Determining Optimal Microwave Antigen Retrieval Conditions for Microtubule-Associated Protein 2 Immunohistochemistry in the Guinea Pig Brain

DTIC Science & Technology

2002-12-01

sections of formalin-fixed guinea pig brains using different MAP-2 monoclonal antibodies. Brain sections were boiled in sodium citrate, citric acid...citric acid solution at pH 6.0 is the optimal microwave-assisted AR method for immunolabeling MAP-2 in formalin-fixed, paraffin-processed guinea pig brain...studies on archival guinea pig brain paraffin blocks, ultimately relaxing the use of additional animals to evaluate changes in MAP-2 expression between chemical warfare nerve agent-treated and control samples.

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

PubMed

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

1981-07-01

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

Human recombinant Fab fragment from combinatorial libraries of a B-cell lymphoma patient recognizes core protein of chondroitin sulphate proteoglycan 4.

PubMed

Egami, Yoko; Narushima, Yuta; Ohshima, Motohiro; Yoshida, Akira; Yoneta, Naruki; Masaki, Yasufumi; Itoh, Kunihiko

2018-01-01

CD antigens are well known as therapeutic targets of B-cell lymphoma. To isolate therapeutic antibodies that recognize novel targets other than CD antigens, we constructed a phage display combinatorial antibody Fab library from bone marrow lymphocytes of B-cell lymphoma patient. To eliminate antibodies reactive with known B-cell lymphoma antigen, non-hematopoietic and patient's sera reactive HeLaS3 cells was selected as a target of whole cell panning. Five rounds of panning against live HeLaS3 cells retrieved single Fab clone, termed AHSA (Antibody to HeLa Surface Antigen). Using phage display random peptide library, LSYLEP was identified as an epitope sequence of AHSA. LC-MS/MS analysis of AHSA-precipitated HeLaS3 cell lysates detected several fragments corresponding to the sequence of chondroitin sulphate proteoglycan 4 (CSPG4) core protein. Since LSYLEP sequence was at the position of 313-318 of CSPG4, we considered that CSPG4 was AHSA-associated antigen. Double staining of CSPG4-postive MDA-MB-435S cells with AHSA and anti-CSPG4 rabbit antibody showed identical staining position, and reduced AHSA reactivity was observed in CSPG4-siRNA treated MDA-MB-435S cells. In conclusion, we retrieved a human Fab from antibody library of B-cell lymphoma patient, and identified CSPG4 as a recognizing antigen. AHSA may have potential benefits for development of CSPG4-targeting theranostics for B-cell lymphoma. © The Authors 2017. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

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

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

PubMed

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

2013-01-01

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

Hemangiosarcoma in a geriatric Labrador retriever

PubMed Central

Sharma, Diya

2012-01-01

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

Receptor for Advanced Glycation End Products (RAGE) as a Novel Target for Inhibiting Breast Cancer Bone Metastasis

DTIC Science & Technology

2013-04-01

SUMMARY: We observed high expression of RAGE in ~50-60% of breast invasive ductal carcinomas compared to benign mammary epithelium. RAGE expression was...of the Ohio State University Department of Pathology. Antigen retrieval on TMA slides was performed by Heat-Induced Epitope Retrieval (HIER,) where...TRAP. Furthermore, the osteoclasts were determined by Real time PCR using gene specific primers against cathepsin K (Cstk). It has been shown that

Antigen Masking During Fixation and Embedding, Dissected

PubMed Central

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

2016-01-01

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

Improved decision making for prioritizing tumor targeting antibodies in human xenografts: Utility of fluorescence imaging to verify tumor target expression, antibody binding and optimization of dosage and application schedule.

PubMed

Dobosz, Michael; Haupt, Ute; Scheuer, Werner

2017-01-01

Preclinical efficacy studies of antibodies targeting a tumor-associated antigen are only justified when the expression of the relevant antigen has been demonstrated. Conventionally, antigen expression level is examined by immunohistochemistry of formalin-fixed paraffin-embedded tumor tissue section. This method represents the diagnostic "gold standard" for tumor target evaluation, but is affected by a number of factors, such as epitope masking and insufficient antigen retrieval. As a consequence, variances and discrepancies in histological staining results can occur, which may influence decision-making and therapeutic outcome. To overcome these problems, we have used different fluorescence-labeled therapeutic antibodies targeting human epidermal growth factor receptor (HER) family members and insulin-like growth factor-1 receptor (IGF1R) in combination with fluorescence imaging modalities to determine tumor antigen expression, drug-target interaction, and biodistribution and tumor saturation kinetics in non-small cell lung cancer xenografts. For this, whole-body fluorescence intensities of labeled antibodies, applied as a single compound or antibody mixture, were measured in Calu-1 and Calu-3 tumor-bearing mice, then ex vivo multispectral tumor tissue analysis at microscopic resolution was performed. With the aid of this simple and fast imaging method, we were able to analyze the tumor cell receptor status of HER1-3 and IGF1R, monitor the antibody-target interaction and evaluate the receptor binding sites of anti-HER2-targeting antibodies. Based on this, the most suitable tumor model, best therapeutic antibody, and optimal treatment dosage and application schedule was selected. Predictions drawn from obtained imaging data were in excellent concordance with outcome of conducted preclinical efficacy studies. Our results clearly demonstrate the great potential of combined in vivo and ex vivo fluorescence imaging for the preclinical development and characterization of monoclonal antibodies.

Multiple immunofluorescence labelling of formalin-fixed paraffin-embedded (FFPE) tissue

PubMed Central

Robertson, David; Savage, Kay; Reis-Filho, Jorge S; Isacke, Clare M

2008-01-01

Background Investigating the expression of candidate genes in tissue samples usually involves either immunohistochemical labelling of formalin-fixed paraffin-embedded (FFPE) sections or immunofluorescence labelling of cryosections. Although both of these methods provide essential data, both have important limitations as research tools. Consequently, there is a demand in the research community to be able to perform routine, high quality immunofluorescence labelling of FFPE tissues. Results We present here a robust optimised method for high resolution immunofluorescence labelling of FFPE tissues, which involves the combination of antigen retrieval, indirect immunofluorescence and confocal laser scanning microscopy. We demonstrate the utility of this method with examples of immunofluorescence labelling of human kidney, human breast and a tissue microarray of invasive human breast cancers. Finally, we demonstrate that stained slides can be stored in the short term at 4°C or in the longer term at -20°C prior to images being collected. This approach has the potential to unlock a large in vivo database for immunofluorescence investigations and has the major advantages over immunohistochemistry in that it provides higher resolution imaging of antigen localization and the ability to label multiple antigens simultaneously. Conclusion This method provides a link between the cell biology and pathology communities. For the cell biologist, it will enable them to utilise the vast archive of pathology specimens to advance their in vitro data into in vivo samples, in particular archival material and tissue microarrays. For the pathologist, it will enable them to utilise multiple antibodies on a single section to characterise particular cell populations or to test multiple biomarkers in limited samples and define with greater accuracy cellular heterogeneity in tissue samples. PMID:18366689

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

PubMed Central

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

1981-01-01

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

Improved Serial Sectioning Techniques for Correlative Light-Electron Microscopy Mapping of Human Langerhans Islets

PubMed Central

Saitoh, Sei; Ohno, Nobuhiko; Saitoh, Yurika; Terada, Nobuo; Shimo, Satoshi; Aida, Kaoru; Fujii, Hideki; Kobayashi, Tetsuro; Ohno, Shinichi

2018-01-01

Combined analysis of immunostaining for various biological molecules coupled with investigations of ultrastructural features of individual cells is a powerful approach for studies of cellular functions in normal and pathological conditions. However, weak antigenicity of tissues fixed by conventional methods poses a problem for immunoassays. This study introduces a method of correlative light and electron microscopy imaging of the same endocrine cells of compact and diffuse islets from human pancreatic tissue specimens. The method utilizes serial sections obtained from Epon-embedded specimens fixed with glutaraldehyde and osmium tetroxide. Double-immunofluorescence staining of thick Epon sections for endocrine hormones (insulin and glucagon) and regenerating islet-derived gene 1 α (REG1α) was performed following the removal of Epoxy resin with sodium ethoxide, antigen retrieval by autoclaving, and de-osmification treatment with hydrogen peroxide. The immunofluorescence images of endocrine cells were superimposed with the electron microscopy images of the same cells obtained from serial ultrathin sections. Immunofluorescence images showed well-preserved secretory granules in endocrine cells, whereas electron microscopy observations demonstrated corresponding secretory granules and intracellular organelles in the same cells. In conclusion, the correlative imaging approach developed by us may be useful for examining ultrastructural features in combination with immunolocalisation of endocrine hormones in the same human pancreatic islets. PMID:29622846

A unique amino acid substitution, T126I, in human genotype C of hepatitis B virus S gene and its possible influence on antigenic structural change.

PubMed

Ren, Fengrong; Tsubota, Asahito; Hirokawa, Takatsugu; Kumada, Hiromitsu; Yang, Ziheng; Tanaka, Hiroshi

2006-11-15

Amino acid substitutions in the S gene of hepatitis B virus (HBV), especially in the 'a' determinant region, have been suggested to affect the antigenicity of the virus and the clinical outcome of the infected patient. However, no convincing evidence has been presented for this hypothesis, partly because the 3D structure of the S protein has not been determined. Comparative analysis of viral genes offers an approach to testing this hypothesis, as it may reveal signals of natural selection and provide insights into the functional significance of the observed amino acid substitutions. In this study, we analyze HBV S gene sequences obtained from 24 patients infected with HBV genotypes B or C, together with 16 representative viral strains of HBV genotypes A-F retrieved from GenBank. We use phylogenetic methods to infer evolutionary changes among HBV genotypes and to identify amino acid residues potentially under positive selective pressure. Furthermore, we employ the fragment assembly method to predict structural changes in the S protein. The results showed that an amino acid substitution within the 'a' determinant, T126I, was unique to genotype C, may affect the antigenicity of the HBsAg, and may result in poorer clinical outcomes of patients infected with genotype C viral strains. We suggest that an integrated approach of evolutionary comparison and structural prediction is useful in generating hypotheses for further laboratory validation.

Antigen retrieval, blocking, detection and visualisation systems in immunohistochemistry: a review and practical evaluation of tyramide and rolling circle amplification systems.

PubMed

Warford, Anthony; Akbar, Hameed; Riberio, Deise

2014-11-01

To achieve specificity and sensitivity using immunohistochemistry it is necessary to combine the application of validated primary antibodies with optimised pre-treatment, detection and visualisation steps. The influence of these surrounding procedures is reviewed. A practical evaluation of tyramide signal amplification and rolling circle amplification detection methods is provided in which formalin fixed paraffin embedded sections of adenocarcinomas of breast, colon and lung together with squamous metaplasia of lung were immunostained with CD20 and CK19 primary antibodies. The results indicate that the detection systems are of comparable sensitivity and specificity. Copyright © 2014 Elsevier Inc. All rights reserved.

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

PubMed

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

2015-03-01

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

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

PubMed

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

2016-01-01

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

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

PubMed

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

2017-11-29

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

Unmasking of complements using proteinase-K in formalin fixed paraffin embedded renal biopsies.

PubMed

Nada, R; Kumar, A; Kumar, V G; Gupta, K L; Joshi, K

2016-01-01

Renal biopsy interpretation requires histopathology, direct immunofluorescence (DIF) and electron microscopy. Formalin-fixed, paraffin-embedded tissue (FFPE) sent for light microscopy can be used for DIF after antigen retrieval. However, complement staining has not been satisfactory. We standardized DIF using proteinase-K for antigen retrieval in FFPE renal biopsies. A pilot study was conducted on known cases of membranous glomerulonephritis (MGN), membranoproliferative type-1 (MPGN-1), immunoglobulin A nephropathy (IgAN), and anti-glomerular basement disease (anti-GBM). Immunofluorescence panel included fluorescein isothiocyanate (FITC) conjugated IgG, IgA, IgM, complements (C3 and C1q), light chains (kappa, lambda) and fibrinogen antibodies. After standardization of the technique, 75 renal biopsies and 43 autopsies cases were stained. Out of 43 autopsy cases, immune-complex mediated glomerulonephritis (GN) was confirmed in 18 cases (Lupus nephritis-11, IgAN-6, MGN-1), complement-mediated dense deposit disease (DDD-1) and monoclonal diseases in 4 cases (amyloidosis-3, cast nephropathy-1). Immune-mediated injury was excluded in 17 cases (focal segmental glomerulosclerosis -3, crescentic GN-6 [pauci-immune-3, anti-GBM-3], thrombotic microangiopathy-5, atherosclerosis-3). Renal biopsies (n-75) where inadequate or no frozen sample was available; this technique classified 52 mesangiocapillary pattern as MPGN type-1-46, DDD-2 and (C3GN-4). Others were diagnosed as IgAN-3, lupus nephritis-2, MGN-4, diffuse proliferative glomerulonephritis (DPGN)-1, Non-IC crescentic GN-1, monoclonal diseases-3. In nine cases, DIF on FFPE tissue could not help in making diagnosis. Proteinase-K enzymatic digestion of FFPE renal biopsies can unmask complements (both C3 and C1q) in immune-complexes mediated and complement-mediated diseases. This method showed good results on autopsy tissues archived for as long as 15 years.

Two Loci on Chromosome 5 Are Associated with Serum IgE Levels in Labrador Retrievers

PubMed Central

Owczarek-Lipska, Marta; Lauber, Béatrice; Molitor, Vivianne; Meury, Sabrina; Kierczak, Marcin; Tengvall, Katarina; Webster, Matthew T.; Jagannathan, Vidhya; Schlotter, Yvette; Willemse, Ton; Hendricks, Anke; Bergvall, Kerstin; Hedhammar, Åke; Andersson, Göran; Lindblad-Toh, Kerstin; Favrot, Claude; Roosje, Petra; Marti, Eliane; Leeb, Tosso

2012-01-01

Crosslinking of immunoglobulin E antibodies (IgE) bound at the surface of mast cells and subsequent mediator release is considered the most important trigger for allergic reactions. Therefore, the genetic control of IgE levels is studied in the context of allergic diseases, such as asthma, atopic rhinitis, or atopic dermatitis (AD). We performed genome-wide association studies in 161 Labrador Retrievers with regard to total and allergen-specific immunoglobulin E (IgE) levels. We identified a genome-wide significant association on CFA 5 with the antigen-specific IgE responsiveness to Acarus siro. We detected a second genome-wide significant association with respect to the antigen-specific IgE responsiveness to Tyrophagus putrescentiae at a different locus on chromosome 5. A. siro and T. putrescentiae both belong to the family Acaridae and represent so-called storage or forage mites. These forage mites are discussed as major allergen sources in canine AD. No obvious candidate gene for the regulation of IgE levels is located under the two association signals. Therefore our studies offer a chance of identifying a novel mechanism controlling the host's IgE response. PMID:22720065

Evaluation of prostate cancer antigen 3 for detecting prostate cancer: a systematic review and meta-analysis

NASA Astrophysics Data System (ADS)

Cui, Yong; Cao, Wenzhou; Li, Quan; Shen, Hua; Liu, Chao; Deng, Junpeng; Xu, Jiangfeng; Shao, Qiang

2016-05-01

Previous studies indicate that prostate cancer antigen 3 (PCA3) is highly expressed in prostatic tumors. However, its clinical value has not been characterized. The aim of this study was to investigate the clinical value of the urine PCA3 test in the diagnosis of prostate cancer by pooling the published data. Clinical trials utilizing the urine PCA3 test for diagnosing prostate cancer were retrieved from PubMed and Embase. A total of 46 clinical trials including 12,295 subjects were included in this meta-analysis. The pooled sensitivity, specificity, positive likelihood ratio (+LR), negative likelihood ratio (-LR), diagnostic odds ratio (DOR) and area under the curve (AUC) were 0.65 (95% confidence interval [CI]: 0.63-0.66), 0.73 (95% CI: 0.72-0.74), 2.23 (95% CI: 1.91-2.62), 0.48 (95% CI: 0.44-0.52), 5.31 (95% CI: 4.19-6.73) and 0.75 (95% CI: 0.74-0.77), respectively. In conclusion, the urine PCA3 test has acceptable sensitivity and specificity for the diagnosis of prostate cancer and can be used as a non-invasive method for that purpose.

Immunohistochemistry for the detection of neural and inflammatory cells in equine brain tissue

PubMed Central

Liu, Junjie; Herrington, Jenna M.; Vallario, Kelsey

2016-01-01

Phenotypic characterization of cellular responses in equine infectious encephalitides has had limited description of both peripheral and resident cell populations in central nervous system (CNS) tissues due to limited species-specific reagents that react with formalin-fixed, paraffin embedded tissue (FFPE). This study identified a set of antibodies for investigating the immunopathology of infectious CNS diseases in horses. Multiple commercially available staining reagents and antibodies derived from antigens of various species for manual immunohistochemistry (IHC) were screened. Several techniques and reagents for heat-induced antigen retrieval, non-specific protein blocking, endogenous peroxidase blocking, and visualization-detection systems were tested during IHC protocol development. Boiling of slides in a low pH, citrate-based buffer solution in a double-boiler system was most consistent for epitope retrieval. Pressure-cooking, microwaving, high pH buffers, and proteinase K solutions often resulted in tissue disruption or no reactivity. Optimal blocking reagents and concentrations of each working antibody were determined. Ultimately, a set of monoclonal (mAb) and polyclonal antibodies (pAb) were identified for CD3+ (pAb A0452, Dako) T-lymphocytes, CD79αcy+ B-lymphocytes (mAb HM57, Dako), macrophages (mAb MAC387, Leica), NF-H+ neurons (mAb NAP4, EnCor Biotechnology), microglia/macrophage (pAb Iba-1, Wako), and GFAP+ astrocytes (mAb 5C10, EnCor Biotechnology). In paraffin embedded tissues, mAbs and pAbs derived from human and swine antigens were very successful at binding equine tissue targets. Individual, optimized protocols are provided for each positively reactive antibody for analyzing equine neuroinflammatory disease histopathology. PMID:26855862

Immune networks: multi-tasking capabilities at medium load

NASA Astrophysics Data System (ADS)

Agliari, E.; Annibale, A.; Barra, A.; Coolen, A. C. C.; Tantari, D.

2013-08-01

Associative network models featuring multi-tasking properties have been introduced recently and studied in the low-load regime, where the number P of simultaneously retrievable patterns scales with the number N of nodes as P ˜ log N. In addition to their relevance in artificial intelligence, these models are increasingly important in immunology, where stored patterns represent strategies to fight pathogens and nodes represent lymphocyte clones. They allow us to understand the crucial ability of the immune system to respond simultaneously to multiple distinct antigen invasions. Here we develop further the statistical mechanical analysis of such systems, by studying the medium-load regime, P ˜ Nδ with δ ∈ (0, 1]. We derive three main results. First, we reveal the nontrivial architecture of these networks: they exhibit a high degree of modularity and clustering, which is linked to their retrieval abilities. Second, by solving the model we demonstrate for δ < 1 the existence of large regions in the phase diagram where the network can retrieve all stored patterns simultaneously. Finally, in the high-load regime δ = 1 we find that the system behaves as a spin-glass, suggesting that finite-connectivity frameworks are required to achieve effective retrieval.

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

NASA Astrophysics Data System (ADS)

Ding, Wenjuan; Zhao, Feng; Yang, Lizi

2017-02-01

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

Aptahistochemistry in diagnostic pathology: technical scrutiny and feasibility.

PubMed

Bukari, Bakhtiar A; Citartan, Marimuthu; Ch'ng, Ewe Seng; Bilibana, Mawethu P; Rozhdestvensky, Timofey; Tang, Thean-Hock

2017-05-01

Antibodies have been the workhorse for diagnostic immunohistochemistry to specifically interrogate the expression of certain protein to aid in histopathological diagnosis. This review introduces another dimension of histochemistry that employs aptamers as the core tool, the so-called aptahistochemistry. Aptamers are an emerging class of molecular recognition elements that could recapitulate the roles of antibodies. The many advantageous properties of aptamers suited for this diagnostic platform are scrutinized. An in-depth discussion on the technical aspects of aptahistochemistry is provided with close step-by-step comparison to the more familiarized immunohistochemical procedures, namely functionalization of the aptamer as a probe, antigen retrieval, optimization with emphasis on incubation parameters and visualization methods. This review offers rationales to overcome the anticipated challenges in transition from immunohistochemistry to aptahistochemistry, which is deemed feasible for an average diagnostic pathology laboratory.

Microwave processing of gustatory tissues for immunohistochemistry

PubMed Central

Bond, Amanda; Kinnamon, John C.

2013-01-01

We use immunohistochemistry to study taste cell structure and function as a means to elucidate how taste receptor cells communicate with nerve fibers and adjacent taste cells. This conventional method, however, is time consuming. In the present study we used taste buds from rat circumvallate papillae to compare conventional immunohistochemical tissue processing with microwave processing for the colocalization of several biochemical pathway markers (PLCβ2, syntaxin-1, IP3R3, α-gustducin) and the nuclear stain, Sytox. The results of our study indicate that in microwave versus conventional immunocytochemistry: (1) fixation quality is improved; (2) the amount of time necessary for processing tissue is decreased; (3) antigen retrieval is no longer needed; (4) image quality is superior. In sum, microwave tissue processing of gustatory tissues is faster and superior to conventional immunohistochemical tissue processing for many applications. PMID:23473796

A new approach to gene therapy using Sleeping Beauty to genetically modify clinical-grade T cells to target CD19

PubMed Central

Singh, Harjeet; Huls, Helen; Cooper, Laurence JN

2014-01-01

Summary The advent of efficient approaches to the genetic modification of T cells has provided investigators with clinically appealing approaches to improve the potency of tumor-specific clinical grade T cells. For example, gene therapy has been successfully used to enforce expression of chimeric antigen receptors (CAR) that provide T cells with ability to directly recognize tumor-associated antigens without the need for presentation by human leukocyte antigen. Gene transfer of CARs can be undertaken using viral-based and non-viral approaches. We have advanced DNA vectors derived from the Sleeping Beauty (SB) system to avoid the expense and manufacturing difficulty associated with transducing T cells with recombinant viral vectors. After electroporation, the transposon/transposase system improves the efficiency of integration of plasmids used to express CAR and other transgenes in T cells. The SB system combined with artificial antigen-presenting cells (aAPC) can selectively propagate and thus retrieve CAR+ T cells suitable for human application. This review describes the translation of the SB system and aAPC for use in clinical trials and highlights how a nimble and cost-effective approach to developing genetically modified T cells can be used to implement clinical trials infusing next-generation T cells with improved therapeutic potential. PMID:24329797

A New Intrusion Detection Method Based on Antibody Concentration

NASA Astrophysics Data System (ADS)

Zeng, Jie; Li, Tao; Li, Guiyang; Li, Haibo

Antibody is one kind of protein that fights against the harmful antigen in human immune system. In modern medical examination, the health status of a human body can be diagnosed by detecting the intrusion intensity of a specific antigen and the concentration indicator of corresponding antibody from human body’s serum. In this paper, inspired by the principle of antigen-antibody reactions, we present a New Intrusion Detection Method Based on Antibody Concentration (NIDMBAC) to reduce false alarm rate without affecting detection rate. In our proposed method, the basic definitions of self, nonself, antigen and detector in the intrusion detection domain are given. Then, according to the antigen intrusion intensity, the change of antibody number is recorded from the process of clone proliferation for detectors based on the antigen classified recognition. Finally, building upon the above works, a probabilistic calculation method for the intrusion alarm production, which is based on the correlation between the antigen intrusion intensity and the antibody concen-tration, is proposed. Our theoretical analysis and experimental results show that our proposed method has a better performance than traditional methods.

How we process trephine biopsy specimens: epoxy resin embedded bone marrow biopsies

PubMed Central

Krenacs, T; Bagdi, E; Stelkovics, E; Bereczki, L; Krenacs, L

2005-01-01

Improved cytomorphology of semithin resin sections over paraffin wax embedded sections may be important in diagnostic haematopathology. However, resin embedding can make immunohistochemical antigen detection or DNA isolation for clonal gene rearrangement assays difficult. This review describes the processing of bone marrow biopsies using buffered formaldehyde based fixation and epoxy resin embedding, with or without EDTA decalcification. Traditional semithin resin sections are completely rehydrated after etching in home made sodium methoxide solution. Resin elimination allows high resolution staining of tissue components with common histological stains. Efficient antigen retrieval and the Envision-HRP system permit the immunohistological detection of many antigens of diagnostic relevance, with retention of high quality cytomorphology. Furthermore, DNA can be extracted for clonality analysis. The technique can be completed within a similar time period to that of paraffin wax processing with only ∼30% increase in cost. This technique has been used for diagnosis in over 4000 bone marrow biopsies over the past 14 years. By meeting traditional and contemporary demands on the haematopathologist, it offers a powerful alternative to paraffin wax processing for diagnosis and research. PMID:16126867

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

PubMed

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

2018-01-30

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

Histological Assessment of PAXgene Tissue Fixation and Stabilization Reagents

PubMed Central

Kap, Marcel; Smedts, Frank; Oosterhuis, Wolter; Winther, Rosa; Christensen, Nanna; Reischauer, Bilge; Viertler, Christian; Groelz, Daniel; Becker, Karl-Friedrich; Zatloukal, Kurt; Langer, Rupert; Slotta-Huspenina, Julia; Bodo, Koppany; de Jong, Bas; Oelmuller, Uwe; Riegman, Peter

2011-01-01

Within SPIDIA, an EC FP7 project aimed to improve pre analytic procedures, the PAXgene Tissue System (PAXgene), was designed to improve tissue quality for parallel molecular and morphological analysis. Within the SPIDIA project promising results were found in both genomic and proteomic experiments with PAXgene-fixed and paraffin embedded tissue derived biomolecules. But, for this technology to be accepted for use in both clinical and basic research, it is essential that its adequacy for preserving morphology and antigenicity is validated relative to formalin fixation. It is our aim to assess the suitability of PAXgene tissue fixation for (immuno)histological methods. Normal human tissue specimens (n = 70) were collected and divided into equal parts for fixation either with formalin or PAXgene. Sections of the obtained paraffin-embedded tissue were cut and stained. Morphological aspects of PAXgene-fixed tissue were described and also scored relative to formalin-fixed tissue. Performance of PAXgene-fixed tissue in immunohistochemical and in situ hybridization assays was also assessed relative to the corresponding formalin-fixed tissues. Morphology of PAXgene-fixed paraffin embedded tissue was well preserved and deemed adequate for diagnostics in most cases. Some antigens in PAXgene-fixed and paraffin embedded sections were detectable without the need for antigen retrieval, while others were detected using standard, formalin fixation based, immunohistochemistry protocols. Comparable results were obtained with in situ hybridization and histochemical stains. Basically all assessed histological techniques were found to be applicable to PAXgene-fixed and paraffin embedded tissue. In general results obtained with PAXgene-fixed tissue are comparable to those of formalin-fixed tissue. Compromises made in morphology can be called minor compared to the advantages in the molecular pathology possibilities. PMID:22110732

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

PubMed Central

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

2016-01-01

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

Epitope enhancement for immunohistochemical demonstration of tartrate-resistant acid phosphatase.

PubMed

Janckila, A J; Lear, S C; Martin, A W; Yam, L T

1996-03-01

We have developed a monoclonal antibody (9C5) for immunohistochemical localization of tartrate-resistant acid phosphatase (TRAcP). This antibody reacts with a denatured epitope of TRAcP and requires enhancement methods to promote antigenicity in paraffin-embedded tissues. We used this antibody to systematically examine proteolytic digestion and heat denaturation conditions for epitope enhancement in both paraffin sections and fixed smears. The goal was to increase the sensitivity of the immunohistochemical stain for TRAcP. Optimal conditions for proteolytic digestion were established. Denaturation in a conventional boiling water bath was compared to microwave irradiation in several commonly used solutions. Immunohistochemistry was compared directly to TRAcP cytochemistry in fixed smears from hairy cell leukemia specimens to gauge the level of sensitivity of our improved method. Attempts were made to "retrieve" the 9C5 epitope from overfixed tissues and aged smears. Maximal immunoreactivity of TRAcP was achieved by microwave irradiation in a citrate or Tris buffer of pH 6.0-8.0 without the need for a subsequent protease digestion step. With this method of epitope enhancement, immunohistochemistry with antibody 9C5 was as sensitive as direct cytochemical staining of TRAcP activity. However, once a tissue specimen had been overfixed or a smear stored for a year or more, the 9C5 epitope was no longer retrievable. The key element in epitope enhancement for 9C5 immunohistochemistry is heat denaturation of the target epitope. Immunohistochemistry of TRAcP in paraffin sections would be a great asset to the study of specialized forms of the monocyte/macrophage lineage and to the process of macrophage activation. It would also provide another means for more precise evaluation of residual disease in bone marrow of patients treated for hairy cell leukemia.

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.

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

PubMed

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

2012-08-01

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

Improved Method for Linear B-Cell Epitope Prediction Using Antigen’s Primary Sequence

PubMed Central

Raghava, Gajendra P. S.

2013-01-01

One of the major challenges in designing a peptide-based vaccine is the identification of antigenic regions in an antigen that can stimulate B-cell’s response, also called B-cell epitopes. In the past, several methods have been developed for the prediction of conformational and linear (or continuous) B-cell epitopes. However, the existing methods for predicting linear B-cell epitopes are far from perfection. In this study, an attempt has been made to develop an improved method for predicting linear B-cell epitopes. We have retrieved experimentally validated B-cell epitopes as well as non B-cell epitopes from Immune Epitope Database and derived two types of datasets called Lbtope_Variable and Lbtope_Fixed length datasets. The Lbtope_Variable dataset contains 14876 B-cell epitope and 23321 non-epitopes of variable length where as Lbtope_Fixed length dataset contains 12063 B-cell epitopes and 20589 non-epitopes of fixed length. We also evaluated the performance of models on above datasets after removing highly identical peptides from the datasets. In addition, we have derived third dataset Lbtope_Confirm having 1042 epitopes and 1795 non-epitopes where each epitope or non-epitope has been experimentally validated in at least two studies. A number of models have been developed to discriminate epitopes and non-epitopes using different machine-learning techniques like Support Vector Machine, and K-Nearest Neighbor. We achieved accuracy from ∼54% to 86% using diverse s features like binary profile, dipeptide composition, AAP (amino acid pair) profile. In this study, for the first time experimentally validated non B-cell epitopes have been used for developing method for predicting linear B-cell epitopes. In previous studies, random peptides have been used as non B-cell epitopes. In order to provide service to scientific community, a web server LBtope has been developed for predicting and designing B-cell epitopes (http://crdd.osdd.net/raghava/lbtope/). PMID:23667458

Advances in Blood Typing.

PubMed

Quraishy, N; Sapatnekar, S

The clinical importance of blood group antigens relates to their ability to evoke immune antibodies that are capable of causing hemolysis. The most important antigens for safe transfusion are ABO and D (Rh), and typing for these antigens is routinely performed for patients awaiting transfusion, prenatal patients, and blood donors. Typing for other blood group antigens, typically of the Kell, Duffy, Kidd, and MNS blood groups, is sometimes necessary, for patients who have, or are likely to develop antibodies to these antigens. The most commonly used typing method is serological typing, based on hemagglutination reactions against specific antisera. This method is generally reliable and practical for routine use, but it has certain drawbacks. In recent years, molecular typing has emerged as an alternative or supplemental typing method. It is based on detecting the polymorphisms and mutations that control the expression of blood group antigens, and using this information to predict the probable antigen type. Molecular typing methods are useful when traditional serological typing methods cannot be used, as when a patient has been transfused and the sample is contaminated with red blood cells from the transfused blood component. Moreover, molecular typing methods can precisely identify clinically significant variant antigens that cannot be distinguished by serological typing; this capability has been exploited for the resolution of typing discrepancies and shows promise for the improved transfusion management of patients with sickle cell anemia. Despite its advantages, molecular typing has certain limitations, and it should be used in conjunction with serological methods. © 2016 Elsevier Inc. All rights reserved.

Regarding retrievals of methane in the atmosphere from IASI/Metop spectra and their comparison with ground-based FTIR measurements data

NASA Astrophysics Data System (ADS)

Khamatnurova, M. Yu.; Gribanov, K. G.; Zakharov, V. I.; Rokotyan, N. V.; Imasu, R.

2017-11-01

The algorithm for atmospheric methane distribution retrieval in atmosphere from IASI spectra has been developed. The feasibility of Levenberg-Marquardt method for atmospheric methane total column amount retrieval from the spectra measured by IASI/METOP modified for the case of lack of a priori covariance matrices for methane vertical profiles is studied in this paper. Method and algorithm were implemented into software package together with iterative estimation of a posteriori covariance matrices and averaging kernels for each individual retrieval. This allows retrieval quality selection using the properties of both types of matrices. Methane (XCH4) retrieval by Levenberg-Marquardt method from IASI/METOP spectra is presented in this work. NCEP/NCAR reanalysis data provided by ESRL (NOAA, Boulder, USA) were taken as initial guess. Surface temperature, air temperature and humidity vertical profiles are retrieved before methane vertical profile retrieval. The data retrieved from ground-based measurements at the Ural Atmospheric Station and data of L2/IASI standard product were used for the verification of the method and results of methane retrieval from IASI/METOP spectra.

Exploiting salient semantic analysis for information retrieval

NASA Astrophysics Data System (ADS)

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

2016-11-01

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

Effective material parameter retrieval of anisotropic elastic metamaterials with inherent nonlocality

NASA Astrophysics Data System (ADS)

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

2016-09-01

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

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

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.

Antibody repertoire development in camelids.

PubMed

De Genst, Erwin; Saerens, Dirk; Muyldermans, Serge; Conrath, Katja

2006-01-01

The humoral immune response of the Camelidae is unique as these animals are the only known mammals that seem to possess functional homodimeric heavy-chain antibodies besides the classical heteromeric antibodies composed of heavy (H) and light (L) chains. By definition, the heavy-chain antibodies lack the L-chain, and it was noticed that their H-chain is devoid of the typical first constant domain (CH1) and contains a dedicated variable domain, referred to as VHH. The VHH exon is assembled from separate V-D-J gene segments. The recombined VHH region is subjected to somatic hypermutations; however, the timing and actual mechanism of the class switch from mu to the dedicated gamma-isotype remains elusive. Interestingly, antigen-specific VHHs are easily retrieved after panning of a phage-displayed rearranged V-gene pool cloned from an immunised camelid. These single-domain antigen binding entities possess a number of biophysical properties that offer particular advantages in various medical and biotechnological applications.

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

NASA Astrophysics Data System (ADS)

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

2016-07-01

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

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

NASA Astrophysics Data System (ADS)

McKague, Darren Shawn

2001-12-01

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

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

PubMed

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

1975-09-01

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

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

ERIC Educational Resources Information Center

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

2003-01-01

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

A demonstration of adjoint methods for multi-dimensional remote sensing of the atmosphere and surface

NASA Astrophysics Data System (ADS)

Martin, William G. K.; Hasekamp, Otto P.

2018-01-01

In previous work, we derived the adjoint method as a computationally efficient path to three-dimensional (3D) retrievals of clouds and aerosols. In this paper we will demonstrate the use of adjoint methods for retrieving two-dimensional (2D) fields of cloud extinction. The demonstration uses a new 2D radiative transfer solver (FSDOM). This radiation code was augmented with adjoint methods to allow efficient derivative calculations needed to retrieve cloud and surface properties from multi-angle reflectance measurements. The code was then used in three synthetic retrieval studies. Our retrieval algorithm adjusts the cloud extinction field and surface albedo to minimize the measurement misfit function with a gradient-based, quasi-Newton approach. At each step we compute the value of the misfit function and its gradient with two calls to the solver FSDOM. First we solve the forward radiative transfer equation to compute the residual misfit with measurements, and second we solve the adjoint radiative transfer equation to compute the gradient of the misfit function with respect to all unknowns. The synthetic retrieval studies verify that adjoint methods are scalable to retrieval problems with many measurements and unknowns. We can retrieve the vertically-integrated optical depth of moderately thick clouds as a function of the horizontal coordinate. It is also possible to retrieve the vertical profile of clouds that are separated by clear regions. The vertical profile retrievals improve for smaller cloud fractions. This leads to the conclusion that cloud edges actually increase the amount of information that is available for retrieving the vertical profile of clouds. However, to exploit this information one must retrieve the horizontally heterogeneous cloud properties with a 2D (or 3D) model. This prototype shows that adjoint methods can efficiently compute the gradient of the misfit function. This work paves the way for the application of similar methods to 3D remote sensing problems.

Individual-specific antibody identification methods

DOEpatents

Francoeur, Ann -Michele

1989-11-14

An identification method, applicable to the identification of animals or inanimate objects, is described. The method takes advantage of a hithertofore unknown set of individual-specific, or IS antibodies, that are part of the unique antibody repertoire present in animals, by reacting an effective amount of IS antibodies with a particular panel, or n-dimensional array (where n is typically one or two) consisting of an effective amount of many different antigens (typically greater than one thousand), to give antibody-antigen complexes. The profile or pattern formed by the antigen-antibody complexes, termed an antibody fingerprint, when revealed by an effective amount of an appropriate detector molecule, is uniquely representative of a particular individual. The method can similarly by used to distinguish genetically, or otherwise similar individuals, or their body parts containing IS antibodies. Identification of inanimate objects, particularly security documents, is similarly affected by associating with the documents, an effective amount of a particular individual's IS antibodies, or conversely, a particular panel of antigens, and forming antibody-antigen complexes with a particular panel of antigens, or a particular individual's IS antibodies, respectively. One embodiment of the instant identification method, termed the blocked fingerprint assay, has applications in the area of allergy testing, autoimmune diagnostics and therapeutics, and the detection of environmental antigens such as pathogens, chemicals, and toxins.

Identification of anti-CD98 antibody mimotopes for inducing antibodies with antitumor activity by mimotope immunization.

PubMed

Saito, Misa; Kondo, Masahiro; Ohshima, Motohiro; Deguchi, Kazuki; Hayashi, Hideki; Inoue, Kazuyuki; Tsuji, Daiki; Masuko, Takashi; Itoh, Kunihiko

2014-04-01

A mimotope is an antibody-epitope-mimicking peptide retrieved from a phage display random peptide library. Immunization with antitumor antibody-derived mimotopes is promising for inducing antitumor immunity in hosts. In this study, we isolated linear and constrained mimotopes from HBJ127, a tumor-suppressing anti-CD98 heavy chain mAb, and determined their abilities for induction of antitumor activity equal to that of the parent antibody. We detected elevated levels of antipeptide responses, but failed to detect reactivity against native CD98-expressing HeLa cells in sera of immunized mice. Phage display panning and selection of mimotope-immunized mouse spleen-derived antibody Fab library showed that HeLa cell-reactive Fabs were successfully retrieved from the library. This finding indicates that native antigen-reactive Fab clones represented an undetectable minor population in mimotope-induced antibody repertoire. Functional and structural analysis of retrieved Fab clones revealed that they were almost identical to the parent antibody. From these results, we confirmed that mimotope immunization was promising for retrieving antitumor antibodies equivalent to the parent antibody, although the co-administration of adjuvant compounds such as T-cell epitope peptides and Toll-like receptor 4 agonist peptides is likely to be necessary for inducing stronger antitumor immunity than mimotope injection alone. © 2014 The Authors. Cancer Science published by Wiley Publishing Asia Pty Ltd on behalf of Japanese Cancer Association.

An Abstraction-Based Data Model for Information Retrieval

NASA Astrophysics Data System (ADS)

McAllister, Richard A.; Angryk, Rafal A.

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

A diagram retrieval method with multi-label learning

NASA Astrophysics Data System (ADS)

Fu, Songping; Lu, Xiaoqing; Liu, Lu; Qu, Jingwei; Tang, Zhi

2015-01-01

In recent years, the retrieval of plane geometry figures (PGFs) has attracted increasing attention in the fields of mathematics education and computer science. However, the high cost of matching complex PGF features leads to the low efficiency of most retrieval systems. This paper proposes an indirect classification method based on multi-label learning, which improves retrieval efficiency by reducing the scope of compare operation from the whole database to small candidate groups. Label correlations among PGFs are taken into account for the multi-label classification task. The primitive feature selection for multi-label learning and the feature description of visual geometric elements are conducted individually to match similar PGFs. The experiment results show the competitive performance of the proposed method compared with existing PGF retrieval methods in terms of both time consumption and retrieval quality.

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

PubMed

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

2018-01-01

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

Sensitivity Analysis for Atmospheric Infrared Sounder (AIRS) CO2 Retrieval

NASA Technical Reports Server (NTRS)

Gat, Ilana

2012-01-01

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

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.

Influence of reaction medium during synthesis of Gantrez AN 119 nanoparticles for oral vaccination.

PubMed

Vandamme, Katrien; Melkebeek, Vesna; Cox, Eric; Deforce, Dieter; Lenoir, Joke; Adriaens, Els; Vervaet, Chris; Remon, Jean Paul

2010-02-01

Two synthesis methods of poly(methyl vinyl ether-co-maleic anhydride) (Gantrez AN 119) nanoparticles (NP) (used for oral vaccination) were compared. Wheat germ agglutinin (WGA) was used as ligand to enhance the bioadhesive properties of NP and beta-galactosidase as antigen. The first method encapsulated beta-galactosidase in NP by co-precipitation in an acetone/water mixture containing 44% acetone. In the second method, antigen addition occurred in 100% acetone. To improve stability, NP were crosslinked with 1,3-diaminopropane. The stability of WGA-conjugated NP with encapsulated antigen diminished at lower pH and when decreasing the amount of crosslinker. The binding type between WGA and polymer depended on the synthesis method: predominantly ionic bonds were formed using the 44% acetone method, whereas synthesis via the 100% acetone method resulted in covalent bonds. The biological activity of the WGA coating, evaluated via a pig gastric mucin binding test, was lower in NP prepared via the 100% acetone method. No release of native antigen was detected after hydrolysis of NP, due to the covalent antigen binding during antigen encapsulation and the high reactivity of the polymer. Moreover, the mucosal irritation capacity was evaluated upon nanoparticle hydrolysis using a slug mucosal irritation assay. Herein, hydrolysed NP of the 44% acetone method were classified as mild irritative. Copyright (c) 2009 Elsevier B.V. All rights reserved.

Anopheles salivary gland proteomes from major malaria vectors

PubMed Central

2012-01-01

Background Antibody responses against Anopheles salivary proteins can indicate individual exposure to bites of malaria vectors. The extent to which these salivary proteins are species-specific is not entirely resolved. Thus, a better knowledge of the diversity among salivary protein repertoires from various malaria vector species is necessary to select relevant genus-, subgenus- and/or species-specific salivary antigens. Such antigens could be used for quantitative (mosquito density) and qualitative (mosquito species) immunological evaluation of malaria vectors/host contact. In this study, salivary gland protein repertoires (sialomes) from several Anopheles species were compared using in silico analysis and proteomics. The antigenic diversity of salivary gland proteins among different Anopheles species was also examined. Results In silico analysis of secreted salivary gland protein sequences retrieved from an NCBInr database of six Anopheles species belonging to the Cellia subgenus (An. gambiae, An. arabiensis, An. stephensi and An. funestus) and Nyssorhynchus subgenus (An. albimanus and An. darlingi) displayed a higher degree of similarity compared to salivary proteins from closely related Anopheles species. Additionally, computational hierarchical clustering allowed identification of genus-, subgenus- and species-specific salivary proteins. Proteomic and immunoblot analyses performed on salivary gland extracts from four Anopheles species (An. gambiae, An. arabiensis, An. stephensi and An. albimanus) indicated that heterogeneity of the salivary proteome and antigenic proteins was lower among closely related anopheline species and increased with phylogenetic distance. Conclusion This is the first report on the diversity of the salivary protein repertoire among species from the Anopheles genus at the protein level. This work demonstrates that a molecular diversity is exhibited among salivary proteins from closely related species despite their common pharmacological activities. The involvement of these proteins as antigenic candidates for genus-, subgenus- or species-specific immunological evaluation of individual exposure to Anopheles bites is discussed. PMID:23148599

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

PubMed Central

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

2013-01-01

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

78 FR 16513 - Application of Advances in Nucleic Acid and Protein Based Detection Methods to Multiplex...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-15

... Transfusion-Transmissible Agents and Blood Cell Antigens in Blood Donations; Public Workshop AGENCY: Food and... Methods to Multiplex Detection of Transfusion- Transmissible Agents and Blood Cell Antigens in Blood... and the use of these tests in blood donor screening and blood cell antigen typing. The public workshop...

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 cirrus.

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.

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

PubMed Central

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

2018-01-01

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

Simultaneous human platelet antigen genotyping and detection of novel single nucleotide polymorphisms by targeted next-generation sequencing.

PubMed

Davey, Sue; Navarrete, Cristina; Brown, Colin

2017-06-01

Twenty-nine human platelet antigen systems have been described to date, but the majority of current genotyping methods are restricted to the identification of those most commonly associated with alloantibody production in a clinical context. This can result in a protracted investigation if causative human platelet antigens are rare or novel. A targeted next-generation sequencing approach was designed to detect all known human platelet antigens with the additional capability of identifying novel mutations in the encoding genes. A targeted enrichment, high-sensitivity HaloPlex assay was designed to sequence all exons and flanking regions of the six genes known to encode human platelet antigens. Indexed DNA libraries were prepared from 47 previously human platelet antigen-genotyped samples and subsequently combined into one of three pools for sequencing on an Illumina MiSeq platform. The generated FASTQ files were aligned and scrutinized for each human platelet antigen polymorphism using SureCall data analysis software. Forty-six samples were successfully genotyped for human platelet antigens 1 through 29bw, with an average per base coverage depth of 1144. Concordance with historical human platelet antigen genotypes was 100%. A putative novel mutation in Exon 10 of the integrin β-3 (ITGB3) gene from an unsolved case of fetal neonatal alloimmune thrombocytopenia was also detected. A next-generation sequencing-based method that can accurately define all known human platelet antigen polymorphisms was developed. With the ability to sequence up to 96 samples simultaneously, our HaloPlex design could be used for high-throughput human platelet antigen genotyping. This method is also applicable for investigating fetal neonatal alloimmune thrombocytopenia when rare or novel human platelet antigens are suspected. © 2017 AABB.

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.

Retrieval of constituent mixing ratios from limb thermal emission spectra

NASA Technical Reports Server (NTRS)

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

1988-01-01

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

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

PubMed

Voevodin, A F; Pácsa, A S

1983-01-01

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

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

IMMUNOGLOBULIN ISOANTIGENS (ALLOTYPES) IN THE MOUSE

PubMed Central

Herzenberg, Leonard A.; Warner, Noel L.; Herzenberg, Leonore A.

1965-01-01

Eight antigens of 7S γ2-immunoglobulins controlled by alleles at a single locus Ig-1, have been identified in mice. This locus has previously been shown to determine antigenic specificities on the F fragments of 7S γ2a-globulins. The reactions of these antigens with various isoantisera have shown that the antigens all cross react with one another. New methods for the analysis of antigenic specificities of soluble proteins are presented in detail. A sensitive method for detecting in the order of 0.01 µg of these isoantigens has been developed, based on the quantitative inhibition of precipitation of I125-labeled antigen. Cross-reactions of the antigens were analysed in inhibition assays and the data is compatible with the existence of a minimum of eight antigenic specificities. Each of the antigens is composed of different combinations of these specificities, with only one antigen having a specificity not present in any other. Sixty-eight mouse strains have been tested with specific isoantisera, and on the basis of the results, have been placed into the eight allele groups. Evidence for close genetic linkage of the Ig-1 locus and 11 chromosome markers has been sought and not found. PMID:14270242

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

NASA Astrophysics Data System (ADS)

Hsieh, Feng-Ju; Wang, Wei-Chih

2012-09-01

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

On the Simulation of Sea States with High Significant Wave Height for the Validation of Parameter Retrieval Algorithms for Future Altimetry Missions

NASA Astrophysics Data System (ADS)

Kuschenerus, Mieke; Cullen, Robert

2016-08-01

To ensure reliability and precision of wave height estimates for future satellite altimetry missions such as Sentinel 6, reliable parameter retrieval algorithms that can extract significant wave heights up to 20 m have to be established. The retrieved parameters, i.e. the retrieval methods need to be validated extensively on a wide range of possible significant wave heights. Although current missions require wave height retrievals up to 20 m, there is little evidence of systematic validation of parameter retrieval methods for sea states with wave heights above 10 m. This paper provides a definition of a set of simulated sea states with significant wave height up to 20 m, that allow simulation of radar altimeter response echoes for extreme sea states in SAR and low resolution mode. The simulated radar responses are used to derive significant wave height estimates, which can be compared with the initial models, allowing precision estimations of the applied parameter retrieval methods. Thus we establish a validation method for significant wave height retrieval for sea states causing high significant wave heights, to allow improved understanding and planning of future satellite altimetry mission validation.

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

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

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

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

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

NASA Technical Reports Server (NTRS)

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

2003-01-01

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

The Use of Mouse Models of Breast Cancer and Quantitative Image Analysis to Evaluate Hormone Receptor Antigenicity after Microwave-assisted Formalin Fixation

PubMed Central

Engelberg, Jesse A.; Giberson, Richard T.; Young, Lawrence J.T.; Hubbard, Neil E.

2014-01-01

Microwave methods of fixation can dramatically shorten fixation times while preserving tissue structure; however, it remains unclear if adequate tissue antigenicity is preserved. To assess and validate antigenicity, robust quantitative methods and animal disease models are needed. We used two mouse mammary models of human breast cancer to evaluate microwave-assisted and standard 24-hr formalin fixation. The mouse models expressed four antigens prognostic for breast cancer outcome: estrogen receptor, progesterone receptor, Ki67, and human epidermal growth factor receptor 2. Using pathologist evaluation and novel methods of quantitative image analysis, we measured and compared the quality of antigen preservation, percentage of positive cells, and line plots of cell intensity. Visual evaluations by pathologists established that the amounts and patterns of staining were similar in tissues fixed by the different methods. The results of the quantitative image analysis provided a fine-grained evaluation, demonstrating that tissue antigenicity is preserved in tissues fixed using microwave methods. Evaluation of the results demonstrated that a 1-hr, 150-W fixation is better than a 45-min, 150-W fixation followed by a 15-min, 650-W fixation. The results demonstrated that microwave-assisted formalin fixation can standardize fixation times to 1 hr and produce immunohistochemistry that is in every way commensurate with longer conventional fixation methods. PMID:24682322

Application of Rough Sets to Information Retrieval.

ERIC Educational Resources Information Center

Miyamoto, Sadaaki

1998-01-01

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

Affinity immunoblotting - High resolution isoelectric focusing analysis of antibody clonotype distribution

NASA Technical Reports Server (NTRS)

Knisley, Keith A.; Rodkey, L. Scott

1986-01-01

A sensitive and specific method is proposed for the analysis of specific antibody clonotype changes occurring during an immune response and for comparing multiple sera for antibody clonotype similarities. Polyclonal serum antibodies separated by isoelectric focusing (IEF) were analyzed by an affinity immunoblotting method using antigen-coated nitrocellulose membranes. Antibodies present on the surface of the acrylamide gels following IEF bind the antigen on the nitrocellulose when the coated nitrocellulose is laid over the gels. The technique has been used to analyze Ig clonotypes specific for five protein antigens and two carbohydrate antigens. Optimal antigen concentrations for coating the nitrocellulose membranes were found to range from 10-100 microgram/ml.

Error analysis applied to several inversion techniques used for the retrieval of middle atmospheric constituents from limb-scanning MM-wave spectroscopic measurements

NASA Technical Reports Server (NTRS)

Puliafito, E.; Bevilacqua, R.; Olivero, J.; Degenhardt, W.

1992-01-01

The formal retrieval error analysis of Rodgers (1990) allows the quantitative determination of such retrieval properties as measurement error sensitivity, resolution, and inversion bias. This technique was applied to five numerical inversion techniques and two nonlinear iterative techniques used for the retrieval of middle atmospheric constituent concentrations from limb-scanning millimeter-wave spectroscopic measurements. It is found that the iterative methods have better vertical resolution, but are slightly more sensitive to measurement error than constrained matrix methods. The iterative methods converge to the exact solution, whereas two of the matrix methods under consideration have an explicit constraint, the sensitivity of the solution to the a priori profile. Tradeoffs of these retrieval characteristics are presented.

Screening individual hybridomas by microengraving to discover monoclonal antibodies

PubMed Central

Ogunniyi, Adebola O; Story, Craig M; Papa, Eliseo; Guillen, Eduardo; Love, J Christopher

2014-01-01

The demand for monoclonal antibodies (mAbs) in biomedical research is significant, but the current methodologies used to discover them are both lengthy and costly. Consequently, the diversity of antibodies available for any particular antigen remains limited. Microengraving is a soft lithographic technique that provides a rapid and efficient alternative for discovering new mAbs. This protocol describes how to use microengraving to screen mouse hybridomas to establish new cell lines producing unique mAbs. Single cells from a polyclonal population are isolated into an array of microscale wells (~105 cells per screen). The array is then used to print a protein microarray, where each element contains the antibodies captured from individual wells. The antibodies on the microarray are screened with antigens of interest, and mapped to the corresponding cells, which are then recovered from their microwells by micromanipulation. Screening and retrieval require approximately 1–3 d (9–12 d including the steps for preparing arrays of microwells). PMID:19528952

Changing practice: red blood cell typing by molecular methods for patients with sickle cell disease.

PubMed

Casas, Jessica; Friedman, David F; Jackson, Tannoa; Vege, Sunitha; Westhoff, Connie M; Chou, Stella T

2015-06-01

Extended red blood cell (RBC) antigen matching is recommended to limit alloimmunization in patients with sickle cell disease (SCD). DNA-based testing to predict blood group phenotypes has enhanced availability of antigen-negative donor units and improved typing of transfused patients, but replacement of routine serologic typing for non-ABO antigens with molecular typing for patients has not been reported. This study compared the historical RBC antigen phenotypes obtained by hemagglutination methods with genotype predictions in 494 patients with SCD. For discrepant results, repeat serologic testing was performed and/or investigated by gene sequencing for silent or variant alleles. Seventy-one typing discrepancies were identified among 6360 antigen comparisons (1.1%). New specimens for repeat serologic testing were obtained for 66 discrepancies and retyping agreed with the genotype in 64 cases. One repeat Jk(b-) serologic phenotype, predicted Jk(b+) by genotype, was found by direct sequencing of JK to be a silenced allele, and one N typing discrepancy remains under investigation. Fifteen false-negative serologic results were associated with alleles encoding weak antigens or single-dose Fy(b) expression. DNA-based RBC typing provided improved accuracy and expanded information on RBC antigens compared to hemagglutination methods, leading to its implementation as the primary method for extended RBC typing for patients with SCD at our institution. © 2015 AABB.

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.

Detection of soluble antigens of Toxoplasma gondii by a four-layer modification of an enzyme immunoassay.

PubMed Central

Turunen, H J

1983-01-01

A sensitive four-layer modification of an enzyme immunoassay for the detection of soluble antigens of Toxoplasma gondii is described. Microtiter plates were sensitized with rabbit anti-toxoplasma immunoglobulins (6 micrograms/ml) used as the primary antibodies; guinea pig anti-toxoplasma immunoglobulins (6 micrograms/ml) were used as the secondary trapping antibodies. Horseradish peroxidase-conjugated anti-guinea pig immunoglobulins were used as the indicator antibodies. The specificity of the antigen assay was confirmed by using guinea pig immunoglobulins from preimmunization sera. The sensitivity of the antigen assay was found to be at least 10 ng of antigen protein per ml. The suitability of the method for detecting antigens of T. gondii in different specimens was studied by experimental toxoplasma infection in mice. Antigenic components of T. gondii could be detected in different tissue specimens from infected animals from the first day after infection onwards. Toxoplasma antigen in serum and urine samples from infected mice reached detectable levels on day 2 after infection followed by a linear increase in antigen concentration in succeeding samples. This method might offer a valuable aid for a rapid etiological diagnosis also in human cases of acute toxoplasmosis. PMID:6345574

Generating Concise Rules for Human Motion Retrieval

NASA Astrophysics Data System (ADS)

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

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

[A retrieval method of drug molecules based on graph collapsing].

PubMed

Qu, J W; Lv, X Q; Liu, Z M; Liao, Y; Sun, P H; Wang, B; Tang, Z

2018-04-18

To establish a compact and efficient hypergraph representation and a graph-similarity-based retrieval method of molecules to achieve effective and efficient medicine information retrieval. Chemical structural formula (CSF) was a primary search target as a unique and precise identifier for each compound at the molecular level in the research field of medicine information retrieval. To retrieve medicine information effectively and efficiently, a complete workflow of the graph-based CSF retrieval system was introduced. This system accepted the photos taken from smartphones and the sketches drawn on tablet personal computers as CSF inputs, and formalized the CSFs with the corresponding graphs. Then this paper proposed a compact and efficient hypergraph representation for molecules on the basis of analyzing factors that directly affected the efficiency of graph matching. According to the characteristics of CSFs, a hierarchical collapsing method combining graph isomorphism and frequent subgraph mining was adopted. There was yet a fundamental challenge, subgraph overlapping during the collapsing procedure, which hindered the method from establishing the correct compact hypergraph of an original CSF graph. Therefore, a graph-isomorphism-based algorithm was proposed to select dominant acyclic subgraphs on the basis of overlapping analysis. Finally, the spatial similarity among graphical CSFs was evaluated by multi-dimensional measures of similarity. To evaluate the performance of the proposed method, the proposed system was firstly compared with Wikipedia Chemical Structure Explorer (WCSE), the state-of-the-art system that allowed CSF similarity searching within Wikipedia molecules dataset, on retrieval accuracy. The system achieved higher values on mean average precision, discounted cumulative gain, rank-biased precision, and expected reciprocal rank than WCSE from the top-2 to the top-10 retrieved results. Specifically, the system achieved 10%, 1.41, 6.42%, and 1.32% higher than WCSE on these metrics for top-10 retrieval results, respectively. Moreover, several retrieval cases were presented to intuitively compare with WCSE. The results of the above comparative study demonstrated that the proposed method outperformed the existing method with regard to accuracy and effectiveness. This paper proposes a graph-similarity-based retrieval approach for medicine information. To obtain satisfactory retrieval results, an isomorphism-based algorithm is proposed for dominant subgraph selection based on the subgraph overlapping analysis, as well as an effective and efficient hypergraph representation of molecules. Experiment results demonstrate the effectiveness of the proposed approach.

Error Analyses of the North Alabama Lightning Mapping Array (LMA)

NASA Technical Reports Server (NTRS)

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

2003-01-01

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

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

PubMed

Hyyti, Janne; Escoto, Esmerando; Steinmeyer, Günter

2017-10-01

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

Infrared Retrievals of Ice Cloud Properties and Uncertainties with an Optimal Estimation Retrieval Method

NASA Astrophysics Data System (ADS)

Wang, C.; Platnick, S. E.; Meyer, K.; Zhang, Z.

2014-12-01

We developed an optimal estimation (OE)-based method using infrared (IR) observations to retrieve ice cloud optical thickness (COT), cloud effective radius (CER), and cloud top height (CTH) simultaneously. The OE-based retrieval is coupled with a fast IR radiative transfer model (RTM) that simulates observations of different sensors, and corresponding Jacobians in cloudy atmospheres. Ice cloud optical properties are calculated using the MODIS Collection 6 (C6) ice crystal habit (severely roughened hexagonal column aggregates). The OE-based method can be applied to various IR space-borne and airborne sensors, such as the Moderate Resolution Imaging Spectroradiometer (MODIS) and the enhanced MODIS Airborne Simulator (eMAS), by optimally selecting IR bands with high information content. Four major error sources (i.e., the measurement error, fast RTM error, model input error, and pre-assumed ice crystal habit error) are taken into account in our OE retrieval method. We show that measurement error and fast RTM error have little impact on cloud retrievals, whereas errors from the model input and pre-assumed ice crystal habit significantly increase retrieval uncertainties when the cloud is optically thin. Comparisons between the OE-retrieved ice cloud properties and other operational cloud products (e.g., the MODIS C6 and CALIOP cloud products) are shown.

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

PubMed

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

1975-10-01

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

Immunocytochemistry associated with oral exfoliative cytology: methodological analysis..

PubMed

da Silva, Alessandra Dutra; Lima, Celina Faig; Maraschin, Bruna Jalfim; Laureano, Natália Koerich; Daroit, Natália Batista; Brochier, Fernanda; Sant'Ana Filho, Manoel; Visioli, Fernanda; Rados, Pantelis Varvaki

2015-04-01

To evaluate different immunocytochemical protocol variations to find the most effective protocol for the analysis of involucrin, epidermal growth factor receptor (EGFR), and E-cadherin antibodies. Exfoliative cytology is a noninvasive method used to monitor and screen for early changes in the oral mucosa of patients exposed to carcinogens such as tobacco and alcohol. It has been postulated that its association with immunocytochemistry may improve the effectiveness of the screening process. Four graduate students from Porto Alegre in southern Brazil had oral smears collected from the border of the tongue using a cytobrush. The following variables were analyzed: cell membrane permeability, antigen retrieval method (microwave oven or water bath), antibody incubation time (overnight or 1 hour), detection system used (Envision or LSAB), and chromogen incubation time (10 seconds or 5 minutes). Best results were obtained with the following combinations: (1) for involucrin: water bath, 1-hour incubation for primary antibody, Envision, and chromogen incubation for 10 seconds; (2)for EGFR: microwave, overnight incubation, LSAB, and chromogen incubation for 5 minutes; and (3) for E-cadherin: water bath, over-night incubation, Envision, and chromogen incubation for 5 minutes. Our findings suggest that each antibody requires a specific immunocytochemical protocol to guarantee optimal results with oral smears.

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.

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.

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

PubMed

Tsaltas, G; Ford, C H

1993-02-01

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

Magnesium Presence Prevents Removal of Antigenic Nuclear-Associated Proteins from Bovine Pericardium for Heart Valve Engineering.

PubMed

Dalgliesh, Ailsa J; Liu, Zhi Zhao; Griffiths, Leigh G

2017-07-01

Current heart valve prostheses are associated with significant complications, including aggressive immune response, limited valve life expectancy, and inability to grow in juvenile patients. Animal derived "tissue" valves undergo glutaraldehyde fixation to mask tissue antigenicity; however, chronic immunological responses and associated calcification still commonly occur. A heart valve formed from an unfixed bovine pericardium (BP) extracellular matrix (ECM) scaffold, in which antigenic burden has been eliminated or significantly reduced, has potential to overcome deficiencies of current bioprostheses. Decellularization and antigen removal methods frequently use sequential solutions extrapolated from analytical chemistry approaches to promote solubility and removal of tissue components from resultant ECM scaffolds. However, the extent to which such prefractionation strategies may inhibit removal of antigenic tissue components has not been explored. We hypothesize that presence of magnesium in prefractionation steps causes DNA precipitation and reduces removal of nuclear-associated antigenic proteins. Keeping all variables consistent bar the addition or absence of magnesium (2 mM magnesium chloride hexahydrate), residual BP ECM scaffold antigenicity and removed antigenicity were assessed, along with residual and removed DNA content, ECM morphology, scaffold composition, and recellularization potential. Furthermore, we used proteomic methods to determine the mechanism by which magnesium presence or absence affects scaffold residual antigenicity. This study demonstrates that absence of magnesium from antigen removal solutions enhances solubility and subsequent removal of antigenic nuclear-associated proteins from BP. We therefore conclude that the primary mechanism of action for magnesium removal during antigen removal processes is avoidance of DNA precipitation, facilitating solubilization and removal of nuclear-associated antigenic proteins. Future studies are necessary to further facilitate solubility and removal of nuclear-associated antigenic proteins from xenogeneic ECM scaffolds, in addition to an in vivo assessing of the material.

Mutual information based feature selection for medical image retrieval

NASA Astrophysics Data System (ADS)

Zhi, Lijia; Zhang, Shaomin; Li, Yan

2018-04-01

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

Retrieving handwriting by combining word spotting and manifold ranking

NASA Astrophysics Data System (ADS)

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

2012-01-01

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

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

NASA Technical Reports Server (NTRS)

Koshak, W.

2016-01-01

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

A glow of HLA typing in organ transplantation

PubMed Central

2013-01-01

The transplant of organs and tissues is one of the greatest curative achievements of this century. In organ transplantation, the adaptive immunity is considered the main response exerted to the transplanted tissue, since the main goal of the immune response is the MHC (major histocompatibility complex) molecules expressed on the surface of donor cells. Cell surface molecules that induce an antigenic stimulus cause the rejection immune response to grafted tissue or organ. A wide variety of transplantation antigens have been described, including the major histocompatibility molecules, minor histocompatibility antigens, ABO blood group antigens and endothelial cell antigens. The sensitization to MHC antigens may be caused by transfusions, pregnancy, or failed previous grafts leading to development of anti-human leukocyte antigen (HLA) antibodies that are important factor responsible for graft rejection in solid organ transplantation and play a role in post-transfusion complication Anti-HLA Abs may be present in healthy individuals. Methods for HLA typing are described, including serological methods, molecular techniques of sequence-specific priming (SSP), sequence-specific oligonucleotide probing (SSOP), Sequence based typing (SBT) and reference strand-based conformation analysis (RSCA) method. Problems with organ transplantation are reservoir of organs and immune suppressive treatments that used to decrease rate of rejection with less side effect and complications. PMID:23432791

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

NASA Astrophysics Data System (ADS)

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

2018-06-01

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

Selecting relevant 3D image features of margin sharpness and texture for lung nodule retrieval.

PubMed

Ferreira, José Raniery; de Azevedo-Marques, Paulo Mazzoncini; Oliveira, Marcelo Costa

2017-03-01

Lung cancer is the leading cause of cancer-related deaths in the world. Its diagnosis is a challenge task to specialists due to several aspects on the classification of lung nodules. Therefore, it is important to integrate content-based image retrieval methods on the lung nodule classification process, since they are capable of retrieving similar cases from databases that were previously diagnosed. However, this mechanism depends on extracting relevant image features in order to obtain high efficiency. The goal of this paper is to perform the selection of 3D image features of margin sharpness and texture that can be relevant on the retrieval of similar cancerous and benign lung nodules. A total of 48 3D image attributes were extracted from the nodule volume. Border sharpness features were extracted from perpendicular lines drawn over the lesion boundary. Second-order texture features were extracted from a cooccurrence matrix. Relevant features were selected by a correlation-based method and a statistical significance analysis. Retrieval performance was assessed according to the nodule's potential malignancy on the 10 most similar cases and by the parameters of precision and recall. Statistical significant features reduced retrieval performance. Correlation-based method selected 2 margin sharpness attributes and 6 texture attributes and obtained higher precision compared to all 48 extracted features on similar nodule retrieval. Feature space dimensionality reduction of 83 % obtained higher retrieval performance and presented to be a computationaly low cost method of retrieving similar nodules for the diagnosis of lung cancer.

Phase retrieval of singular scalar light fields using a two-dimensional directional wavelet transform and a spatial carrier.

PubMed

Federico, Alejandro; Kaufmann, Guillermo H

2008-10-01

We evaluate a method based on the two-dimensional directional wavelet transform and the introduction of a spatial carrier to retrieve optical phase distributions in singular scalar light fields. The performance of the proposed phase-retrieval method is compared with an approach based on Fourier transform. The advantages and limitations of the proposed method are discussed.

Retrieving Liquid Water Path and Precipitable Water Vapor from the Atmospheric Radiation Measurement (ARM) Microwave Radiometers

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

Turner, David D.; Clough, Shepard A.; Liljegren, James C.

2007-11-01

Ground-based two-channel microwave radiometers have been used for over 15 years by the Atmospheric Radiation Measurement (ARM) program to provide observations of downwelling emitted radiance from which precipitable water vapor (PWV) and liquid water path (LWP) – twp geophysical parameters critical for many areas of atmospheric research – are retrieved. An algorithm that utilizes two advanced retrieval techniques, a computationally expensive physical-iterative approach and an efficient statistical method, has been developed to retrieve these parameters. An important component of this Microwave Retrieval (MWRRET) algorithm is the determination of small (< 1K) offsets that are subtracted from the observed brightness temperaturesmore » before the retrievals are performed. Accounting for these offsets removes systematic biases from the observations and/or the model spectroscopy necessary for the retrieval, significantly reducing the systematic biases in the retrieved LWP. The MWRRET algorithm provides significantly more accurate retrievals than the original ARM statistical retrieval which uses monthly retrieval coefficients. By combining the two retrieval methods with the application of brightness temperature offsets to reduce the spurious LWP bias in clear skies, the MWRRET algorithm provides significantly better retrievals of PWV and LWP from the ARM 2-channel microwave radiometers compared to the original ARM product.« less

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

PubMed

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

2005-01-01

The Thomsen-Friedenreich antigen (TF), or more precisely epitope, has been known as a pancarcinoma antigen. It consists of galactose-beta1-3-N-acetylgalactose. We have already described the expression of TF in the normal placenta. TF is expressed by the syncytium and by extravillous trophoblast cells. In this study, we investigated the expression of TF in the abort placenta. Frozen samples of human abort placentas (12 placentas), obtained from the first and second trimesters of pregnancy and, for comparison, samples of normal placentas (17 placentas) from the first, second and third trimesters of pregnancy, were used. Expression of TF was investigated by immunohistochemical methods. For identification of TF-positive cells in abort placentas, immunofluorescence methods were used. Evaluation of simple and double immunofluorescence was performed on a laser scanning microscope. Furthermore, we isolated trophoblast cells from first and third trimester placentas and evaluated cytokeratin 7 and Muc1 expression by immunofluorescence methods. We observed expression of TF antigen in the syncytiotrophoblasts layer of the placenta in all three trimesters of pregnancy in normal and abort placentas evaluated by immunohistochemical methods. There was no expression of TF antigen in the decidua of abort placentas. Immunofluorescence double staining of TF antigen and cytokeratin 7 showed reduced expression of both antigens in the abort decidua and co-expression of both antigens in the syncytiotrophoblast layer of normal and abort placentas. TF expression in the syncytiotrophoblast was reduced in abort placentas. In the isolated trophoblast cells, no TF expression was found, however, Muc1 expression was visualized. Expression of TF antigen was reduced in the first and second trimester abort decidua compared to the normal decidua during the same time of pregnancy. TF antigen was restricted to the syncytiotrophoblast and extravillous trophoblast cells in the decidua. Abort placentas expressed TF antigen on the syncytiotrophoblast layer, but with lower intensity compared to normal placentas. We found a significantly reduced co-expression of TF antigen and cytokeratin 7 in the decidua of abort placentas. These data suggested a reduction of extravillous trophoblast cells in the decidua of abort placentas. In addition, we found higher numbers of CD45-positive cells in the abort decidua compared to normal placentas.

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…

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.

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

PubMed Central

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

2018-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2018-04-01

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

Advances in simultaneous atmospheric profile and cloud parameter regression based retrieval from high-spectral resolution radiance measurements

NASA Astrophysics Data System (ADS)

Weisz, Elisabeth; Smith, William L.; Smith, Nadia

2013-06-01

The dual-regression (DR) method retrieves information about the Earth surface and vertical atmospheric conditions from measurements made by any high-spectral resolution infrared sounder in space. The retrieved information includes temperature and atmospheric gases (such as water vapor, ozone, and carbon species) as well as surface and cloud top parameters. The algorithm was designed to produce a high-quality product with low latency and has been demonstrated to yield accurate results in real-time environments. The speed of the retrieval is achieved through linear regression, while accuracy is achieved through a series of classification schemes and decision-making steps. These steps are necessary to account for the nonlinearity of hyperspectral retrievals. In this work, we detail the key steps that have been developed in the DR method to advance accuracy in the retrieval of nonlinear parameters, specifically cloud top pressure. The steps and their impact on retrieval results are discussed in-depth and illustrated through relevant case studies. In addition to discussing and demonstrating advances made in addressing nonlinearity in a linear geophysical retrieval method, advances toward multi-instrument geophysical analysis by applying the DR to three different operational sounders in polar orbit are also noted. For any area on the globe, the DR method achieves consistent accuracy and precision, making it potentially very valuable to both the meteorological and environmental user communities.

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.

A flower image retrieval method based on ROI feature.

PubMed

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

2004-07-01

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

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

NASA Astrophysics Data System (ADS)

Xiao, Qinhan; Li, Yanjun

2009-12-01

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

Single-step colony assay for screening antibody libraries.

PubMed

Kato, Mieko; Hanyu, Yoshiro

2017-08-10

We describe a method, single-step colony assay, for simple and rapid screening of single-chain Fv fragment (scFv) libraries. Colonies of Escherichia coli expressing the scFv library are formed on a hydrophilic filter that is positioned in contact with a membrane coated with an antigen. scFv expression is triggered upon treatment of colonies with an induction reagent, following which scFvs are secreted from the cells and diffused to the antigen-coated membrane. scFvs that exhibit binding affinity for the antigen are captured by the membrane-immobilized antigen. Lastly, detection of scFv binding of the antigen on the membrane allows identification of the clones on the filter that express antigen-specific scFvs. We tested this methodology by using an anti-rabbit IgG scFv, scFv(A10B), and a rat immune scFv library. Experiments conducted using scFv(A10B) revealed that this method improves scFv expression during the colony assay. By using our method to screen an immune library of 3×10 3 scFv clones, we established several clones exhibiting affinity for the antigen. Moreover, we tested 7 other antigens, including peptides, and successfully identified positive clones. We believe that this simple procedure and controlled scFv expression of the single-step colony assay could make the antibody screening both rapid and reliable and lead to successful isolation of positive clones from antibody libraries. Copyright © 2017 Elsevier B.V. All rights reserved.

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

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

PubMed

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

2017-02-01

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

Development of a generalized algorithm of satellite remote sensing using multi-wavelength and multi-pixel information (MWP method) for aerosol properties by satellite-borne imager

NASA Astrophysics Data System (ADS)

Hashimoto, M.; Nakajima, T.; Morimoto, S.; Takenaka, H.

2014-12-01

We have developed a new satellite remote sensing algorithm to retrieve the aerosol optical characteristics using multi-wavelength and multi-pixel information of satellite imagers (MWP method). In this algorithm, the inversion method is a combination of maximum a posteriori (MAP) method (Rodgers, 2000) and the Phillips-Twomey method (Phillips, 1962; Twomey, 1963) as a smoothing constraint for the state vector. Furthermore, with the progress of computing technique, this method has being combined with the direct radiation transfer calculation numerically solved by each iteration step of the non-linear inverse problem, without using LUT (Look Up Table) with several constraints.Retrieved parameters in our algorithm are aerosol optical properties, such as aerosol optical thickness (AOT) of fine and coarse mode particles, a volume soot fraction in fine mode particles, and ground surface albedo of each observed wavelength. We simultaneously retrieve all the parameters that characterize pixels in each of horizontal sub-domains consisting the target area. Then we successively apply the retrieval method to all the sub-domains in the target area.We conducted numerical tests for the retrieval of aerosol properties and ground surface albedo for GOSAT/CAI imager data to test the algorithm for the land area. The result of the experiment showed that AOTs of fine mode and coarse mode, soot fraction and ground surface albedo are successfully retrieved within expected accuracy. We discuss the accuracy of the algorithm for various land surface types. Then, we applied this algorithm to GOSAT/CAI imager data, and we compared retrieved and surface-observed AOTs at the CAI pixel closest to an AERONET (Aerosol Robotic Network) or SKYNET site in each region. Comparison at several sites in urban area indicated that AOTs retrieved by our method are in agreement with surface-observed AOT within ±0.066.Our future work is to extend the algorithm for analysis of AGEOS-II/GLI and GCOM/C-SGLI data.

Quantifying serum antibody in bird fanciers' hypersensitivity pneumonitis.

PubMed

McSharry, Charles; Dye, George M; Ismail, Tengku; Anderson, Kenneth; Spiers, Elizabeth M; Boyd, Gavin

2006-06-26

Detecting serum antibody against inhaled antigens is an important diagnostic adjunct for hypersensitivity pneumonitis (HP). We sought to validate a quantitative fluorimetric assay testing serum from bird fanciers. Antibody activity was assessed in bird fanciers and control subjects using various avian antigens and serological methods, and the titer was compared with symptoms of HP. IgG antibody against pigeon serum antigens, quantified by fluorimetry, provided a good discriminator of disease. Levels below 10 mg/L were insignificant, and increasing titers were associated with disease. The assay was unaffected by total IgG, autoantibodies and antibody to dietary hen's egg antigens. Antigens from pigeon serum seem sufficient to recognize immune sensitivity to most common pet avian species. Decreasing antibody titers confirmed antigen avoidance. Increasing antibody titer reflected the likelihood of HP, and decreasing titers confirmed antigen avoidance. Quantifying antibody was rapid and the increased sensitivity will improve the rate of false-negative reporting and obviate the need for invasive diagnostic procedures. Automated fluorimetry provides a method for the international standardization of HP serology thereby improving quality control and improving its suitability as a diagnostic adjunct.

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

PubMed Central

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

2015-01-01

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

Soluble Antigen Fluorescent-Antibody Technique

PubMed Central

Toussaint, Andre J.; Anderson, Robert I.

1965-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

SIFT Meets CNN: A Decade Survey of Instance Retrieval.

PubMed

Zheng, Liang; Yang, Yi; Tian, Qi

2018-05-01

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

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.

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

NASA Astrophysics Data System (ADS)

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

2017-02-01

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

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

NASA Technical Reports Server (NTRS)

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

2017-01-01

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

In silico identification and characterization of common epitope-based peptide vaccine for Nipah and Hendra viruses.

PubMed

Saha, Chayan Kumar; Mahbub Hasan, Md; Saddam Hossain, Md; Asraful Jahan, Md; Azad, Abul Kalam

2017-06-01

To explore a common B- and T-cell epitope-based vaccine that can elicit an immune response against encephalitis causing genus Henipaviruses, Hendra virus (HeV) and Nipah virus (NiV). Membrane proteins F, G and M of HeV and NiV were retrieved from the protein database and subjected to different bioinformatics tools to predict antigenic B-cell epitopes. Best B-cell epitopes were then analyzed to predict their T-cell antigenic potentiality. Antigenic B- and T-cell epitopes that shared maximum identity with HeV and NiV were selected. Stability of the selected epitopes was predicted. Finally, the selected epitopes were subjected to molecular docking simulation with HLA-DR to confirm their antigenic potentiality in silico. One epitope from G proteins, one from M proteins and none from F proteins were selected based on their antigenic potentiality. The epitope from the G proteins was stable whereas that from M was unstable. The M-epitope was made stable by adding flanking dipeptides. The 15-mer G-epitope (VDPLRVQWRNNSVIS) showed at least 66% identity with all NiV and HeV G protein sequences, while the 15-mer M-epitope (GKLEFRRNNAIAFKG) with the dipeptide flanking residues showed 73% identity with all NiV and HeV M protein sequences available in the database. Molecular docking simulation with most frequent MHC class-II (MHC II) and class-I (MHC I) molecules showed that these epitopes could bind within HLA binding grooves to elicit an immune response. Data in our present study revealed the notion that the epitopes from G and M proteins might be the target for peptide-based subunit vaccine design against HeV and NiV. However, the biochemical analysis is necessary to experimentally validate the interaction of epitopes individually with the MHC molecules through elucidation of immunity induction. Copyright © 2017 Hainan Medical University. Production and hosting by Elsevier B.V. All rights reserved.

An introduction to the theory of ptychographic phase retrieval methods

NASA Astrophysics Data System (ADS)

Konijnenberg, Sander

2017-12-01

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

Selecting appropriate singular values of transmission matrix to improve precision of incident wavefront retrieval

NASA Astrophysics Data System (ADS)

Fang, Longjie; Zhang, Xicheng; Zuo, Haoyi; Pang, Lin; Yang, Zuogang; Du, Jinglei

2018-06-01

A method of selecting appropriate singular values of the transmission matrix to improve the precision of incident wavefront retrieval in focusing light through scattering media is proposed. The optimal singular values selected by this method can reduce the degree of ill-conditionedness of the transmission matrix effectively, which indicates that the incident wavefront retrieved from the optimal set of singular values is more accurate than the incident wavefront retrieved from other sets of singular values. The validity of this method is verified by numerical simulation and actual measurements of the incident wavefront of coherent light through ground glass.

Diagnostic, therapeutic and economic consequences of a positive urinary antigen test for Legionella spp. in patients admitted with community-acquired pneumonia: a 7-year retrospective evaluation.

PubMed

Engel, M F; van Manen, L; Hoepelman, A I M; Thijsen, S; Oosterheert, J J

2013-09-01

A positive urinary antigen test for Legionella spp. (Legionella urinary antigen test; LUAT) allows an early switch from empiric to targeted treatment (TT) in hospitalised, community-acquired pneumonia (CAP) patients. We aimed to evaluate the diagnostic, therapeutic and economic consequences of this frequently used test 7 years after its implementation. We retrospectively evaluated LUATs performed between 2005 and 2011 in two teaching hospitals. All tests performed in hospitalised CAP patients were used in the economic evaluation and positive tests were included in the treatment evaluation. Data on patient characteristics, admission and outcome were retrieved from the patients' files. The number of days gained by making a rapid aetiological diagnosis, the number of days TT could be provided and their costs were calculated. Of 4485 LUATs, 2504 (56%) were performed for CAP including 55 (1%) positive tests (€1041/positive test). In 26 (60%) of the 43 included positive tests, LUAT was the only test showing Legionella spp. Subsequently, earlier TT was possible in the remaining cases during 209 cumulative admission days (€274/TT day). LUAT led to detection of Legionella spp. 13 days earlier per case (€203/day) as compared with culture/serology alone. Timely LUAT use in accordance with current guidelines allows early detection and treatment of CAP caused by Legionella spp. at considerable expense.

Production of a novel camel single-domain antibody specific for the type III mutant EGFR.

PubMed

Omidfar, K; Rasaee, M J; Modjtahedi, H; Forouzandeh, M; Taghikhani, M; Golmakani, N

2004-01-01

Camelids have a unique immune system capable of producing single-domain heavy-chain antibodies. The antigen-specific domain of these heavy-chain IgGs (VHH) are the smallest binding units produced by the immune system. In this study, we report the isolation and characterization of several binders against the epidermal growth factor receptor (EGFR) vIII retrieved from immune library of camels (Camelus bactrianus and Camelus dromedarius). The EGFRvIII is a ligand-independent, constitutively active, mutated form of the wild-type EGFR. The expression of EGFRvIII has been demonstrated in a wide range of human malignancies, including gliomas, and breast, prostate, ovarian and lung cancer. Camels were immunized with a synthetic peptide corresponding to a mutated sequence and tissue homogenates. Single-domain antibodies (VHH) were directly selected by panning a phage display library on successively decreasing amounts of synthetic peptide immobilized on magnetic beads. The anti-EGFRvIII camel single-domain antibodies selectively bound to the EGFRvIII peptide and reacted specifically with the immunoaffinity-purified antigen from a non-small cell lung cancer patient. These antibodies with affinities in the nanomolar range recognized the EGFRvIII peptide and affinity-purified mutated receptor. We concluded that using the phage display technique, antigen-specific VHH antibody fragments are readily accessible from the camelids. These antibodies may be good candidates for tumor-diagnostic and therapeutic applications. Copyright 2004 S. Karger AG, Basel.

Use of Anti-phospho-girdin Antibodies to Visualize Intestinal Tuft Cells in Free-Floating Mouse Jejunum Cryosections

PubMed Central

Mizutani, Yuka; Kuga, Daisuke; Iida, Machiko; Ushida, Kaori; Takagi, Tsuyoshi; Tokita, Yoshihito; Takahashi, Masahide; Asai, Masato

2018-01-01

The actin binding protein girdin is a cytosolic protein that is required for actin remodeling to trigger cell migration in various tissues. Girdin is phosphorylated by both receptor and non-receptor tyrosine kinases at tyrosine 1798. Omori et al. developed site- and phosphorylation status-specific antibodies against human girdin at tyrosine-1798 (pY1798), which specifically bind to phosphorylated tyrosine-1798, but not to unphosphorylated tyrosine-1798. pY1798 antibodies have been used to specifically label tuft cells (TCs) that are present in mammalian gastrointestinal tissues, but the function of these cells is unclear. This protocol allows the robust visualization of TCs in the jejunum using pY1798 antibodies and immunofluorescence. To ensure successful and simple TC visualization, this protocol includes two histological techniques: production of free-floating cryosections from gelatin-filled jejunum tissue, and low-temperature antigen retrieval at 50 °C for 3 h. Filling the jejunum with gelatin maintains the shape of free-floating sections throughout the staining procedure, whereas low-temperature antigen retrieval ensures robust signals from TCs. Successful use of this protocol results in pY1798 staining of TCs distributed from villus tip to crypt. Stained TCs have a spool-shaped soma and fluorescent signals condense at the lumenal tip, which corresponds to the protruding 'tuft.' Phalloidin staining colocalized with pY1798-positive TCs at the thickened brush border, and corresponds to a rootlet mass extending from the TC tuft. This protocol could be used to examine TCs in human biopsy samples collected with gastrointestinal endoscopes. Furthermore, TCs were recently reported to accumulate following parasite infection in mice, suggesting that this protocol could have applications for diagnosis of parasite infections in the human gut. PMID:29630055

Use of Anti-phospho-girdin Antibodies to Visualize Intestinal Tuft Cells in Free-Floating Mouse Jejunum Cryosections.

PubMed

Mizutani, Yuka; Kuga, Daisuke; Iida, Machiko; Ushida, Kaori; Takagi, Tsuyoshi; Tokita, Yoshihito; Takahashi, Masahide; Asai, Masato

2018-03-21

The actin binding protein girdin is a cytosolic protein that is required for actin remodeling to trigger cell migration in various tissues. Girdin is phosphorylated by both receptor and non-receptor tyrosine kinases at tyrosine 1798. Omori et al. developed site- and phosphorylation status-specific antibodies against human girdin at tyrosine-1798 (pY1798), which specifically bind to phosphorylated tyrosine-1798, but not to unphosphorylated tyrosine-1798. pY1798 antibodies have been used to specifically label tuft cells (TCs) that are present in mammalian gastrointestinal tissues, but the function of these cells is unclear. This protocol allows the robust visualization of TCs in the jejunum using pY1798 antibodies and immunofluorescence. To ensure successful and simple TC visualization, this protocol includes two histological techniques: production of free-floating cryosections from gelatin-filled jejunum tissue, and low-temperature antigen retrieval at 50 °C for 3 h. Filling the jejunum with gelatin maintains the shape of free-floating sections throughout the staining procedure, whereas low-temperature antigen retrieval ensures robust signals from TCs. Successful use of this protocol results in pY1798 staining of TCs distributed from villus tip to crypt. Stained TCs have a spool-shaped soma and fluorescent signals condense at the lumenal tip, which corresponds to the protruding 'tuft.' Phalloidin staining colocalized with pY1798-positive TCs at the thickened brush border, and corresponds to a rootlet mass extending from the TC tuft. This protocol could be used to examine TCs in human biopsy samples collected with gastrointestinal endoscopes. Furthermore, TCs were recently reported to accumulate following parasite infection in mice, suggesting that this protocol could have applications for diagnosis of parasite infections in the human gut.

A Bayesian approach to microwave precipitation profile retrieval

NASA Technical Reports Server (NTRS)

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

1995-01-01

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

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…

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.

Microwave Observations of Precipitation and the Atmosphere

NASA Technical Reports Server (NTRS)

Staelin, David H.; Rosenkranz, Philip W.

2004-01-01

This research effort had three elements devoted to improving satellite-derived passive microwave retrievals of precipitation rate: morphological rain-rate retrievals, warm rain retrievals, and extension of a study of geostationary satellite options. The morphological precipitation-rate retrieval method uses for the first time the morphological character of the observed storm microwave spectra. The basic concept involves: 1) retrieval of point rainfall rates using current algorithms, 2) using spatial feature vectors of the observations over segmented multi-pixel storms to estimate the integrated rainfall rate for that storm (cu m/s), and 3) normalization of the point rain-rate retrievals to ensure consistency with the storm-wide retrieval. This work is ongoing, but two key steps have been completed: development of a segmentation algorithm for defining spatial regions corresponding to single storms for purposes of estimation, and reduction of some of the data from NAST-M that will be used to support this research going forward. The warm rain retrieval method involved extension of Aquai/AIRS/AMSU/HSB algorithmic work on cloud water retrievals. The central concept involves the fact that passive microwave cloud water retrievals over approx. 0.4 mm are very likely associated with precipitation. Since glaciated precipitation is generally detected quite successfully using scattering signatures evident in the surface-blind 54- and 183-GHz bands, this new method complements the first by permitting precipitation retrievals of non-glaciated events. The method is most successful over ocean, but has detected non-glaciated convective cells over land, perhaps in their early formative stages. This work will require additional exploration and validation prior to publication. Passive microwave instrument configurations for use in geostationary orbit were studied. They employ parabolic reflectors between 2 and 4 meters in diameter, and frequencies up to approx.430 GHz; this corresponds to nadir spot diameters as small as 10 km.

Method for detection of antibodies for metallic elements

DOEpatents

Barrick, C.W.; Clarke, S.M.; Nordin, C.W.

1993-11-30

An apparatus and method for detecting antibodies specific to non-protein antigens. The apparatus is an immunological plate containing a plurality of plastic projections coated with a non-protein material. Assays utilizing the plate are capable of stabilizing the non-protein antigens with detection levels for antibodies specific to the antigens on a nanogram level. A screening assay with the apparatus allows for early detection of exposure to non-protein materials. Specifically metallic elements are detected. 10 figures.

Rapid screening and identification of dominant B cell epitopes of HBV surface antigen by quantum dot-based fluorescence polarization assay

NASA Astrophysics Data System (ADS)

Meng, Zhongji; Song, Ruihua; Chen, Yue; Zhu, Yang; Tian, Yanhui; Li, Ding; Cui, Daxiang

2013-03-01

A method for quickly screening and identifying dominant B cell epitopes was developed using hepatitis B virus (HBV) surface antigen as a target. Eleven amino acid fragments from HBV surface antigen were synthesized by 9-fluorenylmethoxy carbonyl solid-phase peptide synthesis strategy, and then CdTe quantum dots were used to label the N-terminals of all peptides. After optimizing the factors for fluorescence polarization (FP) immunoassay, the antigenicities of synthetic peptides were determined by analyzing the recognition and combination of peptides and standard antibody samples. The results of FP assays confirmed that 10 of 11 synthetic peptides have distinct antigenicities. In order to screen dominant antigenic peptides, the FP assays were carried out to investigate the antibodies against the 10 synthetic peptides of HBV surface antigen respectively in 159 samples of anti-HBV surface antigen-positive antiserum. The results showed that 3 of the 10 antigenic peptides may be immunodominant because the antibodies against them existed more widely among the samples and their antibody titers were higher than those of other peptides. Using three dominant antigenic peptides, 293 serum samples were detected for HBV infection by FP assays; the results showed that the antibody-positive ratio was 51.9% and the sensitivity and specificity were 84.3% and 98.2%, respectively. In conclusion, a quantum dot-based FP assay is a very simple, rapid, and convenient method for determining immunodominant antigenic peptides and has great potential in applications such as epitope mapping, vaccine designing, or clinical disease diagnosis in the future.

JAL (RH48) blood group antigen: serologic observations

PubMed Central

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

2009-01-01

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

STUDIES ON THE ANTIGENIC STRUCTURE OF SOME MAMMALIAN SPERMATOZOA

PubMed Central

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

1938-01-01

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

Active immunization against Plasmodium berghei malaria in mice, using different preparations of plasmodial antigen and different pathways of administration*

PubMed Central

Jerusalem, Christoph; Eling, Wynand

1969-01-01

With regard to the effectiveness of the antigens in inducing clinical immunity against malaria parasites, the minimum amount of living antigen developed in mice during controlled low parasitaemia with Plasmodium berghei has been estimated and compared with the amount of non-living antigen obtained by various methods of freeing parasites from their erythrocyte hosts. Whereas about 100 mg of living antigen per kg of body-weight are sufficient to induce a degree of hyperimmunity, 1240 mg/kg of a freshly prepared crude antigen are necessary to enable the mice to survive a challenge infection while 3500 mg—7000 mg/kg of a vaccine prepared from freshly isolated plasmodia are necessary to produce a degree of immunity comparable with hyperimmunity. It appears, therefore, that every manipulation of the parasitized erythrocyte or the isolated plasmodium outside the host organism, as well as a storage time in excess of 36 hours, causes a reduction in antigenicity, up to a factor of 10-2. However, this decrease in antigenicity is disproportionate compared with the reduced rate of infectivity of stored, parasitized erythrocytes and isolated parasites. After an incubation period of 18 hours, the ID100 increases from 2 × 10 to 5 × 107 parasites. Therefore, the differences between the essential amount of living plasmodia and non-living antigen may be due to other, hitherto unknown, factors and not exclusively to degradation of the most important antigen. The saponin method of freeing parasites from their erythrocyte hosts was found to yield the purest antigen. Preparations of parasites obtained by treating parasitized erythrocytes with anti-erythrocyte serum or with formalin were highly contaminated with remnants of the host cells and showed no better antigenic qualities than the parasites isolated by means of saponin. Since the decrease of antigenicity associated with harvesting and isolation procedures is constant, vaccination with a fractionated antigen pool should be possible. ImagesFIG. 4 PMID:5307595

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

NASA Astrophysics Data System (ADS)

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

2012-12-01

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

Errorless Learning in Cognitive Rehabilitation: A Critical Review

PubMed Central

Middleton, Erica L.; Schwartz, Myrna F.

2012-01-01

Cognitive rehabilitation research is increasingly exploring errorless learning interventions, which prioritize the avoidance of errors during treatment. The errorless learning approach was originally developed for patients with severe anterograde amnesia, who were deemed to be at particular risk for error learning. Errorless learning has since been investigated in other memory-impaired populations (e.g., Alzheimer's disease) and acquired aphasia. In typical errorless training, target information is presented to the participant for study or immediate reproduction, a method that prevents participants from attempting to retrieve target information from long-term memory (i.e., retrieval practice). However, assuring error elimination by preventing difficult (and error-permitting) retrieval practice is a potential major drawback of the errorless approach. This review begins with discussion of research in the psychology of learning and memory that demonstrates the importance of difficult (and potentially errorful) retrieval practice for robust learning and prolonged performance gains. We then review treatment research comparing errorless and errorful methods in amnesia and aphasia, where only the latter provides (difficult) retrieval practice opportunities. In each clinical domain we find the advantage of the errorless approach is limited and may be offset by the therapeutic potential of retrieval practice. Gaps in current knowledge are identified that preclude strong conclusions regarding a preference for errorless treatments over methods that prioritize difficult retrieval practice. We offer recommendations for future research aimed at a strong test of errorless learning treatments, which involves direct comparison with methods where retrieval practice effects are maximized for long-term gains. PMID:22247957

Methods and compositions for diagnosing and preventing a group B streptococcal infection

DOEpatents

Brady, Linda Jeannine [Gainesville, FL; Seifert, Kyle N [Harrisonburg, VA; Adderson, Elisabeth E [Memphis, TN; Bohnsack, John F [Salt Lake City, UT

2009-09-15

The present invention provides a group B streptococcal (GBS) surface antigen, designated epsilon antigen, that is co-expressed with the delta antigen on a subset of serotype III GBS. Epsilon is expressed on more pathogenic Restriction Digest Pattern (RDP) III-3 GBS, but not on RDP types 1, 2, or 4. Accordingly, the present invention provides compositions and methods for detecting a group B streptococcus serotype III, RDP III-3 strain. Vaccines and methods of identifying agents which inhibit adhesion of a group B streptococcal cell to a host cell are also provided.

Downscaling Thermal Infrared Radiance for Subpixel Land Surface Temperature Retrieval

PubMed Central

Liu, Desheng; Pu, Ruiliang

2008-01-01

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

Downscaling Thermal Infrared Radiance for Subpixel Land Surface Temperature Retrieval.

PubMed

Liu, Desheng; Pu, Ruiliang

2008-04-06

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

Wet refractivity tomography with an improved Kalman-Filter method

NASA Astrophysics Data System (ADS)

Cao, Yunchang; Chen, Yongqi; Li, Pingwha

2006-10-01

An improved retrieval method, which uses the solution with a Gaussian constraint as the initial state variables for the Kalman Filtering (KF) method, was developed to retrieve the wet refractivity profiles from slant wet delays (SWD) extracted by the double-differenced (DD) GPS method. The accuracy of the GPS-derived SWDs is also tested in this study against the measurements of a water vapor radiometer (WVR) and a weather model. It is concluded that the GPS-derived SWDs have similar accuracy to those measured with WVR and are much higher in quality than those derived from the weather model used. The developed method is used to retrieve the 3D wet refractivity distribution in the Hong Kong region. The retrieved profiles agree well with the radiosonde observations, with a difference of about 4 mm km-1 in the low levels. The accurate profiles obtained with this method are applicable in a number of meteorological applications.

Concept-Based Retrieval from Critical Incident Reports.

PubMed

Denecke, Kerstin

2017-01-01

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

The "RED Versa NIR" Plane to Retrieve Broken-Cloud Optical Depth from Ground-Based Measurements"

NASA Technical Reports Server (NTRS)

Marshak, A.; Knyazikhin, Y.; Evans, K.; Wiscombe, W.

2003-01-01

A new method for retrieving cloud optical depth from ground-based measurements of zenith radiance in the RED and near infrared (MR) spectral regions is introduced. Because zenith radiance does not have a one-to-one relationship with optical depth, it is absolutely impossible to use a monochromatic retrieval. On the other side, algebraic combinations of spectral radiances such as NDCI while largely removing nouniquiness and the radiative effects of cloud inhomogeneity, can result in poor retrievals due to its insensitivity to cloud fraction. Instead, both RED and NIR radiances as points on the 'RED vs. NIR' plane are proposed to be used for retrieval. The proposed retrieval method is applied to Cimel measurements at the Atmospheric Radiation Measurements (ARM) site in Oklahoma. Cimel, a multi-channel sunphotometer, is a part of AERONET - a ground-based network for monitoring aerosol optical properties. The results of retrieval are compared with the ones from Microwave Radiometer (MWR) and Multi-Filter Rotating Shadowband Radiometers (MFRSR) located next to Cimel at the ARM site. In addition, the performance of the retrieval method is assessed using a fractal model of cloud inhomogeneity and broken cloudiness. The preliminary results look very promising both theoretically and from measurements.

Data Compression in Full-Text Retrieval Systems.

ERIC Educational Resources Information Center

Bell, Timothy C.; And Others

1993-01-01

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

Detection of Antigenic Variants of Subtype H3 Swine Influenza A Viruses from Clinical Samples

PubMed Central

Martin, Brigitte E.; Li, Lei; Nolting, Jacqueline M.; Smith, David R.; Hanson, Larry A.

2017-01-01

ABSTRACT A large population of genetically and antigenically diverse influenza A viruses (IAVs) are circulating among the swine population, playing an important role in influenza ecology. Swine IAVs not only cause outbreaks among swine but also can be transmitted to humans, causing sporadic infections and even pandemic outbreaks. Antigenic characterizations of swine IAVs are key to understanding the natural history of these viruses in swine and to selecting strains for effective vaccines. However, influenza outbreaks generally spread rapidly among swine, and the conventional methods for antigenic characterization require virus propagation, a time-consuming process that can significantly reduce the effectiveness of vaccination programs. We developed and validated a rapid, sensitive, and robust method, the polyclonal serum-based proximity ligation assay (polyPLA), to identify antigenic variants of subtype H3N2 swine IAVs. This method utilizes oligonucleotide-conjugated polyclonal antibodies and quantifies antibody-antigen binding affinities by quantitative reverse transcription-PCR (RT-PCR). Results showed the assay can rapidly detect H3N2 IAVs directly from nasal wash or nasal swab samples collected from laboratory-challenged animals or during influenza surveillance at county fairs. In addition, polyPLA can accurately separate the viruses at two contemporary swine IAV antigenic clusters (H3N2 swine IAV-α and H3N2 swine IAV-ß) with a sensitivity of 84.9% and a specificity of 100.0%. The polyPLA can be routinely used in surveillance programs to detect antigenic variants of influenza viruses and to select vaccine strains for use in controlling and preventing disease in swine. PMID:28077698

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

Collaborative Information Retrieval Method among Personal Repositories

NASA Astrophysics Data System (ADS)

Kamei, Koji; Yukawa, Takashi; Yoshida, Sen; Kuwabara, Kazuhiro

In this paper, we describe a collaborative information retrieval method among personal repositorie and an implementation of the method on a personal agent framework. We propose a framework for personal agents that aims to enable the sharing and exchange of information resources that are distributed unevenly among individuals. The kernel of a personal agent framework is an RDF(resource description framework)-based information repository for storing, retrieving and manipulating privately collected information, such as documents the user read and/or wrote, email he/she exchanged, web pages he/she browsed, etc. The repository also collects annotations to information resources that describe relationships among information resources and records of interaction between the user and information resources. Since the information resources in a personal repository and their structure are personalized, information retrieval from other users' is an important application of the personal agent. A vector space model with a personalized concept-base is employed as an information retrieval mechanism in a personal repository. Since a personalized concept-base is constructed from information resources in a personal repository, it reflects its user's knowledge and interests. On the other hand, it leads to another problem while querying other users' personal repositories; that is, simply transferring query requests does not provide desirable results. To solve this problem, we propose a query equalization scheme based on a relevance feedback method for collaborative information retrieval between personalized concept-bases. In this paper, we describe an implementation of the collaborative information retrieval method and its user interface on the personal agent framework.

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

PubMed

Schmitz, H

1981-01-01

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

Genetic diversity of K-antigen gene clusters of Escherichia coli and their molecular typing using a suspension array.

PubMed

Yang, Shuang; Xi, Daoyi; Jing, Fuyi; Kong, Deju; Wu, Junli; Feng, Lu; Cao, Boyang; Wang, Lei

2018-04-01

Capsular polysaccharides (CPSs), or K-antigens, are the major surface antigens of Escherichia coli. More than 80 serologically unique K-antigens are classified into 4 groups (Groups 1-4) of capsules. Groups 1 and 4 contain the Wzy-dependent polymerization pathway and the gene clusters are in the order galF to gnd; Groups 2 and 3 contain the ABC-transporter-dependent pathway and the gene clusters consist of 3 regions, regions 1, 2 and 3. Little is known about the variations among the gene clusters. In this study, 9 serotypes of K-antigen gene clusters (K2ab, K11, K20, K24, K38, K84, K92, K96, and K102) were sequenced and correlated with their CPS chemical structures. On the basis of sequence data, a K-antigen-specific suspension array that detects 10 distinct CPSs, including the above 9 CPSs plus K30, was developed. This is the first report to catalog the genetic features of E. coli K-antigen variations and to develop a suspension array for their molecular typing. The method has a number of advantages over traditional bacteriophage and serum agglutination methods and lays the foundation for straightforward identification and detection of additional K-antigens in the future.

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

PubMed

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

2018-06-01

There are more than 300 known red blood cell (RBC) antigens and 33 platelet antigens that differ between individuals. Sensitisation to antigens is a serious complication that can occur in prenatal medicine and after blood transfusion, particularly for patients who require multiple transfusions. Although pre-transfusion compatibility testing largely relies on serological methods, reagents are not available for many antigens. Methods based on single-nucleotide polymorphism (SNP) arrays have been used, but typing for ABO and Rh-the most important blood groups-cannot be done with SNP typing alone. We aimed to develop a novel method based on whole-genome sequencing to identify RBC and platelet antigens. This whole-genome sequencing study is a subanalysis of data from patients in the whole-genome sequencing arm of the MedSeq Project randomised controlled trial (NCT01736566) with no measured patient outcomes. We created a database of molecular changes in RBC and platelet antigens and developed an automated antigen-typing algorithm based on whole-genome sequencing (bloodTyper). This algorithm was iteratively improved to address cis-trans haplotype ambiguities and homologous gene alignments. Whole-genome sequencing data from 110 MedSeq participants (30 × depth) were used to initially validate bloodTyper through comparison with conventional serology and SNP methods for typing of 38 RBC antigens in 12 blood-group systems and 22 human platelet antigens. bloodTyper was further validated with whole-genome sequencing data from 200 INTERVAL trial participants (15 × depth) with serological comparisons. We iteratively improved bloodTyper by comparing its typing results with conventional serological and SNP typing in three rounds of testing. The initial whole-genome sequencing typing algorithm was 99·5% concordant across the first 20 MedSeq genomes. Addressing discordances led to development of an improved algorithm that was 99·8% concordant for the remaining 90 MedSeq genomes. Additional modifications led to the final algorithm, which was 99·2% concordant across 200 INTERVAL genomes (or 99·9% after adjustment for the lower depth of coverage). By enabling more precise antigen-matching of patients with blood donors, antigen typing based on whole-genome sequencing provides a novel approach to improve transfusion outcomes with the potential to transform the practice of transfusion medicine. National Human Genome Research Institute, Doris Duke Charitable Foundation, National Health Service Blood and Transplant, National Institute for Health Research, and Wellcome Trust. Copyright © 2018 Elsevier Ltd. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

2018-06-01

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

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

Antigen presentation under the influence of 'immune evasion' proteins and its modulation by interferon-gamma: implications for immunotherapy of cytomegalovirus infection with antiviral CD8 T cells.

PubMed

Fink, Annette; Lemmermann, Niels A W; Gillert-Marien, Dorothea; Thomas, Doris; Freitag, Kirsten; Böhm, Verena; Wilhelmi, Vanessa; Reifenberg, Kurt; Reddehase, Matthias J; Holtappels, Rafaela

2012-11-01

Cytomegalovirus (CMV) disease with multiple organ manifestations is the most feared viral complication limiting the success of hematopoietic cell transplantation as a therapy of hematopoietic malignancies. A timely endogenous reconstitution of CD8 T cells controls CMV infection, and adoptive transfer of antiviral CD8 T cells is a therapeutic option to prevent CMV disease by bridging the gap between an early CMV reactivation and delayed endogenous reconstitution of protective immunity. Preclinical research in murine models has provided 'proof of concept' for CD8 T-cell therapy of CMV disease. Protection by CD8 T cells appears to be in conflict with the finding that CMVs encode proteins that inhibit antigen presentation to CD8 T cells by interfering with the constitutive trafficking of peptide-loaded MHC class I molecules (pMHC-I complexes) to the cell surface. Here, we have systematically explored antigen presentation in the presence of the three currently noted immune evasion proteins of murine CMV in all possible combinations and its modulation by pre-treatment of cells with interferon-gamma (IFN-γ). The data reveal improvement in antigen processing by pre-treatment with IFN-γ can almost overrule the inhibitory function of immune evasion molecules in terms of pMHC-I expression levels capable of triggering most of the specific CD8 T cells, though the intensity of stimulation did not retrieve their full functional capacity. Notably, an in vivo conditioning of host tissue cells with IFN-γ in adoptive cell transfer recipients constitutively overexpressing IFN-γ (B6-SAP-IFN-γ mice) enhanced the antiviral efficiency of CD8 T cells in this transgenic cytoimmunotherapy model.

Analysis of the binding loops configuration and surface adaptation of different crystallized single-domain antibodies in response to various antigens.

PubMed

Al Qaraghuli, Mohammed M; Ferro, Valerie A

2017-04-01

Monoclonal antibodies have revolutionized the biomedical field through their ubiquitous utilization in different diagnostics and therapeutic applications. Despite this widespread use, their large size and structural complexity have limited their versatility in specific applications. The antibody variable region that is responsible for binding antigen is embodied within domains that can be rescued individually as single-domain antibody (sdAb) fragments. Because of the unique characteristics of sdAbs, such as low molecular weight, high physicochemical stability, and the ability to bind antigens inaccessible to conventional antibodies, they represent a viable alternative to full-length antibodies. Consequently, 149 crystal structures of sdAbs, originating from human (VH), camelids (VHH), or sharks (VNAR), were retrieved from the Protein Data Bank, and their structures were compared. The 3 types of sdAbs displayed complementarity determining regions (CDRs) with different lengths and configurations. CDR3 of the VHH and VNAR domains were dominated by pleated and extended orientations, respectively. Although VNAR showed the smallest average molecular weight and molecular surface area compared with VHH and VH antibodies. However, the solvent accessible surface area measurements of the 3 tested sdAbs types were very similar. All the antihapten VHH antibodies showed pleated CDR3, which were sufficient to create a binding pocket to accommodate haptens (methotrexate and azo dyes) in terms of shape and electrostatic potential. The sdAbs that recognized lysozyme showed more diversity in their CDR3 orientation to enable them to recognize various topographies of lysozyme. Subsequently, the three sdAb classes were different in size and surface area and have shown distinguishable ability to optimize their CDR length and orientation to recognize different antigen classes. Copyright © 2016 John Wiley & Sons, Ltd.

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

PubMed Central

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

1992-01-01

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

Active learning methods for interactive image retrieval.

PubMed

Gosselin, Philippe Henri; Cord, Matthieu

2008-07-01

Active learning methods have been considered with increased interest in the statistical learning community. Initially developed within a classification framework, a lot of extensions are now being proposed to handle multimedia applications. This paper provides algorithms within a statistical framework to extend active learning for online content-based image retrieval (CBIR). The classification framework is presented with experiments to compare several powerful classification techniques in this information retrieval context. Focusing on interactive methods, active learning strategy is then described. The limitations of this approach for CBIR are emphasized before presenting our new active selection process RETIN. First, as any active method is sensitive to the boundary estimation between classes, the RETIN strategy carries out a boundary correction to make the retrieval process more robust. Second, the criterion of generalization error to optimize the active learning selection is modified to better represent the CBIR objective of database ranking. Third, a batch processing of images is proposed. Our strategy leads to a fast and efficient active learning scheme to retrieve sets of online images (query concept). Experiments on large databases show that the RETIN method performs well in comparison to several other active strategies.

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

PubMed

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

2012-10-04

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

ELISA Methods for the Detection of Ebolavirus Infection.

PubMed

Cross, Robert W; Ksiazek, Thomas G

2017-01-01

Ebola viruses are high-priority pathogens first discovered in rural Africa associated with sporadic outbreaks of severe hemorrhagic disease in humans and nonhuman primates. Little is known about the disease ecology or the prevalence of past exposure of human populations to any of the five species of the genus Ebolavirus. The use of immunologic means of detection for either virus antigens or the host's immune response to antigen associated with prior infections offers a powerful approach at understanding the epidemiology and epizootiology of these agents. Here we describe methods for preparing antigen detection sandwich enzyme-linked immunosorbent assays (ELISAs) as well as IgG and IgM ELISAs for the detection of ebolavirus antigens or antibodies in biological samples.

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

ERIC Educational Resources Information Center

Yu, C. T.; Salton, G.

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

Content-based cell pathology image retrieval by combining different features

NASA Astrophysics Data System (ADS)

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

2004-04-01

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

Joint retrievals of cloud and drizzle in marine boundary layer clouds using ground-based radar, lidar and zenith radiances

DOE PAGES

Fielding, M. D.; Chiu, J. C.; Hogan, R. J.; ...

2015-02-16

Active remote sensing of marine boundary-layer clouds is challenging as drizzle drops often dominate the observed radar reflectivity. We present a new method to simultaneously retrieve cloud and drizzle vertical profiles in drizzling boundary-layer cloud using surface-based observations of radar reflectivity, lidar attenuated backscatter, and zenith radiances. Specifically, the vertical structure of droplet size and water content of both cloud and drizzle is characterised throughout the cloud. An ensemble optimal estimation approach provides full error statistics given the uncertainty in the observations. To evaluate the new method, we first perform retrievals using synthetic measurements from large-eddy simulation snapshots of cumulusmore » under stratocumulus, where cloud water path is retrieved with an error of 31 g m −2. The method also performs well in non-drizzling clouds where no assumption of the cloud profile is required. We then apply the method to observations of marine stratocumulus obtained during the Atmospheric Radiation Measurement MAGIC deployment in the northeast Pacific. Here, retrieved cloud water path agrees well with independent 3-channel microwave radiometer retrievals, with a root mean square difference of 10–20 g m −2.« less

Revising the lower statistical limit of x-ray grating-based phase-contrast computed tomography.

PubMed

Marschner, Mathias; Birnbacher, Lorenz; Willner, Marian; Chabior, Michael; Herzen, Julia; Noël, Peter B; Pfeiffer, Franz

2017-01-01

Phase-contrast x-ray computed tomography (PCCT) is currently investigated as an interesting extension of conventional CT, providing high soft-tissue contrast even if examining weakly absorbing specimen. Until now, the potential for dose reduction was thought to be limited compared to attenuation CT, since meaningful phase retrieval fails for scans with very low photon counts when using the conventional phase retrieval method via phase stepping. In this work, we examine the statistical behaviour of the reverse projection method, an alternative phase retrieval approach and compare the results to the conventional phase retrieval technique. We investigate the noise levels in the projections as well as the image quality and quantitative accuracy of the reconstructed tomographic volumes. The results of our study show that this method performs better in a low-dose scenario than the conventional phase retrieval approach, resulting in lower noise levels, enhanced image quality and more accurate quantitative values. Overall, we demonstrate that the lower statistical limit of the phase stepping procedure as proposed by recent literature does not apply to this alternative phase retrieval technique. However, further development is necessary to overcome experimental challenges posed by this method which would enable mainstream or even clinical application of PCCT.

Monitoring volcanic ash cloud top height through simultaneous retrieval of optical data from polar orbiting and geostationary satellites

NASA Astrophysics Data System (ADS)

Zakšek, K.; Hort, M.; Zaletelj, J.; Langmann, B.

2012-09-01

Volcanic ash cloud top height (ACTH) can be monitored on the global level using satellite remote sensing. Here we propose a photogrammetric method based on the parallax between data retrieved from geostationary and polar orbiting satellites to overcome some limitations of the existing methods of ACTH retrieval. SEVIRI HRV band and MODIS band 1 are a good choice because of their high resolution. The procedure works well if the data from both satellites are retrieved nearly simultaneously. MODIS does not retrieve the data at exactly the same time as SEVIRI. To compensate for advection we use two sequential SEVIRI images (one before and one after the MODIS retrieval) and interpolate the cloud position from SEVIRI data to the time of MODIS retrieval. The proposed method was tested for the case of the Eyjafjallajökull eruption in April 2010. The parallax between MODIS and SEVIRI data can reach over 30 km which implies ACTH of more than 12 km in the beginning of the eruption. In the end of April eruption ACTH of 3-4 km is observed. The accuracy of ACTH was estimated to be 0.6 km.

Monitoring volcanic ash cloud top height through simultaneous retrieval of optical data from polar orbiting and geostationary satellites

NASA Astrophysics Data System (ADS)

Zakšek, K.; Hort, M.; Zaletelj, J.; Langmann, B.

2013-03-01

Volcanic ash cloud-top height (ACTH) can be monitored on the global level using satellite remote sensing. Here we propose a photogrammetric method based on the parallax between data retrieved from geostationary and polar orbiting satellites to overcome some limitations of the existing methods of ACTH retrieval. SEVIRI HRV band and MODIS band 1 are a good choice because of their high resolution. The procedure works well if the data from both satellites are retrieved nearly simultaneously. MODIS does not retrieve the data at exactly the same time as SEVIRI. To compensate for advection we use two sequential SEVIRI images (one before and one after the MODIS retrieval) and interpolate the cloud position from SEVIRI data to the time of MODIS retrieval. The proposed method was tested for the case of the Eyjafjallajökull eruption in April 2010. The parallax between MODIS and SEVIRI data can reach 30 km, which implies an ACTH of approximately 12 km at the beginning of the eruption. At the end of April eruption an ACTH of 3-4 km is observed. The accuracy of ACTH was estimated to be 0.6 km.

Virtual edge illumination and one dimensional beam tracking for absorption, refraction, and scattering retrieval

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

Vittoria, Fabio A., E-mail: fabio.vittoria.12@ucl.ac.uk; Diemoz, Paul C.; Research Complex at Harwell, Harwell Oxford Campus, OX11 0FA Didcot

2014-03-31

We propose two different approaches to retrieve x-ray absorption, refraction, and scattering signals using a one dimensional scan and a high resolution detector. The first method can be easily implemented in existing procedures developed for edge illumination to retrieve absorption and refraction signals, giving comparable image quality while reducing exposure time and delivered dose. The second method tracks the variations of the beam intensity profile on the detector through a multi-Gaussian interpolation, allowing the additional retrieval of the scattering signal.

Phase retrieval using regularization method in intensity correlation imaging

NASA Astrophysics Data System (ADS)

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

2014-11-01

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

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

PubMed Central

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

2015-01-01

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

A humming retrieval system based on music fingerprint

NASA Astrophysics Data System (ADS)

Han, Xingkai; Cao, Baiyu

2011-10-01

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

Theory of retrieving orientation-resolved molecular information using time-domain rotational coherence spectroscopy

NASA Astrophysics Data System (ADS)

Wang, Xu; Le, Anh-Thu; Zhou, Zhaoyan; Wei, Hui; Lin, C. D.

2017-08-01

We provide a unified theoretical framework for recently emerging experiments that retrieve fixed-in-space molecular information through time-domain rotational coherence spectroscopy. Unlike a previous approach by Makhija et al. (V. Makhija et al., arXiv:1611.06476), our method can be applied to the retrieval of both real-valued (e.g., ionization yield) and complex-valued (e.g., induced dipole moment) molecular response information. It is also a direct retrieval method without using iterations. We also demonstrate that experimental parameters, such as the fluence of the aligning laser pulse and the rotational temperature of the molecular ensemble, can be quite accurately determined using a statistical method.

Squamous Cell Carcinoma Antigen-encoding Genes SERPINB3/B4 as Potentially Useful Markers for the Stratification of HNSCC Tumours.

PubMed

Saidak, Zuzana; Morisse, Mony Chenda; Chatelain, Denis; Sauzay, Chloé; Houessinon, Aline; Guilain, Nelly; Soyez, Marion; Chauffert, Bruno; Dakpé, Stéphanie; Galmiche, Antoine

2018-03-01

The squamous cell carcinoma antigen (SCCA), encoded by the genes SERPINB3/B4, is a tumour marker produced by head and neck squamous cell carcinoma (HNSCC). We aimed to examine SERPINB3/B4 mRNA levels and its clinical significance in the therapeutic context. We retrieved mRNA expression levels, clinical, pathological and genomic data for 520 HNSCC from The Cancer Genome Atlas (TCGA). HNSCC tumours express high levels of SERPINB3/B4 mRNA. SERPINB3 expression differs depending on Human papillomavirus (HPV) infection status, primary tumour location, grade and differentiation, extension to lymph nodes and extracapsular spread. Interestingly, we observed an association between SERPINB3/B4 and the presence of tumour immune infiltrate as well as the expression of the immune checkpoint regulators PD-L1/PD-L2 that depended on HPV status. Our findings point to potential interest of SERPINB3/B4 for the stratification of HNSCC patients in the therapeutic context. Copyright© 2018, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

[Current status in the commercialization and application of genetically modified plants and their effects on human and livestock health and phytoremediation].

PubMed

Yoshimatsu, Kayo; Kawano, Noriaki; Kawahara, Nobuo; Akiyama, Hiroshi; Teshima, Reiko; Nishijima, Masahiro

2012-01-01

Developments in the use of genetically modified plants for human and livestock health and phytoremediation were surveyed using information retrieved from Entrez PubMed, Chemical Abstracts Service, Google, congress abstracts and proceedings of related scientific societies, scientific journals, etc. Information obtained was classified into 8 categories according to the research objective and the usage of the transgenic plants as 1: nutraceuticals (functional foods), 2: oral vaccines, 3: edible curatives, 4: vaccine antigens, 5: therapeutic antibodies, 6: curatives, 7: diagnostic agents and reagents, and 8: phytoremediation. In total, 405 cases were collected from 2006 to 2010. The numbers of cases were 120 for nutraceuticals, 65 for oral vaccines, 25 for edible curatives, 36 for vaccine antigens, 36 for therapeutic antibodies, 76 for curatives, 15 for diagnostic agents and reagents, and 40 for phytoremediation (sum of each cases was 413 because some reports were related to several categories). Nutraceuticals, oral vaccines and curatives were predominant. The most frequently used edible crop was rice (51 cases), and tomato (28 cases), lettuce (22 cases), potato (18 cases), corn (15 cases) followed.

Direct covalent attachment of small peptide antigens to enzyme-linked immunosorbent assay plates using radiation and carbodiimide activation.

PubMed

Dagenais, P; Desprez, B; Albert, J; Escher, E

1994-10-01

Direct adsorption of small peptide antigens to unaltered, commercially available polystyrene surfaces may be too weak to permit suitable assay by ELISA. We therefore developed a simple method for the covalent attachment of small, potentially single epitope antigens to polystyrene surfaces. Chemical activation of polystyrene plates with carbodiimide considerably improves the total and covalent attachment of radioactive octapeptides. The covalent attachment was demonstrated by washing with hot detergent. A 3.5 Mrad gamma-irradiation of plates also increases total binding, particularly in combination with chemical activation. The covalent attachment presumably occurs through formation and chemical activation of carboxylate functions on the polystyrene surface which form amide bonds with peptides. ELISA test was performed with CGRP and successive smaller CGRP fragments. Covalent attachment of C-terminal peptide fragments as detection antigens allows optimal recognition and sensitivity even for hexapeptides, while decapeptide antigens were already poorly recognized using a conventional antigen plating technique. Repetitive detergent washes and/or prolonged storage of plates with covalently bound antigens did not reduce their ELISA sensitivity. The method with storage and reutilization capacities that we present here will be useful for the development of preplated antibody screening test.

Phase modulated high density collinear holographic data storage system with phase-retrieval reference beam locking and orthogonal reference encoding.

PubMed

Liu, Jinpeng; Horimai, Hideyoshi; Lin, Xiao; Huang, Yong; Tan, Xiaodi

2018-02-19

A novel phase modulation method for holographic data storage with phase-retrieval reference beam locking is proposed and incorporated into an amplitude-encoding collinear holographic storage system. Unlike the conventional phase retrieval method, the proposed method locks the data page and the corresponding phase-retrieval interference beam together at the same location with a sequential recording process, which eliminates piezoelectric elements, phase shift arrays and extra interference beams, making the system more compact and phase retrieval easier. To evaluate our proposed phase modulation method, we recorded and then recovered data pages with multilevel phase modulation using two spatial light modulators experimentally. For 4-level, 8-level, and 16-level phase modulation, we achieved the bit error rate (BER) of 0.3%, 1.5% and 6.6% respectively. To further improve data storage density, an orthogonal reference encoding multiplexing method at the same position of medium is also proposed and validated experimentally. We increased the code rate of pure 3/16 amplitude encoding method from 0.5 up to 1.0 and 1.5 using 4-level and 8-level phase modulation respectively.

Generating region proposals for histopathological whole slide image retrieval.

PubMed

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

2018-06-01

Content-based image retrieval is an effective method for histopathological image analysis. However, given a database of huge whole slide images (WSIs), acquiring appropriate region-of-interests (ROIs) for training is significant and difficult. Moreover, histopathological images can only be annotated by pathologists, resulting in the lack of labeling information. Therefore, it is an important and challenging task to generate ROIs from WSI and retrieve image with few labels. This paper presents a novel unsupervised region proposing method for histopathological WSI based on Selective Search. Specifically, the WSI is over-segmented into regions which are hierarchically merged until the WSI becomes a single region. Nucleus-oriented similarity measures for region mergence and Nucleus-Cytoplasm color space for histopathological image are specially defined to generate accurate region proposals. Additionally, we propose a new semi-supervised hashing method for image retrieval. The semantic features of images are extracted with Latent Dirichlet Allocation and transformed into binary hashing codes with Supervised Hashing. The methods are tested on a large-scale multi-class database of breast histopathological WSIs. The results demonstrate that for one WSI, our region proposing method can generate 7.3 thousand contoured regions which fit well with 95.8% of the ROIs annotated by pathologists. The proposed hashing method can retrieve a query image among 136 thousand images in 0.29 s and reach precision of 91% with only 10% of images labeled. The unsupervised region proposing method can generate regions as predictions of lesions in histopathological WSI. The region proposals can also serve as the training samples to train machine-learning models for image retrieval. The proposed hashing method can achieve fast and precise image retrieval with small amount of labels. Furthermore, the proposed methods can be potentially applied in online computer-aided-diagnosis systems. Copyright © 2018 Elsevier B.V. All rights reserved.

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.

In situ induction of dendritic cell–based T cell tolerance in humanized mice and nonhuman primates

PubMed Central

Jung, Kyeong Cheon; Jeon, Yoon Kyung; Ban, Young Larn; Min, Hye Sook; Kim, Eun Ji; Kim, Ju Hyun; Kang, Byung Hyun; Bae, Youngmee; Yoon, Il-Hee; Kim, Yong-Hee; Lee, Jae-Il; Kim, Jung-Sik; Shin, Jun-Seop; Yang, Jaeseok; Kim, Sung Joo; Rostlund, Emily; Muller, William A.

2011-01-01

Induction of antigen-specific T cell tolerance would aid treatment of diverse immunological disorders and help prevent allograft rejection and graft versus host disease. In this study, we establish a method of inducing antigen-specific T cell tolerance in situ in diabetic humanized mice and Rhesus monkeys receiving porcine islet xenografts. Antigen-specific T cell tolerance is induced by administration of an antibody ligating a particular epitope on ICAM-1 (intercellular adhesion molecule 1). Antibody-mediated ligation of ICAM-1 on dendritic cells (DCs) led to the arrest of DCs in a semimature stage in vitro and in vivo. Ablation of DCs from mice completely abrogated anti–ICAM-1–induced antigen-specific T cell tolerance. T cell responses to unrelated antigens remained unaffected. In situ induction of DC-mediated T cell tolerance using this method may represent a potent therapeutic tool for preventing graft rejection. PMID:22025302

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

PubMed

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

2005-08-18

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

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

PubMed Central

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

2005-01-01

Background Assays detecting human antigen-specific antibodies are medically useful. However, the usefulness of existing simple immunoassay formats is limited by technical considerations such as sera antibodies to contaminants in insufficiently pure antigen, a problem likely exacerbated when antigen panels are screened to obtain clinically useful data. Results We developed a novel and simple immunoprecipitation technology for identifying clinical sera containing antigen-specific antibodies and for generating quantitative antibody response profiles. This method is based on fusing protein antigens to an enzyme reporter, Renilla luciferase (Ruc), and expressing these fusions in mammalian cells, where mammalian-specific post-translational modifications can be added. After mixing crude extracts, sera and protein A/G beads together and incubating, during which the Ruc-antigen fusion become immobilized on the A/G beads, antigen-specific antibody is quantitated by washing the beads and adding coelenterazine substrate and measuring light production. We have characterized this technology with sera from patients having three different types of cancers. We show that 20–85% of these sera contain significant titers of antibodies against at least one of five frequently mutated and/or overexpressed tumor-associated proteins. Five of six colon cancer sera tested gave responses that were statistically significantly greater than the average plus three standard deviations of 10 control sera. The results of competition experiments, preincubating positive sera with unmodified E. coli-produced antigens, varied dramatically. Conclusion This technology has several advantages over current quantitative immunoassays including its relative simplicity, its avoidance of problems associated with E. coli-produced antigens and its use of antigens that can carry mammalian or disease-specific post-translational modifications. This assay should be generally useful for analyzing sera for antibodies recognizing any protein or its post-translational modifications. PMID:16109166

Biomass Burning Aerosol Absorption Measurements with MODIS Using the Critical Reflectance Method

NASA Technical Reports Server (NTRS)

Zhu, Li; Martins, Vanderlei J.; Remer, Lorraine A.

2010-01-01

This research uses the critical reflectance technique, a space-based remote sensing method, to measure the spatial distribution of aerosol absorption properties over land. Choosing two regions dominated by biomass burning aerosols, a series of sensitivity studies were undertaken to analyze the potential limitations of this method for the type of aerosol to be encountered in the selected study areas, and to show that the retrieved results are relatively insensitive to uncertainties in the assumptions used in the retrieval of smoke aerosol. The critical reflectance technique is then applied to Moderate Resolution Imaging Spectrometer (MODIS) data to retrieve the spectral aerosol single scattering albedo (SSA) in South African and South American 35 biomass burning events. The retrieved results were validated with collocated Aerosol Robotic Network (AERONET) retrievals. One standard deviation of mean MODIS retrievals match AERONET products to within 0.03, the magnitude of the AERONET uncertainty. The overlap of the two retrievals increases to 88%, allowing for measurement variance in the MODIS retrievals as well. The ensemble average of MODIS-derived SSA for the Amazon forest station is 0.92 at 670 nm, and 0.84-0.89 for the southern African savanna stations. The critical reflectance technique allows evaluation of the spatial variability of SSA, and shows that SSA in South America exhibits higher spatial variation than in South Africa. The accuracy of the retrieved aerosol SSA from MODIS data indicates that this product can help to better understand 44 how aerosols affect the regional and global climate.

Ground-based remote sensing of thin clouds in the Arctic

NASA Astrophysics Data System (ADS)

Garrett, T. J.; Zhao, C.

2013-05-01

This paper describes a method for using interferometer measurements of downwelling thermal radiation to retrieve the properties of single-layer clouds. Cloud phase is determined from ratios of thermal emission in three "micro-windows" at 862.5 cm-1, 935.8 cm-1, and 988.4 cm-1 where absorption by water vapour is particularly small. Cloud microphysical and optical properties are retrieved from thermal emission in the first two of these micro-windows, constrained by the transmission through clouds of primarily stratospheric ozone emission at 1040 cm-1. Assuming a cloud does not approximate a blackbody, the estimated 95% confidence retrieval errors in effective radius re, visible optical depth τ, number concentration N, and water path WP are, respectively, 10%, 20%, 38% (55% for ice crystals), and 16%. Applied to data from the Atmospheric Radiation Measurement programme (ARM) North Slope of Alaska - Adjacent Arctic Ocean (NSA-AAO) site near Barrow, Alaska, retrievals show general agreement with both ground-based microwave radiometer measurements of liquid water path and a method that uses combined shortwave and microwave measurements to retrieve re, τ and N. Compared to other retrieval methods, advantages of this technique include its ability to characterise thin clouds year round, that water vapour is not a primary source of retrieval error, and that the retrievals of microphysical properties are only weakly sensitive to retrieved cloud phase. The primary limitation is the inapplicability to thicker clouds that radiate as blackbodies and that it relies on a fairly comprehensive suite of ground based measurements.

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

NASA Astrophysics Data System (ADS)

Miskevich, Alexander A.; Loiko, Valery A.

2015-01-01

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

[Studies on the intradermal reactions with the fractions of Ascaris lumbricoides

PubMed

Lee, Chan Wook

1967-06-01

INTRODUCTION : The studies on allergic reaction with the substances of Ascaris lumbricoides have long been studied by various worers; Conventry(1929), Campbell(1936), Sakei(1949), Miyakawa(1950), Ikeda(1952), Matsumoto and Imawari(1952), Morishita and Kobayashi(1953, 1954), Komiyayama(1954) and Yammoto(1956). Campbell(1936) and some other workers reported that the polysaccharides from ascaris produced the stronger intrademal reactions than protein fraction, though Yamamoto(1954) and others found the reverse results. On the other hand, Hosotani(1954) reported that the crude antigen or mixed antigen with polysaccharide and protein fraction of the ascaris produced the strongest skin reaction than with the other single fraction. As are shown in above reports, the intensity of the allergic reaction with the substances from ascaris is still remained under dipute. The reason might be due to the difference of the method of preparation, technique and evaluation. The aim of the present study is to elucidate the intensity of allergic reactivity fo protein and polysaccharide fration and mixed substance of two fractions and crude antigen of Ascaris lumbricoides. MATERIALS AND METHODS : A Intrdermal Test 1. Human Experiment. The intradermal test was performed on several groups of people. A: Ascaris lumbricoides egg positive cases among adult ages. B: Ascaris lumbricoides egg negative cases but who bad doubtful symptom. C: Ascaris lumbricoides egg negative cases but who had past history of ascaris infection. D: Ascaris lumbricoides egg negative cases and aged 3-8 months old. 2. Animal Experiment: Same breeds of 6 dogs were raised i cages of laboratory for 6 months, During the period, special attention was paid to keep them in parasite free conditon. The body weight was 10kg in average. B. Antigens. The adults worms of Ascaris lumbricoides, which were obtained during laparotomy, were first washed with sterilized saline solution. Each ascaris was placed in 50ml of saline solution and kept in 30 degrees C incubator for 24 hours. Among of them, the active one was seleted and put to sudden freeze at -70 degrees C for 20 hours. the whole body was powdered in a dried condition and kept it in ampoule at -4 degrees C. a) Crude antigen: The ether extract of powdered Ascaris lumbrucoides were motared by adding veronal buffer solution (1:100) and kept in icebox for 48 hours. The suspension was diluted with veronal buffer solution in the ratio of 1:10,000. b) Protein antigen : This antigen was prepared by Chaffee's modified methods and ammonium sulfate extraction mehtod. c) Polysaccharide antigen: Chaffee's modified method and ethanol extration method were applied. d) Mixed antigen : The same amount of preparation of protein and polysaccharide antigen were mixed. C. Intrdermal test 1. The intradermal test : 0.02ml of natigen was injected on the anterior surface of the frearm in human and on the back in aninmal, with tuberculin syringe. The criteria of the skin reaction were determined as follows; wheal: -; 0-4mm, +/-; 5-7mm, +;8-9mm, +; 21-32mm, ++; 33-44mm, +++; 45-56mm, ++++; over 57mm, in diameter. D. Stool examination : All the stool examination was done by formalin-ether concectration(M.G.L) method. E.P.G (egg per gram) was also determined by Stoll's egg counting method. RESULT : The intradermal reaction after the injection of each antigen was observed at 15, 30, 60 minutes and 3, 24 hours. In 58 ascariasis cases, the peak of wheal was appeared at 30 minute; 93.0% with the crude antigen, 15.5% with the mixed antigen, 10.3% with the Protein antigen, but all were negative in the polysaccharide antigen. The erythema reaction paralledled, in general, to the wheal; 75.8% at 15 minutes, 72.5% at 30 minutes and 48.3% at 60 mintues, with the crude antigen. Only 3.4% showed erythema at 15,30, and 60 minutes int the case of mixed antigen, and 1.7% fo positive was appeared at 30 minutes in the case of protein antigen, but none was observed in the polysaccharide antigen. The wheal and erythema revealed correlationship each other. Both of them showed 65.5% positive boundary in the case of crude antigen. Generally, the crude antigen resulted the highest and strongest reaction than the other fractions; the mixed, protein and polysaccharide in decreasing order. In adult age group, who showed egg negative at the time of injection, 81.5% were positive in skin reaction with the crude antigen, and 88.6% in the group who complained doubtful symptom but egg negative. In the group who had past history of ascaris infection showed 66.6% positive and the egg negative infant group with the same crude antigen. The sheal size was not always paralleled with the worm burden. The cross reaction with the antigen from Ascaris lumbricoides and Toxocara canis was examined by the intradermal test. There was no cross reaction between the two antigen. The infected dog with Toxocara canis showed positive reaction by the crude antigen of same species, but mot by the human species. Experimentally, the positive skin reaction was appeared only by the crude antigen at four weeks after the infection of Toxocara canis. CONCLUSION: The intradermal studies with the fraction of Ascaris lumbricoides and Toxocara canis were performed to human and dog, and the following results were observed. 1) Wheal and erythema were appeared in the cases of ascaris infection or who had past history, but not in the ascaris free before. 2) The size of wheal reached to peak 30 minutes after the injection. 3) The crude antigen had specificity and showed no cross reaction. 4) The crude antigen cause the strongest and largest reaction than the other substances; protein, polysaccharide and the mixed antigen. No cutaneous reaction was observed with the fraction of polysaccharides. 5) The size of wheal did not parallel with the worm burden. 6) The skin reaction was appeared four weeks after the infection.

Extraction of Cell-Wall Polysaccharide Antigen from Streptococci

PubMed Central

Slade, Hutton D.

1965-01-01

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

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

PubMed

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

2014-02-01

In this paper, we address the retrieval of multi-modality medical volumes, which consist of two different imaging modalities, acquired sequentially, from the same scanner. One such example, positron emission tomography and computed tomography (PET-CT), provides physicians with complementary functional and anatomical features as well as spatial relationships and has led to improved cancer diagnosis, localisation, and staging. The challenge of multi-modality volume retrieval for cancer patients lies in representing the complementary geometric and topologic attributes between tumours and organs. These attributes and relationships, which are used for tumour staging and classification, can be formulated as a graph. It has been demonstrated that graph-based methods have high accuracy for retrieval by spatial similarity. However, naïvely representing all relationships on a complete graph obscures the structure of the tumour-anatomy relationships. We propose a new graph structure derived from complete graphs that structurally constrains the edges connected to tumour vertices based upon the spatial proximity of tumours and organs. This enables retrieval on the basis of tumour localisation. We also present a similarity matching algorithm that accounts for different feature sets for graph elements from different imaging modalities. Our method emphasises the relationships between a tumour and related organs, while still modelling patient-specific anatomical variations. Constraining tumours to related anatomical structures improves the discrimination potential of graphs, making it easier to retrieve similar images based on tumour location. We evaluated our retrieval methodology on a dataset of clinical PET-CT volumes. Our results showed that our method enabled the retrieval of multi-modality images using spatial features. Our graph-based retrieval algorithm achieved a higher precision than several other retrieval techniques: gray-level histograms as well as state-of-the-art methods such as visual words using the scale- invariant feature transform (SIFT) and relational matrices representing the spatial arrangements of objects. Copyright © 2013 Elsevier B.V. All rights reserved.

Medical image retrieval system using multiple features from 3D ROIs

NASA Astrophysics Data System (ADS)

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

2012-02-01

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

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

NASA Astrophysics Data System (ADS)

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

2016-06-01

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

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 to estimate the retrieval uncertainty from sub-pixel reflectance variations in operational satellite cloud products and to help understand the differences in and re retrievals between two instruments.

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 framework can be used to estimate the retrieval uncertainty from subpixel reflectance variations in operational satellite cloud products and to help understand the differences in t and re retrievals between two instruments.

Multilayered Clouds Identification and Retrieval for CERES Using MODIS

NASA Technical Reports Server (NTRS)

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

2006-01-01

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

Isolation of Small SSEA-4-Positive Putative Stem Cells from the Ovarian Surface Epithelium of Adult Human Ovaries by Two Different Methods

PubMed Central

Virant-Klun, Irma; Skutella, Thomas; Hren, Matjaz; Gruden, Kristina; Cvjeticanin, Branko; Vogler, Andrej; Sinkovec, Jasna

2013-01-01

The adult ovarian surface epithelium has already been proposed as a source of stem cells and germinal cells in the literature, therefore it has been termed the “germinal epithelium”. At present more studies have confirmed the presence of stem cells expressing markers of pluripotency in adult mammalian ovaries, including humans. The aim of this study was to isolate a population of stem cells, based on the expression of pluripotency-related stage-specific embryonic antigen-4 (SSEA-4) from adult human ovarian surface epithelium by two different methods: magnetic-activated cell sorting and fluorescence-activated cell sorting. Both methods made it possible to isolate a similar, relatively homogenous population of small, SSEA-4-positive cells with diameters of up to 4 μm from the suspension of cells retrieved by brushing of the ovarian cortex biopsies in reproductive-age and postmenopausal women and in women with premature ovarian failure. The immunocytochemistry and genetic analyses revealed that these small cells—putative stem cells—expressed some primordial germ cell and pluripotency-related markers and might be related to the in vitro development of oocyte-like cells expressing some oocyte-specific transcription factors in the presence of donated follicular fluid with substances important for oocyte growth and development. The stemness of these cells needs to be further researched. PMID:23509763

Quality control of murine monoclonal antibodies using isoelectric focusing affinity immunoblot analysis

NASA Technical Reports Server (NTRS)

Hamilton, Robert G.; Rodkey, L. Scott; Reimer, Charles B.

1987-01-01

The quality control of murine hybridoma secretory products has been performed using two approaches for isoelectric focusing affinity immunoblot analysis: (1) a method in which antigen-coated nitrocellulose is placed on top of an acrylamide gel containing isoelectrically focused ascites to bind the antigen specific monoclonal antibody; and (2) a method in which focused ascite proteins were passively blotted onto nitrocellulose and specific monoclonal antibodies were detected with enzyme-conjugated antigen. Analysis by both methods of batches of ascites containing antihuman IgG antibodies that were produced by six hybridomas permitted effective monitoring of immunoreactive antibodies for pI microheterogeneity.

Spaced-antenna wind estimation using an X-band active phased-array weather radar

NASA Astrophysics Data System (ADS)

Venkatesh, Vijay

Over the past few decades, several single radar methods have been developed to probe the kinematic structure of storms. All these methods trade angular-resolution to retrieve the wind-field. To date, the spaced-antenna method has been employed for profiling the ionosphere and the precipitation free lower atmosphere. This work focuses on applying the spaced-antenna method on an X-band active phased-array radar for high resolution horizontal wind-field retrieval from precipitation echoes. The ability to segment the array face into multiple displaced apertures allows for flexible spaced-antenna implementations. The methodology employed herein comprises of Monte-Carlo simulations to optimize the spaced-antenna system design and analysis of real data collected with the designed phased-array system. The contribution that underpins this dissertation is the demonstration of qualitative agreement between spaced-antenna and Doppler beam swinging retrievals based on real data. First, simulations of backscattered electric fields at the antenna array elements are validated using theoretical expressions. Based on the simulations, the degrees of freedom in the spaced-antenna system design are optimized for retrieval of mean baseline wind. We show that the designed X-band spaced-antenna system has lower retrieval uncertainty than the existing S-band spaced-antenna implementation on the NWRT. This is because of the flexibility to synthesize small overlapping apertures and the ability to obtain statistically independent samples at a faster rate at X-band. We then demonstrate a technique to make relative phase-center displacement measurements based on simulations and real data from the phased-array spaced-antenna system. This simple method uses statistics of precipitation echoes and apriori beamwidth measurements to make field repeatable phase-center displacement measurements. Finally, we test the hypothesis that wind-field curvature effects are common to both the spaced-antenna and Doppler beam swinging methods. Based on a close-range winter storm data set, we find that the spaced-antenna and fine-resolution Doppler beam swinging retrievals are in qualitative agreement. The correlation between the spaced-antenna and fine-resolution Doppler beam swinging retrievals was 0.57. The lowered correlation coefficient was, in part, due to the high standard deviation of the DBS retrievals. At high wind-speeds, the spaced-antenna retrievals significantly departed from variational retrievals of mean baseline wind.

Towards a true aerosol-and-cloud retrieval scheme

NASA Astrophysics Data System (ADS)

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

2014-05-01

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

Breast Histopathological Image Retrieval Based on Latent Dirichlet Allocation.

PubMed

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

2017-07-01

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

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

NASA Astrophysics Data System (ADS)

Kemp, Z. D. C.

2018-04-01

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

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

PubMed Central

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

2004-01-01

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

Detection of Antigenic Variants of Subtype H3 Swine Influenza A Viruses from Clinical Samples.

PubMed

Martin, Brigitte E; Bowman, Andrew S; Li, Lei; Nolting, Jacqueline M; Smith, David R; Hanson, Larry A; Wan, Xiu-Feng

2017-04-01

A large population of genetically and antigenically diverse influenza A viruses (IAVs) are circulating among the swine population, playing an important role in influenza ecology. Swine IAVs not only cause outbreaks among swine but also can be transmitted to humans, causing sporadic infections and even pandemic outbreaks. Antigenic characterizations of swine IAVs are key to understanding the natural history of these viruses in swine and to selecting strains for effective vaccines. However, influenza outbreaks generally spread rapidly among swine, and the conventional methods for antigenic characterization require virus propagation, a time-consuming process that can significantly reduce the effectiveness of vaccination programs. We developed and validated a rapid, sensitive, and robust method, the polyclonal serum-based proximity ligation assay (polyPLA), to identify antigenic variants of subtype H3N2 swine IAVs. This method utilizes oligonucleotide-conjugated polyclonal antibodies and quantifies antibody-antigen binding affinities by quantitative reverse transcription-PCR (RT-PCR). Results showed the assay can rapidly detect H3N2 IAVs directly from nasal wash or nasal swab samples collected from laboratory-challenged animals or during influenza surveillance at county fairs. In addition, polyPLA can accurately separate the viruses at two contemporary swine IAV antigenic clusters (H3N2 swine IAV-α and H3N2 swine IAV-ß) with a sensitivity of 84.9% and a specificity of 100.0%. The polyPLA can be routinely used in surveillance programs to detect antigenic variants of influenza viruses and to select vaccine strains for use in controlling and preventing disease in swine. Copyright © 2017 American Society for Microbiology.

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

PubMed

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

2017-10-25

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

Database-Centric Method for Automated High-Throughput Deconvolution and Analysis of Kinetic Antibody Screening Data.

PubMed

Nobrega, R Paul; Brown, Michael; Williams, Cody; Sumner, Chris; Estep, Patricia; Caffry, Isabelle; Yu, Yao; Lynaugh, Heather; Burnina, Irina; Lilov, Asparouh; Desroches, Jordan; Bukowski, John; Sun, Tingwan; Belk, Jonathan P; Johnson, Kirt; Xu, Yingda

2017-10-01

The state-of-the-art industrial drug discovery approach is the empirical interrogation of a library of drug candidates against a target molecule. The advantage of high-throughput kinetic measurements over equilibrium assessments is the ability to measure each of the kinetic components of binding affinity. Although high-throughput capabilities have improved with advances in instrument hardware, three bottlenecks in data processing remain: (1) intrinsic molecular properties that lead to poor biophysical quality in vitro are not accounted for in commercially available analysis models, (2) processing data through a user interface is time-consuming and not amenable to parallelized data collection, and (3) a commercial solution that includes historical kinetic data in the analysis of kinetic competition data does not exist. Herein, we describe a generally applicable method for the automated analysis, storage, and retrieval of kinetic binding data. This analysis can deconvolve poor quality data on-the-fly and store and organize historical data in a queryable format for use in future analyses. Such database-centric strategies afford greater insight into the molecular mechanisms of kinetic competition, allowing for the rapid identification of allosteric effectors and the presentation of kinetic competition data in absolute terms of percent bound to antigen on the biosensor.

Geometry Dynamics of α-Helices in Different Class I Major Histocompatibility Complexes

PubMed Central

Karch, Rudolf; Schreiner, Wolfgang

2015-01-01

MHC α-helices form the antigen-binding cleft and are of particular interest for immunological reactions. To monitor these helices in molecular dynamics simulations, we applied a parsimonious fragment-fitting method to trace the axes of the α-helices. Each resulting axis was fitted by polynomials in a least-squares sense and the curvature integral was computed. To find the appropriate polynomial degree, the method was tested on two artificially modelled helices, one performing a bending movement and another a hinge movement. We found that second-order polynomials retrieve predefined parameters of helical motion with minimal relative error. From MD simulations we selected those parts of α-helices that were stable and also close to the TCR/MHC interface. We monitored the curvature integral, generated a ruled surface between the two MHC α-helices, and computed interhelical area and surface torsion, as they changed over time. We found that MHC α-helices undergo rapid but small changes in conformation. The curvature integral of helices proved to be a sensitive measure, which was closely related to changes in shape over time as confirmed by RMSD analysis. We speculate that small changes in the conformation of individual MHC α-helices are part of the intrinsic dynamics induced by engagement with the TCR. PMID:26649324

75 FR 22813 - Guidance for Industry: Requalification Method for Reentry of Blood Donors Deferred Because of...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-30

... Results for Antibody to Hepatitis B Core Antigen (Anti-HBc); Availability AGENCY: Food and Drug... Deferred Because of Reactive Test Results for Antibody to Hepatitis B Core Antigen (Anti- HBc),'' dated May... were repeatedly reactive for antibodies to hepatitis B core antigen (anti-HBc) were falsely positive...

Transfusion Medicine and Molecular Genetic Methods

PubMed Central

Saleh, Rozieyati Mohamed; Zefarina, Zulkafli; Che Mat, Nor Fazila; Chambers, Geoffrey Keith; Edinur, Hisham Atan

2018-01-01

Transfusion procedures are always complicated by potential genetic mismatching between donor and recipient. Compatibility is determined by several major antigens, such as the ABO and Rhesus blood groups. Matching for other blood groups (Kell, Kidd, Duffy, and MNS), human platelet antigens, and human leukocyte antigens (HLAs) also contributes toward the successful transfusion outcomes, especially in multitransfused or highly immunized patients. All these antigens of tissue identity are highly polymorphic and thus present great challenges for finding suitable donors for transfusion patients. The ABO blood group and HLA markers are also the determinants of transplant compatibility, and mismatched antigens will cause graft rejection or graft-versus-host disease. Thus, a single and comprehensive registry covering all of the significant transfusion and transplantation antigens is expected to become an important tool in providing an efficient service capable of delivering safe blood and quickly locating matching organs/stem cells. This review article is intended as an accessible guide for physicians who care for transfusion-dependent patients. In particular, it serves to introduce the new molecular screening methods together with the biology of these systems, which underlies the tests. PMID:29899883

System and method for a parallel immunoassay system

DOEpatents

Stevens, Fred J.

2002-01-01

A method and system for detecting a target antigen using massively parallel immunoassay technology. In this system, high affinity antibodies of the antigen are covalently linked to small beads or particles. The beads are exposed to a solution containing DNA-oligomer-mimics of the antigen. The mimics which are reactive with the covalently attached antibody or antibodies will bind to the appropriate antibody molecule on the bead. The particles or beads are then washed to remove any unbound DNA-oligomer-mimics and are then immobilized or trapped. The bead-antibody complexes are then exposed to a test solution which may contain the targeted antigens. If the antigen is present it will replace the mimic since it has a greater affinity for the respective antibody. The particles are then removed from the solution leaving a residual solution. This residual solution is applied a DNA chip containing many samples of complimentary DNA. If the DNA tag from a mimic binds with its complimentary DNA, it indicates the presence of the target antigen. A flourescent tag can be used to more easily identify the bound DNA tag.

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.

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

PubMed

Li, Changwei; Li, Bangming; Zhang, Sijiong

2014-02-01

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

Content-Based Medical Image Retrieval

NASA Astrophysics Data System (ADS)

Müller, Henning; Deserno, Thomas M.

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

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

NASA Astrophysics Data System (ADS)

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

2018-06-01

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

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

PubMed

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

2004-10-01

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

Inference of Genotype–Phenotype Relationships in the Antigenic Evolution of Human Influenza A (H3N2) Viruses

PubMed Central

Steinbrück, Lars; McHardy, Alice Carolyn

2012-01-01

Distinguishing mutations that determine an organism's phenotype from (near-) neutral ‘hitchhikers’ is a fundamental challenge in genome research, and is relevant for numerous medical and biotechnological applications. For human influenza viruses, recognizing changes in the antigenic phenotype and a strains' capability to evade pre-existing host immunity is important for the production of efficient vaccines. We have developed a method for inferring ‘antigenic trees’ for the major viral surface protein hemagglutinin. In the antigenic tree, antigenic weights are assigned to all tree branches, which allows us to resolve the antigenic impact of the associated amino acid changes. Our technique predicted antigenic distances with comparable accuracy to antigenic cartography. Additionally, it identified both known and novel sites, and amino acid changes with antigenic impact in the evolution of influenza A (H3N2) viruses from 1968 to 2003. The technique can also be applied for inference of ‘phenotype trees’ and genotype–phenotype relationships from other types of pairwise phenotype distances. PMID:22532796

Standardization and validation of a cytometric bead assay to assess antibodies to multiple Plasmodium falciparum recombinant antigens

PubMed Central

2012-01-01

Background Multiplex cytometric bead assay (CBA) have a number of advantages over ELISA for antibody testing, but little information is available on standardization and validation of antibody CBA to multiple Plasmodium falciparum antigens. The present study was set to determine optimal parameters for multiplex testing of antibodies to P. falciparum antigens, and to compare results of multiplex CBA to ELISA. Methods Antibodies to ten recombinant P. falciparum antigens were measured by CBA and ELISA in samples from 30 individuals from a malaria endemic area of Kenya and compared to known positive and negative control plasma samples. Optimal antigen amounts, monoplex vs multiplex testing, plasma dilution, optimal buffer, number of beads required were assessed for CBA testing, and results from CBA vs. ELISA testing were compared. Results Optimal amounts for CBA antibody testing differed according to antigen. Results for monoplex CBA testing correlated strongly with multiplex testing for all antigens (r = 0.88-0.99, P values from <0.0001 - 0.004), and antibodies to variants of the same antigen were accurately distinguished within a multiplex reaction. Plasma dilutions of 1:100 or 1:200 were optimal for all antigens for CBA testing. Plasma diluted in a buffer containing 0.05% sodium azide, 0.5% polyvinylalcohol, and 0.8% polyvinylpyrrolidone had the lowest background activity. CBA median fluorescence intensity (MFI) values with 1,000 antigen-conjugated beads/well did not differ significantly from MFI with 5,000 beads/well. CBA and ELISA results correlated well for all antigens except apical membrane antigen-1 (AMA-1). CBA testing produced a greater range of values in samples from malaria endemic areas and less background reactivity for blank samples than ELISA. Conclusion With optimization, CBA may be the preferred method of testing for antibodies to P. falciparum antigens, as CBA can test for antibodies to multiple recombinant antigens from a single plasma sample and produces a greater range of values in positive samples and lower background readings for blank samples than ELISA. PMID:23259607

42 CFR 71.53 - Requirements for importers of nonhuman primates.

Code of Federal Regulations, 2014 CFR

2014-10-01

... Trade in Endangered Species. ELISA means enzyme-linked immunosorbent assay, a type of laboratory test... serum for immunoglobulin G (IgG) antibodies to filovirus by using an ELISA methodology, or other method... for filovirus antigen by using the antigen-capture ELISA method must be submitted to a qualified...

42 CFR 71.53 - Requirements for importers of nonhuman primates.

Code of Federal Regulations, 2013 CFR

2013-10-01

... Trade in Endangered Species. ELISA means enzyme-linked immunosorbent assay, a type of laboratory test... serum for immunoglobulin G (IgG) antibodies to filovirus by using an ELISA methodology, or other method... for filovirus antigen by using the antigen-capture ELISA method must be submitted to a qualified...

Current Research into Chemical and Textual Information Retrieval at the Department of Information Studies, University of Sheffield.

ERIC Educational Resources Information Center

Lynch, Michael F.; Willett, Peter

1987-01-01

Discusses research into chemical information and document retrieval systems at the University of Sheffield. Highlights include the use of cluster analysis methods for document retrieval and drug design, representation and searching of files of generic chemical structures, and the application of parallel computer hardware to information retrieval.…

Prolonged expression of MHC class I - peptide expression in bone marrow derived retrovirus transfected matured dendritic cells by continuous centrifugation in the presence of IL-4.

PubMed

Hettihewa, L M

2011-11-01

Dendritic cells (DCs) are potent antigen presenting cells which proceed from immature to a mature stage during their differentiation. There are several methods of obtaining long lasting mature antigen expressing DCs and different methods show different levels of antigen expressions. We investigated bone marrow derived DCs for the degree of maturation and genetically engineered antigen presentation in the presence of interleukin-4 (IL-4) as a maturity enhancer. DCs and transfected retrovirus were cultured together in the presence of granulocyte-macrophage colony stimulating factor (GMCSF)-IL4, GMCSF +IL4, lipopolysaccharide (LPS). B 7.1, B7.2 and CD11c were measured by the degree of immune fluorescence using enhanced green fluorescent protein (EGFP) shuttled retrovirus transfected antigen. Degree of MHC class I molecule with antigen presentation of antigen was also evaluated by fluorescence activated cell sorting. The antigen presenting capacity of transfected DCs was investigated. Bone marrow DCs were generated in the presence of GMCSF and IL-4 in vitro. Dividing bone marrow cells were infected with EGFP shuttled retrovirus expressing SSP2 by prolonged centrifugation for three consecutive days from day 5, 6 and 7 and continued to culture in the presence of GMSCF and IL-4 until day 8. IL-4 as a cytokine increased the maturation of retrovirus transfected DCs by high expression of B 7-1 and B 7-2. Also, IL-4 induced DC enhanced by the prolonged centrifugation and it was shown by increased antigen presentation of these dendric cells as antigen presenting cell (APC). Cytolytic effects were significantly higher in cytotoxic T cell response (CTLs) mixed with transfected DCs than CTLs mixed with pulsed DCs. There was an enhanced antigen presentation by prolonged expression of antigen loaded MHC class I receptors in DCs in the presence of IL-4 by prolonged centrifugation.

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

NASA Astrophysics Data System (ADS)

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

2000-05-01

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

Cloud Property Retrieval Products for Graciosa Island, Azores

DOE Data Explorer

Dong, Xiquan

2014-05-05

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

Oriented Immobilization of Fab Fragments by Site-Specific Biotinylation at the Conserved Nucleotide Binding Site for Enhanced Antigen Detection.

PubMed

Mustafaoglu, Nur; Alves, Nathan J; Bilgicer, Basar

2015-09-08

Oriented immobilization of antibodies and antibody fragments has become increasingly important as a result of the efforts to reduce the size of diagnostic and sensor devices to miniaturized dimensions for improved accessibility to the end-user. Reduced dimensions of sensor devices necessitate the immobilized antibodies to conserve their antigen binding activity for proper operation. Fab fragments are becoming more commonly used in small-scaled diagnostic devices due to their small size and ease of manufacture. In this study, we used the previously described UV-NBS(Biotin) method to functionalize Fab fragments with IBA-EG11-Biotin linker utilizing UV energy to initiate a photo-cross-linking reaction between the nucleotide binding site (NBS) on the Fab fragment and IBA-Biotin molecule. Our results demonstrate that immobilization of biotinylated Fab fragments via UV-NBS(Biotin) method generated the highest level of immobilized Fab on surfaces when compared to other typical immobilization methods while preserving antigen binding activity. UV-NBS(Biotin) method provided 432-fold, 114-fold, and 29-fold improved antigen detection sensitivity than physical adsorption, NHS-Biotin, and ε-NH3(+), methods, respectively. Additionally, the limit of detection (LOD) for PSA utilizing Fab fragments immobilized via UV-NBS(Biotin) method was significantly lower than that of the other immobilization methods, with an LOD of 0.4 pM PSA. In summary, site-specific biotinylation of Fab fragments without structural damage or loss in antigen binding activity provides a wide range of application potential for UV-NBS immobilization technique across numerous diagnostic devices and nanotechnologies.

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

NASA Technical Reports Server (NTRS)

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

1975-01-01

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

Aerosol Optical Retrieval and Surface Reflectance from Airborne Remote Sensing Data over Land

PubMed Central

Bassani, Cristiana; Cavalli, Rosa Maria; Pignatti, Stefano

2010-01-01

Quantitative analysis of atmospheric optical properties and surface reflectance can be performed by applying radiative transfer theory in the Atmosphere-Earth coupled system, for the atmospheric correction of hyperspectral remote sensing data. This paper describes a new physically-based algorithm to retrieve the aerosol optical thickness at 550nm (τ550) and the surface reflectance (ρ) from airborne acquired data in the atmospheric window of the Visible and Near-Infrared (VNIR) range. The algorithm is realized in two modules. Module A retrieves τ550 with a minimization algorithm, then Module B retrieves the surface reflectance ρ for each pixel of the image. The method was tested on five remote sensing images acquired by an airborne sensor under different geometric conditions to evaluate the reliability of the method. The results, τ550 and ρ, retrieved from each image were validated with field data contemporaneously acquired by a sun-sky radiometer and a spectroradiometer, respectively. Good correlation index, r, and low root mean square deviations, RMSD, were obtained for the τ550 retrieved by Module A (r2 = 0.75, RMSD = 0.08) and the ρ retrieved by Module B (r2 ≤ 0.9, RMSD ≤ 0.003). Overall, the results are encouraging, indicating that the method is reliable for optical atmospheric studies and the atmospheric correction of airborne hyperspectral images. The method does not require additional at-ground measurements about at-ground reflectance of the reference pixel and aerosol optical thickness. PMID:22163558

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.

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

PubMed

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

2010-03-01

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

Isolation and Characterization of Circulating Tumor Cells in Squamous Cell Carcinoma of the Lung Using a Non-EpCAM-Based Capture Method.

PubMed

Bozzetti, Cecilia; Quaini, Federico; Squadrilli, Anna; Tiseo, Marcello; Frati, Caterina; Lagrasta, Costanza; Azzoni, Cinzia; Bottarelli, Lorena; Galetti, Maricla; Alama, Angela; Belletti, Silvana; Gatti, Rita; Passaro, Antonio; Gradilone, Angela; Cavazzoni, Andrea; Alfieri, Roberta; Petronini, Pier Giorgio; Bonelli, Mara; Falco, Angela; Carubbi, Cecilia; Pedrazzi, Giuseppe; Nizzoli, Rita; Naldi, Nadia; Pinto, Carmine; Ardizzoni, Andrea

2015-01-01

The exclusion of circulating tumor cells (CTCs) that have lost epithelial antigens during the epithelial-to-mesenchymal transition (EMT) process by using Epithelial Cell Adhesion Molecule (EpCAM) based capture methods is still a matter of debate. In this study, cells obtained after depletion procedure from blood samples of squamous cell lung cancer (SQCLC) patients were identified based on morphology and characterized with the combination of FISH assessment and immunophenotypic profile. Five mL blood samples, collected from 55 advanced SQCLC patients, were analyzed by a non-EpCAM-based capture method. After depletion of leukocytes and erythroid cells, the negative fraction was characterized by both FISH using a fibroblast growth factor receptor 1 (FGFR1) probe and by immunocytochemistry. Thirty healthy donors were also tested. Based on morphology (nuclear dimension ≥10 μm, shape and hypercromatic aspect) suspicious circulating cells clearly distinguishable from contaminant leukocytes were observed in 49/55 (89%) SQCLC patients. Thirty-four of the 44 (77%) samples evaluable for FGFR1 FISH showed ≥ 6 FGFR1 gene copy number on average per cell. Vimentin expression involved 43% (18/42) of pooled circulating SQCLC cells, whereas only 29% (14/48) were EpCAM positive. Confocal microscopy confirmed the localization of FGFR1 probe in suspicious circulating cells. Suspicious circulating elements were also observed in healthy donors and did not show any epithelial associated antigens. A significantly lower number of suspicious circulating cells in healthy donors compared to SQCLC patients was found. Among the heterogeneous cell population isolated by depletion procedure, the coexistence of cells with epithelial and/or mesenchymal phenotype suggests that EMT may participate to transendothelial invasion and migration of tumor cells in advanced SQCLC. The finding of cells with neither EpCAM or EMT phenotype, retrieved after non-EpCAM-based systems, underlines the presence of suspicious elements in the blood of both SQCLC patients and healthy donors. Further phenotyping and molecular analyses are necessary to fully characterize these circulating elements.

Investigation of Atmospheric Effects on Retrieval of Sun-Induced Fluorescence Using Hyperspectral Imagery.

PubMed

Ni, Zhuoya; Liu, Zhigang; Li, Zhao-Liang; Nerry, Françoise; Huo, Hongyuan; Sun, Rui; Yang, Peiqi; Zhang, Weiwei

2016-04-06

Significant research progress has recently been made in estimating fluorescence in the oxygen absorption bands, however, quantitative retrieval of fluorescence data is still affected by factors such as atmospheric effects. In this paper, top-of-atmosphere (TOA) radiance is generated by the MODTRAN 4 and SCOPE models. Based on simulated data, sensitivity analysis is conducted to assess the sensitivities of four indicators-depth_absorption_band, depth_nofs-depth_withfs, radiance and Fs/radiance-to atmospheric parameters (sun zenith angle (SZA), sensor height, elevation, visibility (VIS) and water content) in the oxygen absorption bands. The results indicate that the SZA and sensor height are the most sensitive parameters and that variations in these two parameters result in large variations calculated as the variation value/the base value in the oxygen absorption depth in the O₂-A and O₂-B bands (111.4% and 77.1% in the O₂-A band; and 27.5% and 32.6% in the O₂-B band, respectively). A comparison of fluorescence retrieval using three methods (Damm method, Braun method and DOAS) and SCOPE Fs indicates that the Damm method yields good results and that atmospheric correction can improve the accuracy of fluorescence retrieval. Damm method is the improved 3FLD method but considering atmospheric effects. Finally, hyperspectral airborne images combined with other parameters (SZA, VIS and water content) are exploited to estimate fluorescence using the Damm method and 3FLD method. The retrieval fluorescence is compared with the field measured fluorescence, yielding good results (R² = 0.91 for Damm vs. SCOPE SIF; R² = 0.65 for 3FLD vs. SCOPE SIF). Five types of vegetation, including ailanthus, elm, mountain peach, willow and Chinese ash, exhibit consistent associations between the retrieved fluorescence and field measured fluorescence.

Investigation of Atmospheric Effects on Retrieval of Sun-Induced Fluorescence Using Hyperspectral Imagery

PubMed Central

Ni, Zhuoya; Liu, Zhigang; Li, Zhao-Liang; Nerry, Françoise; Huo, Hongyuan; Sun, Rui; Yang, Peiqi; Zhang, Weiwei

2016-01-01

Significant research progress has recently been made in estimating fluorescence in the oxygen absorption bands, however, quantitative retrieval of fluorescence data is still affected by factors such as atmospheric effects. In this paper, top-of-atmosphere (TOA) radiance is generated by the MODTRAN 4 and SCOPE models. Based on simulated data, sensitivity analysis is conducted to assess the sensitivities of four indicators—depth_absorption_band, depth_nofs-depth_withfs, radiance and Fs/radiance—to atmospheric parameters (sun zenith angle (SZA), sensor height, elevation, visibility (VIS) and water content) in the oxygen absorption bands. The results indicate that the SZA and sensor height are the most sensitive parameters and that variations in these two parameters result in large variations calculated as the variation value/the base value in the oxygen absorption depth in the O2-A and O2-B bands (111.4% and 77.1% in the O2-A band; and 27.5% and 32.6% in the O2-B band, respectively). A comparison of fluorescence retrieval using three methods (Damm method, Braun method and DOAS) and SCOPE Fs indicates that the Damm method yields good results and that atmospheric correction can improve the accuracy of fluorescence retrieval. Damm method is the improved 3FLD method but considering atmospheric effects. Finally, hyperspectral airborne images combined with other parameters (SZA, VIS and water content) are exploited to estimate fluorescence using the Damm method and 3FLD method. The retrieval fluorescence is compared with the field measured fluorescence, yielding good results (R2 = 0.91 for Damm vs. SCOPE SIF; R2 = 0.65 for 3FLD vs. SCOPE SIF). Five types of vegetation, including ailanthus, elm, mountain peach, willow and Chinese ash, exhibit consistent associations between the retrieved fluorescence and field measured fluorescence. PMID:27058542

Derivation of Aerosol Columnar Mass from MODIS Optical Depth

NASA Technical Reports Server (NTRS)

Gasso, Santiago; Hegg, Dean A.

2003-01-01

In order to verify performance, aerosol transport models (ATM) compare aerosol columnar mass (ACM) with those derived from satellite measurements. The comparison is inherently indirect since satellites derive optical depths and they use a proportionality constant to derive the ACM. Analogously, ATMs output a four dimensional ACM distribution and the optical depth is linearly derived. In both cases, the proportionality constant requires a direct intervention of the user by prescribing the aerosol composition and size distribution. This study introduces a method that minimizes the direct user intervention by making use of the new aerosol products of MODIS. A parameterization is introduced for the derivation of columnar aerosol mass (AMC) and CCN concentration (CCNC) and comparisons between sunphotometer, MODIS Airborne Simulator (MAS) and in-measurements are shown. The method still relies on the scaling between AMC and optical depth but the proportionality constant is dependent on the MODIS derived r$_{eff}$,\\eta (contribution of the accumulation mode radiance to the total radiance), ambient RH and an assumed constant aerosol composition. The CCNC is derived fkom a recent parameterization of CCNC as a function of the retrieved aerosol volume. By comparing with in-situ data (ACE-2 and TARFOX campaigns), it is shown that retrievals in dry ambient conditions (dust) are improved when using a proportionality constant dependent on r$ {eff}$ and \\eta derived in the same pixel. In high humidity environments, the improvement inthe new method is inconclusive because of the difficulty in accounting for the uneven vertical distribution of relative humidity. Additionally, two detailed comparisons of AMC and CCNC retrieved by the MAS algorithm and the new method are shown. The new method and MAS retrievals of AMC are within the same order of magnitude with respect to the in-situ measurements of aerosol mass. However, the proposed method is closer to the in-situ measurements than the MODIS retrievals. The retrievals of CCNC are also within the same order of magnitude for both methods. The new method is applied to an actual MODIS retrieval and although no in-situ data is available to compare, it is shown that the proposed method yields more credible values than the MODIS retrievals. In addition, recent data available from the PRIDE (Puerto Rico Dust Experiment, July 2000) will be shown by comparing sunphotometer, MODIS and in-situ data.

BIBLIO: A Computerized Retrieval System for Communication Education.

ERIC Educational Resources Information Center

Williams, M. Lee; Edwards, Renee

1983-01-01

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

[Regression analysis to select native-like structures from decoys of antigen-antibody docking].

PubMed

Chen, Zhengshan; Chi, Xiangyang; Fan, Pengfei; Zhang, Guanying; Wang, Meirong; Yu, Changming; Chen, Wei

2018-06-25

Given the increasing exploitation of antibodies in different contexts such as molecular diagnostics and therapeutics, it would be beneficial to unravel properties of antigen-antibody interaction with modeling of computational protein-protein docking, especially, in the absence of a cocrystal structure. However, obtaining a native-like antigen-antibody structure remains challenging due in part to failing to reliably discriminate accurate from inaccurate structures among tens of thousands of decoys after computational docking with existing scoring function. We hypothesized that some important physicochemical and energetic features could be used to describe antigen-antibody interfaces and identify native-like antigen-antibody structure. We prepared a dataset, a subset of Protein-Protein Docking Benchmark Version 4.0, comprising 37 nonredundant 3D structures of antigen-antibody complexes, and used it to train and test multivariate logistic regression equation which took several important physicochemical and energetic features of decoys as dependent variables. Our results indicate that the ability to identify native-like structures of our method is superior to ZRANK and ZDOCK score for the subset of antigen-antibody complexes. And then, we use our method in workflow of predicting epitope of anti-Ebola glycoprotein monoclonal antibody-4G7 and identify three accurate residues in its epitope.

Corrected Panel-Reactive Antibody Positivity Rates for Hypersensitized Patients in Turkish Population With Calculated Panel-Reactive Antibody Software.

PubMed

Karadeniz, S T; Akgul, S U; Ogret, Y; Ciftci, H S; Bayraktar, A; Bakkaloglu, H; Caliskan, Y; Yelekci, K; Turkmen, A; Aydin, A E; Oguz, F S; Carin, M; Aydin, F

2017-04-01

High rates of panel-reactive antibody (PRA) may decrease the chance of kidney transplantation and may result in long waiting periods before transplantation. The calculated PRA (cPRA) is performed based on unacceptable HLA antigens. These antigens are identified by a program that was created based on the antibodies that developed against the HLA antigens circulating in serum and on the risk of binding of these antibodies to antigens. The antigen profile of the population and antigen frequencies can be measured, and more realistic cPRA positivity rates may be obtained using this method. We developed a program based on the HLA antigens of 494 blood donors in 2 European Federation for Immunogenetics-accredited Tissue Typing Laboratories in Turkey. Next-generation sequencing-based tissue typing (HLA-A, -B, -C, -DR, -DQ, 4 digits) of the samples was performed. The PRA screening test was performed on 380 patients who were waiting for organ transplant from a cadaver in Istanbul Faculty of Medicine. The single antigen bead assay testing was performed to identify the antibody profiles on 48 hypersensitized patients. The PRA testing results using the current methods were 44.6% ± 18.5%, and the cPRA rate was 86.2% ± 5.1%. The mean PRA positivity of the sensitized patients using the current methods was 44.6%; however, the rate was 86.2% using the cPRA. cPRA shows the rate of the rejected donors according to all unacceptable antigens. The need for a list of unacceptable antigens in place of the PRA positivity rate is a real change in the sensitization-dependent calculation as cPRA positivity rate. In principal, implementation of cPRA will encourage many centers and laboratories to adopt a standard measurement of sensitization in Turkey. It will increase the chances of better donor match, particularly for hypersensitized patients, by the creation of an unacceptable mismatch program using cPRA software. Copyright © 2017 Elsevier Inc. All rights reserved.

Immune responses to vaccines delivered by encapsulation into and/or adsorption onto cationic lipid-PLGA hybrid nanoparticles.

PubMed

Liu, Lanxia; Ma, Pingchuan; Wang, Hai; Zhang, Chao; Sun, Hongfan; Wang, Chun; Song, Cunxian; Leng, Xigang; Kong, Deling; Ma, Guilei

2016-03-10

In this study, we used cationic lipid-poly(lactide-co-glycolide) acid (PLGA) hybrid nanoparticles as antigen delivery carriers to investigate how antigen-loading methods affect antigen exposure to the immune system and evaluated the resulting antigen-specific immune responses. We formulated three classes of antigen adsorbed and/or encapsulated cationic lipid-PLGA hybrid nanoparticles; we designated antigen-adsorbed (out), antigen-encapsulated (in), and antigen-adsorbed/encapsulated (both) nanoparticles. Our results demonstrate significantly more efficient lysosomal escape and cross-presentation of antigen from dendritic cells (DCs) that were exposed to "both" and "in" nanoparticles. In vivo experiments further revealed that "both" nanoparticles significantly more effectively provided not only adequate initial antigen exposure but also long-term antigen persistence at the injection site. Data from flow cytometry and ELISA analyses demonstrated elevated in vivo immune responses from mice that were immunized with nanoparticles-delivered OVA when compared with free OVA. In addition, "in" and "both" nanoparticles elicited significantly higher antigen-specific immune response than "out" nanoparticles and free OVA. These results suggest that the location of antigen entrapment is an important factor in modulating the immune responses of antigens delivered by nanoparticles. Overall, we propose here a promising approach for the future design of vaccines using cationic lipid-PLGA nanoparticles. Copyright © 2016 Elsevier B.V. All rights reserved.

[The progress in retrieving land surface temperature based on thermal infrared and microwave remote sensing technologies].

PubMed

Zhang, Jia-Hua; Li, Xin; Yao, Feng-Mei; Li, Xian-Hua

2009-08-01

Land surface temperature (LST) is an important parameter in the study on the exchange of substance and energy between land surface and air for the land surface physics process at regional and global scales. Many applications of satellites remotely sensed data must provide exact and quantificational LST, such as drought, high temperature, forest fire, earthquake, hydrology and the vegetation monitor, and the models of global circulation and regional climate also need LST as input parameter. Therefore, the retrieval of LST using remote sensing technology becomes one of the key tasks in quantificational remote sensing study. Normally, in the spectrum bands, the thermal infrared (TIR, 3-15 microm) and microwave bands (1 mm-1 m) are important for retrieval of the LST. In the present paper, firstly, several methods for estimating the LST on the basis of thermal infrared (TIR) remote sensing were synthetically reviewed, i. e., the LST measured with an ground-base infrared thermometer, the LST retrieval from mono-window algorithm (MWA), single-channel algorithm (SCA), split-window techniques (SWT) and multi-channels algorithm(MCA), single-channel & multi-angle algorithm and multi-channels algorithm & multi-angle algorithm, and retrieval method of land surface component temperature using thermal infrared remotely sensed satellite observation. Secondly, the study status of land surface emissivity (epsilon) was presented. Thirdly, in order to retrieve LST for all weather conditions, microwave remotely sensed data, instead of thermal infrared data, have been developed recently, and the LST retrieval method from passive microwave remotely sensed data was also introduced. Finally, the main merits and shortcomings of different kinds of LST retrieval methods were discussed, respectively.

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

NASA Astrophysics Data System (ADS)

Jain, Yogendra Kumar; Singh, Roshan Kumar

2013-12-01

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

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

PubMed

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

2017-11-27

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

INFECTIOUS MYXOMATOSIS OF RABBITS

PubMed Central

Smadel, Joseph E.; Ward, S. M.; Rivers, Thomas M.

1940-01-01

A second soluble antigen, separable from the virus, occurs in extracts of infected skin and in the serum of rabbits acutely ill with infectious myxomatosis. Like the first antigen (A), the second (B) is heat labile and has certain characteristics of a globulin. The two antigens precipitate in different concentrations of ammonium sulfate and can be separated by this method. Neither of the antigens after being heated at 56°C. precipitates in the presence of specific antibody but each is capable of inhibiting the activity of its antibody. PMID:19871012

Induction of human antigen-specific suppressor factors in vitro.

PubMed Central

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

1981-01-01

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

[Retrieve of red tide distributions from MODIS data based on the characteristics of water spectrum].

PubMed

Qiu, Zhong-Feng; Cui, Ting-Wei; He, Yi-Jun

2011-08-01

After comparing the spectral differences between red tide water and normal water, we developed a method to retrieve red tide distributions from MODIS data based on the characteristics of red tide water spectrum. The authors used the 119 series of in situ observations to validate the method and found that only one observation has not been detected correctly. The authors then applied this method to MODIS data on April 4, 2005. In the research areas three locations of red tide water were apparently detected with the total areas about 2 000 km2. The retrieved red tide distributions are in good agreement with the distributions of high chlorophyll a concentrations. The research suggests that the method is available to eliminating the influence of suspended sediments and can be used to retrieve the locations and areas of red tide water.

BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes

PubMed Central

Jespersen, Martin Closter; Peters, Bjoern

2017-01-01

Abstract Antibodies have become an indispensable tool for many biotechnological and clinical applications. They bind their molecular target (antigen) by recognizing a portion of its structure (epitope) in a highly specific manner. The ability to predict epitopes from antigen sequences alone is a complex task. Despite substantial effort, limited advancement has been achieved over the last decade in the accuracy of epitope prediction methods, especially for those that rely on the sequence of the antigen only. Here, we present BepiPred-2.0 (http://www.cbs.dtu.dk/services/BepiPred/), a web server for predicting B-cell epitopes from antigen sequences. BepiPred-2.0 is based on a random forest algorithm trained on epitopes annotated from antibody-antigen protein structures. This new method was found to outperform other available tools for sequence-based epitope prediction both on epitope data derived from solved 3D structures, and on a large collection of linear epitopes downloaded from the IEDB database. The method displays results in a user-friendly and informative way, both for computer-savvy and non-expert users. We believe that BepiPred-2.0 will be a valuable tool for the bioinformatics and immunology community. PMID:28472356

Investigation of vesicle-capsular plague antigen complex formation by elastic laser radiation scattering

NASA Astrophysics Data System (ADS)

Guseva, N. P.; Maximova, Irina S.; Romanov, Sergey V.; Shubochkin, L. P.; Tatarintsev, Sergey N.

1991-05-01

Recently a great deal of attention has been given to the investigation artificial lipid liposomes, due to their application as "containers" for directed transport of biologically active compounds into particular cells, organs and tissues for prophylaxis and therapy of infectious diseases. The use of traditional methods of liposome investigation, such as sedimentation, electrophoresis and chromatography is impeded by low liposome resistivity to different deformations. In conjunction with this, optical methods of laser light scattering are promising as they allow nondisturbing, precise and quick investigations. This paper describes the investigation of vesicle systems prepared from egg lecithin of Serva Corporation and their complexes with the capsular antigen of the plague microbe. The capsular antigen Fl was obtained from EV plague microbe grown at 37° C on Huttinger agar. Fl was isolated by gel-filtration on ASA-22 followed by freeze drying of the preparation. Angular dependences of polarized radiation scattering were measured for several liposome suspension samples in a saline solution before and after the interaction with the plague microbe capsular antigen. The aim of the investigation was to analyze the nature of mutual antigen arrangement in a liposome and to develop methods for measuring its inclusion percentage.

High speed phase retrieval of in-line holograms by the assistance of corresponding off-axis holograms.

PubMed

Orzó, László

2015-06-29

Retrieving correct phase information from an in-line hologram is difficult as the object wave field and the diffractions of the zero order and the conjugate object term overlap. The existing iterative numerical phase retrieval methods are slow, especially in the case of high Fresnel number systems. Conversely, the reconstruction of the object wave field from an off-axis hologram is simple, but due to the applied spatial frequency filtering the achievable resolution is confined. Here, a new, high-speed algorithm is introduced that efficiently incorporates the data of an auxiliary off-axis hologram in the phase retrieval of the corresponding in-line hologram. The efficiency of the introduced combined phase retrieval method is demonstrated by simulated and measured holograms.

Retrieval of seasonal dynamics of forest understory reflectance from semiarid to boreal forests using MODIS BRDF data

NASA Astrophysics Data System (ADS)

Pisek, Jan; Chen, Jing M.; Kobayashi, Hideki; Rautiainen, Miina; Schaepman, Michael E.; Karnieli, Arnon; Sprinstin, Michael; Ryu, Youngryel; Nikopensius, Maris; Raabe, Kairi

2016-03-01

Spatial and temporal patterns of forest background (understory) reflectance are crucial for retrieving biophysical parameters of forest canopies (overstory) and subsequently for ecosystem modeling. In this communication, we retrieved seasonal courses of understory normalized difference vegetation index (NDVI) from multiangular Moderate Resolution Imaging Spectroradiometer bidirectional reflectance distribution function (MODIS BRDF)/albedo data. We compared satellite-based seasonal courses of understory NDVI to understory NDVI values measured in different types of forests distributed along a wide latitudinal gradient (65.12°N-31.35°N). Our results indicated that the retrieval method performs well particularly over open forests of different types. We also demonstrated the limitations of the method for closed canopies, where the understory signal retrieval is much attenuated.

Ground-based remote sensing of thin clouds in the Arctic

NASA Astrophysics Data System (ADS)

Garrett, T. J.; Zhao, C.

2012-11-01

This paper describes a method for using interferometer measurements of downwelling thermal radiation to retrieve the properties of single-layer clouds. Cloud phase is determined from ratios of thermal emission in three "micro-windows" where absorption by water vapor is particularly small. Cloud microphysical and optical properties are retrieved from thermal emission in two micro-windows, constrained by the transmission through clouds of stratospheric ozone emission. Assuming a cloud does not approximate a blackbody, the estimated 95% confidence retrieval errors in effective radius, visible optical depth, number concentration, and water path are, respectively, 10%, 20%, 38% (55% for ice crystals), and 16%. Applied to data from the Atmospheric Radiation Measurement program (ARM) North Slope of Alaska - Adjacent Arctic Ocean (NSA-AAO) site near Barrow, Alaska, retrievals show general agreement with ground-based microwave radiometer measurements of liquid water path. Compared to other retrieval methods, advantages of this technique include its ability to characterize thin clouds year round, that water vapor is not a primary source of retrieval error, and that the retrievals of microphysical properties are only weakly sensitive to retrieved cloud phase. The primary limitation is the inapplicability to thicker clouds that radiate as blackbodies.

Cloud characterization and clear-sky correction from Landsat-7

USGS Publications Warehouse

Cahalan, Robert F.; Oreopoulos, L.; Wen, G.; Marshak, S.; Tsay, S. -C.; DeFelice, Tom

2001-01-01

Landsat, with its wide swath and high resolution, fills an important mesoscale gap between atmospheric variations seen on a few kilometer scale by local surface instrumentation and the global view of coarser resolution satellites such as MODIS. In this important scale range, Landsat reveals radiative effects on the few hundred-meter scale of common photon mean-free-paths, typical of scattering in clouds at conservative (visible) wavelengths, and even shorter mean-free-paths of absorptive (near-infrared) wavelengths. Landsat also reveals shadowing effects caused by both cloud and vegetation that impact both cloudy and clear-sky radiances. As a result, Landsat has been useful in development of new cloud retrieval methods and new aerosol and surface retrievals that account for photon diffusion and shadowing effects. This paper discusses two new cloud retrieval methods: the nonlocal independent pixel approximation (NIPA) and the normalized difference nadir radiance method (NDNR). We illustrate the improvements in cloud property retrieval enabled by the new low gain settings of Landsat-7 and difficulties found at high gains. Then, we review the recently developed “path radiance” method of aerosol retrieval and clear-sky correction using data from the Department of Energy Atmospheric Radiation Measurement (ARM) site in Oklahoma. Nearby clouds change the solar radiation incident on the surface and atmosphere due to indirect illumination from cloud sides. As a result, if clouds are nearby, this extra side-illumination causes clear pixels to appear brighter, which can be mistaken for extra aerosol or higher surface albedo. Thus, cloud properties must be known in order to derive accurate aerosol and surface properties. A three-dimensional (3D) Monte Carlo (MC) radiative transfer simulation illustrates this point and suggests a method to subtract the cloud effect from aerosol and surface retrievals. The main conclusion is that cloud, aerosol, and surface retrievals are linked and must be treated as a combined system. Landsat provides the range of scales necessary to observe the 3D cloud radiative effects that influence joint surface-atmospheric retrievals.

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.

Retrieval of reflections from ambient noise using illumination diagnosis

NASA Astrophysics Data System (ADS)

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

2014-09-01

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

Retrieving the aerosol lidar ratio profile by combining ground- and space-based elastic lidars.

PubMed

Feiyue, Mao; Wei, Gong; Yingying, Ma

2012-02-15

The aerosol lidar ratio is a key parameter for the retrieval of aerosol optical properties from elastic lidar, which changes largely for aerosols with different chemical and physical properties. We proposed a method for retrieving the aerosol lidar ratio profile by combining simultaneous ground- and space-based elastic lidars. The method was tested by a simulated case and a real case at 532 nm wavelength. The results demonstrated that our method is robust and can obtain accurate lidar ratio and extinction coefficient profiles. Our method can be useful for determining the local and global lidar ratio and validating space-based lidar datasets.

Methods of identification employing antibody profiles

DOEpatents

Francoeur, Ann-Michele

1993-12-14

An identification method, applicable to the identification of animals or inanimate objects, is described. The method takes advantage of the set of individual-specific antibodies that are part of the unique antibody repertoire present in animals, by reacting an effective amount of such antibodies with a particular panel, of n-dimensional array (where n is typically one or two) consisting of an effective amount of many different antigens (typically greater than one thousand), to give antibody-antigen complexes. The profile or pattern formed by the antigen-antibody complexes, termed an antibody fingerprint, when revealed by an effective amount of an appropriate detector molecule, is uniquely representative of a particular individual. The method can similarly be used to distinguish genetically, or otherwise similar individuals, or their body parts containing individual-specific antibodies.

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

PubMed

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

2016-10-01

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

Functional analysis of HPV-like particle-activated Langerhans cells in vitro.

PubMed

Yan, Lisa; Woodham, Andrew W; Da Silva, Diane M; Kast, W Martin

2015-01-01

Langerhans cells (LCs) are antigen-presenting cells responsible for initiating an immune response against human papillomaviruses (HPVs) entering the epithelial layer in vivo as they are the first immune cell that HPV comes into contact with. LCs become activated in response to foreign antigens, which causes internal signaling resulting in the increased expression of co-stimulatory molecules and the secretion of inflammatory cytokines. Functionally activated LCs are then capable of migrating to the lymph nodes where they interact with antigen-specific T cells and initiate an adaptive T-cell response in vivo. However, HPV has evolved in a manner that suppresses LC function, and thus the induction of antigen-specific T cells is hindered. While many methods exist to monitor the activity of LCs in vitro, the migration and induction of cytotoxic T cells is ultimately indicative of a functional immune response. Here, methods in analyzing functional migration and induction of antigen-specific T cells after stimulation of LCs with HPV virus-like particles in vitro are described.

Retrieving vertical ozone profiles from measurements of global spectral irradiance

NASA Astrophysics Data System (ADS)

Bernhard, Germar; Petropavlovskikh, Irina; Mayer, Bernhard

2017-12-01

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

Comparisons of Upper Tropospheric Humidity Retrievals from TOVS and METEOSAT

NASA Technical Reports Server (NTRS)

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

1999-01-01

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

A Comparison of High Spectral Resolution Infrared Cloud-Top Pressure Altitude Algorithms Using S-HIS Measurements

NASA Technical Reports Server (NTRS)

Holz, Robert E.; Ackerman, Steve; Antonelli, Paolo; Nagle, Fred; McGill, Matthew; Hlavka, Dennis L.; Hart, William D.

2005-01-01

This paper presents a comparison of cloud-top altitude retrieval methods applied to S-HIS (Scanning High Resolution Interferometer Sounder) measurements. Included in this comparison is an improvement to the traditional CO2 Slicing method. The new method, CO2 Sorting, determines optimal channel pairs to apply the CO2 Slicing. Measurements from collocated samples of the Cloud Physics Lidar (CPL) and Modis Airborne Simulator (MAS) instruments assist in the comparison. For optically thick clouds good correlation between the S-HIS and lidar cloud-top retrievals are found. For tenuous ice clouds there can be large differences between lidar (CPL) and S-HIS retrieved cloud-tops. It is found that CO2 Sorting significantly reduces the cloud height biases for the optically thin cloud (total optical depths less then 1.0). For geometrically thick but optically thin cirrus clouds large differences between the S-HIS infrared cloud top retrievals and the CPL detected cloud top where found. For these cases the cloud height retrieved by the S-HIS cloud retrievals correlated closely with the level the CPL integrated cloud optical depth was approximately 1.0.

The effectiveness of concept mapping and retrieval practice as learning strategies in an undergraduate physiology course.

PubMed

Burdo, Joseph; O'Dwyer, Laura

2015-12-01

Concept mapping and retrieval practice are both educational methods that have separately been reported to provide significant benefits for learning in diverse settings. Concept mapping involves diagramming a hierarchical representation of relationships between distinct pieces of information, whereas retrieval practice involves retrieving information that was previously coded into memory. The relative benefits of these two methods have never been tested against each other in a classroom setting. Our study was designed to investigate whether or not concept mapping or retrieval practice produced a significant learning benefit in an undergraduate physiology course as measured by exam performance and, if so, was the benefit of one method significantly greater than the other. We found that there was a trend toward increased exam scores for the retrieval practice group compared with both the control group and concept mapping group, and that trend achieved statistical significance for one of the four module exams in the course. We also found that women performed statistically better than men on the module exam that contained a substantial amount of material relating to female reproductive physiology. Copyright © 2015 The American Physiological Society.

Kinetic of antigent-antibody reactions with scattering method

NASA Astrophysics Data System (ADS)

Bilyi, Olexander I.; Kiselyov, Yevgen M.; Novikov, Volodymyr P.

2001-07-01

The immune reactions of interaction antigen-antibody represent specific effect of an antigene with an antibody, which outcome are the complex immune aggregates forming precipitate in case of a soluble antigene, or agglutinate in case of a corpuscular antigene. Immunological methods which uses in the quality of carrier protein latex's polymeric microspheresis, gained name and method latex agglutination. Polymeric microspheresis have the array of advantages before biological carries, which consist in the opportunity of the variation of attributes surface and size microspheresis in the broad band of meanings with the preservation of narrow distribution particles behind measurements, the putting of functional groups, necessary for bunch with ligand on stage their synthesis, in ragidity at storage. The quantitative evaluation of parameters of a response of interaction antigen-antibody in immunology is possible by optical methods on a measurement of a modification of intensity of a light stream of a solution in an outcome of a course of a reaction. Concentration of immune complexes determine both on slacking a taking place stream of light, and on a modification of intensity of a stream of light scattering suspended particles in a solution. The process light scattering by colloidal aggregates are formed from suspension microspheresis with adsorbed on their surface protein is described. In report the physics principle of registration immune reaction by light scattering methods is concerned. The results of the effectiveness latex's preparation created on basis of the polymeric carries is described.

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

PubMed

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

2018-01-01

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

Proteomic Identification of Non-Gal Antibody Targets After Pig-to-Primate Cardiac Xenotransplantation

PubMed Central

Byrne, Guerard W.; Stalboerger, Paul G.; Davila, Eduardo; Heppelmann, Carrie J.; Gazi, Mozammel H.; McGregor, Hugh C. J.; LaBreche, Peter T.; Davies, William R.; Rao, Vinay P.; Oi, Keiji; Tazelaar, Henry D.; Logan, John S.; McGregor, Christopher G. A.

2008-01-01

Background Experience with non-antigenic galactose α1,3 galactose (αGal) polymers and development of αGal deficient pigs has reduced or eliminated the significance of this antigen in xenograft rejection. Despite these advances, delayed xenograft rejection (DXR) continues to occur most likely due to antibody responses to non-Gal endothelial cell (EC) antigens. Methods To gauge the diversity of the non-Gal antibody response we used antibody derived from CD46 transgenic heterotopic cardiac xenografts performed without T-cell immunosuppression, Group A (n = 4) and Gal knockout (GT-KO) heart transplants under tacrolimus and sirolimus immunosuppression, Group B (n = 8). Non-Gal antibody was measured by flow cytometry and by Western blots using GT-KO EC membrane antigens. A nanoLC/MS/MS analysis of proteins recovered from 2D gels was used to identify target antigens. Results Group A recipients exhibited a mixed cellular and humoral rejection. Group B recipients mainly exhibited classical DXR. Western blot analysis showed a non-Gal antibody response induced by GT+ and GT-KO hearts to an overlapping set of pig aortic EC membrane antigens. Proteomic analysis identified 14 potential target antigens but failed to define several immunodominant targets. Conclusions These experiments indicate that the non-Gal antibody response is directed to a number of stress response and inflammation related pig EC antigens and a few undefined targets. Further analysis of these antibody specificities using alternative methods is required to more fully define the repertoire of non-Gal antibody responses. PMID:18957049

Compositions, antibodies, asthma diagnosis methods, and methods for preparing antibodies

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

Jin, Hongjun; Zangar, Richard C.

Methods for preparing an antibody are provided with the method including incorporating 3-bromo-4-hydroxy-benzoic acid into a protein to form an antigen, immunizing a mammalian host with the antigen, and recovering an antibody having an affinity for the antigen from the host. Antibodies having a binding affinity for a monohalotyrosine are provided as well as composition comprising an antibody bound with monohalotyrosine. Compositions comprising a protein having a 3-bromo-4-hydroxy-benzoic acid moiety are also provided. Methods for evaluating the severity of asthma are provide with the methods including analyzing sputum of a patient using an antibody having a binding affinity for monohalotyrosine,more » and measuring the amount of antibody bound to protein. Methods for determining eosinophil activity in bodily fluid are also provided with the methods including exposing bodily fluid to an antibody having a binding affinity for monohalotyrosine, and measuring the amount of bound antibody to determine the eosinophil activity.« less

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

PubMed Central

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

2012-01-01

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

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

DOT National Transportation Integrated Search

1998-04-01

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

Retrieving Atmospheric Profiles Data in the Presence of Clouds from Hyperspectral Remote Sensing Data

NASA Technical Reports Server (NTRS)

Liu, Xu; Larar, Allen M.; Zhou, Daniel K.; Kizer, Susan H.; Wu, Wan; Barnet, Christopher; Divakarla, Murty; Guo, Guang; Blackwell, Bill; Smith, William L.;

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 based retrieval. The results were validated using in situ measurements from automatic soil state observation stations in Sodankylä calibration and validation (CAL-VAL) site, which is a reference site for several EO (Earth Observation) data products.

The diversity of H3 loops determines the antigen-binding tendencies of antibody CDR loops.

PubMed

Tsuchiya, Yuko; Mizuguchi, Kenji

2016-04-01

Of the complementarity-determining regions (CDRs) of antibodies, H3 loops, with varying amino acid sequences and loop lengths, adopt particularly diverse loop conformations. The diversity of H3 conformations produces an array of antigen recognition patterns involving all the CDRs, in which the residue positions actually in contact with the antigen vary considerably. Therefore, for a deeper understanding of antigen recognition, it is necessary to relate the sequence and structural properties of each residue position in each CDR loop to its ability to bind antigens. In this study, we proposed a new method for characterizing the structural features of the CDR loops and obtained the antigen-binding ability of each residue position in each CDR loop. This analysis led to a simple set of rules for identifying probable antigen-binding residues. We also found that the diversity of H3 loop lengths and conformations affects the antigen-binding tendencies of all the CDR loops. © 2016 The Protein Society.

Quality by design approach in the development of an ultra-high-performance liquid chromatography method for Bexsero meningococcal group B vaccine.

PubMed

Nompari, Luca; Orlandini, Serena; Pasquini, Benedetta; Campa, Cristiana; Rovini, Michele; Del Bubba, Massimo; Furlanetto, Sandra

2018-02-01

Bexsero is the first approved vaccine for active immunization of individuals from 2 months of age and older to prevent invasive disease caused by Neisseria meningitidis serogroup B. The active components of the vaccine are Neisseria Heparin Binding Antigen, factor H binding protein, Neisseria adhesin A, produced in Escherichia coli cells by recombinant DNA technology, and Outer Membrane Vesicles (expressing Porin A and Porin B), produced by fermentation of Neisseria meningitidis strain NZ98/254. All the Bexsero active components are adsorbed on aluminum hydroxide and the unadsorbed antigens content is a product critical quality attribute. In this paper the development of a fast, selective and sensitive ultra-high-performance liquid chromatography (UHPLC) method for the determination of the Bexsero antigens in the vaccine supernatant is presented. For the first time in the literature, the Quality by Design (QbD) principles were applied to the development of an analytical method aimed to the quality control of a vaccine product. The UHPLC method was fully developed within the QbD framework, the new paradigm of quality outlined in International Conference on Harmonisation guidelines. Critical method attributes (CMAs) were identified with the capacity factor of Neisseria Heparin Binding Antigen, antigens resolution and peak areas. After a scouting phase, aimed at selecting a suitable and fast UHPLC operative mode for the vaccine antigens separation, risk assessment tools were employed to define the critical method parameters to be considered in the screening phase. Screening designs were applied for investigating at first the effects of vial type and sample concentration, and then the effects of injection volume, column type, organic phase starting concentration, ramp time and temperature. Response Surface Methodology pointed out the presence of several significant interaction effects, and with the support of Monte-Carlo simulations led to map out the design space, at a selected probability level, for the desired CMAs. The selected working conditions gave a complete separation of the antigens in about 5min. Robustness testing was carried out by a multivariate approach and a control strategy was implemented by defining system suitability tests. The method was qualified for the analysis of the Bexsero vaccine. Copyright © 2017 Elsevier B.V. All rights reserved.

[HLA A, B, C and DR antigens in a urban population from Santiago of Chile].

PubMed

Rodríguez, L; Scagliotti, P; Quiroga, T

1993-05-01

HLA antigens vary in different ethnical groups and in Chile there are no reports on the frequency of these antigens in a normal representative population. The few existing studies are of indigenous populations and control groups, without including HLA-DR antigens. Therefore, the aim of this study was to study the frequency of HLA A, B and C antigens in 349 individuals and HLA-DR in 257, using the microlymphocytotoxicity method, and compared the results with those on normal caucasian populations (Europe and USA). Significant differences were found for 7 antigens of group A, 10 of group B, 4 of group C and 6 of group DR. The observed difference allow us to conclude that the population from Santiago has a distinct HLA antigen distribution. This fact must be bore in mind future studies in genetics, paternity or autoimmune diseases.

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

PubMed

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

2015-01-01

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

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

PubMed Central

2015-01-01

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

Feasibility study of multi-pixel retrieval of optical thickness and droplet effective radius of inhomogeneous clouds using deep learning

NASA Astrophysics Data System (ADS)

Okamura, Rintaro; Iwabuchi, Hironobu; Schmidt, K. Sebastian

2017-12-01

Three-dimensional (3-D) radiative-transfer effects are a major source of retrieval errors in satellite-based optical remote sensing of clouds. The challenge is that 3-D effects manifest themselves across multiple satellite pixels, which traditional single-pixel approaches cannot capture. In this study, we present two multi-pixel retrieval approaches based on deep learning, a technique that is becoming increasingly successful for complex problems in engineering and other areas. Specifically, we use deep neural networks (DNNs) to obtain multi-pixel estimates of cloud optical thickness and column-mean cloud droplet effective radius from multispectral, multi-pixel radiances. The first DNN method corrects traditional bispectral retrievals based on the plane-parallel homogeneous cloud assumption using the reflectances at the same two wavelengths. The other DNN method uses so-called convolutional layers and retrieves cloud properties directly from the reflectances at four wavelengths. The DNN methods are trained and tested on cloud fields from large-eddy simulations used as input to a 3-D radiative-transfer model to simulate upward radiances. The second DNN-based retrieval, sidestepping the bispectral retrieval step through convolutional layers, is shown to be more accurate. It reduces 3-D radiative-transfer effects that would otherwise affect the radiance values and estimates cloud properties robustly even for optically thick clouds.

Eliciting Epitope-Specific CD8+ T Cell Response by Immunization with Microbial Protein Antigens Formulated with α-Galactosylceramide: Theory, Practice, and Protocols.

PubMed

Gilchuk, Pavlo; Knight, Frances C; Wilson, John T; Joyce, Sebastian

2017-01-01

CD8+ cytotoxic T lymphocytes confer protection against infectious diseases caused by viruses, bacteria, and parasites. Hence, significant efforts have been invested into devising ways to generate CD8+ T cell-targeted vaccines. Generation of microbe-free protein subunit vaccines requires a thorough knowledge of protective target antigens. Such antigens are proteolytically processed peptides presented by MHC class I molecules. To induce a robust antigen-specific CD8+ T cell response through vaccination, it is essential to formulate the antigen with an effective adjuvant. Here, we describe a versatile method for generating high-frequency antigen-specific CD8+ T cells through immunization of mice using the invariant natural killer T cell agonist α-galactosylceramide as the adjuvant.

Improving Retrieval Performance by Relevance Feedback.

ERIC Educational Resources Information Center

Salton, Gerard; Buckley, Chris

1990-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2017-10-01

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

Lightning Charge Retrievals: Dimensional Reduction, LDAR Constraints, and a First Comparison w/ LIS Satellite Data

NASA Technical Reports Server (NTRS)

Koshak, William; Krider, E. Philip; Murray, Natalie; Boccippio, Dennis

2007-01-01

A "dimensional reduction" (DR) method is introduced for analyzing lightning field changes whereby the number of unknowns in a discrete two-charge model is reduced from the standard eight to just four. The four unknowns are found by performing a numerical minimization of a chi-squared goodness-of-fit function. At each step of the minimization, an Overdetermined Fixed Matrix (OFM) method is used to immediately retrieve the best "residual source". In this way, all 8 parameters are found, yet a numerical search of only 4 parameters is required. The inversion method is applied to the understanding of lightning charge retrievals. The accuracy of the DR method has been assessed by comparing retrievals with data provided by the Lightning Detection And Ranging (LDAR) instrument. Because lightning effectively deposits charge within thundercloud charge centers and because LDAR traces the geometrical development of the lightning channel with high precision, the LDAR data provides an ideal constraint for finding the best model charge solutions. In particular, LDAR data can be used to help determine both the horizontal and vertical positions of the model charges, thereby eliminating dipole ambiguities. The results of the LDAR-constrained charge retrieval method have been compared to the locations of optical pulses/flash locations detected by the Lightning Imaging Sensor (LIS).

Comparison of Various Methods in the Diagnosis of Entamoeba histolytica in Stool and Serum Specimens

PubMed Central

Uslu, Hakan; Aktas, Osman; Uyanik, Muhammet Hamidullah

2016-01-01

Objective: Entamoeba histolytica is indistinguishable from Entamoeba dispar in direct microscopic examination. A definitive diagnosis of E. histolytica is important in terms of the treatment of the patient and to avoid unnecessary costs. This study’s aim is to determine the prevalence of E. histolytica and to make a comparison of the different diagnostic tests in the patients specimens defined as E. histolytica/E. dispar infection. Materials and Methods: Faecal and serum specimens of 90 patients defined as E. histolytica/E. dispar with microscopy (wet mount examination with 0.85% saline and Lugol’s iodine) were examined. Stool samples were examined by trichrome staining for trophozoites and cysts and by immunoassay methods for specific adhesin antigens (Wampole ® E. histolytica II antigen testing) and for specific serine-rich 30 kD membrane protein (Serazym® E. histolytica antigen testing). Anti-E. histolytica antibodies were investigated using a latex slide test and indirect hemagglutination methods in serum specimens. Results: Presence of E. histolytica was not confirmed in 31.1% cases with trichrome staining, 62.2% of the Wampole antigen test, 64.4%, of the Serazym antigen test, 73.3% of the indirect hemagglutination test and 75.6%. of the latex agglutination. Considering the common results from Wampole and Serazym antigen testing as a reference standard, the specificity/sensitivity is 100/53.85% for trichrome staining, 75.00/98.11% for the latex agglutination test and 78.57/96.77% for the indirect hemagglutination test. Conclusion: It has been shown that investigation of E. histolytica in stools by direct wet-smear microscopy alone can cause significant false positive results. To obtain a reliable diagnosis for E. histolytica and to avoid unnecessary treatment for this parasite, at least one more specific assay, particularly an antigen testing and microscopy, is required. PMID:27551176

Corrugated Waveguide Mode Content Analysis Using Irradiance Moments

PubMed Central

Jawla, Sudheer K.; Shapiro, Michael A.; Idei, Hiroshi; Temkin, Richard J.

2015-01-01

We present a novel, relatively simple method for determining the mode content of the linearly polarized modes of a corrugated waveguide using the moments of the intensity pattern of the field radiated from the end of the waveguide. This irradiance moment method is based on calculating the low-order irradiance moments, using measured intensity profiles only, of the radiated field from the waveguide aperture. Unlike the phase retrieval method, this method does not use or determine the phase distribution at the waveguide aperture. The new method was benchmarked numerically by comparison with sample mode mixtures. The results predict less than ±0.7% error bar in the retrieval of the mode content. The method was also tested using high-resolution experimental data from beams radiated from 63.5 mm and 19 mm corrugated waveguides at 170 and 250 GHz, respectively. The results showed a very good agreement of the mode content retrieved using the irradiance moment method versus the phase retrieval technique. The irradiance moment method is most suitable for cases where the modal power is primarily in the fundamental HE11 mode, with <8% of the power in high-order modes. PMID:25821260

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…

Medical Subject Headings (MeSH) for indexing and retrieving open-source healthcare data.

PubMed

Marc, David T; Khairat, Saif S

2014-01-01

The US federal government initiated the Open Government Directive where federal agencies are required to publish high value datasets so that they are available to the public. Data.gov and the community site Healthdata.gov were initiated to disperse such datasets. However, data searches and retrieval for these sites are keyword driven and severely limited in performance. The purpose of this paper is to address the issue of extracting relevant open-source data by proposing a method of adopting the MeSH framework for indexing and data retrieval. A pilot study was conducted to compare the performance of traditional keywords to MeSH terms for retrieving relevant open-source datasets related to "mortality". The MeSH framework resulted in greater sensitivity with comparable specificity to the keyword search. MeSH showed promise as a method for indexing and retrieving data, yet future research should conduct a larger scale evaluation of the performance of the MeSH framework for retrieving relevant open-source healthcare datasets.

Retrieval Practice, with or without Mind Mapping, Boosts Fact Learning in Primary School Children

PubMed Central

Ritchie, Stuart J.; Della Sala, Sergio; McIntosh, Robert D.

2013-01-01

Retrieval practice is a method of study in which testing is incorporated into the learning process. This method is known to facilitate recall for facts in adults and in secondary-school-age children, but existing studies in younger children are somewhat limited in their practical applicability. In two studies of primary school-age children of 8–12 years, we tested retrieval practice along with another study technique, mind mapping, which is more widely-used, but less well-evidenced. Children studied novel geographical facts, with or without retrieval practice and with or without mind mapping, in a crossed-factorial between-subjects design. In Experiment 1, children in the retrieval practice condition recalled significantly more facts four days later. In Experiment 2, this benefit was replicated at one and five weeks in a different, larger sample of schoolchildren. No consistent effects of mind mapping were observed. These results underline the effectiveness of retrieval practice for fact learning in young children. PMID:24265738

Methods of preparing and using single chain anti-tumor antibodies

DOEpatents

Cheung, Nai-Kong; Guo, Hong-Fen

2010-02-23

This invention provides a method for identifying cells expressing a target single chain antibody (scFv) directed against a target antigen from a collection of cells that includes cells that do not express the target scFv, comprising the step of combining the collection of cells with an anti-idiotype directed to an antibody specific for the target antigen and detecting interaction, if any, of the anti-idiotype with the cells, wherein the occurrence of an interaction identifies the cell as one which expresses the target scFv. This invention also provides a method for making a single chain antibody (scFv) directed against an antigen, wherein the selection of clones is made based upon interaction of those clones with an appropriate anti-idiotype, and heretofore inaccessible scFv so made. This invention provides the above methods or any combination thereof. Finally, this invention provides various uses of these methods.

Method for preparation of single chain antibodies

DOEpatents

Cheung, Nai-Kong V [New York, NY; Guo, Hong-fen [New York, NY

2012-04-03

This invention provides a method for identifying cells expressing a target single chain antibody (scFv) directed against a target antigen from a collection of cells that includes cells that do not express the target scFv, comprising the step of combining the collection of cells with an anti-idiotype directed to an antibody specific for the target antigen and detecting interaction, if any, of the anti-idiotype with the cells, wherein the occurrence of an interaction identifies the cell as one which expresses the target scFv. This invention also provides a method for making a single chain antibody (scFv) directed against an antigen, wherein the selection of clones is made based upon interaction of those clones with an appropriate anti-idiotype, and heretofore inaccessible scFv so made. This invention provides the above methods or any combination thereof. Finally, this invention provides various uses of these methods.

Neuroendocrine carcinoma of the apocrine glands of the anal sac in a dog.

PubMed

Ogawa, Bunichiro; Taniai, Eriko; Hayashi, Hitomi; Imaoka, Masako; Machida, Noboru; Mitsumori, Kunitoshi; Shibutani, Makoto

2011-07-01

A perianal subcutaneous tumor involving the anal sac developed in an 8-year-old male mixed Labrador Retriever dog. Histologically, this tumor showed typical features of the solid-type carcinoma of the apocrine glands of the anal sac. However, neoplastic cells were immunoreactive for cytokeratin 8, chromogranin A, vasoactive intestinal peptide, neuron-specific enolase, and synaptophysin, and negative for S-100 protein, α-smooth muscle actin, vimentin, glucagon, insulin, somatostatin, carcinoembryonic antigen, serotonin, and parathyroid hormone-related protein. Considering the distribution of chromogranin A-positive cells within the anal sac apocrine glands, this tumor was diagnosed as neuroendocrine carcinoma originating from the apocrine glands of the anal sac.

Diversification of visual media retrieval results using saliency detection

NASA Astrophysics Data System (ADS)

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

2013-03-01

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

Retrieval evaluation and distance learning from perceived similarity between endomicroscopy videos.

PubMed

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

2011-01-01

Evaluating content-based retrieval (CBR) is challenging because it requires an adequate ground-truth. When the available groundtruth is limited to textual metadata such as pathological classes, retrieval results can only be evaluated indirectly, for example in terms of classification performance. In this study we first present a tool to generate perceived similarity ground-truth that enables direct evaluation of endomicroscopic video retrieval. This tool uses a four-points Likert scale and collects subjective pairwise similarities perceived by multiple expert observers. We then evaluate against the generated ground-truth a previously developed dense bag-of-visual-words method for endomicroscopic video retrieval. Confirming the results of previous indirect evaluation based on classification, our direct evaluation shows that this method significantly outperforms several other state-of-the-art CBR methods. In a second step, we propose to improve the CBR method by learning an adjusted similarity metric from the perceived similarity ground-truth. By minimizing a margin-based cost function that differentiates similar and dissimilar video pairs, we learn a weight vector applied to the visual word signatures of videos. Using cross-validation, we demonstrate that the learned similarity distance is significantly better correlated with the perceived similarity than the original visual-word-based distance.

Efficient Retrieval of Massive Ocean Remote Sensing Images via a Cloud-Based Mean-Shift Algorithm.

PubMed

Yang, Mengzhao; Song, Wei; Mei, Haibin

2017-07-23

The rapid development of remote sensing (RS) technology has resulted in the proliferation of high-resolution images. There are challenges involved in not only storing large volumes of RS images but also in rapidly retrieving the images for ocean disaster analysis such as for storm surges and typhoon warnings. In this paper, we present an efficient retrieval of massive ocean RS images via a Cloud-based mean-shift algorithm. Distributed construction method via the pyramid model is proposed based on the maximum hierarchical layer algorithm and used to realize efficient storage structure of RS images on the Cloud platform. We achieve high-performance processing of massive RS images in the Hadoop system. Based on the pyramid Hadoop distributed file system (HDFS) storage method, an improved mean-shift algorithm for RS image retrieval is presented by fusion with the canopy algorithm via Hadoop MapReduce programming. The results show that the new method can achieve better performance for data storage than HDFS alone and WebGIS-based HDFS. Speedup and scaleup are very close to linear changes with an increase of RS images, which proves that image retrieval using our method is efficient.

Image Retrieval Method for Multiscale Objects from Optical Colonoscopy Images

PubMed Central

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

2017-01-01

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

Image Retrieval Method for Multiscale Objects from Optical Colonoscopy Images.

PubMed

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

2017-01-01

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

Efficient Retrieval of Massive Ocean Remote Sensing Images via a Cloud-Based Mean-Shift Algorithm

PubMed Central

Song, Wei; Mei, Haibin

2017-01-01

The rapid development of remote sensing (RS) technology has resulted in the proliferation of high-resolution images. There are challenges involved in not only storing large volumes of RS images but also in rapidly retrieving the images for ocean disaster analysis such as for storm surges and typhoon warnings. In this paper, we present an efficient retrieval of massive ocean RS images via a Cloud-based mean-shift algorithm. Distributed construction method via the pyramid model is proposed based on the maximum hierarchical layer algorithm and used to realize efficient storage structure of RS images on the Cloud platform. We achieve high-performance processing of massive RS images in the Hadoop system. Based on the pyramid Hadoop distributed file system (HDFS) storage method, an improved mean-shift algorithm for RS image retrieval is presented by fusion with the canopy algorithm via Hadoop MapReduce programming. The results show that the new method can achieve better performance for data storage than HDFS alone and WebGIS-based HDFS. Speedup and scaleup are very close to linear changes with an increase of RS images, which proves that image retrieval using our method is efficient. PMID:28737699

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

PubMed

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

2016-09-27

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

Music Retrieval Based on the Relation between Color Association and Lyrics

NASA Astrophysics Data System (ADS)

Nakamur, Tetsuaki; Utsumi, Akira; Sakamoto, Maki

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

Antigenic Structure of Rabbit γ Globulin

PubMed Central

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

1961-01-01

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

Tank Waste Retrieval Lessons Learned at the Hanford Site

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

Dodd, R.A.

One of the environmental remediation challenges facing the nation is the retrieval and permanent disposal of approximately 90 million gallons of radioactive waste stored in underground tanks at the U. S. Department of Energy (DOE) facilities. The Hanford Site is located in southeastern Washington State and stores roughly 60 percent of this waste. An estimated 53 million gallons of high-level, transuranic, and low-level radioactive waste is stored underground in 149 single-shell tanks (SSTs) and 28 newer double-shell tanks (DSTs) at the Hanford Site. These SSTs range in size from 55,000 gallons to 1,000,000 gallon capacity. Approximately 30 million gallons ofmore » this waste is stored in SSTs. The SSTs were constructed between 1943 and 1964 and all have exceeded the nominal 20-year design life. Sixty-seven SSTs are known or suspected to have leaked an estimated 1,000,000 gallons of waste to the surrounding soil. The risk of additional SST leakage has been greatly reduced by removing more than 3 million gallons of interstitial liquids and supernatant and transferring this waste to the DST system. Retrieval of SST salt-cake and sludge waste is underway to further reduce risks and stage feed materials for the Hanford Site Waste Treatment Plant. Regulatory requirements for SST waste retrieval and tank farm closure are established in the Hanford Federal Facility Agreement and Consent Order (HFFACO), better known as the Tri- Party Agreement, or TPA. The HFFACO was signed by the DOE, the State of Washington Department of Ecology (Ecology), and U.S. Environmental Protection Agency (EPA) and requires retrieval of as much waste as technically possible, with waste residues not to exceed 360 ft{sup 3} in 530,000 gallon or larger tanks; 30 ft{sup 3} in 55,000 gallon or smaller tanks; or the limit of waste retrieval technology, whichever is less. If residual waste volume requirements cannot be achieved, then HFFACO Appendix H provisions can be invoked to request Ecology and EPA approval of an exception to the waste retrieval criteria for a specific tank. Tank waste retrieval has been conducted at the Hanford Site over the last few decades using a method referred to as Past Practice Hydraulic Sluicing. Past Practice Hydraulic Sluicing employs large volumes of DST supernatant and water to dislodge, dissolve, mobilize, and retrieve tank waste. Concern over the leak integrity of SSTs resulted in the need for tank waste retrieval methods capable of using smaller volumes of liquid in a more controlled manner. Retrieval of SST waste in accordance with HFFACO requirements was initiated at the Hanford Site in April 2003. New and innovative tank waste retrieval methods that minimize and control the use of liquids are being implemented for the first time. These tank waste retrieval methods replace Past Practice Hydraulic Sluicing and employ modified sluicing, vacuum retrieval, and in-tank vehicle techniques. Waste retrieval has been completed in seven Hanford Site SSTs (C-106, C-103, C-201, C-202, C-203, C-204, and S-112) in accordance with HFFACO requirements. Three additional tanks are currently in the process of being retrieved (C-108, C-109 and S-102) Preparation for retrieval of two additional SSTs (C-104 and C-110) is ongoing with retrieval operations forecasted to start in calendar year 2008. Tank C-106 was retrieved to a residual waste volume of 470 ft{sup 3} using oxalic acid dissolution and modified sluicing. An Appendix H exception request for Tank C-106 is undergoing review. Tank C-103 was retrieved to a residual volume of 351 ft{sup 3} using a modified sluicing technology. This approach was successful at reaching the TPA limits for this tank of less than 360 ft{sup 3}and the limits of the technology. Tanks C-201, C-202, C-203, and C-204 are smaller (55,000 gallon) tanks and waste removal was completed in accordance with HFFACO requirements using a vacuum retrieval system. Residual waste volumes in each of these four tanks were less than 25 ft{sup 3}. Tank S-112 retrieval was completed February 28, 2007, meeting the TPA Limits of less than 360 cu ft using salt-cake dissolution, modified sluicing, in-tank vehicle with high pressure water spray and caustic dissolution. Tanks C-108 and C-109 have been retrieved to 90% and 85% respectively. Modified sluicing was no longer effective at retrieving the remaining 5,000 to 10,000 gallons of residual. A Mobile Retrieval Tool (FoldTrac) is scheduled for installation early in 2008 to assist in breaking up chunks of waste and mobilizing the waste for transfer. Lessons learned from application of new tank waste retrieval methods are being documented and incorporated into future retrieval operations. They address all phases of retrieval including process design, equipment procurement and installation, supporting documentation, and system operations. Information is obtained through interviews with retrieval project personnel, focused workshops, review of problem evaluation requests, and evaluation of retrieval performance data. This paper presents current retrieval successes and lessons learned from retrieval of tank waste at the Hanford Site and discusses how this information is used to optimize retrieval system efficiency, improve overall cost effectiveness of retrieval operations, and ensure that HFFACO requirements are met. (authors)« less

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

PubMed

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

2015-01-01

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

Sensitive typing of reverse ABO blood groups with a waveguide-mode sensor.

PubMed

Uno, Shigeyuki; Tanaka, Torahiko; Ashiba, Hiroki; Fujimaki, Makoto; Tanaka, Mutsuo; Hatta, Yoshihiro; Takei, Masami; Awazu, Koichi; Makishima, Makoto

2018-07-01

Portable, on-site blood typing methods will help provide life-saving blood transfusions to patients during an emergency or natural calamity, such as significant earthquakes. We have previously developed waveguide-mode (WM) sensors for forward ABO and Rh(D) blood typing and detection of antibodies against hepatitis B virus and hepatitis C virus. In this study, we evaluated a WM-sensor for reverse ABO blood typing. Since reverse ABO blood typing is a method for detection of antibodies against type A and type B oligosaccharide antigens on the surface of red blood cells (RBCs), we fixed a synthetic type A or type B trisaccharide antigen on the sensor chip of the WM sensor. We obtained significant changes in the reflectance spectra from a WM sensor on type A antigen with type B plasma and type O plasma and on type B antigen with type A plasma and type O plasma, and no spectrum changes on type A antigen or type B antigen with type AB plasma. Signal enhancement with the addition of a peroxidase reaction failed to increase the sensitivity for detection on oligosaccharide chips. By utilizing hemagglutination detection using regent type A and type B RBCs, we successfully determined reverse ABO blood groups with higher sensitivity compared to a method using oligosaccharide antigens. Thus, functionality of a portable device utilizing a WM sensor can be expanded to include reverse ABO blood typing and, in combination with forward ABO typing and antivirus antibody detection, may be useful for on-site blood testing in emergency settings. Copyright © 2018 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Fleas as an allergen in Egyptian asthmatic patients.

PubMed

el Okbi, L M; Morsy, T A; el-Shayeb, F A; Salama, M M; Abou Gamrah, M M

1991-12-01

Fleas are widely distributed and partially host specific ectoparasites of man and animal. The aim of this work was to study the role of fleas as one of the causative allergens of bronchial asthma in Egyptian patients. Two flea extract antigens were locally prepared. The first from the head and the salivary glands and the second from the abdomen. The sensitivity of the first antigen (head and salivary glands) was evaluated among a known group of flea bite allergic individuals and normal control group using two dilutions 1/50 and 1/100, and proved to be sensitive. Regarding bronchial asthma and fleas, two groups of individuals were examined, asthmatic patients and control ones, using flea extract antigen and common inhalant antigens as skin test as well as precipitin test using flea extract antigen. This test was done by prick method using the routine allergens (house dust, cotton dust, mixed mould, mixed pollens, cat hair, dog hair, wool, feather) and also with locally prepared two flea extracts: one was prepared from the head and salivary glands, the second was prepared from the abdomen. Out of these sixty asthmatic patients, only six (10%) gave positive skin reactions to the antigens of fleas extract. All the control gave negative skin reaction. The precipitin test using the double immuno diffusion method gave positive results with one case who showed reaction to flea extract skin antigen.

Nitrocellulose-bound antigen repeatedly used for the affinity purification of specific polyclonal antibodies for screening DNA expression libraries.

PubMed

Robinson, P A; Anderton, B H; Loviny, T L

1988-04-06

We present a simple, efficient and rapid method for affinity-purifying antibodies from a relatively crude antiserum in quantities large enough to screen a DNA expression library. The method presents a very convenient way to remove crossreacting or contaminating antibody specificities. The affinity matrix, antigen non-covalently bound to nitrocellulose, is prepared by the electrophoretic separation of antigen by sodium dodecyl sulphate-polyacrylamide gel electrophoresis, followed by the transfer of antigen to nitrocellulose. The matrix can be used repeatedly. A brief wash with 6 M guanidine hydrochloride is included between steps to remove residual antibodies which bind with high affinity to nitrocellulose-bound antigen. Various buffer solutions were assessed as antibody/antigen-dissociating agents. Glycine/HCl buffer, pH 2.5, appeared to be the most efficient in our hands, although a number of other less efficient dissociating reagents, including 4.5 M magnesium chloride, pH 7.5, 6 M urea, pH 7, and 0.05 M diethylamine, pH 11.5, also could be used; these may be the elution conditions of choice for other antibody/antigen combinations. The use of affinity-purified antibody solutions instead of the corresponding antisera gave increased signal-to-noise ratios with the detection systems that are commonly used to identify positive signals in screening expression libraries. Protein A- and goat anti-rabbit-alkaline phosphatase conjugates gave the most sensitive signals.

Evaluation of a newly designed sandwich enzyme linked immunosorbent assay for the detection of hydatid antigen in serum, urine and cyst fluid for diagnosis of cystic echinococcosis

PubMed Central

Chaya, DR; Parija, Subhash Chandra

2013-01-01

Introduction: Cystic echinococcosis (CE) is a zoonotic disease of humans with variable clinical manifestations. Imaging and immunological methods are currently the mainstay of diagnosis of this disease. Although the immunological tests for detection of anti-echinococcal antibodies have several disadvantages, they are widely being used. Antigen is far more superior than antibody detection test as they can provide a specific parasitic diagnosis. Materials and Methods: A sandwich enzyme linked immunosorbent assay (ELISA) was designed using antibodies to 24 kDa urinary hydatid antigen for the detection of hydatid antigens in urine, serum and cyst fluid specimens. The performance of this novel test was compared with that of other hydatid antibody detection ELISA and enzyme immune transfer blot (EITB) using radiological and surgical confirmation as the gold standard. Results: The antigen detection ELISA showed 100% sensitivity and specificity when tested with cyst fluid. On testing urine and serum, the antigen detection ELISA was found to be more specific than antibody detection ELISA. EITB was found to be the most sensitive and specific test. Conclusions: ELISA using polyclonal antibodies against 24 kDa urinary hydatid protein was moderately sensitive to detect hydatid antigen in serum and urine. Hence polyclonal antibodies to 24 kDa urinary hydatid antigen can be used as an alternative source of antibody to detect hydatid antigen in serum, urine and cyst fluid. In the present study, EITB was found to be highly specific test for detection of hydatid antibodiesin serum. 24 kDa protein was found to be specific and of diagnostic value in CE. PMID:24470996

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

PubMed Central

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

2018-01-01

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

Techniques for trans-catheter retrieval of embolized Nit-Occlud® PDA-R and ASD-R devices.

PubMed

Sinha, Sanjay; Levi, Daniel; Peirone, Alejandro; Pedra, Carlos

2018-02-15

Nit-Occlud ® (atrial septal defect) ASD-R and (patent ductus arteriosus) PDA-R devices are used outside the United States for percutaneous closure of the patent ductus arteriosus and atrial septal defects. When embolization occurs, these devices have been difficult to retrieve. Bench simulations of retrieval of PDA-R and ASD-R devices were performed in a vascular model. Retrieval of each device was attempted using snare techniques or with bioptome forceps with a range of devices. The same devices were then intentionally embolized in an animal model. Retrieval methods were systematically tested in a range of sheath sizes, and graded in terms of difficulty and retrieval time. Devices that were grasped by the bioptome in the center of the proximal part of the devices were easily retrieved in both models. Bench studies determined the minimum sheath sizes needed for retrieval of each device with this method. In general sheathes two french sizes greater than the delivery sheath were successful with this technique. Three out of the four PDA-R devices were successfully retrieved in vivo. Two were retrieved by grasping the middle of the PA end of the PDA-R device with a Maslanka bioptome and one small PDA-R device was retrieved using a 10 mm Snare. Four of the five ASD-R devices were retrieved successfully grasping the right atrial ASD-R disc or by passing a wire through the device and snaring this loop. For ASD-R 28 and 30 mm devices, a double bioptome technique was needed to retrieve the device. ASD-R and PDA-R devices can be successfully retrieved in the catheterization lab. It is critical to grab the center portion of the right atrial disc of the ASD-R device or pulmonary portion of the PDA-R device and to use adequately sized sheathes. © 2018 Wiley Periodicals, Inc.

Simultaneous and synergistic profiling of cloud and drizzle properties using ground-based observations

NASA Astrophysics Data System (ADS)

Rusli, Stephanie P.; Donovan, David P.; Russchenberg, Herman W. J.

2017-12-01

Despite the importance of radar reflectivity (Z) measurements in the retrieval of liquid water cloud properties, it remains nontrivial to interpret Z due to the possible presence of drizzle droplets within the clouds. So far, there has been no published work that utilizes Z to identify the presence of drizzle above the cloud base in an optimized and a physically consistent manner. In this work, we develop a retrieval technique that exploits the synergy of different remote sensing systems to carry out this task and to subsequently profile the microphysical properties of the cloud and drizzle in a unified framework. This is accomplished by using ground-based measurements of Z, lidar attenuated backscatter below as well as above the cloud base, and microwave brightness temperatures. Fast physical forward models coupled to cloud and drizzle structure parameterization are used in an optimal-estimation-type framework in order to retrieve the best estimate for the cloud and drizzle property profiles. The cloud retrieval is first evaluated using synthetic signals generated from large-eddy simulation (LES) output to verify the forward models used in the retrieval procedure and the vertical parameterization of the liquid water content (LWC). From this exercise it is found that, on average, the cloud properties can be retrieved within 5 % of the mean truth. The full cloud-drizzle retrieval method is then applied to a selected ACCEPT (Analysis of the Composition of Clouds with Extended Polarization Techniques) campaign dataset collected in Cabauw, the Netherlands. An assessment of the retrieval products is performed using three independent methods from the literature; each was specifically developed to retrieve only the cloud properties, the drizzle properties below the cloud base, or the drizzle fraction within the cloud. One-to-one comparisons, taking into account the uncertainties or limitations of each retrieval, show that our results are consistent with what is derived using the three independent methods.

Retrieval of Mid-tropospheric CO2 Directly from AIRS Measurements

NASA Technical Reports Server (NTRS)

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

2008-01-01

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

Web-based multimedia information retrieval for clinical application research

NASA Astrophysics Data System (ADS)

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

2001-08-01

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

Figure mining for biomedical research.

PubMed

Rodriguez-Esteban, Raul; Iossifov, Ivan

2009-08-15

Figures from biomedical articles contain valuable information difficult to reach without specialized tools. Currently, there is no search engine that can retrieve specific figure types. This study describes a retrieval method that takes advantage of principles in image understanding, text mining and optical character recognition (OCR) to retrieve figure types defined conceptually. A search engine was developed to retrieve tables and figure types to aid computational and experimental research. http://iossifovlab.cshl.edu/figurome/.

A Molecular Simulation Study of Antibody-Antigen Interactions on Surfaces for the Rational Design of Next-Generation Antibody Microarrays

NASA Astrophysics Data System (ADS)

Bush, Derek B.

Antibody microarrays constitute a next-generation sensing platform that has the potential to revolutionize the way that molecular detection is conducted in many scientific fields. Unfortunately, current technologies have not found mainstream use because of reliability problems that undermine trust in their results. Although several factors are involved, it is believed that undesirable protein interactions with the array surface are a fundamental source of problems where little detail about the molecular-level biophysics are known. A better understanding of antibody stability and antibody-antigen binding on the array surface is needed to improve microarray technology. Despite the availability of many laboratory methods for studying protein stability and binding, these methods either do not work when the protein is attached to a surface or they do not provide the atomistic structural information that is needed to better understand protein behavior on the surface. As a result, molecular simulation has emerged as the primary method for studying proteins on surfaces because it can provide metrics and views of atomistic structures and molecular motion. Using an advanced, coarse-grain, protein-surface model this study investigated how antibodies react to and function on different types of surfaces. Three topics were addressed: (1) the stability of individual antibodies on surfaces, (2) antibody binding to small antigens while on a surface, and (3) antibody binding to large antigens while on a surface. The results indicate that immobilizing antibodies or antibody fragments in an upright orientation on a hydrophilic surface can provide the molecules with thermal stability similar to their native aqueous stability, enhance antigen binding strength, and minimize the entropic cost of binding. Furthermore, the results indicate that it is more difficult for large antigens to approach the surface than small antigens, that multiple binding sites can aid antigen binding, and that antigen flexiblity simultaneously helps and hinders the binding process as it approaches the surface. The results provide hope that next-generation microarrays and other devices decorated with proteins can be improved through rational design.

Development of monoclonal antibodies to human microsomal epoxide hydrolase and analysis of “preneoplastic antigen”-like molecules

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

Duan, Hongying; Yoshimura, Kazunori; Kobayashi, Nobuharu

2012-04-01

Microsomal epoxide hydrolase (mEH) is a drug metabolizing enzyme which resides on the endoplasmic reticulum (ER) membrane and catalyzes the hydration of reactive epoxide intermediates that are formed by cytochrome P450s. mEH is also thought to have a role in bile acid transport on the plasma membrane of hepatocytes. It is speculated that efficient execution of such multiple functions is secured by its orientation and association with cytochrome P450 enzymes on the ER membrane and formation of a multiple transport system on the plasma membrane. In certain disease status, mEH loses its association with the membrane and can be detectedmore » as distinct antigens in the cytosol of preneoplastic foci of liver (preneoplastic antigen), in the serum in association with hepatitis C virus infection (AN antigen), or in some brain tumors. To analyze the antigenic structures of mEH in physiological and pathological conditions, we developed monoclonal antibodies against different portions of mEH. Five different kinds of antibodies were obtained: three, anti-N-terminal portions; one anti-C-terminal; and one, anti-conformational epitope. By combining these antibodies, we developed antigen detection methods which are specific to either the membrane-bound form or the linearized form of mEH. These methods detected mEH in the culture medium released from a hepatocellular carcinoma cell line and a glioblastoma cell line, which was found to be a multimolecular complex with a unique antigenic structure different from that of the membrane-bound form of mEH. These antibodies and antigen detection methods may be useful to study pathological changes of mEH in various human diseases. -- Highlights: ► Monoclonal antibodies against different portions of mEH were developed. ► They discriminate between the membrane-bound and the linearized forms of mEH. ► We analyze the antigenic structure of the altered form of mEH in tumor cells. ► Preneoplastic antigen is a multimolecular complex of mEH with a unique structure.« less

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.

An integrated content and metadata based retrieval system for art.

PubMed

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

2004-03-01

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

A Ground Flash Fraction Retrieval Algorithm for GLM

NASA Technical Reports Server (NTRS)

Koshak, William J.

2010-01-01

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

Mapping epitopes and antigenicity by site-directed masking

NASA Astrophysics Data System (ADS)

Paus, Didrik; Winter, Greg

2006-06-01

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

BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes.

PubMed

Jespersen, Martin Closter; Peters, Bjoern; Nielsen, Morten; Marcatili, Paolo

2017-07-03

Antibodies have become an indispensable tool for many biotechnological and clinical applications. They bind their molecular target (antigen) by recognizing a portion of its structure (epitope) in a highly specific manner. The ability to predict epitopes from antigen sequences alone is a complex task. Despite substantial effort, limited advancement has been achieved over the last decade in the accuracy of epitope prediction methods, especially for those that rely on the sequence of the antigen only. Here, we present BepiPred-2.0 (http://www.cbs.dtu.dk/services/BepiPred/), a web server for predicting B-cell epitopes from antigen sequences. BepiPred-2.0 is based on a random forest algorithm trained on epitopes annotated from antibody-antigen protein structures. This new method was found to outperform other available tools for sequence-based epitope prediction both on epitope data derived from solved 3D structures, and on a large collection of linear epitopes downloaded from the IEDB database. The method displays results in a user-friendly and informative way, both for computer-savvy and non-expert users. We believe that BepiPred-2.0 will be a valuable tool for the bioinformatics and immunology community. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

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…

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

PubMed

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

1996-06-01

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

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

PubMed Central

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

2010-01-01

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

Using Conceptual Categories of Questions To Measure Differences in Retrieval Performance.

ERIC Educational Resources Information Center

Keyes, John G.

1996-01-01

To investigate the relationship between the retrieval mechanism and the level of question elaboration, this study divided 100 questions from the cystic fibrosis database into five conceptual categories based on their semantic representations. Two retrieval methods were chosen to investigate potential differences in outcomes across conceptual…

The Effectiveness of Concept Mapping and Retrieval Practice as Learning Strategies in an Undergraduate Physiology Course

ERIC Educational Resources Information Center

Burdo, Joseph; O'Dwyer, Laura

2015-01-01

Concept mapping and retrieval practice are both educational methods that have separately been reported to provide significant benefits for learning in diverse settings. Concept mapping involves diagramming a hierarchical representation of relationships between distinct pieces of information, whereas retrieval practice involves retrieving…

Scalable Integrated Region-Based Image Retrieval Using IRM and Statistical Clustering.

ERIC Educational Resources Information Center

Wang, James Z.; Du, Yanping

Statistical clustering is critical in designing scalable image retrieval systems. This paper presents a scalable algorithm for indexing and retrieving images based on region segmentation. The method uses statistical clustering on region features and IRM (Integrated Region Matching), a measure developed to evaluate overall similarity between images…

DIALOG for Electrical Engineers. CTHB Publikation Nr 29 (1982).

ERIC Educational Resources Information Center

Fjallbrant, Nancy

This manual provides electrical and electronic engineers with an introduction to online information retrieval as implemented on the DIALOG information retrieval system. Sections cover: (1) the development of computerized information retrieval; (2) its advantages; (3) the equipment needed, DIALOG hours of availability, methods of access, and cost…

Development of a Global Multilayered Cloud Retrieval System

NASA Technical Reports Server (NTRS)

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

2004-01-01

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

3D object retrieval using salient views

PubMed Central

Shapiro, Linda G.

2013-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2015-08-01

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

Data-driven information retrieval in heterogeneous collections of transcriptomics data links SIM2s to malignant pleural mesothelioma.

PubMed

Caldas, José; Gehlenborg, Nils; Kettunen, Eeva; Faisal, Ali; Rönty, Mikko; Nicholson, Andrew G; Knuutila, Sakari; Brazma, Alvis; Kaski, Samuel

2012-01-15

Genome-wide measurement of transcript levels is an ubiquitous tool in biomedical research. As experimental data continues to be deposited in public databases, it is becoming important to develop search engines that enable the retrieval of relevant studies given a query study. While retrieval systems based on meta-data already exist, data-driven approaches that retrieve studies based on similarities in the expression data itself have a greater potential of uncovering novel biological insights. We propose an information retrieval method based on differential expression. Our method deals with arbitrary experimental designs and performs competitively with alternative approaches, while making the search results interpretable in terms of differential expression patterns. We show that our model yields meaningful connections between biological conditions from different studies. Finally, we validate a previously unknown connection between malignant pleural mesothelioma and SIM2s suggested by our method, via real-time polymerase chain reaction in an independent set of mesothelioma samples. Supplementary data and source code are available from http://www.ebi.ac.uk/fg/research/rex.

Retrieval of tropospheric carbon monoxide for the MOPITT experiment

NASA Astrophysics Data System (ADS)

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

1998-12-01

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

Possible alternative to European Pharmacopoeia's method of analysis Test for Fc Function of Immunoglobulin (2.7.9) by using tetanus toxoid as antigen.

PubMed

Perez-del-Pulgar, S; Lopez, M; Gensana, M; Jorquera, J I

2006-08-01

Preparations of intravenous immunoglobulins must keep functional integrity throughout the purification process. In order to assess Fc fragment functionality, the European Pharmacopoeia proposes the Test for Fc function of immunoglobulin (2.7.9), which is based on a rubella antigen of high titre. Sometimes, such antigen is difficult to obtain. In the present study, we develop the same assay using tetanus toxoid instead of rubella antigen, adapting the procedure for the use of tetanus toxoid. The comparison between rubella-based and tetanus-based assays showed that the slopes of the haemolysis curves were higher if red blood cells had been sensitised with the rubella antigen than with tetanus toxoid. Nonetheless, the tetanus-based assay gave satisfactory results and it could be a good alternative antigen target.

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

PubMed Central

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

2014-01-01

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

A novel algorithm for laser self-mixing sensors used with the Kalman filter to measure displacement

NASA Astrophysics Data System (ADS)

Sun, Hui; Liu, Ji-Gou

2018-07-01

This paper proposes a simple and effective method for estimating the feedback level factor C in a self-mixing interferometric sensor. It is used with a Kalman filter to retrieve the displacement. Without the complicated and onerous calculation process of the general C estimation method, a final equation is obtained. Thus, the estimation of C only involves a few simple calculations. It successfully retrieves the sinusoidal and aleatory displacement by means of simulated self-mixing signals in both weak and moderate feedback regimes. To deal with the errors resulting from noise and estimate bias of C and to further improve the retrieval precision, a Kalman filter is employed following the general phase unwrapping method. The simulation and experiment results show that the retrieved displacement using the C obtained with the proposed method is comparable to the joint estimation of C and α. Besides, the Kalman filter can significantly decrease measurement errors, especially the error caused by incorrectly locating the peak and valley positions of the signal.

Compressed domain indexing of losslessly compressed images

NASA Astrophysics Data System (ADS)

Schaefer, Gerald

2001-12-01

Image retrieval and image compression have been pursued separately in the past. Only little research has been done on a synthesis of the two by allowing image retrieval to be performed directly in the compressed domain of images without the need to uncompress them first. In this paper methods for image retrieval in the compressed domain of losslessly compressed images are introduced. While most image compression techniques are lossy, i.e. discard visually less significant information, lossless techniques are still required in fields like medical imaging or in situations where images must not be changed due to legal reasons. The algorithms in this paper are based on predictive coding methods where a pixel is encoded based on the pixel values of its (already encoded) neighborhood. The first method is based on an understanding that predictively coded data is itself indexable and represents a textural description of the image. The second method operates directly on the entropy encoded data by comparing codebooks of images. Experiments show good image retrieval results for both approaches.

A cheap minimally painful and widely usable alternative for retrieving ureteral stents.

PubMed

Söylemez, Haluk; Sancaktutar, Ahmet Ali; Bozkurt, Yaşar; Atar, Murat; Penbegül, Necmettin; Yildirim, Kadir

2011-01-01

To describe a cheap, minimally painful and widely usable method for retrieving ureteral stents by using an ureteroscope. Sixty-seven patients with ureteral stents were enrolled in this study. The patients were randomized into a cystoscopic (35 patients) and a ureteroscopic (32 patients) group. All stents were retrieved by a flexible cystoscope in the first group and by a ureteroscope in the second group under local anesthesia. Patients in each group were assessed for stented time, stent side, cause of stent placement, operative time, peroperative pain, postoperative pain, irritative voiding symptoms and hematuria. Also costs of instruments were calculated. Stents were successfully retrieved in 67 patients. There were no statistical differences in the two groups regarding patient gender and age or stent side, operative time, stented time, mean operative pain score, irritative voiding symptom scores and hematuria. Total selling price was USD 20.399 for flexible instruments and USD 10.516 for rigid ones. Total maintenance price was higher in flexible instruments than in the rigid ones (USD 197.8 and 51.7 per use, respectively). Ureteroscopic stent retrieval is a minimally painful, safe and highly tolerable method under local anesthesia as well as flexible cystoscopic retrieval. Also, it is a cheap and widely usable method. Copyright © 2011 S. Karger AG, Basel.

Soil Moisture Retrieval Using Convolutional Neural Networks: Application to Passive Microwave Remote Sensing

NASA Astrophysics Data System (ADS)

Hu, Z.; Xu, L.; Yu, B.

2018-04-01

A empirical model is established to analyse the daily retrieval of soil moisture from passive microwave remote sensing using convolutional neural networks (CNN). Soil moisture plays an important role in the water cycle. However, with the rapidly increasing of the acquiring technology for remotely sensed data, it's a hard task for remote sensing practitioners to find a fast and convenient model to deal with the massive data. In this paper, the AMSR-E brightness temperatures are used to train CNN for the prediction of the European centre for medium-range weather forecasts (ECMWF) model. Compared with the classical inversion methods, the deep learning-based method is more suitable for global soil moisture retrieval. It is very well supported by graphics processing unit (GPU) acceleration, which can meet the demand of massive data inversion. Once the model trained, a global soil moisture map can be predicted in less than 10 seconds. What's more, the method of soil moisture retrieval based on deep learning can learn the complex texture features from the big remote sensing data. In this experiment, the results demonstrates that the CNN deployed to retrieve global soil moisture can achieve a better performance than the support vector regression (SVR) for soil moisture retrieval.

Evaluation of a CLEIA automated assay system for the detection of a panel of tumor markers.

PubMed

Falzarano, Renato; Viggiani, Valentina; Michienzi, Simona; Longo, Flavia; Tudini, Silvestra; Frati, Luigi; Anastasi, Emanuela

2013-10-01

Tumor markers are commonly used to detect a relapse of disease in oncologic patients during follow-up. It is important to evaluate new assay systems for a better and more precise assessment, as a standardized method is currently lacking. The aim of this study was to assess the concordance between an automated chemiluminescent enzyme immunoassay system (LUMIPULSE® G1200) and our reference methods using seven tumor markers. Serum samples from 787 subjects representing a variety of diagnoses, including oncologic, were analyzed using LUMIPULSE® G1200 and our reference methods. Serum values were measured for the following analytes: prostate-specific antigen (PSA), alpha-fetoprotein (AFP), carcinoembryonic antigen (CEA), cancer antigen 125 (CA125), carbohydrate antigen 15-3 (CA15-3), carbohydrate antigen 19-9 (CA19-9), and cytokeratin 19 fragment (CYFRA 21-1). For the determination of CEA, AFP, and PSA, an automatic analyzer based on chemiluminescence was applied as reference method. To assess CYFRA 21-1, CA125, CA19-9, and CA15-3, an immunoradiometric manual system was employed. Method comparison by Passing-Bablok analysis resulted in slopes ranging from 0.9728 to 1.9089 and correlation coefficients from 0.9977 to 0.9335. The precision of each assay was assessed by testing six serum samples. Each sample was analyzed for all tumor biomarkers in duplicate and in three different runs. The coefficients of variation were less than 6.3 and 6.2 % for within-run and between-run variation, respectively. Our data suggest an overall good interassay agreement for all markers. The comparison with our reference methods showed good precision and reliability, highlighting its usefulness in clinical laboratory's routine.

Deeply learnt hashing forests for content based image retrieval in prostate MR images

NASA Astrophysics Data System (ADS)

Shah, Amit; Conjeti, Sailesh; Navab, Nassir; Katouzian, Amin

2016-03-01

Deluge in the size and heterogeneity of medical image databases necessitates the need for content based retrieval systems for their efficient organization. In this paper, we propose such a system to retrieve prostate MR images which share similarities in appearance and content with a query image. We introduce deeply learnt hashing forests (DL-HF) for this image retrieval task. DL-HF effectively leverages the semantic descriptiveness of deep learnt Convolutional Neural Networks. This is used in conjunction with hashing forests which are unsupervised random forests. DL-HF hierarchically parses the deep-learnt feature space to encode subspaces with compact binary code words. We propose a similarity preserving feature descriptor called Parts Histogram which is derived from DL-HF. Correlation defined on this descriptor is used as a similarity metric for retrieval from the database. Validations on publicly available multi-center prostate MR image database established the validity of the proposed approach. The proposed method is fully-automated without any user-interaction and is not dependent on any external image standardization like image normalization and registration. This image retrieval method is generalizable and is well-suited for retrieval in heterogeneous databases other imaging modalities and anatomies.

Broadband Phase Retrieval for Image-Based Wavefront Sensing

NASA Technical Reports Server (NTRS)

Dean, Bruce H.

2007-01-01

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

[Measurements of the concentration of atmospheric CO2 based on OP/FTIR method and infrared reflecting scanning Fourier transform spectrometry].

PubMed

Wei, Ru-Yi; Zhou, Jin-Song; Zhang, Xue-Min; Yu, Tao; Gao, Xiao-Hui; Ren, Xiao-Qiang

2014-11-01

The present paper describes the observations and measurements of the infrared absorption spectra of CO2 on the Earth's surface with OP/FTIR method by employing a mid-infrared reflecting scanning Fourier transform spectrometry, which are the first results produced by the first prototype in China developed by the team of authors. This reflecting scanning Fourier transform spectrometry works in the spectral range 2 100-3 150 cm(-1) with a spectral resolution of 2 cm(-1). Method to measure the atmospheric molecules was described and mathematical proof and quantitative algorithms to retrieve molecular concentration were established. The related models were performed both by a direct method based on the Beer-Lambert Law and by a simulating-fitting method based on HITRAN database and the instrument functions. Concentrations of CO2 were retrieved by the two models. The results of observation and modeling analyses indicate that the concentrations have a distribution of 300-370 ppm, and show tendency that going with the variation of the environment they first decrease slowly and then increase rapidly during the observation period, and reached low points in the afternoon and during the sunset. The concentrations with measuring times retrieved by the direct method and by the simulating-fitting method agree with each other very well, with the correlation of all the data is up to 99.79%, and the relative error is no more than 2.00%. The precision for retrieving is relatively high. The results of this paper demonstrate that, in the field of detecting atmospheric compositions, OP/FTIR method performed by the Infrared reflecting scanning Fourier transform spectrometry is a feasible and effective technical approach, and either the direct method or the simulating-fitting method is capable of retrieving concentrations with high precision.

A Method to Retrieve Rainfall Rate over Land from TRMM Observations

NASA Technical Reports Server (NTRS)

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

2002-01-01

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

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

PubMed

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

2018-01-01

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

Design and synthesis of multiple antigenic peptides and their application for dengue diagnosis.

PubMed

Rai, Reeta; Dubey, Sameer; Santosh, K V; Biswas, Ashutosh; Mehrotra, Vinit; Rao, D N

2017-09-01

Major difficulty in development of dengue diagnostics is availability of suitable antigens. To overcome this, we made an attempt to develop a peptide based diagnosis which offers significant advantage over other methods. With the help of in silico methods, two epitopes were selected from envelope protein and three from NS1 protein of dengue virus. These were synthesized in combination as three multiple antigenic peptides (MAPs). We have tested 157 dengue positive sera confirmed for NS1 antigen. MAP1 showed 96.81% sera positive for IgM and 68.15% positive for IgG. MAP2 detected 94.90% IgM and 59.23% IgG positive sera. MAP3 also detected 96.17% IgM and 59.87% IgG positive sera. To the best of our knowledge this is the first study describing the use of synthetic multiple antigenic peptides for the diagnosis of dengue infection. This study describes MAPs as a promising tool for the use in serodiagnosis of dengue. Copyright © 2017 International Alliance for Biological Standardization. Published by Elsevier Ltd. All rights reserved.

Multiview Locally Linear Embedding for Effective Medical Image Retrieval

PubMed Central

Shen, Hualei; Tao, Dacheng; Ma, Dianfu

2013-01-01

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

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

NASA Astrophysics Data System (ADS)

Xiang, Zhongbo; Li, Yanqiu

2017-10-01

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

Phase retrieval by coherent modulation imaging

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

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

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

Phase retrieval by coherent modulation imaging

DOE PAGES

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

2016-11-18

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

Cloud-top height retrieval from polarizing remote sensor POLDER

NASA Astrophysics Data System (ADS)

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

2006-10-01

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

Phase retrieval by coherent modulation imaging.

PubMed

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

2016-11-18

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

A case study of the sensitivity of forecast skill to data and data analysis techniques

NASA Technical Reports Server (NTRS)

Baker, W. E.; Atlas, R.; Halem, M.; Susskind, J.

1983-01-01

A series of experiments have been conducted to examine the sensitivity of forecast skill to various data and data analysis techniques for the 0000 GMT case of January 21, 1979. These include the individual components of the FGGE observing system, the temperatures obtained with different satellite retrieval methods, and the method of vertical interpolation between the mandatory pressure analysis levels and the model sigma levels. It is found that NESS TIROS-N infrared retrievals seriously degrade a rawinsonde-only analysis over land, resulting in a poorer forecast over North America. Less degradation in the 72-hr forecast skill at sea level and some improvement at 500 mb is noted, relative to the control with TIROS-N retrievals produced with a physical inversion method which utilizes a 6-hr forecast first guess. NESS VTPR oceanic retrievals lead to an improved forecast over North America when added to the control.

Retrievals of heavy ozone with MIPAS

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

Learning semantic and visual similarity for endomicroscopy video retrieval.

PubMed

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

2012-06-01

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

A New Neural Network Approach Including First-Guess for Retrieval of Atmospheric Water Vapor, Cloud Liquid Water Path, Surface Temperature and Emissivities Over Land From Satellite Microwave Observations

NASA Technical Reports Server (NTRS)

Aires, F.; Prigent, C.; Rossow, W. B.; Rothstein, M.; Hansen, James E. (Technical Monitor)

2000-01-01

The analysis of microwave observations over land to determine atmospheric and surface parameters is still limited due to the complexity of the inverse problem. Neural network techniques have already proved successful as the basis of efficient retrieval methods for non-linear cases, however, first-guess estimates, which are used in variational methods to avoid problems of solution non-uniqueness or other forms of solution irregularity, have up to now not been used with neural network methods. In this study, a neural network approach is developed that uses a first-guess. Conceptual bridges are established between the neural network and variational methods. The new neural method retrieves the surface skin temperature, the integrated water vapor content, the cloud liquid water path and the microwave surface emissivities between 19 and 85 GHz over land from SSM/I observations. The retrieval, in parallel, of all these quantities improves the results for consistency reasons. A data base to train the neural network is calculated with a radiative transfer model and a a global collection of coincident surface and atmospheric parameters extracted from the National Center for Environmental Prediction reanalysis, from the International Satellite Cloud Climatology Project data and from microwave emissivity atlases previously calculated. The results of the neural network inversion are very encouraging. The r.m.s. error of the surface temperature retrieval over the globe is 1.3 K in clear sky conditions and 1.6 K in cloudy scenes. Water vapor is retrieved with a r.m.s. error of 3.8 kg/sq m in clear conditions and 4.9 kg/sq m in cloudy situations. The r.m.s. error in cloud liquid water path is 0.08 kg/sq m . The surface emissivities are retrieved with an accuracy of better than 0.008 in clear conditions and 0.010 in cloudy conditions. Microwave land surface temperature retrieval presents a very attractive complement to the infrared estimates in cloudy areas: time record of land surface temperature will be produced.

A Wiener-Wavelet-Based filter for de-noising satellite soil moisture retrievals

NASA Astrophysics Data System (ADS)

Massari, Christian; Brocca, Luca; Ciabatta, Luca; Moramarco, Tommaso; Su, Chun-Hsu; Ryu, Dongryeol; Wagner, Wolfgang

2014-05-01

The reduction of noise in microwave satellite soil moisture (SM) retrievals is of paramount importance for practical applications especially for those associated with the study of climate changes, droughts, floods and other related hydrological processes. So far, Fourier based methods have been used for de-noising satellite SM retrievals by filtering either the observed emissivity time series (Du, 2012) or the retrieved SM observations (Su et al. 2013). This contribution introduces an alternative approach based on a Wiener-Wavelet-Based filtering (WWB) technique, which uses the Entropy-Based Wavelet de-noising method developed by Sang et al. (2009) to design both a causal and a non-causal version of the filter. WWB is used as a post-retrieval processing tool to enhance the quality of observations derived from the i) Advanced Microwave Scanning Radiometer for the Earth observing system (AMSR-E), ii) the Advanced SCATterometer (ASCAT), and iii) the Soil Moisture and Ocean Salinity (SMOS) satellite. The method is tested on three pilot sites located in Spain (Remedhus Network), in Greece (Hydrological Observatory of Athens) and in Australia (Oznet network), respectively. Different quantitative criteria are used to judge the goodness of the de-noising technique. Results show that WWB i) is able to improve both the correlation and the root mean squared differences between satellite retrievals and in situ soil moisture observations, and ii) effectively separates random noise from deterministic components of the retrieved signals. Moreover, the use of WWB de-noised data in place of raw observations within a hydrological application confirms the usefulness of the proposed filtering technique. Du, J. (2012), A method to improve satellite soil moisture retrievals based on Fourier analysis, Geophys. Res. Lett., 39, L15404, doi:10.1029/ 2012GL052435 Su,C.-H.,D.Ryu, A. W. Western, and W. Wagner (2013), De-noising of passive and active microwave satellite soil moisture time series, Geophys. Res. Lett., 40,3624-3630, doi:10.1002/grl.50695. Sang Y.-F., D. Wang, J.-C. Wu, Q.-P. Zhu, and L. Wang (2009), Entropy-Based Wavelet De-noising Method for Time Series Analysis, Entropy, 11, pp. 1123-1148, doi:10.3390/e11041123.

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

PubMed

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

2017-01-01

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

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

PubMed Central

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

2017-01-01

Retrieval inhibition hypothesis of directed forgetting effects assumed TBF (to-be-forgotten) items were not retrieved intentionally, while selective rehearsal hypothesis assumed the memory representation of retrieved TBF (to-be-forgotten) items was weaker than TBR (to-be-remembered) items. Previous studies indicated that directed forgetting effects of item-cueing method resulted from selective rehearsal at encoding, but the mechanism of retrieval inhibition that affected directed forgetting of TBF (to-be-forgotten) items was not clear. Strategic retrieval is a control process allowing the selective retrieval of target information, which includes retrieval orientation and strategic recollection. Retrieval orientation via the comparison of tasks refers to the specific form of processing resulted by retrieval efforts. Strategic recollection is the type of strategies to recollect studied items for the retrieval success of targets. Using a “directed forgetting” paradigm combined with a memory exclusion task, our investigation of strategic retrieval in directed forgetting assisted to explore how retrieval inhibition played a role on directed forgetting effects. When TBF items were targeted, retrieval orientation showed more positive ERPs to new items, indicating that TBF items demanded more retrieval efforts. The results of strategic recollection indicated that: (a) when TBR items were retrieval targets, late parietal old/new effects were only evoked by TBR items but not TBF items, indicating the retrieval inhibition of TBF items; (b) when TBF items were retrieval targets, the late parietal old/new effect were evoked by both TBR items and TBF items, indicating that strategic retrieval could overcome retrieval inhibition of TBF items. These findings suggested the modulation of strategic retrieval on retrieval inhibition of directed forgetting, supporting that directed forgetting effects were not only caused by selective rehearsal, but also retrieval inhibition. PMID:28900411

A novel dendritic cell-based direct ex vivo assay for detection and enumeration of circulating antigen-specific human T cells.

PubMed

Carrio, Roberto; Zhang, Ge; Drake, Donald R; Schanen, Brian C

2018-05-07

Although a variety of assays have been used to examine T cell responses in vitro, standardized ex vivo detection of antigen-specific CD4 + T cells from human circulatory PBMCs remains constrained by low-dimensional characterization outputs and the need for polyclonal, mitogen-induced expansion methods to generate detectable response signals. To overcome these limitations, we developed a novel methodology utilizing antigen-pulsed autologous human dendritic target cells in a rapid and sensitive assay to accurately enumerate antigen-specific CD4 + T cell precursor frequency by multiparametric flow cytometry. With this approach, we demonstrate the ability to reproducibly quantitate poly-functional T cell responses following both primary and recall antigenic stimulation. Furthermore, this approach enables more comprehensive phenotypic profiling of circulating antigen-specific CD4 + T cells, providing valuable insights into the pre-existing polarization of antigen-specific T cells in humans. Combined, this approach permits sensitive and detailed ex vivo detection of antigen-specific CD4 + T cells delivering an important tool for advancing vaccine, immune-oncology and other therapeutic studies.

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

PubMed

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

2012-03-01

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

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…

Cloning and expansion of antigen-specific T cells using iPS cell technology: development of "off-the-shelf" T cells for the use in allogeneic transfusion settings.

PubMed

Kawamoto, Hiroshi; Masuda, Kyoko; Nagano, Seiji; Maeda, Takuya

2018-03-01

Recent advances in adoptive immunotherapy using cytotoxic T lymphocytes (CTLs) have led to moderate therapeutic anti-cancer effects in clinical trials. However, a critical issue, namely that CTLs collected from patients are easily exhausted during expansion culture, has yet to be solved. To address this issue, we have been developing a strategy which utilizes induced pluripotent stem cell (iPSC) technology. This strategy is based on the idea that when iPSCs are produced from antigen-specific CTLs, CTLs regenerated from such iPSCs should show the same antigen specificity as the original CTLs. Pursuing this idea, we previously succeeded in regenerating melanoma antigen MART1-specific CTLs, and more recently in producing potent CTLs expressing CD8αβ heterodimer. We are now developing a novel method by which non-T derived iPSCs are transduced with exogenous T cell receptor genes. If this method is applied to Human Leukocyte Antigen (HLA) haplotype-homozygous iPSC stock, it will be possible to prepare "off-the-shelf" T cells. As a first-in-human trial, we are planning to apply our strategy to relapsed acute myeloid leukemia patients by targeting the WT1 antigen.

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

PubMed

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

2017-01-01

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

Synthetic oligonucleotide antigens modified with locked nucleic acids detect disease specific antibodies

NASA Astrophysics Data System (ADS)

Samuelsen, Simone V.; Solov'Yov, Ilia A.; Balboni, Imelda M.; Mellins, Elizabeth; Nielsen, Christoffer Tandrup; Heegaard, Niels H. H.; Astakhova, Kira

2016-10-01

New techniques to detect and quantify antibodies to nucleic acids would provide a significant advance over current methods, which often lack specificity. We investigate the potential of novel antigens containing locked nucleic acids (LNAs) as targets for antibodies. Particularly, employing molecular dynamics we predict optimal nucleotide composition for targeting DNA-binding antibodies. As a proof of concept, we address a problem of detecting anti-DNA antibodies that are characteristic of systemic lupus erythematosus, a chronic autoimmune disease with multiple manifestations. We test the best oligonucleotide binders in surface plasmon resonance studies to analyze binding and kinetic aspects of interactions between antigens and target DNA. These DNA and LNA/DNA sequences showed improved binding in enzyme-linked immunosorbent assay using human samples of pediatric lupus patients. Our results suggest that the novel method is a promising tool to create antigens for research and point-of-care monitoring of anti-DNA antibodies.

High-level generation of polyclonal antibodies by genetic immunization.

PubMed

Chambers, Ross S; Johnston, Stephen Albert

2003-09-01

Antibodies are important tools for investigating the proteome, but current methods for producing them have become a rate-limiting step. A primary obstacle in most methods for generating antibodies or antibody-like molecules is the requirement for at least microgram quantities of purified protein. We have developed a technology for producing antibodies using genetic immunization. Genetic immunization-based antibody production offers several advantages, including high throughput and high specificity. Moreover, antibodies produced from genetically immunized animals are more likely to recognize the native protein. Here we show that a genetic immunization-based system can be used to efficiently raise useful antibodies to a wide range of antigens. We accomplished this by linking the antigen gene to various elements that enhance antigenicity and by codelivering plasmids encoding genetic adjuvants. Our system, which was tested by immunizing mice with >130 antigens, has shown a final success rate of 84%.

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

PubMed Central

Wang, Tongtong; Xiao, Zhiqiang; Liu, Zhigang

2017-01-01

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

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

PubMed

Wang, Tongtong; Xiao, Zhiqiang; Liu, Zhigang

2017-01-01

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

Quantitative Detection of the Foot-And-Mouth Disease Virus Serotype O 146S Antigen for Vaccine Production Using a Double-Antibody Sandwich ELISA and Nonlinear Standard Curves.

PubMed

Feng, Xia; Ma, Jun-Wu; Sun, Shi-Qi; Guo, Hui-Chen; Yang, Ya-Min; Jin, Ye; Zhou, Guang-Qing; He, Ji-Jun; Guo, Jian-Hong; Qi, Shu-yun; Lin, Mi; Cai, Hu; Liu, Xiang-Tao

2016-01-01

The efficacy of an inactivated foot-and-mouth disease (FMD) vaccine is mainly dependent on the integrity of the foot-and-mouth disease virus (FMDV) particles. At present, the standard method to quantify the active component, the 146S antigen, of FMD vaccines is sucrose density gradient (SDG) analysis. However, this method is highly operator dependent and difficult to automate. In contrast, the enzyme-linked immunosorbent assay (ELISA) is a time-saving technique that provides greater simplicity and sensitivity. To establish a valid method to detect and quantify the 146S antigen of a serotype O FMD vaccine, a double-antibody sandwich (DAS) ELISA was compared with an SDG analysis. The DAS ELISA was highly correlated with the SDG method (R2 = 0.9215, P<0.01). In contrast to the SDG method, the DAS ELISA was rapid, robust, repeatable and highly sensitive, with a minimum quantification limit of 0.06 μg/mL. This method can be used to determine the effective antigen yields in inactivated vaccines and thus represents an alternative for assessing the potency of FMD vaccines in vitro. But it still needs to be prospectively validated by analyzing a new vaccine preparation and determining the proper protective dose followed by an in vivo vaccination-challenge study to confirm the ELISA findings.

Quantitative Detection of the Foot-And-Mouth Disease Virus Serotype O 146S Antigen for Vaccine Production Using a Double-Antibody Sandwich ELISA and Nonlinear Standard Curves

PubMed Central

Feng, Xia; Ma, Jun-Wu; Sun, Shi-Qi; Guo, Hui-Chen; Yang, Ya-Min; Jin, Ye; Zhou, Guang-Qing; He, Ji-Jun; Guo, Jian-Hong; Qi, Shu-yun; Lin, Mi; Cai, Hu; Liu, Xiang-Tao

2016-01-01

The efficacy of an inactivated foot-and-mouth disease (FMD) vaccine is mainly dependent on the integrity of the foot-and-mouth disease virus (FMDV) particles. At present, the standard method to quantify the active component, the 146S antigen, of FMD vaccines is sucrose density gradient (SDG) analysis. However, this method is highly operator dependent and difficult to automate. In contrast, the enzyme-linked immunosorbent assay (ELISA) is a time-saving technique that provides greater simplicity and sensitivity. To establish a valid method to detect and quantify the 146S antigen of a serotype O FMD vaccine, a double-antibody sandwich (DAS) ELISA was compared with an SDG analysis. The DAS ELISA was highly correlated with the SDG method (R2 = 0.9215, P<0.01). In contrast to the SDG method, the DAS ELISA was rapid, robust, repeatable and highly sensitive, with a minimum quantification limit of 0.06 μg/mL. This method can be used to determine the effective antigen yields in inactivated vaccines and thus represents an alternative for assessing the potency of FMD vaccines in vitro. But it still needs to be prospectively validated by analyzing a new vaccine preparation and determining the proper protective dose followed by an in vivo vaccination-challenge study to confirm the ELISA findings. PMID:26930597

[Comparative study of the antigens of Streptococcus group A. Rport I. Comparative characteristics of the immunologic activity of partially purified M-protien and the cytoplasmic protective antigen].

PubMed

Evseev, V A; Avdeeva, Zh I; Kondrashov, G I

1975-12-01

Experiments were conducted on mice. A study was made of the protective properties of the cytoplasmic fraction of streptococcus, group A, Type 1 and of an antigen isolated from it by sedimentation with ammonium sulfate, in comparison with M-protein partially purified by the method of Lancefield and Perlman. Cytoplasmic antigen was not inferior by immunogenicity in comparison with M-protein. In difference from the latter, it was thermolabile and sensitive to the action of hydrochloric acid. The protective antigen was revealed in the cytoplasm not only of the virulent, but also of avirulent strains of streptococcus devoid of M-protein.

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

PubMed

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

2014-04-01

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

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

PubMed

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

2000-05-01

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

Searching for evidence or approval? A commentary on database search in systematic reviews and alternative information retrieval methodologies.

PubMed

Delaney, Aogán; Tamás, Peter A

2018-03-01

Despite recognition that database search alone is inadequate even within the health sciences, it appears that reviewers in fields that have adopted systematic review are choosing to rely primarily, or only, on database search for information retrieval. This commentary reminds readers of factors that call into question the appropriateness of default reliance on database searches particularly as systematic review is adapted for use in new and lower consensus fields. It then discusses alternative methods for information retrieval that require development, formalisation, and evaluation. Our goals are to encourage reviewers to reflect critically and transparently on their choice of information retrieval methods and to encourage investment in research on alternatives. Copyright © 2017 John Wiley & Sons, Ltd.

Nonstationary signal analysis in episodic memory retrieval

NASA Astrophysics Data System (ADS)

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

2004-04-01

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

Retrieval of all effective susceptibilities in nonlinear metamaterials

NASA Astrophysics Data System (ADS)

Larouche, Stéphane; Radisic, Vesna

2018-04-01

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

Joint retrievals of cloud and drizzle in marine boundary layer clouds using ground-based radar, lidar and zenith radiances

DOE PAGES

Fielding, M. D.; Chiu, J. C.; Hogan, R. J.; ...

2015-07-02

Active remote sensing of marine boundary-layer clouds is challenging as drizzle drops often dominate the observed radar reflectivity. We present a new method to simultaneously retrieve cloud and drizzle vertical profiles in drizzling boundary-layer clouds using surface-based observations of radar reflectivity, lidar attenuated backscatter, and zenith radiances under conditions when precipitation does not reach the surface. Specifically, the vertical structure of droplet size and water content of both cloud and drizzle is characterised throughout the cloud. An ensemble optimal estimation approach provides full error statistics given the uncertainty in the observations. To evaluate the new method, we first perform retrievalsmore » using synthetic measurements from large-eddy simulation snapshots of cumulus under stratocumulus, where cloud water path is retrieved with an error of 31 g m -2. The method also performs well in non-drizzling clouds where no assumption of the cloud profile is required. We then apply the method to observations of marine stratocumulus obtained during the Atmospheric Radiation Measurement MAGIC deployment in the Northeast Pacific. Here, retrieved cloud water path agrees well with independent three-channel microwave radiometer retrievals, with a root mean square difference of 10–20 g m -2.« less

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

ERIC Educational Resources Information Center

SALTON, GERALD

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

Towards a Theory of Learning for Naming Rehabilitation: Retrieval Practice and Spacing Effects

ERIC Educational Resources Information Center

Middleton, Erica L.; Schwarts, Myrna F.; Rawson, Katherine A.; Traut, Hilary; Verkuilen, Jay

2016-01-01

Purpose: The purpose of this article was to examine how different types of learning experiences affect naming impairment in aphasia. Methods: In 4 people with aphasia with naming impairment, we compared the benefits of naming treatment that emphasized "retrieval practice" (practice retrieving target names from long-term memory) with…

Disposal of Information Seeking and Retrieval Research: Replacement with a Radical Proposition

ERIC Educational Resources Information Center

Budd, John M.; Anstaett, Ashley

2013-01-01

Introduction: Research and theory on the topics of information seeking and retrieval have been plagued by some fundamental problems for several decades. Many of the difficulties spring from mechanistic and instrumental thinking and modelling. Method: Existing models of information retrieval and information seeking are examined for efficacy in a…

Strong Similarity Measures for Ordered Sets of Documents in Information Retrieval.

ERIC Educational Resources Information Center

Egghe, L.; Michel, Christine

2002-01-01

Presents a general method to construct ordered similarity measures in information retrieval based on classical similarity measures for ordinary sets. Describes a test of some of these measures in an information retrieval system that extracted ranked document sets and discuses the practical usability of the ordered similarity measures. (Author/LRW)

A Comparison of Intention and Pantomime Gesture Treatment for Noun Retrieval in People with Aphasia

ERIC Educational Resources Information Center

Ferguson, Neina F.; Evans, Kelli; Raymer, Anastasia M.

2012-01-01

Purpose: The effects of intention gesture treatment (IGT) and pantomime gesture treatment (PGT) on word retrieval were compared in people with aphasia. Method: Four individuals with aphasia and word retrieval impairments subsequent to left-hemisphere stroke participated in a single-participant crossover treatment design. Each participant viewed…

Semantics of User Interface for Image Retrieval: Possibility Theory and Learning Techniques.

ERIC Educational Resources Information Center

Crehange, M.; And Others

1989-01-01

Discusses the need for a rich semantics for the user interface in interactive image retrieval and presents two methods for building such interfaces: possibility theory applied to fuzzy data retrieval, and a machine learning technique applied to learning the user's deep need. Prototypes developed using videodisks and knowledge-based software are…

Digital adaptive optics confocal microscopy based on iterative retrieval of optical aberration from a guidestar hologram

PubMed Central

Liu, Changgeng; Thapa, Damber; Yao, Xincheng

2017-01-01

Guidestar hologram based digital adaptive optics (DAO) is one recently emerging active imaging modality. It records each complex distorted line field reflected or scattered from the sample by an off-axis digital hologram, measures the optical aberration from a separate off-axis digital guidestar hologram, and removes the optical aberration from the distorted line fields by numerical processing. In previously demonstrated DAO systems, the optical aberration was directly retrieved from the guidestar hologram by taking its Fourier transform and extracting the phase term. For the direct retrieval method (DRM), when the sample is not coincident with the guidestar focal plane, the accuracy of the optical aberration retrieved by DRM undergoes a fast decay, leading to quality deterioration of corrected images. To tackle this problem, we explore here an image metrics-based iterative method (MIM) to retrieve the optical aberration from the guidestar hologram. Using an aberrated objective lens and scattering samples, we demonstrate that MIM can improve the accuracy of the retrieved aberrations from both focused and defocused guidestar holograms, compared to DRM, to improve the robustness of the DAO. PMID:28380937

A novel system of artificial antigen-presenting cells efficiently stimulates Flu peptide-specific cytotoxic T cells in vitro

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

Han, Hui; Peng, Ji-Run, E-mail: pengjr@medmail.com.cn; Chen, Peng-Cheng

Highlights: {yields} Adoptive immunotherapy depends on relevant numbers of cytolytic T lymphocytes. {yields} An ideal artificial APCs system was successfully prepared in vivo. {yields} Controlled release of IL-2 leads to much more T-cell expansion. {yields} This system is better than general cellular APCs on T-cell expansion. -- Abstract: Therapeutic numbers of antigen-specific cytotoxic T lymphocytes (CTLs) are key effectors in successful adoptive immunotherapy. However, efficient and reproducible methods to meet the qualification remain poor. To address this issue, we designed the artificial antigen-presenting cell (aAPC) system based on poly(lactic-co-glycolic acid) (PLGA). A modified emulsion method was used for the preparationmore » of PLGA particles encapsulating interleukin-2 (IL-2). Biotinylated molecular ligands for recognition and co-stimulation of T cells were attached to the particle surface through the binding of avidin-biotin. These formed the aAPC system. The function of aAPCs in the proliferation of specific CTLs against human Flu antigen was detected by enzyme-linked immunospot assay (ELISPOT) and MTT staining methods. Finally, we successfully prepared this suitable aAPC system. The results show that IL-2 is released from aAPCs in a sustained manner over 30 days. This dramatically improves the stimulatory capacity of this system as compared to the effect of exogenous addition of cytokine. In addition, our aAPCs promote the proliferation of Flu antigen-specific CTLs more effectively than the autologous cellular APCs. Here, this aAPC platform is proved to be suitable for expansion of human antigen-specific T cells.« less

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

PubMed

Bouadjenek, Mohamed Reda; Verspoor, Karin

2017-01-01

In the context of the bioCADDIE challenge addressing information retrieval of biomedical datasets, we propose a method for retrieval of biomedical data sets with heterogenous schemas through query reformulation. In particular, the method proposed transforms the initial query into a multi-field query that is then enriched with terms that are likely to occur in the relevant datasets. We compare and evaluate two query expansion strategies, one based on the Rocchio method and another based on a biomedical lexicon. We then perform a comprehensive comparative evaluation of our method on the bioCADDIE dataset collection for biomedical retrieval. We demonstrate the effectiveness of our multi-field query method compared to two baselines, with MAP improved from 0.2171 and 0.2669 to 0.2996. We also show the benefits of query expansion, where the Rocchio expanstion method improves the MAP for our two baselines from 0.2171 and 0.2669 to 0.335. We show that the Rocchio query expansion method slightly outperforms the one based on the biomedical lexicon as a source of terms, with an improvement of roughly 3% for MAP. However, the query expansion method based on the biomedical lexicon is much less resource intensive since it does not require computation of any relevance feedback set or any initial execution of the query. Hence, in term of trade-off between efficiency, execution time and retrieval accuracy, we argue that the query expansion method based on the biomedical lexicon offers the best performance for a prototype biomedical data search engine intended to be used at a large scale. In the official bioCADDIE challenge results, although our approach is ranked seventh in terms of the infNDCG evaluation metric, it ranks second in term of P@10 and NDCG. Hence, the method proposed here provides overall good retrieval performance in relation to the approaches of other competitors. Consequently, the observations made in this paper should benefit the development of a Data Discovery Index prototype or the improvement of the existing one. © The Author(s) 2017. Published by Oxford University Press.

Multi-field query expansion is effective for biomedical dataset retrieval

PubMed Central

2017-01-01

Abstract In the context of the bioCADDIE challenge addressing information retrieval of biomedical datasets, we propose a method for retrieval of biomedical data sets with heterogenous schemas through query reformulation. In particular, the method proposed transforms the initial query into a multi-field query that is then enriched with terms that are likely to occur in the relevant datasets. We compare and evaluate two query expansion strategies, one based on the Rocchio method and another based on a biomedical lexicon. We then perform a comprehensive comparative evaluation of our method on the bioCADDIE dataset collection for biomedical retrieval. We demonstrate the effectiveness of our multi-field query method compared to two baselines, with MAP improved from 0.2171 and 0.2669 to 0.2996. We also show the benefits of query expansion, where the Rocchio expanstion method improves the MAP for our two baselines from 0.2171 and 0.2669 to 0.335. We show that the Rocchio query expansion method slightly outperforms the one based on the biomedical lexicon as a source of terms, with an improvement of roughly 3% for MAP. However, the query expansion method based on the biomedical lexicon is much less resource intensive since it does not require computation of any relevance feedback set or any initial execution of the query. Hence, in term of trade-off between efficiency, execution time and retrieval accuracy, we argue that the query expansion method based on the biomedical lexicon offers the best performance for a prototype biomedical data search engine intended to be used at a large scale. In the official bioCADDIE challenge results, although our approach is ranked seventh in terms of the infNDCG evaluation metric, it ranks second in term of P@10 and NDCG. Hence, the method proposed here provides overall good retrieval performance in relation to the approaches of other competitors. Consequently, the observations made in this paper should benefit the development of a Data Discovery Index prototype or the improvement of the existing one. PMID:29220457

Cross-Language Information Retrieval: An Analysis of Errors.

ERIC Educational Resources Information Center

Ruiz, Miguel E.; Srinivasan, Padmini

1998-01-01

Investigates an automatic method for Cross Language Information Retrieval (CLIR) that utilizes the multilingual Unified Medical Language System (UMLS) Metathesaurus to translate Spanish natural-language queries into English. Results indicate that for Spanish, the UMLS Metathesaurus-based CLIR method is at least equivalent to if not better than…

n-Gram-Based Indexing for Korean Text Retrieval.

ERIC Educational Resources Information Center

Lee, Joon Ho; Cho, Hyun Yang; Park, Hyouk Ro

1999-01-01

Discusses indexing methods in Korean text retrieval and proposes a new indexing method based on n-grams which can handle compound nouns effectively without dictionaries and complex linguistic knowledge. Experimental results show that n-gram-based indexing is considerably faster than morpheme-based indexing, and also provides better retrieval…

The Effect of Retrieval on Post-Task Enjoyment of Studying

ERIC Educational Resources Information Center

Clark, Daniel A.; Svinicki, Marilla

2015-01-01

Although active retrieval is an extremely effective study method, students continue to use less effective methods (Karpicke, "Journal of Experimental Psychology General," 138(4), 469-486, 2009; Hartwig and Dunlosky, "Psychonomic Bulletin & Review," 19(1), 126-134, 2012). There are likely many underlying reasons for using…

Study of the temperature dependent immuno-reaction kinetics for the bio-functionalized magnetic nanoparticle assay of bio-markers of colorectal cancer

NASA Astrophysics Data System (ADS)

Yang, S. Y.; Chang, J. F.; Chen, T. C.; Yang, C. C.; Ho, C. S.

2014-01-01

By conjugating antibodies on magnetic nanoparticles, target antigens can be quantitatively detected by measuring the magnetic signals of the magnetic nanoparticles due to their association with target antigens. This method of detection is called magnetically labeled immunoassay. The assay characteristics of magnetically labeled immunoassay have been reported widely. However, the immuno-reaction kinetics of magnetically labeled immunoassay has not been studied. In this work, the reaction rates between magnetic nanoparticles and target antigens are measured at various temperatures. It is found that the temperature dependent reaction rate obeys Arrhenius's equation, which shows the collision frequency and activation energy for the immuno-reaction between antibody-functionalized magnetic nanoparticles and target antigens. The carcinoembryonic antigen, which is a regular blood bio-marker for in-vitro diagnosis of colorectal cancer, is used as a target antigen for the example.

Enzymatic signal amplification for sensitive detection of intracellular antigens by flow cytometry.

PubMed

Karkmann, U; Radbruch, A; Hölzel, V; Scheffold, A

1999-11-19

Flow cytometry is the method of choice for the analysis of single cells with respect to the expression of specific antigens. Antigens can be detected with specific antibodies either on the cell surface or within the cells, after fixation and permeabilization of the cell membrane. Using conventional fluorochrome-labeled antibodies several thousand antigens are required for clear-cut separation of positive and negative cells. More sensitive reagents, e.g., magnetofluorescent liposomes conjugated to specific antibodies permit the detection of less than 200 molecules per cell but cannot be used for the detection of intracellular antigens. Here, we describe an enzymatic amplification technique (intracellular tyramine-based signal amplification, ITSA) for the sensitive cytometric analysis of intracellular cytokines by immunofluorescence. This approach results in a 10 to 15-fold improvement of the signal-to-noise ratio compared to conventional fluorochrome labeled antibodies and permits the detection of as few as 300-400 intracellular antigens per cell.

The joint methane profiles retrieval approach from GOSAT TIR and SWIR spectra

NASA Astrophysics Data System (ADS)

Zadvornykh, Ilya V.; Gribanov, Konstantin G.; Zakharov, Vyacheslav I.; Imasu, Ryoichi

2017-11-01

In this paper we present a method, using methane as example, which allows more accurate greenhouse gases retrieval in the Earth's atmosphere. Using the new version of the FIRE-ARMS software, supplemented with the VLIDORT vector radiation transfer model, we carried out joint methane retrieval from TIR (Thermal Infrared Range) and SWIR (ShortWavelength Infrared Range) GOSAT spectra using optimal estimation method. MACC reanalysis data from the European Center for Medium-Range Forecasts (ECMWF), supplemented by data from aircraft measurements of the HIPPO experiment were used as a statistical ensemble.

Digital micromirror device as amplitude diffuser for multiple-plane phase retrieval

NASA Astrophysics Data System (ADS)

Abregana, Timothy Joseph T.; Hermosa, Nathaniel P.; Almoro, Percival F.

2017-06-01

Previous implementations of the phase diffuser used in the multiple-plane phase retrieval method included a diffuser glass plate with fixed optical properties or a programmable yet expensive spatial light modulator. Here a model for phase retrieval based on a digital micromirror device as amplitude diffuser is presented. The technique offers programmable, convenient and low-cost amplitude diffuser for a non-stagnating iterative phase retrieval. The technique is demonstrated in the reconstructions of smooth object wavefronts.

Content-based video retrieval by example video clip

NASA Astrophysics Data System (ADS)

Dimitrova, Nevenka; Abdel-Mottaleb, Mohamed

1997-01-01

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

A content-based news video retrieval system: NVRS

NASA Astrophysics Data System (ADS)

Liu, Huayong; He, Tingting

2009-10-01

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

Novel use of a radiolabelled antibody against stage specific embryonic antigen for the detection of occult abscesses in mammals

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

Thakur, Madhukar L.

1990-01-01

The invention discloses improved reagents containing antibodies against stage specific embryonic antigen-1 antibodies and improved methods for detection of occult abscess and inflammation using the improved reagents.

Guenter Tulip Filter Retrieval Experience: Predictors of Successful Retrieval

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

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

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

Automatic Evidence Retrieval for Systematic Reviews

PubMed Central

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

2014-01-01

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

Case studies of aerosol and ocean color retrieval using a Markov chain radiative transfer model and AirMSPI measurements

NASA Astrophysics Data System (ADS)

Xu, F.; Diner, D. J.; Seidel, F. C.; Dubovik, O.; Zhai, P.

2014-12-01

A vector Markov chain radiative transfer method was developed for forward modeling of radiance and polarization fields in a coupled atmosphere-ocean system. The method was benchmarked against an independent Successive Orders of Scattering code and linearized through the use of Jacobians. Incorporated with the multi-patch optimization algorithm and look-up-table method, simultaneous aerosol and ocean color retrievals were performed using imagery acquired by the Airborne Multiangle SpectroPolarimetric Imager (AirMSPI) when it was operated in step-and-stare mode with 9 viewing angles ranging between ±67°. Data from channels near 355, 380, 445, 470*, 555, 660*, and 865* nm were used in the retrievals, where the asterisk denotes the polarimetric bands. Retrievals were run for AirMSPI overflights over Southern California and Monterey Bay, CA. For the relatively high aerosol optical depth (AOD) case (~0.28 at 550 nm), the retrieved aerosol concentration, size distribution, water-leaving radiance, and chlorophyll concentration were compared to those reported by the USC SeaPRISM AERONET-OC site off the coast of Southern California on 6 February 2013. For the relatively low AOD case (~0.08 at 550 nm), the retrieved aerosol concentration and size distribution were compared to those reported by the Monterey Bay AERONET site on 28 April 2014. Further, we evaluate the benefits of multi-angle and polarimetric observations by performing the retrievals using (a) all view angles and channels; (b) all view angles but radiances only (no polarization); (c) the nadir view angle only with both radiance and polarization; and (d) the nadir view angle without polarization. Optimized retrievals using different initial guesses were performed to provide a measure of retrieval uncertainty. Removal of multi-angular or polarimetric information resulted in increases in both parameter uncertainty and systematic bias. Potential accuracy improvements afforded by applying constraints on the surface and aerosol parametric models will also be discussed.

Immune Centroids Over-Sampling Method for Multi-Class Classification

DTIC Science & Technology

2015-05-22

recognize to specific antigens . The response of a receptor to an antigen can activate its hosting B-cell. Activated B-cell then proliferates and...modifying N.K. Jerne’s theory. The theory states that in a pre-existing group of lympho- cytes ( specifically B cells), a specific antigen only...the clusters of each small class, which have high data density, called global immune centroids over-sampling (denoted as Global-IC). Specifically

Multiple Strategy Bio-Detection Sensor Platforms Made From Carbon and Polymer Materials

DTIC Science & Technology

2006-08-10

binding of antigens. Further investigations were conducted on the antibody-antigen detection scheme using known test antigens (i.e. bacteria ). While...this method worked in preliminary studies, the use of antibodies was determined not to be feasible for detecting many different types of bacteria in...solution. Also, as the number of bacteria in a solution increased, it became necessary to wash the detection surface more extensively to favor specific

A retrospective analysis of the Alzheimer's disease vaccine progress - The critical need for new development strategies.

PubMed

Marciani, Dante J

2016-06-01

The promising results obtained with aducanumab and solanezumab against Alzheimer's disease (AD) strengthen the vaccine approach to prevent AD, despite of the many clinical setbacks. It has been problematic to use conjugated peptides with Th1/Th2 adjuvants to induce immune responses against conformational epitopes formed by Aβ oligomers, which is critical to induce protective antibodies. Hence, vaccination should mimic natural immunity by using whole or if possible conjugated antigens, but biasing the response to Th2 with anti-inflammatory adjuvants. Also, selection of the carrier and cross-linking agents is important to prevent suppression of the immune response against the antigen. That certain compounds having phosphorylcholine or fucose induce a sole Th2 immunity would allow antigens with T-cell epitopes without inflammatory autoimmune reactions to be used. Another immunization method is DNA vaccines combined with antigenic ones, which favors the clonal selection and expansion of high affinity antibodies needed for immune protection, but this also requires Th2 immunity. Since AD transgenic mouse models have limited value for immunogen selection as shown by the clinical studies, screening may require the use of validated antibodies and biophysical methods to identify the antigens that would be most likely recognized by the human immune system and thus capable to stimulate a protective antibody response. To induce an anti-Alzheimer's disease protective immunity and prevent possible damage triggered by antigens having B-cell epitopes-only, whole antigens might be used; while inducing Th2 immunity with sole anti-inflammatory fucose-based adjuvants. This approach would avert a damaging systemic inflammatory immunity and the suppression of immunoresponse against the antigen because of carrier and cross-linkers; immune requirements that extend to DNA vaccines. © 2016 International Society for Neurochemistry.

The interfacial character of antibody paratopes: analysis of antibody-antigen structures.

PubMed

Nguyen, Minh N; Pradhan, Mohan R; Verma, Chandra; Zhong, Pingyu

2017-10-01

In this study, computational methods are applied to investigate the general properties of antigen engaging residues of a paratope from a non-redundant dataset of 403 antibody-antigen complexes to dissect the contribution of hydrogen bonds, hydrophobic, van der Waals contacts and ionic interactions, as well as role of water molecules in the antigen-antibody interface. Consistent with previous reports using smaller datasets, we found that Tyr, Trp, Ser, Asn, Asp, Thr, Arg, Gly, His contribute substantially to the interactions between antibody and antigen. Furthermore, antibody-antigen interactions can be mediated by interfacial waters. However, there is no reported comprehensive analysis for a large number of structured waters that engage in higher ordered structures at the antibody-antigen interface. From our dataset, we have found the presence of interfacial waters in 242 complexes. We present evidence that suggests a compelling role of these interfacial waters in interactions of antibodies with a range of antigens differing in shape complementarity. Finally, we carry out 296 835 pairwise 3D structure comparisons of 771 structures of contact residues of antibodies with their interfacial water molecules from our dataset using CLICK method. A heuristic clustering algorithm is used to obtain unique structural similarities, and found to separate into 368 different clusters. These clusters are used to identify structural motifs of contact residues of antibodies for epitope binding. This clustering database of contact residues is freely accessible at http://mspc.bii.a-star.edu.sg/minhn/pclick.html. minhn@bii.a-star.edu.sg, chandra@bii.a-star.edu.sg or zhong_pingyu@immunol.a-star.edu.sg. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Cloud Retrieval Intercomparisons Between SEVIRI, MODIS and VIIRS with CHIMAERA PGE06 Data Collection 6 Products

NASA Technical Reports Server (NTRS)

Wind, Galina; Riedi, Jerome; Platnick, Steven; Heidinger, Andrew

2014-01-01

The Cross-platform HIgh resolution Multi-instrument AtmosphEric Retrieval Algorithms (CHIMAERA) system allows us to perform MODIS-like cloud top, optical and microphysical properties retrievals on any sensor that possesses a minimum set of common spectral channels. The CHIMAERA system uses a shared-core architecture that takes retrieval method out of the equation when intercomparisons are made. Here we show an example of such retrieval and a comparison of simultaneous retrievals done using SEVIRI, MODIS and VIIRS sensors. All sensor retrievals are performed using CLAVR-x (or CLAVR-x based) cloud top properties algorithm. SEVIRI uses the SAF_NWC cloud mask. MODIS and VIIRS use the IFF-based cloud mask that is a shared algorithm between MODIS and VIIRS. The MODIS and VIIRS retrievals are performed using a VIIRS branch of CHIMAERA that limits available MODIS channel set. Even though in that mode certain MODIS products such as multilayer cloud map are not available, the cloud retrieval remains fully equivalent to operational Data Collection 6.

Retrieval of an ice water path over the ocean from ISMAR and MARSS millimeter and submillimeter brightness temperatures

NASA Astrophysics Data System (ADS)

Brath, Manfred; Fox, Stuart; Eriksson, Patrick; Chawn Harlow, R.; Burgdorf, Martin; Buehler, Stefan A.

2018-02-01

A neural-network-based retrieval method to determine the snow ice water path (SIWP), liquid water path (LWP), and integrated water vapor (IWV) from millimeter and submillimeter brightness temperatures, measured by using airborne radiometers (ISMAR and MARSS), is presented. The neural networks were trained by using atmospheric profiles from the ICON numerical weather prediction (NWP) model and by radiative transfer simulations using the Atmospheric Radiative Transfer Simulator (ARTS). The basic performance of the retrieval method was analyzed in terms of offset (bias) and the median fractional error (MFE), and the benefit of using submillimeter channels was studied in comparison to pure microwave retrievals. The retrieval is offset-free for SIWP > 0.01 kg m-2, LWP > 0.1 kg m-2, and IWV > 3 kg m-2. The MFE of SIWP decreases from 100 % at SIWP = 0.01 kg m-2 to 20 % at SIWP = 1 kg m-2 and the MFE of LWP from 100 % at LWP = 0.05 kg m-2 to 30 % at LWP = 1 kg m-2. The MFE of IWV for IWV > 3 kg m-2 is 5 to 8 %. The SIWP retrieval strongly benefits from submillimeter channels, which reduce the MFE by a factor of 2, compared to pure microwave retrievals. The IWV and the LWP retrievals also benefit from submillimeter channels, albeit to a lesser degree. The retrieval was applied to ISMAR and MARSS brightness temperatures from FAAM flight B897 on 18 March 2015 of a precipitating frontal system west of the coast of Iceland. Considering the given uncertainties, the retrieval is in reasonable agreement with the SIWP, LWP, and IWV values simulated by the ICON NWP model for that flight. A comparison of the retrieved IWV with IWV from 12 dropsonde measurements shows an offset of 0.5 kg m-2 and an RMS difference of 0.8 kg m-2, showing that the retrieval of IWV is highly effective even under cloudy conditions.

Retrievals of Ice Cloud Microphysical Properties of Deep Convective Systems using Radar Measurements

NASA Astrophysics Data System (ADS)

Tian, J.; Dong, X.; Xi, B.; Wang, J.; Homeyer, C. R.

2015-12-01

This study presents innovative algorithms for retrieving ice cloud microphysical properties of Deep Convective Systems (DCSs) using Next-Generation Radar (NEXRAD) reflectivity and newly derived empirical relationships from aircraft in situ measurements in Wang et al. (2015) during the Midlatitude Continental Convective Clouds Experiment (MC3E). With composite gridded NEXRAD radar reflectivity, four-dimensional (space-time) ice cloud microphysical properties of DCSs are retrieved, which is not possible from either in situ sampling at a single altitude or from vertical pointing radar measurements. For this study, aircraft in situ measurements provide the best-estimated ice cloud microphysical properties for validating the radar retrievals. Two statistical comparisons between retrieved and aircraft in situ measured ice microphysical properties are conducted from six selected cases during MC3E. For the temporal-averaged method, the averaged ice water content (IWC) and median mass diameter (Dm) from aircraft in situ measurements are 0.50 g m-3 and 1.51 mm, while the retrievals from radar reflectivity have negative biases of 0.12 g m-3 (24%) and 0.02 mm (1.3%) with correlations of 0.71 and 0.48, respectively. For the spatial-averaged method, the IWC retrievals are closer to the aircraft results (0.51 vs. 0.47 g m-3) with a positive bias of 8.5%, whereas the Dm retrievals are larger than the aircraft results (1.65 mm vs. 1.51 mm) with a positive bias of 9.3%. The retrieved IWCs decrease from ~0.6 g m-3 at 5 km to ~0.15 g m-3 at 13 km, and Dm values decrease from ~2 mm to ~0.7 mm at the same levels. In general, the aircraft in situ measured IWC and Dm values at each level are within one standard derivation of retrieved properties. Good agreements between microphysical properties measured from aircraft and retrieved from radar reflectivity measurements indicate the reasonable accuracy of our retrievals.

X-ray absorption fine structure of artificial antigens for cadmium

NASA Astrophysics Data System (ADS)

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

2011-11-01

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

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.

Phase-step retrieval for tunable phase-shifting algorithms

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Mass Spectrometry for Paper-Based Immunoassays: Toward On-Demand Diagnosis.

PubMed

Chen, Suming; Wan, Qiongqiong; Badu-Tawiah, Abraham K

2016-05-25

Current analytical methods, either point-of-care or centralized detection, are not able to meet recent demands of patient-friendly testing and increased reliability of results. Here, we describe a two-point separation on-demand diagnostic strategy based on a paper-based mass spectrometry immunoassay platform that adopts stable and cleavable ionic probes as mass reporter; these probes make possible sensitive, interruptible, storable, and restorable on-demand detection. In addition, a new touch paper spray method was developed for on-chip, sensitive, and cost-effective analyte detection. This concept is successfully demonstrated via (i) the detection of Plasmodium falciparum histidine-rich protein 2 antigen and (ii) multiplexed and simultaneous detection of cancer antigen 125 and carcinoembryonic antigen.

The detection of Rh antigens (D,C,c,E,e) on bloodstains by a micro-elution technique using low ionic strength solution (LISS) and papain-treated red cells.

PubMed

Bargagna, M; Sabelli, M; Giacomelli, C

1982-01-01

Ninety experimental bloodstains, were examined, with the intention of detecting the principal Rh antigens, by using a micro-elution method improved by the use of low ionic strength solution (LISS) and papain-treated red cells. This method makes it possible to employ most commercially produced sera in routine forensic haematology laboratory work. The antigens could regularly be detected in stains of the following ages: D, C and c in stains of at least 6 months, E in stains of at least 4 months, and e in stains of at least 2 months.

Superposition-free comparison and clustering of antibody binding sites: implications for the prediction of the nature of their antigen

PubMed Central

Di Rienzo, Lorenzo; Milanetti, Edoardo; Lepore, Rosalba; Olimpieri, Pier Paolo; Tramontano, Anna

2017-01-01

We describe here a superposition free method for comparing the surfaces of antibody binding sites based on the Zernike moments and show that they can be used to quickly compare and cluster sets of antibodies. The clusters provide information about the nature of the bound antigen that, when combined with a method for predicting the number of direct antibody antigen contacts, allows the discrimination between protein and non-protein binding antibodies with an accuracy of 76%. This is of relevance in several aspects of antibody science, for example to select the framework to be used for a combinatorial antibody library. PMID:28338016

Water vapor retrieval from near-IR measurements of polarized scanning atmospheric corrector

NASA Astrophysics Data System (ADS)

Qie, Lili; Ning, Yuanming; Zhang, Yang; Chen, Xingfeng; Ma, Yan; Li, Zhengqiang; Cui, Wenyu

2018-02-01

Water vapor and aerosol are two key atmospheric factors effecting the remote sensing image quality. As water vapor is responsible for most of the solar radiation absorption occurring in the cloudless atmosphere, accurate measurement of water content is important to not only atmospheric correction of remote sensing images, but also many other applications such as the study of energy balance and global climate change, land surface temperature retrieval in thermal remote sensing. A multi-spectral, single-angular, polarized radiometer called Polarized Scanning Atmospheric Corrector (PSAC) were developed in China, which are designed to mount on the same satellite platform with the principle payload and provide essential parameters for principle payload image atmospheric correction. PSAC detect water vapor content via measuring atmosphere reflectance at water vapor absorbing channels (i.e. 0.91 μm) and nearby atmospheric window channel (i.e. 0.865μm). A near-IR channel ratio method was implemented to retrieve column water vapor (CWV) amount from PSAC measurements. Field experiments were performed at Yantai, in Shandong province of China, PSAC aircraft observations were acquired. The comparison between PSAC retrievals and ground-based Sun-sky radiometer measurements of CWV during the experimental flights illustrates that this method retrieves CWV with relative deviations ranging from 4% 13%. This method retrieve CWV more accurate over land than over ocean, as the water reflectance is low.

Novel use of a radiolabelled antibody against stage specific embryonic antigen for the detection of occult abscesses in mammals

DOEpatents

Thakur, M.L.

1990-04-17

The invention discloses improved reagents containing antibodies against stage specific embryonic antigen-1 antibodies and improved methods for detection of occult abscess and inflammation using the improved reagents. No Drawings

A New 1DVAR Retrieval for AMSR2 and GMI: Validation and Sensitivites

NASA Astrophysics Data System (ADS)

Duncan, D.; Kummerow, C. D.

2015-12-01

A new non-raining retrieval has been developed for microwave imagers and applied to the GMI and AMSR2 sensors. With the Community Radiative Transfer Model (CRTM) as the forward model for the physical retrieval, a 1-dimensional variational method finds the atmospheric state which minimizes the difference between observed and simulated brightness temperatures. A key innovation of the algorithm development is a method to calculate the sensor error covariance matrix that is specific to the forward model employed and includes off-diagonal elements, allowing the algorithm to handle various forward models and sensors with little cross-talk. The water vapor profile is resolved by way of empirical orthogonal functions (EOFs) and then summed to get total precipitable water (TPW). Validation of retrieved 10m wind speed, TPW, and sea surface temperature (SST) is performed via comparison with buoys and radiosondes as well as global models and other remotely sensed products. In addition to the validation, sensitivity experiments investigate the impact of ancillary data on the under-constrained retrieval, a concern for climate data records that strive to be independent of model biases. The introduction of model analysis data is found to aid the algorithm most at high frequency channels and affect TPW retrievals, whereas wind and cloud water retrievals show little effect from ingesting further ancillary data.

Uniform Atmospheric Retrievals of Ultracool Late-T and Early-Y dwarfs

NASA Astrophysics Data System (ADS)

Garland, Ryan; Irwin, Patrick

2017-10-01

A significant number of ultracool (<600K) extrasolar objects have been discovered in the past decade thanks to wide-field surveys such as WISE. These objects present a perfect testbed for examining the evolution of atmospheric structure as we transition from typically hot extrasolar temperatures to the temperatures found within our Solar System.By examining these types of objects with a uniform retrieval method, we hope to elucidate any trends and (dis)similarities found in atmospheric parameters, such as chemical abundances, temperature-pressure profile, and cloud structure, for a sample of 7 ultracool brown dwarfs as we transition from hotter (~700K) to colder objects (~450K).We perform atmospheric retrievals on two late-T and five early-Y dwarfs. We use the NEMESIS atmospheric retrieval code coupled to a Nested Sampling algorithm, along with a standard uniform model for all of our retrievals. The uniform model assumes the atmosphere is described by a gray radiative-convective temperature profile, (optionally) a gray cloud, and a number of relevant gases. We first verify our methods by comparing it to a benchmark retrieval for Gliese 570D, which is found to be consistent. Furthermore, we present the retrieved gaseous composition, temperature structure, spectroscopic mass and radius, cloud structure and the trends associated with decreasing temperature found in this small sample of objects.

Kingfisher: a system for remote sensing image database management

NASA Astrophysics Data System (ADS)

Bruzzo, Michele; Giordano, Ferdinando; Dellepiane, Silvana G.

2003-04-01

At present retrieval methods in remote sensing image database are mainly based on spatial-temporal information. The increasing amount of images to be collected by the ground station of earth observing systems emphasizes the need for database management with intelligent data retrieval capabilities. The purpose of the proposed method is to realize a new content based retrieval system for remote sensing images database with an innovative search tool based on image similarity. This methodology is quite innovative for this application, at present many systems exist for photographic images, as for example QBIC and IKONA, but they are not able to extract and describe properly remote image content. The target database is set by an archive of images originated from an X-SAR sensor (spaceborne mission, 1994). The best content descriptors, mainly texture parameters, guarantees high retrieval performances and can be extracted without losses independently of image resolution. The latter property allows DBMS (Database Management System) to process low amount of information, as in the case of quick-look images, improving time performance and memory access without reducing retrieval accuracy. The matching technique has been designed to enable image management (database population and retrieval) independently of dimensions (width and height). Local and global content descriptors are compared, during retrieval phase, with the query image and results seem to be very encouraging.

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…

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

PubMed

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

2018-01-10

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

Improvements to GPS Airborne Radio Occultation in the Lower Troposphere Through Implementation of the Phase Matching Method

NASA Astrophysics Data System (ADS)

Wang, K.-N.; Garrison, J. L.; Haase, J. S.; Murphy, B. J.

2017-10-01

Airborne radio occultation (ARO) is a remote sensing technique for atmospheric sounding using Global Positioning System signals received by an airborne instrument. The atmospheric refractivity profile, which depends on pressure, temperature, and water vapor, can be retrieved by measuring the signal delay due to the refractive medium through which the signal traverses. The ARO system was developed to make repeated observations within an individual meteorological event such as a tropical storm, regardless of the presence of clouds and precipitation, and complements existing observation techniques such as dropsondes and satellite remote sensing. RO systems can suffer multipath ray propagation in the lower troposphere if there are strong refractivity gradients, for example, due to a highly variable moisture distribution or a sharp boundary layer, interfering with continuous carrier phase tracking as well as complicating retrievals. The phase matching method has now been adapted for ARO and is shown to reduce negative biases in the refractivity retrieval by providing robust retrievals of bending angle in the presence of multipath. The retrieval results are presented for a flight campaign in September 2010 for Hurricane Karl in the Caribbean Sea. The accuracy is assessed through comparison with the European Centre for Medium Range Weather Forecasts Interim Reanalysis. The fractional difference in refractivity can be maintained at a standard deviation of 2% from flight level down to a height of 2 km. The phase matching method decreases the negative refractivity bias by as much as 4% over the classical geometrical optics retrieval method.

Automatic evidence retrieval for systematic reviews.

PubMed

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

2014-10-01

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

Feasibility study of complex wavefield retrieval in off-axis acoustic holography employing an acousto-optic sensor

PubMed Central

Rodríguez, Guillermo López; Weber, Joshua; Sandhu, Jaswinder Singh; Anastasio, Mark A.

2011-01-01

We propose and experimentally demonstrate a new method for complex-valued wavefield retrieval in off-axis acoustic holography. The method involves use of an intensity-sensitive acousto-optic (AO) sensor, optimized for use at 3.3 MHz, to record the acoustic hologram and a computational method for reconstruction of the object wavefield. The proposed method may circumvent limitations of conventional implementations of acoustic holography and may facilitate the development of acoustic-holography-based biomedical imaging methods. PMID:21669451

Probing the Energetics of Antigen-Antibody Recognition by Titration Microcalorimetry

PubMed

Jelesarov; Leder; Bosshard

1996-06-01

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

Immunochemical characterization of the "native" type III polysaccharide of group B Streptococcus

PubMed Central

1976-01-01

The type III polysaccharide of -roup B Streptococcus has been isolated and purified by a method that employs washing of intact cells at neutral pH. That the polysaccharide prepared by this procedure is the "native" type III antigen is suggested by its molecular size in excess of 10(6) daltons, its degradation by acid and heat treatment to a fragment with immunologic characteristics of the classical HCl antigen, and its type-specific serologic activity. The type III polysaccharide in native form contains sialic acid, galactose, glucose, glucosamine, heptose, and mannose. It is acidic in nature, is resistant to neuramindiase degradation, contains no O-acetyl groups, and does not share antigenic determinants with capsular type K1 antigen of Escherichia coli or Group B polysaccharide antigen of Neiserria meningitidis. PMID:55450

Automatic video shot boundary detection using k-means clustering and improved adaptive dual threshold comparison

NASA Astrophysics Data System (ADS)

Sa, Qila; Wang, Zhihui

2018-03-01

At present, content-based video retrieval (CBVR) is the most mainstream video retrieval method, using the video features of its own to perform automatic identification and retrieval. This method involves a key technology, i.e. shot segmentation. In this paper, the method of automatic video shot boundary detection with K-means clustering and improved adaptive dual threshold comparison is proposed. First, extract the visual features of every frame and divide them into two categories using K-means clustering algorithm, namely, one with significant change and one with no significant change. Then, as to the classification results, utilize the improved adaptive dual threshold comparison method to determine the abrupt as well as gradual shot boundaries.Finally, achieve automatic video shot boundary detection system.

Comparative evaluation of the diagnostic potential of recombinant envelope proteins and native cell culture purified viral antigens of Chikungunya virus.

PubMed

Khan, Mohsin; Dhanwani, Rekha; Kumar, Jyoti S; Rao, P V Lakshmana; Parida, Manmohan

2014-07-01

Despite the fact that Chikungunya resurgence is associated with epidemic of unprecedented magnitude, there are challenges in the field of its clinical diagnosis. However, serological tests in an ELISA format provide a rapid tool for the diagnosis of Chikungunya infection. Indeed, ELISAs based on recombinant proteins hold a great promise as these methods are cost effective and are free from the risk of handling biohazardous material. In this study, the performance of recombinant CHIKV antigens was compared in various ELISA formats for the diagnosis of Chikungunya. Two recombinant antigens derived from the envelope proteins of Chikungunya virus were prepared and evaluated by comparing their competence for detecting circulating antibodies in serum samples of patients infected with CHIKV using MAC-ELISA and indirect IgM-ELISA. The efficacy of the recombinant antigens was also compared with the native antigen. The indirect antibody capture IgM microplate ELISA revealed ≥90% concordance with the native antigen in detecting the CHIKV specific IgM antibodies whereas the recombinant antigen based MAC-ELISA showed 100% specificity. The recombinant antigens used in this study were effective and reliable targets for the diagnosis of CHIKV infection and also provide an alternative for native antigen use which is potentially biohazardous. © 2013 Wiley Periodicals, Inc.

Assessment of cancer and virus antigens for cross-reactivity in human tissues.

PubMed

Jaravine, Victor; Raffegerst, Silke; Schendel, Dolores J; Frishman, Dmitrij

2017-01-01

Cross-reactivity (CR) or invocation of autoimmune side effects in various tissues has important safety implications in adoptive immunotherapy directed against selected antigens. The ability to predict CR (on-target and off-target toxicities) may help in the early selection of safer therapeutically relevant target antigens. We developed a methodology for the calculation of quantitative CR for any defined peptide epitope. Using this approach, we performed assessment of 4 groups of 283 currently known human MHC-class-I epitopes including differentiation antigens, overexpressed proteins, cancer-testis antigens and mutations displayed by tumor cells. In addition, 89 epitopes originating from viral sources were investigated. The natural occurrence of these epitopes in human tissues was assessed based on proteomics abundance data, while the probability of their presentation by MHC-class-I molecules was modelled by the method of Keşmir et al. which combines proteasomal cleavage, TAP affinity and MHC-binding predictions. The results of these analyses for many previously defined peptides are presented as CR indices and tissue profiles. The methodology thus allows for quantitative comparisons of epitopes and is suggested to be suited for the assessment of epitopes of candidate antigens in an early stage of development of adoptive immunotherapy. Our method is implemented as a Java program, with curated datasets stored in a MySQL database. It predicts all naturally possible self-antigens for a given sequence of a therapeutic antigen (or epitope) and after filtering for predicted immunogenicity outputs results as an index and profile of CR to the self-antigens in 22 human tissues. The program is implemented as part of the iCrossR webserver, which is publicly available at http://webclu.bio.wzw.tum.de/icrossr/ CONTACT: d.frishman@wzw.tum.deSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Biotechnology approaches to produce potent, self-adjuvanting antigen-adjuvant fusion protein subunit vaccines.

PubMed

Moyle, Peter Michael

Traditional vaccination approaches (e.g. live attenuated or killed microorganisms) are among the most effective means to prevent the spread of infectious diseases. These approaches, nevertheless, have failed to yield successful vaccines against many important pathogens. To overcome this problem, methods have been developed to identify microbial components, against which protective immune responses can be elicited. Subunit antigens identified by these approaches enable the production of defined vaccines, with improved safety profiles. However, they are generally poorly immunogenic, necessitating their administration with potent immunostimulatory adjuvants. Since few safe and effective adjuvants are currently used in vaccines approved for human use, with those available displaying poor potency, or an inability to stimulate the types of immune responses required for vaccines against specific diseases (e.g. cytotoxic lymphocytes (CTLs) to treat cancers), the development of new vaccines will be aided by the availability of characterized platforms of new adjuvants, improving our capacity to rationally select adjuvants for different applications. One such approach, involves the addition of microbial components (pathogen-associated molecular patterns; PAMPs), that can stimulate strong immune responses, into subunit vaccine formulations. The conjugation of PAMPs to subunit antigens provides a means to greatly increase vaccine potency, by targeting immunostimulation and antigen to the same antigen presenting cell. Thus, methods that enable the efficient, and inexpensive production of antigen-adjuvant fusions represent an exciting mean to improve immunity towards subunit antigens. Herein we review four protein-based adjuvants (flagellin, bacterial lipoproteins, the extra domain A of fibronectin (EDA), and heat shock proteins (Hsps)), which can be genetically fused to antigens to enable recombinant production of antigen-adjuvant fusion proteins, with a focus on their mechanisms of action, structural or sequence requirements for activity, sequence modifications to enhance their activity or simplify production, adverse effects, and examples of vaccines in preclinical or human clinical trials. Copyright © 2017 Elsevier Inc. All rights reserved.

Comprehensive red blood cell and platelet antigen prediction from whole genome sequencing: proof of principle

PubMed Central

Westhoff, Connie M.; Uy, Jon Michael; Aguad, Maria; Smeland‐Wagman, Robin; Kaufman, Richard M.; Rehm, Heidi L.; Green, Robert C.; Silberstein, Leslie E.

2015-01-01

BACKGROUND There are 346 serologically defined red blood cell (RBC) antigens and 33 serologically defined platelet (PLT) antigens, most of which have known genetic changes in 45 RBC or six PLT genes that correlate with antigen expression. Polymorphic sites associated with antigen expression in the primary literature and reference databases are annotated according to nucleotide positions in cDNA. This makes antigen prediction from next‐generation sequencing data challenging, since it uses genomic coordinates. STUDY DESIGN AND METHODS The conventional cDNA reference sequences for all known RBC and PLT genes that correlate with antigen expression were aligned to the human reference genome. The alignments allowed conversion of conventional cDNA nucleotide positions to the corresponding genomic coordinates. RBC and PLT antigen prediction was then performed using the human reference genome and whole genome sequencing (WGS) data with serologic confirmation. RESULTS Some major differences and alignment issues were found when attempting to convert the conventional cDNA to human reference genome sequences for the following genes: ABO, A4GALT, RHD, RHCE, FUT3, ACKR1 (previously DARC), ACHE, FUT2, CR1, GCNT2, and RHAG. However, it was possible to create usable alignments, which facilitated the prediction of all RBC and PLT antigens with a known molecular basis from WGS data. Traditional serologic typing for 18 RBC antigens were in agreement with the WGS‐based antigen predictions, providing proof of principle for this approach. CONCLUSION Detailed mapping of conventional cDNA annotated RBC and PLT alleles can enable accurate prediction of RBC and PLT antigens from whole genomic sequencing data. PMID:26634332

Systematically Retrieving Research: A Case Study Evaluating Seven Databases

ERIC Educational Resources Information Center

Taylor, Brian; Wylie, Emma; Dempster, Martin; Donnelly, Michael

2007-01-01

Objective: Developing the scientific underpinnings of social welfare requires effective and efficient methods of retrieving relevant items from the increasing volume of research. Method: We compared seven databases by running the nearest equivalent search on each. The search topic was chosen for relevance to social work practice with older people.…

Novel Fourier-domain constraint for fast phase retrieval in coherent diffraction imaging.

PubMed

Latychevskaia, Tatiana; Longchamp, Jean-Nicolas; Fink, Hans-Werner

2011-09-26

Coherent diffraction imaging (CDI) for visualizing objects at atomic resolution has been realized as a promising tool for imaging single molecules. Drawbacks of CDI are associated with the difficulty of the numerical phase retrieval from experimental diffraction patterns; a fact which stimulated search for better numerical methods and alternative experimental techniques. Common phase retrieval methods are based on iterative procedures which propagate the complex-valued wave between object and detector plane. Constraints in both, the object and the detector plane are applied. While the constraint in the detector plane employed in most phase retrieval methods requires the amplitude of the complex wave to be equal to the squared root of the measured intensity, we propose a novel Fourier-domain constraint, based on an analogy to holography. Our method allows achieving a low-resolution reconstruction already in the first step followed by a high-resolution reconstruction after further steps. In comparison to conventional schemes this Fourier-domain constraint results in a fast and reliable convergence of the iterative reconstruction process. © 2011 Optical Society of America

An extended Kalman-Bucy filter for atmospheric temperature profile retrieval with a passive microwave sounder

NASA Technical Reports Server (NTRS)

Ledsham, W. H.; Staelin, D. H.

1978-01-01

An extended Kalman-Bucy filter has been implemented for atmospheric temperature profile retrievals from observations made using the Scanned Microwave Spectrometer (SCAMS) instrument carried on the Nimbus 6 satellite. This filter has the advantage that it requires neither stationary statistics in the underlying processes nor linear production of the observed variables from the variables to be estimated. This extended Kalman-Bucy filter has yielded significant performance improvement relative to multiple regression retrieval methods. A multi-spot extended Kalman-Bucy filter has also been developed in which the temperature profiles at a number of scan angles in a scanning instrument are retrieved simultaneously. These multi-spot retrievals are shown to outperform the single-spot Kalman retrievals.

Combining approaches to on-line handwriting information retrieval

NASA Astrophysics Data System (ADS)

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

2010-01-01

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

Reduction of antigenic protein levels in latex gloves after gamma irradiation.

PubMed

Zehr, B D; Gromelski, S; Beezhold, D

1994-01-01

Gamma irradiation is currently the method most commonly used to sterilize surgical gloves. In this study, the effect of gamma irradiation on antigenic proteins in latex gloves was examined. Protein extraction and quantitation were carried out using latex gloves before and after sterilization. Antigenic protein levels were determined by an ELISA assay specific for latex proteins (LEAP). LEAP analysis revealed a significant decrease after gamma-irradiation sterilization. This observation may partially explain the lower levels of extractable antigenic proteins found in sterile surgical gloves compared with nonsterile examination gloves. However, gamma irradiation was less effective than autoclave sterilization in reducing protein levels.

Evaluation of a surface plasmon resonance imaging-based multiplex O-antigen serogrouping for Escherichia coli using eleven major serotypes of Shiga -toxin-producing E. coli.

PubMed

Nakano, Satoshi; Nagao, Miki; Yamasaki, Tomomi; Morimura, Hiroyuki; Hama, Natsuki; Iijima, Yoshio; Shinomiya, Hiroto; Tanaka, Michio; Yamamoto, Masaki; Matsumura, Yasufumi; Miyake, Shiro; Ichiyama, Satoshi

2018-06-01

The early detection of Shiga toxin-producing Escherichia coli (STEC) is important for early diagnosis and preventing the spread of STEC. Although the confirmatory test for STEC should be based on the detection of Shiga toxin using molecular analysis, isolation permits additional characterization of STEC using a variety of methods, including O:H serotyping. The conventional slide agglutination O-antigen serogrouping used in many clinical laboratories is laborious and time-consuming. Surface plasmon resonance (SPR)-based immunosensors are commonly used to investigate a large variety of bio-interactions such as antibody/antigen, peptide/antibody, DNA/DNA, and antibody/bacteria interactions. SPR imaging (SPRi) is characterized by multiplexing capabilities for rapidly screening (approximately 100 to several hundred sensorgrams in parallel) molecules. SPRi-based O-antigen serogrouping method for STEC was recently developed by detecting the interactions between O-antigen-specific antibodies and bacterial cells themselves. The aim of this study was to evaluate its performance for E. coli serogrouping using clinical STEC isolates by comparing the results of slide agglutination tests. We tested a total of 188 isolates, including O26, O45, O91, O103, O111, O115, O121, O128, O145, O157, and O159. The overall sensitivity of SPRi-based O-antigen serogrouping was 98.9%. Only two O157 isolates were misidentified as nontypeable and O121. The detection limits of all serotypes were distributed between 1.1 × 10 6 and 17.6 × 10 6  CFU/ml. Pulsed-field gel electrophoresis (PFGE) revealed the heterogeneity of the examined isolates. In conclusion, SPRi is a useful method for the O-antigen serogrouping of STEC isolates, but the further evaluation of non-O157 minor serogroups is needed. Copyright © 2018 Japanese Society of Chemotherapy and The Japanese Association for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Quantitative and multiplexed detection for blood typing based on quantum dot-magnetic bead assay.

PubMed

Xu, Ting; Zhang, Qiang; Fan, Ya-Han; Li, Ru-Qing; Lu, Hua; Zhao, Shu-Ming; Jiang, Tian-Lun

2017-01-01

Accurate and reliable blood grouping is essential for safe blood transfusion. However, conventional methods are qualitative and use only single-antigen detection. We overcame these limitations by developing a simple, quantitative, and multiplexed detection method for blood grouping using quantum dots (QDs) and magnetic beads. In the QD fluorescence assay (QFA), blood group A and B antigens were quantified using QD labeling and magnetic beads, and the blood groups were identified according to the R value (the value was calculated with the fluorescence intensity from dual QD labeling) of A and B antigens. The optimized performance of QFA was established by blood typing 791 clinical samples. Quantitative and multiplexed detection for blood group antigens can be completed within 35 min with more than 10 5 red blood cells. When conditions are optimized, the assay performance is satisfactory for weak samples. The coefficients of variation between and within days were less than 10% and the reproducibility was good. The ABO blood groups of 791 clinical samples were identified by QFA, and the accuracy obtained was 100% compared with the tube test. Receiver-operating characteristic curves revealed that the QFA has high sensitivity and specificity toward clinical samples, and the cutoff points of the R value of A and B antigens were 1.483 and 1.576, respectively. In this study, we reported a novel quantitative and multiplexed method for the identification of ABO blood groups and presented an effective alternative for quantitative blood typing. This method can be used as an effective tool to improve blood typing and further guarantee clinical transfusion safety.

Rapid desensitization induces internalization of antigen-specific IgE on mouse mast cells

PubMed Central

Oka, Tatsuya; Rios, Eon J.; Tsai, Mindy; Kalesnikoff, Janet; Galli, Stephen J.

2013-01-01

Background Rapid desensitization transiently prevents severe allergic reactions, allowing administration of life-saving therapies in previously sensitized patients. However, the mechanisms underlying successful rapid desensitization are not fully understood. Objectives We sought to investigate whether the mast cell (MC) is an important target of rapid desensitization in mice sensitized to exhibit IgE-dependent passive systemic anaphylaxis in vivo and to investigate the antigen specificity and underlying mechanisms of rapid desensitization in our mouse model. Methods C57BL/6 mice (in vivo) or primary isolated C57BL/6 mouse peritoneal mast cells (PMCs; in vitro) were passively sensitized with antigen-specific anti–2,4-dinitrophenyl IgE, anti-ovalbumin IgE, or both. MCs were exposed over a short period of time to increasing amounts of antigen (2,4-dinitrophenyl–human serum albumin or ovalbumin) in the presence of extracellular calcium in vitro or by means of intravenous administration to sensitized mice in vivo before challenging the mice with or exposing the PMCs to optimal amounts of specific or irrelevant antigen. Results Rapidly exposing mice or PMCs to progressively increasing amounts of specific antigen inhibited the development of antigen-induced hypothermia in sensitized mice in vivo and inhibited antigen-induced PMC degranulation and prostaglandin D2 synthesis in vitro. Such MC hyporesponsiveness was induced antigen-specifically and was associated with a significant reduction in antigen-specific IgE levels on MC surfaces. Conclusions Rapidly exposing MCs to progressively increasing amounts of antigen can both enhance the internalization of antigen-specific IgE on the MC surface and also desensitize these cells in an antigen-specific manner in vivo and in vitro. PMID:23810240

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

NASA Astrophysics Data System (ADS)

Pelliccia, Daniele; Sen, Tanaji

2014-11-01

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

Advances in the management of infertility in men with spinal cord injury

PubMed Central

Ibrahim, Emad; Brackett, Nancy L; Lynne, Charles M

2016-01-01

Couples with a spinal cord injured male partner require assisted ejaculation techniques to collect semen that can then be further used in various assisted reproductive technology methods to achieve a pregnancy. The majority of men sustaining a spinal cord injury regardless of the cause or the level of injury cannot ejaculate during sexual intercourse. Only a small minority can ejaculate by masturbation. Penile vibratory stimulation and electroejaculation are the two most common methods used to retrieve sperm. Other techniques such as prostatic massage and the adjunct application of other medications can be used, but the results are inconsistent. Surgical sperm retrieval should be considered as a last resort if all other methods fail. Special attention must be paid to patients with T6 and rostral levels of injury due to the risk of autonomic dysreflexia resulting from stimulation below the level of injury. Bladder preparation should be performed before stimulation if retrograde ejaculation is anticipated. Erectile dysfunction is ubiquitous in the spinal cord injured population but is usually easily managed and does not pose a barrier to semen retrieval in these men. Semen analysis parameters of men with spinal cord injury are unique for this population regardless of the method of retrieval, generally presenting as normal sperm concentration but abnormally low sperm motility and viability. When sperm retrieval is desired in this population, emphasis should be placed on initially trying the simple methods of penile vibratory stimulation or electroejaculation before resorting to more advanced and invasive surgical procedures. PMID:27048781

Assessment of imaging quality in magnified phase CT of human bone tissue at the nanoscale

NASA Astrophysics Data System (ADS)

Yu, Boliang; Langer, Max; Pacureanu, Alexandra; Gauthier, Remy; Follet, Helene; Mitton, David; Olivier, Cecile; Cloetens, Peter; Peyrin, Francoise

2017-10-01

Bone properties at all length scales have a major impact on the fracture risk in disease such as osteoporosis. However, quantitative 3D data on bone tissue at the cellular scale are still rare. Here we propose to use magnified X-ray phase nano-CT to quantify bone ultra-structure in human bone, on the new setup developed on the beamline ID16A at the ESRF, Grenoble. Obtaining 3D images requires the application of phase retrieval prior to tomographic reconstruction. Phase retrieval is an ill-posed problem for which various approaches have been developed. Since image quality has a strong impact on the further quantification of bone tissue, our aim here is to evaluate different phase retrieval methods for imaging bone samples at the cellular scale. Samples from femurs of female donors were scanned using magnified phase nano-CT at voxel sizes of 120 and 30 nm with an energy of 33 keV. Four CT scans at varying sample-to-detector distances were acquired for each sample. We evaluated three phase retrieval methods adapted to these conditions: Paganin's method at single distance, Paganin's method extended to multiple distances, and the contrast transfer function (CTF) approach for pure phase objects. These methods were used as initialization to an iterative refinement step. Our results based on visual and quantitative assessment show that the use of several distances (as opposed to single one) clearly improves image quality and the two multi-distance phase retrieval methods give similar results. First results on the segmentation of osteocyte lacunae and canaliculi from such images are presented.

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

PubMed

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

2017-02-01

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

Fusion of Deep Learning and Compressed Domain features for Content Based Image Retrieval.

PubMed

Liu, Peizhong; Guo, Jing-Ming; Wu, Chi-Yi; Cai, Danlin

2017-08-29

This paper presents an effective image retrieval method by combining high-level features from Convolutional Neural Network (CNN) model and low-level features from Dot-Diffused Block Truncation Coding (DDBTC). The low-level features, e.g., texture and color, are constructed by VQ-indexed histogram from DDBTC bitmap, maximum, and minimum quantizers. Conversely, high-level features from CNN can effectively capture human perception. With the fusion of the DDBTC and CNN features, the extended deep learning two-layer codebook features (DL-TLCF) is generated using the proposed two-layer codebook, dimension reduction, and similarity reweighting to improve the overall retrieval rate. Two metrics, average precision rate (APR) and average recall rate (ARR), are employed to examine various datasets. As documented in the experimental results, the proposed schemes can achieve superior performance compared to the state-of-the-art methods with either low- or high-level features in terms of the retrieval rate. Thus, it can be a strong candidate for various image retrieval related applications.

Retrieval and Validation of Aerosol Optical Depth by using the GF-1 Remote Sensing Data

NASA Astrophysics Data System (ADS)

Zhang, L.; Xu, S.; Wang, L.; Cai, K.; Ge, Q.

2017-05-01

Based on the characteristics of GF-1 remote sensing data, the method and data processing procedure to retrieve the Aerosol Optical Depth (AOD) are developed in this study. The surface contribution over dense vegetation and urban bright target areas are respectively removed by using the dark target and deep blue algorithms. Our method is applied for the three serious polluted Beijing-Tianjin-Hebei (BTH), Yangtze River Delta (YRD) and Pearl River Delta (PRD) regions. The retrieved AOD are validated by ground-based AERONET data from Beijing, Hangzhou, Hong Kong sites. Our results show that, 1) the heavy aerosol loadings are usually distributed in high industrial emission and dense populated cities, with the AOD value near 1. 2) There is a good agreement between satellite-retrievals and in-site observations, with the coefficient factors of 0.71 (BTH), 0.55 (YRD) and 0.54(PRD). 3) The GF-1 retrieval uncertainties are mainly from the impact of cloud contamination, high surface reflectance and assumed aerosol model.

Using X-ray Crystallography, Biophysics, and Functional Assays to Determine the Mechanisms Governing T-cell Receptor Recognition of Cancer Antigens.

PubMed

MacLachlan, Bruce J; Greenshields-Watson, Alexander; Mason, Georgina H; Schauenburg, Andrea J; Bianchi, Valentina; Rizkallah, Pierre J; Sewell, Andrew K; Fuller, Anna; Cole, David K

2017-02-06

Human CD8+ cytotoxic T lymphocytes (CTLs) are known to play an important role in tumor control. In order to carry out this function, the cell surface-expressed T-cell receptor (TCR) must functionally recognize human leukocyte antigen (HLA)-restricted tumor-derived peptides (pHLA). However, we and others have shown that most TCRs bind sub-optimally to tumor antigens. Uncovering the molecular mechanisms that define this poor recognition could aid in the development of new targeted therapies that circumnavigate these shortcomings. Indeed, present therapies that lack this molecular understanding have not been universally effective. Here, we describe methods that we commonly employ in the laboratory to determine how the nature of the interaction between TCRs and pHLA governs T-cell functionality. These methods include the generation of soluble TCRs and pHLA and the use of these reagents for X-ray crystallography, biophysical analysis, and antigen-specific T-cell staining with pHLA multimers. Using these approaches and guided by structural analysis, it is possible to modify the interaction between TCRs and pHLA and to then test how these modifications impact T-cell antigen recognition. These findings have already helped to clarify the mechanism of T-cell recognition of a number of cancer antigens and could direct the development of altered peptides and modified TCRs for new cancer therapies.

Generation of cell type-specific monoclonal antibodies for the planarian and optimization of sample processing for immunolabeling.

PubMed

Forsthoefel, David J; Waters, Forrest A; Newmark, Phillip A

2014-12-21

Efforts to elucidate the cellular and molecular mechanisms of regeneration have required the application of methods to detect specific cell types and tissues in a growing cohort of experimental animal models. For example, in the planarian Schmidtea mediterranea, substantial improvements to nucleic acid hybridization and electron microscopy protocols have facilitated the visualization of regenerative events at the cellular level. By contrast, immunological resources have been slower to emerge. Specifically, the repertoire of antibodies recognizing planarian antigens remains limited, and a more systematic approach is needed to evaluate the effects of processing steps required during sample preparation for immunolabeling. To address these issues and to facilitate studies of planarian digestive system regeneration, we conducted a monoclonal antibody (mAb) screen using phagocytic intestinal cells purified from the digestive tracts of living planarians as immunogens. This approach yielded ten antibodies that recognized intestinal epitopes, as well as markers for the central nervous system, musculature, secretory cells, and epidermis. In order to improve signal intensity and reduce non-specific background for a subset of mAbs, we evaluated the effects of fixation and other steps during sample processing. We found that fixative choice, treatments to remove mucus and bleach pigment, as well as methods for tissue permeabilization and antigen retrieval profoundly influenced labeling by individual antibodies. These experiments led to the development of a step-by-step workflow for determining optimal specimen preparation for labeling whole planarians as well as unbleached histological sections. We generated a collection of monoclonal antibodies recognizing the planarian intestine and other tissues; these antibodies will facilitate studies of planarian tissue morphogenesis. We also developed a protocol for optimizing specimen processing that will accelerate future efforts to generate planarian-specific antibodies, and to extend functional genetic studies of regeneration to post-transcriptional aspects of gene expression, such as protein localization or modification. Our efforts demonstrate the importance of systematically testing multiple approaches to species-specific idiosyncracies, such as mucus removal and pigment bleaching, and may serve as a template for the development of immunological resources in other emerging model organisms.

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 compare SIF retrieval results from GOME-2 and SCIAMACHY data as well as results obtained Joiner et al.. 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.

Short-Read Whole-Genome Sequencing for Laboratory-Based Surveillance of Bordetella pertussis.

PubMed

Marchand-Austin, Alex; Tsang, Raymond S W; Guthrie, Jennifer L; Ma, Jennifer H; Lim, Gillian H; Crowcroft, Natasha S; Deeks, Shelley L; Farrell, David J; Jamieson, Frances B

2017-05-01

Bordetella pertussis is a Gram-negative bacterium that causes respiratory infections in humans. Ongoing molecular surveillance of B. pertussis acellular vaccine (aP) antigens is critical for understanding the interaction between evolutionary pressures, disease pathogenesis, and vaccine effectiveness. Methods currently used to characterize aP components are relatively labor-intensive and low throughput. To address this challenge, we sought to derive aP antigen genotypes from minimally processed short-read whole-genome sequencing data generated from 40 clinical B. pertussis isolates and analyzed using the SRST2 bioinformatic package. SRST2 was able to identify aP antigen genotypes for all antigens with the exception of pertactin, possibly due to low read coverage in GC-rich low-complexity regions of variation. Two main genotypes were observed in addition to a singular third genotype that contained an 84-bp deletion that was identified by SRST2 despite the issues in allele calling. This method has the potential to generate large pools of B. pertussis molecular data that can be linked to clinical and epidemiological information to facilitate research of vaccine effectiveness and disease severity in the context of emerging vaccine antigen-deficient strains. Copyright © 2017 American Society for Microbiology.

Evaluation of monoclonal antibody-based sandwich direct ELISA (MSD-ELISA) for antigen detection of foot-and-mouth disease virus using clinical samples.

PubMed

Morioka, Kazuki; Fukai, Katsuhiko; Sakamoto, Kenichi; Yoshida, Kazuo; Kanno, Toru

2014-01-01

A monoclonal antibody-based sandwich direct ELISA (MSD-ELISA) method was previously developed for foot-and-mouth disease (FMD) viral antigen detection. Here we evaluated the sensitivity and specificity of two FMD viral antigen detection MSD-ELISAs and compared them with conventional indirect sandwich (IS)-ELISA. The MSD-ELISAs were able to detect the antigen in saliva samples of experimentally-infected pigs for a longer term compared to the IS-ELISA. We also used 178 RT-PCR-positive field samples from cattle and pigs affected by the 2010 type-O FMD outbreak in Japan, and we found that the sensitivities of both MSD-ELISAs were about 7 times higher than that of the IS-ELISA against each sample (P<0.01). In terms of the FMD-positive farm detection rate, the sensitivities of the MSD-ELISAs were about 6 times higher than that of the IS-ELISA against each farm (P<0.01). Although it is necessary to conduct further validation study using the other virus strains, MSD-ELISAs could be appropriate as a method to replace IS-ELISA for FMD antigen detection.

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.

Analysis and application of Fourier transform spectroscopy in atmospheric remote sensing

NASA Technical Reports Server (NTRS)

Park, J. H.

1984-01-01

An analysis method for Fourier transform spectroscopy is summarized with applications to various types of distortion in atmospheric absorption spectra. This analysis method includes the fast Fourier transform method for simulating the interferometric spectrum and the nonlinear least-squares method for retrieving the information from a measured spectrum. It is shown that spectral distortions can be simulated quite well and that the correct information can be retrieved from a distorted spectrum by this analysis technique.

Immune Repertoire after Immunization As Seen by Next-Generation Sequencing and Proteomics

PubMed Central

VanDuijn, Martijn M.; Dekker, Lennard J.; van IJcken, Wilfred F. J.; Sillevis Smitt, Peter A. E.; Luider, Theo M.

2017-01-01

The immune system produces a diverse repertoire of immunoglobulins in response to foreign antigens. During B-cell development, VDJ recombination and somatic mutations generate diversity, whereas selection processes remove it. Using both proteomic and NGS approaches, we characterized the immune repertoires in groups of rats after immunization with purified antigens. Proteomics and NGS data on the repertoire are in qualitative agreement, but did show quantitative differences that may relate to differences between the biological niches that were sampled for these approaches. Both methods contributed complementary information in the characterization of the immune repertoire. It was found that the immune repertoires resulting from each antigen had many similarities that allowed samples to cluster together, and that mutated immunoglobulin peptides were shared among animals with a response to the same antigen significantly more than for different antigens. However, the number of shared sequences decreased in a log-linear fashion relative to the number of animals that share them, which may affect future applications. A phylogenetic analysis on the NGS reads showed that reads from different individuals immunized with the same antigen populated distinct branches of the phylogram, an indication that the repertoire had converged. Also, similar mutation patterns were found in branches of the phylogenetic tree that were associated with antigen-specific immunoglobulins through proteomics data. Thus, data from different analysis methods and different experimental platforms show that the immunoglobulin repertoires of immunized animals have overlapping and converging features. With additional research, this may enable interesting applications in biotechnology and clinical diagnostics. PMID:29085363

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.

Antigenic Patterns and Evolution of the Human Influenza A (H1N1) Virus

PubMed Central

Liu, Mi; Zhao, Xiang; Hua, Sha; Du, Xiangjun; Peng, Yousong; Li, Xiyan; Lan, Yu; Wang, Dayan; Wu, Aiping; Shu, Yuelong; Jiang, Taijiao

2015-01-01

The influenza A (H1N1) virus causes seasonal epidemics that result in severe illnesses and deaths almost every year. A deep understanding of the antigenic patterns and evolution of human influenza A (H1N1) virus is extremely important for its effective surveillance and prevention. Through development of antigenicity inference method for human influenza A (H1N1), named PREDAC-H1, we systematically mapped the antigenic patterns and evolution of the human influenza A (H1N1) virus. Eight dominant antigenic clusters have been inferred for seasonal H1N1 viruses since 1977, which demonstrated sequential replacements over time with a similar pattern in Asia, Europe and North America. Among them, six clusters emerged first in Asia. As for China, three of the eight antigenic clusters were detected in South China earlier than in North China, indicating the leading role of South China in H1N1 transmission. The comprehensive view of the antigenic evolution of human influenza A (H1N1) virus can help formulate better strategy for its prevention and control. PMID:26412348

Antigenic Patterns and Evolution of the Human Influenza A (H1N1) Virus.

PubMed

Liu, Mi; Zhao, Xiang; Hua, Sha; Du, Xiangjun; Peng, Yousong; Li, Xiyan; Lan, Yu; Wang, Dayan; Wu, Aiping; Shu, Yuelong; Jiang, Taijiao

2015-09-28

The influenza A (H1N1) virus causes seasonal epidemics that result in severe illnesses and deaths almost every year. A deep understanding of the antigenic patterns and evolution of human influenza A (H1N1) virus is extremely important for its effective surveillance and prevention. Through development of antigenicity inference method for human influenza A (H1N1), named PREDAC-H1, we systematically mapped the antigenic patterns and evolution of the human influenza A (H1N1) virus. Eight dominant antigenic clusters have been inferred for seasonal H1N1 viruses since 1977, which demonstrated sequential replacements over time with a similar pattern in Asia, Europe and North America. Among them, six clusters emerged first in Asia. As for China, three of the eight antigenic clusters were detected in South China earlier than in North China, indicating the leading role of South China in H1N1 transmission. The comprehensive view of the antigenic evolution of human influenza A (H1N1) virus can help formulate better strategy for its prevention and control.

Pooled Protein Immunization for Identification of Cell Surface Antigens in Streptococcus sanguinis

PubMed Central

Ge, Xiuchun; Kitten, Todd; Munro, Cindy L.; Conrad, Daniel H.; Xu, Ping

2010-01-01

Background Available bacterial genomes provide opportunities for screening vaccines by reverse vaccinology. Efficient identification of surface antigens is required to reduce time and animal cost in this technology. We developed an approach to identify surface antigens rapidly in Streptococcus sanguinis, a common infective endocarditis causative species. Methods and Findings We applied bioinformatics for antigen prediction and pooled antigens for immunization. Forty-seven surface-exposed proteins including 28 lipoproteins and 19 cell wall-anchored proteins were chosen based on computer algorithms and comparative genomic analyses. Eight proteins among these candidates and 2 other proteins were pooled together to immunize rabbits. The antiserum reacted strongly with each protein and with S. sanguinis whole cells. Affinity chromatography was used to purify the antibodies to 9 of the antigen pool components. Competitive ELISA and FACS results indicated that these 9 proteins were exposed on S. sanguinis cell surfaces. The purified antibodies had demonstrable opsonic activity. Conclusions The results indicate that immunization with pooled proteins, in combination with affinity purification, and comprehensive immunological assays may facilitate cell surface antigen identification to combat infectious diseases. PMID:20668678

Tests for the determination of the effect of antimitotic products on immune reactions*

PubMed Central

Amiel, J. L.; Mathé, G.; Matsukura, M.; Méry, A. M.; Daguet, G.; Tenenbaum, R.; Garattini, S.; Brézin, C.; Palma, V.

1964-01-01

The differences reported by various authors in regard to the inhibitory effect of the same antimitotic product on the production of antibodies, may be attributable in particular to the antigen used and to the technique of administration of the product. These differences have made it necessary to work out a test that is not subject to criticism in these respects. After an investigation of the cytological reactions provoked in the mouse by various antigens, the authors have singled out three of these antigens: human albumin, the poliomyelitis virus and an allogeneic skin graft. The hyperbasophilic cells which are predominantly present in the lymphoid centres are, respectively, lymphocytes for the first, plasmocytes for the second and histiocytes for the third of these antigens. In view of the different mechanisms of action that are possible with the different antimitotic products the authors used three methods of administration: entirely `before' the antigenic stimulus; total dose administered entirely `after' the antigenic stimulus; total dose administered partially `before' and partially `after' the antigenic stimulus. PMID:14218267

Immunization Route Dictates Cross-Priming Efficiency and Impacts the Optimal Timing of Adjuvant Delivery

PubMed Central

Bouvier, Isabelle; Jusforgues-Saklani, Hélène; Lim, Annick; Lemaître, Fabrice; Lemercier, Brigitte; Auriau, Charlotte; Nicola, Marie-Anne; Leroy, Sandrine; Law, Helen K.; Bandeira, Antonio; Moon, James J.; Bousso, Philippe; Albert, Matthew L.

2011-01-01

Delivery of cell-associated antigen represents an important strategy for vaccination. While many experimental models have been developed in order to define the critical parameters for efficient cross-priming, few have utilized quantitative methods that permit the study of the endogenous repertoire. Comparing different strategies of immunization, we report that local delivery of cell-associated antigen results in delayed T cell cross-priming due to the increased time required for antigen capture and presentation. In comparison, delivery of disseminated antigen resulted in rapid T cell priming. Surprisingly, local injection of cell-associated antigen, while slower, resulted in the differentiation of a more robust, polyfunctional, effector response. We also evaluated the combination of cell-associated antigen with poly I:C delivery and observed an immunization route-specific effect regarding the optimal timing of innate immune stimulation. These studies highlight the importance of considering the timing and persistence of antigen presentation, and suggest that intradermal injection with delayed adjuvant delivery is the optimal strategy for achieving CD8+ T cell cross-priming. PMID:22566860

Do Family Physicians Retrieve Synopses of Clinical Research Previously Read as Email Alerts?

PubMed Central

Pluye, Pierre; Johnson-Lafleur, Janique; Granikov, Vera; Shulha, Michael; Bartlett, Gillian; Marlow, Bernard

2011-01-01

Background A synopsis of new clinical research highlights important aspects of one study in a brief structured format. When delivered as email alerts, synopses enable clinicians to become aware of new developments relevant for practice. Once read, a synopsis can become a known item of clinical information. In time-pressured situations, remembering a known item may facilitate information retrieval by the clinician. However, exactly how synopses first delivered as email alerts influence retrieval at some later time is not known. Objectives We examined searches for clinical information in which a synopsis previously read as an email alert was retrieved (defined as a dyad). Our study objectives were to (1) examine whether family physicians retrieved synopses they previously read as email alerts and then to (2) explore whether family physicians purposefully retrieved these synopses. Methods We conducted a mixed-methods study in which a qualitative multiple case study explored the retrieval of email alerts within a prospective longitudinal cohort of practicing family physicians. Reading of research-based synopses was tracked in two contexts: (1) push, meaning to read on email and (2) pull, meaning to read after retrieval from one electronic knowledge resource. Dyads, defined as synopses first read as email alerts and subsequently retrieved in a search of a knowledge resource, were prospectively identified. Participants were interviewed about all of their dyads. Outcomes were the total number of dyads and their type. Results Over a period of 341 days, 194 unique synopses delivered to 41 participants resulted in 4937 synopsis readings. In all, 1205 synopses were retrieved over an average of 320 days. Of the 1205 retrieved synopses, 21 (1.7%) were dyads made by 17 family physicians. Of the 1205 retrieved synopses, 6 (0.5%) were known item type dyads. However, dyads also occurred serendipitously. Conclusion In the single knowledge resource we studied, email alerts containing research-based synopses were rarely retrieved. Our findings help us to better understand the effect of push on pull and to improve the integration of research-based information within electronic resources for clinicians. PMID:22130465

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 determination of the mixing height," Atmospheric Environment, vol. 34, pp. 1352-2310, 2000. [3] D. Lange, J. Tiana-Alsina, U. Saeed, S. Tomás, and F. Rocadenbosch, "Atmospheric-boundary-layer height monitoring using a Kalman filter and backscatter lidar returns," IEEE Transactions on Geoscience and Remote Sensing, vol. 52, no. 8, pp. 4717-4728, 2014. [4] G. Holzworth, "Estimates of mean maximum mixing depths in the contiguous United States," Monthly Weather Review, vol. 92, pp. 235-242, 1964. [5] U. Löhnert, J. H. Schween, C. Acquistapace, K. Ebell, M. Maahn, M. Barrera-Verdejo, A. Hirsikko, B. Bohn, A. Knaps, E. O'Connor, C. Simmer, A. Wahner, and S. Crewell, "JOYCE: Jülich Observatory for Cloud Evolution," Bull. Amer. Meteor. Soc., vol. 96, no. 7, pp. 1157-1174, 2015.

Molecular genotyping of Indian blood group system antigens in Indian blood donors.

PubMed

Gogri, Harita; Pitale, Pranali; Madkaikar, Manisha; Kulkarni, Swati

2018-04-11

Haemagglutination has been the gold standard for defining the blood group status. However, these tests depend upon the availability of specific and reliable antisera. Potent antisera for extended phenotyping are very costly, weakly reacting or available in limited stocks and unavailable for some blood group systems like Indian, Dombrock, Coltan, Diego etc. The Indian blood group system consists of two antithetical antigens, In a and In b . The In a /In b polymorphism arises from 252C > G missense mutation in the CD44 gene. This knowledge has allowed the development of molecular methods for genotyping IN alleles. Blood samples were collected from 715 blood donors from Mumbai. DNA was extracted using phenol-chloroform method and genotyping for Indian (In a /IN*01, In b /IN*02) blood group alleles was done by Sequence Specific PCR. Seventeen donors among 715 were heterozygous for In a antigen i.e. In (a+b+). The In a antigen positivity was confirmed serologically, using anti-In a prepared in-house and the genotype-phenotype results were concordant. The frequency of In a (2.37%) was higher than Caucasians and comparable to those reported among Indians of Bombay. This is the first study reporting molecular screening of Indian blood group antigens in Indian population. The frequency of In a and In b antigens was found to be 2.37% and 100% respectively. Red cells of In a positive donors can be used as in-house reagent red cells for screening and identification of corresponding antibodies. Thus, DNA based methods will help in large scale screening of donors to identify rare blood groups, when commercial antisera are unavailable. Copyright © 2018 Elsevier Ltd. All rights reserved.

Impacts of Cross-Platform Vicarious Calibration on the Deep Blue Aerosol Retrievals for Moderate Resolution Imaging Spectroradiometer Aboard Terra

NASA Technical Reports Server (NTRS)

Jeong, Myeong-Jae; Hsu, N. Christina; Kwiatkowska, Ewa J.; Franz, Bryan A.; Meister, Gerhard; Salustro, Clare E.

2012-01-01

The retrieval of aerosol properties from spaceborne sensors requires highly accurate and precise radiometric measurements, thus placing stringent requirements on sensor calibration and characterization. For the Terra/Moderate Resolution Imaging Spedroradiometer (MODIS), the characteristics of the detectors of certain bands, particularly band 8 [(B8); 412 nm], have changed significantly over time, leading to increased calibration uncertainty. In this paper, we explore a possibility of utilizing a cross-calibration method developed for characterizing the Terral MODIS detectors in the ocean bands by the National Aeronautics and Space Administration Ocean Biology Processing Group to improve aerosol retrieval over bright land surfaces. We found that the Terra/MODIS B8 reflectance corrected using the cross calibration method resulted in significant improvements for the retrieved aerosol optical thickness when compared with that from the Multi-angle Imaging Spectroradiometer, Aqua/MODIS, and the Aerosol Robotic Network. The method reported in this paper is implemented for the operational processing of the Terra/MODIS Deep Blue aerosol products.

Data-driven Green's function retrieval and application to imaging with multidimensional deconvolution

NASA Astrophysics Data System (ADS)

Broggini, Filippo; Wapenaar, Kees; van der Neut, Joost; Snieder, Roel

2014-01-01

An iterative method is presented that allows one to retrieve the Green's function originating from a virtual source located inside a medium using reflection data measured only at the acquisition surface. In addition to the reflection response, an estimate of the travel times corresponding to the direct arrivals is required. However, no detailed information about the heterogeneities in the medium is needed. The iterative scheme generalizes the Marchenko equation for inverse scattering to the seismic reflection problem. To give insight in the mechanism of the iterative method, its steps for a simple layered medium are analyzed using physical arguments based on the stationary phase method. The retrieved Green's wavefield is shown to correctly contain the multiples due to the inhomogeneities present in the medium. Additionally, a variant of the iterative scheme enables decomposition of the retrieved wavefield into its downgoing and upgoing components. These wavefields then enable creation of a ghost-free image of the medium with either cross correlation or multidimensional deconvolution, presenting an advantage over standard prestack migration.

Dictionary Pruning with Visual Word Significance for Medical Image Retrieval

PubMed Central

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

2016-01-01

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

Dictionary Pruning with Visual Word Significance for Medical Image Retrieval.

PubMed

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

2016-02-12

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

Extended capture range for focus-diverse phase retrieval in segmented aperture systems using geometrical optics.

PubMed

Jurling, Alden S; Fienup, James R

2014-03-01

Extending previous work by Thurman on wavefront sensing for segmented-aperture systems, we developed an algorithm for estimating segment tips and tilts from multiple point spread functions in different defocused planes. We also developed methods for overcoming two common modes for stagnation in nonlinear optimization-based phase retrieval algorithms for segmented systems. We showed that when used together, these methods largely solve the capture range problem in focus-diverse phase retrieval for segmented systems with large tips and tilts. Monte Carlo simulations produced a rate of success better than 98% for the combined approach.

Phase retrieval without unwrapping by single-shot dual-wavelength digital holography

NASA Astrophysics Data System (ADS)

Min, Junwei; Yao, Baoli; Zhou, Meiling; Guo, Rongli; Lei, Ming; Yang, Yanlong; Dan, Dan; Yan, Shaohui; Peng, Tong

2014-12-01

A phase retrieval method by using single-shot dual-wavelength digital holography is proposed. Each single wavelength hologram is extracted from the color CCD recorded hologram at one exposure, and the unwrapped phase image of object can be reconstructed directly. Different from the traditional multiple wavelength phase unwrapping techniques, any single complex wave-fronts at different wavelengths have no need to be calculated any more. Thus, the phase retrieval is computationally fast and straightforward, and the limitations on the total optical path difference are significantly relaxed. The practicability of the proposed method is demonstrated by both simulated and experimental results.

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 ignores the cross-covariances between background errors and retrieval errors. We show that interactive retrieval assimilation (where the same background used for assimilation is also used in the retrieval step) is equivalent to direct assimilation of radiances with suboptimal analysis weights. We illustrate and extend these theoretical arguments with several one-dimensional assimilation experiments, where we estimate vertical atmospheric profiles using simulated data from both the High-resolution InfraRed Sounder 2 (HIRS2) and the future Atmospheric InfraRed Sounder (AIRS).

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

NASA Astrophysics Data System (ADS)

Li, Rong; Zhao, Feng

2015-10-01

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

Phase retrieval with the transport-of-intensity equation in an arbitrarily-shaped aperture by iterative discrete cosine transforms

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

Huang, Lei; Zuo, Chao; Idir, Mourad

A novel transport-of-intensity equation (TIE) based phase retrieval method is proposed with putting an arbitrarily-shaped aperture into the optical wavefield. In this arbitrarily-shaped aperture, the TIE can be solved under non-uniform illuminations and even non-homogeneous boundary conditions by iterative discrete cosine transforms with a phase compensation mechanism. Simulation with arbitrary phase, arbitrary aperture shape, and non-uniform intensity distribution verifies the effective compensation and high accuracy of the proposed method. Experiment is also carried out to check the feasibility of the proposed method in real measurement. Comparing to the existing methods, the proposed method is applicable for any types of phasemore » distribution under non-uniform illumination and non-homogeneous boundary conditions within an arbitrarily-shaped aperture, which enables the technique of TIE with hard aperture become a more flexible phase retrieval tool in practical measurements.« less

Phase retrieval with the transport-of-intensity equation in an arbitrarily-shaped aperture by iterative discrete cosine transforms

DOE PAGES

Huang, Lei; Zuo, Chao; Idir, Mourad; ...

2015-04-21

A novel transport-of-intensity equation (TIE) based phase retrieval method is proposed with putting an arbitrarily-shaped aperture into the optical wavefield. In this arbitrarily-shaped aperture, the TIE can be solved under non-uniform illuminations and even non-homogeneous boundary conditions by iterative discrete cosine transforms with a phase compensation mechanism. Simulation with arbitrary phase, arbitrary aperture shape, and non-uniform intensity distribution verifies the effective compensation and high accuracy of the proposed method. Experiment is also carried out to check the feasibility of the proposed method in real measurement. Comparing to the existing methods, the proposed method is applicable for any types of phasemore » distribution under non-uniform illumination and non-homogeneous boundary conditions within an arbitrarily-shaped aperture, which enables the technique of TIE with hard aperture become a more flexible phase retrieval tool in practical measurements.« less

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…

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

Donofrio, David

A method and apparatus for performing stencil computations efficiently are disclosed. In one embodiment, a processor receives an offset, and in response, retrieves a value from a memory via a single instruction, where the retrieving comprises: identifying, based on the offset, one of a plurality of registers of the processor; loading an address stored in the identified register; and retrieving from the memory the value at the address.

Semi-Automated Methods for Refining a Domain-Specific Terminology Base

DTIC Science & Technology

2011-02-01

only as a resource for written and oral translation, but also for Natural Language Processing ( NLP ) applications, text retrieval, document indexing...Natural Language Processing ( NLP ) applications, text retrieval, document indexing, and other knowledge management tasks. The objective of this...also for Natural Language Processing ( NLP ) applications, text retrieval (1), document indexing, and other knowledge management tasks. The National

Identification of HLA Class I Misreads/Dropouts Using Serological Typing, in Comparison with DNA-based Typing.

PubMed

Tipu, Hamid Nawaz; Bashir, Muhammad Mukarram; Noman, Muhammad

2016-10-01

Serology and DNA techniques are employed for Human Leukocyte Antigen (HLA) typing in different transplant centers. Results may not always correlate well and may need retyping with different technique. All the patients (with aplastic anemia, thalassemia, and immunodeficiency) and their donors, requiring HLA typing for bone marrow transplant were enrolled in the study. Serological HLA typing was done by complement-dependent lymphocytotoxicity while DNA-based typing was done with sequence specific primers (SSP). Serology identified 167 HLA A and 165 HLA B antigens while SSP in same samples identified 181 HLA A and 184 HLA B alleles. A11 and B51 were the commonest antigens/alleles by both methods. There were a total of 21 misreads and 32 dropouts on serology, for both HLA A and B loci with HLA A32, B52 and B61 being the most ambiguous antigens. Inherent limitations of serological techniques warrant careful interpretation or use of DNA-based methods for resolution of ambiguous typing.

In Vivo Cytometry of Antigen-Specific T Cells Using 19F MRI

PubMed Central

Srinivas, Mangala; Turner, Michael S.; Janjic, Jelena M.; Morel, Penelope A.; Laidlaw, David H.; Ahrens, Eric T.

2009-01-01

Noninvasive methods to image the trafficking of phenotypically defined immune cells are paramount as we attempt to understand adaptive immunity. A 19F MRI-based methodology for tracking and quantifying cells of a defined phenotype is presented. These methods were applied to a murine inflammation model using antigen-specific T cells. The T cells that were intracellularly labeled ex vivo with a perfluoropolyether (PFPE) nanoemulsion and cells were transferred to a host receiving a localized inoculation of antigen. Longitudinal 19F MRI over 21 days revealed a dynamic accumulation and clearance of T cells in the lymph node (LN) draining the antigen. The apparent T-cell numbers were calculated in the LN from the time-lapse 19F MRI data. The effect of in vivo T-cell division on the 19F MRI cell quantification accuracy was investigated using fluorescence assays. Overall, in vivo cytometry using PFPE labeling and 19F MRI is broadly applicable to studies of whole-body cell biodistribution. PMID:19585593

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.

Detection of urinary Vi antigen as a diagnostic test for typhoid fever.

PubMed Central

Taylor, D N; Harris, J R; Barrett, T J; Hargrett, N T; Prentzel, I; Valdivieso, C; Palomino, C; Levine, M M; Blake, P A

1983-01-01

Since Vi antigen is limited primarily to Salmonella typhi, it has been thought that detection of the antigen may be a useful method for diagnosing acute typhoid fever. The slide coagglutination method and enzyme-linked immunosorbent assay have recently been suggested as ways to detect small quantities of Vi antigen in urine. In Santiago, Chile, we compared the results of these two methods in patients with acute typhoid fever, paratyphoid fever, and other febrile illnesses and in afebrile control subjects. Using a cut-off value that maximally separated typhoid patients from controls, the enzyme-linked immunosorbent assay was positive in 62.4% of 141 patients with culture-proven typhoid infections and in 13.2% of 159 afebrile control subjects. The enzyme-linked immunosorbent assay was false positive in 64.7% of 34 culture-proven paratyphoid A or B patients and 47.1% of 21 patients with other nontyphoidal febrile illnesses. The coagglutination test was positive in 34% of typhoid patients, 14% of afebrile control subjects, and 46% of febrile control subjects. We conclude that these tests when performed with the Vi antibodies employed in this study are of little value for the diagnosis of typhoid fever in this setting. PMID:6630465

A novel UCS memory retrieval-extinction procedure to inhibit relapse to drug seeking.

PubMed

Luo, Yi-xiao; Xue, Yan-xue; Liu, Jian-feng; Shi, Hai-shui; Jian, Min; Han, Ying; Zhu, Wei-li; Bao, Yan-ping; Wu, Ping; Ding, Zeng-bo; Shen, Hao-wei; Shi, Jie; Shaham, Yavin; Lu, Lin

2015-07-14

We recently reported that a conditioned stimulus (CS) memory retrieval-extinction procedure decreases reinstatement of cocaine and heroin seeking in rats and heroin craving in humans. Here we show that non-contingent cocaine or methylphenidate injections (UCS retrieval) 1 h before the extinction sessions decreases cocaine-priming-induced reinstatement, spontaneous recovery, and renewal of cocaine seeking in rats. Unlike the CS-based memory retrieval-extinction procedure, the UCS memory retrieval manipulation decreases renewal and reinstatement of cocaine seeking in the presence of cocaine cues that were not present during extinction training and also decreases cocaine seeking when the procedure commences after 28 days of abstinence. The inhibitory effect of the UCS retrieval manipulation on cocaine-priming-induced reinstatement is mediated by regulation of AMPA-receptor endocytosis in the basolateral amygdala. The UCS memory retrieval-extinction procedure has superior relapse prevention characteristics than the CS memory retrieval-extinction procedure and could be a promising method for decreasing relapse in human addicts.

A novel UCS memory retrieval-extinction procedure to inhibit relapse to drug seeking

PubMed Central

Luo, Yi-xiao; Xue, Yan-xue; Liu, Jian-feng; Shi, Hai-shui; Jian, Min; Han, Ying; Zhu, Wei-li; Bao, Yan-ping; Wu, Ping; Ding, Zeng-bo; Shen, Hao-wei; Shi, Jie; Shaham, Yavin; Lu, Lin

2015-01-01

We recently reported that a conditioned stimulus (CS) memory retrieval-extinction procedure decreases reinstatement of cocaine and heroin seeking in rats and heroin craving in humans. Here we show that non-contingent cocaine or methylphenidate injections (UCS retrieval) 1 h before the extinction sessions decreases cocaine-priming-induced reinstatement, spontaneous recovery, and renewal of cocaine seeking in rats. Unlike the CS-based memory retrieval-extinction procedure, the UCS memory retrieval manipulation decreases renewal and reinstatement of cocaine seeking in the presence of cocaine cues that were not present during extinction training and also decreases cocaine seeking when the procedure commences after 28 days of abstinence. The inhibitory effect of the UCS retrieval manipulation on cocaine-priming-induced reinstatement is mediated by regulation of AMPA-receptor endocytosis in the basolateral amygdala. The UCS memory retrieval-extinction procedure has superior relapse prevention characteristics than the CS memory retrieval-extinction procedure and could be a promising method for decreasing relapse in human addicts. PMID:26169171

Poor readers' retrieval mechanism: efficient access is not dependent on reading skill

PubMed Central

Johns, Clinton L.; Matsuki, Kazunaga; Van Dyke, Julie A.

2015-01-01

A substantial body of evidence points to a cue-based direct-access retrieval mechanism as a crucial component of skilled adult reading. We report two experiments aimed at examining whether poor readers are able to make use of the same retrieval mechanism. This is significant in light of findings that poor readers have difficulty retrieving linguistic information (e.g., Perfetti, 1985). Our experiments are based on a previous demonstration of direct-access retrieval in language processing, presented in McElree et al. (2003). Experiment 1 replicates the original result using an auditory implementation of the Speed-Accuracy Tradeoff (SAT) method. This finding represents a significant methodological advance, as it opens up the possibility of exploring retrieval speeds in non-reading populations. Experiment 2 provides evidence that poor readers do use a direct-access retrieval mechanism during listening comprehension, despite overall poorer accuracy and slower retrieval speeds relative to skilled readers. The findings are discussed with respect to hypotheses about the source of poor reading comprehension. PMID:26528212

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…

Development of an Aerosol Opacity Retrieval Algorithm for Use with Multi-Angle Land Surface Images

NASA Technical Reports Server (NTRS)

Diner, D.; Paradise, S.; Martonchik, J.

1994-01-01

In 1998, the Multi-angle Imaging SpectroRadiometer (MISR) will fly aboard the EOS-AM1 spacecraft. MISR will enable unique methods for retrieving the properties of atmospheric aerosols, by providing global imagery of the Earth at nine viewing angles in four visible and near-IR spectral bands. As part of the MISR algorithm development, theoretical methods of analyzing multi-angle, multi-spectral data are being tested using images acquired by the airborne Advanced Solid-State Array Spectroradiometer (ASAS). In this paper we derive a method to be used over land surfaces for retrieving the change in opacity between spectral bands, which can then be used in conjunction with an aerosol model to derive a bound on absolute opacity.

Multivariate analysis: A statistical approach for computations

NASA Astrophysics Data System (ADS)

Michu, Sachin; Kaushik, Vandana

2014-10-01

Multivariate analysis is a type of multivariate statistical approach commonly used in, automotive diagnosis, education evaluating clusters in finance etc and more recently in the health-related professions. The objective of the paper is to provide a detailed exploratory discussion about factor analysis (FA) in image retrieval method and correlation analysis (CA) of network traffic. Image retrieval methods aim to retrieve relevant images from a collected database, based on their content. The problem is made more difficult due to the high dimension of the variable space in which the images are represented. Multivariate correlation analysis proposes an anomaly detection and analysis method based on the correlation coefficient matrix. Anomaly behaviors in the network include the various attacks on the network like DDOs attacks and network scanning.

Reliable B Cell Epitope Predictions: Impacts of Method Development and Improved Benchmarking

PubMed Central

Kringelum, Jens Vindahl; Lundegaard, Claus; Lund, Ole; Nielsen, Morten

2012-01-01

The interaction between antibodies and antigens is one of the most important immune system mechanisms for clearing infectious organisms from the host. Antibodies bind to antigens at sites referred to as B-cell epitopes. Identification of the exact location of B-cell epitopes is essential in several biomedical applications such as; rational vaccine design, development of disease diagnostics and immunotherapeutics. However, experimental mapping of epitopes is resource intensive making in silico methods an appealing complementary approach. To date, the reported performance of methods for in silico mapping of B-cell epitopes has been moderate. Several issues regarding the evaluation data sets may however have led to the performance values being underestimated: Rarely, all potential epitopes have been mapped on an antigen, and antibodies are generally raised against the antigen in a given biological context not against the antigen monomer. Improper dealing with these aspects leads to many artificial false positive predictions and hence to incorrect low performance values. To demonstrate the impact of proper benchmark definitions, we here present an updated version of the DiscoTope method incorporating a novel spatial neighborhood definition and half-sphere exposure as surface measure. Compared to other state-of-the-art prediction methods, Discotope-2.0 displayed improved performance both in cross-validation and in independent evaluations. Using DiscoTope-2.0, we assessed the impact on performance when using proper benchmark definitions. For 13 proteins in the training data set where sufficient biological information was available to make a proper benchmark redefinition, the average AUC performance was improved from 0.791 to 0.824. Similarly, the average AUC performance on an independent evaluation data set improved from 0.712 to 0.727. Our results thus demonstrate that given proper benchmark definitions, B-cell epitope prediction methods achieve highly significant predictive performances suggesting these tools to be a powerful asset in rational epitope discovery. The updated version of DiscoTope is available at www.cbs.dtu.dk/services/DiscoTope-2.0. PMID:23300419

A comparative laboratory diagnosis of malaria: microscopy versus rapid diagnostic test kits.

PubMed

Azikiwe, C C A; Ifezulike, C C; Siminialayi, I M; Amazu, L U; Enye, J C; Nwakwunite, O E

2012-04-01

To compare the two methods of rapid diagnostic tests (RDTs) and microscopy in the diagnosis of malaria. RDTs and microscopy were carried out to diagnose malaria. Percentage malaria parasitaemia was calculated on thin films and all non-acute cases of plasmodiasis with less than 0.001% malaria parasitaemia were regarded as negative. Results were simply presented as percentage positive of the total number of patients under study. The results of RDTs were compared to those of microscopy while those of RDTs based on antigen were compared to those of RDTs based on antibody. Patients' follow-up was made for all cases. All the 200 patients under present study tested positive to RDTs based on malaria antibodies (serum) method (100%). 128 out of 200 tested positive to RDTs based on malaria antigen (whole blood) method (64%), while 118 out of 200 patients under present study tested positive to visual microscopy of Lieshman and diluted Giemsa (59%). All patients that tested positive to microscopy also tested positive to RDTs based on antigen. All patients on the second day of follow-up were non-febrile and had antimalaria drugs. We conclude based on the present study that the RDTs based on malaria antigen (whole blood) method is as specific as the traditional microscopy and even appears more sensitive than microscopy. The RDTs based on antibody (serum) method is unspecific thus it should not be encouraged. It is most likely that Africa being an endemic region, formation of certain levels of malaria antibody may not be uncommon. The present study also supports the opinion that a good number of febrile cases is not due to malaria. We support WHO's report on cost effectiveness of RDTs but, recommend that only the antigen based method should possibly, be adopted in Africa and other malaria endemic regions of the world.

Lymphocyte and neuronal antigens in neuropsychiatric lupus: presence of an elutable, immunoprecipitable lymphocyte/neuronal 52 kd reactivity.

PubMed Central

Denburg, J A; Behmann, S A

1994-01-01

OBJECTIVE--To examine specific lymphocyte or neuronal antigens immuno-precipitated by systemic lupus erythematosus (SLE) sera. METHOD--SLE sera were screened for the presence of antibodies binding to surface antigens of CD4(+) HUT-78 or SK-N-SH and IMR-6 neuroblastoma cells using Western blotting or radioimmunoprecipitation. RESULTS--IgG eluates from both lymphocytes and neuroblastoma cells recognised a 52 kd band in HUT 78 cell lysates. Eight sera studied further using radioimmunoprecipitation also demonstrated binding to a 52 kd antigen (4/8 on HUT-78, 8/8 on SK-N-SH cells), partially depleted by absorption with viable HUT-78. CONCLUSION--A 52 kd antigen recognised by SLE sera on lymphocytes and neuronal cells may play a role in the pathogenesis of neuropsychiatric-SLE. Images PMID:8017983

Identification of antigen-specific human monoclonal antibodies using high-throughput sequencing of the antibody repertoire.

PubMed

Liu, Ju; Li, Ruihua; Liu, Kun; Li, Liangliang; Zai, Xiaodong; Chi, Xiangyang; Fu, Ling; Xu, Junjie; Chen, Wei

2016-04-22

High-throughput sequencing of the antibody repertoire provides a large number of antibody variable region sequences that can be used to generate human monoclonal antibodies. However, current screening methods for identifying antigen-specific antibodies are inefficient. In the present study, we developed an antibody clone screening strategy based on clone dynamics and relative frequency, and used it to identify antigen-specific human monoclonal antibodies. Enzyme-linked immunosorbent assay showed that at least 52% of putative positive immunoglobulin heavy chains composed antigen-specific antibodies. Combining information on dynamics and relative frequency improved identification of positive clones and elimination of negative clones. and increase the credibility of putative positive clones. Therefore the screening strategy could simplify the subsequent experimental screening and may facilitate the generation of antigen-specific antibodies. Copyright © 2016 Elsevier Inc. All rights reserved.

Culturing and extraction of Coprococcus comes, absorption of serumagglutinins by soluble fractions and relation between agglutinins and antibodies in sera of patients with Crohn's disease.

PubMed

Hazenberg, M P; Pennock-Schröder, A M; van de Merwe, J P

1986-01-01

Agglutinating antibodies to Coprococcus comes and three other obligately anaerobic coccoid rods from the intestinal flora are used in the diagnosis of Crohn's disease. Further studies on the pathogenetic role as well as the development of more sensitive and specific methods for detecting antibodies require extraction of the antigen fractions. Culturing methods to obtain C. comes with optimal antigen presentation and isolation of soluble antigen fractions were therefore developed. Hot water extraction of whole cells and subsequent removal of proteins with trichloroacetic acid provided a fraction that absorbed serum agglutinins, was useful for an enzyme-linked immunosorbent assay and induced agglutinating antibodies in rats.

DELAYED HYPERSENSITIVITY

PubMed Central

Uhr, Jonathan W.; Salvin, S. B.; Pappenheimer, A. M.

1957-01-01

A general method for induction of the delayed hypersensitive state directed against single protein antigens is described. The method consists of intradermal injection of minute amounts of washed immune precipitates containing the antigen in question. Provided the specific precipitates are formed in the region of antibody excess, maximal sensitivity develops at least 2 to 3 weeks before detectable circulating antibody is formed in guinea pigs against the sensitizing antigen. Neither adjuvant nor killed acid-fast bacteria are required for induction of the delayed hypersensitive state although the degree of sensitization is considerably increased when the sensitizing material is incorporated in Freund's complete adjuvant. Characteristics of the "delayed" as opposed to the "immediate" hypersensitive states in the guinea pig are described and implications of the findings are discussed. PMID:13385403

Detection of immune deposits in glomeruli: the masking effect on antigenicity of formalin in the presence of proteins.

PubMed

Hed, J; Eneström, S

1981-01-01

Formalin is known to mask the antigenicity of immune deposits in glomeruli but not of surface immunoglobulins of isolated lymphocytes. We have shown in mice with experimental passive anti-GBM glomerulonephritis that formalin masks the antigenicity of GBM-bound immunoglobulins only if the tissue is fixed before sectioning. The presence of a high concentration of normal bovine serum during fixation of cryostat sections masks the antigenicity of immune deposits, whereas formalin alone has no obvious effect. The same results were obtained with human immunoglobulins (IgG, IgM and IgA) bound to tissue sections. Protease treatment with pepsin and trypsin restored the ability of the immunoglobulins to be stained. The masking effect seems to be due to extensive cross-linking of environmental proteins which prevents fluorescent conjugates reaching their antigens. Methods for detecting immunoglobulins in tissues must, therefore, take into consideration the influence of fixatives not only on epitopes but also on the environment in which the antigenic determinants are localised.

A 1H NMR method for the analysis of antigen-antibody interactions: binding of a peptide fragment of lysozyme to anti-lysozyme monoclonal antibody.

PubMed

Ito, W; Nishimura, M; Sakato, N; Fujio, H; Arata, Y

1987-09-01

A proton nuclear magnetic resonance (NMR) study is reported of the molecular structural basis of antigen-antibody interactions. An immunologically reactive proteolytic fragment corresponding to one of the antigenic regions on hen egg-white lysozyme (HEL) was used in combination with a monoclonal antibody that recognizes this site. Using spin diffusion, we prepared an antibody in which the magnetization of the antigen binding site was saturated by non-specific nuclear Overhauser effect. Under these conditions the effect of the saturation of the antibody was observed to spread over the peptide fragment through the antigen binding site. On the basis of the results obtained for the intermolecular nuclear Overhauser effect, we discuss how the peptide fragment interacts with the antibody. The side chains of aromatic residues, Trp, Tyr, and His, and of ionic residues, especially Arg, Lys, and Glu, are suggested to be important in the antigen-antibody interaction.

Spatiotemporally and Mechanically Controlled Triggering of Mast Cells using Atomic Force Microscopy

PubMed Central

Hu, Kenneth K.; Bruce, Marc A.; Butte, Manish J.

2014-01-01

Mast cells are thought to be sensitive to mechanical forces, for example, coughing in asthma or pressure in “physical urticarias”. Conversion of mechanical forces to biochemical signals could potentially augment antigenic signaling. Studying the combined effects of mechanical and antigenic cues on mast cells and other hematopoietic cells has been elusive. Here, we present an approach using a modified atomic force microscope cantilever to deliver antigenic signals to mast cells while simultaneously applying mechanical forces. We developed a strategy to concurrently record degranulation events by fluorescence microscopy during antigenic triggering. Finally, we also measured the mechanical forces generated by mast cells while antigen receptors are ligated. We showed that mast cells respond to antigen delivered by the AFM cantilever with prompt degranulation and the generation of strong pushing and pulling forces. We did not discern any relationship between applied mechanical forces and the kinetics of degranulation. These experiments present a new method for dissecting the interactions of mechanical and biochemical cues in signaling responses of immune cells. PMID:24777418

Molecular analysis of antigen-independent adhesion forces between T and B lymphocytes.

PubMed Central

Amblard, F; Auffray, C; Sekaly, R; Fischer, A

1994-01-01

The low-affinity interactions underlying antigen recognition by T-cell receptors (TCRs) are thought to involve antigen-independent adhesion mechanisms. Using a hydrodynamic approach, we found that antigen-independent adhesion occurred between human B cells and resting T cells in a transient and temperature-dependent fashion. The mean cell-cell adhesion force was 0.32 x 10(-9) N and was generated by similar contributions (0.16 x 10(-9) N) of the LFA-1- and CD2-dependent adhesion pathways. After T-cell stimulation with a phorbol ester, the force contributed by LFA-1 was drastically increased, while that of CD2 was unaffected. We propose that weak receptor-mediated adhesion initiates antigen-independent intercellular contacts required for antigen recognition by the TCR and is upregulated following TCR engagement. The method used permits adhesion forces between living cells to be resolved at the molecular level and should prove valuable for the rapid assessment of interaction forces between various types of cells and cell-sized particles. Images PMID:7909604

SIMPLE: a sequential immunoperoxidase labeling and erasing method.

PubMed

Glass, George; Papin, Jason A; Mandell, James W

2009-10-01

The ability to simultaneously visualize expression of multiple antigens in cells and tissues can provide powerful insights into cellular and organismal biology. However, standard methods are limited to the use of just two or three simultaneous probes and have not been widely adopted for routine use in paraffin-embedded tissue. We have developed a novel approach called sequential immunoperoxidase labeling and erasing (SIMPLE) that enables the simultaneous visualization of at least five markers within a single tissue section. Utilizing the alcohol-soluble peroxidase substrate 3-amino-9-ethylcarbazole, combined with a rapid non-destructive method for antibody-antigen dissociation, we demonstrate the ability to erase the results of a single immunohistochemical stain while preserving tissue antigenicity for repeated rounds of labeling. SIMPLE is greatly facilitated by the use of a whole-slide scanner, which can capture the results of each sequential stain without any information loss.

[Production of marker-free plants expressing the gene of the hepatitis B virus surface antigen].

PubMed

Rukavtsova, E B; Gaiazova, A R; Chebotareva, E N; Bur'ianova, Ia I

2009-08-01

The pBM plasmid, carrying the gene of hepatitis B virus surface antigen (HBsAg) and free of any selection markers of antibiotic or herbicide resistance, was constructed for genetic transformation of plants. A method for screening transformed plant seedlings on nonselective media was developed. Enzyme immunoassay was used for selecting transgenic plants with HBsAg gene among the produced regenerants; this method provides for a high sensitivity detection of HBsAg in plant extracts. Tobacco and tomato transgenic lines synthesizing this antigen at a level of 0.01-0.05% of the total soluble protein were obtained. The achieved level of HBsAg synthesis is sufficient for preclinical trials of the produced plants as a new generation safe edible vaccine. The developed method for selecting transformants can be used for producing safe plants free of selection markers.