87.50%) secretion measurements. In conclusion, antigen detection methods give better and earlier diagnosis for giardiasis can be performed quickly and do not require an experienced and skilled morphologist.

  14. Effects of antigen retrieval by microwave heating in formalin-fixed tissue sections on a broad panel of antibodies.

    PubMed

    von Wasielewski, R; Werner, M; Nolte, M; Wilkens, L; Georgii, A

    1994-09-01

    Formaldehyde fixation of biopsy specimens for routine purposes has often been held responsible for the poor reproducibility of immunohistochemical studies. Recently, antigen retrieval (AGR) using microwave irradiation was described as a potential tool to enhance immunostaining. A comparison of conventional staining and staining after microwave heating was performed for 52 markers, using tissues fixed in formaldehyde for 24 h, 1 to 6 weeks and 3 years respectively, as well as consultant case material. After adequate duration of fixation (24 h), only a few markers (17%) showed better results after AGR, but this percentage was increased to 50% when tissues were fixed for longer periods. Maximal enhancement was obtained in the group of consultant cases (58% of tested markers demonstrated better staining results), in which the period of fixation and tissue processing was unknown. To achieve reliable enhancement with AGR, continuous heating (100 degrees C) should not be shorter than 20 min. In conclusion, AGR may become the most important tool to simplify and equalize immunohistochemical techniques, if critically evaluated.

  15. An inverse method to retrieve 3D radar reflectivity composites

    NASA Astrophysics Data System (ADS)

    Roca-Sancho, Jordi; Berenguer, Marc; Sempere-Torres, Daniel

    2014-11-01

    Dense radar networks offer the possibility of getting better Quantitative Precipitation Estimates (QPE) than those obtained with individual radars, as they allow increasing the coverage and improving quality of rainfall estimates in overlapping areas. Well-known sources of error such as attenuation by intense rainfall or errors associated with range can be mitigated through radar composites. Many compositing techniques are devoted to operational uses and do not exploit all the information that the network is providing. In this work an inverse method to obtain high-resolution radar reflectivity composites is presented. The method uses a model of radar sampling of the atmosphere that accounts for path attenuation and radar measurement geometry. Two significantly different rainfall situations are used to show detailed results of the proposed inverse method in comparison to other existing methodologies. A quantitative evaluation is carried out in a 12 h-event using two independent sources of information: a radar not involved in the composition process and a raingauge network. The proposed inverse method shows better performance in retrieving high reflectivity values and reproducing variability at convective scales than existing methods.

  16. 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

  17. 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.

  18. 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.

  19. Intelligent Interfaces and Retrieval Methods for Subject Searching in Bibliographic Retrieval Systems.

    ERIC Educational Resources Information Center

    Hildreth, Charles R.

    This study was designed to be a state-of-the-art survey and investigation of intelligent "front end" design approaches and software for improving subject access and subject searching in today's large online bibliographic retrieval systems and online public access catalogs (OPACS). The report begins with an illustrated overview of…

  20. Identification of 5-bromo-2'-deoxyuridine-labeled cells during mouse spermatogenesis by heat-induced antigen retrieval in lectin staining and immunohistochemistry.

    PubMed

    Wakayama, Tomohiko; Nakata, Hiroki; Kumchantuek, Tewarat; Gewaily, Mahmoud Saad; Iseki, Shoichi

    2015-03-01

    DNA replication occurs during S-phase in spermatogonia and preleptotene spermatocytes during spermatogenesis. 5-Bromo-2'-deoxyuridine (BrdU) is incorporated into synthesized DNA and is detectable in the nucleus by immunohistochemistry (IHC). To identify BrdU-labeled spermatogenic cells, the spermatogenic stages must be determined by visualizing acrosomes and detecting cell type-specific marker molecules in the seminiferous tubules. However, the antibody reaction with BrdU routinely requires denaturation of the DNA, which is achieved by pretreating tissue sections with hydrochloric acid; however, this commonly interferes with further histochemical approaches. Therefore, we examined optimal methods for pretreating paraffin sections of the mouse testis to detect incorporated BrdU by an antibody and, at the same time, visualize acrosomes with peanut agglutinin (PNA) or detect several marker molecules with antibodies. We found that the use of heat-induced antigen retrieval (HIAR), which consisted of heating at 95C in 20 mM Tris-HCl buffer (pH 9.0) for 15 min, was superior to the use of 2 N hydrochloric acid for 90 min at room temperature in terms of the quality of subsequent PNA-lectin histochemistry with double IHC for BrdU and an appropriate stage marker protein. With this method, we identified BrdU-labeled spermatogenic cells during mouse spermatogenesis as A1 spermatogonia through to preleptotene spermatocytes.

  1. A TEMPERATURE AND ABUNDANCE RETRIEVAL METHOD FOR EXOPLANET ATMOSPHERES

    SciTech Connect

    Madhusudhan, N.; Seager, S.

    2009-12-10

    We present a new method to retrieve molecular abundances and temperature profiles from exoplanet atmosphere photometry and spectroscopy. We run millions of one-dimensional (1D) atmosphere models in order to cover the large range of allowed parameter space. In order to run such a large number of models, we have developed a parametric pressure-temperature (P-T) profile coupled with line-by-line radiative transfer, hydrostatic equilibrium, and energy balance, along with prescriptions for non-equilibrium molecular composition and energy redistribution. The major difference from traditional 1D radiative transfer models is the parametric P-T profile, which essentially means adopting energy balance only at the top of the atmosphere and not in each layer. We see the parametric P-T model as a parallel approach to the traditional exoplanet atmosphere models that rely on several free parameters to encompass unknown absorbers and energy redistribution. The parametric P-T profile captures the basic physical features of temperature structures in planetary atmospheres (including temperature inversions), and fits a wide range of published P-T profiles, including those of solar system planets. We apply our temperature and abundance retrieval method to the atmospheres of two transiting exoplanets, HD 189733b and HD 209458b, which have the best Spitzer and Hubble Space Telescope data available. For HD 189733b, we find efficient day-night redistribution of energy in the atmosphere, and molecular abundance constraints confirming the presence of H{sub 2}O, CO, CH{sub 4}, and CO{sub 2}. For HD 209458b, we confirm and constrain the dayside thermal inversion in an average 1D temperature profile. We also report independent detections of H{sub 2}O, CO, CH{sub 4}, and CO{sub 2} on the dayside of HD 209458b, based on six-channel Spitzer photometry. We report constraints for HD 189733b due to individual data sets separately; a few key observations are variable in different data sets at similar

  2. Comparison of the Assimilation of Compact Phase Space Retrievals (CPSRs) with Conventional Retrieval Assimilation Methods for MOPITT CO in WRF-Chem/DART

    NASA Astrophysics Data System (ADS)

    Mizzi, A. P.; Arellano, A. F.; Edwards, D. P.; Anderson, J. L.

    2015-12-01

    We introduced "compact phase space retrievals" (CPSRs) for assimilating atmospheric composition observations in Mizzi et al. (2015). CPSRs address many of the challenges associated with assimilating retrievals by: (i) removing the contribution of the retrieval prior, (ii) diagonalizing the associated error covariance, and (iii) compacting the phase space retrievals. Mizzi et al. (2015) showed that the CPSRs reduced assimilation computational costs by approximately one-third while maintaining the relevant forecast skill metrics. In this paper, we examine phase space retrievals and compare CPSRs to more conventional retrieval assimilation methods. Specifically we compare the assimilation of CPSRs with that of (i) raw retrievals where the observation error is based on the diagonal of the retrieval error covariance, (ii) quasi-optimal retrievals (QORs) where the observation error is determined as (i), and (iii) QORs where the observation error is based on an SVD-based transform of the error covariance. Method (i) is the easiest to interpret because the assimilation occurs in retrieval space. Method (ii) explicitly removes the retrieval prior term's contribution but is more difficult to interpret because the assimilated observations are residuals. Finally, method (iii) is the phase space retrieval algorithm of Migliorini et al. (2008). We consider two variants: (i) withholding the inverse square scaling and (ii) using phase space filtering for optimization. We apply those methods to month-long forecast/assimilation experiments with continuous cycling.

  3. Rapid Retrieval of Lung Nodule CT Images Based on Hashing and Pruning Methods.

    PubMed

    Pan, Ling; Qiang, Yan; Yuan, Jie; Wu, Lidong

    2016-01-01

    The similarity-based retrieval of lung nodule computed tomography (CT) images is an important task in the computer-aided diagnosis of lung lesions. It can provide similar clinical cases for physicians and help them make reliable clinical diagnostic decisions. However, when handling large-scale lung images with a general-purpose computer, traditional image retrieval methods may not be efficient. In this paper, a new retrieval framework based on a hashing method for lung nodule CT images is proposed. This method can translate high-dimensional image features into a compact hash code, so the retrieval time and required memory space can be reduced greatly. Moreover, a pruning algorithm is presented to further improve the retrieval speed, and a pruning-based decision rule is presented to improve the retrieval precision. Finally, the proposed retrieval method is validated on 2,450 lung nodule CT images selected from the public Lung Image Database Consortium (LIDC) database. The experimental results show that the proposed pruning algorithm effectively reduces the retrieval time of lung nodule CT images and improves the retrieval precision. In addition, the retrieval framework is evaluated by differentiating benign and malignant nodules, and the classification accuracy can reach 86.62%, outperforming other commonly used classification methods.

  4. Rapid Retrieval of Lung Nodule CT Images Based on Hashing and Pruning Methods

    PubMed Central

    Pan, Ling; Yuan, Jie; Wu, Lidong

    2016-01-01

    The similarity-based retrieval of lung nodule computed tomography (CT) images is an important task in the computer-aided diagnosis of lung lesions. It can provide similar clinical cases for physicians and help them make reliable clinical diagnostic decisions. However, when handling large-scale lung images with a general-purpose computer, traditional image retrieval methods may not be efficient. In this paper, a new retrieval framework based on a hashing method for lung nodule CT images is proposed. This method can translate high-dimensional image features into a compact hash code, so the retrieval time and required memory space can be reduced greatly. Moreover, a pruning algorithm is presented to further improve the retrieval speed, and a pruning-based decision rule is presented to improve the retrieval precision. Finally, the proposed retrieval method is validated on 2,450 lung nodule CT images selected from the public Lung Image Database Consortium (LIDC) database. The experimental results show that the proposed pruning algorithm effectively reduces the retrieval time of lung nodule CT images and improves the retrieval precision. In addition, the retrieval framework is evaluated by differentiating benign and malignant nodules, and the classification accuracy can reach 86.62%, outperforming other commonly used classification methods. PMID:27995140

  5. Association of a dog leukocyte antigen class II haplotype with hypoadrenocorticism in Nova Scotia Duck Tolling Retrievers.

    PubMed

    Hughes, A M; Jokinen, P; Bannasch, D L; Lohi, H; Oberbauer, A M

    2010-06-01

    Canine hypoadrenocorticism (Addison's disease) is due to a deficiency of corticosteroids and mineralocorticoids produced by the adrenals. Although this is a relatively uncommon disease in the general dog population, some breeds, including the Nova Scotia Duck Tolling Retriever (NSDTR), are at increased risk for developing hypoadrenocorticism. A prior study has shown that the increased risk is due to a heritable component. This potentially lethal disorder is hypothesized to have an autoimmune etiology, thus the aim of this study was to determine whether genetic susceptibility to hypoadrenocorticism in NSDTRs is associated with genes of the canine major histocompatibility complex [MHC; dog leukocyte antigen system (DLA)]. Samples were collected from NSDTRs diagnosed with hypoadrenocorticism and healthy siblings or country-matched controls. The DLA class II alleles and haplotypes were determined and compared between cases and controls. We found seven different haplotypes of which the haplotype DLA-DRB1*01502/DQA*00601/DQB1*02301 was significantly more prevalent in the diseased dogs (P = 0.044). In addition, these affected dogs also were more likely to be homozygous across the DLA class II region than the control dogs (OR = 6.7, CI = 1.5-29.3, P = 0.011). We also found that homozygous dogs, regardless of their haplotype, tended to have earlier disease onset compared with heterozygous dogs. These data indicate a limited MHC diversity in North American NSDTRs and suggest that the MHC may play a role in the development of hypoadrenocorticism in the NSDTR, supporting the autoimmune origin of the disease.

  6. Quantitative cell imaging using single beam phase retrieval method

    NASA Astrophysics Data System (ADS)

    Anand, Arun; Chhaniwal, Vani; Javidi, Bahram

    2011-06-01

    Quantitative three-dimensional imaging of cells can provide important information about their morphology as well as their dynamics, which will be useful in studying their behavior under various conditions. There are several microscopic techniques to image unstained, semi-transparent specimens, by converting the phase information into intensity information. But most of the quantitative phase contrast imaging techniques is realized either by using interference of the object wavefront with a known reference beam or using phase shifting interferometry. A two-beam interferometric method is challenging to implement especially with low coherent sources and it also requires a fine adjustment of beams to achieve high contrast fringes. In this letter, the development of a single beam phase retrieval microscopy technique for quantitative phase contrast imaging of cells using multiple intensity samplings of a volume speckle field in the axial direction is described. Single beam illumination with multiple intensity samplings provides fast convergence and a unique solution of the object wavefront. Three-dimensional thickness profiles of different cells such as red blood cells and onion skin cells were reconstructed using this technique with an axial resolution of the order of several nanometers.

  7. Immunolocalization of MAP-2 in Routinely Formalin-Fixed, Paraffin-Embedded Guinea Pig Brain Sections Using Microwave Irradiation: A Comparison of Different Combinations of Antibody Clones and Antigen Retrieval Buffer Solutions

    NASA Astrophysics Data System (ADS)

    Kan, Robert K.; Pleva, Christina M.; Hamilton, Tracey A.; Petrali, John P.

    2005-04-01

    The present study was designed to evaluate the efficacy of different microwave pretreatment methods to retrieve microtubule-associated protein 2 (MAP-2) immunoreactivity in formalin-fixed, paraffin-embedded guinea pig brain sections. Brain sections, microwave pretreated in boiling sodium citrate, citric acid, Tris hydrochloride, and EDTA buffers of pH 4, 6, and 8, were labeled with four different clones of MAP-2 monoclonal antibodies. No MAP-2 immunoreactivity was observed in control sections processed without microwave pretreatment. Optimal MAP-2 immunoreactivity was observed only when MAP-2 antibody clone AP18 was used in conjunction with citric acid buffer of pH 6.0. Using this combination, brain sections from nerve agent soman-exposed guinea pigs were found to exhibit marked reduction in MAP-2 immunostaining in the hippocampus. These observations suggest that the clone of the antibody in addition to the type and pH of antigen retrieval (AR) solution are important variables to be considered for establishing an optimal AR technique. When studying counterpart antigens of species other than that to which the antibodies were originally raised, different antibody clones must be tested in combination with different microwave-assisted AR (MAR) methods. This MAR method makes it possible to conduct retrospective studies on archival guinea pig brain paraffin blocks to evaluate changes in neuronal MAP-2 expression as a consequence of chemical warfare nerve agent toxicity.

  8. Immunolocalization of MAP-2 in routinely formalin-fixed, paraffin-embedded guinea pig brain sections using microwave irradiation: a comparison of different combinations of antibody clones and antigen retrieval buffer solutions.

    PubMed

    Kan, Robert K; Pleva, Christina M; Hamilton, Tracey A; Petrali, John P

    2005-04-01

    The present study was designed to evaluate the efficacy of different microwave pretreatment methods to retrieve microtubule-associated protein 2 (MAP-2) immunoreactivity in formalin-fixed, paraffin-embedded guinea pig brain sections. Brain sections, microwave pretreated in boiling sodium citrate, citric acid, Tris hydrochloride, and EDTA buffers of pH 4, 6, and 8, were labeled with four different clones of MAP-2 monoclonal antibodies. No MAP-2 immunoreactivity was observed in control sections processed without microwave pretreatment. Optimal MAP-2 immunoreactivity was observed only when MAP-2 antibody clone AP18 was used in conjunction with citric acid buffer of pH 6.0. Using this combination, brain sections from nerve agent soman-exposed guinea pigs were found to exhibit marked reduction in MAP-2 immunostaining in the hippocampus. These observations suggest that the clone of the antibody in addition to the type and pH of antigen retrieval (AR) solution are important variables to be considered for establishing an optimal AR technique. When studying counterpart antigens of species other than that to which the antibodies were originally raised, different antibody clones must be tested in combination with different microwave-assisted AR (MAR) methods. This MAR method makes it possible to conduct retrospective studies on archival guinea pig brain paraffin blocks to evaluate changes in neuronal MAP-2 expression as a consequence of chemical warfare nerve agent toxicity.

  9. 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.

  10. 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.

  11. 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.

  12. Image retrieval method based on metric learning for convolutional neural network

    NASA Astrophysics Data System (ADS)

    Wang, Jieyuan; Qian, Ying; Ye, Qingqing; Wang, Biao

    2017-09-01

    At present, the research of content-based image retrieval (CBIR) focuses on learning effective feature for the representations of origin images and similarity measures. The retrieval accuracy and efficiency are crucial to a CBIR. With the rise of deep learning, convolutional network is applied in the domain of image retrieval and achieved remarkable results, but the image visual feature extraction of convolutional neural network exist high dimension problems, this problem makes the image retrieval and speed ineffective. This paper uses the metric learning for the image visual features extracted from the convolutional neural network, decreased the feature redundancy, improved the retrieval performance. The work in this paper is also a necessary part for further implementation of feature hashing to the approximate-nearest-neighbor (ANN) retrieval method.

  13. The Monte Carlo Method and the Evaluation of Retrieval System Performance.

    ERIC Educational Resources Information Center

    Burgin, Robert

    1999-01-01

    Introduces the Monte Carlo method which is shown to represent an attractive alternative to the hypergeometric model for identifying the levels at which random retrieval performance is exceeded in retrieval test collections and for overcoming some of the limitations of the hypergeometric model. Practical matters to consider when employing the Monte…

  14. 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.

  15. Lensless imaging from diffraction intensity measurements by use of a noniterative phase-retrieval method.

    PubMed

    Nakajima, Nobuharu

    2004-03-10

    A method of reconstructing the complex amplitude of an object that is illuminated by a coherent wave from its Fresnel diffraction patterns is proposed for high-frequency wave phenomena such as x-rays and electron waves. A noniterative phase-retrieval method that uses a Gaussian filter is employed here, and it is shown that the object's illumination with amplitude distribution in the Fraunhofer diffraction pattern of a circular aperture can be used as a substitute for the Gaussian filter. This method has an advantage over other noniterative phase-retrieval methods in that it can retrieve phase vortices.

  16. Spatial-light-modulator-based adaptive optical system for the use of multiple phase retrieval methods.

    PubMed

    Lingel, Christian; Haist, Tobias; Osten, Wolfgang

    2016-12-20

    We propose an adaptive optical setup using a spatial light modulator (SLM), which is suitable to perform different phase retrieval methods with varying optical features and without mechanical movement. By this approach, it is possible to test many different phase retrieval methods and their parameters (optical and algorithmic) using one stable setup and without hardware adaption. We show exemplary results for the well-known transport of intensity equation (TIE) method and a new iterative adaptive phase retrieval method, where the object phase is canceled by an inverse phase written into part of the SLM. The measurement results are compared to white light interferometric measurements.

  17. Robust wrapping-free phase retrieval method based on weighted least squares method

    NASA Astrophysics Data System (ADS)

    Wang, Minmin; Zhou, Canlin; Si, Shuchun; Li, XiaoLei; Lei, Zhenkun; Li, YanJie

    2017-10-01

    Phase unwrapping is one of the most challenging processes in many profilometry techniques. To sidestep the phase unwrapping process, Perciante et al. (2015) proposed a wrapping-free method to retrieve the phase based on the direct integration of the spatial derivatives of the fringe patterns. However, this method is only applicable to objects with phase continuity, so it may fail to handle fringe patterns containing complicated singularities such as noise, shadows, shears and surface discontinuities. In the light of this problems, a robust wrapping-free phase retrieval method is proposed that is based on the combined use of Perciante's method and the weighted least squares method. Two partial derivatives of the desired phase are obtained from the fringe patterns, while the carrier is eliminated using the direct phase difference method. The phase singularities are determined using a derivative variance correlation map (DVCM), and the weighting coefficient is obtained from the binary mask of the reverse DVCM. Simulations and experiments are conducted to prove the validity of the proposed method. The results are analyzed and compared with those of Perciante's method demonstrating that in addition to maintaining the advantage of sidestepping the phase unwrapping process, the proposed method is available for measuring objects with some types of singularities sources.

  18. 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.

  19. Comparisons of wind speed retrieval methods on C-band multi-polarization SAR measurements

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

    This paper compares the wind speed retrieval methods on C-band multi-polarization SAR measurements to find out the most appropriate one for each polarization data. The RADARSAT-2 SAR quad-polarization (VV+HH+VH+HV) data and NDBC buoy wind data were collocated. For VVpolarization, the retrieved wind speed are compared among four geophysical model function (GMF). For HH polarization, the retrieved wind speed are compared among four polarization ratio model (PR) based on CMOD5 GMF. For VH polarization, the retrieved wind speed are compared between two linear models. Comparisons show all of three polarimetric SAR data have the ability of retrieving wind speed. Based on the error analysis, the commendatory methods are proposed for each polarization.

  20. Query by Browsing: An Alternative Hypertext Information Retrieval Method

    PubMed Central

    Frisse, Mark E.; Cousins, Steve B.

    1989-01-01

    In this paper we discuss our efforts to develop programs which enhance the ability to navigate through large medical hypertext systems. Our approach organizes hypertext index terms into a belief network and uses reader feedback to update the degree of belief in the index terms' utility to a query. We begin by describing various possible configurations for indexes to hypertext. We then describe how belief network calculations can be applied to these indexes. After a brief discussion of early results using manuscripts from a medical handbook, we close with an analysis of our approach's applicability to a wider range of hypertext information retrieval problems.

  1. Methods for retrieval of sea wave spectra from aerospace image spectra

    NASA Astrophysics Data System (ADS)

    Bondur, V. G.; Murynin, A. B.

    2016-12-01

    An approach to the retrieval of sea wave spatial spectra based on satellite optical imagery in linear and nonlinear approximations is described. Physical mechanisms of the formation of disturbed sea surface brightness fields recorded by remote sensing equipment are analyzed. Wave spectra retrieval methods using brightness field formation models that consider linear and nonlinear dependencies on sea surface slopes are suggested. A method for the construction of operators that retrieve the spatial spectra of surface wave slopes and elevations from aerospace imagery and take into account nonlinear modulations of disturbed sea surface brightness fields is developed. This method is based on the numerical simulation of sea surface images and the construction of a retrieving operator with respect to a set of parameters determined by aerospace imaging conditions. Examples of the use of the developed methods are given.

  2. 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

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

    PubMed

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

    2016-05-13

    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.

  4. [Analysis of antigens recognized by anti-gamma-seminoprotein antibody and anti-prostate-specific antigen antibody by means of Ouchterlony method and western blotting method].

    PubMed

    Deguchi, T; Matsui, H; Ehara, H; Kobayashi, K; Saito, I; Shinoda, I; Takahashi, Y; Kuriyama, M; Ban, Y; Kawada, Y

    1989-03-01

    Antigens recognized by anti-gamma-seminoprotein (gamma-Sm) antibody and anti-prostate-specific antigen (PA) antibody were analyzed immunologically by Ouchterlony method and Western blotting method. The double immunodiffusion test demonstrated that anti-gamma-Sm antibody and anti-PA antibody reacted against an identical antigen in seminal fluid or prostate homogenate. In the immunoblotting examination, anti-gamma-Sm antibody and anti-PA antibody formed a single and identical band, which gave a molecular weight of 33,000, in seminal fluid and prostate homogenate. This study demonstrated that anti-gamma-Sm antibody and anti-PA antibody recognized a single and identical antigen in seminal fluid and prostate homogenate and suggested that an identical material could be measured in sera of patients with prostate cancer by immunoassay systems using anti-gamma-Sm antibody and anti-PA antibody.

  5. 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.

  6. Quantitative interferometric microscopy with two dimensional Hilbert transform based phase retrieval method

    NASA Astrophysics Data System (ADS)

    Wang, Shouyu; Yan, Keding; Xue, Liang

    2017-01-01

    In order to obtain high contrast images and detailed descriptions of label free samples, quantitative interferometric microscopy combining with phase retrieval is designed to obtain sample phase distributions from fringes. As accuracy and efficiency of recovered phases are affected by phase retrieval methods, thus approaches owning higher precision and faster processing speed are still in demand. Here, two dimensional Hilbert transform based phase retrieval method is adopted in cellular phase imaging, it not only reserves more sample specifics compared to classical fast Fourier transform based method, but also overcomes disadvantages of traditional algorithm according to Hilbert transform which is a one dimensional processing causing phase ambiguities. Both simulations and experiments are provided, proving the proposed phase retrieval approach can acquire quantitative sample phases with high accuracy and fast speed.

  7. 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

  8. 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.

  9. Investigating the Bag-of-Words Method for 3D Shape Retrieval

    NASA Astrophysics Data System (ADS)

    Li, Xiaolan; Godil, Afzal

    2010-12-01

    This paper investigates the capabilities of the Bag-of-Words (BWs) method in the 3D shape retrieval field. The contributions of this paper are (1) the 3D shape retrieval task is categorized from different points of view: specific versus generic, partial-to-global retrieval (PGR) versus global-to-global retrieval (GGR), and articulated versus nonarticulated (2) the spatial information, represented as concentric spheres, is integrated into the framework to improve the discriminative ability (3) the analysis of the experimental results on Purdue Engineering Benchmark (PEB) reveals that some properties of the BW approach make it perform better on the PGR task than the GGR task (4) the BW approach is evaluated on nonarticulated database PEB and articulated database McGill Shape Benchmark (MSB) and compared to other methods.

  10. A method for retrieving clouds with satellite infrared radiances using the particle filter

    NASA Astrophysics Data System (ADS)

    Xu, Dongmei; Auligné, Thomas; Descombes, Gaël; Snyder, Chris

    2016-11-01

    Ensemble-based techniques have been widely utilized in estimating uncertainties in various problems of interest in geophysical applications. A new cloud retrieval method is proposed based on the particle filter (PF) by using ensembles of cloud information in the framework of Gridpoint Statistical Interpolation (GSI) system. The PF cloud retrieval method is compared with the Multivariate Minimum Residual (MMR) method that was previously established and verified. Cloud retrieval experiments involving a variety of cloudy types are conducted with the PF and MMR methods with measurements of infrared radiances on multi-sensors onboard both geostationary and polar satellites, respectively. It is found that the retrieved cloud masks with both methods are consistent with other independent cloud products. MMR is prone to producing ambiguous small-fraction clouds, while PF detects clearer cloud signals, yielding closer heights of cloud top and cloud base to other references. More collections of small-fraction particles are able to effectively estimate the semi-transparent high clouds. It is found that radiances with high spectral resolutions contribute to quantitative cloud top and cloud base retrievals. In addition, a different way of resolving the filtering problem over each model grid is tested to better aggregate the weights with all available sensors considered, which is proven to be less constrained by the ordering of sensors. Compared to the MMR method, the PF method is overall more computationally efficient, and the cost of the model grid-based PF method scales more directly with the number of computing nodes.

  11. Simple, flexible, and accurate phase retrieval method for generalized phase-shifting interferometry.

    PubMed

    Yatabe, Kohei; Ishikawa, Kenji; Oikawa, Yasuhiro

    2017-01-01

    This paper presents a non-iterative phase retrieval method from randomly phase-shifted fringe images. By combining the hyperaccurate least squares ellipse fitting method with the subspace method (usually called the principal component analysis), a fast and accurate phase retrieval algorithm is realized. The proposed method is simple, flexible, and accurate. It can be easily coded without iteration, initial guess, or tuning parameter. Its flexibility comes from the fact that totally random phase-shifting steps and any number of fringe images greater than two are acceptable without any specific treatment. Finally, it is accurate because the hyperaccurate least squares method and the modified subspace method enable phase retrieval with a small error as shown by the simulations. A MATLAB code, which is used in the experimental section, is provided within the paper to demonstrate its simplicity and easiness.

  12. Neighbourhood search feature selection method for content-based mammogram retrieval.

    PubMed

    Chandy, D Abraham; Christinal, A Hepzibah; Theodore, Alwyn John; Selvan, S Easter

    2017-03-01

    Content-based image retrieval plays an increasing role in the clinical process for supporting diagnosis. This paper proposes a neighbourhood search method to select the near-optimal feature subsets for the retrieval of mammograms from the Mammographic Image Analysis Society (MIAS) database. The features based on grey level cooccurrence matrix, Daubechies-4 wavelet, Gabor, Cohen-Daubechies-Feauveau 9/7 wavelet and Zernike moments are extracted from mammograms available in the MIAS database to form the combined or fused feature set for testing various feature selection methods. The performance of feature selection methods is evaluated using precision, storage requirement and retrieval time measures. Using the proposed method, a significant improvement is achieved in mean precision rate and feature dimension. The results show that the proposed method outperforms the state-of-the-art feature selection methods.

  13. 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.

  14. 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.

  15. Comparison of an Established Antibody Sandwich Method with an Inhibition Method of Histoplasma capsulatum Antigen Detection

    PubMed Central

    Garringer, Todd O.; Wheat, L. Joseph; Brizendine, Edward J.

    2000-01-01

    The Histoplasma antigen immunoassay utilizes an antibody sandwich method that provides a rapid and reliable means of diagnosing the more severe forms of histoplasmosis. Inhibition assays have been developed for antigen detection and offer at least one potential advantage, namely, reduced antibody requirements. We have developed an inhibition assay using the polyclonal antibody employed in our standard sandwich assay. Urine and serum specimens from patients with culture-proven histoplasmosis and controls were tested using both methods. The two methods had similar sensitivities for detection of antigen in urine (antibody sandwich = 92.5% versus inhibition = 87.5%, P = 0.500) and serum (82.5% versus 80.0%, P = 1.000). With serum, the specificities of both methods were similar (antibody sandwich assay = 95.0% versus inhibition assay = 92.5%, P = 1.000), and with urine, the specificity of the antibody sandwich method was superior (97.5% versus 80.0%, P = 0.039). While the overall reproducibility of both methods was excellent (with urine, antibody sandwich assay intraclass correlation coefficient = 0.9975 and with serum = 0.9949; correlation coefficient of the inhibition assay with urine = 0.9736 and with serum = 0.9850), that of the inhibition method was only fair to poor for the controls: urine = −0.0152, serum = 0.5595. Reproducibility was good for the controls using the sandwich method: urine = 0.7717, serum = 0.9470. Cross-reactivity was observed in specimens from patients infected with Blastomyces dermatitidis, Paracoccidioides brasiliensis, and Penicillium marneffei. In conclusion, the decreased specificity and inferior reproducibility with control specimens suggest that the inhibition assay has poorer precision toward the lower end of the detection range. PMID:10921949

  16. Development of surface profile measurement method for ellipsoidal x-ray mirrors using phase retrieval

    NASA Astrophysics Data System (ADS)

    Saitou, Takahiro; Takei, Yoshinori; Mimura, Hidekazu

    2012-09-01

    An ellipsoidal mirror is a promising type of X-ray mirror, because it can focus X-rays to nanometer size with a very large aperture and no chromatic aberration. However, ideal ellipsoidal mirrors have not yet been realized by any manufacturing method. This is partly because there is no evaluation method for its surface figure profile. In this paper, we propose and develop a method for measuring surface figure profile of ellipsoidal mirrors using phase retrieval. An optical design for soft X-ray focusing, the employed phase retrieval method and an experimental optical system specialized for wavefront measurement using a He-Ne laser are reported.

  17. Mitigating the effect of noise in the hybrid input-output method of phase retrieval.

    PubMed

    Trahan, Russell; Hyland, David

    2013-05-01

    Here a modification to the hybrid input-output (HIO) method of phase retrieval is presented which aides in mitigating the negative effects of low signal-to-noise ratios (SNRs). Various type of interferometers measure diffraction patterns which are used to determine the Fourier transform modulus of an objective. Interferometry often suffers from very low SNRs making phase retrieval difficult because of the sensitivity of most phase retrieval algorithms to local minima. Here we analyze the effect of noise on the HIO method. The result is used as a rationale for the proposed modification to the HIO method. The algorithm presented here introduces a filtering scheme which removes much of the Fourier modulus noise. Examples are shown and the results are compared to the HIO method with and without the proposed modification. Comparisons are also made to other methods of filtering the Fourier modulus noise.

  18. Experimental demonstration of scanning phase retrieval by a noniterative method with a Gaussian-amplitude beam

    NASA Astrophysics Data System (ADS)

    Nakajima, Nobuharu; Yoshino, Masayuki

    2017-01-01

    We present a proof-of-principle experiment of an analytic (noniterative) phase-retrieval method for coherent imaging systems under scanning illumination of a probe beam. This method allows to reconstruct the amplitude and phase distribution of a semi-transparent object over a wide area from intensities measured at three points in the Fourier plane of the object under scanning illumination of a known Gaussian-amplitude beam in the object plane. The present measurement system is very simple in contrast to ones of interferometric techniques, and also the speed of the calculation of phase retrieval in this method is faster than that in iterative algorithms since this method is based on an analytic solution to the phase retrieval. The effectiveness of this method is shown in experimental examples of the object reconstructions of a converging lens and a plastic plate for scratch standards.

  19. Retrieval of Temperature From a Multiple Channel Rayleigh-Scatter Lidar Using an Optimal Estimation Method

    NASA Astrophysics Data System (ADS)

    Sica, R. J.; Haefele, A.

    2014-12-01

    The measurement of temperature in the middle atmosphere with Rayleigh-scatter lidars is an important technique for assessing atmospheric change. Current retrieval schemes for these temperature have several shortcoming which can be overcome using an optimal estimation method (OEM). OEMs are applied to the retrieval of temperature from Rayleigh-scatter lidar measurements using both single and multiple channel measurements. Forward models are presented that completely characterize the measurement and allow the simultaneous retrieval of temperature, dead time and background. The method allows a full uncertainty budget to be obtained on a per profile basis that includes, in addition to the statistical uncertainties, the smoothing error and uncertainties due to Rayleigh extinction, ozone absorption, the lidar constant, nonlinearity in the counting system, variation of the Rayleigh-scatter cross section with altitude, pressure, acceleration due to gravity and the variation of mean molecular mass with altitude. The vertical resolution of the temperature profile is found at each height, and a quantitative determination is made of the maximum height to which the retrieval is valid. A single temperature profile can be retrieved from measurements with multiple channels that cover different height ranges, vertical resolutions and even different detection methods. The OEM employed is shown to give robust estimates of temperature consistent with previous methods, while requiring minimal computational time. This demonstrated success of lidar temperature retrievals using an OEM opens new possibilities in atmospheric science for measurement integration between active and passive remote sensing instruments. We are currently working on extending our method to simultaneously retrieve water vapour and temperature using Raman-scatter lidar measurements.

  20. von Willebrand factor antigen: a radial immunodiffusion method evaluated and compared with an ELISA method.

    PubMed

    Blann, A D

    1992-06-01

    A new commercial kit method for the quantification of von Willebrand factor antigen (vWFAg) by radial immunodiffusion was compared to an established ELISA technique. Major discrepancies were found between the two methods. The radial immunodiffusion method had poorer intra- and inter-assay coefficients of variation than the ELISA method, although there was adequate inter-method agreement when 100 plasma samples from controls and patients were compared. However, there was a great difference in values obtained for vWFAg in the reference sample supplied with the commercial kit and that obtained directly from the National Institute for Biological Standards and Controls. There were also differences in levels of significance when vWFAg was measured by the two techniques in different clinical groups, and standard deviations were larger when the kit method was used. It is suggested that on scientific and economic grounds, the commercial radial immunodiffusion kit does not offer a competitive advantage over the ELISA method.

  1. An Efficient Method for Rare Spectra Retrieval in Astronomical Databases

    NASA Astrophysics Data System (ADS)

    Du, Changde; Luo, Ali; Yang, Haifeng; Hou, Wen; Guo, Yanxin

    2016-03-01

    One of the most important aims of astronomical data mining is to systematically search for specific rare objects in a massive spectral data set, given a small fraction of identified samples with the same type. Most existing methods are mainly based on binary classification, which usually suffers from incompleteness when there are too few known samples. Rank-based methods could provide good solutions for such cases. After investigating several algorithms, a method combining a bipartite ranking model with bootstrap aggregating techniques was developed in this paper. The method was applied while searching for carbon stars in the spectral data of Sloan Digital Sky Survey Data Release 10 and compared with several other popular methods used for data mining. Experimental results validate that the proposed method is not only the most effective but also the least time-consuming technique among its competitors when searching for rare spectra in a large but unlabeled data set.

  2. A novel method of retrieving the polarization qubits after being transmitted in turbid media

    NASA Astrophysics Data System (ADS)

    Xu, Qiang; Guo, Zhongyi; Tao, Qiangqiang; Jiao, Weiyan; Qu, Shiliang; Gao, Jun

    2015-03-01

    In this paper, we have mainly investigated the reconstruction of the polarization states of the incident light which passed through the turbid atmospheric media. Here, a novel polarization retrieve (PR) method is established using a Monte Carlo simulation algorithm, which is proposed to study the influence of particle scattering. The polarization states of the initial field could be retrieved accurately according to the polarization states of the scattered field and the Mueller matrix. In the case of a single homogeneous medium, the mean error of retrieved polarization is close to zero. We have also applied this method to complex atmospheric environments such as random-sized distribution particles and various index of refraction media. By comparison with the existing polarization maintaining method, the results indicate that the PR method is more applicable to disordered media with relatively larger particles. Moreover, the errors of the retrieved degree of polarization are below 0.11%, and the errors of the retrieved angle of polarization are below 0.54% in our mixed media model. So, this work will be very significant for polarizing quantum secure communication in scattering medium over a long-distance scope.

  3. Evaluation of a content-based retrieval system for blood cell images with automated methods.

    PubMed

    Seng, Woo Chaw; Mirisaee, Seyed Hadi

    2011-08-01

    Content-based image retrieval techniques have been extensively studied for the past few years. With the growth of digital medical image databases, the demand for content-based analysis and retrieval tools has been increasing remarkably. Blood cell image is a key diagnostic tool for hematologists. An automated system that can retrieved relevant blood cell images correctly and efficiently would save the effort and time of hematologists. The purpose of this work is to develop such a content-based image retrieval system. Global color histogram and wavelet-based methods are used in the prototype. The system allows users to search by providing a query image and select one of four implemented methods. The obtained results demonstrate the proposed extended query refinement has the potential to capture a user's high level query and perception subjectivity by dynamically giving better query combinations. Color-based methods performed better than wavelet-based methods with regard to precision, recall rate and retrieval time. Shape and density of blood cells are suggested as measurements for future improvement. The system developed is useful for undergraduate education.

  4. Retrieval of Earthshine Spectra Using Evolutionary Computational Methods as Analogs for Extra-Solar Planetary Spectra

    NASA Astrophysics Data System (ADS)

    Terrile, R. J.; Tinetti, G.; Lee, S.; Fink, W.; Huntsberger, T.; von Allmen, P.; Tisdale, E. R.

    2006-05-01

    The spectral information provided by the next generation of extra-solar planet exploration missions will be averaged over the visible disk and the exposure time. Most probably, the interpretation of the observed spectra will not be unique, but families of solutions will provide equally good explanations of the spectral features (degeneracy). Traditional retrieval techniques developed to study the environments of planets in our solar system are inadequate to analyze disk/time-averaged spectra because they assume homogeneous environments, short observational time scales and search only for solutions belonging to the local domain of the initial conditions. We developed an innovative technique that couples evolutionary computational methods to a 3D model that simulates the spectral response of the planet rotating (Tinetti et al., 2005). We have performed a set of preliminary experiments in retrieving the earthshine spectrum recorded by Woolf et al. (2002): nine weighting parameters were retrieved, corresponding to different surface/cloud types (ocean, forest, grass, ground, tundra, ice, high/medium/low clouds) uniformly distributed over 48 planetary pixels. Two distinct retrieval experiments were run: i) evolution of one large solution population with 1000 individuals and ii) evolution of multiple solution islands with 100 individuals in each island. These two experiments returned over 2700 automatically generated retrievals satisfying the error criterion (fitness) of 10% least squares match to the observed spectra. The spectral retrieval procedure with this reduced set of parameters already resulted in a high quality fit of the earthshine spectrum, in agreement with ground truth. The retrieved solutions were divided into classes of spectral fit using clustering tools, which helped visualize the degeneracy in the set of solutions. We have also repeated the experiment using non-uniformly distributed 3 cloud types over ground- truth surface types in 22 illuminated pixels

  5. Retrieval of Extra-Solar Planetary Spectra Using Evolutionary Computational Methods

    NASA Astrophysics Data System (ADS)

    Terrile, R. J.; Fink, W.; Huntsberger, T.; Lee, S.; Tisdale, E. R.; Tinetti, G.; von Allmen, P.

    2005-12-01

    The spectral information provided by the next generation of extra-solar planet exploration missions will be averaged over the visible disk and the exposure time. Most probably, the interpretation of the observed spectra will not be unique, but families of solutions will provide equally good explanations of the spectral features (degeneracy). Traditional retrieval techniques developed to study the environments of planets in our solar system are inadequate to analyze disk/time-averaged spectra because they assume homogeneous environments, short observational time scales and search only for solutions belonging to the local domain of the initial conditions. We developed an innovative technique that couples evolutionary computational methods to a 3D model that simulates the spectral response of the planet rotating (Tinetti et al., 2005). We have performed a set of preliminary experiments in retrieving the earthshine spectrum recorded by Woolf et al. (2002): nine weighting parameters were retrieved, corresponding to different surface/cloud types (ocean, forest, grass, ground, tundra, ice, high/medium/low clouds) uniformly distributed over 48 planetary pixels. Two distinct retrieval experiments were run: i) evolution of one large solution population with 1000 individuals and ii) evolution of multiple solution islands with 100 individuals in each island. These two experiments returned over 2700 automatically generated retrievals satisfying the error criterion (fitness) of 10% least squares match to the observed spectra. The spectral retrieval procedure with this reduced set of parameters already resulted in a high quality fit of the earthshine spectrum, in agreement with ground truth. The retrieved solutions were divided into classes of spectral fit using clustering tools, which helped visualize the degeneracy in the set of solutions. As a next step we are repeating the experiment using non-uniformly distributed 9 surface/cloud types in 12 planetary pixels (108 retrieved

  6. Texture based feature extraction methods for content based medical image retrieval systems.

    PubMed

    Ergen, Burhan; Baykara, Muhammet

    2014-01-01

    The developments of content based image retrieval (CBIR) systems used for image archiving are continued and one of the important research topics. Although some studies have been presented general image achieving, proposed CBIR systems for archiving of medical images are not very efficient. In presented study, it is examined the retrieval efficiency rate of spatial methods used for feature extraction for medical image retrieval systems. The investigated algorithms in this study depend on gray level co-occurrence matrix (GLCM), gray level run length matrix (GLRLM), and Gabor wavelet accepted as spatial methods. In the experiments, the database is built including hundreds of medical images such as brain, lung, sinus, and bone. The results obtained in this study shows that queries based on statistics obtained from GLCM are satisfied. However, it is observed that Gabor Wavelet has been the most effective and accurate method.

  7. Calcium-sensitive immunoaffinity chromatography: Gentle and highly specific retrieval of a scarce plasma antigen, collectin-LK (CL-LK).

    PubMed

    Henriksen, Maiken L; Madsen, Kirstine L; Skjoedt, Karsten; Hansen, Soren

    2014-11-01

    Immunoaffinity chromatography is a powerful fractionation technique that has become indispensable for protein purification and characterization. However, it is difficult to retrieve bound proteins without using harsh or denaturing elution conditions, and the purification of scarce antigens to homogeneity may be impossible due to contamination with abundant antigens. In this study, we purified the scarce, complement-associated plasma protein complex, collectin LK (CL-LK, complex of collectin liver 1 and kidney 1), by immunoaffinity chromatography using a calcium-sensitive anti-collectin-kidney-1 mAb. This antibody was characterized by binding to CL-LK at hypo- and physiological calcium concentrations and dissociated from CK-LK at hyperphysiological concentrations of calcium. We purified CL-LK from plasma to a purity of 41% and a yield of 38%, resulting in a purification factor of more than 88,000 in a single step. To evaluate the efficiency of this new purification scheme, we purified CL-LK using the same calcium-sensitive mAb in combination with acidic elution buffer and by using calcium-dependent anti-CL-K1 mAbs in combination with EDTA elution buffer. We found that calcium-sensitive immunoaffinity chromatography was superior to the traditional immunoaffinity chromatographies and resulted in a nine-fold improvement of the purification factor. The technique is applicable for the purification of proteins in complex mixtures by single-step fractionation without the denaturation of eluted antigens, and it allows for the purification of scarce proteins that would have otherwise been impossible to purify and, hence, to characterize. This technique may also potentially be applied for the purification of proteins that only interact with calcium ions at hyperphysiological concentrations.

  8. 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…

  9. An Information Retrieval Model Based on Vector Space Method by Supervised Learning.

    ERIC Educational Resources Information Center

    Tai, Xiaoying; Ren, Fuji; Kita, Kenji

    2002-01-01

    Proposes a method to improve retrieval performance of the vector space model by using users' relevance feedback. Discusses the use of singular value decomposition and the latent semantic indexing model, and reports the results of two experiments that show the effectiveness of the proposed method. (Author/LRW)

  10. 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…

  11. A neural network based error correction method for radio occultation electron density retrieval

    NASA Astrophysics Data System (ADS)

    Pham, Viet-Cuong; Juang, Jyh-Ching

    2015-12-01

    Abel inversion techniques have been widely employed to retrieve electron density profiles (EDPs) from radio occultation (RO) measurements, which are available by observing Global Navigation Satellite System (GNSS) satellites from low-earth-orbit (LEO) satellites. It is well known that the ordinary Abel inversion might introduce errors in the retrieval of EDPs when the spherical symmetry assumption is violated. The error, however, is case-dependent; therefore it is desirable to associate an error index or correction coefficient with respect to each retrieved EDP. Several error indices have been proposed but they only deal with electron density at the F2 peak and suffer from some drawbacks. In this paper we propose an artificial neural network (ANN) based error correction method for EDPs obtained by the ordinary Abel inversion. The ANN is first trained to learn the relationship between vertical total electron content (TEC) measurements and retrieval errors at the F2 peak, 220 km and 110 km altitudes; correction coefficients are then estimated to correct the retrieved EDPs at these three altitudes. Experiments using the NeQuick2 model and real FORMOSAT-3/COSMIC RO geometry show that the proposed method outperforms existing ones. Real incoherent scatter radar (ISR) measurements at the Jicamarca Radio Observatory and the global TEC map provided by the International GNSS Service (IGS) are also used to valid the proposed method.

  12. [A new retrieval method for ozone concentration at the troposphere based on differential absorption lidar].

    PubMed

    Fan, Guang-Qiang; Liu, Jian-Guo; Liu, Wen-Qing; Lu, Yi-Huai; Zhang, Tian-Shu; Dong, Yun-Sheng; Zhao, Xue-Song

    2012-12-01

    Aerosols interfere with differential absorption lidar ozone concentration measurement and can introduce significant errors. A new retrieval method was introduced, and ozone concentration and aerosol extinction coefficient were gained simultaneously based on the retrieval method. The variables were analyzed by experiment including aerosol lidar ratio, aerosol wavelength exponent, and aerosol-molecular ratio at the reference point. The results show that these parameters introduce error less than 8% below 1 km. The measurement error derives chiefly from signal noise and the parameters introduce error less than 3% above 1 km. Finally the vertical profile of tropospheric ozone concentration and aerosol extinction coefficient were derived by using this algorithm. The retrieval results of the algorithm and traditional dual-wavelength difference algorithm are compared and analyzed. Experimental results indicate that the algorithm is feasible, and the algorithm can reduce differential absorption lidar measurement error introduced by aerosol.

  13. Noninvasive method for retrieval of broken dental implant abutment screw

    PubMed Central

    Gooty, Jagadish Reddy; Palakuru, Sunil Kumar; Guntakalla, Vikram Reddy; Nera, Mahipal

    2014-01-01

    Dental implants made of titanium for replacement of missing teeth are widely used because of ease of technical procedure and high success rate, but are not free of complications and may fail. Fracturing of the prosthetic screw continues to be a problem in restorative practice and great challenge to remove the fractured screw conservatively. This case report describes and demonstrates the technique of using an ultrasonic scaler in the removal of the fracture screw fragment as a noninvasive method without damaging the hex of implants. PMID:24963261

  14. Retrieval of Temperature and Water Vapour from Multiple Channel Lidar Systems Using an Optimal Estimation Method

    NASA Astrophysics Data System (ADS)

    Sica, Robert; Haefele, Alexander

    2016-04-01

    While the application of optimal estimation methods (OEMs) is well-known for the retrieval of atmospheric parameters from passive instruments, active instruments have typically not employed the OEM. For instance, the measurement of temperature in the middle atmosphere with Rayleigh-scatter lidars is an important technique for assessing atmospheric change. Current retrieval schemes for these temperatures have several shortcomings which can be overcome using an OEM. Forward models have been constructed that fully characterize the measurement and allow the simultaneous retrieval of temperature, dead time and background. The OEM allows a full uncertainty budget to be obtained on a per profile basis that includes, in addition to the statistical uncertainties, the smoothing error and uncertainties due to Rayleigh extinction, ozone absorption, the lidar constant, nonlinearity in the counting system, variation of the Rayleigh-scatter cross section with altitude, pressure, acceleration due to gravity and the variation of mean molecular mass with altitude. The vertical resolution of the temperature profile is found at each height, and a quantitative determination is made of the maximum height to which the retrieval is valid. A single temperature profile can be retrieved from measurements with multiple channels that cover different height ranges, vertical resolutions and even different detection methods. The OEM employed is shown to give robust estimates of temperature consistent with previous methods, while requiring minimal computational time. Retrieval of water vapour mixing ratio from vibrational Raman scattering lidar measurements is another example where an OEM offers a considerable advantage over the standard analysis technique, with the same advantages as discussed above for Rayleigh-scatter temperatures but with an additional benefit. The conversion of the lidar measurement into mixing ratio requires a calibration constant to be employed. Using OEM the calibration

  15. Retrieval of Temperature and Water Vapour From Multiple Channel Lidar Systems Using an Optimal Estimation Method

    NASA Astrophysics Data System (ADS)

    Sica, Robert; Haefele, Alexander

    2015-04-01

    While the application of optimal estimation methods (OEMs) is well-known for the retrieval of atmospheric parameters from passive instruments, active instruments have typically not employed the OEM. For instance, the measurement of temperature in the middle atmosphere with Rayleigh-scatter lidars is an important technique for assessing atmospheric change. Current retrieval schemes for these temperatures have several shortcomings which can be overcome using an OEM. Forward models have been constructed that fully characterize the measurement and allow the simultaneous retrieval of temperature, dead time and background. The OEM allows a full uncertainty budget to be obtained on a per profile basis that includes, in addition to the statistical uncertainties, the smoothing error and uncertainties due to Rayleigh extinction, ozone absorption, the lidar constant, nonlinearity in the counting system, variation of the Rayleigh-scatter cross section with altitude, pressure, acceleration due to gravity and the variation of mean molecular mass with altitude. The vertical resolution of the temperature profile is found at each height, and a quantitative determination is made of the maximum height to which the retrieval is valid. A single temperature profile can be retrieved from measurements with multiple channels that cover different height ranges, vertical resolutions and even different detection methods. The OEM employed is shown to give robust estimates of temperature consistent with previous methods, while requiring minimal computational time. Retrieval of water vapour mixing ratio from vibrational Raman scattering lidar measurements is another example where an OEM offers a considerable advantage over the standard analysis technique, with the same advantages as discussed above for Rayleigh-scatter temperatures but with an additional benefit. The conversion of the lidar measurement into mixing ratio requires a calibration constant to be employed. Using OEM the calibration

  16. 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

  17. W-transform method for feature-oriented multiresolution image retrieval

    SciTech Connect

    Kwong, M.K.; Lin, B.

    1995-07-01

    Image database management is important in the development of multimedia technology. Since an enormous amount of digital images is likely to be generated within the next few decades in order to integrate computers, television, VCR, cables, telephone and various imaging devices. Effective image indexing and retrieval systems are urgently needed so that images can be easily organized, searched, transmitted, and presented. Here, the authors present a local-feature-oriented image indexing and retrieval method based on Kwong, and Tang`s W-transform. Multiresolution histogram comparison is an effective method for content-based image indexing and retrieval. However, most recent approaches perform multiresolution analysis for whole images but do not exploit the local features present in the images. Since W-transform is featured by its ability to handle images of arbitrary size, with no periodicity assumptions, it provides a natural tool for analyzing local image features and building indexing systems based on such features. In this approach, the histograms of the local features of images are used in the indexing, system. The system not only can retrieve images that are similar or identical to the query images but also can retrieve images that contain features specified in the query images, even if the retrieved images as a whole might be very different from the query images. The local-feature-oriented method also provides a speed advantage over the global multiresolution histogram comparison method. The feature-oriented approach is expected to be applicable in managing large-scale image systems such as video databases and medical image databases.

  18. Impact of computational methods and spectral models on the retrieval of optical properties via spectral optimization.

    PubMed

    Huang, Shaohui; Li, Yonghong; Shang, Shaoping; Shang, Shaoling

    2013-03-11

    Spectral optimization algorithm (SOA) is a well-accepted scheme for the retrieval of water constituents from the measurement of ocean color radiometry. It defines an error function between the input and output remote sensing reflectance spectrum, with the latter modeled with a few variables that represent the optically active properties, while the variables are solved numerically by minimizing the error function. In this paper, with data from numerical simulations and field measurements as input, we evaluate four computational methods for minimization (optimization) for their efficiency and accuracy on solutions, and illustrate impact of bio-optical models on the retrievals. The four optimization routines are the Levenberg-Marquardt (LM), the Generalized Reduced Gradient (GRG), the Downhill Simplex Method (Amoeba), and the Simulated Annealing-Downhill Simplex (i.e. SA + Amoeba, hereafter abbreviated as SAA). The Garver-Siegel-Maritorena SOA model is used as a base to test these computational methods. It is observed that 1) LM is the fastest method, but SAA has the largest number of valid retrievals; 2) the quality of final solutions are strongly influenced by the forms of spectral models (or eigen functions); and 3) dynamically-varying eigen functions are necessary to obtain smaller errors for both reflectance spectrum and retrievals. Results of this study provide helpful guidance for the selection of a computational method and spectral models if an SOA scheme is to be used to process ocean color images.

  19. 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

  20. Dual-Force ISOMAP: A New Relevance Feedback Method for Medical Image Retrieval

    PubMed Central

    Shen, Hualei; Tao, Dacheng; Ma, Dianfu

    2013-01-01

    With great potential for assisting radiological image interpretation and decision making, content-based image retrieval in the medical domain has become a hot topic in recent years. Many methods to enhance the performance of content-based medical image retrieval have been proposed, among which the relevance feedback (RF) scheme is one of the most promising. Given user feedback information, RF algorithms interactively learn a user’s preferences to bridge the “semantic gap” between low-level computerized visual features and high-level human semantic perception and thus improve retrieval performance. However, most existing RF algorithms perform in the original high-dimensional feature space and ignore the manifold structure of the low-level visual features of images. In this paper, we propose a new method, termed dual-force ISOMAP (DFISOMAP), for content-based medical image retrieval. Under the assumption that medical images lie on a low-dimensional manifold embedded in a high-dimensional ambient space, DFISOMAP operates in the following three stages. First, the geometric structure of positive examples in the learned low-dimensional embedding is preserved according to the isometric feature mapping (ISOMAP) criterion. To precisely model the geometric structure, a reconstruction error constraint is also added. Second, the average distance between positive and negative examples is maximized to separate them; this margin maximization acts as a force that pushes negative examples far away from positive examples. Finally, the similarity propagation technique is utilized to provide negative examples with another force that will pull them back into the negative sample set. We evaluate the proposed method on a subset of the IRMA medical image dataset with a RF-based medical image retrieval framework. Experimental results show that DFISOMAP outperforms popular approaches for content-based medical image retrieval in terms of accuracy and stability. PMID:24391891

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

    SciTech Connect

    Wu, Zhao; Gao, Kun; Chen, Jian; Wang, Dajiang; Wang, Shenghao; Chen, Heng; Bao, Yuan; Shao, Qigang; Wang, Zhili; Zhang, Kai; Zhu, Peiping; Wu, Ziyu

    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 the 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.

  2. 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…

  3. 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…

  4. 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…

  5. 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…

  6. A Proposed Method of Measuring the Utility of Individual Information Retrieval Tools.

    ERIC Educational Resources Information Center

    Meadow, Charles T.

    1996-01-01

    Proposes a method of evaluating information retrieval systems by concentrating on individual tools (commands, their menus or graphic interface equivalents, or a move/stratagem). A user would assess the relative success of a small part of a search, and every tool used in that part would be credited with a contribution to the result. Cumulative…

  7. 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…

  8. Wave propagation retrieval method for metamaterials: Unambiguous restoration of effective parameters

    NASA Astrophysics Data System (ADS)

    Andryieuski, Andrei; Malureanu, Radu; Lavrinenko, Andrei V.

    2009-11-01

    In this Brief report we propose a direct method of effective-parameters restoration that is based on the wave propagation phenomenon. It is easy in implementation, has no unambiguity in retrieving effective properties and is applicable to thick metamaterial (MTM) slabs. The method is validated on the case studies of fishnet, split cube in carcass, and Jerusalem cross MTMs. The constraints of the method are designated.

  9. A Method of Protein Model Classification and Retrieval Using Bag-of-Visual-Features

    PubMed Central

    Ma, Ziping; Kang, Baosheng; Lu, Ke

    2014-01-01

    In this paper we propose a novel visual method for protein model classification and retrieval. Different from the conventional methods, the key idea of the proposed method is to extract image features of proteins and measure the visual similarity between proteins. Firstly, the multiview images are captured by vertices and planes of a given octahedron surrounding the protein. Secondly, the local features are extracted from each image of the different views by the SURF algorithm and are vector quantized into visual words using a visual codebook. Finally, KLD is employed to calculate the similarity distance between two feature vectors. Experimental results show that the proposed method has encouraging performances for protein retrieval and categorization as shown in the comparison with other methods. PMID:25258644

  10. 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.

  11. An overview of the design and methods for retrieving high-quality studies for clinical care

    PubMed Central

    Wilczynski, Nancy L; Morgan, Douglas; Haynes, R Brian

    2005-01-01

    Background With the information explosion, the retrieval of the best clinical evidence from large, general purpose, bibliographic databases such as MEDLINE can be difficult. Both researchers conducting systematic reviews and clinicians faced with a patient care question are confronted with the daunting task of searching for the best medical literature in electronic databases. Many have advocated the use of search filters or "hedges" to assist with the searching process. The purpose of this report is to describe the design and methods of a study that set out to develop optimal search strategies for retrieving sound clinical studies of health disorders in large electronics databases. Objective To describe the design and methods of a study that set out to develop optimal search strategies for retrieving sound clinical studies of health disorders in large electronic databases. Design An analytic survey comparing hand searches of 170 journals in the year 2000 with retrievals from MEDLINE, EMBASE, CINAHL, and PsycINFO for candidate search terms and combinations. The sensitivity, specificity, precision, and accuracy of unique search terms and combinations of search terms were calculated. Conclusion A study design modeled after a diagnostic testing procedure with a gold standard (the hand search of the literature) and a test (the search terms) is an effective way of developing, testing, and validating search strategies for use in large electronic databases. PMID:15969765

  12. 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.

  13. 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.

  14. 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.

  15. Fresnel phase retrieval method using an annular lens array on an SLM

    NASA Astrophysics Data System (ADS)

    Loriot, V.; Mendoza-Yero, O.; Pérez-Vizcaíno, J.; Mínguez-Vega, G.; de Nalda, R.; Bañares, L.; Lancis, J.

    2014-10-01

    Wavefront aberrations play a major role when focusing an ultrashort laser pulse to a high-quality focal spot. Here, we report a novel method to measure and correct wavefront aberrations of a 30-fs pulsed laser beam. The method only requires a programmable liquid-crystal spatial light modulator and a camera. Wavefront retrieval is based on pupil segmentation with an annular lens array, which allows us to determine the local phase that minimizes focusing errors due to wavefront aberrations. Our method provides accurate results even when implemented with low dynamic range cameras and polychromatic beams. Finally, the retrieved phase is added to a diffractive lens codified onto the spatial light modulator to experimentally demonstrate near-diffraction-limited femtosecond beam focusing without refractive components.

  16. Retrieval of particle size distribution in the dependent model using the moment method.

    PubMed

    Sun, Xiaogang; Tang, Hong; Dai, Jingmin

    2007-09-03

    The problem of determining particle size distribution using the moment method in the spectral extinction technique is studied. The feasibility and reliability of the retrieval of spherical particle size distribution using the moment method are investigated. The single spherical particle extinction efficiency, which is derived theoretically using the Mie's solution to Maxwell's equation, is approximated with a higher order polynomial in order to apply the moment method. Simulation and experimental results indicate that a fairly reasonable representation of the particle size distribution can be obtained using the moment method in the dependent model algorithm. The method has advantages of simplicity, rapidity, and suitability for in-line particle size measurement.

  17. Retrieval of Aerosol information from UV measurement by using optimal estimation method

    NASA Astrophysics Data System (ADS)

    KIM, M.; Kim, J.; Jeong, U.; Kim, W. V.; Kim, S. K.; Lee, S. D.; Moon, K. J.

    2014-12-01

    An algorithm to retrieve aerosol optical depth (AOD), single scattering albedo (SSA), and aerosol loading height is developed for GEMS (Geostationary Environment Monitoring Spectrometer) measurement. The GEMS is planned to be launched in geostationary orbit in 2018, and employs hyper-spectral imaging with 0.6 nm resolution to observe solar backscatter radiation in the UV and Visible range. In the UV range, the low surface contribution to the backscattered radiation and strong interaction between aerosol absorption and molecular scattering can be advantageous in retrieving aerosol information such as AOD and SSA [Torres et al., 2007; Torres et al., 2013; Ahn et al., 2014]. However, the large contribution of atmospheric scattering results in the increase of the sensitivity of the backward radiance to aerosol loading height. Thus, the assumption of aerosol loading height becomes important issue to obtain accurate result. Accordingly, this study focused on the simultaneous retrieval of aerosol loading height with AOD and SSA by utilizing the optimal estimation method. For the RTM simulation, the aerosol optical properties were analyzed from AERONET inversion data (level 2.0) at 46 AERONET sites over ASIA. Also, 2-channel inversion method is applied to estimate a priori value of the aerosol information to solve the Lavenberg Marquardt equation. The GEMS aerosol algorithm is tested with OMI level-1B dataset, a provisional data for GEMS measurement, and the result is compared with OMI standard aerosol product and AERONET values. The retrieved AOD and SSA show reasonable distribution compared with OMI products, and are well correlated with the value measured from AERONET. However, retrieval uncertainty in aerosol loading height is relatively larger than other results.

  18. [Concentration retrieving method of SO2 using differential optical absorption spectroscopy based on statistics].

    PubMed

    Liu, Bin; Sun, Chang-Ku; Zhang, Chi; Zhao, Yu-Mei; Liu, Jun-Ping

    2011-01-01

    A concentration retrieving method using statistics is presented, which is applied in differential optical absorption spectroscopy (DOAS) for measuring the concentration of SO2. The method uses the standard deviation of the differential absorption to represents the gas concentration. Principle component analysis (PCA) method is used to process the differential absorption spectrum. In the method, the basis data for the concentration retrieval of SO2 is the combination of the PCA processing result, the correlation coefficient, and the standard deviation of the differential absorption. The method is applied to a continuous emission monitoring system (CEMS) with optical path length of 0.3 m. Its measuring range for SO2 concentration is 0-5 800 mg x m(-3). The nonlinear calibration and the temperature compensation for the system were executed. The full scale error of the retrieving concentration is less than 0.7% FS. And the measuring result is -4.54 mg x m(-3) when the concentration of SO2 is zero.

  19. Method of content-based image retrieval for a spinal x-ray image database

    NASA Astrophysics Data System (ADS)

    Krainak, Daniel M.; Long, L. Rodney; Thoma, George R.

    2002-05-01

    The Lister Hill National Center for Biomedical Communications, a research and development division of the National Library of Medicine (NLM) maintains a digital archive of 17,000 cervical and lumbar spine images collected in the second National Health and Nutrition Examination Survey (NHANES II) conducted by the National Center for Health Statistics (NCHS). Classification of the images for the osteoarthritis research community has been a long-standing goal of researchers at the NLM, collaborators at NCHS, and the National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), and capability to retrieve images based on geometric characteristics of the vertebral bodies is of interest to the vertebral morphometry community. Automated or computer-assisted classification and retrieval methods are highly desirable to offset the high cost of manual classification and manipulation by medical experts. We implemented a prototype system for a database of 118 spine x-rays and health survey text data related to these x-rays. The system supports conventional text retrieval, as well as retrieval based on shape similarity to a user-supplied vertebral image or sketch.

  20. A coordinated retrieval method for sea surface salinity based on SMOS and ocean color data

    NASA Astrophysics Data System (ADS)

    Chen, Peng; Wang, Tianyu; Mao, Zhihua; Bai, Yan; Hao, Zengzhou

    2016-10-01

    A coordinated retrieval method for sea surface salinity based on SMOS and ocean color data was developed. The method retrieved sea surface salinity in open sea based on SMOS data, and those with much RFIs in the coastal area using ocean color data, aCDOM. Tight relationships between surface water salinity and in situ aCDOM were found during the cruises in the Yangtze River estuary on April 2013 and Hangzhou Bay in May 2014, distributions of aCDOM revealed gradual downward trends of magnitudes, as water flowed down the Yangtze River estuary into the ECS coast. A dilution process was detected as water flowed down the Yangtze River and into the ECS coast. Thus, a salinity inversion model from the negative relationship between salinity and aCDOM was developed firstly. Then we matched the SSS products with different spatial resolution retrieved based on SMOS and ocean color and combined them. In the end, we compared the SSS measurements between those based on only SMOS data and those based on method in this paper, and found that the method can make up the phenomenon of lack of data effectively.

  1. A comparison of three retrieval methods with single Doppler radar data

    NASA Astrophysics Data System (ADS)

    Zhou, Shenghui; Wei, Ming; Gao, Li; Wang, Hao; Zeng, Qingfeng; Yang, Kun

    2011-11-01

    In single Doppler radar wind retrieval technique there are three methods proposed in recently years, which is VAP, VPP and SVVP method. Three methods were employed to retrieve wind field with the purpose to find out which one is more suitable in practice according their accuracy by using synthetic data and real data. When tests applied with uniform data, the orders of magnitude for relative error of radial velocity is 10-13 for SVVP, much lower than that of VAP and VPP which both are 10-4. Furthermore, the results under condition of wind direction unchanged and wind velocity varied linearity with altitude are 10-8, 10-3, 10-3 for SVVP, VPP and VAP, respectively. In real wind field of typhoon "Pearl", the authenticity of surrounding wind and wind shear retrieved by SVVP and VPP is better than VAP, the deviation of simulation would be increased at some points missing data. Relative errors of radial velocity achieved by VAP, VPP and SVVP are 7.02, 5.78 and 3.1 respectively. It indicated that SVVP method's performance is better than that of other two and suitable in practical applications.

  2. 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.

  3. Ptychographic phase retrieval method for characterizing ultra-precise ellipsoidal mirrors

    NASA Astrophysics Data System (ADS)

    Takeo, Yoko; Saito, Takahiro; Mimura, Hidekazu

    2015-10-01

    Focusing and imaging optics can be characterized by evaluating the wavefront error of the focused beam. We have bean developing a ptychographic phase retrieval method using a visible laser to measure the wavefront error. In this study, the measurement accuracy of the method is increased by improving both the phase retrieval algorithm and the experimental setup. The system is applied to the characterization of an ellipsoidal mirror used for the focusing of soft X-rays. The posture of the mirror can be measured with a resolution of 1.4 μrad. The wavefront error originating from the surface profile error can be detected with an accuracy of 0.01λ (root mean square).

  4. 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…

  5. 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…

  6. A Method for Unbiased High-Resolution Aerosol Retrieval from Landsat.

    NASA Astrophysics Data System (ADS)

    Lyapustin, Alexei; Williams, D. L.; Markham, B.; Irons, J.; Holben, B.; Wang, Y.

    2004-06-01

    Because the land surface reflectance varies spatially, the atmospheric radiative transfer over land in clear-sky conditions is essentially three-dimensional. This is manifested through horizontal radiative fluxes that blur satellite images. It is important that the atmospheric blurring systematically increases the apparent brightness of the dark pixels. As a consequence, there are systematic biases in the satellite products of aerosol optical thickness and surface albedo over dark targets based on 1D theory, which may have a negative impact on climate research. Below, a new dark target method is presented for unbiased simultaneous retrieval of the aerosol model and optical thickness over land from Landsat Enhanced Thematic Mapper Plus (ETM+) data, based on 3D radiative transfer theory. The method automatically selects an aerosol model from a large set of candidate models using a statistical approach of the probability distribution function. The dark target method of aerosol retrieval in the blue and red bands relies on prediction of the surface reflectance in these bands from the shortwave infrared region (2.1 2.2 μm) based on the linear regression. In the Moderate Resolution Imaging Spectroradiometer (MODIS) algorithm, the regression coefficients are constants, whereas different studies indicate that they have seasonal and geographic variations. The work here shows that the accuracy of aerosol retrieval over land can be significantly increased based on ancillary information on the regional and seasonal distribution of the regression coefficients. This information, which is called surface climatology, can be derived globally around Aerosol Robotic Network (AERONET) sites, using AERONET aerosol and water vapor information for accurate atmospheric correction. This paper describes the developed method in application to Landsat data and its initial validation with AERONET measurements for a set of ETM+ images of the Washington Baltimore area, and studies biases of 1D

  7. [A new method for detection and erradication of Helicobacter pylori infection by stool antigens test].

    PubMed

    Amèndola, R; Doweck, J; Katz, J; Racca, J; Menendez, G; Schenone, L; Farìas, R; Barrantes, C; Quintanta, C; Zerbo, O; Kogan, Z; Valero, J; Bartellini, M A; Questa, U; Luna, P; Corti, R E

    2002-01-01

    Nowadays technics for Helicobacter pylori detection in stools like culture, and PCR, are expensive and difficult to perform. The aim of this study was to evaluate ELISA test efficacy for detection of H. Pylori antigens in stools comparing this results with standarized technics like histology (Giemsa), ureasa test and UBT C 14. 26 patients were evaluated in this study, ages between 15-75 with upper gastrointestinal symptoms; all of them required gastroduodenal endoscopy, status H. Pylori was determined with methods upon mentioned. 24 hours after endoscopy H. Pylori antigens in stools with the technique Premier Platinum Htsa, Elisa were determined. The detection of H. Pylori antigens in stools accurately identified active H. Pylori infection. The performance characteristics of this non-invasive method was similar in sensibility and specificity to conventional tests.

  8. Vibration-resistant phase retrieval method with contrast compensation for phase-shifting interferometry

    NASA Astrophysics Data System (ADS)

    Liu, Qian; He, Huabin; Yuan, Daocheng; He, Jianguo; Ji, Fang

    2017-04-01

    Vibration hinders the application of phase-shifting interferometry (PSI) to on-machine test and large-aperture mirror measurement. The investigation of PSI fringe disturbed by vibration indicates that, besides tilt-shifting error, inter- and intra-frame contrast variation is significant. The contrast variation is another dominant error source in phase retrieval of PSI. An inter- and intra-frame contrast compensation method is proposed here to retrieve wavefront phase from interferograms subjected to vibration. The method constructs algebraic equations with interferogram data and solves equations using iterative procedures. Experiments validate its effectiveness and manifest its capability to suppress vibration-induced error over a large frequency region. To enhance the calculation efficiency, a spatial subsampling strategy is proposed. Practical testing shows that subsampling reduces calculation time exponentially and preserves retrieval accuracy and spatial resolution. The proposed method, of which the unique ability is compensating the tilt-shifting error and fringe blur caused by vibration, predicates an effective and low-cost solution for PSI applied in vibration.

  9. Distributed data organization and parallel data retrieval methods for huge laser scanner point clouds

    NASA Astrophysics Data System (ADS)

    Hongchao, Ma; Wang, Zongyue

    2011-02-01

    This paper proposes a novel method for distributed data organization and parallel data retrieval from huge volume point clouds generated by airborne Light Detection and Ranging (LiDAR) technology under a cluster computing environment, in order to allow fast analysis, processing, and visualization of the point clouds within a given area. The proposed method is suitable for both grid and quadtree data structures. As for distribution strategy, cross distribution of the dataset would be more efficient than serial distribution in terms of non-redundant datasets, since a dataset is more uniformly distributed in the former arrangement. However, redundant datasets are necessary in order to meet the frequent need of input and output operations in multi-client scenarios: the first copy would be distributed by a cross distribution strategy while the second (and later) would be distributed by an iterated exchanging distribution strategy. Such a distribution strategy would distribute datasets more uniformly to each data server. In data retrieval, a greedy algorithm is used to allocate the query task to a data server, where the computing load is lightest if the data block needing to be retrieved is stored among multiple data servers. Experiments show that the method proposed in this paper can satisfy the demands of frequent and fast data query.

  10. Retrieval of Vertical Ozone Profile Using Satellite Solar Occultation Method and Tests of its Sensitivity

    NASA Astrophysics Data System (ADS)

    Cho, Hi-Ku; Yoon, Young-Jun; Park, Jae H.; Lee, Kwang Mok; Tatsuya, Yokota

    1998-06-01

    Recently measurements of atmospheric trace gases from satellite are vigorous. So the development of its data processing algorithm is important. In this study, retrieval of vertical ozone profile from the atmospheric transmittance measured by satellite solar occultation method and its sensitivity to temperature and pressure are investigated. The measured transmittance from satellite is assumed to be given by the limb path transmittance simulated using annual averaged Umkehr data for Seoul. The limb path transmittance between wavelengths 9.89micro m and 10.02micro m is simulated with respect to tangent heights using the ozone data of HALOE SIDS(Hallogen Occultation Experiment Simulated Instrument Data Set) as an initial profile. Other input data such as pressure and temperature are also from HALOE SIDS. Vertical ozone profile is correctly retrieved from the measured transmittance by onion-peeling method from 50km to 11km tangent heights with the vertical resolution of 3km. The bias error of +/- 0.001 in measured transmittance, the forced error of +/- 3K in each layer temperature, and the forced +/- 3% error in each layer pressure are assumed for sensitivity tests. These errors are based on the ADEOS/ILAS error limitation. The error in ozone amount ranges from -6.5% to +6.9% due to transmittance error, from -9.5% to +10.5% due to temperature error, and from -5.1% to +5.4% due to pressure error, respectively. The present study suggests that accurate vertical ozone profile can be retrieved from satellite solar occultation method. Accuracy of vertical temperature profile is especially important in the retrieval of vertical ozone profile.

  11. Development and application of new methods to retrieve vertical structure of precipitation above the ARM CART sites from MMCR measurements

    SciTech Connect

    Matrosov, Sergey

    2010-12-15

    The main objective of this project was to develop, validate and apply remote sensing methods to retrieve vertical profiles of precipitation over the DOE ARM CART sites using currently available remote sensors. While the ARM Program invested very heavily into developments of remote sensing methods and instruments for water vapor and non-precipitating cloud parameter retrievals, precipitation retrievals and studies lagged behind. Precipitation, however, is a crucial part of the water cycle, and without detailed information on rainfall and snowfall, significant improvements in the atmospheric models of different scales (i.e., one of the ARM Program's main goals) is difficult to achieve. Characterization of the vertical atmospheric column above the CART sites is also incomplete without detailed precipitation information, so developments of remote sensing methods for retrievals of parameters in precipitating cloud condition was essential. Providing modelers with retrieval results was also one of the key objectives of this research project.

  12. A comparison of dimensionality reduction methods for retrieval of similar objects in simulation data

    SciTech Connect

    Cantu-Paz, E; Cheung, S S; Kamath, C

    2003-09-23

    High-resolution computer simulations produce large volumes of data. As a first step in the analysis of these data, supervised machine learning techniques can be used to retrieve objects similar to a query that the user finds interesting. These objects may be characterized by a large number of features, some of which may be redundant or irrelevant to the similarity retrieval problem. This paper presents a comparison of six dimensionality reduction algorithms on data from a fluid mixing simulation. The objective is to identify methods that efficiently find feature subsets that result in high accuracy rates. Our experimental results with single- and multi-resolution data suggest that standard forward feature selection produces the smallest feature subsets in the shortest time.

  13. A physical multispectral method for the retrieval of ocean and lake surface temperatures via scanning spectrometer

    NASA Astrophysics Data System (ADS)

    Nalli, Nicholas Rocco

    Accurate measurements of water surface skin temperatures (WST) from satellite are required in numerous research and civil applications. Of particular importance are climate studies which require a high degree of absolute accuracy (≤0.3 K). In this work a physical retrieval methodology is developed for general application to any scanning spectrometer that obtains multispectral IR window radiance measurements. Such instrumentation includes high resolution Fourier transform spectrometer (FTS) systems as well as narrowband channel radiometers. To achieve this a rough surface reflection model is developed to be used in tandem with an emissivity model previously developed by Wu and Smith [1997]. The model assumes the Kirchhoff approximation (valid for IR wavelengths and water surfaces) for rough surface scattering. The wave slope statistics of Cox and Munk [1954, 1955] are then employed for the double integration of reflected rays over zenith and azimuth angle. The otherwise involved computation is performed via Gaussian quadrature using an uplooking fast transmittance model. The full hemispherical model calculation is simplified by the novel concept of a reflection-diffusivity angle. This parameter is a function of wavenumber, viewing angle, wind speed and total uplooking transmittance. A lookup table is generated for convenient application in WST retrieval. The model compares favorably against observed radiance spectra obtained from the Marine Atmospheric Emitted Radiance Interferometer (M-AERI) in the tropical Pacific ocean during the Combined Sensor Program (CSP) research cruise. The improved WST retrieval method which utilizes the reflection model exhibits less scatter and moisture-dependent bias in simulation. The method is applied to microwindow radiance spectra measured by the NPOESS Airborne Sounder Testbed-Interferometer (NAST-I) from the NASA ER-2 during two field campaigns. High resolution lake and sea surface temperature fields are measured which reveal

  14. 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.

  15. Modeling formalin fixation and antigen retrieval with bovine pancreatic ribonuclease A: I—Structural and functional alterations

    PubMed Central

    Rait, Vladimir K; O’Leary, Timothy J; Mason, Jeffrey T

    2006-01-01

    Understanding the chemistry of protein modification by formaldehyde is central to developing improved methods to recover proteins from formalin-fixed paraffin-embedded tissues for proteomic analysis and to improve protein immunoreactivity for immunohistochemical studies. We used biophysical techniques to investigate the effects of formaldehyde treatment on bovine pancreatic ribonuclease A (RNase A). Treatment of RNase A with formaldehyde was shown by gel electrophoresis to lead to the rapid formation of intra- and intermolecular protein cross-links. Thermal studies revealed that these protein cross-links significantly increased the thermal denaturation temperature of RNase A preparations. Analysis of formaldehyde-treated RNase A oligomers isolated by gel chromatography revealed that intramolecular protein cross-links are primarily responsible for the increase in protein thermostability. Formaldehyde treatment also lowered the isoelectric point of the enzyme from 9.45 to the 6.0–7.4 range. Optical spectroscopic studies demonstrated that the formaldehyde-induced modifications did not significantly alter the secondary or tertiary structure of RNase A. Heating formaldehyde-treated RNase A at 65°C resulted in a significant reversal of the protein intra- and intermolecular cross-links and led to a partial restoration of enzymatic activity. PMID:14968117

  16. Evaluation of four methods for the detection of streptococcal group A antigen directly from throat swabs.

    PubMed

    Betriu, C; de la Torre, F; Muñoz, P; Fernández, A; Picazo, J J

    1988-12-01

    We have compared the sensitivity, specificity and reproducibility of four rapid tests for the detection of group A beta-hemolytic streptococci antigen directly from a throat swab. The four methods were very specific, all of them offered reproductibility and surpassed conventional culture in speed and simplicity.

  17. Note: Phase retrieval method for analyzing single-phase displacement interferometry data

    NASA Astrophysics Data System (ADS)

    Chen, X. H.; Zeng, X. L.; Fan, D.; Liu, Q. C.; Bie, B. X.; Zhou, X. M.; Luo, S. N.

    2014-02-01

    We present a phase retrieval method (PRM) for analyzing single-phase displacement interferometry measurements on rapidly changing velocity histories, including photon Doppler velocimetry (PDV). PRM identifies the peaks and valleys as well as zero-crossing points in a PDV time series, performs normalization and extracts point-by-point phase and thus velocity information. PRM does not require a wide time window as in sliding window Fourier transformation, and thus improves the effective temporal resolution. This method is implemented in analyzing PDV data obtained from gas gun experiments, and validated against simultaneous measurements with velocity interferometer system for any reflector.

  18. Note: Phase retrieval method for analyzing single-phase displacement interferometry data

    SciTech Connect

    Chen, X. H.; Zeng, X. L.; Fan, D.; Liu, Q. C.; Bie, B. X.; Zhou, X. M. Luo, S. N.

    2014-02-15

    We present a phase retrieval method (PRM) for analyzing single-phase displacement interferometry measurements on rapidly changing velocity histories, including photon Doppler velocimetry (PDV). PRM identifies the peaks and valleys as well as zero-crossing points in a PDV time series, performs normalization and extracts point-by-point phase and thus velocity information. PRM does not require a wide time window as in sliding window Fourier transformation, and thus improves the effective temporal resolution. This method is implemented in analyzing PDV data obtained from gas gun experiments, and validated against simultaneous measurements with velocity interferometer system for any reflector.

  19. Highly accurate retrieval method of Japanese document images through a combination of morphological analysis and OCR

    NASA Astrophysics Data System (ADS)

    Katsuyama, Yutaka; Takebe, Hiroaki; Kurokawa, Koji; Saitoh, Takahiro; Naoi, Satoshi

    2001-12-01

    We have developed a method that allows Japanese document images to be retrieved more accurately by using OCR character candidate information and a conventional plain text search engine. In this method, the document image is first recognized by normal OCR to produce text. Keyword areas are then estimated from the normal OCR produced text through morphological analysis. A lattice of candidate- character codes is extracted from these areas, and then character strings are extracted from the lattice using a word-matching method in noun areas and a K-th DP-matching method in undefined word areas. Finally, these extracted character strings are added to the normal OCR produced text to improve document retrieval accuracy when u sing a conventional plain text search engine. Experimental results from searches of 49 OHP sheet images revealed that our method has a high recall rate of 98.2%, compared to 90.3% with a conventional method using only normal OCR produced text, while requiring about the same processing time as normal OCR.

  20. 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.

  1. Indirect methods of retrieval of important mesospheric gas constituents from available measurements data

    NASA Astrophysics Data System (ADS)

    Kulikov, Mikhail; Nechaev, Anton; Belikovich, Mikhail; Ermakova, Tatiana; Feigin, Alexander

    2016-04-01

    Observation of minor gas constituents is traditionally considered as one of the fundamental problems in investigations of the Earth's mesosphere and mesopause region. Since direct and regular measurements are still rather scanty, indirect methods are a useful tool. Based on a priori assumptions about possible relationships between measured and retrieved characteristics (for example, photochemical models), they allow one to obtain additional information about the important constituents from available experimental data. In this presentation we discuss, firstly, the restrictions on the use of the ozone steady state equilibrium condition for the retrieval of atomic oxygen and hydrogen concentrations from O2 and OH airglow emissions ratios and O3 concentration measurements. Secondly, we present a statistical Bayesian procedure of retrieving the concentrations of important constituents in mesosphere from available satellite and ground based experimental data. The technique is based on the application of the so-called basic dynamic model of mesospheric photochemistry, which is simplified mathematically correctly in a special manner and describes the most significant reactions between components of the families of odd hydrogen and oxygen. The work was supported by the Russian Science Foundation (Contract No. 15-17-10024).

  2. Enhanced lymph node retrieval from colorectal cancer resections using a simple lymphatic staining method.

    PubMed

    He, Hai-Fei; Zhou, Mei-Qi; Chen, Jun-Qing; Tian, Wei; Cai, Hong-Ke; Chen, Li-Rong; Deng, Yong-Chuan

    2012-01-01

    This study evaluated the effect of lymphatic staining on the number of lymph nodes (LNs) examined and staging in patients with colorectal cancer. Sixty-two consecutive specimens from patients with colorectal cancer resected between February 2009 and April 2010 were randomized to the stained group or the control unstained. Differences in the retrieval, number and size of nodes, and time for retrieval were measured. LN harvest differed significantly with 30±12 and 13±5 (p<0.01) nodes in the stained and the control groups, respectively. Insufficient LN harvest (less than 12 nodes) occurred in 14 cases of the control group and only in 1 case of the stained group (p<0.01). Metastases were confirmed in 57 LNs occurring in 17 cases of the stained group and in 39 nodes occurring in 15 cases of the control group. The mean time for LN retrieval in the stained and control groups were comparable, 27.6±6.9min and 24.7±6.0min (p>0.05), respectively, yet there was a significant difference in the number of LNs (<2mm) (294 vs. 59, respectively, p<0.01) as well as in the number of LNs 2-5mm in size (474 vs. 220, respectively, p<0.01). By lymphatic staining method, more and smaller LNs could be detected, which significantly improved the LN harvest of resected colorectal specimens and reduced cases of insufficient LN harvest.

  3. A Novel Bayesian DNA Motif Comparison Method for Clustering and Retrieval

    PubMed Central

    Margalit, Hanah; Friedman, Nir

    2008-01-01

    Characterizing the DNA-binding specificities of transcription factors is a key problem in computational biology that has been addressed by multiple algorithms. These usually take as input sequences that are putatively bound by the same factor and output one or more DNA motifs. A common practice is to apply several such algorithms simultaneously to improve coverage at the price of redundancy. In interpreting such results, two tasks are crucial: clustering of redundant motifs, and attributing the motifs to transcription factors by retrieval of similar motifs from previously characterized motif libraries. Both tasks inherently involve motif comparison. Here we present a novel method for comparing and merging motifs, based on Bayesian probabilistic principles. This method takes into account both the similarity in positional nucleotide distributions of the two motifs and their dissimilarity to the background distribution. We demonstrate the use of the new comparison method as a basis for motif clustering and retrieval procedures, and compare it to several commonly used alternatives. Our results show that the new method outperforms other available methods in accuracy and sensitivity. We incorporated the resulting motif clustering and retrieval procedures in a large-scale automated pipeline for analyzing DNA motifs. This pipeline integrates the results of various DNA motif discovery algorithms and automatically merges redundant motifs from multiple training sets into a coherent annotated library of motifs. Application of this pipeline to recent genome-wide transcription factor location data in S. cerevisiae successfully identified DNA motifs in a manner that is as good as semi-automated analysis reported in the literature. Moreover, we show how this analysis elucidates the mechanisms of condition-specific preferences of transcription factors. PMID:18463706

  4. Developments of global greenhouse gas retrieval algorithm based on Optimal Estimation Method

    NASA Astrophysics Data System (ADS)

    Kim, W. V.; Kim, J.; Lee, H.; Jung, Y.; Boesch, H.

    2013-12-01

    After the industrial revolution, atmospheric carbon dioxide concentration increased drastically over the last 250 years. It is still increasing and over than 400ppm of carbon dioxide was measured at Mauna Loa observatory for the first time which value was considered as important milestone. Therefore, understanding the source, emission, transport and sink of global carbon dioxide is unprecedentedly important. Currently, Total Carbon Column Observing Network (TCCON) is operated to observe CO2 concentration by ground base instruments. However, the number of site is very few and concentrated to Europe and North America. Remote sensing of CO2 could supplement those limitations. Greenhouse Gases Observing SATellite (GOSAT) which was launched 2009 is measuring column density of CO2 and other satellites are planned to launch in a few years. GOSAT provide valuable measurement data but its low spatial resolution and poor success rate of retrieval due to aerosol and cloud, forced the results to cover less than half of the whole globe. To improve data availability, accurate aerosol information is necessary, especially for East Asia region where the aerosol concentration is higher than other region. For the first step, we are developing CO2 retrieval algorithm based on optimal estimation method with VLIDORT the vector discrete ordinate radiative transfer model. Proto type algorithm, developed from various combinations of state vectors to find best combination of state vectors, shows appropriate result and good agreement with TCCON measurements. To reduce calculation cost low-stream interpolation is applied for model simulation and the simulation time is drastically reduced. For the further study, GOSAT CO2 retrieval algorithm will be combined with accurate GOSAT-CAI aerosol retrieval algorithm to obtain more accurate result especially for East Asia.

  5. Method for the location of primary wear scars from retrieved metal on metal hip replacements.

    PubMed

    Govind, Garima; Henckel, Johann; Hothi, Harry; Sabah, Shiraz; Skinner, John; Hart, Alister

    2015-07-30

    Retrieved metal-on-metal acetabular cups are valuable resources in investigating the wear behaviour of failed hip implants, but adequate methods to do so are lacking. To further contribute to addressing this issue, we developed a method to detect the in vivo location of the primary wear scar of an explanted cup. We proposed a new method in which thirteen patients with failed metal hip resurfacings were recruited, and their acetabular components retrieved. A 3D wear map was generated and the precise location of the primary wear scar in each cup was identified using a coordinate measuring machine. This wear scar location was noted in relation to the features on the acetabular cup. Having identified the location of the wear scar, this 3D positional map was co-registered to the implant on the patient's pelvic 3D CT scan. Using our proposed technique, we were able to demonstrate that the in vivo position of the primary wear scar in explanted metal acetabular cups can be variable. This method has utilised existing techniques to better understand the three-dimensional properties of wear behaviour, and may be a method which can be used in further studies to investigate variables that affect the position of the primary wear scar.

  6. 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

  7. 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.

  8. 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.

  9. Influenza virus titration, antigenic characterization, and serological methods for antibody detection.

    PubMed

    Klimov, Alexander; Balish, Amanda; Veguilla, Vic; Sun, Hong; Schiffer, Jarad; Lu, Xiuhua; Katz, Jacqueline M; Hancock, Kathy

    2012-01-01

    This chapter describes some commonly used methods of influenza virus titration, antigenic characterization, and serological methods by antibody detection. These methods are essential not only for virus characterization but also for identifying new antigenic variants, vaccine strain selection, and sero-epidemiologic studies of influenza virus transmission and prevalence. Virus titration methods such as the hemagglutination assay, 50% egg or tissue culture infectious dose, and plaque assay are employed to determine the amount of virus particles in a sample. The hemagglutination inhibition assay is a reliable, relatively simple and inexpensive technique to antigenically characterize isolates of influenza viruses. Serological methods such as virus neutralization and hemagglutination inhibition are the fundamental tools used in sero-epidemiologic studies of influenza virus transmission and prevalence and in the evaluation of vaccine immunogenicity. While serological methods rarely yield an early diagnosis of acute influenza virus infection, well-timed, paired acute, and convalescent serum samples may establish the diagnosis of a recent influenza infection even when attempts to detect the virus are negative.

  10. 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

  11. 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.

  12. Pulse retrieval in frequency-resolved optical gating based on the method of generalized projections

    SciTech Connect

    DeLong, K.W.; Fittinghoff, D.N.; Trebino, R. ); Kohler, B.; Wilson, K. )

    1994-12-15

    We use the algorithmic method of generalized projections (GP's) to retrieve the intensity and phase of an ultrashort laser pulse from the experimental trace in frequency-resolved optical gating (FROG). Using simulations, we show that the use of GP's improves significantly the convergence properties of the algorithm over the basic FROG algorithm. In experimental measurements, the GP-based algorithm achieves significantly lower errors than previous algorithms. The use of GP's also permits the inclusion of an arbitrary material response function in the FROG problem.

  13. A Valuable Antigen Detection Method for Diagnosis of Acute Hepatitis E

    PubMed Central

    Wen, Gui-Ping; Tang, Zi-Min; Yang, Fan; Zhang, Ke; Ji, Wen-Fang; Cai, Wei; Huang, Shou-Jie; Wu, Ting; Zhang, Jun

    2014-01-01

    Hepatitis E virus (HEV) is a serious public health problem. The commonly used tests that are specific for current HEV infection diagnosis include the detection of anti-HEV IgM and HEV RNA. Here, we report an improved enzyme-linked immunosorbent assay (ELISA) method for HEV antigen detection with a linear range equivalent to 6.3 × 103 to 9.2 × 105 RNA copies per ml. The monoclonal antibody (MAb) 12F12, a high-ability MAb that binds HEV virus, was selected as the capture antibody from a panel of 95 MAbs. The positive period of HEV antigenemia in infected monkeys using this test was, on average, 3 weeks longer than previously reported and covered the majority of the acute phase. The positive detection rates of IgM, RNA, and new antigen from the first serum samples collected from 16 confirmed acute hepatitis E patients were 81% (13/16), 81% (13/16), and 100% (16/16), respectively. In three patients, the initial serum specimens that tested negative for IgM, despite the presence of symptoms of acute hepatitis and elevated alanine aminotransferase (ALT) levels, were positive for HEV antigen and HEV RNA. In contrast, the serum samples of the three RNA-negative patients were antigen positive (and IgM positive), possibly due to the degradation of HEV nucleic acids. Our results suggest that this new antigen detection method has acceptable concordance with RNA detection and could serve as an important tool for diagnosing acute hepatitis E. PMID:25540394

  14. A nonlinear spectral unmixing method for abundance retrieval of mineral mixtures

    NASA Astrophysics Data System (ADS)

    Zhang, Xia; Lin, Honglei; Cen, Yi; Yang, Hang

    2016-05-01

    Minerals are generally present as intimate mixtures. The spectra of intimate mixtures in visible-infrared are complex function of abundance, grain size, and optical constants et.al, making the linear spectral unmixing model inapplicable. In this paper, we presented a nonlinear unmixing method by combining Shkuratov model (SK99) and Hapke model (H81) to unmix the mineral mixtures. For obtaining the abundances of mineral endmembers, we built up a look-up table (LUT) in the following steps: First, the optical constants were derived by SK99 model and then single scattering albedos of endmembers were computed. Second, the approximation of multiple scattering was derived by the Chandrasekhar H-function. Finally, LUT was established using H81 model. The root-mean-square error (RMSE) was calculated to find the best match between the reflectance of mixtures and LUT. We used the laboratory mineral mixtures to verify the accuracy of abundance estimation. The results show that RMSEs are less than 1% and the absolute errors of abundance retrieval are within 5%. The presented method can retrieve mineral abundance effectively and rapidly. It can be a potential method applying for hyperspectral images of the earth and planetary.

  15. An online aerosol retrieval algorithm using OMI near-UV observations based on the optimal estimation method

    NASA Astrophysics Data System (ADS)

    Jeong, U.; Kim, J.; Ahn, C.; Torres, O.; Liu, X.; Bhartia, P. K.; Spurr, R. J. D.; Haffner, D.; Chance, K.; Holben, B. N.

    2015-06-01

    An online version of the OMI (Ozone Monitoring Instrument) near-ultraviolet (UV) aerosol retrieval algorithm was developed to retrieve aerosol optical thickness (AOT) and single scattering albedo (SSA) based on the optimal estimation (OE) method. Instead of using the traditional look-up tables for radiative transfer calculations, it performs online radiative transfer calculations with the Vector Linearized Discrete Ordinate Radiative Transfer (VLIDORT) model to eliminate interpolation errors and improve stability. The OE-based algorithm has the merit of providing useful estimates of uncertainties simultaneously with the inversion products. The measurements and inversion products of the Distributed Regional Aerosol Gridded Observation Network campaign in Northeast Asia (DRAGON NE-Asia 2012) were used to validate the retrieved AOT and SSA. The retrieved AOT and SSA at 388 nm have a correlation with the Aerosol Robotic Network (AERONET) products that is comparable to or better than the correlation with the operational product during the campaign. The estimated retrieval noise and smoothing error perform well in representing the envelope curve of actual biases of AOT at 388 nm between the retrieved AOT and AERONET measurements. The forward model parameter errors were analyzed separately for both AOT and SSA retrievals. The surface albedo at 388 nm, the imaginary part of the refractive index at 354 nm, and the number fine mode fraction (FMF) were found to be the most important parameters affecting the retrieval accuracy of AOT, while FMF was the most important parameter for the SSA retrieval. The additional information provided with the retrievals, including the estimated error and degrees of freedom, is expected to be valuable for future studies.

  16. A Novel Medical Freehand Sketch 3D Model Retrieval Method by Dimensionality Reduction and Feature Vector Transformation

    PubMed Central

    Jing, Zhang; Sheng, Kang Bao

    2016-01-01

    To assist physicians to quickly find the required 3D model from the mass medical model, we propose a novel retrieval method, called DRFVT, which combines the characteristics of dimensionality reduction (DR) and feature vector transformation (FVT) method. The DR method reduces the dimensionality of feature vector; only the top M low frequency Discrete Fourier Transform coefficients are retained. The FVT method does the transformation of the original feature vector and generates a new feature vector to solve the problem of noise sensitivity. The experiment results demonstrate that the DRFVT method achieves more effective and efficient retrieval results than other proposed methods. PMID:27293478

  17. A Novel Medical Freehand Sketch 3D Model Retrieval Method by Dimensionality Reduction and Feature Vector Transformation.

    PubMed

    Jing, Zhang; Sheng, Kang Bao

    2015-01-01

    To assist physicians to quickly find the required 3D model from the mass medical model, we propose a novel retrieval method, called DRFVT, which combines the characteristics of dimensionality reduction (DR) and feature vector transformation (FVT) method. The DR method reduces the dimensionality of feature vector; only the top M low frequency Discrete Fourier Transform coefficients are retained. The FVT method does the transformation of the original feature vector and generates a new feature vector to solve the problem of noise sensitivity. The experiment results demonstrate that the DRFVT method achieves more effective and efficient retrieval results than other proposed methods.

  18. Inverse problem of the multislice method in retrieving projected complex potentials from the exit-wave function.

    PubMed

    Lin, Fang; Jin, Chuanhong

    2014-03-01

    We proposed a new algorithm that retrieves the projected potentials from the EW of object. This algorithm is based on the traditional multislice method which involves the convolution operation in calculation. The retrieved potential is complex including both the electrostatic and absorptive components. Tests with the simulated exit waves of a 200 K InP crystal prove the algorithm effective for objects in wide thickness range. For thick specimen where dynamical electron diffraction prevails, the retrieved potential could present structure and chemical information of object by completely mapping an atom's scattering potential during interaction with incident electrons.

  19. A Comparative Analysis of Retrieval Effectiveness for Three Methods of Indexing AIDS-Related Abstracts.

    ERIC Educational Resources Information Center

    Hersh, William R.; Hickam, David H.

    1991-01-01

    Describes SAPHIRE, an experimental information retrieval system featuring concept-based automated indexing, natural language input, and relevance-based retrieval; and compares its retrieval effectiveness with other indexing approaches in a Boolean-based searching environment. Indexing in MEDLINE is described, and a test collection of AIDS…

  20. 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.

  1. 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.

  2. 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

  3. Evaluation of shape indexing methods for content-based retrieval of x-ray images

    NASA Astrophysics Data System (ADS)

    Antani, Sameer; Long, L. Rodney; Thoma, George R.; Lee, Dah-Jye

    2003-01-01

    Efficient content-based image retrieval of biomedical images is a challenging problem of growing research interest. Feature representation algorithms used in indexing medical images on the pathology of interest have to address conflicting goals of reducing feature dimensionality while retaining important and often subtle biomedical features. At the Lister Hill National Center for Biomedical Communications, a R&D division of the National Library of Medicine, we are developing a content-based image retrieval system for digitized images of a collection of 17,000 cervical and lumbar x-rays taken as a part of the second National Health and Nutrition Examination Survey (NHANES II). Shape is the only feature that effectively describes various pathologies identified by medical experts as being consistently and reliably found in the image collection. In order to determine if the state of the art in shape representation methods is suitable for this application, we have evaluated representative algorithms selected from the literature. The algorithms were tested on a subset of 250 vertebral shapes. In this paper we present the requirements of an ideal algorithm, define the evaluation criteria, and present the results and our analysis of the evaluation. We observe that while the shape methods perform well on visual inspection of the overall shape boundaries, they fall short in meeting the needs of determining similarity between the vertebral shapes based on the pathology.

  4. [Quantitative retrieval of chlorophyll a concentration in Taihu Lake using machine learning methods].

    PubMed

    Zhang, Yu-Chao; Qian, Xin; Qian, Yu; Liu, Jian-Ping; Kong, Fan-Xiang

    2009-05-15

    We evaluated the performance of two machine learning methods, artificial neural net (ANN) and support vector machine (SVM), for estimation of chlorophyll a in Taihu Lake from remote sensing data. The theoretical analysis has been done from basic theory and learning target of these two methods first. Then two empirical algorithms have been developed to relate reflectance of MODIS to in situ concentrations of chlorophyll a. The performance of ANN and SVM is comparatively analyzed in terms of validation, stability and robustness assessment and chlorophyll a distribution of Taihu Lake from two algorithms. The root of mean square deviation (RMSE) and average relative error (ARE) of validation data is only 5.85 and 26.5% of SVM retrieval model, however, RMSE and ARE of ANN model is 13.04 and 46.8%. Stability and robustness assessment suggest that SVM provides the better performance than ANN. And the retrieval results show that the chlorophyll a distribution of the whole lake from two algorithms is similar, however, the chlorophyll a concentration in the eastern region and central region of Taihu Lake is distorted by ANN model because of the limitations, such as learning target setting and over-learning in net construction.

  5. List-method directed forgetting: the forget cue improves both encoding and retrieval of postcue information.

    PubMed

    Pastötter, Bernhard; Kliegl, Oliver; Bäuml, Karl-Heinz T

    2012-08-01

    In list-method directed forgetting, people are cued to forget a previously studied item list and to learn a new list instead. Such cuing typically leads to forgetting of the first list and to memory enhancement of the second, referred to as list 1 forgetting and list 2 enhancement. In the present study, two experiments are reported that examined influences of items' serial learning position in a list and the two lists' output order on list-method directed forgetting. The results show that list output order influences list 2 enhancement but not list 1 forgetting. The enhancement was higher when list 2 was recalled first than when list 1 was recalled first and, in both cases, was higher for early list 2 items than for middle and late list 2 items. In contrast, the forgetting was equally present for all list 1 items and did not depend on the two lists' output order. The findings suggest that two separate factors can contribute to list 2 enhancement: one (encoding) factor that is restricted to early list 2 items and does not depend on list output order, and another (retrieval) factor that pertains to all list 2 items and varies with the two lists' output order. A new two-mechanism account of directed forgetting is suggested that reconciles previous (encoding or retrieval) views on list 2 enhancement.

  6. Tropospheric CO Observations Using IASI datasets and an Optimal Estimation Retrieval Method

    NASA Astrophysics Data System (ADS)

    Illingworth, S. M.

    2009-04-01

    Carbon monoxide (CO) in the troposphere acts as a marker of large-scale influences of pollution on both the regional and global scale, whilst acting as a reference source for incomplete combustion. Through its reactions with the hydroxyl radical OH, the concentration of CO is also related to the oxidizing capacity of the troposphere, hence providing a chemical marker for the "local" chemical environment and its state. Investigations into perturbations of the sources, sinks and net surface fluxes of CO are therefore of increasing importance. CO exhibits strong locally elevated concentrations in the vicinity of sources due to its relatively short life time of weeks to months. Global measurements of CO from satellites will therefore allow to identify the main source regions and to quantify their source strength. The Infrared Atmospheric Sounding Interferometer (IASI) is a high-resolution (0.25 cm-1 unapodized) Michelson interferometer which was launched in 2007 on the European polar Meteorological Operational Platform (METEOP-1) satellite. The IASI instrument has a swath of about 2200 km, ensuring 99% global coverage twice a day, and is the first of a series of three instruments launched every five years, ensuring a continuity of data for a planned period of 15 years. The IASI instrument thus offers the possibility of high-spectral resolution infrared monitoring of CO over a very long time period. This work presents a new Optimal Estimation Method (OEM) retrieval of CO profiles in the mid-troposphere from observations of the IASI instrument. First retrieval results, as well as a validation of these results with ground-based sites and other satellites are included, and error characterization as well as the effects of noise in the retrievals is also discussed.

  7. Experimental Sentinel-2 LAI estimation using parametric, non-parametric and physical retrieval methods - A comparison

    NASA Astrophysics Data System (ADS)

    Verrelst, Jochem; Rivera, Juan Pablo; Veroustraete, Frank; Muñoz-Marí, Jordi; Clevers, Jan G. P. W.; Camps-Valls, Gustau; Moreno, José

    2015-10-01

    Given the forthcoming availability of Sentinel-2 (S2) images, this paper provides a systematic comparison of retrieval accuracy and processing speed of a multitude of parametric, non-parametric and physically-based retrieval methods using simulated S2 data. An experimental field dataset (SPARC), collected at the agricultural site of Barrax (Spain), was used to evaluate different retrieval methods on their ability to estimate leaf area index (LAI). With regard to parametric methods, all possible band combinations for several two-band and three-band index formulations and a linear regression fitting function have been evaluated. From a set of over ten thousand indices evaluated, the best performing one was an optimized three-band combination according to (ρ560 -ρ1610 -ρ2190) / (ρ560 +ρ1610 +ρ2190) with a 10-fold cross-validation RCV2 of 0.82 (RMSECV : 0.62). This family of methods excel for their fast processing speed, e.g., 0.05 s to calibrate and validate the regression function, and 3.8 s to map a simulated S2 image. With regard to non-parametric methods, 11 machine learning regression algorithms (MLRAs) have been evaluated. This methodological family has the advantage of making use of the full optical spectrum as well as flexible, nonlinear fitting. Particularly kernel-based MLRAs lead to excellent results, with variational heteroscedastic (VH) Gaussian Processes regression (GPR) as the best performing method, with a RCV2 of 0.90 (RMSECV : 0.44). Additionally, the model is trained and validated relatively fast (1.70 s) and the processed image (taking 73.88 s) includes associated uncertainty estimates. More challenging is the inversion of a PROSAIL based radiative transfer model (RTM). After the generation of a look-up table (LUT), a multitude of cost functions and regularization options were evaluated. The best performing cost function is Pearson's χ -square. It led to a R2 of 0.74 (RMSE: 0.80) against the validation dataset. While its validation went fast

  8. A Method to Estimate Crop Effects in Passive Microwave Soil Moisture Retrieval Above C-band

    NASA Astrophysics Data System (ADS)

    Zhang, Z.; Xu, Y.; Shi, J.

    2009-12-01

    moisture) directly to the observed Brightness Temperature. On the other hand, τ-ω model is simple in formula and are widely used in soil moisture retrieval at L- or C-band. To characterize ω and t of short vegetation above C-band, we setup a Brightness Temperature database with M-D model by a variety of parameters. Then results from M-D model were matched with those from τ-ω model at the same environmental conditions by least-square deviation, so as to retrieve ω and t of vegetation above C-band. To verify the derived effective single scattering albedo ω and transmissivity t, they were used, together with the Brightness Temperature data during SMEX02/PSR flight, in τ-ω model. The results of the equation were emissivity of soil, which were then used by a Qp model to retrieve soil moisture in the same area where PSR flight passed. The retrieved soil moisture matched the measurement very good, the rmse is 0.0458. This showed our method to retrieve ω and t are reliable.

  9. Novel antigen identification method for discovery of protective malaria antigens by rapid testing of DNA vaccines encoding exons from the parasite genome.

    PubMed

    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

    2004-03-01

    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.

  10. 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.

  11. Tropospheric ozone retrieval by using SCIAMACHY Limb-Nadir-Matching method

    NASA Astrophysics Data System (ADS)

    Jia, Jia; Ladstätter-Weissenmayer, Annette; Ebojie, Felix; Rozanov, Alexei; Burrows, John

    2014-05-01

    Tropospheric ozone is photochemically produced during pollution events and transported from the stratosphere towards the troposphere. It is the third most important green house gases and the main component of summer smog. Global covered satellite measurements are well suitable to investigate sources, sinks, and transport mechanisms of tropospheric ozone in a global view, and to study a characteristic behaviour of the tropospheric ozone in regions. However, the usage of satellite data is associated to a large uncertainty as 90% ozone is located in the stratosphere and only the remaining part of 10% can be observed in the troposphere. The limb-nadir matching (LNM) technique is one of the methods suitable to retrieve tropospheric ozone distributions from space borne observations of the scattered solar light in the UV-visible spectral range. In this study we apply the LNM approach to alternating limb and nadir measurements performed by the SCIAMACHY instrument. A precise tropopause height is used to subtract the stratospheric ozone from the total ozone amount for each matching point. The focus of this work is to reduce the uncertainty of the resulting tropospheric ozone distributions by analysing possible error sources, refining both limb and nadir retrievals and the matching technique.

  12. Wind Profile Retrieval Method for Incoherent Doppler LIDAR in Partly Cloudy Conditions

    NASA Astrophysics Data System (ADS)

    Feng, Changzhong; Liu, Bingyi; Liu, Zhishen

    2014-11-01

    After the launch of ESA's spaceborne Doppler lidar ALADIN, Ocean University of China is going to perform the ground validation using a ground based Doppler wind lidar which utilizes an iodine absorption filter as frequency discriminator to derive Doppler frequency shift of atmospheric wind from combined molecular and aerosol backscatter. Under circumstance of non-uniform aerosol horizontal distribution, such as partly cloudy conditions, the accuracy of wind measurements is seriously influenced. Therefore, an improved VAD (Velocity-Azimuth Display) method for retrieving wind profiles is developed, which significantly increases the accuracy. With the atmospheric return signal obtained from the line-of- sight velocity PPI (Plan Position Indicator) measurements, the spatial distribution of aerosol optical parameters can be derived and considered as a reference for the quality control of line-of-sight velocity. Consequently, the wind profile in partly cloudy conditions can be retrieved by using the quality controlled line-of-sight velocity. As a result, the applicability of the ground based Doppler lidar is improved.

  13. Wind Profile Retrieval Method for Incoherent Doppler LIDAR in Partly Cloudy Conditions

    NASA Astrophysics Data System (ADS)

    Feng, Changzhong; Liu, Bingyi; Liu, Zhishen

    2014-11-01

    After the launch of ESA’s spaceborne Doppler lidar ALADIN, Ocean University of China is going to perform the ground validation using a ground based Doppler wind lidar which utilizes an iodine absorption filter as frequency discriminator to derive Doppler frequency shift of atmospheric wind from combined molecular and aerosol backscatter. Under circumstance of non-uniform aerosol horizontal distribution, such as partly cloudy conditions, the accuracy of wind measurements is seriously influenced. Therefore, an improved VAD (Velocity-Azimuth Display) method for retrieving wind profiles is developed, which significantly increases the accuracy. With the atmospheric return signal obtained from the line-of-sight velocity PPI (Plan Position Indicator) measurements, the spatial distribution of aerosol optical parameters can be derived and considered as a reference for the quality control of line-of-sight velocity. Consequently, the wind profile in partly cloudy conditions can be retrieved by using the quality controlled line-of-sight velocity. As a result, the applicability of the ground based Doppler lidar is improved.

  14. Improved poliovirus D-antigen yields by application of different Vero cell cultivation methods.

    PubMed

    Thomassen, Yvonne E; Rubingh, Olaf; Wijffels, René H; van der Pol, Leo A; Bakker, Wilfried A M

    2014-05-19

    Vero cells were grown adherent to microcarriers (Cytodex 1; 3 g L(-1)) using animal component free media in stirred-tank type bioreactors. Different strategies for media refreshment, daily media replacement (semi-batch), continuous media replacement (perfusion) and recirculation of media, were compared with batch cultivation. Cell densities increased using a feed strategy from 1×10(6) cells mL(-1) during batch cultivation to 1.8, 2.7 and 5.0×10(6) cells mL(-1) during semi-batch, perfusion and recirculation, respectively. The effects of these different cell culture strategies on subsequent poliovirus production were investigated. Increased cell densities allowed up to 3 times higher D-antigen levels when compared with that obtained from batch-wise Vero cell culture. However, the cell specific D-antigen production was lower when cells were infected at higher cell densities. This cell density effect is in good agreement with observations for different cell lines and virus types. From the evaluated alternative culture methods, application of a semi-batch mode of operations allowed the highest cell specific D-antigen production. The increased product yields that can easily be reached using these higher cell density cultivation methods, showed the possibility for better use of bioreactor capacity for the manufacturing of polio vaccines to ultimately reduce vaccine cost per dose. Further, the use of animal-component-free cell- and virus culture media shows opportunities for modernization of human viral vaccine manufacturing.

  15. Analysis of sperm antigens by sodium dodecyl sulfate gel/protein blot radioimmunobinding method

    SciTech Connect

    Lee, C.Y.G.; Huang, Y.S.; Hu, P.C.; Gomel, V.; Menge, A.C.

    1982-06-01

    A radioimmunobinding method based on the blotting of renatured proteins from sodium dodecyl sulfate gels on to nitrocellulose filter papers was developed to analyze the sperm antigens that elicit serum anti-sperm antibodies. In rabbits, serum anti-sperm antibodies were raised by immunization with homologous epididymal spermatozoa mixed with complete Freund's adjuvant. The raised antisera from either male or female rabbits were shown to react with three major sperm protein bands on sodium dodecyl sulfate gels with the corresponding molecular weights of about 70,000 +/- 5000, 14,000, and 13,000, respectively. In humans, the monoclonal antibodies against human sperm were raised by a hybridoma technique. Out of six independent hybrid cell lines that were generated, three of them were shown to secrete immunoglobulins that react with the same two protein bands on sodium dodecyl sulfate gels, which have the approximate molecular weight of 10,000. The same procedure was also used to analyze human serum samples that were shown to contain anti-sperm antibodies by the known techniques. Unique sperm antigens that elicit anti-sperm antibodies in humans were identified and correlated. The results of this study suggest that sodium dodecyl sulfate gel/protein blot radioimmunobinding method may be a sensitive and useful tool for the study of sperm antigens that elicit autoimmune responses and their association with human infertility.

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. Retrieval of water vapor mixing ratio from a multiple channel Raman-scatter lidar using an optimal estimation method.

    PubMed

    Sica, R J; Haefele, A

    2016-02-01

    Lidar measurements of the atmospheric water vapor mixing ratio provide an excellent complement to radiosoundings and passive, ground-based remote sensors. Lidars are now routinely used that can make high spatial-temporal resolution measurements of water vapor from the surface to the stratosphere. Many of these systems can operate during the day and night, with operation only limited by clouds thick enough to significantly attenuate the laser beam. To enhance the value of these measurements for weather and climate studies, this paper presents an optimal estimation method (OEM) to retrieve the water vapor mixing ratio, aerosol optical depth profile, Ångstrom exponent, lidar constants, detector dead times, and measurement backgrounds from multichannel vibrational Raman-scatter lidars. The OEM retrieval provides the systematic uncertainties due to the overlap function, calibration factor, air density and Rayleigh-scatter cross sections, in addition to the random uncertainties of the retrieval due to measurement noise. The OEM also gives the vertical resolution of the retrieval as a function of height, as well as the height to which the contribution of the a priori is small. The OEM is applied to measurements made by the Meteoswiss Raman Lidar for Meteorological Observations (RALMO) in the day and night for clear and cloudy conditions. The retrieved water vapor mixing ratio is in excellent agreement with both the traditional lidar retrieval method and coincident radiosoundings.

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

    PubMed

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

    2015-06-08

    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.

  2. 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

  3. Steady method to retrieve effective electromagnetic parameters of bianisotropic metamaterials at one incident direction in the terahertz region

    NASA Astrophysics Data System (ADS)

    Zhao, Jingyin; Jing, Xufeng; Wang, Weimin; Tian, Ying; Zhu, Dongshuo; Shi, Guohua

    2017-10-01

    We propose a steady method to extract the effective constitutive parameters of a slab of bianisotropic split-ring resonator metamaterial from reflection and transmission coefficients. The effective permittivity, permeability and magnetoelectric coupling coefficient of bianisotropic metamaterial can be simply retrieved by our derived analytical inversion equations. In our retrieval method, the transmission and reflection coefficients in only one direction of wave propagation were applied. The method was verified by the retrieval constitutive parameters for different metamaterials, among which one is isotropic structure and the other one is bianisotropic metamaterial. The intrinsic difference between the normal isotropic metamaterial and the bianisotropic metamaterial was evidently revealed. The resonant characteristic of the split ring resonator metamaterial including electric coupling to magnetic resonance was verified by the extracted effective constitutive parameters. The proposed method can be effectively applied in investigation of bianisotropic performance of metamaterials.

  4. Screening and determinations of tissue polypeptide antigen by label-free optical immunosensing method.

    PubMed

    Yao, Zufu; Huang, Kelong; Guo, Jun; Li, Yanhua; Yu, Jingang; Wu, Fangping

    2012-01-01

    Based on the specificity of the immunoreaction of anti-body and antigen, and the resulting localized surface plasmon resonance extinction response of functionalized nano-Au monolayer on glass chip, a novel label-free optical immunosensor with amplified sensitivity has been developed for the detection of tissue polypeptide antigen (TPA). The nano-Au monolayer on glass chip was controllably prepared using 3-mercaptopropyltrimethoxysilane (MPTMOS) as linker by a solution self-assembly method. To analyze its quality, the nano-Au monolayer was characterized by UV-visible spectrum and atomic force microscopy (AFM). The resulting chip was modified by tissue polypeptide antigen antibody (anti-TPA), and then bovine serum albumin (BSA) was employed to block the possible remaining active sites of the nano-Au monolayer. An immunosensor was constructed with biocompatible monolayer nano-Au membrane and the desirable TPA antibody/BSA composite membrane, and it showed good selectivity, high sensitivity and a wide linear response to TPA in the range of 1-1000 ng L(-1) with a detection limit of 1.2 x 10(-3) ng L(-1), as well as good stability and long-term life. Owing to its ease of operation, low detection limit and low cost, it is expected that the proposed procedure may hold great promise in both research-based and clinical assays.

  5. Demonstration of retrieval methods for Westinghouse Hanford Corporation October 20, 1995

    SciTech Connect

    1996-10-01

    Westinghouse Hanford Corporation has been pursuing strategies to break up and retrieve the radioactive waste material in single shell storage tanks at the Hanford Nuclear Reservation, by working with non-radioactive ``saltcake`` and sludge material that simulate the actual waste. It has been suggested that the use of higher volumes of water than used in the past (10 gpm nozzles at 10,000 psi) might be successful in breaking down the hard waste simulants. Additionally, the application of these higher volumes of water might successfully be applied through commercially available tooling using methods similar to those used in the deslagging of large utility boilers. NMW Industrial Services, Inc., has proposed a trial consisting of three approaches each to dislodging both the solid (saltcake) simulant and the sludge simulant.

  6. An automatic Planetary Boundary Layer height retrieval method with compact EZ backscattering Lidar

    NASA Astrophysics Data System (ADS)

    Loaec, S.; Sauvage, L.; Boquet, M.; Lolli, S.; Rouget, V.

    2009-09-01

    Bigger strongly urbanized cities in the world are often exposed to atmospheric pollution events. To understand the chemical and physical processes that are taking place in these areas it is necessary to describe correctly the Planetary Boundary Layer (PBL) dynamics and the PBL height evolution. For these proposals, a compact and rugged eye safe UV Lidar, the EZLIDAR™, was developed together by CEA/LMD and LEOSPHERE (France) to study and investigate structural and optical properties of clouds and aerosols and PBL time evolution. EZLIDAR™ has been validated by different remote and in-situ instruments as MPL Type-4 Lidar manufactured by NASA at ARM/SGP site or the LNA (Lidar Nuage Aerosol) at the Laboratoire de Metereologie Dynamique LMD (France) and during several intercomparison campaigns. EZLIDAR™ algorithm retrieves automatically the PBL height in real-time. The method is based on the detection of the slope of the signal linked to a sharp change in concentration of the aerosols. Once detected, the different layers are filtered on a 15mn sample and classified between nocturnal, convective or residual layer, depending on the time and date. This method has been validated against those retrieved by the algorithm STRAT from data acquired at IPSL, France, showing 95% of correlation. In this paper are presented the results of the intercomparison campaign that took place in Orleans, France and Mace Head, Ireland in the framework of ICOS (Integrated Carbon Observation System) project, where the EZ Lidar™ worked under all weather conditions, clear sky, fog, low clouds, during the whole month of October 2008. Moreover, thanks to its 3D scanning capability, the EZLIDAR was able to provide the variability of the PBL height around the site, enabling the scientists to estimate the flux intensities that play a key role in the radiative transfer budget and in the atmospheric pollutants dispersion.

  7. 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.

  8. 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.

  9. 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.

    2016-06-01

    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.

  10. 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.

  11. Validation of GOES-Derived Surface Radiation Using NOAA's Physical Retrieval Method

    SciTech Connect

    Habte, A.; Sengupta, M.; Wilcox, S.

    2013-01-01

    This report was part of a multiyear collaboration with the University of Wisconsin and the National Oceanic and Atmospheric Administration (NOAA) to produce high-quality, satellite-based, solar resource datasets for the United States. High-quality, solar resource assessment accelerates technology deployment by making a positive impact on decision making and reducing uncertainty in investment decisions. Satellite-based solar resource datasets are used as a primary source in solar resource assessment. This is mainly because satellites provide larger areal coverage and longer periods of record than ground-based measurements. With the advent of newer satellites with increased information content and faster computers that can process increasingly higher data volumes, methods that were considered too computationally intensive are now feasible. One class of sophisticated methods for retrieving solar resource information from satellites is a two-step, physics-based method that computes cloud properties and uses the information in a radiative transfer model to compute solar radiation. This method has the advantage of adding additional information as satellites with newer channels come on board. This report evaluates the two-step method developed at NOAA and adapted for solar resource assessment for renewable energy with the goal of identifying areas that can be improved in the future.

  12. 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.

  13. Immunoelectron microscopy of skin basement membrane zone antigens: a pre-embedding method using 1-nm immunogold with silver enhancement.

    PubMed

    McGrath, J A; Ishida-Yamamoto, A; Shimizu, H; Fine, J D; Eady, R A

    1994-05-01

    There is no single immunoelectron microscopical method for invariably effective localization of both intracellular and extracellular antigens. We describe a simple and practicable immunogold technique that can be used to localize various skin basement membrane zone antigens at the ultrastructural level. Small pieces of skin were incubated with primary antibodies recognizing epitopes on a range of basement membrane zone-related antigens (two different lamina lucida-associated antigens, laminin, type VII collagen, fibrillin and keratin 14). This was followed by incubation with 1-nm colloidal gold-conjugated secondary antibody and subsequent silver intensification. The specimens were then processed for transmission electron microscopy. Precise immunolocalization with good ultrastructural preservation was achieved for all basement membrane zone antibodies tested. The results of basal cell keratin immunostaining showed that this microscopic approach could also be applied to some extent in the characterization of intracellular antigens. This immunoelectron microscopy technique provides a useful approach to the study of macromolecules at the basement membrane zone.

  14. A reliable method to retrieve accident & emergency data stored on a free-text basis.

    PubMed

    Premaratne, U N; Marks, G B; Austin, E J; Burney, P G

    1997-02-01

    Accident & Emergency (A & E) data on asthma-related attendances are useful for studies on the effectiveness of asthma interventions, and to determine the relationship of environmental factors to asthma and asthma epidemics. The final diagnoses made in the A & E departments are not usually coded when entered into hospital databases in the U.K., although the "presenting complaint' can be retrieved from the computerized Hospital Information & Support Systems (HISS), from a free-text attendance diagnosis field entered by the reception clerk when the patient arrives at the A & E department. The validity of this as an indication of the final diagnosis is unevaluated. The aim of this study was to measure the validity of the string "asth' in the A & E attendance diagnosis field for identifying patients attending the A & E departments of two hospitals for asthma-related conditions. A list of patients who attended the A & E department of two hospitals was retrieved from the HISS along with the attendance diagnosis field. If the attendance diagnosis field contained the text string "asth', mentioned wheeze or breathing problems, or the patients were referred by their GP without any diagnostic information entered on HISS, the records were selected for evaluation. The remaining attendances, which were not evaluated further, were attributed to another diagnosis based on the evidence of the recorded attendance diagnosis. The results indicated that the string "asth' in the attendance diagnosis field had a sensitivity of 80.3% (95% CI 75.1-85.5%) and a specificity of 96.7% (95% CI 95.6-97.8%) for a final diagnosis of asthma. It is concluded that free-text attendance diagnosis fields in hospital databases can be searched with suitable strings to obtain reliable data on attendance with asthma. As part of another investigation, the present authors attempted to retrieve a list of the attendances with asthma at the same two A & E departments at a time that was reportedly associated with

  15. Retrieval of the pulse amplitude and phase from cross-phase modulation spectrograms using the simulated annealing method.

    PubMed

    Honzatko, Pavel; Kanka, J; Vrany, B

    2004-11-29

    The simulated annealing method is used for retrieving the amplitude and phase from cross-phase modulation spectrograms. The method allows us to take into account the birefringence of the measurement fiber and resolution of the optical spectrum analyzer. The influence of the birefringence and analyzer resolution are discussed.

  16. A simple and versatile cloud-screening method for MAX-DOAS retrievals

    NASA Astrophysics Data System (ADS)

    Gielen, C.; Van Roozendael, M.; Hendrick, F.; Pinardi, G.; Vlemmix, T.; De Bock, V.; De Backer, H.; Fayt, C.; Hermans, C.; Gillotay, D.; Wang, P.

    2014-10-01

    We present a cloud-screening method based on differential optical absorption spectroscopy (DOAS) measurements, more specifically using intensity measurements and O4 differential slant-column densities (DSCDs). Using the colour index (CI), i.e. the ratio of the radiance at two wavelengths, we define different sky conditions including clear, thin clouds/polluted, fully-cloudy, and heavily polluted. We also flag the presence of broken and scattered clouds. The O4 absorption is a good tracer for cloud-induced light-path changes and is used to detect clouds and discriminate between instances of high aerosol optical depth (AOD) and high cloud optical depth (COD). We apply our cloud screening to MAX-DOAS (multi-axis DOAS) retrievals at three different sites with different typical meteorological conditions, more specifically suburban Beijing (39.75° N, 116.96° E), Brussels (50.78° N, 4.35° E) and Jungfraujoch (46.55° N, 7.98° E). We find that our cloud screening performs well characterizing the different sky conditions. The flags based on the colour index are able to detect changes in visibility due to aerosols and/or (scattered) clouds. The O4-based multiple-scattering flag is able to detect optically thick clouds, and is needed to correctly identify clouds for sites with extreme aerosol pollution. Removing data taken under cloudy conditions results in a better agreement, in both correlation and slope, between the MAX-DOAS AOD retrievals and measurements from other co-located instruments.

  17. A simple and versatile cloud-screening method for MAX-DOAS retrievals

    NASA Astrophysics Data System (ADS)

    Gielen, C.; Van Roozendael, M.; Hendrick, F.; Pinardi, G.; Vlemmix, T.; De Bock, V.; De Backer, H.; Fayt, C.; Hermans, C.; Gillotay, D.; Wang, P.

    2014-06-01

    We present a cloud-screening method based on differential optical absorption spectroscopy (DOAS) measurements, more specifically using zenith sky spectra and O4 differential slant-column densities (DSCDs). Using the colour index (CI), i.e. the ratio of the radiance at two wavelengths, we define different sky conditions including clear, thin clouds/polluted, fully-cloudy, and heavily polluted. We also flag the presence of broken and scattered clouds. The O4 absorption is a good tracer for cloud-induced light-path changes and is used to detect clouds and discriminate between instances of high aerosol optical depth (AOD) and high cloud optical depth (COD). We apply our cloud screening to MAX-DOAS (multi-axis DOAS) retrievals at three different sites with different typical meteorological conditions, more specifically suburban Beijing (39.75° N, 116.96° E), Brussels (50.78° N, 4.35° E) and Jungfraujoch (46.55° N, 7.98° E). We find that our cloud screening performs well characterizing the different sky conditions. The flags based on the colour index are able to detect changes in visibility due to aerosols and/or (scattered) clouds. The O4-based multiple-scattering flag is able to detect optically thick clouds, and is needed to correctly identify clouds for sites with extreme aerosol pollution. Removing data taken under cloudy conditions results in a better agreement, in both correlation and slope, between the AOD retrievals and measurements from other co-located instruments.

  18. The Günther-Tulip retrievable filter: a method for assessing tilting of the filter.

    PubMed

    Semiz-Oysu, Aslihan; Cho, Kyung J

    2010-04-01

    Tilting of the Günther-Tulip filter may be responsible for failure or difficulty to retrieve. Assessment of the filter tilt can be difficult when only AP imaging is available. This study is performed in vitro to develop a simple method to assess the Günther-Tulip filter for tilting. A model consisting of a plastic tube was used to simulate vena cava. A Günther-Tulip filter was placed centred or tilted within the tube at various positions and radiograms were taken in AP, lateral, and craniocaudally angled projections. The images were analysed to determine the actual degree of tilt, the distance between the limb hooks on AP radiograms and the craniocaudal angulation degree needed to align the limb hooks linearly. When the filter was centred or tilted laterally, all limb hooks of the filter were aligned linearly on AP radiograms. When the filter was tilted in AP or oblique direction, linear alignment of the limb hooks was lost and the ventral and dorsal limb hooks showed separation on AP projection. The amount of separation and the craniocaudal angles to align the filter hooks corresponded to actual tilt angles. Loss of linear alignment of limb hooks in AP radiograms may suggest the presence of tilt in the AP plane. Significant separation of limb hooks should be alarming for significant filter tilt, and further evaluation of the filter position by CT scan or lateral cavogram should be obtained prior to planning of the retrieval. Copyright 2009 Australasian Society of Cardiac and Thoracic Surgeons and the Cardiac Society of Australia and New Zealand. Published by Elsevier B.V. All rights reserved.

  19. Stabilization of Transfected Cells Expressing Low-Incidence Blood Group Antigens: Novel Methods Facilitating Their Use as Reagent-Cells

    PubMed Central

    González, Cecilia; Esteban, Rosa; Canals, Carme; Muñiz-Díaz, Eduardo; Nogués, Núria

    2016-01-01

    Background The identification of erythrocyte antibodies in the serum of patients rely on panels of human red blood cells (RBCs), which coexpress many antigens and are not easily available for low-incidence blood group phenotypes. These problems have been addressed by generating cell lines expressing unique blood group antigens, which may be used as an alternative to human RBCs. However, the use of cell lines implies several drawbacks, like the requirement of cell culture facilities and the high cost of cryopreservation. The application of cell stabilization methods could facilitate their use as reagent cells in clinical laboratories. Methods We generated stably-transfected cells expressing low-incidence blood group antigens (Dia and Lua). High-expresser clones were used to assess the effect of TransFix® treatment and lyophilization as cell preservation methods. Cells were kept at 4°C and cell morphology, membrane permeability and antigenic properties were evaluated at several time-points after treatment. Results TransFix® addition to cell suspensions allows cell stabilization and proper antigen detection for at least 120 days, despite an increase in membrane permeability and a reduction in antigen expression levels. Lyophilized cells showed minor morphological changes and antigen expression levels were rather conserved at days 1, 15 and 120, indicating a high stability of the freeze-dried product. These stabilized cells have been proved to react specifically with human sera containing alloantibodies. Conclusions Both stabilization methods allow long-term preservation of the transfected cells antigenic properties and may facilitate their distribution and use as reagent-cells expressing low-incidence antigens, overcoming the limited availability of such rare RBCs. PMID:27603310

  20. 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

  1. A Comparison of Two Methods for Indexing and Retrieval from a Full-Text Medical Database.

    ERIC Educational Resources Information Center

    Hersh, William R.; Hickman, David H.

    1992-01-01

    Describes a study that compared two information retrieval systems on a full-text medical database: one featured concept-based automatic indexing and statistical retrieval techniques, and the second used traditional word-based Boolean techniques. Evaluation of search results by calculating relative recall and precision is discussed, and user…

  2. 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…

  3. 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…

  4. 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…

  5. 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.

  6. 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…

  7. The impact of the choice of radiative transfer model and inversion method on the OSIRIS ozone and nitrogen dioxide retrievals

    NASA Astrophysics Data System (ADS)

    Haley, Craig; McLinden, Chris; Sioris, Christopher; Brohede, Samuel

    Key to the retrieval of stratospheric minor species information from limb-scatter measurements are the selections of a radiative transfer model (RTM) and inversion method (solver). Here we assess the impact of choice of RTM and solver on the retrievals of stratospheric ozone and nitrogen dioxide from the OSIRIS instrument using the ‘Ozone Triplet' and Differential Optical Absorption Spectroscopy (DOAS) techniques that are used in the operational Level 2 processing algorithms. The RTMs assessed are LIMBTRAN, VECTOR, SCIARAYS, and SASKTRAN. The solvers studied include the Maximum A Posteriori (MAP), Maximum Likelihood (ML), Iterative Least Squares (ILS), and Chahine methods.

  8. Active on-demand service method based on event-driven architecture for geospatial data retrieval

    NASA Astrophysics Data System (ADS)

    Fan, Minghu; Fan, Hong; Chen, Nengcheng; Chen, Zeqiang; Du, Wu

    2013-07-01

    Timely on-demand access to geospatial data is necessary for environmental observation and disaster response. However, traditional service methods for acquiring geospatial data are inefficient and cumbersome, which is not beneficial for timely data acquisition. In these service methods, data are obtained and published by managers and are then left to users to discover and to retrieve them. To solve this problem, we propose an event-driven active on-demand data service method, for which a prototype based on sensor web technologies is demonstrated. First, we select a subset of observed properties as the attributes of an observation event of a data service system. Event-filtering technologies are then employed to find the data desired by users. Finally, the data that meet the subscription requirement are pushed to subscribers on time. The aims of the implementation of the method are to test the suitability of the observation and measurement (O&M) profile for Earth observation and OGC event pattern markup language (EML) specification. We determined the attributes of observation events according to the requirement of the data service and encoded observation event information using the OGC Observations and Measurements specification. We encoded the information under filtering conditions using the OGC Event Pattern Markup Language specification. We implemented a data service method that is based on event-driven architecture via a combination of some sensor web enablement services. Finally, we verified the feasibility of the method using MODIS data from the forest fires that occurred on February 7, 2009, in Victoria, Australia. The results show that the proposed method can achieve actively pushing the desired data to subscribers in the shortest possible time. O&M profiles for Earth observation and EML are suitable for the metadata encoding of observation events and the encoding of subscription information respectively. They match well for the data service in the system.

  9. Real-time measurement of laser beam quality factor by the Fresnel phase-retrieval method

    NASA Astrophysics Data System (ADS)

    Yang, Pao-Keng; Liu, Jian-You; Chen, Yung-Chieh; Hsu, Chia-En

    2016-09-01

    Conventionally, it is a tedious work to measure the beam quality factor for a laser beam because one needs to move a camera-based beam profiler from one location to another for many times to record intensity profiles at different positions around the beam waist. We present a simple method for determining the laser beam quality factor from only two laser intensity profiles at different cross sections around the waist. We first used an iterative phase-retrieval algorithm, based on the Huygens-Fresnel principle, to reconstruct the phase profiles at the two cross sections where the intensity profiles had been measured. Once the optical field amplitude (the square root of intensity) and phase distribution functions at certain cross section of a laser beam had been determined, we can propagate the light wave at this cross section by using the Fresnel diffraction formula to obtain the intensity profiles at different positions, from which the beam quality factor can be determined. Using a HeNe laser for test, we had experimentally demonstrated the feasibility of our idea by showing that the result from our proposed method is in good agreement with that obtained from the conventional method. Our setup is capable of executing a real-time measurement of the beam quality factor because the two intensity profiles can be simultaneously recorded by using a beam splitter and two beam-profilers controlled by the same computer.

  10. Stabilization of Transfected Cells Expressing Low-Incidence Blood Group Antigens: Novel Methods Facilitating Their Use as Reagent-Cells.

    PubMed

    González, Cecilia; Esteban, Rosa; Canals, Carme; Muñiz-Díaz, Eduardo; Nogués, Núria

    2016-01-01

    The identification of erythrocyte antibodies in the serum of patients rely on panels of human red blood cells (RBCs), which coexpress many antigens and are not easily available for low-incidence blood group phenotypes. These problems have been addressed by generating cell lines expressing unique blood group antigens, which may be used as an alternative to human RBCs. However, the use of cell lines implies several drawbacks, like the requirement of cell culture facilities and the high cost of cryopreservation. The application of cell stabilization methods could facilitate their use as reagent cells in clinical laboratories. We generated stably-transfected cells expressing low-incidence blood group antigens (Dia and Lua). High-expresser clones were used to assess the effect of TransFix® treatment and lyophilization as cell preservation methods. Cells were kept at 4°C and cell morphology, membrane permeability and antigenic properties were evaluated at several time-points after treatment. TransFix® addition to cell suspensions allows cell stabilization and proper antigen detection for at least 120 days, despite an increase in membrane permeability and a reduction in antigen expression levels. Lyophilized cells showed minor morphological changes and antigen expression levels were rather conserved at days 1, 15 and 120, indicating a high stability of the freeze-dried product. These stabilized cells have been proved to react specifically with human sera containing alloantibodies. Both stabilization methods allow long-term preservation of the transfected cells antigenic properties and may facilitate their distribution and use as reagent-cells expressing low-incidence antigens, overcoming the limited availability of such rare RBCs.

  11. Automatic query generation using word embeddings for retrieving passages describing experimental methods

    PubMed Central

    Aydın, Ferhat; Hüsünbeyi, Zehra Melce; Özgür, Arzucan

    2017-01-01

    Information regarding the physical interactions among proteins is crucial, since protein–protein interactions (PPIs) are central for many biological processes. The experimental techniques used to verify PPIs are vital for characterizing and assessing the reliability of the identified PPIs. A lot of information about PPIs and the experimental methods are only available in the text of the scientific publications that report them. In this study, we approach the problem of identifying passages with experimental methods for physical interactions between proteins as an information retrieval search task. The baseline system is based on query matching, where the queries are generated by utilizing the names (including synonyms) of the experimental methods in the Proteomics Standard Initiative–Molecular Interactions (PSI-MI) ontology. We propose two methods, where the baseline queries are expanded by including additional relevant terms. The first method is a supervised approach, where the most salient terms for each experimental method are obtained by using the term frequency–relevance frequency (tf.rf) metric over 13 articles from our manually annotated data set of 30 full text articles, which is made publicly available. On the other hand, the second method is an unsupervised approach, where the queries for each experimental method are expanded by using the word embeddings of the names of the experimental methods in the PSI-MI ontology. The word embeddings are obtained by utilizing a large unlabeled full text corpus. The proposed methods are evaluated on the test set consisting of 17 articles. Both methods obtain higher recall scores compared with the baseline, with a loss in precision. Besides higher recall, the word embeddings based approach achieves higher F-measure than the baseline and the tf.rf based methods. We also show that incorporating gene name and interaction keyword identification leads to improved precision and F-measure scores for all three evaluated

  12. Automatic query generation using word embeddings for retrieving passages describing experimental methods.

    PubMed

    Aydın, Ferhat; Hüsünbeyi, Zehra Melce; Özgür, Arzucan

    2017-01-01

    Information regarding the physical interactions among proteins is crucial, since protein-protein interactions (PPIs) are central for many biological processes. The experimental techniques used to verify PPIs are vital for characterizing and assessing the reliability of the identified PPIs. A lot of information about PPIs and the experimental methods are only available in the text of the scientific publications that report them. In this study, we approach the problem of identifying passages with experimental methods for physical interactions between proteins as an information retrieval search task. The baseline system is based on query matching, where the queries are generated by utilizing the names (including synonyms) of the experimental methods in the Proteomics Standard Initiative-Molecular Interactions (PSI-MI) ontology. We propose two methods, where the baseline queries are expanded by including additional relevant terms. The first method is a supervised approach, where the most salient terms for each experimental method are obtained by using the term frequency-relevance frequency (tf.rf) metric over 13 articles from our manually annotated data set of 30 full text articles, which is made publicly available. On the other hand, the second method is an unsupervised approach, where the queries for each experimental method are expanded by using the word embeddings of the names of the experimental methods in the PSI-MI ontology. The word embeddings are obtained by utilizing a large unlabeled full text corpus. The proposed methods are evaluated on the test set consisting of 17 articles. Both methods obtain higher recall scores compared with the baseline, with a loss in precision. Besides higher recall, the word embeddings based approach achieves higher F-measure than the baseline and the tf.rf based methods. We also show that incorporating gene name and interaction keyword identification leads to improved precision and F-measure scores for all three evaluated methods

  13. Use of thermal infrared pictures for retrieving intertidal DEM by the waterline method: advantages and limitations

    NASA Astrophysics Data System (ADS)

    Gaudin, D.; Delacourt, C.; Allemand, P.

    2010-12-01

    Digital Elevation Models (DEM) of the intertidal zones have a growing interest for ecological and land development purposes. They are also a fundamental tool for monitoring current sedimentary movements in those low energy environments. Such DEMs have to be constructed with a centimetric resolution as the topographic changes are not predictable and as sediment displacements are weak. Direct construction of DEM by GPS in these muddy environment is difficult: photogrammetric techniques are not efficient on uniform coloured surfaces and terrestrial laser scans are difficult to stabilize on the mud, due to humidity. In this study, we propose to improve and to apply the waterline method to retrieve DEMs in intertidal zones. This technique is based on monitoring accurately the boundary between sand and water during a whole tide rise with thermal infrared images. The DEM is made by stacking all these lines calibrated by an immersed pressure sensor. Using thermal infrared pictures, instead of optical ones, improves the detection of the waterline, since mud and water have very different responses to sun heating and a large emissivity contrast. However, temperature retrieving from thermal infrared data is not trivial, since the luminance of an object is the sum of a radiative part and a reflexive part, whose relative proportions are given by the emissivity. In the following equation, B accounts for the equivalent blackbody luminance, and Linc is the incident luminance : Ltot}=L{rad}+L_{refl=ɛ B+(1-ɛ )Linc The infrared waterline technique has been used for the monitoring of a beach located on the Aber Benoit, 8.5km away from the open sea. The site is mainly constituted of mud, and waves are very small (less than one centimeter high), which are the ideal conditions for using the waterline method. A few measurements have been made to make differential heigh maps of sediments. We reached a mean resolution of 2cm and a vertical accuracy better than one centimeter. The results

  14. Information Retrieval.

    ERIC Educational Resources Information Center

    National Archives and Records Service (GSA), Washington, DC. Office of the National Archives.

    It is the purpose of this handbook to provide managers and their assistants with guidelines for determining where new information processing systems (dissemination, storage and retrieval) might profitably be employed in Government offices and with criteria for selecting the right methods and equipment. While the main objective is to encourage…

  15. Regional content-based image retrieval for solar images: Traditional versus modern methods

    NASA Astrophysics Data System (ADS)

    Banda, J. M.; Angryk, R. A.

    2015-11-01

    This work presents an extensive evaluation between conventional (distance-based) and modern (search-engine) information retrieval techniques in the context of finding similar Solar image regions within the Solar Dynamics Observatory (SDO) mission image repository. We compare pre-computed image descriptors (image features) extracted from the SDO mission images in two very different ways: (1) similarity retrieval using multiple distance-based metrics and (2) retrieval using Lucene, a general purpose scalable retrieval engine. By transforming image descriptors into histogram-like signatures and into Lucene-compatible text strings, we are able to effectively evaluate the retrieval capabilities of both methodologies. Using the image descriptors alongside a labeled image dataset, we present an extensive evaluation under the criteria of performance, scalability and retrieval precision of experimental retrieval systems in order to determine which implementation would be ideal for a production level system. In our analysis we performed key transformations to our sample datasets to properly evaluate rotation invariance and scalability. At the end of this work we conclude which technique is the most robust and would yield the best performing system after an extensive experimental evaluation, we also point out the strengths and weaknesses of each approach and theorize on potential improvements.

  16. 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.

  17. 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

  18. 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.

  19. One Question, Multiple Answers: Biochemical and Biophysical Screening Methods Retrieve Deviating Fragment Hit Lists.

    PubMed

    Schiebel, Johannes; Radeva, Nedyalka; Köster, Helene; Metz, Alexander; Krotzky, Timo; Kuhnert, Maren; Diederich, Wibke E; Heine, Andreas; Neumann, Lars; Atmanene, Cedric; Roecklin, Dominique; Vivat-Hannah, Valérie; Renaud, Jean-Paul; Meinecke, Robert; Schlinck, Nina; Sitte, Astrid; Popp, Franziska; Zeeb, Markus; Klebe, Gerhard

    2015-09-01

    Fragment-based lead discovery is gaining momentum in drug development. Typically, a hierarchical cascade of several screening techniques is consulted to identify fragment hits which are then analyzed by crystallography. Because crystal structures with bound fragments are essential for the subsequent hit-to-lead-to-drug optimization, the screening process should distinguish reliably between binders and non-binders. We therefore investigated whether different screening methods would reveal similar collections of putative binders. First we used a biochemical assay to identify fragments that bind to endothiapepsin, a surrogate for disease-relevant aspartic proteases. In a comprehensive screening approach, we then evaluated our 361-entry library by using a reporter-displacement assay, saturation-transfer difference NMR, native mass spectrometry, thermophoresis, and a thermal shift assay. While the combined results of these screening methods retrieve 10 of the 11 crystal structures originally predicted by the biochemical assay, the mutual overlap of individual hit lists is surprisingly low, highlighting that each technique operates on different biophysical principles and conditions.

  20. Recursive method for phase retrieval using transport of intensity and its applications.

    PubMed

    Basunia, Mahmudunnabi; Banerjee, Partha P; Abeywickrema, Ujitha; Poon, Ting-Chung; Zhang, Hongbo

    2016-11-20

    Propagation of optical fields is governed by the Helmholtz equation or the paraxial wave equation. Transport of intensity is a noninterferometric method to find the phase of an object by recording optical intensities at different distances of propagation. The transport of intensity equation results from the imaginary part of the complex paraxial wave equation and is equivalent to the principle of conservation of energy. The real part of the paraxial wave equation yields the Eikonal equation in the presence of diffraction. The amplitude and phase of the optical field must therefore simultaneously satisfy both the real and imaginary parts of the paraxial wave equation during propagation. In this paper, we demonstrate, with illustrative examples, how to exploit this to retrieve the phase through recursive calculations of the phase and intensity. This is achieved using the transport of intensity equation, which is solved using standard techniques, and the real part of the paraxial wave equation, or the transport of phase equation, which is solved using a Gauss-Seidel iterative method. Examples include calculation of the imaged phase induced through self-phase modulation of a focused laser beam in a liquid and the imaged phase of light reflected from a surface, which yields the 3D surface profile.

  1. A novel method for efficient archiving and retrieval of biomedical images using MPEG-7

    NASA Astrophysics Data System (ADS)

    Meyer, Joerg; Pahwa, Ash

    2004-10-01

    Digital archiving and efficient retrieval of radiological scans have become critical steps in contemporary medical diagnostics. Since more and more images and image sequences (single scans or video) from various modalities (CT/MRI/PET/digital X-ray) are now available in digital formats (e.g., DICOM-3), hospitals and radiology clinics need to implement efficient protocols capable of managing the enormous amounts of data generated daily in a typical clinical routine. We present a method that appears to be a viable way to eliminate the tedious step of manually annotating image and video material for database indexing. MPEG-7 is a new framework that standardizes the way images are characterized in terms of color, shape, and other abstract, content-related criteria. A set of standardized descriptors that are automatically generated from an image is used to compare an image to other images in a database, and to compute the distance between two images for a given application domain. Text-based database queries can be replaced with image-based queries using MPEG-7. Consequently, image queries can be conducted without any prior knowledge of the keys that were used as indices in the database. Since the decoding and matching steps are not part of the MPEG-7 standard, this method also enables searches that were not planned by the time the keys were generated.

  2. Comparative analysis of different retrieval methods for mapping grassland leaf area index using airborne imaging spectroscopy

    NASA Astrophysics Data System (ADS)

    Atzberger, Clement; Darvishzadeh, Roshanak; Immitzer, Markus; Schlerf, Martin; Skidmore, Andrew; le Maire, Guerric

    2015-12-01

    Fine scale maps of vegetation biophysical variables are useful status indicators for monitoring and managing national parks and endangered habitats. Here, we assess in a comparative way four different retrieval methods for estimating leaf area index (LAI) in grassland: two radiative transfer model (RTM) inversion methods (one based on look-up-tables (LUT) and one based on predictive equations) and two statistical modelling methods (one partly, the other entirely based on in situ data). For prediction, spectral data were used that had been acquired over Majella National Park in Italy by the airborne hyperspectral HyMap instrument. To assess the performance of the four investigated models, the normalized root mean squared error (nRMSE) and coefficient of determination (R2) between estimates and in situ LAI measurements are reported (n = 41). Using a jackknife approach, we also quantified the accuracy and robustness of empirical models as a function of the size of the available calibration data set. The results of the study demonstrate that the LUT-based RTM inversion yields higher accuracies for LAI estimation (R2 = 0.91, nRMSE = 0.18) as compared to RTM inversions based on predictive equations (R2 = 0.79, nRMSE = 0.38). The two statistical methods yield accuracies similar to the LUT method. However, as expected, the accuracy and robustness of the statistical models decrease when the size of the calibration database is reduced to fewer samples. The results of this study are of interest for the remote sensing community developing improved inversion schemes for spaceborne hyperspectral sensors applicable to different vegetation types. The examples provided in this paper may also serve as illustrations for the drawbacks and advantages of physical and empirical models.

  3. A single-image retrieval method for edge illumination X-ray phase-contrast imaging: Application and noise analysis.

    PubMed

    Diémoz, Paul C; Vittoria, Fabio A; Hagen, Charlotte K; Endrizzi, Marco; Coan, Paola; Bravin, Alberto; Wagner, Ulrich H; Rau, Christoph; Robinson, Ian K; Olivo, Alessandro

    2016-12-01

    Edge illumination (EI) X-ray phase-contrast imaging (XPCI) has been under development at University College London in recent years, and has shown great potential for both laboratory and synchrotron applications. In this work, we propose a new acquisition and processing scheme. Contrary to existing retrieval methods for EI, which require as input two images acquired in different setup configurations, the proposed approach can retrieve an approximate map of the X-ray phase from a single image, thus significantly simplifying the acquisition procedure and reducing data collection times. The retrieval method is analytically derived, based on the assumption of a quasi-homogeneous object, i.e. an object featuring a constant ratio between refractive index and absorption coefficient. The noise properties of the input and retrieved images are also theoretically analyzed under the developed formalism. The method is applied to experimental synchrotron images of a biological object. The experimental results show that the method can provide high-quality images, where the "edge" signal typical of XPCI images is transformed to an "area" contrast that enables an easier interpretation of the sample geometry. Moreover, the retrieved images confirm that the method is highly stable against noise. We anticipate that the developed approach will become the method of choice for a variety of applications of EI XPCI, thanks to its ability to simplify the acquisition procedure and reduce acquisitions time and dose to the sample. Future work will focus on the adaptation of the method to computed tomography and to polychromatic radiation from X-ray tubes. Copyright © 2016 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

  4. 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.

  5. 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.

  6. 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

  7. A new method for information retrieval in two-dimensional grating-based X-ray phase contrast imaging

    NASA Astrophysics Data System (ADS)

    Wang, Zhi-Li; Gao, Kun; Chen, Jian; Ge, Xin; Zhu, Pei-Ping; Tian, Yang-Chao; Wu, Zi-Yu

    2012-11-01

    Grating-based X-ray phase contrast imaging has been demonstrated to be an extremely powerful phase-sensitive imaging technique. By using two-dimensional (2D) gratings, the observable contrast is extended to two refraction directions. Recently, we have developed a novel reverse-projection (RP) method, which is capable of retrieving the object information efficiently with one-dimensional (1D) grating-based phase contrast imaging. In this contribution, we present its extension to the 2D grating-based X-ray phase contrast imaging, named the two-dimensional reverse-projection (2D-RP) method, for information retrieval. The method takes into account the nonlinear contributions of two refraction directions and allows the retrieval of the absorption, the horizontal and the vertical refraction images. The obtained information can be used for the reconstruction of the three-dimensional phase gradient field, and for an improved phase map retrieval and reconstruction. Numerical experiments are carried out, and the results confirm the validity of the 2D-RP method.

  8. Cirrus heterogeneity effects on cloud optical properties retrieved with an optimal estimation method from MODIS VIS to TIR channels

    NASA Astrophysics Data System (ADS)

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

    2017-02-01

    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 µm, 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.

  9. 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.

  10. Toxoplasma gondii from liquid nitrogen for continuous cell culture: methods to maximise efficient retrieval.

    PubMed

    Mavin, S; Evans, R; Chatterton, J M W; Ashburn, D; Joss, A W L; Ho-Yen, D O

    2003-01-01

    This study aims to increase the efficiency of continuous growth of Toxoplasma gondii in HeLa cells from tachyzoite stocks frozen in liquid nitrogen. Freezing and retrieval of tachyzoites for continuous cell culture requires more stringent protocols than those published for animal culture. The freezing and retrieval conditions are optimised so that a quality harvest (> or = 1 x 10(6) tachyzoites/mL, > or = 90% viability) can be produced using T. gondii recovered from liquid nitrogen as fast and reliably as possible. Retrieval success rate increased from 36% to 100%. An improved freezing procedure using chilled reagents and freshly harvested parasites, and adoption of an effective recovery protocol with retrieval of 3 x 10(7) tachyzoites into 75 cm2 flasks, change of maintenance media after six hours and subsequent blind passage all contributed to this success. The result is faster and more dependable production of T. gondii for diagnostic and experimental use.

  11. Toxoplasma gondii from liquid nitrogen for continuous cell culture:methods to maximise efficient retrieval.

    PubMed

    Mavin, S; Evans, R; Chatterton, J M W; Ashburn, D; Joss, A W L; Ho-Yen, D O

    2003-01-01

    This study aims to increase the efficiency of continuous growth of Toxoplasma gondii in HeLa cells from tachyzoite stocks frozen in liquid nitrogen. Freezing and retrieval of tachyzoites for continuous cell culture requires more stringent protocols than those published for animal culture. The freezing and retrieval conditions are optimised so that a quality harvest (≥ 1 x 10(6) tachyzoites/mL, ≥ 90% viability) can be produced using T. gondii recovered from liquid nitrogen as fast and reliably as possible. Retrieval success rate increased from 36% to 100%. An improved freezing procedure using chilled reagents and freshly harvested parasites, and adoption of an effective recovery protocol with retrieval of 3 x 10(7) tachyzoites into 75cm(2) flasks, change of maintenance media after six hours and subsequent blind passage all contributed to this success. The result is faster and more dependable production of T. gondii for diagnostic and experimental use.

  12. Method for analysis of antigen-antibody precipitins in double immunodiffusion.

    PubMed

    Treadwell, E L; Swanson, M S; Byrd, A W

    1988-01-01

    Ribonucleoprotein (RNP) antigen-antibody precipitin bands obtained by two-dimensional double immunodiffusion were systematically analyzed and compared using a microcomputer and a SPSS-PC statistical analysis package. Precipitins rated in respective agarose concentrations ranging from 0.3% to 1.5% were obtained from twofold dilutions of a calf thymus nuclear extract (CTNE) containing RNP antigen. These dilutions were reacted against the same dilutions of plasma containing anti-RNP antibody. A Mean Quality Index Score was calculated at each agarose concentration from the sum of ratings assigned for the intensity (thickness) of precipitin bands times the sum of ratings assigned for the clarity (clearness and sharpness) of the precipitin bands. This product was divided by the total number of possible precipitin reactions. The Mean Quality Index Score for the 0.4% agarose was significantly higher than the other concentrations (p less than or equal to 0.05). This method or similar approaches may allow a more systematic way of comparing precipitins developed in gel immunodiffusion.

  13. A novel method for rapid detection of Streptococcus pneumoniae antigens in blood.

    PubMed

    Fukushima, Kiyoyasu; Kubo, Toru; Ehara, Naomi; Nakano, Reiji; Matsutake, Toyoshi; Ishimatu, Yuji; Tanaka, Yumi; Akamatsu, Suguru; Izumikawa, Koichi; Kohno, Shigeru

    2016-03-01

    In this study, we used "RAPIRUN(®)Streptococcus pneumoniae HS (otitis media/sinusitis) (RAPIRUN-HS)," a rapid S. pneumoniae antigen detection kit, to investigate methods for detecting S. pneumoniae antigens in blood of 32 bacterial pneumonia patients. We simultaneously performed PCR to detect S. pneumoniae in blood samples. The results of these tests were compared based on pneumonia severity, determined using the Pneumonia Severity Index (PSI) score classification. Four S. pneumoniae PCR-positive patients of the six severe pneumococcal pneumonia patients (PSI risk class IV/V) also tested positive using RAPIRUN-HS. Twenty-four mild to moderate pneumonia patients (PSI risk class I-III) were S. pneumoniae PCR-negative; of these, 21 tested negative using RAPIRUN-HS. The pneumococcal pneumonia patients testing positive using RAPIRUN-HS had low leukocyte counts and elevated C-reactive protein and procalcitonin levels, indicating that RAPIRUN-HS results were correlated with pneumonia severity. The time course evaluations of the laboratory tests for severe pneumococcal pneumonia patients showed that RAPIRUN-HS and S. pneumoniae PCR yielded positive results earlier than the changes in procalcitonin and IL-6. Thus, concomitant pneumococcal bacteremia was strongly suspected in patients testing positive using RAPIRUN-HS. In conclusion, RAPIRUN-HS may be useful for determining whether to admit patients into hospitals and selecting the appropriate antimicrobial agents.

  14. 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.

  15. 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.

  16. Microwave brightness temperature and thermal inertia - towards synergistic method of high-resolution soil moisture retrieval

    NASA Astrophysics Data System (ADS)

    Lukowski, Mateusz; Usowicz, Boguslaw; Sagan, Joanna; Szlazak, Radoslaw; Gluba, Lukasz; Rojek, Edyta

    2017-04-01

    Soil moisture is an important parameter in many environmental studies, as it influences the exchange of water and energy at the interface between the land surface and the atmosphere. Accurate assessment of the soil moisture spatial and temporal variations is crucial for numerous studies; starting from a small scale of single field, then catchment, mesoscale basin, ocean conglomeration, finally ending at the global water cycle. Despite numerous advantages, such as fine accuracy (undisturbed by clouds or daytime conditions) and good temporal resolution, passive microwave remote sensing of soil moisture, e.g. SMOS and SMAP, are not applicable to a small scale - simply because of too coarse spatial resolution. On the contrary, thermal infrared-based methods of soil moisture retrieval have a good spatial resolution, but are often disturbed by clouds and vegetation interferences or night effects. The methods that base on point measurements, collected in situ by monitoring stations or during field campaigns, are sometimes called "ground truth" and may serve as a reference for remote sensing, of course after some up-scaling and approximation procedures that are, unfortunately, potential source of error. Presented research concern attempt to synergistic approach that join two remote sensing methods: passive microwave and thermal infrared, supported by in situ measurements. Microwave brightness temperature of soil was measured by ELBARA, the radiometer at 1.4 GHz frequency, installed at 6 meters high tower at Bubnow test site in Poland. Thermal inertia around the tower was modelled using the statistical-physical model whose inputs were: soil physical properties, its water content, albedo and surface temperatures measured by an infrared pyrometer, directed at the same footprint as ELBARA. The results coming from this method were compared to in situ data obtained during several field campaigns and by the stationary agrometeorological stations. The approach seems to be

  17. A simple and reliable immunohistochemical method for colocalization of 2 antigens in the same cells of paraffin-embedded tissues.

    PubMed

    Yan, Jun; Catts, Vibeke S; Chan, Anthony; McCombe, Pamela A

    2013-10-01

    Immunohistochemistry (IHC) lacks an efficient technique for colocalizing multiple antigens in the same cells of a single tissue section. The development of a methodology which combines the advantage of low cost, high sensitivity, and specificity would benefit clinical diagnosis and general research. On the basis of a newly published method of visualizing 2 antigens on a single paraffin-embedded tissue section, we have further developed a novel sequential technique for colocalizing 2 different antigens in a same cell in a paraffin-embedded tissue section. In this technique, we combined the microwave heating technique (MVT) with normal IHC methods to sequentially double stain a paraffin section; and colocalize 2 antigens in a single cell through result comparison stored in a digital management system. This MVT colocalization method has a higher degree of sensitivity and specificity comparable with conventional staining of both immunofluorescence and IHC systems. The primary advantage of this method is that it is inexpensive and convenient; the antibody(s) used in this method can be generated from the same or different species; it allows colocalization or comparison of different results of cell morphology for any single cell of the section on 2 images, avoids uncertainty when overlapping 2 antigens on a single image.

  18. Evaluation of the Secretor Status of ABO Blood Group Antigens in Saliva among Southern Rajasthan Population Using Absorption Inhibition Method

    PubMed Central

    Khajuria, Nidhi; Mamta; Ramesh, Gayathri

    2016-01-01

    Introduction The ABO blood group system was the significant element for forensic serological examination of blood and body fluids in the past before the wide adaptation of DNA typing. A significant proportion of individuals (80%) are secretors, meaning that antigens present in the blood are also found in other body fluids such as saliva. Absorption inhibition is one such method that works by reducing strength of an antiserum based on type and amount of antigen present in the stains. Aim To check the efficacy of identifying the blood group antigens in saliva and to know the secretor status using absorption inhibition method among southern Rajasthan population. Materials and Methods Blood and saliva samples were collected from 80 individuals comprising 20 individuals in each blood group. The absorption inhibition method was used to determine the blood group antigens in the saliva and then the results were correlated with the blood group of the collected blood sample. The compiled data was statistically analysed using chi-square test. Results Blood groups A & O revealed 100% secretor status for both males and females. While blood groups B and AB revealed 95% secretor status. Conclusion Secretor status evaluation of the ABO blood group antigen in saliva using absorption inhibition method can be a useful tool in forensic examination. PMID:27042574

  19. A Novel Method to Assess Wear Rates of Retrieved Tibial Inserts Following in-vivo Use

    NASA Astrophysics Data System (ADS)

    Paniogue, Tanille J.

    Ultra-high molecular weight polyethylene (UHMWPE) on cobalt chrome is the bearing couple of choice for total knee arthroplasty. The number of patients undergoing total knee arthroplasty has been steadily growing and is projected to continue increasing rapidly in the near future. Many of these patients are younger and more active and therefore need a longer lasting device. However, many of these devices fail prematurely and often the primary reason for failure and ultimately revision is due to wear related issues. Therefore, examining how wear rates of the UHMWPE tibial insert change during in-vivo use can help elucidate the mechanisms of accelerated wear and hopefully aid in finding solutions to combat wear related failures. Different crosslinking treatments have been employed by manufacturers to improve wear resistance of the polyethylene. While this has been shown to be an effective way to reduce wear, crosslinking has led to other issues such as oxidative instability and a decline in mechanical properties. The purpose of this body of work is to examine how changes in oxidation, after in-vivo use, affect wear resistance. A novel testing method was developed to test the native articular surface from retrieved tibial inserts in a laboratory Pin-on-Disk (POD) simulator. The method was validated using short-duration implant articular surfaces and non-articular control pins. In the absence of high surface oxidation or severe surface damage, the articular surface pins had comparable steady state wear rates to their bulk counterparts. Tests of devices with longer in-vivo service show chemical changes consistent with a free-radical mediated oxidation mechanism. Tribological assessment of the articular surfaces shows increasing wear rates as a function of oxidation. While this relationship has been hypothesized in the literature, these experiments represent the first physical demonstration of the phenomenon. The wear mechanism is further explored through infrared

  20. To Clone or Not To Clone: Method Analysis for Retrieving Consensus Sequences In Ancient DNA Samples

    PubMed Central

    Winters, Misa; Barta, Jodi Lynn; Monroe, Cara; Kemp, Brian M.

    2011-01-01

    The challenges associated with the retrieval and authentication of ancient DNA (aDNA) evidence are principally due to post-mortem damage which makes ancient samples particularly prone to contamination from “modern” DNA sources. The necessity for authentication of results has led many aDNA researchers to adopt methods considered to be “gold standards” in the field, including cloning aDNA amplicons as opposed to directly sequencing them. However, no standardized protocol has emerged regarding the necessary number of clones to sequence, how a consensus sequence is most appropriately derived, or how results should be reported in the literature. In addition, there has been no systematic demonstration of the degree to which direct sequences are affected by damage or whether direct sequencing would provide disparate results from a consensus of clones. To address this issue, a comparative study was designed to examine both cloned and direct sequences amplified from ∼3,500 year-old ancient northern fur seal DNA extracts. Majority rules and the Consensus Confidence Program were used to generate consensus sequences for each individual from the cloned sequences, which exhibited damage at 31 of 139 base pairs across all clones. In no instance did the consensus of clones differ from the direct sequence. This study demonstrates that, when appropriate, cloning need not be the default method, but instead, should be used as a measure of authentication on a case-by-case basis, especially when this practice adds time and cost to studies where it may be superfluous. PMID:21738625

  1. 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

  2. New method for simultaneous gas and aerosol retrievals from space limb-scanning spectral observation of the atmosphere.

    PubMed

    Oshchepkov, Sergey; Sasano, Yasuhiro; Yokota, Tatsuya

    2002-07-20

    This study concerns the development of a new inversion method for simultaneous gas and aerosol retrievals in the upper layers of the atmosphere from limb-viewing multiwavelength-transmission infrared measurements. In this method, concentrations of gas species such as O3, NO2, HNO3, N2O, CH4, and H2O, and spectral dependences of the aerosol extinction coefficient are retrieved simultaneously. When this is done, smoothness constraints on the desired spectral dependencies of the aerosol extinction coefficient are used as an a priori assumption. The method is used in the treating of synthetic transmission spectra of the Improved Limb Atmospheric Spectrometer, which is based on the solar occultation technique and was on board the Advanced Earth Observing Satellite. A set of numerical tests shows the efficiency of the method.

  3. 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…

  4. 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…

  5. [Preparation of Staphylococcus aureus antigens for evaluation of their immunological reactivity with the human sera by the western blot method].

    PubMed

    Tyski, S; Jarecka, K; Gut, W; Hryniewicz, W

    1991-01-01

    Extracellular antigens as well as cell wall extracts of 4 S. aureus strains isolated from different kinds of infection were analysed by Western-Blott technique. Materials obtained in two systems of bacteria cultivation (with and without aeration) were compared. Four systems of PAGE (native conditions, with 8.0 M urea, with SDS and SDS after previous reduction of the material with 2-mercaptoethanol) were compared in order to get the best differentiation of proteins and antigens. Immunological reactivity of the antigens mixture with two human sera: highly positive (with three S. aureus antigens in ELISA) from patient with staphylococcal sepsis and negative (from blood donor) were analysed. The best results were obtained after reduction of the cell wall extracted material in SDS-PAGE. The different protein patterns depending on the strain and the method of bacteria cultivation were observed. The standardisation of Western-Blott technique was performed, including titration of the sera to get the best differentiation of the antigens. The difference in immunological reactivity of the positive and negative sera with staphylococcal antigens mixture showed rather quantitative than qualitative character.

  6. Implementation of the common phrase index method on the phrase query for information retrieval

    NASA Astrophysics Data System (ADS)

    Fatmawati, Triyah; Zaman, Badrus; Werdiningsih, Indah

    2017-08-01

    As the development of technology, the process of finding information on the news text is easy, because the text of the news is not only distributed in print media, such as newspapers, but also in electronic media that can be accessed using the search engine. In the process of finding relevant documents on the search engine, a phrase often used as a query. The number of words that make up the phrase query and their position obviously affect the relevance of the document produced. As a result, the accuracy of the information obtained will be affected. Based on the outlined problem, the purpose of this research was to analyze the implementation of the common phrase index method on information retrieval. This research will be conducted in English news text and implemented on a prototype to determine the relevance level of the documents produced. The system is built with the stages of pre-processing, indexing, term weighting calculation, and cosine similarity calculation. Then the system will display the document search results in a sequence, based on the cosine similarity. Furthermore, system testing will be conducted using 100 documents and 20 queries. That result is then used for the evaluation stage. First, determine the relevant documents using kappa statistic calculation. Second, determine the system success rate using precision, recall, and F-measure calculation. In this research, the result of kappa statistic calculation was 0.71, so that the relevant documents are eligible for the system evaluation. Then the calculation of precision, recall, and F-measure produces precision of 0.37, recall of 0.50, and F-measure of 0.43. From this result can be said that the success rate of the system to produce relevant documents is low.

  7. Retrieving microphysical properties and air motion of cirrus clouds based on the doppler moments method using cloud radar

    NASA Astrophysics Data System (ADS)

    Zhong, Lingzhi; Liu, Liping; Deng, Min; Zhou, Xiuji

    2012-05-01

    Radar parameters including radar reflectivity, Doppler velocity, and Doppler spectrum width were obtained from Doppler spectrum moments. The Doppler spectrum moment is the convolution of both the particle spectrum and the mean air vertical motion. Unlike strong precipitation, the motion of particles in cirrus clouds is quite close to the air motion around them. In this study, a method of Doppler moments was developed and used to retrieve cirrus cloud microphysical properties such as the mean air vertical velocity, mass-weighted diameter, effective particle size, and ice content. Ice content values were retrieved using both the Doppler spectrum method and classic Z-IWC (radar reflectivity-ice water content) relationships; however, the former is a more reasonable method.

  8. Coherent diffractive imaging beyond the Fresnel approximation using a deterministic phase-retrieval method with an aperture-array filter.

    PubMed

    Nakajima, Nobuharu

    2013-03-01

    Previously, we have proposed a lensless coherent imaging using a nonholographic and noniterative phase-retrieval method that allows the reconstruction of a complex-valued object from a single diffraction intensity measured with an aperture-array filter. The proof-of-concept experiment of this method has been demonstrated under the Fresnel diffraction approximation. In applications to microscopy, however, the measurement of the diffraction intensity with high numerical aperture beyond the Fresnel approximation is required to obtain the object information at high spatial resolution. Thus we have also presented an extension procedure to apply the method to the cases beyond the Fresnel approximation by means of computer simulations. Here the effectiveness of the procedure is demonstrated by the experiments, in which the reconstruction with about 10 times the resolution of our previous experiment has been achieved and the object information in depth direction has been retrieved.

  9. CODA METHOD AT HIGH FREQUENCIES: RETRIEVING SOURCE PARAMETERS OF SMALL (M1-M2) EARTHQUAKES

    NASA Astrophysics Data System (ADS)

    Viegas, G.; Abercrombie, R. E.; Mayeda, K. M.

    2009-12-01

    We calculate source parameters of small earthquakes from coda derived source spectrum ratios, extending the coda method to higher frequencies and smaller crustal volumes. To validate our high frequency results, we compare our source parameters estimates to the ones obtained with a direct wave study for the same set of earthquakes. We investigate earthquake source scaling relationships using local and regional good quality recordings of the M5 2002 Au Sable Forks, NY, mainshock and aftershocks sequence (M4-M1), and regional recordings of other moderate Eastern North America (ENA) earthquakes. We successfully retrieve spectral ratios, with a clear corner frequency and omega squared fall off, for the small (M2) Au Sable Forks aftershocks recorded locally (~3 km to 12 km epicentral distances) at a high sampling rate (200 sps). The local data have maximum coda duration of 15 s after the S wave onset (triggered recording). We investigate if the records are long enough, by first testing the method with Parkfield, CA, earthquakes, a dataset with similar dimensions in terms of station epicentral distances, earthquake magnitudes, and instrument sampling rate, for which records with long codas are available. The method holds for both datasets at high frequencies (up to 80 Hz), with a small increase of inter-station coda amplitude instability (0.5 standard deviation), expected for smaller earthquakes. We obtain in average higher corner frequencies and stress drops estimates (factor of 1.7 for corner frequency and 4.3 for stress drop) for the small (~M2) locally recorded Au Sable Forks earthquakes, than the values obtained with a direct wave study, and in average lower corner frequencies and stress drops for the moderate regionally recorded earthquakes (factor of 0.7 for corner frequency and 0.4 for stress drop). The corner frequencies of the mainshock and M3 earthquakes are close to the usable band limit and so uncertainties in the estimates of corner frequency and stress drop

  10. [Research on serum prostate-specific antigen measurement by characteristic spectral absorption method].

    PubMed

    Zhu, Jian-ming; Chen, Zhen-cheng

    2012-01-01

    A serum prostate-specific antigen (PSA) measurement method was studied using immunochromatography-based colloidal gold-marked test-strips and characteristic spectral absorption method. Some LEDs in the range from 520 to 535 nm irradiated the test-strips sampled by PSA, and then a photodiode in the range from 520 to 540 nm measured the reflex light at the specific area. Accordingly, the absorbency of the strip could be calculated, then the relationship between PSA level and strip absorbency could be ascertained by linear fit method. The experimental measurement system was calibrated by different PSA standard solutions in this research. As a result, in the range between 5 to 50 ng x mL(-1), the levels of PSA have a linear relationship with the absorbency of test-strips. Some experiments were completed by 21 different PSA standard solutions within that range, and then the correlation coefficient of the results is equal to 0.910, which proves that the proposed method for serum PSA level measurement is feasible.

  11. A simple method for retrieving significant wave height from Dopplerized X-band radar

    NASA Astrophysics Data System (ADS)

    Carrasco, Ruben; Streßer, Michael; Horstmann, Jochen

    2017-02-01

    Retrieving spectral wave parameters such as the peak wave direction and wave period from marine radar backscatter intensity is very well developed. However, the retrieval of significant wave height is difficult because the radar image spectrum (a backscatter intensity variance spectrum) has to be transferred to a wave spectrum (a surface elevation variance spectrum) using a modulation transfer function (MTF) which requires extensive calibration for each individual radar setup. In contrast to the backscatter intensity, the Doppler velocity measured by a coherent radar is induced by the radial velocity (or line-of-sight velocity) of the surface scattering and its periodic component is mainly the contribution of surface waves. Therefore, the variance of the Doppler velocity can be utilized to retrieve the significant wave height. Analyzing approximately 100 days of Doppler velocity measurements of a coherent-on-receive radar operating at X-band with vertical polarization in transmit and receive, a simple relation was derived and validated to retrieve significant wave heights. Comparison to wave measurements of a wave rider buoy as well as an acoustic wave and current profiler resulted in a root mean square error of 0.24 m with a bias of 0.08 m. Furthermore, the different sources of error are discussed and investigated.

  12. Applying Information-Retrieval Methods to Software Reuse: A Case Study.

    ERIC Educational Resources Information Center

    Stierna, Eric J.; Rowe, Neil C.

    2003-01-01

    Discusses reuse of existing software for new purposes as a key aspect of efficient software engineering by matching formal written requirements used to define the new and the old software. Explores two matching methodologies that use information retrieval techniques and describes test results from a comparison of two military systems. (Author/LRW)

  13. Applying Information-Retrieval Methods to Software Reuse: A Case Study.

    ERIC Educational Resources Information Center

    Stierna, Eric J.; Rowe, Neil C.

    2003-01-01

    Discusses reuse of existing software for new purposes as a key aspect of efficient software engineering by matching formal written requirements used to define the new and the old software. Explores two matching methodologies that use information retrieval techniques and describes test results from a comparison of two military systems. (Author/LRW)

  14. User-Centered Perspective of Information Retrieval Research and Analysis Methods.

    ERIC Educational Resources Information Center

    Sugar, William

    1995-01-01

    Reviews information retrieval (IR) studies since 1986 from the user's perspective. Identifies two main approaches that advocate user-centered design theory: (1) the cognitive approach; and (2) the holistic approach. Also explores other approaches--systems thinking/action research and usability techniques that may have potential for IR research and…

  15. Comparing different methods to retrieve cloud top height from Meteosat satellite data

    NASA Astrophysics Data System (ADS)

    Tabone, I.; Briz, S.; Anzalone, A.; De Castro, A. J.; Lopez, F.; Ferrarese, S.; Isgrò, F.; Cassardo, C.; Cremonini, R.; Bertaina, M.

    2015-10-01

    Cloud parameters such as the Cloud Top Height (CTH), Cloud Top Temperature (CTT), emissivity, particle size and optical depth have always been matter of interest for the atmospheric community. Particularly the CTH provides information leading to better understand the cloud radiative effects. Although there are many meteorological satellites providing the CTH, there are other sensors, not devoted to this purpose, that give some information from which this crucial parameter can be estimated. In this contribution we will describe three different methodologies to retrieve the CTH. The first technique is based on stereo-vision algorithms and requires two different views of the same scene and does not need of extra atmospheric information. In the second one, brightness temperatures in two IR spectral bands are converted to real cloud temperature by means of the proposed algorithms. From the CTT, the CTH is estimated using temperature vertical profiles (measured or modeled). The third technique retrieves the CTH from the output parameters of post event simulations performed by a Numerical Weather Prediction (NWP) model that in this work will be the mesoscale model WRF (Weather Research Forecast). This article presents a preliminary work, in which the heights retrieved by the three methodologies applied to the geostationary satellite Meteosat 10 are compared with the heights given by MODIS sensor installed on the polar satellite AQUA. This promising results show that valuable information about CTH can be retrieved from Meteosat which provide high frequency and large scale data useful for weather and climate research.

  16. 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.

  17. Anti-noise algorithm of lidar data retrieval by combining the ensemble Kalman filter and the Fernald method.

    PubMed

    Mao, Feiyue; Gong, Wei; Li, Chen

    2013-04-08

    The lidar signal-to-noise ratio decreases rapidly with an increase in range, which severely affects the retrieval accuracy and the effective measure range of a lidar based on the Fernald method. To avoid this issue, an alternative approach is proposed to simultaneously retrieve lidar data accurately and obtain a de-noised signal as a by-product by combining the ensemble Kalman filter and the Fernald method. The dynamical model of the new algorithm is generated according to the lidar equation to forecast backscatter coefficients. In this paper, we use the ensemble sizes as 60 and the factor δ(1/2) as 1.2 after being weighed against the accuracy and the time cost based on the performance function we define. The retrieval and de-noising results of both simulated and real signals demonstrate that our method is practical and effective. An extensive application of our method can be useful for the long-term determining of the aerosol optical properties.

  18. Retrieval of diffusing surface by two-frame interferometric method with blind phase shift of a reference wave

    NASA Astrophysics Data System (ADS)

    Muravsky, Leonid I.; Kmet', Arkady B.; Voronyak, Taras I.

    2011-08-01

    Two-frame interferometric method with blind phase shift of a reference wave for smooth surfaces retrieval is considered. The ability of this method to reconstruct a macrorelief of diffusing surfaces with a given roughness is studied. Computer simulations have testified the ability of reliable low-noise reconstruction of the diffusing surface macrorelief with standard deviation of the roughness heights up to λ/10 by using the developed interferogram processing algorithm. The simulations have shown that the proposed correlation approach, which is used to determine the reference wave blind phase shift, is more suitable for a diffusing surface than for a smooth one and the increase of surface roughness leads to a quadruple decrease of this error in comparison with that for the smooth surface. Experimental verification of the interferometric method performance to retrieve real diffusing surface macroreliefs with given roughness has been done by using the experimental setup based on a Twyman-Green interferometer and roughness comparison specimen. The obtained experimental results virtually have coincided with the computer simulation results that prove the performance of the considered method to retrieve not only smooth, but also diffusing surfaces.

  19. 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

  20. 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.

  1. Surface Plasmon Resonance is an Analytically Sensitive Method for Antigen Profiling of Extracellular Vesicles.

    PubMed

    Gool, Elmar L; Stojanovic, Ivan; Schasfoort, Richard B M; Sturk, Auguste; van Leeuwen, Ton G; Nieuwland, Rienk; Terstappen, Leon W M M; Coumans, Frank A W

    2017-10-01

    Identification, enumeration, and characterization of extracellular vesicles (EVs) are hampered by the small size of EVs, a low refractive index, and low numbers of antigens on their surface. We investigated the potential of a 48-multiplex surface plasmon resonance imaging (SPRi) system to perform EV phenotyping. Antigen surface density of 11 antigens was measured on the human breast cancer cell lines HS578T, MCF7, and SKBR3 and their EVs by use of both SPRi and the widely used flow cytometry (FCM). For cells, the SPRi and FCM signals for antigen exposure correlated (RHS578T cells(2) = 0.66, RMCF7 cells(2) = 0.78, RSKBR3 cells(2) = 0.60). With regard to EVs, SPRi detected 31 out of 33 tested antibody-EV pairs, whereas our flow cytometer detected 5 antibody-EV pairs because of high blank and isotype control signals. For HS578T-derived EVs, the SPRi and FCM signals correlated (R(2)HS578T EVs = 0.98). However, on MCF7- and SKBR3-derived EVs, insufficient antigens were detected by our flow cytometer. To confirm that the SPRi responses correlated with mean antigen density on EVs, the SPRi responses of EVs were correlated with antigen density on parental cells as measured by FCM (RHS578T(2) = 0.77, RMCF7(2) = 0.49, RSKBR3(2) = 0.52). SPRi responses correlate with mean antigen density. Moreover, SPRi detects lower antigen-exposure levels than FCM because SPRi measures an ensemble of EVs binding to the sensor surface, whereas FCM detects antigens of single EV. © 2017 American Association for Clinical Chemistry.

  2. A new method for the evaluation of antibody affinity based on serial dilutions of studied antibody-antigen mixture.

    PubMed

    Bobrovnik, S A

    2002-01-01

    A new method for the evaluation of the affinity of bivalent antibodies were suggested. This method is based on the previously published by the author the idea of using so-called coordinates of dilutions. It was shown that the suggested method allows to evaluate the affinity of antibodies with high accuracy using this simple approach. It is supposed that at some conditions the suggested method could have substantial advantages in comparison to the traditional methods. This method allows to analyze situations when antibodies are already in a mixture with antigen, for example in the bloodstream in the case of infections or autoimmune diseases. The method provides useful approach for the evaluation not only antibody affinity, but also the concentration of circulated antigen.

  3. A Sense Retrieving Method from a Noun for the Commonsense Feeling Judgment System

    NASA Astrophysics Data System (ADS)

    Watabe, Hirokazu; Horiguchi, Atsushi; Kawaoka, Tsukasa

    When we humans receive uncertain information, we interpret it properly, so we can expand the conversation, and take proper actions. This is possible because we have "commonsense" concerning the word, which is built up from knowledge that is stored through long time experience. Among the commonsense we use in our every day lives it is thought that there are the commonsense concerning; quantity such as size, weight, speed, time, or place; sense or feeling such as hot, beautiful, or loud; and moreover emotion such as happy or sad. In order for computers to understand the meaning and become closer to human beings, it is thought that the construction of a "Commonsense Judgment System" which deals with these "commonsense" is necessary. A subsystem needed for the "Commonsense Judgment System" is the system that judges the commonsense concerning the characteristics of words, namely the "Commonsense Feeling Judgment System." This paper proposes a mechanism to associate the characteristics of a word based on our five senses, such as an apple is red, with a knowledge base consisting of basic words. When aiming to realize this "Commonsense Feeling Judgment System" and trying to make a computer have the same commonsense and judgment ability as human beings, a very important factor is the handling of unknown words. Judgment concerning words, which are given to the computer as knowledge before hand, is not a problem since it can refer to that knowledge. But when an unknown word, non-registered knowledge, is inputted, how to process that word is a very difficult problem. In this paper, a method of unknown word processing, which connects an inputted unknown word to a word that is registered in the judgment knowledge base, is proposed. By using a concept base, which is made from several electric dictionaries, the closeness of meaning is put into consideration. With this process, it is possible to understand a word that does not exist in the knowledge base. This study aims to

  4. An inversion method for retrieving soil moisture information from satellite altimetry observations

    NASA Astrophysics Data System (ADS)

    Uebbing, Bernd; Forootan, Ehsan; Kusche, Jürgen; Braakmann-Folgmann, Anne

    2016-04-01

    Soil moisture represents an important component of the terrestrial water cycle that controls., evapotranspiration and vegetation growth. Consequently, knowledge on soil moisture variability is essential to understand the interactions between land and atmosphere. Yet, terrestrial measurements are sparse and their information content is limited due to the large spatial variability of soil moisture. Therefore, over the last two decades, several active and passive radar and satellite missions such as ERS/SCAT, AMSR, SMOS or SMAP have been providing backscatter information that can be used to estimate surface conditions including soil moisture which is proportional to the dielectric constant of the upper (few cm) soil layers . Another source of soil moisture information are satellite radar altimeters, originally designed to measure sea surface height over the oceans. Measurements of Jason-1/2 (Ku- and C-Band) or Envisat (Ku- and S-Band) nadir radar backscatter provide high-resolution along-track information (~ 300m along-track resolution) on backscatter every ~10 days (Jason-1/2) or ~35 days (Envisat). Recent studies found good correlation between backscatter and soil moisture in upper layers, especially in arid and semi-arid regions, indicating the potential of satellite altimetry both to reconstruct and to monitor soil moisture variability. However, measuring soil moisture using altimetry has some drawbacks that include: (1) the noisy behavior of the altimetry-derived backscatter (due to e.g., existence of surface water in the radar foot-print), (2) the strong assumptions for converting altimetry backscatters to the soil moisture storage changes, and (3) the need for interpolating between the tracks. In this study, we suggest a new inversion framework that allows to retrieve soil moisture information from along-track Jason-2 and Envisat satellite altimetry data, and we test this scheme over the Australian arid and semi-arid regions. Our method consists of: (i

  5. Evaluation of antigen-capture ELISA and immunohistochemical methods for avian surveillance of West Nile virus.

    PubMed

    Godhardt, Jennifer A; Beheler, Kerry; O'Connor, Michael J; Whyte, T J; Reisdorf, Erik S; Ubl, Susan J; Bochsler, Philip N; Toohey-Kurth, Kathy L

    2006-01-01

    Accurate detection of West Nile virus (WNV) in corvids is essential for monitoring the spread of virus during the mosquito season. Viremia in corvids is very high, with titers approaching 10(8) viral particles/ml. In the presence of such marked viremia, the sensitivity of real-time reverse transcription-polymerase chain reaction (RT-PCR) analysis is unnecessary, and more cost-effective methods should be assessed. To this end, antigen-capture ELISA (ACE) and immunohistochemical (IHC) assays were evaluated. Skin, cloacal swab specimens, and feathers from corvids were tested by use of ACE, and results were compared with results obtained from use of real-time RT-PCR analysis. Of the 3 sample types, skin gave the best sensitivity (98%) and specificity (100%). Skin, brain, kidney, and spleen from corvids were analyzed by IHC, and results were compared with real-time RT-PCR results. Kidney and spleen were more often positive by use of IHC than were brain and skin tissue; however, IHC did not perform as well as ACE in the identification of virus-positive birds. Results of this study support the use of a skin sample in an ACE format as an effective surveillance method for corvids.

  6. 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.

  7. A simple method for the biochemical purification of Ro/SS-A antigen.

    PubMed

    Wu, D H; Tavoni, A; Garzelli, C; Neri, R; Vitali, C; Bombardieri, S

    1989-07-26

    In the present study, Ro/SS-A antigen has been isolated from human spleen by a two-step procedure. In the first step most of the non-antigenic material was removed by means of ammonium sulphate precipitation and ion exchange chromatography. The final purification was obtained by passing the Ro/SS-A-containing fractions twice through a Mono Q ion exchange fast protein liquid chromatography (FPLC) column. The purified antigen showed identical immunoreactivity with crude material on CIE and was composed of two polypeptides with a molecular weight of approximately 60,000 and 55,000 respectively on SDS-PAGE, both reacting on Western blotting with a panel of anti-Ro/SS-A antisera. This system permits milligrams of highly purified antigen to be obtained from grams of human spleen.

  8. A novel method to identify and characterise peptide mimotopes of heat shock protein 70-associated antigens.

    PubMed

    Arnaiz, Blanca; Madrigal-Estebas, Laura; Todryk, Stephen; James, Tharappel C; Doherty, Derek G; Bond, Ursula

    2006-04-08

    The heat shock protein, Hsp70, has been shown to play an important role in tumour immunity. Vaccination with Hsp70-peptide complexes (Hsp70-PCs), isolated from autologous tumour cells, can induce protective immune responses. We have developed a novel method to identify synthetic mimic peptides of Hsp70-PCs and to test their ability to activate T-cells. Peptides (referred to as "recognisers") that bind to Hsp70-PCs from the human breast carcinoma cell line, MDA-MB-231, were identified by bio-panning a random peptide M13 phage display library. Synthetic recogniser peptides were subsequently used as bait in a reverse bio-panning experiment to identify potential Hsp70-PC mimic peptides. The ability of the recogniser and mimic peptides to prime human lymphocyte responses against tumour cell antigens was tested by stimulating lymphocytes with autologous peptide-loaded monocyte-derived dendritic cells (DCs). Priming and subsequent stimulation with either the recogniser or mimic peptide resulted in interferon-gamma (IFN-gamma) secretion by the lymphocytes. Furthermore, DCs loaded with Hsp70, Hsp70-PC or the recogniser or the mimic peptide primed the lymphocytes to respond to soluble extracts from breast cells. These results highlight the potential application of synthetic peptide-mimics of Hsp70-PCs, as modulators of the immune response against tumours.

  9. A novel method for evaluating natural and vaccine induced serological responses to Bordetella pertussis antigens.

    PubMed

    Berbers, G A M; van de Wetering, M S E; van Gageldonk, P G M; Schellekens, J F P; Versteegh, F G A; Teunis, P F M

    2013-08-12

    We studied the time course of serum IgG antibodies against 3 different pertussis vaccine antigens: PT (pertussis toxin), FHA (filamentous hemagglutinin), Prn (pertactin) in sera from individuals vaccinated with four different pertussis vaccines at 4 years of age: (N=44, 44, 23 and 23, respectively,) and compared the responses to/after natural infection with Bordetella pertussis (N=44, age 1-8 years). These longitudinal data were analyzed with a novel method, using a mathematical model to describe the observed responses, and their variation among subjects. This allowed us to estimate biologically meaningful characteristics of the serum antibody response, like peak level and decay rate, and to compare these among natural infections and vaccine responses. Compared to natural infection, responses to PT after vaccination with the tested vaccines are smaller in magnitude and tend to decay slightly faster. When present in vaccines, FHA and Prn tend to produce high peak levels, higher than those in naturally infected patients, but these decay faster. As expected, the Dutch whole cell vaccine produced lower antibody responses than the acellular vaccines. This model allows a better comparison of the kinetics of vaccine induced antibody responses and after natural infection over a long follow up period.

  10. Nonadherent culture method downregulates stem cell antigen-1 expression in mouse bone marrow mesenchymal stem cells

    PubMed Central

    DENG, BAOPING; DENG, WEIPING; XIAO, PINGNAN; ZENG, KUAN; ZHANG, SHINING; ZHANG, HONGWU; DENG, DAVID YB; YANG, YANQI

    2015-01-01

    Mesenchymal stem cells (MSCs) are primarily isolated by their adherence to plastic and their in vitro growth characteristics. Expansion of these cells from an adherent culture is the only method to obtain a sufficient number of cells for use in clinical practice and research. However, little is known with regard to the effect of adherence to plastic on the phenotype of the cells. In the present study, bone marrow CD45−CD31−CD44− stem cell antigen (Sca)-1+ MSCs were sorted by flow cytometry and expanded in adherent cultures. The expression levels of the adhesion molecule, Sca-1, in the adherent cultures were compared with those from nonadherent cultures at different time points. The flow cytometry results indicated that the expression levels of Sca-1 decreased in the MSCs in the nonadherent cultures grown in ultra-low-adherent plates. Furthermore, the result was confirmed by quantitative polymerase chain reaction at the same time points. Therefore, the results demonstrated that the loss of plastic adherence downregulated the expression of Sca-1. The observations may provide novel insights into the molecular mechanisms underlying plastic adherent culture. PMID:26170908

  11. Hepatitis C virus core antigen assay: an alternative method for hepatitis C diagnosis.

    PubMed

    Wang, Lijuan; Lv, Hong; Zhang, Guojun

    2017-03-01

    Background The study aimed to evaluate a fully automated chemiluminescent immunoassay and compared it with a quantitative RNA assay and anti-HCV assay to verify the utility of this automated Ag assay as an alternative method for hepatitis C diagnosis. Methods A total of 229 serum samples previously tested for anti-HCV concentrations by the Architect Anti-HCV assay, were selected for HCV RNA testing by real time RT-PCR kit (Shanghai ZJ Bio-Tec Co., Ltd) and 125 specimens were tested for HCV Ag by the Architect HCV core Antigen kit. Results The log10 HCVAg and HCV RNA concentrations were highly correlated [ r = 0.834); with HCV RNA as the comparator test, HCVAg had 100% specificity, 100% positive predictive value (PPV) and 94.8% sensitivity. We found 1 pg/mL of total HCV core Ag is equivalent to approximately 6607HCV RNA international units (IU)/mL. Receiver operator characteristic curve analysis showed that the area under the curve of HCV core Ag (0.989) was greater than HCV Ab (0.871). HCV Ag concentrations and RNA-to-Ag ratio of the groups for HCV RNA concentrations ≤10(5) and >10(5 )IU/mL were both significantly different from each other ( P < 0.05). Conclusion The Architect HCV core Ag assay may be an alternative method for hepatitis C diagnosis, performed on the same analytical platform and sample as the anti-HCV assay, shortening the diagnostic window period, demonstrating good correlation with HCV RNA assay with high specificity and positive predictive value.

  12. De-noising and retrieving algorithm of Mie lidar data based on the particle filter and the Fernald method.

    PubMed

    Li, Chen; Pan, Zengxin; Mao, Feiyue; Gong, Wei; Chen, Shihua; Min, Qilong

    2015-10-05

    The signal-to-noise ratio (SNR) of an atmospheric lidar decreases rapidly as range increases, so that maintaining high accuracy when retrieving lidar data at the far end is difficult. To avoid this problem, many de-noising algorithms have been developed; in particular, an effective de-noising algorithm has been proposed to simultaneously retrieve lidar data and obtain a de-noised signal by combining the ensemble Kalman filter (EnKF) and the Fernald method. This algorithm enhances the retrieval accuracy and effective measure range of a lidar based on the Fernald method, but sometimes leads to a shift (bias) in the near range as a result of the over-smoothing caused by the EnKF. This study proposes a new scheme that avoids this phenomenon using a particle filter (PF) instead of the EnKF in the de-noising algorithm. Synthetic experiments show that the PF performs better than the EnKF and Fernald methods. The root mean square error of PF are 52.55% and 38.14% of that of the Fernald and EnKF methods, and PF increases the SNR by 44.36% and 11.57% of that of the Fernald and EnKF methods, respectively. For experiments with real signals, the relative bias of the EnKF is 5.72%, which is reduced to 2.15% by the PF in the near range. Furthermore, the suppression impact on the random noise in the far range is also made significant via the PF. An extensive application of the PF method can be useful in determining the local and global properties of aerosols.

  13. Differential uncertainty analysis for evaluating the accuracy of S-parameter retrieval methods for electromagnetic properties of metamaterial slabs.

    PubMed

    Hasar, Ugur Cem; Barroso, Joaquim J; Sabah, Cumali; Kaya, Yunus; Ertugrul, Mehmet

    2012-12-17

    We apply a complete uncertainty analysis, not studied in the literature, to investigate the dependences of retrieved electromagnetic properties of two MM slabs (the first one with only split-ring resonators (SRRs) and the second with SRRs and a continuous wire) with single-band and dual-band resonating properties on the measured/simulated scattering parameters, the slab length, and the operating frequency. Such an analysis is necessary for the selection of a suitable retrieval method together with the correct examination of exotic properties of MM slabs especially in their resonance regions. For this analysis, a differential uncertainty model is developed to monitor minute changes in the dependent variables (electromagnetic properties of MM slabs) in functions of independent variables (scattering (S-) parameters, the slab length, and the operating frequency). Two complementary approaches (the analytical approach and the dispersion model approach) each with different strengths are utilized to retrieve the electromagnetic properties of various MM slabs, which are needed for the application of the uncertainty analysis. We note the following important results from our investigation. First, uncertainties in the retrieved electromagnetic properties of the analyzed MM slabs drastically increase when values of electromagnetic properties shrink to zero or near resonance regions where S-parameters exhibit rapid changes. Second, any low-loss or medium-loss inside the MM slabs due to an imperfect dielectric substrate or a finite conductivity of metals can decrease these uncertainties near resonance regions because these losses hinder abrupt changes in S-parameters. Finally, we note that precise information of especially the slab length and the operating frequency is a prerequisite for accurate analysis of exotic electromagnetic properties of MM slabs (especially multiband MM slabs) near resonance regions.

  14. Information storage medium and method of recording and retrieving information thereon

    DOEpatents

    Marchant, D. D.; Begej, Stefan

    1986-01-01

    Information storage medium comprising a semiconductor doped with first and second impurities or dopants. Preferably, one of the impurities is introduced by ion implantation. Conductive electrodes are photolithographically formed on the surface of the medium. Information is recorded on the medium by selectively applying a focused laser beam to discrete regions of the medium surface so as to anneal discrete regions of the medium containing lattice defects introduced by the ion-implanted impurity. Information is retrieved from the storage medium by applying a focused laser beam to annealed and non-annealed regions so as to produce a photovoltaic signal at each region.

  15. New Term Weighting Formulas for the Vector Space Method in Information Retrieval

    SciTech Connect

    Chisholm, E.; Kolda, T.G.

    1999-03-01

    The goal in information retrieval is to enable users to automatically and accurately find data relevant to their queries. One possible approach to this problem i use the vector space model, which models documents and queries as vectors in the term space. The components of the vectors are determined by the term weighting scheme, a function of the frequencies of the terms in the document or query as well as throughout the collection. We discuss popular term weighting schemes and present several new schemes that offer improved performance.

  16. Epstein-Barr virus viral capsid antigen titer by immunofluorescence with microplates: new semiautomated method based on the microtiter system.

    PubMed Central

    Lamy, M E; Favart, A M; Burtonboy, G; Arana, A

    1977-01-01

    A semiautomated method of an indirect immunofluorescence technique for the titration of antibodies directed against viral capsid antigens of Epstein-Barr virus has been developed with Microtiter system units. By this method, a technician is able to titrate some hundred samples daily. The technique is safe, easy, and reproducible. The various procedures are described, and the sensitivity of the test is discussed. Images PMID:195981

  17. 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.

  18. New Automated Methods for Detecting Volcanic Ash and Retrieving its Macro- and Micro-physical Properties

    NASA Astrophysics Data System (ADS)

    Pavolonis, M. J.; Sieglaff, J.

    2009-12-01

    Suspended volcanic ash poses significant threats to the aviation community. These threats include loss of life and severe damage to aircraft. Current operational volcanic ash detection techniques used at the various Volcanic Ash Advisory Centers (VAACs) are generally qualitative and require manual analysis. Reliable satellite-based automated ash detection techniques are few and far between due to the difficult nature of separating volcanic clouds from meteorological clouds and other non-volcanic features using reflectance or brightness temperature measurements alone. In order to better isolate the volcanic cloud signal, it is necessary to account for the background conditions and use a combination of spatial and spectral information. In addition, to forecast the dispersion of volcanic ash clouds, an estimate of the cloud height, effective particle size, and mass loading is needed. These parameters can be retrieved using infrared radiances and volcanic ash microphysical models. We will present results of an optimal estimation technique used to retrieve these parameters. Overall, this work has focused on developing operational quality volcanic ash remote sensing techniques that can be applied to a variety of sensors (e.g. AVHRR, GOES, MODIS, SEVIRI, MTSAT, GOES-R ABI, VIIRS, etc…). Beginning in the Fall of 2009, these products will be made available to the Anchorage and Washington VAACs for evaluation and collaborative efforts to assimilate these products into dynamical models are underway.

  19. Sucrose density gradient centrifugation and cross-flow filtration methods for the production of arbovirus antigens inactivated by binary ethylenimine

    PubMed Central

    Pyke, Alyssa T; Phillips, Debra A; Chuan, Teck F; Smith, Greg A

    2004-01-01

    Background Sucrose density gradient centrifugation and cross-flow filtration methods have been developed and standardised for the safe and reproducible production of inactivated arbovirus antigens which are appropriate for use in diagnostic serological applications. Methods To optimise the maximum titre of growth during the propagation of arboviruses, the multiplicity of infection and choice of cell line were investigated using stocks of Ross River virus and Barmah Forest virus grown in both mosquito and mammalian cell lines. To standardise and improve the efficacy of the inactivation of arboviral suspensions, stocks of Ross River virus, Barmah Forest virus, Japanese encephalitis virus, Murray Valley encephalitis virus and Alfuy virus were chemically inactivated using binary ethylenimine at a final concentration of 3 mM. Aliquots were then taken at hourly intervals and crude inactivation rates were determined for each virus using a plaque assay. To ensure complete inactivation, the same aliquots were each passaged 3 times in Aedes albopictus C6/36 cells and the presence of viral growth was detected using an immunofluorescent assay. For larger quantities of viral suspensions, centrifugation on an isopycnic sucrose density gradient or cross-flow filtration was used to produce concentrated, pure antigens or partially concentrated, semi-purified antigens respectively. Results The results of the propagation experiments suggested that the maximum viral titres obtained for both Ross River virus and Barmah Forest virus were affected by the incubation period and choice of cell line, rather than the use of different multiplicity of infection values. Results of the binary ethylenimine inactivation trial suggested that standardised periods of 5 or 8 hours would be suitable to ensure effective and complete inactivation for a number of different arboviral antigens. Conclusion Two methods used to prepare inactivated arbovirus antigens have been standardised to minimise production

  20. Soil Moisture Retrieval from Polarimetric SAR Data: A Short Review of Existing Methods and a New One

    NASA Astrophysics Data System (ADS)

    Di Martino, Gerardo; Iodice, Antonio; Poreh, Davod; Riccio, Daniele

    2016-08-01

    Soil moisture retrieval from SAR data is not an easy task, especially in presence of vegetation cover. Accordingly, in recent years several methods for soil-moisture retrieval under vegetation cover have been developed, relying on model-based or hybrid polarimetric target- decomposition techniques. However, most of these decomposition techniques suffer from the so-called negative-power problem, which is mainly related to poor modelling of surface- and/or volume-scattering contributions. In this paper we, first, analyse the Polarimetric Two-Scale Two-Component Model and the Iterative Generalized Hybrid Decomposition method, proposing a way to combine the estimation results of the methods so that most vegetation conditions can be accounted for. Then, we introduce a method that tries to solve the case of dominant surface scattering and non- negligible dihedral scattering, which is the case not covered by the abovementioned model combination. Meaningful estimation results are presented and discussed using polarimetric L-band SAR data of the AgriSAR 2006 campaign.

  1. Novel methods for expression of foreign antigens in live vector vaccines

    PubMed Central

    Wang, Jin Yuan; Harley, Regina H.; Galen, James E.

    2013-01-01

    Bacterial live vector vaccines represent a vaccine development strategy that offers exceptional flexibility. In this approach, genes encoding protective antigens of unrelated bacterial, viral or parasitic pathogens are expressed in an attenuated bacterial vaccine strain that delivers these foreign antigens to the immune system, thereby eliciting relevant immune responses. Rather than expressing these antigens using low copy expression plasmids, here we pursue expression of foreign proteins from the live vector chromosome. Our strategy is designed to compensate for the inherent disadvantage of loss of gene dosage (vs. plasmid-based expression) by integrating antigen-encoding gene cassettes into multiple chromosomal sites already inactivated in an attenuated Salmonella enterica serovar Typhi vaccine candidate. We tested expression of a cassette encoding the green fluorescent protein (GFPuv) integrated separately into native guaBA, htrA or clyA chromosomal loci. Using single integrations, we show that expression levels of GFPuv are significantly affected by the site of integration, regardless of the inclusion of additional strong promoters within the incoming cassette. Using cassettes integrated into both guaBA and htrA, we observe cumulative synthesis levels from two integration sites superior to single integrations. Most importantly, we observe that GFPuv expression increases in a growth phase-dependent manner, suggesting that foreign antigen synthesis may be “tuned” to the physiology of the live vaccine. We expect this novel platform expression technology to prove invaluable in the development of a wide variety of multivalent live vector vaccines, capable of expressing multiple antigens from both chromosomal and plasmid-based expression systems within a single strain. PMID:23406777

  2. [Detection and quantification of weak concentrations of antigens using a sensitive and direct method of demonstrating immunoprecipitation reactions].

    PubMed

    Rochu, D; Crespeau, H; Fine, A; Marneux, M; Fine, J M

    1989-09-01

    Using agarose gel coated on GelBond film sheets, and using Coomassie blue stain followed by silver stain, a sensitive microassay has been developed for detecting small amounts of antigen-antibody precipitates, and for quantitating low concentrations of antigen. In order to obtain a high sensitivity, antigen-antibody ratios were adjusted imperatively close to the equivalence in double-diffusion, and for quantitative estimation, single radial immunodiffusion was performed, according to Mancini, by measuring circles at the end point. The use of a double staining procedure allows to detect as little as 8 micrograms/ml antigen by Ouchterlony and 200 ng/ml by Mancini technique. The sensitivity of the method is 100 times greater than classical techniques and other advantages such as the need for minimal amounts of unconcentrated samples, the absence of radioactive labelling, and the absence of interference due to a second or a third antibody coat, make this assay useful for analyzing and quantitating monoclonal antibodies obtained by hybridoma or B-cell immortalization.

  3. Sucrose density gradient centrifugation and cross-flow filtration methods for the production of arbovirus antigens inactivated by binary ethylenimine.

    PubMed

    Pyke, Alyssa T; Phillips, Debra A; Chuan, Teck F; Smith, Greg A

    2004-01-14

    Sucrose density gradient centrifugation and cross-flow filtration methods have been developed and standardised for the safe and reproducible production of inactivated arbovirus antigens which are appropriate for use in diagnostic serological applications. To optimise the maximum titre of growth during the propagation of arboviruses, the multiplicity of infection and choice of cell line were investigated using stocks of Ross River virus and Barmah Forest virus grown in both mosquito and mammalian cell lines. To standardise and improve the efficacy of the inactivation of arboviral suspensions, stocks of Ross River virus, Barmah Forest virus, Japanese encephalitis virus, Murray Valley encephalitis virus and Alfuy virus were chemically inactivated using binary ethylenimine at a final concentration of 3 mM. Aliquots were then taken at hourly intervals and crude inactivation rates were determined for each virus using a plaque assay. To ensure complete inactivation, the same aliquots were each passaged 3 times in Aedes albopictus C6/36 cells and the presence of viral growth was detected using an immunofluorescent assay. For larger quantities of viral suspensions, centrifugation on an isopycnic sucrose density gradient or cross-flow filtration was used to produce concentrated, pure antigens or partially concentrated, semi-purified antigens respectively. The results of the propagation experiments suggested that the maximum viral titres obtained for both Ross River virus and Barmah Forest virus were affected by the incubation period and choice of cell line, rather than the use of different multiplicity of infection values. Results of the binary ethylenimine inactivation trial suggested that standardised periods of 5 or 8 hours would be suitable to ensure effective and complete inactivation for a number of different arboviral antigens. Two methods used to prepare inactivated arbovirus antigens have been standardised to minimise production failure and expenditure and to

  4. Enzyme-labeled Antigen Method: Development and Application of the Novel Approach for Identifying Plasma Cells Locally Producing Disease-specific Antibodies in Inflammatory Lesions

    PubMed Central

    Mizutani, Yasuyoshi; Shiogama, Kazuya; Onouchi, Takanori; Sakurai, Kouhei; Inada, Ken-ichi; Tsutsumi, Yutaka

    2016-01-01

    In chronic inflammatory lesions of autoimmune and infectious diseases, plasma cells are frequently observed. Antigens recognized by antibodies produced by the plasma cells mostly remain unclear. A new technique identifying these corresponding antigens may give us a breakthrough for understanding the disease from a pathophysiological viewpoint, simply because the immunocytes are seen within the lesion. We have developed an enzyme-labeled antigen method for microscopic identification of the antigen recognized by specific antibodies locally produced in plasma cells in inflammatory lesions. Firstly, target biotinylated antigens were constructed by the wheat germ cell-free protein synthesis system or through chemical biotinylation. Next, proteins reactive to antibodies in tissue extracts were screened and antibody titers were evaluated by the AlphaScreen method. Finally, with the enzyme-labeled antigen method using the biotinylated antigens as probes, plasma cells producing specific antibodies were microscopically localized in fixed frozen sections. Our novel approach visualized tissue plasma cells that produced 1) autoantibodies in rheumatoid arthritis, 2) antibodies against major antigens of Porphyromonas gingivalis in periodontitis or radicular cyst, and 3) antibodies against a carbohydrate antigen, Strep A, of Streptococcus pyogenes in recurrent tonsillitis. Evaluation of local specific antibody responses expectedly contributes to clarifying previously unknown processes in inflammatory disorders. PMID:27006517

  5. An improved tropospheric ozone database retrieved from SCIAMACHY Limb-Nadir-Matching method

    NASA Astrophysics Data System (ADS)

    Jia, Jia; Rozanov, Alexei; Ladstätter-Weißenmayer, Annette; Ebojie, Felix; Rahpoe, Nabiz; Bötel, Stefan; Burrows, John

    2015-04-01

    Tropospheric ozone is one of the most important green-house gases and the main component of photochemical smog. It is either transported from the stratosphere or photochemically produced during pollution events in the troposphere that threaten the respiratory system. To investigate sources, transport mechanisms of tropospheric ozone in a global view, limb nadir matching (LNM) technique applied with SCIAMACHY instrument is used to retrieve tropospheric ozone. With the fact that 90% ozone is located in the stratosphere and only about 10% can be observed in the troposphere, the usage of satellite data requires highly qualified nadir and limb data. In this study we show an improvement of SCIAMACHY limb data as well as its influence on tropospheric ozone results. The limb nadir matching technique is also refined to increase the quality of the tropospheric ozone. The results are validated with ozone sonde measurements.

  6. [Retrieval method for estimating snow depth using hyperspectral data in snowmelt period].

    PubMed

    Xu, Qian; Liu, Zhi-Hui; Fang, Shi-Feng

    2013-07-01

    The snow surface reflectance spectra with different depth in snowmelt period and snow depth data were measured and its correlation was analyzed. The characteristic absorption band data of the valley with higher correlation were used to establish a single band snow depth regression model. The highest contribution rate of the band was selected as the input variable of the neural network model to retrieve snow depth. The results show that in Juntang Lake area, near 1 022, 1 241 and 1 492 nm exists characteristic absorption valley of snow, and compared to estimation accuracy of the single-band inversion of snow depth model (R2 = 0.53), ANN-BP model has a higher inversion level, and determination coefficient (R2 = 0.86, RMSE = 0.67) was obtained with 4 nodes in hidden layers, indicating that ANN-BP model can greatly improve the ability of inversion of snow depth with hyperspectral data.

  7. Idea Retrieval.

    ERIC Educational Resources Information Center

    Shively, Daniel

    1988-01-01

    Discusses the need to retrieve ideas in addition to content retrieval by such means as classification, subject headings, and keywords. Three models for idea retrieval are described, and a new model is proposed which combines selection, a controlled vocabulary, and logical structure. (seven references) (CLB)

  8. Application of the Markov Chain Monte Carlo method for snow water equivalent retrieval based on passive microwave measurements

    NASA Astrophysics Data System (ADS)

    Pan, J.; Durand, M. T.; Vanderjagt, B. J.

    2015-12-01

    Markov Chain Monte Carlo (MCMC) method is a retrieval algorithm based on Bayes' rule, which starts from an initial state of snow/soil parameters, and updates it to a series of new states by comparing the posterior probability of simulated snow microwave signals before and after each time of random walk. It is a realization of the Bayes' rule, which gives an approximation to the probability of the snow/soil parameters in condition of the measured microwave TB signals at different bands. Although this method could solve all snow parameters including depth, density, snow grain size and temperature at the same time, it still needs prior information of these parameters for posterior probability calculation. How the priors will influence the SWE retrieval is a big concern. Therefore, in this paper at first, a sensitivity test will be carried out to study how accurate the snow emission models and how explicit the snow priors need to be to maintain the SWE error within certain amount. The synthetic TB simulated from the measured snow properties plus a 2-K observation error will be used for this purpose. It aims to provide a guidance on the MCMC application under different circumstances. Later, the method will be used for the snowpits at different sites, including Sodankyla, Finland, Churchill, Canada and Colorado, USA, using the measured TB from ground-based radiometers at different bands. Based on the previous work, the error in these practical cases will be studied, and the error sources will be separated and quantified.

  9. The use of measured RF power signals to evaluate feasibility of inverse methods to retrieve refractivity parameters

    NASA Astrophysics Data System (ADS)

    Gustafsson, Ove K. S.; Eriksson, Gunnar; Holm, Peter; Waern, Åsa; von Schoenberg, Pontus; Thaning, Lennart; Nordstrand, Melker; Persson, Rolf

    2006-09-01

    Radio wave propagation over sea paths is influenced by the local meteorological condition at the atmospheric layer near the surface, especially during ducts. Duct condition can be determined by measurements of local meteorological parameters, by weather forecast models or by using inverse methods. In order to evaluate the feasibility of using inverse methods to retrieve the refractivity profiles a measurement of RF signals and meteorological parameters were carried out at a test site in the Baltic. During the measurements, signal power from two broadcast antennas, one at Visby and one at Vastervik, were received at Musko, an island south of Stockholm. The measurements were performed during the summer 2005 and the data was used to test the software package for inversion methods, SAGA (Seismo Acoustic inversion using Genetic Algorithms, by Peter Gerstoft UCSD, US). Refractivity profiles retrieved by SAGA were compared with the refractivity profiles calculated from measured parameters, during parts of the experiment, from rocket sounding, radio sounding, local meteorological measurements using bulk model calculations, and also obtained by the Swedish operational weather forecast model HIRLAM. Surface based duct height are predicted in relative many situations even though the number of frequencies or antennas height has to be increased to diminish the ambiguous of the refractive index profile.

  10. 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

  11. Retrieval of Sea-Bed Parameters by the Method of Matching Acoustic Fields on the Basis of Vertical Angular Spectra

    NASA Astrophysics Data System (ADS)

    Kerzhakov, B. V.; Kulinich, V. V.

    2016-08-01

    We use the field matching method to solve the inverse problem of estimating the geoacoustic parameters of a stratified sea bed using the objective function based on the norm of difference between the experimental and simulated vertical angular spectra of the acoustic field and combination of the rapid-annealing method with direct search methods for localization of the global minimum of the objective function. To reduce the influence of the ravine effects of the objective function, we use regularization on the basis of mutual correlations of the experimental and simulated vertical angular spectra of the acoustic field. The numerical experiment has been performed to retrieve the parameters of the model waveguide, e.g., the thickness of the water layer and the layer of sediments, the velocity and attenuation coefficients of longitudinal waves, and the density of the sediment layer and the subjacent half-space in the presence of noise interference of different intensity levels.

  12. Human factors analysis and design methods for nuclear waste retrieval systems. Human factors design methodology and integration plan

    SciTech Connect

    Casey, S.M.

    1980-06-01

    The purpose of this document is to provide an overview of the recommended activities and methods to be employed by a team of human factors engineers during the development of a nuclear waste retrieval system. This system, as it is presently conceptualized, is intended to be used for the removal of storage canisters (each canister containing a spent fuel rod assembly) located in an underground salt bed depository. This document, and the others in this series, have been developed for the purpose of implementing human factors engineering principles during the design and construction of the retrieval system facilities and equipment. The methodology presented has been structured around a basic systems development effort involving preliminary development, equipment development, personnel subsystem development, and operational test and evaluation. Within each of these phases, the recommended activities of the human engineering team have been stated, along with descriptions of the human factors engineering design techniques applicable to the specific design issues. Explicit examples of how the techniques might be used in the analysis of human tasks and equipment required in the removal of spent fuel canisters have been provided. Only those techniques having possible relevance to the design of the waste retrieval system have been reviewed. This document is intended to provide the framework for integrating human engineering with the rest of the system development effort. The activities and methodologies reviewed in this document have been discussed in the general order in which they will occur, although the time frame (the total duration of the development program in years and months) in which they should be performed has not been discussed.

  13. A content based video retrieval method for surveillance and forensic applications

    NASA Astrophysics Data System (ADS)

    Vadakkeveedu, Kalyan; Xu, Peng; Fernandes, Ronald; Mayer, Richard J.

    2007-04-01

    The advances in video surveillance technology have lead to the proliferation of surveillance video cameras for the purposes of viewing areas of interest. Counter terrorism and surveillance applications require video forensics capabilities like querying and searching video data for events, people or objects of interest. A human analyst may accurately spot a suspicious activity in a small segment of video. However, due to the large volume of data collected in real-time video surveillance, it is impractical for human analysts to watch or tag the entire video collected as this can lead to human errors, lower throughput and inconsistencies in the level of scrutiny. In this paper, we introduce an ontology-based video retrieval approach, which represents videos with object ontologies and event ontologies, and annotates videos accordingly. We also describe a user-friendly interface for querying surveillance videos using event dictionaries. Our approach leverages the capabilities of ontologies in specifying knowledge at different levels, and, in this way, provides flexibility to a user while forming a query. It is also capable of detecting undefined events such as not previously conceived abnormal events.

  14. Phase retrieval and time-frequency methods in the measurement of ultrashort laser pulses

    SciTech Connect

    DeLong, K.W.; Fittinghoff, D.N.; Ladera, C.L.; Trebino, R.

    1995-02-01

    Recently several techniques have become available to measure the time- (or frequency-) dependent intensity and phase of ultrashort laser pulses. One of these, Frequency-Resolved Optical Gating (FROG), is rigorous and has achieved single-laser-shot operation. FROG combines the concepts of time-frequency analysis in the form of spectrogram generation (in order to create a two-dimensional problem), and uses a phase-retrieval-based algorithm to invert the experimental data to yield the intensity and phase of the laboratory laser pulse. In FROG it is easy to generate a spectrogram of the unknown signal, and inversion of the spectrogram to recover the signal is the main goal. Because the temporal width of a femtosecond laser pulse is much shorter than anything achievable by electronics, FROG uses the pulse to measure itself. In FROG, the laser pulse is split into two replicas of itself by a partially reflecting beamsplitter, and the two replicas interact with each other in a medium with an instantaneous nonlinear-optical response. This interaction generates a signal field that is then frequency-resolved using a spectrometer. The spectrum of the signal field is measured for all relevant values of the temporal delay between the two pulses. Here, the authors employ FROG and FROG related techniques to measure the time-dependent intensity and phase of an ultrashort laser pulse.

  15. A comparison of retrieval effectiveness for three methods of indexing medical literature.

    PubMed

    Hersh, W R; Hickam, D H

    1992-05-01

    Conventional approaches to indexing medical literature include the human assignment of terms from a controlled vocabulary, such as MeSH, or the computer assignment of all words in the title and abstract as indexing terms. Human indexing suffers from inconsistency, while word-based indexing suffers from the multiple meanings of words. SAPHIRE is a computer program designed to provide indexing using controlled terms that are assigned by computer, based on their occurrence in the title and abstract. In this first evaluation of SAPHIRE, the authors compared the retrieval performance of the three indexing approaches--human-based MEDLINE with text words; machine-based SAPHIRE with text words; and text words only--for searches by measuring recall and precision for each search using a test collection of 200 abstracts. The abstracts were judged by human reviewers for relevance as applied to 12 literature queries. The results suggest that text word indexing is more effective than indexing with MeSH terms. SAPHIRE's indexing performance was slightly inferior but the program has other advantageous features.

  16. A Comparison Between Heliosat-2 and Artificial Neural Network Methods for Global Horizontal Irradiance Retrievals over Desert Environments

    NASA Astrophysics Data System (ADS)

    Ghedira, H.; Eissa, Y.

    2012-12-01

    Global horizontal irradiance (GHI) retrievals at the surface of any given location could be used for preliminary solar resource assessments. More accurately, the direct normal irradiance (DNI) and diffuse horizontal irradiance (DHI) are also required to estimate the global tilt irradiance, mainly used for fixed flat plate collectors. Two different satellite-based models for solar irradiance retrievals have been applied over the desert environment of the United Arab Emirates (UAE). Both models employ channels of the SEVIRI instrument, onboard the geostationary satellite Meteosat Second Generation, as their main inputs. The satellite images used in this study have a temporal resolution of 15-min and a spatial resolution of 3-km. The objective of this study is to compare between the GHI retrieved using the Heliosat-2 method and an artificial neural network (ANN) ensemble method over the UAE. The high-resolution visible channel of SEVIRI is used in the Heliosat-2 method to derive the cloud index. The cloud index is then used to compute the cloud transmission, while the cloud-free GHI is computed from the Linke turbidity factor. The product of the cloud transmission and the cloud-free GHI denotes the estimated GHI. A constant underestimation is observed in the estimated GHI over the dataset available in the UAE. Therefore, the cloud-free DHI equation in the model was recalibrated to fix the bias. After recalibration, results over the UAE show a root mean square error (RMSE) value of 10.1% and a mean bias error (MBE) of -0.5%. As for the ANN approach, six thermal channels of SEVIRI were used to estimate the DHI and the total optical depth of the atmosphere (δ). An ensemble approach is employed to obtain a better generalizability of the results, as opposed to using one single weak network. The DNI is then computed from the estimated δ using the Beer-Bouguer-Lambert law. The GHI is computed from the DNI and DHI estimates. The RMSE for the estimated GHI obtained over an

  17. Immunonucleochemistry: a new method for in situ detection of antigens in the nucleus of cells in culture.

    PubMed

    Moon, Il Soo; Lee, Hyunsook; Park, Sung Dong; Seog, Dae-Hyun

    2010-04-01

    The advancement of immunocytochemistry (ICC) allows one to observe detailed spatial distribution of cellular antigens, but, with some limitations. Using conventional ICC, it is difficult to distinguish the nuclear localization from cytoplasm, as two large subcellular compartments overlap on the z-axis. In this study, we have investigated whether in situ immunostaining of 'naked' nuclei could provide an unambiguous method for detection of nuclear antigens. We have designed a protocol that efficiently lyses plasmalemma, while keeping the nuclear envelope intact. The optimal condition for lysing the plasmalemma was 0.5% Nonidet P-40 for 5 min in both neuronal and non-neuronal cultured cells. Using this protocol, we could unambiguously isolate nuclear from cytoplasmic ICC signals. Since the present protocol has been designed for immunostaining of 'naked' nuclei from cultured or isolated cells, we have coined a new term to refer to this procedure as 'immunonucleochemistry' ('INC' for abbreviation).

  18. In situ visualization of plasma cells producing antibodies reactive to Porphyromonas gingivalis in periodontitis: the application of the enzyme-labeled antigen method

    PubMed Central

    Mizutani, Y; Tsuge, S; Takeda, H; Hasegawa, Y; Shiogama, K; Onouchi, T; Inada, K; Sawasaki, T; Tsutsumi, Y

    2014-01-01

    Porphyromonas gingivalis is a keystone periodontal pathogen. Histologocally, the gingival tissue in periodontitis shows dense infiltration of plasma cells. However, antigens recognized by antibodies secreted from the immunocytes remain unknown. The enzyme-labeled antigen method was applied to detecting plasma cells producing P. gingivalis-specific antibodies in biopsied gingival tissue of periodontitis. N-terminally biotinylated P. gingivalis antigens, Ag53 and four gingipain domains (Arg-pro, Arg-hgp, Lys-pro and Lys-hgp) were prepared by the cell-free protein synthesis system using wheatgerm extract. With these five labeled proteins as probes, 20 lesions of periodontitis were evaluated. With the AlphaScreen method, antibodies against any one of the five P. gingivalis antigens were detected in 11 (55%) serum samples and 17 (85%) tissue extracts. Using the enzyme-labeled antigen method on paraformaldehyde-fixed frozen sections of gingival tissue, plasma cells were labeled with any one of the five antigens in 17 (94%) of 18 specimens, in which evaluable plasma cells were detected. The positivity rates in periodontitis were significantly higher than those found previously in radicular cysts (20% in sera and 33% in tissue extracts with the AlphaScreen method, and 25% with the enzyme-labeled antigen method). Our findings directly indicate that antibodies reactive to P. gingivalis are locally produced in the gingival lesions, and that inflammatory reactions against P. gingivalis are involved in periodontitis. PMID:24698402

  19. The limits of ultrahigh-resolution x-ray mapping: estimating uncertainties in thin-film and interface structures determined by phase retrieval methods

    SciTech Connect

    Zhou H.; Pindak R.; Clarke, R.; Steinberg, D.NM.; Yacoby, Y.

    2012-04-25

    Capturing subtle details at the sub-Angstrom level is key to understanding the structural basis of many intriguing interfacial phenomena in epitaxial thin films and nanostructures. X-ray phase retrieval methods are ideally suited to this task but the usual approaches for determination of uncertainties, based on refining a parametrized model, are not applicable in this case. Here we describe a method to estimate the uncertainties of the system electron density, obtained by phase retrieval, and of parameters of interest obtained from it. The method is based on the bootstrap approach and it can be generally applied to surface x-ray scattering data. Several examples are given which illustrate the method's utility in determining uncertainties arising from random and systematic errors. The approach also provides a quantitative measure of the validity of structural solutions obtained by phase retrieval methods.

  20. The limits of ultrahigh-resolution x-ray mapping: estimating uncertainties in thin-film and interface structures determined by phase retrieval methods

    NASA Astrophysics Data System (ADS)

    Zhou, Hua; Pindak, Ron; Clarke, Roy; Steinberg, David M.; Yacoby, Yizhak

    2012-05-01

    Capturing subtle details at the sub-Angstrom level is key to understanding the structural basis of many intriguing interfacial phenomena in epitaxial thin films and nanostructures. X-ray phase retrieval methods are ideally suited to this task but the usual approaches for determination of uncertainties, based on refining a parametrized model, are not applicable in this case. Here we describe a method to estimate the uncertainties of the system electron density, obtained by phase retrieval, and of parameters of interest obtained from it. The method is based on the bootstrap approach and it can be generally applied to surface x-ray scattering data. Several examples are given which illustrate the method's utility in determining uncertainties arising from random and systematic errors. The approach also provides a quantitative measure of the validity of structural solutions obtained by phase retrieval methods.

  1. Particle size and refractive index retrieval from the backscattering spectrum of white light using the Twomey iterative method: simulation and experiment

    NASA Astrophysics Data System (ADS)

    Zhou, Jing; Moshary, Fred; Gross, Barry; Ahmed, Samir

    2006-09-01

    The Twomey iterative method has been applied to the retrieval of hydrosol microphysical properties. In particular, we focused on the retrieval of single and multimode particle size distributions from both simulated and experimental backscattering spectra in the 400-800 nm wavelength range. Assuming a known refractive index, both single-mode and multimode distributions were successfully retrieved through the introduction of an initial distribution biased toward larger particles. The simulation results were experimentally verified with standard polystyrene particles suspended in water within the diameter range of 0.2-2 μm for both narrow and broad monomodal distributions as well as more complicated multimode distributions. Finally, the technique was extended to the retrieval of an unknown refractive index.

  2. 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

  3. Methods for Retrievals of CO2 Mixing Ratios from JPL Laser Absorption Spectrometer Flights During a Summer 2011 Campaign

    NASA Technical Reports Server (NTRS)

    Menzies, Robert T.; Spiers, Gary D.; Jacob, Joseph C.

    2013-01-01

    The JPL airborne Laser Absorption Spectrometer instrument has been flown several times in the 2007-2011 time frame for the purpose of measuring CO2 mixing ratios in the lower atmosphere. This instrument employs CW laser transmitters and coherent detection receivers in the 2.05- micro m spectral region. The Integrated Path Differential Absorption (IPDA) method is used to retrieve weighted CO2 column mixing ratios. We present key features of the evolving LAS signal processing and data analysis algorithms and the calibration/validation methodology. Results from 2011 flights in various U.S. locations include observed mid-day CO2 drawdown in the Midwest and high spatial resolution plume detection during a leg downwind of the Four Corners power plant in New Mexico.

  4. Methods for Retrievals of CO2 Mixing Ratios from JPL Laser Absorption Spectrometer Flights During a Summer 2011 Campaign

    NASA Technical Reports Server (NTRS)

    Menzies, Robert T.; Spiers, Gary D.; Jacob, Joseph C.

    2013-01-01

    The JPL airborne Laser Absorption Spectrometer instrument has been flown several times in the 2007-2011 time frame for the purpose of measuring CO2 mixing ratios in the lower atmosphere. This instrument employs CW laser transmitters and coherent detection receivers in the 2.05- micro m spectral region. The Integrated Path Differential Absorption (IPDA) method is used to retrieve weighted CO2 column mixing ratios. We present key features of the evolving LAS signal processing and data analysis algorithms and the calibration/validation methodology. Results from 2011 flights in various U.S. locations include observed mid-day CO2 drawdown in the Midwest and high spatial resolution plume detection during a leg downwind of the Four Corners power plant in New Mexico.

  5. An automatic Planetary Boundary Layer height retrieval method with compact EZ backscattering Lidar in the frame of ICOS campaign

    NASA Astrophysics Data System (ADS)

    Loaec, S.; Lolli, S.; Sauvage, L.; Boquet, M.; Xueref-Remy, I.

    2009-12-01

    Bigger strongly urbanized cities in the world are often exposed to atmospheric pollution events. To understand the chemical and physical processes that are taking place in these areas it is necessary to describe correctly the Planetary Boundary Layer (PBL) dynamics and the PBL height evolution. For these proposals, a compact and rugged eye safe UV Lidar, the EZLIDAR™, was developed together by CEA/LMD and LEOSPHERE (France) to study and investigate structural and optical properties of clouds and aerosols and PBL time evolution. EZLIDAR™ has been validated by different remote and in-situ instruments as MPL Type-4 Lidar manufactured by NASA at ARM/SGP site or the LNA (Lidar Nuage Aerosol) at the Laboratoire de Metereologie Dynamique LMD (France) and during several intercomparison campaigns. EZLIDAR™ algorithm retrieves automatically the PBL height in real-time. The method is based on the detection of the slope of the signal linked to a sharp change in concentration of the aerosols. Once detected, the different layers are filtered on a 15mn sample and classified between nocturnal, convective or residual layer, depending on the time and date. This method has been validated against those retrieved by the algorithm STRAT from data acquired at IPSL, France, showing 95% of correlation. In this paper are presented the results of the intercomparison campaign that took place in Orleans, France and Mace Head, Ireland in the framework of ICOS (Integrated Carbon Observation System) project, where the EZ Lidar™ worked under all weather conditions, clear sky, fog, low clouds, during the whole month of October 2008. Moreover, thanks to its 3D scanning capability, the EZLIDAR was able to provide the variability of the PBL height around the site, enabling the scientists to estimate the flux intensities that play a key role in the radiative transfer budget and in the atmospheric pollutants dispersion.

  6. [METHODS FOR DETECTION OF ANTIBODIES TO HLA ANTIGENS IN PATIENTS AWAITING KIDNEY TRANSPLANTATION AND COMBINED PANCREAS-KIDNEY TRANSPLANTATION].

    PubMed

    Ančić, Mirela; Maravić, Blaženko; Radman, Maja; Kovačić, Vedran

    2014-12-01

    The best possibility to treat chronic renal disease is renal transplantation. Especially important fact in transplantation is the percentage of so-called panel reactive antibody (PRA) that is focused on the human leukocyte antigen. There are several methods to determine the percentage of PRA in sensitized patients awaiting kidney transplants. The most important is the complement-dependent cytotoxicity. A higher value of PRA implies greater likelihood of positive cross-match with random donor and lower probability of receiving a transplant. Comparing the sensitivity of laboratory tests for determination of PRA percentage in patient serum, it is concluded that ELISA and flow cytometry proved to be more sensitive and specific.

  7. A new method to retrieve the aerosol layer absorption coefficient from airborne flux density and actinic radiation measurements

    NASA Astrophysics Data System (ADS)

    Bierwirth, Eike; Wendisch, Manfred; JäKel, Evelyn; Ehrlich, André; Schmidt, K. Sebastian; Stark, Harald; Pilewskie, Peter; Esselborn, Michael; Gobbi, Gian Paolo; Ferrare, Richard; Müller, Thomas; Clarke, Antony

    2010-07-01

    A new method is presented to derive the mean value of the spectral absorption coefficient of an aerosol layer from combined airborne measurements of spectral net irradiance and actinic flux density. While the method is based on a theoretical relationship of radiative transfer theory, it is applied to atmospheric radiation measurements for the first time. The data have been collected with the Spectral Modular Airborne Radiation Measurement System (SMART-Albedometer), the Solar Spectral Flux Radiometer (SSFR), and the Actinic Flux Spectroradiometer (AFSR) during four field campaigns between 2002 and 2008 (the Saharan Mineral Dust Experiment (SAMUM), the Influence of Clouds on the Spectral Actinic Flux in the Lower Troposphere (INSPECTRO) project, and the Arctic Research of the Composition of the Troposphere from Aircraft and Satellites and Aerosol, Radiation, and Cloud Processes Affecting Arctic Climate (ARCTAS/ARCPAC) projects). The retrieval algorithm is tested in a series of radiative transfer model runs and then applied to measurement cases with different aerosol species and loading. The method is shown to be a feasible approach to obtain the mean aerosol absorption coefficient across a given accessible altitude range. The results indicate that the method is viable whenever the difference of the net irradiance at the top and bottom of a layer is equal to or higher than the measurement uncertainty for net irradiance. This can be achieved by a high optical depth or a low single-scattering albedo within the layer.

  8. Comparison of Different Approach of Back Projection Method in Retrieving the Rupture Process of Large Earthquakes

    NASA Astrophysics Data System (ADS)

    Tan, F.; Wang, G.; Chen, C.; Ge, Z.

    2016-12-01

    Back-projection of teleseismic P waves [Ishii et al., 2005] has been widely used to image the rupture of earthquakes. Besides the conventional narrowband beamforming in time domain, approaches in frequency domain such as MUSIC back projection (Meng 2011) and compressive sensing (Yao et al, 2011), are proposed to improve the resolution. Each method has its advantages and disadvantages and should be properly used in different cases. Therefore, a thorough research to compare and test these methods is needed. We write a GUI program, which puts the three methods together so that people can conveniently use different methods to process the same data and compare the results. Then we use all the methods to process several earthquake data, including 2008 Wenchuan Mw7.9 earthquake and 2011 Tohoku-Oki Mw9.0 earthquake, and theoretical seismograms of both simple sources and complex ruptures. Our results show differences in efficiency, accuracy and stability among the methods. Quantitative and qualitative analysis are applied to measure their dependence on data and parameters, such as station number, station distribution, grid size, calculate window length and so on. In general, back projection makes it possible to get a good result in a very short time using less than 20 lines of high-quality data with proper station distribution, but the swimming artifact can be significant. Some ways, for instance, combining global seismic data, could help ameliorate this method. Music back projection needs relatively more data to obtain a better and more stable result, which means it needs a lot more time since its runtime accumulates obviously faster than back projection with the increase of station number. Compressive sensing deals more effectively with multiple sources in a same time window, however, costs the longest time due to repeatedly solving matrix. Resolution of all the methods is complicated and depends on many factors. An important one is the grid size, which in turn influences

  9. Methods for Semi-automated Indexing for High Precision Information Retrieval

    PubMed Central

    Berrios, Daniel C.; Cucina, Russell J.; Fagan, Lawrence M.

    2002-01-01

    Objective. To evaluate a new system, ISAID (Internet-based Semi-automated Indexing of Documents), and to generate textbook indexes that are more detailed and more useful to readers. Design. Pilot evaluation: simple, nonrandomized trial comparing ISAID with manual indexing methods. Methods evaluation: randomized, cross-over trial comparing three versions of ISAID and usability survey. Participants. Pilot evaluation: two physicians. Methods evaluation: twelve physicians, each of whom used three different versions of the system for a total of 36 indexing sessions. Measurements. Total index term tuples generated per document per minute (TPM), with and without adjustment for concordance with other subjects; inter-indexer consistency; ratings of the usability of the ISAID indexing system. Results. Compared with manual methods, ISAID decreased indexing times greatly. Using three versions of ISAID, inter-indexer consistency ranged from 15% to 65% with a mean of 41%, 31%, and 40% for each of three documents. Subjects using the full version of ISAID were faster (average TPM: 5.6) and had higher rates of concordant index generation. There were substantial learning effects, despite our use of a training/run-in phase. Subjects using the full version of ISAID were much faster by the third indexing session (average TPM: 9.1). There was a statistically significant increase in three-subject concordant indexing rate using the full version of ISAID during the second indexing session (p < 0.05). Summary. Users of the ISAID indexing system create complex, precise, and accurate indexing for full-text documents much faster than users of manual methods. Furthermore, the natural language processing methods that ISAID uses to suggest indexes contributes substantially to increased indexing speed and accuracy. PMID:12386114

  10. Methods for semi-automated indexing for high precision information retrieval.

    PubMed

    Berrios, Daniel C; Cucina, Russell J; Fagan, Lawrence M

    2002-01-01

    To evaluate a new system, ISAID (Internet-based Semi-automated Indexing of Documents), and to generate textbook indexes that are more detailed and more useful to readers. Pilot evaluation: simple, nonrandomized trial comparing ISAID with manual indexing methods. Methods evaluation: randomized, cross-over trial comparing three versions of ISAID and usability survey. Pilot evaluation: two physicians. Methods evaluation: twelve physicians, each of whom used three different versions of the system for a total of 36 indexing sessions. Total index term tuples generated per document per minute (TPM), with and without adjustment for concordance with other subjects; inter-indexer consistency; ratings of the usability of the ISAID indexing system. Compared with manual methods, ISAID decreased indexing times greatly. Using three versions of ISAID, inter-indexer consistency ranged from 15% to 65% with a mean of 41%, 31%, and 40% for each of three documents. Subjects using the full version of ISAID were faster (average TPM: 5.6) and had higher rates of concordant index generation. There were substantial learning effects, despite our use of a training/run-in phase. Subjects using the full version of ISAID were much faster by the third indexing session (average TPM: 9.1). There was a statistically significant increase in three-subject concordant indexing rate using the full version of ISAID during the second indexing session (p < 0.05). Users of the ISAID indexing system create complex, precise, and accurate indexing for full-text documents much faster than users of manual methods. Furthermore, the natural language processing methods that ISAID uses to suggest indexes contributes substantially to increased indexing speed and accuracy.

  11. Methods for semi-automated indexing for high precision information retrieval

    NASA Technical Reports Server (NTRS)

    Berrios, Daniel C.; Cucina, Russell J.; Fagan, Lawrence M.

    2002-01-01

    OBJECTIVE: To evaluate a new system, ISAID (Internet-based Semi-automated Indexing of Documents), and to generate textbook indexes that are more detailed and more useful to readers. DESIGN: Pilot evaluation: simple, nonrandomized trial comparing ISAID with manual indexing methods. Methods evaluation: randomized, cross-over trial comparing three versions of ISAID and usability survey. PARTICIPANTS: Pilot evaluation: two physicians. Methods evaluation: twelve physicians, each of whom used three different versions of the system for a total of 36 indexing sessions. MEASUREMENTS: Total index term tuples generated per document per minute (TPM), with and without adjustment for concordance with other subjects; inter-indexer consistency; ratings of the usability of the ISAID indexing system. RESULTS: Compared with manual methods, ISAID decreased indexing times greatly. Using three versions of ISAID, inter-indexer consistency ranged from 15% to 65% with a mean of 41%, 31%, and 40% for each of three documents. Subjects using the full version of ISAID were faster (average TPM: 5.6) and had higher rates of concordant index generation. There were substantial learning effects, despite our use of a training/run-in phase. Subjects using the full version of ISAID were much faster by the third indexing session (average TPM: 9.1). There was a statistically significant increase in three-subject concordant indexing rate using the full version of ISAID during the second indexing session (p < 0.05). SUMMARY: Users of the ISAID indexing system create complex, precise, and accurate indexing for full-text documents much faster than users of manual methods. Furthermore, the natural language processing methods that ISAID uses to suggest indexes contributes substantially to increased indexing speed and accuracy.

  12. Methods for semi-automated indexing for high precision information retrieval

    NASA Technical Reports Server (NTRS)

    Berrios, Daniel C.; Cucina, Russell J.; Fagan, Lawrence M.

    2002-01-01

    OBJECTIVE: To evaluate a new system, ISAID (Internet-based Semi-automated Indexing of Documents), and to generate textbook indexes that are more detailed and more useful to readers. DESIGN: Pilot evaluation: simple, nonrandomized trial comparing ISAID with manual indexing methods. Methods evaluation: randomized, cross-over trial comparing three versions of ISAID and usability survey. PARTICIPANTS: Pilot evaluation: two physicians. Methods evaluation: twelve physicians, each of whom used three different versions of the system for a total of 36 indexing sessions. MEASUREMENTS: Total index term tuples generated per document per minute (TPM), with and without adjustment for concordance with other subjects; inter-indexer consistency; ratings of the usability of the ISAID indexing system. RESULTS: Compared with manual methods, ISAID decreased indexing times greatly. Using three versions of ISAID, inter-indexer consistency ranged from 15% to 65% with a mean of 41%, 31%, and 40% for each of three documents. Subjects using the full version of ISAID were faster (average TPM: 5.6) and had higher rates of concordant index generation. There were substantial learning effects, despite our use of a training/run-in phase. Subjects using the full version of ISAID were much faster by the third indexing session (average TPM: 9.1). There was a statistically significant increase in three-subject concordant indexing rate using the full version of ISAID during the second indexing session (p < 0.05). SUMMARY: Users of the ISAID indexing system create complex, precise, and accurate indexing for full-text documents much faster than users of manual methods. Furthermore, the natural language processing methods that ISAID uses to suggest indexes contributes substantially to increased indexing speed and accuracy.

  13. Effects of histoplasmin M antigen chemical and enzymatic deglycosylation on cross-reactivity in the enzyme-linked immunoelectrotransfer blot method.

    PubMed Central

    Zancopé-Oliveira, R M; Bragg, S L; Reiss, E; Wanke, B; Peralta, J M

    1994-01-01

    The enzyme-linked immunoelectrotransfer blot (EITB) method was evaluated as a suitable method for detecting antibodies against M antigen of Histoplasma capsulatum by use of both glycosylated and deglycosylated M protein of histoplasmin (HMIN). Sera from patients with histoplasmosis, paracoccidioidomycosis, blastomycosis, coccidioidomycosis, and aspergillosis were tested by the EITB with glycosylated M protein of HMIN. This assay demonstrated 100% sensitivity with histoplasmosis serum samples, all of which reacted with the 94-kDa glycoprotein (M antigen). Although the EITB is highly sensitive, it is not specific for histoplasmosis when glycosylated M protein is used as an antigen. A total of 81% of paracoccidioidomycosis, 25% of blastomycosis, 33% of coccidioidomycosis, 73% of aspergillosis, and 16% of tuberculosis serum samples cross-reacted with M protein of HMIN and yielded patterns indistinguishable from those obtained with histoplasmosis serum samples. The EITB reactions with both untreated M antigen and M antigen altered by periodate oxidation or by deglycosylation with endoglycosidases were compared. Cross-reactions with heterologous sera in the EITB could be attributed to periodate-sensitive carbohydrate epitopes, as reflected by the increase in the test specificity from 46.1 to 91.2% after periodate treatment of M protein. The EITB for the detection of antibodies to M antigen is a potential diagnostic test for histoplasmosis, provided that periodate-treated M protein is used as an antigen. Images PMID:8556474

  14. Flow cytometry-based methods for assessing soluble scFv activities and detecting pathogen antigens in solution

    SciTech Connect

    Gray, Sean; Weigel, Kris M.; Miller, Keith D.; Ndung'u, Joseph; Buscher, Philippe; Tran, Thao N.; Baird, Cheryl L.; Cangelosi, Gerard A.

    2010-04-01

    Novel methods are reported for evaluating and utilizing single chain fragment variable (scFv) antibodies derived from yeast-display libraries. Yeast-display was used to select scFv specific to invariant surface glycoproteins (ISG) of Trypanosoma brucei. A limiting step in the isolation of scFv from nonimmune libraries is the conversion of highly active yeast-displayed scFv into soluble antibodies that can be used in standard immunoassays. Challenges include limited solubility or activity following secretion and purification of scFv. For this reason, few scFv derived from yeast-display platforms have moved into development and implementation as diagnostic reagents. To address this problem, assays were developed that employ both yeastdisplayed and secreted scFv as analytical reagents. The first is a competitive inhibition flow cytometry (CIFC) assay that detects secreted scFv by virtue of its ability to competitively inhibit the binding of biotinylated antigen to yeast-displayed scFv. The second is an epitope binning assay that uses secreted scFv toidentify additional yeast-displayed scFv that bind nonoverlapping or noncompeting epitopes on an antigen. The epitope binning assay was used not only to identify sandwich assay pairs with yeast-displayed scFv, but also to identify active soluble scFv present in low concentration in a crude expression extract. Finally, a CIFC assay was developed that bypasses entirely the need for soluble scFv expression, by using yeast displayed scFv to detect unlabeled antigen in samples. These methods will facilitate the continued development and practical implementation of scFv derived from yeast-display libraries.

  15. A new method to retrieve spectral absorption coefficient of highly-scattering and weakly-absorbing materials

    NASA Astrophysics Data System (ADS)

    Dombrovsky, Leonid A.

    2016-03-01

    A significant uncertainty in the absorption coefficient of highly scattering dispersed materials is typical in the spectral ranges of very weak absorption. The traditional way to identify the main absorption and scattering characteristics of semi-transparent materials is based on spectral measurements of normal-hemispherical reflectance and transmittance for the material sample. Unfortunately this way cannot be used in the case of in vivo measurements of optical properties of biological tissues. A method suggested in the present paper is based on thermal response to the periodic radiative heating of the open surface of a semi-transparent material. It is shown that the period of a variation of the surface temperature is sensitive to the value of an average absorption coefficient in the surface layer. As a result, the monochromatic external irradiation combined with the surface temperature measurements can be used to retrieve the spectral values of absorption coefficient. Possible application of this method to porous semi-transparent ceramics is considered. An example problem is also solved to illustrate the applicability of this method to human skin. The approach suggested enables one to estimate an average absorption coefficient of human skin of a patient just before the thermal processing.

  16. Potential of a spectroscopic measurement method using adding-doubling to retrieve the bulk optical properties of dense microalgal media.

    PubMed

    Bellini, Sarah; Bendoula, Ryad; Latrille, Eric; Roger, Jean-Michel

    2014-01-01

    In the context of algal mass cultivation, current techniques used for the characterization of algal cells require time-consuming sample preparation and a large amount of costly, standard instrumentation. As the physical and chemical properties of the algal cells strongly affect their optical properties, the optical characterization is seen as a promising method to provide an early diagnosis in the context of mass cultivation monitoring. This article explores the potential of a spectroscopic measurement method coupled with the inversion of the radiative transfer theory for the retrieval of the bulk optical properties of dense algal samples. Total transmittance and total reflectance measurements were performed over the 380-1020 nm range on dense algal samples with a double integrating sphere setup. The bulk absorption and scattering coefficients were thus extracted over the 380-1020 nm range by inverting the radiative transfer theory using inverse-adding-doubling computations. The experimental results are presented and discussed; the configuration of the optical setup remains a critical point. The absorption coefficients obtained for the four samples of this study appear not to be more informative about pigment composition than would be classical methods in analytical spectroscopy; however, there is a real added value in measuring the reduced scattering coefficient, as it appears to be strongly correlated to the size distribution of the algal cells.

  17. Method for Face-Emotion Retrieval Using A Cartoon Emotional Expression Approach

    NASA Astrophysics Data System (ADS)

    Kostov, Vlaho; Yanagisawa, Hideyoshi; Johansson, Martin; Fukuda, Shuichi

    A simple method for extracting emotion from a human face, as a form of non-verbal communication, was developed to cope with and optimize mobile communication in a globalized and diversified society. A cartoon face based model was developed and used to evaluate emotional content of real faces. After a pilot survey, basic rules were defined and student subjects were asked to express emotion using the cartoon face. Their face samples were then analyzed using principal component analysis and the Mahalanobis distance method. Feature parameters considered as having relations with emotions were extracted and new cartoon faces (based on these parameters) were generated. The subjects evaluated emotion of these cartoon faces again and we confirmed these parameters were suitable. To confirm how these parameters could be applied to real faces, we asked subjects to express the same emotions which were then captured electronically. Simple image processing techniques were also developed to extract these features from real faces and we then compared them with the cartoon face parameters. It is demonstrated via the cartoon face that we are able to express the emotions from very small amounts of information. As a result, real and cartoon faces correspond to each other. It is also shown that emotion could be extracted from still and dynamic real face images using these cartoon-based features.

  18. The influence of sterilization method on articular surface damage of retrieved cruciate-retaining tibial inserts.

    PubMed

    Greulich, Matthew T; Roy, Marcel E; Whiteside, Leo A

    2012-06-01

    This observational study was designed to determine the importance of sterilization method and insert thickness as predictors of articular damage of cruciate-retaining polyethylene components used in total knee arthroplasty. Ninety-nine explanted tibial inserts were evaluated for surface damage. Severe damage modes were observed in 36 of 52 of γ-irradiated inserts but none of those sterilized by ethylene oxide. Articular damage significantly correlated to time in vivo but not to insert thickness. Inserts sterilized by ethylene oxide gas in gas-permeable packaging exhibited a significantly lower damage accumulation rate compared with inserts sterilized by γ radiation and stored in air or an inert environment. γ irradiation and storage in argon instead of air reduced the frequency of severe damage such as delamination but not the overall damage rate. Copyright © 2012 Elsevier Inc. All rights reserved.

  19. 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

  20. Fast method of retrieving the asymmetry factor and scattering albedo from the maximum time-resolved reflectance of participating media.

    PubMed

    Qi, Hong; Ren, Ya-Tao; Chen, Qin; Ruan, Li-Ming

    2015-06-01

    This research presents a parametric study of the time-resolved hemispherical reflectance of a semi-infinite plane-parallel slab of homogeneous, nonemitting, absorbing, and anisotropic scattering medium exposed to a collimated Gaussian pulse. The one-dimensional transient radiative transfer equation was solved by using the finite volume method. The internal reflection at the medium-air interface caused by the mismatch of the refractive indices was considered. In particular, this work focused on the maximum diffuse hemispherical reflectance. Three different optical regions were identified according to the dimensionless pulsewidth βctp. The correlation between the normalized maximum hemispherical reflectance and βctp was conformed to the Boltzmann function. The coefficients in the correlating functions of the match and mismatch refractive index cases were fitted as polynomial fitting functions of the single scattering albedo ω and Henyey-Greenstein asymmetric factor g. Thus, ω and g can be simultaneously reconstructed by the semi-empirical correlations without solving the forward model. In conclusion, the proposed method can potentially retrieve the asymmetry factor and single scattering albedo of participating media accurately and efficiently.

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

    SciTech Connect

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

    2013-07-01

    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 is 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)

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

    SciTech Connect

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

    2013-01-11

    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 is 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.

  3. Methods of atomic oxygen and ozone retrieval from observations of the O2 dayglow emissions in the MLT region

    NASA Astrophysics Data System (ADS)

    Yankovsky, Valentine; Martyshenko, Kseniia; Manuilova, Rada

    2015-04-01

    The problem of creating the new methods of remote sensing of altitude profile of the [O(3P)] and [O3] in the daytime is actual for the mesosphere and lower thermosphere range. Currently there is no reliable method for remote sensing of altitude profile of the [O(3P)], but atomic oxygen is a key component in the mechanism of the atmosphere cooling by quenching of vibrationally excited CO2 molecules and also one of basic quencher of excited components in MLT region. The airglow emission in 1.27 µm IR Atm(0 - 0) band from [O2(a1Δg, v=0)] has been used as a proxy for [O3] in MLT for over a decade. However, lifetime of O2(a1Δg, v=0) is more than 1 hour, therefore this method is not suitable for detecting of relatively rapid [O3] variations which occur due to the variability of the solar spectrum in the UV range (120 - 320 nm) and other space factors. The aim of this study is revealing of proxies for retrievals of [O(3P)] and [O3]. In the framework of developed model of electronic vibrational kinetics of excited products of O3 and O2 photolysis in MLT of the Earth (model YM-2011) [1] we consider the photolysis of O2 in the Schumann-Runge continuum and Lyaman-A H atom and of O3 in Hartley band and for excited products of photolysis ( O2(a1Δg, v=0 - 5), O2(b1Σ+g, v=0, 1, 2) and excited oxygen atom O(1D)) we took into account more than 60 aeronomical reactions of photoexcitation and deexcitation by energy transfer between the excited levels and of quenching of the levels in collisions with O(3P) O2, N2, O(3P), O3, CO2. We tested 5 excited components, namely, O2(b1Σ+g, v=0, 1, 2), O2(a1Δg, v=0 - 5) and O(1D) as the O(3P) and O3 proxies. The total system of kinetic equations for 10 components has been solved and altitude profiles of concentrations of O(1D), O2(b1Σ+g, v=0, 1, 2), and O2(a1Δg, v=0 - 5) have been calculated. To compare characteristics of assumed proxies we used sensitivity analysis of the proxy concentrations altitude profiles to variations of [O3] and

  4. 300 The Method of Antigen Specific Damage of Leucocytes by Food Additives in Patients with Bronchial Asthma

    PubMed Central

    Titova, Nadya

    2012-01-01

    Background Diagnosis of adverse reactions to food additives is difficult due to a variety of mechanisms involved and the lack of sufficiently reliable methods for their determination. The diagnosis of intolerance to food additives is still based only on placebo-controlled oral provocation. Methods The aim of this study was to determine the incidence of intolerance to ponceau 4R (E124), indigo carmine (E132), azorubine (E122), tartrazine (E102), sunset yellow (E110) and sodium benzoate (E211) among patients with bronchial asthma. We studied 114 patients with bronchial asthma using clinical and laboratory methods. Also we used the method of antigen specific damage of leucocytes by food additives. After the incubation of leucocytes with solutions of food additives to leucocytes was added 0.05 mL of trypan blue and counted the percentage of stained (damaged) granulocytes with the food dye and in control tests. If damaging leucocytes were more than 20% in comparison with controls - the test considered positive. Results It was found that positive to ponceau 4R were 6 of 114 patients, to indigo carmine–3 of 73, to sodium benzoate–4 of 73, to azorubine–11 of 114, to tartrazine–7 of 114 and to sunset yellow–9 of 114. There was a correlation between the results obtained and data history. Between experienced and control group (the patients without allergic diseases) were the reliable differences (P < 0.05). Conclusions 1. Under influence of the food additives leukocytes of patients with bronchial asthma are damaged and painted by trypan blue. 2. The method of antigen specific damage of leucocytes by food additives can be used for diagnostics of the allergies to food dyes, sodium benzoate and other gaptens.

  5. Comparing the Precision of Information Retrieval of MeSH-Controlled Vocabulary Search Method and a Visual Method in the Medline Medical Database.

    PubMed

    Hariri, Nadjla; Ravandi, Somayyeh Nadi

    2014-01-01

    Medline is one of the most important databases in the biomedical field. One of the most important hosts for Medline is Elton B. Stephens CO. (EBSCO), which has presented different search methods that can be used based on the needs of the users. Visual search and MeSH-controlled search methods are among the most common methods. The goal of this research was to compare the precision of the retrieved sources in the EBSCO Medline base using MeSH-controlled and visual search methods. This research was a semi-empirical study. By holding training workshops, 70 students of higher education in different educational departments of Kashan University of Medical Sciences were taught MeSH-Controlled and visual search methods in 2012. Then, the precision of 300 searches made by these students was calculated based on Best Precision, Useful Precision, and Objective Precision formulas and analyzed in SPSS software using the independent sample T Test, and three precisions obtained with the three precision formulas were studied for the two search methods. The mean precision of the visual method was greater than that of the MeSH-Controlled search for all three types of precision, i.e. Best Precision, Useful Precision, and Objective Precision, and their mean precisions were significantly different (P <0.001). Sixty-five percent of the researchers indicated that, although the visual method was better than the controlled method, the control of keywords in the controlled method resulted in finding more proper keywords for the searches. Fifty-three percent of the participants in the research also mentioned that the use of the combination of the two methods produced better results. For users, it is more appropriate to use a natural, language-based method, such as the visual method, in the EBSCO Medline host than to use the controlled method, which requires users to use special keywords. The potential reason for their preference was that the visual method allowed them more freedom of action.

  6. An osmium-free method of epon embedment that preserves both ultrastructure and antigenicity for post-embedding immunocytochemistry.

    PubMed

    Phend, K D; Rustioni, A; Weinberg, R J

    1995-03-01

    Immunocytochemistry for amino acids with post-embedding gold is compatible with glutaraldehyde fixation, osmication, and embedding in epoxy-based plastics, but immunogold detection of larger molecules in the central nervous system commonly requires special procedures, e.g. minimizing exposure to glutaraldehyde, eliminating osmium, cryosectioning, and/or embedding in acrylic plastics. These make samples more difficult to prepare and view and may compromise structural preservation. We report a new technique, fixing with high levels of glutaraldehyde, replacing osmium with tannic acid followed by other heavy metals and p-phenylenediamine, and embedding in Epon. This method optimizes antigenicity while retaining the structural preservation and convenient handling of standard embedding techniques. Compared to standard Epon embedment, labeling for neuropeptides in brain and spinal cord is improved. Moreover, the present method yields excellent labeling of glutamate receptors (difficult to identify with traditional post-embedding techniques) and enables simultaneous visualization of associated neurotransmitters.

  7. 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

  8. Characterization of anthropogenic methane plumes with the Hyperspectral Thermal Emission Spectrometer (HyTES): a retrieval method and error analysis

    NASA Astrophysics Data System (ADS)

    Kuai, Le; Worden, John R.; Li, King-Fai; Hulley, Glynn C.; Hopkins, Francesca M.; Miller, Charles E.; Hook, Simon J.; Duren, Riley M.; Aubrey, Andrew D.

    2016-07-01

    We introduce a retrieval algorithm to estimate lower tropospheric methane (CH4) concentrations from the surface to 1 km with uncertainty estimates using Hyperspectral Thermal Emission Spectrometer (HyTES) airborne radiance measurements. After resampling, retrievals have a spatial resolution of 6 × 6 m2. The total error from a single retrieval is approximately 20 %, with the uncertainties determined primarily by noise and spectral interferences from air temperature, surface emissivity, and atmospheric water vapor. We demonstrate retrievals for a HyTES flight line over storage tanks near Kern River Oil Field (KROF), Kern County, California, and find an extended plume structure in the set of observations with elevated methane concentrations (3.0 ± 0.6 to 6.0 ± 1.2 ppm), well above mean concentrations (1.8 ± 0.4 ppm) observed for this scene. With typically a 20 % estimated uncertainty, plume enhancements with more than 1 ppm are distinguishable from the background values with its uncertainty. HyTES retrievals are consistent with simultaneous airborne and ground-based in situ CH4 mole fraction measurements within the reported accuracy of approximately 0.2 ppm (or ˜ 8 %), due to retrieval interferences related to air temperature, emissivity, and H2O.

  9. Variations in definition and method of retrieval of complications influence outcomes statistics after pancreatoduodenectomy: comparison of NSQIP with non-NSQIP methods.

    PubMed

    Sanford, Dominic E; Woolsey, Cheryl A; Hall, Bruce L; Linehan, David C; Hawkins, William G; Fields, Ryan C; Strasberg, Steven M

    2014-09-01

    NSQIP and the Accordion Severity Grading System have recently been used to develop quantitative methods for measuring the burden of postoperative complications. However, other audit methods such as chart reviews and prospective institutional databases are commonly used to gather postoperative complications. The purpose of this study was to evaluate discordance between different audit methods in pancreatoduodenectomy--a common major surgical procedure. The chief aim was to determine how these different methods could affect quantitative evaluations of postoperative complications. Three common audit methods were compared with NSQIP in 84 patients who underwent pancreatoduodenectomy. The methods were use of a prospective database, a chart review based on discharge summaries only, and a detailed retrospective chart review. The methods were evaluated for discordance with NSQIP and among themselves. Severity grading was performed using the Modified Accordion System. Fifty-three complications were listed by NSQIP and 31 complications were identified that were not listed by NSQIP. There was poor agreement for NSQIP-type complications between NSQIP and the other audit methods for mild and moderate complications (kappa 0.381 to 0.744), but excellent agreement for severe complications (kappa 0.953 to 1.00). Discordance was usually due to variations in definition of the complications in non-NSQIP methods. There was good agreement among non-NSQIP methods for non-NSQIP complications for moderate and severe complications, but not for mild complications. There are important differences in perceived surgical outcomes based on the method of complication retrieval. The non-NSQIP methods used in this study could not be substituted for NSQIP in a quantitative analysis unless that analysis was limited to severe complications. Copyright © 2014 American College of Surgeons. Published by Elsevier Inc. All rights reserved.

  10. A new method for fusion, denoising and enhancement of x-ray images retrieved from Talbot-Lau grating interferometry.

    PubMed

    Scholkmann, Felix; Revol, Vincent; Kaufmann, Rolf; Baronowski, Heidrun; Kottler, Christian

    2014-03-21

    This paper introduces a new image denoising, fusion and enhancement framework for combining and optimal visualization of x-ray attenuation contrast (AC), differential phase contrast (DPC) and dark-field contrast (DFC) images retrieved from x-ray Talbot-Lau grating interferometry. The new image fusion framework comprises three steps: (i) denoising each input image (AC, DPC and DFC) through adaptive Wiener filtering, (ii) performing a two-step image fusion process based on the shift-invariant wavelet transform, i.e. first fusing the AC with the DPC image and then fusing the resulting image with the DFC image, and finally (iii) enhancing the fused image to obtain a final image using adaptive histogram equalization, adaptive sharpening and contrast optimization. Application examples are presented for two biological objects (a human tooth and a cherry) and the proposed method is compared to two recently published AC/DPC/DFC image processing techniques. In conclusion, the new framework for the processing of AC, DPC and DFC allows the most relevant features of all three images to be combined in one image while reducing the noise and enhancing adaptively the relevant image features. The newly developed framework may be used in technical and medical applications.

  11. A new method for fusion, denoising and enhancement of x-ray images retrieved from Talbot-Lau grating interferometry

    NASA Astrophysics Data System (ADS)

    Scholkmann, Felix; Revol, Vincent; Kaufmann, Rolf; Baronowski, Heidrun; Kottler, Christian

    2014-03-01

    This paper introduces a new image denoising, fusion and enhancement framework for combining and optimal visualization of x-ray attenuation contrast (AC), differential phase contrast (DPC) and dark-field contrast (DFC) images retrieved from x-ray Talbot-Lau grating interferometry. The new image fusion framework comprises three steps: (i) denoising each input image (AC, DPC and DFC) through adaptive Wiener filtering, (ii) performing a two-step image fusion process based on the shift-invariant wavelet transform, i.e. first fusing the AC with the DPC image and then fusing the resulting image with the DFC image, and finally (iii) enhancing the fused image to obtain a final image using adaptive histogram equalization, adaptive sharpening and contrast optimization. Application examples are presented for two biological objects (a human tooth and a cherry) and the proposed method is compared to two recently published AC/DPC/DFC image processing techniques. In conclusion, the new framework for the processing of AC, DPC and DFC allows the most relevant features of all three images to be combined in one image while reducing the noise and enhancing adaptively the relevant image features. The newly developed framework may be used in technical and medical applications.

  12. Comparison between the ESFT method and LBL method of CO2 retrieval for high-resolution satellite

    NASA Astrophysics Data System (ADS)

    Li, Yanfen; Zhang, Chunmin; Wang, Dingyi; Chen, Jie; Liu, Dongdong; Rong, Piao

    2015-02-01

    The spectra of O2 A-band (0.76 μm) and CO2 near-infrared emissions (1.6 μm) for Medium-resolution Satellite (SCIAMACHY) are simulated by the SCIATRAN model (V3.1.29), and compared with the ESFT and LBL method, as the inversion accuracy and time consuming. The time consuming of LBL was more than ESFT with the relative error less than 1%, especially for the CO2 band. But for the CO2 (2.0 um) of High-resolution Satellite, the opposite result was found. That is to say, the LBL method was more suitable for High-resolution Satellite. Different wavelength intervals and integral wavelength steps are applied to the LBL to select the most appropriate combination for High-resolution SatelliteO2 A-band (0.76 μm) and CO2 near-infrared band (1.58 μm).

  13. Localization of hepatitis B surface antigen in conventional paraffin sections of the liver. Comparison of immunofluorescence, immunoperoxidase, and orcein staining methods with regard to their specificity and reliability as antigen marker.

    PubMed Central

    Nayak, N. C.; Sachdeva, R.

    1975-01-01

    Hepatitis B antigen (HBAg) has been demonstrated in conventional formalin-fixed paraffin-embedded liver tissue by peroxidase and fluorescent immunostaining as well as by orcein. Complete locational and morphologic identity is seen between material stained by specific immunologic methods and by orcein. The antigen is restricted to the cytoplasm and is generally observed in the hepatocyte; it is present in three morphologic forms. Certain morphologic forms can even be identified in hematoxylin and eosin-stained tissue. Results of immunostaining procedures indicate that the antigen demonstrated in this study consists entirely of surface coat of hepatitis B virus (HBsAg). This seems to be the only component revealed by orcein staining. The latter is considered to be a good marker of the surface antigen and to have certain advantages over immunostaining. It is suggested that suitability of conventional paraffin sections for the detection of HBAg has wide and important implications. Images Figures 1-5 Figure 6 Figure 7 Figure 8 Figure 9 Figure 10 PMID:55076

  14. Evaluation of a rapid method for the detection of streptococcal group A antigen directly from throat swabs.

    PubMed Central

    Venezia, R A; Ryan, A; Alward, S; Kostun, W A

    1985-01-01

    Throat swabs from 196 pediatric patients were processed by a direct extraction-latex agglutination method (Group A Strep Direct Antigen Identification Test [DAI]) that detects group A streptococci in the specimen. The method requires a 45-min enzymatic extraction period at 37 degrees C and a 4-min reaction period with antibody-linked latex particles. The results were compared with those of the culture and fluorescent antibody methods and the clinical presentation of the patient for pharyngitis. Ninety-three percent of the specimens resulted in agreement by all tests, and 28% were culture positive for group A streptococci. Compared with the culture method, the DAI had a sensitivity and a specificity of 83% and 99%, respectively. The positive predictive values were 98% versus the culture method and 93% versus the fluorescent antibody method, whereas the negative predictive values were 94% versus both other methods. Of the 14 discrepant results when both clinical presentation of an acute pharyngitis and the test results were compared, the culture method provided the best correlation. An additional 64 specimens were processed by the DAI and another direct extraction-latex agglutination method (Culturette Ten-Minute Group A Strep ID Test), and the results were compared with those of the culture method. This group had a 40.6% culture isolation rate for group A streptococci. The sensitivity and specificity of the DAI and Strep ID methods versus the culture method were 81 and 100%, and 77 and 97%, respectively. These results indicate that the DAI is accurate for diagnosing group A streptococcal pharyngitis directly from throat swabs. However, negative results in the presence of a symptomatic patient must be confirmed by standard culture techniques. PMID:3884656

  15. A new and robust method of tethering IgG surrogate antigens on lipid bilayer membranes to facilitate the TIRFM based live cell and single molecule imaging experiments.

    PubMed

    Zhang, Shaosen; Xu, Liling; Zhao, Xingwang; Chen, Xin; Fan, Yilin; Wan, Zhengpeng; Xu, Yinsheng; Liu, Wanli

    2013-01-01

    Our understanding of cell-cell interactions has been significantly improved in the past years with the help of Total Internal Reflection Fluorescence Microscope (TIRFM) in combination with an antigen presenting system supported by planar lipid bilayer (PLB) membranes, which are used to mimic the extensive receptor and ligand interactions within cell-cell contact interface. In TIRFM experiments, it is a challenge to uniformly present ligand molecules in monomeric format on the surface of PLB membranes. Here, we introduce a new and robust method of tethering IgG surrogate antigen ligands on the surface of Ni(2+)-containing PLB membranes. In this method, we use a modified D domain from staphylococcal protein A molecule that is fused with an N-terminus polyhistidine tag (H12-D-domain) to tether IgG surrogate antigens on Ni(2+)-containing PLB membranes. We systematically assessed the specificity and capability of H12-D-domain construct to capture IgG molecules from different species through live cell and single molecule TIRFM imaging. We find that these IgG surrogate antigens tethered by H12-D-domain show better lateral mobility and are more uniformly distributed on PLB membranes than the ones tethered by streptavidin. Neither IgM molecules, nor Fab or F(ab')2 fragments of IgG molecules can be tethered on PLB membranes by H12-D-domain construct. These tethered IgG surrogate antigens strongly induce the formation and accumulation of signaling active antigen receptor microclusters within the immunological synapse in B or T lymphocyte cells. Thus our method provides a new and robust method to tether IgG surrogate antigens or other molecules fused with IgG Fc portion on PLB membranes for TIRFM based molecule imaging experiments.

  16. 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.

  17. Application of an indirect immunofluorescent staining method for detection of Salmonella enteritidis in paraffin slices and antigen location in infected duck tissues.

    PubMed

    Yan, Bin; Cheng, An-Chun; Wang, Ming-Shu; Deng, Shu-Xuan; Zhang, Zhen-Hua; Yin, Nian-Chun; Cao, Ping; Cao, Sheng-Yan

    2008-02-07

    To detect Salmonella enteritidis (S. enteritidis) in paraffin slices and antigen location in infected duck tissues. The rabbits were immunized with purified bacillus to obtain S. enteritidis-specific antibody, which were then extracted by the caprylic-ammonium sulphate method, purified through High-Q columns. An indirect immuno-fluorescent staining method (IFA) was established to detect the S. enteritidis antigen in paraffin slices. Detected S. enteritidis in each organ tissue of ducklings experimentally infected with S. enteritidis. The gland of Garder, heart, kidney, spleen, liver, brain, ileum, jejunum, bursa of Fabricius from S. enteritidis experimentally infected ducklings were positive or strongly positive, and the S. enteritidis antigen mainly distributed in the infected cell cytoplasm. IFA is an intuitionist, sensitive and specific method in detecting S. enteritidis antigen in paraffin wax slices, and it is a good method in diagnosis and antigen location of S. enteritidis. We also conclude that the gland of Garder, heart, kidney, spleen, liver, ileum, jejunum are target organs in S. enteritidis infections of duck, and S. enteritidis is an intracellular parasitic bacterium.

  18. Comparing the Precision of Information Retrieval of MeSH-Controlled Vocabulary Search Method and a Visual Method in the Medline Medical Database

    PubMed Central

    Hariri, Nadjla; Ravandi, Somayyeh Nadi

    2014-01-01

    Background: Medline is one of the most important databases in the biomedical field. One of the most important hosts for Medline is Elton B. Stephens CO. (EBSCO), which has presented different search methods that can be used based on the needs of the users. Visual search and MeSH-controlled search methods are among the most common methods. The goal of this research was to compare the precision of the retrieved sources in the EBSCO Medline base using MeSH-controlled and visual search methods. Methods: This research was a semi-empirical study. By holding training workshops, 70 students of higher education in different educational departments of Kashan University of Medical Sciences were taught MeSH-Controlled and visual search methods in 2012. Then, the precision of 300 searches made by these students was calculated based on Best Precision, Useful Precision, and Objective Precision formulas and analyzed in SPSS software using the independent sample T Test, and three precisions obtained with the three precision formulas were studied for the two search methods. Results: The mean precision of the visual method was greater than that of the MeSH-Controlled search for all three types of precision, i.e. Best Precision, Useful Precision, and Objective Precision, and their mean precisions were significantly different (P <0.001). Sixty-five percent of the researchers indicated that, although the visual method was better than the controlled method, the control of keywords in the controlled method resulted in finding more proper keywords for the searches. Fifty-three percent of the participants in the research also mentioned that the use of the combination of the two methods produced better results. Conclusion: For users, it is more appropriate to use a natural, language-based method, such as the visual method, in the EBSCO Medline host than to use the controlled method, which requires users to use special keywords. The potential reason for their preference was that the visual

  19. Retrievable Inferior Vena Cava Filters: Factors that Affect Retrieval Success

    SciTech Connect

    Geisbuesch, Philipp Benenati, James F.; Pena, Constantino S.; Couvillon, Joseph; Powell, Alex; Gandhi, Ripal; Samuels, Shaun; Uthoff, Heiko

    2012-10-15

    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 had 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.

  20. Golden Retrievers.

    ERIC Educational Resources Information Center

    Christensen, Deborah

    1999-01-01

    Provides a basic definition of metadata, including the usefulness of metatags for online information retrieval and documentation. Defines the elements of the Dublin Core, the next level of metadata. Discusses how librarians can take advantage of metadata. Describes the Gateway to Educational Materials (GEM) Project whose goal is to use metadata to…

  1. Exploring a new method for the retrieval of urban thermophysical properties using thermal infrared remote sensing and deterministic modeling

    NASA Astrophysics Data System (ADS)

    De Ridder, K.; Bertrand, C.; Casanova, G.; Lefebvre, W.

    2012-09-01

    Increasingly, mesoscale meteorological and climate models are used to predict urban weather and climate. Yet, large uncertainties remain regarding values of some urban surface properties. In particular, information concerning urban values for thermal roughness length and thermal admittance is scarce. In this paper, we present a method to estimate values for thermal admittance in combination with an optimal scheme for thermal roughness length, based on METEOSAT-8/SEVIRI thermal infrared imagery in conjunction with a deterministic atmospheric model containing a simple urbanized land surface scheme. Given the spatial resolution of the SEVIRI sensor, the resulting parameter values are applicable at scales of the order of 5 km. As a study case we focused on the city of Paris, for the day of 29 June 2006. Land surface temperature was calculated from SEVIRI thermal radiances using a new split-window algorithm specifically designed to handle urban conditions, as described inAppendix A, including a correction for anisotropy effects. Land surface temperature was also calculated in an ensemble of simulations carried out with the ARPS mesoscale atmospheric model, combining different thermal roughness length parameterizations with a range of thermal admittance values. Particular care was taken to spatially match the simulated land surface temperature with the SEVIRI field of view, using the so-called point spread function of the latter. Using Bayesian inference, the best agreement between simulated and observed land surface temperature was obtained for the Zilitinkevich (1970) and Brutsaert (1975) thermal roughness length parameterizations, the latter with the coefficients obtained by Kanda et al. (2007). The retrieved thermal admittance values associated with either thermal roughness parameterization were, respectively, 1843 ± 108 J m-2 s-1/2 K-1 and 1926 ± 115 J m-2 s-1/2 K-1.

  2. Detection of Chlamydia psittaci (ovis) antigen in tissue sections and McCoy cells using streptavidin-biotin and the IMAGEN staining method.

    PubMed

    Amin, J D; Wilsmore, A J

    1994-01-01

    Two procedures for identifying chlamydial antigen in infected McCoy cells and tissue sections are described. Both the streptavidin-biotin method and the IMAGEN test clearly detected chlamydial antigen in ovine placental tissue sections and in infected McCoy cells before they could be detected by conventional stains. The streptavidin-biotin method is lengthy, but specific and sensitive, and the slides can be kept indefinitely for later examination. By contrast, the IMAGEN test is a single step procedure which requires fluorescent microscopy and slides can only be kept for up to 1 week before examination.

  3. A method for retrieving vertical distribution of aerosol mass concentration in atmosphere from results of lidar sensing at Nd:YAG laser wavelengths

    NASA Astrophysics Data System (ADS)

    Lisenko, S. A.; Kugeiko, M. M.

    2011-03-01

    A method for retrieving the vertical profiles of atmospheric aerosol concentration from the results of lidar sensing at Ng:YAG laser wavelengths is developed based on the found multiple regressions between the optical location characteristics of aerosol at wavelengths of 0.355, 0.532, and 1.064 nm, as well as between the aerosol backscattering coefficient at these wavelengths and the concentration of aerosol particles. The method does not require solving ill-posed inverse problems and minimizes the use of a priori information. The reliability and generality of regressions obtained are confirmed by their good agreement with the AERO-NET data. The method efficiency is demonstrated by numerical experiments on retrieving profiles of back-scattering coefficients and concentration that corresponds to different optical models of aerosol.

  4. A comparison of DNA collection and retrieval from two swab types (cotton and nylon flocked swab) when processed using three QIAGEN extraction methods.

    PubMed

    Brownlow, Robert J; Dagnall, Kathryn E; Ames, Carole E

    2012-05-01

    The Metropolitan Police Service currently uses cotton swabs to retrieve DNA for forensic profiling. Recently, a new nylon flocked swab type has become available from Copan (MicroRheologics, Brescia, Italy) that it is claimed, offers increased sample recovery and release yields. If true, the flocked swab may have important applications in DNA evidence retrieval. This study examines the DNA retrieval capability of cotton and nylon flocked swabs when extracted using three common extraction platforms (QIAcube, BioRobot EZ1 and manually processed QIAamp DNA investigator kit). Results indicate that both swab types are capable of recovering high percentages of DNA (>50%); however, the extraction platform selected was shown to have a significant effect upon DNA retrieval. Across all experiments, the cotton swab combined with the spin-column extractions was shown to be most effective, with the nylon swab and BioRobot EZ1 combination being the least effective. These findings illustrate the importance of extraction method selection. © 2011 American Academy of Forensic Sciences.

  5. Guenter Tulip Filter Retrieval Experience: Predictors of Successful Retrieval

    SciTech Connect

    Turba, Ulku Cenk Arslan, Bulent Meuse, Michael Sabri, Saher; Macik, Barbara Gail

    2010-08-15

    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 relationship 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.

  6. A New Method to Retrieve the Data Requirements of the Remote Sensing Community – Exemplarily Demonstrated for Hyperspectral User Needs

    PubMed Central

    Nieke, Jens; Reusen, Ils

    2007-01-01

    User-driven requirements for remote sensing data are difficult to define, especially details on geometric, spectral and radiometric parameters. Even more difficult is a decent assessment of the required degrees of processing and corresponding data quality. It is therefore a real challenge to appropriately assess data costs and services to be provided. In 2006, the HYRESSA project was initiated within the framework 6 programme of the European Commission to analyze the user needs of the hyperspectral remote sensing community. Special focus was given to finding an answer to the key question, “What are the individual user requirements for hyperspectral imagery and its related data products?”. A Value-Benefit Analysis (VBA) was performed to retrieve user needs and address open items accordingly. The VBA is an established tool for systematic problem solving by supporting the possibility of comparing competing projects or solutions. It enables evaluation on the basis of a multidimensional objective model and can be augmented with expert's preferences. After undergoing a VBA, the scaling method (e.g., Law of Comparative Judgment) was applied for achieving the desired ranking judgments. The result, which is the relative value of projects with respect to a well-defined main objective, can therefore be produced analytically using a VBA. A multidimensional objective model adhering to VBA methodology was established. Thereafter, end users and experts were requested to fill out a Questionnaire of User Needs (QUN) at the highest level of detail - the value indicator level. The end user was additionally requested to report personal preferences for his particular research field. In the end, results from the experts' evaluation and results from a sensor data survey can be compared in order to understand user needs and the drawbacks of existing data products. The investigation – focusing on the needs of the hyperspectral user community in Europe – showed that a VBA is a

  7. Retrieval with gene queries.

    PubMed

    Sehgal, Aditya K; Srinivasan, Padmini

    2006-04-21

    Accuracy of document retrieval from MEDLINE for gene queries is crucially important for many applications in bioinformatics. We explore five information retrieval-based methods to rank documents retrieved by PubMed gene queries for the human genome. The aim is to rank relevant documents higher in the retrieved list. We address the special challenges faced due to ambiguity in gene nomenclature: gene terms that refer to multiple genes, gene terms that are also English words, and gene terms that have other biological meanings. Our two baseline ranking strategies are quite similar in performance. Two of our three LocusLink-based strategies offer significant improvements. These methods work very well even when there is ambiguity in the gene terms. Our best ranking strategy offers significant improvements on three different kinds of ambiguities over our two baseline strategies (improvements range from 15.9% to 17.7% and 11.7% to 13.3% depending on the baseline). For most genes the best ranking query is one that is built from the LocusLink (now Entrez Gene) summary and product information along with the gene names and aliases. For others, the gene names and aliases suffice. We also present an approach that successfully predicts, for a given gene, which of these two ranking queries is more appropriate. We explore the effect of different post-retrieval strategies on the ranking of documents returned by PubMed for human gene queries. We have successfully applied some of these strategies to improve the ranking of relevant documents in the retrieved sets. This holds true even when various kinds of ambiguity are encountered. We feel that it would be very useful to apply strategies like ours on PubMed search results as these are not ordered by relevance in any way. This is especially so for queries that retrieve a large number of documents.

  8. 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.

  9. 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.

  10. A microarray method for identifying tumor antigens by screening a tumor cDNA expression library against cancer sera

    PubMed Central

    Whittemore, Kurt; Sykes, Kathryn

    2013-01-01

    The immune system responds to tumor cells. The challenge has been how to effectively use these responses to treat or protect against cancer. Toward the goal of developing a cancer vaccine, we are pursuing methodologies for the discovery and testing of useful antigens. We present an array-based approach for discovering these B cell antigens by directly screening for specific host-sera reactivity to lysates from tumor-derived cDNA expression libraries. Several cancer-specific antigens were identified, and these are currently being validated as potential candidates. PMID:23851590

  11. A microarray method for identifying tumor antigens by screening a tumor cDNA expression library against cancer sera.

    PubMed

    Whittemore, Kurt; Sykes, Kathryn

    2013-10-01

    The immune system responds to tumor cells. The challenge has been how to effectively use these responses to treat or protect against cancer. Toward the goal of developing a cancer vaccine, we are pursuing methodologies for the discovery and testing of useful antigens. We present an array-based approach for discovering these B cell antigens by directly screening for specific host-sera reactivity to lysates from tumor-derived cDNA expression libraries. Several cancer-specific antigens were identified, and these are currently being validated as potential candidates.

  12. Differential Scanning Calorimetry - A Method for Assessing the Thermal Stability and Conformation of Protein Antigen.

    PubMed

    Durowoju, Ibrahim B; Bhandal, Kamaljit S; Hu, Jian; Carpick, Bruce; Kirkitadze, Marina

    2017-03-04

    Differential scanning calorimetry (DSC) is an analytical technique that measures the molar heat capacity of samples as a function of temperature. In the case of protein samples, DSC profiles provide information about thermal stability, and to some extent serves as a structural "fingerprint" that can be used to assess structural conformation. It is performed using a differential scanning calorimeter that measures the thermal transition temperature (melting temperature; Tm) and the energy required to disrupt the interactions stabilizing the tertiary structure (enthalpy; ∆H) of proteins. Comparisons are made between formulations as well as production lots, and differences in derived values indicate differences in thermal stability and structural conformation. Data illustrating the use of DSC in an industrial setting for stability studies as well as monitoring key manufacturing steps are provided as proof of the effectiveness of this protocol. In comparison to other methods for assessing the thermal stability of protein conformations, DSC is cost-effective, requires few sample preparation steps, and also provides a complete thermodynamic profile of the protein unfolding process.

  13. Differential Scanning Calorimetry — A Method for Assessing the Thermal Stability and Conformation of Protein Antigen

    PubMed Central

    Durowoju, Ibrahim B.; Bhandal, Kamaljit S.; Hu, Jian; Carpick, Bruce; Kirkitadze, Marina

    2017-01-01

    Differential scanning calorimetry (DSC) is an analytical technique that measures the molar heat capacity of samples as a function of temperature. In the case of protein samples, DSC profiles provide information about thermal stability, and to some extent serves as a structural “fingerprint” that can be used to assess structural conformation. It is performed using a differential scanning calorimeter that measures the thermal transition temperature (melting temperature; Tm) and the energy required to disrupt the interactions stabilizing the tertiary structure (enthalpy; ∆H) of proteins. Comparisons are made between formulations as well as production lots, and differences in derived values indicate differences in thermal stability and structural conformation. Data illustrating the use of DSC in an industrial setting for stability studies as well as monitoring key manufacturing steps are provided as proof of the effectiveness of this protocol. In comparison to other methods for assessing the thermal stability of protein conformations, DSC is cost-effective, requires few sample preparation steps, and also provides a complete thermodynamic profile of the protein unfolding process. PMID:28287565

  14. Generalized amplitude-phase retrieval algorithm attack on 'double images encryption method with resistance against the special attack based on an asymmetric algorithm'

    NASA Astrophysics Data System (ADS)

    Zhang, Chenggong; He, Wenqi; Cai, Zewei; Peng, Xiang

    2016-09-01

    A generalized amplitude-phase retrieval algorithm (GAPRA) attack on `double images encryption method with resistance against the special attack based on an asymmetric algorithm' (DIEM) is presented in this paper. The analysis shows that the DIEM is a cascaded cryptosystem, which consist of a joint transform correlator architecture and a phasetruncated Fourier transform scheme. A GAPRA attack is proposed and the potential risk of the cascaded cryptosystems is discussed. By using our method, an attacker could crack high-quality results of the plaintexts. A set of simulation results demonstrate the validity and feasibility of the proposed method.

  15. Human factors analysis and design methods for nuclear waste retrieval systems: Human factors design methodology and integration plan

    NASA Astrophysics Data System (ADS)

    Casey, S. M.

    1980-06-01

    The nuclear waste retrieval system intended to be used for the removal of storage canisters (each canister containing a spent fuel rod assembly) located in an underground salt bed depository is discussed. The implementation of human factors engineering principles during the design and construction of the retrieval system facilities and equipment is reported. The methodology is structured around a basic system development effort involving preliminary development, equipment development, personnel subsystem development, and operational test and evaluation. Examples of application of the techniques in the analysis of human tasks, and equipment required in the removal of spent fuel canisters is provided. The framework for integrating human engineering with the rest of the system development effort is documented.

  16. A two-channel method for retrieval of the Black Sea surface temperature from Landsat-8 measurements

    NASA Astrophysics Data System (ADS)

    Aleskerova, A. A.; Kubryakov, A. A.; Stanichny, S. V.

    2016-12-01

    The present work is devoted to the development of a retrieval algorithm for the sea surface temperature from the two-channel measurements of the Landsat-8 satellite on the basis of a comparison with MODIS satellite data. The algorithm makes it possible to reconstruct the surface temperature with a 100 m resolution, which enables analysis of the spatial structure of various phenomena on the ocean surface at small scales (upwelling, submesoscale vortices, etc.). The magnitude of the standard deviation between the reconstructed temperature and the temperature derived from the MODIS satellite is 0.58°C. The sources of inconsistency between temperatures retrieved from the MODIS and Landsat-8 measurements were investigated: diurnal temperature variation, which leads to an increase in the standard deviation in the summer period because of the mismatch in time ( 2 hours) between measurements; the presence of specific bands in the Landsat data, which is probably related to instrumental errors of the device.

  17. A high-throughput optomechanical retrieval method for sequence-verified clonal DNA from the NGS platform.

    PubMed

    Lee, Howon; Kim, Hyoki; Kim, Sungsik; Ryu, Taehoon; Kim, Hwangbeom; Bang, Duhee; Kwon, Sunghoon

    2015-02-02

    Writing DNA plays a significant role in the fields of synthetic biology, functional genomics and bioengineering. DNA clones on next-generation sequencing (NGS) platforms have the potential to be a rich and cost-effective source of sequence-verified DNAs as a precursor for DNA writing. However, it is still very challenging to retrieve target clonal DNA from high-density NGS platforms. Here we propose an enabling technology called 'Sniper Cloning' that enables the precise mapping of target clone features on NGS platforms and non-contact rapid retrieval of targets for the full utilization of DNA clones. By merging the three cutting-edge technologies of NGS, DNA microarray and our pulse laser retrieval system, Sniper Cloning is a week-long process that produces 5,188 error-free synthetic DNAs in a single run of NGS with a single microarray DNA pool. We believe that this technology has potential as a universal tool for DNA writing in biological sciences.

  18. A method to identify protein antigens of Dermanyssus gallinae for the protection of birds from poultry mites.

    PubMed

    Makert, Gustavo R; Vorbrüggen, Susanne; Krautwald-Junghanns, Maria-Elisabeth; Voss, Matthias; Sohn, Kai; Buschmann, Tilo; Ulbert, Sebastian

    2016-07-01

    The poultry red mite (PRM) Dermanyssus gallinae causes high economic losses and is among the most important parasites in poultry farming worldwide. Different chemical, physical, and biological strategies try to control the expansion of PRM. However, effective solutions to this problem still have to be found. Here, we present a method for the development of an immunological control strategy, based on the identification of mite protein antigens which elicit antibodies with anti-mite activity in the immunized chicken. Hens were immunized with different PRM protein extracts formulated with two different adjuvants, and IgY-antibodies were isolated from the eggs. A PRM in vitro feeding assay which used chicken blood spiked with these IgY-preparations was used to detect antibodies which caused PRM mortality. In vitro feeding of mites with IgY isolated from hens immunized with PRM extract formulated with one of the adjuvants showed a statistically significant increase in the mortality as compared to control mites. After the separation of total PRM extracts in two-dimensional gels, several protein spots were recognized by such IgY preparations. Ten protein spots were subjected to mass spectrometry (MS/MS) for the identification of the corresponding proteins. Complete protein sequences were deduced from genomic and transcriptomic assemblies derived from high throughput sequencing of total PRM DNA and RNA. The results may contribute to the development of an immunological control strategy of D. gallinae.

  19. Snow depth and snow cover retrieval from FengYun3B microwave radiation imagery based on a snow passive microwave unmixing method in Northeast China

    NASA Astrophysics Data System (ADS)

    Gu, Lingjia; Ren, Ruizhi; Zhao, Kai; Li, Xiaofeng

    2014-01-01

    The precision of snow parameter retrieval is unsatisfactory for current practical demands. The primary reason is because of the problem of mixed pixels that are caused by low spatial resolution of satellite passive microwave data. A snow passive microwave unmixing method is proposed in this paper, based on land cover type data and the antenna gain function of passive microwaves. The land cover type of Northeast China is partitioned into grass, farmland, bare soil, forest, and water body types. The component brightness temperatures (CBT), namely unmixed data, with 1 km data resolution are obtained using the proposed unmixing method. The snow depth determined by the CBT and three snow depth retrieval algorithms are validated through field measurements taken in forest and farmland areas of Northeast China in January 2012 and 2013. The results show that the overall of the retrieval precision of the snow depth is improved by 17% in farmland areas and 10% in forest areas when using the CBT in comparison with the mixed pixels. The snow cover results based on the CBT are compared with existing MODIS snow cover products. The results demonstrate that more snow cover information can be obtained with up to 86% accuracy.

  20. Adaptive MGS Phase Retrieval

    NASA Technical Reports Server (NTRS)

    Basinger, Scott A.; Bikkannavar, Siddarayappa; Cohen, David; Green, Joseph J.; Lou, John; Ohara, Catherine; Redding, David; Shi, Fang

    2008-01-01

    Adaptive MGS Phase Retrieval software uses the Modified Gerchberg-Saxton (MGS) algorithm, an image-based sensing method that can turn any focal plane science instrument into a wavefront sensor, avoiding the need to use external metrology equipment. Knowledge of the wavefront enables intelligent control of active optical systems.

  1. Retrieving similar color images

    NASA Astrophysics Data System (ADS)

    Gagliardi, Isabella; Schettini, Raimondo

    1998-09-01

    There is a great demand for efficient tools that can, on the basis of the pictorial content, organize large quantities of images and rapidly retrieve those of interest. With that goal in mind we present a method for indexing complex color images. The basic idea is to exploit image data decomposition and compression based on the standard Haar multiresolution wavelet transform to describe image content. In this way we are able to effectively eliminate data redundancy and concisely represent the salient features of the image in image signatures of predefined lengths. In the retrieval phase image signatures are compared using a similarity measure that the system has 'learned' from user's. Experimental results confirm the feasibility of our approach, which outperforms more standard procedures, in retrieval accuracy and at lower computational costs.

  2. Automatic Classification in Information Retrieval.

    ERIC Educational Resources Information Center

    van Rijsbergen, C. J.

    1978-01-01

    Addresses the application of automatic classification methods to the problems associated with computerized document retrieval. Different kinds of classifications are described, and both document and term clustering methods are discussed. References and notes are provided. (Author/JD)

  3. Rapid method for detection of influenza a and B virus antigens by use of a two-photon excitation assay technique and dry-chemistry reagents.

    PubMed

    Koskinen, Janne O; Vainionpää, Raija; Meltola, Niko J; Soukka, Jori; Hänninen, Pekka E; Soini, Aleksi E

    2007-11-01

    New separation-free assay methods for the rapid detection of influenza A and B virus antigens are presented. The methods employ dry-chemistry reagents and the recently developed two-photon excitation (TPX) fluorescence detection technology. According to the assay scheme, virus antigens are sandwiched by capture antibody onto polymer microspheres and fluorescently labeled antibody conjugate. Consequently, fluorescent immunocomplexes are formed on the surface of microspheres in proportion to the concentration of the analyte in the sample. The fluorescence signal from individual microspheres is measured, separation free, by means of two-photon excited fluorescence detection. In order to demonstrate the applicability of the new assay technique for virus antigen detection, methods for influenza A and B viruses were constructed. The assay method for influenza A virus applied a molecular fluorescent label, whereas the method for influenza B virus required a nanoparticle fluorescent reporter to reach sufficient clinical sensitivity. The new methods utilize a dry-chemistry approach, where all assay-specific reagents are dispensed into assay wells already in the manufacturing process of the test kits. The performance of the assay methods was tested with nasopharyngeal specimens using a time-resolved fluoroimmunoassay as a reference method. The results suggest that the new technique enables the rapid detection of influenza virus antigens with sensitivity and specificity comparable to that of the reference method. The dose-response curves showed linear responses with slopes equal to unity and dynamic assay ranges of 3 orders of magnitude. Applicability of the novel TPX technique for rapid multianalyte testing of respiratory infections is discussed.

  4. Rapid Method for Detection of Influenza A and B Virus Antigens by Use of a Two-Photon Excitation Assay Technique and Dry-Chemistry Reagents▿

    PubMed Central

    Koskinen, Janne O.; Vainionpää, Raija; Meltola, Niko J.; Soukka, Jori; Hänninen, Pekka E.; Soini, Aleksi E.

    2007-01-01

    New separation-free assay methods for the rapid detection of influenza A and B virus antigens are presented. The methods employ dry-chemistry reagents and the recently developed two-photon excitation (TPX) fluorescence detection technology. According to the assay scheme, virus antigens are sandwiched by capture antibody onto polymer microspheres and fluorescently labeled antibody conjugate. Consequently, fluorescent immunocomplexes are formed on the surface of microspheres in proportion to the concentration of the analyte in the sample. The fluorescence signal from individual microspheres is measured, separation free, by means of two-photon excited fluorescence detection. In order to demonstrate the applicability of the new assay technique for virus antigen detection, methods for influenza A and B viruses were constructed. The assay method for influenza A virus applied a molecular fluorescent label, whereas the method for influenza B virus required a nanoparticle fluorescent reporter to reach sufficient clinical sensitivity. The new methods utilize a dry-chemistry approach, where all assay-specific reagents are dispensed into assay wells already in the manufacturing process of the test kits. The performance of the assay methods was tested with nasopharyngeal specimens using a time-resolved fluoroimmunoassay as a reference method. The results suggest that the new technique enables the rapid detection of influenza virus antigens with sensitivity and specificity comparable to that of the reference method. The dose-response curves showed linear responses with slopes equal to unity and dynamic assay ranges of 3 orders of magnitude. Applicability of the novel TPX technique for rapid multianalyte testing of respiratory infections is discussed. PMID:17855571

  5. [Detection of Aspergillus antigen galactomannan using ELISA method: validation of the performances of the method for accreditation].

    PubMed

    Kauffmann-Lacroix, C; Arvier, M; Charron, M; Rodier, M-H; Vassault, A

    2013-03-01

    Diagnosis of invasive aspergillosis for patients with high risk of infection is based on the monitoring of Aspergillus antigenemia assessed by the detection of galactomannan in serum by a sandwich-type ELISA (Biorad(®)). The validation of the method was displayed according to the guide COFRAC SH GTA 04. The internal quality control system settled, involves two quality control samples made of pools of sera (negative and positive). The repeatability of the measurements, as estimated by the coefficients of variation (CV), obtained by two different technicians was found from 9 to 13.7% for the positive control. The CV of the negative control, for which the provider indicates it is not useful in the analytical process, was found from 7.1 to 30%. In our experience it could be an indicator of environmental contamination. The evaluation of the intermediary fidelity was 15.7% for the positive control and 22.5% for the negative one. In the lack of reference material (International Standard) and recommendation from scientific societies, performances obtained will be discussed according to the results reported in the technical form of the supplier and those obtained by 39 laboratories participating in the only available external quality assessment program organized in France by ProBioQual(®) where the CV of reproducibility are 44.7% of unit (mean index 0.131) for the negative control and 18% (mean index 1.089) for the positive one in 2011.

  6. Rapid and Accurate Determination of Lipopolysaccharide O-Antigen Types in Klebsiella pneumoniae with a Novel PCR-Based O-Genotyping Method

    PubMed Central

    Shih, Yun-Jui; Cheong, Cheng-Man; Yi, Wen-Ching

    2015-01-01

    Klebsiella pneumoniae, a Gram-negative bacillus that causes life-threatening infections in both hospitalized patients and ambulatory persons, can be classified into nine lipopolysaccharide (LPS) O-antigen serotypes. The O-antigen type has important clinical and epidemiological significance. However, K. pneumoniae O serotyping is cumbersome, and the reagents are not commercially available. To overcome the limitations of conventional serotyping methods, we aimed to create a rapid and accurate PCR method for K. pneumoniae O genotyping. We sequenced the genetic determinants of LPS O antigen from serotypes O1, O2a, O2ac, O3, O4, O5, O8, O9, and O12. We established a two-step genotyping scheme, based on the two genomic regions associated with O-antigen biosynthesis. The first set of PCR primers, which detects alleles at the wzm-wzt loci of the wb gene cluster, distinguishes between O1/O2, O3, O4, O5, O8, O9, and O12. The second set of PCR primers, which detects alleles at the wbbY region, further differentiates between O1, O2a, and O2ac. We verified the specificity of O genotyping against the O-serotype reference strains. We then tested the sensitivity and specificity of O genotyping in K. pneumoniae, using the 56 K-serotype reference strains with known O serotypes determined by an inhibition enzyme-linked immunosorbent assay (iELISA). There is a very good correlation between the O genotypes and classical O serotypes. Three discrepancies were observed and resolved by nucleotide sequencing—all in favor of O genotyping. The PCR-based O genotyping, which can be easily performed in clinical and research microbiology laboratories, is a rapid and accurate method for determining the LPS O-antigen types of K. pneumoniae isolates. PMID:26719438

  7. Osteosarcoma Microenvironment: Whole-Slide Imaging and Optimized Antigen Detection Overcome Major Limitations in Immunohistochemical Quantification

    PubMed Central

    Kunz, Pierre; Fellenberg, Jörg; Moskovszky, Linda; Sápi, Zoltan; Krenacs, Tibor; Poeschl, Johannes; Lehner, Burkhard; Szendrõi, Miklos; Ewerbeck, Volker; Kinscherf, Ralf; Fritzsching, Benedikt

    2014-01-01

    Background In osteosarcoma survival rates could not be improved over the last 30 years. Novel biomarkers are warranted to allow risk stratification of patients for more individual treatment following initial diagnosis. Although previous studies of the tumor microenvironment have identified promising candidates, novel biomarkers have not been translated into routine histopathology. Substantial difficulties regarding immunohistochemical detection and quantification of antigens in decalcified and heterogeneous osteosarcoma might largely explain this translational short-coming. Furthermore, we hypothesized that conventional hot spot analysis is often not representative for the whole section when applied to heterogeneous tissues like osteosarcoma. We aimed to overcome these difficulties for major biomarkers of the immunovascular microenvironment. Methods Immunohistochemistry was systematically optimized for cell surface (CD31, CD8) and intracellular antigens (FOXP3) including evaluation of 200 different antigen retrieval conditions. Distribution patterns of these antigens were analyzed in formalin-fixed and paraffin-embedded samples from 120 high-grade central osteosarcoma biopsies and computer-assisted whole-slide analysis was compared with conventional quantification methods including hot spot analysis. Results More than 96% of osteosarcoma samples were positive for all antigens after optimization of immunohistochemistry. In contrast, standard immunohistochemistry retrieved false negative results in 35–65% of decalcified osteosarcoma specimens. Standard hot spot analysis was applicable for homogeneous distributed FOXP3+ and CD8+ cells. However, heterogeneous distribution of vascular CD31 did not allow reliable quantification with hot spot analysis in 85% of all samples. Computer-assisted whole-slide analysis of total CD31- immunoreactive area proved as the most appropriate quantification method. Conclusion Standard staining and quantification procedures are not

  8. Optimal retrieval method to estimate ozone vertical profile in the mesosphere and lower thermosphere (MLT) region from submillimeter-wave limb emission spectra

    NASA Astrophysics Data System (ADS)

    Kuribayashi, K.; Yoshida, N.; Jin, H.; Orsolini, Y. J.; Kasai, Y.

    2017-05-01

    Spectrum width and intensity of ozone (O3) observed in the MLT region behaves quite differently than in the stratosphere for submillimeter-wave limb emission spectroscopic observation. For example, O3 spectra in the stratosphere are stronger during the day than at night. Conversely, spectra in the MLT region at night are stronger than those occurring during the day due to diurnal variations in O3 behavior. These opposing behaviors cause problems, including oscillations and inaccuracies particularly for O3 vertical profiles in the MLT region retrieved with an application of one retrieval procedure for the entire vertical range (stratosphere to thermosphere). Recently, we developed an optimal retrieval method for O3 in the MLT region for spectra, observed by the Superconducting Submillimeter-Wave Limb-Emission Sounder (SMILES) instrument on the International Space Station. Optimizations were performed for frequency window range, retrieval vertical range, vertical grids, and a priori information for O3 and temperature. Precision and accuracy were evaluated by error analysis and comparisons with previous products. The random error was estimated to be about 5% and 35% in the mesosphere and lower thermosphere, respectively, for nighttime O3 profiles in the MLT region. The total systematic error was about 6% in the MLT region. Certain improvements for both random noise (from 50% to 35%) and systematic error (from 10% to 6%) were obtained. We succeeded in revealing the positive correlation between O3 and ClO at nighttime in the upper mesosphere using the optimized O3 profiles; furthermore, its chemical mechanism was explained quantitatively.

  9. Phase 2, Solid waste retrieval strategy

    SciTech Connect

    Johnson, D.M.

    1994-09-29

    Solid TRU retrieval, Phase 1 is scheduled to commence operation in 1998 at 218W-4C-T01 and complete recovery of the waste containers in 2001. Phase 2 Retrieval will recover the remaining buried TRU waste to be retrieved and provide the preliminary characterization by non-destructive means to allow interim storage until processing for disposal. This document reports on researching the characterization documents to determine the types of wastes to be retrieved and where located, waste configurations, conditions, and required methods for retrieval. Also included are discussions of wastes encompassed by Phase 2 for which there are valid reasons to not retrieve.

  10. New Methods for Retrieval of Chlorophyll Red Fluorescence from Hyperspectral Satellite Instruments: Simulations and Application to GOME-2 and SCIAMACHY

    NASA Technical Reports Server (NTRS)

    Joiner, Joanna; Yoshida, Yasuko; Guanter, Luis; Middleton, Elizabeth M.

    2016-01-01

    Global satellite measurements of solar-induced fluorescence (SIF) from chlorophyll over land and ocean have proven useful for a number of different applications related to physiology, phenology, and productivity of plants and phytoplankton. Terrestrial chlorophyll fluorescence is emitted throughout the red and far-red spectrum, producing two broad peaks near 683 and 736nm. From ocean surfaces, phytoplankton fluorescence emissions are entirely from the red region (683nm peak). Studies using satellite-derived SIF over land have focused almost exclusively on measurements in the far red (wavelengths greater than 712nm), since those are the most easily obtained with existing instrumentation. Here, we examine new ways to use existing hyperspectral satellite data sets to retrieve red SIF (wavelengths less than 712nm) over both land and ocean. Red SIF is thought to provide complementary information to that from the far red for terrestrial vegetation. The satellite instruments that we use were designed to make atmospheric trace-gas measurements and are therefore not optimal for observing SIF; they have coarse spatial resolution and only moderate spectral resolution (0.5nm). Nevertheless, these instruments, the Global Ozone Monitoring Instrument 2 (GOME-2) and the SCanning Imaging Absorption spectroMeter for Atmospheric CHartographY (SCIAMACHY), offer a unique opportunity to compare red and far-red terrestrial SIF at regional spatial scales. Terrestrial SIF has been estimated with ground-, aircraft-, or satellite-based instruments by measuring the filling-in of atmospheric andor solar absorption spectral features by SIF. Our approach makes use of the oxygen (O2) gamma band that is not affected by SIF. The SIF-free O2 gamma band helps to estimate absorption within the spectrally variable O2 B band, which is filled in by red SIF. SIF also fills in the spectrally stable solar Fraunhofer lines (SFLs) at wavelengths both inside and just outside the O2 B band, which further helps

  11. New Methods for Retrieval of Chlorophyll Red Fluorescence from Hyperspectral Satellite Instruments: Simulations and Application to GOME-2 and SCIAMACHY

    NASA Technical Reports Server (NTRS)

    Joiner, Joanna; Yoshida, Yasuko; Guanter, Luis; Middleton, Elizabeth M.

    2016-01-01

    Global satellite measurements of solar-induced fluorescence (SIF) from chlorophyll over land and ocean have proven useful for a number of different applications related to physiology, phenology, and productivity of plants and phytoplankton. Terrestrial chlorophyll fluorescence is emitted throughout the red and far-red spectrum, producing two broad peaks near 683 and 736nm. From ocean surfaces, phytoplankton fluorescence emissions are entirely from the red region (683nm peak). Studies using satellite-derived SIF over land have focused almost exclusively on measurements in the far red (wavelengths greater than 712nm), since those are the most easily obtained with existing instrumentation. Here, we examine new ways to use existing hyperspectral satellite data sets to retrieve red SIF (wavelengths less than 712nm) over both land and ocean. Red SIF is thought to provide complementary information to that from the far red for terrestrial vegetation. The satellite instruments that we use were designed to make atmospheric trace-gas measurements and are therefore not optimal for observing SIF; they have coarse spatial resolution and only moderate spectral resolution (0.5nm). Nevertheless, these instruments, the Global Ozone Monitoring Instrument 2 (GOME-2) and the SCanning Imaging Absorption spectroMeter for Atmospheric CHartographY (SCIAMACHY), offer a unique opportunity to compare red and far-red terrestrial SIF at regional spatial scales. Terrestrial SIF has been estimated with ground-, aircraft-, or satellite-based instruments by measuring the filling-in of atmospheric andor solar absorption spectral features by SIF. Our approach makes use of the oxygen (O2) gamma band that is not affected by SIF. The SIF-free O2 gamma band helps to estimate absorption within the spectrally variable O2 B band, which is filled in by red SIF. SIF also fills in the spectrally stable solar Fraunhofer lines (SFLs) at wavelengths both inside and just outside the O2 B band, which further helps

  12. Flexible montage retrieval for image data

    NASA Astrophysics Data System (ADS)

    Sakamoto, Hiroaki; Suzuki, Hideharu; Uemori, Akira

    1994-04-01

    Academic and photo libraries require the reuse of images. If the database is large, similarity retrieval and retrieval by sketch are effective. However, similarity retrieval can retrieve images that are similar to only one key image. Retrieval by sketch can retrieve images that are similar to the sketch, but it is not always easy to make a sketch sufficiently similar to the desired image. To overcome these limitations, we propose a new flexible montage retrieval method (FMR) that allows the user to retrieve images by appropriately combining characteristics of the key images in the same way that a montage picture of a criminal is constructed. In FMR, the user selects one or more key images and specifies areas (called `key regions') manually or by using image manipulating tools. He then indicates the retrieval conditions, for example, the requirement that the image to be retrieved includes specified areas. This paper describes an FMR algorithm that uses a color histogram and texture to quantify the similarity between a key region and an image in the database. The effectiveness of FMR is then statistically demonstrated by comparing its correct retrieval rate with that of retrieval by sketch. The retrieval rate is calculated from the result of retrieving the images that include a specified sky image from among more than 150 images containing various sky images.

  13. Retrieving the relief of a low-roughness surface using a two-step interferometric method with blind phase shift of a reference wave

    NASA Astrophysics Data System (ADS)

    Muravsky, Leonid I.; Kmet', Arkady B.; Voronyak, Taras I.

    2012-11-01

    A two-step interferometric method with blind phase shift of a reference wave for surface relief retrieval is considered. The possibility of using this method to reconstruct a macrorelief and microrelief of low-roughness surfaces is studied. Computer simulations have testified to the possibility of obtaining a reliable low-noise reconstruction of a low-roughness surface macrorelief and microrelief with standard deviation of the roughness heights up to λ/10 by using the developed interferogram-processing algorithm. The simulations have shown that the correlation approach, which is used to determine the reference wave blind phase shift, is more suitable for a rough surface than for a smooth one and the increase of surface roughness leads to a sharp decrease of error in comparison with that for a smooth surface. The experiment-based verification of the performance of the proposed interferometric method has been done using an experiment setup based on a Twyman-Green interferometer. Peculiarities of choosing the sampling interval for a rough surface recording are discussed. The experimental results that were obtained virtually coincided with the computer simulation results, proving the feasibility of retrieving both smooth and low-roughness surfaces by the considered method.

  14. Preferentially expressed antigen of melanoma (PRAME) in the development of diagnostic and therapeutic methods for hematological malignancies.

    PubMed

    Matsushita, Maiko; Yamazaki, Rie; Ikeda, Hideyuki; Kawakami, Yutaka

    2003-03-01

    PRAME (Preferentially expressed antigen of melanoma), highly expressed in various solid tumor cells and normal testis, was first isolated as a human melanoma antigen recognized by cytotoxic T cells (CTL). This gene was also expressed in some of the hematological malignancies, including acute myelogenous leukemia (AML) and multiple myeloma. We and others have extensively evaluated the PRAME expression in various hematological malignancies and demonstrated high expression of the PRAME gene in subsets of AML, chronic myelogenous leukemia, acute lymphocytic leukemia, lymphoma and multiple myeloma. In addition, we have demonstrated that PRAME was a useful marker for detection of minimal residual disease (MRD) in patients with leukemia, particularly those leukemias in which tumor specific markers are currently unavailable. Since PRAME was first identified as a tumor antigen recognized by T cells, the possibility that PRAME is a leukemia antigen recognized by T cells was evaluated, and it was found that PRAME-positive leukemia cell lines and fresh leukemia cells were susceptible to lysis by the PRAME-specific CTL. Five CTL epitopes associated with either HLA-A*0201 or HLA-A*2402 have recently been identified. It is, therefore, an attractive strategy to apply PRAME specific immunotherapy on patients with PRAME positive leukemia in MRD condition.

  15. Label-free and real-time detection of antigen-antibody interactions by Oblique-incidence Reflectivity Difference (OIRD) method

    NASA Astrophysics Data System (ADS)

    He, LiPing; Sun, Yue; Dai, Jun; Wang, JingYi; Lü, HuiBin; Wang, ShuFang; Jin, KuiJuan; Zhou, YueLiang; Yang, GuoZhen

    2012-09-01

    We label-free and real-time detected three interaction processes of antigen-antibodies, Human Immunoglobulin G (IgG), Rabbit IgG, and Mouse IgG as the targets, and Goat Anti-human IgG, Goat Anti-rabbit IgG, and Goat Anti-mouse IgG as the probe, by the Oblique-incidence Reflectivity Difference (OIRD) method. The interaction dynamic curves of the OIRD signal, corresponding to the interaction processes of antigen-antibodies, are generated. The reaction times from beginning to equilibrium state are about 1800, 900, and 1200 s for Human IgG, Rabbit IgG, and Mouse IgG, respectively. The experimental results demonstrate that the OIRD method not only can distinguish biomolecular interactions, but also can be used in real-time detection of interactions and dynamic processes of biomolecules.

  16. A new storage and retrieval method to support editing operations in a multi-disk-based video server

    SciTech Connect

    Chien-I Lee; Wei-Pang Yang; Ye-In Chang

    1996-12-31

    Since the storage ordering is assumed the same as the retrieval ordering in all the previous storage placement strategies, there is a requirement of a large amount of file copying or merging operations when users insert/delete some data into/from the media data. The observation is also important for video applications because features, like video editing, require the support of random access on individual video frames. In this paper, we propose a new strategy for the insert/delete operations on continuous media that are striped into multidisks without reorganization of the whole data. From our performance analysis and simulation, the proposed algorithms for insertion/deletion may require only some additional movement cost.

  17. Tangent height registration method for the Version 1.4 data retrieval algorithm of the solar occultation sensor ILAS-II.

    PubMed

    Tanaka, Tomoaki; Nakajima, Hideaki; Sugita, Takafumi; Ejiri, Mitsumu K; Irie, Hitoshi; Saitoh, Naoko; Terao, Yukio; Kawasaki, Hiroyuki; Usami, Masatoshi; Yokota, Tatsuya; Kobayashi, Hirokazu; Sasano, Yasuhiro

    2007-10-10

    The Improved Limb Atmospheric Spectrometer-II (ILAS-II) is a satellite-borne solar occultation sensor onboard the Advanced Earth Observing Satellite-II (ADEOS-II). The ILAS-II succeeded the ILAS. The ILAS-II used four grating spectrometers to observe vertical profiles of gas volume mixing ratios of trace constituents and was also equipped with a Sun-edge sensor to determine tangent heights geometrically with high precision. The accuracy of gas volume mixing ratios depends on the accuracy of the tangent height determination. The combination method is a tangent height registration method that was developed to give appropriate tangent heights for the ILAS-II Version 1.4 data retrieval algorithm. This study describes the method used in the ILAS-II Version 1.4 retrieval algorithm to register tangent heights. The root-sum-square total random error is estimated to be 30 m, and the total systematic error is 180 m at an altitude of 30 km. The influence of the tangent height errors on the vertical profiles of gas volume mixing ratios in ILAS-II Version 1.4 is estimated by using the relative difference. The relative difference for each species is within 7% (20%) for an altitude shift of +/-100 m(+/-300 m).

  18. Evaluating the Utility of Satellite Soil Moisture Retrievals over Irrigated Areas and the Ability of Land Data Assimilation Methods to Correct for Unmodeled Processes

    NASA Technical Reports Server (NTRS)

    Kumar, S. V.; Peters-Lidard, C. D.; Santanello, J. A.; Reichle, R. H.; Draper, C. S.; Koster, R. D.; Nearing, G.; Jasinski, M. F.

    2015-01-01

    Earth's land surface is characterized by tremendous natural heterogeneity and human-engineered modifications, both of which are challenging to represent in land surface models. Satellite remote sensing is often the most practical and effective method to observe the land surface over large geographical areas. Agricultural irrigation is an important human-induced modification to natural land surface processes, as it is pervasive across the world and because of its significant influence on the regional and global water budgets. In this article, irrigation is used as an example of a human-engineered, often unmodeled land surface process, and the utility of satellite soil moisture retrievals over irrigated areas in the continental US is examined. Such retrievals are based on passive or active microwave observations from the Advanced Microwave Scanning Radiometer for the Earth Observing System (AMSR-E), the Advanced Microwave Scanning Radiometer 2 (AMSR2), the Soil Moisture Ocean Salinity (SMOS) mission, WindSat and the Advanced Scatterometer (ASCAT). The analysis suggests that the skill of these retrievals for representing irrigation effects is mixed, with ASCAT-based products somewhat more skillful than SMOS and AMSR2 products. The article then examines the suitability of typical bias correction strategies in current land data assimilation systems when unmodeled processes dominate the bias between the model and the observations. Using a suite of synthetic experiments that includes bias correction strategies such as quantile mapping and trained forward modeling, it is demonstrated that the bias correction practices lead to the exclusion of the signals from unmodeled processes, if these processes are the major source of the biases. It is further shown that new methods are needed to preserve the observational information about unmodeled processes during data assimilation.

  19. Evaluating the Utility of Satellite Soil Moisture Retrievals over Irrigated Areas and the Ability of Land Data Assimilation Methods to Correct for Unmodeled Processes

    NASA Technical Reports Server (NTRS)

    Kumar, S. V.; Peters-Lidard, C. D.; Santanello, J. A.; Reichle, R. H.; Draper, C. S.; Koster, R. D.; Nearing, G.; Jasinski, M. F.

    2015-01-01

    Earth's land surface is characterized by tremendous natural heterogeneity and human-engineered modifications, both of which are challenging to represent in land surface models. Satellite remote sensing is often the most practical and effective method to observe the land surface over large geographical areas. Agricultural irrigation is an important human-induced modification to natural land surface processes, as it is pervasive across the world and because of its significant influence on the regional and global water budgets. In this article, irrigation is used as an example of a human-engineered, often unmodeled land surface process, and the utility of satellite soil moisture retrievals over irrigated areas in the continental US is examined. Such retrievals are based on passive or active microwave observations from the Advanced Microwave Scanning Radiometer for the Earth Observing System (AMSR-E), the Advanced Microwave Scanning Radiometer 2 (AMSR2), the Soil Moisture Ocean Salinity (SMOS) mission, WindSat and the Advanced Scatterometer (ASCAT). The analysis suggests that the skill of these retrievals for representing irrigation effects is mixed, with ASCAT-based products somewhat more skillful than SMOS and AMSR2 products. The article then examines the suitability of typical bias correction strategies in current land data assimilation systems when unmodeled processes dominate the bias between the model and the observations. Using a suite of synthetic experiments that includes bias correction strategies such as quantile mapping and trained forward modeling, it is demonstrated that the bias correction practices lead to the exclusion of the signals from unmodeled processes, if these processes are the major source of the biases. It is further shown that new methods are needed to preserve the observational information about unmodeled processes during data assimilation.

  20. Evaluating the utility of satellite soil moisture retrievals over irrigated areas and the ability of land data assimilation methods to correct for unmodeled processes

    NASA Astrophysics Data System (ADS)

    Kumar, S. V.; Peters-Lidard, C. D.; Santanello, J. A.; Reichle, R. H.; Draper, C. S.; Koster, R. D.; Nearing, G.; Jasinski, M. F.

    2015-11-01

    Earth's land surface is characterized by tremendous natural heterogeneity and human-engineered modifications, both of which are challenging to represent in land surface models. Satellite remote sensing is often the most practical and effective method to observe the land surface over large geographical areas. Agricultural irrigation is an important human-induced modification to natural land surface processes, as it is pervasive across the world and because of its significant influence on the regional and global water budgets. In this article, irrigation is used as an example of a human-engineered, often unmodeled land surface process, and the utility of satellite soil moisture retrievals over irrigated areas in the continental US is examined. Such retrievals are based on passive or active microwave observations from the Advanced Microwave Scanning Radiometer for the Earth Observing System (AMSR-E), the Advanced Microwave Scanning Radiometer 2 (AMSR2), the Soil Moisture Ocean Salinity (SMOS) mission, WindSat and the Advanced Scatterometer (ASCAT). The analysis suggests that the skill of these retrievals for representing irrigation effects is mixed, with ASCAT-based products somewhat more skillful than SMOS and AMSR2 products. The article then examines the suitability of typical bias correction strategies in current land data assimilation systems when unmodeled processes dominate the bias between the model and the observations. Using a suite of synthetic experiments that includes bias correction strategies such as quantile mapping and trained forward modeling, it is demonstrated that the bias correction practices lead to the exclusion of the signals from unmodeled processes, if these processes are the major source of the biases. It is further shown that new methods are needed to preserve the observational information about unmodeled processes during data assimilation.

  1. Evaluating the utility of satellite soil moisture retrievals over irrigated areas and the ability of land data assimilation methods to correct for unmodeled processes

    NASA Astrophysics Data System (ADS)

    Kumar, S. V.; Peters-Lidard, C. D.; Santanello, J. A.; Reichle, R. H.; Draper, C. S.; Koster, R. D.; Nearing, G.; Jasinski, M. F.

    2015-06-01

    The Earth's land surface is characterized by tremendous natural heterogeneity and human engineered modifications, both of which are challenging to represent in land surface models. Satellite remote sensing is often the most practical and effective method to observe the land surface over large geographical areas. Agricultural irrigation is an important human induced modifications to natural land surface processes, as it is pervasive across the world and because of its significant influence on the regional and global water budgets. In this article, irrigation is used as an example of a human engineered, unmodeled land surface process, and the utility of satellite soil moisture retrievals over irrigated areas in the continental US is examined. Such retrievals are based on passive or active microwave observations from the Advanced Microwave Scanning Radiometer for the Earth Observing System (AMSR-E), the Advanced Microwave Scanning Radiometer 2 (AMSR2), the Soil Moisture Ocean Salinity (SMOS) mission, WindSat and the Advanced Scatterometer (ASCAT). The analysis suggests that the skill of these retrievals for representing irrigation artifacts is mixed, with ASCAT based products somewhat more skillful than SMOS and AMSR2 products. The article then examines the suitability of typical bias correction strategies in current land data assimilation systems when unmodeled processes dominate the bias between the model and the observations. Using a suite of synthetic experiments that includes bias correction strategies such as quantile mapping and trained forward modeling, it is demonstrated that the bias correction practices lead to the exclusion of the signals from unmodeled processes, if these processes are the major source of the biases. It is further shown that new methods are needed to preserve the observational information about unmodeled processes during data assimilation.

  2. Identification of the size and antigenic determinants of the human C4 gene by a polymerase chain-reaction-based amplification method.

    PubMed

    Lee, Hsien-Hsiung; Chang, Shwu-Fen; Tseng, Yung-Te; Lee, Yann-Jinn

    2006-10-01

    The human C4 complement components of the C4 locus are encoded by two genes, C4A and C4B, located on chromosome 6p21.3 of the major histocompatibility complex of the human leukocyte antigen class III region. The size difference between the two genes is due to the presence of HERV-K (C4), an endogenous retroviral sequence (6.7 kb long), in intron 9 of the long C4 gene. Whether the C4 is the long (L) or short (S) gene was determined by the Southern blot method, and the antigenic determinants in residues 1,054-1,106 of Rodgers and Chido were generally identified by immunoblot analysis. Herein, we explore a polymerase chain reaction (PCR) amplification method for directly determining the size of C4 loci adjacent to the respective RP1 and RP2 genes and antigenic determinants by DNA sequencing. From the results of this study, we concluded that all of the C4 genes adjacent to the RP1 gene presented the long gene. In addition, 47% of the C4 genes adjacent to the RP2 gene were the short gene and 53% were the long gene. This result was consistent with that of the Southern blot analysis. The PCR method is practical for identifying the C4 genotype and can be used to detect other polymorphisms among variants of C4 genes.

  3. Sensitivities of antigen detection and PCR assays greatly increased compared to that of the standard culture method for screening for group B streptococcus carriage in pregnant women.

    PubMed

    Rallu, Fabien; Barriga, Peter; Scrivo, Carole; Martel-Laferrière, Valérie; Laferrière, Céline

    2006-03-01

    Group B streptococcus (GBS) is a major cause of serious infections in neonates. The 2002 revised guidelines of the Centers for Disease Control and Prevention (CDC) for the prevention of perinatal GBS disease recommend that all pregnant women be screened for GBS carriage at between 35 and 37 weeks of gestation and that intrapartum antibiotic prophylaxis be given to carriers. We studied the performances of four different GBS detection assays in the context of antenatal screening. Between May and August 2004, the 605 vaginorectal swab specimens received at our bacteriology laboratory for GBS antenatal detection were tested by the four assays. The standard culture method was done according to the CDC recommendations. The three experimental assays performed with the growth from the selective enrichment (LIM) broth (Todd-Hewitt broth with 15 mug/ml nalidixic acid and 10 mug/ml colistin) after overnight incubation were a GBS antigen detection assay (PathoDx) and two PCR assays (for cfb and scpB). The most accurate assay was the scpB PCR (sensitivity, 99.6%; specificity, 100%), followed by the cfb PCR (sensitivity, 75.3%; specificity, 100%), GBS antigen detection (sensitivity, 57.3%; specificity, 99.5%), and standard culture (sensitivity, 42.3%; specificity, 100%). The GBS antigen detection assay was found to be more sensitive than the standard culture method, and moreover, the assay has a low cost and is easy to perform in all obstetrical centers which have access to the most basic of diagnostic microbiology services. We believe that antigen detection on incubated LIM broth should replace the standard culture method for screening for GBS carriage at 35 to 37 weeks of gestation. The impact of the greater sensitivities of PCR assays on the diminution of neonatal GBS infections remains to be demonstrated.

  4. Development of a streptavidin-anti-carcinoembryonic antigen antibody, radiolabeled biotin pretargeting method for radioimmunotherapy of colorectal cancer. Reagent development.

    PubMed

    Karacay, H; Sharkey, R M; Govindan, S V; McBride, W J; Goldenberg, D M; Hansen, H J; Griffiths, G L

    1997-01-01

    With pretargeting, radioisotope delivery to tumor is decoupled from the long antibody localization process, and this can increase tumor:blood ratios dramatically. Several reagents were prepared for each step of a "two-step" pretargeting method, and their properties were investigated. For pretargeting tumor, streptavidin-monoclonal antibody (StAv-mab) conjugates were prepared by cross-linking sulfo-SMCC-derivatized streptavidin to a free thiol (SH) group on MN-14 [a high-affinity anti-carcinoembryonic antigen (CEA) mab]. Thiolated mabs were generated either by reaction of 2-iminothiolane (2-IT) with mab lysine residues or by reduction of mab disulfide bonds with (2-mercaptoethyl)amine (MEA). Both procedures gave protein-protein conjugates isolated in relatively low yields (20-25%) after preparative size-exclusion (SE) chromatography purification with conservative peak collection. Both StAv-MN-14 conjugates retained their ability to bind to CEA, to an anti-idiotypic antibody to MN-14 (WI2), and to biotin, as demonstrated by SE-HPLC. Two clearing agents, WI2 mab and a biotin-human serum albumin (biotin-HSA) conjugate, were developed to remove excess circulating StAv-MN-14 conjugates in animals. Both clearing proteins were also modified with galactose residues, introduced using an activated thioimidate derivative, to produce clearing agents which would clear rapidly and clear primary mab rapidly. At least 14 galactose residues on WI2 were required to reduce blood levels to 5.9 +/- 0.7% ID/g in 1 h. Faster blood clearance (0.7 +/- 0.2% ID/g) was observed in 1 h using 44 galactose units per WI2. For the delivery of radioisotope to tumor, several biotinylated conjugates consisting of biotin, a linker, and a chelate were prepared. Conjugates showed good in vitro and in vivo stability when D-amino acid peptides were used as linkers, biotin-peptide-DOTA-indium-111 had a slightly longer blood circulation time (0.09 +/- 0.02% ID/g in 1 h) than biotin-peptide-DTPA-indium-111 (0

  5. 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

  6. A numerical method for retrieving high oxygen isotope temperatures from plutonic igneous rocks: An example from the Laramie Anorthosite Complex, Wyoming, USA

    SciTech Connect

    Farquhar, J.; Chacko, T. . Dept. of Geology); Frost, B.R. )

    1992-01-01

    The Sybille Pit is a late-stage magnetite-ilmenite-plagioclase-bearing differentiate of the Laramie Anorthosite with a wide range of grain sizes and modal mineralogy. This variability makes Sybille an ideal locality in which to study the factors that affect isotopic thermometry in plutonic environments. The authors have developed a numerical model based on isotope exchange trajectories that retrieves close to magmatic temperatures for samples from Sybille. This method is based on the premise that hand sample-scale sub-systems close to exchange with each other at temperatures that exceed those of the constituent minerals. The temperature of hand-sample scale closure is retrieved by back calculating the isotope exchange trajectories to the temperature at which two samples with widely different model compositions are in isotopic equilibrium. Application of these methods to samples from Sybille provides promising results. Whereas conventional isotopic thermometry of individual samples yields a wide range of temperatures ([approximately]600 to > 1000 C) depending on the mineral-pair chosen, application of this numerical model to multiple samples yields temperatures of 1,070 [+-] 100 C which corresponds closely to the inferred solidus for these rocks.

  7. ClearColi BL21(DE3)-based expression of Zika virus antigens illustrates a rapid method of antibody production against emerging pathogens.

    PubMed

    Viranaicken, Wildriss; Nativel, Brice; Krejbich-Trotot, Pascale; Harrabi, Wissal; Bos, Sandra; El Kalamouni, Chaker; Roche, Marjolaine; Gadea, Gilles; Desprès, Philippe

    2017-09-20

    Available rapid, simple and accurate methods for detection and diagnosis of emerging viral diseases are required. Recently, there was an urgent need for specific antibodies against mosquito-borne Zika virus (ZIKV), which is an emerging zoonotic disease of medical concern in different regions of the world. Here, we showed that overexpression of ZIKV antigens in ClearColi BL21(DE3), a bacteria strain expressing a non-endotoxic form of LPS, is suitable for the production of specific ZIKV antisera. Two major ZIKV antigenic domains, the domain III from envelope E glycoprotein, which brings the virus-specific epitopes, and the N-terminal region of nonstructural NS1 glycoprotein, which is responsible for pathophysiological conditions, were overexpressed in ClearColi BL21(DE3). Immunization of adult rat with insoluble recombinant ZIKV antigens in inclusion bodies resulted in the production of specific antibodies in a few weeks. Anti-E and anti-NS1 antibodies are efficient as biological tools for ZIKV detection by indirect ELISA and immunoblot assay. This method could successfully be applied to any emerging viruses. Copyright © 2017 Elsevier B.V. and Societe Francaise de Biochimie et Biologie Moleculaire (SFBBM). All rights reserved.

  8. Significance of specific IgG against sensitizing antigens in extrinsic allergic alveolitis: serological methods in EAA.

    PubMed

    Sterclova, M; Vasakova, M; Metlicka, M

    2011-01-01

    The aim of our study is to find differences in IgG in sera of potentially exposed and nonexposed individuals and to detect differences in concentrations of specific serum IgG among subjects with and without EAA. Seventy-two patients being followed for suspected interstitial lung disease were included. Specific IgG in sera were established by ImmunoCAP. Serum concentrations of Aspergillus fumigatus, Candida albicans IgG and mixture of moulds IgG were higher in subjects with exposure to relevant inhalation antigens (p<0.05). Patients exposed to parrot and mammal hair mixture had higher serum concentration of specific IgG (p<0.05). Subjects without exposure to mites had lower serum IgG to Dermatophagoides pteronyssinus, Dermatophagoides farinae, Dermatophagoides microceras and Glycophagus domesticus (p<0.05). Higher concentration of serum specific IgG may show previous exposure to this antigen. Even though mite specific IgG are not commonly tested in EAA patients, we suggest their immunomodulatory activity may influence susceptibility to other inhalation antigens. Copyright © 2010. Published by Elsevier España.

  9. 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

  10. 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

  11. 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

  12. 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

  13. Iodine-filter-based mobile Doppler lidar to make continuous and full-azimuth-scanned wind measurements: data acquisition and analysis system, data retrieval methods, and error analysis.

    PubMed

    Wang, Zhangjun; Liu, Zhishen; Liu, Liping; Wu, Songhua; Liu, Bingyi; Li, Zhigang; Chu, Xinzhao

    2010-12-20

    An incoherent Doppler wind lidar based on iodine edge filters has been developed at the Ocean University of China for remote measurements of atmospheric wind fields. The lidar is compact enough to fit in a minivan for mobile deployment. With its sophisticated and user-friendly data acquisition and analysis system (DAAS), this lidar has made a variety of line-of-sight (LOS) wind measurements in different operational modes. Through carefully developed data retrieval procedures, various wind products are provided by the lidar, including wind profile, LOS wind velocities in plan position indicator (PPI) and range height indicator (RHI) modes, and sea surface wind. Data are processed and displayed in real time, and continuous wind measurements have been demonstrated for as many as 16 days. Full-azimuth-scanned wind measurements in PPI mode and full-elevation-scanned wind measurements in RHI mode have been achieved with this lidar. The detection range of LOS wind velocity PPI and RHI reaches 8-10 km at night and 6-8 km during daytime with range resolution of 10 m and temporal resolution of 3 min. In this paper, we introduce the DAAS architecture and describe the data retrieval methods for various operation modes. We present the measurement procedures and results of LOS wind velocities in PPI and RHI scans along with wind profiles obtained by Doppler beam swing. The sea surface wind measured for the sailing competition during the 2008 Beijing Olympics is also presented. The precision and accuracy of wind measurements are estimated through analysis of the random errors associated with photon noise and the systematic errors introduced by the assumptions made in data retrieval. The three assumptions of horizontal homogeneity of atmosphere, close-to-zero vertical wind, and uniform sensitivity are made in order to experimentally determine the zero wind ratio and the measurement sensitivity, which are important factors in LOS wind retrieval. Deviations may occur under certain

  14. Validation of MODIS C6 AOD products retrieved by the Dark Target method in the Beijing-Tianjin-Hebei urban agglomeration, China

    NASA Astrophysics Data System (ADS)

    Zhang, Jie; Xin, Jinyuan; Zhang, Wenyu; Wang, Shigong; Wang, Lili; Xie, Wei; Xiao, Guojie; Pan, Hela; Kong, Lingbin

    2017-08-01

    The quality of the MODIS C6 3-km and 10-km aerosol optical depth (AOD) products retrieved by the Dark Target (DT) method is discussed using ground-based observations in the Beijing-Tianjin-Hebei region from 1 August 2007 to 31 July 2008. Good consistency exists between the 3-km and 10-km products and ground-based observations. The retrieval accuracy of the two products both show distinctive seasonality. The percentage falling within the expected error (EE) is largest in the winter, moderate in the spring and autumn, and smallest in the summer. A worse overestimation appears in the spring and summer (27%-66%). However, the 3-km and 10-km products over different surfaces still exhibit obvious deviations. The 10-km product performs better in the large cities, while the 3-km product has advantages in the suburbs. In urban areas, the percentage falling within EE of the 3-km AOD product (18%-59%) is lower than that for the 10-km AOD product (31%-69%). However, in suburban areas, the percentage falling within EE of the 3-km AOD product (61%-84%) is higher than for the 10 km AOD product (54%-83%).The percentages falling within EE differ considerably when the AOD is greater than 1.5 (73% and 63% for the 3-km and 10-km products, respectively). On the whole, the 3-km (10-km) AOD product performs better in suburban (urban) areas.

  15. A persistent scatterer method for retrieving accurate InSAR ground deformation map over vegetation-decorrelated areas

    NASA Astrophysics Data System (ADS)

    Chen, J.; Zebker, H. A.; Knight, R. J.

    2015-12-01

    InSAR is commonly used to measure surface deformation between different radar passes at cm-scale accuracy and m-scale resolution. However, InSAR measurements are often decorrelated due to vegetation growth, which greatly limits high quality InSAR data coverage. Here we present an algorithm for retrieving InSAR deformation measurements over areas with significant vegetation decorrelation through the use of adaptive interpolation between persistent scatterer (PS) pixels, those points at which surface scattering properties do not change much over time and thus decorrelation artifacts are minimal. The interpolation filter restores phase continuity in space and greatly reduces errors in phase unwrapping. We apply this algorithm to process L-band ALOS interferograms acquired over the San Luis Valley, Colorado and the Tulare Basin, California. In both areas, groundwater extraction for irrigation results in land deformation that can be detected using InSAR. We show that the PS-based algorithm reduces the artifacts from vegetation decorrelation while preserving the deformation signature. The spatial sampling resolution achieved over agricultural fields is on the order of hundreds of meters, usually sufficient for groundwater studies. The improved InSAR data allow us further to reconstruct the SBAS ground deformation time series and transform the measured deformation to head levels using the skeletal storage coefficient and time delay constant inferred from a joint InSAR-well data analysis. The resulting InSAR-head and well-head measurements in the San Luis valley show good agreement with primary confined aquifer pumping activities. This case study demonstrates that high quality InSAR deformation data can be obtained over vegetation-decorrrelated region if processed correctly.

  16. Invasive brain-machine interfaces: a survey of paralyzed patients’ attitudes, knowledge and methods of information retrieval

    NASA Astrophysics Data System (ADS)

    Lahr, Jacob; Schwartz, Christina; Heimbach, Bernhard; Aertsen, Ad; Rickert, Jörn; Ball, Tonio

    2015-08-01

    Objective. Brain-machine interfaces (BMI) are an emerging therapeutic option that can allow paralyzed patients to gain control over assistive technology devices (ATDs). BMI approaches can be broadly classified into invasive (based on intracranially implanted electrodes) and noninvasive (based on skin electrodes or extracorporeal sensors). Invasive BMIs have a favorable signal-to-noise ratio, and thus allow for the extraction of more information than noninvasive BMIs, but they are also associated with the risks related to neurosurgical device implantation. Current noninvasive BMI approaches are typically concerned, among other issues, with long setup times and/or intensive training. Recent studies have investigated the attitudes of paralyzed patients eligible for BMIs, particularly patients affected by amyotrophic lateral sclerosis (ALS). These studies indicate that paralyzed patients are indeed interested in BMIs. Little is known, however, about the degree of knowledge among paralyzed patients concerning BMI approaches or about how patients retrieve information on ATDs. Furthermore, it is not yet clear if paralyzed patients would accept intracranial implantation of BMI electrodes with the premise of decoding improvements, and what the attitudes of a broader range of patients with diseases such as stroke or spinal cord injury are towards this new kind of treatment. Approach. Using a questionnaire, we surveyed 131 paralyzed patients for their opinions on invasive BMIs and their attitude toward invasive BMI treatment options. Main results. The majority of the patients knew about and had a positive attitude toward invasive BMI approaches. The group of ALS patients was especially open to the concept of BMIs. The acceptance of invasive BMI technology depended on the improvements expected from the technology. Furthermore, the survey revealed that for paralyzed patients, the Internet is an important source of information on ATDs. Significance. Websites tailored to

  17. Invasive brain-machine interfaces: a survey of paralyzed patients' attitudes, knowledge and methods of information retrieval.

    PubMed

    Lahr, Jacob; Schwartz, Christina; Heimbach, Bernhard; Aertsen, Ad; Rickert, Jörn; Ball, Tonio

    2015-08-01

    Brain-machine interfaces (BMI) are an emerging therapeutic option that can allow paralyzed patients to gain control over assistive technology devices (ATDs). BMI approaches can be broadly classified into invasive (based on intracranially implanted electrodes) and noninvasive (based on skin electrodes or extracorporeal sensors). Invasive BMIs have a favorable signal-to-noise ratio, and thus allow for the extraction of more information than noninvasive BMIs, but they are also associated with the risks related to neurosurgical device implantation. Current noninvasive BMI approaches are typically concerned, among other issues, with long setup times and/or intensive training. Recent studies have investigated the attitudes of paralyzed patients eligible for BMIs, particularly patients affected by amyotrophic lateral sclerosis (ALS). These studies indicate that paralyzed patients are indeed interested in BMIs. Little is known, however, about the degree of knowledge among paralyzed patients concerning BMI approaches or about how patients retrieve information on ATDs. Furthermore, it is not yet clear if paralyzed patients would accept intracranial implantation of BMI electrodes with the premise of decoding improvements, and what the attitudes of a broader range of patients with diseases such as stroke or spinal cord injury are towards this new kind of treatment. Using a questionnaire, we surveyed 131 paralyzed patients for their opinions on invasive BMIs and their attitude toward invasive BMI treatment options. The majority of the patients knew about and had a positive attitude toward invasive BMI approaches. The group of ALS patients was especially open to the concept of BMIs. The acceptance of invasive BMI technology depended on the improvements expected from the technology. Furthermore, the survey revealed that for paralyzed patients, the Internet is an important source of information on ATDs. Websites tailored to prospective BMI users should be further developed to

  18. 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.

  19. A critical review of published methods for analysis of red cell antigen-antibody reactions by flow cytometry, and approaches for resolving problems with red cell agglutination.

    PubMed

    Arndt, Patricia A; Garratty, George

    2010-07-01

    Flow cytometry operators often apply familiar white blood cell (WBC) methods when studying red blood cell (RBC) antigens and antibodies. Some WBC methods are not appropriate for RBCs, as the analysis of RBCs requires special considerations, for example, avoidance of agglutination. One hundred seventy-six published articles from 88 groups studying RBC interactions were reviewed. Three fourths of groups used at least one unnecessary WBC procedure for RBCs, and about one fourth did not use any method to prevent/disperse RBC agglutination. Flow cytometric studies were performed to determine the effect of RBC agglutination on results and compare different methods of preventing and/or dispersing agglutination. The presence of RBC agglutinates have been shown to be affected by the type of pipette tip used for mixing RBC suspensions, the number of antigen sites/RBC, the type and concentration of primary antibody, and the type of secondary antibody. For quantitation methods, for example, fetal maternal hemorrhage, the presence of agglutinates have been shown to adversely affect results (fewer fetal D+ RBCs detected).

  20. Interaction Information Retrieval.

    ERIC Educational Resources Information Center

    Dominich, Sandor

    1994-01-01

    Discussion of information retrieval focuses on an Interaction Information Retrieval model in which documents are interconnected; queries and documents are treated in the same way; and retrieval is the result of the interconnection between query and documents. A theoretical mathematical formulation of this type of retrieval is given. (Contains 31…

  1. B cell antigen extraction is regulated by physical properties of antigen-presenting cells

    PubMed Central

    2017-01-01

    Antibody production and affinity maturation are driven by B cell extraction and internalization of antigen from immune synapses. However, the extraction mechanism remains poorly understood. Here we develop DNA-based nanosensors to interrogate two previously proposed mechanisms, enzymatic liberation and mechanical force. Using antigens presented by either artificial substrates or live cells, we show that B cells primarily use force-dependent extraction and resort to enzymatic liberation only if mechanical forces fail to retrieve antigen. The use of mechanical forces renders antigen extraction sensitive to the physical properties of the presenting cells. We show that follicular dendritic cells are stiff cells that promote strong B cell pulling forces and stringent affinity discrimination. In contrast, dendritic cells are soft and promote acquisition of low-affinity antigens through low forces. Thus, the mechanical properties of B cell synapses regulate antigen extraction, suggesting that distinct properties of presenting cells support different stages of B cell responses. PMID:27923880

  2. An improved method for the detection of cell surface antigens in samples of low viability using flow cytometry.

    PubMed

    Wing, M G; Montgomery, A M; Songsivilai, S; Watson, J V

    1990-01-24

    A high non-specific background fluorescence signal was observed when cell surface antigen analysis was carried out using flow cytometry on a cell sample which contained a high proportion of dead and dying cells. To overcome this problem it was necessary to analyse the cells in three stages. First the intact cells were identified by their forward (FWD) and 90 degree scatter profile. These cells were gated-on, then analysed on the basis of their FWD scatter and propidium iodide (PI) signal, allowing the dead PI positive cells to be gated out. The PI negative cells were then displayed using their 90 degree scatter and fluorescence signals following staining with the irrelevant antibody control. This revealed a population of dead cells, which despite being PI negative, were non-specifically binding antibody molecules. Such multiparameter analysis permitted the successful analysis of cell surface antigens in preparations of low viability by gating out the high background fluorescence associated with dead PI positive and negative cells.

  3. Accuracy of methods for calculating volumetric wear from coordinate measuring machine data of retrieved metal-on-metal hip joint implants.

    PubMed

    Lu, Zhen; McKellop, Harry A

    2014-03-01

    This study compared the accuracy and sensitivity of several numerical methods employing spherical or plane triangles for calculating the volumetric wear of retrieved metal-on-metal hip joint implants from coordinate measuring machine measurements. Five methods, one using spherical triangles and four using plane triangles to represent the bearing and the best-fit surfaces, were assessed and compared on a perfect hemisphere model and a hemi-ellipsoid model (i.e. unworn models), computer-generated wear models and wear-tested femoral balls, with point spacings of 0.5, 1, 2 and 3 mm. The results showed that the algorithm (Method 1) employing spherical triangles to represent the bearing surface and to scale the mesh to the best-fit surfaces produced adequate accuracy for the wear volume with point spacings of 0.5, 1, 2 and 3 mm. The algorithms (Methods 2-4) using plane triangles to represent the bearing surface and to scale the mesh to the best-fit surface also produced accuracies that were comparable to that with spherical triangles. In contrast, if the bearing surface was represented with a mesh of plane triangles and the best-fit surface was taken as a smooth surface without discretization (Method 5), the algorithm produced much lower accuracy with a point spacing of 0.5 mm than Methods 1-4 with a point spacing of 3 mm.

  4. DNA extraction from archival formalin-fixed, paraffin-embedded tissues: heat-induced retrieval in alkaline solution.

    PubMed

    Shi, Shan-Rong; Datar, Ram; Liu, Cheng; Wu, Lin; Zhang, Zina; Cote, Richard J; Taylor, Clive R

    2004-09-01

    Based on the antigen retrieval principle, our previous study has demonstrated that heating archival formalin-fixed, paraffin-embedded (FFPE) tissues at a higher temperature and at higher pH value of the retrieval solution may achieve higher efficiency of extracted DNA, when compared to the traditional enzyme digestion method. Along this line of heat-induced retrieval, this further study is focused on development of a simpler and more effective heat-induced DNA retrieval technique by testing various retrieval solutions. Three major experiments using a high temperature heating method to extract DNA from FFPE human lymphoid and other tissue sections were performed to compare: (1) different concentrations of alkaline solution (NaOH or KOH, pH 11.5-12) versus Britton and Robinson type of buffer solution (BR buffer) of pH 12 that was the only retrieval solution tested in our previous study; (2) several chemical solutions (SDS, Tween 20, and GITC of various concentrations) versus BR buffer or alkaline solution; and (3) alkaline solution mixed with chemicals versus BR buffer or single alkaline solution. Efficiency of DNA extraction was evaluated by measuring yields using spectrophotometry, electrophoretic pattern, semiquantitation of tissue dissolution, PCR amplification, and kinetic thermocycling-PCR methods. Results showed that boiling tissue sections in 0.1 M NaOH or KOH or its complex retrieval solutions produced higher yields and better quality of DNA compared to BR buffer or chemical solutions alone. The conclusion was that boiling FFPE tissue sections in 0.1 M alkaline solution is a simpler and more effective heat-induced retrieval protocol for DNA extraction. Combination with some chemicals (detergents) may further significantly improve efficiency of the heat-induced retrieval technique.

  5. Developing Atmospheric Retrieval Methods for Direct Imaging Spectroscopy of Gas Giants in Reflected Light. I. Methane Abundances and Basic Cloud Properties

    NASA Astrophysics Data System (ADS)

    Lupu, Roxana E.; Marley, Mark S.; Lewis, Nikole; Line, Michael; Traub, Wesley A.; Zahnle, Kevin

    2016-12-01

    Upcoming space-based coronagraphic instruments in the next decade will perform reflected light spectroscopy and photometry of cool directly imaged extrasolar giant planets. We are developing a new atmospheric retrieval methodology to help assess the science return and inform the instrument design for such future missions, and ultimately interpret the resulting observations. Our retrieval technique employs a geometric albedo model coupled with both a Markov chain Monte Carlo Ensemble Sampler (emcee) and a multimodal nested sampling algorithm (MultiNest) to map the posterior distribution. This combination makes the global evidence calculation more robust for any given model and highlights possible discrepancies in the likelihood maps. As a proof of concept, our current atmospheric model contains one or two cloud layers, methane as a major absorber, and a H2-He background gas. This 6-to-9 parameter model is appropriate for Jupiter-like planets and can be easily expanded in the future. In addition to deriving the marginal likelihood distribution and confidence intervals for the model parameters, we perform model selection to determine the significance of methane and cloud detection as a function of expected signal-to-noise ratio in the presence of spectral noise correlations. After internal validation, the method is applied to realistic spectra of Jupiter, Saturn, and HD 99492c, a model observing target. We find that the presence or absence of clouds and methane can be determined with high confidence, while parameter uncertainties are model dependent and correlated. Such general methods will also be applicable to the interpretation of direct imaging spectra of cloudy terrestrial planets.

  6. Energy fluxes retrieval on an Alaskan Arctic and Sub-Arctic vegetation by means MODIS imagery and the DTD method

    NASA Astrophysics Data System (ADS)

    Cristobal, J.; Prakash, A.; Starkenburg, D. P.; Fochesatto, G. J.; Anderson, M. C.; Gens, R.; Kane, D. L.; Kustas, W.; Alfieri, J. G.

    2012-12-01

    Evapotranspiration (ET) plays a significant role in the hydrologic cycle of Arctic and Sub-Arctic basins. Surface-atmosphere exchanges due to ET are estimated from water balance computations to be about 74% of summer precipitation or 50% of annual precipitation. Even though ET is a significant component of the hydrologic cycle in this region, the bulk estimates don't accurately account for spatial and temporal variability due to vegetation type, topography, etc. (Kane and Yang, 2004). Nowadays, remote sensing is the only technology capable of providing the necessary radiometric measurements for the calculation of the ET at global scales and in a feasible economic way, especially in Arctic and Sub-Arctic Alaskan basins with a very sparse network of both meteorological and flux towers. In this work we present the implementation and validation of the Dual-Time-Difference model (Kustas et al., 2001) to retrieve energy fluxes (ET, sensible heat flux, net radiation and soil heat flux) in tundra vegetation in Arctic conditions and in a black spruce (Picea mariana) forest in Sub-Arctic conditions. In order to validate the model in tundra vegetation we used a flux tower from the Imnavait Creek sites of the Arctic Observatory Network (Euskirchen et al. 2012). In the case of the black spruce forest, on September 2011 we installed a flux tower in the University of Alaska Fairbanks north campus that includes an eddy-covariance system as well a net radiometer, air temperature probes, soil heat flux plates, soil moisture sensors and thermistors to fully estimate energy fluxes in the field (see http://www.et.alaska.edu/ for further details). Additionally, in order to upscale energy fluxes into MODIS spatial resolution, a scintillometer was also installed covering 1.2 km across the flux tower. DTD model mainly requires meteorological inputs as well as land surface temperature (LST) and leaf area index (LAI) data, both coming from satellite imagery, at two different times: after

  7. Retrieval Testing with Hypergeometric Document Models.

    ERIC Educational Resources Information Center

    Wilbur, W. John

    1993-01-01

    Presents a method of modeling the relevance relationship in information retrieval to answer the question of the theoretical limits of certain statistical methods. Hypergeometric probability distribution is used to construct an abstract model of a database of MEDLINE records, and results of tests of vector retrieval methods are reported. (28…

  8. 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

  9. Two methods for retrieving UV index for all cloud conditions from sky imager products or total SW radiation measurements.

    PubMed

    Badosa, Jordi; Calbó, Josep; Mckenzie, Richard; Liley, Ben; González, Josep-Abel; Forgan, Bruce; Long, Charles N

    2014-01-01

    Cloud effects on UV Index (UVI) and total solar radiation (TR) as a function of cloud cover and sunny conditions (from sky images) as well as of solar zenith angle (SZA) are assessed. These analyses are undertaken for a southern-hemisphere mid-latitude site where a 10-years dataset is available. It is confirmed that clouds reduce TR more than UV, in particular for obscured Sun conditions, low cloud fraction (<60%) and large SZA (>60°). Similarly, local short-time enhancement effects are stronger for TR than for UV, mainly for visible Sun conditions, large cloud fraction and large SZA. Two methods to estimate UVI are developed: (1) from sky imaging cloud cover and sunny conditions, and (2) from TR measurements. Both methods may be used in practical applications, although Method 2 shows overall the best performance, as TR allows considering cloud optical properties. The mean absolute (relative) differences of Method 2 estimations with respect to measured values are 0.17 UVI units (6.7%, for 1 min data) and 0.79 Standard Erythemal Dose (SED) units (3.9%, for daily integrations). Method 1 shows less accurate results but it is still suitable to estimate UVI: mean absolute differences are 0.37 UVI units (15%) and 1.6 SED (8.0%).

  10. Two Methods for Retrieving UV Index for All Cloud Conditions from Sky Imager Products or Total SW Radiation Measurements

    SciTech Connect

    Badosa, Jordi; Calbo, J.; McKenzie, R. L.; Liley, Ben; Gonzalez, J. A.; Forgan, B. W.; Long, Charles N.

    2014-07-01

    In the present study, we assess the cloud effects on UV Index (UVI) and total solar radiation (TR) as a function of cloud cover estimations and sunny conditions (from sky imaging products) as well as of solar zenith angle (SZA). These analyses are undertaken for a southern-hemisphere mid-latitude site where a 10-years dataset is available. It is confirmed that clouds reduce TR more than UV, in particular for obscured Sun conditions, low cloud fraction (< 60%) and large SZA (> 60º). Similarly, clouds enhance TR more than UV, mainly for visible Sun conditions, large cloud fraction and large SZA. Two methods to estimate UVI are developed: 1) from sky imaging cloud cover and sunny conditions, and 2) from TR measurements. Both methods may be used in practical operational applications, although Method 2 shows overall the best performance, since TR allows accounting for cloud optical properties. The mean absolute differences of Method 2 estimations with respect to measured values are 0.17 UVI units (for 1-minute data) and 0.79 Standard Erythemal Dose (SED) units (for daily integrations). Method 1 shows less accurate results but it is still suitable to estimate UVI: mean absolute differences are 0.37 UVI units and 1.6 SED.

  11. Developing Atmospheric Retrieval Methods for Direct Imaging Spectroscopy of Gas Giants in Reflected Light I: Methane Abundances and Basic Cloud Properties

    NASA Technical Reports Server (NTRS)

    Lupu, R. E.; Marley, M. S.; Lewis, N.; Line, M.; Traub, W.; Zahnle, K.

    2016-01-01

    Reflected light spectroscopy and photometry of cool, directly imaged extrasolar giant planets are expected to be performed in the next decade by space-based telescopes equipped with optical wavelength coronagraphs and integral field spectrographs, such as the Wide-Field Infrared Survey Telescope (WFIRST). We are developing a new atmospheric retrieval methodology to help assess the science return and inform the instrument design for such future missions, and ultimately interpret the resulting observations. Our retrieval technique employs an albedo model coupled with both a Markov chain Monte Carlo Ensemble Sampler (emcee) and a multimodal nested sampling algorithm (MultiNest) to map the posterior distribution. This combination makes the global evidence calculation more robust for any given model, and highlights possible discrepancies in the likelihood maps. Here we apply this methodology to simulated spectra of cool giant planets. As a proof-of-concept, our current atmospheric model contains 1 or 2 cloud layers, methane as a major absorber, and a H2-He background gas. This 6-to-9 parameter model is appropriate for Jupiter-like planets and can be easily expanded in the future. In addition to deriving the marginal likelihood distribution and confidence intervals for the model parameters, we perform model selection to determine the significance of methane and cloud detection as a function of expected signal-to-noise, in the presence of spectral noise correlations. After internal validation, the method is applied to realistic reflected-light spectra of Jupiter, Saturn, and HD 99492 c, a likely observing target. We find that the presence or absence of clouds and methane can be determined with high accuracy, while parameters uncertainties are model-dependent.

  12. Kyoto islet isolation method: the optimized one for non-heart-beating donors with highly efficient islet retrieval.

    PubMed

    Okitsu, T; Matsumoto, S; Iwanaga, Y; Noguchi, H; Nagata, H; Yonekawa, Y; Maekawa, T; Tanaka, K

    2005-10-01

    The availability of pancreata for clinical cadaveric islet transplantation is restricted to non-heart-beating donors (NHBDs) in Japan. This forced us to modify the current standard islet isolation protocol that was made up for brain-dead donors and make it suitable for NHBDs. The Kyoto islet isolation method is the one with induction of several steps based on the ideas both already reported literally and invented originally by ourselves. Using this islet isolation method, we isolated islets from 13 human pancreata of NHBDs and transplanted 11 preparations to six type-1 diabetic patients. The rate to meet release criteria of Edmonton protocol was 84.6%. Establishment of this method allowed us to begin a clinical islet transplantation program in Japan and to continue to perform the preparation of islets from NHBDs with high rate to meet the release criteria of the Edmonton protocol.

  13. Use of In Situ Cloud Condensation Nuclei, Extinction, and Aerosol Size Distribution Measurements to Test a Method for Retrieving Cloud Condensation Nuclei Profiles From Surface Measurements

    NASA Technical Reports Server (NTRS)

    Ghan, Stephen J.; Rissman, Tracey A.; Ellman, Robert; Ferrare, Richard A.; Turner, David; Flynn, Connor; Wang, Jian; Ogren, John; Hudson, James; Jonsson, Haflidi H.; VanReken, Timothy; Flagan, Richard C.; Seinfeld, John H.

    2006-01-01

    If the aerosol composition and size distribution below cloud are uniform, the vertical profile of cloud condensation nuclei (CCN) concentration can be retrieved entirely from surface measurements of CCN concentration and particle humidification function and surface-based retrievals of relative humidity and aerosol extinction or backscatter. This provides the potential for long-term measurements of CCN concentrations near cloud base. We have used a combination of aircraft, surface in situ, and surface remote sensing measurements to test various aspects of the retrieval scheme. Our analysis leads us to the following conclusions. The retrieval works better for supersaturations of 0.1% than for 1% because CCN concentrations at 0.1% are controlled by the same particles that control extinction and backscatter. If in situ measurements of extinction are used, the retrieval explains a majority of the CCN variance at high supersaturation for at least two and perhaps five of the eight flights examined. The retrieval of the vertical profile of the humidification factor is not the major limitation of the CCN retrieval scheme. Vertical structure in the aerosol size distribution and composition is the dominant source of error in the CCN retrieval, but this vertical structure is difficult to measure from remote sensing at visible wavelengths.

  14. Use of In Situ Cloud Condensation Nuclei, Extinction, and Aerosol Size Distribution Measurements to Test a Method for Retrieving Cloud Condensation Nuclei Profiles From Surface Measurements

    NASA Technical Reports Server (NTRS)

    Ghan, Stephen J.; Rissman, Tracey A.; Ellman, Robert; Ferrare, Richard A.; Turner, David; Flynn, Connor; Wang, Jian; Ogren, John; Hudson, James; Jonsson, Haflidi H.; hide

    2006-01-01

    If the aerosol composition and size distribution below cloud are uniform, the vertical profile of cloud condensation nuclei (CCN) concentration can be retrieved entirely from surface measurements of CCN concentration and particle humidification function and surface-based retrievals of relative humidity and aerosol extinction or backscatter. This provides the potential for long-term measurements of CCN concentrations near cloud base. We have used a combination of aircraft, surface in situ, and surface remote sensing measurements to test various aspects of the retrieval scheme. Our analysis leads us to the following conclusions. The retrieval works better for supersaturations of 0.1% than for 1% because CCN concentrations at 0.1% are controlled by the same particles that control extinction and backscatter. If in situ measurements of extinction are used, the retrieval explains a majority of the CCN variance at high supersaturation for at least two and perhaps five of the eight flights examined. The retrieval of the vertical profile of the humidification factor is not the major limitation of the CCN retrieval scheme. Vertical structure in the aerosol size distribution and composition is the dominant source of error in the CCN retrieval, but this vertical structure is difficult to measure from remote sensing at visible wavelengths.

  15. A Highly Selective and Sensitive Fluorescence Detection Method of Glyphosate Based on an Immune Reaction Strategy of Carbon Dot Labeled Antibody and Antigen Magnetic Beads.

    PubMed

    Wang, Duo; Lin, Bixia; Cao, Yujuan; Guo, Manli; Yu, Ying

    2016-08-03

    A sensitive fluorescence detection method for glyphosate (GLY) was established based on immune reaction. First, carbon dot labeled antibodies (lgG-CDs) which were able to specifically identify glyphosate were prepared with the environmentally friendly carbon dots (CDs) and glyphosate antibody (lgG). lgG-CDs could be used to in situ visualize the distribution of glyphosate in plant tissues. In order to eliminate the effects of excess lgG-CDs on the determination of GLY, antigen magnetic beads Fe3O4-GLY based on magnetic nanoparticles Fe3O4 and glyphosate were constructed and utilized to couple with the excess lgG-CDs. After magnetic separation to remove antigen magnetic beads, there was a linear relationship between the fluorescence intensity of lgG-CDs and the logarithmic concentration of glyphosate in the range of 0.01-80 μg/mL with a detection limit of 8 ng/mL. The method was used for the detection of glyphosate in Pearl River water, tea, and soil samples with satisfactory recovery ratio between 87.4% and 103.7%.

  16. Use of the maximum entropy method to retrieve the vertical atmospheric ozone profile and predict atmospheric ozone content

    NASA Technical Reports Server (NTRS)

    Turner, B. Curtis

    1992-01-01

    A method is developed for prediction of ozone levels in planetary atmospheres. This method is formulated in terms of error covariance matrices, and is associated with both direct measurements, a priori first guess profiles, and a weighting function matrix. This is described by the following linearized equation: y = A(matrix) x X + eta, where A is the weighting matrix and eta is noise. The problems to this approach are: (1) the A matrix is near singularity; (2) the number of unknowns in the profile exceeds the number of data points, therefore, the solution may not be unique; and (3) even if a unique solution exists, eta may cause the solution to be ill conditioned.

  17. Human liver nucleolar antigens.

    PubMed

    Busch, R K; Busch, H

    1981-10-01

    In an extension of previous studies on the antigens in rat liver nucleoli (R. K. Busch, R. C. Reddy, D. H. Henning, and H. Busch, Proc. Soc. Exp. Biol. Med. 160, 185 (1979); R. K. Busch and H. Busch, Tumori 63, 347 (1977); F. M. Davis, R. K. Busch, L. C. Yeoman, and H. Busch, Cancer Res. 38, 1906 (1978), rabbit antibodies were elicited to human liver nucleoli isolated by the sucrose--Mg2+ method (10). Fluorescent nucleoli were found in liver cryostat sections treated with rabbit anti-human liver nucleolar antibodies followed by fluorescein-conjugated goat anti-rabbit antibodies. In HeLa cells, fluorescence was distributed throughout the nucleus and in a nuclear network but was not localized to the nucleolus. In placental cryostat sections, an overall nuclear fluorescence was observed with some localization to nucleoli. Immunodiffusion analysis revealed two immunoprecipitin bands which appeared to be liver specific. Other immunoprecipitin bands were common to liver, placenta, and HeLa nuclear extracts. Rocket immunoelectrophoresis revealed two liver-specific antigens, one migrating to the cathode and the other to the anode Other rockets exhibited identity to antigens of other nuclear extracts. These results demonstrate the presence of human liver nucleolar-specific antigens which were not found in the HeLa and placental cells.

  18. Wear measurement of retrieved polyethylene ABG 1 cups by universal-type measuring microscope and X-ray methods.

    PubMed

    Gallo, Jiri; Havranek, Vitezslav; Cechova, Ivana; Zapletalova, Jana

    2006-11-01

    Polyethylene wear is considered a most important part of periprosthetic osteolysis development. Thus, its measurement is central to contemporary orthopaedics. The aim of this paper was to compare the accuracy of three radiographic techniques for wear measurement. Secondly, the influence of the abduction angle of the cup on measurement accuracy was investigated. Wear was measured manually in 80 patients by a single observer according to the Livermore, Charnley, and Dorr description. A multi-component statistical analysis was used to test the hypothesis that the Livermore technique was superior. In vitro data obtained from a Universal-type measuring microscope served as a gold standard. In vitro measurements showed an average linear wear of 0.363 mm per year (0.000-0.939, SD 0.241) with a corresponding volumetric wear rate of 161 mm3 per year (0-467, SD 118.2). The Livermore technique showed the least deviation from the optical reference standard and a superior position from the viewpoint of error analysis but the correlation coefficient was slightly less (r = 0.761) than for the Dorr and Charnley techniques (r = 0.795 and r = 0.778, respectively). In addition, the mean error of the Dorr method differed significantly from zero (p = 0.036). Overall, the Livermore technique was the most accurate method for polyethylene wear measurement regardless of the abduction angle of the cup. The Livermore technique performed manually was more accurate than the Charnley and Dorr methods. Nevertheless, we consider the Dorr technique an adequate tool for day-to-day wear measurements, mainly due to its simplicity.

  19. Method of in situ retrieval of contaminants or other substances using a barrier system and leaching solutions

    SciTech Connect

    Nickelson, Reva A.; Walsh, Stephanie; Richardson, John G.; Dick, John R.; Sloan, Paul A.

    2006-12-26

    Processes and methods relating to treating contaminants and collecting desired substances from a zone of interest using subterranean collection and containment barriers. Tubular casings having interlock structures are used to create subterranean barriers for containing and treating buried waste and its effluents. The subterranean barrier includes an effluent collection system. Treatment solutions provided to the zone of interest pass therethrough and are collected by the barrier and treated or recovered, allowing on-site remediation. Barrier components may be used to in the treatment by collecting or removing contaminants or other materials from the zone of interest.

  20. 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.

  1. Inter-comparison of four remote sensing based surface energy balance methods to retrieve surface evapotranspiration and water stress of irrigated fields in semi-arid climate

    NASA Astrophysics Data System (ADS)

    Chirouze, J.; Boulet, G.; Jarlan, L.; Fieuzal, R.; Rodriguez, J. C.; Ezzahar, J.; Er-Raki, S.; Bigeard, G.; Merlin, O.; Garatuza-Payan, J.; Watts, C.; Chehbouni, G.

    2013-01-01

    Remotely sensed surface temperature can provide a good proxy for water stress level and is therefore particularly useful to estimate spatially distributed evapotranspiration. Instantaneous stress levels or instantaneous latent heat flux are deduced from the surface energy balance equation constrained by this equilibrium temperature. Pixel average surface temperature depends on two main factors: stress and vegetation fraction cover. Methods estimating stress vary according to the way they treat each factor. Two families of methods can be defined: the contextual methods, where stress levels are scaled on a given image between hot/dry and cool/wet pixels for a particular vegetation cover, and single-pixel methods which evaluate latent heat as the residual of the surface energy balance for one pixel independently from the others. Four models, two contextual (S-SEBI and a triangle method, inspired by Moran et al., 1994) and two single-pixel (TSEB, SEBS) are applied at seasonal scale over a four by four km irrigated agricultural area in semi-arid northern Mexico. Their performances, both at local and spatial standpoints, are compared relatively to energy balance data acquired at seven locations within the area, as well as a more complex soil-vegetation-atmosphere transfer model forced with true irrigation and rainfall data. Stress levels are not always well retrieved by most models, but S-SEBI as well as TSEB, although slightly biased, show good performances. Drop in model performances is observed when vegetation is senescent, mostly due to a poor partitioning both between turbulent fluxes and between the soil/plant components of the latent heat flux and the available energy. As expected, contextual methods perform well when extreme hydric and vegetation conditions are encountered in the same image (therefore, esp. in spring and early summer) while they tend to exaggerate the spread in water status in more homogeneous conditions (esp. in winter).

  2. A Variational Method to Retrieve the Extinction Profile in Liquid Clouds Using Multiple Field-of-View Lidar

    NASA Technical Reports Server (NTRS)

    Pounder, Nicola L.; Hogan, Robin J.; Varnai, Tamas; Battaglia, Alessandro; Cahalan, Robert F.

    2011-01-01

    While liquid clouds playa very important role in the global radiation budget, it's been very difficult to remotely determine their internal cloud structure. Ordinary lidar instruments (similar to radars but using visible light pulses) receive strong signals from such clouds, but the information is limited to a thin layer near the cloud boundary. Multiple field-of-view (FOV) lidars offer some new hope as they are able to isolate photons that were scattered many times by cloud droplets and penetrated deep into a cloud before returning to the instrument. Their data contains new information on cloud structure, although the lack of fast simulation methods made it challenging to interpret the observations. This paper describes a fast new technique that can simulate multiple-FOV lidar signals and can even estimate the way the signals would change in response to changes in cloud properties-an ability that allows quick refinements in our initial guesses of cloud structure. Results for a hypothetical airborne three-FOV lidar suggest that this approach can help determine cloud structure for a deeper layer in clouds, and can reliably determine the optical thickness of even fairly thick liquid clouds. The algorithm is also applied to stratocumulus observations by the 8-FOV airborne "THOR" lidar. These tests demonstrate that the new method can determine the depth to which a lidar provides useful information on vertical cloud structure. This work opens the way to exploit data from spaceborne lidar and radar more rigorously than has been possible up to now.

  3. Molecular epidemiology of human hepatitis A virus defined by an antigen-capture polymerase chain reaction method.

    PubMed Central

    Jansen, R W; Siegl, G; Lemon, S M

    1990-01-01

    We describe an immunoaffinity-linked nucleic acid amplification system (antigen-capture/polymerase chain reaction, or AC/PCR) for detection of viruses in clinical specimens and its application to the study of the molecular epidemiology of a picornavirus, hepatitis A virus (HAV). Immunoaffinity capture of virus, synthesis of viral cDNA, and amplification of cDNA by a polymerase chain reaction (PCR) were carried out sequentially in a single reaction vessel. This approach simplified sample preparation and enhanced the specificity of conventional PCR. AC/PCR detected less than one cell culture infectious unit of virus in 80 microliters of sample. Sequencing of AC/PCR reaction products from 34 virus strains demonstrated remarkable conservation at the nucleotide level among most strains but revealed hitherto unsuspected genetic diversity among human isolates. Epidemiologically related strains were identical or closely related in sequence. Virus strains recovered from epidemics of hepatitis A in the United States and Germany were identical in sequence, providing evidence for a previously unrecognized epidemiologic link between these outbreaks. Images PMID:2158093

  4. Antibodies on demand: a fast method for the production of human scFvs with minimal amounts of antigen.

    PubMed

    Babel, Ingrid; Barderas, Rodrigo; Peláez-García, Alberto; Casal, J Ignacio

    2011-06-02

    Antibodies constitute a powerful tool to study protein function, protein localization and protein-protein interactions, as well as for diagnostic and therapeutic purposes. High-throughput antibody development requires faster methodologies with lower antigen consumption. Here, we describe a novel methodology to select human monoclonal recombinant antibodies by combining in vitro protein expression, phage display antibody libraries and antibody microarrays. The application of this combination of methodologies permitted us to generate human single-chain variable fragments (scFvs) against two proteins: green fluorescent protein (GFP) and thioredoxin (Trx) in a short time, using as low as 5 μg of purified protein. These scFvs showed specific reactivity against their respective targets and worked well by ELISA and western blot. The scFvs were able to recognise as low as 31 ng of protein of their respective targets by western blot. This work describes a novel and miniaturized methodology to obtain human monoclonal recombinant antibodies against any target in a shorter time than other methodologies using only 5 μg of protein. The protocol could be easily adapted to a high-throughput procedure for antibody production.

  5. Antibodies on demand: a fast method for the production of human scFvs with minimal amounts of antigen

    PubMed Central

    2011-01-01

    Background Antibodies constitute a powerful tool to study protein function, protein localization and protein-protein interactions, as well as for diagnostic and therapeutic purposes. High-throughput antibody development requires faster methodologies with lower antigen consumption. Results Here, we describe a novel methodology to select human monoclonal recombinant antibodies by combining in vitro protein expression, phage display antibody libraries and antibody microarrays. The application of this combination of methodologies permitted us to generate human single-chain variable fragments (scFvs) against two proteins: green fluorescent protein (GFP) and thioredoxin (Trx) in a short time, using as low as 5 μg of purified protein. These scFvs showed specific reactivity against their respective targets and worked well by ELISA and western blot. The scFvs were able to recognise as low as 31 ng of protein of their respective targets by western blot. Conclusion This work describes a novel and miniaturized methodology to obtain human monoclonal recombinant antibodies against any target in a shorter time than other methodologies using only 5 μg of protein. The protocol could be easily adapted to a high-throughput procedure for antibody production. PMID:21635725

  6. PICTURES OF A SUSPECT-TRU RETRIEVAL

    SciTech Connect

    GADD, R.R.

    2007-05-24

    Retrieving ''suspect'' transuranic (TRU) waste from the Hanford Site's low-level waste burial grounds is a tall order, due to conditions that have changed as the work progresses. Project personnel developed several new methods for handling the waste that other retrieval operations may find useful. The Waste Retrieval Project is operated by Fluor Hanford, a prime contractor for the U.S. Department of Energy's Richland Operations Office since 1996.

  7. 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

  8. 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.

  9. Microfilm and Information Retrieval.

    ERIC Educational Resources Information Center

    Teplitz, Arthur

    This paper was prepared to provide a frame of reference to the role of microfilm within the information retrieval world and to provide an opportunity for evaluation of the use of microforms for active retrieval applications. The paper discusses the principles of information retrieval, considers subject and classification indexing, and describes…

  10. Immunohistowax processing, a new fixation and embedding method for light microscopy, which preserves antigen immunoreactivity and morphological structures: visualisation of dendritic cells in peripheral organs

    PubMed Central

    Pajak, B.; De Smedt, T.; Moulin, V.; De Trez, C.; Maldonado-Lopez, R.; Vansanten, G.; Briend, E.; Urbain, J.; Leo, O.; Moser, M.

    2000-01-01

    Aims—To describe a new fixation and embedding method for tissue samples, immunohistowax processing, which preserves both morphology and antigen immunoreactivity, and to use this technique to investigate the role of dendritic cells in the immune response in peripheral tissues. Methods—This technique was used to stain a population of specialised antigen presenting cells (dendritic cells) that have the unique capacity to sensitise naive T cells, and therefore to induce primary immune responses. The numbers of dendritic cells in peripheral organs of mice either untreated or injected with live Escherichia coli were compared. Results—Numbers of dendritic cells were greatly decreased in heart, kidney, and intestine after the inoculation of bacteria. The numbers of dendritic cells in the lung did not seem to be affected by the injection of E coli. However, staining of lung sections revealed that some monocyte like cells acquired morphological and phenotypic features of dendritic cells, and migrated into blood vessels. Conclusions—These observations suggest that the injection of bacteria induces the activation of dendritic cells in peripheral organs, where they play the role of sentinels, and/or their movement into lymphoid organs, where T cell priming is likely to occur. Key Words: dendritic cell • Escherichia coli • immunohistochemistry PMID:10961175

  11. The antigens - Volume VII

    SciTech Connect

    Sela, M. )

    1987-01-01

    This book contains four chapters. They are: Ir Genes: Antigen-Specific Genetic Regulation of the Immune Response; Molecular Genetics of Class II (Ia) Antigens; Antigen-Specific T Cell Clones and T Cell Factors; and Infection and Autoimmunity.

  12. A novel method to retrieve Aerosol Optical Thickness from high-resolution optical satellite images using an extended version of the Haze Optimized Transform (HOTBAR)

    NASA Astrophysics Data System (ADS)

    Wilson, Robin; Milton, Edward; Nield, Joanna

    2016-04-01

    Aerosol Optical Thickness (AOT) data has many important applications including atmospheric correction of satellite imagery and monitoring of particulate matter air pollution. Current data products are generally available at a kilometre-scale resolution, but many applications require far higher resolutions. For example, particulate matter concentrations vary on a metre-scale, and thus data products at a similar scale are required to provide accurate assessments of particle densities and allow effective monitoring of air quality and analysis of local air quality effects on health. A novel method has been developed which retrieves per-pixel AOT values from high-resolution (~30m) satellite data. This method is designed to work over a wide range of land covers - including both bright and dark surfaces - and requires only standard visible and near-infrared data, making it applicable to a range of data from sensors such as Landsat, SPOT and Sentinel-2. The method is based upon an extension of the Haze Optimized Transform (HOT). The HOT was originally designed for assessing areas of thick haze in satellite imagery by calculating a 'haziness' value for each pixel in an image as the distance from a 'Clear Line' in feature space, defined by the high correlation between visible bands. Here, we adapt the HOT method and use it to provide AOT data instead. Significant extensions include Monte Carlo estimation of the 'Clear Line', object-based correction for land cover, and estimation of AOT from the haziness values through radiative transfer modelling. This novel method will enable many new applications of AOT data that were impossible with previously available low-resolution data, and has the potential to contribute significantly to our understanding of the air quality on health, the accuracy of satellite image atmospheric correction and the role of aerosols in the climate system.

  13. Intercomparison of four remote-sensing-based energy balance methods to retrieve surface evapotranspiration and water stress of irrigated fields in semi-arid climate

    NASA Astrophysics Data System (ADS)

    Chirouze, J.; Boulet, G.; Jarlan, L.; Fieuzal, R.; Rodriguez, J. C.; Ezzahar, J.; Er-Raki, S.; Bigeard, G.; Merlin, O.; Garatuza-Payan, J.; Watts, C.; Chehbouni, G.

    2014-03-01

    Instantaneous evapotranspiration rates and surface water stress levels can be deduced from remotely sensed surface temperature data through the surface energy budget. Two families of methods can be defined: the contextual methods, where stress levels are scaled on a given image between hot/dry and cool/wet pixels for a particular vegetation cover, and single-pixel methods, which evaluate latent heat as the residual of the surface energy balance for one pixel independently from the others. Four models, two contextual (S-SEBI and a modified triangle method, named VIT) and two single-pixel (TSEB, SEBS) are applied over one growing season (December-May) for a 4 km × 4 km irrigated agricultural area in the semi-arid northern Mexico. Their performance, both at local and spatial standpoints, are compared relatively to energy balance data acquired at seven locations within the area, as well as an uncalibrated soil-vegetation-atmosphere transfer (SVAT) model forced with local in situ data including observed irrigation and rainfall amounts. Stress levels are not always well retrieved by most models, but S-SEBI as well as TSEB, although slightly biased, show good performance. The drop in model performance is observed for all models when vegetation is senescent, mostly due to a poor partitioning both between turbulent fluxes and between the soil/plant components of the latent heat flux and the available energy. As expected, contextual methods perform well when contrasted soil moisture and vegetation conditions are encountered in the same image (therefore, especially in spring and early summer) while they tend to exaggerate the spread in water status in more homogeneous conditions (especially in winter). Surface energy balance models run with available remotely sensed products prove to be nearly as accurate as the uncalibrated SVAT model forced with in situ data.

  14. A versatile method for protein-based antigen bioanalysis in non-clinical pharmacokinetics studies of a human monoclonal antibody drug by an immunoaffinity liquid chromatography-tandem mass spectrometry.

    PubMed

    Onami, Ichio; Ayabe, Miho; Murao, Naoaki; Ishigai, Masaki

    2014-03-21

    A versatile immunoaffinity liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was developed to quantify the total concentration of a protein-based antigen in non-clinical pharmacokinetics (PK) studies of a human monoclonal antibody drug. The method combines using magnetic beads that have been coated with a commercial anti-human Fc region antibody to capture an immune complex of the antigen and antibody drug, with subsequent digestion and quantification of the antigen-derived tryptic peptide via LC-MS/MS. Although a typical immunoassay or an immunoaffinity LC-MS/MS assay requires an antigen-specific antibody that uses a different epitope from the antibody drug, this method requires only a commercial anti-human Fc region antibody. The method was applied to quantify total receptor activator of nuclear factor-κB ligand (RANKL) in the presence of denosumab, a humanized monoclonal antibody (mAb) specific to RANKL. The assay was validated as fit-for-purpose and found to be accurate (<115% interbatch accuracies) and precise (<15%, interbatch coefficient of variation) across a range of 3.13-200ng/mL RANKL. Commercial enzyme-linked immunosorbent assay (ELISA) kit was not able to determine the total RANKL because interference by denosumab decreased recovery. In contrast, the antibody drug had less effect on the LC-MS/MS method. The method now provides a bioanalytical platform for developing other protein-based antigen assays in the early drug stage.

  15. Evaluating the Effectiveness of Information Retrieval Systems Using Simulated Queries.

    ERIC Educational Resources Information Center

    Gordon, Michael D.

    1990-01-01

    Describes a simulation method for estimating recall and fallout in a document retrieval system. Earlier research on simulating document retrieval systems is reviewed, examples are presented of the current method, a probabilistic justification of the method is given, theoretical concerns dealing with retrieval precision are discussed, and further…

  16. The Evaluation of Two Methods to Facilitate Shared Decision Making for Men Considering the Prostate-Specific Antigen Test

    PubMed Central

    Frosch, Dominick L; Kaplan, Robert M; Felitti, Vincent

    2001-01-01

    OBJECTIVE California law (Grant H. Kenyon Prostate Cancer Detection Act) requires physicians to inform all patients older than aged 50 years who receive a prostate examination about the availability of the prostate-specific antigen (PSA) test. Physicians are not given guidance on how this information should be presented. We sought to evaluate the effects upon PSA screening rates of informing patients about PSA testing by 2 different techniques. DESIGN Factorial comparison of discussion versus video formats for presenting information about the PSA test. SETTING Patients were recruited through the Health Appraisal screening program in the Department for Preventive Medicine, Kaiser Permanente, San Diego, Calif. PARTICIPANTS Male patients undergoing health appraisal screening participated in 1 of 4 groups providing information about PSA screening: usual care ( n =43), discussion about risks and benefits of PSA ( n =45), shared decision-making video ( n =46), or video plus discussion ( n =42). Participants were sequentially assigned to 1 of the 4 groups. RESULTS No significant differences in demographics or family history was demonstrated between the groups at the time of group assignment. Participants in the intervention groups rated the information as clear, balanced, and fair. There were significant differences in the number of men requesting a PSA test, with the highest rate in the usual care group (97.7%), followed by discussion (82.2%), video (60.0%), and video plus discussion (50.0%). CONCLUSION Providing information about PSA screening in the form of video or discussion is feasible and significantly alters PSA screening rates. PMID:11422636

  17. Retrieval of mixed layer height (MLH) from lidar using analytical methods and estimation of MLH growth rates over a tropical site Gadanki

    NASA Astrophysics Data System (ADS)

    Vishnu, R.; Bhavani Kumar, Y.; Sinha, P. R.; Narayana Rao, T.; James Jebaseelan Samuel, E.

    2016-05-01

    A single channel elastic-backscatter lidar system was developed in-house at National Atmospheric Research Laboratory, an institution under Department of Space and Government of India, for studies on boundary layer dynamics during convective periods. The developed lidar system operates at the second harmonic wavelength of Nd: YAG laser and uses biaxial configuration. The lidar system utilizes a mini PMT for detecting laser returns from the atmosphere and operates in the analogue mode of data acquisition. The analogue recorder operates at 20 MHz sampling and uses a 12 bit A to D converter. The lidar system capable to operate at a maximum vertical resolution 7.5 m and 1-sec time sampling. However, in the present study, the lidar was operated with 30 m vertical resolution and 30-sec time sampling to understand the boundary layer dynamics during convective periods. The lidar measurements conducted between January and March 2014 were used in the present study. The laser backscatters obtained at 532 nm wavelength were corrected for noise and range before application of above mentioned analytical methods. This study presents evaluation of mixed layer height (MLH) from lidar using different analytical methods such as gradient, variance and wavelet techniques and presentation of inter-comparison between methods to achieve suitable method for assessment of MLH. The estimated MLH is then compared with the simultaneous radiosonde observations and empirical model values. We computed the MLH growth rates and observed that a significant enhancement was seen during the transition from winter to pre-monsoon period which could be attributed to increased convective activity over the tropical site. We present the lidar measurements and discuss the MLH retrieval and growth rates over Gadanki using lidar measurements.

  18. 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

  19. 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.

  20. ARM Cloud Retrieval Ensemble Data Set (ACRED)

    SciTech Connect

    Zhao, C; Xie, S; Klein, SA; McCoy, R; Comstock, JM; Delanoë, J; Deng, M; Dunn, M; Hogan, RJ; Jensen, MP; Mace, GG; McFarlane, SA; O’Connor, EJ; Protat, A; Shupe, MD; Turner, D; Wang, Z

    2011-09-12

    This document describes a new Atmospheric Radiation Measurement (ARM) data set, the ARM Cloud Retrieval Ensemble Data Set (ACRED), which is created by assembling nine existing ground-based cloud retrievals of ARM measurements from different cloud retrieval algorithms. The current version of ACRED includes an hourly average of nine ground-based retrievals with vertical resolution of 45 m for 512 layers. The techniques used for the nine cloud retrievals are briefly described in this document. This document also outlines the ACRED data availability, variables, and the nine retrieval products. Technical details about the generation of ACRED, such as the methods used for time average and vertical re-grid, are also provided.

  1. A Novel Method of Safely Measuring Influenza Virus Aerosol Using Antigen-Capture Enzyme-Linked Immunosorbent Assay for the Performance Evaluation of Protective Clothing Materials.

    PubMed

    Shimasaki, Noriko; Nojima, Yasuhiro; Okaue, Akira; Takahashi, Hitoshi; Kageyama, Tsutomu; Hamamoto, Itsuki; Shinohara, Katsuaki

    2016-01-01

    Currently, threats caused by pathogens are serious public health problems worldwide. Protective clothing is essential when one is treating infected patients or dealing with unknown pathogens. Therefore, it is necessary to evaluate the performance of protective clothing against pathogens. In Japan, some methods for evaluating the performance of protective clothing have been established in the Japanese Industrial Standards (JIS). However, a test method against virus aerosols has not been established. Because there is a risk of infection from a live virus during the test, it is necessary to devise a safe method for the virus-aerosol-based test. Here, we propose a new method of safely measuring virus aerosols for the performance evaluation of protective clothing materials. To ensure safety, an inactivated virus was used. As a model virus, the influenza virus was selected owing to the proper small diameter of the virus particles. To quantitatively measure the particle-amount of the inactivated influenza virus, we developed an antigen-capture enzyme-linked immunosorbent assay (ELISA) targeting the M1 protein. Furthermore, we evaluated two materials using our method. Significant differences in the protection performance against the virus aerosol were observed between different sample materials, thereby confirming the applicability of our new method for performance evaluation.

  2. Retrieving soil surface temperature under snowpack using special sensor microwave/imager brightness temperature in forested areas of Heilongjiang, China: an improved method

    NASA Astrophysics Data System (ADS)

    Zheng, Xingming; Li, Xiaofeng; Jiang, Tao; Ding, Yanling; Wu, Lili; Zhang, Shiyi; Zhao, Kai

    2016-04-01

    Soil surface temperature (Ts) is an important indicator of global temperature change and a key input parameter for retrieving land surface variables using remote sensing techniques. Due to the masking in the thermal infrared band and the scattering in the microwave band of snow, the temperature of soil surfaces covered by snow is difficult to infer from remote sensing data. We attempted to estimate Ts under snow cover using brightness temperature data from the special sensor microwave/imager. Ts under snow cover was underestimated due to the strong scattering effect of snow on upward soil microwave emissions at 37 GHz. The underestimated portion of Ts is related to snow properties, such as depth, grain size, and moisture. Based on the microwave emission model of layered snowpacks, the simulated results revealed a linear relationship between the underestimated Ts and the brightness temperature difference (TBD) at 19 and 37 GHz. When TBDs at 19 and 37 GHz were introduced to the Ts estimation method, accuracy improved, i.e., the root mean square error and bias of the estimated Ts decreased greatly, especially for dry snow. This improvement allows Ts estimation of snow-covered surfaces from 37 GHz microwave brightness temperature.

  3. Canopy Water Content retrieval at different scales from empirical and physically-based remote sensing methods in the SMOS VAS cal/val site

    NASA Astrophysics Data System (ADS)

    Camacho de Coca, Fernando

    based on the ground data. Finally, to produce the VWC maps over the whole site, the HR maps have been remapped to the spatial resolution of MODIS MCD43B4 product (1 km). A linear relationship between the SIWSI MODIS index and ground maps has been found, with a correlation coefficient better than 0.9. 2. A coupled version of the radiative transfer models PROSPECT and SAILH was used to derive spatially distributed estimates of CWC variables from CHRIS/PROBA data acquired during the ESA Sen3Exp campaign. Model inversion through a feed forward artificial neural network, was applied to selected bands of the CHRIS sensor. The network was trained using a backpropagation algorithmn based on simulated spectra to relate the canopy variables as independently and simultaneously outputs. Different combinations of spectral bands were evaluated too as input variables. Other network structural properties such as the number of hidden layers, the number of neurons or the activation function have been studied to optimize the results. Finally, a comparison of retrievals from empirical and physically-based methods is conducted, and the performance and limitations of each approach for mapping CWC analyzed.

  4. Genotyping of coeliac-specific human leucocyte antigen in children with type 1 diabetes: does this screening method make sense?

    PubMed

    Binder, Elisabeth; Loinger, Martina; Mühlbacher, Annelies; Edlinger, Michael; Steichen, Elisabeth; Meraner, Dagmar; Loacker, Lorin; Weigel, Guenter; Müller, Thomas; Fröhlich-Reiterer, Elke; Hofer, Sabine E

    2017-07-01

    Due to a high linkage disequilibrium of diabetes and coeliac-specific human leucocyte antigen (HLA) genotypes, the prevalence of coeliac disease (CD) in children and adolescents with diabetes mellitus type 1 (T1D) is much higher than in the general population. Recently, the European Society for Paediatric Gastroenterology, Hepatology and Nutrition (ESPGHAN) revised new screening guidelines in which genotyping for coeliac-specific HLA alleles is recommended for high-risk patients as patients with T1D. The aim of our study was to investigate the frequency and distribution of coeliac-specific HLA genotypes in paediatric patients with T1D. HLA genotyping was performed on paediatric p