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Sample records for affinity tagging method

  1. An automated method for high-throughput protein purification applied to a comparison of His-tag and GST-tag affinity chromatography

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    Büssow Konrad

    2003-07-01

    Full Text Available Abstract Background Functional Genomics, the systematic characterisation of the functions of an organism's genes, includes the study of the gene products, the proteins. Such studies require methods to express and purify these proteins in a parallel, time and cost effective manner. Results We developed a method for parallel expression and purification of recombinant proteins with a hexahistidine tag (His-tag or glutathione S-transferase (GST-tag from bacterial expression systems. Proteins are expressed in 96-well microplates and are purified by a fully automated procedure on a pipetting robot. Up to 90 microgram purified protein can be obtained from 1 ml microplate cultures. The procedure is readily reproducible and 96 proteins can be purified in approximately three hours. It avoids clearing of crude cellular lysates and the use of magnetic affinity beads and is therefore less expensive than comparable commercial systems. We have used this method to compare purification of a set of human proteins via His-tag or GST-tag. Proteins were expressed as fusions to an N-terminal tandem His- and GST-tag and were purified by metal chelating or glutathione affinity chromatography. The purity of the obtained protein samples was similar, yet His-tag purification resulted in higher yields for some proteins. Conclusion A fully automated, robust and cost effective method was developed for the purification of proteins that can be used to quickly characterise expression clones in high throughput and to produce large numbers of proteins for functional studies. His-tag affinity purification was found to be more efficient than purification via GST-tag for some proteins.

  2. Comparison of a Label-Free Quantitative Proteomic Method Based on Peptide Ion Current Area to the Isotope Coded Affinity Tag Method

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    Young Ah Goo

    2008-01-01

    Full Text Available Recently, several research groups have published methods for the determination of proteomic expression profiling by mass spectrometry without the use of exogenously added stable isotopes or stable isotope dilution theory. These so-called label-free, methods have the advantage of allowing data on each sample to be acquired independently from all other samples to which they can later be compared in silico for the purpose of measuring changes in protein expression between various biological states. We developed label free software based on direct measurement of peptide ion current area (PICA and compared it to two other methods, a simpler label free method known as spectral counting and the isotope coded affinity tag (ICAT method. Data analysis by these methods of a standard mixture containing proteins of known, but varying, concentrations showed that they performed similarly with a mean squared error of 0.09. Additionally, complex bacterial protein mixtures spiked with known concentrations of standard proteins were analyzed using the PICA label-free method. These results indicated that the PICA method detected all levels of standard spiked proteins at the 90% confidence level in this complex biological sample. This finding confirms that label-free methods, based on direct measurement of the area under a single ion current trace, performed as well as the standard ICAT method. Given the fact that the label-free methods provide ease in experimental design well beyond pair-wise comparison, label-free methods such as our PICA method are well suited for proteomic expression profiling of large numbers of samples as is needed in clinical analysis.

  3. Several Affinity Tags Commonly Used in Chromatographic Purification

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    Xinyu Zhao

    2013-01-01

    Full Text Available Affinity tags have become powerful tools from basic biological research to structural and functional proteomics. They were widely used to facilitate the purification and detection of proteins of interest, as well as the separation of protein complexes. Here, we mainly discuss the benefits and drawbacks of several affinity or epitope tags frequently used, including hexahistidine tag, FLAG tag, Strep II tag, streptavidin-binding peptide (SBP tag, calmodulin-binding peptide (CBP, glutathione S-transferase (GST, maltose-binding protein (MBP, S-tag, HA tag, and c-Myc tag. In some cases, a large-size affinity tag, such as GST or MBP, can significantly impact on the structure and biological activity of the fusion partner protein. So it is usually necessary to excise the tag by protease. The most commonly used endopeptidases are enterokinase, factor Xa, thrombin, tobacco etch virus, and human rhinovirus 3C protease. The proteolysis features of these proteases are described in order to provide a general guidance on the proteolytic removal of the affinity tags.

  4. Differential profiling of breast cancer plasma proteome by isotope-coded affinity tagging method reveals biotinidase as a breast cancer biomarker

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    Yu Myeong-Hee

    2010-03-01

    Full Text Available Abstract Background Breast cancer is one of the leading causes of women's death worldwide. It is important to discover a reliable biomarker for the detection of breast cancer. Plasma is the most ideal source for cancer biomarker discovery since many cells cross-communicate through the secretion of soluble proteins into blood. Methods Plasma proteomes obtained from 6 breast cancer patients and 6 normal healthy women were analyzed by using the isotope-coded affinity tag (ICAT labeling approach and tandem mass spectrometry. All the plasma samples used were depleted of highly abundant 6 plasma proteins by immune-affinity column chromatography before ICAT labeling. Several proteins showing differential abundance level were selected based on literature searches and their specificity to the commercially available antibodies, and then verified by immunoblot assays. Results A total of 155 proteins were identified and quantified by ICAT method. Among them, 33 proteins showed abundance changes by more than 1.5-fold between the plasmas of breast cancer patients and healthy women. We chose 5 proteins for the follow-up confirmation in the individual plasma samples using immunoblot assay. Four proteins, α1-acid glycoprotein 2, monocyte differentiation antigen CD14, biotinidase (BTD, and glutathione peroxidase 3, showed similar abundance ratio to ICAT result. Using a blind set of plasmas obtained from 21 breast cancer patients and 21 normal healthy controls, we confirmed that BTD was significantly down-regulated in breast cancer plasma (Wilcoxon rank-sum test, p = 0.002. BTD levels were lowered in all cancer grades (I-IV except cancer grade zero. The area under the receiver operating characteristic curve of BTD was 0.78. Estrogen receptor status (p = 0.940 and progesterone receptor status (p = 0.440 were not associated with the plasma BTD levels. Conclusions Our study suggests that BTD is a potential serological biomarker for the detection of breast cancer.

  5. Affinity Purification of Protein Complexes Using TAP Tags

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    Gerace, Erica; Moazed, Danesh

    2016-01-01

    This protocol is used for the isolation and analysis of protein complexes using the tandem affinity purification (TAP) tag system. The protocol describes the purification of a protein fused to a TAP tag comprised of two protein A domains and the calmodulin binding peptide separated by a TEV cleavage site. This is a powerful technique for rapid purification of protein complexes and the analysis of their stoichiometric composition, posttranslational modifications, structure, and functional activities. PMID:26096502

  6. Heparin-binding peptide as a novel affinity tag for purification of recombinant proteins.

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    Morris, Jacqueline; Jayanthi, Srinivas; Langston, Rebekah; Daily, Anna; Kight, Alicia; McNabb, David S; Henry, Ralph; Kumar, Thallapuranam Krishnaswamy Suresh

    2016-10-01

    Purification of recombinant proteins constitutes a significant part of the downstream processing in biopharmaceutical industries. Major costs involved in the production of bio-therapeutics mainly depend on the number of purification steps used during the downstream process. Affinity chromatography is a widely used method for the purification of recombinant proteins expressed in different expression host platforms. Recombinant protein purification is achieved by fusing appropriate affinity tags to either N- or C- terminus of the target recombinant proteins. Currently available protein/peptide affinity tags have proved quite useful in the purification of recombinant proteins. However, these affinity tags suffer from specific limitations in their use under different conditions of purification. In this study, we have designed a novel 34-amino acid heparin-binding affinity tag (HB-tag) for the purification of recombinant proteins expressed in Escherichia coli (E. coli) cells. HB-tag fused recombinant proteins were overexpressed in E. coli in high yields. A one-step heparin-Sepharose-based affinity chromatography protocol was developed to purify HB-fused recombinant proteins to homogeneity using a simple sodium chloride step gradient elution. The HB-tag has also been shown to facilitate the purification of target recombinant proteins from their 8 M urea denatured state(s). The HB-tag has been demonstrated to be successfully released from the fusion protein by an appropriate protease treatment to obtain the recombinant target protein(s) in high yields. Results of the two-dimensional NMR spectroscopy experiments indicate that the purified recombinant target protein(s) exist in the native conformation. Polyclonal antibodies raised against the HB-peptide sequence, exhibited high binding specificity and sensitivity to the HB-fused recombinant proteins (∼10 ng) in different crude cell extracts obtained from diverse expression hosts. In our opinion, the HB-tag provides a

  7. NiCoMnO4: A Bifunctional Affinity Probe for His-Tagged Protein Purification and Phosphorylation Sites Recognition.

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    Qi, Xiaoyue; Chen, Long; Zhang, Chaoqun; Xu, Xinyuan; Zhang, Yiding; Bai, Yu; Liu, Huwei

    2016-07-27

    A bifunctional affinity probe NiCoMnO4 was designed and prepared with controllable morphology and size using facile methods. It was observed that the probe could be applied in His-tagged proteins purification and phosphopeptides enrichment simply through the buffer modulation. NiCoMnO4 particles showed satisfactory cycling performance for His-tagged proteins purification and broad pH-tolerance of loading buffer for phosphopeptides affinity. Therefore, a high-throughput, cost-effective, and efficient protein/peptide purification method was developed within 10 min based on the novel bifunctional affinity probe. PMID:27381638

  8. A photocleavable affinity tag for the enrichment of alkyne-modified biomolecules

    NARCIS (Netherlands)

    Koopmans, Timo; Dekker, Frank J.; Martin, Nathaniel I.

    2012-01-01

    A new photocleavable affinity tag for use in the enrichment of alkyne-labelled biomolecules is reported. The tag is prepared via a concise synthetic route using readily available materials. The photolytic conditions employed for cleavage of the tag provide for a clean release of enriched biomolecule

  9. A dual-tagging system for the affinity purification of mammalian protein complexes

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    Giannone, Richard J [ORNL; McDonald, W Hayes [ORNL; Hurst, Gregory {Greg} B [ORNL; Huang, Ying [ORNL; Wu, Jun [ORNL; Liu, Yie [National Institute on Aging, Baltimore; Wang, Yisong [ORNL

    2007-01-01

    One popular method to elucidate protein-protein interactions involves the native co-purification of an affinity tagged protein and its interacting partners, which are subsequently identified through mass spectrometry (MS) (1). Although straightforward, reproducible, and broadly employed, this strategy is hampered by the efficacy of protein recoveries both in terms of sensitivity and specificity. This is especially pertinent to methodologies that employ a single-step of purification, where suboptimal enrichment of the bait protein and its partners over background can lead to masking of their signals. Although improvements to MS instrumentation generally increase peptide detection sensitivities, the problem of specificity, i.e. distinguishing specific from non-specific interacting proteins, remains. Thus ultimately, the limiting factor in the identification of specific interacting proteins lies with the purification itself. An effort to resolve this specificity issue has been made with the introduction of the Tandem Affinity Purification (TAP) tag. This construct consists of an IgG-binding domain and calmodulin binding peptide domain separated by a tobacco etch virus (TEV) protease cleavage site (2). The TAP method was originally developed in yeast and has best demonstrated its utility in the systematic identification of numerous multiprotein complexes in the yeast proteome (3). Although modifications to the original TAP have been successful in examining the protein networks of mammalian cells (4-7), the strategy offers a relatively low yield of bait and specific interacting proteins (8), and the success rate are usually on case-by-case basis. In addition, problems inherent to any protein tagging strategy remain, such as variable exposure of the affinity tag, disruption of the bait protein's ability to fold properly, steric exclusion of interacting partners, and/or ectopic overexpression of the fusion protein, which can lead to complications in both the

  10. A Method to Site-Specifically Identify and Quantitate Carbonyl End Products of Protein Oxidation Using Oxidation-Dependent Element Coded Affinity Tags (O-ECAT) and NanoLiquid Chromatography Fourier Transform Mass Spectrometry

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    Lee, S; Young, N L; Whetstone, P A; Cheal, S M; Benner, W H; Lebrilla, C B; Meares, C F

    2005-08-25

    Protein oxidation is linked to cellular stress, aging, and disease. Protein oxidations that result in reactive species are of particular interest, since these reactive oxidation products may react with other proteins or biomolecules in an unmediated and irreversible fashion, providing a potential marker for a variety of disease mechanisms. We have developed a novel system to identify and quantitate, relative to other states, the sites of oxidation on a given protein. A specially designed Oxidation-dependent carbonyl-specific Element-Coded Affinity Mass Tag (O-ECAT), AOD, ((S)-2-(4-(2-aminooxy)-acetamido)-benzyl)-1, 4, 7, 10-tetraazacyclododecane-N, N', N'', N'''-tetraacetic acid, is used to covalently tag the residues of a protein oxidized to aldehyde or keto end products. After proteolysis, the resulting AOD-tagged peptides are affinity purified, and analyzed by nanoLC-FTICR-MS, which provides high specificity in extracting co-eluting AOD mass pairs with a unique mass difference and affords relative quantitation based on isotopic ratios. Using this methodology, we have mapped the surface oxidation sites on a model protein, recombinant human serum albumin (rHSA) in its native form (as purchased) and after FeEDTA oxidation. A variety of modified amino acid residues including lysine, arginine, proline, histidine, threonine, aspartic and glutamic acids, were found to be oxidized to aldehyde and keto end products. The sensitivity of this methodology is shown by the number of peptides identified, twenty peptides on the native protein and twenty-nine after surface oxidation using FeEDTA and ascorbate. All identified peptides map to the surface of the HSA crystal structure validating this method for identifying oxidized amino acids on protein surfaces. In relative quantitation experiments between FeEDTA oxidation and native protein oxidation, identified sites showed different relative propensities towards oxidation independent of amino acid

  11. Application of Ni(II-assisted peptide bond hydrolysis to non-enzymatic affinity tag removal.

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    Edyta Kopera

    Full Text Available In this study, we demonstrate a non-enzymatic method for hydrolytic peptide bond cleavage, applied to the removal of an affinity tag from a recombinant fusion protein, SPI2-SRHWAP-His(6. This method is based on a highly specific Ni(II reaction with (S/TXHZ peptide sequences. It can be applied for the protein attached to an affinity column or to the unbound protein in solution. We studied the effect of pH, temperature and Ni(II concentration on the efficacy of cleavage and developed an analytical protocol, which provides active protein with a 90% yield and ∼100% purity. The method works well in the presence of non-ionic detergents, DTT and GuHCl, therefore providing a viable alternative for currently used techniques.

  12. Dual-tagging system for the affinity purification of mammalian protein complexes

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    Giannone, Richard J [ORNL; McDonald, W Hayes [ORNL; Hurst, Gregory {Greg} B [ORNL; Huang, Ying [ORNL; Wu, Jun [ORNL; Liu, Yie [National Institute on Aging, Baltimore; Wang, Yisong [ORNL

    2007-01-01

    Although affinity purification coupled with mass spectrometry (MS) provides a powerful tool to study protein-protein interactions, this strategy has encountered numerous difficulties when adapted to mammalian cells. Here we describe a Gateway{reg_sign}-compatible dual-tag affinity purification system that integrates regulatable expression, tetracysteine motifs, and various combinations of affinity tags to facilitate the cloning, detection, and purification of bait proteins and their interacting partners. Utilizing the human telomere binding protein TRF2 as a benchmark, we demonstrate bait protein recoveries upwards of approximately 16% from as little as 1-7 x 10{sup 7} cells and successfully identify known TRF2 interacting proteins, suggesting that our dual-tag affinity purification approach is a capable new tool for expanding the capacity to explore mammalian proteomic networks.

  13. A chimeric affinity tag for efficient expression and chromatographic purification of heterologous proteins from plants

    OpenAIRE

    Frank eSainsbury; Philippe V. Jutras; Juan eVorster; Marie-Claire eGoulet; Dominique eMichaud

    2016-01-01

    The use of plants as expression hosts for recombinant proteins is an increasingly attractive option for the production of complex and challenging biopharmaceuticals. Tools are needed at present to marry recent developments in high-yielding gene vectors for heterologous expression with routine protein purification techniques. In this study we designed the Cysta-tag, a new purification tag for immobilized metal affinity chromatography (IMAC) of plant-made proteins based on the protein-stabilizi...

  14. Affinity purification of in vitro transcribed RNA with homogeneous ends using a 3'-ARiBo tag.

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    Di Tomasso, Geneviève; Salvail-Lacoste, Alix; Bouvette, Jonathan; Omichinski, James G; Legault, Pascale

    2014-01-01

    Common approaches for purification of RNAs synthesized in vitro by the T7 RNA polymerase often denature the RNA and produce RNAs with chemically heterogeneous 5'- and 3'-ends. Thus, native affinity purification strategies that incorporate 5' and 3' trimming technologies provide a solution to two main disadvantages that arise from standard approaches for RNA purification. This chapter describes procedures for nondenaturing affinity purification of in vitro transcribed RNA using a 3'-ARiBo tag, which yield RNAs with a homogeneous 3'-end. The applicability of the method to RNAs of different sequences, secondary structures, and sizes (29-614 nucleotides) is described, including suggestions for troubleshooting common problems. In addition, this chapter presents three complementary approaches to producing 5'-homogeneity of the affinity-purified RNA: (1) selection of the starting sequence; (2) Cse3 endoribonuclease cleavage of a 5'-CRISPR tag; or (3) self-cleavage of a 5'-hammerhead ribozyme tag. The additional steps to express and purify the Cse3 endonuclease are detailed. In light of recent results, the advantages and limitations of current approaches to achieve 5'-homogeneity of affinity-purified RNA are discussed, such that one can select a suitable strategy to purify the RNA of interest. PMID:25432744

  15. The Monitoring and Affinity Purification of Proteins Using Dual Tags with Tetracysteine Motifs

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    Giannone, Richard J.; Liu, Yie; Wang, Yisong

    Identification and characterization of protein-protein interaction networks is essential for the elucidation of biochemical mechanisms and cellular function. Affinity purification in combination with liquid chromatography-tandem mass spectrometry (LC-MS/MS) has emerged as a very powerful tactic for the identification of specific protein-protein interactions. In this chapter, we describe a comprehensive methodology that uses our recently developed dual-tag affinity purification system for the enrichment and identification of mammalian protein complexes. The protocol covers a series of separate but sequentially related techniques focused on the facile monitoring and purification of a dual-tagged protein of interest and its interacting partners via a system built with tetracysteine motifs and various combinations of affinity tags. Using human telomeric repeat binding factor 2 (TRF2) as an example, we demonstrate the power of the system in terms of bait protein recovery after dual-tag affinity purification, detection of bait protein subcellular localization and expression, and successful identification of known and potentially novel TRF2 interacting proteins. Although the protocol described here has been optimized for the identification and characterization of TRF2-associated proteins, it is, in principle, applicable to the study of any other mammalian protein complexes that may be of interest to the research community.

  16. The Monitoring and Affinity Purification of Proteins Using Dual-Tags with Tetracysteine Motifs

    Energy Technology Data Exchange (ETDEWEB)

    Giannone, Richard J [ORNL; Liu, Yie [ORNL; Wang, Yisong [ORNL

    2009-01-01

    Identification and characterization of protein-protein interaction networks is essential for the elucidation of biochemical mechanisms and cellular function. Affinity purification in combination with liquid chromatography-tandem mass spectrometry (LC-MS/MS) has emerged as a very powerful tactic for the identification of specific protein-protein interactions. In this chapter we describe a comprehensive methodology that utilizes our recently developed dual-tag affinity purification system for the enrichment and identification of mammalian protein complexes. The protocol covers a series of separate but sequentially related techniques focused on the facile monitoring and purification of a dual-tagged protein of interest and its interacting partners via a system built with tetracysteine motifs and various combinations of affinity tags. Using human telomeric repeat binding factor 2 (TRF2) as an example, we have demonstrated the power of the system in terms of bait protein recovery after dual-tag affinity purification, detection of bait protein subcellular localization and expression, and successful identification of known and potentially novel TRF2 interacting proteins. Although the protocol described here has been optimized for the identification and characterization of TRF2-associated proteins, it is, in principle, applicable to the study of any other mammalian protein complexes that may be of interest to the research community.

  17. Evaluation of Affinity-Tagged Protein Expression Strategies using Local and Global Isotope Ratio Measurements

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    Hervey, IV, William Judson [ORNL; Khalsa-Moyers, Gurusahai K [ORNL; Lankford, Patricia K [ORNL; Owens, Elizabeth T [ORNL; McKeown, Catherine K [ORNL; Lu, Tse-Yuan S [ORNL; Foote, Linda J [ORNL; Morrell-Falvey, Jennifer L [ORNL; McDonald, W Hayes [ORNL; Pelletier, Dale A [ORNL; Hurst, Gregory {Greg} B [ORNL

    2009-01-01

    Protein enrichments of engineered, affinity-tagged (or bait ) fusion proteins with interaction partners are often laden with background, non-specific proteins, due to interactions that occur in vitro as an artifact of the technique. Furthermore, the in vivo expression of the bait protein may itself affect physiology or metabolism. In this study, intrinsic affinity purification challenges were investigated in a model protein complex, DNA-dependent RNA polymerase (RNAP), encompassing chromosome- and plasmid-encoding strategies for bait proteins in two different microbial species: Escherichia coli and Rhodopseudomonas palustris. Isotope ratio measurements of bait protein expression strains relative to native, wild-type strains were performed by liquid chromatography tandem mass spectrometry (LC-MS-MS) to assess bait protein expression strategies in each species. Authentic interacting proteins of RNAP were successfully discerned from artifactual co-isolating proteins by the isotopic differentiation of interactions as random or targeted (I-DIRT) method (A. J. Tackett et al. J. Proteome Res. 2005, 4 (5), 1752-1756). To investigate broader effects of bait protein production in the bacteria, we compared proteomes from strains harboring a plasmid that encodes an affinity-tagged subunit (RpoA) of the RNAP complex with the corresponding wild-type strains using stable isotope metabolic labeling. The ratio of RpoA abundance in plasmid strains versus wild type was 0.8 for R. palustris and 1.7 for E. coli. While most other proteins showed no appreciable difference, proteins significantly increased in abundance in plasmid-encoded bait-expressing strains of both species included the plasmid encoded antibiotic resistance protein, GenR and proteins involved in amino acid biosynthesis. Together, these local, complex-specific and more global, whole proteome isotopic abundance ratio measurements provided a tool for evaluating both in vivo and in vitro effects of plasmid

  18. A chimeric affinity tag for efficient expression and chromatographic purification of heterologous proteins from plants

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    Frank eSainsbury

    2016-02-01

    Full Text Available The use of plants as expression hosts for recombinant proteins is an increasingly attractive option for the production of complex and challenging biopharmaceuticals. Tools are needed at present to marry recent developments in high-yielding gene vectors for heterologous expression with routine protein purification techniques. In this study we designed the Cysta-tag, a new purification tag for immobilized metal affinity chromatography (IMAC of plant-made proteins based on the protein-stabilizing fusion partner SlCYS8. We show that the Cysta-tag may be used to rapidly purify proteins under native conditions, and then be removed enzymatically to isolate the protein of interest. We also show that commonly used protease recognition sites for linking purification tags are differentially stable in leaves of the commonly used expression host Nicotiana benthamiana, with those linkers susceptible to cysteine proteases being less stable then serine protease-cleavable linkers. As an example we describe a Cysta-tag experimental scheme for the one-step purification of a clinically useful protein, human α1-antitrypsin, transiently expressed in N. benthamiana. With potential applicability to the variety of chromatography formats commercially available for IMAC-based protein purification, the Cysta-tag provides a convenient means for the efficient and cost-effective purification of recombinant proteins from plant tissues.

  19. In-house preparation of hydrogels for batch affinity purification of glutathione S-transferase tagged recombinant proteins

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    Buhrman Jason S

    2012-09-01

    Full Text Available Abstract Background Many branches of biomedical research find use for pure recombinant proteins for direct application or to study other molecules and pathways. Glutathione affinity purification is commonly used to isolate and purify glutathione S-transferase (GST-tagged fusion proteins from total cellular proteins in lysates. Although GST affinity materials are commercially available as glutathione immobilized on beaded agarose resins, few simple options for in-house production of those systems exist. Herein, we describe a novel method for the purification of GST-tagged recombinant proteins. Results Glutathione was conjugated to low molecular weight poly(ethylene glycol diacrylate (PEGDA via thiol-ene “click” chemistry. With our in-house prepared PEGDA:glutathione (PEGDA:GSH homogenates, we were able to purify a glutathione S-transferase (GST green fluorescent protein (GFP fusion protein (GST-GFP from the soluble fraction of E. coli lysate. Further, microspheres were formed from the PEGDA:GSH hydrogels and improved protein binding to a level comparable to purchased GSH-agarose beads. Conclusions GSH containing polymers might find use as in-house methods of protein purification. They exhibited similar ability to purify GST tagged proteins as purchased GSH agarose beads.

  20. A strategy to enhance the binding affinity of fluorophore-aptamer pairs for RNA tagging with neomycin conjugation.

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    Jeon, Jongho; Lee, Kyung Hyun; Rao, Jianghong

    2012-10-14

    Fluorogenic sulforhodamine-neomycin conjugates have been designed and synthesized for RNA tagging. Conjugates were fluorescently activated by binding to RNA aptamers and exhibited greater than 250-400 fold enhancement in binding affinity relative to corresponding unconjugated fluorophores.

  1. High Affinity Immobilization of Proteins Using the CrAsH/TC Tag

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    Janine Schulte-Zweckel

    2016-06-01

    Full Text Available Protein microarrays represent important tools for biomedical analysis. We have recently described the use of the biarsenical-tetracysteine (TC tag for the preparation of protein microarrays. The unique feature of this tag enables the site-specific immobilization of TC-containing proteins on biarsenical-modified surfaces, resulting in a fluorescence enhancement that allows the direct quantification of the immobilized proteins. Moreover, the reversibility of the binding upon incubation with large quantities of thiols permits the detachment of the proteins from the surface, thereby enabling recovery of the substrate to extend the life time of the slide. Herein, we describe our recent results that further extend the applicability of the CrAsH/TC tag to the fabrication of biochips. With this aim, the immobilization of proteins on surfaces has been investigated using two different spacers and two TC tags, the minimal TC sequence (CCPGCC and an optimized motif (FLNCCPGCCMEP. While the minimal peptide motif enables a rapid recycling of the slide, the optimized TC sequence reveals an increased affinity due to its greater resistance to displacement by thiols. Moreover, the developed methodology was applied to the immobilization of proteins via on-chip ligation of recombinant protein thioesters.

  2. SNAP-Tag Technology: A Useful Tool To Determine Affinity Constants and Other Functional Parameters of Novel Antibody Fragments.

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    Niesen, Judith; Sack, Markus; Seidel, Melanie; Fendel, Rolf; Barth, Stefan; Fischer, Rainer; Stein, Christoph

    2016-08-17

    Antibody derivatives, such as the single chain fragment variable (scFv), can be developed as diagnostic and therapeutic tools in cancer research, especially in the form of fusion proteins. Such derivatives are easier to produce and modify than monoclonal antibodies (mAbs) and achieve better tissue/tumor penetration. The genetic modification of scFvs is also much more straightforward than the challenging chemical modification of mAbs. Therefore, we constructed two scFvs derived from the approved monoclonal antibodies cetuximab (scFv2112) and panitumumab (scFv1711), both of which are specific for the epidermal growth factor receptor (EGFR), a well-characterized solid tumor antigen. Both scFvs were genetically fused to the SNAP-tag, an engineered version of the human DNA repair enzyme O(6)-alkylguanine DNA alkyltransferase that allows the covalent coupling of benzylguanine (BG)-modified substrates such as fluorescent dyes. The SNAP-tag achieves controllable and irreversible protein modification and is an important tool for experimental studies in vitro and in vivo. The affinity constant of a scFv is a key functional parameter, especially in the context of a fusion protein. Therefore, we developed a method to define the affinity constants of scFv-SNAP fusion proteins by surface plasmon resonance (SPR) spectroscopy. We could confirm that both scFvs retained their functionality after fusion to the SNAP-tag in a variety of procedures and assays, including ELISA, flow cytometry, and confocal microscopy. The experimental procedures described herein, and the new protocol for affinity determination by SPR spectroscopy, are suitable for the preclinical evaluation of diverse antibody formats and derivatives. PMID:27391930

  3. Proteomic analysis of Trypanosoma cruzi developmental stages using isotope-coded affinity tag reagents.

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    Paba, Jaime; Ricart, Carlos A O; Fontes, Wagner; Santana, Jaime M; Teixeira, Antonio R L; Marchese, Jason; Williamson, Brian; Hunt, Tony; Karger, Barry L; Sousa, Marcelo V

    2004-01-01

    Comparative proteome analysis of developmental stages of the human pathogen Trypanosoma cruzi was carried out by isotope-coded affinity tag technology (ICAT) associated with liquid cromatography-mass spectrometry peptide sequencing (LC-MS/MS). Protein extracts of the protozoan trypomastigote and amastigote stages were labeled with heavy (D8) and light (D0) ICAT reagents and subjected to cation exchange and avidin affinity chromatographies followed by LC-MS/MS analysis. High confidence sequence information and expression levels for 41 T. cruzi polypeptides, including metabolic enzymes, paraflagellar rod components, tubulins, and heat-shock proteins were reported. Twenty-nine proteins displayed similar levels of expression in both forms of the parasite, nine proteins presented higher levels in trypomastigotes, whereas three were more expressed in amastigotes. PMID:15253433

  4. A photo-cleavable biotin affinity tag for the facile release of a photo-crosslinked carbohydrate-binding protein.

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    Chang, Tsung-Che; Adak, Avijit K; Lin, Ting-Wei; Li, Pei-Jhen; Chen, Yi-Ju; Lai, Chain-Hui; Liang, Chien-Fu; Chen, Yu-Ju; Lin, Chun-Cheng

    2016-03-15

    The use of photo-crosslinking glycoprobes represents a powerful strategy for the covalent capture of labile protein complexes and allows detailed characterization of carbohydrate-mediated interactions. The selective release of target proteins from solid support is a key step in functional proteomics. We envisaged that light activation can be exploited for releasing labeled protein in a dual photo-affinity probe-based strategy. To investigate this possibility, we designed a trifunctional, galactose-based, multivalent glycoprobe for affinity labeling of carbohydrate-binding proteins. The resulting covalent protein-probe adduct is attached to a photo-cleavable biotin affinity tag; the biotin moiety enables specific presentation of the conjugate on streptavidin-coated beads, and the photolabile linker allows the release of the labeled proteins. This dual probe promotes both the labeling and the facile cleavage of the target protein complexes from the solid surfaces and the remainder of the cell lysate in a completely unaltered form, thus eliminating many of the common pitfalls associated with traditional affinity-based purification methods.

  5. Tags, wireless communication systems, tag communication methods, and wireless communications methods

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    Scott; Jeff W. , Pratt; Richard M.

    2006-09-12

    Tags, wireless communication systems, tag communication methods, and wireless communications methods are described. In one aspect, a tag includes a plurality of antennas configured to receive a plurality of first wireless communication signals comprising data from a reader, a plurality of rectifying circuits coupled with. respective individual ones of the antennas and configured to provide rectified signals corresponding to the first wireless communication signals, wherein the rectified signals are combined to produce a composite signal, an adaptive reference circuit configured to vary a reference signal responsive to the composite signal, a comparator coupled with the adaptive reference circuit and the rectifying circuits and configured to compare the composite signal with respect to the reference signal and to output the data responsive to the comparison, and processing circuitry configured to receive the data from the comparator and to process the data.

  6. Hybrid Method for Tagging Arabic Text

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    Yamina Tlili-Guiassa

    2006-01-01

    Full Text Available Many natural language expressions are ambiguous and need to draw on other sources of information to be interpreted. Interpretation of the word ﺗﻌﺎون to be considered as a noun or a verb depends on the presence of contextual cues. This study proposes a hybrid method of based- rules and a machine learning method for tagging Arabic words. So this method is based firstly on rules (that considered the post-position, ending of a word and patterns and then the anomaly is corrected by adopting a memory-based learning method (MBL. The memory based learning is an efficient method to integrate various sources of information and handling exceptional data in natural language processing tasks. Secondly checking the exceptional cases of rules and more information is made available to the learner for treating those exceptional cases. To evaluate the proposed method a number of experiments has been run and in order, to improve the importance of the various information in learning.

  7. Characterization of the diatomite binding domain in the ribosomal protein L2 from E. coli and functions as an affinity tag.

    Science.gov (United States)

    Li, Junhua; Zhang, Yang; Yang, Yanjun

    2013-03-01

    The ribosomal protein L2, a constituent protein of the 50S large ribosomal subunit, can be used as Si-tag using silica particles for the immobilization and purification of recombinant proteins (Ikeda et al. (Protein Expr Purif 71:91-95, 2010); Taniguchi et al. (Biotechnol Bioeng 96:1023-1029, 2007)). We applied a diatomite powder, a sedimentary rock mainly composed with diatoms silica, as an affinity solid phase and small ubiquitin-like modifier (SUMO) technology to release a target protein from the solid phase. The L2 (203-273) was the sufficient region for the adsorption of ribosomal protein L2 on diatomite. We comparatively analyzed the different adsorption properties of the two deleted proteins of L2 (L2 (1-60, 203-273) and L2 (203-273)) on diatomite. The time required to reach adsorption equilibrium of L2 (203-273) fusion protein on diatomite was shorter than that of L2 (1-60, 203-273) fusion protein. The maximum adsorption capacity of L2 (203-273) fusion protein was larger than that of L2 (1-60, 203-273) fusion protein. In order to study whether the L2 (203-273) can function as an affinity purification tag, SUMO was introduced as one specific protease cleavage site between the target protein and the purification tags. The L2 (203-273) and SUMO fusion protein purification method was tested using enhanced green fluorescent protein as a model protein; the result shows that the purification performance of this affinity purification method was good. The strong adsorption characteristic of L2 (203-273) on diatomite also provides a potential protein fusion tag for the immobilization of enzyme.

  8. Novel peptide sequence ("IQ-tag" with high affinity for NIR fluorochromes allows protein and cell specific labeling for in vivo imaging.

    Directory of Open Access Journals (Sweden)

    Kimberly A Kelly

    Full Text Available BACKGROUND: Probes that allow site-specific protein labeling have become critical tools for visualizing biological processes. METHODS: Here we used phage display to identify a novel peptide sequence with nanomolar affinity for near infrared (NIR (benzindolium fluorochromes. The developed peptide sequence ("IQ-tag" allows detection of NIR dyes in a wide range of assays including ELISA, flow cytometry, high throughput screens, microscopy, and optical in vivo imaging. SIGNIFICANCE: The described method is expected to have broad utility in numerous applications, namely site-specific protein imaging, target identification, cell tracking, and drug development.

  9. [Archival tags and geolocation methods for marine animals: A review].

    Science.gov (United States)

    Zhang, Tian-feng; Fan, Wei; Dai, Yang

    2015-11-01

    Archival tags, a group of data storable electronic tags, are widely used as strong tools for obtaining long term and large scale activity information of marine animals, specifically highly migratory oceanic fishes, and corresponding environmental data. Though retrieving tags is an indispensable step for obtaining data, which is a shortage of archival tags, a series of achievements have been made on marine animals by using archival tags since the 1990s. With the appearance of pop-up satellite tag, which solved the problem of data retrieving and was fully independent of the fishing, both breadth and depth of marine animals' studies are extended by the end of the 1990s. Geolocation based on light intensity is the key to estimate marine animals' movement and has achieved some progress in the past 20 years. However, the accuracy of geolocation for latitude is not high enough, and there is still much room for improvement. To date, most geolocation methods that use ambient daylight involve identifying the times when the sun is at a precisely known zenith angle (e.g., sunrise and sunset). The problem of estimating longitude has been proved easy to solve, but accurate latitude estimates remain elusive. This paper mainly introduced two tags, i. e., archival tags and pop-up tags, and three geolocation methods, i.e. , 1) the "fixed reference" method, 2) the "variable reference" method, and 3) the "reflection" method. We also presented a prospect analysis on archival tags and possible research direction of geolocation methods. We believed that miniaturization and multi-sensor integration are the trends for electronic tags while more environmental factors such as depth, SST (sea surface temperature) or magnetic field intensity, instead of single factor, as auxiliary parameters would be used for improving the geolocation accuracy in the future.

  10. Methods for Improving Aptamer Binding Affinity

    OpenAIRE

    Hijiri Hasegawa; Nasa Savory; Koichi Abe; Kazunori Ikebukuro

    2016-01-01

    Aptamers are single stranded oligonucleotides that bind a wide range of biological targets. Although aptamers can be isolated from pools of random sequence oligonucleotides using affinity-based selection, aptamers with high affinities are not always obtained. Therefore, further refinement of aptamers is required to achieve desired binding affinities. The optimization of primary sequences and stabilization of aptamer conformations are the main approaches to refining the binding properties of a...

  11. Application of a new dual localization-affinity purification tag reveals novel aspects of protein kinase biology in Aspergillus nidulans.

    Directory of Open Access Journals (Sweden)

    Colin P De Souza

    Full Text Available Filamentous fungi occupy critical environmental niches and have numerous beneficial industrial applications but devastating effects as pathogens and agents of food spoilage. As regulators of essentially all biological processes protein kinases have been intensively studied but how they regulate the often unique biology of filamentous fungi is not completely understood. Significant understanding of filamentous fungal biology has come from the study of the model organism Aspergillus nidulans using a combination of molecular genetics, biochemistry, cell biology and genomic approaches. Here we describe dual localization-affinity purification (DLAP tags enabling endogenous N or C-terminal protein tagging for localization and biochemical studies in A. nidulans. To establish DLAP tag utility we endogenously tagged 17 protein kinases for analysis by live cell imaging and affinity purification. Proteomic analysis of purifications by mass spectrometry confirmed association of the CotA and NimXCdk1 kinases with known binding partners and verified a predicted interaction of the SldABub1/R1 spindle assembly checkpoint kinase with SldBBub3. We demonstrate that the single TOR kinase of A. nidulans locates to vacuoles and vesicles, suggesting that the function of endomembranes as major TOR cellular hubs is conserved in filamentous fungi. Comparative analysis revealed 7 kinases with mitotic specific locations including An-Cdc7 which unexpectedly located to mitotic spindle pole bodies (SPBs, the first such localization described for this family of DNA replication kinases. We show that the SepH septation kinase locates to SPBs specifically in the basal region of apical cells in a biphasic manner during mitosis and again during septation. This results in gradients of SepH between G1 SPBs which shift along hyphae as each septum forms. We propose that SepH regulates the septation initiation network (SIN specifically at SPBs in the basal region of G1 cells and that

  12. Hepatitis C virus expressing flag-tagged envelope protein 2 has unaltered infectivity and density, is specifically neutralized by flag antibodies and can be purified by affinity chromatography

    DEFF Research Database (Denmark)

    Prentø, Jannick Cornelius; Bukh, Jens

    2011-01-01

    Hepatitis C virus (HCV) purification by ultracentrifugation is difficult because of the low and heterogeneous density of native and cultured viruses. It was recently shown that inserting flag tag into envelope protein 2 (E2) of HCV permitted virus purification by affinity chromatography. However,...... physiochemical properties of flag-tagged HCV is an important improvement for utilizing these viruses for imaging, virion composition analysis and possibly vaccine development....

  13. Image analysis methods for tagged MRI cardiac studies

    Science.gov (United States)

    Guttman, Michael A.; Prince, Jerry L.

    1990-07-01

    Tracking of magnetic resonance (MR) tags in myocardial tissue promises to be an effective tool in the assessment of myocardial motion. The amount of data acquired is very large and the measurements are numerous and must be precise requiring automated tracking methods. We describe a hierarchy of image processing steps that estimate both the endocardial and epicardial boundaries of the left ventricle and also estimate the spines of radial tags that emanate outward from the left ventricular cavity. The first stage determines the position of the myocardial boundaries for each of 128 rays emanating from the origin. To counter the deleterious effects of noise and the presence of the tags when determining the boundary positions we use nonlinear filtering concepts from mathematical morphology together with a prion knowledge related to boundary smoothness to improve the estimates. The second stage estimates the tag spines by matching a template in a direction orthogonal to the expected tag direction. We show results on tagged images and discuss further research directions. 1.

  14. Affinity Purification of a Recombinant Protein Expressed as a Fusion with the Maltose-Binding Protein (MBP) Tag

    Science.gov (United States)

    Duong-Ly, Krisna C.; Gabelli, Sandra B.

    2015-01-01

    Expression of fusion proteins such as MBP fusions can be used as a way to improve the solubility of the expressed protein in E. coli (Fox and Waugh, 2003; Nallamsetty et al., 2005; Nallamsetty and Waugh, 2006) and as a way to introduce an affinity purification tag. The protocol that follows was designed by the authors as a first step in the purification of a recombinant protein fused with MBP, using fast protein liquid chromatography (FPLC). Cells should have been thawed, resuspended in binding buffer, and lysed by sonication or microfluidization before mixing with the amylose resin or loading on the column. Slight modifications to this protocol may be made to accommodate both the protein of interest and the availability of equipment. PMID:26096500

  15. Immobilised metal-ion affinity chromatography purification of histidine-tagged recombinant proteins : a wash step with a low concentration of EDTA

    NARCIS (Netherlands)

    Westra, DF; Welling, GW; Koedijk, DGAM; Scheffer, AJ; The, TH; Welling-Wester, S

    2001-01-01

    Immobilised metal-ion affinity chromatography (IMAC) is widely used for the purification of recombinant proteins in which a poly-histidine tag is introduced. However, other proteins may also bind to IMAC columns. We describe the use of a washing buffer with a low concentration of EDTA (0.5 mM) for t

  16. Detection of diamonds in kimberlite by the tagged neutron method

    Energy Technology Data Exchange (ETDEWEB)

    Alexakhin, V.Yu.; Bystritsky, V.M.; Zamyatin, N.I.; Zubarev, E.V.; Krasnoperov, A.V.; Rapatsky, V.L. [Neutron Technologies LLC, Dubna, Joint Institute for Nuclear Research, Dubna (Russian Federation); Rogov, Yu.N., E-mail: Yury.Rogov@cern.ch [Neutron Technologies LLC, Dubna, Joint Institute for Nuclear Research, Dubna (Russian Federation); Sadovsky, A.B.; Salamatin, A.V.; Salmin, R.A.; Sapozhnikov, M.G.; Slepnev, V.M.; Khabarov, S.V. [Neutron Technologies LLC, Dubna, Joint Institute for Nuclear Research, Dubna (Russian Federation); Razinkov, E.A.; Tarasov, O.G. [Neutron Technologies LLC, Dubna (Russian Federation); Nikitin, G.M. [Institute “Yakutniproalmaz”, ALROSA JSC, Mirny (Russian Federation)

    2015-06-11

    A new technology for diamond detection in kimberlite based on the tagged neutron method is proposed. The results of experimental researches on irradiation of kimberlite samples with 14.1-MeV tagged neutrons are discussed. The source of the tagged neutron flux is a portable neutron generator with a built-in 64-pixel silicon alpha-detector with double-sided stripped readout. Characteristic gamma rays resulting from inelastic neutron scattering on nuclei of elements included in the composition of kimberlite are registered by six gamma-detectors based on BGO crystals. The criterion for diamond presence in kimberlite is an increased carbon concentration within a certain volume of the kimberlite sample.

  17. Detection of diamonds in kimberlite by the tagged neutron method

    International Nuclear Information System (INIS)

    A new technology for diamond detection in kimberlite based on the tagged neutron method is proposed. The results of experimental researches on irradiation of kimberlite samples with 14.1-MeV tagged neutrons are discussed. The source of the tagged neutron flux is a portable neutron generator with a built-in 64-pixel silicon alpha-detector with double-sided stripped readout. Characteristic gamma rays resulting from inelastic neutron scattering on nuclei of elements included in the composition of kimberlite are registered by six gamma-detectors based on BGO crystals. The criterion for diamond presence in kimberlite is an increased carbon concentration within a certain volume of the kimberlite sample

  18. Ni(2+)-zeolite/ferrosphere and Ni(2+)-silica/ferrosphere beads for magnetic affinity separation of histidine-tagged proteins.

    Science.gov (United States)

    Vereshchagina, T A; Fedorchak, M A; Sharonova, O M; Fomenko, E V; Shishkina, N N; Zhizhaev, A M; Kudryavtsev, A N; Frank, L A; Anshits, A G

    2016-01-28

    Magnetic Ni(2+)-zeolite/ferrosphere and Ni(2+)-silica/ferrosphere beads (Ni-ferrosphere beads - NFB) of a core-shell structure were synthesized starting from coal fly ash ferrospheres having diameters in the range of 0.063-0.050 mm. The strategy of NFB fabrication is an oriented chemical modification of the outer surface preserving the magnetic core of parent beads with the formation of micro-mesoporous coverings. Two routes of ferrosphere modification were realized, such as (i) hydrothermal treatment in an alkaline medium resulting in a NaP zeolite layer and (ii) synthesis of micro-mesoporous silica on the glass surface using conventional methods. Immobilization of Ni(2+) ions in the siliceous porous shell of the magnetic beads was carried out via (i) the ion exchange of Na(+) for Ni(2+) in the zeolite layer or (ii) deposition of NiO clusters in the zeolite and silica pores. The final NFB were tested for affinity in magnetic separation of the histidine-tagged green fluorescent protein (GFP) directly from a cell lysate. Results pointed to the high affinity of the magnetic beads towards the protein in the presence of 10 mM EDTA. The sorption capacity of the ferrosphere-based Ni-beads with respect to GFP was in the range 1.5-5.7 mg cm(-3).

  19. Communication methods, systems, apparatus, and devices involving RF tag registration

    Science.gov (United States)

    Burghard, Brion J.; Skorpik, James R.

    2008-04-22

    One technique of the present invention includes a number of Radio Frequency (RF) tags that each have a different identifier. Information is broadcast to the tags from an RF tag interrogator. This information corresponds to a maximum quantity of tag response time slots that are available. This maximum quantity may be less than the total number of tags. The tags each select one of the time slots as a function of the information and a random number provided by each respective tag. The different identifiers are transmitted to the interrogator from at least a subset of the RF tags.

  20. Integrative refolding and purification of histidine-tagged protein by like-charge facilitated refolding and metal-chelate affinity adsorption.

    Science.gov (United States)

    Liu, Hu; Du, Wen-Jie; Dong, Xiao-Yan; Sun, Yan

    2014-05-30

    This work proposed an integrative method of protein refolding and purification by like-charged resin facilitated refolding and metal-chelate affinity adsorption. Hexahistidine-tagged enhanced green fluorescence protein (EGFP) was overexpressed in Escherichia coli as inclusion bodies (IBs), and then the protein was refolded and purified from urea-solubilized IBs by this method. A metal-chelating resin was fabricated by coupling iminodiacetic acid (IDA) to agarose gel (Sepharose FF). The anionic resin was used to facilitate the refolding of like-charged EGFP from IBs. After refolding, nickel ions were introduced for the affinity purification of the target protein by metal-chelating adsorption. It was found that the resin was effective in facilitating EGFP refolding. For 0.1mg/mL EGFP IBs refolding, the fluorescence recovery (FR) by direct dilution was only 64%; addition of only 0.05 g/mL resin increased the FR to over 90%. Moreover, the FR increased with increasing resin concentration. Owning to the shielding effect of the oppositely charged impurities embedded in IBs on the surface charges of the IDA resin, more resin particles were required to exert an aggregation inhibition effect in the IBs protein refolding. Additionally, compared with direct-dilution refolding, inclusion of like-charged resins not only offered an enhanced FR of EGFP, but also bound some opposite-charged contaminant proteins, leading to a preliminary purification effect. Afterwards, the refolded EGFP was recovered by metal-chelating adsorption at an FR of 85% and purity of 93%. This work has thus extended the like-charge facilitated protein refolding strategy to the integrative protein refolding and purification.

  1. Studies with an immobilized metal affinity chromatography cassette system involving binuclear triazacyclononane-derived ligands: automation of batch adsorption measurements with tagged recombinant proteins.

    Science.gov (United States)

    Petzold, Martin; Coghlan, Campbell J; Hearn, Milton T W

    2014-07-18

    This study describes the determination of the adsorption isotherms and binding kinetics of tagged recombinant proteins using a recently developed IMAC cassette system and employing automated robotic liquid handling procedures for IMAC resin screening. These results confirm that these new IMAC resins, generated from a variety of different metal-charged binuclear 1,4,7-triaza-cyclononane (tacn) ligands, interact with recombinant proteins containing a novel N-terminal metal binding tag, NT1A, with static binding capacities similar to those obtained with conventional hexa-His tagged proteins, but with significantly increased association constants. In addition, higher kinetic binding rates were observed with these new IMAC systems, an attribute that can be positively exploited to increase process productivity. The results from this investigation demonstrate that enhancements in binding capacities and affinities were achieved with these new IMAC resins and chosen NT1A tagged protein. Further, differences in the binding performances of the bis(tacn) xylenyl-bridged ligands were consistent with the distance between the metal binding centres of the two tacn moieties, the flexibility of the ligand and the potential contribution from the aromatic ring of the xylenyl group to undergo π/π stacking interactions with the tagged proteins.

  2. A statistical method for assessing peptide identification confidence in accurate mass and time tag proteomics.

    Science.gov (United States)

    Stanley, Jeffrey R; Adkins, Joshua N; Slysz, Gordon W; Monroe, Matthew E; Purvine, Samuel O; Karpievitch, Yuliya V; Anderson, Gordon A; Smith, Richard D; Dabney, Alan R

    2011-08-15

    Current algorithms for quantifying peptide identification confidence in the accurate mass and time (AMT) tag approach assume that the AMT tags themselves have been correctly identified. However, there is uncertainty in the identification of AMT tags, because this is based on matching LC-MS/MS fragmentation spectra to peptide sequences. In this paper, we incorporate confidence measures for the AMT tag identifications into the calculation of probabilities for correct matches to an AMT tag database, resulting in a more accurate overall measure of identification confidence for the AMT tag approach. The method is referenced as Statistical Tools for AMT Tag Confidence (STAC). STAC additionally provides a uniqueness probability (UP) to help distinguish between multiple matches to an AMT tag and a method to calculate an overall false discovery rate (FDR). STAC is freely available for download, as both a command line and a Windows graphical application.

  3. Use of the myosin motor domain as large-affinity tag for the expression and purification of proteins in Dictyostelium discoideum.

    Science.gov (United States)

    Kollmar, Martin

    2006-08-15

    The cellular slime mold Dictyostelium discoideum is increasingly be used for the overexpression of proteins. Dictyostelium is amenable to classical and molecular genetic approaches and can easily be grown in large quantities. It contains a variety of chaperones and folding enzymes, and is able to perform all kinds of post-translational protein modifications. Here, new expression vectors are presented that have been designed for the production of proteins in large quantities for biochemical and structural studies. The expression cassettes of the most successful vectors are based on a tandem affinity purification tag consisting of an octahistidine tag followed by the myosin motor domain tag. The myosin motor domain not only strongly enhances the production of fused proteins but is also used for a fast affinity purification step through its ATP-dependent binding to actin. The applicability of the new system has been demonstrated for the expression and purification of subunits of the dynein-dynactin motor protein complex from different species. PMID:16516959

  4. A Quick and Affine Invariance Matching Method for Oblique Images

    Directory of Open Access Journals (Sweden)

    XIAO Xiongwu

    2015-04-01

    Full Text Available This paper proposed a quick, affine invariance matching method for oblique images. It calculated the initial affine matrix by making full use of the two estimated camera axis orientation parameters of an oblique image, then recovered the oblique image to a rectified image by doing the inverse affine transform, and left over by the SIFT method. We used the nearest neighbor distance ratio(NNDR, normalized cross correlation(NCC measure constraints and consistency check to get the coarse matches, then used RANSAC method to calculate the fundamental matrix and the homography matrix. And we got the matches that they were interior points when calculating the homography matrix, then calculated the average value of the matches' principal direction differences. During the matching process, we got the initial matching features by the nearest neighbor(NN matching strategy, then used the epipolar constrains, homography constrains, NCC measure constrains and consistency check of the initial matches' principal direction differences with the calculated average value of the interior matches' principal direction differences to eliminate false matches. Experiments conducted on three pairs of typical oblique images demonstrate that our method takes about the same time as SIFT to match a pair of oblique images with a plenty of corresponding points distributed evenly and an extremely low mismatching rate.

  5. Parameters of explosives detection through tagged neutron method

    Energy Technology Data Exchange (ETDEWEB)

    Bagdasaryan, Kh.E.; Batyaev, V.F.; Belichenko, S.G., E-mail: consul757@mail.ru; Bestaev, R.R.; Gavryuchenkov, A.V.; Karetnikov, M.D.

    2015-06-01

    The potentialities of tagged neutron method (TNM) for explosives detection are examined on the basis of an idealized geometrical model. The model includes ING-27 14 MeV neutron generator with a built-in α-detector, a LYSO γ-detector and samples of material to be identified of approximately 0.3 kg each: explosives imitators (trinitrotoluene - TNT, tetryl, RDX and ammonium nitrate), legal materials (sugar, water, silk and polyethylene). The samples were unshielded or shielded by a paper layer of various thicknesses. The experimental data were interpreted by numerical simulation using a Poisson distribution of signals with the statistical parameters defined experimentally. The detection parameters were obtained by a pattern classification theory and a Bayes classifier.

  6. Peculiarities of Thermodynamic Simulation with the Method of Bound Affinity

    CERN Document Server

    Zilbergleyt, B

    2004-01-01

    Thermodynamic simulation of chemical and metallurgical systems is the only method to predict their equilibrium composition and is the most important application of chemical thermodynamics. The conventional strategy of simulation is always to find the most probable composition of the system, corresponding to thermodynamic equilibrium. Traditional simulation methods do not account for interactions within the chemical system. The Method of Bound Affinity (MBA) is based on the theory that explicitly takes into account interactions between subsystems of a complex chemical system and leads sometimes to essential differences in simulation results. This article discusses peculiarities of MBA application, exemplified by results for a complex system with a set of subsystems.

  7. A novel affinity purification method to isolate peptide specific antibodies

    DEFF Research Database (Denmark)

    Karlsen, Alan E; Lernmark, A; Kofod, Hans;

    1990-01-01

    with the beads and after a wash step the bound antibodies were eluted in 1 M acetic acid. The eluted material was composed predominantly of intact immunoglobulin as evidenced by the presence of heavy and light chain bands in SDS-PAGE. The eluted antibodies were peptide specific in ELISA and bound only to intact......Site-specific, high affinity polyclonal antisera are effectively and successfully produced by immunizing rabbits with synthetic peptides. The use of these antisera in subsequent immune analysis is often limited because of non-specific binding. We describe a new and simple method to effectively...... affinity-purify anti-peptide antibodies. To test our system, rabbits were immunized with model peptides representing sequences of the putative rabbit growth hormone receptor and several HLA-DQ beta-chain molecules. Polystyrene plastic beads were coated with peptides. Immune serum was incubated...

  8. An angular momentum conserving Affine-Particle-In-Cell method

    CERN Document Server

    Jiang, Chenfanfu; Teran, Joseph

    2016-01-01

    We present a new technique for transferring momentum and velocity between particles and grid with Particle-In-Cell (PIC) calculations which we call Affine-Particle-In-Cell (APIC). APIC represents particle velocities as locally affine, rather than locally constant as in traditional PIC. We show that this representation allows APIC to conserve linear and angular momentum across transfers while also dramatically reducing numerical diffusion usually associated with PIC. Notably, conservation is achieved with lumped mass, as opposed to the more commonly used Fluid Implicit Particle (FLIP) transfers which require a 'full' mass matrix for exact conservation. Furthermore, unlike FLIP, APIC retains a filtering property of the original PIC and thus does not accumulate velocity modes on particles as FLIP does. In particular, we demonstrate that APIC does not experience velocity instabilities that are characteristic of FLIP in a number of Material Point Method (MPM) hyperelasticity calculations. Lastly, we demonstrate th...

  9. Affinity purification and partial characterization of a yeast multiprotein complex for nucleotide excision repair using histidine-tagged Rad14 protein

    International Nuclear Information System (INIS)

    The nucleotide excision repair (NER) pathway of eukaryotes involves approximately 30 polypeptides. Reconstitution of this pathway with purified components is consistent with the sequential assembly of NER proteins at the DNA lesion. However, recent studies have suggested that NER proteins may be pre-assembled in a high molecular weight complex in the absence of DNA damage. To examine this model further, we have constructed a histidine-tagged version of the yeast DNA damage recognition protein Rad14. Affinity purification of this protein from yeast nuclear extracts resulted in the co-purification of Rad1, Rad7, Rad10, Rad16, Rad23, RPA, RPB1, and TFIIH proteins, whereas none of these proteins bound to the affinity resin in the absence of recombinant Rad14. Furthermore, many of the co-purifying proteins were present in approximately equimolar amounts. Co-elution of these proteins was also observed when the nuclear extract was fractionated by gel filtration, indicating that the NER proteins were associated in a complex with a molecular mass of >1000 kDa prior to affinity chromatography. The affinity purified NER complex catalyzed the incision of UV-irradiated DNA in an ATP-dependent reaction. We conclude that active high molecular weight complexes of NER proteins exist in undamaged yeast cells

  10. Design, synthesis, and application of a hydrazide-functionalized isotope-coded affinity tag for the quantification of oxylipid-protein conjugates.

    Science.gov (United States)

    Han, Bingnan; Stevens, Jan F; Maier, Claudia S

    2007-05-01

    An isotopically coded affinity probe was developed and evaluated for the characterization and quantification of proteins adducted by 2-alkenals derived from lipid peroxidation (LPO) processes. Lipid-derived 2-alkenals, such as acrolein and 4-hydroxy-2-nonenal (HNE), have the ability to react with cysteine, histidine, and lysine residues in proteins, thus causing protein damage and loss of protein function. Such modifications of proteins are difficult to characterize in biological samples by mass spectrometry due to the complexity of protein extracts and the low abundance of adducted proteins. The novel aldehyde-reactive, hydrazide-functionalized, isotope-coded affinity tag (HICAT) described in this study was found effective for the selective isolation, detection, and quantification of Michael-type adducts of 2-alkenals with proteins using a combination of affinity isolation, nanoLC, and matrix-assisted laser desorption ionization tandem mass spectrometry (MALDI-MS/MS). The chemical and mass spectrometric properties of the new probe are demonstrated on a model protein treated with HNE. The efficacy of HICAT for the analysis of complex samples was tested using preparations of mitochondrial proteins that were modified in vitro with HNE. The potential of the HICAT strategy for the identification, characterization, and quantification of in vivo oxylipid-protein conjugates is demonstrated on cardiac mitochondrial protein preparations, in which, for example, the ADP/ATP translocase 1 was found adducted to the 2-alkenals, acrolein and 4-hydroxy-2-hexenal, at Cys-256.

  11. System Virtualization and Efficient ID Transmission Method for RFID Tag Infrastructure Network

    Directory of Open Access Journals (Sweden)

    Shin-ichi Kuribayashi

    2010-11-01

    Full Text Available The use of RFID tag which identifies a thing and an object will be expanded with progress of ubiquitoussociety, and it is necessary to study how to construct RFID network system as a social infrastructure likethe Internet. First, this paper proposes the virtualization method of RFID tag network system to enablethe same physical RFID network system to be used by multiple different service systems. The systemvirtualization not only reduces the system cost but also can dramatically reduce the installation space ofphysical readers and the operation cost. It is proposed that all equipments in the RFID network systemexcept RFID tag could be shared with the conventional virtual technologies. Then, this paper proposesthe conditional tag ID processing and the efficient tag ID transmission method which can greatly reducethe processing time and processing load in RFID tag Infrastructure network The conditional tag IDprocessing allows that tag ID is valid only at a certain time zone of day or in a certain area. The efficienttag ID transmission method uses the virtual network address of the service center as a part of the ID of anRF tag, which allows the direct ID forwarding to the service center.

  12. Detection of protein-protein interactions using tandem affinity purification.

    Science.gov (United States)

    Goodfellow, Ian; Bailey, Dalan

    2014-01-01

    Tandem affinity purification (TAP) is an invaluable technique for identifying interaction partners for an affinity tagged bait protein. The approach relies on the fusion of dual tags to the bait before separate rounds of affinity purification and precipitation. Frequently two specific elution steps are also performed to increase the specificity of the overall technique. In the method detailed here, the two tags used are protein G and a short streptavidin binding peptide; however, many variations can be employed. In our example the tags are separated by a cleavable tobacco etch virus protease target sequence, allowing for specific elution after the first round of affinity purification. Proteins isolated after the final elution step in this process are concentrated before being identified by mass spectrometry. The use of dual affinity tags and specific elution in this technique dramatically increases both the specificity and stringency of the pull-downs, ensuring a low level of background nonspecific interactions.

  13. 一种改进图像标注的新方法%A Novel Method for Improving Tagging

    Institute of Scientific and Technical Information of China (English)

    朱松豪; 邹黎明

    2013-01-01

    Social media webs,such as Flicker and Zoomer,allow users to describe image content with semantic tags.However,tagging all the images in the same category is a task that takes time and patience.Tagging all the images in the same category with unified tags will greatly degrade the accuracy of the tagging.In this paper,a novel scheme is proposed to automatically tagging images in the same category.An affinity propagation algorithm is utilized to achieve a group of representative images,where the number of representative images depends on the semantic content.Then,the information of both visual appearance and semantic appearance is adopted to estimate the relevance of each tag of each representative image.A random walk algorithm is adopted to refine the achieved relevance.Finally,tags of the rest images in the same category are accessed by using a graph-based semi-supervise method.The experimental results on the Flickr image sets demonstrate the effectiveness and efficiency of the proposed scheme.%社会媒体共享网站允许用户上传图片的同时,也鼓励用户对上传图片内容加以标注.不过要对网站中所有图片进行内容标注,将是一项非常费时的任务;而如对同一类型图片统一进行标注则会大大降低内容标注的准确性.因此,文中提出了一个内容标注的新方法.首先,采用仿射传播聚类算法,从同一类型图片中获取一组具有代表性的图像;然后,利用图像内容的视觉信息和语义信息,对能够表示代表性图像内容标签的相关值进行估计,并依据随机游走算法改进标签的相关值;最后,通过半监督学习方法自动为同一类型的其它图片分配标签.基于Flickr图片集的实验结果表明所提方案的有效性.

  14. Improved affinity of engineered streptavidin for the Strep-tag II peptide is due to a fixed open conformation of the lid-like loop at the binding site

    OpenAIRE

    Korndörfer, Ingo P.; Skerra, Arne

    2002-01-01

    The Strep-tag II is a nine-amino acid peptide that was developed as an affinity tool for the purification of corresponding fusion proteins on streptavidin columns. The peptide recognizes the same pocket of streptavidin where the natural ligand is normally bound so that biotin or its chemical derivatives can be used for competitive elution. We report here the crystal structures of the streptavidin mutants `1' and `2,' which had been engineered for 10-fold higher affinity towards the Strep-tag ...

  15. System Virtualization and Efficient ID Transmission Method for RFID Tag Infrastructure Network

    CERN Document Server

    Kuribayashi, Shin-ichi

    2010-01-01

    The use of RFID tag which identifies a thing and an object will be expanded with progress of ubiquitous society, and it is necessary to study how to construct RFID network system as a social infrastructure like the Internet. First, this paper proposes the virtualization method of RFID tag network system to enable the same physical RFID network system to be used by multiple different service systems. The system virtualization not only reduces the system cost but also can dramatically reduce the installation space of physical readers and the operation cost. It is proposed that all equipments in the RFID network system except RFID tag could be shared with the conventional virtual technologies. Then, this paper proposes the conditional tag ID processing and the efficient tag ID transmission method which can greatly reduce the processing time and processing load in RFID tag Infrastructure network The conditional tag ID processing allows that tag ID is valid only at a certain time zone of day or in a certain area. ...

  16. Identification of protein partners in mycobacteria using a single-step affinity purification method.

    Directory of Open Access Journals (Sweden)

    Przemysław Płociński

    Full Text Available Tuberculosis is a leading cause of death in developing countries. Efforts are being made to both prevent its spread and improve curability rates. Understanding the biology of the bacteria causing the disease, Mycobacterium tuberculosis (M. tuberculosis, is thus vital. We have implemented improved screening methods for protein-protein interactions based on affinity purification followed by high-resolution mass spectrometry. This method can be efficiently applied to both medium- and high-throughput studies aiming to characterize protein-protein interaction networks of tubercle bacilli. Of the 4 tested epitopes FLAG, enhanced green fluorescent protein (eGFP, protein A and haemagglutinin, the eGFP tag was found to be most useful on account of its easily monitored expression and its ability to function as a simultaneous tool for subcellular localization studies. It presents a relatively low background with cost-effective purification. RNA polymerase subunit A (RpoA was used as a model for investigation of a large protein complex. When used as bait, it co-purified with all remaining RNA polymerase core subunits as well as many accessory proteins. The amount of RpoA strongly correlated with the amount of quantification peptide used as part of the tagging system in this study (SH, making it applicable for semi-quantification studies. Interactions between the components of the RpoA-eGFP protein complex were further confirmed using protein cross-linking. Dynamic changes in the composition of protein complexes under induction of UV damage were observed when UvrA-eGFP expressing cells treated with UV light were used to co-purify UvrA interaction partners.

  17. A Practical Method for UHF RFID Interrogation Area Measurement Using Battery Assisted Passive Tag

    Science.gov (United States)

    Mitsugi, Jin; Tokumasu, Osamu

    For the success of a large deployment of UHF RFID, easyto-use and low-cost engineering tools to facilitate the performance evaluation are demanded particularly in installations and for trouble shooting. The measurement of interrogation area is one of the most typical industrial demands to establish the stable readability of UHF RFID. Exhaustive repetition of tag position change with a read operation and a usage of expensive measurement equipment or special interrogators are common practices to measure the interrogation area. In this paper, a practical method to measure the interrogation area of a UHF RFID by using a battery assisted passive tag (BAP) is presented. After introducing the fundamental design and performances of the BAP that we have developed, we introduce the measurement method. In the method, the target tag in the target installation is continuously traversed either manually or automatically while it is subjected to a repetitive read of a commercial interrogator. During the target tag traversal, the interrogator's commands are continuously monitored by a BAP. With an extensive analysis on interrogator commands, the BAP can differentiate between its own read timings and those of the target tag. The read timings of the target tag collected by the BAP are recorded synchronously with the target tag position, yielding a map of the interrogation area. The present method does not entail a measurement burden. It is also independent of the choice of interrogator and tag. The method is demonstrated in a practical UHF RFID installation to show that the method can measure a 40mm resolution interrogation area measurement just by traversing the target tag at a slow walking speed, 300mm/sec.

  18. Development of a Method for Tissue Elasticity Imaging Using Tagged Magnetic Resonance Imaging

    CERN Document Server

    Takeuchi, Tomoki; Murase, Kenya

    2016-01-01

    The purpose of this study was to develop a method for tissue elasticity imaging using tagged magnetic resonance imaging (MRI). First, we developed a cyclic pressure device that used air to remotely transmit the power to generate cyclic deformation in an object. The pressure induced by the cyclic pressure device was measured by MRI-compatible force sensors. Second, we developed a software to calculate Young's modulus from tagged MRI data using the harmonic phase (HARP) method and the finite element method (FEM). We also developed a software to extract tag-cross points from tagged MRI data. Finally, we evaluated the usefulness of our method using three homogeneous silicone gel phantoms with different degrees of stiffness in comparison with Young's moduli measured by a material testing machine. The coefficient of variation of the pressure data measured by MRI-compatible force sensors was within 5 %, indicating that the reproducibility of the pressure generated by our cyclic pressure device was good. The Young's ...

  19. Tag Selection of Tandem Affinity Purification and Its Application in Plant Protein-Protein Interactions%TAP亲和标签选择及其在植物蛋白互作研究中的应用

    Institute of Scientific and Technical Information of China (English)

    张志飞; 赵志丽; 文昭竹

    2014-01-01

    Tandem affinity purification(TAP)is a technology for the purification of protein complex under the normal physiological conditions, which has been extensively utilized to identify protein-protein interactions(PPIs)and reveal interaction network of protein complexes. In recent years, TAP technology has been improving in the PPIs study, with the development of new labels, TAP method improvements and jointed use with other technologies associated. TAP technology is also being increasingly used in the studies of plant PPIs. This paper reviews the selection of TAP affinity tag and advance of research that TAP has been successful used in the study of plant PPIs.%串联亲和纯化法(TAP)是一种纯化生理条件下蛋白复合物的技术,已广泛应用于鉴定蛋白相互作用和揭示蛋白复合物互作网络。近年来,随着TAP新型标签的不断出现以及与其他技术的联用,TAP技术正逐渐应用于植物蛋白质互作研究中。综述了TAP亲和标签选择,并介绍其在植物蛋白互作研究中的成功应用。

  20. Method of remote powering and detecting multiple UWB passive tags in an RFID system

    Science.gov (United States)

    Dowla, Farid U.; Nekoogar, Faranak; Benzel, David M.; Dallum, Gregory E.; Spiridon, Alex

    2012-05-29

    A new Radio Frequency Identification (RFID), tracking, powering apparatus/system and method using coded Ultra-wideband (UWB) signaling is introduced. The proposed hardware and techniques disclosed herein utilize a plurality of passive UWB transponders in a field of an RFID-radar system. The radar system itself enables multiple passive tags to be remotely powered (activated) at about the same time frame via predetermined frequency UWB pulsed formats. Once such tags are in an activated state, an UWB radar transmits specific "interrogating codes" to put predetermined tags in an awakened status. Such predetermined tags can then communicate by a unique "response code" so as to be detected by an UWB system using radar methods.

  1. Modified PCR methods for 3' end amplification from serial analysis of gene expression (SAGE) tags.

    Science.gov (United States)

    Xu, Wang-Jie; Wang, Zhao-Xia; Qiao, Zhong-Dong

    2009-05-01

    Serial analysis of gene expression (SAGE) is a powerful technique to study gene expression at the genome level. However, a disadvantage of the shortness of SAGE tags is that it prevents further study of SAGE library data, thus limiting extensive application of the SAGE method in gene expression studies. However, this problem can be solved by extension of the SAGE tags to 3' cDNAs. Therefore, several methods based on PCR have been developed to generate a 3' longer fragment cDNA corresponding to a SAGE tag. The list of modified methods is extensive, and includes rapid RT-PCR analysis of unknown SAGE tags (RAST-PCR), generation of longer cDNA fragments from SAGE tags for gene identification (GLGI), a high-throughput GLGI procedure, reverse SAGE (rSAGE), two-step analysis of unknown SAGE tags (TSAT-PCR), etc. These procedures are constantly being updated because they have characteristics and advantages that can be shared. Development of these methods has promoted the widespread use of the SAGE technique, and has accelerated the speed of studies of large-scale gene expression.

  2. Prediction of peptide bonding affinity: kernel methods for nonlinear modeling

    CERN Document Server

    Bergeron, Charles; Sundling, C Matthew; Krein, Michael; Katt, Bill; Sukumar, Nagamani; Breneman, Curt M; Bennett, Kristin P

    2011-01-01

    This paper presents regression models obtained from a process of blind prediction of peptide binding affinity from provided descriptors for several distinct datasets as part of the 2006 Comparative Evaluation of Prediction Algorithms (COEPRA) contest. This paper finds that kernel partial least squares, a nonlinear partial least squares (PLS) algorithm, outperforms PLS, and that the incorporation of transferable atom equivalent features improves predictive capability.

  3. Cyanine-based probe\\tag-peptide pair fluorescence protein imaging and fluorescence protein imaging methods

    Science.gov (United States)

    Mayer-Cumblidge, M. Uljana; Cao, Haishi

    2013-01-15

    A molecular probe comprises two arsenic atoms and at least one cyanine based moiety. A method of producing a molecular probe includes providing a molecule having a first formula, treating the molecule with HgOAc, and subsequently transmetallizing with AsCl.sub.3. The As is liganded to ethanedithiol to produce a probe having a second formula. A method of labeling a peptide includes providing a peptide comprising a tag sequence and contacting the peptide with a biarsenical molecular probe. A complex is formed comprising the tag sequence and the molecular probe. A method of studying a peptide includes providing a mixture containing a peptide comprising a peptide tag sequence, adding a biarsenical probe to the mixture, and monitoring the fluorescence of the mixture.

  4. Measurement of B- -> tau- nu_tau-bar Decay With a Semileptonic Tagging Method

    CERN Document Server

    Adachi, I; Anipko, D; Arinstein, K; Aso, T; Aulchenko, V; Aushev, T; Aziz, T; Bahinipati, S; Bakich, A M; Balagura, V; Ban, Y; Barberio, E; Bay, A; Bedny, I; Belous, K S; Bhardwaj, V; Bitenc, U; Blyth, S; Bondar, A; Bozek, A; Bracko, M; Brodzicka, J; Browder, T E; Chang, M C; Chang, P; Chang, Y W; Chao, Y; Chen, A; Chen, K F; Cheon, B G; Chiang, C C; Chistov, R; Cho, I S; Choi, S K; Choi, Y; Choi, Y K; Cole, S; Dalseno, J; Danilov, M; Das, A; Dash, M; Drutskoy, A; Dungel, W; Eidelman, S; Epifanov, D; Esen, S; Fratina, S; Fujii, H; Fujikawa, M; Gabyshev, N; Garmash, A; Goldenzweig, P; Golob, B; Grosse-Perdekamp, M; Guler, H; Guo, H; Ha, H; Haba, J; Hara, K; Hara, T; Hasegawa, Y; Hastings, N C; Hayasaka, K; Hayashii, H; Hazumi, M; Heffernan, D; Higuchi, T; Hodlmoser, H; Hokuue, T; Horii, Y; Hoshi, Y; Hoshina, K; Hou, W S; Hsiung, Y B; Hyun, H J; Igarashi, Y; Iijima, T; Ikado, K; Inami, K; Ishikawa, A; Ishino, H; Itoh, R; Iwabuchi, M; Iwasaki, M; Iwasaki, Y; Jacoby, C; Joshi, N J; Kaga, M; Kah, D H; Kaji, H; Kakuno, H; Kang, J H; Kapusta, P; Kataoka, S U; Katayama, N; Kawai, H; Kawasaki, T; Kibayashi, A; Kichimi, H; Kim, H J; Kim, H O; Kim, J H; Kim, S K; Kim, Y I; Kim, Y J; Kinoshita, K; Korpar, S; Kozakai, Y; Krizan, P; Krokovny, P; Kumar, R; Kurihara, E; Kuroki, Y; Kuzmin, A; Kwon, Y J; Kyeong, S H; Lange, J S; Leder, G; Lee, J; Lee, J S; Lee, M J; Lee, S E; Lesiak, T; Li, J; Limosani, A; Lin, S W; Liu, C; Liu, Y; Liventsev, D; MacNaughton, J; Mandl, F; Marlow, D; Matsumura, T; Matyja, A; McOnie, S; Medvedeva, T; Mikami, Y; Miyabayashi, K; Miyata, H; Miyazaki, Y; Mizuk, R; Moloney, G R; Mori, T; Nagamine, T; Nagasaka, Y; Nakahama, Y; Nakamura, I; Nakano, E; Nakao, M; Nakayama, H; Nakazawa, H; Natkaniec, Z; Neichi, K; Nishida, S; Nishimura, K; Nishio, Y; Nishizawa, I; Nitoh, O; Noguchi, S; Nozaki, T; Ogawa, A; Ogawa, S; Ohshima, T; Okuno, S; Olsen, S L; Ono, S; Ostrowicz, W; Ozaki, H; Pakhlov, P; Pakhlova, G; Palka, H; Park, C W; Park, H; Park, H K; Park, K S; Parslow, N; Peak, L S; Pernicka, M; Pestotnik, R; Peters, M; Piilonen, L E; Poluektov, A; Rorie, J; Rózanska, M; Sahoo, H; Sakai, Y; Sasao, N; Sayeed, K; Schietinger, T; Schneider, O; Schonmeier, P; Schümann, J; Schwanda, C; Schwartz, A J; Seidl, R; Sekiya, A; Senyo, K; Sevior, M E; Shang, L; Shapkin, M; Shebalin, V; Shen, C P; Shibuya, H; Shinomiya, S; Shiu, J G; Shwartz, B; Sidorov, V; Singh, J B; Sokolov, A; Somov, A; Stanic, S; Staric, M; Stypula, J; Sugiyama, A; Sumisawa, K; Sumiyoshi, T; Suzuki, S; Suzuki, S Y; Tajima, O; Takasaki, F; Tamai, K; Tamura, N; Tanaka, M; Taniguchi, N; Taylor, G N; Teramoto, Y; Tikhomirov, I; Trabelsi, K; Tse, Y F; Tsuboyama, T; Uchida, Y; Uehara, S; Ueki, Y; Ueno, K; Uglov, T; Unno, Y; Uno, S; Urquijo, P; Ushiroda, Y; Usov, Yu; Varner, G; Varvell, K E; Vervink, K; Villa, S; Vinokurova, A; Wang, C C; Wang, C H; Wang, J; Wang, M Z; Wang, P; Wang, X L; Watanabe, M; Watanabe, Y; Wedd, R; Wei, J T; Wicht, J; Widhalm, L; Wiechczynski, J; Won, E; Yabsley, B D; Yamaguchi, A; Yamamoto, H; Yamaoka, M; Yamashita, Y; Yamauchi, M; Yuan, C Z; Yusa, Y; Zhang, C C; Zhang, L M; Zhang, Z P; Zhilich, V; Zhulanov, V; Zivko, T; Zupanc, A; Zwahlen, N; Zyukova, O

    2008-01-01

    We present a new measurement of the decay B- -> tau- nu_tau-bar with a semileptonic B tagging method, using a data sample containing 657*10^6 BB-bar pairs collected at the (4S) resonance with the Belle detector at the KEKB asymmetric e+e- collider. A sample of BB pairs are tagged by reconstructing one B meson decaying semileptonically. We detect the B- -> tau- nu_tau-bar candidate in the recoil. We obtain a signal with a signicance of 3.8 standard deviations including systematics, and measure the branching fraction to be B(B- -> tau- nu_tau-bar)=(1.65+0.38-0.37(stat)+0.35-0.37(syst))*10^4. This result confirms the evidence for B- -> tau- nu_tau-bartained in the previous Belle measurement with a hadronic B tagging method.

  5. Improved affinity of engineered streptavidin for the Strep-tag II peptide is due to a fixed open conformation of the lid-like loop at the binding site

    Science.gov (United States)

    Korndörfer, Ingo P.; Skerra, Arne

    2002-01-01

    The Strep-tag II is a nine-amino acid peptide that was developed as an affinity tool for the purification of corresponding fusion proteins on streptavidin columns. The peptide recognizes the same pocket of streptavidin where the natural ligand is normally bound so that biotin or its chemical derivatives can be used for competitive elution. We report here the crystal structures of the streptavidin mutants `1' and `2,' which had been engineered for 10-fold higher affinity towards the Strep-tag II. Both streptavidin mutants carry mutations at positions 44, 45, and 47, that is, in a flexible loop region close to the binding site. The crystal structures of the two apo-proteins and their complexes with the Strep-tag II peptide were refined at resolutions below 2 Å. Both in the presence and absence of the peptide, the lid-like loop next to the ligand pocket—comprising residues 45 through 52—adopts an `open' conformation in all four subunits within the asymmetric unit. The same loop was previously described to be disordered in the wild-type apo-streptavidin and to close over the pocket upon complexation of the natural ligand biotin. Our findings suggest that stabilization of the `open' loop conformation in the absence of a ligand abolishes the need for conformational rearrangement prior to the docking of the voluminous peptide. Because no direct contacts between the flexible part of the loop and the peptide ligand were detected, it seems likely that the higher affinity of the two streptavidin mutants for the Strep-tag II is caused by a predominantly entropic mechanism. PMID:11910031

  6. Biochemical method for fast affinity diagnosis in grape-vine transplantation

    International Nuclear Information System (INIS)

    Long term experiments have proved the affinity of cv. Mavroud in transplantations on various root stocks. Best affinity was observed in the combination cv. Mavroud X Riparia tomanteau, followed, in a descending order, by the combinations Mavroud X Mavroud (autotransplantation), Mavroud X Berlandieri X Riparia Kobber SBB and Mavroud X Riparia 33 EM. In view to establish indices for predicting the transplantation affinity a great number of physiological-biochemical and morphological-anatomical studies were carried out. The results obtained showed that a most clearly expressed positive, statistically significant correlation exists between the amount of 15N transported from the root stock to the scions, shoots and leaves. As a result, a biochemical method for fast affinity diagnosis in grape-vine transplantation has been developed. The reliability of the method has been checked up also with other cultivars. Up to the present no such method was known in grape-vine science and practice. (author)

  7. A new method to identify flanking sequence tags in chlamydomonas using 3’-RACE

    OpenAIRE

    Meslet-Cladière Laurence; Vallon Olivier

    2012-01-01

    Abstract Background The green alga Chlamydomonas reinhardtii, although a premier model organism in biology, still lacks extensive insertion mutant libraries with well-identified Flanking Sequence Tags (FSTs). Rapid and efficient methods are needed for FST retrieval. Results Here, we present a novel method to identify FSTs in insertional mutants of Chlamydomonas. Transformants can be obtained with a resistance cassette lacking a 3’ untranslated region (UTR), suggesting that the RNA that is pro...

  8. Particle Display: A Quantitative Screening Method for Generating High-Affinity Aptamers**

    OpenAIRE

    Wang, J.; Gong, Q; N Maheshwari; Eisenstein, M; Arcila, ML; Kosik, KS; Soh, HT

    2014-01-01

    We report an aptamer discovery technology that reproducibly yields higher affinity aptamers in fewer rounds compared to conventional selection. Our method (termed particle display) transforms libraries of solution-phase aptamers into "aptamer particles", each displaying many copies of a single sequence on its surface. We then use fluorescence-activated cell sorting (FACS) to individually measure the relative affinities of >108 aptamer particles and sort them in a high-throughput manner. Throu...

  9. A comparison of implantation methods for large PIT tags or injectable acoustic transmitters in juvenile Chinook salmon

    Energy Technology Data Exchange (ETDEWEB)

    Cook, Katrina V.; Brown, Richard S.; Deng, Zhiqun; Klett, Ryan S.; Li, Huidong; Seaburg, Adam; Eppard, M. B.

    2014-04-15

    The miniaturization of acoustic transmitters may allow greater flexibility in terms of the size and species of fish available to tag. New downsized injectable acoustic tags similar in shape to passive integrated transponder tags can be rapidly injected rather than surgically implanted through a sutured incision, as is current practice. Before wide-scale field use of these injectable transmitters, standard protocols to ensure the most effective and least damaging methods of implantation must be developed. Three implantation methods were tested in various sizes of juvenile Chinook salmon Oncorhynchus tschawytscha. Methods included a needle bevel-down injection, a needle bevel-up injection with a 90-degree rotation, and tag implantation through an unsutured incision. Tagged fish were compared to untagged control groups. Weight and wound area were measured at tagging and every week for 3 weeks; holding tanks were checked daily for mortalities and tag losses. No differences among treatments were found in growth, tag loss, or survival, but wound area was significantly reduced among incision-treated fish. The bevel-up injection had the worst results in terms of tag loss and wound area and also had high mortality. Implantation through an incision resulted in the lowest tag loss but the highest mortality. Fish from the bevel-down treatment group had the least mortality; wound areas also were smaller than the bevel-up treatment group. Cumulatively, the data suggest that the unsutured incision and bevel-down injection methods were the most effective; the drawbacks of both methods are described in detail. However, we further recommend larger and longer studies to find more robust thresholds for tagging size that include more sensitive measures.

  10. Protein-protein binding affinities calculated using the LIE method

    OpenAIRE

    Andberg, Tor Arne Heim

    2011-01-01

    Absolute binding free energies for the third domain of the turkey ovomucoid inhibitor in complex with Streptomyces griseus proteinase B and porcine pancreatic elastase has been calculated using the linear interaction energy method.

  11. Tag Correspondence Model for User Tag Suggestion

    Institute of Scientific and Technical Information of China (English)

    涂存超; 刘知远; 孙茂松

    2015-01-01

    Some microblog services encourage users to annotate themselves with multiple tags, indicating their attributes and interests. User tags play an important role for personalized recommendation and information retrieval. In order to better understand the semantics of user tags, we propose Tag Correspondence Model (TCM) to identify complex correspondences of tags from the rich context of microblog users. The correspondence of a tag is referred to as a unique element in the context which is semantically correlated with this tag. In TCM, we divide the context of a microblog user into various sources (such as short messages, user profile, and neighbors). With a collection of users with annotated tags, TCM can automatically learn the correspondences of user tags from multiple sources. With the learned correspondences, we are able to interpret implicit semantics of tags. Moreover, for the users who have not annotated any tags, TCM can suggest tags according to users’ context information. Extensive experiments on a real-world dataset demonstrate that our method can effciently identify correspondences of tags, which may eventually represent semantic meanings of tags.

  12. Top tagging: a method for identifying boosted hadronically decaying top quarks.

    Science.gov (United States)

    Kaplan, David E; Rehermann, Keith; Schwartz, Matthew D; Tweedie, Brock

    2008-10-01

    A method is introduced for distinguishing top jets (boosted, hadronically decaying top quarks) from light-quark and gluon jets using jet substructure. The procedure involves parsing the jet cluster to resolve its subjets and then imposing kinematic constraints. With this method, light-quark or gluon jets with p{T} approximately 1 TeV can be rejected with an efficiency of around 99% while retaining up to 40% of top jets. This reduces the dijet background to heavy tt[over ] resonances by a factor of approximately 10 000, thereby allowing resonance searches in tt[over ] to be extended into the all-hadronic channel. In addition, top tagging can be used in tt[over ] events when one of the top quarks decays semileptonically, in events with missing energy, and in studies of b-tagging efficiency at high p{T}.

  13. Computational methods for the analysis of tag sequences in metagenomics studies.

    Science.gov (United States)

    Chang, Qin; Luan, Yihui; Chen, Ting; Fuhrman, Jed A; Sun, Fengzhu

    2012-06-01

    Metagenomics commonly refers to the study of genetic materials directly derived from environments without culturing. Several ongoing large-scale metagenomics projects related to human and marine life, as well as pedology studies, have generated enormous amounts of data, posing a key challenge for efficient analysis, as we try to 1) understand microbial organism assemblage under different conditions, 2) compare different communities, and 3) understand how microbial organisms associate with each other and the environment.To address such questions, investigators are using new sequencing technologies, including Sanger, Illumina Solexa, and Roche 454, to sequence either particular genes, called tag sequences, mostly 16S or 18S ribosomal RNA sequences or other conserved genes, or whole metagenome shotgun sequences of all the genetic materials in a given community. In this paper, we review computational methods used for the analysis of tag sequences.

  14. A Statistical Method for Assessing Peptide Identification Confidence in Accurate Mass and Time Tag Proteomics

    Energy Technology Data Exchange (ETDEWEB)

    Stanley, Jeffrey R.; Adkins, Joshua N.; Slysz, Gordon W.; Monroe, Matthew E.; Purvine, Samuel O.; Karpievitch, Yuliya V.; Anderson, Gordon A.; Smith, Richard D.; Dabney, Alan R.

    2011-07-15

    High-throughput proteomics is rapidly evolving to require high mass measurement accuracy for a variety of different applications. Increased mass measurement accuracy in bottom-up proteomics specifically allows for an improved ability to distinguish and characterize detected MS features, which may in turn be identified by, e.g., matching to entries in a database for both precursor and fragmentation mass identification methods. Many tools exist with which to score the identification of peptides from LC-MS/MS measurements or to assess matches to an accurate mass and time (AMT) tag database, but these two calculations remain distinctly unrelated. Here we present a statistical method, Statistical Tools for AMT tag Confidence (STAC), which extends our previous work incorporating prior probabilities of correct sequence identification from LC-MS/MS, as well as the quality with which LC-MS features match AMT tags, to evaluate peptide identification confidence. Compared to existing tools, we are able to obtain significantly more high-confidence peptide identifications at a given false discovery rate and additionally assign confidence estimates to individual peptide identifications. Freely available software implementations of STAC are available in both command line and as a Windows graphical application.

  15. An efficient weighted tag SNP-set analytical method in genome-wide association studies

    OpenAIRE

    Yan, Bin; Wang, Shudong; Jia, Huaqian; Liu, Xing; Wang, Xinzeng

    2015-01-01

    Background Single-nucleotide polymorphism (SNP)-set analysis in Genome-wide association studies (GWAS) has emerged as a research hotspot for identifying genetic variants associated with disease susceptibility. But most existing methods of SNP-set analysis are affected by the quality of SNP-set, and poor quality of SNP-set can lead to low power in GWAS. Results In this research, we propose an efficient weighted tag-SNP-set analytical method to detect the disease associations. In our method, we...

  16. Proteomic analysis of nipple aspirate fluid from women with early-stage breast cancer using isotope-coded affinity tags and tandem mass spectrometry reveals differential expression of vitamin D binding protein

    Directory of Open Access Journals (Sweden)

    Hunt Kelly K

    2006-03-01

    Full Text Available Abstract Background Isotope-coded affinity tag (ICAT tandem mass spectrometry (MS allows for qualitative and quantitative analysis of paired protein samples. We sought to determine whether ICAT technology could quantify and identify differential expression of tumor-specific proteins in nipple aspirate fluid (NAF from the tumor-bearing and contralateral disease-free breasts of patients with unilateral early-stage breast cancer. Methods Paired NAF samples from 18 women with stage I or II unilateral invasive breast carcinoma and 4 healthy volunteers were analyzed using ICAT labeling, sodium dodecyl sulfate-polyacrylamide gel (SDS-PAGE, liquid chromatography, and MS. Proteins were identified by sequence database analysis. Western blot analysis of NAF from an independent sample set from 12 women (8 with early-stage breast cancer and 4 healthy volunteers was also performed. Results 353 peptides were identified from tandem mass spectra and matched to peptide sequences in the National Center for Biotechnology Information database. Equal numbers of peptides were up- versus down-regulated. Alpha2HS-glycoprotein [Heavy:Light (H:L ratio 0.63] was underexpressed in NAF from tumor-bearing breasts, while lipophilin B (H:L ratio 1.42, beta-globin (H:L ratio 1.98, hemopexin (H:L ratio 1.73, and vitamin D-binding protein precursor (H:L ratio 1.82 were overexpressed. Western blot analysis of pooled samples of NAF from healthy volunteers versus NAF from women with breast cancer confirmed the overexpression of vitamin D-binding protein in tumor-bearing breasts. Conclusion ICAT tandem MS was able to identify and quantify differences in specific protein expression between NAF samples from tumor-bearing and disease-free breasts. Proteomic screening techniques using ICAT and NAF may be used to find markers for diagnosis of breast cancer.

  17. Accurate Ionization Potentials and Electron Affinities of Acceptor Molecules IV: Electron-Propagator Methods.

    Science.gov (United States)

    Dolgounitcheva, O; Díaz-Tinoco, Manuel; Zakrzewski, V G; Richard, Ryan M; Marom, Noa; Sherrill, C David; Ortiz, J V

    2016-02-01

    Comparison of ab initio electron-propagator predictions of vertical ionization potentials and electron affinities of organic, acceptor molecules with benchmark calculations based on the basis set-extrapolated, coupled cluster single, double, and perturbative triple substitution method has enabled identification of self-energy approximations with mean, unsigned errors between 0.1 and 0.2 eV. Among the self-energy approximations that neglect off-diagonal elements in the canonical, Hartree-Fock orbital basis, the P3 method for electron affinities, and the P3+ method for ionization potentials provide the best combination of accuracy and computational efficiency. For approximations that consider the full self-energy matrix, the NR2 methods offer the best performance. The P3+ and NR2 methods successfully identify the correct symmetry label of the lowest cationic state in two cases, naphthalenedione and benzoquinone, where some other methods fail. PMID:26730459

  18. An incremental community detection method for social tagging systems using locality-sensitive hashing.

    Science.gov (United States)

    Wu, Zhenyu; Zou, Ming

    2014-10-01

    An increasing number of users interact, collaborate, and share information through social networks. Unprecedented growth in social networks is generating a significant amount of unstructured social data. From such data, distilling communities where users have common interests and tracking variations of users' interests over time are important research tracks in fields such as opinion mining, trend prediction, and personalized services. However, these tasks are extremely difficult considering the highly dynamic characteristics of the data. Existing community detection methods are time consuming, making it difficult to process data in real time. In this paper, dynamic unstructured data is modeled as a stream. Tag assignments stream clustering (TASC), an incremental scalable community detection method, is proposed based on locality-sensitive hashing. Both tags and latent interactions among users are incorporated in the method. In our experiments, the social dynamic behaviors of users are first analyzed. The proposed TASC method is then compared with state-of-the-art clustering methods such as StreamKmeans and incremental k-clique; results indicate that TASC can detect communities more efficiently and effectively. PMID:24930583

  19. Sense Tagging Semantic Tagging with a Lexicon

    CERN Document Server

    Wilks, Y A; Wilks, Yorick; Stevenson, Mark

    1997-01-01

    Sense tagging, the automatic assignment of the appropriate sense from some lexicon to each of the words in a text, is a specialised instance of the general problem of semantic tagging by category or type. We discuss which recent word sense disambiguation algorithms are appropriate for sense tagging. It is our belief that sense tagging can be carried out effectively by combining several simple, independent, methods and we include the design of such a tagger. A prototype of this system has been implemented, correctly tagging 86% of polysemous word tokens in a small test set, providing evidence that our hypothesis is correct.

  20. Tagging French comparing a statistical and a constraint-based method

    CERN Document Server

    Chanod, J P; Chanod, Jean-Pierre; Tapanainen, Pasi

    1995-01-01

    In this paper we compare two competing approaches to part-of-speech tagging, statistical and constraint-based disambiguation, using French as our test language. We imposed a time limit on our experiment: the amount of time spent on the design of our constraint system was about the same as the time we used to train and test the easy-to-implement statistical model. We describe the two systems and compare the results. The accuracy of the statistical method is reasonably good, comparable to taggers for English. But the constraint-based tagger seems to be superior even with the limited time we allowed ourselves for rule development.

  1. Superlinearly Convergent Affine Scaling Interior Trust-Region Method for Linear Constrained LC1 Minimization

    Institute of Scientific and Technical Information of China (English)

    De Tong ZHU

    2008-01-01

    We extend the classical affine scaling interior trust region algorithm for the linear con-strained smooth minimization problem to the nonsmooth case where the gradient of objective function is only locally Lipschitzian. We propose and analyze a new affine scaling trust-region method in associ-ation with nonmonotonic interior backtracking line search technique for solving the linear constrained LC1 optimization where the second-order derivative of the objective function is explicitly required to be locally Lipschitzian. The general trust region subproblem in the proposed algorithm is defined by minimizing an augmented affine scaling quadratic model which requires both first and second order information of the objective function subject only to an affine scaling ellipsoidal constraint in a null subspace of the augmented equality constraints. The global convergence and fast local convergence rate of the proposed algorithm are established under some reasonable conditions where twice smoothness of the objective function is not required. Applications of the algorithm to some nonsmooth optimization problems are discussed.

  2. Tagged Chromosomal Insertion Site System: A Method to Study Lamina-Associated Chromatin.

    Science.gov (United States)

    Harr, Jennifer C; Reddy, Karen L

    2016-01-01

    The three-dimensional (3D) organization of the genome is important for chromatin regulation. This organization is nonrandom and appears to be tightly correlated with or regulated by chromatin state and scaffolding proteins. To understand how specific DNA and chromatin elements contribute to the functional organization of the genome, we developed a new tool-the tagged chromosomal insertion site (TCIS) system-to identify and study minimal DNA sequences that drive nuclear compartmentalization and applied this system to specifically study the role of cis elements in targeting DNA to the nuclear lamina. The TCIS system allows Cre-recombinase-mediated site-directed integration of any DNA fragment into a locus tagged with lacO arrays, thus enabling both functional molecular studies and positional analysis of the altered locus. This system can be used to study the minimal DNA sequences that target the nuclear periphery (or other nuclear compartments), allowing researchers to understand how genome-wide results obtained, for example, by DNA adenine methyltransferase identification, chromosome conformation capture (HiC), or related methods, connect to the actual organization of DNA and chromosomes at the single-cell level. Finally, TCIS allows one to test roles for specific proteins in chromatin reorganization and to determine how changes in nuclear environment affect chromatin state and gene regulation at a single locus.

  3. A Lyapunov method for stability analysis of piecewise-affine systems over non-invariant domains

    Science.gov (United States)

    Rubagotti, Matteo; Zaccarian, Luca; Bemporad, Alberto

    2016-05-01

    This paper analyses stability of discrete-time piecewise-affine systems, defined on possibly non-invariant domains, taking into account the possible presence of multiple dynamics in each of the polytopic regions of the system. An algorithm based on linear programming is proposed, in order to prove exponential stability of the origin and to find a positively invariant estimate of its region of attraction. The results are based on the definition of a piecewise-affine Lyapunov function, which is in general discontinuous on the boundaries of the regions. The proposed method is proven to lead to feasible solutions in a broader range of cases as compared to a previously proposed approach. Two numerical examples are shown, among which a case where the proposed method is applied to a closed-loop system, to which model predictive control was applied without a-priori guarantee of stability.

  4. A Phosphorylation Tag for Uranyl Mediated Protein Purification and Photo Assisted Tag Removal

    DEFF Research Database (Denmark)

    Zhang, Qiang; Jørgensen, Thomas. J. D.; Nielsen, Peter E;

    2014-01-01

    Most protein purification procedures include an affinity tag fused to either the N or C-terminal end of the protein of interest as well as a procedure for tag removal. Tag removal is not straightforward and especially tag removal from the C-terminal end is a challenge due to the characteristics o...

  5. Billfish Tagging

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The SWFSC's constituent-based Billfish Tagging Program began in 1963 and since that time has provided conventional spaghetti type tags and tagging supplies to...

  6. A method for rapidly screening functionality of actin mutants and tagged actins

    Directory of Open Access Journals (Sweden)

    Rommelaere Heidi

    2004-01-01

    Full Text Available Recombinant production and biochemical analysis of actin mutants has been hampered by the fact that actin has an absolute requirement for the eukaryotic chaperone CCT to reach its native state. We therefore have developed a method to rapidly screen the folding capacity and functionality of actin variants, by combining in vitro expression of labelled actin with analysis on native gels, band shift assays or copolymerization tests. Additionally, we monitor, using immuno-fluorescence, incorporation of actin variants in cytoskeletal structures in transfected cells. We illustrate the method by two examples. In one we show that tagged versions of actin do not always behave native-like and in the other we study some of the molecular defects of three &bgr;-actin mutants that have been associated with diseases.

  7. A Personalized Tag-Based Recommendation in Social Web Systems

    DEFF Research Database (Denmark)

    Durao, Frederico; Dolog, Peter

    2009-01-01

    -based recommender system which suggests similar Web pages based on the similarity of their tags from a Web 2.0 tagging application. The proposed approach extends the basic similarity calculus with external factors such as tag popularity, tag representativeness and the affinity between user and tag. In order...

  8. Simplified, enhanced protein purification using an inducible, autoprocessing enzyme tag.

    Directory of Open Access Journals (Sweden)

    Aimee Shen

    Full Text Available We introduce a new method for purifying recombinant proteins expressed in bacteria using a highly specific, inducible, self-cleaving protease tag. This tag is comprised of the Vibrio cholerae MARTX toxin cysteine protease domain (CPD, an autoprocessing enzyme that cleaves exclusively after a leucine residue within the target protein-CPD junction. Importantly, V. cholerae CPD is specifically activated by inositol hexakisphosphate (InsP(6, a eukaryotic-specific small molecule that is absent from the bacterial cytosol. As a result, when His(6-tagged CPD is fused to the C-terminus of target proteins and expressed in Escherichia coli, the full-length fusion protein can be purified from bacterial lysates using metal ion affinity chromatography. Subsequent addition of InsP(6 to the immobilized fusion protein induces CPD-mediated cleavage at the target protein-CPD junction, releasing untagged target protein into the supernatant. This method condenses affinity chromatography and fusion tag cleavage into a single step, obviating the need for exogenous protease addition to remove the fusion tag(s and increasing the efficiency of tag separation. Furthermore, in addition to being timesaving, versatile, and inexpensive, our results indicate that the CPD purification system can enhance the expression, integrity, and solubility of intractable proteins from diverse organisms.

  9. Improved native affinity purification of RNA.

    Science.gov (United States)

    Batey, Robert T; Kieft, Jeffrey S

    2007-08-01

    RNA biochemical or structural studies often require an RNA sample that is chemically pure, and most protocols for its in vitro production use denaturing polyacrylamide gel electrophoresis to achieve this. Unfortunately, many RNAs do not quantitatively refold into an active conformation after denaturation, creating significant problems for downstream characterization or use. In addition, this traditional purification method is not amenable to studies demanding high-throughput RNA production. Recently, we presented the first general method for producing almost any RNA sequence that employs an affinity tag that is removed during the purification process. Because technical difficulties prevented application of this method to many RNAs, we have developed an improved version that utilizes a different activatable ribozyme and affinity tag that are considerably more robust, rapid, and broadly applicable. PMID:17548432

  10. Cyanine-based probe\\tag-peptide pair for fluorescence protein imaging and fluorescence protein imaging methods

    Science.gov (United States)

    Mayer-Cumblidge, M. Uljana; Cao, Haishi

    2010-08-17

    A molecular probe comprises two arsenic atoms and at least one cyanine based moiety. A method of producing a molecular probe includes providing a molecule having a first formula, treating the molecule with HgOAc, and subsequently transmetallizing with AsCl.sub.3. The As is liganded to ethanedithiol to produce a probe having a second formula. A method of labeling a peptide includes providing a peptide comprising a tag sequence and contacting the peptide with a biarsenical molecular probe. A complex is formed comprising the tag sequence and the molecular probe. A method of studying a peptide includes providing a mixture containing a peptide comprising a peptide tag sequence, adding a biarsenical probe to the mixture, and monitoring the fluorescence of the mixture.

  11. Elliptical modification of trilateration method based on linear model of distance vs power ratio for RFID tags spatial localization

    Directory of Open Access Journals (Sweden)

    Yu. B. Gimpilevich

    2013-12-01

    Full Text Available Introduction. Radio-frequency identification (RFID systems can be applied for a 2D spatial localization of objects in indoor spaces. For implementing the known localization method of trilateration one needs to build a model of ratio of distance between antenna and RFID tag versus power level of tag response signal. To maximize the accuracy of the model, one needs to collect measurement data from RFID tags placed at known positions. Due to the labor intensity of this process we aim to develop an alternative modification of elliptical trilateration method resulting in elimination of the preliminary data collecting stage. Theory part. We propose to use a linear model of distance vs power ratio for localization of passive RFID tags with small read ranges. Additionally, our model takes into account the possible ellipticity of position figures which happens because of antennas directivity. Also we propose some heuristics for solving the estimates ambiguity problem which arises when response signals from RFID tags are received by one or two antennas. Experimental part. We carried out the experimental analysis of the proposed trilateration variant using the previously developed RFID system in the 5 m ´ 5 m localization field. During the experiment, we compared our variant with a classical trilateration which was based on the polynomial model of distance vs power ratio formed by analyzing preliminarily gathered measurement data from RFID tags. The comparison indicated that our variant had a bigger by 1.6 cm mean localization error. Furthermore, taking into account ellipticity of position figures resulted in decrease of localization error for 18 of the 24 analyzed cases. Conclusions. It was determined that the proposed trilateration modification produced a slightly bigger mean localization error compared to the classical variant of trilateration. However, our approach allows one to eliminate the preliminary labor-intensive stage of collecting

  12. DEVELOPMENT OF DECISION MAKING ALGORITHM FOR CONTROL OF SEA CARGO CONTAINERS BY 'TAGGED' NEUTRON METHOD

    International Nuclear Information System (INIS)

    Nowadays in Russia and abroad there are several groups of scientists, engaged in development of systems based on 'tagged' neutron method (API method) and intended for detection of dangerous materials, including high explosives (HE). Particular attention is paid to possibility of detection of dangerous objects inside a sea cargo container. Energy gamma-spectrum, registered from object under inspection is used for determination of oxygen/carbon and nitrogen/carbon chemical ratios, according to which dangerous object is distinguished from not dangerous one. Material of filled container, however, gives rise to additional effects of rescattering and moderation of 14 MeV primary neutrons of generator, attenuation of secondary gamma-radiation from reactions of inelastic neutron scattering on objects under inspection. These effects lead to distortion of energy gamma-response from examined object and therefore prevent correct recognition of chemical ratios. These difficulties are taken into account in analytical method, presented in the paper. Method has been validated against experimental data, obtained by the system for HE detection in sea cargo, based on API method and developed in VNIIA. Influence of shielding materials on results of HE detection and identification is considered. Wood and iron were used as shielding materials. Results of method application for analysis of experimental data on HE simulator measurement (tetryl, trotyl, hexogen) are presented.

  13. A new method to identify flanking sequence tags in chlamydomonas using 3’-RACE

    Directory of Open Access Journals (Sweden)

    Meslet-Cladière Laurence

    2012-06-01

    Full Text Available Abstract Background The green alga Chlamydomonas reinhardtii, although a premier model organism in biology, still lacks extensive insertion mutant libraries with well-identified Flanking Sequence Tags (FSTs. Rapid and efficient methods are needed for FST retrieval. Results Here, we present a novel method to identify FSTs in insertional mutants of Chlamydomonas. Transformants can be obtained with a resistance cassette lacking a 3’ untranslated region (UTR, suggesting that the RNA that is produced from the resistance marker terminates in the flanking genome when it encounters a cleavage/polyadenylation signal. We have used a robust 3’-RACE method to specifically amplify such chimeric cDNAs. Out of 38 randomly chosen transformants, 27 (71% yielded valid FSTs, of which 23 could be unambiguously mapped to the genome. Eighteen of the mutants lie within a predicted gene. All but two of the intragenic insertions occur in the sense orientation with respect to transcription, suggesting a bias against situations of convergent transcription. Among the 14 insertion sites tested by genomic PCR, 12 could be confirmed. Among these are insertions in genes coding for PSBS3 (possibly involved in non-photochemical quenching, the NimA-related protein kinase CNK2, the mono-dehydroascorbate reductase MDAR1, the phosphoglycerate mutase PGM5 etc.. Conclusion We propose that our 3’-RACE FST method can be used to build large scale FST libraries in Chlamydomonas and other transformable organisms.

  14. Advances and applications of binding affinity prediction methods in drug discovery.

    Science.gov (United States)

    Parenti, Marco Daniele; Rastelli, Giulio

    2012-01-01

    Nowadays, the improvement of R&D productivity is the primary commitment in pharmaceutical research, both in big pharma and smaller biotech companies. To reduce costs, to speed up the discovery process and to increase the chance of success, advanced methods of rational drug design are very helpful, as demonstrated by several successful applications. Among these, computational methods able to predict the binding affinity of small molecules to specific biological targets are of special interest because they can accelerate the discovery of new hit compounds. Here we provide an overview of the most widely used methods in the field of binding affinity prediction, as well as of our own work in developing BEAR, an innovative methodology specifically devised to overtake some limitations in existing approaches. The BEAR method was successfully validated against different biological targets, and proved its efficacy in retrieving active compounds from virtual screening campaigns. The results obtained so far indicate that BEAR may become a leading tool in the drug discovery pipeline. We primarily discuss advantages and drawbacks of each technique and show relevant examples and applications in drug discovery.

  15. Studies of top tagging identification methods and development of a new heavy object tagger

    International Nuclear Information System (INIS)

    At the Large Hadron Collider (LHC), precision tests of the standard model of particle physics and searches for new phenomena are performed. To make optimal use of the proton-proton collisions delivered by the LHC and its increasing collision rate, both the detectors and the reconstruction algorithms have to be optimized. The identification of heavy quarks is a key component in many measurements. This thesis describes a hardware and a software project which both aim at improving the identification of heavy quarks. In the first part of this thesis, the Phase 1 upgrade of the CMS pixel detector is introduced. One of the main motivations of the replacement of the Pixel detector is the improved b jet identification at large collision rates. The Phase 1 upgrade involves several production and calibration steps. An X-ray calibration procedure has been developed and the corresponding experimental setup is described. Measurements show that the calibration of the pixel modules is temperature independent and can be performed at room temperature. The stability of the setup is tested in order to fulfill the requirements for mass production of the pixel modules. A method to stabilize the calibration is introduced which is shown to reduce the systematic uncertainty. In the second part, algorithms to identify heavily boosted top quarks (''top tagger'') are described and their performance is compared. The OptimalR HEP top tagger and the shower deconstruction tagger show a better performance than existing tagging algorithms. They can be used in Run II with increased centre-of-mass energies of 13 and 14 TeV. It is also shown that existing top tagging algorithms can be improved by the usage of multivariate analysis methods. New algorithms are commissioned using CMS data with a centre-of-mass energy of 8 TeV, corresponding to an integrated luminosity of 19.7 fb-1. In order to validate these new algorithms in data, two selections are made to measure the efficiency

  16. Studies of top tagging identification methods and development of a new heavy object tagger

    Energy Technology Data Exchange (ETDEWEB)

    Lapsien, Tobias

    2016-05-15

    At the Large Hadron Collider (LHC), precision tests of the standard model of particle physics and searches for new phenomena are performed. To make optimal use of the proton-proton collisions delivered by the LHC and its increasing collision rate, both the detectors and the reconstruction algorithms have to be optimized. The identification of heavy quarks is a key component in many measurements. This thesis describes a hardware and a software project which both aim at improving the identification of heavy quarks. In the first part of this thesis, the Phase 1 upgrade of the CMS pixel detector is introduced. One of the main motivations of the replacement of the Pixel detector is the improved b jet identification at large collision rates. The Phase 1 upgrade involves several production and calibration steps. An X-ray calibration procedure has been developed and the corresponding experimental setup is described. Measurements show that the calibration of the pixel modules is temperature independent and can be performed at room temperature. The stability of the setup is tested in order to fulfill the requirements for mass production of the pixel modules. A method to stabilize the calibration is introduced which is shown to reduce the systematic uncertainty. In the second part, algorithms to identify heavily boosted top quarks (''top tagger'') are described and their performance is compared. The OptimalR HEP top tagger and the shower deconstruction tagger show a better performance than existing tagging algorithms. They can be used in Run II with increased centre-of-mass energies of 13 and 14 TeV. It is also shown that existing top tagging algorithms can be improved by the usage of multivariate analysis methods. New algorithms are commissioned using CMS data with a centre-of-mass energy of 8 TeV, corresponding to an integrated luminosity of 19.7 fb{sup -1}. In order to validate these new algorithms in data, two selections are made to measure the

  17. Transcriptome analysis in primary neural stem cells using a tag cDNA amplification method

    Directory of Open Access Journals (Sweden)

    Wikström Lilian

    2005-04-01

    Full Text Available Abstract Background Neural stem cells (NSCs can be isolated from the adult mammalian brain and expanded in culture, in the form of cellular aggregates called neurospheres. Neurospheres provide an in vitro model for studying NSC behaviour and give information on the factors and mechanisms that govern their proliferation and differentiation. They are also a promising source for cell replacement therapies of the central nervous system. Neurospheres are complex structures consisting of several cell types of varying degrees of differentiation. One way of characterising neurospheres is to analyse their gene expression profiles. The value of such studies is however uncertain since they are heterogeneous structures and different populations of neurospheres may vary significantly in their gene expression. Results To address this issue, we have used cDNA microarrays and a recently reported tag cDNA amplification method to analyse the gene expression profiles of neurospheres originating from separate isolations of the lateral ventricle wall of adult mice and passaged to varying degrees. Separate isolations as well as consecutive passages yield a high variability in gene expression while parallel cultures yield the lowest variability. Conclusions We demonstrate a low technical amplification variability using the employed amplification strategy and conclude that neurospheres from the same isolation and passage are sufficiently similar to be used for comparative gene expression analysis.

  18. Expression of cold-adapted β-1,3-xylanase as a fusion protein with a ProS2 tag and purification using immobilized metal affinity chromatography with a high concentration of ArgHCl.

    Science.gov (United States)

    Kudou, Motonori; Okazaki, Fumiyoshi; Asai-Nakashima, Nanami; Ogino, Chiaki; Kondo, Akihiko

    2015-01-01

    Cold-adapted β-1,3-xylanase (P.t.Xyn26A) from the psychrotrophic bacterium, Psychroflexus torquis, was expressed as a fusion protein with tandem repeats of the N-terminal domain of Protein S from Myxocuccus xanthus (ProS2) in Escherichia coli. After cell lysis in phosphate buffer, most of the ProS2-P.t.Xyn26A was located in the insoluble fraction and aggregated during purification. Arginine hydrochloride (ArgHCl) efficiently solubilized the ProS2-P.t.Xyn26A. The solubilized ProS2-P.t.Xyn26A was purified using immobilized metal affinity chromatography (IMAC) with 500 mM ArgHCl. After cleavage of ProS2-P.t.Xyn26A by human rhinovirus 3C protease, we confirmed that recombinant P.t.Xyn26A maintained its native fold. This is the first report of the expression of a cold-adapted enzyme fused with a ProS2 tag under IMAC purification using a high concentration of ArgHCl. These insights into the expression and purification should be useful during the handling of cold-adapted enzymes. PMID:25214227

  19. Extracting tag hierarchies

    CERN Document Server

    Tibély, Gergely; Vicsek, Tamás; Palla, Gergely

    2014-01-01

    Tagging items with descriptive annotations or keywords is a very natural way to compress and highlight information about the properties of the given entity. Over the years several methods have been proposed for extracting a hierarchy between the tags for systems with a "flat", egalitarian organization of the tags, which is very common when the tags correspond to free words given by numerous independent people. Here we present a complete framework for automated tag hierarchy extraction based on tag occurrence statistics. Along with proposing new algorithms, we are also introducing different quality measures enabling the detailed comparison of competing approaches from different aspects. Furthermore, we set up a synthetic, computer generated benchmark providing a versatile tool for testing, with a couple of tunable parameters capable of generating a wide range of test beds. Beside the computer generated input we also use real data in our studies, including a biological example with a pre-defined hierarchy betwe...

  20. Methods for Fault Diagnosability Analysis of a Class of Affine Nonlinear Systems

    Directory of Open Access Journals (Sweden)

    Xiafu Peng

    2015-01-01

    Full Text Available The fault diagnosability analysis for a given model, before developing a diagnosis algorithm, can be used to answer questions like “can the fault fi be detected by observed states?” and “can it separate fault fi from fault fj by observed states?” If not, we should redesign the sensor placement. This paper deals with the problem of the evaluation of detectability and separability for the diagnosability analysis of affine nonlinear system. First, we used differential geometry theory to analyze the nonlinear system and proposed new detectability criterion and separability criterion. Second, the related matrix between the faults and outputs of the system and the fault separable matrix are designed for quantitative fault diagnosability calculation and fault separability calculation, respectively. Finally, we illustrate our approach to exemplify how to analyze diagnosability by a certain nonlinear system example, and the experiment results indicate the effectiveness of the fault evaluation methods.

  1. Affinity capillary electrophoresis method for investigation of bile salts complexation with sulfobutyl ether-ß-cyclodextrin

    DEFF Research Database (Denmark)

    Østergaard, Jesper; Jensen, Henrik; Holm, Rene

    2012-01-01

    Sulfobutyl ether-ß-cyclodextrin (SBEßCD) is utilized in preformulation and drug formulation as an excipient for solubilization of drugs with poor aqueous solubility. Approximately seven negative charges of SBEßCD play a role with respect to solubilization and complexation, but also have...... an influence on the ionic strength of the background electrolyte when the cyclodextrin is used in capillary electrophoresis. Mobility-shift affinity capillary methods for investigation of the complexation of taurocholate and taurochenodeoxycholate with the negatively charged cyclodextrin derivative applying...... for the bile salts were in the same range as those previously reported for the interaction with neutral ß-cyclodextrins derivatives, i.e. the positions of the negative charges on SBEßCD and the bile salts within the complex did not lead to significant electrostatic repulsion....

  2. Methodological study of affine transformations of gene expression data with proposed robust non-parametric multi-dimensional normalization method

    Directory of Open Access Journals (Sweden)

    Hössjer Ola

    2006-03-01

    Full Text Available Abstract Background Low-level processing and normalization of microarray data are most important steps in microarray analysis, which have profound impact on downstream analysis. Multiple methods have been suggested to date, but it is not clear which is the best. It is therefore important to further study the different normalization methods in detail and the nature of microarray data in general. Results A methodological study of affine models for gene expression data is carried out. Focus is on two-channel comparative studies, but the findings generalize also to single- and multi-channel data. The discussion applies to spotted as well as in-situ synthesized microarray data. Existing normalization methods such as curve-fit ("lowess" normalization, parallel and perpendicular translation normalization, and quantile normalization, but also dye-swap normalization are revisited in the light of the affine model and their strengths and weaknesses are investigated in this context. As a direct result from this study, we propose a robust non-parametric multi-dimensional affine normalization method, which can be applied to any number of microarrays with any number of channels either individually or all at once. A high-quality cDNA microarray data set with spike-in controls is used to demonstrate the power of the affine model and the proposed normalization method. Conclusion We find that an affine model can explain non-linear intensity-dependent systematic effects in observed log-ratios. Affine normalization removes such artifacts for non-differentially expressed genes and assures that symmetry between negative and positive log-ratios is obtained, which is fundamental when identifying differentially expressed genes. In addition, affine normalization makes the empirical distributions in different channels more equal, which is the purpose of quantile normalization, and may also explain why dye-swap normalization works or fails. All methods are made available in

  3. The physiological response of chinook salmon smolts to two methods of radio-tagging

    DEFF Research Database (Denmark)

    Jepsen, Niels; Davis, L.E.; Schreck, C.B.;

    2001-01-01

    Smolts of hatchery-reared chinook salmon Oncorhynchus tshawytscha were radio-tagged by gastric insertion or surgical implant, and their physiological response was measured and compared to that of control insertion or surgical implant, and their physiological response was measured and compared to...

  4. Highly specific purification of N-glycans using phosphate-based derivatization as an affinity tag in combination with Ti(4+)-SPE enrichment for mass spectrometric analysis.

    Science.gov (United States)

    Zhang, Ying; Peng, Ye; Bin, Zhichao; Wang, Huijie; Lu, Haojie

    2016-08-31

    N-linked protein glycosylation is involved in regulation of a wide variety of cellular processes and associated with numerous diseases. Highly specific identification of N-glycome remains a challenge while its biological significance is acknowledged. The relatively low abundance of glycan in complex biological mixtures, lack of basic sites for protonation, and suppression by other highly abundant proteins/peptides lead to the particularly poor detection sensitivity of N-glycans in the MS analysis. Therefore, the highly specific purification procedure becomes a crucial step prior to MS analysis of the N-glycome. Herein, a novel N-glycans enrichment approach based on phosphate derivatization combined with Ti(4+)-SPE (solid phase extraction) was developed. Briefly, in this strategy, N-glycans were chemically labeled with a phospho-group at their reducing ends, such that the Ti(4+)-SPE microspheres were able to capture the phospho-containing glycans. The enrichment method was developed and optimized using model oligosaccharides (maltoheptaose DP7 and sialylated glycan A1) and also glycans from a standard glycoprotein (asialofetuin, ASF). This method experimentally showed high derivatization efficiency (almost 100%), excellent selectivity (analyzing DP7 in the digests of bovine serum albumin at a mass ratio of 1:100), high enriching recovery (90%), good reproducibility (CVN-glycome in human serum, in which a total of 31 N-glycan masses were identified.

  5. 可伸缩TAGS%Scalable TAGS

    Institute of Scientific and Technical Information of China (English)

    闵帆; 张君雁; 杨国纬

    2003-01-01

    In a distributed Web server system where tasks are unpreemptible,the most important issue for improving quality of service (QoS) is how to realize fairness and reduce average slow down. In this paper we present an algorithm named Scalable TAGS by integrating Central Queue algorithm and Task Assignment by Guessing Size (TAGS), together with its performance analysis, system parameter setting algorithm subject to fairness requirement, and optimal grouping method.

  6. An extended affinity propagation clustering method based on different data density types.

    Science.gov (United States)

    Zhao, XiuLi; Xu, WeiXiang

    2015-01-01

    Affinity propagation (AP) algorithm, as a novel clustering method, does not require the users to specify the initial cluster centers in advance, which regards all data points as potential exemplars (cluster centers) equally and groups the clusters totally by the similar degree among the data points. But in many cases there exist some different intensive areas within the same data set, which means that the data set does not distribute homogeneously. In such situation the AP algorithm cannot group the data points into ideal clusters. In this paper, we proposed an extended AP clustering algorithm to deal with such a problem. There are two steps in our method: firstly the data set is partitioned into several data density types according to the nearest distances of each data point; and then the AP clustering method is, respectively, used to group the data points into clusters in each data density type. Two experiments are carried out to evaluate the performance of our algorithm: one utilizes an artificial data set and the other uses a real seismic data set. The experiment results show that groups are obtained more accurately by our algorithm than OPTICS and AP clustering algorithm itself.

  7. Using seed-tagging methods for assessing post-dispersal seed fate in rodent-dispersed trees

    NARCIS (Netherlands)

    Xiao, ZS; Jansen, PA; Zhang, ZB

    2006-01-01

    Seed tagging is widely used for tracking seeds during dispersal by seed-caching animals. No studies, however, have fully examined the effects of seed tagging on post-dispersal seed fate. We studied how two seed tagging techniques - thread-marking and wire tin-tagging - affected seed fate by placing

  8. Using seed-tagging methods for assessing post-dispersal seed fate in rodent-dispersed trees.

    NARCIS (Netherlands)

    Xiao, Z.; Jansen, P.A.; Zhang, Z.

    2006-01-01

    Seed tagging is widely used for tracking seeds during dispersal by seed-caching animals. No studies, however, have fully examined the effects of seed tagging on post-dispersal seed fate. We studied how two seed tagging techniques – thread-marking and wire tin-tagging – affected seed fate by placing

  9. The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities

    Science.gov (United States)

    Genheden, Samuel; Ryde, Ulf

    2015-01-01

    Introduction: The molecular mechanics energies combined with the Poisson–Boltzmann or generalized Born and surface area continuum solvation (MM/PBSA and MM/GBSA) methods are popular approaches to estimate the free energy of the binding of small ligands to biological macromolecules. They are typically based on molecular dynamics simulations of the receptor–ligand complex and are therefore intermediate in both accuracy and computational effort between empirical scoring and strict alchemical perturbation methods. They have been applied to a large number of systems with varying success. Areas covered: The authors review the use of MM/PBSA and MM/GBSA methods to calculate ligand-binding affinities, with an emphasis on calibration, testing and validation, as well as attempts to improve the methods, rather than on specific applications. Expert opinion: MM/PBSA and MM/GBSA are attractive approaches owing to their modular nature and that they do not require calculations on a training set. They have been used successfully to reproduce and rationalize experimental findings and to improve the results of virtual screening and docking. However, they contain several crude and questionable approximations, for example, the lack of conformational entropy and information about the number and free energy of water molecules in the binding site. Moreover, there are many variants of the method and their performance varies strongly with the tested system. Likewise, most attempts to ameliorate the methods with more accurate approaches, for example, quantum-mechanical calculations, polarizable force fields or improved solvation have deteriorated the results. PMID:25835573

  10. The use of external electronic tags on fish: an evaluation of tag retention and tagging effects

    DEFF Research Database (Denmark)

    Jepsen, Niels; Thorstad, Eva B.; Havn, Torgeir;

    2015-01-01

    growth and survival have also been recorded, but direct mortality caused by external tagging seems rare. Most of the studies reviewed evaluate tag retention, survival, and tissue reactions. There is a general need for more research on the effects of external tagging of fish with electronic tags......External tagging of fish with electronic tags has been used for decades for a wide range of marine and freshwater species. In the early years of fish telemetry research, it was the most commonly used attachment method, but later internal implants became preferred. Recently, the number of telemetry...... unsuitable for surgical implantation, or when using tags with sensors recording the external environment. The most commonly reported problems with external tags are tissue damage, premature tag loss, and decreased swimming capacity, but the effects are highly context dependent and species specific. Reduced...

  11. A general method of community detection by identifying community centers with affinity propagation

    Science.gov (United States)

    Guo, Wei-Feng; Zhang, Shao-Wu

    2016-04-01

    Detection of community structures is beneficial to analyzing the structures and properties of networks. It is of theoretical interest and practical significance in modern science. So far, a large number of algorithms have been proposed to detect community structures in complex networks, but most of them are suitable for a specific network structure. In this paper, a novel method (called CDMIC) is proposed to detect the communities in un-weighted, weighted, un-directed, directed and signed networks by constructing a dissimilarity distance matrix of network and identifying community centers with maximizing modularity. For a given network, we first estimate the distance between all pairs of nodes for constructing the dissimilarity distance matrix of the network. Then, this distance matrix is input to the affinity propagation (AP) algorithm to extract a candidate center set of community. Thirdly, we rank these centers in descending order according to the sum of their availability and responsibility. Finally, we determine the community structure by selecting the center subset from the candidate center set in an incremental manner to make the modularity maximization. On three real-world networks and some synthetic networks, experimental results show that our CDMIC method has higher performance in terms of classification accuracy and normalized mutual information (NMI), and ability to tolerate the resolution limitation.

  12. A Measurement of $R_{b}$ using a Double Tagging Method

    CERN Document Server

    Abbiendi, G; Alexander, Gideon; Allison, J; Altekamp, N; Anderson, K J; Anderson, S; Arcelli, S; Asai, S; Ashby, S F; Axen, D A; Azuelos, Georges; Ball, A H; Barberio, E; Barlow, R J; Bartoldus, R; Batley, J Richard; Baumann, S; Bechtluft, J; Behnke, T; Bell, K W; Bella, G; Bellerive, A; Bentvelsen, Stanislaus Cornelius Maria; Bethke, Siegfried; Betts, S; Biebel, O; Biguzzi, A; Bird, S D; Blobel, Volker; Bloodworth, Ian J; Bobinski, M; Bock, P; Böhme, J; Bonacorsi, D; Boutemeur, M; Braibant, S; Bright-Thomas, P G; Brigliadori, L; Brown, R M; Burckhart, Helfried J; Burgard, C; Bürgin, R; Capiluppi, P; Carnegie, R K; Carter, A A; Carter, J R; Chang, C Y; Charlton, D G; Chrisman, D; Ciocca, C; Clarke, P E L; Clay, E; Cohen, I; Conboy, J E; Cooke, O C; Couyoumtzelis, C; Coxe, R L; Cuffiani, M; Dado, S; Dallavalle, G M; Davis, R; De Jong, S; del Pozo, L A; de Roeck, A; Desch, Klaus; Dienes, B; Dixit, M S; Dubbert, J; Duchovni, E; Duckeck, G; Duerdoth, I P; Eatough, D; Estabrooks, P G; Etzion, E; Evans, H G; Fabbri, Franco Luigi; Fanti, M; Faust, A A; Fiedler, F; Fierro, M; Fleck, I; Folman, R; Fürtjes, A; Futyan, D I; Gagnon, P; Gary, J W; Gascon, J; Gascon-Shotkin, S M; Gaycken, G; Geich-Gimbel, C; Giacomelli, G; Giacomelli, P; Gibson, V; Gibson, W R; Gingrich, D M; Glenzinski, D A; Goldberg, J; Gorn, W; Grandi, C; Gross, E; Grunhaus, Jacob; Gruwé, M; Hanson, G G; Hansroul, M; Hapke, M; Harder, K; Hargrove, C K; Hartmann, C; Hauschild, M; Hawkes, C M; Hawkings, R; Hemingway, Richard J; Herndon, M; Herten, G; Heuer, R D; Hildreth, M D; Hill, J C; Hillier, S J; Hobson, P R; Höcker, Andreas; Homer, R James; Honma, A K; Horváth, D; Hossain, K R; Howard, R; Hüntemeyer, P; Igo-Kemenes, P; Imrie, D C; Ishii, K; Jacob, F R; Jawahery, A; Jeremie, H; Jimack, Martin Paul; Jones, C R; Jovanovic, P; Junk, T R; Karlen, D A; Kartvelishvili, V G; Kawagoe, K; Kawamoto, T; Kayal, P I; Keeler, Richard K; Kellogg, R G; Kennedy, B W; Klier, A; Kluth, S; Kobayashi, T; Kobel, M; Koetke, D S; Kokott, T P; Kolrep, M; Komamiya, S; Kowalewski, R V; Kress, T; Krieger, P; Von Krogh, J; Kühl, T; Kyberd, P; Lafferty, G D; Lanske, D; Lauber, J; Lautenschlager, S R; Lawson, I; Layter, J G; Lazic, D; Lee, A M; Lellouch, Daniel; Letts, J; Levinson, L; Liebisch, R; List, B; Littlewood, C; Lloyd, A W; Lloyd, S L; Loebinger, F K; Long, G D; Losty, Michael J; Ludwig, J; Liu, D; Macchiolo, A; MacPherson, A L; Mader, W F; Mannelli, M; Marcellini, S; Markopoulos, C; Martin, A J; Martin, J P; Martínez, G; Mashimo, T; Mättig, P; McDonald, W J; McKenna, J A; McKigney, E A; McMahon, T J; McPherson, R A; Meijers, F; Menke, S; Merritt, F S; Mes, H; Meyer, J; Michelini, Aldo; Mihara, S; Mikenberg, G; Miller, D J; Mir, R; Mohr, W; Montanari, A; Mori, T; Nagai, K; Nakamura, I; Neal, H A; Nellen, B; Nisius, R; O'Neale, S W; Oakham, F G; Odorici, F; Ögren, H O; Oreglia, M J; Orito, S; Pálinkás, J; Pásztor, G; Pater, J R; Patrick, G N; Patt, J; Pérez-Ochoa, R; Petzold, S; Pfeifenschneider, P; Pilcher, J E; Pinfold, James L; Plane, D E; Poffenberger, P R; Polok, J; Przybycien, M B; Rembser, C; Rick, Hartmut; Robertson, S; Robins, S A; Rodning, N L; Roney, J M; Roscoe, K; Rossi, A M; Rozen, Y; Runge, K; Runólfsson, O; Rust, D R; Sachs, K; Saeki, T; Sahr, O; Sang, W M; Sarkisyan-Grinbaum, E; Sbarra, C; Schaile, A D; Schaile, O; Scharf, F; Scharff-Hansen, P; Schieck, J; Schmitt, B; Schmitt, S; Schöning, A; Schröder, M; Schumacher, M; Schwick, C; Scott, W G; Seuster, R; Shears, T G; Shen, B C; Shepherd-Themistocleous, C H; Sherwood, P; Siroli, G P; Sittler, A; Skuja, A; Smith, A M; Snow, G A; Sobie, Randall J; Söldner-Rembold, S; Sproston, M; Stahl, A; Stephens, K; Steuerer, J; Stoll, K; Strom, D; Ströhmer, R; Surrow, B; Talbot, S D; Tanaka, S; Taras, P; Tarem, S; Teuscher, R; Thiergen, M; Thomson, M A; Von Törne, E; Torrence, E; Towers, S; Trigger, I; Trócsányi, Z L; Tsur, E; Turcot, A S; Turner-Watson, M F; Van Kooten, R; Vannerem, P; Verzocchi, M; Voss, H; Wäckerle, F; Wagner, A; Ward, C P; Ward, D R; Watkins, P M; Watson, A T; Watson, N K; Wells, P S; Wermes, N; White, J S; Wilson, G W; Wilson, J A; Wyatt, T R; Yamashita, S; Yekutieli, G; Zacek, V; Zer-Zion, D

    1999-01-01

    The fraction of Z to bbbar events in hadronic Z decays has been measured by the OPAL experiment using the data collected at LEP between 1992 and 1995. The Z to bbbar decays were tagged using displaced secondary vertices, and high momentum electrons and muons. Systematic uncertainties were reduced by measuring the b-tagging efficiency using a double tagging technique. Efficiency correlations between opposite hemispheres of an event are small, and are well understood through comparisons between real and simulated data samples. A value of Rb = 0.2178 +- 0.0011 +- 0.0013 was obtained, where the first error is statistical and the second systematic. The uncertainty on Rc, the fraction of Z to ccbar events in hadronic Z decays, is not included in the errors. The dependence on Rc is Delta(Rb)/Rb = -0.056*Delta(Rc)/Rc where Delta(Rc) is the deviation of Rc from the value 0.172 predicted by the Standard Model. The result for Rb agrees with the value of 0.2155 +- 0.0003 predicted by the Standard Model.

  13. Development of an aptamer-based affinity purification method for vascular endothelial growth factor

    Directory of Open Access Journals (Sweden)

    Maren Lönne

    2015-12-01

    Full Text Available Since aptamers bind their targets with high affinity and specificity, they are promising alternative ligands in protein affinity purification. As aptamers are chemically synthesized oligonucleotides, they can be easily produced in large quantities regarding GMP conditions allowing their application in protein production for therapeutic purposes. Several advantages of aptamers compared to antibodies are described in general within this paper. Here, an aptamer directed against the human Vascular Endothelial Growth Factor (VEGF was used as affinity ligand for establishing a purification platform for VEGF in small scale. The aptamer was covalently immobilized on magnetic beads in a controlled orientation resulting in a functional active affinity matrix. Target binding was optimized by introduction of spacer molecules and variation of aptamer density. Further, salt-induced target elution was demonstrated as well as VEGF purification from a complex protein mixture proving the specificity of protein-aptamer binding.

  14. Combining biophysical methods for the analysis of protein complex stoichiometry and affinity in SEDPHAT

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Huaying, E-mail: zhaoh3@mail.nih.gov; Schuck, Peter, E-mail: zhaoh3@mail.nih.gov [National Institutes of Health, Bethesda, MD 20892 (United States)

    2015-01-01

    Global multi-method analysis for protein interactions (GMMA) can increase the precision and complexity of binding studies for the determination of the stoichiometry, affinity and cooperativity of multi-site interactions. The principles and recent developments of biophysical solution methods implemented for GMMA in the software SEDPHAT are reviewed, their complementarity in GMMA is described and a new GMMA simulation tool set in SEDPHAT is presented. Reversible macromolecular interactions are ubiquitous in signal transduction pathways, often forming dynamic multi-protein complexes with three or more components. Multivalent binding and cooperativity in these complexes are often key motifs of their biological mechanisms. Traditional solution biophysical techniques for characterizing the binding and cooperativity are very limited in the number of states that can be resolved. A global multi-method analysis (GMMA) approach has recently been introduced that can leverage the strengths and the different observables of different techniques to improve the accuracy of the resulting binding parameters and to facilitate the study of multi-component systems and multi-site interactions. Here, GMMA is described in the software SEDPHAT for the analysis of data from isothermal titration calorimetry, surface plasmon resonance or other biosensing, analytical ultracentrifugation, fluorescence anisotropy and various other spectroscopic and thermodynamic techniques. The basic principles of these techniques are reviewed and recent advances in view of their particular strengths in the context of GMMA are described. Furthermore, a new feature in SEDPHAT is introduced for the simulation of multi-method data. In combination with specific statistical tools for GMMA in SEDPHAT, simulations can be a valuable step in the experimental design.

  15. Combining biophysical methods for the analysis of protein complex stoichiometry and affinity in SEDPHAT

    International Nuclear Information System (INIS)

    Global multi-method analysis for protein interactions (GMMA) can increase the precision and complexity of binding studies for the determination of the stoichiometry, affinity and cooperativity of multi-site interactions. The principles and recent developments of biophysical solution methods implemented for GMMA in the software SEDPHAT are reviewed, their complementarity in GMMA is described and a new GMMA simulation tool set in SEDPHAT is presented. Reversible macromolecular interactions are ubiquitous in signal transduction pathways, often forming dynamic multi-protein complexes with three or more components. Multivalent binding and cooperativity in these complexes are often key motifs of their biological mechanisms. Traditional solution biophysical techniques for characterizing the binding and cooperativity are very limited in the number of states that can be resolved. A global multi-method analysis (GMMA) approach has recently been introduced that can leverage the strengths and the different observables of different techniques to improve the accuracy of the resulting binding parameters and to facilitate the study of multi-component systems and multi-site interactions. Here, GMMA is described in the software SEDPHAT for the analysis of data from isothermal titration calorimetry, surface plasmon resonance or other biosensing, analytical ultracentrifugation, fluorescence anisotropy and various other spectroscopic and thermodynamic techniques. The basic principles of these techniques are reviewed and recent advances in view of their particular strengths in the context of GMMA are described. Furthermore, a new feature in SEDPHAT is introduced for the simulation of multi-method data. In combination with specific statistical tools for GMMA in SEDPHAT, simulations can be a valuable step in the experimental design

  16. Methods for optimizing over the efficient and weakly efficient sets of an affine fractional vector optimization program

    DEFF Research Database (Denmark)

    Le, T.H.A.; Pham, D. T.; Canh, Nam Nguyen;

    2010-01-01

    Both the efficient and weakly efficient sets of an affine fractional vector optimization problem, in general, are neither convex nor given explicitly. Optimization problems over one of these sets are thus nonconvex. We propose two methods for optimizing a real-valued function over the efficient a...

  17. Flavour Tagging at LHCb

    CERN Multimedia

    Grabalosa Gandara, M

    2009-01-01

    To do precise CP violation measurements, the most possible accurate knowledge of the flavour at production of the reconstructed B meson is required. This poster summarizes the flavour tagging performances for the LHCb experiment. We use same side an opposite side algorithms to establish wheter the meson contained a b or a b\\bar quark. The final decision is obtained through a combination of several methods. The use of control channels, decays to a flavour specific final state, will allow to determine the wrong tag fraction \\omega (the probability of a tag to be wrong), which can be used as input for the determination of CKM unitary triangle angles.

  18. Identification of High Affinity Fatty Acid Binding Sites on Human Serum Albumin by MM-PBSA Method

    OpenAIRE

    Fujiwara, Shin-ichi; Amisaki, Takashi

    2007-01-01

    Human serum albumin (HSA) has seven common fatty acid (FA) binding sites. In this study, we used the molecular mechanics Poisson-Boltzmann surface area method to identify high affinity FA binding sites on HSA in terms of binding free energy. Using multiple HSA-FA (myristate, palmitate) complex models constructed by molecular dynamics simulations, two methods were performed in molecular mechanics Poisson-Boltzmann surface area, the “three-trajectory method” and the “single-trajectory method”. ...

  19. Method to produce acetyldiacylglycerols (ac-TAGs) by expression of an acetyltransferase gene isolated from Euonymus alatus (burning bush)

    Energy Technology Data Exchange (ETDEWEB)

    Durrett, Timothy; Ohlrogge, John; Pollard, Michael

    2016-05-03

    The present invention relates to novel diacylglycerol acyltransferase genes and proteins, and methods of their use. In particular, the invention describes genes encoding proteins having diacylglycerol acetyltransferase activity, specifically for transferring an acetyl group to a diacylglycerol substrate to form acetyl-Triacylglycerols (ac-TAGS), for example, a 3-acetyl-1,2-diacyl-sn-glycerol. The present invention encompasses both native and recombinant wild-type forms of the transferase, as well as mutants and variant forms. The present invention also relates to methods of using novel diacylglycerol acyltransferase genes and proteins, including their expression in transgenic organisms at commercially viable levels, for increasing production of 3-acetyl-1,2-diacyl-sn-glycerols in plant oils and altering the composition of oils produced by microorganisms, such as yeast, by increasing ac-TAG production. Additionally, oils produced by methods of the present inventions comprising genes and proteins are contemplated for use as biodiesel fuel, in polymer production and as naturally produced food oils with reduced calories.

  20. Expression of Epitope-Tagged Proteins in Mammalian Cells in Culture.

    Science.gov (United States)

    Bhatt, Jay M; Styers, Melanie L; Sztul, Elizabeth

    2016-01-01

    Before the advent of molecular methods to tag proteins, visualization of proteins within cells required the use of antibodies directed against the protein of interest. Thus, only proteins for which antibodies were available could be visualized. Epitope tagging allows the detection of all proteins with existing sequence information, irrespective of the availability of antibodies directed against them. This technique involves the generation of DNA constructs that express the protein of interest tagged with an epitope that can be recognized by a commercially available antibody. Proteins can be tagged with a wide variety of epitopes using commercially available vectors that allow expression in mammalian cells. Epitope-tagged proteins are easily transfected into mammalian cell lines and, in most cases, tightly mimic the behavior of the endogenous protein. Tagged proteins exogenously expressed in cells provide different types of information depending on the subsequent detection approaches. Using immunofluorescence and immunoelectron microscopy with anti-tag antibodies, relative to known markers of cellular organelles, can provide information on the subcellular localization of the tagged protein and may provide clues regarding the protein's function. Immunofluorescence with anti-tag antibodies can also be utilized to assess the tagged protein's responses to cellular signals and pharmacological treatments. Immunoprecipitations with anti-tag antibodies can recover protein complexes containing the protein of interest, resulting in the identification of interacting proteins. Recovery of tagged proteins on affinity matrices allows their purification for use in biochemical assays. In addition, specialized fluorescent tags, such as the green fluorescent protein (GFP) allow the analysis of cellular dynamics in live cells in real time. PMID:27515071

  1. Geometrical and P.D.E. Methods in the Treatment of the Theory of Shells: Comparing Euclidean and Affine Approaches

    Directory of Open Access Journals (Sweden)

    Salvador Gigena

    2014-01-01

    Full Text Available The use of differential equations methods in the approach, treatment, and solution of problems in diverse areas of geometry, particularly in affine differential geometry is well known and prolific, where they have proven to be quite fruitful when it comes to the obtainment of definite results. It is perhaps lesser known that the same kind of those very same methods has been and is currently being used to treat developments in some specific areas of applied sciences, such as the theory of shells where, similarly, they can be proven to be quite effective as well. In this paper we precisely show that such is the case in two particular, related instances: the historic approach of the classical, Euclidean part of the theory pursued by Fritz John, in the past century, and the more recent expositions that we ourselves have dedicated to the affine counterpart of the theory.

  2. Prediction of SAMPL3 Host-Guest Affinities with the Binding Energy Distribution Analysis Method (BEDAM)

    OpenAIRE

    Gallicchio, Emilio; Ronald M Levy

    2012-01-01

    BEDAM calculations are described to predict the free energies of binding of a series of anaesthetic drugs to a recently characterized acyclic cucurbituril host. The modeling predictions, conducted as part of the SAMPL3 host-guest affinity blind challenge, are generally in good quantitative agreement with the experimental measurements. The correlation coefficient between computed and measured binding free energies is 70% with high statistical significance. Multiple conformational stereoisomers...

  3. Affinity Induced Surface Functionalization of Liposomes Using Cu-Free Click Chemistry

    DEFF Research Database (Denmark)

    Bak, Martin; Jølck, Rasmus Irming; Eliasen, Rasmus;

    2016-01-01

    be used for functionalization of other nanoparticles or solid surfaces. The method exploits a synergistic effect of having both affinity and covalent anchoring tags on the surface of the liposome. This was achieved by synthesizing a peptide linker system that uses Cu-free strain-promoted click chemistry...

  4. The Method of Selecting tagSNPs Based on Linkage Disequilibrium%一种基于连锁不平衡的tagSNPs选择算法

    Institute of Scientific and Technical Information of China (English)

    王钧峰; 王新赠

    2016-01-01

    进行全基因组关联研究(genome-wide association studies,简记为GWAS)时,我们需要获得一个足够密集的单核苷酸多态性(single-nucleotide polymorphism,简记为SNP)标记集来解释常见疾病遗传风险的一部分.候选基因中SNP的数量是有限的,但是直接分析所有现存的SNPs是无效的,因为在这些位点上的基因型有很强的关联性,会导致大量的冗余信息,并且会造成基因分型成本的增加,消耗大量的时间.所以我们在进行关联检验时,没有必要对所有的SNPs进行基因分型,只需要选择出具有代表性,并且数量很少的SNPs进行分型,并对这些SNPs进行关联检验.这里选择出的SNPs称为标签SNPs(记为tagSNPs),它为SNPs的一个小的子集,在每个单体型区域中足以捕获单体型的信息.选择tagSNPs的方法有很多,本文我们提出了一种新的tagSNPs选择方法,通过使用基于连锁不平衡(linkage disequilibrium,简记为LD)的两两r2准则对单体型分组,分成不相交的组,并在每个组中选择标签SNPs.与基于原始SNPs集的检验方法比较,我们的方法产生了更少的tagSNPs,在最大化所选标记提供信息含量的同时,降低了基因分型成本,提高了效率.

  5. NONMONOTONIC REDUCED PROJECTED HESSIAN METHOD VIA AN AFFINE SCALING INTERIOR MODIFIED GRADIENT PATH FOR BOUNDED-CONSTRAINED OPTIMIZATION

    Institute of Scientific and Technical Information of China (English)

    Peihua GUO; Detong ZHU

    2008-01-01

    The authors propose an affine scaling modified gradient path method in association with reduced projective Hessian and nonmonotonic interior backtracking line search techniques for solving the linear equality constrained optimization subject to bounds on variables. By employing the QR decomposition of the constraint matrix and the eigensystem decomposition of reduced projective Hes-sian matrix in the subproblem, the authors form affine scaling modified gradient curvilinear path very easily. By using interior backtracking line search technique, each iterate switches to trial step of strict interior feasibility. The global convergence and fast local superlinear/quadratical convergence rates of the proposed algorithm are established under some reasonable conditions. A nonmonotonic criterion should bring about speeding up the convergence progress in some ill-conditioned cases. The results of numerical experiments are reported to show the effectiveness of the proposed algorithm.

  6. EXPRESSION OF SV40 Tag AND FORMATION Tag-p53 AND Tag-Rb COMPLEXES IN CHINESE BRAIN TUMORS

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Objective: To investigate the expression of SV40 Tag andformation of Tag-p53 and Tag-Rb complexes in Chinese brain tumors. Methods: SV40 large tumor antigen (Tag) were investigated by immunoprecipitation, silver staining and Western blot in 65 cases of Chinese brain tumors and 8 cases of normal brain tissues. Tag-p53 and Tag-Rb complexes were screened by the same way in 20 and 15 Tag positive tumor tissues respectively. Results: Tag was found in all of 8 ependymomas and 2 choroid plexus papillomas, 90% (9/10) of pituitary adenomas, 73% (11/15) of astrocytomas, 70% (7/10) of meningiomas, 50% (4/8) of glioblastoma multiform, 33% (2/6) of medulloblastomas, 5 oligodendrogliomas, 1 pineocytoma and 8 normal brain tissues were negative for Tag. Tag-p53 complex was detected in all of 20 Tag positive tumors as well as Tag-Rb complex in all of 15 Tag positive tumors. Conclusion: SV40 Tag is not only expressed in human brain tumors, but also it can form specific complexes with tumor suppressors p53 and Rb. SV40 is correlated to human brain tumorigenesis. The inactivation of p53 and Rb due to the formation of Tag-p53 and Tag-Rb complexes is possibly an important mechanism in the etiopathogenesis of human brain tumors.

  7. Tagging of MADS domain proteins for chromatin immunoprecipitation

    Directory of Open Access Journals (Sweden)

    van Zuijlen Lisette GC

    2007-09-01

    Full Text Available Abstract Background Most transcription factors fulfill their role in complexes and regulate their target genes upon binding to DNA motifs located in upstream regions or introns. To date, knowledge about transcription factor target genes and their corresponding transcription factor binding sites are still very limited. Two related methods that allow in vivo identification of transcription factor binding sites are chromatin immunoprecipitation (ChIP and chromatin affinity purification (ChAP. For ChAP, the protein of interest is tagged with a peptide or protein, which can be used for affinity purification of the protein-DNA complex and hence, the identification of the target gene. Results Here, we present the results of experiments aiming at the development of a generic tagging approach for the Arabidopsis MADS domain proteins AGAMOUS, SEPALLATA3, and FRUITFULL. For this, Arabidopsis wild type plants were transformed with constructs containing a MADS-box gene fused to either a double Strep-tag® II-FLAG-tag, a triple HA-tag, or an eGFP-tag, all under the control of the constitutive double 35S Cauliflower Mosaic Virus (CaMV promoter. Strikingly, in all cases, the number of transformants with loss-of-function phenotypes was much larger than those with an overexpression phenotype. Using endogenous promoters in stead of the 35S CaMV resulted in a dramatic reduction in the frequency of loss-of-function phenotypes. Furthermore, pleiotropic defects occasionally caused by an overexpression strategy can be overcome by using the native promoter of the gene. Finally, a ChAP result is presented using GFP antibody on plants carrying a genomic fragment of a MADS-box gene fused to GFP. Conclusion This study revealed that MADS-box proteins are very sensitive to fusions with small peptide tags and GFP tags. Furthermore, for the expression of chimeric versions of MADS-box genes it is favorable to use the entire genomic region in frame to the tag of choice

  8. Top Tagging with New Approaches

    CERN Document Server

    CMS Collaboration

    2016-01-01

    Methods for boosted hadronically decaying top quark identification (top tagging) are tested in view of the 13 TeV data-taking run of the LHC. In addition to evaluating the discrimination power of single observables, the gain from combining different substructure techniques is quantified. The interplay between different top tagging variables and b tagging is evaluated and the performance of selected observables for high transverse momentum jets is studied. Aditionally, a comparison of top tagging variables between data and simulation is performed, using collision events with a center-of-mass energy of 8 TeV.

  9. A Simple Three-Step Method for Design and Affinity Testing of New Antisense Peptides: An Example of Erythropoietin

    Directory of Open Access Journals (Sweden)

    Nikola Štambuk

    2014-05-01

    Full Text Available Antisense peptide technology is a valuable tool for deriving new biologically active molecules and performing peptide–receptor modulation. It is based on the fact that peptides specified by the complementary (antisense nucleotide sequences often bind to each other with a higher specificity and efficacy. We tested the validity of this concept on the example of human erythropoietin, a well-characterized and pharmacologically relevant hematopoietic growth factor. The purpose of the work was to present and test simple and efficient three-step procedure for the design of an antisense peptide targeting receptor-binding site of human erythropoietin. Firstly, we selected the carboxyl-terminal receptor binding region of the molecule (epitope as a template for the antisense peptide modeling; Secondly, we designed an antisense peptide using mRNA transcription of the epitope sequence in the 3'→5' direction and computational screening of potential paratope structures with BLAST; Thirdly, we evaluated sense–antisense (epitope–paratope peptide binding and affinity by means of fluorescence spectroscopy and microscale thermophoresis. Both methods showed similar Kd values of 850 and 816 µM, respectively. The advantages of the methods were: fast screening with a small quantity of the sample needed, and measurements done within the range of physicochemical parameters resembling physiological conditions. Antisense peptides targeting specific erythropoietin region(s could be used for the development of new immunochemical methods. Selected antisense peptides with optimal affinity are potential lead compounds for the development of novel diagnostic substances, biopharmaceuticals and vaccines.

  10. Exploring the Long Tail of Social Media Tags

    NARCIS (Netherlands)

    S. Kordumova; J. van Gemert; C.G.M. Snoek

    2016-01-01

    There are millions of users who tag multimedia content, generating a large vocabulary of tags. Some tags are frequent, while other tags are rarely used following a long tail distribution. For frequent tags, most of the multimedia methods that aim to automatically understand audio-visual content, giv

  11. Simple Protein Complex Purification and Identification Method Suitable for High- throughput Mapping of Protein Interaction Networks

    Energy Technology Data Exchange (ETDEWEB)

    Markillie, Lye Meng; Lin, Chiann Tso; Adkins, Joshua N.; Auberry, Deanna L.; Hill, Eric A.; Hooker, Brian S.; Moore, Priscilla A.; Moore, Ronald J.; Shi, Liang; Wiley, H. S.; Kery, Vladimir

    2005-04-11

    Most of the current methods for purification and identification of protein complexes use endogenous expression of affinity tagged bait, tandem affinity tag purification of protein complexes followed by specific elution of complexes from beads, gel separation, in-gel digestion and mass spectrometric analysis of protein interactors. We propose a single affinity tag in vitro pulldown assay with denaturing elution, trypsin digestion in organic solvent and LC ESI MS/MS protein identification using SEQUEST analysis. Our method is simple, easy to scale up and automate thus suitable for high throughput mapping of protein interaction networks and functional proteomics.

  12. Two-dimensional Length Extraction of Ballistic Target from ISAR Images Using a New Scaling Method by Affine Registration

    Directory of Open Access Journals (Sweden)

    Jin Guanghu

    2014-09-01

    Full Text Available The length of ballistic target is one of the most important features for target recognition. It can be extracted from ISAR Images. Unlike from the optical image, the length extraction from ISAR image has two difficulties. The first one is that it is hard to get the actual position of scattering centres by the traditional target extraction method. The second one is that the ISAR image’s cross scale is not known because of the target’s complex rotation. Here we propose two methods to solve these problems. Firstly, we use clustering method to get scattering centers. Secondly we propose to get cross scale of the ISAR images by affine registration. Experiments verified that our approach is realisable and has good performance.Defence Science Journal, Vol. 64, No. 5, September 2014, pp.458-463, DOI:http://dx.doi.org/10.14429/dsj.64.5001

  13. A simple enzyme-substrate localized conjugation method to generate immobilized, functional glutathione S-transferase fusion protein columns for affinity enrichment.

    Science.gov (United States)

    Coughlin, John; Masci, Allyson; Gronke, Robert S; Bergelson, Svetlana; Co, Carl

    2016-07-15

    Immobilized protein receptors and enzymes are tools for isolating or enriching ligands and substrates based on affinity. For example, glutathione S-transferase (GST) is fused to proteins as a tag for binding to its substrate glutathione (GSH) linked to solid supports. One issue with this approach is that high-affinity interactions between receptors and ligands require harsh elution conditions such as low pH, which can result in leached receptor. Another issue is the inherent nonspecific chemical conjugation of reactive groups such as N-hydroxysuccinimide (NHS) that couple lysines to solid supports; the nonspecificity of NHS may result in residue modifications near the binding site(s) of the receptor that can affect ligand specificity. In this study, a simple conjugation procedure is presented that overcomes these limitations and results in immobilized GST fusion proteins that are functional and specific. Here, the affinity of GST for GSH was used to generate an enzyme-substrate site-specific cross-linking reaction; GSH-Sepharose was preactivated with 1-ethyl-3-(dimethylaminopropyl)carbodiimide (EDC) and then incubated Fc gamma receptor IIIa (FcγRIIIa)-GST. The immobilized FcγRIIIa-GST more specifically bound glycosylated immunoglobulin G1s (IgG1s) and was used to enrich nonfucosylated IgG1s from weaker binding species. This technique can be used when modifications of amino acids lead to changes in activity. PMID:27063248

  14. Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method

    Directory of Open Access Journals (Sweden)

    Lund Ole

    2007-07-01

    Full Text Available Abstract Background Antigen presenting cells (APCs sample the extra cellular space and present peptides from here to T helper cells, which can be activated if the peptides are of foreign origin. The peptides are presented on the surface of the cells in complex with major histocompatibility class II (MHC II molecules. Identification of peptides that bind MHC II molecules is thus a key step in rational vaccine design and developing methods for accurate prediction of the peptide:MHC interactions play a central role in epitope discovery. The MHC class II binding groove is open at both ends making the correct alignment of a peptide in the binding groove a crucial part of identifying the core of an MHC class II binding motif. Here, we present a novel stabilization matrix alignment method, SMM-align, that allows for direct prediction of peptide:MHC binding affinities. The predictive performance of the method is validated on a large MHC class II benchmark data set covering 14 HLA-DR (human MHC and three mouse H2-IA alleles. Results The predictive performance of the SMM-align method was demonstrated to be superior to that of the Gibbs sampler, TEPITOPE, SVRMHC, and MHCpred methods. Cross validation between peptide data set obtained from different sources demonstrated that direct incorporation of peptide length potentially results in over-fitting of the binding prediction method. Focusing on amino terminal peptide flanking residues (PFR, we demonstrate a consistent gain in predictive performance by favoring binding registers with a minimum PFR length of two amino acids. Visualizing the binding motif as obtained by the SMM-align and TEPITOPE methods highlights a series of fundamental discrepancies between the two predicted motifs. For the DRB1*1302 allele for instance, the TEPITOPE method favors basic amino acids at most anchor positions, whereas the SMM-align method identifies a preference for hydrophobic or neutral amino acids at the anchors. Conclusion

  15. A new real-time method for investigation of affinity properties and binding kinetics of magnetic nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Orlov, Alexey V. [Prokhorov General Physics Institute, Russian Academy of Sciences, 38 Vavilov St, 119991 Moscow (Russian Federation); Nikitin, Maxim P. [Prokhorov General Physics Institute, Russian Academy of Sciences, 38 Vavilov St, 119991 Moscow (Russian Federation); Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St, 117997 Moscow (Russian Federation); Moscow Institute of Physics and Technology, 9 Institutskii per., Dolgoprudny, Moscow Region 141700 (Russian Federation); Bragina, Vera A.; Znoyko, Sergey L.; Zaikina, Marina N.; Ksenevich, Tatiana I.; Gorshkov, Boris G. [Prokhorov General Physics Institute, Russian Academy of Sciences, 38 Vavilov St, 119991 Moscow (Russian Federation); Nikitin, Petr I., E-mail: nikitin@kapella.gpi.ru [Prokhorov General Physics Institute, Russian Academy of Sciences, 38 Vavilov St, 119991 Moscow (Russian Federation); National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), 31 Kashirskoe shosse, 115409 Moscow (Russian Federation)

    2015-04-15

    A method for quantitative investigation of affinity constants of receptors immobilized on magnetic nanoparticles (MP) is developed based on spectral correlation interferometry (SCI). The SCI records with a picometer resolution the thickness changes of a layer of molecules or nanoparticles due to a biochemical reaction on a cover slip, averaged over the sensing area. The method is compatible with other types of sensing surfaces employed in biosensing. The measured values of kinetic association constants of magnetic nanoparticles are 4 orders of magnitude higher than those of molecular antibody association with antigen. The developed method also suggests highly sensitive detection of antigens in a wide dynamic range. The limit of detection of 92 pg/ml has been demonstrated for prostate-specific antigen (PSA) with 50-nm MP employed as labels, which produce 3-order amplification of the SCI signals. The calibration curve features high sensitivity (slope) of 3-fold signal raise per 10-fold increase of PSA concentration within 4-order dynamic range, which is an attractive compromise for precise quantitative and highly sensitive immunoassay. The proposed biosensing technique offers inexpensive disposable sensor chips of cover slips and represents an economically sound alternative to traditional immunoassays for disease diagnostics, detection of pathogens in food and environmental monitoring. - Highlights: • Method for study of affinity constants of magnetic nanoparticles with receptors is proposed. • Association constants of such particles are 4 orders higher than for biomolecules. • Method is compatible with widely used biosensor surfaces and affordable consumables. • It has high sensitivity: 3-fold signal increasing per 10-fold of PSA concentration. • Limit of detection for PSA is 92 pg/ml, dynamic range – 4 orders of concentration.

  16. A Review on Chipless RFID Tag Design

    Directory of Open Access Journals (Sweden)

    Ali Hashemi

    2013-06-01

    Full Text Available The demand for RFID tags has recently increased due to the development of the RFID. Over the past decade, great efforts have been devoted to the design of RFID tags without chip inside. The concept of chipless RFID tags appears to be a promising solution for low cost item tagging because the cost of active RFID tag depends mainly on the chip used in them. This paper presents the progress of the chipless RFID tag and introduces major studies in this filed. Advantages and disadvantages of these methods are pointed out.

  17. Protein Complex Purification by Affinity Capture.

    Science.gov (United States)

    LaCava, John; Fernandez-Martinez, Javier; Hakhverdyan, Zhanna; Rout, Michael P

    2016-01-01

    Affinity capture has become a powerful technique for consistently purifying endogenous protein complexes, facilitating biochemical and biophysical assays on otherwise inaccessible biological assemblies, and enabling broader interactomic exploration. For this procedure, cells are broken and their contents separated and extracted into a solvent, permitting access to target macromolecular complexes thus released in solution. The complexes are specifically enriched from the extract onto a solid medium coupled with an affinity reagent-usually an antibody-that recognizes the target either directly or through an appended affinity tag, allowing subsequent characterization of the complex. Here, we discuss approaches and considerations for purifying endogenous yeast protein complexes by affinity capture. PMID:27371601

  18. Shark Tagging Activities.

    Science.gov (United States)

    Current: The Journal of Marine Education, 1998

    1998-01-01

    In this group activity, children learn about the purpose of tagging and how scientists tag a shark. Using a cut-out of a shark, students identify, measure, record data, read coordinates, and tag a shark. Includes introductory information about the purpose of tagging and the procedure, a data sheet showing original tagging data from Tampa Bay, and…

  19. High-Throughput Melanin-Binding Affinity and In Silico Methods to Aid in the Prediction of Drug Exposure in Ocular Tissue.

    Science.gov (United States)

    Reilly, John; Williams, Sarah L; Forster, Cornelia J; Kansara, Viral; End, Peter; Serrano-Wu, Michael H

    2015-12-01

    Drugs possessing the ability to bind to melanin-rich tissue, such as the eye, are linked with higher ocular exposure, and therefore have the potential to affect the efficacy and safety profiles of therapeutics. A high-throughput melanin chromatographic affinity assay has been developed and validated, which has allowed the rapid melanin affinity assessment for a large number of compounds. Melanin affinity of compounds can be quickly assigned as low, medium, or high melanin binders. A high-throughput chromatographic method has been developed and fully validated to assess melanin affinity of pharmaceuticals and has been useful in predicting ocular tissue distribution in vivo studies. The high-throughput experimental approach has also allowed for a specific training set of 263 molecules for a quantitative structure-affinity relationships (QSAR) method to be developed, which has also been shown to be a predictor of ocular tissue exposure. Previous studies have reported the development of in silico QSAR models based on training sets of relatively small and mostly similar compounds; this model covers a broader range of melanin-binding affinities than what has been previously published and identified several physiochemical descriptors to be considered in the design of compounds where melanin-binding modulation is desired.

  20. Fast Modeling of Binding Affinities by Means of Superposing Significant Interaction Rules (SSIR Method

    Directory of Open Access Journals (Sweden)

    Emili Besalú

    2016-05-01

    Full Text Available The Superposing Significant Interaction Rules (SSIR method is described. It is a general combinatorial and symbolic procedure able to rank compounds belonging to combinatorial analogue series. The procedure generates structure-activity relationship (SAR models and also serves as an inverse SAR tool. The method is fast and can deal with large databases. SSIR operates from statistical significances calculated from the available library of compounds and according to the previously attached molecular labels of interest or non-interest. The required symbolic codification allows dealing with almost any combinatorial data set, even in a confidential manner, if desired. The application example categorizes molecules as binding or non-binding, and consensus ranking SAR models are generated from training and two distinct cross-validation methods: leave-one-out and balanced leave-two-out (BL2O, the latter being suited for the treatment of binary properties.

  1. A method for the chemical modification of polychlorinated biphenyls for improved affinity towards noble metal surfaces

    DEFF Research Database (Denmark)

    2015-01-01

    The present application discloses a method for the modification and analysis of a field sample suspected of containing contaminant(s) like polychlorinated biphenyls (PCBs). The invention also relates to a corresponding kit for the modification of samples suspected of containing such contaminant(s)....

  2. A comparison of protein kinases inhibitor screening methods using both enzymatic activity and binding affinity determination

    DEFF Research Database (Denmark)

    Rudolf, Amalie Frederikke; Skovgaard, Tine; Knapp, Stefan;

    2014-01-01

    Binding assays are increasingly used as a screening method for protein kinase inhibitors; however, as yet only a weak correlation with enzymatic activity-based assays has been demonstrated. We show that the correlation between the two types of assays can be improved using more precise screening...

  3. Restriction site extension PCR: a novel method for high-throughput characterization of tagged DNA fragments and genome walking.

    Directory of Open Access Journals (Sweden)

    Jiabing Ji

    Full Text Available BACKGROUND: Insertion mutant isolation and characterization are extremely valuable for linking genes to physiological function. Once an insertion mutant phenotype is identified, the challenge is to isolate the responsible gene. Multiple strategies have been employed to isolate unknown genomic DNA that flanks mutagenic insertions, however, all these methods suffer from limitations due to inefficient ligation steps, inclusion of restriction sites within the target DNA, and non-specific product generation. These limitations become close to insurmountable when the goal is to identify insertion sites in a high throughput manner. METHODOLOGY/PRINCIPAL FINDINGS: We designed a novel strategy called Restriction Site Extension PCR (RSE-PCR to efficiently conduct large-scale isolation of unknown genomic DNA fragments linked to DNA insertions. The strategy is a modified adaptor-mediated PCR without ligation. An adapter, with complementarity to the 3' overhang of the endonuclease (KpnI, NsiI, PstI, or SacI restricted DNA fragments, extends the 3' end of the DNA fragments in the first cycle of the primary RSE-PCR. During subsequent PCR cycles and a second semi-nested PCR (secondary RSE-PCR, touchdown and two-step PCR are combined to increase the amplification specificity of target fragments. The efficiency and specificity was demonstrated in our characterization of 37 tex mutants of Arabidopsis. All the steps of RSE-PCR can be executed in a 96 well PCR plate. Finally, RSE-PCR serves as a successful alternative to Genome Walker as demonstrated by gene isolation from maize, a plant with a more complex genome than Arabidopsis. CONCLUSIONS/SIGNIFICANCE: RSE-PCR has high potential application in identifying tagged (T-DNA or transposon sequence or walking from known DNA toward unknown regions in large-genome plants, with likely application in other organisms as well.

  4. The biological activity of a recombinantly expressed (His)(6)-tagged peanut allergen (rAra h 1) is unaffected by endotoxin removal

    DEFF Research Database (Denmark)

    Jensen, Louise Bjerremann; Torp, Anna Maria; Andersen, Sven Bode;

    2008-01-01

    The application of recombinant (His)(6)-tagged proteins in cell culture assays is associated with problems due to lipopolysaccharide (LPS) contamination. LPS stimulates cells of the immune system, thereby masking antigen-specific activation of T cells. Due to the affinity of LPS for histidine...... it is associated with difficulties to remove LPS from recombinant (His)(6)-tagged proteins. Here we describe that the Triton X-114 phase separation method can be used to remove LPS from (His)(6)-tagged proteins and that the recombinant proteins retain their biological activity....

  5. Image registration for recovering affine transformation using Nelder Mead Simplex method for optimization.

    Directory of Open Access Journals (Sweden)

    Mehfuza Holia

    2009-11-01

    Full Text Available In computer vision system sets of data acquired by sampling of the same sceneor object at different times or from different perspectives, will be in differentcoordinate systems. Image registration is the process of transforming thedifferent sets of data into one coordinate system. Registration is necessaryin order to be able to compare or integrate the data obtained from differentmeasurements such as different view points, different times, different sensorsetc. Image Registration is an important problem and a fundamental task in imageprocessing technique. This paper presents an algorithm for recovering translationparameter from two images that differ by Rotation, Scaling, Transformation andRotation-scale-Translation (RST also known as similarity transformation. It is atransformation expressed as a pixel mapping function that maps a referenceimage into a pattern image. The images having rotational, scaling, translationdifferences are registered using correlation with Nelder-mead method for functionminimization. The algorithm finds the correlation between original image andsensed images. It applies the transformation parameters on sensed images sothat maximum correlation between original image and sensed images areachieved. Simulation results (Using Matlab on images show the Performancesof the method.

  6. Study of the interactions between fluoroquinolones and human serum albumin by affinity capillary electrophoresis and fluorescence method

    Energy Technology Data Exchange (ETDEWEB)

    Zhang Liwei; Wang Kun [Beijing National Laboratory for Molecular Sciences (BNLMS), College of Chemistry, Peking University, Beijing 100871 (China); Zhang Xinxiang [Beijing National Laboratory for Molecular Sciences (BNLMS), College of Chemistry, Peking University, Beijing 100871 (China)], E-mail: zxx@pku.edu.cn

    2007-11-05

    The interactions between fluoroquinolones and human serum albumin (HSA) were investigated by affinity capillary electrophoresis (ACE) and fluorescence quenching technique. Based on the efficient separation of several fluoroquinolones using a simple phosphate buffer, the binding constants of fluoroquinolones with HSA were determined simultaneously during one set of electrophoresis by ACE method. The thermodynamic parameters were obtained from data at different temperatures, and the negative {delta}H and {delta}S values showed that both hydrogen bonds and van der Waals interaction played major roles in the binding of fluoroquinolones to HSA. The interactions were also studied by fluorescence quenching technique. The results of fluorescence titration revealed that fluoroquinolones had the strong ability to quenching the intrinsic fluorescence of HSA through the static quenching procedure. The binding site number n, apparent binding constant K{sub b} and the Stern-Volmer quenching constant K{sub sv} were determined. The thermodynamic parameters were also studied by fluorescence method, and the results were consonant with that of ACE.

  7. Fluorinated carbon tag derivatization combined with fluorous solid-phase extraction: a new method for the highly sensitive and selective mass spectrometric analysis of glycans.

    Science.gov (United States)

    Li, Lulu; Jiao, Jing; Cai, Yan; Zhang, Ying; Lu, Haojie

    2015-01-01

    The sensitive and specific detection of glycans via mass spectrometry (MS) remains a significant challenge due to their low abundance in complex biological mixtures, inherent lack of hydrophobicity, and suppression by other, more abundant biological molecules (proteins/peptides) or contaminants. A new strategy for the sensitive and selective MS analysis of glycans based on fluorous chemistry is reported. Glycan reducing ends were derivatized with a hydrophobic fluorinated carbon tag, increasing glycan ionization efficiency during MS by more than an order of magnitude. More importantly, the fluorinated carbon tag enabled efficient fluorous solid-phase extraction (FSPE) to specifically enrich the glycans from contaminated solutions and protein mixtures. Finally, we successfully analyzed the N-glycome in human serum using this new method. PMID:25884104

  8. b-tagging in DELPHI at LEP

    CERN Document Server

    Abdallah, J; Adam, W; Adye, T; Adzic, P; Albrecht, T; Alderweireld, T; Alemany-Fernandez, R; Allmendinger, T; Allport, P P; Almehed, S; Amaldi, Ugo; Amapane, N; Amato, S; Anashkin, E; Andreazza, A; Andringa, S; Anjos, N; Antilogus, P; Apel, W D; Arnoud, Y; Ask, S; Åsman, B; Augustin, J E; Augustinus, A; Baillon, Paul; Ballestrero, A; Bambade, P; Barbier, R; Bardin, Dimitri Yuri; Barker, G; Baroncelli, A; Bates, M; Battaglia, Marco; Baubillier, M; Becks, K H; Begalli, M; Behrmann, A; Benekos, N C; Benvenuti, Alberto C; Bérat, C; Berggren, M; Berntzon, L; Bertrand, D; Besançon, M; Besson, N; Bibby, J; Biffi, P; Bloch, D; Blom, M; Bonesini, M; Boonekamp, M; Booth, P S L; Borisov, G; Botner, O; Bouquet, B; Bowcock, T J V; Boyko, I; Bracko, M; Branchini, P; Brenner, R; Brodet, E; Brückman, P; Brunet, J M; Bugge, L; Buschmann, P; Caccia, M; Calvi, M; Camporesi, T; Canale, V; Carena, F; Castro, N; Cavallo, F R; Chabaud, V; Chapkin, M M; Charpentier, P; Checchia, P; Chierici, R; Shlyapnikov, P; Chudoba, J; Chung, S U; Cieslik, K; Collins, P; Contri, R; Cosme, G; Cossutti, F; Costa, M J; Couchot, F; Crawley, B; Crennell, D J; Cuevas-Maestro, J; D'Almagne, B; D'Hondt, J; Dalmau, J; Da Silva, T; Da Silva, W; Della Ricca, G; De Angelis, A; de Boer, Wim; De Clercq, C; De Lotto, B; De Maria, N; De Min, A; De Paula, L S; Di Ciaccio, Lucia; Dijkstra, H; Di Simone, A; Doroba, K; Drees, J; Dris, M; Eigen, G; Ekelöf, T J C; Ellert, M; Elsing, M; Espirito-Santo, M C; Fanourakis, G K; Fassouliotis, D; Feindt, M; Fernández, J; Ferrer, A; Ferro, F; Flagmeyer, U; Föth, H; Fokitis, E; Fulda-Quenzer, F; Fuster, J A; Gandelman, M; García, C; Gavillet, P; Gazis, E N; Geralis, T; Gokieli, R; Golob, B; Gómez-Cadenas, J J; Gómez-Ceballos, G; Gonçalves, P; Graziani, E; Grosdidier, G; Grzelak, K; Guy, J; Haag, C; Hallgren, A; Hamacher, K; Hamilton, K; Hansen, J; Haug, S; Hauler, F; Hedberg, V; Hennecke, M; Hernando, J A; Herr, H; Heuser, J M; Holmgren, S O; Holt, P J; Houlden, M A; Hultqvist, K; Jackson, J N; Jalocha, P; Jarlskog, C; Jarlskog, G; Jarry, P; Jeans, D; Johansson, E K; Johansson, P D; Jonsson, P; Joram, C; Jungermann, L; Kapusta, F; Karlsson, M; Katsanevas, S; Katsoufis, E C; Keränen, R; Kernel, G; Kersevan, Borut P; Kiiskinen, A P; King, B T; Kjaer, N J; Kluit, P; Kokkinias, P; Kourkoumelis, C; Kuznetsov, O; Krumshtein, Z; Kucharczyk, M; Kucewicz, W; Kurowska, J; Lamsa, J; Leder, G; Ledroit, F; Leinonen, L; Leitner, R; Lemonne, J; Lepeltier, V; Lesiak, T; Liebig, W; Liko, D; Lipniacka, A; Lopes, J H; López, J M; Loukas, D; Lutz, P; Lyons, L; MacNaughton, J; Malek, A; Maltezos, S; Mandl, F; Marco, J; Marco, R; Maréchal, B; Margoni, M; Marin, J C; Mariotti, C; Markou, A; Martínez-Rivero, C; Martínez-Vidal, F; Masik, J; Mastroyiannopoulos, N; Matorras, F; Matteuzzi, C; Mazzucato, F; Mazzucato, M; McNulty, R; Meroni, C; Meyer, W T; Migliore, E; Mitaroff, W A; Mjörnmark, U; Moa, T; Moch, M; Mönig, K; Monge, R; Montenegro, J; Moraes, D; Moreno, S; Morettini, P; Müller, U; Münich, K; Mulders, M; Mundim, L; Murray, W; Muryn, B; Myatt, Gerald; Myklebust, T; Nassiakou, M; Navarria, Francesco Luigi; Nawrocki, K; Nicolaidou, R; Niezurawski, P; Nikolenko, M; Nomerotski, A; Norman, A; Nygren, A; Oblakowska-Mucha, A; Obraztsov, V F; Olshevskii, A G; Onofre, A; Orava, Risto; Österberg, K; Ouraou, A; Oyanguren, A; Paganoni, M; Paiano, S; Palacios, J P; Palka, H; Papadopoulou, T D; Pape, L; Parkes, C; Parodi, F; Parzefall, U; Passeri, A; Passon, O; Peralta, L; Perepelitsa, V F; Perrotta, A; Petrolini, A; Piedra, J; Pieri, L; Pierre, F; Pimenta, M; Piotto, E; Podobnik, T; Poireau, V; Pol, M E; Polok, G; Poropat, P; Pozdnyakov, V; Pukhaeva, N; Pullia, Antonio; Rames, J; Ramler, L; Read, A; Rebecchi, P; Rehn, J; Reid, D; Reinhardt, R; Renton, P B; Richard, F; Rídky, J; Rivero, M; Rodríguez, D; Romero, A; Ronchese, P; Rosenberg, E I; Roudeau, Patrick; Rovelli, T; Ruhlmann-Kleider, V; Ryabtchikov, D; Sadovskii, A; Salmi, L; Salt, J; Savoy-Navarro, A; Schwickerath, U; Segar, A; Sekulin, R L; Siebel, M; Sissakian, A N; Smadja, G; Smirnova, O G; Sokolov, A; Sopczak, A; Sosnowski, R; Spassoff, Tz; Stanitzki, M; Stavitski, I; Stocchi, A; Strauss, J; Stugu, B; Szczekowski, M; Szeptycka, M; Szumlak, T; Tabarelli de Fatis, T; Taffard, A C; Tegenfeldt, F; Timmermans, J; Tinti, N; Tkatchev, L G; Tobin, M; Todorovova, S; Tomaradze, A G; Tomé, B; Tonazzo, A; Tortosa, P; Travnicek, P; Treille, D; Trischuk, W; Tristram, G; Trochimczuk, M; Troncon, C; Turluer, M L; Tyapkin, I A; Tyapkin, P; Tyndel, M; Tzamarias, S; Uvarov, V; Valenti, G; van Dam, P; Van Eldik, J; Van Lysebetten, A; Van Remortel, N; Van Vulpen, I B; Vegni, G; Veloso, F; Venus, W A; Verbeure, F; Verdier, P; Verzi, V; Vilanova, D; Vitale, L; Vrba, V; Wahlen, H; Washbrook, A J; Weilhammer, Peter; Weiser, C; Wicke, D; Wickens, J H; Wilkinson, G; Winter, M; Witek, M; Yushchenko, O P; Zalewska-Bak, A; Zalewski, Piotr; Zavrtanik, D; Zimin, N I; Zinchenko, A I; Zupan, M

    2004-01-01

    The standard method used for tagging b-hadrons in the DELPHI experiment at the CERN LEP Collider is discussed in detail. The main ingredient of b-tagging is the impact parameters of tracks, which relies mostly on the vertex detector. Additional information, such as the mass of particles associated to a secondary vertex, significantly improves the selection efficiency and the background suppression. The paper describes various discriminating variables used for the tagging and the procedure of their combination. In addition, applications of b-tagging to some physics analyses, which depend crucially on the performance and reliability of b-tagging, are described briefly.

  9. LOMA: A fast method to generate efficient tagged-random primers despite amplification bias of random PCR on pathogens

    Directory of Open Access Journals (Sweden)

    Lee Wah

    2008-09-01

    Full Text Available Abstract Background Pathogen detection using DNA microarrays has the potential to become a fast and comprehensive diagnostics tool. However, since pathogen detection chips currently utilize random primers rather than specific primers for the RT-PCR step, bias inherent in random PCR amplification becomes a serious problem that causes large inaccuracies in hybridization signals. Results In this paper, we study how the efficiency of random PCR amplification affects hybridization signals. We describe a model that predicts the amplification efficiency of a given random primer on a target viral genome. The prediction allows us to filter false-negative probes of the genome that lie in regions of poor random PCR amplification and improves the accuracy of pathogen detection. Subsequently, we propose LOMA, an algorithm to generate random primers that have good amplification efficiency. Wet-lab validation showed that the generated random primers improve the amplification efficiency significantly. Conclusion The blind use of a random primer with attached universal tag (random-tagged primer in a PCR reaction on a pathogen sample may not lead to a successful amplification. Thus, the design of random-tagged primers is an important consideration when performing PCR.

  10. Affinity Chromatography Method for Determination of Binding of Drugs to Melanin and Evaluation of Side Effect Potential of Antipsychotic Agents

    OpenAIRE

    Marszałł, Michał Piotr; Proszowska, Anna; Buciński, Adam; Kaliszan, Roman

    2014-01-01

    The extrapyramidal side effect parameters of typical and atypical antypsychotics were correlated with affinity chromatographic data determined on the melanin-based column. The chromatographic study was performed according to the hypothesis that extrapyramidal symptoms (EPS) as side effects of the use of antipsychotic drugs at clinically effective doses are correlated to the affinity of these drugs to neuromelanin. For that aim the polymerization product of L-DOPA (melanin) was immobilized ont...

  11. A Methodology for Simultaneous Fluorogenic Derivatization and Boronate Affinity Enrichment of 3-Nitrotyrosine Containing Peptides

    OpenAIRE

    Dremina, Elena S.; Li, Xiaobao; Galeva, Nadezhda A.; Sharov, Victor S.; Stobaugh, John F.; Schöneich, Christian

    2011-01-01

    We synthesized and characterized a new tagging reagent, (3R,4S)-1-(4-(aminomethyl)phenylsulfonyl)pyrrolidine-3,4-diol (APPD), for the selective fluorogenic derivatization of 3-nitrotyrosine (3-NT) residues in peptides (after reduction to 3-aminotyrosine) and affinity enrichment. The synthetic 3-NT-containing peptide, FSAY(3-NO2)LER, was employed as a model for method validation. Further, this derivatization protocol was successfully tested for analysis of 3-NT-containing proteins exposed to p...

  12. Toward a Universal Method for Preparing Molecularly Imprinted Polymer Nanoparticles with Antibody-like Affinity for Proteins.

    Science.gov (United States)

    Xu, Jingjing; Ambrosini, Serena; Tamahkar, Emel; Rossi, Claire; Haupt, Karsten; Tse Sum Bui, Bernadette

    2016-01-11

    We describe a potentially universal, simple and cheap method to prepare water-compatible molecularly imprinted polymer nanoparticles (MIP-NPs) as synthetic antibodies against proteins. The strategy is based on a solid phase synthesis approach where glass beads (GBs) are functionalized with a metal chelate, acting as a general affinity ligand to attract surface-bound histidines present on proteins. This configuration enables an oriented immobilization of the proteins, upon which thermoresponsive MIP-NPs are synthesized. The GBs play the role of both a reactor and a separation column since, after synthesis, the MIP-NPs are released from the support by a simple temperature change, resulting in protein-free polymers. The resulting MIP-NPs are endowed with improved binding site homogeneity, since the binding sites have the same orientation. Moreover, they are stable (no aggregation) in a buffer solution for prolonged storage time and exhibit apparent dissociation constants in the nanomolar range, with little or no cross-reactivity toward other proteins. PMID:26644006

  13. Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers

    DEFF Research Database (Denmark)

    Lundegaard, Claus; Lund, Ole; Nielsen, Morten

    2008-01-01

    Several accurate prediction systems have been developed for prediction of class I major histocompatibility complex (MHC):peptide binding. Most of these are trained on binding affinity data of primarily 9mer peptides. Here, we show how prediction methods trained on 9mer data can be used for accurate...

  14. Microplanktonic community structure in a coastal system relative to a Phaeocystis bloom inferred from morphological and tag pyrosequencing methods.

    Directory of Open Access Journals (Sweden)

    Sébastien Monchy

    Full Text Available BACKGROUND: Massive phytoplankton blooms, like the recurrent Phaeocystis proliferation observed every year in the Eastern English Channel (EEC, have a significant influence on the overall planktonic community structure and their food web dynamics. As well as being an important area for local fisheries, the EEC is an ideal ecosystem for work on microbial diversity. This is because, although its environmental context is relatively complex, it is reasonably well understood due to several years of monitoring and morphological observations of its planktonic organisms. The objective of our study was to better understand the under-explored microbial eukaryotic diversity relative to the Phaeocystis bloom. METHODOLOGY AND PRINCIPAL FINDINGS: The community structure of microplankton (diatoms, haptophytes, ciliates and dinoflagellates was studied through morphological observations and tag pyrosequencing. During the annual Phaeocystis spring bloom, the phytoplankton biomass increased by 34-fold, while the microzooplankton biomass showed a 4-fold increase, representing on average about 4.6% of the biomass of their phytoplankton prey. Tag pyrosequencing unveiled an extensive diversity of Gymnodiniaceae, with G. spirale and G. fusiformis representing the most abundant reads. An extended diversity of Phaeocystales, with partial 18S rDNA genes sequence identity as low as 85% was found, with taxa corresponding to P. globosa, but also to unknown Phaeocystaceae. CONCLUSIONS: Morphological analyses and pyrosequencing were generally in accordance with capturing frequency shifts of abundant taxa. Tag pyrosequencing allowed highlighting the maintenance of microplankton diversity during the Phaeocystis bloom and the increase of the taxa presenting low number of reads (minor taxa along with the dominant ones in response to biotic and/or abiotic changing conditions. Although molecular approaches have enhanced our perception on diversity, it has come to light that the

  15. Application of a constrained regularization method to extraction of affinity distributions: proton and metal binding to humic substances.

    Science.gov (United States)

    Orsetti, Silvia; Andrade, Estela María; Molina, Fernando V

    2009-08-15

    The binding of proton and metal cations to humic substances has been analyzed with a regularized fitting procedure (using the CONTIN software package) to extract conditional affinity distributions, valid at a given ionic strength, from binding (titration) curves. The procedure was previously tested with simulated titration curves using a simple bi-Gaussian model, the NICA-Donnan model, and the Stockholm humic model. Application to literature data for proton binding shows that in several cases the affinity distribution found is bimodal (carboxylic and phenolic sites) as usually assumed; however in other cases, specially for fulvic acids, a trimodal distribution is clearly discerned, with a smaller peak between the two noted above attributed to the presence of vicinal carboxylic groups. The analysis of metal binding curves has been performed in a few cases where the available data could be reliably processed, separating the proton affinity distribution and obtaining the conditional affinity spectra. For Cd(II) and Pb(II) a bimodal distribution is found, attributed in principle to mono- and bidentate binding, based on spectroscopic data. In the case of Cu(II), a more complex affinity distribution is found showing 3-4 peaks; this is consistent with spectroscopic studies, where different binding modes, up to tetradentate, have been observed. PMID:19477457

  16. 利用生物信息学方法挑选MCPH1基因标签单核苷酸多态性(tag-SNPs)位点%Bioinformatics methods for selecting the MCHPH1 gene tag single nucleotide polymorphisms(tag-SNPs)sites

    Institute of Scientific and Technical Information of China (English)

    刘跃亮; 曾照芳

    2011-01-01

    目的:为考察汉族人群MCPH1基因与原发性小头畸形病的关系,利用生物信息学方法挑选汉族人群中的MCPH1基因标签单核苷酸多态性(tag-SNPs)位点。方法:利用NCBI数据库,确定MCPHl基因研究范围:利用Hapmap数据库获取汉族人群的MCPHl基因SNPs数据;应用Haploview4.2对MCPH1基因进行连锁不平衡分析;在D′值95%可信区间内构建单倍域(haplotype block):根据单倍域内SNPs之间的r2值和LOD值,挑选标签SNP。结果:在汉族人群中,MCPH1全基因范围内共构建35个单倍域,挑选出122个标签SNPs,确定了各个单倍域内的代表单倍型。结论:汉族人群MCPH1基因的122个SNPs位点是较具代表性的标志性位点,可被选为标签SNPs,并作为汉族人群MCPHl基因与原发性小头畸形病的关联研究。%Objective:Han population for the study MCPH1 primary microcephaly genes and the relationship between disease,the use of bioinformatics methods for selecting the Han population MCPH1 gene tag single nucleotide polymorphisms(tag-SNPs) sites.Methods:Using NCBI databases,to determine the scope of genetic research MCPH1;use Hapmap database for the Han population MCPH1 gene SNPs data;application Haploview4.2 MCPH1 gene on linkage disequilibrium analysis;in the D'value of the 95% confidence interval constructed single-fold domain(haplotype block);based on the single-fold within the r2 values between SNPs and the LOD value,tag SNP selection.Results:In the Han population,MCPH 1 genome were constructed within the domain of 35 haplotypes,selected 122 tag SNPs,identified representatives of the various haplotypes within haplotype.Conclusion:MCPH1 gene in Han population of 122 SNPs loci are more representative of the landmark site,can be selected as tag SNPs,Han population MCPH1 favor of primary microcephaly genes and disease association studies.

  17. Gas tagging system development in Japan

    International Nuclear Information System (INIS)

    The Gas tagging method has been considered to be most desirable for a failed fuel location system for the fast breeder reactor, regarding the component reduction in the reactor vessel and rapid location during reactor operation. The gas tagging system has been designed by referring to R and D results obtained in Japan and other countries. The designed system is comprised of tag gas filling pins, cover gas sampling system, tag gas recovery and enrichment system, tag gas analyzer and system control and data handling computers. The main specifications for this system have been decided as follows; 1) Main function is location of failed fuels in core and a part of blanket region, 2) Identification capability is each subassembly, 3) Time for identification is within a few days, 4) Continuous operation with automatic start at fuel failure, 5) Detection sensitivity must cover both gas leak and pin burst. In designing the gas tagging system, the following R and D items were selected; 1) System design study, 2) Tag gas capsule development, 3) Modeling the tag gas behavior in reactor primary cooling system, 4) Tag gas recovery and enrichment system, 5) Computer code development for tag gas isotope ratio change estimation. Details of the Japanese gas tagging system development appear in this paper. (author)

  18. A novel method to isolate protein N-terminal peptides from proteome samples using sulfydryl tagging and gold-nanoparticle-based depletion.

    Science.gov (United States)

    Li, Lanting; Wu, Runqing; Yan, Guoquan; Gao, Mingxia; Deng, Chunhui; Zhang, Xiangmin

    2016-01-01

    A novel method to isolate global N-termini using sulfydryl tagging and gold-nanoparticle-based depletion (STagAu method) is presented. The N-terminal and lysine amino groups were first completely dimethylated at the protein level, after which the proteins were digested. The newly generated internal peptides were tagged with sulfydryl by Traut's reagent through digested N-terminal amines in yields of 96%. The resulting sulfydryl peptides were depleted through binding onto nano gold composite materials. The Au-S bond is stable and widely used in materials science. Nano gold composite materials showed nearly complete depletion of sulfydryl peptides. A set of the acetylated and dimethylated N-terminal peptides were analyzed by liquid chromatography-tandem mass spectrometry. This method was demonstrated to be an efficient N-terminus enrichment method because of the use of an effective derivatization reaction, in combination with robust and relative easy to implement Au-S coupling. We identified 632 N-terminal peptides from 386 proteins in a mouse liver sample. The STagAu approach presented is therefore a facile and efficient method for mass-spectrometry-based analysis of proteome N-termini or protease-generated cleavage products.

  19. Preserving Privacy in Social Tagging

    Directory of Open Access Journals (Sweden)

    Pradnya M. Deshmane

    2015-12-01

    Full Text Available Our system works on the collaborative tagging technique which is very famous in online system or social networking system. This system works on the bottle neck area of some previous tagging method. Our system contains the module that extends the tagging functionality capacity and features. Our system is having one policy layer that analyzes the collaborative tagging before it is into action. Our system required this layer to consider user preferences, deliberately defining sources on the basis of tag categories associated with them, and, some other parameters considering their trust worthiness. Along with this our systems try to preserve the user’s sensitive information which is predictable from his feedback and comments. Hence our system also provides one privacy protection layer. Along with this there is an issue in some social networking sites like facebook. These social networking sites are using user’s profile to analysis and extract behavioral aspect of user. This type of profile sometimes may contain sensitive information. Our system avoids misuse of such profile by using technology namely tag suppression. Hence our system first filter tags using our policy layer and then for user interest it uses our privacy layer and finally from user interest respective tag is shared. We contribute one phase using which user can view social network status / reputation of particular user. Based on this online social network status / reputation of particular user we can take decision whether to allow such user or not. It is completely preventive approach that helps user to take decision whether to block particular user or not.

  20. Affinity Induced Surface Functionalization of Liposomes Using Cu-Free Click Chemistry.

    Science.gov (United States)

    Bak, Martin; Jølck, Rasmus I; Eliasen, Rasmus; Andresen, Thomas L

    2016-07-20

    Functionalization of nanoparticles is a key element for improving specificity of drug delivery systems toward diseased tissue or cells. In the current study we report a highly efficient and chemoselective method for post-functionalization of liposomes with biomacromolecules, which equally well can be used for functionalization of other nanoparticles or solid surfaces. The method exploits a synergistic effect of having both affinity and covalent anchoring tags on the surface of the liposome. This was achieved by synthesizing a peptide linker system that uses Cu-free strain-promoted click chemistry in combination with histidine affinity tags. The investigation of post-functionalization of PEGylated liposomes was performed with a cyclic RGDfE peptide. By exploring both affinity and covalent tags a 98 ± 2.0% coupling efficiency was achieved, even a diluted system showed a coupling efficiency of 87 ± 0.2%. The reaction kinetics and overall yield were quantified by HPLC. The results presented here open new possibilities for constructing complex nanostructures and functionalized surfaces. PMID:27269516

  1. TagCombine:Recommending Tags to Contents in Software Information Sites

    Institute of Scientific and Technical Information of China (English)

    王新宇; 夏鑫; David Lo

    2015-01-01

    Nowadays, software engineers use a variety of online media to search and become informed of new and interesting technologies, and to learn from and help one another. We refer to these kinds of online media which help software engineers improve their performance in software development, maintenance, and test processes as software information sites. In this paper, we propose TagCombine, an automatic tag recommendation method which analyzes objects in software information sites. TagCombine has three different components: 1) multi-label ranking component which considers tag recommendation as a multi-label learning problem; 2) similarity-based ranking component which recommends tags from similar objects; 3) tag-term based ranking component which considers the relationship between different terms and tags, and recommends tags after analyzing the terms in the objects. We evaluate TagCombine on four software information sites, Ask Different, Ask Ubuntu, Freecode, and Stack Overflow. On averaging across the four projects, TagCombine achieves recall@5 and recall@10 to 0.619 8 and 0.762 5 respectively, which improves TagRec proposed by Al-Kofahi et al. by 14.56% and 10.55% respectively, and the tag recommendation method proposed by Zangerle et al. by 12.08% and 8.16% respectively.

  2. A mix-and-read drop-based in vitro two-hybrid method for screening high-affinity peptide binders.

    Science.gov (United States)

    Cui, Naiwen; Zhang, Huidan; Schneider, Nils; Tao, Ye; Asahara, Haruichi; Sun, Zhiyi; Cai, Yamei; Koehler, Stephan A; de Greef, Tom F A; Abbaspourrad, Alireza; Weitz, David A; Chong, Shaorong

    2016-01-01

    Drop-based microfluidics have recently become a novel tool by providing a stable linkage between phenotype and genotype for high throughput screening. However, use of drop-based microfluidics for screening high-affinity peptide binders has not been demonstrated due to the lack of a sensitive functional assay that can detect single DNA molecules in drops. To address this sensitivity issue, we introduced in vitro two-hybrid system (IVT2H) into microfluidic drops and developed a streamlined mix-and-read drop-IVT2H method to screen a random DNA library. Drop-IVT2H was based on the correlation between the binding affinity of two interacting protein domains and transcriptional activation of a fluorescent reporter. A DNA library encoding potential peptide binders was encapsulated with IVT2H such that single DNA molecules were distributed in individual drops. We validated drop-IVT2H by screening a three-random-residue library derived from a high-affinity MDM2 inhibitor PMI. The current drop-IVT2H platform is ideally suited for affinity screening of small-to-medium-sized libraries (10(3)-10(6)). It can obtain hits within a single day while consuming minimal amounts of reagents. Drop-IVT2H simplifies and accelerates the drop-based microfluidics workflow for screening random DNA libraries, and represents a novel alternative method for protein engineering and in vitro directed protein evolution. PMID:26940078

  3. Methodologies for Improved Tag Cloud Generation with Clustering

    DEFF Research Database (Denmark)

    Leginus, Martin; Dolog, Peter; Lage, Ricardo Gomes;

    2012-01-01

    Tag clouds are useful means for navigation in the social web systems. Usually the systems implement the tag cloud generation based on tag popularity which is not always the best method. In this paper we propose methodologies on how to combine clustering into the tag cloud generation to improve...... coverage and overlap. We study several clustering algorithms to generate tag clouds. We show that by extending cloud generation based on tag popularity with clustering we slightly improve coverage. We also show that if the cloud is generated by clustering independently of the tag popularity baseline we...

  4. Objective evaluation of methods to track motion from clinical cardiac-gated tagged MRI without the use of a gold standard

    Science.gov (United States)

    Parages, Felipe M.; Denney, Thomas S.; Brankov, Jovan G.

    2015-03-01

    Cardiac-gated MRI is widely used for the task of measuring parameters related to heart motion. More specifically, gated tagged MRI is the preferred modality to estimate local deformation (strain) and rotational motion (twist) of myocardial tissue. Many methods have been proposed to estimate cardiac motion from gated MRI sequences. However, when dealing with clinical data, evaluation of these methods is problematic due to the absence of gold-standards for cardiac motion. To overcome that, a linear regression scheme known as regression-without-truth (RWT) was proposed in the past. RWT uses priors to model the distribution of true values, thus enabling us to assess image-analysis algorithms without knowledge of the ground-truth. Furthermore, it allows one to rank methods by means of an objective figure-of-merit γ (i.e. precision). In this work we apply RWT to compare the performance of several gated MRI motion-tracking methods (e.g. non-rigid registration, feature based, harmonic phase) at the task of estimating myocardial strain and left-ventricle (LV) twist, from a population of 18 clinical human cardiac-gated tagged MRI studies.

  5. Simple method for Shiga toxin 2e purification by affinity chromatography via binding to the divinyl sulfone group.

    Directory of Open Access Journals (Sweden)

    Hideyuki Arimitsu

    Full Text Available Here we describe a simple affinity purification method for Shiga toxin 2e (Stx2e, a major causative factor of edema disease in swine. Escherichia coli strain MV1184 transformed with the expression plasmid pBSK-Stx2e produced Stx2e when cultivated in CAYE broth containing lincomycin. Stx2e bound to commercial D-galactose gel, containing α-D-galactose immobilized on agarose resin via a divinyl sulfone linker, and was eluted with phosphate-buffered saline containing 4.5 M MgCl2. A small amount of Stx2e bound to another commercial α-galactose-immobilized agarose resin, but not to β-galactose-immobilized resin. In addition, Stx2e bound to thiophilic adsorbent resin containing β-mercaptoethanol immobilized on agarose resin via a divinyl sulfone, and was purified in the same manner as from D-galactose gel, but the Stx2e sample contained some contamination. These results indicate that Stx2e bound to D-galactose gel mainly through the divinyl sulfone group on the resin and to a lesser extent through α-D-galactose. With these methods, the yields of Stx2e and attenuated mutant Stx2e (mStx2e from 1 L of culture were approximately 36 mg and 27.7 mg, respectively, and the binding capacity of the D-galactose gel and thiophilic adsorbent resin for Stx2e was at least 20 mg per 1 ml of resin. In addition, using chimeric toxins with prototype Stx2 which did not bind to thiophilic adsorbent resin and some types of mutant Stx2e and Stx2 which contained inserted mutations in the B subunits, we found that, at the least, asparagine (amino acid 17 of the B subunits was associated with Stx2e binding to the divinyl sulfone group. The mStx2e that was isolated exhibited vaccine effects in ICR mice, indicating that these methods are beneficial for large-scale preparation of Stx2e toxoid, which protects swine from edema disease.

  6. Gaussian Affine Feature Detector

    OpenAIRE

    Xu, Xiaopeng; Zhang, Xiaochun

    2011-01-01

    A new method is proposed to get image features' geometric information. Using Gaussian as an input signal, a theoretical optimal solution to calculate feature's affine shape is proposed. Based on analytic result of a feature model, the method is different from conventional iterative approaches. From the model, feature's parameters such as position, orientation, background luminance, contrast, area and aspect ratio can be extracted. Tested with synthesized and benchmark data, the method achieve...

  7. Cooperative Tagging Center (CTC)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Cooperative Tagging Center (CTC) began as the Cooperative Game Fish Tagging Program (GTP) at Woods Hole Oceanographic Institute (WHOI) in 1954. The GTP was...

  8. Satellite Tags- Hawaii EEZ

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Satellite tagging was implemented in 2013. Satellite tagging is conducted using a Dan Inject air rifle and deployment arrows designed by Wildlife Computers. Two...

  9. Gillnet Tag Program

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Certain fishery management programs require vessels to obtain gillnet tags to be used with their gillnet gear. Gillnet tag data is a collection of requests and...

  10. North Pacific Albacore Tagging

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Conventional tagging data are available from 1971 to 1996. Electronic tagging data are available from 2000 to present. The data are managed by SWFSC in Access...

  11. Using Interference to Block RFID Tags

    DEFF Research Database (Denmark)

    Krigslund, Rasmus; Popovski, Petar; Pedersen, Gert Frølund;

    We propose a novel method to block RFID tags from responding, using intentional interference. We focus on the experimental evaluation, where we impose interference on the download and uplink, respectively. The results are positive, where modulated CCI shows most effective to block a tag.......We propose a novel method to block RFID tags from responding, using intentional interference. We focus on the experimental evaluation, where we impose interference on the download and uplink, respectively. The results are positive, where modulated CCI shows most effective to block a tag....

  12. Comparative Study of Three Methods for Affinity Measurements: Capillary Electrophoresis Coupled with UV Detection and Mass Spectrometry, and Direct Infusion Mass Spectrometry

    Science.gov (United States)

    Mironov, Gleb G.; Logie, Jennifer; Okhonin, Victor; Renaud, Justin B.; Mayer, Paul M.; Berezovski, Maxim V.

    2012-07-01

    We present affinity capillary electrophoresis and mass spectrometry (ACE-MS) as a comprehensive separation technique for label-free solution-based affinity analysis. The application of ACE-MS for measuring affinity constants between eight small molecule drugs [ibuprofen, s-flurbiprofen, diclofenac, phenylbutazone, naproxen, folic acid, resveratrol, and 4,4'-(propane-1,3-diyl) dibenzoic acid] and β-cyclodextrin is described. We couple on-line ACE with MS to combine the separation and kinetic capability of ACE together with the molecular weight and structural elucidation of MS in one system. To understand the full potential of ACE-MS, we compare it with two other methods: Direct infusion mass spectrometry (DIMS) and ACE with UV detection (ACE-UV). After the evaluation, DIMS provides less reliable equilibrium dissociation constants than separation-based ACE-UV and ACE-MS, and cannot be used solely for the study of noncovalent interactions. ACE-MS determines apparent dissociation constants for all reacting small molecules in a mixture, even in cases when drugs overlap with each other during separation. The ability of ACE-MS to interact, separate, and rapidly scan through m/z can facilitate the simultaneous affinity analysis of multiple interacting pairs, potentially leading to the high-throughput screening of drug candidates.

  13. Cutaneous skin tag

    Science.gov (United States)

    Skin tag; Acrochordon; Fibroepithelial polyp ... have diabetes. They are thought to occur from skin rubbing against skin. ... The tag sticks out of the skin and may have a short, narrow stalk connecting it to the surface of the skin. Some skin tags are as long as ...

  14. Hierarchical Affinity Propagation

    CERN Document Server

    Givoni, Inmar; Frey, Brendan J

    2012-01-01

    Affinity propagation is an exemplar-based clustering algorithm that finds a set of data-points that best exemplify the data, and associates each datapoint with one exemplar. We extend affinity propagation in a principled way to solve the hierarchical clustering problem, which arises in a variety of domains including biology, sensor networks and decision making in operational research. We derive an inference algorithm that operates by propagating information up and down the hierarchy, and is efficient despite the high-order potentials required for the graphical model formulation. We demonstrate that our method outperforms greedy techniques that cluster one layer at a time. We show that on an artificial dataset designed to mimic the HIV-strain mutation dynamics, our method outperforms related methods. For real HIV sequences, where the ground truth is not available, we show our method achieves better results, in terms of the underlying objective function, and show the results correspond meaningfully to geographi...

  15. Mobile Application Partition Method Based on Tag in Cloud Environment%云环境下基于标记的移动应用划分方法

    Institute of Scientific and Technical Information of China (English)

    樊新; 高曙

    2015-01-01

    In order to solve the resource -constrained problem to mobile devices and save the energy consumption , a tag-based mobile application partition method was proposed .It is a way to partition the mobile application according to its functional structure in advance and tag the transferable application module .The abundant resources and strong ability of cloud computing technology were employed to process the information .And combining with transfer energy consumption model , it was determined whether the mobile application tag module was transferred to the cloud to remote execution or not .At last, through wireless net-work, the cloud execution results were return so as to extend equipment resources and save the energy consumption .%针对移动设备资源受限及节省其能耗的问题,提出了一种基于标记的移动应用划分方法。该方法根据移动应用功能结构对其进行划分,将可转移执行的应用模块进行标记,利用云计算丰富的资源和强大的信息处理能力,结合转移能耗模型,决定移动应用标记模块是否转移到云端远程执行,通过无线网络,返回云端执行结果,从而达到扩展移动设备资源,节省其能耗的目的。

  16. Analysis of tag-based Recommendation Performance for a Semantic Wiki

    DEFF Research Database (Denmark)

    Durao, Frederico; Dolog, Peter

    2009-01-01

    Recommendations play a very important role for revealing related topics addressed in the wikis beyond the currently viewed page. In this paper, we extend KiWi, a semantic wiki with three different recommendation approaches. The first approach is implemented as a traditional tag-based retrieval......, the second takes into account external factors such as tag popularity, tag representativeness and the affinity between user and tag and the third approach recommends pages in grouped by tag. The experiment evaluates the wiki performance in different scenarios regarding the amount of pages, tags and users...

  17. Semantic Analysis of Tag Similarity Measures in Collaborative Tagging Systems

    CERN Document Server

    Cattuto, Ciro; Hotho, Andreas; Stumme, Gerd

    2008-01-01

    Social bookmarking systems allow users to organise collections of resources on the Web in a collaborative fashion. The increasing popularity of these systems as well as first insights into their emergent semantics have made them relevant to disciplines like knowledge extraction and ontology learning. The problem of devising methods to measure the semantic relatedness between tags and characterizing it semantically is still largely open. Here we analyze three measures of tag relatedness: tag co-occurrence, cosine similarity of co-occurrence distributions, and FolkRank, an adaptation of the PageRank algorithm to folksonomies. Each measure is computed on tags from a large-scale dataset crawled from the social bookmarking system del.icio.us. To provide a semantic grounding of our findings, a connection to WordNet (a semantic lexicon for the English language) is established by mapping tags into synonym sets of WordNet, and applying there well-known metrics of semantic similarity. Our results clearly expose differe...

  18. Graph based techniques for tag cloud generation

    DEFF Research Database (Denmark)

    Leginus, Martin; Dolog, Peter; Lage, Ricardo Gomes

    2013-01-01

    Tag cloud is one of the navigation aids for exploring documents. Tag cloud also link documents through the user defined terms. We explore various graph based techniques to improve the tag cloud generation. Moreover, we introduce relevance measures based on underlying data such as ratings...... or citation counts for improved measurement of relevance of tag clouds. We show, that on the given data sets, our approach outperforms the state of the art baseline methods with respect to such relevance by 41 % on Movielens dataset and by 11 % on Bibsonomy data set....

  19. Measurement of tag confidence in user generated contents retrieval

    Science.gov (United States)

    Lee, Sihyoung; Min, Hyun-Seok; Lee, Young Bok; Ro, Yong Man

    2009-01-01

    As online image sharing services are becoming popular, the importance of correctly annotated tags is being emphasized for precise search and retrieval. Tags created by user along with user-generated contents (UGC) are often ambiguous due to the fact that some tags are highly subjective and visually unrelated to the image. They cause unwanted results to users when image search engines rely on tags. In this paper, we propose a method of measuring tag confidence so that one can differentiate confidence tags from noisy tags. The proposed tag confidence is measured from visual semantics of the image. To verify the usefulness of the proposed method, experiments were performed with UGC database from social network sites. Experimental results showed that the image retrieval performance with confidence tags was increased.

  20. Binding affinities in the SAMPL3 trypsin and host-guest blind tests estimated with the MM/PBSA and LIE methods.

    OpenAIRE

    Mikulskis, Paulius; Genheden, Samuel; Rydberg, Patrik; Sandberg, Lars; Olsen, Lars; Ryde, Ulf

    2012-01-01

    We have estimated affinities for the binding of 34 ligands to trypsin and nine guest molecules to three different hosts in the SAMPL3 blind challenge, using the MM/PBSA, MM/GBSA, LIE, continuum LIE, and Glide score methods. For the trypsin challenge, none of the methods were able to accurately predict the experimental results. For the MM/GB(PB)SA and LIE methods, the rankings were essentially random and the mean absolute deviations were much worse than a null hypothesis giving the same affini...

  1. Tag Based Audio Search Engine

    Directory of Open Access Journals (Sweden)

    Parameswaran Vellachu

    2012-03-01

    Full Text Available The volume of the music database is increasing day by day. Getting the required song as per the choice of the listener is a big challenge. Hence, it is really hard to manage this huge quantity, in terms of searching, filtering, through the music database. It is surprising to see that the audio and music industry still rely on very simplistic metadata to describe music files. However, while searching audio resource, an efficient "Tag Based Audio Search Engine" is necessary. The current research focuses on two aspects of the musical databases 1. Tag Based Semantic Annotation Generation using the tag based approach.2. An audio search engine, using which the user can retrieve the songs based on the users choice. The proposed method can be used to annotation and retrieve songs based on musical instruments used , mood of the song, theme of the song, singer, music director, artist, film director, instrument, genre or style and so on.

  2. One-step purification of twin-strep-tagged proteins and their complexes on strep-tactin resin cross-linked with bis(sulfosuccinimidyl) suberate (BS3).

    Science.gov (United States)

    Ivanov, Konstantin I; Bašić, Marta; Varjosalo, Markku; Mäkinen, Kristiina

    2014-01-01

    Affinity purification of Strep-tagged fusion proteins on resins carrying an engineered streptavidin (Strep-Tactin) has become a widely used method for isolation of protein complexes under physiological conditions. Fusion proteins containing two copies of Strep-tag II, designated twin-Strep-tag or SIII-tag, have the advantage of higher affinity for Strep-Tactin compared to those containing only a single Strep-tag, thus allowing more efficient protein purification. However, this advantage is offset by the fact that elution of twin-Strep-tagged proteins with biotin may be incomplete, leading to low protein recovery. The recovery can be dramatically improved by using denaturing elution with sodium dodecyl sulfate (SDS), but this leads to sample contamination with Strep-Tactin released from the resin, making the assay incompatible with downstream proteomic analysis. To overcome this limitation, we have developed a method whereby resin-coupled tetramer of Strep-Tactin is first stabilized by covalent cross-linking with Bis(sulfosuccinimidyl) suberate (BS3) and the resulting cross-linked resin is then used to purify target protein complexes in a single batch purification step. Efficient elution with SDS ensures good protein recovery, while the absence of contaminating Strep-Tactin allows downstream protein analysis by mass spectrometry. As a proof of concept, we describe here a protocol for purification of SIII-tagged viral protein VPg-Pro from nuclei of virus-infected N. benthamiana plants using the Strep-Tactin polymethacrylate resin cross-linked with BS3. The same protocol can be used to purify any twin-Strep-tagged protein of interest and characterize its physiological binding partners. PMID:24796313

  3. Realization of Fractal Affine Transformation

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    This paper gives the definition of fractal affine transformation and presents a specific method for its realization and its cor responding mathematical equations which are essential in fractal image construction.

  4. Production of biologically active IgG hinge-tag soluble epidermal growth factor receptors (ErbB).

    Science.gov (United States)

    Otani, Takayuki; Hashizume, Toshihiro; Nagaoka, Tadahiro; Fukuda, Tomoko; Tang, Careen K; Salomon, David S; Seno, Masaharu

    2010-03-01

    The extracellular domains (ECD) of epidermal growth factor receptors, ErbB1, 2, 3 and 4, were designed as soluble dimeric forms. Each ECD was fused to a short hinge region derived from IgG, such that the stable dimer could be formed with disulfide bridges. This hinge-tagged design minimized the molecular weight to approximately 50% of the conventional Fc-fusion design without an Fc domain of IgG. The refolded dimers could be easily analyzed and characterized by SDS-PAGE. Hinge-tagged soluble ErbBs demonstrated significant affinity for betacellulin and heregulin. The IgG hinge-tag should be a simple method to design soluble dimers that would be useful for high throughput screening of ligands, antagonists or derivatives.

  5. Tagging vs. Controlled Vocabulary

    DEFF Research Database (Denmark)

    Bogers, Toine; Petras, Vivien

    2015-01-01

    elements like core bibliographic data, controlled vocabulary terms, reviews, and tags to the retrieval performance. Our comparison is done using a test collection of over 2 million book records with information elements from Amazon, the British Library, the Library of Congress, and LibraryThing. We find...... that tags and controlled vocabulary terms do not actually outperform each other consistently, but seem to provide complementary contributions: some information needs are best addressed using controlled vocabulary terms whereas other are best addressed using tags....

  6. Multilabel Learning for Automatic Web Services Tagging

    Directory of Open Access Journals (Sweden)

    Mustapha AZNAG

    2014-08-01

    Full Text Available Recently, some web services portals and search engines as Biocatalogue and Seekda!, have allowed users to manually annotate Web services using tags. User Tags provide meaningful descriptions of services and allow users to index and organize their contents. Tagging technique is widely used to annotate objects in Web 2.0 applications. In this paper we propose a novel probabilistic topic model (which extends the CorrLDA model - Correspondence Latent Dirichlet Allocation- to automatically tag web services according to existing manual tags. Our probabilistic topic model is a latent variable model that exploits local correlation labels. Indeed, exploiting label correlations is a challenging and crucial problem especially in multi-label learning context. Moreover, several existing systems can recommend tags for web services based on existing manual tags. In most cases, the manual tags have better quality. We also develop three strategies to automatically recommend the best tags for web services. We also propose, in this paper, WS-Portal; An Enriched Web Services Search Engine which contains 7063 providers, 115 sub-classes of category and 22236 web services crawled from the Internet. In WS-Portal, severals technologies are employed to improve the effectiveness of web service discovery (i.e. web services clustering, tags recommendation, services rating and monitoring. Our experiments are performed out based on real-world web services. The comparisons of Precision@n, Normalised Discounted Cumulative Gain (NDCGn values for our approach indicate that the method presented in this paper outperforms the method based on the CorrLDA in terms of ranking and quality of generated tags.

  7. A Self-Adaptive Steered Molecular Dynamics Method Based on Minimization of Stretching Force Reveals the Binding Affinity of Protein–Ligand Complexes

    Directory of Open Access Journals (Sweden)

    Junfeng Gu

    2015-10-01

    Full Text Available Binding affinity prediction of protein–ligand complexes has attracted widespread interest. In this study, a self-adaptive steered molecular dynamics (SMD method is proposed to reveal the binding affinity of protein–ligand complexes. The SMD method is executed through adjusting pulling direction to find an optimum trajectory of ligand dissociation, which is realized by minimizing the stretching force automatically. The SMD method is then used to simulate the dissociations of 19 common protein–ligand complexes which are derived from two homology families, and the binding free energy values are gained through experimental techniques. Results show that the proposed SMD method follows a different dissociation pathway with lower a rupture force and energy barrier when compared with the conventional SMD method, and further analysis indicates the rupture forces of the complexes in the same protein family correlate well with their binding free energy, which reveals the possibility of using the proposed SMD method to identify the active ligand.

  8. Prediction of binding affinity and efficacy of thyroid hormone receptor ligands using QSAR and structure-based modeling methods

    International Nuclear Information System (INIS)

    The thyroid hormone receptor (THR) is an important member of the nuclear receptor family that can be activated by endocrine disrupting chemicals (EDC). Quantitative Structure–Activity Relationship (QSAR) models have been developed to facilitate the prioritization of THR-mediated EDC for the experimental validation. The largest database of binding affinities available at the time of the study for ligand binding domain (LBD) of THRβ was assembled to generate both continuous and classification QSAR models with an external accuracy of R2 = 0.55 and CCR = 0.76, respectively. In addition, for the first time a QSAR model was developed to predict binding affinities of antagonists inhibiting the interaction of coactivators with the AF-2 domain of THRβ (R2 = 0.70). Furthermore, molecular docking studies were performed for a set of THRβ ligands (57 agonists and 15 antagonists of LBD, 210 antagonists of the AF-2 domain, supplemented by putative decoys/non-binders) using several THRβ structures retrieved from the Protein Data Bank. We found that two agonist-bound THRβ conformations could effectively discriminate their corresponding ligands from presumed non-binders. Moreover, one of the agonist conformations could discriminate agonists from antagonists. Finally, we have conducted virtual screening of a chemical library compiled by the EPA as part of the Tox21 program to identify potential THRβ-mediated EDCs using both QSAR models and docking. We concluded that the library is unlikely to have any EDC that would bind to the THRβ. Models developed in this study can be employed either to identify environmental chemicals interacting with the THR or, conversely, to eliminate the THR-mediated mechanism of action for chemicals of concern. - Highlights: • This is the largest curated dataset for ligand binding domain (LBD) of the THRβ. • We report the first QSAR model for antagonists of AF-2 domain of THRβ. • A combination of QSAR and docking enables prediction of both

  9. Prediction of binding affinity and efficacy of thyroid hormone receptor ligands using QSAR and structure-based modeling methods

    Energy Technology Data Exchange (ETDEWEB)

    Politi, Regina [Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, University of North Carolina, Chapel Hill, NC 27599 (United States); Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, NC 27599 (United States); Rusyn, Ivan, E-mail: iir@unc.edu [Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, NC 27599 (United States); Tropsha, Alexander, E-mail: alex_tropsha@unc.edu [Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, University of North Carolina, Chapel Hill, NC 27599 (United States)

    2014-10-01

    The thyroid hormone receptor (THR) is an important member of the nuclear receptor family that can be activated by endocrine disrupting chemicals (EDC). Quantitative Structure–Activity Relationship (QSAR) models have been developed to facilitate the prioritization of THR-mediated EDC for the experimental validation. The largest database of binding affinities available at the time of the study for ligand binding domain (LBD) of THRβ was assembled to generate both continuous and classification QSAR models with an external accuracy of R{sup 2} = 0.55 and CCR = 0.76, respectively. In addition, for the first time a QSAR model was developed to predict binding affinities of antagonists inhibiting the interaction of coactivators with the AF-2 domain of THRβ (R{sup 2} = 0.70). Furthermore, molecular docking studies were performed for a set of THRβ ligands (57 agonists and 15 antagonists of LBD, 210 antagonists of the AF-2 domain, supplemented by putative decoys/non-binders) using several THRβ structures retrieved from the Protein Data Bank. We found that two agonist-bound THRβ conformations could effectively discriminate their corresponding ligands from presumed non-binders. Moreover, one of the agonist conformations could discriminate agonists from antagonists. Finally, we have conducted virtual screening of a chemical library compiled by the EPA as part of the Tox21 program to identify potential THRβ-mediated EDCs using both QSAR models and docking. We concluded that the library is unlikely to have any EDC that would bind to the THRβ. Models developed in this study can be employed either to identify environmental chemicals interacting with the THR or, conversely, to eliminate the THR-mediated mechanism of action for chemicals of concern. - Highlights: • This is the largest curated dataset for ligand binding domain (LBD) of the THRβ. • We report the first QSAR model for antagonists of AF-2 domain of THRβ. • A combination of QSAR and docking enables

  10. Comparing the hierarchy of author given tags and repository given tags in a large document archive

    CERN Document Server

    Tibély, Gergely; Palla, Gergely

    2015-01-01

    Folksonomies - large databases arising from collaborative tagging of items by independent users - are becoming an increasingly important way of categorizing information. In these systems users can tag items with free words, resulting in a tripartite item-tag-user network. Although there are no prescribed relations between tags, the way users think about the different categories presumably has some built in hierarchy, in which more special concepts are descendants of some more general categories. Several applications would benefit from the knowledge of this hierarchy. Here we apply a recent method to check the differences and similarities of hierarchies resulting from tags given by independent individuals and from tags given by a centrally managed repository system. The results from out method showed substantial differences between the lower part of the hierarchies, and in contrast, a relatively high similarity at the top of the hierarchies.

  11. A Novel User Classification Method for Femtocell Network by Using Affinity Propagation Algorithm and Artificial Neural Network

    Directory of Open Access Journals (Sweden)

    Afaz Uddin Ahmed

    2014-01-01

    Full Text Available An artificial neural network (ANN and affinity propagation (AP algorithm based user categorization technique is presented. The proposed algorithm is designed for closed access femtocell network. ANN is used for user classification process and AP algorithm is used to optimize the ANN training process. AP selects the best possible training samples for faster ANN training cycle. The users are distinguished by using the difference of received signal strength in a multielement femtocell device. A previously developed directive microstrip antenna is used to configure the femtocell device. Simulation results show that, for a particular house pattern, the categorization technique without AP algorithm takes 5 indoor users and 10 outdoor users to attain an error-free operation. While integrating AP algorithm with ANN, the system takes 60% less training samples reducing the training time up to 50%. This procedure makes the femtocell more effective for closed access operation.

  12. Electrochemical immobilization of Fluorescent labelled probe molecules on a FTO surface for affinity detection based on photo-excited current

    Energy Technology Data Exchange (ETDEWEB)

    Haruyama, Tetsuya; Wakabayashi, Ryo; Cho, Takeshi; Matsuyama, Sho-taro, E-mail: haruyama@life.kyutech.as.jp [Kyushu Institute of Technology, Department of Biological Functions and Engineering, Kitakyushu Science and Research Park, Hibikino, Kitakyushu, Fukuoka 808-0196 (Japan)

    2011-10-29

    Photo-excited current can be generated at a molecular interface between a photo-excited molecules and a semi-conductive material in appropriate condition. The system has been recognized for promoting photo-energy devices such as an organic dye sensitized solar-cell. The photo-current generated reactions are totally dependent on the interfacial energy reactions, which are in a highly fluctuated interfacial environment. The authors investigated the photo-excited current reaction to develop a smart affinity detection method. However, in order to perform both an affinity reaction and a photo-excited current reaction at a molecular interface, ordered fabrications of the functional (affinity, photo-excitation, etc.) molecules layer on a semi-conductive surface is required. In the present research, we would like to present the fabrication and functional performance of photo-excited current-based affinity assay device and its application for detection of endocrine disrupting chemicals. On the FTO surface, fluorescent pigment labelled affinity peptide was immobilized through the EC tag (electrochemical-tag) method. The modified FTO produced a current when it was irradiated with diode laser light. However, the photo current decreased drastically when estrogen (ES) coexisted in the reaction solution. In this case, immobilized affinity probe molecules formed a complex with ES and estrogen receptor (ER). The result strongly suggests that the photo-excited current transduction between probe molecule-labelled cyanine pigment and the FTO surface was partly inhibited by a complex that formed at the affinity oligo-peptide region in a probe molecule on the FTO electrode. The bound bulky complex may act as an impediment to perform smooth transduction of photo-excited current in the molecular interface. The present system is new type of photo-reaction-based analysis. This system can be used to perform simple high-sensitive homogeneous assays.

  13. Hydroxyl Tagging Velocimetry for Rocket Plumes Project

    Data.gov (United States)

    National Aeronautics and Space Administration — A non-intrusive method for measuring velocities in a rocket exhaust is proposed in a joint effort by MetroLaser and Vanderbilt University. Hydroxyl Tagging...

  14. AccQ-Tag-HPLC法测定烟叶生长过程中游离氨基酸的变化%Detection of Free Amino Acids in Tobacco Leaves during Growth Process by Using AccQ-Tag-HPLC Method

    Institute of Scientific and Technical Information of China (English)

    李方楼; 姬小明; 魏跃伟; 杨永锋; 刘国顺

    2011-01-01

    [目的]在AccQ-Tag分析包的基础上建立一种适合烟草中游离氨基酸测定的方法.[方法]采用WATERS公司的AccQ-Tg试剂包作为构建方法的基本条件,通过优化烟草中游离氨基酸的前处理和色谱条件,以6-氨基喹啉-N-羟基琥珀酰亚胺基甲酸酯(AQC)为衍生试剂与各氨基酸柱前定量衍生后,再用AccQ-TagTM柱梯度洗脱,建立了烟叶中游离氨基酸的AccQ-Tag-HPLC测试方法.[结果]用该方法测定烟叶杀青样品中的游离氨基酸,能够分离检测烟叶中的16种游离氨基酸,其回收率均在82.8%~105.3%,标准偏差均在2.5%以内,具有较好的重现性和回收率.烤烟杀青样中游离氨基酸以脯氨酸、天门冬氨酸、丝氨酸和丙氨酸含量较高.[结论] AccQ-Tag-HPLC法是一种实用的烟草中游离氨基酸的分析方法,适于烟叶中游离氨基酸从旺长期到成熟期的不同时段含量变化的测试.%[Objective] The study aimed to establish a method for the detection of free amino acids in tobacco by using AccQ-Tag-HPLC sys tem. [ Method] With the AccQ-Tag reagent bag from WATERS company as the basic condition of building method, through the optimization of pretreatment and chromatographic conditions for the free amino acid in the tobacco, the 6-amino decoquinate-N-hydroxyl succinyl imide formic ether (AQC) was taken as the derivative reagent to make for the column quantitative derivatization with each amino acid and then to elute by using AccQ-TagTM column gradient, thus, a AccQ-Tag-HPLC determining method for the detection of free amino acids in tobacco was estab lished. [ Result ] When the method was used to determine the free amino acids in the kill out samples of tobacco, 16 kinds of free amino acids in tobacco leaves were separated and detected by the method, with the recovery of 82. 8% - 105. 3% and the standard deviation values of be low 2.5% , showing a better reproducibility and recovery. The contents of proline, aspartate

  15. Survival and tag loss in Moapa White River springfish implanted with passive integrated transponder tags

    Science.gov (United States)

    Dixon, Christopher J.; Mesa, Matthew G.

    2011-01-01

    We monitored survival and tag loss among Moapa White River springfish Crenichthys baileyi moapae that were surgically implanted with passive integrated transponder (PIT; 9 × 2 mm) tags. The fish used in the study ranged from 40 to 67 mm in total length and from 1.0 to 6.5 g in mass; the PIT tag: body weight ratios were 1.0–6.1%. Fish were held for 41 d in live cages within a small, warm desert stream. Survival did not differ between untagged control fish (94.5%) and tagged fish (95.6%). Survival did not appear to be influenced by fish size or PIT tag: body weight ratio, but the small number of fish that died precluded a detailed analysis. Tag retention was 100% among the 86 fish that survived over the 41 d. Our results suggest that surgically implanting 9-mm PIT tags into Moapa White River springfish as small as 40 mm is an effective method for marking them because it has minimal impacts on survival and tag retention is high. More work is needed on the effects of PIT tagging on growth and other performance metrics of springfish and other small desert fishes.

  16. TAG Advertisement Hardware

    Science.gov (United States)

    1994-01-01

    LaRc SI Material Overall photograph showing the material specimens, the graphite composite, the gold composite and the molded gears on a black background. These photos were used for the TAG CO-OP Public Relations and promotions

  17. Tagged Vector Contour (TVC)

    Data.gov (United States)

    Kansas Data Access and Support Center — The Kansas Tagged Vector Contour (TVC) dataset consists of digitized contours from the 7.5 minute topographic quadrangle maps. Coverage for the state is incomplete....

  18. Efficient biotinylation and single-step purification of tagged transcription factors in mammalian cells and transgenic mice

    Science.gov (United States)

    de Boer, Ernie; Rodriguez, Patrick; Bonte, Edgar; Krijgsveld, Jeroen; Katsantoni, Eleni; Heck, Albert; Grosveld, Frank; Strouboulis, John

    2003-06-01

    Proteomic approaches require simple and efficient protein purification methodologies that are amenable to high throughput. Biotinylation is an attractive approach for protein complex purification due to the very high affinity of avidin/streptavidin for biotinylated templates. Here, we describe an approach for the single-step purification of transcription factor complex(es) based on specific in vivo biotinylation. We expressed the bacterial BirA biotin ligase in mammalian cells and demonstrated very efficient biotinylation of a hematopoietic transcription factor bearing a small (23-aa) artificial peptide tag. Biotinylation of the tagged transcription factor altered neither the factor's protein interactions or DNA binding properties in vivo nor its subnuclear distribution. Using this approach, we isolated the biotin-tagged transcription factor and at least one other known interacting protein from crude nuclear extracts by direct binding to streptavidin beads. Finally, this method works efficiently in transgenic mice, thus raising the prospect of using biotinylation tagging in protein complex purification directly from animal tissues. Therefore, BirA-mediated biotinylation of tagged proteins provides the basis for the single-step purification of proteins from mammalian cells.

  19. New tags for recombinant protein detection and O-glycosylation reporters.

    Directory of Open Access Journals (Sweden)

    Gianluca Petris

    Full Text Available Monoclonal antibodies (mAbs, because of their unique specificity, are irreplaceable tools for scientific research. Precise mapping of the antigenic determinants allows the development of epitope tagging approaches to be used with recombinant proteins for several purposes. Here we describe a new family of tags derived from the epitope recognized by a single highly specific mAb (anti-roTag mAb, which was obtained from a pool of mAbs reacting with the rotavirus nonstructural protein 5 (NSP5. The variable regions of the anti-roTag mAb were identified and their binding capacity verified upon expression as a single-chain/miniAb. The minimal epitope, termed roTag, was identified as a 10 amino acid sequence (SISSSIFKNE. The affinity of the anti-roTag/roTag interaction was found to be comparable to that of the anti-SV5/SV5 tag interaction. roTag was successfully used for detection of several recombinant cytosolic, secretory and membrane proteins. Two additional variants of roTag of 10 and 13 amino acids containing O-glycosylation susceptible sites (termed OG-tag and roTagO were constructed and characterised. These tags were useful to detect proteins passing through the Golgi apparatus, the site of O-glycosylation.

  20. A Tag Ranking Method Based on HITS and Random Walk%一种基于HITS和随机跳转的网页标签排序方法

    Institute of Scientific and Technical Information of China (English)

    汪兆鹏; 胡侠; 倪宁; 王灿

    2011-01-01

    Web 2.0应用的兴起,推进了情报学科由"文献组织"向"知识组织"演化.网页标签作为重要的Web 2 0应用之一,已经成为大众组织知识的常用途径.然而,现有的标签排序方法难以有效满足知识组织的需求.本文在三核协同标签模型的基础上,充分考虑标签和用户、标签和标签、标签和文档之间的关系,提出了一种结合HITS和随机跳转的标签排序方法.该方法利用高质量标签和高质量用户之间的相互加强关系,根据标签之间的相似性来找出高质量相关标签,有效提高标签排序的质量.在Delicious数据集上的实验结果表明,该方法能较大提高标签排序的准确度.%With the rise of Web 2. 0 applications, a new trend in information science, namely the evolution from "organizing document" to "organizing knowledge" , is looming on the horizon. One of' important Web 2. 0 applications,social tag, is making this trend a reality by adding meaningful annotations to Web pages. However, existing tag ranking methods are not efficient in knowledge organization. To improve tag ranking performance , this paper proposes a new ranking algorithm by utilizing relationships among users, tags and Web documents in a tripartite collaborative tagging model. By combining HITS and random walk, we effectively exploit the mutual reinforcement between quality users and quality tags and retrieve related tags by measuring similarity between tags. Experimental results on Delicious dataset demonstrate the effectiveness of our algorithm.

  1. Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method

    DEFF Research Database (Denmark)

    Nielsen, Morten; Lundegaard, Claus; Lund, Ole

    2007-01-01

    by favoring binding registers with a minimum PFR length of two amino acids. Visualizing the binding motif as obtained by the SMM-align and TEPITOPE methods highlights a series of fundamental discrepancies between the two predicted motifs. For the DRB1*1302 allele for instance, the TEPITOPE method favors basic...... benchmark data set, and SMM-align prediction method (NetMHCII) are made publicly available....

  2. Tag loss and short-term mortality associated with passive integrated transponder tagging of juvenile Lost River suckers

    Science.gov (United States)

    Burdick, Summer M.

    2011-01-01

    Passive integrated transponder (PIT) tags are commonly used to mark small catostomids, but tag loss and the effect of tagging on mortality have not been assessed for juveniles of the endangered Lost River sucker Deltistes luxatus. I evaluated tag loss and short-term (34-d) mortality associated with the PIT tagging of juvenile Lost River suckers in the laboratory by using a completely randomized design and three treatment groups (PIT tagged, positive control, and control). An empty needle was inserted into each positive control fish, whereas control fish were handled but not tagged. Only one fish expelled its PIT tag. Mortality rate averaged 9.8 ± 3.4% (mean ± SD) for tagged fish; mortality was 0% for control and positive control fish. All tagging mortalities occurred in fish with standard lengths of 71 mm or less, and most of the mortalities occurred within 48 h of tagging. My results indicate that 12.45- × 2.02-mm PIT tags provide a viable method of marking juvenile Lost River suckers that are 72 mm or larger.

  3. Dark-lumen MR colonography with fecal tagging: a comparison of water enema and air methods of colonic distension for detecting colonic neoplasms

    Energy Technology Data Exchange (ETDEWEB)

    Rodriguez Gomez, Sonia; Pages Llinas, Mario; Juan Garcia, Carmen de; Rimola Gibert, Jordi; Ayuso Colella, Juan R.; Ayuso Colella, Carmen [Hospital Clinico of Barcelona, Department of Radiology, Barcelona (Spain); Castells Garangou, Antoni; Bordas Alsina, Josep M. [Hospital Clinico of Barcelona, Department of Gastroenterology, Barcelona (Spain)

    2008-07-15

    The purpose was to evaluate MR colonography (MRC) with barium fecal tagging in detecting colorectal pathology and to determine how air-based and water-based colonic distension influences MRC. We studied 83 patients with high risk of colonic neoplasms. All received oral barium sulfate for colonic preparation before unenhanced and enhanced T1-weighted gradient-echo MRC using either water (n=54) or air (n=29) for colonic distension. Fecal tagging, distension, and artifacts were recorded. All patients underwent conventional colonoscopy within 2 weeks of MRC; the techniques were compared for detection of malignant neoplasms and polyps {>=}1 cm, 6-9 mm, and {<=}5 mm. Fecal tagging was ''good'' in 76% of the colonic segments in water-distended patients and 46% of air-distended patients. The degree of distension was ''good'' in 90.7% of water-distended patients and 44% of air-distended patients. Severe artifacts were present in 15% air-distended patients and 0.3% of water-distended patients. Both water-distended and air-distended MRC detected all malignant neoplasms and polyps {>=}1 cm, but more air-distended MRC were excluded for poor quality. MRC with fecal tagging is useful for detecting lesions {>=}1 cm. Air distension was inferior to water distension in most aspects. Water-based colonic distension should be used for barium-tagging MRC. (orig.)

  4. Personalized Tag Recommendation Using Social Influence

    Institute of Scientific and Technical Information of China (English)

    Jun Hu; Bing Wang; Yu Liu; De-Yi Li

    2012-01-01

    Tag recommendation encourages users to add more tags in bridging the semantic gap between human concept and the features of media object,which provides a feasible solution for content-based multimedia information retrieval.In this paper,we study personalized tag recommendation in a popular online photo sharing site Flickr.Social relationship information of users is collected to generate an online social network. From the perspective of network topology,we propose node topological potential to characterize user's social influence.With this metric,we distinguish different social relations between users and find out those who really have influence on the target users.Tag recommendations are based on tagging history and the latent personalized preference learned from those who have most influence in user's social network.We evaluate our method on large scale real-world data.The experimental results demonstrate that our method can outperform the non-personalized global co-occurrence method and other two state-of-the-art personalized approaches using social networks.We also analyze the further usage of our approach for the cold-start problem of tag recommendation.

  5. 一种基于词语搭配的语义消歧方法%Word sense tagging method based on word relationships

    Institute of Scientific and Technical Information of China (English)

    郑杰; 茅于杭

    2001-01-01

    The paper proposes a word sense tagging method using a hybrid strategy combining rule-based and statistic-based methods. A mathematical model is constructed to remove the word ambiguity in term of its relationship to other words. By evaluating each possible sense combination according to bilingual corpus, the model can select the most reasonable word sense. Then, a rules learning algorithm is proposed and an application algorithm of the learned rules is provided which can increase recall. Its application in English-Chinese machine translation system proved a 10% increase in precision.%提出一种利用规则与统计相结合的方法用于英汉机译系统中以消解语义级歧义,建立了一种根据单词之间的词语搭配关系以消除歧义的模型。该模型利用英汉双语语料选择合理的词组语义,对有歧义的单词作出标注。在此基础上给出了语义消歧的学习算法,并建立了一套有效的提高召回率的消歧算法。算法在英汉机译系统中的实际应用使正确率提高了约10%,效果显著。

  6. Tagging of Explosives for Detection

    Directory of Open Access Journals (Sweden)

    J. S. Gharia

    2000-01-01

    Full Text Available This paper gives the results of a study on estimation of shelf life of2,3-dimethyI2,3-dinitrobutane (DMNB-tagged RDX and PETN expiosives by monitoring DMNB depletion by high performanceliquid chromatography and simultaneously recording the detectability of the tagged explosive composition using explosive vapoUf detector Model-97 HS. DMNB was incorporated in the explosive using methanol as solvent for DMNB and the explosive compositions were stored at 35,55 and 75 °C over a long period. Methods developed for preparing the homogeneously tagged composition with DMNB at 0.5 per cent level and for the analysis ofDMNB for ensuring homogeneity of DMNB in the composition are described. The results show no change in compatibility and sensitivity on the incorporation of DMNB in the explosive. Estimation of shelf life of DMNB in the explosive was done for a period of storage of 202-304 days at different temperatures.

  7. Tandem affinity purification to identify cytosolic and nuclear gβγ-interacting proteins.

    Science.gov (United States)

    Campden, Rhiannon; Pétrin, Darlaine; Robitaille, Mélanie; Audet, Nicolas; Gora, Sarah; Angers, Stéphane; Hébert, Terence E

    2015-01-01

    It has become clear in recent years that the Gβγ subunits of heterotrimeric proteins serve broad roles in the regulation of cellular activity and interact with many proteins in different subcellular locations including the nucleus. Protein affinity purification is a common method to identify and confirm protein interactions. When used in conjugation with mass spectrometry it can be used to identify novel protein interactions with a given bait protein. The tandem affinity purification (TAP) technique identifies partner proteins bound to tagged protein bait. Combined with protocols to enrich the nuclear fraction of whole cell lysate through sucrose cushions, TAP allows for purification of interacting proteins found specifically in the nucleus. Here we describe the use of the TAP technique on cytosolic and nuclear lysates to identify candidate proteins, through mass spectrometry, that bind to Gβ1 subunits.

  8. A new affine transformation parameters estimation method%一种新的仿射变换参数估计方法

    Institute of Scientific and Technical Information of China (English)

    何凯; 远中文; 牟聪翀

    2011-01-01

    仿射变换参数的精确估计是进行图像配准的关键,传统基于超定方程的参数估计方法对误匹配点比较敏感,对匹配准确率提出了很高的要求。针对这种情况,本文利用改进后的牛顿法对仿射变换参数估计算法进行了研究,建立了迭代模型,并推导了相关的数学公式,通过与SIFT特征点提取方法相结合,构建了新的图像配准算法仿真实验结果表明,与传统求解超定方程的方法相比,该方法能够有效减少误匹配点对估计结果的影响,参数估计更加准确,且估计时间缩短了一个数量级。利用新的图像配准方法实现了实际航空影像的精确配准,表明本文方法具有很高的精度,能够满足实际工程的需要。%The precise estimation of affine transformation parameter is most significant in image matching. Since the traditional parameters estimation method based on solving over determined equation is sensitive to mismatch points, high precision of matching is required. In view of this situation, the improved Newton method is studied to estimate the affine transformation parameters the relevant mathematical model is established, and the formulas are deduced. Besides that, by combining the parameter estimation method with SIFT feature extraction algorithm, a new image registration algorithm is proposed. The simulation results show that this estimation algorithm is robust to mismatch points, and the estimated parameters are more accurate than traditional method. Besides that, an order of magnitude improvement is made in time consuming. With the improved registration method, precise registration of actual aviation images are realized, therefore this method is high precise and suitable in practical engineering.

  9. Ordinary differential equations in affine geometry

    Directory of Open Access Journals (Sweden)

    Salvador Gigena

    1996-05-01

    Full Text Available The method of qualitative analysis is used, as applied to a class of fourth order, nonlinear ordinary differential equations, in order to classify, both locally and globally, two classes of hypersurfaces of decomposable type in affine geometry: those with constant unimodular affine mean curvature L , and those with constant Riemannian scalar curvature R. This allows to provide a large number of new examples of hypersurfaces in affine geometry.

  10. Ordinary differential equations in affine geometry

    OpenAIRE

    Salvador Gigena

    1996-01-01

    The method of qualitative analysis is used, as applied to a class of fourth order, nonlinear ordinary differential equations, in order to classify, both locally and globally, two classes of hypersurfaces of decomposable type in affine geometry: those with constant unimodular affine mean curvature L , and those with constant Riemannian scalar curvature R. This allows to provide a large number of new examples of hypersurfaces in affine geometry.

  11. A universal SI-traceable isotope dilution mass spectrometry method for protein quantitation in a matrix by tandem mass tag technology.

    Science.gov (United States)

    Li, Jiale; Wu, Liqing; Jin, Youxun; Su, Ping; Yang, Bin; Yang, Yi

    2016-05-01

    Isotope dilution mass spectrometry (IDMS), an important metrological method, is widely used for absolute quantification of peptides and proteins. IDMS employs an isotope-labeled peptide or protein as an internal standard although the use of a protein provides improved accuracy. Generally, the isotope-labeled protein is obtained by stable isotope labeling by amino acids in cell culture (SILAC) technology. However, SILAC is expensive, laborious, and time-consuming. To overcome these drawbacks, a novel universal SI-traceable IDMS method for absolute quantification of proteins in a matrix is described with human transferrin (hTRF). The hTRF and a human serum sample were labeled with different tandem mass tags (TMTs). After mixing the TMT-labeled hTRF and serum sample together followed by digestion, the peptides were separated by nano-liquid chromatography and analyzed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Using the signature peptides, we calculated the ratios of reporter ions from the TMT-labeled peptides which, in turn, allowed determination of the mass fraction of hTRF. The recovery ranged from 97% to 105% with a CV of 3.9%. The LOD and LOQ were 1.71 × 10(-5) g/g and 5.69 × 10(-5) g/g of hTRF in human serum, respectively, and the relative expanded uncertainty was 4.7% with a mass fraction of 2.08 mg/g. For comparison, an enzyme-linked immunosorbent assay (ELISA) method for hTRF yielded a mass fraction of 2.03 mg/g. This method provides a starting point for establishing IDMS technology to accurately determine the mass fractions of protein biomarkers in a matrix with traceability to SI units. This technology should support the development of a metrological method useful for quantification of a wide variety of proteins. PMID:26942737

  12. Reduced-basis method (RBM) for non-affine elliptic parametrized PDEs - (motivated by optimization in hydromechanics)

    OpenAIRE

    Tonn, Timo

    2012-01-01

    This work has been motivated by optimizing the efficiency of a ship-propulsion device, the Voith-Schneider Propeller, w.r.t. its steering (determined by the so-called blade-steering curve). We consider a simplified model (stationary convection-diffusion problem), which is transformed to a reference domain in a first step. This transformation shifts the parametric dependency into the coefficients of the PDE, which is key for the application of the reduced-basis method (RBM), and results in a n...

  13. In Silico Prediction of Estrogen Receptor Subtype Binding Affinity and Selectivity Using Statistical Methods and Molecular Docking with 2-Arylnaphthalenes and 2-Arylquinolines

    Directory of Open Access Journals (Sweden)

    Yonghua Wang

    2010-09-01

    Full Text Available Over the years development of selective estrogen receptor (ER ligands has been of great concern to researchers involved in the chemistry and pharmacology of anticancer drugs, resulting in numerous synthesized selective ER subtype inhibitors. In this work, a data set of 82 ER ligands with ERα and ERβ inhibitory activities was built, and quantitative structure-activity relationship (QSAR methods based on the two linear (multiple linear regression, MLR, partial least squares regression, PLSR and a nonlinear statistical method (Bayesian regularized neural network, BRNN were applied to investigate the potential relationship of molecular structural features related to the activity and selectivity of these ligands. For ERα and ERβ, the performances of the MLR and PLSR models are superior to the BRNN model, giving more reasonable statistical properties (ERα: for MLR, Rtr2 = 0.72, Qte2 = 0.63; for PLSR, Rtr2 = 0.92, Qte2 = 0.84. ERβ: for MLR, Rtr2 = 0.75, Qte2 = 0.75; for PLSR, Rtr2 = 0.98, Qte2 = 0.80. The MLR method is also more powerful than other two methods for generating the subtype selectivity models, resulting in Rtr2 = 0.74 and Qte2 = 0.80. In addition, the molecular docking method was also used to explore the possible binding modes of the ligands and a relationship between the 3D-binding modes and the 2D-molecular structural features of ligands was further explored. The results show that the binding affinity strength for both ERα and ERβ is more correlated with the atom fragment type, polarity, electronegativites and hydrophobicity. The substitutent in position 8 of the naphthalene or the quinoline plane and the space orientation of these two planes contribute the most to the subtype selectivity on the basis of similar hydrogen bond interactions between binding ligands and both ER subtypes. The QSAR models built together with the docking procedure should be of great advantage for screening and designing ER ligands with improved affinity

  14. 固定RFID电子标签探测定位方法%A Method about Detecting the Fixed Tag to Realize Localization

    Institute of Scientific and Technical Information of China (English)

    汪勇

    2012-01-01

    研究了一种无线通信的定位方法,介绍了利用移动阅读器探测固定RFID(射频识别技术)电子标签的定位技术,建立了系统基本模型。并介绍了该定位方法在车载系统的导航定位系统及室内三维定位系统中的应用。提出的新定位方法是对传统GPS/北斗卫星定位系统的有益补充。可弥补卫星定位在城市“峡谷”区域工作时由于阴影、多路径等因素所导致的定位误差。%The purpose of this paper is to propose a new kind of positioning method based on wireless communication. In this study, attempts were made to use mobile reader to detect the fixed tag to realize localization and build the basic model of the system. At the same time, tlle applications of navigation system on vehicle and indoor three dimensional positioning are presented. This study can also supplement the traditional GPS/Beidou satellite positioning system beneficially, because it can make up the positioning error which led to by shadow, multipath and other factors in the city positioning.

  15. Affine Grassmann codes

    DEFF Research Database (Denmark)

    Høholdt, Tom; Beelen, Peter; Ghorpade, Sudhir Ramakant

    2010-01-01

    We consider a new class of linear codes, called affine Grassmann codes. These can be viewed as a variant of generalized Reed-Muller codes and are closely related to Grassmann codes.We determine the length, dimension, and the minimum distance of any affine Grassmann code. Moreover, we show that...... affine Grassmann codes have a large automorphism group and determine the number of minimum weight codewords....

  16. Isolation of Human Antibodies Against Hepatitis E From Phage Display Library by Metal Affinity Chromatography

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Objective To isolate human antibodies against hepatitis E virus from phage display library by a new method of panning phage antibody library based on immobilized metal affinity chromatography (IMAC). Methods Phage antibody library was allowed to mix with hex-His tagged expressed HEV specific antigen, NE2, in solution for adequate binding before affinity resin for hex-His was added. The non-specific phage antibodies were removed by extensive washing and the specific bound phage antibodies could then be eluted to infect TG1 or repeat the binding process for subsequent rounds of purification. The specificity of the selected human antibodies were tested by antigen competitive ELISA, human sera blocking ELISA, scFv expression, and sequence analysis. Results His-NE2 specific recombinant phages were successfully enriched after panning procedure. Two individual phage clones, 126 and 138, showed 50% inhibition in NE2 antigen competition ELISA and obvious blocking effect by HEV positive serum in blocking ELISA. Soluble scFv of 126, 138 bound to NE2 specifically. Conclusion Two specific human phage antibodies against hepatitis E virus (HEV) from phage display library were isolated by immobilized metal affinity chromatography. The immobilized metal affinity chromatography applied to phage antibody selection was a helpful supplement to the selection in solution.

  17. Improved methodology for the affinity isolation of human protein complexes expressed at near endogenous levels

    DEFF Research Database (Denmark)

    Domanski, Michal; Molloy, Kelly; Jiang, Hua;

    2012-01-01

    An efficient and reliable procedure for the capture of affinity-tagged proteins and associated complexes from human cell lines is reported. Through multiple optimizations, high yield and low background affinity-purifications are achieved from modest quantities of human cells expressing endogenous...

  18. Analysis of tag-position bias in MPSS technology

    Directory of Open Access Journals (Sweden)

    Rattray Magnus

    2006-04-01

    Full Text Available Abstract Background Massively Parallel Signature Sequencing (MPSS technology was recently developed as a high-throughput technology for measuring the concentration of mRNA transcripts in a sample. It has previously been observed that the position of the signature tag in a transcript (distance from 3' end can affect the measurement, but this effect has not been studied in detail. Results We quantify the effect of tag-position bias in Classic and Signature MPSS technology using published data from Arabidopsis, rice and human. We investigate the relationship between measured concentration and tag-position using nonlinear regression methods. The observed relationship is shown to be broadly consistent across different data sets. We find that there exist different and significant biases in both Classic and Signature MPSS data. For Classic MPSS data, genes with tag-position in the middle-range have highest measured abundance on average while genes with tag-position in the high-range, far from the 3' end, show a significant decrease. For Signature MPSS data, high-range tag-position genes tend to have a flatter relationship between tag-position and measured abundance. Thus, our results confirm that the Signature MPSS method fixes a substantial problem with the Classic MPSS method. For both Classic and Signature MPSS data there is a positive correlation between measured abundance and tag-position for low-range tag-position genes. Compared with the effects of mRNA length and number of exons, tag-position bias seems to be more significant in Arabadopsis. The tag-position bias is reflected both in the measured abundance of genes with a significant tag count and in the proportion of unexpressed genes identified. Conclusion Tag-position bias should be taken into consideration when measuring mRNA transcript abundance using MPSS technology, both in Classic and Signature MPSS methods.

  19. A combination of docking, QM/MM methods, and MD simulation for binding affinity estimation of metalloprotein ligands.

    Science.gov (United States)

    Khandelwal, Akash; Lukacova, Viera; Comez, Dogan; Kroll, Daniel M; Raha, Soumyendu; Balaz, Stefan

    2005-08-25

    To alleviate the problems in the receptor-based design of metalloprotein ligands due to inadequacies in the force-field description of coordination bonds, a four-tier approach was devised. Representative ligand-metalloprotein interaction energies are obtained by subsequent application of (1) docking with metal-binding-guided selection of modes, (2) optimization of the ligand-metalloprotein complex geometry by combined quantum mechanics and molecular mechanics (QM/MM) methods, (3) conformational sampling of the complex with constrained metal bonds by force-field-based molecular dynamics (MD), and (4) a single point QM/MM energy calculation for the time-averaged structures. The QM/MM interaction energies are, in a linear combination with the desolvation-characterizing changes in the solvent-accessible surface areas, correlated with experimental data. The approach was applied to structural correlation of published binding free energies of a diverse set of 28 hydroxamate inhibitors to zinc-dependent matrix metalloproteinase 9 (MMP-9). Inclusion of steps 3 and 4 significantly improved both correlation and prediction. The two descriptors explained 90% of variance in inhibition constants of all 28 inhibitors, ranging from 0.08 to 349 nM, with the average unassigned error of 0.318 log units. The structural and energetic information obtained from the time-averaged MD simulation results helped understand the differences in binding modes of related compounds.

  20. Affine connections, midpoint formation, and point reflection

    DEFF Research Database (Denmark)

    Kock, Anders

    2011-01-01

    We describe some differential-geometric structures in combinatorial terms: namely affine connections and their torsion and curvature, and we show that torsion free affine connections may equivalently be presented in terms of some simpler combinatorial structure: midpoint formation, and point refl...... reflection (geodesic symmetry). The method employed is that of synthetic differential geometry, which is briefly explained.......We describe some differential-geometric structures in combinatorial terms: namely affine connections and their torsion and curvature, and we show that torsion free affine connections may equivalently be presented in terms of some simpler combinatorial structure: midpoint formation, and point...

  1. Der erste Tag

    Institute of Scientific and Technical Information of China (English)

    HugoLoetscher

    2004-01-01

    Der erste Tag in einer fremden Stadtdas sind nicht nur Stunden der Liebe und des Urteils auf den ersten Blick, gespannte Erwartung, wer wen enttiiuscht, Bestaetigung von Vorstellungen und Korrekturen davon, das Aufkommen neue Vorurteile, fluechtiger Eindruck und doch nachhaltige Erfahrung.

  2. Personalization of tagging systems

    NARCIS (Netherlands)

    Wang, J.; Clements, M.; Yang, J.; Vries, A.P. de; Reinders, M.J.T.

    2010-01-01

    Social media systems have encouraged end user participation in the Internet, for the purpose of storing and distributing Internet content, sharing opinions and maintaining relationships. Collaborative tagging allows users to annotate the resulting user-generated content, and enables effective retrie

  3. Tag Completion for Image Retrieval.

    Science.gov (United States)

    Wu, Lei; Jin, Rong; Jain, Anil K

    2013-03-01

    Many social image search engines are based on keyword/tag matching. This is because tag-based image retrieval (TBIR) is not only efficient but also effective. The performance of TBIR is highly dependent on the availability and quality of manual tags. Recent studies have shown that manual tags are often unreliable and inconsistent. In addition, since many users tend to choose general and ambiguous tags in order to minimize their efforts in choosing appropriate words, tags that are specific to the visual content of images tend to be missing or noisy, leading to a limited performance of TBIR. To address this challenge, we study the problem of tag completion, where the goal is to automatically fill in the missing tags as well as correct noisy tags for given images. We represent the image-tag relation by a tag matrix, and search for the optimal tag matrix consistent with both the observed tags and the visual similarity. We propose a new algorithm for solving this optimization problem. Extensive empirical studies show that the proposed algorithm is significantly more effective than the state-of-the-art algorithms. Our studies also verify that the proposed algorithm is computationally efficient and scales well to large databases. PMID:22641703

  4. Expression and affinity purification of recombinant proteins from plants

    Science.gov (United States)

    Desai, Urvee A.; Sur, Gargi; Daunert, Sylvia; Babbitt, Ruth; Li, Qingshun

    2002-01-01

    With recent advances in plant biotechnology, transgenic plants have been targeted as an inexpensive means for the mass production of proteins for biopharmaceutical and industrial uses. However, the current plant purification techniques lack a generally applicable, economic, large-scale strategy. In this study, we demonstrate the purification of a model protein, beta-glucuronidase (GUS), by employing the protein calmodulin (CaM) as an affinity tag. In the proposed system, CaM is fused to GUS. In the presence of calcium, the calmodulin fusion protein binds specifically to a phenothiazine-modified surface of an affinity column. When calcium is removed with a complexing agent, e.g., EDTA, calmodulin undergoes a conformational change allowing the dissociation of the calmodulin-phenothiazine complex and, therefore, permitting the elution of the GUS-CaM fusion protein. The advantages of this approach are the fast, efficient, and economical isolation of the target protein under mild elution conditions, thus preserving the activity of the target protein. Two types of transformation methods were used in this study, namely, the Agrobacterium-mediated system and the viral-vector-mediated transformation system. Copyright 2002 Elsevier Science (USA).

  5. Ontologies and tag-statistics

    International Nuclear Information System (INIS)

    Due to the increasing popularity of collaborative tagging systems, the research on tagged networks, hypergraphs, ontologies, folksonomies and other related concepts is becoming an important interdisciplinary area with great potential and relevance for practical applications. In most collaborative tagging systems the tagging by the users is completely ‘flat’, while in some cases they are allowed to define a shallow hierarchy for their own tags. However, usually no overall hierarchical organization of the tags is given, and one of the interesting challenges of this area is to provide an algorithm generating the ontology of the tags from the available data. In contrast, there are also other types of tagged networks available for research, where the tags are already organized into a directed acyclic graph (DAG), encapsulating the ‘is a sub-category of’ type of hierarchy between each other. In this paper, we study how this DAG affects the statistical distribution of tags on the nodes marked by the tags in various real networks. The motivation for this research was the fact that understanding the tagging based on a known hierarchy can help in revealing the hidden hierarchy of tags in collaborative tagging systems. We analyse the relation between the tag-frequency and the position of the tag in the DAG in two large sub-networks of the English Wikipedia and a protein-protein interaction network. We also study the tag co-occurrence statistics by introducing a two-dimensional (2D) tag-distance distribution preserving both the difference in the levels and the absolute distance in the DAG for the co-occurring pairs of tags. Our most interesting finding is that the local relevance of tags in the DAG (i.e. their rank or significance as characterized by, e.g., the length of the branches starting from them) is much more important than their global distance from the root. Furthermore, we also introduce a simple tagging model based on random walks on the DAG, capable of

  6. Basis set limit electronic excitation energies, ionization potentials, and electron affinities for the 3d transition metal atoms: Coupled cluster and multireference methods

    Science.gov (United States)

    Balabanov, Nikolai B.; Peterson, Kirk A.

    2006-08-01

    Recently developed correlation consistent basis sets for the first row transition metal elements Sc-Zn have been utilized to determine complete basis set (CBS) scalar relativistic electron affinities, ionization potentials, and 4s23dn -2-4s1dn -1 electronic excitation energies with single reference coupled cluster methods [CCSD(T), CCSDT, and CCSDTQ] and multireference configuration interaction with three reference spaces: 3d4s, 3d4s4p, and 3d4s4p3d'. The theoretical values calculated with the highest order coupled cluster techniques at the CBS limit, including extrapolations to full configuration interaction, are well within 1kcal/mol of the corresponding experimental data. For the early transition metal elements (Sc-Mn) the internally contracted multireference averaged coupled pair functional method yielded excellent agreement with experiment; however, the atomic properties for the late transition metals (Mn-Zn) proved to be much more difficult to describe with this level of theory, even with the largest reference function of the present work.

  7. Phosphopeptide enrichment by immobilized metal affinity chromatography

    DEFF Research Database (Denmark)

    Thingholm, Tine E.; Larsen, Martin R.

    2016-01-01

    Immobilized metal affinity chromatography (IMAC) has been the method of choice for phosphopeptide enrichment prior to mass spectrometric analysis for many years and it is still used extensively in many laboratories. Using the affinity of negatively charged phosphate groups towards positively...

  8. Associated Particle Tagging (APT) in Magnetic Spectrometers

    Energy Technology Data Exchange (ETDEWEB)

    Jordan, David V.; Baciak, James E.; Stave, Sean C.; Chichester, David; Dale, Daniel; Kim, Yujong; Harmon, Frank

    2012-10-16

    alpha-particle spectrometer concept, and outlines challenges involved in the magnetic field design. Tagged photon interrogation: • We investigated a method for discriminating fissile from benign cargo-material response to an energy-tagged photon beam. The method relies upon coincident detection of the tagged photon and a photoneutron or photofission neutron produced in the target material. The method exploits differences in the shape of the neutron production cross section as a function of incident photon energy in order to discriminate photofission yield from photoneutrons emitted by non-fissile materials. Computational tests of the interrogation method as applied to material composition assay of a simple, multi-layer target suggest that the tagged-photon information facilitates precise (order 1% thickness uncertainty) reconstruction of the constituent thicknesses of fissile (uranium) and high-Z (Pb) constituents of the test targets in a few minutes of photon-beam exposure. We assumed an 18-MeV endpoint tagged photon beam for these simulations. • The report addresses several candidate design and data analysis issues for beamline infrastructure required to produce a tagged photon beam in a notional AI-dedicated facility, including the accelerator and tagging spectrometer.

  9. Self-Powered Wireless Affinity-Based Biosensor Based on Integration of Paper-Based Microfluidics and Self-Assembled RFID Antennas.

    Science.gov (United States)

    Yuan, Mingquan; Alocilja, Evangelyn C; Chakrabartty, Shantanu

    2016-08-01

    This paper presents a wireless, self-powered, affinity-based biosensor based on the integration of paper-based microfluidics with our previously reported method for self-assembling radio-frequency (RF) antennas. At the core of the proposed approach is a silver-enhancement technique that grows portions of a RF antenna in regions where target antigens hybridize with target specific affinity probes. The hybridization regions are defined by a network of nitrocellulose based microfluidic channels which implement a self-powered approach to sample the reagent and control its flow and mixing. The integration substrate for the biosensor has been constructed using polyethylene and the patterning of the antenna on the substrate has been achieved using a low-cost ink-jet printing technique. The substrate has been integrated with passive radio-frequency identification (RFID) tags to demonstrate that the resulting sensor-tag can be used for continuous monitoring in a food supply-chain where direct measurement of analytes is typically considered to be impractical. We validate the proof-of-concept operation of the proposed sensor-tag using IgG as a model analyte and using a 915 MHz Ultra-high-frequency (UHF) RFID tagging technology.

  10. Self-Powered Wireless Affinity-Based Biosensor Based on Integration of Paper-Based Microfluidics and Self-Assembled RFID Antennas.

    Science.gov (United States)

    Yuan, Mingquan; Alocilja, Evangelyn C; Chakrabartty, Shantanu

    2016-08-01

    This paper presents a wireless, self-powered, affinity-based biosensor based on the integration of paper-based microfluidics with our previously reported method for self-assembling radio-frequency (RF) antennas. At the core of the proposed approach is a silver-enhancement technique that grows portions of a RF antenna in regions where target antigens hybridize with target specific affinity probes. The hybridization regions are defined by a network of nitrocellulose based microfluidic channels which implement a self-powered approach to sample the reagent and control its flow and mixing. The integration substrate for the biosensor has been constructed using polyethylene and the patterning of the antenna on the substrate has been achieved using a low-cost ink-jet printing technique. The substrate has been integrated with passive radio-frequency identification (RFID) tags to demonstrate that the resulting sensor-tag can be used for continuous monitoring in a food supply-chain where direct measurement of analytes is typically considered to be impractical. We validate the proof-of-concept operation of the proposed sensor-tag using IgG as a model analyte and using a 915 MHz Ultra-high-frequency (UHF) RFID tagging technology. PMID:27214914

  11. TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets

    Directory of Open Access Journals (Sweden)

    Lim Yan

    2010-06-01

    Full Text Available Abstract Background Sequencing metagenomes that were pre-amplified with primer-based methods requires the removal of the additional tag sequences from the datasets. The sequenced reads can contain deletions or insertions due to sequencing limitations, and the primer sequence may contain ambiguous bases. Furthermore, the tag sequence may be unavailable or incorrectly reported. Because of the potential for downstream inaccuracies introduced by unwanted sequence contaminations, it is important to use reliable tools for pre-processing sequence data. Results TagCleaner is a web application developed to automatically identify and remove known or unknown tag sequences allowing insertions and deletions in the dataset. TagCleaner is designed to filter the trimmed reads for duplicates, short reads, and reads with high rates of ambiguous sequences. An additional screening for and splitting of fragment-to-fragment concatenations that gave rise to artificial concatenated sequences can increase the quality of the dataset. Users may modify the different filter parameters according to their own preferences. Conclusions TagCleaner is a publicly available web application that is able to automatically detect and efficiently remove tag sequences from metagenomic datasets. It is easily configurable and provides a user-friendly interface. The interactive web interface facilitates export functionality for subsequent data processing, and is available at http://edwards.sdsu.edu/tagcleaner.

  12. An audio file tagging mobile game, mTagATune

    OpenAIRE

    Díaz, Francisco Javier; Queiruga, Claudia Alejandra; Ferraresso, Alejandro; Larghi, José

    2011-01-01

    mTagATune is a mobile game based on TagATune. mTagATune implements the concept of GWAP and seizes the capabilities and wide acceptance of current smartphones. GWAP promotes the creation of computer games that encourage people to do voluntary work. mTagATune implements a game that collects information on audio files to facilitate future searches on them. By means of a collaborative game, mTagATune enables an ubiquitous collection of information on audio files that can later be used in searc...

  13. An improved toolbox to unravel the plant cellular machinery by tandem affinity purification of Arabidopsis protein complexes.

    Science.gov (United States)

    Van Leene, Jelle; Eeckhout, Dominique; Cannoot, Bernard; De Winne, Nancy; Persiau, Geert; Van De Slijke, Eveline; Vercruysse, Leen; Dedecker, Maarten; Verkest, Aurine; Vandepoele, Klaas; Martens, Lennart; Witters, Erwin; Gevaert, Kris; De Jaeger, Geert

    2015-01-01

    Tandem affinity purification coupled to mass spectrometry (TAP-MS) is one of the most advanced methods to characterize protein complexes in plants, giving a comprehensive view on the protein-protein interactions (PPIs) of a certain protein of interest (bait). The bait protein is fused to a double affinity tag, which consists of a protein G tag and a streptavidin-binding peptide separated by a very specific protease cleavage site, allowing highly specific protein complex isolation under near-physiological conditions. Implementation of this optimized TAP tag, combined with ultrasensitive MS, means that these experiments can be performed on small amounts (25 mg of total protein) of protein extracts from Arabidopsis cell suspension cultures. It is also possible to use this approach to isolate low abundant protein complexes from Arabidopsis seedlings, thus opening perspectives for the exploration of protein complexes in a plant developmental context. Next to protocols for efficient biomass generation of seedlings (∼7.5 months), we provide detailed protocols for TAP (1 d), and for sample preparation and liquid chromatography-tandem MS (LC-MS/MS; ∼5 d), either from Arabidopsis seedlings or from cell cultures. For the identification of specific co-purifying proteins, we use an extended protein database and filter against a list of nonspecific proteins on the basis of the occurrence of a co-purified protein among 543 TAP experiments. The value of the provided protocols is illustrated through numerous applications described in recent literature.

  14. Development of techniques for tagging precursor and essential chemicals

    Energy Technology Data Exchange (ETDEWEB)

    Swansiger, W.A.; Shepodd, T.J. [Sandia National Labs., Livermore, CA (United States); Phillips, M.L.F. [Sandia National Labs., Albuquerque, NM (United States)

    1994-01-01

    The ability to identify the manufacturers and distributors of chemicals seized in raids of illicit drug labs would be of great value in controlling the diversion of these chemicals. We developed a tagging scheme based on the addition of sub-ppM concentrations of various combinations of rare-earth elements to the target chemicals and evaluated a number of techniques for detecting the tags. We developed soluble tags for tagging liquids and selected Inductively Coupled Plasma-Mass Spectrometry (ICP-MS) as the preferred detection technique. We developed insoluble tags for tagging solids and developed methods to analyze them and mix them into solid precursors. We have successfully demonstrated the tagging of several solvents and two of the precursor chemicals used in one of the most popular clandestine methamphetamine syntheses (ephedrine reacting with hydriodic acid/red phosphorus). The tagging scheme is capable of yielding tens of thousands of signatures (using holmium as an internal standard and up to 9 rare-earths at up to 3 concentrations yields 3{sup 9} {minus} 1 = 19,682 signatures) and is applicable to most of the chemicals on the precursor and essential chemicals list. In the concentrations employed, the tags are safe enough to be added to pharmaceuticals and cheap enough to tag tanker loads of chemicals.

  15. Software for tag single nucleotide polymorphism selection

    Directory of Open Access Journals (Sweden)

    Stram Daniel O

    2005-06-01

    Full Text Available Abstract This paper reviews the theoretical basis for single nucleotide polymorphism (SNP tagging and considers the use of current software made freely available for this task. A distinction between haplotype block-based and non-block-based approaches yields two classes of procedures. Analysis of two different sets of SNP genotype data from the HapMap is used to judge the practical aspects of using each of the programs considered, as well as to make some general observations about the performance of the programs in finding optimal sets of tagging SNPs. Pairwise R2 methods, while the simplest of those considered, do tend to pick more tagging SNPs than are strictly needed to predict unmeasured (non-tagging SNPs, since a combination of two or more tagging SNPs can form a prediction of SNPs that have no direct (pairwise surrogate. Block-based methods that exploit the linkage disequilibrium structure within haplotype blocks exploit this sort of redundancy, but run a risk of over-fitting if used without some care. A compromise approach which eliminates the need first to analyse block structure, but which still exploits simple relationships between SNPs, appears promising.

  16. Native Elution of Yeast Protein Complexes Obtained by Affinity Capture.

    Science.gov (United States)

    LaCava, John; Fernandez-Martinez, Javier; Rout, Michael P

    2016-01-01

    This protocol describes two options for the native (nondenaturing) elution of protein complexes obtained by affinity capture. The first approach involves the elution of complexes purified through a tag that includes a human rhinovirus 3C protease (PreScission protease) cleavage site sequence between the protein of interest and the tag. Incubation with the protease cleaves immobilized complexes from the affinity medium. The second approach involves the release of protein A-tagged protein complexes using a competitive elution reagent called PEGylOx. The degree of purity of the native assemblies eluted is sample dependent and strongly influenced by the affinity capture. It should be noted that the efficiency of native elution is commonly lower than that of elution by a denaturing agent (e.g., SDS) and the release of the complex will be limited by the activity of the protease or the inhibition constant (Ki) of the competitive release agent. However, an advantage of native release is that some nonspecifically bound materials tend to stay adsorbed to the affinity medium, providing an eluted fraction of higher purity. Finally, keep in mind that the presence of the protease or elution peptide could potentially affect downstream applications; thus, their removal should be considered. PMID:27371597

  17. Affine dynamics with torsion

    Energy Technology Data Exchange (ETDEWEB)

    Gueltekin, Kemal [Izmir Institute of Technology, Department of Physics, Izmir (Turkey)

    2016-03-15

    In this study, we give a thorough analysis of a general affine gravity with torsion. After a brief exposition of the affine gravities considered by Eddington and Schroedinger, we construct and analyze different affine gravities based on the determinants of the Ricci tensor, the torsion tensor, the Riemann tensor, and their combinations. In each case we reduce equations of motion to their simplest forms and give a detailed analysis of their solutions. Our analyses lead to the construction of the affine connection in terms of the curvature and torsion tensors. Our solutions of the dynamical equations show that the curvature tensors at different points are correlated via non-local, exponential rescaling factors determined by the torsion tensor. (orig.)

  18. Tag cloud generation for results of multiple keywords queries

    DEFF Research Database (Denmark)

    Leginus, Martin; Dolog, Peter; Lage, Ricardo Gomes

    2013-01-01

    In this paper we study tag cloud generation for retrieved results of multiple keyword queries. It is motivated by many real world scenarios such as personalization tasks, surveillance systems and information retrieval tasks defined with multiple keywords. We adjust the state-of-the-art tag cloud...... generation techniques for multiple keywords query results. Consequently, we conduct the extensive evaluation on top of three distinct collaborative tagging systems. The graph-based methods perform significantly better for the Movielens and Bibsonomy datasets. Tag cloud generation based on maximal coverage...

  19. Versatile protein tagging in cells with split fluorescent protein

    OpenAIRE

    Kamiyama, Daichi; Sekine, Sayaka; Barsi-Rhyne, Benjamin; Hu, Jeffrey; Chen, Baohui; Gilbert, Luke A.; Ishikawa, Hiroaki; Leonetti, Manuel D.; Marshall, Wallace F.; Jonathan S Weissman; Huang, Bo

    2016-01-01

    In addition to the popular method of fluorescent protein fusion, live cell protein imaging has now seen more and more application of epitope tags. The small size of these tags may reduce functional perturbation and enable signal amplification. To address their background issue, we adapt self-complementing split fluorescent proteins as epitope tags for live cell protein labelling. The two tags, GFP11 and sfCherry11 are derived from the eleventh β-strand of super-folder GFP and sfCherry, respec...

  20. Tag-elese or The Language of Tags

    Directory of Open Access Journals (Sweden)

    Jan Simons

    2008-01-01

    Full Text Available The core "meme" of Web 2.0 from which almost all other memes radiated was: 'You control your own data' (O'Reilly, 2005, 3. Key instruments for this user control are tagging systems that allow users to freely assign keywords of their own choosing to Internet resources of their own making as well as to documents produced by others. Of course, freely chosen keywords tags do not necessarily follow prefixed taxonomies or classification systems. But going by the maxim that interaction creates similarity and similarity creates interaction, the idea - or hope - is, however, that the tagging practices of individual users will eventually converge into an emergent common vocabulary or folksonomy (Merholz, 2004; Shirky, 2005; Vander Wal, 2005b; Mika, 2007. It is far from clear, however, that free tagging systems will eventually yield controlled vocabularies, and there are many incentives for idiosyncratic, ambiguous, and inconsistent uses of tags. Left to themselves, free tagging systems seem to be too wild and too chaotic for any order to emerge. But are these free tagging systems really as "feral" as they seem to be, or do they only look uncontrolled because one has been looking for order in the wrong place? I have done a quick-and-dirty" analysis of Flickr's tag cloud. The concept was: if folksonomies encourage users to tap on their own vernacular, everyday natural language must somehow "guide" the tagging practices of users of tagging systems. Flickr's tag cloud has been choosen because it may teach us something about tagging systems and folksonomies, and not - or not primarily - because of what tags may tell us about pictures.

  1. Security Techniques for Prevention of Rank Manipulation in Social Tagging Services including Robotic Domains

    Directory of Open Access Journals (Sweden)

    Okkyung Choi

    2014-01-01

    Full Text Available With smartphone distribution becoming common and robotic applications on the rise, social tagging services for various applications including robotic domains have advanced significantly. Though social tagging plays an important role when users are finding the exact information through web search, reliability and semantic relation between web contents and tags are not considered. Spams are making ill use of this aspect and put irrelevant tags deliberately on contents and induce users to advertise contents when they click items of search results. Therefore, this study proposes a detection method for tag-ranking manipulation to solve the problem of the existing methods which cannot guarantee the reliability of tagging. Similarity is measured for ranking the grade of registered tag on the contents, and weighted values of each tag are measured by means of synonym relevance, frequency, and semantic distances between tags. Lastly, experimental evaluation results are provided and its efficiency and accuracy are verified through them.

  2. Affine and degenerate affine BMW algebras: Actions on tensor space

    CERN Document Server

    Daugherty, Zajj; Virk, Rahbar

    2012-01-01

    The affine and degenerate affine Birman-Murakami-Wenzl (BMW) algebras arise naturally in the context of Schur-Weyl duality for orthogonal and symplectic quantum groups and Lie algebras, respectively. Cyclotomic BMW algebras, affine and cyclotomic Hecke algebras, and their degenerate versions are quotients. In this paper we explain how the affine and degenerate affine BMW algebras are tantalizers (tensor power centralizer algebras) by defining actions of the affine braid group and the degenerate affine braid algebra on tensor space and showing that, in important cases, these actions induce actions of the affine and degenerate affine BMW algebras. We then exploit the connection to quantum groups and Lie algebras to determine universal parameters for the affine and degenerate affine BMW algebras. Finally, we show that the universal parameters are central elements--the higher Casimir elements for orthogonal and symplectic enveloping algebras and quantum groups.

  3. Improving image segmentation by learning region affinities

    Energy Technology Data Exchange (ETDEWEB)

    Prasad, Lakshman [Los Alamos National Laboratory; Yang, Xingwei [TEMPLE UNIV.; Latecki, Longin J [TEMPLE UNIV.

    2010-11-03

    We utilize the context information of other regions in hierarchical image segmentation to learn new regions affinities. It is well known that a single choice of quantization of an image space is highly unlikely to be a common optimal quantization level for all categories. Each level of quantization has its own benefits. Therefore, we utilize the hierarchical information among different quantizations as well as spatial proximity of their regions. The proposed affinity learning takes into account higher order relations among image regions, both local and long range relations, making it robust to instabilities and errors of the original, pairwise region affinities. Once the learnt affinities are obtained, we use a standard image segmentation algorithm to get the final segmentation. Moreover, the learnt affinities can be naturally unutilized in interactive segmentation. Experimental results on Berkeley Segmentation Dataset and MSRC Object Recognition Dataset are comparable and in some aspects better than the state-of-art methods.

  4. Fast and scalable image auto-tagging

    CERN Document Server

    Frejaville, Camille; Lepetit, Vincent

    Inside Invenio, the web-based integrated system for handling digital libraries developed at CERN, there is a media module, enabling users to upload photos and videos. Especially in CDS, the Invenio instance used at CERN, people use this digital library to upload pictures of official events that took place at CERN. However, so far, there was no way of tagging what’s inside these photos. This project is meant to solve the problem of tagging persons in a photo in an easy and fast way. First, by implementing a complete tagging interface that allows the user to square parts of the photo, resize them, move them and give them a name. Second, by running face detection so that squares already appear on faces and the user just has to fill the title field. Finally, by running a face recognition system that learned from previous tags created by users. In this report, we will show how we implemented the tagging interface, how we improved the existing face detector to make it more efficient, which face detection methods ...

  5. Protein isolation using affinity chromatography

    OpenAIRE

    Besselink, T.

    2012-01-01

    Many product or even waste streams in the food industry contain components that may have potential for e.g. functional foods. These streams are typically large in volume and the components of interest are only present at low concentrations. A robust and highly selective separation process should be developed for efficient isolation of the components. Affinity chromatography is such a selective method. Ligands immobilized to a stationary phase (e.g., a resin or membrane) are used to bind the c...

  6. Affinity Proteomics in the mountains: Alpbach 2015.

    Science.gov (United States)

    Taussig, Michael J

    2016-09-25

    The 2015 Alpbach Workshop on Affinity Proteomics, organised by the EU AFFINOMICS consortium, was the 7th workshop in this series. As in previous years, the focus of the event was the current state of affinity methods for proteome analysis, including complementarity with mass spectrometry, progress in recombinant binder production methods, alternatives to classical antibodies as affinity reagents, analysis of proteome targets, industry focus on biomarkers, and diagnostic and clinical applications. The combination of excellent science with Austrian mountain scenery and winter sports engender an atmosphere that makes this series of workshops exceptional. The articles in this Special Issue represent a cross-section of the presentations at the 2015 meeting. PMID:27118167

  7. Upper Tag Ontology (UTO) For Integrating Social Tagging Data

    CERN Document Server

    Ding, Ying; Fried, Michael; Toma, Ioan; Yan, Erjia; Foo, Schubert

    2010-01-01

    Data integration and mediation have become central concerns of information technology over the past few decades. With the advent of the Web and the rapid increases in the amount of data and the number of Web documents and users, researchers have focused on enhancing the interoperability of data through the development of metadata schemes. Other researchers have looked to the wealth of metadata generated by bookmarking sites on the Social Web. While several existing ontologies capitalize on the semantics of metadata created by tagging activities, the Upper Tag Ontology (UTO) emphasizes the structure of tagging activities to facilitate modeling of tagging data and the integration of data from different bookmarking sites as well as the alignment of tagging ontologies. UTO is described and its utility in harvesting, modeling, integrating, searching and analyzing data is demonstrated with metadata harvested from three major social tagging systems (Delicious, Flickr and YouTube).

  8. Identifying Nuclear Materials Using Tagged Muons

    CERN Document Server

    Morris, C L; Borodzin, K; Durham, J M; Fabritius, J M; Guardincerri, E; Hecht, A; Milner, E C; Miyadera, H; Perry, J O; Poulson, D

    2014-01-01

    Experimental results from a new technique that uses neutrons generated by stopped cosmic-ray muons to identify nuclear materials are described. The neutrons are used to tag muon-induced fission events in actinides and laminography is used to form images of the stopping material. This technique allows the imaging of uranium objects tagged using muon tracking detectors located above or to the side of the objects. The specificity of the technique to significant quantities of nuclear material along with its insensitivity to spatial details may provide a new method for the task of warhead verification for future arms reduction treaties.

  9. Imaging mass spectrometer with mass tags

    Science.gov (United States)

    Felton, James S.; Wu, Kuang Jen J.; Knize, Mark G.; Kulp, Kristen S.; Gray, Joe W.

    2013-01-29

    A method of analyzing biological material by exposing the biological material to a recognition element, that is coupled to a mass tag element, directing an ion beam of a mass spectrometer to the biological material, interrogating at least one region of interest area from the biological material and producing data, and distributing the data in plots.

  10. Improving Web Document Clustering through Employing User-Related Tag Expansion Techniques

    Institute of Scientific and Technical Information of China (English)

    Peng Li; Bin Wang; Wei Jin

    2012-01-01

    As high quality descriptors of web page semantics,social annotations or tags have been used for web document clustering and achieved promising results.However,most web pages have few tags (less than 10).This sparsity seriously limits the usage of tags for clustering.In this work,we propose a user-related tag expansion method to overcome this problem,which incorporates additional useful tags into the original tag document by utilizing user tagging data as background knowledge.Unfortunately,simply adding tags may cause topic drift,i.e.,the dominant topic(s) of the original document may be changed.To tackle this problem,we have designed a novel generative model called Folk-LDA,which jointly models original and expanded tags as independent observations.ExPerimental results show that 1) our user-related tag expansion method can be effectively applied to over 90% tagged web documents; 2) Folk-LDA can alleviate topic drift in expansion,especially for those topic-specific documents; 3) the proposed tag-based clustering methods significantly outperform the word-based methods,which indicates that tags could be a better resource for the clustering task.

  11. Preparation of recombinant firefly luciferase by a simple and rapid expression and purification method and its application in bacterial detection

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    A simple and rapid expression and purification method of recombinant firefly luciferase was developed for bacteria detection. A modified luciferase gene from North American firefly Photinus pyralis was cloned into pET28a expression vector and the recombinant protein was produced in Escherichia coli BL21. The recombinant luciferase,equipped with a polyhistidine affinity tag,was purified by immobilized metal ion affinity chromatography (IMAC). The approach generated an abundant expression and an efficient pur...

  12. Buddy Tag CONOPS and Requirements.

    Energy Technology Data Exchange (ETDEWEB)

    Brotz, Jay Kristoffer [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Deland, Sharon M. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2015-12-01

    This document defines the concept of operations (CONOPS) and the requirements for the Buddy Tag, which is conceived and designed in collaboration between Sandia National Laboratories and Princeton University under the Department of State Key VerificationAssets Fund. The CONOPS describe how the tags are used to support verification of treaty limitations and is only defined to the extent necessary to support a tag design. The requirements define the necessary functions and desired non-functional features of the Buddy Tag at a high level

  13. Spectral affinity in protein networks

    Directory of Open Access Journals (Sweden)

    Teng Shang-Hua

    2009-11-01

    Full Text Available Abstract Background Protein-protein interaction (PPI networks enable us to better understand the functional organization of the proteome. We can learn a lot about a particular protein by querying its neighborhood in a PPI network to find proteins with similar function. A spectral approach that considers random walks between nodes of interest is particularly useful in evaluating closeness in PPI networks. Spectral measures of closeness are more robust to noise in the data and are more precise than simpler methods based on edge density and shortest path length. Results We develop a novel affinity measure for pairs of proteins in PPI networks, which uses personalized PageRank, a random walk based method used in context-sensitive search on the Web. Our measure of closeness, which we call PageRank Affinity, is proportional to the number of times the smaller-degree protein is visited in a random walk that restarts at the larger-degree protein. PageRank considers paths of all lengths in a network, therefore PageRank Affinity is a precise measure that is robust to noise in the data. PageRank Affinity is also provably related to cluster co-membership, making it a meaningful measure. In our experiments on protein networks we find that our measure is better at predicting co-complex membership and finding functionally related proteins than other commonly used measures of closeness. Moreover, our experiments indicate that PageRank Affinity is very resilient to noise in the network. In addition, based on our method we build a tool that quickly finds nodes closest to a queried protein in any protein network, and easily scales to much larger biological networks. Conclusion We define a meaningful way to assess the closeness of two proteins in a PPI network, and show that our closeness measure is more biologically significant than other commonly used methods. We also develop a tool, accessible at http://xialab.bu.edu/resources/pnns, that allows the user to

  14. Optimized Affinity Capture of Yeast Protein Complexes.

    Science.gov (United States)

    LaCava, John; Fernandez-Martinez, Javier; Hakhverdyan, Zhanna; Rout, Michael P

    2016-01-01

    Here, we describe an affinity isolation protocol. It uses cryomilled yeast cell powder for producing cell extracts and antibody-conjugated paramagnetic beads for affinity capture. Guidelines for determining the optimal extraction solvent composition are provided. Captured proteins are eluted in a denaturing solvent (sodium dodecyl sulfate polyacrylamide gel electrophoresis sample buffer) for gel-based proteomic analyses. Although the procedures can be modified to use other sources of cell extract and other forms of affinity media, to date we have consistently obtained the best results with the method presented. PMID:27371596

  15. Affinity Purification and Characterization of a G-Protein Coupled Receptor, Saccharomyces cerevisiae Ste2p

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Byung-Kwon [University of Tennessee, Knoxville (UTK); Jung, Kyung-Sik [University of Tennessee, Knoxville (UTK); Son, Cagdas D [ORNL; Kim, Heejung [University of Tennessee, Knoxville (UTK); Verberkmoes, Nathan C [ORNL; Arshava, Boris [College of Staten Island; Naider, Fred [College of Staten Island; Becker, Jeffrey Marvin [ORNL

    2007-01-01

    We present a rare example of a biologically active G protein coupled receptor (GPCR) whose purity and identity were verified by mass spectrometry after being purified to near homogeneity from its native system. An overexpression vector was constructed to encode the Saccharomyces cerevisiae GPCR -factor receptor (Ste2p, the STE2 gene product) containing a 9-amino acid sequence of rhodopsin that served as an epitope/affinity tag. In the construct, two glycosylation sites and two cysteine residues were removed to aid future structural and functional studies. The receptor was expressed in yeast cells and was detected as a single band in a western blot indicating the absence of glycosylation. Tests of the epitope-tagged, mutated receptor showed it maintained its full biological activity. For extraction of Ste2p, yeast membranes were solubilized with 0.5 % n-dodecyl maltoside (DM). Approximately 120 g of purified -factor receptor was obtained per liter of culture by single-step affinity chromatography using a monoclonal antibody to the rhodopsin epitope. The binding affinity (Kd) of the purified -factor receptor in DM micelles was 28 nM as compared to Kd = 12.7 nM for Ste2p in cell membranes, and approximately 40 % of the purified receptor was correctly folded as judged by ligand saturation binding. About 50 % of the receptor sequence was retrieved from MALDITOF and nanospray mass spectrometry after CNBr digestion of the purified receptor. The methods described will enable structural studies of the -factor receptor and may provide an efficient technique to purify other GPCRs that have been functionally expressed in yeast.

  16. Using an explicit emission tagging method in global modeling of source-receptor relationships for black carbon in the Arctic: Variations, sources, and transport pathways

    Science.gov (United States)

    Wang, Hailong; Rasch, Philip J.; Easter, Richard C.; Singh, Balwinder; Zhang, Rudong; Ma, Po-Lun; Qian, Yun; Ghan, Steven J.; Beagley, Nathaniel

    2014-11-01

    We introduce an explicit emission tagging technique in the Community Atmosphere Model to quantify source-region-resolved characteristics of black carbon (BC), focusing on the Arctic. Explicit tagging of BC source regions without perturbing the emissions provides a physically consistent and computationally efficient approach to establish source-receptor relationships and transport pathways. Our analysis shows that the contributions of major source regions to the global BC burden are not proportional to the respective emissions due to strong region-dependent removal rates and lifetimes, while the contributions to BC direct radiative forcing show a near-linear dependence on their respective contributions to the burden. Arctic BC concentrations, deposition, and source contributions all have strong seasonal variations. Eastern Asia contributes the most to the wintertime Arctic BC burden, but has much less impact on lower-level concentrations and deposition. Northern Europe emissions are more important to both surface concentration and deposition in winter than in summer. The largest contribution to Arctic BC in the summer is from Northern Asia. Although local emissions contribute less than 10% to the annual mean BC burden and deposition within the Arctic, the per-emission efficiency is much higher than for non-Arctic sources. The interannual variability (1996-2005) due to meteorology is small in annual mean BC burden and radiative forcing but is significant in yearly seasonal means over the Arctic. When a slow aging treatment of BC is introduced, the increase of BC lifetime and burden is source dependent. Global BC forcing-per-burden efficiency also increases primarily due to changes in BC vertical distributions.

  17. Online encyclopedia entities tagging method based on page struc-ture and content%融合页面结构与内容的在线百科实体标注方法

    Institute of Scientific and Technical Information of China (English)

    李晓静; 林海伦; 贾岩涛; 王元卓; 程学旗

    2015-01-01

    Online encyclopedia entity tagging aims to label online encyclopedia pages with standard named entity tags such as person, location and organization. It is crucial for a wide range of applications such as entity disambigu-ation, entity relation inference and knowledge base construction and so on. Features of encyclopedia pages can be divided as structure features (e.g., Infobox, title, and category) and content features (i.e., page content). Existing methods that only take one feature or simply combine both features in one classification cause low F1 value. These methods don’t make full use of the difference of these features. This paper presents an online encyclopedia entities tagging method based on page structure and content. This method firstly builds two classifiers with the two kinds of features respectively, and then builds a new classifier by linear combination of these two classifiers, so this method can accurately realize entities tagging. The experimental results show that this method can achieve F1 value improve-ment over the baseline methods on the task of encyclopedia entity tagging.%在线百科实体标注目的是标注出属于特定类别(如人名、地名、机构名等)的实体。百科实体标注对大量的应用,诸如实体消歧、实体关系挖掘、知识库构建都很重要。百科实体特征可以分为结构特征(属性框、标题、类别等)和内容特征(页面正文)。现有的标注方法大多只考虑一种特征或者一种分类器,导致F1值较低,无法充分发挥两种特征的优势。因此,提出了融合页面结构特征和内容特征的在线百科实体标注方法。该方法考虑了两种特征对标注结果的影响,分别构造分类器,并且对结果进行线性组合,能够更准确地实现百科实体的实体标注。实验表明,该方法在实体标注中F1值较其他对比实验方法均有所提高。

  18. 融合页面结构与内容的在线百科实体标注方法%Online encyclopedia entities tagging method based on page struc-ture and content

    Institute of Scientific and Technical Information of China (English)

    李晓静; 林海伦; 贾岩涛; 王元卓; 程学旗

    2015-01-01

    Online encyclopedia entity tagging aims to label online encyclopedia pages with standard named entity tags such as person, location and organization. It is crucial for a wide range of applications such as entity disambigu-ation, entity relation inference and knowledge base construction and so on. Features of encyclopedia pages can be divided as structure features (e.g., Infobox, title, and category) and content features (i.e., page content). Existing methods that only take one feature or simply combine both features in one classification cause low F1 value. These methods don’t make full use of the difference of these features. This paper presents an online encyclopedia entities tagging method based on page structure and content. This method firstly builds two classifiers with the two kinds of features respectively, and then builds a new classifier by linear combination of these two classifiers, so this method can accurately realize entities tagging. The experimental results show that this method can achieve F1 value improve-ment over the baseline methods on the task of encyclopedia entity tagging.%在线百科实体标注目的是标注出属于特定类别(如人名、地名、机构名等)的实体。百科实体标注对大量的应用,诸如实体消歧、实体关系挖掘、知识库构建都很重要。百科实体特征可以分为结构特征(属性框、标题、类别等)和内容特征(页面正文)。现有的标注方法大多只考虑一种特征或者一种分类器,导致F1值较低,无法充分发挥两种特征的优势。因此,提出了融合页面结构特征和内容特征的在线百科实体标注方法。该方法考虑了两种特征对标注结果的影响,分别构造分类器,并且对结果进行线性组合,能够更准确地实现百科实体的实体标注。实验表明,该方法在实体标注中F1值较其他对比实验方法均有所提高。

  19. Tag Gardening for Folksonomy Enrichment and Maintenance

    Directory of Open Access Journals (Sweden)

    Katrin Weller

    2008-09-01

    Full Text Available As social tagging applications continuously gain in popularity, it becomes more and more accepted that models and tools for (re-organizing tags are needed. Some first approaches are already practically implemented. Recently, activities to edit and organize tags have been described as "tag gardening". We discuss different ways to subsequently revise and reedit tags and thus introduce different "gardening activities"; among them models that allow gradually adding semantic structures to folksonomies and/or that combine them with more complex forms of knowledge organization systems. Moreover, power tags are introduced as tag gardening candidates and the personal tag repository TagCare is presented.

  20. Novel and efficient tag SNPs selection algorithms.

    Science.gov (United States)

    Chen, Wen-Pei; Hung, Che-Lun; Tsai, Suh-Jen Jane; Lin, Yaw-Ling

    2014-01-01

    SNPs are the most abundant forms of genetic variations amongst species; the association studies between complex diseases and SNPs or haplotypes have received great attention. However, these studies are restricted by the cost of genotyping all SNPs; thus, it is necessary to find smaller subsets, or tag SNPs, representing the rest of the SNPs. In fact, the existing tag SNP selection algorithms are notoriously time-consuming. An efficient algorithm for tag SNP selection was presented, which was applied to analyze the HapMap YRI data. The experimental results show that the proposed algorithm can achieve better performance than the existing tag SNP selection algorithms; in most cases, this proposed algorithm is at least ten times faster than the existing methods. In many cases, when the redundant ratio of the block is high, the proposed algorithm can even be thousands times faster than the previously known methods. Tools and web services for haplotype block analysis integrated by hadoop MapReduce framework are also developed using the proposed algorithm as computation kernels. PMID:24212035

  1. Affine stochastic mortality

    NARCIS (Netherlands)

    D.F. Schrager

    2006-01-01

    We propose a new model for stochastic mortality. The model is based on the literature on affine term structure models. It satisfies three important requirements for application in practice: analytical tractibility, clear interpretation of the factors and compatibility with financial option pricing m

  2. LHCb Tag Collector

    CERN Document Server

    Fuente Fernàndez, P; Cousin, N

    2011-01-01

    The LHCb physics software consists of hundreds of packages, each of which is developed by one or more physicists. When the developers have some code changes that they would like released, they commit them to the version control system, and enter the revision number into a database. These changes have to be integrated into a new release of each of the physics analysis applications. Tests are then performed by a nightly build system, which rebuilds various configurations of the whole software stack and executes a suite of run-time functionality tests. A Tag Collector system has been developed using solid standard technologies to cover both the use cases of developers and integration managers. A simple Web interface, based on an AJAX-like technology, is available. Integration with software management and Nightly Build programs is possible via a Python API. Data are stored in a relational database with the help of an ORM (Object-Relational Mapping) library.

  3. An Overview of Social Tagging and Applications

    Science.gov (United States)

    Gupta, Manish; Li, Rui; Yin, Zhijun; Han, Jiawei

    Social tagging on online portals has become a trend now. It has emerged as one of the best ways of associating metadata with web objects. With the increase in the kinds of web objects becoming available, collaborative tagging of such objects is also developing along new dimensions. This popularity has led to a vast literature on social tagging. In this survey paper, we would like to summarize different techniques employed to study various aspects of tagging. Broadly, we would discuss about properties of tag streams, tagging models, tag semantics, generating recommendations using tags, visualizations of tags, applications of tags, integration of different tagging systems and problems associated with tagging usage. We would discuss topics like why people tag, what influences the choice of tags, how to model the tagging process, kinds of tags, different power laws observed in tagging domain, how tags are created and how to choose the right tags for recommendation. Metadata generated in the form of tags can be efficiently used to improve web search, for web object classification, for generating ontologies, for enhanced browsing etc. We would discuss these applications and conclude with thoughts on future work in the area.

  4. A Methodology for Simultaneous Fluorogenic Derivatization and Boronate Affinity Enrichment of 3-Nitrotyrosine Containing Peptides

    Science.gov (United States)

    Dremina, Elena S.; Li, Xiaobao; Galeva, Nadezhda A.; Sharov, Victor S.; Stobaugh, John F.; Schöneich, Christian

    2011-01-01

    We synthesized and characterized a new tagging reagent, (3R,4S)-1-(4-(aminomethyl)phenylsulfonyl)pyrrolidine-3,4-diol (APPD), for the selective fluorogenic derivatization of 3-nitrotyrosine (3-NT) residues in peptides (after reduction to 3-aminotyrosine) and affinity enrichment. The synthetic 3-NT-containing peptide, FSAY(3-NO2)LER, was employed as a model for method validation. Further, this derivatization protocol was successfully tested for analysis of 3-NT-containing proteins exposed to peroxynitrite in the total protein lysate of cultured C2C12 cells. The quantitation of 3-NT content in samples was achieved through either fluorescence spectrometry or boronate affinity chromatography with detection by specific fluorescence (excitation and emission wavelengths of 360 and 510 nm, respectively); the respective limits of detection were 95 and 68 nM (19 and 13 pmol total amount) of 3-NT. Importantly, the derivatized peptides show a strong retention on a synthetic boronate affinity column, containing sulfonamide-phenylboronic acid, under mild chromatographic conditions, affording a route to separate the derivatized peptides from large amounts (milligrams) of non-derivatized peptides, and to enrich them for fluorescent detection and MS identification. Tandem MS analysis identified chemical structures of peptide 3-NT fluorescent derivatives and revealed that the fluorescent derivatives undergo efficient backbone fragmentations, permitting sequence-specific identification of protein nitration at low concentrations of 3-NT in complex protein mixtures. PMID:21855526

  5. A methodology for simultaneous fluorogenic derivatization and boronate affinity enrichment of 3-nitrotyrosine-containing peptides.

    Science.gov (United States)

    Dremina, Elena S; Li, Xiaobao; Galeva, Nadezhda A; Sharov, Victor S; Stobaugh, John F; Schöneich, Christian

    2011-11-15

    We synthesized and characterized a new tagging reagent, (3R,4S)-1-(4-(aminomethyl)phenylsulfonyl)pyrrolidine-3,4-diol (APPD), for the selective fluorogenic derivatization of 3-nitrotyrosine (3-NT) residues in peptides (after reduction to 3-aminotyrosine) and affinity enrichment. The synthetic 3-NT-containing peptide, FSAY(3-NO(2))LER, was employed as a model for method validation. Furthermore, this derivatization protocol was successfully tested for analysis of 3-NT-containing proteins exposed to peroxynitrite in the total protein lysate of cultured C2C12 cells. The quantitation of 3-NT content in samples was achieved through either fluorescence spectrometry or boronate affinity chromatography with detection by specific fluorescence (excitation and emission wavelengths of 360 and 510 nm, respectively); the respective limits of detection were 95 and 68 nM (19 and 13 pmol total amount) of 3-NT. Importantly, the derivatized peptides show a strong retention on a synthetic boronate affinity column, containing sulfonamide-phenylboronic acid, under mild chromatographic conditions, affording a route to separate the derivatized peptides from large amounts (milligrams) of nonderivatized peptides and to enrich them for fluorescent detection and mass spectrometry (MS) identification. Tandem MS analysis identified chemical structures of peptide 3-NT fluorescent derivatives and revealed that the fluorescent derivatives undergo efficient backbone fragmentations, permitting sequence-specific identification of protein nitration at low concentrations of 3-NT in complex protein mixtures. PMID:21855526

  6. Methyl-CpG island-associated genome signature tags

    Science.gov (United States)

    Dunn, John J

    2014-05-20

    Disclosed is a method for analyzing the organismic complexity of a sample through analysis of the nucleic acid in the sample. In the disclosed method, through a series of steps, including digestion with a type II restriction enzyme, ligation of capture adapters and linkers and digestion with a type IIS restriction enzyme, genome signature tags are produced. The sequences of a statistically significant number of the signature tags are determined and the sequences are used to identify and quantify the organisms in the sample. Various embodiments of the invention described herein include methods for using single point genome signature tags to analyze the related families present in a sample, methods for analyzing sequences associated with hyper- and hypo-methylated CpG islands, methods for visualizing organismic complexity change in a sampling location over time and methods for generating the genome signature tag profile of a sample of fragmented DNA.

  7. Tagging, Encoding, and Jones Optimality

    DEFF Research Database (Denmark)

    Danvy, Olivier; López, Pablo Ernesto Martínes

    2003-01-01

    is typed, however, residual programs are cluttered with type tags. To obtain the original source program, these tags must be removed. A number of sophisticated solutions have already been proposed. We observe, however, that with a simple representation shift, ordinary partial evaluation is already Jones...

  8. Design and Analysis of Salmonid Tagging Studies in the Columbia Basin, Volume XXI; A Summary of Methods for Conducting Salmonid Fry Mark-Recapture Studies for Estimating Survival in Tributaries, Technical Report 2005-2006.

    Energy Technology Data Exchange (ETDEWEB)

    Skalski, John

    2007-02-01

    Productivity and early fry survival can have a major influence on the dynamics of fish stocks. To investigate the early life history of fish, numerous methods have been developed or adapted to these much smaller fish. Some of the marking techniques provide individual identification; many others, only class identification. Some of the tagging techniques require destructive sampling to identify a mark; other methods permit benign examination and rerelease of captured fish. Sixteen alternative release-recapture designs for conducting fry survival investigations were examined. Eleven approaches were found capable of estimating survival parameters; five were not. Of those methods capable of estimating fry survival, five required unique marks, four required batch-specific marks, and two approaches required remarking and rereleasing captured fry. No approach based on a simple batch mark was capable of statistically estimating survival.

  9. Versatile protein tagging in cells with split fluorescent protein.

    Science.gov (United States)

    Kamiyama, Daichi; Sekine, Sayaka; Barsi-Rhyne, Benjamin; Hu, Jeffrey; Chen, Baohui; Gilbert, Luke A; Ishikawa, Hiroaki; Leonetti, Manuel D; Marshall, Wallace F; Weissman, Jonathan S; Huang, Bo

    2016-03-18

    In addition to the popular method of fluorescent protein fusion, live cell protein imaging has now seen more and more application of epitope tags. The small size of these tags may reduce functional perturbation and enable signal amplification. To address their background issue, we adapt self-complementing split fluorescent proteins as epitope tags for live cell protein labelling. The two tags, GFP11 and sfCherry11 are derived from the eleventh β-strand of super-folder GFP and sfCherry, respectively. The small size of FP11-tags enables a cost-effective and scalable way to insert them into endogenous genomic loci via CRISPR-mediated homology-directed repair. Tandem arrangement FP11-tags allows proportional enhancement of fluorescence signal in tracking intraflagellar transport particles, or reduction of photobleaching for live microtubule imaging. Finally, we show the utility of tandem GFP11-tag in scaffolding protein oligomerization. These experiments illustrate the versatility of FP11-tag as a labelling tool as well as a multimerization-control tool for both imaging and non-imaging applications.

  10. Versatile protein tagging in cells with split fluorescent protein

    Science.gov (United States)

    Kamiyama, Daichi; Sekine, Sayaka; Barsi-Rhyne, Benjamin; Hu, Jeffrey; Chen, Baohui; Gilbert, Luke A.; Ishikawa, Hiroaki; Leonetti, Manuel D.; Marshall, Wallace F.; Weissman, Jonathan S.; Huang, Bo

    2016-01-01

    In addition to the popular method of fluorescent protein fusion, live cell protein imaging has now seen more and more application of epitope tags. The small size of these tags may reduce functional perturbation and enable signal amplification. To address their background issue, we adapt self-complementing split fluorescent proteins as epitope tags for live cell protein labelling. The two tags, GFP11 and sfCherry11 are derived from the eleventh β-strand of super-folder GFP and sfCherry, respectively. The small size of FP11-tags enables a cost-effective and scalable way to insert them into endogenous genomic loci via CRISPR-mediated homology-directed repair. Tandem arrangement FP11-tags allows proportional enhancement of fluorescence signal in tracking intraflagellar transport particles, or reduction of photobleaching for live microtubule imaging. Finally, we show the utility of tandem GFP11-tag in scaffolding protein oligomerization. These experiments illustrate the versatility of FP11-tag as a labelling tool as well as a multimerization-control tool for both imaging and non-imaging applications. PMID:26988139

  11. Versatile protein tagging in cells with split fluorescent protein.

    Science.gov (United States)

    Kamiyama, Daichi; Sekine, Sayaka; Barsi-Rhyne, Benjamin; Hu, Jeffrey; Chen, Baohui; Gilbert, Luke A; Ishikawa, Hiroaki; Leonetti, Manuel D; Marshall, Wallace F; Weissman, Jonathan S; Huang, Bo

    2016-01-01

    In addition to the popular method of fluorescent protein fusion, live cell protein imaging has now seen more and more application of epitope tags. The small size of these tags may reduce functional perturbation and enable signal amplification. To address their background issue, we adapt self-complementing split fluorescent proteins as epitope tags for live cell protein labelling. The two tags, GFP11 and sfCherry11 are derived from the eleventh β-strand of super-folder GFP and sfCherry, respectively. The small size of FP11-tags enables a cost-effective and scalable way to insert them into endogenous genomic loci via CRISPR-mediated homology-directed repair. Tandem arrangement FP11-tags allows proportional enhancement of fluorescence signal in tracking intraflagellar transport particles, or reduction of photobleaching for live microtubule imaging. Finally, we show the utility of tandem GFP11-tag in scaffolding protein oligomerization. These experiments illustrate the versatility of FP11-tag as a labelling tool as well as a multimerization-control tool for both imaging and non-imaging applications. PMID:26988139

  12. In situ tagging technique for fishes provides insight into growth and movement of invasive lionfish

    OpenAIRE

    John L Akins; Morris, James A.; Green, Stephanie J.

    2014-01-01

    Information on fish movement and growth is primarily obtained through the marking and tracking of individuals with external tags, which are usually affixed to anesthetized individuals at the surface. However, the quantity and quality of data obtained by this method is often limited by small sample sizes owing to the time associated with the tagging process, high rates of tagging-related mortality, and displacement of tagged individuals from the initial capture location. To address these issue...

  13. Using an Explicit Emission Tagging Method in Global Modeling of Source-Receptor Relationships for Black Carbon in the Arctic: Variations, Sources and Transport Pathways

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Hailong; Rasch, Philip J.; Easter, Richard C.; Singh, Balwinder; Zhang, Rudong; Ma, Po-Lun; Qian, Yun; Ghan, Steven J.; Beagley, Nathaniel

    2014-11-27

    We introduce an explicit emission tagging technique in the Community Atmosphere Model to quantify source-region-resolved characteristics of black carbon (BC), focusing on the Arctic. Explicit tagging of BC source regions without perturbing the emissions makes it straightforward to establish source-receptor relationships and transport pathways, providing a physically consistent and computationally efficient approach to produce a detailed characterization of the destiny of regional BC emissions and the potential for mitigation actions. Our analysis shows that the contributions of major source regions to the global BC burden are not proportional to the respective emissions due to strong region-dependent removal rates and lifetimes, while the contributions to BC direct radiative forcing show a near-linear dependence on their respective contributions to the burden. Distant sources contribute to BC in remote regions mostly in the mid- and upper troposphere, having much less impact on lower-level concentrations (and deposition) than on burden. Arctic BC concentrations, deposition and source contributions all have strong seasonal variations. Eastern Asia contributes the most to the wintertime Arctic burden. Northern Europe emissions are more important to both surface concentration and deposition in winter than in summer. The largest contribution to Arctic BC in the summer is from Northern Asia. Although local emissions contribute less than 10% to the annual mean BC burden and deposition within the Arctic, the per-emission efficiency is much higher than for major non-Arctic sources. The interannual variability (1996-2005) due to meteorology is small in annual mean BC burden and radiative forcing but is significant in yearly seasonal means over the Arctic. When a slow aging treatment of BC is introduced, the increase of BC lifetime and burden is source-dependent. Global BC forcing-per-burden efficiency also increases primarily due to changes in BC vertical distributions. The

  14. Sediment tracing from small torrential channels to gravel-bed rivers using pit tags method. A case study from the upper Guil catchment.

    Science.gov (United States)

    Graff, Kévin; Viel, Vincent; Carlier, Benoit; Lissak, Candide; Arnaud-Fassetta, Gilles; Fort, Monique; Madelin, Malika

    2016-04-01

    In mountainous areas, especially in large catchments with torrential tributaries, the production and sediment transport significantly increase flood impacts in the valley bottoms. The quantification and characterisation of sedimentary transfers are therefore major challenges to provide better flood risk management. As a part of SAMCO (ANR 12 SENV-0004 SAMCO) project, for mountain hazard assessment in a context of global changes, we tried to improve the knowledge of these hydromorphological systems at both spatial and temporal scales, by identifying sediment supply and sediment dynamics from torrential tributaries to the main channel. A sediment budget was used as a tool for quantifying erosion, transport and deposition processes. This research is focused on the upper Guil catchment (Queyras, Southern French Alps - 317 km2) entrenched in "schistes lustrés" and ophiolitic bedrock. This catchment is prone to catastrophic summer floods [June 1957 (>R.I. 100 yr), June 2000 (R.I. 30 yr)] characterised by huge sediment transport from tributaries to downvalley, very much facilitated by strong hillslope-channel connectivity (about 12,000 m3 volume of sediment aggraded in the Peyronnelle fan during the June 2000 RI-30 year flood event). We intend to highlight sediment dynamics on small torrential channels and its connection with gravel-bed streams. Four study sites characterised by avalanche and debris flow-dominated channels located in the upper Guil catchment were investigated. In order to better assess sediment movement, we used the pit-tags technique. In total, 560 pit-tags (pt) have been implemented in four catchments: Peyronnelle (320pt), Combe Morel (40pt), Bouchouse (120pt), and Maloqueste (80pt). Distances and trajectories of gravels sediments have been monitored since two years during summer periods. We specifically describe results obtained along the Peyronnelle channel affected by a large debris-flow during august 2015. Data are used to discuss lag time

  15. Affine and degenerate affine BMW algebras: The center

    CERN Document Server

    Daugherty, Zajj; Virk, Rahbar

    2011-01-01

    The degenerate affine and affine BMW algebras arise naturally in the context of Schur-Weyl duality for orthogonal and symplectic Lie algebras and quantum groups, respectively. Cyclotomic BMW algebras, affine Hecke algebras, cyclotomic Hecke algebras, and their degenerate versions are quotients. In this paper the theory is unified by treating the orthogonal and symplectic cases simultaneously; we make an exact parallel between the degenerate affine and affine cases via a new algebra which takes the role of the affine braid group for the degenerate setting. A main result of this paper is an identification of the centers of the affine and degenerate affine BMW algebras in terms of rings of symmetric functions which satisfy a "cancellation property" or "wheel condition" (in the degenerate case, a reformulation of a result of Nazarov). Miraculously, these same rings also arise in Schubert calculus, as the cohomology and K-theory of isotropic Grassmanians and symplectic loop Grassmanians. We also establish new inte...

  16. Antibody affinity maturation

    DEFF Research Database (Denmark)

    Skjødt, Mette Louise

    linker for yeast surface display of scFv and scFab fragments, we compared a series of different Gly-Ser-based linkers in display and antigen binding proficiency. We show that these formats of the model antibody can accommodate linkers of different lengths and that introduction of alanine or glutamate......-2. Based on the presented data we suggest that affinity maturation of the model antibody proceeds through multiple incremental steps of subtle improvements. We moreover conclude that the best affinity improved candidates are likely to be obtained through optimization of both the antigen...... fragments by in vivo homologous recombination large combinatorial antibody libraries can easily be generated. We have optimized ordered assembly of three CDR fragments into a gapped vector and observed increased transformation efficiency in a yeast strain carrying a deletion of the SGS1 helicase...

  17. Measuring an antibody affinity distribution molecule by molecule

    Energy Technology Data Exchange (ETDEWEB)

    Bradbury, Andrew M [Los Alamos National Laboratory; Werner, James H [Los Alamos National Laboratory; Temirov, Jamshid [INVITROGEN

    2008-01-01

    Single molecule fluorescence mIcroscopy was used to observe the binding and unbinding of hapten decorated quantum dots with individual surface immobilized antibodies. The fluorescence time history from an individual antibody site can be used to calculate its binding affinity. While quantum dot blinking occurs during these measurements, we describe a simple empirical method to correct the apparent/observed affinity to account for the blinking contribution. The combination of many single molecule affinity measurements from different antibodies yields not only the average affinity, it directly measures the full shape and character of the surface affinity distribution function.

  18. Affinity driven social networks

    Science.gov (United States)

    Ruyú, B.; Kuperman, M. N.

    2007-04-01

    In this work we present a model for evolving networks, where the driven force is related to the social affinity between individuals of a population. In the model, a set of individuals initially arranged on a regular ordered network and thus linked with their closest neighbors are allowed to rearrange their connections according to a dynamics closely related to that of the stable marriage problem. We show that the behavior of some topological properties of the resulting networks follows a non trivial pattern.

  19. RAC-tagging: Recombineering And Cas9-assisted targeting for protein tagging and conditional analyses.

    Science.gov (United States)

    Baker, Oliver; Gupta, Ashish; Obst, Mandy; Zhang, Youming; Anastassiadis, Konstantinos; Fu, Jun; Stewart, A Francis

    2016-01-01

    A fluent method for gene targeting to establish protein tagged and ligand inducible conditional loss-of-function alleles is described. We couple new recombineering applications for one-step cloning of gRNA oligonucleotides and rapid generation of short-arm (~1 kb) targeting constructs with the power of Cas9-assisted targeting to establish protein tagged alleles in embryonic stem cells at high efficiency. RAC (Recombineering And Cas9)-tagging with Venus, BirM, APEX2 and the auxin degron is facilitated by a recombineering-ready plasmid series that permits the reuse of gene-specific reagents to insert different tags. Here we focus on protein tagging with the auxin degron because it is a ligand-regulated loss-of-function strategy that is rapid and reversible. Furthermore it includes the additional challenge of biallelic targeting. Despite high frequencies of monoallelic RAC-targeting, we found that simultaneous biallelic targeting benefits from long-arm (>4 kb) targeting constructs. Consequently an updated recombineering pipeline for fluent generation of long arm targeting constructs is also presented. PMID:27216209

  20. Affine morphisms at zero level

    CERN Document Server

    Das, Paramita; Gupta, Ved Prakash

    2010-01-01

    Given a finite index subfactor, we show that the {\\em affine morphisms at zero level} in the affine category over the planar algebra associated to the subfactor is isomorphic to the fusion algebra of the subfactor as a *-algebra.

  1. On the Affine Isoperimetric Inequalities

    Indian Academy of Sciences (India)

    Wuyang Yu; Gangsong Leng

    2011-11-01

    We obtain an isoperimetric inequality which estimate the affine invariant -surface area measure on convex bodies. We also establish the reverse version of -Petty projection inequality and an affine isoperimetric inequality of $_{-p}K$.

  2. Regional assessment of left ventricular torsion by CMR tagging

    OpenAIRE

    Marcus J Tim; Kuijer Joost P; Götte Marco J; Rüssel Iris K

    2008-01-01

    Abstract Purpose To introduce a standardized method for calculation of left ventricular torsion by CMR tagging and to determine the accuracy of torsion analysis in regions using an analytical model. Methods Torsion between base and apex, base and mid, and mid and apex levels was calculated using CSPAMM tagging and Harmonic Phase tracking. The accuracy of torsion analysis on a regional basis (circumferential segments and transmural layers) was analyzed using an analytical model of a deforming ...

  3. Adjoint affine fusion and tadpoles

    OpenAIRE

    Urichuk, Andrew; Walton, Mark A.

    2016-01-01

    We study affine fusion with the adjoint representation. For simple Lie algebras, elementary and universal formulas determine the decomposition of a tensor product of an integrable highest-weight representation with the adjoint representation. Using the (refined) affine depth rule, we prove that equally striking results apply to adjoint affine fusion. For diagonal fusion, a coefficient equals the number of nonzero Dynkin labels of the relevant affine highest weight, minus 1. A nice lattice-pol...

  4. Affine Patches on Positroid Varieties and Affine Pipe Dreams (Thesis)

    CERN Document Server

    Snider, Michelle

    2010-01-01

    The objects of interest in this thesis are positroid varieties in the Grassmannian, which are indexed by juggling patterns. In particular, we study affine patches on these positroid varieties. Our main result corresponds these affine patches to Kazhdan-Lusztig varieties in the affine Grassmannian. We develop a new term order and study how these spaces are related to subword complexes and Stanley-Reisner ideals. We define an extension of pipe dreams to the affine case and conclude by showing how our affine pipe dreams are generalizations of Cauchon and Le diagrams.

  5. Affine and quasi-affine frames for rational dilations

    DEFF Research Database (Denmark)

    Bownik, Marcin; Lemvig, Jakob

    2011-01-01

    , the corresponding family of quasi-affine systems are frames with uniform frame bounds. We also prove a similar equivalence result between pairs of dual affine frames and dual quasi-affine frames. Finally, we uncover some fundamental differences between the integer and rational settings by exhibiting an example......In this paper we extend the investigation of quasi-affine systems, which were originally introduced by Ron and Shen [J. Funct. Anal. 148 (1997), 408-447] for integer, expansive dilations, to the class of rational, expansive dilations. We show that an affine system is a frame if, and only if...

  6. Search for the Higgs boson in the ZH→v$\\bar{v}$b$\\bar{b}$ channel: Development of a b-tagging method based on soft muons

    Energy Technology Data Exchange (ETDEWEB)

    Jamin, David [Univ. of the Mediterranean, Marseille (France)

    2010-09-30

    In the Standard Model of particle physics, the Higgs boson generates elementary particle masses. Current theoretical and experimental constraints lead to a Higgs boson mass between 114.4 and 158 GeV with 95% confidence level. Moreover, Tevatron has recently excluded the mass ranges between 100 and 109 GeV, 158 and 175 GeV with 95% confidence level. These results gives a clear indication to search for a Higgs boson at low mass. The D0 detector is located near Chicago, at the Tevatron, a proton-antiproton collider with an energy in the center of mass of 1.96 TeV. The topic of this thesis is the search for a Higgs boson in association with a Z boson. This channel is sensitive to low mass Higgs boson (<135 GeV) which has a branching ratio H → bb varies between 50% and 90% in this mass range. The decay channel ZH → v$\\bar{v}$b$\\bar{b}$ studied has in the final state 2 heavy-flavor jets and some missing transverse energy due to escaping neutrinos. The heavy-flavor jets identification ('b-tagging') is done with a new algorithm (SLTNN) developed specifically for semi-leptonic decay of b quarks. The Higgs boson search analysis was performed with 3 fb-1 of data. The use of SLTNN increases by 10% the Higgs boson signal efficiency. The global analysis sensitivity improvement, however, is rather low (<1%) after taking into account the backgrounds and systematic uncertainties.

  7. Search for the Higgs boson in the ZH->nunubb channel: Development of a b-tagging method based on soft muons

    Energy Technology Data Exchange (ETDEWEB)

    Jamin, David; /Marseille, CPPM

    2010-10-01

    In the Standard Model of particle physics, the Higgs boson generates elementary particle masses. Current theoretical and experimental constraints lead to a Higgs boson mass between 114.4 and 158 GeV with 95% confidence level. Moreover, Tevatron has recently excluded the mass ranges between 100 and 109 GeV, 158 and 175 GeV with 95% confidence level. These results gives a clear indication to search for a Higgs boson at low mass. The D0 detector is located near Chicago, at the Tevatron, a proton-antiproton collider with an energy in the center of mass of 1.96 TeV. The topic of this thesis is the search for a Higgs boson in association with a Z boson. This channel is sensitive to low mass Higgs boson (<135 GeV) which has a branching ratio H {yields} bb varies between 50% and 90% in this mass range. The decay channel ZH {yields} {nu}{bar {nu}}b{bar b} studied has in the final state 2 heavy-flavor jets and some missing transverse energy due to escaping neutrinos. The heavy-flavor jets identification ('b-tagging') is done with a new algorithm (SLTNN) developped specifically for semi-leptonic decay of b quarks. The Higgs boson search analysis was performed with 3 fb{sup -1} of data. The use of SLTNN increases by 10% the Higgs boson signal efficiency. The global analysis sensitivity improvement, however, is rather low (<1%) after taking into account the backgrounds and systematic uncertainties.

  8. Aptamer Affinity Maturation by Resampling and Microarray Selection.

    Science.gov (United States)

    Kinghorn, Andrew B; Dirkzwager, Roderick M; Liang, Shaolin; Cheung, Yee-Wai; Fraser, Lewis A; Shiu, Simon Chi-Chin; Tang, Marco S L; Tanner, Julian A

    2016-07-19

    Aptamers have significant potential as affinity reagents, but better approaches are critically needed to discover higher affinity nucleic acids to widen the scope for their diagnostic, therapeutic, and proteomic application. Here, we report aptamer affinity maturation, a novel aptamer enhancement technique, which combines bioinformatic resampling of aptamer sequence data and microarray selection to navigate the combinatorial chemistry binding landscape. Aptamer affinity maturation is shown to improve aptamer affinity by an order of magnitude in a single round. The novel aptamers exhibited significant adaptation, the complexity of which precludes discovery by other microarray based methods. Honing aptamer sequences using aptamer affinity maturation could help optimize a next generation of nucleic acid affinity reagents. PMID:27346322

  9. The affine quantum gravity programme

    International Nuclear Information System (INIS)

    The central principle of affine quantum gravity is securing and maintaining the strict positivity of the matrix { g-hat ab(x)} composed of the spatial components of the local metric operator. On spectral grounds, canonical commutation relations are incompatible with this principle, and they must be replaced by noncanonical, affine commutation relations. Due to the partial second-class nature of the quantum gravitational constraints, it is advantageous to use the recently developed projection operator method, which treats all quantum constraints on an equal footing. Using this method, enforcement of regularized versions of the gravitational operator constraints is formulated quite naturally by means of a novel and relatively well-defined functional integral involving only the same set of variables that appears in the usual classical formulation. It is anticipated that skills and insight to study this formulation can be developed by studying special, reduced-variable models that still retain some basic characteristics of gravity, specifically a partial second-class constraint operator structure. Although perturbatively nonrenormalizable, gravity may possibly be understood nonperturbatively from a hard-core perspective that has proved valuable for specialized models. Finally, developing a procedure to pass to the genuine physical Hilbert space involves several interconnected steps that require careful coordination

  10. Tagging behaviour with support from controlled vocabulary

    DEFF Research Database (Denmark)

    Lykke, Marianne; Høj, Anne Lyhne; Madsen, Line Nørgaard;

    2011-01-01

    The paper investigates how knowledge structures from a controlled vocabulary affect tagging. The study is a comparative analysis of tags assigned in two tagging systems, a simple tagging system (control system) that provides suggestions from two tag clouds (all users tags and my tags) and an enha......The paper investigates how knowledge structures from a controlled vocabulary affect tagging. The study is a comparative analysis of tags assigned in two tagging systems, a simple tagging system (control system) that provides suggestions from two tag clouds (all users tags and my tags...... vocabulary might help taggers in being more specific in their tagging, allowing more precise information searching based on user tags. In addition, the results indicate that structured controlled suggestions might encourage taggers to add synonym variations enhancing the variety and number of access points....... Furthermore, controlled vocabularies might be useful for automatic spell checking. Future study should explore in what direction the different kinds of suggestions lead the tagger and whether it is possible to identify scope or patterns between related tags from the two systems....

  11. Behavioral tagging of extinction learning.

    Science.gov (United States)

    de Carvalho Myskiw, Jociane; Benetti, Fernando; Izquierdo, Iván

    2013-01-15

    Extinction of contextual fear in rats is enhanced by exposure to a novel environment at 1-2 h before or 1 h after extinction training. This effect is antagonized by administration of protein synthesis inhibitors anisomycin and rapamycin into the hippocampus, but not into the amygdala, immediately after either novelty or extinction training, as well as by the gene expression blocker 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole administered after novelty training, but not after extinction training. Thus, this effect can be attributed to a mechanism similar to synaptic tagging, through which long-term potentiation can be enhanced by other long-term potentiations or by exposure to a novel environment in a protein synthesis-dependent fashion. Extinction learning produces a tag at the appropriate synapses, whereas novelty learning causes the synthesis of plasticity-related proteins that are captured by the tag, strengthening the synapses that generated this tag. PMID:23277583

  12. Chemical tags for site-specific fluorescent labeling of biomolecules.

    Science.gov (United States)

    Freidel, Christoph; Kaloyanova, Stefka; Peneva, Kalina

    2016-06-01

    This review focuses on the various approaches to covalently attach a chromophore to a biomolecule of interest in site-specific manner. Novel methods like inverse electron-demand Diels-Alder reaction, Pictet-Spengler ligation and enzyme tags like SNAP and Halo-tags are critically discussed and compared to established techniques like copper-free click reaction and native chemical ligation. Selected examples in which the tags have been exploited for in vitro or in vivo imaging are reviewed and evaluated. PMID:26969255

  13. Device-free object tracking using passive tags

    CERN Document Server

    Han, Jinsong; Zhao, Kun; Jiang, Zhiping

    2014-01-01

    This SpringerBrief examines the use of cheap commercial passive RFID tags to achieve accurate device-free object-tracking. It presents a sensitive detector, named Twins, which uses a pair of adjacent passive tags to detect uncooperative targets (such as intruders). Twins leverages a newly observed phenomenon called critical state that is caused by interference among passive tags.The author expands on the previous object tracking methods, which are mostly device-based, and reveals a new interference model and their extensive experiments for validation. A prototype implementation of the Twins-ba

  14. Human P-glycoprotein exhibits reduced affinity for substrates during a catalytic transition state.

    Science.gov (United States)

    Ramachandra, M; Ambudkar, S V; Chen, D; Hrycyna, C A; Dey, S; Gottesman, M M; Pastan, I

    1998-04-01

    Human P-glycoprotein (Pgp), a plasma membrane protein that confers multidrug resistance, functions as an ATP-dependent drug efflux pump. Pgp contains two ATP binding/utilization sites and exhibits ATPase activity that is stimulated in the presence of substrates and modulating agents. The mechanism of coupling of ATP hydrolysis to drug transport is not known. To understand the role of ATP hydrolysis in drug binding, it is necessary to develop methods for purifying and reconstituting Pgp that retains properties including stimulation of ATPase activity by known substrates to an extent similar to that in the native membrane. In this study, (His)6-tagged Pgp was expressed in Trichoplusia ni (High Five) cells using the recombinant baculovirus system and purified by metal affinity chromatography. Upon reconstitution into phospholipid vesicles, purified Pgp exhibited specific binding to analogues of substrates and ATP in affinity labeling experiments and displayed a high level of drug-stimulated ATPase activity (specific activity ranging from 4.5 to 6.5 micromol min-1 mg-1). The ATPase activity was inhibited by ADP in a competitive manner, and by vanadate and N-ethylmaleimide at low concentrations. Vanadate which is known to inhibit ATPase activity by trapping MgADP at the catalytic site inhibited photoaffinity labeling of Pgp with substrate analogues, [125I]iodoarylazidoprazosin and [3H]azidopine, only under ATP hydrolysis conditions. Because vanadate-trapped Pgp is known to resemble the ADP and phosphate-bound catalytic transition state, our findings indicate that ATP hydrolysis results in a conformation with reduced affinity for substrates. A catalytic transition conformation with reduced affinity would essentially result in substrate dissociation and supports a model for drug transport in which an ATP hydrolysis-induced conformational change leads to drug release toward the extracellular medium.

  15. Preparation of silica coated cobalt ferrite magnetic nanoparticles for the purification of histidine-tagged proteins

    Science.gov (United States)

    Aygar, Gülfem; Kaya, Murat; Özkan, Necati; Kocabıyık, Semra; Volkan, Mürvet

    2015-12-01

    Surface modified cobalt ferrite (CoFe2O4) nanoparticles containing Ni-NTA affinity group were synthesized and used for the separation of histidine tag proteins from the complex matrices through the use of imidazole side chains of histidine molecules. Firstly, CoFe2O4 nanoparticles with a narrow size distribution were prepared in an aqueous solution using the controlled co-precipitation method. In order to obtain small CoFe2O4 agglomerates, oleic acid and sodium chloride were used as dispersants. The CoFe2O4 particles were coated with silica and subsequently the surface of these silica coated particles (SiO2-CoFe2O4) was modified by amine (NH2) groups in order to add further functional groups on the silica shell. Then, carboxyl (-COOH) functional groups were added to the SiO2-CoFe2O4 magnetic nanoparticles through the NH2 groups. After that Nα,Nα-Bis(carboxymethyl)-L-lysine hydrate (NTA) was attached to carboxyl ends of the structure. Finally, the surface modified nanoparticles were labeled with nickel (Ni) (II) ions. Furthermore, the modified SiO2-CoFe2O4 magnetic nanoparticles were utilized as a new system that allows purification of the N-terminal His-tagged recombinant small heat shock protein, Tpv-sHSP 14.3.

  16. A Novel Recombinant DNA System for High Efficiency Affinity Purification of Proteins in Saccharomyces cerevisiae.

    Science.gov (United States)

    Carrick, Brian H; Hao, Linxuan; Smaldino, Philip J; Engelke, David R

    2016-03-01

    Isolation of endogenous proteins from Saccharomyces cerevisiae has been facilitated by inserting encoding polypeptide affinity tags at the C-termini of chromosomal open reading frames (ORFs) using homologous recombination of DNA fragments. Tagged protein isolation is limited by a number of factors, including high cost of affinity resins for bulk isolation and low concentration of ligands on the resin surface, leading to low isolation efficiencies and trapping of contaminants. To address this, we have created a recombinant "CelTag" DNA construct from which PCR fragments can be created to easily tag C-termini of S. cerevisiae ORFs using selection for a nat1 marker. The tag has a C-terminal cellulose binding module to be used in the first affinity step. Microgranular cellulose is very inexpensive and has an effectively continuous ligand on its surface, allowing rapid, highly efficient purification with minimal background. Cellulose-bound proteins are released by specific cleavage of an included site for TEV protease, giving nearly pure product. The tag can be lifted from the recombinant DNA construct either with or without a 13x myc epitope tag between the target ORF and the TEV protease site. Binding of CelTag protein fusions to cellulose is stable to high salt, nonionic detergents, and 1 M urea, allowing stringent washing conditions to remove loosely associated components, as needed, before specific elution. It is anticipated that this reagent could allow isolation of protein complexes from large quantities of yeast extract, including soluble, membrane-bound, or nucleic acid-associated assemblies.

  17. HAMS: High-Affinity Mass Spectrometry Screening. A High-Throughput Screening Method for Identifying the Tightest-Binding Lead Compounds for Target Proteins with No False Positive Identifications

    Science.gov (United States)

    Imaduwage, Kasun P.; Go, Eden P.; Zhu, Zhikai; Desaire, Heather

    2016-09-01

    A major challenge in drug discovery is the identification of high affinity lead compounds that bind a particular target protein; these leads are typically identified by high throughput screens. Mass spectrometry has become a detection method of choice in drug screening assays because the target and the ligand need not be modified. Label-free assays are advantageous because they can be developed more rapidly than assays requiring labels, and they eliminate the risk of the label interfering with the binding event. However, in commonly used MS-based screening methods, detection of false positives is a major challenge. Here, we describe a detection strategy designed to eliminate false positives. In this approach, the protein and the ligands are incubated together, and the non-binders are separated for detection. Hits (protein binders) are not detectable by MS after incubation with the protein, but readily identifiable by MS when the target protein is not present in the incubation media. The assay was demonstrated using three different proteins and hundreds of non-inhibitors; no false positive hits were identified in any experiment. The assay can be tuned to select for ligands of a particular binding affinity by varying the quantity of protein used and the immobilization method. As examples, the method selectively detected inhibitors that have Ki values of 0.2 μM, 50 pM, and 700 pM. These findings demonstrate that the approach described here compares favorably with traditional MS-based screening methods.

  18. Evolving effective behaviours to interact with tag-based populations

    Science.gov (United States)

    Yucel, Osman; Crawford, Chad; Sen, Sandip

    2015-07-01

    Tags and other characteristics, externally perceptible features that are consistent among groups of animals or humans, can be used by others to determine appropriate response strategies in societies. This usage of tags can be extended to artificial environments, where agents can significantly reduce cognitive effort spent on appropriate strategy choice and behaviour selection by reusing strategies for interacting with new partners based on their tags. Strategy selection mechanisms developed based on this idea have successfully evolved stable cooperation in games such as the Prisoner's Dilemma game but relies upon payoff sharing and matching methods that limit the applicability of the tag framework. Our goal is to develop a general classification and behaviour selection approach based on the tag framework. We propose and evaluate alternative tag matching and adaptation schemes for a new, incoming individual to select appropriate behaviour against any population member of an existing, stable society. Our proposed approach allows agents to evolve both the optimal tag for the environment as well as appropriate strategies for existing agent groups. We show that these mechanisms will allow for robust selection of optimal strategies by agents entering a stable society and analyse the various environments where this approach is effective.

  19. Rational self-affine tiles

    CERN Document Server

    Steiner, Wolfgang

    2012-01-01

    An integral self-affine tile is the solution of a set equation $\\mathbf{A} \\mathcal{T} = \\bigcup_{d \\in \\mathcal{D}} (\\mathcal{T} + d)$, where $\\mathbf{A}$ is an $n \\times n$ integer matrix and $\\mathcal{D}$ is a finite subset of $\\mathbb{Z}^n$. In the recent decades, these objects and the induced tilings have been studied systematically. We extend this theory to matrices $\\mathbf{A} \\in \\mathbb{Q}^{n \\times n}$. We define rational self-affine tiles as compact subsets of the open subring $\\mathbb{R}^n\\times \\prod_\\mathfrak{p} K_\\mathfrak{p}$ of the ad\\'ele ring $\\mathbb{A}_K$, where the factors of the (finite) product are certain $\\mathfrak{p}$-adic completions of a number field $K$ that is defined in terms of the characteristic polynomial of $\\mathbf{A}$. Employing methods from classical algebraic number theory, Fourier analysis in number fields, and results on zero sets of transfer operators, we establish a general tiling theorem for these tiles. We also associate a second kind of tiles with a rational matr...

  20. Myocardial MR tagging. Analysis of regional and global myocardial function; Kardiales MR-Tagging. Analyse regionaler und globaler Myokardfunktion

    Energy Technology Data Exchange (ETDEWEB)

    Kramer, U.; Fenchel, M. [Universitaet Tuebingen, Abt. fuer Diagnostische und Interventionelle Radiologie, Radiologische Klinik, Tuebingen (Germany); Hennemuth, A. [Fraunhofer MEVIS, Bremen (Germany)

    2010-06-15

    Myocardial MR tagging is a powerful method which allows for assessment of myocardial function and may become an important tool for clinical evaluation of cardiac dysfunction, particularly in ischemic heart disease. In addition to visual assessment it allows direct quantification of myocardial deformation and strain to measure contractility. The use of myocardial tagging has provided new insights into the (patho)physiology of regional wall motion, and several parameters have been described as being useful to identify an ischemic response of the myocardium. One challenge encountered with tagging at 1.5 T is the fading of tags at end-diastole, greatly limiting the evaluation of myocardial function during diastole. Due to longer T{sub 1} relaxation times of the myocardium, tagging at 3 T has shown to have a higher CNR{sub Tag} and better tag persistence when compared to current clinical gradient-echo tagging protocols at 1.5 T. As a consequence, tagging at higher field strengths may be well suited for the characterization of the diastolic portion of the cardiac cycle in future applications. (orig.) [German] Das myokardiale Tagging mittels der kardialen Magnetresonanztomographie (MRT) stellt ein spezielles Verfahren dar, das eine quantitative Analyse der regionalen Myokardfunktion erlaubt. Mit der Analyse der regionalen Wandbewegung koennen pathologische Bewegungsablaeufe fruehzeitig erkannt und kardiale Dysfunktionen differenziert werden. Neben der visuellen Analyse ist es in erster Linie die quantitative Bestimmung der aus der Echokardiographie bekannten Funktionsparameter, die den Vorteil des Taggings bei der Charakterisierung der myokardialen Funktion ausmachen. Die quantitative Erfassung des Rotations- und Kontraktionsverhaltens mit dem myokardialen Tagging eroeffnet bei verschiedenen Erkrankungen des Herzens neue Einblicke in die Pathophysiologie. Eine intrinsische Limitation dieses Verfahrens besteht in dem insbesondere in der diastolischen Phase des Herzzyklus

  1. Tempting To Tag: An Experimental Comparison Of Four Tagging Input Mechanisms

    Directory of Open Access Journals (Sweden)

    Mark Melenhorst

    2010-01-01

    Full Text Available Tagging helps achieve improved indexing and recommendation of resources (e.g., videos or pictures in large data collections. In order to reap the benefits of tagging, people must be persuaded to label the resources they consume. This paper reports on a study in which four different tagging input mechanisms and their effect on users' motivation to tag were compared. The mechanisms consisted of a standard tag input box, a chatbot-like environment, a bookmarking mechanism, and a "tag and vote" game. The results of our experiment show that the use of the nonstandard tagging input mechanisms does not affect users' motivation to tag. In some instances tagging mechanisms were found to distract users from their primary task: consuming resources. Persuading people to tag might be accomplished more effectively by using other motivating tagging mechanisms (e.g., tagging games, or motivation could be created by explaining the usefulness of tagging.

  2. Classification of neocortical interneurons using affinity propagation

    Science.gov (United States)

    Santana, Roberto; McGarry, Laura M.; Bielza, Concha; Larrañaga, Pedro; Yuste, Rafael

    2013-01-01

    In spite of over a century of research on cortical circuits, it is still unknown how many classes of cortical neurons exist. In fact, neuronal classification is a difficult problem because it is unclear how to designate a neuronal cell class and what are the best characteristics to define them. Recently, unsupervised classifications using cluster analysis based on morphological, physiological, or molecular characteristics, have provided quantitative and unbiased identification of distinct neuronal subtypes, when applied to selected datasets. However, better and more robust classification methods are needed for increasingly complex and larger datasets. Here, we explored the use of affinity propagation, a recently developed unsupervised classification algorithm imported from machine learning, which gives a representative example or exemplar for each cluster. As a case study, we applied affinity propagation to a test dataset of 337 interneurons belonging to four subtypes, previously identified based on morphological and physiological characteristics. We found that affinity propagation correctly classified most of the neurons in a blind, non-supervised manner. Affinity propagation outperformed Ward's method, a current standard clustering approach, in classifying the neurons into 4 subtypes. Affinity propagation could therefore be used in future studies to validly classify neurons, as a first step to help reverse engineer neural circuits. PMID:24348339

  3. Part-of-Speech Tagging with Neural Networks

    CERN Document Server

    Schmid, H

    1994-01-01

    Text corpora which are tagged with part-of-speech information are useful in many areas of linguistic research. In this paper, a new part-of-speech tagging method based on neural networks (Net- Tagger) is presented and its performance is compared to that of a HMM-tagger and a trigram-based tagger. It is shown that the Net- Tagger performs as well as the trigram-based tagger and better than the HMM-tagger.

  4. Affinity Purification of Insulin by Peptide-Ligand Affinity Chromatography

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The affinity heptapeptide (HWWWPAS) for insulin, selected from phage display library,was coupled to EAH Sepharose 4B gel and packed to a 1-mL column. The column was used for the affinity purification of insulin from protein mixture and commercial insulin preparation. It was observed that the minor impurity in the commercial insulin was removed by the affinity chromatography. Nearly 40 mg of insulin could be purified with the 1-mL affinity column. The results revealed the high specificity and capacity of the affinity column for insulin purification. Moreover, based on the analysis of the amino acids in the peptide sequence, shorter peptides were designed and synthesized for insulin chromatography. As a result, HWWPS was found to be a good alternative to HWWWPAS, while the other two peptides with three or four amino acids showed weak affinity for insulin. The results indicated that the peptide sequence of HWWWPAS was quite conservative for specific binding of insulin.

  5. The Utility of Affine Variables and Affine Coherent States

    CERN Document Server

    Klauder, John R

    2011-01-01

    Affine coherent states are generated by affine kinematical variables much like canonical coherent states are generated by canonical kinematical variables. Although all classical and quantum formalisms normally entail canonical variables, it is shown that affine variables can serve equally well for many classical and quantum studies. This general purpose analysis provides tools to discuss two major applications: (1) the completely successful quantization of a nonrenormalizable scalar quantum field theory by affine techniques, in complete contrast to canonical techniques which only offer triviality; and (2) a formulation of the kinematical portion of quantum gravity that favors affine kinematical variables over canonical kinematical variables, and which generates a framework in which a favorable analysis of the constrained dynamical issues can take place. All this is possible because of the close connection between the affine and the canonical stories, while the few distinctions can be used to advantage when ap...

  6. Affinity Pull-Down of Proteins Using Anti-FLAG M2 Agarose Beads

    Science.gov (United States)

    Gerace, Erica; Moazed, Danesh

    2016-01-01

    FLAG is an affinity tag widely used for rapid and highly specific one-step protein purification. Native elution of protein from anti-FLAG antibody resins allows the identification of protein and nucleic acid binding partners and functional analysis using biochemical activity assays. PMID:26096505

  7. Jacobi Structures on Affine Bundles

    Institute of Scientific and Technical Information of China (English)

    J. GRABOWSKI; D. IGLESIAS; J. C. MARRERO; E. PADR(O)N; P. URBA(N)SKI

    2007-01-01

    We study affine Jacobi structures (brackets) on an affine bundle π: A→M, i.e. Jacobi brackets that close on affine functions. We prove that if the rank of A is non-zero, there is a one-to- one correspondence between affine Jacobi structures on A and Lie algebroid structures on the vector bundle A+=∪p∈M Aff(Ap, R) of affine functionals. In the case rank A = 0, it is shown that there is a one-to-one correspondence between affins Jacobi structures on A and local Lie algebras on A+. Some examples and applications, also for the linear case, are discussed. For a special type of affine Jacobi structures which are canonically exhibited (strongly-affine or affine-homogeneous Jacobi structures) over a real vector space of finite dimension, we describe the leaves of its characteristic foliation as the orbits of an affine representation. These afline Jacobi structures can be viewed as an analog of the Kostant-Arnold-LiouviUe linear Poisson structure on the dual space of a real finite-dimensional Lie algebra.

  8. Removal of PCR error products and unincorporated primers by metal-chelate affinity chromatography.

    Directory of Open Access Journals (Sweden)

    Indhu Kanakaraj

    Full Text Available Immobilized Metal Affinity Chromatography (IMAC has been used for decades to purify proteins on the basis of amino acid content, especially surface-exposed histidines and "histidine tags" genetically added to recombinant proteins. We and others have extended the use of IMAC to purification of nucleic acids via interactions with the nucleotide bases, especially purines, of single-stranded RNA and DNA. We also have demonstrated the purification of plasmid DNA from contaminating genomic DNA by IMAC capture of selectively-denatured genomic DNA. Here we describe an efficient method of purifying PCR products by specifically removing error products, excess primers, and unincorporated dNTPs from PCR product mixtures using flow-through metal-chelate affinity adsorption. By flowing a PCR product mixture through a Cu(2+-iminodiacetic acid (IDA agarose spin column, 94-99% of the dNTPs and nearly all the primers can be removed. Many of the error products commonly formed by Taq polymerase also are removed. Sequencing of the IMAC-processed PCR product gave base-calling accuracy comparable to that obtained with a commercial PCR product purification method. The results show that IMAC matrices (specifically Cu(2+-IDA agarose can be used for the purification of PCR products. Due to the generality of the base-specific mechanism of adsorption, IMAC matrices may also be used in the purification of oligonucleotides, cDNA, mRNA and micro RNAs.

  9. Quantitative Evaluation of His-Tag Purification and Immunoprecipitation of Tristetraprolin and Its Mutant Proteins from Transfected Human Cells

    OpenAIRE

    Cao, Heping; Lin, Rui

    2009-01-01

    Histidine (His)-tag is widely used for affinity purification of recombinant proteins, but the yield and purity of expressed proteins are quite different. Little information is available about quantitative evaluation of this procedure. The objective of current study was to evaluate His-tag procedure quantitatively and to compare it with immunoprecipitation using radiolabeled tristetraprolin (TTP), a zinc finger protein with anti-inflammatory property. Human embryonic kidney 293 cells were tran...

  10. Determining the ice-binding planes of antifreeze proteins by fluorescence-based ice plane affinity.

    Science.gov (United States)

    Basu, Koli; Garnham, Christopher P; Nishimiya, Yoshiyuki; Tsuda, Sakae; Braslavsky, Ido; Davies, Peter

    2014-01-15

    Antifreeze proteins (AFPs) are expressed in a variety of cold-hardy organisms to prevent or slow internal ice growth. AFPs bind to specific planes of ice through their ice-binding surfaces. Fluorescence-based ice plane affinity (FIPA) analysis is a modified technique used to determine the ice planes to which the AFPs bind. FIPA is based on the original ice-etching method for determining AFP-bound ice-planes. It produces clearer images in a shortened experimental time. In FIPA analysis, AFPs are fluorescently labeled with a chimeric tag or a covalent dye then slowly incorporated into a macroscopic single ice crystal, which has been preformed into a hemisphere and oriented to determine the a- and c-axes. The AFP-bound ice hemisphere is imaged under UV light to visualize AFP-bound planes using filters to block out nonspecific light. Fluorescent labeling of the AFPs allows real-time monitoring of AFP adsorption into ice. The labels have been found not to influence the planes to which AFPs bind. FIPA analysis also introduces the option to bind more than one differently tagged AFP on the same single ice crystal to help differentiate their binding planes. These applications of FIPA are helping to advance our understanding of how AFPs bind to ice to halt its growth and why many AFP-producing organisms express multiple AFP isoforms.

  11. Traceless affinity labeling of endogenous proteins for functional analysis in living cells.

    Science.gov (United States)

    Hayashi, Takahiro; Hamachi, Itaru

    2012-09-18

    Protein labeling and imaging techniques have provided tremendous opportunities to study the structure, function, dynamics, and localization of individual proteins in the complex environment of living cells. Molecular biology-based approaches, such as GFP-fusion tags and monoclonal antibodies, have served as important tools for the visualization of individual proteins in cells. Although these techniques continue to be valuable for live cell imaging, they have a number of limitations that have only been addressed by recent progress in chemistry-based approaches. These chemical approaches benefit greatly from the smaller probe sizes that should result in fewer perturbations to proteins and to biological systems as a whole. Despite the research in this area, so far none of these labeling techniques permit labeling and imaging of selected endogenous proteins in living cells. Researchers have widely used affinity labeling, in which the protein of interest is labeled by a reactive group attached to a ligand, to identify and characterize proteins. Since the first report of affinity labeling in the early 1960s, efforts to fine-tune the chemical structures of both the reactive group and ligand have led to protein labeling with excellent target selectivity in the whole proteome of living cells. Although the chemical probes used for affinity labeling generally inactivate target proteins, this strategy holds promise as a valuable tool for the labeling and imaging of endogenous proteins in living cells and by extension in living animals. In this Account, we summarize traceless affinity labeling, a technique explored mainly in our laboratory. In our overview of the different labeling techniques, we emphasize the challenge of designing chemical probes that allow for dissociation of the affinity module (often a ligand) after the labeling reaction so that the labeled protein retains its native function. This feature distinguishes the traceless labeling approach from the traditional

  12. Adjoint affine fusion and tadpoles

    Science.gov (United States)

    Urichuk, Andrew; Walton, Mark A.

    2016-06-01

    We study affine fusion with the adjoint representation. For simple Lie algebras, elementary and universal formulas determine the decomposition of a tensor product of an integrable highest-weight representation with the adjoint representation. Using the (refined) affine depth rule, we prove that equally striking results apply to adjoint affine fusion. For diagonal fusion, a coefficient equals the number of nonzero Dynkin labels of the relevant affine highest weight, minus 1. A nice lattice-polytope interpretation follows and allows the straightforward calculation of the genus-1 1-point adjoint Verlinde dimension, the adjoint affine fusion tadpole. Explicit formulas, (piecewise) polynomial in the level, are written for the adjoint tadpoles of all classical Lie algebras. We show that off-diagonal adjoint affine fusion is obtained from the corresponding tensor product by simply dropping non-dominant representations.

  13. Adjoint affine fusion and tadpoles

    CERN Document Server

    Urichuk, Andrew

    2016-01-01

    We study affine fusion with the adjoint representation. For simple Lie algebras, elementary and universal formulas determine the decomposition of a tensor product of an integrable highest-weight representation with the adjoint representation. Using the (refined) affine depth rule, we prove that equally striking results apply to adjoint affine fusion. For diagonal fusion, a coefficient equals the number of nonzero Dynkin labels of the relevant affine highest weight, minus 1. A nice lattice-polytope interpretation follows, and allows the straightforward calculation of the genus-1 1-point adjoint Verlinde dimension, the adjoint affine fusion tadpole. Explicit formulas, (piecewise) polynomial in the level, are written for the adjoint tadpoles of all classical Lie algebras. We show that off-diagonal adjoint affine fusion is obtained from the corresponding tensor product by simply dropping non-dominant representations.

  14. Unsupervised mining of frequent tags for clinical eligibility text indexing.

    Science.gov (United States)

    Miotto, Riccardo; Weng, Chunhua

    2013-12-01

    Clinical text, such as clinical trial eligibility criteria, is largely underused in state-of-the-art medical search engines due to difficulties of accurate parsing. This paper proposes a novel methodology to derive a semantic index for clinical eligibility documents based on a controlled vocabulary of frequent tags, which are automatically mined from the text. We applied this method to eligibility criteria on ClinicalTrials.gov and report that frequent tags (1) define an effective and efficient index of clinical trials and (2) are unlikely to grow radically when the repository increases. We proposed to apply the semantic index to filter clinical trial search results and we concluded that frequent tags reduce the result space more efficiently than an uncontrolled set of UMLS concepts. Overall, unsupervised mining of frequent tags from clinical text leads to an effective semantic index for the clinical eligibility documents and promotes their computational reuse.

  15. Global navigation system with RFID tags

    Science.gov (United States)

    Tsukiyama, Toshifumi

    2002-02-01

    A new navigation system is described for a mobile robot moving around in man-made environments such as hallways in a building. The system is based on a commercial three-wheel mobile platform with the addition of a Linux-based laptop computer, a Radio Frequency Identification (RDID) tag sensor and a vision system. At critical junctions such as the intersection of two passages the navigation system must identify the robot's location on a given map. We propose a method using RFID tags as landmarks. Each RFID tag has a unique ID number corresponding to its location on the map. The navigation system can decide the next movement (left-turn, right-turn and so on) toward a given goal based on this number. The navigation system also can automatically follow walls using the vision system. Since the equipment setup is very simple and the navigation system is easily combined with general mobile robot systems, our proposed technique would be useful for real-world robotic applications such as intelligent navigation for motorized wheelchairs.

  16. Affine Invariant Character Recognition by Progressive Removing

    Science.gov (United States)

    Iwamura, Masakazu; Horimatsu, Akira; Niwa, Ryo; Kise, Koichi; Uchida, Seiichi; Omachi, Shinichiro

    Recognizing characters in scene images suffering from perspective distortion is a challenge. Although there are some methods to overcome this difficulty, they are time-consuming. In this paper, we propose a set of affine invariant features and a new recognition scheme called “progressive removing” that can help reduce the processing time. Progressive removing gradually removes less feasible categories and skew angles by using multiple classifiers. We observed that progressive removing and the use of the affine invariant features reduced the processing time by about 60% in comparison to a trivial one without decreasing the recognition rate.

  17. Neutral B meson flavor tagging

    CERN Document Server

    Wilson, R J

    2001-01-01

    We present an investigation of the use of net charge and kaon identification to tag the flavor of neutral B mesons. The net charge of the neutral B meson decay products is zero if all charged particles are used and slightly non-zero if only undiscriminated hadronic final states are used. The net charge of the kaons alone correctly tags the identity of the neutral meson in at least a third of all decays. We have parametrized the particle identification capability of several techniques, such as dE/dx in time projection chambers, LEP/SLC ring-imaging chambers and an enhanced BaBar DIRC. Using these parametrisations we compare the relative tagging power of each technique to that of an ideal detector. (8 refs).

  18. Tissue-specific tagging of endogenous loci in Drosophila melanogaster

    Directory of Open Access Journals (Sweden)

    Kate Koles

    2016-01-01

    Full Text Available Fluorescent protein tags have revolutionized cell and developmental biology, and in combination with binary expression systems they enable diverse tissue-specific studies of protein function. However these binary expression systems often do not recapitulate endogenous protein expression levels, localization, binding partners and/or developmental windows of gene expression. To address these limitations, we have developed a method called T-STEP (tissue-specific tagging of endogenous proteins that allows endogenous loci to be tagged in a tissue specific manner. T-STEP uses a combination of efficient CRISPR/Cas9-enhanced gene targeting and tissue-specific recombinase-mediated tag swapping to temporally and spatially label endogenous proteins. We have employed this method to GFP tag OCRL (a phosphoinositide-5-phosphatase in the endocytic pathway and Vps35 (a Parkinson's disease-implicated component of the endosomal retromer complex in diverse Drosophila tissues including neurons, glia, muscles and hemocytes. Selective tagging of endogenous proteins allows, for the first time, cell type-specific live imaging and proteomics in complex tissues.

  19. AUTOMATIC TAGGING OF PERSIAN WEB PAGES BASED ON N-GRAM LANGUAGE MODELS USING MAPREDUCE

    Directory of Open Access Journals (Sweden)

    Saeed Shahrivari

    2015-07-01

    Full Text Available Page tagging is one of the most important facilities for increasing the accuracy of information retrieval in the web. Tags are simple pieces of data that usually consist of one or several words, and briefly describe a page. Tags provide useful information about a page and can be used for boosting the accuracy of searching, document clustering, and result grouping. The most accurate solution to page tagging is using human experts. However, when the number of pages is large, humans cannot be used, and some automatic solutions should be used instead. We propose a solution called PerTag which can automatically tag a set of Persian web pages. PerTag is based on n-gram models and uses the tf-idf method plus some effective Persian language rules to select proper tags for each web page. Since our target is huge sets of web pages, PerTag is built on top of the MapReduce distributed computing framework. We used a set of more than 500 million Persian web pages during our experiments, and extracted tags for each page using a cluster of 40 machines. The experimental results show that PerTag is both fast and accurate

  20. Tagging, Encoding, and Jones Optimality

    DEFF Research Database (Denmark)

    Danvy, Olivier; Lopez, Pablo E. Martinez

    2003-01-01

    A partial evaluator is said to be Jones-optimal if the result of specializing a self-interpreter with respect to a source program is textually identical to the source program, modulo renaming. Jones optimality has already been obtained if the self-interpreter is untyped. If the selfinterpreter...... a residual program that is textually identical to the source program, modulo renaming....... is typed, however, residual programs are cluttered with type tags. To obtain the original source program, these tags must be removed. A number of sophisticated solutions have already been proposed. We observe, however, that with a simple representation shift, ordinary partial evaluation is already Jones...

  1. A Novel Recombinant DNA System for High Efficiency Affinity Purification of Proteins in Saccharomyces cerevisiae

    Directory of Open Access Journals (Sweden)

    Brian H. Carrick

    2016-03-01

    Full Text Available Isolation of endogenous proteins from Saccharomyces cerevisiae has been facilitated by inserting encoding polypeptide affinity tags at the C-termini of chromosomal open reading frames (ORFs using homologous recombination of DNA fragments. Tagged protein isolation is limited by a number of factors, including high cost of affinity resins for bulk isolation and low concentration of ligands on the resin surface, leading to low isolation efficiencies and trapping of contaminants. To address this, we have created a recombinant “CelTag” DNA construct from which PCR fragments can be created to easily tag C-termini of S. cerevisiae ORFs using selection for a nat1 marker. The tag has a C-terminal cellulose binding module to be used in the first affinity step. Microgranular cellulose is very inexpensive and has an effectively continuous ligand on its surface, allowing rapid, highly efficient purification with minimal background. Cellulose-bound proteins are released by specific cleavage of an included site for TEV protease, giving nearly pure product. The tag can be lifted from the recombinant DNA construct either with or without a 13x myc epitope tag between the target ORF and the TEV protease site. Binding of CelTag protein fusions to cellulose is stable to high salt, nonionic detergents, and 1 M urea, allowing stringent washing conditions to remove loosely associated components, as needed, before specific elution. It is anticipated that this reagent could allow isolation of protein complexes from large quantities of yeast extract, including soluble, membrane-bound, or nucleic acid-associated assemblies.

  2. WebTag: Web browsing into sensor tags over NFC.

    Science.gov (United States)

    Echevarria, Juan Jose; Ruiz-de-Garibay, Jonathan; Legarda, Jon; Alvarez, Maite; Ayerbe, Ana; Vazquez, Juan Ignacio

    2012-01-01

    Information and Communication Technologies (ICTs) continue to overcome many of the challenges related to wireless sensor monitoring, such as for example the design of smarter embedded processors, the improvement of the network architectures, the development of efficient communication protocols or the maximization of the life cycle autonomy. This work tries to improve the communication link of the data transmission in wireless sensor monitoring. The upstream communication link is usually based on standard IP technologies, but the downstream side is always masked with the proprietary protocols used for the wireless link (like ZigBee, Bluetooth, RFID, etc.). This work presents a novel solution (WebTag) for a direct IP based access to a sensor tag over the Near Field Communication (NFC) technology for secure applications. WebTag allows a direct web access to the sensor tag by means of a standard web browser, it reads the sensor data, configures the sampling rate and implements IP based security policies. It is, definitely, a new step towards the evolution of the Internet of Things paradigm.

  3. WebTag: Web Browsing into Sensor Tags over NFC

    Science.gov (United States)

    Echevarria, Juan Jose; Ruiz-de-Garibay, Jonathan; Legarda, Jon; Álvarez, Maite; Ayerbe, Ana; Vazquez, Juan Ignacio

    2012-01-01

    Information and Communication Technologies (ICTs) continue to overcome many of the challenges related to wireless sensor monitoring, such as for example the design of smarter embedded processors, the improvement of the network architectures, the development of efficient communication protocols or the maximization of the life cycle autonomy. This work tries to improve the communication link of the data transmission in wireless sensor monitoring. The upstream communication link is usually based on standard IP technologies, but the downstream side is always masked with the proprietary protocols used for the wireless link (like ZigBee, Bluetooth, RFID, etc.). This work presents a novel solution (WebTag) for a direct IP based access to a sensor tag over the Near Field Communication (NFC) technology for secure applications. WebTag allows a direct web access to the sensor tag by means of a standard web browser, it reads the sensor data, configures the sampling rate and implements IP based security policies. It is, definitely, a new step towards the evolution of the Internet of Things paradigm. PMID:23012511

  4. WebTag: Web Browsing into Sensor Tags over NFC

    Directory of Open Access Journals (Sweden)

    Juan Jose Echevarria

    2012-06-01

    Full Text Available Information and Communication Technologies (ICTs continue to overcome many of the challenges related to wireless sensor monitoring, such as for example the design of smarter embedded processors, the improvement of the network architectures, the development of efficient communication protocols or the maximization of the life cycle autonomy. This work tries to improve the communication link of the data transmission in wireless sensor monitoring. The upstream communication link is usually based on standard IP technologies, but the downstream side is always masked with the proprietary protocols used for the wireless link (like ZigBee, Bluetooth, RFID, etc.. This work presents a novel solution (WebTag for a direct IP based access to a sensor tag over the Near Field Communication (NFC technology for secure applications. WebTag allows a direct web access to the sensor tag by means of a standard web browser, it reads the sensor data, configures the sampling rate and implements IP based security policies. It is, definitely, a new step towards the evolution of the Internet of Things paradigm.

  5. European and international collaboration in affinity proteomics.

    Science.gov (United States)

    Stoevesandt, Oda; Taussig, Michael J

    2012-06-15

    In affinity proteomics, specific protein-binding molecules (a.k.a. binders), principally antibodies, are applied as reagents in proteome analysis. In recent years, advances in binder technologies have created the potential for an unprecedented view on protein expression and distribution patterns in plasma, cells and tissues and increasingly on protein function. Particular strengths of affinity proteomics methods include detecting proteins in their natural environments of cell or tissue, high sensitivity and selectivity for detection of low abundance proteins and exploiting binding actions such as functional interference in living cells. To maximise the use and impact of affinity reagents, it will be essential to create comprehensive, standardised binder collections. With this in mind, the EU FP7 programme AFFINOMICS (http://www.affinomics.org), together with the preceding EU programmes ProteomeBinders and AffinityProteome, aims to extend affinity proteomics research by generating a large-scale resource of validated protein-binding molecules for characterisation of the human proteome. Activity is directed at producing binders to about 1000 protein targets, primarily in signal transduction and cancer, by establishing a high throughput, coordinated production pipeline. An important aspect of AFFINOMICS is the development of highly efficient recombinant selection methods, based on phage, cell and ribosome display, capable of producing high quality binders at greater throughput and lower cost than hitherto. The programme also involves development of innovative and sensitive technologies for specific detection of target proteins and their interactions, and deployment of binders in proteomics studies of clinical relevance. The need for such binder generation programmes is now recognised internationally, with parallel initiatives in the USA for cancer (NCI) and transcription factors (NIH) and within the Human Proteome Organisation (HUPO). The papers in this volume of New

  6. Robust segmentation of 4D cardiac MRI-tagged images via spatio-temporal propagation

    Science.gov (United States)

    Qian, Zhen; Huang, Xiaolei; Metaxas, Dimitris N.; Axel, Leon

    2005-04-01

    In this paper we present a robust method for segmenting and tracking cardiac contours and tags in 4D cardiac MRI tagged images via spatio-temporal propagation. Our method is based on two main techniques: the Metamorphs Segmentation for robust boundary estimation, and the tunable Gabor filter bank for tagging lines enhancement, removal and myocardium tracking. We have developed a prototype system based on the integration of these two techniques, and achieved efficient, robust segmentation and tracking with minimal human interaction.

  7. Tagging the European eel Anguilla anguilla (L.) with coded wire tags

    DEFF Research Database (Denmark)

    Thomassen, S.; Pedersen, Michael Ingemann; Holdensgaard, G.

    2000-01-01

    The coded wire tag (CWT) system was examined as a possible tool for tagging European eels (Anguilla anguilla). Two size groups of eels (3.8 and 10.2 g) were tagged with CWTs in the dorsal musculature, Tag loss 28 days after tagging was 3.1% for the small and 0.7% for the large groups of eels....... Of the tag loss in the small eels, 61% were lost during the first 2 h after tagging. In the small group, eels that lost tags were significantly (P...

  8. DNA tagged microparticles

    Science.gov (United States)

    Farquar, George Roy; Leif, Roald N; Wheeler, Elizabeth

    2015-05-05

    A simulant that includes a carrier and DNA encapsulated in the carrier. Also a method of making a simulant including the steps of providing a carrier and encapsulating DNA in the carrier to produce the simulant.

  9. In situ tagging technique for fishes provides insight into growth and movement of invasive lionfish.

    Science.gov (United States)

    Akins, John L; Morris, James A; Green, Stephanie J

    2014-10-01

    Information on fish movement and growth is primarily obtained through the marking and tracking of individuals with external tags, which are usually affixed to anesthetized individuals at the surface. However, the quantity and quality of data obtained by this method is often limited by small sample sizes owing to the time associated with the tagging process, high rates of tagging-related mortality, and displacement of tagged individuals from the initial capture location. To address these issues, we describe a technique for applying external streamer and dart tags in situ, which uses SCUBA divers to capture and tag individual fish on the sea floor without the use of anesthetic. We demonstrate this method for Indo-Pacific lionfish (Pterois volitans/P. miles), species which are particularly vulnerable to barotrauma when transported to and handled at the surface. To test our method, we tagged 161 individuals inhabiting 26 coral reef locations in the Bahamas over a period of 3 years. Our method resulted in no instances of barotrauma, reduced handling and recovery time, and minimal post-tagging release displacement compared with conventional ex situ tag application. Opportunistic resighting and recapture of tagged individuals reveals that lionfish exhibit highly variable site fidelity, movement patterns, and growth rates on invaded coral reef habitats. In total, 24% of lionfish were resighted between 29 and 188 days after tagging. Of these, 90% were located at the site of capture, while the remaining individuals were resighted between 200 m and 1.1 km from initial site of capture over 29 days later. In situ growth rates ranged between 0.1 and 0.6 mm/day. While individuals tagged with streamer tags posted slower growth rates with increasing size, as expected, there was no relationship between growth rate and fish size for individuals marked with dart tags, potentially because of large effects of tag presence on the activities of small bodied lionfish (i.e., <150

  10. Tag-Aware Recommender Systems: A State-of-the-Art Survey

    Institute of Scientific and Technical Information of China (English)

    Zi-Ke Zhang; Tao Zhou; Yi-Cheng Zhang

    2011-01-01

    In the past decade,Social Tagging Systems have attracted increasing attention from both physical and computer science communities.Besides the underlying structure and dynamics of tagging systems,many efforts have been addressed to unify tagging information to reveal user behaviors and preferences,extract the latent semantic relations among items,make recommendations,and so on.Specifically,this article summarizes recent progress about tag-aware recommender systems,emphasizing on the contributions from three mainstream perspectives and approaches:network-based methods,tensor-based methods,and the topic-based methods.Finally,we outline some other tag-related studies and future challenges of tag-aware recommendation algorithms.

  11. EXPLOITING SOCIAL TAGS TO OVERCOME COLD START RECOMMENDATION PROBLEM

    Directory of Open Access Journals (Sweden)

    A. S. Ghabayen

    2014-01-01

    Full Text Available The practice and method of collaboratively creating and managing tags to annotate and categorize content has resulted in the creation of folksonomy. Folksonomies provide new opportunities and challenges in the field of recommender systems. Despite the considerable amount of researches done in the context of recommender systems, the specific problem of integrating tags into standard recommender system algorithms is less explored than the problem of recommending tags. Collaborative filtering is one of the popular approaches for providing recommendation. However, despite the popularity of collaborative filtering, to some extent, it could not recognize the preferences of users in cold-start scenarios, where insufficient preferences are associated to certain users or items, which leads to degraded recommendation quality. This study presents a collaborative filtering approach based on the expansion of users’ tags. In this case, semantics between tags can be unveiled which subsequently resulted in the identification of semantically similar users. Experiment on real-life dataset shows that our approach outperforms the state-of-the-art tag-aware collaborative filtering approaches in terms of recommendation quality particularly in the cold-start situation.

  12. ePAT: A simple method to tag adenylated RNA to measure poly(A)-tail length and other 3′ RACE applications

    OpenAIRE

    Jänicke, Amrei; Vancuylenberg, John; Boag, Peter R.; Traven, Ana; Traude H Beilharz

    2012-01-01

    The length of the poly(A)-tail that terminates most mRNA can serve as a readout of its metabolism. A long poly(A)-tail is generally associated with actively translating mRNA, whereas a short poly(A)-tail often indicates a translationally repressed state. Here, the authors present a simple new method to measure transcript-specific poly(A)-tail length using standard molecular biology reagents.

  13. MR Colonography with fecal tagging: Barium vs. barium ferumoxsil

    DEFF Research Database (Denmark)

    Achiam, M.P.; Chabanova, E.; Logager, V.B.;

    2008-01-01

    and Methods. Twenty patients referred to CC underwent dark lumen MRC prior to the colonoscopy. Two groups of patients received two different oral contrast agents (barium sulfate and barium sulfate/ferumoxsil) as a laxative-free fecal tagging prior to the MRC. After MRC, the contrast agent was rated...... qualitatively (with the standard method using contrast-to-wall ratio) and subjectively (using a visual analog scale [VAS]) by three different blinded observers. Results. Evaluated both qualitatively and subjectively, the tagging efficiency of barium sulfate/ferumoxsil was significantly better (P ... barium sulfate alone. The VAS method for evaluating the tagging efficiency of contrast agents showed a high correlation (observer 11, r = 0.91) to the standard method using contrast-to-wall ratio and also a high interclass correlation (observer 11 and III = 0.89/0.85). MRC found I of 22 (5%) polyps

  14. Peptide Nucleic Acids Having Enhanced Binding Affinity and Sequence Specificity

    DEFF Research Database (Denmark)

    1998-01-01

    A novel class of compounds, known as peptide nucleic acids, bind complementary DNA and RNA strands more strongly than a corresponding DNA strand, and exhibit increased sequence specificity and binding affinity. Methods of increasing binding affinity and sequence specificity of peptide nucleic aci...

  15. Satellite Tags- Guam/CNMI EEZ

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Satellite tagging was implemented in 2013. Satellite tagging is conducted using a Dan Inject air rifle and deployment arrows designed by Wildlife Computers. Two...

  16. HMSRP Hawaiian Monk Seal Tag Data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains records for all tags applied to Hawaiian monk seals since 1981. These tags were applied by PSD personnel and cooperating scientists as part...

  17. Design and Analysis of Salmonid Tagging Studies in the Columbia Basin, Volume IX; Comparison of Statistical Methods of Estimating Treatment-Control Ratios Using Coded-Wire Tags, Based on Spring Chinook Salmon on the Columbia River, 1986-1988 Technical Report.

    Energy Technology Data Exchange (ETDEWEB)

    Townsend, Richard L.; Skalski, John R. (University of Washington, School of Fisheries, Seattle, WA)

    2000-06-01

    The strength of a salmon run is often measured as the adult return rate from some previous brood year (i.e. the percent of a smolt population returning to spawn or captured in fisheries). The U.S. Army Corp of Engineers (ACOE) program of barge transportation of smolts from collector dams is one mitigation measure used to improve smolt survival. Using Coded Wire-tags, the adult return rates of transported and untransported smolt have been tracked. A ratio of the recovered percentages of adult salmon, those transported in the smolt stage over the salmon not transported (controls), is often used to summarize the program effectiveness. There are a number of ways to estimate this transportation/control (T/C) ratio, and this paper explores six alternative statistical models to improve accuracy and precision of the estimate. Assuming the proportion of adult recoveries are binomially distributed, the data were analyzed using linear regression of arc-sine square-root and logit transformations; general linear model regression (GLM) with logit- and log-links; and a maximum-likelihood estimation (MLE) of the T/C ratio. Profile likelihood intervals were calculated to generate 95% confidence interval estimates of the T/C ratio. Depending on the analytical method, T/C ratios varied greatly. Arc-sine square-root and logit transformations gave individual release T/C ratios which ranged from 1.0934 to 4.0076 and {minus}1.2193 to 1.9057, respectively. The negative T/C ratio is due to the back-transformation properties of the logit transformation. The GLM and MLE approaches produced mean T/C ratios (after adjusting for the individual release batch effects) ranging from 1.4964 to 1.4974. The recommended method from this analysis, a binomial maximum likelihood estimate adjusted for over-dispersion, produced a T/C ratio of 1.4965 with a 95% confidence interval of (1.0618, 1.9312).

  18. Categorical and Specificity Differences between User-Supplied Tags and Search Query Terms for Images. An Analysis of "Flickr" Tags and Web Image Search Queries

    Science.gov (United States)

    Chung, EunKyung; Yoon, JungWon

    2009-01-01

    Introduction: The purpose of this study is to compare characteristics and features of user supplied tags and search query terms for images on the "Flickr" Website in terms of categories of pictorial meanings and level of term specificity. Method: This study focuses on comparisons between tags and search queries using Shatford's categorization…

  19. HaloTag protein-mediated specific labeling of living cells with quantum dots

    International Nuclear Information System (INIS)

    Quantum dots emerge as an attractive alternative to small molecule fluorophores as fluorescent tags for in vivo cell labeling and imaging. This communication presents a method for specific labeling of live cells using quantum dots. The labeling is mediated by HaloTag protein expressed at the cell surface which forms a stable covalent adduct with its ligand (HaloTag ligand). The labeling can be performed in one single step with quantum dot conjugates that are functionalized with HaloTag ligand, or in two steps with biotinylated HaloTag ligand first and followed by streptavidin coated quantum dots. Live cell fluorescence imaging indicates that the labeling is specific and takes place at the cell surface. This HaloTag protein-mediated cell labeling method should facilitate the application of quantum dots for live cell imaging

  20. Exploiting tag correlations to improve multilabel learning

    OpenAIRE

    Payne, Brent

    2011-01-01

    This thesis looks at applying tags to musical songs as a multilabeling problem. We focus on the CAL500 dataset which summarizes 1704 student reviews into tags for 502 songs. This summarization loses information, so we create the CAL1700 dataset which uses each of the student reviews to generate a single multilabel. We develop a two-layer technique to exploit tag correlations. The first layer makes tag predictions based on data features. The second layer applies correlation information to thes...

  1. Towards EPC compatible plastic RFID tags

    NARCIS (Netherlands)

    Myny, K.; Steudel, S.; Vicca, P.; Smout, S.; Beenhakkers, M.J.; Aerle, N.A.J.M. van; Furthner, F.; Putten, B. van der; Tripathi, A.K.; Gelinck, G.H.; Genoe, J.; Dehaene, W.; Heremans, P.

    2010-01-01

    A target application for plastic RFID tags is Electronic Product Coding (EPC). The EPC-specifications set some demanding requirements for RFID tags. In this work, we review the work that has been done to fulfill some of these specifications. We describe a complete 64-bit RFID tag that is inductively

  2. 50 CFR 635.33 - Archival tags.

    Science.gov (United States)

    2010-10-01

    ... 50 Wildlife and Fisheries 8 2010-10-01 2010-10-01 false Archival tags. 635.33 Section 635.33..., DEPARTMENT OF COMMERCE ATLANTIC HIGHLY MIGRATORY SPECIES Management Measures § 635.33 Archival tags. (a) Implantation report. Any person affixing or implanting an archival tag into a regulated species must...

  3. Motion analysis of both ventricles using tagged MRI

    Science.gov (United States)

    Ozturk, Cengizhan; McVeigh, Elliot R.

    2000-04-01

    Although several methods exist for the analysis of tagged MRI images of the left ventricle (LV), analysis of the right ventricle (RV) remains challenging due to its complex anatomy and significant through plane motion. We present here preliminary results of our new motion analysis method, both for RV and LV, in healthy human volunteers. In this method, following standard myocardial and tag segmentation of cardiac gated cine tagged MR images; a 4D B-spline based parametric motion field was computed for a volume of interest encompassing both ventricles. Using this motion field, 3D displacements and strains were calculated on the RV and LV. We observed that for both chambers the circumferential strain (Ecc) decreased with a constant rate throughout systole. The systolic strain rate displayed spatial similarity not only for the LV but also for the RV. For RV free wall, mean systolic Ecc was -0.19 +/- 0.05 with an average coefficient of variability of 20%. The 4D B-spline based motion analysis technique for tagged MRI yields compatible results for the LV and gives consistent circumferential strain measures for the RV free wall. Tagged MRI based RV mechanical analysis can be used along with LV results for a more complete cardiac evaluation.

  4. Classification of neocortical interneurons using affinity propagation

    Directory of Open Access Journals (Sweden)

    Roberto eSantana

    2013-12-01

    Full Text Available In spite of over a century of research on cortical circuits, it is still unknown how many classes of cortical neurons exist. Neuronal classification has been a difficult problem because it is unclear what a neuronal cell class actually is and what are the best characteristics are to define them. Recently, unsupervised classifications using cluster analysis based on morphological, physiological or molecular characteristics, when applied to selected datasets, have provided quantitative and unbiased identification of distinct neuronal subtypes. However, better and more robust classification methods are needed for increasingly complex and larger datasets. We explored the use of affinity propagation, a recently developed unsupervised classification algorithm imported from machine learning, which gives a representative example or exemplar for each cluster. As a case study, we applied affinity propagation to a test dataset of 337 interneurons belonging to four subtypes, previously identified based on morphological and physiological characteristics. We found that affinity propagation correctly classified most of the neurons in a blind, non-supervised manner. In fact, using a combined anatomical/physiological dataset, our algorithm differentiated parvalbumin from somatostatin interneurons in 49 out of 50 cases. Affinity propagation could therefore be used in future studies to validly classify neurons, as a first step to help reverse engineer neural circuits.

  5. Top tagging algorithms in CMS

    Energy Technology Data Exchange (ETDEWEB)

    Haller, Johannes; Kogler, Roman; Lapsien, Tobias [University of Hamburg (Germany)

    2015-07-01

    Top quarks with high transverse momenta will be produced abundantly at the LHC with increasing center of mass energy. The identification of hadronically decaying top quarks (t → bW → bq anti q) imposes various challenges, since at high transverse momenta all decay products are collimated in one jet. Various algorithms to identify these top quarks, while rejecting light flavour jets, have been studied and employed in CMS. New developments in jet substructure techniques make it possible to improve these existing top taggers significantly. In this talk, various improvements of top tagging algorithms are shown and results are presented based on the shower deconstruction tagger and the MultiR HEP Top tagger. Also measurements of efficiency and misidentification rates of these new top tagging algorithms in the √(s) = 8 TeV dataset are shown.

  6. ATLAS boosted object tagging 2

    CERN Document Server

    Caudron, Julien; The ATLAS collaboration

    2015-01-01

    A detailed study into the optimal techniques for identifying boosted hadronically decaying W or Z bosons is presented. Various algorithms for reconstructing, grooming and tagging bosonic jets are compared for W bosons with a wide range of transverse momenta using 8 TeV data and 8 TeV and 13 TeV MC simulations. In addition, given that a hadronic jet has been identified as resulting from the hadronic decay of a W or Z, a technique is developed to discriminate between W and Z bosons. The modeling of the tagging variables used in this technique is studied using 8 TeV pp collision data and systematic uncertainties for the tagger efficiency and fake rates are evaluated.

  7. A new approach to tag design in dolphin telemetry: Computer simulations to minimise deleterious effects

    Science.gov (United States)

    Pavlov, V. V.; Wilson, R. P.; Lucke, K.

    2007-02-01

    Remote-sensors and transmitters are powerful devices for studying cetaceans at sea. However, despite substantial progress in microelectronics and miniaturisation of systems, dolphin tags are imperfectly designed; additional drag from tags increases swim costs, compromises swimming capacity and manoeuvrability, and leads to extra loads on the animal's tissue. We propose a new approach to tag design, elaborating basic principles and incorporating design stages to minimise device effects by using computer-aided design. Initially, the operational conditions of the device are defined by quantifying the shape, hydrodynamics and range of the natural deformation of the dolphin body at the tag attachment site (such as close to the dorsal fin). Then, parametric models of both of the dorsal fin and a tag are created using the derived data. The link between parameters of the fin and a tag model allows redesign of tag models according to expected changes of fin geometry (difference in fin shape related with species, sex, and age peculiarities, simulation of the bend of the fin during manoeuvres). A final virtual modelling stage uses iterative improvement of a tag model in a computer fluid dynamics (CFD) environment to enhance tag performance. This new method is considered as a suitable tool of tag design before creation of the physical model of a tag and testing with conventional wind/water tunnel technique. Ultimately, tag materials are selected to conform to the conditions identified by the modelling process and thus help create a physical model of a tag, which should minimise its impact on the animal carrier and thus increase the reliability and quality of the data obtained.

  8. A Novel Multilayered RFID Tagged Cargo Integrity Assurance Scheme.

    Science.gov (United States)

    Yang, Ming Hour; Luo, Jia Ning; Lu, Shao Yong

    2015-01-01

    To minimize cargo theft during transport, mobile radio frequency identification (RFID) grouping proof methods are generally employed to ensure the integrity of entire cargo loads. However, conventional grouping proofs cannot simultaneously generate grouping proofs for a specific group of RFID tags. The most serious problem of these methods is that nonexistent tags are included in the grouping proofs because of the considerable amount of time it takes to scan a high number of tags. Thus, applying grouping proof methods in the current logistics industry is difficult. To solve this problem, this paper proposes a method for generating multilayered offline grouping proofs. The proposed method provides tag anonymity; moreover, resolving disputes between recipients and transporters over the integrity of cargo deliveries can be expedited by generating grouping proofs and automatically authenticating the consistency between the receipt proof and pick proof. The proposed method can also protect against replay attacks, multi-session attacks, and concurrency attacks. Finally, experimental results verify that, compared with other methods for generating grouping proofs, the proposed method can efficiently generate offline grouping proofs involving several parties in a supply chain using mobile RFID. PMID:26512673

  9. Soft lepton tagging for Bd mixing at CDF

    International Nuclear Information System (INIS)

    The authors present a study of heavy flavor tagging using soft lepton identification. They optimize their soft lepton identification method for use in a time-dependent Bd mixing measurement. In events triggered by a high Pt lepton from one B hadron, they search for a soft lepton from the semileptonic decay of the other B hadron. The charge of each lepton tags the flavor of its parent B hadron at the time of that parent's decay. The authors present the resulting efficiency and dilution for their optimized method

  10. Tag Clusters as Information Retrieval Interfaces

    CERN Document Server

    Knautz, Kathrin; Stock, Wolfgang G

    2010-01-01

    The paper presents our design of a next generation information retrieval system based on tag co-occurrences and subsequent clustering. We help users getting access to digital data through information visualization in the form of tag clusters. Current problems like the absence of interactivity and semantics between tags or the difficulty of adding additional search arguments are solved. In the evaluation, based upon SERVQUAL and IT systems quality indicators, we found out that tag clusters are perceived as more useful than tag clouds, are much more trustworthy, and are more enjoyable to use.

  11. Representations of affine Hecke algebras

    CERN Document Server

    Xi, Nanhua

    1994-01-01

    Kazhdan and Lusztig classified the simple modules of an affine Hecke algebra Hq (q E C*) provided that q is not a root of 1 (Invent. Math. 1987). Ginzburg had some very interesting work on affine Hecke algebras. Combining these results simple Hq-modules can be classified provided that the order of q is not too small. These Lecture Notes of N. Xi show that the classification of simple Hq-modules is essentially different from general cases when q is a root of 1 of certain orders. In addition the based rings of affine Weyl groups are shown to be of interest in understanding irreducible representations of affine Hecke algebras. Basic knowledge of abstract algebra is enough to read one third of the book. Some knowledge of K-theory, algebraic group, and Kazhdan-Lusztig cell of Cexeter group is useful for the rest

  12. Infinite transitivity on affine varieties

    OpenAIRE

    Arzhantsev, Ivan; Flenner, Hubert; Kaliman, Shulim; Kutzschebauch, Frank; ZAIDENBERG, MIKHAIL

    2012-01-01

    In this note we survey recent results on automorphisms of affine algebraic varieties, infinitely transitive group actions and flexibility. We present related constructions and examples, and discuss geometric applications and open problems.

  13. Plastic-casting intrinsic-surface unique identifier (tag)

    International Nuclear Information System (INIS)

    This report describes the development of an authenticated intrinsic-surf ace tagging method for unique- identification of controlled items. Although developed for control of items limited by an arms control treaty, this method has other potential applications to keep track of critical or high-value items. Each tag (unique-identifier) consists of the intrinsic, microscopic surface topography of a small designated area on a controlled item. It is implemented by making a baseline plastic casting of the designated tag area and usually placing a cover (for example, a bar-code label) over this area to protect the surface from environmental alteration. The plastic casting is returned to a laboratory and prepared for high-resolution scanning electron microscope imaging. Several images are digitized and stored for use as a standard for authentication of castings taken during future inspections. Authentication is determined by numerically comparing digital images. Commercially available hardware and software are used for this tag. Tag parameters are optimized, so unique casting images are obtained from original surfaces, and images obtained from attempted duplicate surfaces are detected. This optimization uses the modulation transfer function, a first principle of image analysis, to determine the parameters. Surface duplication experiments confirmed the optimization

  14. Approximation properties of haplotype tagging

    Directory of Open Access Journals (Sweden)

    Dreiseitl Stephan

    2006-01-01

    Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs are locations at which the genomic sequences of population members differ. Since these differences are known to follow patterns, disease association studies are facilitated by identifying SNPs that allow the unique identification of such patterns. This process, known as haplotype tagging, is formulated as a combinatorial optimization problem and analyzed in terms of complexity and approximation properties. Results It is shown that the tagging problem is NP-hard but approximable within 1 + ln((n2 - n/2 for n haplotypes but not approximable within (1 - ε ln(n/2 for any ε > 0 unless NP ⊂ DTIME(nlog log n. A simple, very easily implementable algorithm that exhibits the above upper bound on solution quality is presented. This algorithm has running time O((2m - p + 1 ≤ O(m(n2 - n/2 where p ≤ min(n, m for n haplotypes of size m. As we show that the approximation bound is asymptotically tight, the algorithm presented is optimal with respect to this asymptotic bound. Conclusion The haplotype tagging problem is hard, but approachable with a fast, practical, and surprisingly simple algorithm that cannot be significantly improved upon on a single processor machine. Hence, significant improvement in computatational efforts expended can only be expected if the computational effort is distributed and done in parallel.

  15. B-tagging in CMS

    International Nuclear Information System (INIS)

    The CMS experiment investigates high-energetic proton-proton collisions at the LHC, in order to broaden the knowledge of the Standard Model (SM) of particle physics and to discover possible new physics beyond the SM. A large fraction of the CMS physics program relies on the identification of jets containing the decay of a B-hadron (b-jets). The b-jets can be discriminated from jets produced by the hadronization of light quarks based on characteristic properties of B-hadrons, such as the long lifetime or the presence of soft leptons produced during their decay. The CMS detector, with its excellent tracking system, robust lepton identification and finely segmented calorimeters, is well suited to the task of identification of b-jets (b-tagging). This talk gives an overview of the large variety of b-tagging algorithms and the measurement of their performance with data collected in 2011 and 2012. The algorithms described are based either on the identification of tracks displaced from the primary proton-proton collision, the reconstruction of secondary vertices or the presence of soft leptons inside jets. Some algorithms combine this information using multivariate techniques. This talk discusses also the performance of b-tagging with upgraded CMS detector and high pile-up conditions, which will be faced during the high-energy collisions at 13 TeV planned to start in 2014.

  16. Glutamate dehydrogenase isoforms with N-terminal (His)6- or FLAG-tag retain their kinetic properties and cellular localization

    DEFF Research Database (Denmark)

    Pajęcka, Kamilla; Nielsen, Camilla Wendel; Hauge, Anne;

    2014-01-01

    containing N-terminal (His)6 tags were successfully expressed in Sf9 cells and the recombinant proteins were isolated to ≥95 % purity in a two-step procedure involving ammonium sulfate precipitation and Ni(2+)-based immobilized metal ion affinity chromatography. To explore whether the presence of the FLAG...

  17. Development of an epitope tag for the gentle purification of proteins by immunoaffinity chromatography: application to epitope-tagged green fluorescent protein.

    Science.gov (United States)

    Thompson, Nancy E; Arthur, Terrance M; Burgess, Richard R

    2003-12-15

    Polyol-responsive monoclonal antibodies (mAbs) are useful tools for the gentle purification of proteins and protein complexes. These are high-affinity mAbs that release the antigen in the presence of a nonchaotropic salt and a low-molecular-weight polyhydroxylated compound (polyol). The epitope for the polyol-responsive mAb NT73, which reacts with Escherichia coli RNA polymerase, was located at the C terminus of the beta' subunit. Using recombinant DNA techniques, we have identified the epitope to be within the 13-amino-acid sequence SLAELLNAGLGGS and have developed an epitope tag that can be fused to a protein of interest for use as a purification tag. This epitope tag (designated Softag1) was fused to either the N or the C terminus of the green fluorescent protein. These tagged proteins were expressed in E. coli, and the tagged proteins were purified from the soluble fraction by a single-step immunoaffinity chromatography procedure. This approach extends the powerful technique of gentle-release immunoaffinity chromatography to many expressed proteins. PMID:14656522

  18. Enhancing Navigation on Wikipedia with Social Tags

    CERN Document Server

    Zubiaga, Arkaitz

    2012-01-01

    Social tagging has become an interesting approach to improve search and navigation over the actual Web, since it aggregates the tags added by different users to the same resource in a collaborative way. This way, it results in a list of weighted tags describing its resource. Combined to a classical taxonomic classification system such as that by Wikipedia, social tags can enhance document navigation and search. On the one hand, social tags suggest alternative navigation ways, including pivot-browsing, popularity-driven navigation, and filtering. On the other hand, it provides new metadata, sometimes uncovered by documents' content, that can substantially improve document search. In this work, the inclusion of an interface to add user-defined tags describing Wikipedia articles is proposed, as a way to improve article navigation and retrieval. As a result, a prototype on applying tags over Wikipedia is proposed in order to evaluate its effectiveness.

  19. Parsing of Myanmar sentences with function tagging

    CERN Document Server

    Thant, Win Win; Thein, Ni Lar

    2012-01-01

    This paper describes the use of Naive Bayes to address the task of assigning function tags and context free grammar (CFG) to parse Myanmar sentences. Part of the challenge of statistical function tagging for Myanmar sentences comes from the fact that Myanmar has free-phrase-order and a complex morphological system. Function tagging is a pre-processing step for parsing. In the task of function tagging, we use the functional annotated corpus and tag Myanmar sentences with correct segmentation, POS (part-of-speech) tagging and chunking information. We propose Myanmar grammar rules and apply context free grammar (CFG) to find out the parse tree of function tagged Myanmar sentences. Experiments show that our analysis achieves a good result with parsing of simple sentences and three types of complex sentences.

  20. Lipid Vesicle-mediated Affinity Chromatography using Magnetic Activated Cell Sorting (LIMACS): a Novel Method to Analyze Protein-lipid Interaction

    OpenAIRE

    Bieberich, Erhard

    2011-01-01

    The analysis of lipid protein interaction is difficult because lipids are embedded in cell membranes and therefore, inaccessible to most purification procedures. As an alternative, lipids can be coated on flat surfaces as used for lipid ELISA and Plasmon resonance spectroscopy. However, surface coating lipids do not form microdomain structures, which may be important for the lipid binding properties. Further, these methods do not allow for the purification of larger amounts of proteins bindin...

  1. Reduced Basis Methods for Partial Differential Equations: Evaluation of multiple non-compliant flux-type output functionals for a non-affine electrostatics problem

    OpenAIRE

    Eftang, Jens Lohne

    2008-01-01

    A method for rapid evaluation of flux-type outputs of interest from solutions to partial differential equations (PDEs) is presented within the reduced basis framework for linear, elliptic PDEs. The central point is a Neumann-Dirichlet equivalence that allows for evaluation of the output through the bilinear form of the weak formulation of the PDE. Through a comprehensive example related to electrostatics, we consider multiple outputs, a posteriori error estimators and empirical interpolation...

  2. POLYFAIL: a program for identification of multiple fuel failures with gas tagging

    International Nuclear Information System (INIS)

    This report describes the development of the computer code POLYFAIL for identification of fuel failures in fast reactors or light-water reactors that use gas tagging. POLYFAIL implements a sophisticated numerical algorithm known as the method of barycentric coordinates. The code can treat problems involving up to four simultaneous tag releases in a tagging system characterized by three independent tag ratios. The sensitivity of the multiple-failure-resolution technique has been optimized by incorporation of a newly developed ratio weighting scheme. Several example problems are provided to demonstrate operation of the code under single-leaker and various postulated multiple-leaker situations

  3. Profile-QSAR: a novel meta-QSAR method that combines activities across the kinase family to accurately predict affinity, selectivity, and cellular activity.

    Science.gov (United States)

    Martin, Eric; Mukherjee, Prasenjit; Sullivan, David; Jansen, Johanna

    2011-08-22

    Profile-QSAR is a novel 2D predictive model building method for kinases. This "meta-QSAR" method models the activity of each compound against a new kinase target as a linear combination of its predicted activities against a large panel of 92 previously studied kinases comprised from 115 assays. Profile-QSAR starts with a sparse incomplete kinase by compound (KxC) activity matrix, used to generate Bayesian QSAR models for the 92 "basis-set" kinases. These Bayesian QSARs generate a complete "synthetic" KxC activity matrix of predictions. These synthetic activities are used as "chemical descriptors" to train partial-least squares (PLS) models, from modest amounts of medium-throughput screening data, for predicting activity against new kinases. The Profile-QSAR predictions for the 92 kinases (115 assays) gave a median external R²(ext) = 0.59 on 25% held-out test sets. The method has proven accurate enough to predict pairwise kinase selectivities with a median correlation of R²(ext) = 0.61 for 958 kinase pairs with at least 600 common compounds. It has been further expanded by adding a "C(k)XC" cellular activity matrix to the KxC matrix to predict cellular activity for 42 kinase driven cellular assays with median R²(ext) = 0.58 for 24 target modulation assays and R²(ext) = 0.41 for 18 cell proliferation assays. The 2D Profile-QSAR, along with the 3D Surrogate AutoShim, are the foundations of an internally developed iterative medium-throughput screening (IMTS) methodology for virtual screening (VS) of compound archives as an alternative to experimental high-throughput screening (HTS). The method has been applied to 20 actual prospective kinase projects. Biological results have so far been obtained in eight of them. Q² values ranged from 0.3 to 0.7. Hit-rates at 10 uM for experimentally tested compounds varied from 25% to 80%, except in K5, which was a special case aimed specifically at finding "type II" binders, where none of the compounds were predicted to be

  4. Affinity Monolith-Integrated Microchips for Protein Purification and Concentration.

    Science.gov (United States)

    Gao, Changlu; Sun, Xiuhua; Wang, Huaixin; Qiao, Wei; Hu, Bo

    2016-01-01

    Affinity chromatography is a valuable method to purify and concentrate minute amount of proteins. Monoliths with epoxy groups for affinity immobilization were prepared by direct in-situ photopolymerization of glycidyl methacrylate and ethylene glycol dimethacrylate in porogenic solvents consisting of 1-dodecanol and cyclohexanol. By integrating affinity monoliths onto a microfluidic system, targeted biomolecules can be captured and retained on affinity column, while other biomolecules having no specific interactions toward the immobilized ligands flow through the microchannel. Therefore, proteins which remain on the affinity column are purified and concentrated, and then eluted by appropriate solutions and finally, separated by microchip capillary electrophoresis. This integrated microfluidic device has been applied to the purification and separation of specific proteins (FITC-labeled human serum albumin and IgG) in a mixture.

  5. An inexpensive and simple method for thermally stable immobilization of DNA on an unmodified glass surface: UV linking of poly(T)10-poly(C)10-tagged DNA probes

    DEFF Research Database (Denmark)

    Guðnason, Haukur; Dufva, Hans Martin; Bang, Dang Duong;

    2008-01-01

    Microarrays printed on glass slides are often constructed by covalently linking modified oligonucleotide probes to a derivatized surface at considerable expense. In this article, we demonstrate that 14-base oligonucleotides with a poly(T)10 - poly(C)10 tail (TC tag), but otherwise unmodified, can...... be linked by UV light irradiation onto a plain, unmodified glass surface. Probes immobilized onto unmodified glass microscope slides performed similarly to probes bound to commercial amino-silane-coated slides and had comparable detection limits. The TC-tagged probes linked to unmodified glass did not show...

  6. AFFINE TRANSFORMATION IN RANDOM ITERATED FUNCTION SYSTEMS

    Institute of Scientific and Technical Information of China (English)

    熊勇; 史定华

    2001-01-01

    Random iterated function systems (IFSs) is discussed, which is one of the methods for fractal drawing. A certain figure can be reconstructed by a random IFS. One approach is presented to determine a new random IFS, that the figure reconstructed by the new random IFS is the image of the origin figure reconstructed by old IFS under a given affine transformation. Two particular examples are used to show this approach.

  7. Is It Reliable to Use Common Molecular Docking Methods for Comparing the Binding Affinities of Enantiomer Pairs for Their Protein Target?

    Science.gov (United States)

    Ramírez, David; Caballero, Julio

    2016-01-01

    Molecular docking is a computational chemistry method which has become essential for the rational drug design process. In this context, it has had great impact as a successful tool for the study of ligand-receptor interaction modes, and for the exploration of large chemical datasets through virtual screening experiments. Despite their unquestionable merits, docking methods are not reliable for predicting binding energies due to the simple scoring functions they use. However, comparisons between two or three complexes using the predicted binding energies as a criterion are commonly found in the literature. In the present work we tested how wise is it to trust the docking energies when two complexes between a target protein and enantiomer pairs are compared. For this purpose, a ligand library composed by 141 enantiomeric pairs was used, including compounds with biological activities reported against seven protein targets. Docking results using the software Glide (considering extra precision (XP), standard precision (SP), and high-throughput virtual screening (HTVS) modes) and AutoDock Vina were compared with the reported biological activities using a classification scheme. Our test failed for all modes and targets, demonstrating that an accurate prediction when binding energies of enantiomers are compared using docking may be due to chance. We also compared pairs of compounds with different molecular weights and found the same results. PMID:27104528

  8. Multifunctional g3p-peptide tag for current phage display systems.

    Science.gov (United States)

    Beckmann, C; Haase, B; Timmis, K N; Tesar, M

    1998-03-15

    . The high sensitivity of the antibody for the peptide tag was reflected in the antibody affinity constant K(D) of 6.80 x 10(-10) M, which was determined by real time biomolecular interaction analysis (BIA) based on surface plasmon resonance (SPR) [Karlsson, R., Fält, A., 1997. Experimental design for kinetic analysis of protein-protein interactions with surface plasmon resonance biosensors. J. Immunol. Methods 200, 121-133]. Finally, recombinant proteins in E. coli periplasmic extracts could be purified in a single step by affinity purification using immobilized mAb 10C3. These studies demonstrated that the new peptide-tag and its corresponding mAb represents a versatile tool for the detection of recombinant proteins selected by phage display technology.

  9. Myocardial motion estimation of tagged cardiac magnetic resonance images using tag motion constraints and multi-level b-splines interpolation.

    Science.gov (United States)

    Liu, Hong; Yan, Meng; Song, Enmin; Wang, Jie; Wang, Qian; Jin, Renchao; Jin, Lianghai; Hung, Chih-Cheng

    2016-05-01

    Myocardial motion estimation of tagged cardiac magnetic resonance (TCMR) images is of great significance in clinical diagnosis and the treatment of heart disease. Currently, the harmonic phase analysis method (HARP) and the local sine-wave modeling method (SinMod) have been proven as two state-of-the-art motion estimation methods for TCMR images, since they can directly obtain the inter-frame motion displacement vector field (MDVF) with high accuracy and fast speed. By comparison, SinMod has better performance over HARP in terms of displacement detection, noise and artifacts reduction. However, the SinMod method has some drawbacks: 1) it is unable to estimate local displacements larger than half of the tag spacing; 2) it has observable errors in tracking of tag motion; and 3) the estimated MDVF usually has large local errors. To overcome these problems, we present a novel motion estimation method in this study. The proposed method tracks the motion of tags and then estimates the dense MDVF by using the interpolation. In this new method, a parameter estimation procedure for global motion is applied to match tag intersections between different frames, ensuring specific kinds of large displacements being correctly estimated. In addition, a strategy of tag motion constraints is applied to eliminate most of errors produced by inter-frame tracking of tags and the multi-level b-splines approximation algorithm is utilized, so as to enhance the local continuity and accuracy of the final MDVF. In the estimation of the motion displacement, our proposed method can obtain a more accurate MDVF compared with the SinMod method and our method can overcome the drawbacks of the SinMod method. However, the motion estimation accuracy of our method depends on the accuracy of tag lines detection and our method has a higher time complexity. PMID:26712656

  10. Identifying novel genes in C. elegans using SAGE tags

    Directory of Open Access Journals (Sweden)

    Chen Nansheng

    2010-12-01

    Full Text Available Abstract Background Despite extensive efforts devoted to predicting protein-coding genes in genome sequences, many bona fide genes have not been found and many existing gene models are not accurate in all sequenced eukaryote genomes. This situation is partly explained by the fact that gene prediction programs have been developed based on our incomplete understanding of gene feature information such as splicing and promoter characteristics. Additionally, full-length cDNAs of many genes and their isoforms are hard to obtain due to their low level or rare expression. In order to obtain full-length sequences of all protein-coding genes, alternative approaches are required. Results In this project, we have developed a method of reconstructing full-length cDNA sequences based on short expressed sequence tags which is called sequence tag-based amplification of cDNA ends (STACE. Expressed tags are used as anchors for retrieving full-length transcripts in two rounds of PCR amplification. We have demonstrated the application of STACE in reconstructing full-length cDNA sequences using expressed tags mined in an array of serial analysis of gene expression (SAGE of C. elegans cDNA libraries. We have successfully applied STACE to recover sequence information for 12 genes, for two of which we found isoforms. STACE was used to successfully recover full-length cDNA sequences for seven of these genes. Conclusions The STACE method can be used to effectively reconstruct full-length cDNA sequences of genes that are under-represented in cDNA sequencing projects and have been missed by existing gene prediction methods, but their existence has been suggested by short sequence tags such as SAGE tags.

  11. Influence of Histidine-Containing Tags on the Biodistribution of ADAPT Scaffold Proteins.

    Science.gov (United States)

    Lindbo, Sarah; Garousi, Javad; Åstrand, Mikael; Honarvar, Hadis; Orlova, Anna; Hober, Sophia; Tolmachev, Vladimir

    2016-03-16

    Engineered scaffold proteins (ESP) are high-affinity binders that can be used as probes for radionuclide imaging. Histidine-containing tags enable both efficient purification of ESP and radiolabeling with (99m)Tc(CO)3. Earlier studies demonstrated that the use of a histidine-glutamate-histidine-glutamate-histidine-glutamate (HE)3-tag instead of the commonly used hexahistidine (H6)-tag reduces hepatic uptake of radiolabeled ESP and short peptides. Here, we investigated the influence of histidine-containing tags on the biodistribution of a novel type of ESP, ADAPTs. A series of anti-HER2 ADAPT probes having H6- or (HE)3-tags in the N-termini were prepared. The constructs, (HE)3-ADAPT6 and H6-ADAPT6, were labeled with two different nuclides, (99m)Tc or (111)In. The labeling with (99m)Tc(CO)3 utilized the histidine-containing tags, while (111)In was attached through a maleimido derivative of DOTA conjugated to the N-terminus. For (111)In-labeled ADAPTs, the use of (HE)3 provided a significantly (p < 0.05) lower hepatic uptake at 1 h after injection, but there was no significant difference in hepatic uptake of (111)In-(HE)3-ADAPT6 and H6-ADAPT6 at later time points. Interestingly, in the case of (99m)Tc, (99m)Tc(CO)3-H6-ADAPT6 provided significantly (p < 0.05) lower uptake in a number of normal tissues and was more suitable as an imaging probe. Thus, the influence of histidine-containing tags on the biodistribution of the novel ADAPT scaffold proteins was different compared to its influence on other ESPs studied so far. Apparently, the effect of a histidine-containing tag on the biodistribution is highly dependent on the scaffold composition of the ESP. PMID:26781756

  12. Measurement of $R_{b}$ using a Vertex Mass Tag

    CERN Document Server

    Abe, K; Akagi, T; Allen, N J; Ash, W W; Aston, D; Baird, K G; Baltay, C; Band, H R; Barakat, M B; Baranko, G; Bardon, O; Barklow, T L; Bashindzhagian, G L; Bazarko, A O; Ben-David, R; Benvenuti, Alberto C; Bilei, G M; Bisello, D; Blaylock, G; Bogart, J R; Bolen, B; Bolton, T; Bower, G R; Brau, J E; Breidenbach, M; Bugg, W M; Burke, D; Burnett, T H; Burrows, P N; Busza, W; Calcaterra, A; Caldwell, D O; Calloway, D; Camanzi, B; Carpinelli, M; Cassell, R; Castaldi, R; Castro, A; Cavalli-Sforza, M; Chou, A; Church, E; Cohn, H O; Coller, J A; Cook, V; Cotton, R; Cowan, R F; Coyne, D G; Crawford, G; de Oliveira, A; Damerell, C J S; Daoudi, M; De Groot, N; De Sangro, R; Dell'Orso, R; Dervan, P J; Dima, M; Dong, D N; Du, P Y C; Dubois, R; Eisenstein, B I; Elia, R; Etzion, E; Fahey, S; Falciai, D; Fan, C; Fernández, J P; Fero, M J; Frey, R; Gillman, T; Gladding, G; González, S; Hart, E L; Harton, J L; Hasan, A; Hasegawa, Y; Hasuko, K; Hedges, S J; Hertzbach, S S; Hildreth, M D; Huber, J; Huffer, M E; Hughes, E W; Hwang, H; Iwasaki, Y; Jackson, D J; Jacques, P; Jaros, J A; Jiang, Z Y; Johnson, A S; Johnson, J R; Johnson, R A; Junk, T R; Kajikawa, R; Kalelkar, M; Kang, H J; Karliner, I; Kawahara, H; Kendall, H W; Kim, Y D; King, M E; King, R; Kofler, R R; Krishna, N M; Kroeger, R S; Labs, J F; Langston, M; Lath, A; Lauber, J A; Leith, D W G S; Lia, V; Liu, M X; Liu, X; Loreti, M; Lu, A; Lynch, H L; Ma, J; Mancinelli, G; Manly, S; Mantovani, G C; Markiewicz, T W; Maruyama, T; Masuda, H; Mazzucato, E; McKemey, A K; Meadows, B T; Messner, R; Mockett, P M; Moffeit, K C; Moore, T B; Müller, D; Nagamine, T; Narita, S; Nauenberg, U; Neal, H; Nussbaum, M; Ohnishi, Y; Oishi, N; Onoprienko, D; Osborne, L S; Panvini, R S; Park, C H; Park, H; Pavel, T J; Peruzzi, I; Piccolo, M; Piemontese, L; Pieroni, E; Pitts, K T; Plano, R J; Prepost, R; Prescott, C Y; Punkar, G D; Quigley, J; Ratcliff, B N; Reeves, T W; Reidy, J; Reinertsen, P L; Rensing, P E; Rochester, L S; Rowson, P C; Russell, J J; Saxton, O H; Schalk, T; Schindler, R H; Schumm, B A; Schwiening, J; Sen, S; Serbo, V V; Shaevitz, M H; Shank, J T; Shapiro, G; Sherden, D J; Shmakov, K D; Simopoulos, C; Sinev, N B; Smith, S R; Smy, M B; Snyder, J A; Stängle, H; Stamer, P; Steiner, H; Steiner, R; Strauss, M G; Su, D; Suekane, F; Sugiyama, A; Suzuki, S; Swartz, M; Szumilo, A; Takahashi, T; Taylor, F E; Torrence, E; Trandafir, A I; Turk, J D; Usher, T; Vavra, J; Vannini, C; Vella, E; Venuti, J P; Verdier, R; Verdini, P G; Wagner, D L; Wagner, S R; Waite, A P; Watts, S J; Weidemann, A W; Weiss, E R; Whitaker, J S; White, S L; Wickens, F J; Williams, D C; Williams, S H; Willocq, S; Wilson, R J; Wisniewski, W J; Woods, M; Word, G B; Wyss, J; Yamamoto, R K; Yamartino, J M; Yang, X; Yashima, J; Yellin, S J; Young, C C; Yuta, H; Zapalac, G; Zdarko, R W; Zhou, J

    1998-01-01

    We report a new measurement of Rb = Gamma(Z0->b-bbar) / Gamma(Z0->hadrons) using a double tag technique, where the b hemisphere selection is based on the reconstructed mass of the B hadron decay vertex. The measurement was performed using a sample of 130k hadronic Z0 events, collected with the SLD at the SLC. The method utilizes the 3-D vertexing abilities of the CCD pixel vertex detector and the small stable SLC beams to obtain a high b-tagging efficiency and purity. We obtain Rb=0.2142+/-0.0034(stat.)+/-0.0015(syst.)+/-0.0002(R_c).

  13. The lifetime probability tag measurement of Rb using the SLD

    International Nuclear Information System (INIS)

    The authors present a new measurement of Rb = ΛZdegree→bantib/ΛZdegree→hadrons using a lifetime double tag on 150k hadronic Z degree events collected from the SLD 1993 and 1994 runs. The method utilizes the high precision 3-D position measurements provided by the CCD vertex detector and the small stable SLC beams to obtain a b hemisphere tagging efficiency of 31% for a purity of 94%. The b-Hemisphere tagging efficiency is measured from the data reducing dependence on the B-decay model and detector simulation. They obtain a result of Rb = 0.2171 ± 0.0040statistical ± 0.0037systematic ± 0.0023Rc

  14. Treelicious: a System for Semantically Navigating Tagged Web Pages

    CERN Document Server

    Mullins, Matt; 10.1109/WI-IAT.2010.289

    2011-01-01

    Collaborative tagging has emerged as a popular and effective method for organizing and describing pages on the Web. We present Treelicious, a system that allows hierarchical navigation of tagged web pages. Our system enriches the navigational capabilities of standard tagging systems, which typically exploit only popularity and co-occurrence data. We describe a prototype that leverages the Wikipedia category structure to allow a user to semantically navigate pages from the Delicious social bookmarking service. In our system a user can perform an ordinary keyword search and browse relevant pages but is also given the ability to broaden the search to more general topics and narrow it to more specific topics. We show that Treelicious indeed provides an intuitive framework that allows for improved and effective discovery of knowledge.

  15. In vitro affinity screening of protein and peptide binders by megavalent bead surface display.

    Science.gov (United States)

    Diamante, Letizia; Gatti-Lafranconi, Pietro; Schaerli, Yolanda; Hollfelder, Florian

    2013-10-01

    The advent of protein display systems has provided access to tailor-made protein binders by directed evolution. We introduce a new in vitro display system, bead surface display (BeSD), in which a gene is mounted on a bead via strong non-covalent (streptavidin/biotin) interactions and the corresponding protein is displayed via a covalent thioether bond on the DNA. In contrast to previous monovalent or low-copy bead display systems, multiple copies of the DNA and the protein or peptide of interest are displayed in defined quantities (up to 10(6) of each), so that flow cytometry can be used to obtain a measure of binding affinity. The utility of the BeSD in directed evolution is validated by library selections of randomized peptide sequences for binding to the anti-hemagglutinin (HA) antibody that proceed with enrichments in excess of 10(3) and lead to the isolation of high-affinity HA-tags within one round of flow cytometric screening. On-bead K(d) measurements suggest that the selected tags have affinities in the low nanomolar range. In contrast to other display systems (such as ribosome, mRNA and phage display) that are limited to affinity panning selections, BeSD possesses the ability to screen and rank binders by their affinity in vitro, a feature that hitherto has been exclusive to in vivo multivalent cell display systems (such as yeast display).

  16. Social Tagging in a Scholarly Digital Library Environment: Users' Perspectives

    Science.gov (United States)

    Noorhidawati, A.; Hanum, N. Fariza; Zohoorian-Fooladi, N.

    2013-01-01

    Introduction: This paper reports an exploratory study examining how users participate in social tagging activities in a scholarly digital library environment to learn about their motivations, behaviour, and practices. Method: This study was conducted in two phases: a survey to investigate usage and attitudes of social tagging tool, and a…

  17. Recent Results Regarding Affine Quantum Gravity

    CERN Document Server

    Klauder, John R

    2012-01-01

    Recent progress in the quantization of nonrenormalizable scalar fields has found that a suitable non-classical modification of the ground state wave function leads to a result that eliminates term-by-term divergences that arise in a conventional perturbation analysis. After a brief review of both the scalar field story and the affine quantum gravity program, examination of the procedures used in the latter surprisingly shows an analogous formulation which already implies that affine quantum gravity is not plagued by divergences that arise in a standard perturbation study. Additionally, guided by the projection operator method to deal with quantum constraints, trial reproducing kernels are introduced that satisfy the diffeomorphism constraints. Furthermore, it is argued that the trial reproducing kernels for the diffeomorphism constraints may also satisfy the Hamiltonian constraint as well.

  18. Intein Applications: From Protein Purification and Labeling to Metabolic Control Methods*

    OpenAIRE

    Wood, David W.; Camarero, Julio A.

    2014-01-01

    The discovery of inteins in the early 1990s opened the door to a wide variety of new technologies. Early engineered inteins from various sources allowed the development of self-cleaving affinity tags and new methods for joining protein segments through expressed protein ligation. Some applications were developed around native and engineered split inteins, which allow protein segments expressed separately to be spliced together in vitro. More recently, these early applications have been expand...

  19. Mass spectrometry-based methods for detection and differentiation of botulinum neurotoxins

    Science.gov (United States)

    Schmidt, Jurgen G.; Boyer, Anne E.; Kalb, Suzanne R.; Moura, Hercules; Barr, John R.; Woolfitt, Adrian R.

    2009-11-03

    The present invention is directed to a method for detecting the presence of clostridial neurotoxins in a sample by mixing a sample with a peptide that can serve as a substrate for proteolytic activity of a clostridial neurotoxin; and measuring for proteolytic activity of a clostridial neurotoxin by a mass spectroscopy technique. In one embodiment, the peptide can have an affinity tag attached at two or more sites.

  20. Chasing polys: Interdisciplinary affinity and its connection to physics identity

    Science.gov (United States)

    Scott, Tyler D.

    This research is based on two motivations that merge by means of the frameworks of interdisciplinary affinity and physics identity. First, a goal of education is to develop interdisciplinary abilities in students' thinking and work. But an often ignored factor is students interests and beliefs about being interdisciplinary. Thus, this work develops and uses a framework called interdisciplinary affinity. It encompasses students interests in making connections across disciplines and their beliefs about their abilities to make those connections. The second motivation of this research is to better understand how to engage more students with physics. Physics identity describes how a student sees themselves in relation to physics. By understanding how physics identity is developed, researchers and educators can identify factors that increase interest and engagement in physics classrooms. Therefore, physics identity was used in conjunction with interdisciplinary affinity. Using a mixed methods approach, this research used quantitative data to identify the relationships interdisciplinary affinity has with physics identity and the physics classroom. These connections were explored in more detail using a case study of three students in a high school physics class. Results showed significant and positive relationships between interdisciplinary affinity and physics identity, including the individual interest and recognition components of identity. It also identified characteristics of physics classrooms that had a significant, positive relationship with interdisciplinary affinity. The qualitative case study highlighted the importance of student interest to the relationship between interdisciplinary affinity and physics identity. It also identified interest and mastery orientation as key to understanding the link between interdisciplinary affinity and the physics classroom. These results are a positive sign that by understanding interdisciplinary affinity and physics identity

  1. Study of b-jet tagging performance in ALICE

    CERN Document Server

    Feldkamp, Linus

    2014-01-01

    We present the current status and Monte Carlo study based performance estimates of b-jet tagging using ALICE, as obtained using both impact parameter as well as secondary vertex methods. We also address the prospects of the identification of electrons from heavy-flavour hadron decays to obtain b-jet enhanced jet samples.

  2. Genetic Algorithm-based Affine Parameter Estimation for Shape Recognition

    Directory of Open Access Journals (Sweden)

    Yuxing Mao

    2014-06-01

    Full Text Available Shape recognition is a classically difficult problem because of the affine transformation between two shapes. The current study proposes an affine parameter estimation method for shape recognition based on a genetic algorithm (GA. The contributions of this study are focused on the extraction of affine- invariant features, the individual encoding scheme, and the fitness function construction policy for a GA. First, the affine-invariant characteristics of the centroid distance ratios (CDRs of any two opposite contour points to the barycentre are analysed. Using different intervals along the azimuth angle, the different numbers of CDRs of two candidate shapes are computed as representations of the shapes, respectively. Then, the CDRs are selected based on predesigned affine parameters to construct the fitness function. After that, a GA is used to search for the affine parameters with optimal matching between candidate shapes, which serve as actual descriptions of the affine transformation between the shapes. Finally, the CDRs are resampled based on the estimated parameters to evaluate the similarity of the shapes for classification. The experimental results demonstrate the robust performance of the proposed method in shape recognition with translation, scaling, rotation and distortion.

  3. Simple conjugation and outgrowth procedures for tagging vibrios with GFP, and factors affecting the stable expression of the gfp tag

    OpenAIRE

    Sawabe, T.; Fukui, Y.; Stabb, E.V.

    2006-01-01

    Aim: Our goal was to develop a simple system for tagging wild-type marine bacteria with gfp. Methods and Results: Escherichia coli strain CC118λpir carrying the conjugative helper plasmid pEVS104 and the gfp-containing plasmid pKV111 was used to transfer gfp to Vibrio recipients. Four different media were tested for their ability to support the growth of recipients, but not the E. coli donor, to allow powerful enrichment of gfp-tagged wild-type vibrios from mating mixes. Forty-three vibrio...

  4. Onboard tagging for smart medical devices.

    Science.gov (United States)

    Li, Kejia; Warren, Steve

    2011-01-01

    Most medical devices are 'dumb:' their role is to acquire, display, and forward data. They make few if any operational decisions based on those data. Onboard tagging is a means whereby a device can embed information about itself, its data, and the sensibility of those data into its data stream. This diagnostic add-on offers a move toward 'smart' devices that will have the ability to affect changes in operational modes based on onboard contextual decision making, such as decisions to avoid needless wireless transmission of corrupt data. This paper presents a description of three types of onboard tags that relate to device hardware (type I tag), signal statistics (type II tag), and signal viability for the intended application (type III tag). A custom wireless pulse oximeter is presented as a use case to show how type II and III tags that convey photoplethysmogram (PPG) statistics and usability specifiers can be calculated and embedded into the data stream without degrading performance.

  5. Building Tag Clouds in Perl and PHP

    CERN Document Server

    Bumgardner, Jim

    2006-01-01

    Tag clouds are everywhere on the web these days. First popularized by the web sites Flickr, Technorati, and del.icio.us, these amorphous clumps of words now appear on a slew of web sites as visual evidence of their membership in the elite corps of "Web 2.0." This PDF analyzes what is and isn't a tag cloud, offers design tips for using them effectively, and then goes on to show how to collect tags and display them in the tag cloud format. Scripts are provided in Perl and PHP. Yes, some have said tag clouds are a fad. But as you will see, tag clouds, when used properly, have real merits. More

  6. Learner Corpora without Error Tagging

    Directory of Open Access Journals (Sweden)

    Rastelli, Stefano

    2009-01-01

    Full Text Available The article explores the possibility of adopting a form-to-function perspective when annotating learner corpora in order to get deeper insights about systematic features of interlanguage. A split between forms and functions (or categories is desirable in order to avoid the "comparative fallacy" and because – especially in basic varieties – forms may precede functions (e.g., what resembles to a "noun" might have a different function or a function may show up in unexpected forms. In the computer-aided error analysis tradition, all items produced by learners are traced to a grid of error tags which is based on the categories of the target language. Differently, we believe it is possible to record and make retrievable both words and sequence of characters independently from their functional-grammatical label in the target language. For this purpose at the University of Pavia we adapted a probabilistic POS tagger designed for L1 on L2 data. Despite the criticism that this operation can raise, we found that it is better to work with "virtual categories" rather than with errors. The article outlines the theoretical background of the project and shows some examples in which some potential of SLA-oriented (non error-based tagging will be possibly made clearer.

  7. Spam Fighting in Social Tagging Systems

    OpenAIRE

    Yazdani, Sasan; Ivanov, Ivan; Analoui, Morteza; Berangi, Reza; Ebrahimi, Touradj

    2012-01-01

    Tagging in online social networks is very popular these days, as it facilitates search and retrieval of diverse resources available online. However, noisy and spam annotations often make it difficult to perform an efficient search. Users may make mistakes in tagging and irrelevant tags and resources may be maliciously added for advertisement or self-promotion. Since filtering spam annotations and spammers is time-consuming if it is done manually, machine learning approaches can be employed to...

  8. Circularly Polarized Broadband RFID Microstrip Tag Antenna

    OpenAIRE

    B. Rajini; G. V. Subrahmanyam

    2014-01-01

    In recent years, the application of radio frequency identification (RFID) operating in the ultra-high frequency (UHF) band (860-960MHz) are expanding exponentially, due to the advantages such as long reading distance, high data transfer rate, and small tag size. So the design of a CP tag antenna with broadband characteristic is presently one of the most challenging topics. This project presents a square patch passive RFID tag antenna designed for UHF band. To a...

  9. Tagging diversity in personal learning environments

    OpenAIRE

    Cao, Yiwei; Kovachev, Dejan; Klamma, Ralf; Jarke, Matthias; Lau, Rynson W. H.

    2015-01-01

    Tagging is a prevalent practice in the Web 2.0. It has been widely usedto annotate different media like video. However, in personal learning environments(PLEs), tagging is supporting not only content indexing but also the self-regulatedlearning process consisting of different phases like planning, learning, and reflecting.In particular, in the reflection phase, tags support the organization of learningoutcomes. We have researched the interrelations of learning content, learningprocesses, and ...

  10. Trinity:Walking on a User-Ob ject-Tag Heterogeneous Network for Personalised Recommendations

    Institute of Scientific and Technical Information of China (English)

    Ming-Xin Gan; Lily Sun; Rui Jiang

    2016-01-01

    The rapid evolution of the Internet has been appealing for effective recommender systems to pinpoint useful information from online resources. Although historical rating data has been widely used as the most important information in recommendation methods, recent advancements have been demonstrating the improvement in recommendation performance with the incorporation of tag information. Furthermore, the availability of tag annotations has been well addressed by such fruitful online social tagging applications as CiteULike, MovieLens and BibSonomy, which allow users to express their preferences, upload resources and assign their own tags. Nevertheless, most existing tag-aware recommendation approaches model relationships among users, objects and tags using a tripartite graph, and hence overlook relationships within the same types of nodes. To overcome this limitation, we propose a novel approach, Trinity, to integrate historical data and tag information towards personalised recommendation. Trinity constructs a three-layered object-user-tag network that considers not only interconnections between different types of nodes but also relationships within the same types of nodes. Based on this heterogeneous network, Trinity adopts a random walk with restart model to assign the strength of associations to candidate objects, thereby providing a means of prioritizing the objects for a query user. We validate our approach via a series of large-scale 10-fold cross-validation experiments and evaluate its performance using three comprehensive criteria. Results show that our method outperforms several existing methods, including supervised random walk with restart, simulation of resource allocating processes, and traditional collaborative filtering.

  11. Affinity tagging & purification of the fucose binding LecB protein

    OpenAIRE

    Creavin, Aileen; O'Connor, Brendan

    2007-01-01

    The fucose binding LecB protein is one of two identified lectins produced by the opportunistic pathogen Pseudomonas aeruginosa (PA01) and is implicated in contributing to its virulence. A large number of homologous proteins have been identified in other bacterial species that exhibit extremely high sequence identity and similarity to LecB. However, key amino acid residues known to participate in fucose binding in LecB are altered in many of these proteins. Some of these proteins have been sho...

  12. Optimization of tagged MRI for quantification of liver stiffness using computer simulated data.

    Directory of Open Access Journals (Sweden)

    Serena Monti

    Full Text Available The heartbeat has been proposed as an intrinsic source of motion that can be used in combination with tagged Magnetic Resonance Imaging (MRI to measure displacements induced in the liver as an index of liver stiffness. Optimizing a tagged MRI acquisition protocol in terms of sensitivity to these displacements, which are in the order of pixel size, is necessary to develop the method as a quantification tool for staging fibrosis. We reproduced a study of cardiac-induced strain in the liver at 3T and simulated tagged MR images with different grid tag patterns to evaluate the performance of the Harmonic Phase (HARP image analysis method and its dependence on the parameters of tag spacing and grid angle. The Partial Volume Effect (PVE, T1 relaxation, and different levels of noise were taken into account. Four displacement fields of increasing intensity were created and applied to the tagged MR images of the liver. These fields simulated the deformation at different liver stiffnesses. An Error Index (EI was calculated to evaluate the estimation accuracy for various parameter values. In the absence of noise, the estimation accuracy of the displacement fields increased as tag spacings decreased. EIs for each of the four displacement fields were lower at 0° and the local minima of the EI were found to correspond to multiples of pixel size. The accuracy of the estimation decreased for increasing levels of added noise; as the level increased, the improved estimation caused by decreasing the tag spacing tended to zero. The optimal tag spacing turned out to be a compromise between the smallest tag period that is a multiple of the pixel size and is achievable in a real acquisition and the tag spacing that guarantees an accurate liver displacement measure in the presence of realistic levels of noise.

  13. Stability of the Neurotensin Receptor NTS1 Free in Detergent Solution and Immobilized to Affinity Resin

    OpenAIRE

    White, Jim F.; Reinhard Grisshammer

    2010-01-01

    BACKGROUND: Purification of recombinant membrane receptors is commonly achieved by use of an affinity tag followed by an additional chromatography step if required. This second step may exploit specific receptor properties such as ligand binding. However, the effects of multiple purification steps on protein yield and integrity are often poorly documented. We have previously reported a robust two-step purification procedure for the recombinant rat neurotensin receptor NTS1 to give milligram q...

  14. Stability of the Neurotensin Receptor NTS1 Free in Detergent Solution and Immobilized to Affinity Resin

    OpenAIRE

    White, Jim F.; Grisshammer, Reinhard

    2010-01-01

    Background Purification of recombinant membrane receptors is commonly achieved by use of an affinity tag followed by an additional chromatography step if required. This second step may exploit specific receptor properties such as ligand binding. However, the effects of multiple purification steps on protein yield and integrity are often poorly documented. We have previously reported a robust two-step purification procedure for the recombinant rat neurotensin receptor NTS1 to give milligram qu...

  15. Tagging: An Organization Scheme for the Internet

    OpenAIRE

    Visser, Marijke A.

    2010-01-01

    How should the information on the Internet be organized? This question and the possible solutions spark debates among people concerned with how we identify, classify, and retrieve Internet content. This paper discusses the benefits and the controversies of using a tagging system to organize Internet resources. Tagging refers to a classification system where individual Internet users apply labels, or tags, to digital resources. Tagging increased in popularity with the advent of Web 2.0 applica...

  16. Modeling Consensus Semantics in Social Tagging Systems

    Institute of Scientific and Technical Information of China (English)

    Bin Zhang; Yin Zhang; Ke-Ning Gao

    2011-01-01

    In social tagging systems,people can annotate arbitrary tags to online data to categorize and index them.However,the lack of the "a priori" set of words makes it difficult for people to reach consensus about the semantics of tags and how to categorize data.Ontologies based approaches can help reaching such consensus,but they are still facing problems such as inability of model ambiguous and new concepts properly.For tags that are used very few times,since they can only be used in very specific contexts,their semantics are very clear and detailed.Although people have no consensus on these tags,it is still possible to leverage these detailed semantics to model the other tags.In this paper we introduce a random walk and spreading activation like model to represent the semantics of tags using semantics of unpopular tags.By comparing the proposed model to the classic Latent Semantic Analysis approach in a concept clustering task,we show that the proposed model can properly capture the semantics of tags.

  17. Artifacts reduction in strain maps of tagged magnetic resonance imaging using harmonic phase

    Directory of Open Access Journals (Sweden)

    Wang Daolei

    2015-01-01

    Full Text Available Tagged Magnetic Resonance Imaging (MRI is a noninvasive technique for examining myocardial function and deformation. Tagged MRI can also be used in quasistatic MR elastography to acquire strain maps of other biological soft tissues. Harmonic phase (HARP provides automatic and rapid analysis of tagged MR images for the quantification and visualization of myocardial strain. We propose a new artifact reduction method in strain maps. Image intensity of the DC component is estimated and subtracted from spatial modulation of magnetization (SPAMM tagged MR images. DC peak interference in harmonic phase extraction is greatly reduced after DC component subtraction. The proposed method is validated using both simulated and MR acquired tagged images. Strain maps are obtained with better accuracy and smoothness after DC component subtraction.

  18. Improved statistical analysis of budding yeast TAG microarrays revealed by defined spike-in pools.

    Science.gov (United States)

    Peyser, Brian D; Irizarry, Rafael A; Tiffany, Carol W; Chen, Ou; Yuan, Daniel S; Boeke, Jef D; Spencer, Forrest A

    2005-09-15

    Saccharomyces cerevisiae knockout collection TAG microarrays are an emergent platform for rapid, genome-wide functional characterization of yeast genes. TAG arrays report abundance of unique oligonucleotide 'TAG' sequences incorporated into each deletion mutation of the yeast knockout collection, allowing measurement of relative strain representation across experimental conditions for all knockout mutants simultaneously. One application of TAG arrays is to perform genome-wide synthetic lethality screens, known as synthetic lethality analyzed by microarray (SLAM). We designed a fully defined spike-in pool to resemble typical SLAM experiments and performed TAG microarray hybridizations. We describe a method for analyzing two-color array data to efficiently measure the differential knockout strain representation across two experimental conditions, and use the spike-in pool to show that the sensitivity and specificity of this method exceed typical current approaches.

  19. In Tags We Trust: Trust modeling in social tagging of multimedia content

    OpenAIRE

    Ivanov, Ivan; Vajda, Péter; Lee, Jong Seok; Ebrahimi, Touradj

    2012-01-01

    Tagging in online social networks is very popular these days, as it facilitates search and retrieval of multimedia content. However, noisy and spam annotations often make it difficult to perform an efficient search. Users may make mistakes in tagging and irrelevant tags and content may be maliciously added for advertisement or self-promotion. This article surveys recent advances in techniques for combatting such noise and spam in social tagging. We classify the state-of-the-art approaches int...

  20. Nitric oxide flow tagging in unseeded air.

    Science.gov (United States)

    Dam, N; Klein-Douwel, R J; Sijtsema, N M; Meulen, J J

    2001-01-01

    A scheme for molecular tagging velocimetry is presented that can be used in air flows without any kind of seeding. The method is based on the local and instantaneous creation of nitric oxide (NO) molecules from N(2) and O(2) in the waist region of a focused ArF excimer laser beam. This NO distribution is advected by the flow and can be visualized any time later by laser-induced fluorescence in the gamma bands. The creation of NO is confirmed by use of an excitation spectrum. Two examples of the application of the new scheme for air-flow velocimetry are given in which single laser pulses are used for creation and visualization of NO. PMID:18033499

  1. Reconciling Knowledge in Social Tagging Web Services

    Science.gov (United States)

    Aranda-Corral, Gonzalo A.; Borrego-Díaz, Joaquín

    Sometimes we want to search for new information about topics but we can not find relevant results using our own knowledge (for example, our personal bookmarks). A potential solution could be the use of knowledge from other users to find what we are searching for. This solution implies that we can achieve some agreement on implicit semantics used by the other users. We call it Reconciliation of Knowledge. The aim of this paper is to show an agent-based method which lets us reconcile two different knowledge basis (associated with tagging systems) into a common language, obtaining a new one that allows the reconcilitiation of (part of) this knowledge. The agents use Formal Concept Analysis concepts and tools and it has been implemented on the JADE multiagent platform.

  2. External tagging does not affect the feeding behavior of a coral reef fish, Chaetodon vagabundus (Pisces: Chaetodontidae)

    KAUST Repository

    Berumen, Michael L.

    2009-11-10

    Increasingly, the ability to recognize individual fishes is important for studies of population dynamics, ecology, and behavior. Although a variety of methods exist, external tags remain one of the most widely applied because they are both effective and cost efficient. However, a key assumption is that neither the tagging procedure nor the presence of a tag negatively affects the individual. While this has been demonstrated for relatively coarse metrics such as growth and survival, few studies have examined the impact of tags and tagging on more subtle aspects of behavior. We tagged adult vagabond butterflyfish (Chaetodon vagabundus) occupying a 30-ha insular reef in Kimbe Bay, Papua New Guinea, using a commonly-utilized t-bar anchor tag. We quantified and compared feeding behavior (bite rate), which is sensitive to stress, of tagged and untagged individuals over four separate sampling periods spanning 4 months post-tagging. Bite rates did not differ between tagged and untagged individuals at each sampling period and, combined with additional anecdotal observations of normal pairing behavior and successful reproduction, suggest that tagging did not adversely affect individuals. © Springer Science+Business Media B.V. 2009.

  3. Extending birthday paradox theory to estimate the number of tags in RFID systems.

    Directory of Open Access Journals (Sweden)

    Masoud Shakiba

    Full Text Available The main objective of Radio Frequency Identification systems is to provide fast identification for tagged objects. However, there is always a chance of collision, when tags transmit their data to the reader simultaneously. Collision is a time-consuming event that reduces the performance of RFID systems. Consequently, several anti-collision algorithms have been proposed in the literature. Dynamic Framed Slotted ALOHA (DFSA is one of the most popular of these algorithms. DFSA dynamically modifies the frame size based on the number of tags. Since the real number of tags is unknown, it needs to be estimated. Therefore, an accurate tag estimation method has an important role in increasing the efficiency and overall performance of the tag identification process. In this paper, we propose a novel estimation technique for DFSA anti-collision algorithms that applies birthday paradox theory to estimate the number of tags accurately. The analytical discussion and simulation results prove that the proposed method increases the accuracy of tag estimation and, consequently, outperforms previous schemes.

  4. Extending birthday paradox theory to estimate the number of tags in RFID systems.

    Science.gov (United States)

    Shakiba, Masoud; Singh, Mandeep Jit; Sundararajan, Elankovan; Zavvari, Azam; Islam, Mohammad Tariqul

    2014-01-01

    The main objective of Radio Frequency Identification systems is to provide fast identification for tagged objects. However, there is always a chance of collision, when tags transmit their data to the reader simultaneously. Collision is a time-consuming event that reduces the performance of RFID systems. Consequently, several anti-collision algorithms have been proposed in the literature. Dynamic Framed Slotted ALOHA (DFSA) is one of the most popular of these algorithms. DFSA dynamically modifies the frame size based on the number of tags. Since the real number of tags is unknown, it needs to be estimated. Therefore, an accurate tag estimation method has an important role in increasing the efficiency and overall performance of the tag identification process. In this paper, we propose a novel estimation technique for DFSA anti-collision algorithms that applies birthday paradox theory to estimate the number of tags accurately. The analytical discussion and simulation results prove that the proposed method increases the accuracy of tag estimation and, consequently, outperforms previous schemes.

  5. Peculiarities of Matter Motion in Metric-Affine Gravitational Theory

    OpenAIRE

    Babourova, O. V.; Frolov, B. N.; Koroliov, M. Yu.

    1995-01-01

    On the basis of the Lie derivative method in a metric-affine space-time it is shown that in the metric-affine gravitational theory the energy-momentum conservation law and therefore the equations of the matter motion are the consequence (as in the GR) of the gravitational field equations. The possi- bility of the detection of the space-time non-metric properties is discussed.

  6. Monodisperse REPO4 (RE = Yb, Gd, Y) hollow microspheres covered with nanothorns as affinity probes for selectively capturing and labeling phosphopeptides.

    Science.gov (United States)

    Cheng, Gong; Zhang, Ji-Lin; Liu, Yan-Lin; Sun, De-Hui; Ni, Jia-Zuan

    2012-02-13

    Rare-earth phosphate microspheres with unique structures were developed as affinity probes for the selective capture and tagging of phosphopeptides. Prickly REPO(4) (RE = Yb, Gd, Y) monodisperse microspheres, that have hollow structures, low densities, high specific surface areas, and large adsorptive capacities were prepared by an ion-exchange method. The elemental compositions and crystal structures of these affinity probes were confirmed by energy-dispersive spectroscopy (EDS), powder X-ray diffraction (XRD), and Fourier-transform infrared (FTIR) spectroscopy. The morphologies of these compounds were investigated using scanning electron microscopy (SEM), transmission electron microscopy (TEM), and nitrogen-adsorption isotherms. The potential ability of these microspheres for selectively capturing and labeling target biological molecules was evaluated by using protein-digestion analysis and a real sample as well as by comparison with the widely used TiO(2) affinity microspheres. These results show that these porous rare-earth phosphate microspheres are highly promising probes for the rapid purification and recognition of phosphopeptides.

  7. Monodisperse REPO4 (RE = Yb, Gd, Y) hollow microspheres covered with nanothorns as affinity probes for selectively capturing and labeling phosphopeptides.

    Science.gov (United States)

    Cheng, Gong; Zhang, Ji-Lin; Liu, Yan-Lin; Sun, De-Hui; Ni, Jia-Zuan

    2012-02-13

    Rare-earth phosphate microspheres with unique structures were developed as affinity probes for the selective capture and tagging of phosphopeptides. Prickly REPO(4) (RE = Yb, Gd, Y) monodisperse microspheres, that have hollow structures, low densities, high specific surface areas, and large adsorptive capacities were prepared by an ion-exchange method. The elemental compositions and crystal structures of these affinity probes were confirmed by energy-dispersive spectroscopy (EDS), powder X-ray diffraction (XRD), and Fourier-transform infrared (FTIR) spectroscopy. The morphologies of these compounds were investigated using scanning electron microscopy (SEM), transmission electron microscopy (TEM), and nitrogen-adsorption isotherms. The potential ability of these microspheres for selectively capturing and labeling target biological molecules was evaluated by using protein-digestion analysis and a real sample as well as by comparison with the widely used TiO(2) affinity microspheres. These results show that these porous rare-earth phosphate microspheres are highly promising probes for the rapid purification and recognition of phosphopeptides. PMID:22241661

  8. SERS-active nanoparticle aggregate technology for tags and seals

    Energy Technology Data Exchange (ETDEWEB)

    Brown, Leif O [Los Alamos National Laboratory; Montoya, Velma M [Los Alamos National Laboratory; Havrilla, George J [Los Alamos National Laboratory; Doorn, Stephen K [Los Alamos National Laboratory

    2010-06-03

    In this paper, we describe our efforts to create a modern tagging and sealing technology for international safeguards application. Our passive tagging methods are based on SANAs (SERS-Active Nanoparticle Aggregates; SERS: Surface Enhanced Raman Scattering). These SANAs offer robust spectral barcoding capability in an inexpensive tag/seal, with the possibility of rapid in-field verification that requires no human input. At INMM 2009, we introduced SANAs, and showed approaches to integrating our technology with tags under development at Sandia National Laboratories (SNL). Here, we will focus on recent LANL development work, as well as adding additional dimensionality to the barcoding technique. The field of international safeguards employs a broad array of tags, seals, and tamper-indicating devices to assist with identification, tracking, and verification of components and materials. These devices each have unique strengths suited to specific applications, and span a range of technologies from passive metal cup seals and adhesive seals to active, remotely monitored fiber optic seals. Regardless of the technology employed, essential characteristics center around security, environmental and temporal stability, ease of use, and the ability to provide confidence to all parties. Here, we present a new inexpensive tagging technology that will deliver these attributes, while forming the basis of either a new seal, or as a secure layer added to many existing devices. Our approach uses the Surface Enhanced Raman Scattering (SERS) response from SANAs (SERS-Active Nanoparticle Aggregates, Figure 1) to provide a unique identifier or signature for tagging applications. SANAs are formed from gold or silver nanoparticles in the 40-80 nm size range. A chemical dye is installed on the nanoparticle surface, and the nanoparticles are then aggregated into ensembles of {approx}100 to 500 nm diameter, prior to being coated with silica. The silica shell protects the finished SANA from

  9. To tag or not to tag: animal welfare, conservation and stakeholder considerations in fish tracking studies that use electronic tags

    Energy Technology Data Exchange (ETDEWEB)

    Cooke, Steven J.; Nguyen, Vivian M.; Murchie, Karen J.; Thiem, Jason D.; Donaldson, Michael R.; Hinch, Scott G.; Brown, Richard S.; Fisk, Aaron

    2013-11-01

    The advent and widespread adoption of electronic tags (including biotelemetry and biologging devices) for tracking animals has provided unprecedented information on the biology, management, and conservation of fish in the world’s oceans and inland waters. However, use of these tools is not without controversy. Even when scientific and management objectives may best be achieved using electronic tags, it is increasingly important to further consider other factors such as the welfare of tagged animals (i.e., the role of training and science-based surgical guidelines, anesthetic use, inability to maintain sterile conditions in field environments), the ethics of tagging threatened species vs. using surrogates, stakeholder perspectives on tagging (including aboriginals), as well as use of data emanating from such studies (e.g., by fishers to facilitate exploitation). Failure to do so will have the potential to create conflict and undermine scientific, management and public confidence in the use of this powerful tool. Indeed, there are already a number of examples of where tracking studies using electronic tags have been halted based on concerns raised by researchers, authorities, or stakeholders. Here we present a candid evaluation of several factors that should be considered when determining when to tag or not to tag fish with electronic devices. It is not our objective to judge the merit of previous studies. Rather, we hope to stimulate debate and discussion regarding the use of electronic tags to study fish. Relatedly, there is a need for more research to address these questions (e.g., what level of cleanliness is needed when conducting surgeries, what type of training should be required for fish surgery) including human dimensions studies to understand perspectives of different actors including society as a whole with respect to tagging and tracking studies.

  10. CT colonography with rectal iodine tagging: Feasibility and comparison with oral tagging in a colorectal cancer screening population

    Energy Technology Data Exchange (ETDEWEB)

    Neri, Emanuele, E-mail: emanuele.neri@med.unipi.it [Diagnostic and Interventional Radiology – Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa (Italy); Mantarro, Annalisa; Faggioni, Lorenzo; Scalise, Paola; Bemi, Pietro; Pancrazi, Francesca [Diagnostic and Interventional Radiology – Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa (Italy); D’Ippolito, Giuseppe [Federal University of São Paulo – Sena Madureira 1500 – Vila Mariana, UNIFESP, São Paulo, SP (Brazil); Bartolozzi, Carlo [Diagnostic and Interventional Radiology – Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa (Italy)

    2015-09-15

    Highlights: • In the group receiving rectal tagging, mean per-polyp sensitivity, specificity were 96.1% and 95.3%; while in the group receiving oral tagging, mean per-polyp sensitivity, specificity were 89.4% and 95.8%. The difference between the two groups was not statistically significant (p = 0.549). • Rectal tagging can be an effective alternative to oral tagging. • Rectal tagging allowed greater patient acceptance and lower overall examination time. - Abstract: Purpose: To evaluate feasibility, diagnostic performance, patient acceptance, and overall examination time of CT colonography (CTC) performed through rectal administration of iodinated contrast material. Materials and methods: Six-hundred asymptomatic subjects (male:female = 270:330; mean 63 years) undergoing CTC for colorectal cancer screening on an individual basis were consecutively enrolled in the study. Out of them, 503 patients (group 1) underwent CTC with rectal tagging, of which 55 had a total of 77 colonic lesions. The remaining 97 patients (group 2) were randomly selected to receive CTC with oral tagging of which 15 had a total of 20 colonic lesions. CTC findings were compared with optical colonoscopy, and per-segment image quality was visually assessed using a semi-quantitative score (1 = poor, 2 = adequate, 3 = excellent). In 70/600 patients (11.7%), CTC was performed twice with both types of tagging over a 5-year follow-up cancer screening program. In this subgroup, patient acceptance was rated via phone interview two weeks after CTC using a semi-quantitative scale (1 = poor, 2 = fair, 3 = average, 4 = good, 5 = excellent). Results: Mean per-polyp sensitivity, specificity, positive and negative predictive values of CTC with rectal vs oral tagging were 96.1% (CI{sub 95%} 85.4 ÷ 99.3%) vs 89.4% (CI{sub 95%} 65.4 ÷ 98.1%), 95.3% (CI{sub 95%} 90.7 ÷ 97.8%) vs 95.8% (CI{sub 95%} 87.6 ÷ 98.9%), 86.0% (CI{sub 95%} 73.6 ÷ 93.3) vs 85.0% (CI{sub 95%} 61.1 ÷ 96.0%), and 98.8% (CI{sub 95

  11. CT colonography with rectal iodine tagging: Feasibility and comparison with oral tagging in a colorectal cancer screening population

    International Nuclear Information System (INIS)

    Highlights: • In the group receiving rectal tagging, mean per-polyp sensitivity, specificity were 96.1% and 95.3%; while in the group receiving oral tagging, mean per-polyp sensitivity, specificity were 89.4% and 95.8%. The difference between the two groups was not statistically significant (p = 0.549). • Rectal tagging can be an effective alternative to oral tagging. • Rectal tagging allowed greater patient acceptance and lower overall examination time. - Abstract: Purpose: To evaluate feasibility, diagnostic performance, patient acceptance, and overall examination time of CT colonography (CTC) performed through rectal administration of iodinated contrast material. Materials and methods: Six-hundred asymptomatic subjects (male:female = 270:330; mean 63 years) undergoing CTC for colorectal cancer screening on an individual basis were consecutively enrolled in the study. Out of them, 503 patients (group 1) underwent CTC with rectal tagging, of which 55 had a total of 77 colonic lesions. The remaining 97 patients (group 2) were randomly selected to receive CTC with oral tagging of which 15 had a total of 20 colonic lesions. CTC findings were compared with optical colonoscopy, and per-segment image quality was visually assessed using a semi-quantitative score (1 = poor, 2 = adequate, 3 = excellent). In 70/600 patients (11.7%), CTC was performed twice with both types of tagging over a 5-year follow-up cancer screening program. In this subgroup, patient acceptance was rated via phone interview two weeks after CTC using a semi-quantitative scale (1 = poor, 2 = fair, 3 = average, 4 = good, 5 = excellent). Results: Mean per-polyp sensitivity, specificity, positive and negative predictive values of CTC with rectal vs oral tagging were 96.1% (CI95% 85.4 ÷ 99.3%) vs 89.4% (CI95% 65.4 ÷ 98.1%), 95.3% (CI95% 90.7 ÷ 97.8%) vs 95.8% (CI95% 87.6 ÷ 98.9%), 86.0% (CI95% 73.6 ÷ 93.3) vs 85.0% (CI95% 61.1 ÷ 96.0%), and 98.8% (CI95% 95.3 ÷ 99.8%) vs 97.2% (CI95% 89.4 ÷ 99

  12. Reducing fungal infections and testing tag loss in juvenile Pacific lampreys implanted with passive integrated transponders.

    Science.gov (United States)

    Christiansen, H.E.; Gee, L.P.; Mesa, M.G.

    2012-01-01

    Pacific lamprey Entosphenus tridentatus are facing severe population declines, yet little is known about juvenile lamprey passage, life history, or adult return rates because until now, these small fish could not be tagged for unique identification of live individuals. Previously, we developed a simple and effective method for tagging juvenile lampreys with passive integrated transponder (PIT) tags and showed that tagging per se did not affect survival. Mortality in tagged and untagged control fish, however, was frequently associated with fungal infection. In this study, we addressed two outstanding issues related to handling and tagging juvenile lampreys. First, we tried to mitigate freshwater fungal infections by reducing irritation and stress from anesthesia and by treating tagged fish briefly with a prophylactic immediately after tagging. We tested four anesthetics at three concentrations each and determined that 100 mg/L MS-222 and 60 mg/L BENZOAK® (benzocaine) were the most effective for anesthetizing juvenile lampreys to handleable while minimizing irritation. We also showed that fish anesthetized with BENZOAK® may have lower rates of fungal infection than those anesthetized with MS-222 or AQUI-S® 20E (eugenol). When fish anesthetized with MS-222 or BENZOAK® were given a 30 min prophylactic treatment with Stress Coat®, hydrogen peroxide, or salt immediately after tagging, few fish presented with fungal infections. However, untreated, tagged control fish also showed few fungal infections, making it difficult to determine if the prophylactic treatments were successful. The second question we addressed was whether activity would increase tag loss in PIT-tagged lampreys. We found that active swimming did not cause tag loss if fish were first held for 20–24 h after tagging. Therefore, we recommend anesthesia with MS-222 or BENZOAK® and then tagging with a 20–24 h recovery period followed by immediate release. If field studies show that lampreys are not

  13. Towards EPC-compatible organic RFID tags

    NARCIS (Netherlands)

    Myny, K.; Steudel, S.; Vicca, P.; Smout, S.; Beenhakkers, M.J.; Aerle, N.A.J.M. van; Furthner, F.; Putten, B. van der; Tripathi, A.K.; Gelinck, G.H.; Genoe, J.; Dehaene, W.; Heremans, P.L.

    2011-01-01

    In this chapter, fully integrated organic RFID tags are demonstrated. These tags are inductively-coupled at a base frequency of 13.56 MHz and can be read out at distances up to 10 cm, which is the expected readout distance for proximity readers. We also demonstrate next generation transponder chips,

  14. TAG (Teaching Active Games) for the Holidays

    Science.gov (United States)

    Erwin, Heather E.; Bachtel, Amy

    2007-01-01

    Holidays present the perfect opportunity for physical educators to utilize creative TAG (Teaching Active Games) games to offer maximum physical activity opportunities for their students. The TAG ideas in this article offer physical education teachers quick, instant activities that involve very little equipment, time management, or instruction. At…

  15. Evaluation of PIT-tagging in cyprinids

    DEFF Research Database (Denmark)

    Skov, Christian; Brodersen, J.; Brönmark, C.;

    2005-01-01

    Laboratory and field experiments were used to investigate how different marking procedures, with 23 mm PIT (passive integrated transponders) - tags. affected mortality, body condition and tag expulsion in small roach Rutilus rutilus and rudd Scardinus erythrophthalmus (117 to 163 mm total length...

  16. A Radio Tag for Big Whales

    Science.gov (United States)

    Watkins, William A.

    1978-01-01

    Radio tags to track wildlife have been used for years. However, such tagging of whales has been more complicated and less successful. This article explores the latest technology that is designed to give information over a long period of time. (MA)

  17. Expression and purification of recombinant proteins in Escherichia coli tagged with the metal-binding protein CusF.

    Science.gov (United States)

    Cantu-Bustos, J Enrique; Vargas-Cortez, Teresa; Morones-Ramirez, Jose Ruben; Balderas-Renteria, Isaias; Galbraith, David W; McEvoy, Megan M; Zarate, Xristo

    2016-05-01

    Production of recombinant proteins in Escherichia coli has been improved considerably through the use of fusion proteins, because they increase protein solubility and facilitate purification via affinity chromatography. In this article, we propose the use of CusF as a new fusion partner for expression and purification of recombinant proteins in E. coli. Using a cell-free protein expression system, based on the E. coli S30 extract, Green Fluorescent Protein (GFP) was expressed with a series of different N-terminal tags, immobilized on self-assembled protein microarrays, and its fluorescence quantified. GFP tagged with CusF showed the highest fluorescence intensity, and this was greater than the intensities from corresponding GFP constructs that contained MBP or GST tags. Analysis of protein production in vivo showed that CusF produces large amounts of soluble protein with low levels of inclusion bodies. Furthermore, fusion proteins can be exported to the cellular periplasm, if CusF contains the signal sequence. Taking advantage of its ability to bind copper ions, recombinant proteins can be purified with readily available IMAC resins charged with this metal ion, producing pure proteins after purification and tag removal. We therefore recommend the use of CusF as a viable alternative to MBP or GST as a fusion protein/affinity tag for the production of soluble recombinant proteins in E. coli.

  18. Expression and purification of recombinant proteins in Escherichia coli tagged with the metal-binding protein CusF.

    Science.gov (United States)

    Cantu-Bustos, J Enrique; Vargas-Cortez, Teresa; Morones-Ramirez, Jose Ruben; Balderas-Renteria, Isaias; Galbraith, David W; McEvoy, Megan M; Zarate, Xristo

    2016-05-01

    Production of recombinant proteins in Escherichia coli has been improved considerably through the use of fusion proteins, because they increase protein solubility and facilitate purification via affinity chromatography. In this article, we propose the use of CusF as a new fusion partner for expression and purification of recombinant proteins in E. coli. Using a cell-free protein expression system, based on the E. coli S30 extract, Green Fluorescent Protein (GFP) was expressed with a series of different N-terminal tags, immobilized on self-assembled protein microarrays, and its fluorescence quantified. GFP tagged with CusF showed the highest fluorescence intensity, and this was greater than the intensities from corresponding GFP constructs that contained MBP or GST tags. Analysis of protein production in vivo showed that CusF produces large amounts of soluble protein with low levels of inclusion bodies. Furthermore, fusion proteins can be exported to the cellular periplasm, if CusF contains the signal sequence. Taking advantage of its ability to bind copper ions, recombinant proteins can be purified with readily available IMAC resins charged with this metal ion, producing pure proteins after purification and tag removal. We therefore recommend the use of CusF as a viable alternative to MBP or GST as a fusion protein/affinity tag for the production of soluble recombinant proteins in E. coli. PMID:26805756

  19. Emergent Community Structure in Social Tagging Systems

    CERN Document Server

    Cattuto, Ciro; Servedio, Vito D P; Loreto, Vittorio

    2008-01-01

    A distributed classification paradigm known as collaborative tagging has been widely adopted in new Web applications designed to manage and share online resources. Users of these applications organize resources (Web pages, digital photographs, academic papers) by associating with them freely chosen text labels, or tags. Here we leverage the social aspects of collaborative tagging and introduce a notion of resource distance based on the collective tagging activity of users. We collect data from a popular system and perform experiments showing that our definition of distance can be used to build a weighted network of resources with a detectable community structure. We show that this community structure clearly exposes the semantic relations among resources. The communities of resources that we observe are a genuinely emergent feature, resulting from the uncoordinated activity of a large number of users, and their detection paves the way for mapping emergent semantics in social tagging systems.

  20. Flavor tagging TeV jets for physics beyond the Standard Model

    Science.gov (United States)

    Sullivan, Zack; Pedersen, Keith

    2016-07-01

    We present a new scheme for tagging boosted heavy flavor jets called "µx tagging." At the LHC, the primary method to tag b-jets relies on tracking their charged constituents. However, when highly boosted, track-based b-tags lose efficiency, and the probability to mistag light jets rises dramatically. Using muons from B hadron decay and defining a particular combination "x" of angular information and boost estimation, we find fairly flat efficiencies to tag b-jets, c-jets, light-quark jets, and light-heavy jets (containing B hadrons from gluon splitting) of ɛb = 14%, ɛc = 6:5%, ɛlight-light = 0:1%, and ɛlight-heavy = 0:5%, respectively. We demonstrate the usefulness of this new scheme by showing the reach for discovery of a leptophobic Z' → bb¯ in the dijet channel.

  1. Use of the Nanofitin Alternative Scaffold as a GFP-Ready Fusion Tag.

    Directory of Open Access Journals (Sweden)

    Simon Huet

    Full Text Available With the continuous diversification of recombinant DNA technologies, the possibilities for new tailor-made protein engineering have extended on an on-going basis. Among these strategies, the use of the green fluorescent protein (GFP as a fusion domain has been widely adopted for cellular imaging and protein localization. Following the lead of the direct head-to-tail fusion of GFP, we proposed to provide additional features to recombinant proteins by genetic fusion of artificially derived binders. Thus, we reported a GFP-ready fusion tag consisting of a small and robust fusion-friendly anti-GFP Nanofitin binding domain as a proof-of-concept. While limiting steric effects on the carrier, the GFP-ready tag allows the capture of GFP or its blue (BFP, cyan (CFP and yellow (YFP alternatives. Here, we described the generation of the GFP-ready tag from the selection of a Nanofitin variant binding to the GFP and its spectral variants with a nanomolar affinity, while displaying a remarkable folding stability, as demonstrated by its full resistance upon thermal sterilization process or the full chemical synthesis of Nanofitins. To illustrate the potential of the Nanofitin-based tag as a fusion partner, we compared the expression level in Escherichia coli and activity profile of recombinant human tumor necrosis factor alpha (TNFα constructs, fused to a SUMO or GFP-ready tag. Very similar expression levels were found with the two fusion technologies. Both domains of the GFP-ready tagged TNFα were proved fully active in ELISA and interferometry binding assays, allowing the simultaneous capture by an anti-TNFα antibody and binding to the GFP, and its spectral mutants. The GFP-ready tag was also shown inert in a L929 cell based assay, demonstrating the potent TNFα mediated apoptosis induction by the GFP-ready tagged TNFα. Eventually, we proposed the GFP-ready tag as a versatile capture and labeling system in addition to expected applications of anti

  2. Design of a covert RFID tag network for target discovery and target information routing.

    Science.gov (United States)

    Pan, Qihe; Narayanan, Ram M

    2011-01-01

    Radio frequency identification (RFID) tags are small electronic devices working in the radio frequency range. They use wireless radio communications to automatically identify objects or people without the need for line-of-sight or contact, and are widely used in inventory tracking, object location, environmental monitoring. This paper presents a design of a covert RFID tag network for target discovery and target information routing. In the design, a static or very slowly moving target in the field of RFID tags transmits a distinct pseudo-noise signal, and the RFID tags in the network collect the target information and route it to the command center. A map of each RFID tag's location is saved at command center, which can determine where a RFID tag is located based on each RFID tag's ID. We propose the target information collection method with target association and clustering, and we also propose the information routing algorithm within the RFID tag network. The design and operation of the proposed algorithms are illustrated through examples. Simulation results demonstrate the effectiveness of the design.

  3. A versatile PCR-based tandem epitope tagging system for Streptomyces coelicolor genome.

    Science.gov (United States)

    Kim, Ji-Nu; Yi, Jeong Sang; Lee, Bo-Rahm; Kim, Eun-Jung; Kim, Min Woo; Song, Yoseb; Cho, Byung-Kwan; Kim, Byung-Gee

    2012-07-20

    Epitope tagging approaches have been widely used for the analysis of functions, interactions and subcellular distributions of proteins. However, incorporating epitope sequence into protein loci in Streptomyces is time-consuming procedure due to the absence of the versatile tagging methods. Here, we developed a versatile PCR-based tandem epitope tagging tool for the Streptomyces genome engineering. We constructed a series of template plasmids that carry repeated sequence of c-myc epitope, Flp recombinase target (FRT) sites, and apramycin resistance marker to insert epitope tags into any desired spot of the chromosomal loci. A DNA module which includes the tandem epitope-encoding sequence and a selectable marker was amplified by PCR with primers that carry homologous extensions to the last portion and downstream region of the targeted gene. We fused the epitope tags at the 3' region of global transcription factors of Streptomyces coelicolor to test the validity of this system. The proper insertion of the epitope tag was confirmed by PCR and western blot analysis. The recombinants showed the identical phenotype to the wild-type that proved the conservation of in vivo function of the tagged proteins. Finally, the direct binding targets were successfully detected by chromatin immunoprecipitation with the increase in the signal-to-noise ratio. The epitope tagging system describes here would provide wide applications to study the protein functions in S. coelicolor. PMID:22704935

  4. Affine density in wavelet analysis

    CERN Document Server

    Kutyniok, Gitta

    2007-01-01

    In wavelet analysis, irregular wavelet frames have recently come to the forefront of current research due to questions concerning the robustness and stability of wavelet algorithms. A major difficulty in the study of these systems is the highly sensitive interplay between geometric properties of a sequence of time-scale indices and frame properties of the associated wavelet systems. This volume provides the first thorough and comprehensive treatment of irregular wavelet frames by introducing and employing a new notion of affine density as a highly effective tool for examining the geometry of sequences of time-scale indices. Many of the results are new and published for the first time. Topics include: qualitative and quantitative density conditions for existence of irregular wavelet frames, non-existence of irregular co-affine frames, the Nyquist phenomenon for wavelet systems, and approximation properties of irregular wavelet frames.

  5. Query-Driven Approach to Face Clustering and Tagging.

    Science.gov (United States)

    Zhang, Liyan; Wang, Xikui; Kalashnikov, Dmitri V; Mehrotra, Sharad; Ramanan, Deva

    2016-10-01

    In the era of big data, a traditional offline setting to processing image data is simply not tenable. We simply do not have the computational power to process every image with every possible tag; moreover, we will not have the manpower to clean up the potentially noisy results. In this paper, we introduce a query-driven approach to visual tagging, focusing on the application of face tagging and clustering. We integrate active learning with query-driven probabilistic databases. Rather than asking a user to provide manual labels so as to minimize the uncertainty of labels (face tags) across the entire data set, we ask the user to provide labels that minimize the uncertainty of his/her query result (e.g., "How many times did Bob and Jim appear together?"). We use a data-driven Gaussian process model of facial appearance to write the probabilistic estimates of facial identity into a probabilistic database, which can then support inference through query answering. Importantly, the database is augmented with contextual constraints (faces in the same image cannot be the same identity, while faces in the same track must be identical). Experiments on the real-world photo collections demonstrate the effectiveness of the proposed method. PMID:27448352

  6. Job optimization in ATLAS TAG-based distributed analysis

    International Nuclear Information System (INIS)

    The ATLAS experiment is projected to collect over one billion events/year during the first few years of operation. The efficient selection of events for various physics analyses across all appropriate samples presents a significant technical challenge. ATLAS computing infrastructure leverages the Grid to tackle the analysis across large samples by organizing data into a hierarchical structure and exploiting distributed computing to churn through the computations. This includes events at different stages of processing: RAW, ESD (Event Summary Data), AOD (Analysis Object Data), DPD (Derived Physics Data). Event Level Metadata Tags (TAGs) contain information about each event stored using multiple technologies accessible by POOL and various web services. This allows users to apply selection cuts on quantities of interest across the entire sample to compile a subset of events that are appropriate for their analysis. This paper describes new methods for organizing jobs using the TAGs criteria to analyze ATLAS data. It further compares different access patterns to the event data and explores ways to partition the workload for event selection and analysis. Here analysis is defined as a broader set of event processing tasks including event selection and reduction operations ('skimming', 'slimming' and 'thinning') as well as DPD making. Specifically it compares analysis with direct access to the events (AOD and ESD data) to access mediated by different TAG-based event selections. We then compare different ways of splitting the processing to maximize performance.

  7. Geographical Topics Learning of Geo-Tagged Social Images.

    Science.gov (United States)

    Zhang, Xiaoming; Ji, Shufan; Wang, Senzhang; Li, Zhoujun; Lv, Xueqiang

    2016-03-01

    With the availability of cheap location sensors, geotagging of images in online social media is very popular. With a large amount of geo-tagged social images, it is interesting to study how these images are shared across geographical regions and how the geographical language characteristics and vision patterns are distributed across different regions. Unlike textual document, geo-tagged social image contains multiple types of content, i.e., textual description, visual content, and geographical information. Existing approaches usually mine geographical characteristics using a subset of multiple types of image contents or combining those contents linearly, which ignore correlations between different types of contents, and their geographical distributions. Therefore, in this paper, we propose a novel method to discover geographical characteristics of geo-tagged social images using a geographical topic model called geographical topic model of social images (GTMSIs). GTMSI integrates multiple types of social image contents as well as the geographical distributions, in which image topics are modeled based on both vocabulary and visual features. In GTMSI, each region of the image would have its own topic distribution, and hence have its own language model and vision pattern. Experimental results show that our GTMSI could identify interesting topics and vision patterns, as well as provide location prediction and image tagging. PMID:25861092

  8. Engineering Protein Hydrogels Using SpyCatcher-SpyTag Chemistry.

    Science.gov (United States)

    Gao, Xiaoye; Fang, Jie; Xue, Bin; Fu, Linglan; Li, Hongbin

    2016-09-12

    Constructing hydrogels from engineered proteins has attracted significant attention within the material sciences, owing to their myriad potential applications in biomedical engineering. Developing efficient methods to cross-link tailored protein building blocks into hydrogels with desirable mechanical, physical, and functional properties is of paramount importance. By making use of the recently developed SpyCatcher-SpyTag chemistry, we successfully engineered protein hydrogels on the basis of engineered tandem modular elastomeric proteins. Our resultant protein hydrogels are soft but stable, and show excellent biocompatibility. As the first step, we tested the use of these hydrogels as a drug carrier, as well as in encapsulating human lung fibroblast cells. Our results demonstrate the robustness of the SpyCatcher-SpyTag chemistry, even when the SpyTag (or SpyCatcher) is flanked by folded globular domains. These results demonstrate that SpyCatcher-SpyTag chemistry can be used to engineer protein hydrogels from tandem modular elastomeric proteins that can find applications in tissue engineering, in fundamental mechano-biological studies, and as a controlled drug release vehicle.

  9. Using DEDICOM for completely unsupervised part-of-speech tagging.

    Energy Technology Data Exchange (ETDEWEB)

    Chew, Peter A.; Bader, Brett William; Rozovskaya, Alla (University of Illinois, Urbana, IL)

    2009-02-01

    A standard and widespread approach to part-of-speech tagging is based on Hidden Markov Models (HMMs). An alternative approach, pioneered by Schuetze (1993), induces parts of speech from scratch using singular value decomposition (SVD). We introduce DEDICOM as an alternative to SVD for part-of-speech induction. DEDICOM retains the advantages of SVD in that it is completely unsupervised: no prior knowledge is required to induce either the tagset or the associations of terms with tags. However, unlike SVD, it is also fully compatible with the HMM framework, in that it can be used to estimate emission- and transition-probability matrices which can then be used as the input for an HMM. We apply the DEDICOM method to the CONLL corpus (CONLL 2000) and compare the output of DEDICOM to the part-of-speech tags given in the corpus, and find that the correlation (almost 0.5) is quite high. Using DEDICOM, we also estimate part-of-speech ambiguity for each term, and find that these estimates correlate highly with part-of-speech ambiguity as measured in the original corpus (around 0.88). Finally, we show how the output of DEDICOM can be evaluated and compared against the more familiar output of supervised HMM-based tagging.

  10. Inhomogeneous self-affine carpets

    OpenAIRE

    Fraser, Jonathan M.

    2013-01-01

    We investigate the dimension theory of inhomogeneous self-affine carpets. Through the work of Olsen, Snigireva and Fraser, the dimension theory of inhomogeneous self-similar sets is now relatively well-understood, however, almost no progress has been made concerning more general non-conformal inhomogeneous attractors. If a dimension is countably stable, then the results are immediate and so we focus on the upper and lower box dimensions and compute these explicitly for large classes of inhomo...

  11. Pop-up Archival Transmitting (PAT) fish tag data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The cooperative tagging center (CTC) began deploying electronic tags in 2002. To date over 300 tags have been deployed. The following species have been monitored:...

  12. Lectin affinity chromatography of glycolipids

    Energy Technology Data Exchange (ETDEWEB)

    Torres, B.V.; Smith, D.F.

    1987-05-01

    Since glycolipids (GLs) are either insoluble or form mixed micelles in water, lectin affinity chromatography in aqueous systems has not been applied to their separation. They have overcome this problem by using tetrahydrofuran (THF) in the mobile phase during chromatography. Affinity columns prepared with the GalNAc-specific Helix pomatia agglutinin (HPA) and equilibrated in THF specifically bind the (/sup 3/H)oligosaccharide derived from Forssman GL indicating that the immobilized HPA retained its carbohydrate-binding specificity in this solvent. Intact Forssman GL was bound by the HPA-column equilibrated in THF and was specifically eluted with 0.1 mg/ml GalNAc in THF. Purification of the Forssman GL was achieved when a crude lipid extract of sheep erythrocyte membranes was applied to the HPA-column in THF. Non-specifically bound GLs were eluted from the column using a step gradient of aqueous buffer in THF, while the addition of GalNAc was required to elute the specifically bound GLs. Using this procedure the A-active GLs were purified from a crude lipid extract of type A human erythrocytes in a single chromatographic step. The use of solvents that maintain carbohydrate-binding specificity and lipid solubility will permit the application of affinity chromatography on immobilized carbohydrate-binding proteins to intact GLs.

  13. The use of coded wire tags to estimate cormorant predation on fish stocks in an estuary

    DEFF Research Database (Denmark)

    Jepsen, Niels; Klenke, Reinhard; Sonnesen, Per Michael;

    2010-01-01

    One of the main obstacles to resolving the conflict between an increasing population of cormorants, Phalacrocorax carbo sinensis, and the fishing industry is the lack of documentation of the effect of the birds’ predation on fish stocks. Tagging and releasing fish with coded wire tags followed...... by intensive cormorant pellet sampling may be a viable method to measure the impact of cormorants on fish populations. To test this new method, we studied cormorant predation in a shallow estuary, where nearly 100 000 fish were tagged and more than 10 000 cormorant pellets were collected over a 3-year study...

  14. Affinity chromatography and capillary electrophoresis for analysis of the yeast ribosomal proteins

    Directory of Open Access Journals (Sweden)

    Miriam S. Goyder

    2012-04-01

    Full Text Available We present a top down separation platform for yeast ribosomalproteins using affinity chromatography and capillary electrophoresiswhich is designed to allow deposition of proteins ontoa substrate. FLAG tagged ribosomes were affinity purified, andrRNA acid precipitation was performed on the ribosomes followedby capillary electrophoresis to separate the ribosomalproteins. Over 26 peaks were detected with excellent reproducibility(<0.5% RSD migration time. This is the first reportedseparation of eukaryotic ribosomal proteins using capillaryelectrophoresis. The two stages in this workflow, affinity chromatographyand capillary electrophoresis, share the advantagesthat they are fast, flexible and have small sample requirementsin comparison to more commonly used techniques. This methodis a remarkably quick route from cell to separation that hasthe potential to be coupled to high throughput readout platformsfor studies of the ribosomal proteome. [BMB reports2012; 45(4: 233-238

  15. Production of N-acetyl-D-neuraminic acid using two sequential enzymes overexpressed as double-tagged fusion proteins

    Directory of Open Access Journals (Sweden)

    Cheng Chung-Hsien

    2009-07-01

    Full Text Available Abstract Background Two sequential enzymes in the production of sialic acids, N-acetyl-D-glucosamine 2-epimerase (GlcNAc 2-epimerase and N-acetyl-D-neuraminic acid aldolase (Neu5Ac aldolase, were overexpressed as double-tagged gene fusions. Both were tagged with glutathione S-transferase (GST at the N-terminus, but at the C-terminus, one was tagged with five contiguous aspartate residues (5D, and the other with five contiguous arginine residues (5R. Results Both fusion proteins were overexpressed in Escherichia coli and retained enzymatic activity. The fusions were designed so their surfaces were charged under enzyme reaction conditions, which allowed isolation and immobilization in a single step, through a simple capture with either an anionic or a cationic exchanger (Sepharose Q or Sepharose SP that electrostatically bound the 5D or 5R tag. The introduction of double tags only marginally altered the affinity of the enzymes for their substrates, and the double-tagged proteins were enzymatically active in both soluble and immobilized forms. Combined use of the fusion proteins led to the production of N-acetyl-D-neuraminic acid (Neu5Ac from N-acetyl-D-glucosamine (GlcNAc. Conclusion Double-tagged gene fusions were overexpressed to yield two enzymes that perform sequential steps in sialic acid synthesis. The proteins were easily immobilized via ionic tags onto ionic exchange resins and could thus be purified by direct capture from crude protein extracts. The immobilized, double-tagged proteins were effective for one-pot enzymatic production of sialic acid.

  16. Folksonomy-based tag recommendation for online audio clip sharing

    OpenAIRE

    Font, Frederic; Serr?? Juli??, Joan; Serra, Xavier

    2012-01-01

    Collaborative tagging has emerged as an efficient way to semantically describe online resources shared by a community of users. However, tag descriptions present some drawbacks such as tag scarcity or concept inconsistencies. In these situations, tag recommendation strategies can help users in adding meaningful tags to the resources being described. Freesound is an online audio clip sharing site that uses collaborative tagging to describe a collection of more than 140,...

  17. Alternative affinity tools: more attractive than antibodies?

    NARCIS (Netherlands)

    Ruigrok, V.J.B.; Levisson, M.; Eppink, M.H.M.; Smidt, H.; Oost, van der J.

    2011-01-01

    Antibodies are the most successful affinity tools used today, in both fundamental and applied research (diagnostics, purification and therapeutics). Nonetheless, antibodies do have their limitations, including high production costs and low stability. Alternative affinity tools based on nucleic acids

  18. Direct Labeling of Polyphosphate at the Ultrastructural Level in Saccharomyces cerevisiae by Using the Affinity of the Polyphosphate Binding Domain of Escherichia coli Exopolyphosphatase

    OpenAIRE

    Saito, Katsuharu; Ohtomo, Ryo; Kuga-Uetake, Yukari; Aono, Toshihiro; Saito, Masanori

    2005-01-01

    Inorganic polyphosphate (polyP) is a linear polymer of orthophosphate and has many biological functions in prokaryotic and eukaryotic organisms. To investigate polyP localization, we developed a novel technique using the affinity of the recombinant polyphosphate binding domain (PPBD) of Escherichia coli exopolyphosphatase to polyP. An epitope-tagged PPBD was expressed and purified from E. coli. Equilibrium binding assay of PPBD revealed its high affinity for long-chain polyP and its weak affi...

  19. Enhanced UHF RFID tags for drug tracing.

    Science.gov (United States)

    Catarinucci, Luca; Colella, Riccardo; De Blasi, Mario; Patrono, Luigi; Tarricone, Luciano

    2012-12-01

    Radio Frequency Identification (RFID) technology is playing a crucial role for item-level tracing systems in healthcare scenarios. The pharmaceutical supply chain is a fascinating application context, where RFID can guarantee transparency in the drug flow, supporting both suppliers and consumers against the growing counterfeiting problem. In such a context, the choice of the most adequate RFID tag, in terms of shape, frequency, size and reading range, is crucial. The potential presence of items containing materials hostile to the electromagnetic propagation exasperates the problem. In addition, the peculiarities of the different RFID-based checkpoints make even more stringent the requirements for the tag. In this work, the performance of several commercial UHF RFID tags in each step of the pharmaceutical supply chain has been evaluated, confirming the expected criticality. On such basis, a guideline for the electromagnetic design of new high-performance tags capable to overcome such criticalities has been defined. Finally, driven by such guidelines, a new enhanced tag has been designed, realized and tested. Due to patent pending issues, the antenna shape is not shown. Nevertheless, the optimal obtained results do not lose their validity. Indeed, on the one hand they demonstrate that high performance item level tracing systems can actually be implemented also in critical operating conditions. On the other hand, they encourage the tag designer to follow the identified guidelines so to realize enhanced UHF tags.

  20. Tags and seals for arms control verification

    Energy Technology Data Exchange (ETDEWEB)

    DeVolpi, A.

    1990-09-18

    Tags and seals have long been recognized as important tools in arms control. The trend in control of armaments is to limit militarily significant equipment that is capable of being verified through direct and cooperative means, chiefly on-site inspection or monitoring. Although this paper will focus on the CFE treaty, the role of tags and seals for other treaties will also be addressed. Published technology and concepts will be reviewed, based on open sources. Arms control verification tags are defined as unique identifiers designed to be tamper-revealing; in that respect, seals are similar, being used as indicators of unauthorized access. Tamper-revealing tags might be considered as single-point markers, seals as two-point couplings, and nets as volume containment. The functions of an arms control tag can be considered to be two-fold: to provide field verification of the identity of a treaty-limited item (TLI), and to have a means of authentication of the tag and its tamper-revealing features. Authentication could take place in the field or be completed elsewhere. For CFE, the goal of tags and seals can be to reduce the overall cost of the entire verification system.

  1. Satellite tagging and biopsy sampling of killer whales at subantarctic Marion Island: effectiveness, immediate reactions and long-term responses.

    Directory of Open Access Journals (Sweden)

    Ryan R Reisinger

    Full Text Available Remote tissue biopsy sampling and satellite tagging are becoming widely used in large marine vertebrate studies because they allow the collection of a diverse suite of otherwise difficult-to-obtain data which are critical in understanding the ecology of these species and to their conservation and management. Researchers must carefully consider their methods not only from an animal welfare perspective, but also to ensure the scientific rigour and validity of their results. We report methods for shore-based, remote biopsy sampling and satellite tagging of killer whales Orcinus orca at Subantarctic Marion Island. The performance of these methods is critically assessed using 1 the attachment duration of low-impact minimally percutaneous satellite tags; 2 the immediate behavioural reactions of animals to biopsy sampling and satellite tagging; 3 the effect of researcher experience on biopsy sampling and satellite tagging; and 4 the mid- (1 month and long- (24 month term behavioural consequences. To study mid- and long-term behavioural changes we used multievent capture-recapture models that accommodate imperfect detection and individual heterogeneity. We made 72 biopsy sampling attempts (resulting in 32 tissue samples and 37 satellite tagging attempts (deploying 19 tags. Biopsy sampling success rates were low (43%, but tagging rates were high with improved tag designs (86%. The improved tags remained attached for 26±14 days (mean ± SD. Individuals most often showed no reaction when attempts missed (66% and a slight reaction-defined as a slight flinch, slight shake, short acceleration, or immediate dive-when hit (54%. Severe immediate reactions were never observed. Hit or miss and age-sex class were important predictors of the reaction, but the method (tag or biopsy was unimportant. Multievent trap-dependence modelling revealed considerable variation in individual sighting patterns; however, there were no significant mid- or long-term changes

  2. Novel Use of PIT Tags in Sea Cucumbers: Promising Results with the Commercial Species Cucumaria frondosa.

    Science.gov (United States)

    Gianasi, Bruno L; Verkaik, Katie; Hamel, Jean-François; Mercier, Annie

    2015-01-01

    The lack of a reliable and innocuous mark-recapture method has limited studies that would provide essential information for the management of commercial sea cucumbers. Tagging sea cucumbers is notoriously difficult because of their plastic nature and autolysis capacities. The markers that have so far been tested, mainly on or through the body wall, were either lost rapidly or had major drawbacks (e.g. suitable only for batch identification, requiring complex analysis, causing infections, necrosis, behavioural changes and mortality). The present study explored the efficacy of passive integrated transponder (PIT) tags for individually marking sea cucumbers by assessing retention rates and long-term side effects of tags inserted in previously unstudied tissues/organs. Individuals of the species Cucumaria frondosa were tagged in the body wall, aquapharyngeal bulb and at the base of the oral tentacles. They were monitored closely for evidence of stress, infection, change in feeding and spawning behaviour and tag retention rate. Implanting the tag in an oral tentacle to reach the hydrovascular system of the aquapharyngeal bulb achieved the best retention rates in full-size individuals: from a maximum of 92% after 30 days to 68% at the end of the experimental period (300 days). Efficacy was lower in smaller individuals (84% after 30 d and 42% after 300 d). Following a slight increase in cloacal movements for 15 h post tagging, no side effect was noted in sea cucumbers tagged in the aquapharyngeal bulb via the tentacles. Feeding and spawning behaviours were not affected and no signs of infections or abnormal cell development in the vicinity of the tags were observed. This study indicates that marking sea cucumbers with 8.2 mm long PIT tags implanted via the oral tentacle is an effective technique, yielding relatively high retention rates over long periods without any detectable physiological or behavioural effects. PMID:26011165

  3. Novel Use of PIT Tags in Sea Cucumbers: Promising Results with the Commercial Species Cucumaria frondosa.

    Directory of Open Access Journals (Sweden)

    Bruno L Gianasi

    Full Text Available The lack of a reliable and innocuous mark-recapture method has limited studies that would provide essential information for the management of commercial sea cucumbers. Tagging sea cucumbers is notoriously difficult because of their plastic nature and autolysis capacities. The markers that have so far been tested, mainly on or through the body wall, were either lost rapidly or had major drawbacks (e.g. suitable only for batch identification, requiring complex analysis, causing infections, necrosis, behavioural changes and mortality. The present study explored the efficacy of passive integrated transponder (PIT tags for individually marking sea cucumbers by assessing retention rates and long-term side effects of tags inserted in previously unstudied tissues/organs. Individuals of the species Cucumaria frondosa were tagged in the body wall, aquapharyngeal bulb and at the base of the oral tentacles. They were monitored closely for evidence of stress, infection, change in feeding and spawning behaviour and tag retention rate. Implanting the tag in an oral tentacle to reach the hydrovascular system of the aquapharyngeal bulb achieved the best retention rates in full-size individuals: from a maximum of 92% after 30 days to 68% at the end of the experimental period (300 days. Efficacy was lower in smaller individuals (84% after 30 d and 42% after 300 d. Following a slight increase in cloacal movements for 15 h post tagging, no side effect was noted in sea cucumbers tagged in the aquapharyngeal bulb via the tentacles. Feeding and spawning behaviours were not affected and no signs of infections or abnormal cell development in the vicinity of the tags were observed. This study indicates that marking sea cucumbers with 8.2 mm long PIT tags implanted via the oral tentacle is an effective technique, yielding relatively high retention rates over long periods without any detectable physiological or behavioural effects.

  4. Manifolds with integrable affine shape operator

    Directory of Open Access Journals (Sweden)

    Daniel A. Joaquín

    2005-05-01

    Full Text Available This work establishes the conditions for the existence of vector fields with the property that theirs covariant derivative, with respect to the affine normal connection, be the affine shape operatorS in hypersurfaces. Some results are obtained from this property and, in particular, for some kind of affine decomposable hypersurfaces we explicitely get the actual vector fields.

  5. Tagging Water Sources in Atmospheric Models

    Science.gov (United States)

    Bosilovich, M.

    2003-01-01

    Tagging of water sources in atmospheric models allows for quantitative diagnostics of how water is transported from its source region to its sink region. In this presentation, we review how this methodology is applied to global atmospheric models. We will present several applications of the methodology. In one example, the regional sources of water for the North American Monsoon system are evaluated by tagging the surface evaporation. In another example, the tagged water is used to quantify the global water cycling rate and residence time. We will also discuss the need for more research and the importance of these diagnostics in water cycle studies.

  6. Recommender Systems for Social Tagging Systems

    CERN Document Server

    Balby Marinho, Leandro

    2012-01-01

    Social Tagging Systems are web applications in which users upload resources (e.g., bookmarks, videos, photos, etc.) and annotate it with a list of freely chosen keywords called tags. This is a grassroots approach to organize a site and help users to find the resources they are interested in. Social tagging systems are open and inherently social; features that have been proven to encourage participation. However, with the large popularity of these systems and the increasing amount of user-contributed content, information overload rapidly becomes an issue. Recommender Systems are well known appl

  7. Exploratory Analysis of the Main Characteristics of Tags and Tagging of Educational Resources in a Multi-lingual Context

    OpenAIRE

    Vuorikari, Riina; Ochoa, Xavier

    2009-01-01

    Although social, collaborative classification through tagging has been the focus of recent research, the effect of multi-linguality is often overlooked. This work presents an exploratory study of the production and use of tags in multiple languages in a context of European Learning Resources Exchange. We describe a tagging tool used by teachers from 6 countries and study the main characteristics of tags and how users tag when multiple languages are presented. We find early indication that tag...

  8. Methodology optimizing SAGE library tag-to-gene mapping: application to Leishmania

    Directory of Open Access Journals (Sweden)

    Smandi Sondos

    2012-01-01

    Full Text Available Abstract Background Leishmaniasis are widespread parasitic-diseases with an urgent need for more active and less toxic drugs and for effective vaccines. Understanding the biology of the parasite especially in the context of host parasite interaction is a crucial step towards such improvements in therapy and control. Several experimental approaches including SAGE (Serial analysis of gene expression have been developed in order to investigate the parasite transcriptome organisation and plasticity. Usual SAGE tag-to-gene mapping techniques are inadequate because almost all tags are normally located in the 3'-UTR outside the CDS, whereas most information available for Leishmania transcripts is restricted to the CDS predictions. The aim of this work is to optimize a SAGE libraries tag-to-gene mapping technique and to show how this development improves the understanding of Leishmania transcriptome. Findings The in silico method implemented herein was based on mapping the tags to Leishmania genome using BLAST then mapping the tags to their gene using a data-driven probability distribution. This optimized tag-to-gene mappings improved the knowledge of Leishmania genome structure and transcription. It allowed analyzing the expression of a maximal number of Leishmania genes, the delimitation of the 3' UTR of 478 genes and the identification of biological processes that are differentially modulated during the promastigote to amastigote differentiation. Conclusion The developed method optimizes the assignment of SAGE tags in trypanosomatidae genomes as well as in any genome having polycistronic transcription and small intergenic regions.

  9. Affine trajectory correction for nonholonomic mobile robots

    CERN Document Server

    Pham, Quang-Cuong

    2011-01-01

    Planning trajectories for nonholonomic systems is difficult and computationally expensive. When facing unexpected events, it may therefore be preferable to deform in some way the initially planned trajectory rather than to re-plan entirely a new one. We suggest here a method based on affine transformations to make such deformations. This method is exact and fast: the deformations and the resulting trajectories can be computed algebraically, in one step, and without any trajectory re-integration. To demonstrate the possibilities offered by this new method, we use it to derive position correction, orientation correction, obstacle avoidance and feedback control algorithms for the general class of planar wheeled robots and for a tridimensional underwater vehicle.

  10. Towards Enhancing Supportive E-Learning Courses using Smart Tags

    Directory of Open Access Journals (Sweden)

    Hayel Khafajeh

    2016-08-01

    Full Text Available E-learning management systems have emerged as a method of education development in many universities in the Arab world. E-learning management system tools provide a basic environment for interaction between faculty members and students, and these tools require information technology to obtain the most benefit. This paper proposes a method for enhancing the delivery of supportive e-learning courses using smart tags, such as NFC technique. The study sample comprises students at a supportive E-learning course in King Khaled University. This study aims to propose a technique to enhance the delivery of E-learning courses using these tags, which enable teachers and students to interact with the educational material and track their academic performance. The conducted experiments used receiver operating characteristic (ROC prediction quality measurements to evaluate the proposed technique.

  11. Comparative Performance of Acoustic-tagged and PIT-tagged Juvenile Salmonids

    Energy Technology Data Exchange (ETDEWEB)

    Hockersmith, Eric E.; Brown, Richard S.; Liedtke, Theresa L.

    2008-02-01

    Numerous research tools and technologies are currently being used to evaluate fish passage and survival to determine the impacts of the Federal Columbia River Power System (FCRPS) on endangered and threatened juvenile salmonids, including PIT tags, balloon tags, hydroacoustic evaluations, radio telemetry, and acoustic telemetry. Each has advantages and disadvantages, but options are restricted in some situations because of limited capabilities of a specific technology, lack of detection capability downstream, or availability of adequate numbers of fish. However, there remains concern about the comparative effects of the tag or the tagging procedure on fish performance. The recently developed Juvenile Salmonid Acoustic Telemetry System (JSATS) acoustic transmitter is the smallest active acoustic tag currently available. The goal of this study was to determine whether fish tagged with the JSATS acoustic-telemetry tag can provide unbiased estimates of passage behavior and survival within the performance life of the tag. We conducted both field and laboratory studies to assess tag effects. For the field evaluation we released a total of 996 acoustic-tagged fish in conjunction with 21,026 PIT-tagged fish into the tailrace of Lower Granite Dam on 6 and 13 May. Travel times between release and downstream dams were not significantly different for the majority of the reaches between acoustic-tagged and PIT-tagged fish. In addition to the field evaluation, a series of laboratory experiments were conducted to determine if growth and survival of juvenile Chinook salmon surgically implanted with acoustic transmitters is different than untagged or PIT tagged juvenile Chinook salmon. Only yearling fish with integrated and non-integrated transmitters experienced mortalities, and these were low (<4.5%). Mortality among sub-yearling control and PIT-tag treatments ranged up to 7.7% while integrated and non-integrated treatments had slightly higher rates (up to 8.3% and 7

  12. Unbiased Selective Isolation of Protein N-Terminal Peptides from Complex Proteome Samples Using Phospho Tagging PTAG) and TiO2-based Depletion

    NARCIS (Netherlands)

    Mommen, G.P.M.; Waterbeemd, van de B.; Meiring, H.D.; Kersten, G.; Heck, A.J.R.; Jong, de A.P.J.M.

    2012-01-01

    A positional proteomics strategy for global N-proteome analysis is presented based on phospho tagging (PTAG) of internal peptides followed by depletion by titanium dioxide (TiO2) affinity chromatography. Therefore, N-terminal and lysine amino groups are initially completely dimethylated with formald

  13. System and method for acquisition management of subject position information

    Energy Technology Data Exchange (ETDEWEB)

    Carrender, Curt (Morgan Hill, CA)

    2007-01-23

    A system and method for acquisition management of subject position information that utilizes radio frequency identification (RF ID) to store position information in position tags. Tag programmers receive position information from external positioning systems, such as the Global Positioning System (GPS), from manual inputs, such as keypads, or other tag programmers. The tag programmers program each position tag with the received position information. Both the tag programmers and the position tags can be portable or fixed. Implementations include portable tag programmers and fixed position tags for subject position guidance, and portable tag programmers for collection sample labeling. Other implementations include fixed tag programmers and portable position tags for subject route recordation. Position tags can contain other associated information such as destination address of an affixed subject for subject routing.

  14. System and method for acquisition management of subject position information

    Energy Technology Data Exchange (ETDEWEB)

    Carrender, Curt

    2005-12-13

    A system and method for acquisition management of subject position information that utilizes radio frequency identification (RF ID) to store position information in position tags. Tag programmers receive position information from external positioning systems, such as the Global Positioning System (GPS), from manual inputs, such as keypads, or other tag programmers. The tag programmers program each position tag with the received position information. Both the tag programmers and the position tags can be portable or fixed. Implementations include portable tag programmers and fixed position tags for subject position guidance, and portable tag programmers for collection sample labeling. Other implementations include fixed tag programmers and portable position tags for subject route recordation. Position tags can contain other associated information such as destination address of an affixed subject for subject routing.

  15. Flavour Tagging with the LHCb experiment

    CERN Multimedia

    Birnkraut, Alex

    2015-01-01

    Measurements of flavour oscillations and time-dependent CP asymmetries in neutral B meson systems require knowledge of the b quark production flavour. This identification is performed by the Flavour Tagging.

  16. P systems based on tag operations

    Directory of Open Access Journals (Sweden)

    Yurii Rogozhin

    2012-10-01

    Full Text Available In this article we introduce P systems using Post's tag operation on strings.We show that the computational completeness can be achieved even if the deletion length is equal to one.

  17. User Interface Program for secure electronic tags

    International Nuclear Information System (INIS)

    This report summarizes and documents the efforts of Argonne National Laboratory (ANL) in developing a secure tag communication user interface program comprising a tag monitor and a communication tool. This program can perform the same functions as the software that was developed at the Lawrence Livermore National Laboratory (LLNL), but it is enhanced with a user-friendly screen. It represents the first step in updating the TRANSCOM Tracking System (TRANSCOM) by incorporating a tag communication screen menu into the main menu of the TRANSCOM user program. A working version of TRANSCOM, enhanced with ANL secure-tag graphics, will strongly support the Department of Energy Warhead Dismantlement/Special Nuclear Materials Control initiatives. It will allow commercial satellite tracking of the movements and operational activities of treaty-limited items and transportation vehicles throughout Europe and the former USSR, as well as the continental US

  18. Believing Your Eyes: Strengthening the Reliability of Tags and Seals

    Energy Technology Data Exchange (ETDEWEB)

    Brim, Cornelia P.; Denlinger, Laura S.

    2013-07-01

    NNSA’s Office of Nonproliferation and International Security (NIS) is working together with scientific experts at the DOE national laboratories to develop the tools needed to safeguard and secure nuclear material from diversion, theft, and sabotage--tasks critical to support future arms control treaties that may involve the new challenge of monitoring nuclear weapons dismantlement. Use of optically stimulated luminescent material is one method to enhance the security and robustness of existing tamper indicating devices such as tags and seals.

  19. A new RF tagging pulse based on the Frank poly-phase perfect sequence

    DEFF Research Database (Denmark)

    Laustsen, Christoffer; Greferath, Marcus; Ringgaard, Steffen;

    2014-01-01

    Radio frequency (RF) spectrally selective multiband pulses or tagging pulses, are applicable in a broad range of magnetic resonance methods. We demonstrate through simulations and experiments a new phase-modulation-only RF pulse for RF tagging based on the Frank poly-phase perfect sequence. In...... addition, we introduce an extended version with a WURST modulation (Frank-WURST). The new pulses exhibit interesting and flexible spin tagging properties and are easily implemented in existing MR sequences, where they can substitute slice-selective pulses with no additional alterations....

  20. A Security Mechanism for library management system using low cost RFID tags

    OpenAIRE

    V. Nagalakshmi; I. Rameshbabu; D. Lalithabhaskari

    2007-01-01

    Radio Frequency Identification (RFID) systems will become pervasive in our daily lives due to their low cost and easy to use characteristics[1]. This paper presents a methodology of using low cost RFID tags for a library management system to protect the books from unauthorized capturing and usage. Every object to be identified in the RFID system is physically labeled with a tag. In the proposed method a book or a magazine or a CD is identified with the RFID tag. Whenever a book is issued to a...

  1. Reconfigurable Control of Input Affine Nonlinear Systems under Actuator Fault

    DEFF Research Database (Denmark)

    Tabatabaeipour, Mojtaba; Galeazzi, Roberto

    2015-01-01

    This paper proposes a fault tolerant control method for input-affine nonlinear systems using a nonlinear reconfiguration block (RB). The basic idea of the method is to insert the RB between the plant and the nominal controller such that fault tolerance is achieved without re-designing the nominal...

  2. Antibody-free magnetic cell sorting of genetically modified primary human CD4+ T cells by one-step streptavidin affinity purification.

    Directory of Open Access Journals (Sweden)

    Nicholas J Matheson

    Full Text Available Existing methods for phenotypic selection of genetically modified mammalian cells suffer disadvantages of time, cost and scalability and, where antibodies are used to bind exogenous cell surface markers for magnetic selection, typically yield cells coated with antibody-antigen complexes and beads. To overcome these limitations we have developed a method termed Antibody-Free Magnetic Cell Sorting in which the 38 amino acid Streptavidin Binding Peptide (SBP is displayed at the cell surface by the truncated Low Affinity Nerve Growth Receptor (LNGFRF and used as an affinity tag for one-step selection with streptavidin-conjugated magnetic beads. Cells are released through competition with the naturally occurring vitamin biotin, free of either beads or antibody-antigen complexes and ready for culture or use in downstream applications. Antibody-Free Magnetic Cell Sorting is a rapid, cost-effective, scalable method of magnetic selection applicable to either viral transduction or transient transfection of cell lines or primary cells. We have optimised the system for enrichment of primary human CD4+ T cells expressing shRNAs and exogenous genes of interest to purities of >99%, and used it to isolate cells following Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR/Cas9 genome editing.

  3. b-flavour tagging in pp collisions

    CERN Multimedia

    Birnkraut, Alex

    2015-01-01

    An essential ingredient of all time-dependent CP violation studies of B mesons is the ability to tag the initial flavour of the B meson. The harsh environment of 7 and 8 TeV pp collisions makes this a particularly difficult enterprise. We report progresses in the flavour tagging of B0 and Bs mesons, including developments of novel techniques like the use of an opposite side charm tagger.

  4. Accurate and unambiguous tag-to-gene mapping in serial analysis of gene expression

    Directory of Open Access Journals (Sweden)

    Melo Francisco

    2006-11-01

    Full Text Available Abstract Background In this study, we present a robust and reliable computational method for tag-to-gene assignment in serial analysis of gene expression (SAGE. The method relies on current genome information and annotation, incorporation of several new features, and key improvements over alternative methods, all of which are important to determine gene expression levels more accurately. The method provides a complete annotation of potential virtual SAGE tags within a genome, along with an estimation of their confidence for experimental observation that ranks tags that present multiple matches in the genome. Results We applied this method to the Saccharomyces cerevisiae genome, producing the most thorough and accurate annotation of potential virtual SAGE tags that is available today for this organism. The usefulness of this method is exemplified by the significant reduction of ambiguous cases in existing experimental SAGE data. In addition, we report new insights from the analysis of existing SAGE data. First, we found that experimental SAGE tags mapping onto introns, intron-exon boundaries, and non-coding RNA elements are observed in all available SAGE data. Second, a significant fraction of experimental SAGE tags was found to map onto genomic regions currently annotated as intergenic. Third, a significant number of existing experimental SAGE tags for yeast has been derived from truncated cDNAs, which are synthesized through oligo-d(T priming to internal poly-(A regions during reverse transcription. Conclusion We conclude that an accurate and unambiguous tag mapping process is essential to increase the quality and the amount of information that can be extracted from SAGE experiments. This is supported by the results obtained here and also by the large impact that the erroneous interpretation of these data could have on downstream applications.

  5. RATC: A Robust Automated Tag Clustering Technique

    Science.gov (United States)

    Boratto, Ludovico; Carta, Salvatore; Vargiu, Eloisa

    Nowadays, the most dominant and noteworthy web information sources are developed according to the collaborative-web paradigm, also known as Web 2.0. In particular, it represents a novel paradigm in the way users interact with the web. Users (also called prosumers) are no longer passive consumers of published content, but become involved, implicitly and explicitly, as they cooperate by providing their own resources in an “architecture of participation”. In this scenario, collaborative tagging, i.e., the process of classifying shared resources by using keywords, becomes more and more popular. The main problem in such task is related to well-known linguistic phenomena, such as polysemy and synonymy, making effective content retrieval harder. In this paper, an approach that monitors users activity in a tagging system and dynamically quantifies associations among tags is presented. The associations are then used to create tags clusters. Experiments are performed comparing the proposed approach with a state-of-the-art tag clustering technique. Results -given in terms of classical precision and recall- show that the approach is quite effective in the presence of strongly related tags in a cluster.

  6. A hypergraph model of social tagging networks

    International Nuclear Information System (INIS)

    The past few years have witnessed the great success of a new family of paradigms, so-called folksonomy, which allows users to freely associate tags with resources and efficiently manage them. In order to uncover the underlying structures and user behaviors in folksonomy, in this paper, we propose an evolutionary hypergraph model for explaining the emerging statistical properties. The present model introduces a novel mechanism that can not only assign tags to resources, but also retrieve resources via collaborative tags. We then compare the model with a real-world data set: Del.icio.us. Indeed, the present model shows considerable agreement with the empirical data in the following aspects: power-law hyperdegree distributions, negative correlation between clustering coefficients and hyperdegrees, and small average distances. Furthermore, the model indicates that most tagging behaviors are motivated by labeling tags on resources, and the tag plays a significant role in effectively retrieving interesting resources and making acquaintances with congenial friends. The proposed model may shed some light on the in-depth understanding of the structure and function of folksonomy

  7. Smart-tag Based Data Dissemination

    DEFF Research Database (Denmark)

    Bonnet, Philippe; Beaufour, Allan; Leopold, Martin

    2002-01-01

    Monitoring wide, hostile areas requires disseminating data between fixed, disconnected clusters of sensor nodes. It is not always possible to install long-range radios in order to cover the whole area. We propose to leverage the movement of mobile individuals, equipped with smart-tags, to dissemi......-tag based data dissemination. We use simulation to study the characteristics of the model we propose. Finally, we present an implementation based on Bluetooth smart-tags.......Monitoring wide, hostile areas requires disseminating data between fixed, disconnected clusters of sensor nodes. It is not always possible to install long-range radios in order to cover the whole area. We propose to leverage the movement of mobile individuals, equipped with smart......-tags, to disseminate data across disconnected static nodes spread across a wide area. Static nodes and mobile smart-tags exchange data when they are in the vicinity of each other; smart-tags disseminate data as they move around. In this paper, we propose an algorithm for update propagation and a model for smart...

  8. TagSmart: analysis and visualization for yeast mutant fitness data measured by tag microarrays

    Directory of Open Access Journals (Sweden)

    Xie Dan

    2007-04-01

    Full Text Available Abstract Background A nearly complete collection of gene-deletion mutants (96% of annotated open reading frames of the yeast Saccharomyces cerevisiae has been systematically constructed. Tag microarrays are widely used to measure the fitness of each mutant in a mutant mixture. The tag array experiments can have a complex experimental design, such as time course measurements and drug treatment with multiple dosages. Results TagSmart is a web application for analysis and visualization of Saccharomyces cerevisiae mutant fitness data measured by tag microarrays. It implements a robust statistical approach to assess the concentration differences among S. cerevisiae mutant strains. It also provides an interactive environment for data analysis and visualization. TagSmart has the following advantages over previously described analysis procedures: 1 it is user-friendly software rather than merely a description of analytical procedure; 2 It can handle complicated experimental designs, such as multiple time points and treatment with multiple dosages; 3 it has higher sensitivity and specificity; 4 It allows users to mask out "bad" tags in the analysis. Two biological tests were performed to illustrate the performance of TagSmart. First, we generated titration mixtures of mutant strains, in which the relative concentration of each strain was controlled. We used tag microarrays to measure the numbers of tag copies in each titration mixture. The data was analyzed with TagSmart and the result showed high precision and recall. Second, TagSmart was applied to a dataset in which heterozygous deletion strain mixture pools were treated with a new drug, Cincreasin. TagSmart identified 53 mutant strains as sensitive to Cincreasin treatment. We individually tested each identified mutant, and found 52 out of the 53 predicted mutants were indeed sensitive to Cincreasin. Conclusion TagSmart is provided "as is" to analyze tag array data produced by Affymetrix and Agilent

  9. Graded electron affinity electron source

    Energy Technology Data Exchange (ETDEWEB)

    Shaw, J.L.; Gray, H.F.; Jensen, K.L.; Jung, T.M. [Naval Research Laboratory, Washington, DC 20375 (United States)

    1996-05-01

    We describe a new electron source using electric field and low electron affinity semiconductor materials to bring charge to potential energy levels near the vacuum level while still in the solid. The basic idea involves moving some of the potential barrier from the surface to the bulk, and distributing the barrier over a thin layer below the surface. In so doing, the emission physics is changed fundamentally from a quantum mechanical tunneling process largely controlled by surface properties to a classical transport process largely controlled by the band structure of a wide bandgap semiconductor. The composition of the thin layer below the surface would be graded such that the conduction band minimum changes from an energy close to the substrate Fermi level to an energy significantly closer to the vacuum level. Electrons from the substrate would be drawn into the graded composition layer with an electric field produced by a pointed emitter structure and extraction gate similar to that used in field emitter arrays. Relative to a conventional field emitter array, the new source is expected to require lower extraction fields and exhibit improved emission uniformity, stability, and noise. The {ital I}{endash}{ital V} characteristics are not Fowler{endash}Nordheim and may include a saturation effect at high current densities that could be engineered to improve reliability and uniformity. The group III nitrides can be grown with a continuous range of composition that provides the range of electron affinity needed to produce the proposed electronic structure. {copyright} {ital 1996 American Vacuum Society}

  10. Thermo-mechanical actuator-based miniature tagging module for localization in capsule endoscopy

    Science.gov (United States)

    Chandrappan, Jayakrishnan; Ruiqi, Lim; Su, Nandar; Yen Yi, Germaine Hoe; Vaidyanathan, Kripesh

    2011-04-01

    Capsule endoscopy is a frontline medical diagnostic tool for the gastro intestinal tract disorders. During diagnosis, efficient localization techniques are essential to specify a pathological area that may require further diagnosis or treatment. This paper presents the development of a miniature tagging module that relies on a novel concept to label the region of interest and has the potential to integrate with a capsule endoscope. The tagging module is a compact thermo-mechanical actuator loaded with a biocompatible micro tag. A low power microheater attached to the module serves as the thermal igniter for the mechanical actuator. At optimum temperature, the actuator releases the micro tag instantly and penetrates the mucosa layer of a GI tract, region of interest. Ex vivo animal trials are conducted to verify the feasibility of the tagging module concept. X-ray imaging is used to detect the location of the micro tag embedded in the GI tract wall. The method is successful, and radiopaque micro tags can provide valuable pre-operative position information on the infected area to facilitate further clinical procedures.

  11. The value of LibraryThing tags for academic libraries

    NARCIS (Netherlands)

    H. Voorbij

    2012-01-01

    Purpose - The purpose of this paper is to determine the percentage of recently published books provided with tags drawn from LibraryThing for Libraries, the nature of these tags, the relation of the tags with keywords in the record and the percentage of records actually enhanced by tags. Design/meth

  12. Human-centered implicit tagging: overview and perspectives

    NARCIS (Netherlands)

    Soleymani, Mohammad; Pantic, Maja

    2012-01-01

    Tags are an effective form of metadata which help users to locate and browse multimedia content of interest. Tags can be generated by users (user-generated explicit tags), automatically from the content (content-based tags), or assigned automatically based on non-verbal behavioral reactions of users

  13. Estimation of 3D myocardial motion from tagged MRI using LDDMM

    Science.gov (United States)

    Kotamraju, Vinay; McVeigh, Elliot; Beg, Mirza Faisal

    2007-03-01

    Non-invasive estimation of regional cardiac function is important for assessment of myocardial contractility. The use of MR tagging technique enables acquisition of intra-myocardial tissue motion by placing a spatially modulated pattern of magnetization whose deformation with the myocardium over the cardiac cycle can be imaged. Quantitative computation of parameters such as wall thickening, shearing, rotation, torsion and strain within the myocardium is traditionally achieved by processing the tag-marked MR image frames to 1) segment the tag lines and 2) detect the correspondence between points across the time-indexed frames. In this paper, we describe our approach to solving this problem using the Large Deformation Diffeomorphic Metric Mapping (LDDMM) algorithm in which tag-line segmentation and motion reconstruction occur simultaneously. Our method differs from earlier proposed non rigid registration based cardiac motion estimation methods in that our matching cost incorporates image intensity overlap via the L2 norm and the estimated tranformations are diffeomorphic. We also present a novel method of generating synthetic tag line images with known ground truth and motion characteristics that closely follow those in the original data; these can be used for validation of motion estimation algorithms. Initial validation shows that our method is able to accurately segment tag-lines and estimate a dense 3D motion field describing the motion of the myocardium in both the left and the right ventricle.

  14. Rhodamine-labeled 2beta-carbomethoxy-3beta-(3,4-dichlorophenyl)tropane analogues as high-affinity fluorescent probes for the dopamine transporter

    DEFF Research Database (Denmark)

    Cha, Joo Hwan; Zou, Mu-Fa; Adkins, Erika M;

    2005-01-01

    Novel fluorescent ligands were synthesized to identify a high-affinity probe that would enable visualization of the dopamine transporter (DAT) in living cells. Fluorescent tags were extended from the N- or 2-position of 2beta-carbomethoxy-3beta-(3,4-dichlorophenyl)tropane, using an ethylamino...

  15. Predicting hospital visits from geo-tagged Internet search logs

    Science.gov (United States)

    Agarwal, Vibhu; Han, Lichy; Madan, Isaac; Saluja, Shaurya; Shidham, Aaditya; Shah, Nigam H.

    2016-01-01

    The steady rise in healthcare costs has deprived over 45 million Americans of healthcare services (1, 2) and has encouraged healthcare providers to look for opportunities to improve their operational efficiency. Prior studies have shown that evidence of healthcare seeking intent in Internet searches correlates well with healthcare resource utilization. Given the ubiquitous nature of mobile Internet search, we hypothesized that analyzing geo-tagged mobile search logs could enable us to machine-learn predictors of future patient visits. Using a de-identified dataset of geo-tagged mobile Internet search logs, we mined text and location patterns that are predictors of healthcare resource utilization and built statistical models that predict the probability of a user’s future visit to a medical facility. Our efforts will enable the development of innovative methods for modeling and optimizing the use of healthcare resources—a crucial prerequisite for securing healthcare access for everyone in the days to come.

  16. Predicting hospital visits from geo-tagged Internet search logs.

    Science.gov (United States)

    Agarwal, Vibhu; Han, Lichy; Madan, Isaac; Saluja, Shaurya; Shidham, Aaditya; Shah, Nigam H

    2016-01-01

    The steady rise in healthcare costs has deprived over 45 million Americans of healthcare services (1, 2) and has encouraged healthcare providers to look for opportunities to improve their operational efficiency. Prior studies have shown that evidence of healthcare seeking intent in Internet searches correlates well with healthcare resource utilization. Given the ubiquitous nature of mobile Internet search, we hypothesized that analyzing geo-tagged mobile search logs could enable us to machine-learn predictors of future patient visits. Using a de-identified dataset of geo-tagged mobile Internet search logs, we mined text and location patterns that are predictors of healthcare resource utilization and built statistical models that predict the probability of a user's future visit to a medical facility. Our efforts will enable the development of innovative methods for modeling and optimizing the use of healthcare resources-a crucial prerequisite for securing healthcare access for everyone in the days to come. PMID:27570641

  17. Maximum Likelihood Approach for RFID Tag Set Cardinality Estimation with Detection Errors

    DEFF Research Database (Denmark)

    Nguyen, Chuyen T.; Hayashi, Kazunori; Kaneko, Megumi;

    2013-01-01

    Abstract Estimation schemes of Radio Frequency IDentification (RFID) tag set cardinality are studied in this paper using Maximum Likelihood (ML) approach. We consider the estimation problem under the model of multiple independent reader sessions with detection errors due to unreliable radio...... is evaluated under dierent system parameters and compared with that of the conventional method via computer simulations assuming flat Rayleigh fading environments and framed-slotted ALOHA based protocol. Keywords RFID tag cardinality estimation maximum likelihood detection error...

  18. Co-evolution of affinity and stability of grafted amyloid-motif domain antibodies.

    Science.gov (United States)

    Julian, Mark C; Lee, Christine C; Tiller, Kathryn E; Rabia, Lilia A; Day, Evan K; Schick, Arthur J; Tessier, Peter M

    2015-10-01

    An attractive approach for designing lead antibody candidates is to mimic natural protein interactions by grafting peptide recognition motifs into the complementarity-determining regions (CDRs). We are using this approach to generate single-domain (VH) antibodies specific for amyloid-forming proteins such as the Alzheimer's Aβ peptide. Here, we use random mutagenesis and yeast surface display to improve the binding affinity of a lead VH domain grafted with Aβ residues 33-42 in CDR3. Interestingly, co-selection for improved Aβ binding and VH display on the surface of yeast yields antibody domains with improved affinity and reduced stability. The highest affinity VH domains were strongly destabilized on the surface of yeast as well as unfolded when isolated as autonomous domains. In contrast, stable VH domains with improved affinity were reliably identified using yeast surface display by replacing the display antibody that recognizes a linear epitope tag at the terminus of both folded and unfolded VH domains with a conformational ligand (Protein A) that recognizes a discontinuous epitope on the framework of folded VH domains. Importantly, we find that selection for improved stability using Protein A without simultaneous co-selection for improved Aβ binding leads to strong enrichment for stabilizing mutations that reduce antigen binding. Our findings highlight the importance of simultaneously optimizing affinity and stability to improve the rapid isolation of well-folded and specific antibody fragments. PMID:26386257

  19. Tagging b jets associated with heavy neutral MSSM Higgs bosons

    International Nuclear Information System (INIS)

    Since a neural network (NN) approach has been shown to be applicable to the problem of Higgs boson detection at LHC [I. Iashvili, A. Kharchilava, CMS TN-1996/100; M. Mjahed, Nucl. Phys. B 140 (2005) 799], we study the use of NNs in the problem of tagging b jets in pp->bb-bar HSUSY, HSUSY->ττ in the Compact Muons Solenoid experiment [F. Hakl, et al., Nucl. Instr. and Meth. A 502 (2003) 489; S. Lehti, CMS NOTE-2001/019; G. Segneri, F. Palla, CMS NOTE-2002/046]. B tagging is an important tool for separating the Higgs events with associated b jets from the Drell-Yan background Z,γ*->ττ, for which the associated jets are mostly light quark and gluon jets. We teach multi-layer perceptrons (MLPs) available in the object oriented implementation of data analysis framework ROOT [ROOT-An Object Oriented Data Analysis Framework, in: Proceedings of the AIHENP'96 Workshop, Lausanne, September 1996, Nucl. Instr. and Meth. A 389 (1997) 81]. The following learning methods are evaluated: steepest descent algorithm (BFGS) Broyden-Fletcher-Goldfarb-Shanno algorithm, and variants of conjugate gradients. The ROOT code generation feature of standalone C++ classifiers is utilized. We compare the b tagging performance of MLPs with another ROOT based feed forward NN tool NeuNet [J.P. Ernenwein, NeuNet software for ROOT], which uses a common back-propagation learning method. In addition, we demonstrate the use of the self-organizing map program package (SOMPAK) and the learning vector quantization program package (LVQPAK) [T. Kohonen, et al., SOMPAK: the self-organizing map program package, Technical Report A31; T. Kohonen, et al., LVQPAK: the learning vector quantization program package, Technical Report A30, Laboratory of Computer and Information Science, Helsinki University of Technology, FIN-02150 Espoo, Finland, 1996] in the b tagging problem

  20. Tagging b jets associated with heavy neutral MSSM Higgs bosons

    Science.gov (United States)

    Heikkinen, A.; Lehti, S.

    2006-04-01

    Since a neural network (NN) approach has been shown to be applicable to the problem of Higgs boson detection at LHC [I. Iashvili, A. Kharchilava, CMS TN-1996/100; M. Mjahed, Nucl. Phys. B 140 (2005) 799], we study the use of NNs in the problem of tagging b jets in pp →bb¯HSUSY, HSUSY→ττ in the Compact Muons Solenoid experiment [F. Hakl, et al., Nucl. Instr. and Meth. A 502 (2003) 489; S. Lehti, CMS NOTE-2001/019; G. Segneri, F. Palla, CMS NOTE-2002/046]. B tagging is an important tool for separating the Higgs events with associated b jets from the Drell-Yan background Z,γ*→ττ, for which the associated jets are mostly light quark and gluon jets. We teach multi-layer perceptrons (MLPs) available in the object oriented implementation of data analysis framework ROOT [ROOT—An Object Oriented Data Analysis Framework, in: Proceedings of the AIHENP'96 Workshop, Lausanne, September 1996, Nucl. Instr. and Meth. A 389 (1997) 81]. The following learning methods are evaluated: steepest descent algorithm, (BFGS) Broyden-Fletcher-Goldfarb-Shanno algorithm, and variants of conjugate gradients. The ROOT code generation feature of standalone C++ classifiers is utilized. We compare the b tagging performance of MLPs with another ROOT based feed forward NN tool NeuNet [J.P. Ernenwein, NeuNet software for ROOT], which uses a common back-propagation learning method. In addition, we demonstrate the use of the self-organizing map program package (SOM_PAK) and the learning vector quantization program package (LVQ_PAK) [T. Kohonen, et al., SOM_PAK: the self-organizing map program package, Technical Report A31; T. Kohonen, et al., LVQ_PAK: the learning vector quantization program package, Technical Report A30, Laboratory of Computer and Information Science, Helsinki University of Technology, FIN-02150 Espoo, Finland, 1996] in the b tagging problem.

  1. A brief examination of optical tagging technologies.

    Energy Technology Data Exchange (ETDEWEB)

    Ackermann, Mark R.; Cahill, Paul A. (Aspecular Optics, Dayton, OH); Drummond, Timothy J.; Wilcoxon, Jess Patrick

    2003-07-01

    Presented within this report are the results of a brief examination of optical tagging technologies funded by the Laboratory Directed Research and Development (LDRD) program at Sandia National Laboratories. The work was performed during the summer months of 2002 with total funding of $65k. The intent of the project was to briefly examine a broad range of approaches to optical tagging concentrating on the wavelength range between ultraviolet (UV) and the short wavelength infrared (SWIR, {lambda} < 2{micro}m). Tagging approaches considered include such things as simple combinations of reflective and absorptive materials closely spaced in wavelength to give a high contrast over a short range of wavelengths, rare-earth oxides in transparent binders to produce a narrow absorption line hyperspectral tag, and fluorescing materials such as phosphors, dies and chemically precipitated particles. One technical approach examined in slightly greater detail was the use of fluorescing nano particles of metals and semiconductor materials. The idea was to embed such nano particles in an oily film or transparent paint binder. When pumped with a SWIR laser such as that produced by laser diodes at {lambda}=1.54{micro}m, the particles would fluoresce at slightly longer wavelengths, thereby giving a unique signal. While it is believed that optical tags are important for military, intelligence and even law enforcement applications, as a business area, tags do not appear to represent a high on return investment. Other government agencies frequently shop for existing or mature tag technologies but rarely are interested enough to pay for development of an untried technical approach. It was hoped that through a relatively small investment of laboratory R&D funds, enough technologies could be identified that a potential customers requirements could be met with a minimum of additional development work. Only time will tell if this proves to be correct.

  2. On the Analysis of Tag Questions in English Teaching

    Institute of Scientific and Technical Information of China (English)

    朱虹

    2013-01-01

    Tag question is often used in English conversation, but it is also a very complicated syntactic structure in English which becomes the difficulty of English learners. Tag question involves various grammatical factors. A full linguistic analysis of tag ques⁃tions includes the classification, construction and meanings of intonations of the tag questions in English. The study of tag ques⁃tion aims at providing substantial contribution to the teaching and learning of English syntax.

  3. Extracting Usage Patterns and the Analysis of Tag Connection Dynamics within Collaborative Tagging Systems

    Directory of Open Access Journals (Sweden)

    Daniel MICAN

    2013-01-01

    Full Text Available Collaborative tagging has become a very popular way of annotation, thanks to the fact that any entity may be labeled by any individual based on his own reason. In this paper we present the results of the case study carried out on the basis of data gathered at different time intervals from the social tagging system developed and implemented on Întelepciune.ro. Analyzing collective data referring to the way in which community members associate different tags, we have observed that between tags, links are formed which become increasingly stable with the passing of time. Following the application of methodology specific to network analysis, we have managed to extract information referring to tag popularity, their influence within the network and the degree to which a tag depends upon another. As such, we have succeeded in determining different semantic structures within the collective tagging system and see their evolution at different stages in time. Furthermore, we have pictured the way in which tag rec-ommendations can be executed and that they can be integrated within recommendation sys-tems. Thus, we will be able to identify experts and trustworthy content based on different cat-egories of interest.

  4. Tag4M, a Wi-Fi RFID Active Tag Optimized for Sensor Measurements

    OpenAIRE

    Folea, Silviu; Ghercioiu, Marius

    2010-01-01

    This presentation introduces a Wi-Fi tag named Tag4M. The novelty of the design is Wi-Fi with ultra-low power, in a very small package that is running on a battery for years and offers a platform for sensor measurements using the existing (Internet) network

  5. Efficient expression of codon-adapted human acetaldehyde dehydrogenase 2 cDNA with 6×His tag in Pichia pastoris

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Human mitochondrial acetaldehyde dehydrogenase 2 (ALDH2) catalyzes the oxidation of acetaldehyde to acetic acid. Therefore, ALDH2 has therapeutic potential in detoxification of acetaldehyde. Further-more, ALDH2 catalyzes nitroglycerin to nitrate and 1, 2-glyceryldinitrate during therapy for angina pectoris, myocardial infarction, and heart failure. Large quantities of ALDH2 will be needed for potential clinical practice. In this study, Pichia pastoris was used as a platform for expression of human ALDH2. Based on the ALDH2*1 cDNA sequence, we designed ALDH2 cDNA by choosing the P. pastoris preferred codons and by decreasing the G + C content level. The sequence was synthesized using the overlap extension PCR method. The cDNA and 6×His tags were subcloned into the plasmid pPIC9K. The recombinant protein was expressed in P. pastoris GS115 and purified using Ni2+-Sepharose affinity chromatography. The amount of secreted protein in the culture was 80 mg/L in shake-flask cultivation and 260 mg/L in high-density bioreactor fermentation. Secreted ALDH2 was easily purified from the culture supernatant by using Ni2+-Sepharose affinity chromatography. After purification of the fermentation supernatant, the enzyme had a specific activity of 1.2 U/mg protein. The yield was about 16 mg/L in a shake flask culture of P. pastoris GS115 which contained the original human ALDH2*1 cDNA.

  6. Efficient expression of codon-adapted human acetaldehyde dehydrogenase 2 cDNA with 6×His tag in Pichia pastoris

    Institute of Scientific and Technical Information of China (English)

    ZHAO YuFeng; LEI MingKe; WU YuanXin; ZHANG ZiSheng; WANG CunWen

    2009-01-01

    Human mitochondrial acetaldehyde dehydrogenase 2 (ALDH2) catalyzes the oxidation of acetaldehyde to acetic acid. Therefore, ALDH2 has therapeutic potential in detoxification of acetaldehyde. Furthermore, ALDH2 catalyzes nitroglycerin to nitrate and 1, 2-glyceryldinitrate during therapy for angina pectoris, myocardial infarction, and heart failure. Large quantities of ALDH2 will be needed for potential clinical practice. In this study, Pichia pastoris was used as a platform for expression of human ALDH2.Based on the ALDH2~*1 cDNA sequence, we designed ALDH2 cDNA by choosing the P. pastoris preferred codons and by decreasing the G + C content level. The sequence was synthesized using the overlap extension PCR method. The cDNA and 6×His tags were subcloned into the plasmid pPIC9K.The recombinant protein was expressed in P. pastoris GS115 and purified using Ni~(2+)-Sepharose affinity chromatography. The amount of secreted protein in the culture was 80 mg/L in shake-flask cultivation and 260 mglL in high-density bioreactor fermentation. Secreted ALDH2 was easily purified from the culture supernatant by using Ni2+-Sepharose affinity chromatography. After purification of the fermentation supernatant, the enzyme had a specific activity of 1.2 U/mg protein. The yield was about 16 mg/L in a shake flask culture of P. pastoris GS115 which contained the original human ALDH2~*1 cDNA.

  7. Circularly Polarized Broadband RFID Microstrip Tag Antenna

    Directory of Open Access Journals (Sweden)

    B. Rajini

    2014-04-01

    Full Text Available In recent years, the application of radio frequency identification (RFID operating in the ultra-high frequency (UHF band (860-960MHz are expanding exponentially, due to the advantages such as long reading distance, high data transfer rate, and small tag size. So the design of a CP tag antenna with broadband characteristic is presently one of the most challenging topics. This project presents a square patch passive RFID tag antenna designed for UHF band. To achieve compact size broadband and circular polarization (CP radiation, the square patch is embedded with a cross slot, while an L-shaped open-end microstrip line coupled to the patch. By selecting an appropriate length for the microstrip line and its coupling distance with the radiating element, easy control on the input impedance of the designed tag antenna which leads to excellent impedance matching is achieved. The measured 10-dB return-loss bandwidth of the tag antenna is 27MHz (from 901–928 MHz.

  8. Electronic tagging and integrated product intelligence

    Science.gov (United States)

    Swerdlow, Martin; Weeks, Brian

    1996-03-01

    The advent of 'intelligent,' electronic data bearing tags is set to revolutionize the way industrial and retail products are identified and tracked throughout their life cycles. The dominant system for unique identification today is the bar code, which is based on printed symbology and regulated by the International Article Numbering Association. Bar codes provide users with significant operational advantages and generate considerable added value to packaging companies, product manufacturers, distributors and retailers, across supply chains in many different sectors, from retailing, to baggage handling and industrial components, e.g., for vehicles or aircraft. Electronic tags offer the potential to: (1) record and store more complex data about the product or any modifications which occur during its life cycle; (2) access (and up-date) stored data in real time in a way which does not involve contact with the product or article; (3) overcome the limitations imposed by systems which rely on line-of-sight access to stored data. Companies are now beginning to consider how electronic data tags can be used, not only to improve the efficiency of their supply chain processes, but also to revolutionize the way they do business. This paper reviews the applications and business opportunities for electronic tags and outlines CEST's strategy for achieving an 'open' standard which will ensure that tags from different vendors can co-exist on an international basis.

  9. Purification and Refolding to Amyloid Fibrils of (His)6-tagged Recombinant Shadoo Protein Expressed as Inclusion Bodies in E. coli.

    Science.gov (United States)

    Li, Qiaojing; Richard, Charles-Adrien; Moudjou, Mohammed; Vidic, Jasmina

    2015-12-19

    The Escherichia coli expression system is a powerful tool for the production of recombinant eukaryotic proteins. We use it to produce Shadoo, a protein belonging to the prion family. A chromatographic method for the purification of (His)6-tagged recombinant Shadoo expressed as inclusion bodies is described. The inclusion bodies are solubilized in 8 M urea and bound to a Ni(2+)-charged column to perform ion affinity chromatography. Bound proteins are eluted by a gradient of imidazole. Fractions containing Shadoo protein are subjected to size exclusion chromatography to obtain a highly purified protein. In the final step purified Shadoo is desalted to remove salts, urea and imidazole. Recombinant Shadoo protein is an important reagent for biophysical and biochemical studies of protein conformation disorders occurring in prion diseases. Many reports demonstrated that prion neurodegenerative diseases originate from the deposition of stable, ordered amyloid fibrils. Sample protocols describing how to fibrillate Shadoo into amyloid fibrils at acidic and neutral/basic pHs are presented. The methods on how to produce and fibrillate Shadoo can facilitate research in laboratories working on prion diseases, since it allows for production of large amounts of protein in a rapid and low cost manner.

  10. Affine diffusions and related processes simulation, theory and applications

    CERN Document Server

    Alfonsi, Aurélien

    2015-01-01

    This book gives an overview of affine diffusions, from Ornstein-Uhlenbeck processes to Wishart processes and it considers some related diffusions such as Wright-Fisher processes. It focuses on different simulation schemes for these processes, especially second-order schemes for the weak error. It also presents some models, mostly in the field of finance, where these methods are relevant and provides some numerical experiments. The book explains the mathematical background to understand affine diffusions and analyze the accuracy of the schemes.  

  11. A Novel Vertex Affinity for Community Detection

    Energy Technology Data Exchange (ETDEWEB)

    Yoo, Andy [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Sanders, Geoffrey [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Henson, Van [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Vassilevski, Panayot [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2015-10-05

    We propose a novel vertex affinity measure in this paper. The new vertex affinity quantifies the proximity between two vertices in terms of their clustering strength and is ideal for such graph analytics applications as community detection. We also developed a framework that combines simple graph searches and resistance circuit formulas to compute the vertex affinity efficiently. We study the properties of the new affinity measure empirically in comparison to those of other popular vertex proximity metrics. Our results show that the existing metrics are ill-suited for community detection due to their lack of fundamental properties that are essential for correctly capturing inter- and intra-cluster vertex proximity.

  12. Properties of the Affine Invariant Ensemble Sampler in high dimensions

    CERN Document Server

    Huijser, David; Brewer, Brendon J

    2015-01-01

    We present theoretical and practical properties of the affine-invariant ensemble sampler Markov chain Monte Carlo method. In high dimensions the affine-invariant ensemble sampler shows unusual and undesirable properties. We demonstrate this with an $n$-dimensional correlated Gaussian toy problem with a known mean and covariance structure, and analyse the burn-in period. The burn-in period seems to be short, however upon closer inspection we discover the mean and the variance of the target distribution do not match the expected, known values. This problem becomes greater as $n$ increases. We therefore conclude that the affine-invariant ensemble sampler should be used with caution in high dimensional problems. We also present some theoretical results explaining this behaviour.

  13. Evaluation Codes from an Affine Veriety Code Perspective

    DEFF Research Database (Denmark)

    Geil, Hans Olav

    2008-01-01

    Evaluation codes (also called order domain codes) are traditionally introduced as generalized one-point geometric Goppa codes. In the present paper we will give a new point of view on evaluation codes by introducing them instead as particular nice examples of affine variety codes. Our study inclu...... includes a reformulation of the usual methods to estimate the minimum distances of evaluation codes into the setting of affine variety codes. Finally we describe the connection to the theory of one-pointgeometric Goppa codes. Contents 4.1 Introduction...... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153 4.2 Affine variety codes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154 4.3 Some Gr¨obner basis theoretical tools . . . . . . . . . . . . . . . . . . . . . . . 155 4.4 A bound on the minimum distance of C(I,L) . . . . . . . . . . . . . . . . . . 157 4.5 The Feng-Rao bound...... for C(I,L)? . . . . . . . . . . . . . . . . . . . . . . . . 160 4.6 Using weighted degree orderings . . . . . . . . . . . . . . . . . . . . . . . . . 163 4.7 The order domain conditions . . . . . . . . . . . . . . . . . . . . . . . . . . . 168 4.8 Weight functions and order domains...

  14. Semisupervised Clustering for Networks Based on Fast Affinity Propagation

    Directory of Open Access Journals (Sweden)

    Mu Zhu

    2013-01-01

    Full Text Available Most of the existing clustering algorithms for networks are unsupervised, which cannot help improve the clustering quality by utilizing a small number of prior knowledge. We propose a semisupervised clustering algorithm for networks based on fast affinity propagation (SCAN-FAP, which is essentially a kind of similarity metric learning method. Firstly, we define a new constraint similarity measure integrating the structural information and the pairwise constraints, which reflects the effective similarities between nodes in networks. Then, taking the constraint similarities as input, we propose a fast affinity propagation algorithm which keeps the advantages of the original affinity propagation algorithm while increasing the time efficiency by passing only the messages between certain nodes. Finally, by extensive experimental studies, we demonstrate that the proposed algorithm can take fully advantage of the prior knowledge and improve the clustering quality significantly. Furthermore, our algorithm has a superior performance to some of the state-of-art approaches.

  15. Direct calculation of 2D components of myocardial strain using sinusoidal MR tagging

    Science.gov (United States)

    Osman, Nael F.; Prince, Jerry L.

    1998-07-01

    A new technique to measure local planar strain in left ventricular myocardium using two-dimensional tagged MR images is presented. This new technique is computationally fast, is fully automated, and generates dense motion estimates. It is based on using a 1-1 SPAMM tag pattern which comprise several one-dimensional sinusoidal tag patterns at different frequencies. A local deformation of the myocardium produces a variation in the local frequencies of these patterns, which can be used to compute strain components in the image plane. Local frequency is measured by scanning certain spectral peaks to create complex images, for which the local frequency is the gradient of the angle associated with their complex data points. The method is demonstrated using both simulations and real tagged MR images, and a discussion of these results and of directions for future research is provided.

  16. Measurement of Bd mixing using opposite-side flavor tagging

    CERN Document Server

    Abazov, V M; Abolins, M; Acharya, B S; Adams, M; Adams, T; Agelou, M; Aguiló, E; Ahn, S H; Ahsan, M; Alexeev, G D; Alkhazov, G; Alton, A; Alverson, G; Alves, G A; Anastasoaie, M; Andeen, T; Anderson, S; Andrieu, B; Anzelc, M S; Arnoud, Y; Arov, M; Askew, A; Åsman, B; Assis-Jesus, A C S; Atramentov, O; Autermann, C; Avila, C; Ay, C; Badaud, F; Baden, A; Bagby, L; Baldin, B; Bandurin, D V; Banerjee, P; Banerjee, S; Barberis, E; Bargassa, P; Baringer, P; Barnes, C; Barreto, J; Bartlett, J F; Bassler, U; Bauer, D; Beale, S; Bean, A; Begalli, M; Begel, M; Belanger-Champagne, C; Bellantoni, L; Bellavance, A; Benítez, J A; Beri, S B; Bernardi, G; Bernhard, R; Berntzon, L; Bertram, I; Besançon, M; Beuselinck, R; Bezzubov, V A; Bhat, P C; Bhatnagar, V; Binder, M; Biscarat, C; Black, K M; Blackler, I; Blazey, G; Blekman, F; Blessing, S; Bloch, D; Bloom, K; Blumenschein, U; Böhnlein, A; Boeriu, O; Bolton, T A; Borissov, G; Bos, K; Bose, T; Brandt, A; Brock, R; Brooijmans, G; Bross, A; Brown, D; Buchanan, N J; Buchholz, D; Bühler, M; Büscher, V; Burdin, S; Burke, S; Burnett, T H; Busato, E; Buszello, C P; Butler, J M; Calfayan, P; Calvet, S; Cammin, J; Caron, S; Carvalho, W; Casey, B C K; Cason, N M; Castilla-Valdez, H; Chakrabarti, S; Chakraborty, D; Chan, K M; Chandra, A; Charles, F; Cheu, E; Chevallier, F; Cho, D K; Choi, S; Choudhary, B; Christofek, L; Claes, D; Clement, B; Clément, C; Coadou, Y; Cooke, M; Cooper, W E; Coppage, D; Corcoran, M; Cousinou, M C; Cox, B; Crepe-Renaudin, S; Cutts, D; Cwiok, M; Da Motta, H; Das, A; Das, M; Davies, B; Davies, G; Davis, G A; De, K; de Jong, P; De Jong, S J; De La Cruz-Burelo, E; De Oliveira Martins, C; Degenhardt, J D; Déliot, F; Demarteau, M; Demina, R; Demine, P; Denisov, D; Denisov, S P; Desai, S; Diehl, H T; Diesburg, M; Doidge, M; Dominguez, A; Dong, H; Dudko, L V; Duflot, L; Dugad, S R; Duggan, D; Duperrin, A; Dyer, J; Dyshkant, A; Eads, M; Edmunds, D; Edwards, T; Ellison, J; Elmsheuser, J; Elvira, V D; Eno, S; Ermolov, P; Evans, H; Evdokimov, A; Evdokimov, V N; Fatakia, S N; Feligioni, L; Ferapontov, A V; Ferbel, T; Fiedler, F; Filthaut, F; Fisher, W; Fisk, H E; Fleck, I; Ford, M; Fortner, M; Fox, H; Fu, S; Fuess, S; Gadfort, T; Galea, C F; Gallas, E; Galyaev, E; García, C; García-Bellido, A; Gardner, J; Gavrilov, V; Gay, A; Gay, P; Gelé, D; Gelhaus, R; Gerber, C E; Gershtein, Yu; Gillberg, D; Ginther, G; Gollub, N; Gómez, B; Goussiou, A; Grannis, P D; Greenlee, H; Greenwood, Z D; Gregores, E M; Grenier, G; Gris, P; Grivaz, J F; Grünendahl, S; Grünewald, M W; Guo, F; Guo, J; Gutíerrez, G; Gutíerrez, P; Haas, A; Hadley, N J; Haefner, P; Hagopian, S; Haley, J; Hall, I; Hall, R E; Han, L; Hanagaki, K; Hansson, P; Harder, K; Harel, A; Harrington, R; Hauptman, J M; Hauser, R; Hays, J; Hebbeker, T; Hedin, D; Hegeman, J G; Heinmiller, J M; Heinson, A P; Heintz, U; Hensel, C; Herner, K; Hesketh, G; Hildreth, M D; Hirosky, R; Hobbs, J D; Hoeneisen, B; Hoeth, H; Hohlfeld, M; Hong, S J; Hooper, R; Houben, P; Hu, Y; Hubacek, Z; Hynek, V; Iashvili, I; Illingworth, R; Ito, A S; Jabeen, S; Jaffré, M; Jain, S; Jakobs, K; Jarvis, C; Jenkins, A; Jesik, R; Johns, K; Johnson, C; Johnson, M; Jonckheere, A; Jonsson, P; Juste, A; Käfer, D; Kahn, S; Kajfasz, E; Kalinin, A M; Kalk, J M; Kalk, J R; Kappler, S; Karmanov, D; Kasper, J; Kasper, P; Katsanos, I; Kau, D; Kaur, R; Kehoe, R; Kermiche, S; Khalatyan, N; Khanov, A; Kharchilava, A I; Kharzheev, Yu M; Khatidze, D; Kim, H; Kim, T J; Kirby, M H; Klima, B; Kohli, J M; Konrath, J P; Kopal, M; Korablev, V M; Kotcher, J; Kothari, B; Koubarovsky, A; Kozelov, A V; Krop, D; Kryemadhi, A; Kühl, T; Kumar, A; Kunori, S; Kupco, A; Kurca, T; Kvita, J; Lammers, S; Landsberg, G L; Lazoflores, J; Le Bihan, A C; Lebrun, P; Lee, W M; Leflat, A; Lehner, F; Lesne, V; Lévêque, J; Lewis, P; Li, J; Li, Q Z; Lima, J G R; Lincoln, D; Linnemann, J; Lipaev, V V; Lipton, R; Liu, Z; Lobo, L; Lobodenko, A; Lokajícek, M; Lounis, A; Love, P; Lubatti, H J; Lynker, M; Lyon, A L; Maciel, A K A; Madaras, R J; Mättig, P; Magass, C; Magerkurth, A; Magnan, A M; Makovec, N; Mal, P K; Malbouisson, H B; Malik, S; Malyshev, V L; Mao, H S; Maravin, Y; Martens, M; McCarthy, R; Meder, D; Melnitchouk, A; Mendes, A; Mendoza, L; Merkin, M; Merritt, K W; Meyer, A; Meyer, J; Michaut, M; Miettinen, H; Millet, T; Mitrevski, J; Molina, J; Mondal, N K; Monk, J; Moore, R W; Moulik, T; Muanza, G S; Mulders, M; Mulhearn, M; Mundal, O; Mundim, L; Mutaf, Y D; Nagy, E; Naimuddin, M; Narain, M; Naumann, N A; Neal, H A; Negret, J P; Neustroev, P; Nöding, C; Nomerotski, A; Novaes, S F; Nunnemann, T; O'Dell, V; O'Neil, D C; Obrant, G; Oguri, V; Oliveira, N; Onoprienko, D; Oshima, N; Otec, R; Oteroy-Garzon, G J; Owen, M; Padley, P; Parashar, N; Park, S J; Park, S K; Parsons, J; Partridge, R; Parua, N; Patwa, A; Pawloski, G; Perea, P M; Pérez, E; Peters, K; Petroff, P; Petteni, M; Piegaia, R; Piper, J; Pleier, M A; Podesta-Lerma, P L M; Podstavkov, V M; Pogorelov, Y; Pol, M E; Pompos, A; Pope, B G; Popov, A V; Potter, C; Prado da Silva, W L; Prosper, H B; Protopopescu, S D; Qian, J; Quadt, A; Quinn, B; Rangel, M S; Rani, K J; Ranjan, K; Ratoff, P N; Renkel, P; Reucroft, S; Rijssenbeek, M; Ripp-Baudot, I; Rizatdinova, F K; Robinson, S; Rodrigues, R F; Royon, C; Rubinov, P; Ruchti, R; Rud, V I; Sajot, G; Sánchez-Hernández, A; Sanders, M P; Santoro, A F S; Savage, G; Sawyer, L; Scanlon, T; Schaile, A D; Schamberger, R D; Scheglov, Y; Schellman, H; Schieferdecker, P; Schmitt, C; Schwanenberger, C; Schwartzman, A; Schwienhorst, R; Sekaric, J; Sen-Gupta, S; Severini, H; Shabalina, E; Shamim, M; Shary, V; Shchukin, A A; Shephard, W D; Shivpuri, R K; Shpakov, D; Siccardi, V; Sidwell, R A; Simák, V; Sirotenko, V I; Skubic, P L; Slattery, P F; Smith, R P; Snow, G R; Snow, J; Snyder, S; Söldner-Rembold, S; Song, X; Sonnenschein, L; Sopczak, A; Sosebee, M; Soustruznik, K; Souza, M; Spurlock, B; Stark, J; Steele, J; Stolin, V; Stone, A; Stoyanova, D A; Strandberg, J; Strandberg, S; Strang, M A; Strauss, M; Ströhmer, R; 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Zhao, T; Zhou, B; Zhu, J; Zielinski, M; Zieminska, D; Zieminski, A; Zutshi, V; Zverev, E G

    2006-01-01

    We report on a measurement of the $B^0_d$ mixing frequency and the calibration of an opposite-side flavor tagger in the D{\\O}experiment. Various properties associated with the $b$ quark on the opposite side of the reconstructed $B$ meson were combined using a likelihood-ratio method into a single variable with enhanced tagging power. Its performance was tested with data, using a large sample of reconstructed semileptonic $B \\to \\mu \\dzero X$ and $B \\to \\mu \\dst X$ decays, corresponding to an integrated luminosity of approximately 1 fb$^{-1}$. The events were divided into groups depending on the value of the combined tagging variable, and an independent analysis was performed in each group. Combining the results of these analyses, the overall effective tagging power was found to be eD^2 = (2.48 \\pm 0.21 (stat.) ^{+0.08}_{-0.06} (syst.))%. The measured $B^0_d$ mixing frequency dmd = 0.506 \\pm 0.020 {\\rm (stat) \\pm 0.016 (syst) ps}^{-1} is in good agreement with the world average value.

  17. Affinity purification of polysaccharide degrading enzymes with crosslinked substrates.

    NARCIS (Netherlands)

    Rozie, H.J.

    1992-01-01

    The aim of this work was to find economically favourable, affinity based, purification methods for several polysaccharide splitting bulk enzymes. The framework in which this study is done is described in Chapter 1.Chapter 2 describes the adsorption of endo-polygalacturonase (endoPG) from a commercia

  18. Higher-order momentum distributions and locally affine LDDMM registration

    DEFF Research Database (Denmark)

    Sommer, Stefan Horst; Nielsen, Mads; Darkner, Sune;

    2013-01-01

    description of affine transformations and subsequent compact description of non-translational movement in a globally nonrigid deformation. The resulting representation contains directly interpretable information from both mathematical and modeling perspectives. We develop the mathematical construction...... higher-order momenta lead to natural modeling of articulated movement, and the method promises to be useful for quantifying ventricle expansion and progressing atrophy during Alzheimer's disease....

  19. On global asymptotic controllability of planar affine nonlinear systems

    Institute of Scientific and Technical Information of China (English)

    SUN Yimin; GUO Lei

    2005-01-01

    In this paper, we present a necessary and sufficient condition for globally asymptotic controllability of the general planar affine nonlinear systems with single-input.This result is obtained by introducing a new method in the analysis, which is based on the use of some basic results in planar topology and in the geometric theory of ordinary differential equations.

  20. Passive UHF RFID Tag for Multispectral Assessment

    Directory of Open Access Journals (Sweden)

    Pablo Escobedo

    2016-07-01

    Full Text Available This work presents the design, fabrication, and characterization of a passive printed radiofrequency identification tag in the ultra-high-frequency band with multiple optical sensing capabilities. This tag includes five photodiodes to cover a wide spectral range from near-infrared to visible and ultraviolet spectral regions. The tag antenna and circuit connections have been screen-printed on a flexible polymeric substrate. An ultra-low-power microcontroller-based switch has been included to measure the five magnitudes issuing from the optical sensors, providing a spectral fingerprint of the incident electromagnetic radiation from ultraviolet to infrared, without requiring energy from a battery. The normalization procedure has been designed applying illuminants, and the entire system was tested by measuring cards from a colour chart and sensing fruit ripening.