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1

Quantitative analysis of complex protein mixtures using isotope-coded affinity tags  

Microsoft Academic Search

We describe an approach for the accurate quantification and concurrent sequence identification of the individual proteins within complex mixtures. The method is based on a class of new chemical reagents termed isotope-coded affinity tags (ICATs) and tandem mass spectrometry. Using this strategy, we compared protein expression in the yeast Saccharomyces cerevisiae, using either ethanol or galactose as a carbon source.

Steven P. Gygi; Beate Rist; Scott A. Gerber; Frantisek Turecek; Michael H. Gelb; Ruedi Aebersold

1999-01-01

2

Isotope-Coded and Affinity-Tagged Cross-Linking (ICATXL): An Efficient Strategy to Probe Protein Interaction Surfaces  

E-print Network

Isotope-Coded and Affinity-Tagged Cross-Linking (ICATXL): An Efficient Strategy to Probe Protein; E-mail: alb@cgl.ucsf.edu Protein bait affinity studies on the yeast proteome have begun to reveal of the cross-linked products sought. Incorporation of affinity tags into cross-linkers can reduce

Craik, Charles S.

3

Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry  

Microsoft Academic Search

An approach to the systematic identification and quantification of the proteins contained in the microsomal fraction of cells is described. It consists of three steps: (1) preparation of microsomal fractions from cells or tissues representing different states; (2) covalent tagging of the proteins with isotope-coded affinity tag (ICAT) reagents followed by proteolysis of the combined labeled protein samples; and (3)

David K. Han; Jimmy Eng; Huilin Zhou; Ruedi Aebersold

2001-01-01

4

Phosphoprotein isotope-coded affinity tag approach for isolating and quantitating phosphopeptides in proteome-wide analyses.  

PubMed

A method has been developed that utilizes phosphoprotein isotope-coded affinity tags (PhIAT) that combines stable isotope and biotin labeling to enrich and quantitatively measure differences in the O-phosphorylation states of proteins. The PhIAT labeling approach involves hydroxide ion-mediated beta-elimination of the O-phosphate moiety and the addition of 1,2-ethanedithiol containing either four alkyl hydrogens (EDT-D0) or four alkyl deuteriums (EDT-D4) followed by biotinylation of the EDT-D0/D4 moiety using (+)-biotinyl-iodoacetamidyl-3,6-dioxaoctanediamine. The PhIAT reagent, which contains the nucleophilic sulfhydryl and isotopic label covalently linked to a biotin moiety, was synthesized and has the potential utility to reduce the O-phosphorylation derivatization into a one-step process. The PhIAT labeling approach was initially demonstrated using the model phosphoprotein beta-casein. After proteolytic digestion, the PhIAT-labeled peptides were affinity isolated using immobilized avidin and analyzed using capillary reversed-phase liquid chromatography-mass spectrometry. PhIAT-labeled beta-casein peptides corresponding to peptides containing known sites of O-phosphorylation were isolated and identified. The PhIAT labeling method was also applied to a yeast protein extract. The PhIAT labeling technique provides a reliable method for making quantitative measurements of differences in the O-phosphorylation state of proteins. PMID:11403303

Goshe, M B; Conrads, T P; Panisko, E A; Angell, N H; Veenstra, T D; Smith, R D

2001-06-01

5

Identification of thioredoxin disulfide targets using a quantitative proteomics approach based on isotope-coded affinity tags.  

PubMed

Thioredoxin (Trx) is a ubiquitous protein disulfide reductase involved in a wide range of cellular redox processes. A large number of putative target proteins have been identified using proteomics approaches, but insight into target specificity at the molecular level is lacking since the reactivity of Trx toward individual disulfides has not been quantified. Here, a novel proteomics procedure is described for quantification of Trx-mediated target disulfide reduction based on thiol-specific differential labeling with the iodoacetamide-based isotope-coded affinity tag (ICAT) reagents. Briefly, protein extract of embryos from germinated barley seeds was treated +/- Trx, and thiols released from target protein disulfides were irreversibly blocked with iodoacetamide. The remaining cysteine residues in the Trx-treated and the control (-Trx) samples were then chemically reduced and labeled with the "light" (12C) and "heavy" (13C) ICAT reagent, respectively. The extent of Trx-mediated reduction was thus quantified for individual cysteine residues based on ratios of tryptic peptides labeled with the two ICAT reagents as measured by liquid chromatography coupled with mass spectrometry (LC-MS). A threshold for significant target reduction was set and disulfide targets were identified in 104 among a total of 199 identified ICAT-labeled peptides. Trx-reduced disulfides were found in several previously identified target proteins, for example, peroxiredoxin and cyclophilin, as well as from a wide range of new targets including several ribosomal proteins that point to a link between Trx h and translation. The catalytic cysteine in dehydroascorbate reductase constituted the most extensively reduced target suggesting that Trx h has an important role in the ascorbate-glutathione cycle. PMID:19367707

Hägglund, Per; Bunkenborg, Jakob; Maeda, Kenji; Svensson, Birte

2008-12-01

6

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

PubMed Central

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, ?1-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. PMID:20346108

2010-01-01

7

Comparative Glycomics using A Tetraplex Stable-Isotope Coded Tag  

PubMed Central

This study illustrates the utility of tetraplex stable isotope coded tags in mass spectrometric glycomics using three carbohydrate classes. The teteraplex tags allow for the direct comparison of glycan compositions within four samples using capillary scale hydrophilic interaction chromatography with on-line mass spectrometry. In addition, the ability to discern glycan structural isomers is shown based on the tandem mass spectra of each composition using nanospray ionization. Results are shown for chondroitin sulfate proteoglycans, low molecular weight heparins, full length heparins, and N-glycans from ?-1-acid glycoproteins from four mammalian species. The data demonstrate the value of the tetraplex stable isotope tagging approach for producing high quality glycomics compositional profiling and fine structural analysis. PMID:20230064

Bowman, Michael J.; Zaia, Joseph

2010-01-01

8

Phosphoprotein isotope-coded solid-phase tag approach for enrichment and quantitative analysis of phosphopeptides from complex mixtures.  

PubMed

Many cellular processes are regulated by reversible protein phosphorylation, and the ability to broadly identify and quantify phosphoproteins from proteomes would provide a basis for gaining a better understanding of these dynamic cellular processes. However, such a sensitive, efficient, and global method capable of addressing the phosphoproteome has yet to be developed. Here we describe an improved stable-isotope labeling method using a phosphoprotein isotope-coded solid-phase tag (PhIST) for isolating and measuring the relative abundances of phosphorylated peptides from complex peptide mixtures resulting from the enzymatic digestion of extracted proteins. The PhIST approach is an extension of the previously reported phosphoprotein isotope-coded affinity tag (PhIAT) approach developed by our laboratory, where phosphoseryl and phosphothreonyl residues were derivatized by hydroxide ion-mediated beta-elimination followed by the Michael addition of 1,2-ethanedithiol (EDT). Instead of using the biotin affinity tag, peptides containing the EDT moiety were captured and labeled in one step using isotope-coded solid-phase reagents containing either light (12C6, 14N) or heavy (13C6, 15N) stable isotopes. The captured peptides labeled with the isotope-coded tags were released from the solid-phase support by UV photocleavage and analyzed by capillary liquid chromatography-tandem mass spectrometry. The efficiency and sensitivity of the PhIST labeling approach for identification of phosphopeptides from mixtures were determined using casein proteins. Its utility for proteomic applications was demonstrated by the labeling of soluble phosphoproteins from a human breast cancer cell line. PMID:14714534

Qian, Wei-Jun; Goshe, Michael B; Camp, David G; Yu, Li-Rong; Tang, Keqi; Smith, Richard D

2003-10-15

9

Combining protein identification and quantification: C-terminal isotope-coded tagging using sulfanilic acid.  

PubMed

Two methods of differential isotopic coding of carboxylic groups have been developed to date. The first approach uses d0- or d3-methanol to convert carboxyl groups into the corresponding methyl esters. The second relies on the incorporation of two 18O atoms into the C-terminal carboxylic group during tryptic digestion of proteins in H(2)18O. However, both methods have limitations such as chromatographic separation of 1H and 2H derivatives or overlap of isotopic distributions of light and heavy forms due to small mass shifts. Here we present a new tagging approach based on the specific incorporation of sulfanilic acid into carboxylic groups. The reagent was synthesized in a heavy form (13C phenyl ring), showing no chromatographic shift and an optimal isotopic separation with a 6 Da mass shift. Moreover, sulfanilic acid allows for simplified fragmentation in matrix-assisted laser desorption/ionization (MALDI) due the charge fixation of the sulfonate group at the C-terminus of the peptide. The derivatization is simple, specific and minimizes the number of sample treatment steps that can strongly alter the sample composition. The quantification is reproducible within an order of magnitude and can be analyzed either by electrospray ionization (ESI) or MALDI. Finally, the method is able to specifically identify the C-terminal peptide of a protein by using GluC as the proteolytic enzyme. PMID:16628568

Panchaud, Alexandre; Guillaume, Elisabeth; Affolter, Michael; Robert, Fabien; Moreillon, Philippe; Kussmann, Martin

2006-01-01

10

Affinity Chromatography GST-tagged Proteins  

E-print Network

Affinity Chromatography GST-tagged Proteins His-tagged Proteins Antibody Immobilization Nucleotide binding Proteins Phospho-Aminoacid binding Proteins www.jenabioscience.com #12;Table of Contents AffinityChromatography Affinity Chromatography 3 GST-tagged Proteins 4 Glutathione ChroMatrixTM, Fast Flow 4 GST Cleavage Capture

Lebendiker, Mario

11

Making the most of affinity tags David S. Waugh  

E-print Network

Making the most of affinity tags David S. Waugh Protein Engineering Section, Macromolecular of their diverse physio- chemical properties. Consequently, affinity tags have become indispensable tools and purification of recombinant proteins, in recent years it has become clear that affinity tags can have

12

Quantification of tryptic peptides in quadrupole ion trap using high-mass signals derived from isotope-coded N-acetyl dipeptide tags.  

PubMed

Isotope-labeled N-acetyl dipeptides (Ac-Xxx-Ala) are coupled to the primary amines of tryptic peptides and then analyzed by tandem mass spectrometry. Amide bond cleavage between Xxx and Ala provides both low- and high-mass isotope-coded signals for quantification of peptides. Especially, facile cleavage at the modified lysine side chain yields very strong high-mass quantitation signals in a noise-free region. Tagging tryptic peptides with isobaric N-acetyl dipeptides is a viable strategy for accurate quantification of proteins, which can be used with most quadrupole ion trap mass spectrometers carrying the 1/3 mass cut-off problem. PMID:21953270

Seo, Jongcheol; Yoon, Hye-Joo; Shin, Seung Koo

2011-09-01

13

Several Affinity Tags Commonly Used in Chromatographic Purification  

PubMed Central

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. PMID:24490106

Zhao, Xinyu; Liang, Shufang

2013-01-01

14

Several affinity tags commonly used in chromatographic purification.  

PubMed

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. PMID:24490106

Zhao, Xinyu; Li, Guoshun; Liang, Shufang

2013-01-01

15

One-Step Metal-Affinity Purification of Histidine-Tagged Proteins by  

E-print Network

One-Step Metal-Affinity Purification of Histidine-Tagged Proteins by Temperature method for the purification of histidine (His)-tagged proteins. The principle of the single-step metal-affinity purification; metal affinity; His-tag INTRODUCTION Many systems have been developed in recent years

Chen, Wilfred

16

Challenges and recent advances in affinity purification of tag-free proteins.  

PubMed

There is currently no generic, simple, lowcost method for affinity chromatographic purification of proteins in which the purified product is free of appended tags. Existing approaches for the purification of tagless proteins fall into two broad categories: (1) direct affinity-based capture of tag-free proteins that utilize affinity ligands specific to the target protein or class of target protein, and (2) removal of an appended affinity tag following tag-mediated protein capture. This paper reviews current state-of-the-art approaches for tagless protein purification in both categories, including specific examples of affinity ligands used for the capture of different classes of proteins and cleavage systems for affinity tag removal following chromatographic capture. A particular focus of this review is on recent developments in affinity tag removal systems utilizing split inteins. PMID:24658742

Guan, Dongli; Chen, Zhilei

2014-07-01

17

The AviD-tag, a NeutrAvidin/avidin specific peptide affinity tag for the immobilization and purification of recombinant proteins  

E-print Network

The AviD-tag, a NeutrAvidin/avidin specific peptide affinity tag for the immobilization Available online 30 July 2007 Abstract The widespread success of affinity tags throughout the biological sciences has prompted interest in developing new and convenient labeling strategies. Affinity tags are well

Ghosh, Indraneel

18

A tailor-made "tag-receptor" affinity pair for the purification of fusion proteins.  

PubMed

A novel affinity "tag-receptor" pair was developed as a generic platform for the purification of fusion proteins. The hexapeptide RKRKRK was selected as the affinity tag and fused to green fluorescent protein (GFP). The DNA fragments were designed, cloned in Pet-21c expression vector and expressed in E. coli host as soluble protein. A solid-phase combinatorial library based on the Ugi reaction was synthesized: 64 affinity ligands displaying complementary functionalities towards the designed tag. The library was screened by affinity chromatography in a 96-well format for binding to the RKRKRK-tagged GFP protein. Lead ligand A7C1 was selected for the purification of RKRKRK fusion proteins. The affinity pair RKRKRK-tagged GFP with A7C1 emerged as a promising solution (Ka of 2.45×10(5) ?M(-1) ). The specificity of the ligand towards the tag was observed experimentally and theoretically through automated docking and molecular dynamics simulations. PMID:24903894

Pina, Ana S; Guilherme, Márcia; Pereira, Alice S; Fernandes, Cláudia S F M; Branco, Ricardo J F; El Khoury, Graziella; Lowe, Christopher R; Roque, A Cecília A

2014-07-01

19

CABM Symposium Differential effects of supplementary affinity tags on the solubility of MBP  

E-print Network

CABM Symposium Differential effects of supplementary affinity tags on the solubility of MBP fusion, maltose binding protein, solubility, structural genomics Abstract It is difficult to imagine any strategy affinity tags. Because of its ability to enhance the solubility and promote the proper folding of its

20

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

SciTech Connect

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.

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

21

PA tag: a versatile protein tagging system using a super high affinity antibody against a dodecapeptide derived from human podoplanin.  

PubMed

Peptide-based epitope tagging technology is universally used in nearly all kind of research projects that involve biochemical characterization of a target protein, but not many systems are fully compatible with purification purpose. By utilizing an anti-human podoplanin antibody NZ-1, we constructed a novel epitope tag system. NZ-1 possesses exceptionally high affinity toward a dodecapeptide dubbed "PA tag", with a characteristic slow dissociation kinetics. Because of its high affinity, PA-tagged proteins in a dilute sample can be captured by immobilized NZ-1 resin in a near complete fashion and eluted by a solution of free PA peptide. This enabled efficient one-step purification of various proteins including soluble (an ectodomain fragment of neuropilin-1) and membrane (epidermal growth factor receptor) proteins expressed in mammalian cells. Mild regeneration condition of the peptide-bound antibody ensures repeated use of the antibody resin, indicating a cost-efficient nature of the system. Together with its outstanding performance in the immunodetection experiments (i.e., Western blotting and flow cytometry), PA tag/NZ-1 system will offer a great chance to facilitate protein production in many biomedical research projects. PMID:24480187

Fujii, Yuki; Kaneko, Mika; Neyazaki, Makiko; Nogi, Terukazu; Kato, Yukinari; Takagi, Junichi

2014-03-01

22

Tris-Nitrilotriacetic Acids of Sub-nanomolar Affinity Toward Hexahistidine Tagged Molecules  

PubMed Central

Nitrilotriacetic acid (NTA) has moderate affinity (10 µM) for hexahistidine (His6) and is widely used in the purification of His6-tagged proteins. The affinity can be increased significantly (10 nM) through multivalency such as using a tris-NTA. We show that the binding affinity of tris-NTA is dependent on the flexibility and length of the spacer between the mono-NTA and the scaffold: the shorter the spacer, the higher the affinity. A series of biotinylated tris-NTA having different spacers were synthesized and used to prepare tris-NTA sensor chips for surface plasmon resonance measurement of binding affinity. Sub-nanomolar affinity can be achieved with a short spacer. The new high affinity tris-NTA enables the formation of stable complexes with hexahistidine containing molecules and provides a convenient method to non-covalently attach proteins to various surfaces. PMID:19650657

Huang, Zhaohua; Hwang, Peter; Watson, Douglas S.; Cao, Limin; Szoka, Francis C.

2009-01-01

23

Export, purification, and activities of affinity tagged Lactobacillus reuteri levansucrase produced by Bacillus megaterium.  

PubMed

Fructosyltransferases, like the Lactobacillus reteri levansucrase, are important for the production of new fructosyloligosaccharides. Various His(6)- and Strep-tagged variants of this enzyme were recombinantly produced and exported into the growth medium using the Gram-positive bacterium Bacillus megaterium. Nutrient-rich growth medium significantly enhanced levansucrase production and export. The B. megaterium signal peptide of the extracellular esterase LipA mediated better levansucrase export compared to the one of the penicillin amidase Pac. The combination of protein export via the LipA signal peptide with the coexpression of the signal peptidase gene sipM further increased the levansucrase secretion. Fused affinity tags allowed the efficient one-step purification of the recombinant proteins from the growth medium. However, fused peptide tags led to slightly decreased secretion of tested fusion proteins. After upscaling 2 to 3 mg affinity tagged levansucrase per liter culture medium was produced and exported. Up to 1 mg of His(6)-tagged and 0.7 mg of Strep-tagged levansucrase per liter were recovered by affinity chromatography. Finally, the purified levansucrase was shown to synthesize new fructosyloligosaccharides from the novel donor substrates D-Gal-Fru, D-Xyl-Fru, D-Man-Fru, and D-Fuc-Fru. PMID:17245578

Biedendieck, Rebekka; Beine, Rafael; Gamer, Martin; Jordan, Eva; Buchholz, Klaus; Seibel, Jürgen; Dijkhuizen, Lubbert; Malten, Marco; Jahn, Dieter

2007-04-01

24

Immobilized metal affinity chromatography of histidine-tagged lentiviral vectors using monolithic adsorbents  

Microsoft Academic Search

Histidine-tagged lentiviral vectors were separated from crude cell culture supernatant using labscale monolithic adsorbents by immobilized metal affinity chromatography. The capture capacity, concentration factor, purification factor, and elution efficiency of a supermacroporous cryogel monolith were evaluated against the BIA Separations convective interaction media (CIM) disc, which is a commercial macroporous monolith. The morphology of the polymeric cryogel material was characterised

M. C. Cheeks; N. Kamal; A. Sorrell; D. Darling; F. Farzaneh; N. K. H. Slater

2009-01-01

25

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

SciTech Connect

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.

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

2009-01-01

26

The variable detergent sensitivity of proteases that are utilized for recombinant protein affinity tag removal.  

PubMed

Recombinant proteins typically include one or more affinity tags to facilitate purification and/or detection. Expression constructs with affinity tags often include an engineered protease site for tag removal. Like other enzymes, the activities of proteases can be affected by buffer conditions. The buffers used for integral membrane proteins contain detergents, which are required to maintain protein solubility. We examined the detergent sensitivity of six commonly-used proteases (enterokinase, factor Xa, human rhinovirus 3C protease, SUMOstar, tobacco etch virus protease, and thrombin) by use of a panel of 94 individual detergents. Thrombin activity was insensitive to the entire panel of detergents, thus suggesting it as the optimal choice for use with membrane proteins. Enterokinase and factor Xa were only affected by a small number of detergents, making them good choices as well. PMID:21539919

Vergis, James M; Wiener, Michael C

2011-08-01

27

SnAvi - a new tandem tag for high-affinity protein-complex purification  

PubMed Central

Systematic tandem-affinity-purification (TAP) of protein complexes was tremendously successful in yeast and has changed the general concept of how we understand protein function in eukaryotic cells. The transfer of this method to other model organisms has been difficult and may require specific adaptations. We were especially interested to establish a cell-type-specific TAP system for Caenorhabditis elegans, a model animal well suited to high-throughput analysis, proteomics and systems biology. By combining the high-affinity interaction between in vivo biotinylated target-proteins and streptavidin with the usage of a newly identified epitope of the publicly shared SB1 monoclonal antibody we created a novel in vivo fluorescent tag, the SnAvi-Tag. We show the versatile application of the SnAvi-Tag in Escherichia coli, vertebrate cells and in C. elegans for tandem affinity purification of protein complexes, western blotting and also for the in vivo sub-cellular localization of labelled proteins. PMID:20047968

Schaffer, Ursula; Schlosser, Andreas; Muller, Kristian M.; Schafer, Angelika; Katava, Nenad; Baumeister, Ralf; Schulze, Ekkehard

2010-01-01

28

A cleavable silica-binding affinity tag for rapid and inexpensive protein purification.  

PubMed

We describe a new affinity purification tag called Car9 that confers proteins to which it is fused micromolar affinity for unmodified silica. When appended to the C-terminus of GFPmut2 through a flexible linker, Car9 promotes efficient adsorption to silica gel and the fusion protein can be released from the particles by incubation with L-lysine. Using a silica gel column and the lysine elution approach in fast protein liquid chromatography (FPLC) mode, Car9-tagged versions of GFPmut2, mCherry and maltose binding protein (MBP) can be recovered from clarified lysates with a purity of 80-90%. Capitalizing on silica's ability to handle large pressure drops, we further show that it is possible to go from cell lysates to purified protein in less than 15?min using a fully disposable device. Finally, we demonstrate that the linker-Car9 region is susceptible to proteolysis by E. coli OmpT and take advantage of this observation to excise the C-terminal extension of GFPmut2-Car9 by incubating purified fusion protein with cells that overproduce the outer membrane protease OmpT. The set of strategies described herein, should reduce the cost of affinity purification by at least 10-fold, cut down purification times to minutes, and allow for the production of proteins with native (or nearly native) termini from their C-terminally-tagged versions. Biotechnol. Bioeng. 2014;111: 2019-2026. © 2014 Wiley Periodicals, Inc. PMID:24777569

Coyle, Brandon L; Baneyx, François

2014-10-01

29

A Bacillus megaterium plasmid system for the production, export, and one-step purification of affinity-tagged heterologous levansucrase from growth medium.  

PubMed

A multiple vector system for the production and export of recombinant affinity-tagged proteins in Bacillus megaterium was developed. Up to 1 mg/liter of a His6-tagged or Strep-tagged Lactobacillus reuteri levansucrase was directed into the growth medium, using the B. megaterium esterase LipA signal peptide, and recovered by one-step affinity chromatography. PMID:16461726

Malten, Marco; Biedendieck, Rebekka; Gamer, Martin; Drews, Ann-Christin; Stammen, Simon; Buchholz, Klaus; Dijkhuizen, Lubbert; Jahn, Dieter

2006-02-01

30

Reprint of: Influence of the protein oligomericity on final yield after affinity tag removal in purification of recombinant proteins.  

PubMed

The new aspect concerning the applicability of histidine and other affinity tags for the purification of oligomeric proteins, with particular emphasis on cleavage efficiency and final yield, is presented in this study. The final yield depends on both the cleavage efficiency and the degree of oligomerization of the protein. Cleavage procedures that are good enough for monomeric proteins can be problematic for oligomeric proteins. Random distribution of uncleaved or partially cleaved affinity tags among oligomers is the main cause of reduced yields. A trimeric protein, tumour necrosis factor alpha (TNF-alpha), bearing different histidine tags, was used as a model protein to explore and confirm this theoretical concept. Analysis of mixed TNF trimers, prepared from tag-free TNF doped with various amounts of histidine-tagged TNF, revealed an increased retention of the trimeric protein on immobilized metal-ion affinity chromatography (IMAC) columns. When 20% of histidine-tagged TNF was added, more than 50% of the protein was retained on the IMAC column. Thus, the applicability of histidine- and other affinity tags for purifying oligomeric proteins is significantly prejudiced in the case of higher oligomers. Various histidine-tags were fused to the N-terminus of full-length TNF-alpha and to the truncated form (dN6) of TNF-alpha. Two-step IMAC separation was used for purification. In the first step, IMAC-1, over 95% purity of histidine-tagged protein was achieved in all cases. Endo- and exoproteolytic removal of histidine tags with enterokinase (EKmax) and aminodipeptidase (DAPase) was studied and the major parameters affecting cleavage efficiency, microheterogeneity and final yield are critically discussed. IMAC-2 was used as the second and final step for removing the cleavage enzyme, cleaved tags, unprocessed protein and some other impurities. Selection of the optimal cleavage enzyme depends on the amino acid composition of the N-terminus and the intended use of the purified protein. The main conclusion is that special caution should be taken when introducing affinity tags to oligomeric proteins, with the final goal to produce pure, tag-free protein with acceptable yields. Given the same enzyme cleavage efficiency one can expect progressively reduced final protein yields with increasing degree of oligomerization. This should be considered as a general rule. PMID:21893202

Kenig, Maja; Peternel, Spela; Gaberc-Porekar, Vladka; Menart, Viktor

2011-09-01

31

Cancer cell sensing and therapy using affinity tag-conjugated gold nanorods  

PubMed Central

Through the developments in controlling the shape of gold nanoparticles, synthesis of gold nanorods (AuNRs) can be considered as a milestone discovery in the area of nanomaterial-based cancer treatments. Besides having tuneable absorption maxima at near infrared (NIR) range, AuNRs have superior absorption cross section at NIR frequencies compared with other gold nanoparticles. When this unique optical property is combined with the specificity against cancer cells used by affinity tag conjugations, AuNRs become one of the most important nanoparticles used in both cancer cell sensing and in therapy. In this review, the impact of size and shape control of nanoparticles, especially AuNRs, on cancer cell treatments and a range of aptamer-conjugated AuNR applications in this regard are reviewed. PMID:24427543

Yasun, Emir; Kang, Huaizhi; Erdal, Huseyin; Cansiz, Sena; Ocsoy, Ismail; Huang, Yu-Fen; Tan, Weihong

2013-01-01

32

Immobilized palladium(II) ion affinity chromatography for recovery of recombinant proteins with peptide tags containing histidine and cysteine.  

PubMed

Fusion of peptide-based tags to recombinant proteins is currently one of the most used tools for protein production. Also, immobilized metal ion affinity chromatography (IMAC) has a huge application in protein purification, especially in research labs. The combination of expression systems of recombinant tagged proteins with this robust chromatographic system has become an efficient and rapid tool to produce milligram-range amounts of proteins. IMAC-Ni(II) columns have become the natural partners of 6xHis-tagged proteins. The Ni(II) ion is considered as the best compromise of selectivity and affinity for purification of a recombinant His-tagged protein. The palladium(II) ion is also able to bind to side chains of amino acids and form ternary complexes with iminodiacetic acid and free amino acids and other sulfur-containing molecules. In this work, we evaluated two different cysteine- and histidine-containing six amino acid tags linked to the N-terminal group of green fluorescent protein (GFP) and studied the adsorption and elution conditions using novel eluents. Both cysteine-containing tagged GFPs were able to bind to IMAC-Pd(II) matrices and eluted successfully using a low concentration of thiourea solution. The IMAC-Ni(II) system reaches less than 20% recovery of the cysteine-containing tagged GFP from a crude homogenate of recombinant Escherichia coli, meanwhile the IMAC-Pd(II) yields a recovery of 45% with a purification factor of 13. Copyright © 2014 John Wiley & Sons, Ltd. PMID:25277090

Kikot, Pamela; Polat, Aise; Achilli, Estefania; Fernandez Lahore, Marcelo; Grasselli, Mariano

2014-11-01

33

Affinity-based isolation of tagged nuclei from Drosophila tissues for gene expression analysis.  

PubMed

Drosophila melanogaster embryonic and larval tissues often contain a highly heterogeneous mixture of cell types, which can complicate the analysis of gene expression in these tissues. Thus, to analyze cell-specific gene expression profiles from Drosophila tissues, it may be necessary to isolate specific cell types with high purity and at sufficient yields for downstream applications such as transcriptional profiling and chromatin immunoprecipitation. However, the irregular cellular morphology in tissues such as the central nervous system, coupled with the rare population of specific cell types in these tissues, can pose challenges for traditional methods of cell isolation such as laser microdissection and fluorescence-activated cell sorting (FACS). Here, an alternative approach to characterizing cell-specific gene expression profiles using affinity-based isolation of tagged nuclei, rather than whole cells, is described. Nuclei in the specific cell type of interest are genetically labeled with a nuclear envelope-localized EGFP tag using the Gal4/UAS binary expression system. These EGFP-tagged nuclei can be isolated using antibodies against GFP that are coupled to magnetic beads. The approach described in this protocol enables consistent isolation of nuclei from specific cell types in the Drosophila larval central nervous system at high purity and at sufficient levels for expression analysis, even when these cell types comprise less than 2% of the total cell population in the tissue. This approach can be used to isolate nuclei from a wide variety of Drosophila embryonic and larval cell types using specific Gal4 drivers, and may be useful for isolating nuclei from cell types that are not suitable for FACS or laser microdissection. PMID:24686501

Ma, Jingqun; Weake, Vikki Marie

2014-01-01

34

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

SciTech Connect

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-encoding strategies for bait protein expression. This approach has the potential for enabling discovery of protein-protein interactions among the growing number of sequenced microbial species without the need for development of chromosomal insertion systems.

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

35

A Method for the Rapid and Efficient Elution of Native Affinity-Purified Protein A Tagged Complexes  

E-print Network

A Method for the Rapid and Efficient Elution of Native Affinity-Purified Protein A Tagged Complexes and protein complexes from IgG-Sepharose. We show that Bio-Ox elution is a robust method for the efficient or in complexes with its in vivo binding partners.4-6 The yield of these purifica- tion methods is often high

Chait, Brian T.

36

Description T7Tag Affinity Purification KIt 69025-3 The T7Tag Affinity Purification Kit is designed for rapid immunoaffinity purification of  

E-print Network

monoclonal anti- body which is covalently coupled to cross-linked agarose beads, washing away unbound, but the beads are standardized to bind a minimum of 300µg T7·Tag -galactosidase per ml of settled resin. The beads can be used in either batch or col- umn modes and can be recycled a minimum of five times without

Lebendiker, Mario

37

Bidirectional immobilization of affinity-tagged cytochrome c on electrode surfaces.  

PubMed

Here, we report a new strategy for the directed bivalent immobilization of cyt c on or between gold electrodes. C-terminal modification with cys- or his-tag did not affect the functional integrity of the protein. In combination with electrostatic protein binding, these tags enable a bifunctional immobilization between two electrodes or alternatively one electrode and interacting enzymes. PMID:20563352

Schröper, Florian; Baumann, Arnd; Offenhäusser, Andreas; Mayer, Dirk

2010-08-01

38

Microarrays based on affinity-tagged single-chain Fv antibodies: sensitive detection of analyte in complex proteomes.  

PubMed

Protein-based microarrays are among the novel class of rapidly emerging proteomic technologies that will allow us to efficiently perform global proteome analysis. However, the process of designing adequate protein microarrays is a major inherent problem. In this study, we have evaluated a protein microarray platform based on nonpurified affinity-tagged single-chain (sc) Fv antibody fragments to generate proof-of-principle and to demonstrate the specificity and sensitivity of the array design. To this end, we used our human recombinant scFv antibody library genetically constructed around one framework, the n-CoDeR library containing 2 x 10(10) clones, as a source for our probes. The probes were immobilized via engineered C-terminal affinity tags, his- or myc-tags, to either Ni(2+)-coated slides or anti-tag antibody coated substrates. The results showed that highly functional microarrays were generated and that nonpurified scFvs readily could be applied as probes. Specific and sensitive microarrays were obtained, providing a limit of detection in the pM to fM range, using fluorescence as the mode of detection. Further, the results showed that spotting the analyte on top of the arrayed probes, instead of incubating the array with large sample volumes (333 pL vs. 40 microL), could reduce the amount of analyte required 4000 times, from 1200 attomole to 300 zeptomole. Finally, we showed that a highly complex proteome, such as human sera containing several thousand different proteins, could be directly fluorescently labeled and successfully analyzed without compromising the specificity and sensitivity of the antibody microarrays. This is a prerequisite for the design of high-density antibody arrays applied in high-throughput proteomics. PMID:15732136

Wingren, Christer; Steinhauer, Cornelia; Ingvarsson, Johan; Persson, Erik; Larsson, Katrin; Borrebaeck, Carl A K

2005-04-01

39

Journal of Chromatography B, 715 (1998) 8591 Genetic engineering of streptavidin, a versatile affinity tag  

E-print Network

and molecules of a small water-soluble vitamin, D-biotin their ligands. Streptavidin is also one of the most. The efficacy of streptavidin is derived from its extremely high binding affinity for the vitamin biotin (vitamin H), with a remarkably high affinity [3,4]. stable proteins known. For example, it can maintain its

Vajda, Sandor

40

Affinity-based SDS PAGE identification of phosphorylated Arabidopsis MAPKs and substrates by acrylamide pendant Phos-Tag™.  

PubMed

Protein phosphorylation is the most abundant and best studied protein posttranslational modification, dedicated to the regulation of protein function and subcellular localization as well as to protein-protein interactions. Identification and quantitation of the dynamic, conditional protein phosphorylation can be achieved by either metabolic labeling of the protein of interest with (32)P-labeled ATP followed by autoradiographic analysis, the use of specific monoclonal or polyclonal antibodies against the phosphorylated protein species and finally by phosphoproteome delineation using mass spectrometry.Hereby we present a fourth alternative which relies on the enforced-affinity-based-electrophoretic separation of phosphorylated from non-phosphorylated protein species by standard SDS-PAGE systems co-polymerized with Phos-Tag™ and Mn(2+) or Zn(2+) cations. Phosphate groups of phosphorylated Ser, Thr, and Tyr residues form complexes with Mn(2+) and Zn(2+) cations with polyacrylamide immobilized Phos-Tag™. Following appropriate treatment of the gels, separated proteins can be quantitatively transferred to PVDF or nitrocellulose membranes and probed with common-not phosphorylation state specific-antibodies and delineate the occurrence of a certain phosphoprotein species against its non-phosphorylated counterpart. PMID:24908119

Komis, George; Taká?, Tomáš; Bekešová, Slávka; Vadovi?, Pavol; Samaj, Jozef

2014-01-01

41

Qualitative and quantitative proteomics by two-dimensional gel electrophoresis, peptide mass fingerprint and a chemically-coded affinity tag (CCAT)  

Microsoft Academic Search

The chemically-coded affinity tag (CCAT) method combines standard electrophoresis protocols with MALDI-TOF-MS analysis to identify and quantify protein abundances in complex samples in one step. This method is designed to fit into the workflow of SDS-PAGE or two-dimensional electrophoresis (2-DE) only requiring basic proteome laboratory equipment. Prior to electrophoresis two protein samples are separately labelled with a heavy or a

Steven Alexander Watt; Thomas Patschkowski; Jörn Kalinowski; Karsten Niehaus

2003-01-01

42

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

PubMed

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. PMID:22926644

Li, Junhua; Zhang, Yang; Yang, Yanjun

2013-03-01

43

Enzyme-linked immunosorbent assay-based selection and optimization of elution buffer for TAG72-affinity chromatography  

Microsoft Academic Search

An enzyme-linked immunosorbent assay (ELISA)-elution assay was developed to screen a large variety of elution buffers for selection of a suitable one for purification of the fusion protein FV\\/TNF-? by affinity chromatography. Various commonly used buffer systems utilizing widely differing conditions such as extreme pH, denaturants, chaotropic ions and polarity reducing reagents were investigated. Ammonia solution (1 M, pH 11.5)

Junbao Yang; Terence Moyana; Jim Xiang

1999-01-01

44

Specific and Reversible Immobilization of Proteins Tagged to the Affinity Polypeptide C-LytA on Functionalized Graphite Electrodes  

PubMed Central

We have developed a general method for the specific and reversible immobilization of proteins fused to the choline-binding module C-LytA on functionalized graphite electrodes. Graphite electrode surfaces were modified by diazonium chemistry to introduce carboxylic groups that were subsequently used to anchor mixed self-assembled monolayers consisting of N,N-diethylethylenediamine groups, acting as choline analogs, and ethanolamine groups as spacers. The ability of the prepared electrodes to specifically bind C-LytA-tagged recombinant proteins was tested with a C-LytA-?-galactosidase fusion protein. The binding, activity and stability of the immobilized protein was evaluated by electrochemically monitoring the formation of an electroactive product in the enzymatic hydrolysis of the synthetic substrate 4-aminophenyl ?-D-galactopyranoside. The hybrid protein was immobilized in an specific and reversible way, while retaining the catalytic activity. Moreover, these functionalized electrodes were shown to be highly stable and reusable. The method developed here can be envisaged as a general, immobilization procedure on the protein biosensor field. PMID:24498237

Bello-Gil, Daniel; Maestro, Beatriz; Fonseca, Jennifer; Feliu, Juan M.; Climent, Victor; Sanz, Jesus M.

2014-01-01

45

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

PubMed

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. PMID:24768124

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

2014-05-30

46

Qualitative and quantitative proteomics by two-dimensional gel electrophoresis, peptide mass fingerprint and a chemically-coded affinity tag (CCAT).  

PubMed

The chemically-coded affinity tag (CCAT) method combines standard electrophoresis protocols with MALDI-TOF-MS analysis to identify and quantify protein abundances in complex samples in one step. This method is designed to fit into the workflow of SDS-PAGE or two-dimensional electrophoresis (2-DE) only requiring basic proteome laboratory equipment. Prior to electrophoresis two protein samples are separately labelled with a heavy or a light version of the CCAT reagent via reduced cysteines in the proteins. Equal amounts are then combined and electrophoretically separated. Proteins can then be excised from the gel to obtain their peptide mass fingerprint by mass spectrometry. This fingerprint enabled not only identification, but also quantification by comparing relative peak intensities of CCAT-labelled peptides. In this article, we display how the CCAT method can be used to analyse two protein samples in one gel and that the peak intensities of labelled peptides reflect the abundance of a protein in it. PMID:14651868

Watt, Steven Alexander; Patschkowski, Thomas; Kalinowski, Jörn; Niehaus, Karsten

2003-12-19

47

Observed octameric assembly of a Plasmodium yoelii peroxiredoxin can be explained by the replacement of native "ball-and-socket" interacting residues by an affinity tag.  

PubMed

Peroxiredoxins (Prxs) are ubiquitous and efficient antioxidant enzymes crucial for redox homeostasis in most organisms, and are of special importance for disease-causing parasites that must protect themselves against the oxidative weapons of the human immune system. Here, we describe reanalyses of crystal structures of two Prxs from malaria parasites. In addition to producing improved structures, we provide normalizing explanations for features that had been noted as unusual in the original report of these structures (Qiu et al., BMC Struct Biol 2012;12:2). Most importantly, we provide evidence that the unusual octameric assembly seen for Plasmodium yoelii Prx1a is not physiologically relevant, but arises because the structure is not of authentic P. yoelii Prx1a, but a variant we designate PyPrx1a(N*) that has seven native N-terminal residues replaced by an affinity tag. This N-terminal modification disrupts a previously unrecognized, hydrophobic "ball-and-socket" interaction conserved at the B-type dimer interface of Prx1 subfamily enzymes, and is accommodated by a fascinating two-residue "?-slip" type register shift in the ?-strand association at a dimer interface. The resulting change in the geometry of the dimer provides a simple explanation for octamer formation. This study illustrates how substantive impacts can occur in protein variants in which native residues have been altered. PMID:23934758

Gretes, Michael C; Karplus, P Andrew

2013-10-01

48

Observed octameric assembly of a Plasmodium yoelii peroxiredoxin can be explained by the replacement of native "ball-and-socket" interacting residues by an affinity tag  

PubMed Central

Peroxiredoxins (Prxs) are ubiquitous and efficient antioxidant enzymes crucial for redox homeostasis in most organisms, and are of special importance for disease-causing parasites that must protect themselves against the oxidative weapons of the human immune system. Here, we describe reanalyses of crystal structures of two Prxs from malaria parasites. In addition to producing improved structures, we provide normalizing explanations for features that had been noted as unusual in the original report of these structures (Qiu et al., BMC Struct Biol 2012;12:2). Most importantly, we provide evidence that the unusual octameric assembly seen for Plasmodium yoelii Prx1a is not physiologically relevant, but arises because the structure is not of authentic P. yoelii Prx1a, but a variant we designate PyPrx1aN* that has seven native N-terminal residues replaced by an affinity tag. This N-terminal modification disrupts a previously unrecognized, hydrophobic “ball-and-socket” interaction conserved at the B-type dimer interface of Prx1 subfamily enzymes, and is accommodated by a fascinating two-residue “?-slip” type register shift in the ?-strand association at a dimer interface. The resulting change in the geometry of the dimer provides a simple explanation for octamer formation. This study illustrates how substantive impacts can occur in protein variants in which native residues have been altered. PMID:23934758

Gretes, Michael C; Karplus, P Andrew

2013-01-01

49

Metal Affinity Chromatography (MAC)  

E-print Network

Fractogel® Metal Affinity Chromatography (MAC) Resins and Cartridges Tools for His·Tag® Fusion-MACTM Cartridges #12;2 Novagen · Fractogel Metal Affinity Chromatography (MAC) Resins Ni-MACTM , Co-MACTM and u-MACTM Metal Affinity Chromatography (MAC) Resins and Cartridges HI Ni2+ Ni2+ Ni2+ HISHISHI SHISHISHIS Ni2

Lebendiker, Mario

50

Affinity partitioning of a poly(histidine)-tagged integral membrane protein, cytochrome bo3 ubiquinol oxidase, in a detergent--polymer aqueous two-phase system containing metal-chelating polymer.  

PubMed

A system has been developed for selective partitioning of membrane proteins. For the first time, an integral membrane protein, cytochrome bo3 ubiquinol oxidase from Escherichia coli, has been affinity partitioned in an aqueous two-phase system. The systems used were different detergent/polymer aqueous two-phase systems containing a metal-chelating polymer, such as poly(ethyleneglycol)-iminodiacetic acid-Cu(II) as well as dextran-iminodiacetic acid-Cu(II). Many non-ionic detergents, such as alkyl(polyethyleneoxide) (CmEOn), Triton, Tween and alkylglucosides, form two-phase systems in mixture with polymers, such as dextran and poly(ethyleneglycol), i.e., a micelle-enriched phase in equilibrium with a polymer-enriched phase are formed. In general, membrane proteins partition strongly to the micelle phase. We show that it is possible to selectively partition a poly(histidine)-tagged integral membrane protein into the polymer phase by metal affinity partitioning, with a shift in the partitioning coefficient from 0.015 to 4.8 (300-fold). The affinity partitioning was characterized and the effects of ligand concentration, pH, time, salts, buffer type, imidazole and charged detergent are discussed. Thus, a fast and mild affinity procedure for the purification of integral membrane proteins can be developed in affinity detergent/polymer aqueous two-phase systems, and the method is especially suitable for the purification of labile integral membrane proteins, such as receptors. PMID:10942301

Sivars, U; Abramson, J; Iwata, S; Tjerneld, F

2000-06-23

51

Metallophore mapping in complex matrices by metal isotope coded profiling of organic ligands.  

PubMed

Metal isotope coded profiling (MICP) introduces a universal discovery platform for metal chelating natural products that act as metallophores, ion buffers or sequestering agents. The detection of cation and oxoanion complexing ligands is facilitated by the identification of unique isotopic signatures created by the application of isotopically pure metals. PMID:25298978

Deicke, Michael; Mohr, Jan Frieder; Bellenger, Jean-Philippe; Wichard, Thomas

2014-12-01

52

Yolk-Shell Nanostructured Fe3O4@NiSiO3 for Selective Affinity and Magnetic Separation of His-Tagged Proteins.  

PubMed

Recent developments of nanotechnology encourage novel materials for facile separations and purifications of recombinant proteins, which are of great importance in disease diagnoses and treatments. We find that Fe3O4@NiSiO3 with yolk-shell nanostructure can be used to specifically purify histidine-tagged (His-tagged) proteins from mixtures of lysed cells with a recyclable process. Each individual nanoparticle composes by a mesoporous nickel silicate shell and a magnetic Fe3O4 core in the hollow inner, which is featured by its great loading efficiency and rapid response toward magnetic fields. The abundant Ni(2+) cations on the shell provide docking sites for selective coordination of histidine and the reversible release is induced by excess imidazole solution. Because of the Fe3O4 cores, the separation, concentration, and recycling of the nanocomposites become feasible under the controls of magnets. These characteristics would be highly beneficial in nanoparticle-based biomedical applications for targeted-drug delivery and biosensors. PMID:25303145

Wang, Yang; Wang, Guangchuan; Xiao, Yun; Yang, Yuling; Tang, Ruikang

2014-11-12

53

NLS-tagging: an alternative strategy to tag nuclear proteins.  

PubMed

The characterization of transcription factor complexes and their binding sites in the genome by affinity purification has yielded tremendous new insights into how genes are regulated. The affinity purification requires either the use of antibodies raised against the factor of interest itself or by high-affinity binding of a C- or N-terminally added tag sequence to the factor. Unfortunately, fusing extra amino acids to the termini of a factor can interfere with its biological function or the tag may be inaccessible inside the protein. Here, we describe an effective solution to that problem by integrating the 'tag' close to the nuclear localization sequence domain of the factor. We demonstrate the effectiveness of this approach with the transcription factors Fli-1 and Irf2bp2, which cannot be tagged at their extremities without loss of function. This resulted in the identification of novel proteins partners and a new hypothesis on the contribution of Fli-1 to hematopoiesis. PMID:25260593

Giraud, Guillaume; Stadhouders, Ralph; Conidi, Andrea; Dekkers, Dick H W; Huylebroeck, Danny; Demmers, Jeroen A A; Soler, Eric; Grosveld, Frank G

2014-12-01

54

Evaluation of IDA-PEVA hollow fiber membrane metal ion affinity chromatography for purification of a histidine-tagged human proinsulin.  

PubMed

Inabilities to process particulate material and to allow the use of high flow rates are limitations of conventional chromatography. Membranes have been suggested as matrix for affinity separation due to advantages such as allowing high flow rates and low-pressure drops. This work evaluated the feasibility of using an iminodiacetic acid linked poly(ethylenevinyl alcohol) membrane in the immobilized metal ion affinity chromatography (IMAC) purification of a human proinsulin(His)(6) of an industrial insulin production process. The screening of metal ions showed Ni(2+) as metal with higher selectivity and capacity among the Cu(2+), Ni(2+), Zn(2+) and Co(2+). The membrane showed to be equivalent to conventional chelating beads in terms of selectivity and had a lower capacity (3.68 mg/g versus 12.26 mg/g). The dynamic adsorption capacity for human proinsulin(His)(6) was unaffected by the mode of operation (dead-end and cross-flow filtration). PMID:16531127

de Aquino, Luciana Cristina Lins; de Sousa, Heloisa Ribeiro Tunes; Miranda, Everson Alves; Vilela, Luciano; Bueno, Sônia Maria Alves

2006-04-13

55

Targeted purification of SnAvi-tagged proteins.  

PubMed

Tandem affinity purification (TAP) is a powerful technique to identify protein complex members. The modular composition of TAP-tags allows two sequential protein enrichment steps and thereby drastically reduces the amount of contaminants. Here, we describe the application of the SnAvi-tag-a TAP-tag useful in different expression systems. Due to its modular composition, this tag is multifunctional and facilitates among others the in vivo visualization of tagged proteins and their cell type specific activation. PMID:24943322

Schäffer, Ursula; Baumeister, Ralf; Schulze, Ekkehard

2014-01-01

56

Quantitative Proteomics Employing Primary Amine Affinity Tags  

PubMed Central

A proteomics-based method using stable isotope labeling to assess the relative abundance of peptides or proteins is described. Bradykinin and carbonic anhydrase were labeled with sulfosuccinimidyl-2-(biotinamido) ethyl-1,3-dithiopropionate, a membrane impermeant reagent that is reactive with primary amines. Specificity of the label to primary amines was demonstrated using tandem mass spectrometry. Also, relative quantitation was achieved by secondary labeling with natural isotopic abundance and stable isotope-labeled methyl iodide. We believe this to be an effective stable isotope-labeling method for quantitative proteomics. PMID:13678152

Hoang, Van M.; Conrads, Thomas P.; Veenstra, Timothy D.; Blonder, Josip; Terunuma, Atsushi; Vogel, Jonathan C.; Fisher, Robert J.

2003-01-01

57

Developing new isotope-coded mass spectrometry-cleavable cross-linkers for elucidating protein structures.  

PubMed

Structural characterization of protein complexes is essential for the understanding of their function and regulation. However, it remains challenging due to limitations in existing tools. With recent technological improvements, cross-linking mass spectrometry (XL-MS) has become a powerful strategy to define protein-protein interactions and elucidate structural topologies of protein complexes. To further advance XL-MS studies, we present here the development of new isotope-coded MS-cleavable homobifunctional cross-linkers: d0- and d10-labeled dimethyl disuccinimidyl sulfoxide (DMDSSO). Detailed characterization of DMDSSO cross-linked peptides further demonstrates that sulfoxide-containing MS-cleavable cross-linkers offer robust and predictable MS2 fragmentation of cross-linked peptides, permitting subsequent MS3 analysis for simplified, unambiguous identification. Concurrent usage of these reagents provides a characteristic doublet pattern of DMDSSO cross-linked peptides, thus aiding in the confidence of cross-link identification by MS(n) analysis. More importantly, the unique isotopic profile permits quantitative analysis of cross-linked peptides and therefore expands the capability of XL-MS strategies to analyze both static and dynamic protein interactions. Together, our work has established a new XL-MS workflow for future studies toward the understanding of structural dynamics of protein complexes. PMID:24471733

Yu, Clinton; Kandur, Wynne; Kao, Athit; Rychnovsky, Scott; Huang, Lan

2014-02-18

58

Affinity Chromatography  

NSDL National Science Digital Library

This is an experiment showing the application of affinity chromatography to the separation of albumin from horse serum. A brief introduction of affinity chromatography and how it is being used in this specific experiment is given. This appears to be a good experiment to show the advantages of affinity chromatography in separating specific proteins from a complex matrix and would be useful in a biochemistry course or a course that is specifically looking at differing types of chromatography.

Diresta, Dan

2011-05-23

59

tagging, communities, vocabulary, evolution  

Microsoft Academic Search

A tagging community's vocabulary of tags forms the basis for social navigation and shared expression. We present a user-centric model of vocabulary evolution in tagging com- munities based on community influence and personal ten- dency. We evaluate our model in an emergent tagging sys- tem by introducing tagging features into the MovieLens rec- ommender system. We explore four tag selection

Shilad Sen; Shyong K. Lam; Al Mamunur Rashid; Dan Cosley; Dan Frankowski; Jeremy Osterhouse; F. Maxwell Harper; John Riedl

2006-01-01

60

Germ Tag  

NSDL National Science Digital Library

In this version of tag, a large group of learners model how the body fights infection. Learners act as germs, as lymphocytes, and as the body's cells threatened by germs. After playing one round, subsequent rounds can use different numbers of germs and/or lymphocytes to see how the infection rate is changed. When learners set up a free account at Kinetic City, they can answer bonus questions at the end of the activity as a quick assessment. They can also keep track of their progress in all of the Kinetic City activities, and compare their progress to other participants worldwide.

Science, American A.

2009-01-01

61

Shark Tagging Activities.  

ERIC Educational Resources Information Center

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…

Current: The Journal of Marine Education, 1998

1998-01-01

62

Identification of Candidate Angiogenic Inhibitors Processed by Matrix Metalloproteinase 2 (MMP-2) in Cell-Based Proteomic Screens: Disruption of Vascular Endothelial Growth Factor (VEGF)/Heparin Affin Regulatory Peptide (Pleiotrophin) and VEGF/Connective Tissue Growth Factor Angiogenic Inhibitory Complexes by MMP-2 Proteolysis? †  

PubMed Central

Matrix metalloproteinases (MMPs) exert both pro- and antiangiogenic functions by the release of cytokines or proteolytically generated angiogenic inhibitors from extracellular matrix and basement membrane remodeling. In the Mmp2?/? mouse neovascularization is greatly reduced, but the mechanistic aspects of this remain unclear. Using isotope-coded affinity tag labeling of proteins analyzed by multidimensional liquid chromatography and tandem mass spectrometry we explored proteome differences between Mmp2?/? cells and those rescued by MMP-2 transfection. Proteome signatures that are hallmarks of proteolysis revealed cleavage of many known MMP-2 substrates in the cellular context. Proteomic evidence of MMP-2 processing of novel substrates was found. Insulin-like growth factor binding protein 6, follistatin-like 1, and cystatin C protein cleavage by MMP-2 was biochemically confirmed, and the cleavage sites in heparin affin regulatory peptide (HARP; pleiotrophin) and connective tissue growth factor (CTGF) were sequenced by matrix-assisted laser desorption ionization-time of flight mass spectrometry. MMP-2 processing of HARP and CTGF released vascular endothelial growth factor (VEGF) from angiogenic inhibitory complexes. The cleaved HARP N-terminal domain increased HARP-induced cell proliferation, whereas the HARP C-terminal domain was antagonistic and decreased cell proliferation and migration. Hence the unmasking of cytokines, such as VEGF, by metalloproteinase processing of their binding proteins is a new mechanism in the control of cytokine activation and angiogenesis. PMID:17908800

Dean, Richard A.; Butler, Georgina S.; Hamma-Kourbali, Yamina; Delbé, Jean; Brigstock, David R.; Courty, José; Overall, Christopher M.

2007-01-01

63

Isotope-coded carbamidomethylation for quantification of N-glycoproteins with online microbore hollow fiber enzyme reactor-nanoflow liquid chromatography-tandem mass spectrometry.  

PubMed

This paper introduces a simple, inexpensive, and robust quantitative proteomic method for quantifying N-linked glycoproteins based on isotope-coded carbamidomethylation (iCCM) incorporated into an online microbore hollow fiber enzyme reactor and nanoflow liquid chromatography-tandem mass spectrometry (mHFER-nLC-MS/MS). The iCCM quantitation uses carbamidomethylation (CM; a routine protection of thiol groups before proteolysis) of the Cys residue of proteins with iodoacetamide (IAA) or its isotope (IAA-(13)C2,D2: 4 Da difference). CM-/iCCM-labeled proteome samples are mixed for proteolysis; then, online enrichment of N-glycopeptides using lectin affinity is carried out in an mHFER before nLC-MS/MS for quantification using multiple reaction monitoring (MRM). Initial evaluation of the iCCM method varying the mixing ratio of CM-/iCCM-labeled bovine serum albumin (BSA) standards yielded successful quantification of 18 peptides with less than 2% variation in the calculated ratio of light/heavy-labeled peptides. The iCCM quantitation with mHFER-nLC-MS/MS was evaluated with three standard glycoproteins (?-1-acid glycoproteins, fetuin and transferrin) and then applied to serum glycoproteins from liver cancer patients and controls, resulting in successful quantification of 73 N-glycopeptides (from 49 N-glycoproteins), among which 19 N-glycopeptides from 14 N-glycoproteins showed more than a 2.5-fold aberrant change in liver cancer patients' sera compared with the pooled control. Although iCCM quantitation with mHFER-nLC-MS/MS applies only to glycopeptides with Cys residue, the method can offer several advantages over other labeling methods when applied to targeted glycoproteins: The iCCM method does not require an additional labeling reaction under special conditions nor complicated procedures to purify labeled products using additional columns. Isotope labeling at the protein level can minimize potential uncertainty originating from unequal efficiencies in protein digestion in separate vials and retrieval of each labeled peptide when labeling takes place at the peptide level. In addition, the labeling reagents for the iCCM method are readily obtained at a reasonable cost, which can make protein quantification easily accessible. PMID:24960276

Kim, Jin Yong; Oh, Donggeun; Kim, Sook-Kyung; Kang, Dukjin; Moon, Myeong Hee

2014-08-01

64

Conversational tagging in twitter  

Microsoft Academic Search

Users on Twitter, a microblogging service, started the phenomenon of adding tags to their messages sometime around February 2008. These tags are distinct from those in other Web 2.0 systems because users are less likely to index messages for later retrieval. We compare tagging patterns in Twitter with those in Delicious to show that tagging behavior in Twitter is different

Jeff Huang; Katherine M. Thornton; Efthimis N. Efthimiadis

2010-01-01

65

Tag switching architecture overview  

Microsoft Academic Search

Tag switching is a way to combine the label-swapping forwarding paradigm with network-layer routing with particular application to the Internet. This has several advantages. Tags can have a wide spectrum of forwarding granularities, so at one end of the spectrum a tag could be associated with a group of destinations, while at the other end, a tag could be associated

YAKOV REKHTER; BRUCE DAVIE; ERIC ROSEN; GEORGE SWALLOW; DINO FARINACCI; DAVE KATZ

1997-01-01

66

Multipurpose peptide tags for protein isolation.  

PubMed

A multifunctional peptide tag (HYDHYD) consisting of histidine, tyrosine and aspartate residues was fused to the N-terminal ends of green fluorescent protein (GFP), lactate dehydrogenase (LDH) and human hemoglobin (Hb), proteins which were subjected to ion-exchange chromatography (IEC), aqueous two-phase system partition, immobilized metal-ion affinity chromatography (IMAC), and hydrophobic interaction chromatography (HIC). Tagged GFP was retained significantly longer (>1 column volume) in both HIC and IEC. It exhibited 3x greater partition in favor of the hydrophobic phase in a two-phase system and 96% could be bound to an IMAC column which did not bind native GFP. PMID:18635190

Becker, Kristian; Van Alstine, James; Bülow, Leif

2008-08-15

67

A novel affinity gene fusion system allowing protein A-based recovery of non-immunoglobulin gene products  

Microsoft Academic Search

An expression vector system has been developed, taking advantage of a novel, Staphylococcus aureus protein A (SPA)-binding affinity tag ZSPA-1, enabling straightforward affinity blotting procedures and efficient recovery by affinity purification of expressed gene products on readily available reagents and chromatography media. The 58 amino acid SPA-binding affinity tag ZSPA-1, was previously selected from a library constructed by combinatorial mutagenesis

Susanne Gräslund; Malin Eklund; Ronny Falk; Mathias Uhlén; Per-Åke Nygren; Stefan Ståhl

2002-01-01

68

Donor Tag Game  

MedlinePLUS

... Games > Donor Tag Game Printable Version Donor Tag Game This feature requires version 6 or later of ... Needles Blood Donor Community Donor Stories Recipient Stories Games Facebook Fanbox Avatars and Badges Banners eCards Enter ...

69

Protein structure modeling indicates hexahistidine-tag interference with enzyme activity.  

PubMed

Unusual kinetic characteristics of tropinone reductase, an enzyme in the family of short chain dehydrogenases, prompted to investigate a possible impact of the hexahistidine affinity tag on catalytic properties. Comparison of enzymes from Solanum dulcamara, Solanaceae, tagged at the N-terminus or at the C-terminus revealed that the C-terminally tagged form was functionally impaired. Protein modeling indicated that the hexahistidine tag attached at the C-terminus but not at the N-terminus of the polypeptide can interfere with the active site by steric or electrostatic interactions. In consequence, protein modeling is suggested before enzyme expression with affinity tags to estimate possible interactions of affinity tags with the active center. PMID:18214963

Freydank, Anna-Carolin; Brandt, Wolfgang; Dräger, Birgit

2008-07-01

70

RFID Tag Ownership Transfer  

Microsoft Academic Search

In some applications, the bearer of a radio frequency identi- fication (RFID) tag might change, with corresponding changes required in the RFID system infrastructure. We survey the security requirements for RFID tag ownership transfer, and propose novel authentication pro- tocols for tag ownership and authorisation transfer. The proposed proto- cols satisfy most of the requirements that we present, and have

Boyeon Song

71

Extracting Tag Hierarchies  

PubMed Central

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 between the tags. The encouraging similarity between the pre-defined and reconstructed hierarchy, as well as the seemingly meaningful hierarchies obtained for other real systems indicate that tag hierarchy extraction is a very promising direction for further research with a great potential for practical applications. Tags have become very prevalent nowadays in various online platforms ranging from blogs through scientific publications to protein databases. Furthermore, tagging systems dedicated for voluntary tagging of photos, films, books, etc. with free words are also becoming popular. The emerging large collections of tags associated with different objects are often referred to as folksonomies, highlighting their collaborative origin and the “flat” organization of the tags opposed to traditional hierarchical categorization. Adding a tag hierarchy corresponding to a given folksonomy can very effectively help narrowing or broadening the scope of search. Moreover, recommendation systems could also benefit from a tag hierarchy. PMID:24391901

Tibely, Gergely; Pollner, Peter; Vicsek, Tamas; Palla, Gergely

2013-01-01

72

Improved -Elimination-Based Affinity Purification Strategy for Enrichment of Phosphopeptides  

E-print Network

Improved -Elimination-Based Affinity Purification Strategy for Enrichment of Phosphopeptides Derek followed by addition of an affinity tag has recently been pursued as a strategy for enriching for affinity purification via disulfide exchange with an activated thiol resin and the develop- ment

Chait, Brian T.

73

Extracting tag hierarchies  

E-print Network

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...

Tibély, Gergely; Vicsek, Tamás; Palla, Gergely

2014-01-01

74

Tandem affinity purification vectors for use in gram positive bacteria.  

PubMed

Tandem affinity purification has become a valuable tool for the isolation of protein complexes. Here we describe the construction and use of a series of plasmid vectors for Gram positive bacteria. The vectors utilize the SPA tag as well as variants containing a 3C rather than the TEV protease site as 3C protease has been shown to work efficiently at the low temperatures (4 degrees C) used to isolate protein complexes. In addition, a further vector incorporates a GST moiety in place of the 3xFLAG of the SPA tag which provides an additional tagging option for situations where SPA binding may be inefficient. The vectors are all compatible with previously constructed fluorescent protein fusion vectors enabling construction of a suite of affinity and fluorescently tagged genes using a single PCR product. PMID:18093654

Yang, Xiao; Doherty, Geoff P; Lewis, Peter J

2008-01-01

75

Personalization of tagging systems  

Microsoft Academic Search

Social media systems have encouraged end user participation in the Inter- net, 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 re- trieval of otherwise uncategorised data. However, compared to professional web content production, collaborative tagging systems face the challenge that end-users

Jun Wang; Maarten Clements; Jie Yang; Arjen P. De Vries; Marcel J. T. Reinders

2010-01-01

76

New Tags for Recombinant Protein Detection and O-Glycosylation Reporters  

PubMed Central

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. PMID:24802141

Arnoldi, Francesca; Burrone, Oscar R.

2014-01-01

77

Affinity Propagation Brendan Frey  

E-print Network

Affinity Propagation Brendan Frey University of Toronto Where is the exemplar? An interpretation of affinity propagation by Marc Mezard, Laboratoire de Physique Théorique et Modeles Statistique, Paris Number of clusters, k Squared error #12;Let's close the gap! Source: MSNBC #12;Affinity Propagation

Haykin, Simon

78

Affine Stanley symmetric functions  

Microsoft Academic Search

We define a new family of symmetric functions which are affine analogues of Stanley symmetric functions. We establish basic properties of these functions including symmetry, dominance and conjugation. We conjecture certain positivity properties in terms of a subfamily of symmetric functions called affine Schur functions. As applications, we show how affine Stanley symmetric functions generalise the (dual of the) $k$-Schur

Thomas Lam

2005-01-01

79

TAG Advertisement Hardware  

NASA Technical Reports Server (NTRS)

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

1994-01-01

80

Neuron Chain Tag  

NSDL National Science Digital Library

In this outdoor activity, learners play a game of Tag to discover how neurons attach themselves to each other to form a chain. The game starts with one learner who is "it" and represents the first neuron. When "it" tags another player, the tagger player must hold the hand of "it" and work together to form a long a chain. The game ends when all the players are part of the neuron chain.

Yoshioka, Melissa

2009-01-01

81

TECHNICAL ADVANCE An alternative tandem affinity purification strategy applied to  

E-print Network

, the second purification step can now be performed through two different affinity tags: a six His repeat of the TAPa system to allow efficient multi-protein complex isolation from stably transformed Arabidopsis isolated from bacteria (Gully et al., 2003), mammalian cells (Knuesel et al., 2003), insect cells (Forler

Deng, Xing-Wang

82

Tag-switching architecture: overview  

Microsoft Academic Search

Tag switching is a way to combine the label-swapping forwarding paradigm with network layer routing. This has several advantages. Tags can have a wide spectrum of forwarding granularities, so at one end of the spectrum a tag could be associated with a group of desti-nations, while at the other a tag could be associated with a single application flow. At

Yakov Rekhter; B. Davie; E. Rosen; G. Swallow; D. Farinacci; D. Katz

1997-01-01

83

Development of a hexahistidine-3× FLAG-tandem affinity purification method for endogenous protein complexes in Pichia pastoris.  

PubMed

We developed a method for efficient chromosome tagging in Pichia pastoris, using a useful tandem affinity purification (TAP) tag. The TAP tag, designated and used here as the THF tag, contains a thrombin protease cleavage site for removal of the TAP tag and a hexahistidine sequence (6× His) followed by three copies of the FLAG sequence (3× FLAG) for affinity purification. Using this method, THF-tagged RNA polymerases I, II, and III were successfully purified from P. pastoris. The method also enabled us to purify the tagged RNA polymerase II on a large scale, for its crystallization and preliminary X-ray crystallographic analysis. The method described here will be widely useful for the rapid and large-scale preparation of crystallization grade eukaryotic multi-subunit protein complexes. PMID:25398586

Higo, Toshiaki; Suka, Noriyuki; Ehara, Haruhiko; Wakamori, Masatoshi; Sato, Shin; Maeda, Hideaki; Sekine, Shun-Ichi; Umehara, Takashi; Yokoyama, Shigeyuki

2014-12-01

84

Colorizing Tags in Tag Cloud: A Novel Query-by-Tag Music Search System  

E-print Network

of preference (denoted as an MTML query) by colorizing desired tags in a web-based tag cloud interface. When) on a desired tag, the color of the tag will change cyclically according to a color map (from dark blue]: Web-based interaction; H.5.5 [Sound and Music Computing]: System. General Terms Algorithms

Wang, Hsin-Min

85

Affinity Through Instant Messaging  

E-print Network

document contains the author’s accepted manuscript. For the publisher’s version, see the link in the header of this document.] Affinity Through Instant Messaging By Jason P. Grebe, M.A. and Jeffrey A. Hall, Ph.D. Department of Communication... Studies University of Kansas Paper citation: Grebe, J. P. and Hall, J.A. (in press). “Affinity In Instant Messaging.” Northwest Journal of Communication. Abstract: The present manuscript explores affinity seeking, testing, and signaling...

Grebe, Jason P.; Hall, Jeffrey A.

2012-01-01

86

A Reliable Tag Anti-Collision Algorithm for Mobile Tags  

NASA Astrophysics Data System (ADS)

As RFID technology is being more widely adopted, it is fairly common to read mobile tags using RFID systems, such as packages on conveyer belt and unit loads on pallet jack or forklift truck. In RFID systems, multiple tags use a shared medium for communicating with a reader. It is quite possible that tags will exit the reading area without being read, which results in tag leaking. In this letter, a reliable tag anti-collision algorithm for mobile tags is proposed. It reliably estimates the expectation of the number of tags arriving during a time slot when new tags continually enter the reader's reading area and no tag leaves without being read. In addition, it gives priority to tags that arrived early among read cycles and applies the expectation of the number of tags arriving during a time slot to the determination of the number of slots in the initial inventory round of the next read cycle. Simulation results show that the reliability of the proposed algorithm is close to that of DFSA algorithm when the expectation of the number of tags entering the reading area during a time slot is a given, and is better than that of DFSA algorithm when the number of time slots in the initial inventory round of next read cycle is set to 1 assuming that the number of tags arriving during a time slot follows Poisson distribution.

Deng, Xiaodong; Rong, Mengtian; Liu, Tao

87

Deciphering Systemic Wound Responses of the Pumpkin Extrafascicular Phloem by Metabolomics and Stable Isotope-Coded Protein Labeling1[C][W  

PubMed Central

In cucurbits, phloem latex exudes from cut sieve tubes of the extrafascicular phloem (EFP), serving in defense against herbivores. We analyzed inducible defense mechanisms in the EFP of pumpkin (Cucurbita maxima) after leaf damage. As an early systemic response, wounding elicited transient accumulation of jasmonates and a decrease in exudation probably due to partial sieve tube occlusion by callose. The energy status of the EFP was enhanced as indicated by increased levels of ATP, phosphate, and intermediates of the citric acid cycle. Gas chromatography coupled to mass spectrometry also revealed that sucrose transport, gluconeogenesis/glycolysis, and amino acid metabolism were up-regulated after wounding. Combining ProteoMiner technology for the enrichment of low-abundance proteins with stable isotope-coded protein labeling, we identified 51 wound-regulated phloem proteins. Two Sucrose-Nonfermenting1-related protein kinases and a 32-kD 14-3-3 protein are candidate central regulators of stress metabolism in the EFP. Other proteins, such as the Silverleaf Whitefly-Induced Protein1, Mitogen Activated Protein Kinase6, and Heat Shock Protein81, have known defensive functions. Isotope-coded protein labeling and western-blot analyses indicated that Cyclophilin18 is a reliable marker for stress responses of the EFP. As a hint toward the induction of redox signaling, we have observed delayed oxidation-triggered polymerization of the major Phloem Protein1 (PP1) and PP2, which correlated with a decline in carbonylation of PP2. In sum, wounding triggered transient sieve tube occlusion, enhanced energy metabolism, and accumulation of defense-related proteins in the pumpkin EFP. The systemic wound response was mediated by jasmonate and redox signaling. PMID:23085839

Gaupels, Frank; Sarioglu, Hakan; Beckmann, Manfred; Hause, Bettina; Spannagl, Manuel; Draper, John; Lindermayr, Christian; Durner, Jorg

2012-01-01

88

Pseudo affine Wigner distributions  

Microsoft Academic Search

We define a new set of tools for time-varying spectral analysis: the pseudo affine Wigner distributions. Based on the affine Wigner distributions of J. and P. Bertrand (1992), these new time-frequency distributions support efficient online operation at the same computational cost as the continuous wavelet transform. Moreover, they take advantage of the proportional bandwidth smoothing inherent in the sliding structure

P. Goncalves; Richard G. Baraniuk

1996-01-01

89

Tagging mammalian transcription complexity  

Microsoft Academic Search

The nature of the 'transcriptome' is more complex than first realized. Although CAGE, various tagging technol- ogies and tiling arrays show that most of the mammalian genome is transcribed, a large proportion of transcripts do not encode proteins and are either poorly polyade- nylated, involved in sense-antisense pairs or never leave the nucleus. In this article, I review the various

Piero Carninci

2006-01-01

90

Tags are not Metadata, but \\  

Microsoft Academic Search

The authoring of tags - unlike the authoring of traditional metadata - is highly popular among users. This harbours un- precedented opportunities for organizing content. However, tags are still poorly understood. What do they \\

Bettina Berendt; Christoph Hanser

2007-01-01

91

Higher Affine Connections  

E-print Network

For a smooth manifold $M$, it was shown in \\cite{BPH} that every affine connection on the tangent bundle $TM$ naturally gives rise to covariant differentiation of multivector fields (MVFs) and differential forms along MVFs. In this paper, we generalize the covariant derivative of \\cite{BPH} and construct covariant derivatives along MVFs which are not induced by affine connections on $TM$. We call this more general class of covariant derivatives \\textit{higher affine connections}. Related notions of \\textit{higher torsion} and \\textit{higher curvature} are considered also.

David N. Pham

2014-08-18

92

Designing new metal affinity peptides by random mutagenesis of a natural metal-binding site.  

PubMed

The metal-binding site of a Helicobacter pylori ATPase 439 (heli(WT)-tag) was successfully used as a new fusion peptide for immobilized metal ion affinity chromatography (IMAC). It produced higher yields than the frequently used his6-tag. Due to stronger binding of the peptide to metal ions, harsher elution conditions were, however, necessary. This undesired side-effect was overcome by modifying the heli(WT)-tag by polymerase chain reaction-directed mutagenesis. The modified tags were screened by an automated high-throughput IMAC system, leading to a heliM14-tag peptide that could be eluted under conditions similar to those of the his6-tag but at the same time produced 20% higher yields of the desired protein. PMID:11185626

Enzelberger, M M; Minning, S; Schmid, R D

2000-11-10

93

A probabilistic model for personalized tag prediction  

Microsoft Academic Search

Social tagging systems have become increasingly popular for sharing and organizing web resources. Tag prediction is a common feature of social tagging systems. Social tagging by nature is an incremental process, meaning that once a user has saved a web page with tags, the tagging system can provide more accurate predictions for the user, based on user's incremental behaviors. However,

Dawei Yin; Zhenzhen Xue; Liangjie Hong; Brian D. Davison

2010-01-01

94

Extreme affine transformations  

Microsoft Academic Search

We classify the extreme points of the compact convex set of affine maps of IRn which map into itself the closed unit ball. This work is a preliminary step towards solving the problem of finding the extreme points of the compact convex set of affine maps of theN×N density matrices (dynamical maps of anN-level system) and forn=3 furnishes the solution

Vittorio Gorini; E. C. G. Sudarshan

1976-01-01

95

application note Affinity chromatography  

E-print Network

columns, prepacked with Chelating SepharoseTM High Performance, are effective and convenient tools, and the position of the histidine tag on the protein--were investigated for their effect on purification protein varied somewhat depending on the ion used, several different ions were effective for purifying

Lebendiker, Mario

96

Social Tagging of Mission Data  

NASA Technical Reports Server (NTRS)

Mars missions will generate a large amount of data in various forms, such as daily plans, images, and scientific information. Often, there is a semantic linkage between images that cannot be captured automatically. Software is needed that will provide a method for creating arbitrary tags for this mission data so that items with a similar tag can be related to each other. The tags should be visible and searchable for all users. A new routine was written to offer a new and more flexible search option over previous applications. This software allows users of the MSLICE program to apply any number of arbitrary tags to a piece of mission data through a MSLICE search interface. The application of tags creates relationships between data that did not previously exist. These tags can be easily removed and changed, and contain enough flexibility to be specifically configured for any mission. This gives users the ability to quickly recall or draw attention to particular pieces of mission data, for example: Give a semantic and meaningful description to mission data; for example, tag all images with a rock in them with the tag "rock." Rapidly recall specific and useful pieces of data; for example, tag a plan as"driving template." Call specific data to a user s attention; for example, tag a plan as "for:User." This software is part of the MSLICE release, which was written in Java. It will run on any current Windows, Macintosh, or Linux system.

Norris, Jeffrey S.; Wallick, Michael N.; Joswig, Joseph C.; Powell, Mark W.; Torres, Recaredo J.; Mittman, David S.; Abramyan, Lucy; Crockett, Thomas M.; Shams, Khawaja S.; Fox, Jason M.; Pyrzak, Guy; Vaughn, Michael B.

2010-01-01

97

Why do people tag?: motivations for photo tagging  

Microsoft Academic Search

Introduction Tagging, or using keywords to add metadata to shared content, is gaining much popularity in recent years. Tags are used to annotate various types of content, including images, videos, bookmarks, and blogs, through web-based systems such as Flickr, YouTube, del.icio.us, and Technorati, respectively. The popularity of tagging is attributed, at least in part, to the benefits users gain from

Oded Nov; Chen Ye

2010-01-01

98

Affine hypersurfaces with parallel difference tensor relative to affine ?-connection  

NASA Astrophysics Data System (ADS)

Li and Zhang (2014) studied affine hypersurfaces of R with parallel difference tensor relative to the affine ?-connection ?, and characterized the generalized Cayley hypersurfaces by K?0 and ?K=0 for some nonzero constant ?, where the affine ?-connection ? of information geometry was introduced on affine hypersurface. In this paper, by a slightly different method we continue to study affine hypersurfaces with ?K=0, if ?=0 we further assume that the Pick invariant vanishes and affine metric is of constant sectional curvature. It is proved that they are either hyperquadrics or improper affine hypersphere with flat indefinite affine metric, the latter can be locally given as a graph of a polynomial of at most degree n+1 with constant Hessian determinant. In particular, if the affine metric is definite, Lorentzian, or its negative index is 2, we complete the classification of such hypersurfaces.

Li, Cece

2014-12-01

99

Fish Tagging Forum Draft Compilation of Tagging Infrastructure  

E-print Network

Fish Tagging Forum Draft Compilation of Tagging Infrastructure 2012_11_06 v0 One of the items in the Forum or easily gleaned from internet research (e.g., PTAGIS site). As with other synthesis documents I have shared, this is merely a starting point for the Forum participants to add, subtract

100

An Overview of Social Tagging and Applications  

NASA Astrophysics Data System (ADS)

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.

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

101

Geometry of affine distributions  

Microsoft Academic Search

Bilinear affine distributions are considered from the point of view of their geometry in the time-frequency plane. General construction rules are established for interference terms, with further interpretations in terms of localization properties and generalized means. In the case of frequency modulated signals, it is shown how the pointwise application of these rules can be refined by the study of

Patrick Flandrin; P. Goncalves

1994-01-01

102

Impact of clostridial glucosylating toxins on the proteome of colonic cells determined by isotope-coded protein labeling and LC-MALDI  

PubMed Central

Background The anaerobe Clostridium difficile produces two major virulence factors toxin A and B that inactivate Rho proteins by glucosylation of a pivotal threonine residue. Purified toxins induce reorganization of the cytoskeleton and cell death in colonic cells. Whether all toxin effects on target cells depend on catalytic glucosyltransferase activity is unclear at present. Thus, we conducted a proteome approach to compare the protein profile of target cells treated either with wild type toxin A (rTcdA wt) or with a catalytically inactive mutant toxin A (mutant rTcdA). Relative protein quantification was feasible using isotope-coded protein labeling techniques (ICPL) and mass spectrometry (LC-MALDI). Results Altogether we found a significant differential expression of thirty proteins after treatment with rTcdA wt or mutant rTcdA. Mutant rTcdA caused up-regulation of seven proteins and sixteen proteins were responsive to rTcdA wt after 5 h. Long-term effect of rTcdA wt on protein expression was the down-regulation of eleven proteins. Up- or down-regulation of several proteins was verified by western blot analysis confirming the MS results. Conclusion Our results indicate incubation time-dependent effects of the clostridial glucosylating toxin A on colonic cells. The rTcdA wt impact more cellular functions than actin cytoskeleton reorganization and apoptosis. Furthermore, these data give insight into glucosyltransferase independent effects of clostridial glucosylating toxins on target cells after short incubation time. Additionally, our data reveal pro-inflammatory and proliferative effects of mutant rTcdA after short-term incubation. PMID:21849038

2011-01-01

103

Development of a Dehalogenase-Based Protein Fusion Tag Capable of Rapid, Selective and Covalent Attachment to Customizable Ligands  

PubMed Central

Our fundamental understanding of proteins and their biological significance has been enhanced by genetic fusion tags, as they provide a convenient method for introducing unique properties to proteins so that they can be examinedin isolation. Commonly used tags satisfy many of the requirements for applications relating to the detection and isolation of proteins from complex samples. However, their utility at low concentration becomes compromised if the binding affinity for a detection or capture reagent is not adequate to produce a stable interaction. Here, we describe HaloTag® (HT7), a genetic fusion tag based on a modified haloalkane dehalogenase designed and engineered to overcome the limitation of affinity tags by forming a high affinity, covalent attachment to a binding ligand. HT7 and its ligand have additional desirable features. The tag is relatively small, monomeric, and structurally compatible with fusion partners, while the ligand is specific, chemically simple, and amenable to modular synthetic design. Taken together, the design features and molecular evolution of HT7 have resulted in a superior alternative to common tags for the overexpression, detection, and isolation of target proteins. PMID:23248739

Encell, Lance P; Friedman Ohana, Rachel; Zimmerman, Kris; Otto, Paul; Vidugiris, Gediminas; Wood, Monika G; Los, Georgyi V; McDougall, Mark G; Zimprich, Chad; Karassina, Natasha; Learish, Randall D; Hurst, Robin; Hartnett, James; Wheeler, Sarah; Stecha, Pete; English, Jami; Zhao, Kate; Mendez, Jacqui; Benink, Helene A; Murphy, Nancy; Daniels, Danette L; Slater, Michael R; Urh, Marjeta; Darzins, Aldis; Klaubert, Dieter H; Bulleit, Robert F; Wood, Keith V

2012-01-01

104

Cobalt carbonyl complexes as probes for alkyne-tagged lipids.  

PubMed

Monitoring lipid distribution and metabolism in cells and biological fluids poses many challenges because of the many molecular species and metabolic pathways that exist. This study describes the synthesis and study of molecules that contain an alkyne functional group as surrogates for natural lipids in cultured cells. Thus, hexadec-15-ynoic and hexadec-7-ynoic acids were readily incorporated into RAW 264.7 cells, principally as phosphocholine esters; the alkyne was used as a "tag" that could be transformed to a stable dicobalt-hexacarbonyl complex; and the complex could then be detected by HPLC/MS or HPLC/UV(349nm). The 349 nm absorbance of the cobalt complexes was used to provide qualitative and quantitative information about the distribution and cellular concentrations of the alkyne lipids. The alkyne group could also be used as an affinity tag for the lipids by a catch-and-release strategy on phosphine-coated silica beads. Lipid extracts were enriched in the tagged lipids in this way, making the approach of potential utility to study lipid transformations in cell culture. Both terminal alkynes and internal alkynes were used in this affinity "pull-down" strategy. This method facilitates measuring lipid species that might otherwise fall below limits of detection. PMID:23307946

Tallman, Keri A; Armstrong, Michelle D; Milne, Stephen B; Marnett, Lawrence J; Brown, H Alex; Porter, Ned A

2013-03-01

105

Hierarchical Affinity Propagation  

E-print Network

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...

Givoni, Inmar; Frey, Brendan J

2012-01-01

106

Herpetological PIT Tag Migration in Seaturtle Flippers  

E-print Network

Herpetological Review PIT Tag Migration in Seaturtle Flippers JEANETTE WYNEKEN* Florida Atlantic and Reptiles PIT Tag Migration in Seaturtle Flippers JEANETTE WYNEKEN* Florida Atlantic University, Biological

Wyneken, Wyneken Jeanette

107

Overview of tag protein fusions: from molecular and biochemical fundamentals to commercial systems  

Microsoft Academic Search

. In response to the rapidly growing field of proteomics, the use of recombinant proteins has increased greatly in recent years. Recombinant hybrids containing a polypeptide fusion partner, termed affinity tag, to facilitate the purification of the target polypeptides are widely used. Many different proteins, domains, or peptides can be fused with the target protein. The advantages of using fusion

K. Terpe

2003-01-01

108

Purification of Tag-Free Recombinant Proteins Using the Profinity eXactTM  

E-print Network

activities. This is a generic approach that differs from traditional chromatography, where specific materials be challenging. Alternative systems using intein-mediated self-processing of fusion proteins have been designed-column proteolytic cleavage of the affinity tag, and the overall efficiency and simplicity of the purification

Lebendiker, Mario

109

Adaptive Affinity Propagation Clustering  

Microsoft Academic Search

Affinity propagation clustering (AP) has two limitations: it is hard to know\\u000awhat value of parameter 'preference' can yield an optimal clustering solution,\\u000aand oscillations cannot be eliminated automatically if occur. The adaptive AP\\u000amethod is proposed to overcome these limitations, including adaptive scanning\\u000aof preferences to search space of the number of clusters for finding the\\u000aoptimal clustering solution,

Kaijun Wang; Junying Zhang; Dan Li; Xinna Zhang; Tao Guo

2008-01-01

110

Purely affine Gravity  

E-print Network

We develop a topological theory of gravity with torsion where metric has a dynamical rather than a kinematical origin. This approach towards gravity resembles pre-geometrical approaches in which a fundamental metric does not exist, but the affine connection gives place to a local inertial structure. Such feature reminds us of Mach's principle, that assumes the inertial forces should have dynamical origin. Additionally, a Newtonian gravitational force is obtained in the non-relativistic limit of the theory.

Skirzewski, Aureliano

2014-01-01

111

ChemTeacher: Electron Affinity  

NSDL National Science Digital Library

ChemTeacher compiles background information, videos, articles, demonstrations, worksheets and activities for high school teachers to use in their classrooms. The Electron Affinity page includes resources for teaching students about the concept of electron affinity.

2011-01-01

112

Antibodies with infinite affinity  

PubMed Central

Here we report an approach to the design and production of antibody/ligand pairs, to achieve functional affinity far greater than avidin/biotin. Using fundamental chemical principles, we have developed antibody/ligand pairs that retain the binding specificity of the antibody, but do not dissociate. Choosing a structurally characterized antibody/ligand pair as an example, we engineered complementary reactive groups in the antibody binding pocket and the ligand, so that they would be in close proximity in the antibody/ligand complex. Cross-reactions with other molecules in the medium are averted because of the low reactivity of these groups; however, in the antibody/ligand complex the effective local concentrations of the complementary reactive groups are very large, allowing a covalent reaction to link the two together. By eliminating the dissociation of the ligand from the antibody, we have made the affinity functionally infinite. This chemical manipulation of affinity is applicable to other biological binding pairs. PMID:11447282

Chmura, Albert J.; Orton, Molly S.; Meares, Claude F.

2001-01-01

113

Quantized Affinely Rigid Bodies  

E-print Network

Developed are the main ideas of the quantized version of affinely-rigid motion. We base on the usual Schr\\"odinger formulation of quantum mechanics in the configuration manifold. The latter is given, in our case, by the affine group or equivalently by the semi-direct product of the linear group ${\\rm GL}(n,\\mathbb{R})$ and the space of translations $\\mathbb{R}^{n}$, where $n$ equals the dimension of the "physical space". In particular, we discuss the problem of the dynamical invariance of the kinetic energy under the action of affine group, not only under the isometry subgroup. Technically, the treatment is based on the two-polar decomposition of the matrix of the internal configuration space and on the Peter-Weyl theory of generalized Fourier series on Lie groups. One can hope that our results may be applied in quantum problems of nuclear dynamics or even in apparently exotic phenomena in vibrating neutron stars. And, of course, some more prosaic applications in molecular dynamics are possible.

J. J. S\\lawianowski; B. Go\\lubowska; V. Kovalchuk; A. Martens; E. E. Ro?ko

2014-05-12

114

D-TAG: erasing the tag of gang membership.  

PubMed

Gangs are noted for establishing their territory, flaunting gang affiliation, intimidating nonmembers, and documenting their "services performed." These examples are a few reasons for the practice of "tagging," the labeling of an area, person, or object with gang-related graffiti or markings, such as tattoos. This article describes a school nurse's response to gang "tagging" and her efforts to assist former gang members who request removal of their tattoos, to get them removed-in essence to D-TAG themselves from their gang affiliation. D-TAG is a volunteer rehabilitation program utilizing family and community interaction to support gang tattoo removal and direct activities away from gang affiliations toward alternative educational programs and life styles. PMID:9146217

Gurke, B; Armstrong, M L

1997-04-01

115

Quantum tagging for tags containing secret classical data  

SciTech Connect

Various authors have considered schemes for quantum tagging, that is, authenticating the classical location of a classical tagging device by sending and receiving quantum signals from suitably located distant sites, in an environment controlled by an adversary whose quantum information processing and transmitting power is potentially unbounded. All of the schemes proposed elsewhere in the literature assume that the adversary is able to inspect the interior of the tagging device. All of these schemes have been shown to be breakable if the adversary has unbounded predistributed entanglement. We consider here the case in which the tagging device contains a finite key string shared with distant sites but kept secret from the adversary, and show this allows the location of the tagging device to be authenticated securely and indefinitely. Our protocol relies on quantum key distribution between the tagging device and at least one distant site, and demonstrates a new practical application of quantum key distribution. It also illustrates that the attainable security in position-based cryptography can depend crucially on apparently subtle details in the security scenario considered.

Kent, Adrian [Centre for Quantum Information and Foundations, DAMTP, University of Cambridge, Cambridge (United Kingdom) and Perimeter Institute for Theoretical Physics, Waterloo, Ontario (Canada)

2011-08-15

116

Targeted tandem affinity purification of PSD95 recovers core postsynaptic complexes and schizophrenia susceptibility proteins  

Microsoft Academic Search

The molecular complexity of mammalian proteomes demands new methods for mapping the organization of multiprotein complexes. Here, we combine mouse genetics and proteomics to characterize synapse protein complexes and interaction networks. New tandem affinity purification (TAP) tags were fused to the carboxyl terminus of PSD-95 using gene targeting in mice. Homozygous mice showed no detectable abnormalities in PSD-95 expression, subcellular

Esperanza Fernández; Mark O Collins; Rachel T Uren; Maksym V Kopanitsa; Noboru H Komiyama; Mike D R Croning; Lysimachos Zografos; J Douglas Armstrong; Jyoti S Choudhary; Seth G N Grant

2009-01-01

117

Adaptive Affinity Propagation Clustering  

E-print Network

Affinity propagation clustering (AP) has two limitations: it is hard to know what value of parameter 'preference' can yield an optimal clustering solution, and oscillations cannot be eliminated automatically if occur. The adaptive AP method is proposed to overcome these limitations, including adaptive scanning of preferences to search space of the number of clusters for finding the optimal clustering solution, adaptive adjustment of damping factors to eliminate oscillations, and adaptive escaping from oscillations when the damping adjustment technique fails. Experimental results on simulated and real data sets show that the adaptive AP is effective and can outperform AP in quality of clustering results.

Wang, Kaijun; Li, Dan; Zhang, Xinna; Guo, Tao

2008-01-01

118

TAG Based Skimming In ATLAS  

NASA Astrophysics Data System (ADS)

The ATLAS detector at the LHC takes data at 200-500 Hz for several months per year accumulating billions of events for hundreds of physics analyses. TAGs are event-level metadata allowing a quick search for interesting events based on selection criteria defined by the user. They are stored in a file-based format as well as in relational databases. The overall TAG system architecture encompasses a range of interconnected services that provide functionality for the required use cases such as event selection, display, extraction and skimming. Skimming can be used to navigate to any of the pre-TAG data products. The services described in this paper address use cases that range in scale from selecting a handful of interesting events for an analysis specific study to creating physics working group samples on the ATLAS production system. This paper will focus on the workflow aspects involved in creating pre and post TAG data products from a TAG selection using the Grid in the context of the overall TAG system architecture. The emphasis will be on the range of demands that the implemented use cases place on these workflows and on the infrastructure. The tradeoffs of various workflow strategies will be discussed including scalability issues and other concerns that occur when integrating with data management and production systems.

Doherty, T.; Cranshaw, J.; Hrivnac, J.; Slater, M.; Nowak, M.; Quilty, D.; Zhang, Q.

2012-12-01

119

Affinity chromatography using biocompatible and reusable biotinylated membranes.  

PubMed

A novel, reusable biotinylated affinity chromatography strategy for the bio-specific binding of bioactive avidin tagged enzymes or polypeptides is reported. Using an avidin coupled peroxidase fusion protein as a test system; non-specific protein shielding and matrix regeneration were also shown. The amphiphilic surfactant Pluronic F108 was used as an affinity linker, by non-covalent binding to membrane chromatographic matrices while the terminal hydroxyl groups of Pluronic were covalently coupled to the biological ligand biotin. Planar nonporous membranes of varying surface chemistry were synthesised to test the matrix dependent affinity binding of biotinylated Pluronic and their respective ability to resist non-specific protein adsorption. Membrane regeneration using sodium dodecyl sulphate (SDS) was capable of displacing both adsorbed proteins and Pluronic. SDS micelles (34 mM) were effective in desorbing membrane bound protein while 5mM SDS removed up to 85% of the bound ligand after 20 h incubation at 20 degrees C. In this study, polyvinylidene membranes had the highest ligand binding capacity of 0.22 mg cm(-2) and specific, competitive affinity binding of avidin-peroxidase was shown in the presence of up to 0.2 mg ml(-1) 'contaminant' proteins. The resultant biocompatible affinity chromatographic system was regenerated and reused with no significant change in performance for up to five cycles. PMID:17875407

Govender, S; Jacobs, E P; Bredenkamp, M W; Swart, P

2007-11-01

120

Avidity-mediated virus separation using a hyperthermophilic affinity ligand.  

PubMed

Immunoaffinity separation of large multivalent species such as viruses is limited by the stringent elution conditions necessary to overcome their strong and highly avid interaction with immobilized affinity ligands on the capture surface. Here we present an alternate strategy that harnesses the avidity effect to overcome this limitation. Red clover necrotic mosaic virus (RCNMV), a plant virus relevant to drug delivery applications, was chosen as a model target for this study. An RCNMV binding protein (RBP) with modest binding affinity (K(D) ~100 nM) was generated through mutagenesis of the Sso7d protein from Sulfolobus solfataricus and used as the affinity ligand. In our separation scheme, RCNMV is captured by a highly avid interaction with RBP immobilized on a nickel surface through a hexahistidine (6xHis) tag. Subsequently, disruption of the multivalent interaction and release of RCNMV is achieved by elution of RBP from the nickel surface. Finally, RCNMV is separated from RBP by exploiting the large difference in their molecular weights (~8 MDa vs. ~10 kDa). Our strategy not only eliminates the need for harsh elution conditions, but also bypasses chemical conjugation of the affinity ligand to the capture surface. Stable non-antibody affinity ligands to a wide spectrum of targets can be generated through mutagenesis of Sso7d and other hyperthermophilic proteins. Therefore, our approach may be broadly relevant to cases where capture of large multivalent species from complex mixtures and subsequent release without the use of harsh elution conditions is necessary. PMID:23125177

Hussain, Mahmud; Lockney, Dustin; Wang, Ruqi; Gera, Nimish; Rao, Balaji M

2013-01-01

121

Hybrid Content and Tag-based Profiles for Recommendation in Collaborative Tagging Systems  

Microsoft Academic Search

Collaborative tagging systems have grown in popularity over the Web in the last years on account of their simplicity to categorize and retrieve content using open-ended tags. The increasing number of users providing information about themselves through social tagging activities caused the emergence of tag-based profiling approaches, which assume that users expose their preferences for certain contents through tag assignments.

Daniela Godoy; Anal ´ õa Amandi

2008-01-01

122

Dimerization Capacities of FGF2 Purified with or without Heparin-Affinity Chromatography  

PubMed Central

Fibroblast growth factor-2 (FGF2) is a pleiotropic growth factor exhibiting a variety of biological activities. In this article, we studied the capacity of FGF2 purified with or without heparin affinity chromatography to self-associate. Analyzing the NMR HSQC spectra for different FGF2 concentrations, heparin-affinity purified FGF2 showed perturbations that indicate dimerization and are a higher-order oligomerization state. HSQC perturbation observed with different FGF2 concentrations revealed a heparin-binding site and two dimer interfaces. Thus, with increasing protein concentrations, FGF2 monomers make contacts with each other and form dimers or higher order oligomers. On the contrary, FGF2 purified with ion-exchange chromatography did not show similar perturbation indicating that self-association of FGF2 is eliminated if purification is done without heparin-affinity chromatography. The HSQC spectra of heparin-affinity purified FGF2 can be reproduced to some extent by adding heparin tetra-saccharide to ion exchange chromatography purified FGF2. Heparin-affinity purified FGF2 bound to acceptor and donor beads in a tagged form using His-tagged or GST-tagged proteins, also dimerized in the AlphaScreen™ assay. This assay was further validated using different experimental conditions and competitors. The assay constitutes an interesting tool to study dimerization of other FGF forms as well. PMID:25299071

Chiu, Liang-Yuan; Taouji, Said; Moroni, Elisabetta; Colombo, Giorgio; Chevet, Eric; Sue, Shih-Che; Bikfalvi, Andreas

2014-01-01

123

In vivo investigation of protein-protein interactions for helicases using tandem affinity purification.  

PubMed

A key component in determining the functional role of any protein is the elucidation of its binding partners using protein-protein interaction (PPI) data. Here we examine the use of tandem affinity purification (TAP) tagging to study RNA/DNA helicase PPIs in Escherichia coli. The tag, which consists of a calmodulin-binding region, a TEV protease recognition sequence, and an IgG-binding domain, is introduced into E. coli using a lambdared recombination system. This method prevents the overproduction of the target protein, which could generate false interactions. The interacting proteins are then affinity purified using double affinity purification steps and are separated by SDS-PAGE followed by mass spectrometry identification. Each protein identified would represent a physical interaction in the cell. These interactions may potentially be mediated by an RNA/DNA template, for which the helicase would likely be needed to disrupt the secondary structures. PMID:20225144

Jessulat, Matthew; Buist, Terry; Alamgir, Md; Hooshyar, Mohsen; Xu, Jianhua; Aoki, Hiroyuki; Ganoza, M Clelia; Butland, Gareth; Golshani, Ashkan

2010-01-01

124

Taking down the FLAG! How insect cell expression challenges an established tag-system.  

PubMed

In 1988 the preceding journal of Nature Biotechnology, Bio/Technology, reported a work by Hopp and co-workers about a new tag system for the identification and purification of recombinant proteins: the FLAG-tag. Beside the extensively used hexa-his tag system the FLAG-tag has gained broad popularity due to its small size, its high solubility, the presence of an internal Enterokinase cleavage site, and the commercial availability of high-affinity anti-FLAG antibodies. Surprisingly, considering the heavy use of FLAG in numerous laboratories world-wide, we identified in insect cells a post-translational modification (PTM) that abolishes the FLAG-anti-FLAG interaction rendering this tag system ineffectual for secreted proteins. The present publication shows that the tyrosine that is part of the crucial FLAG epitope DYK is highly susceptible to sulfation, a PTM catalysed by the enzyme family of Tyrosylprotein-Sulfo-transferases (TPSTs). We showed that this modification can result in less than 20% of secreted FLAG-tagged protein being accessible for purification questioning the universal applicability of this established tag system. PMID:22701579

Schmidt, Peter M; Sparrow, Lindsay G; Attwood, Rebecca M; Xiao, Xiaowen; Adams, Tim E; McKimm-Breschkin, Jennifer L

2012-01-01

125

Social image tagging with diverse semantics.  

PubMed

We have witnessed the popularity of image-sharing websites for sharing personal experiences through photos on the Web. These websites allow users describing the content of their uploaded images with a set of tags. Those user-annotated tags are often noisy and biased. Social image tagging aims at removing noisy tags and suggests new relevant tags. However, most existing tag enrichment approaches predominantly focus on tag relevance and overlook tag diversity problem. How to make the top-ranked tags covering a wide range of semantic is still an opening, yet challenging, issue. In this paper, we propose an approach to retag social images with diverse semantics. Both the relevance of a tag to image as well as its semantic compensations to the already determined tags are fused to determine the final tag list for a given image. Different from existing image tagging approaches, the top-ranked tags are not only highly relevant to the image but also have significant semantic compensations with each other. Experiments show the effectiveness of the proposed approach. PMID:25415950

Qian, Xueming; Hua, Xian-Sheng; Tang, Yuan Yan; Mei, Tao

2014-12-01

126

A low-cost affinity purification system using ?-1,3-glucan recognition protein and curdlan beads  

PubMed Central

Silkworm ?-1,3-glucan recognition protein (?GRP) tightly and specifically associates with ?-1,3-glucan. We report here an affinity purification system named the ‘GRP system’, which uses the association between the ?-1,3-glucan recognition domain of ?GRP (GRP-tag), as an affinity tag, and curdlan beads. Curdlan is a water-insoluble ?-1,3-glucan reagent, the low cost of which (about 100 JPY/g) allows the economical preparation of beads. Curdlan beads can be readily prepared by solubilization in an alkaline solution, followed by neutralization, sonication and centrifugation. We applied the GRP system to preparation of several proteins and revealed that the expression levels of the GRP-tagged proteins in soluble fractions were two or three times higher than those of the glutathione S-transferase (GST)-tagged proteins. The purity of the GRP-tagged proteins on the curdlan beads was comparable to that of the GST-tagged proteins on glutathione beads. The chemical stability of the GRP system was more robust than conventional affinity systems under various conditions, including low pH (4–6). Biochemical and structural analyses revealed that proteins produced using the GRP system were structurally and functionally active. Thus, the GRP system is suitable for both the large- and small-scale preparation of recombinant proteins for functional and structural analyses. PMID:22706764

Horiuchi, Masataka; Takahasi, Kiyohiro; Kobashigawa, Yoshihiro; Ochiai, Masanori; Inagaki, Fuyuhiko

2012-01-01

127

Characterization of polystyrene-binding peptides (PS-tags) for site-specific immobilization of proteins.  

PubMed

In this study, we characterized polystyrene-binding peptides (PS-tags) that possess a specific binding affinity for hydrophilic polystyrene (phi-PS) plates. Both the FITC-labeled PS19-1 (RAFIASRRIKRP) and PS19-6 (RIIIRRIRR) peptides showed strong binding affinity for commercially available hydrophilic, but not hydrophobic, PS plates in the presence of the non-ionic surfactant Tween 20. The dissociation constants (K(d)) of the PS19-1 and PS19-6 peptides for the hydrophilic PS-A plate were 169 and 86 nM, respectively, and the K(d) of both peptides increased with the concentration of NaCl or urea. Based on adsorption yield and residual activity of glutathione S-transferase (GST) after fusion with the PS19-6 peptide or its variants, it was found that the basic amino acid in the PS-tags, i.e., Arg was essential for the strong binding affinity of PS-tags in both the peptide and peptide-fused protein forms The aliphatic amino acids in PS19-6 and PS19-6L, such as Ile or Leu, were also effective. Thus, a series of PS-tags that possess this unusual feature, especially the peptides PS19-6 (RIIIRRIRR) and PS19-6L (RLLLRRLRR), are potential candidate affinity peptide tags for site-specific immobilization of proteins onto hydrophilic PS plates, which show potential as solid supports for protein-based biochips. PMID:20471598

Kumada, Yoichi; Kuroki, Daisuke; Yasui, Hidefumi; Ohse, Takuhito; Kishimoto, Michimasa

2010-06-01

128

Visible and Controllable RFID Tags Radio frequency identification (RFID) tags containing  

E-print Network

;Introduction and Motivation Since its invention in the early 20th century, radio frequency identification (RFIDVisible and Controllable RFID Tags Abstract Radio frequency identification (RFID) tags containing

Greenberg, Saul

129

Synaptic Tagging During Memory Allocation  

PubMed Central

There is now compelling evidence that the allocation of memory to specific neurons (neuronal allocation) and synapses (synaptic allocation) in a neurocircuit is not random and that instead specific mechanisms, such as increases in neuronal excitability and synaptic tagging and capture, determine the exact sites where memories are stored. We propose an integrated view of these processes, such that neuronal allocation, synaptic tagging and capture, spine clustering and metaplasticity reflect related aspects of memory allocation mechanisms. Importantly, the properties of these mechanisms suggest a set of rules that profoundly affect how memories are stored and recalled. PMID:24496410

Rogerson, Thomas; Cai, Denise; Frank, Adam; Sano, Yoshitake; Shobe, Justin; Aranda, Manuel L.; Silva, Alcino J.

2014-01-01

130

WebTag: Web browsing into sensor tags over NFC.  

PubMed

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

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

2012-01-01

131

WebTag: Web Browsing into Sensor Tags over NFC  

PubMed Central

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

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

2012-01-01

132

Electron Affinity Calculations for Thioethers  

NASA Technical Reports Server (NTRS)

Previous work indicated that polyphenyl thioethers possessed chemical properties, related to their electron affinities, which could allow them to function as vapor phase lubricants (VPL). Indeed, preliminary tribological tests revealed that the thioethers could function as vapor phase lubricants but not over a wide temperature and hertzian pressure range. Increasing the electron affinity of the thioethers may improve their VPL properties over this range. Adding a substituent group to the thioether will alter its electron affinity in many cases. Molecular orbital calculations were undertaken to determine the effect of five different substituent groups on the electron affinity of polyphenyl thioethers. It was found that the NO2, F, and I groups increased the thioethers electron affinity by the greatest amount. Future work will involve the addition of these groups to the thioethers followed by tribological testing to assess their VPL properties.

Sulton, Deley L.; Boothe, Michael; Ball, David W.; Morales, Wilfredo

1997-01-01

133

Quantifying Visual-Representativeness of Social Image Tags Using Image Tag Clarity  

NASA Astrophysics Data System (ADS)

Tags associated with images in various social media sharing web sites are valuable information source for superior image retrieval experiences. Due to the nature of tagging, many tags associated with images are not visually descriptive. In this chapter, we propose Image Tag Clarity to evaluate the effectiveness of a tag in describing the visual content of its annotated images, which is also known as the image tag visual-representativeness. It is measured by computing the zero-mean normalized distance between the tag language model estimated from the images annotated by the tag and the collection language model. The tag/collection language models are derived from the bag of visual-word local content features of the images. The visual-representative tags that are commonly used to annotate visually similar images are given high tag clarity scores. Evaluated on a large real-world dataset containing more than 269K images and their associated tags, we show that the image tag clarity score can effectively identify the visual-representative tags from all tags contributed by users. Based on the tag clarity scores, we have made a few interesting observations that could be used to support many tag-based applications.

Sun, Aixin; Bhowmick, Sourav S.

134

What Do Tag Games Teach?  

ERIC Educational Resources Information Center

Tag games have been described as "Chasing, fleeing, and dodging" type activities. Most "fleeing" activities involve dramatic play, use of movement concepts (such as quick and light), or movement changes without a partner, while many of the chasing and dodging activities utilize dodging concepts between partners or within small groups and are…

Belka, David

2006-01-01

135

Vibrationally excited hydroxyl tagging velocimetry.  

PubMed

A new molecular-based velocity method is developed for high-temperature flame gases based on the hydroxyl tagging velocimetry (HTV) technique. In vibrationally excited HTV (VE-HTV), two photons from a KrF laser (248 nm) dissociate H2O into a tag line of vibrationally excited OH (v=1). The excited state OH tag is selectively detected in a background of naturally occurring ground state OH (v=0). In atmospheric pressure laboratory burners, the OH (v=1) tag persists for 5-10 ?s, allowing single-shot velocity measurements along a 2 cm line under lean, stoichiometric, and rich flame conditions with temperatures reaching 2300 K. Mean velocity measurements are demonstrated in a lean (?=0.78) premixed H2/air turbulent flame (Re=26,550) laboratory flame. The VE-HTV method is best suited to measure high-speed velocities in hot combustion environments in the presence of background OH. PMID:25402874

Grady, Nathan; Pitz, Robert W

2014-11-01

136

Freedom System Text and Graphics System (TAGS)  

NASA Technical Reports Server (NTRS)

The Text and Graphics System (TAGS) is a high-resolution facsimile system that scans text or graphics material and converts the analog SCAN data into serial digital data. This video shows the TAGS in operation.

1989-01-01

137

HCI gesture tracking using wearable passive tags  

E-print Network

In this thesis. a wearable system is developed to track hand gestures with passive RFID sensor tags. This system was composed of an ultra-high frequency reader and small, passive, finger-worn tags powered by scavenged RFID ...

Bainbridge, Rachel M

2010-01-01

138

OpenTag: Privacy protection for RFID  

E-print Network

Radio frequency identification's use in retail is good for pervasive computing, but raises considerable privacy issues. OpenTag programmable tags address privacy issues while remaining fully compatible with the supply-chain ...

Holtzman, Henry N.

139

WhaleNet's Satellite Tagging Program  

NSDL National Science Digital Library

This extensive, easy to use site contains information on satellite tags and tagging, data from current and archived tagging projects on whales, porpoises, seals, and turtles, and questions and activities to help use the data in the classroom. Follow these marine mammals up and down the coast or use the archived data to study distribution and migration patterns of dolphins, seals, etc. Site also links to other tagging and monitoring programs.

140

Fish Tagging Forum March 22, 2012  

E-print Network

1 Fish Tagging Forum March 22, 2012 Portland, OR Draft Meeting Notes Background The Northwest Power and Conservation Council convened the Fish Tagging Forum (FTF) to address regional fish tagging issues (see July 13 of the Forum's overall Evaluation Framework. The subcommittee reviewed the management questions and indicators

141

Social Tags and Music Information Retrieval  

Microsoft Academic Search

Social tags are free text labels that are applied to items such as artists, albums and songs. Captured in these tags is a great deal of information that is highly relevant to Music Information Retrieval (MIR) researchers including information about genre, mood, instrumentation, and quality. Unfortunately there is also a great deal of irrelevant information and noise in the tags.

Paul Lamere; Elias Pampalk

2008-01-01

142

Emergent Community Structure in Social Tagging Systems  

Microsoft Academic Search

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, aca- demic papers) by associating with them freely chosen text labels, or tags .H ere we leverage the social aspects of collaborative tagging and introduce a notion

Ciro Cattuto; Andrea Baldassarri; Vito Domenico Pietro Servedio; Vittorio Loreto

2008-01-01

143

RFID Performance Tag Analysis Dan Deavours,  

E-print Network

phones. The intended application is to use RFID tags to keep unauthorized cell phones from restricted continued operation. · We found that in ideal situations (i.e., not on a cell phone), all but the Avery tag that we could consistently find good placement on cell phones. · All tags showed a dipole radiation

Kansas, University of

144

Hybrid tag recommendation for social annotation systems  

Microsoft Academic Search

Social annotation systems allow users to annotate resources with personalized tags and to navigate large and complex information spaces without the need to rely on predefined hierarchies. These systems help users organize and share their own resources, as well as discover new ones annotated by other users. Tag recommenders in such systems assist users in finding appropriate tags for resources

Jonathan Gemmell; Thomas Schimoler; Bamshad Mobasher; Robin D. Burke

2010-01-01

145

Method for designing gas tag compositions  

DOEpatents

For use in the manufacture of gas tags such as employed in a nuclear reactor gas tagging failure detection system, a method for designing gas tagging compositions utilizes an analytical approach wherein the final composition of a first canister of tag gas as measured by a mass spectrometer is designated as node No. 1. Lattice locations of tag nodes in multi-dimensional space are then used in calculating the compositions of a node No. 2 and each subsequent node so as to maximize the distance of each node from any combination of tag components which might be indistinguishable from another tag composition in a reactor fuel assembly. Alternatively, the measured compositions of tag gas numbers 1 and 2 may be used to fix the locations of nodes 1 and 2, with the locations of nodes 3-N then calculated for optimum tag gas composition. A single sphere defining the lattice locations of the tag nodes may be used to define approximately 20 tag nodes, while concentric spheres can extend the number of tag nodes to several hundred. 5 figures.

Gross, K.C.

1995-04-11

146

Available Tagging Products www.beeworks.com  

E-print Network

that each inject a tag, used for mass tagging an area of tissue Syringe implanters - used to inject bulk tags into tissue Needles ­ for the syringe implanters Rapid Implant Gun ­ a more effective and no doubt of the larger readers that are more portable, suffer from lower memory also Antenna ­ a variety of types

Mayes, Keith

147

Picture Tags and World Knowledge Learning Tag Relations from Visual Semantic Sources  

E-print Network

Picture Tags and World Knowledge Learning Tag Relations from Visual Semantic Sources Lexing Xie in analyzing picture tags and everyday semantic knowledge. Potential other appli- cations include generating, improved picture annotation and tag sugges- tion, and enriching encyclopedic knowledge-bases with more

He, Xuming

148

NiceTag Ontology: tags as named graphs Freddy Limpens1  

E-print Network

NiceTag Ontology: tags as named graphs Freddy Limpens1 , Alexandre Monnin2,3 , David Laniado4 National des Arts et Metiers (CNAM) 4 DEI, Politecnico di Milano david.laniado@elet.polimi.it Abstract general manner, and as an immediate consequence, to describe tags as modelled by other tag models (SCOT

Boyer, Edmond

149

Abstract.North Pacific albacore tag-ging data from a tag-release program  

E-print Network

by the U.S. National Marine Fisheries Ser- Estimates of exploitation rates for north Pacific albacore exploitation rates and related parameters. In this paper, we develop tag-attrition models (Kleiber et al., 1987 to 1989 were ana- lyzed to obtain estimates of exploitation rates and related parameters. The ma- jor

150

His-tag protein monitoring by a fast mix-and-measure immunoassay.  

PubMed

Here, we present a fast mix-and-measure immunoassay for the specific semiquantitative detection of His-tagged proteins, for example in E. coli cell lysate. The assay is based on Förster resonance energy transfer (FRET) between a lanthanide dye-labeled low-affinity His-peptide and an acceptor-labeled anti-His-tag antibody. The targeted His-tag protein in the sample displaces the donor-labeled peptide and leads to a concentration-dependent time-resolved fluorescence signal. The assay has a total assay time of less than two minutes including sample preparation. The assay recognizes both, N- and C-terminally tagged proteins. The detection limit is comparable to those obtained in SDS-PAGE or Western Blot, which are used as standard methods for the characterization of His-tag protein expression. Additionally, we demonstrate a full compatibility of the developed assay to cell lysate, and a correlation to detectable bands in a western blot application. In conclusion, this fast, sensitive, specific and affordable mix-and-measure assay provides a timesaving and user-friendly way to quantify recombinant protein expression. It substantially reduces the workload for recombinant protein detection, especially when His-tag-protein-containing fractions in manual chromatographic purifications have to be identified. PMID:25000910

Kreisig, Thomas; Prasse, Agneta A; Zscharnack, Kristin; Volke, Daniela; Zuchner, Thole

2014-01-01

151

48 CFR 908.7101-7 - Government license tags.  

Code of Federal Regulations, 2013 CFR

...Special Items 908.7101-7 Government license tags. (a) Government license tags shall be procured...made by UNICOR via the UNICOR online vehicle license tag...District of Columbia, official Government tags shall be...

2013-10-01

152

Co-evolution of multipartite interactions between an extended tmRNA tag and a robust Lon protease in Mycoplasma.  

PubMed

Messenger RNAs that lack in-frame stop codons promote ribosome stalling and accumulation of aberrant and potentially harmful polypeptides. The SmpB-tmRNA quality control system has evolved to solve problems associated with non-stop mRNAs, by rescuing stalled ribosomes and directing the addition of a peptide tag to the C-termini of the associated proteins, marking them for proteolysis. In Escherichia coli, the ClpXP system is the major contributor to disposal of tmRNA-tagged proteins. We have shown that the AAA+ Lon protease can also degrade tmRNA-tagged proteins, but with much lower efficiency. Here, we present a unique case of enhanced recognition and degradation of an extended Mycoplasma pneumoniae (MP) tmRNA tag by the MP-Lon protease. We demonstrate that MP-Lon can efficiently and selectively degrade MP-tmRNA-tagged proteins. Most significantly, our studies reveal that the larger (27 amino acids long) MP-tmRNA tag contains multiple discrete signalling motifs for efficient recognition and rapid degradation by Lon. We propose that higher-affinity multipartite interactions between MP-Lon and the extended MP-tmRNA tag have co-evolved from pre-existing weaker interactions, as exhibited by Lon in E. coli, to better fulfil the function of MP-Lon as the sole soluble cytoplasmic protease responsible for the degradation of tmRNA-tagged proteins. PMID:19912542

Ge, Zhiyun; Karzai, A Wali

2009-12-01

153

FIGURE S1. Biochemical purification and identification of the interaction between A3G and MOV10. A, The A3G-containing protein complexes were double-affinity-purified from 293T cells transfected with  

E-print Network

, The A3G-containing protein complexes were double-affinity-purified from 293T cells transfected with FLAG-tagged A3G (lane 2) and HA-tagged GFP (lane 1) were co-transfected with FLAG-tagged MOV10 (lanes 1 and 2). C, The transfected 293T cells co-expressing A3G-HA and MOV10-FLAG were lysed and immunoprecipitated

Bedwell, David M.

154

pAUL: a gateway-based vector system for adaptive expression and flexible tagging of proteins in Arabidopsis.  

PubMed

Determination of protein function requires tools that allow its detection and/or purification. As generation of specific antibodies often is laborious and insufficient, protein tagging using epitopes that are recognized by commercially available antibodies and matrices appears more promising. Also, proper spatial and temporal expression of tagged proteins is required to prevent falsification of results. We developed a new series of binary Gateway cloning vectors named pAUL1-20 for C- and N-terminal in-frame fusion of proteins to four different tags: a single (i) HA epitope and (ii) Strep-tagIII, (iii) both epitopes combined to a double tag, and (iv) a triple tag consisting of the double tag extended by a Protein A tag possessing a 3C protease cleavage site. Expression can be driven by either the 35 S CaMV promoter or, for C-terminal fusions, promoters from genes encoding the chloroplast biogenesis factors HCF107, HCF136, or HCF173. Fusions of the four promoters to the GUS gene showed that endogenous promoter sequences are functional and drive expression more moderately and consistently throughout different transgenic lines when compared to the 35 S CaMV promoter. By testing complementation of mutations affected in chloroplast biogenesis factors HCF107 and HCF208, we found that the effect of different promoters and tags on protein function strongly depends on the protein itself. Single-step and tandem affinity purification of HCF208 via different tags confirmed the integrity of the cloned tags. PMID:23326506

Lyska, Dagmar; Engelmann, Kerstin; Meierhoff, Karin; Westhoff, Peter

2013-01-01

155

49 CFR 236.76 - Tagging of wires and interference of wires or tags with signal apparatus.  

Code of Federal Regulations, 2012 CFR

... false Tagging of wires and interference of wires or tags with signal apparatus. 236.76 ...APPLIANCES Rules and Instructions: All Systems Wires and Cables § 236.76 Tagging of wires and interference of wires or tags with...

2012-10-01

156

49 CFR 236.76 - Tagging of wires and interference of wires or tags with signal apparatus.  

Code of Federal Regulations, 2010 CFR

... false Tagging of wires and interference of wires or tags with signal apparatus. 236.76 ...APPLIANCES Rules and Instructions: All Systems Wires and Cables § 236.76 Tagging of wires and interference of wires or tags with...

2010-10-01

157

49 CFR 236.76 - Tagging of wires and interference of wires or tags with signal apparatus.  

Code of Federal Regulations, 2013 CFR

... false Tagging of wires and interference of wires or tags with signal apparatus. 236.76 ...APPLIANCES Rules and Instructions: All Systems Wires and Cables § 236.76 Tagging of wires and interference of wires or tags with...

2013-10-01

158

49 CFR 236.76 - Tagging of wires and interference of wires or tags with signal apparatus.  

Code of Federal Regulations, 2011 CFR

... false Tagging of wires and interference of wires or tags with signal apparatus. 236.76 ...APPLIANCES Rules and Instructions: All Systems Wires and Cables § 236.76 Tagging of wires and interference of wires or tags with...

2011-10-01

159

Affine invariant scale-space  

Microsoft Academic Search

A newaffine invariant scale-space for planar curves is presented in this work. The scale-space is obtained from the solution of a novel nonlinear curve evolution equation which admits affine invariant solutions. This flow was proved to be the affine analogue of the well knownEuclidean shortening flow. The evolution also satisfies properties such ascausality, which makes it useful in defining a

Guillermo Sapiro; Allen Tannenbaum

1993-01-01

160

Tetherless Microgrippers With Transponder Tags  

Microsoft Academic Search

We describe the concept of utilizing tetherless mi- crostructured grippers with attached silicon (Si)-based chips for event-based gripping. Grippers were fabricated using photolitho- graphy, and Si chips were bonded to them using a solder-based directed assembly approach. Because we propose the use of these grippers as tags or to attach electronic devices to various sur- faces, we also attached commercial

Kate E. Laflin; Christopher J. Morris; Noy Bassik; Mustapha Jamal; David H. Gracias

2011-01-01

161

Infrared tag and track technique  

DOEpatents

A method of covertly tagging an object for later tracking includes providing a material capable of at least one of being applied to the object and being included in the object, which material includes deuterium; and performing at least one of applying the material to the object and including the material in the object in a manner in which in the appearance of the object is not changed, to the naked eye.

Partin, Judy K. (Idaho Falls, ID); Stone, Mark L. (Idaho Falls, ID); Slater, John (Albuquerque, NM); Davidson, James R. (Idaho Falls, ID)

2007-12-04

162

Electronic Tag and Position Sensor  

SciTech Connect

The intent of this study phase program was to adequately define the Electronic Tag and Position Sensor chip so as to be able to price and schedule the full design and development culminating in a silicon IC. Therefore, even though Hughes Aircraft Company feels that the approach submitted in this document is what should be developed, it is still considered preliminary and could change as the full design is developed.

Not Available

1992-01-20

163

Parsing of Myanmar sentences with function tagging  

E-print Network

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.

Thant, Win Win; Thein, Ni Lar

2012-01-01

164

RNase One Gene Isolation, Expression, and Affinity Purification Models Research Experimental Progression and Culminates with Guided Inquiry-Based Experiments  

ERIC Educational Resources Information Center

This new biochemistry laboratory course moves through a progression of experiments that generates a platform for guided inquiry-based experiments. RNase One gene is isolated from prokaryotic genomic DNA, expressed as a tagged protein, affinity purified, and tested for activity and substrate specificity. Student pairs present detailed explanations…

Bailey, Cheryl P.

2009-01-01

165

A "click" chemistry constructed affinity system for 2-oxoglutaric acid receptors and binding proteins.  

PubMed

An ingenious and specific affinity resin designed to capture the 2-oxoglutaric acid (2-OG) binding proteins was constructed by appending a 2-OG tag to the solid resin via a Cu-catalyzed Huisgen "click" reaction. The so-obtained affinity resin was able to recognize, retain and separate the established 2-OG binding protein NtcA in both the pure form and crude cellular extract, thus constituting a valuable means of searching for novel 2-OG receptors with a view to exploring the signalling pathways of 2-OG, a key Krebs cycle intermediate with unprecedented signalling functions. PMID:25019277

Wang, Yang; Assaf, Zeinab; Liu, Xinjun; Ziarelli, Fabio; Latifi, Amel; Lamrabet, Otmane; Quéléver, Gilles; Qu, Fanqi; Zhang, Cheng-Cai; Peng, Ling

2014-09-01

166

False positive RNA binding activities after Ni-affinity purification from Escherichia coli  

PubMed Central

A His-tag is often added by means of recombinant DNA technology to a heterologous protein of interest, which is then over-produced in Escherchia coli and purified by one-step immobilized metal-affinity chromatography (IMAC). Owing to the presence of 24 histidines at the C-termini of the hexameric E. coli RNA chaperone Hfq, the protein co-purifies with His-tagged proteins of interest. As Hfq can bind to distinct RNA substrates with high affinity, its presence can obscure studies performed with (putative) RNA binding activities purified by IMAC. Here, we present results for a seemingly positive RNA-binding activity, exemplifying that false-positive results can be avoided if the protein of interest is either subjected to further purification step(s) or produced in an E. coli hfq- strain. PMID:23770724

Milojevic, Tetyana; Sonnleitner, Elisabeth; Romeo, Alessandra; Djinovic-Carugo, Kristina; Blasi, Udo

2013-01-01

167

LIVING AND LEARNING & AFFINITY HOUSING COMMUNITIES  

E-print Network

LIVING AND LEARNING & AFFINITY HOUSING COMMUNITIES What are Living and Learning Communities and Affinity Housing Communities? Living and Learning Communities (LLC) and Affinity Housing Communities (AHC are the Affinity Housing Communities? Fraternity and Sorority Floors in Callahan Hall Please visit: http

Boyce, Richard L.

168

Tagged-weak {pi} method  

SciTech Connect

A new 'tagged-weak {pi} method' is proposed for determination of electromagnetic transition probabilities B(E2) and B(M1) of the hypernuclear states with lifetimes of {approx}10{sup -10} s. With this method, we are planning to measure B(E2) and B(M1) for light hypernuclei at JLab. The results of Monte Carlo simulations for the case of E2(5/2{sup +}, 3/2{sup +} {yields} 1/2{sup +}) transitions in {sub {Lambda}}{sup 7}He hypernuclei are presented.

Margaryan, A., E-mail: mat@yerphi.am [Yerevan Physics Institute (Armenia); Hashimoto, O. [Tohoku University, Department of Physics (Japan); Kakoyan, V.; Knyazyan, S. [Yerevan Physics Institute (Armenia); Tang, L. [Hampton University, Department of Physics (United States)

2011-02-15

169

Not All Sequence Tags Are Created Equal: Designing and Validating Sequence Identification Tags Robust to Indels  

PubMed Central

Ligating adapters with unique synthetic oligonucleotide sequences (sequence tags) onto individual DNA samples before massively parallel sequencing is a popular and efficient way to obtain sequence data from many individual samples. Tag sequences should be numerous and sufficiently different to ensure sequencing, replication, and oligonucleotide synthesis errors do not cause tags to be unrecoverable or confused. However, many design approaches only protect against substitution errors during sequencing and extant tag sets contain too few tag sequences. We developed an open-source software package to validate sequence tags for conformance to two distance metrics and design sequence tags robust to indel and substitution errors. We use this software package to evaluate several commercial and non-commercial sequence tag sets, design several large sets (maxcount?=?7,198) of edit metric sequence tags having different lengths and degrees of error correction, and integrate a subset of these edit metric tags to polymerase chain reaction (PCR) primers and sequencing adapters. We validate a subset of these edit metric tagged PCR primers and sequencing adapters by sequencing on several platforms and subsequent comparison to commercially available alternatives. We find that several commonly used sets of sequence tags or design methodologies used to produce sequence tags do not meet the minimum expectations of their underlying distance metric, and we find that PCR primers and sequencing adapters incorporating edit metric sequence tags designed by our software package perform as well as their commercial counterparts. We suggest that researchers evaluate sequence tags prior to use or evaluate tags that they have been using. The sequence tag sets we design improve on extant sets because they are large, valid across the set, and robust to the suite of substitution, insertion, and deletion errors affecting massively parallel sequencing workflows on all currently used platforms. PMID:22900027

Faircloth, Brant C.; Glenn, Travis C.

2012-01-01

170

Understanding why users tag: A survey of tagging motivation literature and results from an empirical study.  

PubMed

While recent progress has been achieved in understanding the structure and dynamics of social tagging systems, we know little about the underlying user motivations for tagging, and how they influence resulting folksonomies and tags. This paper addresses three issues related to this question. (1) What distinctions of user motivations are identified by previous research, and in what ways are the motivations of users amenable to quantitative analysis? (2) To what extent does tagging motivation vary across different social tagging systems? (3) How does variability in user motivation influence resulting tags and folksonomies? In this paper, we present measures to detect whether a tagger is primarily motivated by categorizing or describing resources, and apply these measures to datasets from seven different tagging systems. Our results show that (a) users' motivation for tagging varies not only across, but also within tagging systems, and that (b) tag agreement among users who are motivated by categorizing resources is significantly lower than among users who are motivated by describing resources. Our findings are relevant for (1) the development of tag-based user interfaces, (2) the analysis of tag semantics and (3) the design of search algorithms for social tagging systems. PMID:23471473

Strohmaier, Markus; Körner, Christian; Kern, Roman

2012-12-01

171

Scalable Faceted Ranking in Tagging Systems  

NASA Astrophysics Data System (ADS)

Nowadays, web collaborative tagging systems which allow users to upload, comment on and recommend contents, are growing. Such systems can be represented as graphs where nodes correspond to users and tagged-links to recommendations. In this paper we analyze the problem of computing a ranking of users with respect to a facet described as a set of tags. A straightforward solution is to compute a PageRank-like algorithm on a facet-related graph, but it is not feasible for online computation. We propose an alternative: (i) a ranking for each tag is computed offline on the basis of tag-related subgraphs; (ii) a faceted order is generated online by merging rankings corresponding to all the tags in the facet. Based on the graph analysis of YouTube and Flickr, we show that step (i) is scalable. We also present efficient algorithms for step (ii), which are evaluated by comparing their results with two gold standards.

Orlicki, José I.; Alvarez-Hamelin, J. Ignacio; Fierens, Pablo I.

172

Protein Purification with Polymeric Affinity Membranes Containing Functionalized Poly(acid) Brushes  

PubMed Central

Porous nylon membranes modified with poly(acid) brushes and their derivatives can rapidly purify proteins via ion-exchange and metal-ion affinity interactions. Membranes containing poly(2-(methacryloyloxy)ethyl succinate) (poly(MES)) brushes bind 118 ± 8 mg of lysozyme per cm3 of membrane and facilitate purification of lysozyme from chicken egg white. Moreover, functionalization of the poly(MES) brushes with nitrilotriacetate (NTA)-Ni2+ complexes yields membranes that bind poly(histidine)-tagged (His-tagged) ubiquitin with a capacity of 85 ± 2 mg of protein per cm3 of membrane. Most importantly, the membranes modified with poly(MES)-NTA-Ni2+ allow isolation of His-tagged cellular retinaldehyde-binding protein directly from a cell extract in less than 10 min, and the protein purity is comparable to that achieved with commercial affinity columns. Thus, porous nylon membranes containing functionalized poly(MES) brushes are attractive candidates for rapid, high-capacity purification of His-tagged proteins from cell extracts. PMID:20187657

Jain, Parul; Vyas, Mukesh Kumar; Geiger, James H.; Baker, Gregory L.; Bruening, Merlin L.

2010-01-01

173

Identification of secreted bacterial proteins by noncanonical amino acid tagging.  

PubMed

Pathogenic microbes have evolved complex secretion systems to deliver virulence factors into host cells. Identification of these factors is critical for understanding the infection process. We report a powerful and versatile approach to the selective labeling and identification of secreted pathogen proteins. Selective labeling of microbial proteins is accomplished via translational incorporation of azidonorleucine (Anl), a methionine surrogate that requires a mutant form of the methionyl-tRNA synthetase for activation. Secreted pathogen proteins containing Anl can be tagged by azide-alkyne cycloaddition and enriched by affinity purification. Application of the method to analysis of the type III secretion system of the human pathogen Yersinia enterocolitica enabled efficient identification of secreted proteins, identification of distinct secretion profiles for intracellular and extracellular bacteria, and determination of the order of substrate injection into host cells. This approach should be widely useful for the identification of virulence factors in microbial pathogens and the development of potential new targets for antimicrobial therapy. PMID:24347637

Mahdavi, Alborz; Szychowski, Janek; Ngo, John T; Sweredoski, Michael J; Graham, Robert L J; Hess, Sonja; Schneewind, Olaf; Mazmanian, Sarkis K; Tirrell, David A

2014-01-01

174

Identification of secreted bacterial proteins by noncanonical amino acid tagging  

PubMed Central

Pathogenic microbes have evolved complex secretion systems to deliver virulence factors into host cells. Identification of these factors is critical for understanding the infection process. We report a powerful and versatile approach to the selective labeling and identification of secreted pathogen proteins. Selective labeling of microbial proteins is accomplished via translational incorporation of azidonorleucine (Anl), a methionine surrogate that requires a mutant form of the methionyl-tRNA synthetase for activation. Secreted pathogen proteins containing Anl can be tagged by azide-alkyne cycloaddition and enriched by affinity purification. Application of the method to analysis of the type III secretion system of the human pathogen Yersinia enterocolitica enabled efficient identification of secreted proteins, identification of distinct secretion profiles for intracellular and extracellular bacteria, and determination of the order of substrate injection into host cells. This approach should be widely useful for the identification of virulence factors in microbial pathogens and the development of potential new targets for antimicrobial therapy. PMID:24347637

Mahdavi, Alborz; Szychowski, Janek; Ngo, John T.; Sweredoski, Michael J.; Graham, Robert L. J.; Hess, Sonja; Schneewind, Olaf; Mazmanian, Sarkis K.; Tirrell, David A.

2014-01-01

175

Noncovalent tagging proteins with paramagnetic lanthanide complexes for protein study.  

PubMed

The site-specific labeling of proteins with paramagnetic lanthanides offers unique opportunities for NMR spectroscopic analysis in structural biology. Herein, we report an interesting way of obtaining paramagnetic structural restraints by employing noncovalent interaction between a lanthanide metal complex, [Ln(L)3](n-) (L=derivative of dipicolinic acid, DPA), and a protein. These complexes formed by lanthanides and DPA derivatives, which have different substitution patterns on the DPA derivatives, produce diverse thermodynamic and paramagnetic properties when interacting with proteins. The binding affinity of [Ln(L)3](n-) with proteins, as well as the determined paramagnetic tensor, are tunable by changing the substituents on the ligands. These noncovalent interactions between [Ln(L)3](n-) and proteins offer great opportunities in the tagging of proteins with paramagnetic lanthanides. We expect that this method will be useful for obtaining multiple angles and distance restraints of proteins in structural biology. PMID:23450718

Wei, Zhen; Yang, Yin; Li, Qing-Feng; Huang, Feng; Zuo, Hui-Hui; Su, Xun-Cheng

2013-04-26

176

Scalable Faceted Ranking in Tagging Systems  

Microsoft Academic Search

\\u000a Nowadays, web collaborative tagging systems which allow users to upload, comment on and recommend contents, are growing. Such\\u000a systems can be represented as graphs where nodes correspond to users and tagged-links to recommendations. In this paper we\\u000a analyze the problem of computing a ranking of users with respect to a facet described as a set of tags. A straightforward\\u000a solution

José Ignacio Orlicki; J. Ignacio Alvarez-Hamelin; Pablo Ignacio Fierens

2009-01-01

177

MUBs inequivalence and affine planes  

NASA Astrophysics Data System (ADS)

There are fairly large families of unitarily inequivalent complete sets of N + 1 mutually unbiased bases (MUBs) known in {C}N for various prime powers N. The number of such sets is not bounded above by any polynomial as a function of N. While it is standard that there is a superficial similarity between complete sets of MUBs and finite affine planes, there is an intimate relationship between these large families and affine planes. This note briefly summarizes "old" results that do not appear to be well known concerning known families of complete sets of MUBs and their associated planes.

Kantor, W. M.

2012-03-01

178

MUBs inequivalence and affine planes  

E-print Network

There are fairly large families of unitarily inequivalent complete sets of N+1 mutually unbiased bases (MUBs) in C^N for various prime powers N. The number of such sets is not bounded above by any polynomial as a function of N. While it is standard that there is a superficial similarity between complete sets of MUBs and finite affine planes, there is an intimate relationship between these large families and affine planes. This note briefly summarizes "old" results that do not appear to be well-known concerning known families of complete sets of MUBs and their associated planes.

W. K. Kantor

2011-04-18

179

Applications of a peptide ligand for streptavidin: the Strep-tag.  

PubMed

The Strep-tag constitutes a nine amino acid-peptide that binds specifically to streptavidin and occupies the same pocket where biotin is normally complexed. Since the Strep-tag participates in a reversible interaction it can be applied for the efficient purification of corresponding fusion proteins on affinity columns with immobilized streptavidin. Elution of the bound recombinant protein can be effected under mild buffer conditions by competition with biotin or a suitable derivative. In addition, Strep-tag fusion proteins can be easily detected in immunochemical assays, like Western blots or ELISAs, by means of commercially available streptavidin-enzyme conjugates. The Strep-tag/streptavidin system has been systematically optimized over the past years, including the engineering of streptavidin itself. Structural insight into the molecular mimicry between the peptide and biotin was furthermore gained from X-ray crystallographic analysis. As a result the system provides a reliable and versatile tool in recombinant protein chemistry. Exemplary applications of the Strep-tag are discussed in this review. PMID:10796988

Skerra, A; Schmidt, T G

1999-12-31

180

Chemical binding affinity estimation using MSB  

NASA Astrophysics Data System (ADS)

Binding affinity can be estimated in several ways in the laboratory but there is no viable way to estimate binding affinity in vivo without assumptions on the number of binding sites. Magnetic spectroscopy of nanoparticle Brownian motion, MSB, measures the rotational Brownian motion. The MSB signal is affected by nanoparticle binding affinity so it provides a mechanism to measure the chemical binding affinity. We present a possible mechanism to quantify the binding affinity and test that mechanism using viscous solutions.

Weaver, John B.; Rauwerdink, Adam M.

2011-03-01

181

Engineering Escherichia coli BL21(DE3) Derivative Strains To Minimize E. coli Protein Contamination after Purification by Immobilized Metal Affinity Chromatography ? † ‡  

PubMed Central

Recombinant His-tagged proteins expressed in Escherichia coli and purified by immobilized metal affinity chromatography (IMAC) are commonly coeluted with native E. coli proteins, especially if the recombinant protein is expressed at a low level. The E. coli contaminants display high affinity to divalent nickel or cobalt ions, mainly due to the presence of clustered histidine residues or biologically relevant metal binding sites. To improve the final purity of expressed His-tagged protein, we engineered E. coli BL21(DE3) expression strains in which the most recurring contaminants are either expressed with an alternative tag or mutated to decrease their affinity to divalent cations. The current study presents the design, engineering, and characterization of two E. coli BL21(DE3) derivatives, NiCo21(DE3) and NiCo22(DE3), which express the endogenous proteins SlyD, Can, ArnA, and (optionally) AceE fused at their C terminus to a chitin binding domain (CBD) and the protein GlmS, with six surface histidines replaced by alanines. We show that each E. coli CBD-tagged protein remains active and can be efficiently eliminated from an IMAC elution fraction using a chitin column flowthrough step, while the modification of GlmS results in loss of affinity for nickel-containing resin. The “NiCo” strains uniquely complement existing methods for improving the purity of recombinant His-tagged protein. PMID:21602383

Robichon, Carine; Luo, Jianying; Causey, Thomas B.; Benner, Jack S.; Samuelson, James C.

2011-01-01

182

Tag-based web photo retrieval improved by batch mode re-tagging  

Microsoft Academic Search

Web photos in social media sharing websites such as Flickr are generally accompanied by rich but noisy textual descriptions (tags, captions, categories, etc.). In this pa- per, we proposed a tag-based photo retrieval framework to improve the retrieval performance for Flickr photos by em- ploying a novel batch mode re-tagging method. The pro- posed batch mode re-tagging method can automatically

Dong Xu; Ivor Wai-Hung Tsang; Jiebo Luo

2010-01-01

183

Strategy for improvement of enteropeptidase efficiency in tag removal processes.  

PubMed

Enteropeptidase (synonym: enterokinase, EC 3.4.21.9) is a heterodimeric serine protease of the intestinal brush border that activates trypsinogen by highly specific cleavage of the trypsinogen activation peptide following the sequence (Asp)(4)-Lys. It has also great biotechnological interest because of the unique substrate specificity of the serine protease domain. The high degree of specificity exhibited by enteropeptidase makes it a suitable reagent for cleaving recombinant proteins to remove affinity or other tags. However often unwanted cleavages elsewhere in the protein occurred during cleavage of fusions when high amount of enzyme is required. In this study we have improved the efficiency of fusion proteins cleavage by enteropeptidase by substitution of the Lys residue by Arg in specific cleavage sequence (Asp)(4)-Lys. We have demonstrated that 3-6-fold lower amounts of the catalytic subunit of human and bovine enteropeptidase is required for 95% cleavage of Trx/TRAIL and Trx/FGF-2 fusions with (Asp)(4)-Arg cleavage sequence in comparison to native sequence (Asp)(4)-Lys. As a result, reduced amount of non-specifically cleaved peptide fragments were observed during cleavage of (Asp)(4)-Lys/Arg mutated fusions. These findings overcome limitations of enteropeptidase in tag removal processes during recombinant proteins purification and extend its commercial benefit in the biopharmaceutical industry. PMID:21515380

Gasparian, Marine E; Bychkov, Maxim L; Dolgikh, Dmitry A; Kirpichnikov, Mikhail P

2011-10-01

184

Enzymatically amplified mass tags for tissue mass spectrometry imaging.  

PubMed

Tissue mass spectrometry imaging (MSI) is a rapidly developing technology which promises to provide biomarker molecular information within tissue context, which is an unmet medical need in the era of personalized medicine. However, challenges associated with tissue specimens as well as the MSI technical limitations have hindered the practical applications of this technology. We report here a mass tag based MSI method that combines the strength of signal amplification by immuno-enzymatic reactions with the superior detection characteristics of mass spectrometry to enable matrix-free MSI of protein biomarkers in formalin fixed paraffin embedded (FFPE) tissues. The method involves binding of the target protein with a primary antibody with high affinity and specificity, followed by binding with a secondary antibody-enzyme conjugate. Enzyme substrates suitable for mass spectrometry detection are locally deposited at the site of the target through enzymatically catalyzed transformation. The precipitates thus serve as mass tags to be detected in mass spectrometry to represent the target biomolecule in tissue. Two enzymes and various substrates have been identified and successfully used to demonstrate the feasibility of this novel MSI method to image protein targets in FFPE tissue samples. PMID:24410597

Hong, Rui; True, Jan; Bieniarz, Christopher

2014-02-01

185

Affinity purification of binding miRNAs for messenger RNA fused with a common tag.  

PubMed

Prediction of microRNA-mRNA interaction typically relies on bioinformatic methods, but these methods only suggest the possibility of microRNA binding and may miss important interactions as well as falsely predict others. A major obstacle to the miRNA research has been the lack of experimental procedures for the identification of miRNA-mRNA interactions. Recently, a few studies have attempted to explore experimental methods to isolate and identify miRNA targets or miRNAs targeting a single gene. Here, we developed an more convenient experimental approach for the isolation and identification of miRNAs targeting a single gene by applying short biotinylated DNA anti-sense oligonucleotides mix to enhanced green fluorescent protein (EGFP) mRNA which was fused to target gene mRNA. This method does not require a design of different anti-sense oligonucleotides to any mRNA. This is a simple and an efficient method to potentially identify miRNAs targeting specific gene mRNA combined with chip screen. PMID:25153630

Wei, Ke; Yan, Feng; Xiao, Hui; Yang, Xiaoxu; Xie, Guie; Xiao, Ye; Wang, Tingting; Xun, Yu; Huang, Zhaoqin; Han, Mei; Zhang, Jian; Xiang, Shuanglin

2014-01-01

186

Affinity Purification of Binding miRNAs for Messenger RNA Fused with a Common Tag  

PubMed Central

Prediction of microRNA–mRNA interaction typically relies on bioinformatic methods, but these methods only suggest the possibility of microRNA binding and may miss important interactions as well as falsely predict others. A major obstacle to the miRNA research has been the lack of experimental procedures for the identification of miRNA–mRNA interactions. Recently, a few studies have attempted to explore experimental methods to isolate and identify miRNA targets or miRNAs targeting a single gene. Here, we developed an more convenient experimental approach for the isolation and identification of miRNAs targeting a single gene by applying short biotinylated DNA anti-sense oligonucleotides mix to enhanced green fluorescent protein (EGFP) mRNA which was fused to target gene mRNA. This method does not require a design of different anti-sense oligonucleotides to any mRNA. This is a simple and an efficient method to potentially identify miRNAs targeting specific gene mRNA combined with chip screen. PMID:25153630

Wei, Ke; Yan, Feng; Xiao, Hui; Yang, Xiaoxu; Xie, Guie; Xiao, Ye; Wang, Tingting; Xun, Yu; Huang, Zhaoqin; Han, Mei; Zhang, Jian; Xiang, Shuanglin

2014-01-01

187

Using association rules for discovering tag bundles in social tagging data  

Microsoft Academic Search

Social tagging has become very popular with the rise of Web 2.0, making it an important piece of the puzzle that makes up the web phenomenon. In contrast to more elaborate ways of organizing resources, such as taxonomies or ontologies, tagging is very easy to use and understand. Because of its simplicity tagging does not create explicit, formalized, structures. By

Walter Christian Kammergruber; Maximilian Viermetz; Karsten Ehms; Manfred Langen

2010-01-01

188

Recent advances in conventional tag-ging and ultrasonic telemetry meth-  

E-print Network

405 Recent advances in conventional tag- ging and ultrasonic telemetry meth- ods have substantially found along the Gulf and Atlantic coasts, conventional tagging and ultrasonic telemetry have been ocellatus) inferred from conventional tagging and ultrasonic telemetry Nathan M. Bacheler (contact author)1

189

Evacuation of Passive Integrated Transponder (PIT) Tags from Northern Pikeminnow Consuming Tagged Juvenile Chinook Salmon  

Microsoft Academic Search

Prey fish implanted with passive integrated transponder (PIT) tags can be used in predation studies if the timing of tag evacuation from the predators is understood. Laboratory experiments were conducted to determine how PIT tags in juvenile Chinook salmon Oncorhynchus tshawytscha that were consumed by northern pikeminnow Ptychocheilus oregonensis were evacuated in relation to various parameters. The rate of evacuation

James H. Petersen; Craig A. Barfoot

2003-01-01

190

Mixture Modeling by Affinity Propagation  

Microsoft Academic Search

Clustering is a fundamental problem in machine learning and has been approached in many ways. Two general and quite different approaches include iteratively fitting a mixture model ( e.g., using EM) and linking to- gether pairs of training cases that have high affinity ( e.g., using spectral methods). Pair-wise clustering algorithms need not compute sufficient statistics and avoid poor solutions

Brendan J. Frey; Delbert Dueck

2005-01-01

191

Analyzing microblogs with affinity propagation  

Microsoft Academic Search

Recently, there has been a great deal of interest in analyzing inherent structures in posts on microblogs such as Twitter. While many works utilize a well-known topic modeling technique, we instead propose to apply Affinity Propagation [4] (AP) to analyze such a corpus, and we hypothesize that AP may provide different perspective to the traditional approach. Our preliminary analysis raises

Jeon Hyung Kang; Kristina Lerman; Anon Plangprasopchok

2010-01-01

192

Scaling analysis of affinity propagation  

Microsoft Academic Search

We analyze and exploit some scaling properties of the affinity propagation (AP) clustering algorithm proposed by Frey and Dueck [Science 315, 972 (2007)]. Following a divide and conquer strategy we setup an exact renormalization-based approach to address the question of clustering consistency, in particular, how many cluster are present in a given data set. We first observe that the divide

Cyril Furtlehner; Michèle Sebag; Xiangliang Zhang

2010-01-01

193

SOLVABLE AFFINE TERM STRUCTURE MODELS  

Microsoft Academic Search

An Affine Term Structure Model (ATSM) is said to be solvable if the pricing problem has an explicit solution, i.e., the corresponding Riccati ordinary differential equations have a regular globally integrable flow. We identify the parametric restrictions which are necessary and sufficient for an ATSM with continuous paths, to be solvable in a state space , where , the domain

Martino Grasselli; Claudio Tebaldi

2008-01-01

194

The fast affine projection algorithm  

Microsoft Academic Search

This paper discusses a new adaptive filtering algorithm called fast affine projections (FAP). FAP's key features include LMS like complexity and memory requirements (low), and RLS like convergence (fast) for the important case where the excitation signal is speech. Another of FAP's important features is that it causes no delay in the input or output signals. In addition, the algorithm

Steven L. Gay; Sanjeev Tavathia

1995-01-01

195

Phosphorylation of serine residues in histidine-tag sequences attached to recombinant protein kinases: a cause of heterogeneity in mass and complications in function.  

PubMed

High-level recombinant expression of protein kinases in eukaryotic cells or Escherichia coli commonly gives products that are phosphorylated by autocatalysis or by the action of endogenous kinases. Here, we report that phosphorylation occurred on serine residues adjacent to hexahistidine affinity tags (His-tags) derived from several commercial expression vectors and fused to overexpressed kinases. The result was observed with a variety of recombinant kinases expressed in either insect cells or E. coli. Multiple phosphorylations of His-tagged full-length Aurora A, a protein serine/threonine kinase, were detected by mass spectrometry when it was expressed in insect cells in the presence of okadaic acid, a protein phosphatase inhibitor. Peptide mapping by liquid chromatography-mass spectrometry detected phosphorylations on all three serine residues in an N-terminal tag, alpha-N-acetyl-MHHHHHHSSGLPRGS. The same sequence was also phosphorylated, but only at a low level, when a His-tagged protein tyrosine kinase, Pyk2 was expressed in insect cells and activated in vitro. When catalytic domains of Aurora A and several other protein serine/threonine kinases were expressed in E. coli, serines in the affinity tag sequence GSSHHHHHHSSGLVPRGS were also variably phosphorylated. His-Aurora A with hyperphosphorylation of the serine residues in the tag aggregated and resisted thrombin-catalyzed removal of the tag. Treatment with alkaline phosphatase partly restored sensitivity to thrombin. The same His-tag sequence was also detected bearing alpha-N-d-gluconoylation in addition to multiple phosphorylations. The results show that histidine-tag sequences can receive complicated posttranslational modification, and that the hyperphosphorylation and resulting heterogeneity of the recombinant fusion proteins can interfere with downstream applications. PMID:15946859

Du, Ping; Loulakis, Pat; Luo, Chun; Mistry, Anil; Simons, Samuel P; LeMotte, Peter K; Rajamohan, Francis; Rafidi, Kristina; Coleman, Kevin G; Geoghegan, Kieran F; Xie, Zhi

2005-12-01

196

Evaluation of visible implant elastomer tags in zebrafish (Danio rerio)  

PubMed Central

Summary The use of the visible implant elastomer (VIE) tagging system in zebrafish (Danio rerio) was examined. Two tag orientations (horizontal and vertical) at the dorsal fin base were tested for tag retention, tag fragmentation and whether VIE tags affected growth and survival of juvenile zebrafish (1–4 month post hatch). Six tag locations (abdomen, anal fin base, caudal peduncle, dorsal fin base, pectoral fin base, isthmus) and 5 tag colors (yellow, red, pink, orange, blue) were evaluated for ease of VIE tag application and tag visibility in adult zebrafish. Long-term retention (1 year) and multiple tagging sites (right and left of dorsal fin and pectoral fin base) were examined in adult zebrafish. Lastly, survival of recombination activation gene 1?/? (rag1?/?) zebrafish was evaluated after VIE tagging. The best tag location was the dorsal fin base, and the most visible tag color was pink. Growth rate of juvenile zebrafish was not affected by VIE tagging. Horizontal tagging is recommended in early stages of fish growth (1–2 months post hatch). VIE tags were retained for 1 year and tagging did not interfere with long-term growth and survival. There was no mortality associated with VIE tagging in rag1?/? zebrafish. The VIE tagging system is highly suitable for small-sized zebrafish. When familiar with the procedure, 120 adult zebrafish can be tagged in one hour. It does not increase mortality in adult zebrafish or interfere with growth in juvenile or adult zebrafish. PMID:24285706

Hohn, Claudia; Petrie-Hanson, Lora

2013-01-01

197

To tag or not to tag: animal welfare, conservation and stakeholder considerations in fish tracking studies that use electronic tags  

SciTech Connect

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.

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

198

Technical Note Pulmonary Kinematics From Tagged Hyperpolarized  

E-print Network

assessment of disease progression. Key Words: helium-3; registration; pulmonary kinematics; tagging J. MagnTechnical Note Pulmonary Kinematics From Tagged Hyperpolarized Helium-3 MRI Nicholas J. Tustison the feasibility of a novel method for quantifying 3D regional pulmonary kinematics from hyperpolarized helium-3

Utah, University of

199

Page 1 of 1 Fish Tagging Forum  

E-print Network

Page 1 of 1 AGENDA Fish Tagging Forum Northwest Power and Conservation Council Meeting:30 Opening Remarks Forum Manager, Forum Chair, and Participants will share their perspectives and expectations related to the Fish Tagging Forum. BREAK 10:45 to 11:15 Forum Ground Rules, Participation

200

SOCIAL TAGGING AND MUSIC INFORMATION RETRIEVAL  

Microsoft Academic Search

Social tags are free text labels that are applied to items such as artists, albums and songs. Captured in these tags is a great deal of information that is highly relevant to Music Information Retrieval (MIR) researchers including infor- mation about genre, mood, instrumentation, and quality. Unfortunately there is also a great deal of irrelevant in- formation and noise in

Paul Lamere

201

MFR PAPER 1069 Coded wire tagging  

E-print Network

additional or different fins removed . The use of thermal marks (hot and cold) on juvenile Pacific salmon of the magneti zed wire tag for automatic detection and eparation of tagged adult almon . y tem. or de ice ucce - fully operated in fish ladder on the Snake River at Ice Harbor and Little Goose Dam from 1970

202

Method and apparatus for manufacturing gas tags  

DOEpatents

For use in the manufacture of gas tags employed in a gas tagging failure detection system for a nuclear reactor, a plurality of commercial feed gases each having a respective noble gas isotopic composition are blended under computer control to provide various tag gas mixtures having selected isotopic ratios which are optimized for specified defined conditions such as cost. Using a new approach employing a discrete variable structure rather than the known continuous-variable optimization problem, the computer controlled gas tag manufacturing process employs an analytical formalism from condensed matter physics known as stochastic relaxation, which is a special case of simulated annealing, for input feed gas selection. For a tag blending process involving M tag isotopes with N distinct feed gas mixtures commercially available from an enriched gas supplier, the manufacturing process calculates the cost difference between multiple combinations and specifies gas mixtures which approach the optimum defined conditions. The manufacturing process is then used to control tag blending apparatus incorporating tag gas canisters connected by stainless-steel tubing with computer controlled valves, with the canisters automatically filled with metered quantities of the required feed gases.

Gross, Kenny C. (Bolingbrook, IL); Laug, Matthew T. (Idaho Falls, ID)

1996-01-01

203

Method and apparatus for manufacturing gas tags  

DOEpatents

For use in the manufacture of gas tags employed in a gas tagging failure detection system for a nuclear reactor, a plurality of commercial feed gases each having a respective noble gas isotopic composition are blended under computer control to provide various tag gas mixtures having selected isotopic ratios which are optimized for specified defined conditions such as cost. Using a new approach employing a discrete variable structure rather than the known continuous-variable optimization problem, the computer controlled gas tag manufacturing process employs an analytical formalism from condensed matter physics known as stochastic relaxation, which is a special case of simulated annealing, for input feed gas selection. For a tag blending process involving M tag isotopes with N distinct feed gas mixtures commercially available from an enriched gas supplier, the manufacturing process calculates the cost difference between multiple combinations and specifies gas mixtures which approach the optimum defined conditions. The manufacturing process is then used to control tag blending apparatus incorporating tag gas canisters connected by stainless-steel tubing with computer controlled valves, with the canisters automatically filled with metered quantities of the required feed gases. 4 figs.

Gross, K.C.; Laug, M.T.

1996-12-17

204

Notes on SAW Tag Interrogation Techniques.  

National Technical Information Service (NTIS)

We consider the problem of interrogating a single SAW RFID tag with a known ID and known range in the presence of multiple interfering tags under the following assumptions: (1) The RF propagation environment is well approximated as a simple delay channel ...

R. J. Barton

2010-01-01

205

50 CFR 20.36 - Tagging requirement.  

Code of Federal Regulations, 2010 CFR

...WILDLIFE AND PLANTS (CONTINUED) MIGRATORY BIRD HUNTING Possession § 20.36 Tagging...person shall put or leave any migratory game birds at any place (other than at his personal...taxidermy services performed, unless such birds have a tag attached, signed by the...

2010-10-01

206

50 CFR 20.36 - Tagging requirement.  

Code of Federal Regulations, 2012 CFR

...WILDLIFE AND PLANTS (CONTINUED) MIGRATORY BIRD HUNTING Possession § 20.36 Tagging...person shall put or leave any migratory game birds at any place (other than at his personal...taxidermy services performed, unless such birds have a tag attached, signed by the...

2012-10-01

207

50 CFR 20.36 - Tagging requirement.  

Code of Federal Regulations, 2011 CFR

...WILDLIFE AND PLANTS (CONTINUED) MIGRATORY BIRD HUNTING Possession § 20.36 Tagging...person shall put or leave any migratory game birds at any place (other than at his personal...taxidermy services performed, unless such birds have a tag attached, signed by the...

2011-10-01

208

USE OF DYNAMITE TO RECOVER TAGGED SALMON  

E-print Network

353 USE OF DYNAMITE TO RECOVER TAGGED SALMON Marine Biological Laboratory LIBRARY Of. zi 1960 WOODS of Commercial Fisheries, Donald L. McKernan, Director USE OF DYNAMITE TO RECOVER TAGGED SALMON by Richard W Page The effect of dynamite on salmon 2 Description and results of variables tested 3 Effect of water

209

Harnessing Collective Knowledge Inherent in Tag Clouds  

ERIC Educational Resources Information Center

Tagging systems represent the conceptual knowledge of a community. We experimentally tested whether people harness this collective knowledge when navigating through the Web. As a within-factor we manipulated people's prior knowledge (no knowledge vs. prior knowledge that was congruent/incongruent to the collective knowledge inherent in the tags).…

Cress, U.; Held, C.

2013-01-01

210

Affinity chromatography and capillary electrophoresis for analysis of the yeast ribosomal proteins.  

PubMed

We present a top down separation platform for yeast ribosomal proteins using affinity chromatography and capillary electrophoresis which is designed to allow deposition of proteins onto a substrate. FLAG tagged ribosomes were affinity purified, and rRNA acid precipitation was performed on the ribosomes followed by capillary electrophoresis to separate the ribosomal proteins. Over 26 peaks were detected with excellent reproducibility (<0.5% RSD migration time). This is the first reported separation of eukaryotic ribosomal proteins using capillary electrophoresis. The two stages in this workflow, affinity chromatography and capillary electrophoresis, share the advantages that they are fast, flexible and have small sample requirements in comparison to more commonly used techniques. This method is a remarkably quick route from cell to separation that has the potential to be coupled to high throughput readout platforms for studies of the ribosomal proteome. PMID:22531133

Goyder, Miriam S; Willison, Keith R; Klug, David R; Demello, Andrew J; Ces, Oscar

2012-04-01

211

RNA mango aptamer-fluorophore: a bright, high-affinity complex for RNA labeling and tracking.  

PubMed

Because RNA lacks strong intrinsic fluorescence, it has proven challenging to track RNA molecules in real time. To address this problem and to allow the purification of fluorescently tagged RNA complexes, we have selected a high affinity RNA aptamer called RNA Mango. This aptamer binds a series of thiazole orange (fluorophore) derivatives with nanomolar affinity, while increasing fluorophore fluorescence by up to 1,100-fold. Visualization of RNA Mango by single-molecule fluorescence microscopy, together with injection and imaging of RNA Mango/fluorophore complex in C. elegans gonads demonstrates the potential for live-cell RNA imaging with this system. By inserting RNA Mango into a stem loop of the bacterial 6S RNA and biotinylating the fluorophore, we demonstrate that the aptamer can be used to simultaneously fluorescently label and purify biologically important RNAs. The high affinity and fluorescent properties of RNA Mango are therefore expected to simplify the study of RNA complexes. PMID:25101481

Dolgosheina, Elena V; Jeng, Sunny C Y; Panchapakesan, Shanker Shyam S; Cojocaru, Razvan; Chen, Patrick S K; Wilson, Peter D; Hawkins, Nancy; Wiggins, Paul A; Unrau, Peter J

2014-10-17

212

Visible Implant Elastomer Color Determination, Tag Visibility, and Tag Loss: Potential Sources of Error for Mark–Recapture Studies  

Microsoft Academic Search

Errors in visible implant elastomer (VIE) color determination may exert stronger influences on mark–recapture data quality than poor tag visibility and tag loss. I applied individual VIE tags to 567 wild long-snouted seahorses Hippocampus guttulatus using four fluorescent colors (red, orange, green, and yellow). Given VIE tag data were compared with tag data recorded by observers as they released recently

Janelle M. R. Curtis

2006-01-01

213

Engineering the ATLAS TAG Browser  

NASA Astrophysics Data System (ADS)

ELSSI is a web-based event metadata (TAG) browser and event-level selection service for ATLAS. In this paper, we describe some of the challenges encountered in the process of developing ELSSI, and the software engineering strategies adopted to address those challenges. Approaches to management of access to data, browsing, data rendering, query building, query validation, execution, connection management, and communication with auxiliary services are discussed. We also describe strategies for dealing with data that may vary over time, such as run-dependent trigger decision decoding. Along with examples, we illustrate how programming techniques in multiple languages (PHP, JAVASCRIPT, XML, AJAX, and PL/SQL) have been blended to achieve the required results. Finally, we evaluate features of the ELSSI service in terms of functionality, scalability, and performance.

Zhang, Qizhi; ATLAS Collaboration

2011-12-01

214

Transposon tagging in diploid strawberry.  

PubMed

Fragaria vesca was transformed with a transposon tagging construct harbouring amino terminally deleted maize transposase and EGFP (Ac element), NPTII, CaMV 35S promoter (P35S) driving transposase and mannopine synthase promoter (Pmas) driving EGFP (Ds element). Of 180 primary transgenics, 48 were potential launch pads, 72 were multiple insertions or chimaeras, and 60 exhibited somatic transposition. T? progeny of 32 putative launch pads were screened by multiplex PCR for transposition. Evidence of germ-line transposition occurred in 13 putative launch pads; however, the transposition frequency was too low in three for efficient recovery of transposants. The transposition frequency in the remaining launch pads ranged from 16% to 40%. After self-pollination of the T? launch pads, putative transposants in the T? generation were identified by multiplex PCR. Sequencing of hiTAIL-PCR products derived from nested primers within the Ds end sequences (either P35S at the left border or the inverted repeat at the right border) of T? plants revealed transposition of the Ds element to distant sites in the strawberry genome. From more than 2400 T? plants screened, 103 unique transposants have been identified, among which 17 were somatic transpositions observed in the T? generation. Ds insertion sites were dispersed among various gene elements [exons (15%), introns (23%), promoters (30%), 3' UTRs (17%) as well as intergenically (15%)]. Three-primer (one on either side of the Ds insertion and one within the Ds T-DNA) PCR could be used to identify homozygous T? transposon-tagged plants. The mutant collection has been catalogued in an on-line database. PMID:22845757

Veilleux, Richard E; Mills, Kerri P; Baxter, Aaron J; Upham, Kendall T; Ferguson, Tammy J; Holt, Sarah Hudson; Lu, Nan; Ruiz-Rojas, Juan J; Pantazis, Christopher J; Davis, Cherish M; Lindsay, Robert C; Powell, Frankie L; Dan, Yinghui; Dickerman, Allan W; Oosumi, Teruko; Shulaev, Vladimir

2012-10-01

215

Cobalt carbonyl complexes as probes for alkyne-tagged lipids[S  

PubMed Central

Monitoring lipid distribution and metabolism in cells and biological fluids poses many challenges because of the many molecular species and metabolic pathways that exist. This study describes the synthesis and study of molecules that contain an alkyne functional group as surrogates for natural lipids in cultured cells. Thus, hexadec-15-ynoic and hexadec-7-ynoic acids were readily incorporated into RAW 264.7 cells, principally as phosphocholine esters; the alkyne was used as a “tag” that could be transformed to a stable dicobalt-hexacarbonyl complex; and the complex could then be detected by HPLC/MS or HPLC/UV349nm. The 349 nm absorbance of the cobalt complexes was used to provide qualitative and quantitative information about the distribution and cellular concentrations of the alkyne lipids. The alkyne group could also be used as an affinity tag for the lipids by a catch-and-release strategy on phosphine-coated silica beads. Lipid extracts were enriched in the tagged lipids in this way, making the approach of potential utility to study lipid transformations in cell culture. Both terminal alkynes and internal alkynes were used in this affinity “pull-down” strategy. This method facilitates measuring lipid species that might otherwise fall below limits of detection. PMID:23307946

Tallman, Keri A.; Armstrong, Michelle D.; Milne, Stephen B.; Marnett, Lawrence J.; Brown, H. Alex; Porter, Ned A.

2013-01-01

216

Data Streaming with Affinity Propagation  

Microsoft Academic Search

This paper proposed StrAP (Streaming AP), extending Affinity Propagation (AP) to data steaming. AP, a new clustering algorithm, extracts the data items,\\u000a or exemplars, that best represent the dataset using a message passing method. Several steps are made to build StrAP. The first one (Weighted AP) extends AP to weighted items with no loss of generality. The second one (Hierarchical

Xiangliang Zhang; Cyril Furtlehner; Michèle Sebag

2008-01-01

217

Genetic algorithm with affinity propagation  

Microsoft Academic Search

Classical genetic algorithm suffers heavy pressure of fitness evaluation for time-consuming optimization problems, e.g., aerodynamic design optimization, qualitative model learning in bioinformatics. To address this problem, we present a combination between genetic algorithms and clustering methods. Specifically, the clustering method used in this paper is affinity propagation. The numerical experiments demonstrate that the proposed method performs promisingly for well-known benchmark

Chunguo Wu; Hao Gao; Lianjiang Yu; Yanchun Liang; Rongwu Xiang

2010-01-01

218

Graded electron affinity semiconductor field emitter  

NASA Astrophysics Data System (ADS)

A field emitter is disclosed comprising a graded electron affinity surface layer. The graded electron affinity layer provides for increased transconductance, reduced energy distribution of emitted electrons, reduced noise and increased uniformity in its operation.

Shaw, Jonathan L.; Jesen, Kevin; Gray, Henry F.

1995-07-01

219

Identification of novel protein-protein interactions using a versatile mammalian tandem affinity purification expression system.  

PubMed

Identification of protein-protein interactions is essential for elucidating the biochemical mechanism of signal transduction. Purification and identification of individual proteins in mammalian cells have been difficult, however, due to the sheer complexity of protein mixtures obtained from cellular extracts. Recently, a tandem affinity purification (TAP) method has been developed as a tool that allows rapid purification of native protein complexes expressed at their natural level in engineered yeast cells. To adapt this method to mammalian cells, we have created a TAP tag retroviral expression vector to allow stable expression of the TAP-tagged protein at close to physiological levels. To demonstrate the utility of this vector, we have fused a TAP tag, consisting of a protein A tag, a cleavage site for the tobacco etch virus (TEV) protease, and the FLAG epitope, to the N terminus of human SMAD3 and SMAD4. We have stably expressed these proteins in mammalian cells at desirable levels by retroviral gene transfer and purified native SMAD3 protein complexes from cell lysates. The combination of two different affinity tags greatly reduced the number of nonspecific proteins in the mixture. We have identified HSP70 as a specific interacting protein of SMAD3. We demonstrated that SMAD3, but not SMAD1, binds HSP70 in vivo, validating the TAP purification approach. This method is applicable to virtually any protein and provides an efficient way to purify unknown proteins to homogeneity from the complex mixtures found in mammalian cell lysates in preparation for identification by mass spectrometry. PMID:12963786

Knuesel, Matthew; Wan, Yong; Xiao, Zhan; Holinger, Eric; Lowe, Nick; Wang, Wei; Liu, Xuedong

2003-11-01

220

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

DOEpatents

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.

Burghard, Brion J. (W. Richland, WA); Skorpik, James R. (Kennewick, WA)

2008-04-22

221

Transcriptome annotation using tandem SAGE tags  

PubMed Central

Analysis of several million expressed gene signatures (tags) revealed an increasing number of different sequences, largely exceeding that of annotated genes in mammalian genomes. Serial analysis of gene expression (SAGE) can reveal new Poly(A) RNAs transcribed from previously unrecognized chromosomal regions. However, conventional SAGE tags are too short to identify unambiguously unique sites in large genomes. Here, we design a novel strategy with tags anchored on two different restrictions sites of cDNAs. New transcripts are then tentatively defined by the two SAGE tags in tandem and by the spanning sequence read on the genome between these tagged sites. Having developed a new algorithm to locate these tag-delimited genomic sequences (TDGS), we first validated its capacity to recognize known genes and its ability to reveal new transcripts with two SAGE libraries built in parallel from a single RNA sample. Our algorithm proves fast enough to experiment this strategy at a large scale. We then collected and processed the complete sets of human SAGE tags to predict yet unknown transcripts. A cross-validation with tiling arrays data shows that 47% of these TDGS overlap transcriptional active regions. Our method provides a new and complementary approach for complex transcriptome annotation. PMID:17709346

Rivals, Eric; Boureux, Anthony; Lejeune, Mireille; Ottones, Florence; Pecharroman Perez, Oscar; Tarhio, Jorma; Pierrat, Fabien; Ruffle, Florence; Commes, Therese; Marti, Jacques

2007-01-01

222

Tags and seals for arms control verification  

SciTech Connect

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.

DeVolpi, A.

1990-09-18

223

Annotating nonspecific SAGE tags with microarray data.  

PubMed

SAGE (serial analysis of gene expression) detects transcripts by extracting short tags from the transcripts. Because of the limited length, many SAGE tags are shared by transcripts from different genes. Relying on sequence information in the general gene expression database has limited power to solve this problem due to the highly heterogeneous nature of the deposited sequences. Considering that the complexity of gene expression at a single tissue level should be much simpler than that in the general expression database, we reasoned that by restricting gene expression to tissue level, the accuracy of gene annotation for the nonspecific SAGE tags should be significantly improved. To test the idea, we developed a tissue-specific SAGE annotation database based on microarray data (). This database contains microarray expression information represented as UniGene clusters for 73 normal human tissues and 18 cancer tissues and cell lines. The nonspecific SAGE tag is first matched to the database by the same tissue type used by both SAGE and microarray analysis; then the multiple UniGene clusters assigned to the nonspecific SAGE tag are searched in the database under the matched tissue type. The UniGene cluster presented solely or at higher expression levels in the database is annotated to represent the specific gene for the nonspecific SAGE tags. The accuracy of gene annotation by this database was largely confirmed by experimental data. Our study shows that microarray data provide a useful source for annotating the nonspecific SAGE tags. PMID:16314072

Ge, Xijin; Jung, Yong-Chul; Wu, Qingfa; Kibbe, Warren A; Wang, San Ming

2006-01-01

224

A new generation of lock and tag  

SciTech Connect

The safety culture of an organization needs to change to achieve full implementation of Chapter 9, ``Lockout and Tagouts`` of DOE Order 5480.19, Conduct of Operations Requirements for DOE Facilities (DOE 1990). You can implement this change of culture through Conduct of Operations training in the classroom, in organized group discussions, and with on-the-job training. In many facilities, lock and tag is viewed as an administration function that is not directly tied to individual employee safety. Often, lock and tag is seen as an obstacle to getting the job done, a roadblock in the way of progress that has been placed there by unseen forces for unknown reasons. Because lock and tag is not always viewed as part of the personal safety standards of the employee, the necessary attention to detail is lacking. We are presenting you with three useful methods for introducing and reinforcing a new generation of safety culture and lock and tag safety. The method will help your fellow workers view lock and tag and as a safety tool. Lock and tag will become part of their safety foundation. However, you may need to do some foundation building regarding safety, personal standards, and worker attitude before the principles of lock and tag training can become an integral part of your safety culture.

Wells, P.A.; Bickford, J.C.

1992-04-01

225

A new generation of lock and tag  

SciTech Connect

The safety culture of an organization needs to change to achieve full implementation of Chapter 9, Lockout and Tagouts'' of DOE Order 5480.19, Conduct of Operations Requirements for DOE Facilities (DOE 1990). You can implement this change of culture through Conduct of Operations training in the classroom, in organized group discussions, and with on-the-job training. In many facilities, lock and tag is viewed as an administration function that is not directly tied to individual employee safety. Often, lock and tag is seen as an obstacle to getting the job done, a roadblock in the way of progress that has been placed there by unseen forces for unknown reasons. Because lock and tag is not always viewed as part of the personal safety standards of the employee, the necessary attention to detail is lacking. We are presenting you with three useful methods for introducing and reinforcing a new generation of safety culture and lock and tag safety. The method will help your fellow workers view lock and tag and as a safety tool. Lock and tag will become part of their safety foundation. However, you may need to do some foundation building regarding safety, personal standards, and worker attitude before the principles of lock and tag training can become an integral part of your safety culture.

Wells, P.A.; Bickford, J.C.

1992-04-01

226

Constructing Treatment Portfolios Using Affinity Propagation  

E-print Network

Constructing Treatment Portfolios Using Affinity Propagation Delbert Dueck1 , Brendan J. Frey1 the recently-published affinity propagation algorithm work quite well for clustering tasks. We demonstrate. In particular, we show how the affinity propagation algorithm [1] can be used to effectively to approach

Frey, Brendan J.

227

AFFINITY PROPAGATION: CLUSTERING DATA BY PASSING MESSAGES  

E-print Network

AFFINITY PROPAGATION: CLUSTERING DATA BY PASSING MESSAGES by Delbert Dueck A thesis submitted. This thesis describes a method called "affinity propagation" that simultaneously considers all data points of exemplars and corresponding clusters gradually emerges. Affinity propagation takes as input a set

Dueck, Delbert

228

Tag retention, growth, and survival of red swamp crayfish Procambarus clarkii marked with coded wire tags  

USGS Publications Warehouse

Juvenile red swamp crayfish (or crawfish), Procambarus clarkii (20-41 mm in total length) were collected from a crayfish culture pond by dipnetting and tagged with sequentially numbered, standard length, binary-coded wire tags. Four replicates of 50 crayfish were impaled perpendicular to the long axis of the abdomen with a fixed needle. Tags were injected transversely into the ventral surface of the first or second abdominal segment and were imbedded in the musculature just beneath the abdominal sternum. Tags were visible upon inspection. Additionally, two replicates of 50 crayfish were not tagged and were used as controls. Growth, survival, and tag retention were evaluated after 7 d in individual containers, after 100 d in aquaria, and after 200 d in field cages. Tag retention during each sample period was 100%, and average mortality of tagged crayfish within 7 d of tagging was 1%. Mortality during the remainder of the study was high (75-91%) but was similar between treatment and control samples. Most of the deaths were probably due to cannibalism. Average total length increased threefold during the course of the study, and crayfish reached maturity. Because crayfish were mature by the end of the study, we concluded that the coded wire tag was retained through the life history of the crayfish.

Isely, J. J.; Eversole, A. G.

1998-01-01

229

Expression and affinity purification of recombinant proteins from plants  

NASA Technical Reports Server (NTRS)

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).

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

2002-01-01

230

The connection between metal ion affinity and ligand affinity in integrin I domains  

E-print Network

The connection between metal ion affinity and ligand affinity in integrin I domains Thomas Vorup in regulating ligand binding has been reported, the relationship between metal ion binding affinity and ligand binding affinity has not been elucidated. Metal and ligand binding by several I domain mutants

Springer, Timothy A.

231

Directed Evolution of Human Estrogen Receptor Variants with Significantly Enhanced Androgen Specificity and Affinity*S  

E-print Network

Specificity and Affinity*S Received for publication, February 25, 2004, and in revised form, May 17, 2004 a directed evolution ap- proach to create hER variants with enhanced androgen specificity and affinity yeast and mammalian cells. These variants showed up to 7,600-fold improvement in the binding affinity

Zhao, Huimin

232

Time-Tag Generation Script  

NASA Technical Reports Server (NTRS)

Time-Tag Generation Script (TTaGS) is an application program, written in the AWK scripting language, for generating commands for aiming one Ku-band antenna and two S-band antennas for communicating with spacecraft. TTaGS saves between 2 and 4 person-hours per every 24 hours by automating the repetitious process of building between 150 and 180 antenna-control commands. TTaGS reads a text database of communication satellite schedules and a text database of satellite rise and set times and cross-references items in the two databases. It then compares the scheduled start and stop with the geometric rise and set to compute the times to execute antenna control commands. While so doing, TTaGS determines whether to generate commands for guidance, navigation, and control computers to tell them which satellites to track. To help prevent Ku-band irradiation of the Earth, TTaGS accepts input from the user about horizon tolerance and accordingly restricts activation and effects deactivation of the transmitter. TTaGS can be modified easily to enable tracking of additional satellites and for such other tasks as reading Sun-rise/set tables to generate commands to point the solar photovoltaic arrays of the International Space Station at the Sun.

Jackson, Dan E.

2010-01-01

233

Optimization of expression of untagged and histidine-tagged human recombinant thrombin precursors in Escherichia coli.  

PubMed

The present study is focused on preparation of proper Escherichia coli expression system to ensure high yields of various modified precursors of human recombinant thrombin, a potential biopharmaceutical reagent. Two thrombin precursors, the smallest single-chain ?-thrombin precursor prethrombin-2 and its shortened form prethrombin-2?13, and their His-tagged forms were used. In order to determine the effect of the different lengths and amino acid compositions of affinity His-tag on the target protein expression level, a variety of the His-tag sequences were used. We found out that the protein expression efficiency was closely related to the codons used for encoding of amino acids of fusion histidine tag. Optimization of culture medium composition is another way to increase yield of the target protein. Suitable medium composition can ensure cell growth to high densities which is related to total yield of expressed protein. In this study, a new optimized complex medium for batch fermentation was developed. Addition of nutrients like a yeast extract and enzymatic casein hydrolysate to the defined medium components had a positive impact on protein expression, where relatively high expression level of the target protein from total amount of cellular proteins was achieved. Further, we have focused on trace element solution composition, and the optimized nickel and selenium concentrations were determined. Our results show that the composition of essential trace metal solution has a major impact not only on expression level, but it can also affect cell growth rate. PMID:24878753

Osadská, Michaela; Bo?ková, Hana; Krahulec, Ján; Stuchlík, Stanislav; Tur?a, Ján

2014-11-01

234

Immunoaffinity purification of epitope-tagged human beta 2-adrenergic receptor to homogeneity.  

PubMed

To obtain large quantities of pure human beta 2-adrenergic receptor (beta 2-AR) needed for structural studies, an efficient method for beta 2-AR purification was developed using a recombinant receptor with an eight amino acid epitope at its C-terminus. This epitope is recognized by KT3-monoclonal antibody. The epitope tagged beta 2-AR was expressed in Sf9 cells with a specific activity of 5-20 pmol/mg of membrane protein. The epitope-tagged and wild-type receptors had identical ligand binding properties. The tagged receptor was solubilized using dodecyl-beta-maltoside with a quantitative yield. Solubilized epitope-tagged receptors were partially purified by KT3-mAb immunoaffinity in 60-70% yield. Further purification of the receptors on an alprenolol-affinity column resulted in a homogenous preparation with an overall yield of > 30%. The purified receptor was concentrated to > 1 mg/ml without loss of ligand binding activity. PMID:8746622

Kwatra, M M; Schreurs, J; Schwinn, D A; Innis, M A; Caron, M G; Lefkowitz, R J

1995-12-01

235

Efficient and versatile one-step affinity purification of in vivo biotinylated proteins: Expression, characterization and structure analysis of recombinant human glutamate carboxypeptidase II  

SciTech Connect

Affinity purification is a useful approach for purification of recombinant proteins. Eukaryotic expression systems have become more frequently used at the expense of prokaryotic systems since they afford recombinant eukaryotic proteins with post-translational modifications similar or identical to the native ones. Here, we present a one-step affinity purification set-up suitable for the purification of secreted proteins. The set-up is based on the interaction between biotin and mutated streptavidin. Drosophila Schneider 2 cells are chosen as the expression host, and a biotin acceptor peptide is used as an affinity tag. This tag is biotinylated by Escherichia coli biotin-protein ligase in vivo. We determined that localization of the ligase within the ER led to the most effective in vivo biotinylation of the secreted proteins. We optimized a protocol for large-scale expression and purification of AviTEV-tagged recombinant human glutamate carboxypeptidase II (Avi-GCPII) with milligram yields per liter of culture. We also determined the 3D structure of Avi-GCPII by X-ray crystallography and compared the enzymatic characteristics of the protein to those of its non-tagged variant. These experiments confirmed that AviTEV tag does not affect the biophysical properties of its fused partner. Purification approach, developed here, provides not only a sufficient amount of highly homogenous protein but also specifically and effectively biotinylates a target protein and thus enables its subsequent visualization or immobilization.

Tykvart, J.; Sacha, P.; Barinka, C.; Knedlik, T.; Starkova, J.; Lubkowski, J.; Konvalinka, J. (Gilead); (NCI); (Czech Academy)

2012-02-07

236

Evacuation of Passive Integrated Transponder (PIT) Tags from Northern Pikeminnow Consuming Tagged Juvenile Chinook Salmon  

USGS Publications Warehouse

Prey fish implanted with passive integrated transponder (PIT) tags can be used in predation studies if the timing of tag evacuation from the predators is understood. Laboratory experiments were conducted to determine how PIT tags in juvenile Chinook salmon Oncorhynchus tshawytscha that were consumed by northern pikeminnow Ptychocheilus oregonensis were evacuated in relation to various parameters. The rate of evacuation was directly related to temperature, while predator size and the number of prey consumed had less effect on the timing of tag evacuation. A power model was fitted to predict the proportion of tags expected to be evacuated at different intervals after ingestion. These results could be used in planning field or laboratory predation experiments with PIT-tagged prey fish.

Petersen, J.H.; Barfoot, C.A.

2003-01-01

237

Do-it-yourself histidine-tagged bovine enterokinase: A handy member of the protein engineer's toolbox?  

PubMed Central

Enterokinase, a two-chain duodenal serine protease, activates trypsinogen by removing its N-terminal propeptide. Due to a clean cut after the non-primed site recognition sequence, the enterokinase light chain is frequently employed in biotechnology to separate N-terminal affinity tags from target proteins with authentic N-termini. In order to obtain large quantities of this protease, we adapted an in vitro folding protocol for a pentahistidine-tagged triple mutant of the bovine enterokinase light chain. The purified, highly active enzyme successfully processed recombinant target proteins, while the pentahistidine-tag facilitated post-cleavage removal. Hence, we conclude that producing enterokinase in one's own laboratory is an efficient alternative to the commercial enzyme. PMID:24184090

Skala, Wolfgang; Goettig, Peter; Brandstetter, Hans

2013-01-01

238

Do-it-yourself histidine-tagged bovine enterokinase: a handy member of the protein engineer's toolbox.  

PubMed

Enterokinase, a two-chain duodenal serine protease, activates trypsinogen by removing its N-terminal propeptide. Due to a clean cut after the non-primed site recognition sequence, the enterokinase light chain is frequently employed in biotechnology to separate N-terminal affinity tags from target proteins with authentic N-termini. In order to obtain large quantities of this protease, we adapted an in vitro folding protocol for a pentahistidine-tagged triple mutant of the bovine enterokinase light chain. The purified, highly active enzyme successfully processed recombinant target proteins, while the pentahistidine-tag facilitated post-cleavage removal. Hence, we conclude that producing enterokinase in one's own laboratory is an efficient alternative to the commercial enzyme. PMID:24184090

Skala, Wolfgang; Goettig, Peter; Brandstetter, Hans

2013-12-01

239

A fluorogenic probe for SNAP-tagged plasma membrane proteins based on the solvatochromic molecule Nile Red.  

PubMed

A fluorogenic probe for plasma membrane proteins based on the dye Nile Red and SNAP-tag is introduced. It takes advantage of Nile Red, a solvatochromic molecule highly fluorescent in an apolar environment, such as cellular membranes, but almost dark in a polar aqueous environment. The probe possesses a tuned affinity for membranes allowing its Nile Red moiety to insert into the lipid bilayer of the plasma membrane, becoming fluorescent, only after its conjugation to a SNAP-tagged plasma membrane protein. The fluorogenic character of the probe was demonstrated for different SNAP-tag fusion proteins, including the human insulin receptor. This work introduces a new approach for generating a powerful turn-on probe for "no-wash" labeling of plasma membrane proteins with numerous applications in bioimaging. PMID:24471525

Prifti, Efthymia; Reymond, Luc; Umebayashi, Miwa; Hovius, Ruud; Riezman, Howard; Johnsson, Kai

2014-03-21

240

50 CFR 20.81 - Tagging requirement.  

Code of Federal Regulations, 2012 CFR

...EXPORTATION, AND IMPORTATION OF WILDLIFE AND PLANTS (CONTINUED) MIGRATORY BIRD HUNTING Migratory Bird Preservation Facilities § 20.81 Tagging requirement. No migratory bird preservation facility shall receive or have in custody any...

2012-10-01

241

Mass-producible micro-holographic tags  

SciTech Connect

Microtags are microscopic computer-generated holograms with 130-nm features and are mass-producible with EUVL. This fabrication method renders microtags difficult to counterfeit. Applications includ tagging and tracking of microprocessors, memory chips, currencey, and credit cards.

Sweatt, W.C.; Ray-Chaudhuri, A.K.; Kravitz, S.H.; Warren, M.E.; Stulen, R.H.; Tichenor, D.A.; Krenz, K.D. [Sandia National Labs., Albuquerque, NM (United States)]|[Sandia National Labs., Livermore, CA (United States); Descour, M.R. [Arizona Univ., Tucson, AZ (United States). Optical Sciences Center; Underwood, J.H. [Lawrence Berkeley Lab., CA (United States)

1996-06-01

242

Modeling social tagging using latent interaction potential  

NASA Astrophysics Data System (ADS)

Modeling social tagging plays a critical role in identifying statistical regularities and structural principles common to social tagging systems. Existing modeling approaches only consider imitations or background knowledge of users. However, common interests among users are ignored. In this paper, latent interactions are applied to present the common interests, and dynamic patterns in empirical data are investigated. Furthermore, the latent interaction driven model (LIDM) is proposed to model social tagging. Experimental results show that the tag frequency distribution generated by LIDM is consistent with that in real-world data. Moreover, the latent interaction graph generated by LIDM has a higher average clustering coefficient and lower average shortest path compared with that generated by preferential attachment methods. This demonstrates that LIDM outperforms traditional methods.

Wu, Zhenyu; Zou, Ming

2014-11-01

243

Lanthanide-tagged proteins – An illuminating partnership  

E-print Network

Lanthanide-tagged proteins are valuable for exploiting the unique properties of Ln ions for investigating protein structure, function, and dynamics. Introduction of the Ln into the target is accomplished via chemical ...

Imperiali, Barbara

244

Harvesting Intelligence in Multimedia Social Tagging Systems  

Microsoft Academic Search

\\u000a As more people adopt tagging practices, social tagging systems tend to form rich knowledge repositories that enable the extraction\\u000a of patterns reflecting the way content semantics is perceived by the web users. This is of particular importance, especially\\u000a in the case of multimedia content, since the availability of such content in the web is very high and its efficient retrieval

Eirini Giannakidou; Foteini Kaklidou; Elisavet Chatzilari; Ioannis Kompatsiaris; Athena Vakali

2010-01-01

245

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

USGS Publications Warehouse

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.

Dixon, Christopher J.; Mesa, Matthew G.

2011-01-01

246

Z-path SAW RFID tag.  

PubMed

Surface acoustic wave (SAW) radio-frequency identification (RFID) tags are soon expected to be produced in very high volumes. The size and cost of a SAW RFID tag will be key parameters for many applications. Therefore, it is of primary importance to reduce the chip size. In this work, we describe the design principles of a 2.4-GHz SAW RFID tag that is significantly smaller than earlier reported tags. We also present simulated and experimental results. The coded signal should arrive at the reader with a certain delay (typically about 1 micros), i.e., after the reception of environmental echoes. If the tag uses a bidirectional interdigital transducer (IDT), space for the initial delay is needed on both sides of the IDT. In this work, we replace the bidirectional IDT by a unidirectional one. This halves the space required by the initial delay because all the code reflectors must now be placed on the same side of the IDT. We reduce tag size even further by using a Z-path geometry in which the same space in x-direction is used for both the initial delay and the code reflectors. Chip length is thus determined only by the space required by the code reflectors. PMID:18334326

Härmä, Sanna; Plessky, Victor P; Hartmann, Clinton S; Steichen, William

2008-01-01

247

SNAP-tagging the retrograde route.  

PubMed

We have developed a chemical biology strategy to identify proteins that follow the retrograde transport route from the plasma membrane to the Golgi apparatus, via endosomes. The general principle is the following: plasma membrane proteins are covalently tagged with a first probe. Only the ones that are then transported to trans-Golgi/TGN membranes are covalently bound to a capture reagent that has been engineered into this compartment. Specifically, the first probe is benzylguanine (BG) that is conjugated onto primary amino groups of plasma-membrane proteins. The capture reagent includes an O(6)-alkylguanine-DNA alkyltransferase-derived fragment, the SNAP-tag, which forms a covalent linkage with BG. The SNAP-tag is fused to the GFP-tagged Golgi membrane anchor from galactosyl transferase for proper targeting to trans-Golgi/TGN membranes. Cell-surface BG-tagged proteins that are transported to trans-Golgi/TGN membranes (i.e., that are retrograde cargoes) are thereby covalently captured by the SNAP-tag fusion protein. For identification, the latter is immunopurified using GFP-Trap, and associated retrograde cargo proteins are identified by mass spectrometry. We here provide a step-by-step protocol of this method. PMID:24295305

Johannes, Ludger; Shafaq-Zadah, Massiullah

2013-01-01

248

Large Scale Tag Recommendation Using Different Image Representations  

Microsoft Academic Search

Abstract. Nowadays, geographical coordinates (geo-tags), social anno- tations (tags), and low-level features are available in large image datasets. In our paper, we exploit these three kinds of image descriptions to sug- gest possible annotations for new images uploaded to a social tagging system. In order to compare the benefits each of these description types brings to a tag recommender system

Rabeeh Abbasi; Marcin Grzegorzek; Steffen Staab

2009-01-01

249

Tagged particle processes and their non-explosion criteria  

E-print Network

We give a derivation of tagged particle processes from unlabeled interacting Brownian motions. We give a criteria of the non-explosion property of tagged particle processes. We prove the quasi-regularity of Dirichlet forms describing the environment seen from the tagged particle, which were used in previous papers to prove the invariance principle of tagged particles of interacting Brownian motions.

Hirofumi Osada

2009-05-25

250

Leveraging Collective Intelligence through Community Detection in Tag Networks  

Microsoft Academic Search

The paper studies the problem of community detection in tag networks, i.e. networks consisting of associations between tags that are used within Social Tagging Sys- tems (STS) to annotate online resources (e.g. book- marks, pictures, videos, etc.). Community detection methods aim at uncovering densely connected groups of tags, which can reveal the topic structure emerging in the STS. In this

Symeon Papadopoulos; Yiannis Kompatsiaris; Athena Vakali

251

The Internet of Tags: Energy-Harvesting Adaptive Algorithms  

E-print Network

(IoTags). We believe that IoTags will be a key component of the Internet of Things (IoT). In the nearThe Internet of Tags: Energy-Harvesting Adaptive Algorithms Robert Margolies Ph.D. Candidate a top-down approach and develop energy harvesting adaptive algorithms to support the Internet of Tags

Hone, James

252

Rule Based Part of Speech Tagging of Sindhi Language  

Microsoft Academic Search

Part of speech (POS) tagging is a process of assigning correct syntactic categories to each word in the text. Tag set and word disambiguation rules are fundamental parts of any POS tagger. No work has hitherto been published of tag set in Sindhi language. The Sindhi lexicon for computational processing is also not available. In this study, the tag set

Javed Ahmed Mahar; Ghulam Qadir Memon

2010-01-01

253

Indian Craniometric Variability and Affinities  

PubMed Central

Recently published craniometric and genetic studies indicate a predominantly indigenous ancestry of Indian populations. We address this issue with a fuller coverage of Indian craniometrics than any done before. We analyse metrical variability within Indian series, Indians' sexual dimorphism, differences between northern and southern Indians, index-based differences of Indian males from other series, and Indians' multivariate affinities. The relationship between a variable's magnitude and its variability is log-linear. This relationship is strengthened by excluding cranial fractions and series with a sample size less than 30. Male crania are typically larger than female crania, but there are also shape differences. Northern Indians differ from southern Indians in various features including narrower orbits and less pronounced medial protrusion of the orbits. Indians resemble Veddas in having small crania and similar cranial shape. Indians' wider geographic affinities lie with “Caucasoid” populations to the northwest, particularly affecting northern Indians. The latter finding is confirmed from shape-based Mahalanobis-D distances calculated for the best sampled male and female series. Demonstration of a distinctive South Asian craniometric profile and the intermediate status of northern Indians between southern Indians and populations northwest of India confirm the predominantly indigenous ancestry of northern and especially southern Indians. PMID:24455409

Raghavan, Pathmanathan; Bulbeck, David; Pathmanathan, Gayathiri; Rathee, Suresh Kanta

2013-01-01

254

Multi-exemplar affinity propagation.  

PubMed

The affinity propagation (AP) clustering algorithm has received much attention in the past few years. AP is appealing because it is efficient, insensitive to initialization, and it produces clusters at a lower error rate than other exemplar-based methods. However, its single-exemplar model becomes inadequate when applied to model multisubclasses in some situations such as scene analysis and character recognition. To remedy this deficiency, we have extended the single-exemplar model to a multi-exemplar one to create a new multi-exemplar affinity propagation (MEAP) algorithm. This new model automatically determines the number of exemplars in each cluster associated with a super exemplar to approximate the subclasses in the category. Solving the model is NP-hard and we tackle it with the max-sum belief propagation to produce neighborhood maximum clusters, with no need to specify beforehand the number of clusters, multi-exemplars, and superexemplars. Also, utilizing the sparsity in the data, we are able to reduce substantially the computational time and storage. Experimental studies have shown MEAP's significant improvements over other algorithms on unsupervised image categorization and the clustering of handwritten digits. PMID:23868781

Wang, Chang-Dong; Lai, Jian-Huang; Suen, Ching Y; Zhu, Jun-Yong

2013-09-01

255

Multi-Exemplar Affinity Propagation.  

PubMed

Affinity Propagation (AP) clustering algorithm has received much attention in the past few years. AP is appealing because it is efficient, insensitive to initialization, and it produces clusters at a lower error rate than other exemplar-based methods. However, its single-exemplar model becomes inadequate when applied to model multi-subclasses in some situations such as scene analysis and character recognition. To remedy this deficiency, we have extended the single-exemplar model to a multi-exemplar one to create a new Multi-Exemplar Affinity Propagation (MEAP) algorithm. This new model determines automatically the number of exemplars in each cluster associated with a super exemplar to approximate the subclasses in the category. Solving the model is NP-hard and we tackle it with the max-sum belief propagation to produce neighborhood maximum clusters, with no need to specify beforehand the number of clusters, multi-exemplars, and super-exemplars. Also, utilizing the sparsity in the data, we are able to reduce substantially the computational time and storage. Experimental studies have shown MEAP's significant improvements over other algorithms on unsupervised image categorization and the clustering of handwritten digits. PMID:23358283

Wang, Chang-Dong; Lai, Jian-Huang; Suen, Ching Y; Zhu, Jun-Yong

2013-01-24

256

Neural net controlled tag gas sampling system for nuclear reactors  

DOEpatents

A method and system are disclosed for providing a tag gas identifier to a nuclear fuel rod and analyze escaped tag gas to identify a particular failed nuclear fuel rod. The method and system include disposing a unique tag gas composition into a plenum of a nuclear fuel rod, monitoring gamma ray activity, analyzing gamma ray signals to assess whether a nuclear fuel rod has failed and is emitting tag gas, activating a tag gas sampling and analysis system upon sensing tag gas emission from a failed nuclear rod and evaluating the escaped tag gas to identify the particular failed nuclear fuel rod. 12 figs.

Gross, K.C.; Laug, M.T.; Lambert, J.B.; Herzog, J.P.

1997-02-11

257

Neural net controlled tag gas sampling system for nuclear reactors  

DOEpatents

A method and system for providing a tag gas identifier to a nuclear fuel rod and analyze escaped tag gas to identify a particular failed nuclear fuel rod. The method and system include disposing a unique tag gas composition into a plenum of a nuclear fuel rod, monitoring gamma ray activity, analyzing gamma ray signals to assess whether a nuclear fuel rod has failed and is emitting tag gas, activating a tag gas sampling and analysis system upon sensing tag gas emission from a failed nuclear rod and evaluating the escaped tag gas to identify the particular failed nuclear fuel rod.

Gross, Kenneth C. (Bolingbrook, IL); Laug, Matthew T. (Idaho Fall, ID); Lambert, John D. B. (Wheaton, IL); Herzog, James P. (Downers Grove, IL)

1997-01-01

258

Convergent evidence identifying MAP\\/microtubule affinity-regulating kinase 1 (MARK1) as a susceptibility gene for autism  

Microsoft Academic Search

Autism spectrum disorders (ASDs) are common, heritable, but genetically heterogeneous neurodevelopmen- tal conditions. We recently defined a susceptibility locus for ASDs on chromosome 1q41-q42. High- resolution single-nucleotide polymorphisms (126 SNPs) genotyping across the chromosome 1q41-q42 region, followed by a MARK1 (microtubule affinity-regulating kinase 1)-tagged-SNP association study in 276 families with autism from the Autism Genetic Research Exchange, showed that several

Gilles Maussion; J erome Carayol; Aude-Marie Lepagnol-Bestel; Frederic Tores; Yann Loe-Mie; Ulla Milbreta; Francis Rousseau; Karine Fontaine; Julie Renaud; Jean-Marie Moalic; Anne Philippi; Alain Chedotal; Philip Gorwood; Nicolas Ramoz; Jorg Hager; Michel Simonneau

2008-01-01

259

Passive Tag-to-Tag Communication Pavel V. Nikitin, Shashi Ramamurthy, Rene Martinez, K. V. S. Rao  

E-print Network

as "Gen2") has been largely adopted as the UHF RFID protocol standard. Despite this progress, transacting intelligence to both tags and readers to go beyond standard tag reading and writing protocol. For readerPassive Tag-to-Tag Communication Pavel V. Nikitin, Shashi Ramamurthy, Rene Martinez, K. V. S. Rao

Hochberg, Michael

260

L'ontologie NiceTag : les tags en tant que graphes nomms Alexandre Monnin*, Freddy Limpens**  

E-print Network

L'ontologie NiceTag : les tags en tant que graphes nomm�s Alexandre Monnin*, Freddy Limpens** David Milano david.laniado@elet.polimi.it R�sum�. Notre analyse part du constat selon lequel les mod, quelque soit le mod�le sur lequel repose leur description (SCOT, CommonTag, etc.). 1 Introduction Les tags

Paris-Sud XI, Université de

261

Stille couplings in supercritical CO 2 catalyzed with perfluoro-tagged and un-tagged Pd complexes  

Microsoft Academic Search

Stille CC-couplings in supercritical CO2 (scCO2) were performed with perfluoro-tagged and un-tagged Pd complexes in high yields. With fluoro-tagged complexes yields were generally slightly higher. A recycling of the perfluoro-tagged catalyst was also achieved.

Thomas Osswald; Siegfried Schneider; Shaoning Wang; Willi Bannwarth

2001-01-01

262

New plant vectors for protein tagging with E2 epitope  

Microsoft Academic Search

E2Tag has been used for tagging of bacterial, yeast, and mammalian proteins. A set of plant expression vectors was constructed\\u000a for tagging proteins with E2Tag. Detection of E2-tagged proteins with specific antibodies inNicotiana benthamiana andNicotiana tabacum was easily done without any nonspecific background activity. No effect on the biological activity of the enzyme GUS, used\\u000a as a marker, was detected.

Lenne Nigul; Allan Olspert; Merike Meier; Heiti Paves; Tiit Talpsep; Erkki Truve

2004-01-01

263

Associated Particle Tagging (APT) in Magnetic Spectrometers  

SciTech Connect

Summary In Brief The Associated Particle Tagging (APT) project, a collaboration of Pacific Northwest National Laboratory (PNNL), Idaho National Laboratory (INL) and the Idaho State University (ISU)/Idaho Accelerator Center (IAC), has completed an exploratory study to assess the role of magnetic spectrometers as the linchpin technology in next-generation tagged-neutron and tagged-photon active interrogation (AI). The computational study considered two principle concepts: (1) the application of a solenoidal alpha-particle spectrometer to a next-generation, large-emittance neutron generator for use in the associated particle imaging technique, and (2) the application of tagged photon beams to the detection of fissile material via active interrogation. In both cases, a magnetic spectrometer momentum-analyzes charged particles (in the neutron case, alpha particles accompanying neutron generation in the D-T reaction; in the tagged photon case, post-bremsstrahlung electrons) to define kinematic properties of the relevant neutral interrogation probe particle (i.e. neutron or photon). The main conclusions of the study can be briefly summarized as follows: Neutron generator: • For the solenoidal spectrometer concept, magnetic field strengths of order 1 Tesla or greater are required to keep the transverse size of the spectrometer smaller than 1 meter. The notional magnetic spectrometer design evaluated in this feasibility study uses a 5-T magnetic field and a borehole radius of 18 cm. • The design shows a potential for 4.5 Sr tagged neutron solid angle, a factor of 4.5 larger than achievable with current API neutron-generator designs. • The potential angular resolution for such a tagged neutron beam can be less than 0.5o for modest Si-detector position resolution (3 mm). Further improvement in angular resolution can be made by using Si-detectors with better position resolution. • The report documents several features of a notional generator design incorporating the 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.

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

2012-10-16

264

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

NASA Astrophysics Data System (ADS)

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.

Haruyama, Tetsuya; Wakabayashi, Ryo; Cho, Takeshi; Matsuyama, Sho-taro

2011-10-01

265

Learning by tagging: The role of social tagging in group knowledge formation1  

Microsoft Academic Search

This research presents a case study on the use of Social Tagging in an undergraduate classroom at the University of Michigan during the Fall 2005 semester. Students were between 20 and 22 years of age. Stude- nts tagged their individual blog posts to contribute to themes and conversa- tions in an online learning environment. Using content analysis of the blog

Jude Yew; Faison P. Gibson; Stephanie Teasley

266

24: Development of tag sets for part-of-speech tagging Eric Atwell, University of Leeds.  

E-print Network

language family, Urdu; then for a non-Indo-European language with a highly inflexional grammar, Arabic; then for a contrasting non-Indo-European language with isolating grammar, Malay. Finally, we present some conclusions-of-Speech tagging service for English; then design of a tag-set for another language from the same broad Indo-European

Bennett, Brandon

267

Assistive tagging: A survey of multimedia tagging with human-computer joint exploration  

Microsoft Academic Search

Along with the explosive growth of multimedia data, automatic multimedia tagging has attracted great interest of various research communities, such as computer vision, multimedia, and information retrieval. However, despite the great progress achieved in the past two decades, automatic tagging technologies still can hardly achieve satisfactory performance on real-world multimedia data that vary widely in genre, quality, and content. Meanwhile,

Meng Wang; Bingbing Ni; Xian-Sheng Hua; Tat-Seng Chua

268

Supporting Information A dipicolinic acid tag for rigid lanthanide tagging of proteins and paramagnetic  

E-print Network

S1 Supporting Information A dipicolinic acid tag for rigid lanthanide tagging of proteins,6-pyridine dicarboxylic acid General Procedures Dipicolinic acid and p-toluenesulfonyl chloride were of literature NMR data. To a round bottom flask containing a solution of sulfuric acid (30% v/v, 30 ml

Otting, Gottfried

269

Robust Speaker Clustering Using Affinity Propagation  

NASA Astrophysics Data System (ADS)

In this letter, a recently proposed clustering algorithm named affinity propagation is introduced for the task of speaker clustering. This novel algorithm exhibits fast execution speed and finds clusters with low error. However, experiments show that the speaker purity of affinity propagation is not satisfying. Thus, we propose a hybrid approach that combines affinity propagation with agglomerative hierarchical clustering to improve the clustering performance. Experiments show that compared with traditional agglomerative hierarchical clustering, the hybrid method achieves better performance on the test corpora.

Zhang, Xiang; Lu, Ping; Suo, Hongbin; Zhao, Qingwei; Yan, Yonghong

270

Tags to Track Illicit Uranium and Plutonium  

SciTech Connect

With the expansion of nuclear power, it is essential to avoid nuclear materials from falling into the hands of rogue nations, terrorists, and other opportunists. This paper examines the idea of detection and attribution tags for nuclear materials. For a detection tag, it is proposed to add small amounts [about one part per billion (ppb)] of {sup 232}U to enriched uranium to brighten its radioactive signature. Enriched uranium would then be as detectable as plutonium and thus increase the likelihood of intercepting illicit enriched uranium. The use of rare earth oxide elements is proposed as a new type of 'attribution' tag for uranium and thorium from mills, uranium and plutonium fuels, and other nuclear materials. Rare earth oxides are chosen because they are chemically compatible with the fuel cycle, can survive high-temperature processing operations in fuel fabrication, and can be chosen to have minimal neutronic impact within the nuclear reactor core. The mixture of rare earths and/or rare earth isotopes provides a unique 'bar code' for each tag. If illicit nuclear materials are recovered, the attribution tag can identify the source and lot of nuclear material, and thus help police reduce the possible number of suspects in the diversion of nuclear materials based on who had access. (authors)

Haire, M. Jonathan; Forsberg, Charles W. [Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831-6166 (United States)

2007-07-01

271

Electronic tagging and integrated product intelligence  

NASA Astrophysics Data System (ADS)

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.

Swerdlow, Martin; Weeks, Brian

1996-03-01

272

Immunopaleontology reveals how affinity enhancement is achieved during affinity maturation of antibodies to influenza virus  

E-print Network

The Abs made by B lymphocytes on first encountering an antigen bind it with low intrinsic affinity, and, over time, the average affinity of the Abs made against that antigen gradually increases. These changes, known as ...

Eisen, Herman N.

273

Molecular tagging velocimetry in turbulence using biacetyl  

NASA Astrophysics Data System (ADS)

We evaluate various molecular tagging velocimetry (MTV) techniques for application in turbulent flows of gases where the smallest length scales must be resolved. We argue that tracer diffusion dictates the use of large complex molecules and discuss a few candidate molecules. The accuracy of MTV is determined by the profile of written lines which widen due to molecular dynamics, including both diffusion and chemical reaction. We evaluate these profiles for tagging with phosphorescing biacetyl molecules, which is a commonly used probe in MTV. For relatively large laser power, these profiles are determined not by molecular diffusion, but by the triplet-triplet annihilation reaction of excited biacetyl molecules. We identify a new reaction pathway, and present a model for the observed line shapes. The rapid widening of tagged lines of biacetyl molecules due to chemical reaction restricts this MTV technique to large-scale turbulent motion in gases of comparable molecular weight.

Mirzaei, M.; Dam, N. J.; van de Water, W.

2012-10-01

274

Ultrafast tissue staining with chemical tags  

PubMed Central

Genetically encoded fluorescent proteins and immunostaining are widely used to detect cellular and subcellular structures in fixed biological samples. However, for thick or whole-mount tissue, each approach suffers from limitations, including limited spectral flexibility and lower signal or slow speed, poor penetration, and high background labeling, respectively. We have overcome these limitations by using transgenically expressed chemical tags for rapid, even, high-signal and low-background labeling of thick biological tissues. We first construct a platform of widely applicable transgenic Drosophila reporter lines, demonstrating that chemical labeling can accelerate staining of whole-mount fly brains by a factor of 100. Using viral vectors to deliver chemical tags into the mouse brain, we then demonstrate that this labeling strategy works well in mice. Thus this tag-based approach drastically improves the speed and specificity of labeling genetically marked cells in intact and/or thick biological samples. PMID:25157152

Kohl, Johannes; Ng, Julian; Cachero, Sebastian; Ciabatti, Ernesto; Dolan, Michael-John; Sutcliffe, Ben; Tozer, Adam; Ruehle, Sabine; Krueger, Daniel; Frechter, Shahar; Branco, Tiago; Tripodi, Marco; Jefferis, Gregory S. X. E.

2014-01-01

275

Functional wild-type and carboxyl-terminal-tagged rat substance P receptors expressed in baculovirus-infected insect Sf9 cells.  

PubMed

The rat substance P (SP) receptor (SPR) was expressed in insect Sf9 cells by infection with recombinant baculovirus. The receptor bound SP with high affinity (KD = 360 pM) and had a rank order of affinity of SP > neurokinin A > neurokinin B. Ligand activation of the receptor resulted in an increase in both inositol lipid hydrolysis and intracellular Ca2+ concentration ([Ca2+]i). However, high-level expression of the receptor, in the absence of ligand, was correlated with increased basal turnover of inositol lipids and an elevated rate of Ca2+ influx. These results demonstrate that the Sf9 cells provide a suitable environment for the high-level expression of a functionally active SPR. Two carboxy-terminal epitope-tagged receptors (SPR-KT3 = SPR-TPPPEPET, COOH; SPR-Glu = SPR-EEEEYMPME, COOH) were also expressed. The affinity of the KT3-tagged receptor for ligand was similar to that of the wild-type receptor (KD = 405 pM), and that of the Glu-tagged receptor was slightly lower (KD = 1,082 pM). The high-affinity SP binding site of all three receptors was sensitive to guanosine 5'-O-(3-thiotriphosphate) pretreatment. The maximal signal-transducing ability of the epitope-tagged receptors was comparable to that of the wild-type receptor ([Ca2+]i rise as a percentage of wild-type: SPR-KT3, 80-100%; SPR-Glu, 88-100%). These data show that heterologous expression in the baculovirus system results in high expression of functional wild-type and tagged receptors. PMID:7891090

Schreurs, J; Yamamoto, R; Lyons, J; Munemitsu, S; Conroy, L; Clark, R; Takeda, Y; Krause, J E; Innis, M

1995-04-01

276

One source of uncertainty in fishery assessments based on tag release and  

E-print Network

from tag shed- ding--the loss of tags from fish from the time of tagging until tag recovery. Inde, it reduces the number of tags ini- tially put out to sea. Type-II shedding is the loss of a tag or both tags- fectively than others, and some may be- come firmly embedded (with growth of muscle tissues

277

bumpy, caution with merging: an exploration of tagging in a geowiki  

Microsoft Academic Search

We introduced tags into the Cyclopath geographic wiki for bicyclists. To promote the creation of useful tags, we made tags wiki objects, giving ownership of tag applications to the community, not to individuals. We also introduced a novel interface that lets users fine-tune their routing preferences with tags. We analyzed the Cyclopath tagging vocabulary, the relationship of tags to existing

Fernando Torre; S. Andrew Sheppard; Reid Priedhorsky; Loren G. Terveen

2010-01-01

278

Identifying Nuclear Materials Using Tagged Muons  

E-print Network

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.

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

279

Tags to Track Illicit Uranium and Plutonium  

SciTech Connect

With the expansion of nuclear power, it is essential to avoid diversion of nuclear materials into the hands of 'rogue nations,' terrorists, and other opportunists. This paper describes (1) the use of a detection tag to make it easier to detect smuggled material by creating a nuclear fingerprint and (2) the use of attribution tags to enable law enforcement to determine where any recovered stolen nuclear materials came from, identify the individuals responsible for the unlawful diversion, and reduce future loss of nuclear materials.

Haire, Marvin Jonathan [ORNL

2007-01-01

280

Identifying Nuclear Materials Using Tagged Muons  

E-print Network

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.

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

2014-06-04

281

Projecting Farsi POS Data To Tag Pashto  

E-print Network

We present our findings on projecting part of speech (POS) information from a well resourced language, Farsi, to help tag a lower resourced language, Pashto, following Feldman and Hana (2010). We make a series of modifications to both tag transition and lexical emission parameter files generated from a hidden Markov model tagger, TnT, trained on the source language (Farsi). Changes to the emission parameters are immediately effective, whereas changes made to the transition information are most effective when we introduce a custom tagset. We reach our best results of 70.84 % when we employ all emission and transition modifications to the Farsi corpus with the custom tagset. 1

Mohammad Khan; Eric Baucom; Anthony Meyer; Lwin Moe

282

Seamless gene tagging by endonuclease-driven homologous recombination.  

PubMed

Gene tagging facilitates systematic genomic and proteomic analyses but chromosomal tagging typically disrupts gene regulatory sequences. Here we describe a seamless gene tagging approach that preserves endogenous gene regulation and is potentially applicable in any species with efficient DNA double-strand break repair by homologous recombination. We implement seamless tagging in Saccharomyces cerevisiae and demonstrate its application for protein tagging while preserving simultaneously upstream and downstream gene regulatory elements. Seamless tagging is compatible with high-throughput strain construction using synthetic genetic arrays (SGA), enables functional analysis of transcription antisense to open reading frames and should facilitate systematic and minimally-invasive analysis of gene functions. PMID:21915245

Khmelinskii, Anton; Meurer, Matthias; Duishoev, Nurlanbek; Delhomme, Nicolas; Knop, Michael

2011-01-01

283

Loop realizations of quantum affine algebras  

E-print Network

We give a simplified description of quantum affine algebras in their loop presentation. This description is related to Drinfeld's new realization via halves of vertex operators. We also define an idempotent version of the quantum affine algebra which is suitable for categorification.

Cautis, Sabin

2011-01-01

284

Loop realizations of quantum affine algebras  

SciTech Connect

We give a simplified description of quantum affine algebras in their loop presentation. This description is related to Drinfeld's new realization via halves of vertex operators. We also define an idempotent version of the quantum affine algebra which is suitable for categorification.

Cautis, Sabin [Department of Mathematics, University of Southern California, Los Angeles, California, 90089 (United States); Licata, Anthony [Department of Mathematics, Australian National University, Canberra (Australia)

2012-12-15

285

An adaptive affinity propagation document clustering  

Microsoft Academic Search

The standard affinity propagation clustering algorithm suffers from one limitation that it is hard to know the value of the parameter ¿preference¿ which can yield an optimal clustering solution. To overcome this limitation, in this paper we proposes an adaptive affinity propagation method. The method first finds out the range of ¿preference¿, then searches the space of ¿preference¿ to find

Yancheng He; Qingcai Chen; Xiaolong Wang; Ruifeng Xu; Xiaohua Bai; Xianjun Meng

2010-01-01

286

Scaling Analysis of Affinity Propagation Cyril Furtlehner,  

E-print Network

Scaling Analysis of Affinity Propagation Cyril Furtlehner, Mich`ele Sebag, and Xiangliang Zhang (Dated: June 9, 2010) We analyze and exploit some scaling properties of the Affinity Propagation (AP counterpart is known to be the belief-propagation (BP) algorithm of Pearl [4, 5]. This algorithm was initially

Paris-Sud XI, Université de

287

Affine Invariant Features from Self-Flow  

Microsoft Academic Search

The paper introduces the Self Affine Feature Transform (SAFT), which finds features on images in a novel way. Image features are represented by 6*6 block-symmetric matrices having only 18 independent parameters. Feature descriptors are extracted from the affine flows which do not change image content. The streamlines of these flows and their invariant subspaces move together with the image plane

Zoltan Prohaszka

2008-01-01

288

Affine\\/ Photometric Invariants for Planar Intensity Patterns  

Microsoft Academic Search

The paper contributes to the viewpoint invariant recognition of planar patterns, especially labels and signs under affine deformations. By their nature, the information of such eye-catchers is not contained in the outline or frame — they often are affinely equivalent like parallelograms and ellipses — but in the intensity content within. Moment invariants are well suited for their recognition. They

Luc J. Van Gool; Theo Moons; Dorin Ungureanu

1996-01-01

289

An affine invariant interest point detector  

Microsoft Academic Search

This paper presents a novel approach for detecting affine invariant interest points. Our method can deal with significant affine transformations including large scale changes. Such transformations in- troduce significant changes in the point location as well as in the scale and the shape of the neighbourhood of an interest point. Our approach allows to solve for these problems simultaneously. It

Krystian Mikolajczyk; Cordelia Schmid

2002-01-01

290

A Comparison of Affine Region Detectors  

Microsoft Academic Search

The paper gives a snapshot of the state of the art in affine covariant region detectors, and compares their performance on a set of test images under varying imaging conditions. Six types of detectors are included: detectors based on affine normalization around Harris (Mikolajczyk and Schmid, 2002; Schaffalitzky and Zisserman, 2002) and Hessian points (Mikolajczyk and Schmid, 2002), a detector

Krystian Mikolajczyk; Tinne Tuytelaars; Cordelia Schmid; Andrew Zisserman; Jiri Matas; Frederik Schaffalitzky; Timor Kadir; Luc J. Van Gool; J. Matas

2005-01-01

291

Affinity Chromatography Media CellufineTM Sulfate  

E-print Network

, chondroitin sulfate or heparin. Matrex Cellufine Sulfate consists of a rigid spherical cellulose matrix of 3Affinity Chromatography Media Matrex® CellufineTM Sulfate For Concentration, Purification and viral or microbial antigens. Matrex Cellufine Sulfate affinity media is a simple, rapid and effective

Lebendiker, Mario

292

Scaling Analysis of Affinity Propagation  

E-print Network

We analyze and exploit some scaling properties of the Affinity Propagation (AP) clustering algorithm proposed by Frey and Dueck (2007). First we observe that a divide and conquer strategy, used on a large data set hierarchically reduces the complexity ${\\cal O}(N^2)$ to ${\\cal O}(N^{(h+2)/(h+1)})$, for a data-set of size $N$ and a depth $h$ of the hierarchical strategy. For a data-set embedded in a $d$-dimensional space, we show that this is obtained without notably damaging the precision except in dimension $d=2$. In fact, for $d$ larger than 2 the relative loss in precision scales like $N^{(2-d)/(h+1)d}$. Finally, under some conditions we observe that there is a value $s^*$ of the penalty coefficient, a free parameter used to fix the number of clusters, which separates a fragmentation phase (for $ss^*$) of the underlying hidden cluster structure. At this precise point holds a self-similarity property which can be exploited by the hierarchical strategy to actually locate its position. From this observation, ...

Furtlehner, Cyril; Zhang, Xiangliang

2009-01-01

293

Improving image segmentation by learning region affinities  

SciTech Connect

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.

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

2010-11-03

294

AtKUP1: an Arabidopsis gene encoding high-affinity potassium transport activity.  

PubMed Central

Because plants grow under many different types of soil and environmental conditions, we investigated the hypothesis that multiple pathways for K+ uptake exist in plants. We have identified a new family of potassium transporters from Arabidopsis by searching for homologous sequences among the expressed sequence tags of the GenBank database. The deduced amino acid sequences of AtKUP (for Arabidopsis thaliana K+ uptake transporter) cDNAs are highly homologous to the non-plant Kup and HAK1 potassium transporters from Escherichia coli and Schwanniomyces occidentalis, respectively. Interestingly, AtKUP1 and AtKUP2 are able to complement the potassium transport deficiency of an E. coli triple mutant. In addition, transgenic Arabidopsis suspension cells overexpressing AtKUP1 showed increased Rb+ uptake at micromolar concentrations with an apparent K(m) of approximately 22 microM, indicating that AtKUP1 encodes a high-affinity potassium uptake activity in vivo. A small, low-affinity Rb+ uptake component was also detected in AtKUP1-expressing cells. RNA gel blot analysis showed that the various members of the AtKUP family have distinct patterns of expression, with AtKUP3 transcript levels being strongly induced by K+ starvation. It is proposed that plants contain multiple potassium transporters for high-affinity uptake and that the AtKUP family may provide important components of high- and low-affinity K+ nutrition and uptake into various plant cell types. PMID:9477571

Kim, E J; Kwak, J M; Uozumi, N; Schroeder, J I

1998-01-01

295

Optimization of SERS tag intensity, binding footprint, and emittance.  

PubMed

Nanoparticle surface enhanced Raman scattering (SERS) tags have attracted interest as labels for use in a variety of applications, including biomolecular assays. An obstacle to progress in this area is a lack of standardized approaches to compare the brightness of different SERS tags within and between laboratories. Here we present an approach based on binding of SERS tags to beads with known binding capacities that allows evaluation of the average intensity, the relative binding footprint of particles in a SERS tag preparation, and the size-normalized intensity or emittance. We tested this on four different SERS tag compositions and show that aggregated gold nanorods produce SERS tags that are 2-4 times brighter than relatively more monodisperse nanorods, but that the aggregated nanorods are also correspondingly larger, which may negate the intensity if steric hindrance limits the number of tags bound to a target. By contrast, SERS tags prepared from smaller gold nanorods coated with a silver shell produce SERS tags that are 2-3 times brighter, on a size-normalized basis, than the Au nanorod-based tags, resulting in labels with improved performance in SERS-based image and flow cytometry assays. SERS tags based on red-resonant Ag plates showed similarly bright signals and small footprint. This approach to evaluating SERS tag brightness is general, uses readily available reagents and instruments, and should be suitable for interlab comparisons of SERS tag brightness. PMID:24892497

Nolan, John P; Duggan, Erika; Condello, Danilo

2014-07-16

296

Rapid, continuous purification of proteins in a microfluidic device using genetically-engineered partition tags.  

PubMed

High-throughput screening assays of native and recombinant proteins are increasingly crucial in life science research, including fields such as drug screening and enzyme engineering. These assays are typically highly parallel, and require minute amounts of purified protein per assay. To address this need, we have developed a rapid, automated microscale process for isolating specific proteins from sub-microlitre volumes of E. Coli cell lysate. Recombinant proteins are genetically tagged to drive partitioning into the PEG-rich phase of a flowing aqueous two-phase system, which removes approximately 85% of contaminating proteins, as well as unwanted nucleic acids and cell debris, on a simple microfluidic device. Inclusion of the genetic tag roughly triples recovery of the autofluorescent protein AcGFP1, and also significantly improves recovery of the enzyme glutathione S-transferase (GST), from nearly zero recovery for the wild-type enzyme, up to 40% with genetic tagging. The extraction process operates continuously, with only a single step from cell lysate to purified protein, and does not require expensive affinity reagents or troublesome chromatographic steps. The two-phase system is mild and does not disrupt protein function, as evidenced by recovery of active enzymes and functional fluorescent protein from our microfluidic process. The microfluidic aqueous two-phase extraction forms the core component of an integrated lab-on-a-chip device comprising cell culture, lysis, purification and analysis on a single device. PMID:18369506

Meagher, Robert J; Light, Yooli K; Singh, Anup K

2008-04-01

297

Nickel nanoparticle decorated graphene for highly selective isolation of polyhistidine-tagged proteins  

NASA Astrophysics Data System (ADS)

Nickel nanoparticle decorated graphene (GP-Ni) is prepared by one-pot hydrothermal reduction of graphene oxide and nickel cations by hydrazine hydrate in the presence of poly(sodium-p-styrenesulfonate) (PSS). The GP-Ni hybrid is characterized by XRD, TEM, SEM, XPS, Raman and FT-IR spectra, demonstrating the formation of poly-dispersed nickel nanoparticles with an average size of 83 nm attached on the surface of graphene sheets. The GP-Ni hybrid exhibits ferromagnetic behavior with a magnetization saturation of 31.1 emu g-1 at 10?000 Oersted (Oe). The GP-Ni also possesses favorable stability in aqueous medium and rapid magnetic response to an external magnetic field. These make it a novel magnetic adsorbent for the separation/isolation of His6-tagged recombinant proteins from a complex sample matrix (cell lysate). The targeted protein species is captured onto the surface of the GP-Ni hybrid via specific metal affinity force between polyhistidine groups and nickel nanoparticles. The SDS-PAGE assay indicates highly selective separation of His6-tagged Smt A from cell lysate. The GP-Ni hybrid displays favorable performance on the separation/isolation of His6-tagged recombinant proteins with respect to the commercial NTA-Ni2+ column.

Liu, Jia-Wei; Yang, Ting; Ma, Lin-Yu; Chen, Xu-Wei; Wang, Jian-Hua

2013-12-01

298

Measurement Protocols for Optimized Fuel Assembly Tags  

SciTech Connect

This report describes the measurement protocols for optimized tags that can be applied to standard fuel assemblies used in light water reactors. This report describes work performed by the authors at Pacific Northwest National Laboratory for NA-22 as part of research to identify specific signatures that can be developed to support counter-proliferation technologies.

Gerlach, David C.; Mitchell, Mark R.; Reid, Bruce D.; Gesh, Christopher J.; Hurley, David E.

2008-11-01

299

Techniques for Tagging and Tracking Deepwater Rockfishes  

Microsoft Academic Search

Using scuba in August and September 1997 and 1998, we surgically implanted acoustic transmitters (Vemco V16 series) in 6 greenspotted rockfish Sebastes chlorostictus and 16 bocaccio S. paucispinis on the flank of Soquel Canyon in Monterey Bay, California. In 1997 we used longline gear to capture and tag greenspotted rockfish, and in 1998 we worked with a commercial fisherman who

Richard M. Starr; John N. Heine; Korie A. Johnson

2000-01-01

300

Page 1 of 1 Fish Tagging Forum  

E-print Network

Page 1 of 1 AGENDA Fish Tagging Forum Northwest Power and Conservation Council Meeting Date: Monday Question and Indicator Network Diagram, the Forum will explore the value of genetic marking by identifying, the Forum will explore the value of CWT by identifying the theoretical consequences of not investing

301

Page 1 of 1 Fish Tagging Forum  

E-print Network

Page 1 of 1 AGENDA Fish Tagging Forum Northwest Power and Conservation Council Meeting Forum Manager and Forum Chair will report back to the group on their first briefing on progress questions. LUNCH 1:15 to 3:45 Continued Discussion of Forum Process The State agencies and Nez Perce

302

Page 1 of 9 Fish Tagging Forum  

E-print Network

Page 1 of 9 Fish Tagging Forum Northwest Power and Conservation Council Wednesday August 29, 2012. These new definitions are: o Required: required by a forum to be done o Funds: entity that funds the work out the action that collects the information. o Interest-Uses: forum that uses the information

303

TAGGING, TRACKING AND LOCATING WITHOUT GPS  

Microsoft Academic Search

The Savannah River National Laboratory (SRNL) was requested to lead a Law Enforcement Working Group that was formed to collaborate on common operational needs. All agencies represented on the working group ranked their need to tag, track, and locate a witting or unwitting target as their highest priority. Specifically, they were looking for technologies more robust than Global Positioning Satellite

J. Cordaro; T. Coleman; D. Shull

2012-01-01

304

Efficient Object Identification with Passive RFID Tags  

E-print Network

frequency identification systems with passive tags are power- ful tools for object identification. However such as asset tracking (e.g. libraries, ani- mals), automated inventory and stock-keeping, toll collecting, however. As examples, consider laundry services, warehouses, or the su- permarket checkout. We have

305

Closeup of Solar Tadpoles with time tags  

NSDL National Science Digital Library

Here is a close-up view of dark tentacles or tadpoles moving towards the solar surface in this solar flare of April 21, 2002 seen by TRACE. One theory proposed in this press release is that they are due to voids created by magnetic reconnection in the flare. This version of the visualization displays the instrument clock time tags.

Bridgman, Tom; Deluca, Edward; Mckenzie, David; Cooper, Fenwick; Nakariakov, Valery; Seaton, Daniel

2003-04-11

306

Closeup of Solar Tadpoles without time tags  

NSDL National Science Digital Library

Here is a close-up view of dark tentacles or tadpoles moving towards the solar surface in this solar flare of April 21, 2002 seen by TRACE. One theory proposed in this press release is that they are due to voids created by magnetic reconnection in the flare. This version of the visualization does not display the instrument clock time tags.

Bridgman, Tom; Deluca, Edward; Mckenzie, David; Cooper, Fenwick; Nakariakov, Valery; Seaton, Daniel

2003-04-11

307

Semantic Enhancement of Social Tagging Systems  

NASA Astrophysics Data System (ADS)

Social tagging systems have shown an impressive potential for information discovery and exploration. Enriched with Semantic Web technologies, they enable to tap valuable metadata about Web resources and to detect hidden relations, thus, to capture information about both content and context of the resources. In this article, we propose a novel way to combine semantic technologies with Web 2.0 paradigms. We introduce the GroupMe! system, which extends current social tagging systems by giving users more flexibility in organizing and maintaining Web content. In GroupMe!, users can create groups of Web resources they consider relevant by simple drag & drop operations. They can tag and share their groups and Web content with fellow users and benefit from improved search and retrieval capabilities. We evaluate the GroupMe! approach and investigate on the effect of grouping resources for search in tag-based social systems. Our experiments show that the quality of search result ranking can be significantly improved by introducing and exploiting the grouping of resources.

Abel, Fabian; Henze, Nicola; Krause, Daniel; Kriesell, Matthias

308

RFID tag antenna based temperature sensing  

Microsoft Academic Search

Temperature monitoring is important in a number of fields, particularly cold supply chain applications. Most commercial wireless temperature sensors consist of transceivers, memory and batteries to maintain a temperature time history but this is expensive and allows for limited sensor deployment. In this paper, we propose a low cost temperature sensor based on the paradigm of passive RFID tag antenna

Rahul Bhattacharyya; Christian Floerkemeier; Sanjay Sarma

2010-01-01

309

Automated Data Tagging in the HLA  

NASA Astrophysics Data System (ADS)

One of the more powerful and popular forms of data organization implemented in most popular information sharing web applications is data tagging. With a rich user base from which to gather and digest tags, many interesting and often unanticipated yet very useful associations are revealed. With regard to an existing information, the astronomical community has a rich pool of existing digitally stored and searchable data than any of the currently popular web community, such as You Tube or My Space, had when they started. In initial experiments with the search engine for the Hubble Legacy Archive, we have created a simple yet powerful scheme by which the information from a footprint service, the NED and SIMBAD catalog services, and the ADS abstracts and keywords can be used to initially tag data with standard keywords. By then ingesting this into a public ally available information search engine, such as Apache Lucene, one can create a simple and powerful data tag search engine and association system. By then augmenting this with user provided keys and usage pattern analysis, one can produce a powerful modern data mining system for any astronomical data warehouse.

Gaffney, N. I.; Miller, W. W.

2008-08-01

310

AUTOMATIC TAG IDENTIFICATION IN WEB SERVICE DESCRIPTIONS  

E-print Network

technique to smooth browsing experience in large document collections. Some service search engines, like of services is becoming a time-consuming task. Web services are usually described with a standard XML- dispensible. Tagging is a mechanism that has been introduced in search engines and digital libraries

Paris-Sud XI, Université de

311

AFRICAN AMERICAN AFFINITY GROUP ARTICLES OF THE CONSTITUTION & BYLAWS  

E-print Network

AFRICAN AMERICAN AFFINITY GROUP ARTICLES OF THE CONSTITUTION & BYLAWS Date: May 22, 2012 African-American Affinity Group #12;AFRICAN AMERICAN AFFINITY GROUP ARTICLES OF THE CONSTITUTION - 2 - Revised and accepted is the "African -American Affinity Group" (AAAG). ARTICLE II � MISSION SECTION 1 The African-American Affinity

312

OpenTag : privacy control methods in RFID  

E-print Network

The work documented in this thesis is part of the OpenTag project, which has the goal of designing and developing a flexible and more powerful RFID system to meet the needs of the approaching ubiquitous tagging of everyday ...

Shen, Daniel Z

2006-01-01

313

PAP: A Privacy and Authentication Protocol for Passive RFID Tags  

E-print Network

transmission using a battery. Semi-Passive tags are battery assisted tags that use some battery power useful when the transaction history of each item needs to be maintained or when individual items need

Liu, Alex X.

314

Low-cost electromagnetic tagging : design and implementation  

E-print Network

Several implementations of chipless RFID (Radio Frequency Identification) tags are presented and discussed as low-cost alternatives to chip-based RFID tags and sensors. An overview of present-day near-field electromagnetic ...

Fletcher, Richard R. (Richard Ribon)

2002-01-01

315

Facette : using facets to improve tag-based bookmarking  

E-print Network

Facette is a web service that uses facets to enhance the organizational capabilities of tag-based bookmarking systems. As with other bookmarking services, Facette allows users to associate tags with bookmarks to assist the ...

Lai, Peter (Peter J.)

2009-01-01

316

Comparative Performance of Acoustic-Tagged and Passive Integrated Transponder-Tagged Juvenile Salmonids.  

National Technical Information Service (NTIS)

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, balloo...

E. E. Hockersmith, R. S. Brown, T. L. Liedtke

2008-01-01

317

9 CFR 2.51 - Form of official tag.  

Code of Federal Regulations, 2011 CFR

...Identification of Animals § 2.51 Form of official tag. (a) The official tag shall be made of a durable alloy such as brass, bronze, or steel, or of a durable plastic. Aluminum of a sufficient thickness to assure the tag is durable and...

2011-01-01

318

9 CFR 2.51 - Form of official tag.  

Code of Federal Regulations, 2012 CFR

...Identification of Animals § 2.51 Form of official tag. (a) The official tag shall be made of a durable alloy such as brass, bronze, or steel, or of a durable plastic. Aluminum of a sufficient thickness to assure the tag is durable and...

2012-01-01

319

9 CFR 2.51 - Form of official tag.  

...Identification of Animals § 2.51 Form of official tag. (a) The official tag shall be made of a durable alloy such as brass, bronze, or steel, or of a durable plastic. Aluminum of a sufficient thickness to assure the tag is durable and...

2014-01-01

320

9 CFR 2.51 - Form of official tag.  

Code of Federal Regulations, 2013 CFR

...Identification of Animals § 2.51 Form of official tag. (a) The official tag shall be made of a durable alloy such as brass, bronze, or steel, or of a durable plastic. Aluminum of a sufficient thickness to assure the tag is durable and...

2013-01-01

321

Temperature Sensor Tag for Passive UHF RFID Systems  

E-print Network

Temperature Sensor Tag for Passive UHF RFID Systems Juha Virtanen, Leena Ukkonen, Toni Björninen sensor tag for passive UHF RFID systems and discusses a method to perform measurements in practice. The developed sensor tag is fabricated from cost-efficient and commercially available materials. Distilled water

Elsherbeni, Atef Z.

322

Linear Reduction Method for Predictive and Informative Tag SNP Selection  

E-print Network

Linear Reduction Method for Predictive and Informative Tag SNP Selection Jingwu He, Kelly measure the quality of our tag SNP selection algorithm by com- paring actual SNPs with SNPs predicted from: Single nucleotide polymorphism, tag SNP, linear independence. 1 Introduction Genome-wide SNP scans

Zelikovsky, Alexander

323

CS229 Project Report: Automated photo tagging in Facebook  

E-print Network

CS229 Project Report: Automated photo tagging in Facebook Sebastian Schuon, Harry Robertson, Hao identifying and tagging users in photos on a social networking environment known as Facebook. The presented au- tomatic facial tagging system is split into three subsys- tems: obtaining image data from Facebook

Pratt, Vaughan

324

RFID Indoor Tracking based on Inter-tags Distance Measurement  

Microsoft Academic Search

Summary form only given. Indoor tracking and localization is a crucial ingredient in many ubiquitous computing applications and robotics. In many applications there is the need to know the location of the objects. While in the near future everything will be tagged with radio frequency identification (RFID) tags, the localization of these tags in their environment is becoming an important

A. Bekkali; M. Matsumoto

2007-01-01

325

Infrastructure Concepts for Tag-Based Ubiquitous Computing Applications  

E-print Network

amount (Icode tags currently provide about 60 bytes) of non-volatile read/write memory. Such tagging like smart games, home and office automation. Our first prototype systems were implemented from scratch Chef Grocery items are equipped with RFID tags (instead of the bar- codes that are commonly used today

326

RFID tag antennas with stable impedance to mounted material  

Microsoft Academic Search

The following study presents two UHF RFID tag antennas for the identification of mass retailing produces. The antenna is composed of two elements, a planar dipole based antenna matched with a small inductive coil. These tags have the particularity to have stable performances to mounted material. Simulations studied the performance of tag antennas depending on the permittivity and thickness of

T. Deleruyelle; P. Pannier; J. Alarcon; M. Egels; E. Bergeret

2010-01-01

327

NINDS Data Definition for Disorders Content Top Level Tag  

E-print Network

NINDS Data Definition for Disorders Content Top Level Tag data> Container Tag surrounding the particular disorder needs to be singular or plural... example "What is autism" vs. "What have a synonym of Lou Gehrig's Disease. set> Container tag for the set of NINDS partner

328

A SEMANTIC SPACE FOR MUSIC DERIVED FROM SOCIAL TAGS  

Microsoft Academic Search

In this paper we investigate social tags as a novel high- volume source of semantic metadata for music, using tech- niques from the fields of information retrieval and multi- variate data analysis. We show that, despite the ad hoc and informal language of tagging, tags define a low-dimensional semantic space that is extremely well-behaved at the track level, in particular

Mark Sandler

2007-01-01

329

2012 UEC Tokyo. Visual Analysis of Tag Co-occurrence  

E-print Network

-search with the tags. but Query word: blue & car "blue car" Relevant Query word: blue & car "red car" "blue sky; 2012 UEC Tokyo. Basic idea · Prepare many tag pairs of nouns and adjectives ­ e.g. "red + car", "blue + sky", ... · Search web image database for the images corresponding to each of the prepared tag pairs

Yanai, Keiji

330

A New Continuous Multimodal Musical Controller Using Wireless Magnetic Tags  

E-print Network

-negligible size, weight, complication, and current drain. 2) Magnetically-Coupled Tags Magnetically-coupled "tags amounts of magnetic material or conductors that carry eddy currents). This enables essentially any objectA New Continuous Multimodal Musical Controller Using Wireless Magnetic Tags Kai-Yuh Hsiao

331

Tag Normalization and Prediction for Effective Social Media Retrieval  

Microsoft Academic Search

In this paper, we propose a tag normalization algorithm to unify the userspsila annotations. Meanwhile, we explore some general phenomena in a social annotation system and propose a supervised tag prediction model to predict the stabilized tag set of a resource, with feedback of a small amount of user annotation records. The experiments show that a large potion of the

Ming-hung Hsu; Hsin-hsi Chen

2008-01-01

332

Exploiting Flickr Tags and Groups for Finding Landmark Photos  

Microsoft Academic Search

Many people take pictures of different city landmarks and post them to photo-sharing systems like Flickr. They also add tags and place photos in Flickr groups, created around particular themes. Using tags, other people can search for representative landmark images of places of interest. Searching for landmarks using tags results into many non-landmark photos and provides poor landmark summary for

Rabeeh Abbasi; Sergey Chernov; Wolfgang Nejdl; Raluca Paiu; Steffen Staab

2009-01-01

333

Affinity-based Protein Surface Pattern Formation by Ligand Self-Selection from Mixed Protein Solutions**  

PubMed Central

Photolithographically prepared surface patterns of two affinity ligands (biotin and chloroalkane) specific for two proteins (streptavidin and HaloTag®, respectively) are used to spontaneously form high-fidelity surface patterns of the two proteins from their mixed solution. High affinity protein-surface self-selection onto patterned ligands on surfaces exhibiting low non-specific adsorption rapidly yields the patterned protein surfaces. Fluorescence images after protein immobilization show high specificity of the target proteins to their respective surface patterned ligands. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) imaging further supports the chemical specificity of streptavidin and HaloTag® for their surface patterned ligands from mixed protein solutions. However, ToF-SIMS did detect some non-specific adsorption of bovine serum albumin, a masking protein present in excess in the adsorbing solutions, on the patterned surfaces. Protein amino acid composition, surface coverage, density and orientation are important parameters that determine the relative ToF-SIMS fragmentation pattern yields. ToF-SIMS amino acid-derived ion fragment yields summed to produce surface images can reliably determine which patterned surface regions contain bound proteins, but do not readily discriminate between different co-planar protein regions. Principal component analysis (PCA) of these ToF-SIMS data, however, improves discrimination of ions specific to each protein, facilitating surface pattern discrimination and contrast. PMID:23504611

Dubey, Manish; Emoto, Kazunori; Takahashi, Hironobu

2013-01-01

334

Monodisperse, "highly" positively charged protein polymer drag-tags generated in an intein-mediated purification system used in free-solution electrophoretic separations of DNA  

PubMed Central

Free-solution conjugate electrophoresis (FSCE) is a method of DNA sequencing that eliminates the need for viscous polymer solutions by tethering a carefully designed, mobility modifying “drag-tag” to each DNA molecule to achieve size-based separations of DNA. The most successful drag-tags to date are genetically engineered, highly repetitive polypeptides (“protein polymers”) that are designed to be large, water-soluble, and completely monodisperse. Positively charged arginines were deliberately introduced at regular intervals into the amino acid sequence to increase the hydrodynamic drag without increasing drag-tag length. Additionally, a one-step purification method that combines affinity chromatography and on-column tag cleavage was devised to achieve the required drag-tag monodispersity. Sequencing with a read length of approximately 180 bases was successfully achieved with a known sequence in free-solution electrophoresis using one of these positively charged drag-tags. This preliminary result is expected to lead to further progress in FSCE sequencing with ~400 bases read length possible when more “highly” positively charged protein polymers of larger size are generated with the intein system. PMID:22168388

Wang, Xiaoxiao; Albrecht, Jennifer Coyne; Lin, Jennifer S.; Barron, Annelise E.

2012-01-01

335

Faceted Ranking in Collaborative Tagging Systems - Efficient Algorithms for Ranking Users based on a Set of Tags  

Microsoft Academic Search

Multimedia content is uploaded, tagged and recommended by users of collaborative systems such as YouTube and Flickr. These systems can be represented as tagged-graphs, where nodes correspond to users and tagged- links to recommendations. In this paper we analyze the online computation of user-rankings associated to a set of tags, called a facet. A simple approach to faceted ranking is

José Ignacio Orlicki; Pablo Ignacio Fierens; J. Ignacio Alvarez-hamelin

2009-01-01

336

RESEARCH ARTICLE Open Access Using affinity propagation for identifying  

E-print Network

RESEARCH ARTICLE Open Access Using affinity propagation for identifying subspecies among clonal the support of each spoligotype family among the previous classification using affinity propagation shows how the new clustering algorithm Affinity Propagation can help building or refining clonal

Paris-Sud XI, Université de

337

Beyond Affinity Propagation: Message Passing Algorithms for Clustering  

E-print Network

Beyond Affinity Propagation: Message Passing Algorithms for Clustering by Inmar-Ella Givoni Beyond Affinity Propagation: Message Passing Algorithms for Clustering Inmar-Ella Givoni Doctor of Philosophy Graduate Department of Computer Science University of Toronto 2012 Affinity propagation

Frey, Brendan J.

338

Affinity Purification of Plasmid DNA by Temperature-Triggered Precipitation  

E-print Network

Affinity Purification of Plasmid DNA by Temperature-Triggered Precipitation Jan Kostal, Ashok purification method, which takes advantage of the DNA- binding affinity and specificity of the bacterial purifi- cation; affinity precipitation; Elastin-like proteins (ELPs) INTRODUCTION Medical applications

Chen, Wilfred

339

Subcellular Localization and Function of an Epitope-Tagged p7 Viroporin in Hepatitis C Virus-Producing Cells  

PubMed Central

The hepatitis C virus (HCV) viroporin p7 is crucial for production of infectious viral progeny. However, its role in the viral replication cycle remains incompletely understood, in part due to the poor availability of p7-specific antibodies. To circumvent this obstacle, we inserted two consecutive hemagglutinin (HA) epitope tags at its N terminus. HA-tagged p7 reduced peak virus titers ca. 10-fold and decreased kinetics of virus production compared to the wild-type virus. However, HA-tagged p7 rescued virus production of a mutant virus lacking p7, thus providing formal proof that the tag does not disrupt p7 function. In HCV-producing cells, p7 displayed a reticular staining pattern which colocalized with the HCV envelope glycoprotein 2 (E2) but also partially with viral nonstructural proteins 2, 3, and 5A. Using coimmunoprecipitation, we confirmed a specific interaction between p7 and NS2, whereas we did not detect a stable interaction with core, E2, or NS5A. Moreover, we did not observe p7 incorporation into affinity-purified virus particles. Consistently, there was no evidence supporting a role of p7 in viral entry, as an anti-HA antibody was not able to neutralize Jc1 virus produced from an HA-p7-tagged genome. Collectively, these findings highlight a stable interaction between p7 and NS2 which is likely crucial for production of infectious HCV particles. Use of this functional epitope-tagged p7 variant should facilitate the analysis of the final steps of the HCV replication cycle. PMID:23175364

Vieyres, Gabrielle; Brohm, Christiane; Friesland, Martina; Gentzsch, Juliane; Wolk, Benno; Roingeard, Philippe; Steinmann, Eike

2013-01-01

340

Subcellular localization and function of an epitope-tagged p7 viroporin in hepatitis C virus-producing cells.  

PubMed

The hepatitis C virus (HCV) viroporin p7 is crucial for production of infectious viral progeny. However, its role in the viral replication cycle remains incompletely understood, in part due to the poor availability of p7-specific antibodies. To circumvent this obstacle, we inserted two consecutive hemagglutinin (HA) epitope tags at its N terminus. HA-tagged p7 reduced peak virus titers ca. 10-fold and decreased kinetics of virus production compared to the wild-type virus. However, HA-tagged p7 rescued virus production of a mutant virus lacking p7, thus providing formal proof that the tag does not disrupt p7 function. In HCV-producing cells, p7 displayed a reticular staining pattern which colocalized with the HCV envelope glycoprotein 2 (E2) but also partially with viral nonstructural proteins 2, 3, and 5A. Using coimmunoprecipitation, we confirmed a specific interaction between p7 and NS2, whereas we did not detect a stable interaction with core, E2, or NS5A. Moreover, we did not observe p7 incorporation into affinity-purified virus particles. Consistently, there was no evidence supporting a role of p7 in viral entry, as an anti-HA antibody was not able to neutralize Jc1 virus produced from an HA-p7-tagged genome. Collectively, these findings highlight a stable interaction between p7 and NS2 which is likely crucial for production of infectious HCV particles. Use of this functional epitope-tagged p7 variant should facilitate the analysis of the final steps of the HCV replication cycle. PMID:23175364

Vieyres, Gabrielle; Brohm, Christiane; Friesland, Martina; Gentzsch, Juliane; Wölk, Benno; Roingeard, Philippe; Steinmann, Eike; Pietschmann, Thomas

2013-02-01

341

Universality of affine formulation in general relativity  

NASA Astrophysics Data System (ADS)

The affine variational principle for general relativity, proposed in 1978 by one of us, is a good remedy for the nonuniversal properties of the standard, metric formulation, arising when the matter Lagrangian depends upon the metric derivatives. The affine version of the theory cures the standard drawback of the metric version, where the leading (second-order) term of the field equations depends upon the matter fields and its causal structure violates the light cone structure of the metric. Choosing the affine connection (and not the metric one) as the gravitational configuration, simplifies considerably the canonical structure of the theory and is more suitable for the purposes of its quantization along the lines of Ashtekar and Lewandowski. We show how the affine formulation provides a simple method to handle boundary integrals in general relativity theory.

Kijowski, Jerzy; Werpachowski, Roman

2007-02-01

342

PRINCIPLES OF AFFINITY-BASED BIOSENSORS  

EPA Science Inventory

Despite the amount of resources that have been invested by national and international academic, government, and commercial sectors to develop affinity-based biosensor products, little obvious success has been realized through commercialization of these devices for specific applic...

343

Clustering by evidence accumulation on affinity propagation  

Microsoft Academic Search

Affinity propagation (AP) is a clustering algorithm which has much better performance than traditional clustering approach such as k-means algorithm. In this paper, we present an algorithm called voting partition affinity propagation (voting-PAP) which is a method for clustering using evidence accumulation based on AP. Resulting clusters by voting-PAP are not constrained to be hyper-spherically shaped. Voting-PAP consists of three

Xuqing Zhang; Fei Wu; Yueting Zhuang

2008-01-01

344

Affinity Electrophoresis Using Ligands Attached To Polymers  

NASA Technical Reports Server (NTRS)

In new technique, reduction of electrophoretic mobilities by addition of polyethylene glycol to ligands increases electrophoretic separabilities. In immuno-affinity electrophoresis, modification of ligands extends specificity of electrophoretic separation to particles having surface electric-charge structures otherwise making them electrophoretically inseparable. Modification of antibodies by polyethylene glycol greatly reduces ability to aggregate while enhancing ability to affect electrophoretic mobilities of cells. In hydrophobic-affinity electrophoresis, addition of polyethylene glycol reduces tendency toward aggregation of cells or macromolecules.

Van Alstine, James M.; Snyder, Robert S.; Harris, J. M.; Brooks, D. E.

1990-01-01

345

Two-dimensional gel electrophoresis; better than a poke in the ICAT?  

Microsoft Academic Search

To date, the most widely used technology for conducting proteomic studies has been two-dimensional gel electrophoresis (2DGE), but this approach does have drawbacks. Isotope-coded affinity tagging (ICAT) is starting to challenge 2DGE as a new proteomic tool for the analysis of proteins in complex biological specimens. An appraisal of these two methodologies reveals that neither ICAT nor 2DGE provide comprehensive

Wayne F Patton; Birte Schulenberg; Thomas H Steinberg

2002-01-01

346

Dynamic changes in transcription factor complexes during erythroid differentiation revealed by quantitative proteomics  

Microsoft Academic Search

During erythroid differentiation, ?-globin gene expression is regulated by the locus control region (LCR). The transcription factor NF-E2p18\\/MafK binds within this region and is essential for ?-globin expression in murine erythroleukemia (MEL) cells. Here we use the isotope-coded affinity tag (ICAT) technique of quantitative mass spectrometry to compare proteins interacting with NF-E2p18\\/MafK during differentiation. Our results define MafK as a

Marjorie Brand; Jeffrey A Ranish; Nicolas T Kummer; Joan Hamilton; Kazuhiko Igarashi; Claire Francastel; Tian H Chi; Gerald R Crabtree; Ruedi Aebersold; Mark Groudine

2003-01-01

347

Evidence for the Presence of Disease-Perturbed Networks in Prostate Cancer Cells by Genomic and Proteomic Analyses: A Systems Approach to Disease  

Microsoft Academic Search

Prostate cancer is initially responsive to androgen ablation therapy and progresses to androgen-unresponsive states that arerefractory to treatment. The mechanism of thistransition is unknown. A systems approach to disease begins with the quantitativedelineation oftheinformational elements (mRNAs and proteins) in various disease states. We employed two recently developed high-throughput technologies, massively parallel signature sequencing (MPSS) and isotope-coded affinity tag, to gain

Biaoyang Lin; James T. White; Tao Xie; Angelita G. Utleg; Xiaowei Yan; Eugene C. Yi; Paul Shannon; Irina Khrebtukova; Paul H. Lange; David R. Goodlett; Daixing Zhou; Thomas J. Vasicek; Leroy Hood

2005-01-01

348

Selected Isotopes for Optimized Fuel Assembly Tags  

SciTech Connect

In support of our ongoing signatures project we present information on 3 isotopes selected for possible application in optimized tags that could be applied to fuel assemblies to provide an objective measure of burnup. 1. Important factors for an optimized tag are compatibility with the reactor environment (corrosion resistance), low radioactive activation, at least 2 stable isotopes, moderate neutron absorption cross-section, which gives significant changes in isotope ratios over typical fuel assembly irradiation levels, and ease of measurement in the SIMS machine 2. From the candidate isotopes presented in the 3rd FY 08 Quarterly Report, the most promising appear to be Titanium, Hafnium, and Platinum. The other candidate isotopes (Iron, Tungsten, exhibited inadequate corrosion resistance and/or had neutron capture cross-sections either too high or too low for the burnup range of interest.

Gerlach, David C.; Mitchell, Mark R.; Reid, Bruce D.; Gesh, Christopher J.; Hurley, David E.

2008-10-01

349

Chemoenzymatic Fc Glycosylation via Engineered Aldehyde Tags  

PubMed Central

Glycoproteins with chemically defined glycosylation sites and structures are important biopharmaceutical targets and critical tools for glycobiology. One approach toward constructing such molecules involves chemical glycosylation of aldehyde-tagged proteins. Here, we report the installation of a genetically encoded aldehyde tag at the internal glycosylation site of the crystallizable fragment (Fc) of IgG1. We replaced the natural Fc N-glycosylation sequon with a five amino-acid sequence that was efficiently converted by recombinant formylglycine generating enzyme in vitro, thereby introducing aldehyde groups for subsequent chemical elaboration. Oxime-linked glycoconjugates were synthesized by conjugating aminooxy N-acetylglucosamine to the modified Fc followed by enzymatic transfer of complex N-glycans from corresponding glycan oxazolines by an EndoS-derived glycosynthase. In this manner we generated specific Fc glycoforms without relying on natural protein glycosylation machineries. PMID:24702330

2014-01-01

350

Vulnerability Analysis of PAP for RFID Tags  

E-print Network

In this paper, we analyze the security of an RFID authentication protocol proposed by Liu and Bailey [1], called Privacy and Authentication Protocol (PAP), and show its vulnerabilities and faulty assumptions. PAP is a privacy and authentication protocol designed for passive tags. The authors claim that the protocol, being resistant to commonly assumed attacks, requires little computation and provides privacy protection and authentication. Nevertheless, we propose two traceability attacks and an impersonation attack, in which the revealing of secret information (i.e., secret key and static identifier) shared between the tag and the reader is unnecessary. Moreover, we review all basic assumptions on which the design of the protocol resides, and show how many of them are incorrect and are contrary to the common assumptions in RFID systems.

Naser, Mu'awya; Rafie, Mohammd; van der Lubbe, Jan

2010-01-01

351

Molecular Tagging Velocimetry in a Microchannel  

NASA Astrophysics Data System (ADS)

The majority of velocity measurements in microchannel geometries have been typically obtained using particle-based techniques. We report preliminary data from Molecular Tagging Velocimetry (MTV) in high aspect ratio rectangular channels with a gap width of order 100 micron. The aqueous flow is driven either electroosmotically or by a pressure differential. Results will be presented for the variation of flow speed versus applied potential, for the electroosmotic flow, and friction factor versus Reynolds number for the pressure driven flow.

Lum, C.; Koochesfahani, M.

2003-11-01

352

Prospects for Barium Tagging in Gaseous Xenon  

NASA Astrophysics Data System (ADS)

Tagging events with the coincident detection of a barium ion would greatly reduce the background for a neutrino-less double beta decay search in xenon. This paper describes progress towards realizing this goal. It outlines a source that can produce large quantities of Ba++ in gas, shows that this can be extracted to vacuum, and demonstrates a mechanism by which the Ba++ can be efficiently converted to Ba+ as required for laser identification.

Sinclair, D.; Rollin, E.; Smith, J.; Mommers, A.; Ackeran, N.; Aharmin, B.; Auger, M.; Barbeau, P. S.; Benitez-Medina, C.; Breidenbach, M.; Burenkov, A.; Cook, S.; Coppens, A.; Daniels, T.; DeVoe, R.; Dobi, A.; Dolinski, M. J.; Donato, K.; Fairbank, W., Jr.; Farine, J.; Giroux, G.; Gornea, G.; Graham, K.; Gratta, G.; Green, M.; Hagemann, C.; Hall, C.; Hall, K.; Hallman, D.; Hargrove, C.; Herrin, S.; Kaufman, L. K.; Leonard, D. S.; LePort, F.; Mackay, D.; MacLennan, R.; Mong, B.; Montero Díez, M.; Müller, A. R.; Neilson, R.; Niner, E.; Odian, A.; O'Sullivan, K.; Ouellet, C.; Piepke, A.; Pocar, A.; Prescott, C. Y.; Pushkin, K.; Rowson, P. C.; Slutsky, S.; Stekhanov, V.; Twelker, K.; Voskanian, N.; Vuilleumier, J.-L.; Wichoski, U.; Wodin, J.; Yang, L.; Yen, Y.-R.

2011-08-01

353

RADIO-TAGGING FALCONIFORM AND STRIGIFORM BIRDS  

Microsoft Academic Search

This paper describes techniques for radio-tagging and monitoring birds of prey. Several recent papers briefly discuss radio-telemetric techniques for study- ing behavior of raptoffal birds. Nicholls and Warner (1966, 1968) commented on the use of radio-telemetry for studying the natural history of Great Horned Owls (Bubo virginianus), Barred Owls (Strix varia), and Saw-whet Owls (Aegol- ius acadica). Southern (1963, 1964,

Thomas C. Dunstan

1972-01-01

354

A fractal circular polarized RFID tag antenna  

NASA Astrophysics Data System (ADS)

In this paper, we present a novel fractal antenna for radiofrequency identification (RFID) tags. The proposed antenna has a resonant frequency equal to 2.45GHz and circular polarization. The fractal technique was very useful to obtain a miniaturization of antenna size by more than 30%. The gain and directivity of the antenna are acceptable for the desired RFID application. All the results are obtained using CST Microwave simulation tool.

Chaouki, Guesmi; Ferchichi, Abdelhak; Gharsallah, Ali

2013-09-01

355

The use of tags in monitoring limits on mobile missiles  

SciTech Connect

Three tagging systems were considered in this paper: as a supplement to on-site inspection (OSI), as a supplement to national technical means (NTM), and as a supplement to site surveillance systems. Each system would require a different type of tag, perhaps ranging from microchip tags with infrared transponders to navigation receivers. Use of tags as a supplement to OSIs may be the simplest system to implement because it places the least demands on technology. Tags may make OSI more acceptable by replacing humans with remote sensors, thereby decreasing the perceived potential for espionage. Using tags as a supplement to NTM decreases the necessity for human OSI even further, but places higher demands on technology and may affect the normal operation of deployment areas. Site surveillance systems using tags have the potential for excellent missile verification, but they may be excessively intrusive and expensive, and could have a large effect on the normal operation of declared facilities.

Fetter, S.

1987-03-01

356

Single tag for total carbohydrate analysis.  

PubMed

Anthranilic acid (2-aminobenzoic acid, 2-AA) has the remarkable property of reacting rapidly with every type of reducing carbohydrate. Reactivity of 2-AA with carbohydrates in aqueous solutions surpasses all other tags reported to date. This unique capability is attributed to the strategically located -COOH which accelerates Schiff base formation. Monosaccharides, oligosaccharides (N-, O-, and lipid linked and glycans in secretory fluids), glycosaminoglycans, and polysaccharides can be easily labeled with 2-AA. With 2-AA, labeling is simple in aqueous solutions containing proteins, peptides, buffer salts, and other ingredients (e.g., PNGase F, glycosidase, and transferase reaction mixtures). In contrast, other tags require relatively pure glycans for labeling in anhydrous dimethyl sulfoxide-acetic acid medium. Acidic conditions are known to cause desialylation, thus requiring a great deal of attention to sample preparation. Simpler labeling is achieved with 2-AA within 30-60 min in mild acetate-borate buffered solution. 2-AA provides the highest sensitivity and resolution in chromatographic methods for carbohydrate analysis in a simple manner. Additionally, 2-AA is uniquely qualified for quantitative analysis by mass spectrometry in the negative mode. Analyses of 2-AA-labeled carbohydrates by electrophoresis and other techniques have been reported. Examples cited here demonstrate that 2-AA is the universal tag for total carbohydrate analysis. PMID:24769375

Anumula, Kalyan Rao

2014-07-15

357

Comparison of weak affinity chromatography and surface plasmon resonance in determining affinity of small molecules.  

PubMed

In this study, we compared affinity data from surface plasmon resonance (SPR) and weak affinity chromatography (WAC), two established techniques for determination of weak affinity (mM-?M) small molecule-protein interactions. In the current comparison, thrombin was used as target protein. In WAC the affinity constant (KD) was determined from retention times, and in SPR it was determined by Langmuir isotherm fitting of steady-state responses. Results indicate a strong correlation between the two methods (R(2)=0.995, P<0.0001). PMID:24915639

Duong-Thi, Minh-Dao; Bergström, Gunnar; Mandenius, Carl-Fredrik; Bergström, Maria; Fex, Tomas; Ohlson, Sten

2014-09-15

358

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

SciTech Connect

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.

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

359

The affinity purification and characterization of ATP synthase complexes from mitochondria  

PubMed Central

The mitochondrial F1-ATPase inhibitor protein, IF1, inhibits the hydrolytic, but not the synthetic activity of the F-ATP synthase, and requires the hydrolysis of ATP to form the inhibited complex. In this complex, the ?-helical inhibitory region of the bound IF1 occupies a deep cleft in one of the three catalytic interfaces of the enzyme. Its N-terminal region penetrates into the central aqueous cavity of the enzyme and interacts with the ?-subunit in the enzyme's rotor. The intricacy of forming this complex and the binding mode of the inhibitor endow IF1 with high specificity. This property has been exploited in the development of a highly selective affinity procedure for purifying the intact F-ATP synthase complex from mitochondria in a single chromatographic step by using inhibitor proteins with a C-terminal affinity tag. The inhibited complex was recovered with residues 1–60 of bovine IF1 with a C-terminal green fluorescent protein followed by a His-tag, and the active enzyme with the same inhibitor with a C-terminal glutathione-S-transferase domain. The wide applicability of the procedure has been demonstrated by purifying the enzyme complex from bovine, ovine, porcine and yeast mitochondria. The subunit compositions of these complexes have been characterized. The catalytic properties of the bovine enzyme have been studied in detail. Its hydrolytic activity is sensitive to inhibition by oligomycin, and the enzyme is capable of synthesizing ATP in vesicles in which the proton-motive force is generated from light by bacteriorhodopsin. The coupled enzyme has been compared by limited trypsinolysis with uncoupled enzyme prepared by affinity chromatography. In the uncoupled enzyme, subunits of the enzyme's stator are degraded more rapidly than in the coupled enzyme, indicating that uncoupling involves significant structural changes in the stator region. PMID:23407638

Runswick, Michael J.; Bason, John V.; Montgomery, Martin G.; Robinson, Graham C.; Fearnley, Ian M.; Walker, John E.

2013-01-01

360

Modeling data from double-tagging experiments to estimate heterogeneous rates of tag shedding in lake trout (Salvelinus namaycush)  

USGS Publications Warehouse

Data from mark-recapture studies are used to estimate population rates such as exploitation, survival, and growth. Many of these applications assume negligible tag loss, so tag shedding can be a significant problem. Various tag shedding models have been developed for use with data from double-tagging experiments, including models to estimate constant instantaneous rates, time-dependent rates, and type I and II shedding rates. In this study, we used conditional (on recaptures) multinomial models implemented using the program SURVIV (G.C. White. 1983. J. Wildl. Manage. 47: 716-728) to estimate tag shedding rates of lake trout (Salvelinus namaycush) and explore various potential sources of variation in these rates. We applied the models to data from several long-term double-tagging experiments with Lake Superior lake trout and estimated shedding rates for anchor tags in hatchery-reared and wild fish and for various tag types applied in these experiments. Estimates of annual tag retention rates for lake trout were fairly high (80-90%), but we found evidence (among wild fish only) that retention rates may be significantly lower in the first year due to type I losses. Annual retention rates for some tag types varied between male and female fish, but there was no consistent pattern across years. Our estimates of annual tag retention rates will be used in future studies of survival rates for these fish.

Fabrizio, Mary C.; Nichols, James D.; Hines, James E.; Swanson, Bruce L.; Schram, Stephen T.

1999-01-01

361

Modeling data from double-tagging experiments to estimate heterogeneous rates of tag-shedding in lake trout (Salvelinus namaycush)  

USGS Publications Warehouse

Data from mark-recapture studies are used to estimate population rates such as exploitation, survival, and growth. Many of these applications assume negligible tag loss, so tag shedding can be a significant problem. Various tag shedding models have been developed for use with data from double-tagging experiments, including models to estimate constant instantaneous rates, time-dependent rates, and type I and II shedding rates. I n this study, we used conditional (on recaptures) multinomial models implemented using the program SURVIV (G.C. White. 1983. J. Wildl. Manage. 47: 716-728) to estimate tag shedding rates of lake trout (Salvelinus namaycush) and explore various potential sources of variation in these rates. We applied the models to data from several long-term double-tagging experiments with Lake Superior lake trout and estimated shedding rates for anchor tags in hatchery-reared and wild fish and for various tag types applied in these experiments. Estimates of annual tag retention rates for lake trout were fairly high (80-90%), but we found evidence (among wild fish only) that retention rates may be significantly lower in the first year due to type I losses. Annual retention rates for some tag types varied between male and female fish, but there was no consistent pattern across years. Our estimates of annual tag retention rates will be used in future studies of survival rates for these fish.

Fabrizio, M.C.; Nichols, J.D.; Hines, J.E.; Swanson, B.L.; Schram, S.T.

1999-01-01

362

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

DOEpatents

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.

Scott; Jeff W. (Pasco, WA), Pratt; Richard M. (Richland, WA)

2006-09-12

363

Triosephosphate isomerase is a common crystallization contaminant of soluble His-tagged proteins produced in Escherichia coli  

PubMed Central

Attempts to crystallize several mammalian proteins overexpressed in Escherichia coli revealed a common contaminant, triosephosphate isomerase, a protein involved in glucose metabolism. Even with triosephosphate isomerase present in very small amounts, similarly shaped crystals appeared in the crystallization drops in a number of polyethylene glycol-containing conditions. All of the target proteins were His-tagged and their purification involved immobilized metal-affinity chromatography (IMAC), a step that was likely to lead to triosephos­phate isomerase contamination. Analysis of the triosephosphate isomerase crystals led to the structure of E. coli triosephosphate isomerase at 1.85?Å resolution, which is a significant improvement over the previous structure. PMID:23695562

Kozlov, Guennadi; Vinaik, Roohi; Gehring, Kalle

2013-01-01

364

Classification of neocortical interneurons using affinity propagation.  

PubMed

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

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

2013-01-01

365

Classification of neocortical interneurons using affinity propagation  

PubMed Central

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

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

2013-01-01

366

The effect of ligand affinity on integrins' lateral diffusion in cultured cells.  

PubMed

The role of ligand affinity in altering ?PS2C?PS integrins' lateral mobility was studied using single particle tracking (SPT) with ligand-functionalized quantum dots (QDs) and fluorescence recovery after photobleaching (FRAP) with fluorescent protein tagged integrins. Integrins are ubiquitous transmembrane proteins that are vital for numerous cellular functions, including bidirectional signaling and cell anchorage. Wild-type and high ligand affinity mutant (?PS2C?PS-V409D) integrins were studied in S2 cells. As measured by SPT, the integrin mobile fraction decreased by 22% and had a 4× slower diffusion coefficient for ?PS2C?PS-V409D compared to wild-type integrins. These differences are partially the result of ?PS2C?PS-V409D integrins' increased clustering. For the wild-type integrins, the average of all diffusion coefficients measured by SPT was statistically similar to the ensemble FRAP results. A 75% slower average diffusion coefficient was measured by SPT compared to FRAP for ?PS2C?PS-V409D integrins, and this may be the result of SPT measuring only ligand-bound integrins, in contrast all ligand-bound and ligand-unbound integrins are averaged in FRAP measurements. Specific binding of the ligand-functionalized QDs was 99% for integrin expressing cells. The results prove that the ligand binding affinity affects the lateral dynamics of a subset of integrins based on the complementary SPT and FRAP data. PMID:23242168

Mainali, Dipak; Smith, Emily A

2013-04-01

367

Fluorescent Boronic Acid Polymer Grafted on Silica Particles for Affinity Separation of Saccharides  

PubMed Central

Boronic acid affinity gels are important for effective separation of biological active cis-diols, and are finding applications both in biotech industry and in biomedical research areas. To increase the efficacy of boronate affinity separation, it is interesting to introduce repeating boronic acid units in flexible polymer chains attached on solid materials. In this work, we synthesize polymer brushes containing boronic acid repeating units on silica gels using surface-initiated atom transfer radical polymerization (ATRP). A fluorescent boronic acid monomer is first prepared from an azide-tagged fluorogenic boronic acid and an alkyne-containing acrylate by Cu(I)-catalyzed 1,3-dipolar cycloaddition reaction (the CuAAC click chemistry). The boronic acid monomer is then grafted to the surface of silica gel modified with an ATRP initiator. The obtained composite material contains boronic acid polymer brushes on surface and shows favorable saccharide binding capability under physiological pH conditions, and displays interesting fluorescence intensity change upon binding fructose and glucose. In addition to saccharide binding, the flexible polymer brushes on silica also enable fast separation of a model glycoprotein based on selective boronate affinity interaction. The synthetic approach and the composite functional material developed in this work should open new opportunities for high efficiency detection, separation, and analysis of not only simple saccharides, but also glycopeptides and large glycoproteins. PMID:24444898

2014-01-01

368

Active sensor tags for global visibility of asset readiness  

NASA Astrophysics Data System (ADS)

The era of wireless communication and discrete, autonomous sensors platforms is upon us. Advances in radio-frequency (RF) technology from simple two-way personal communications to smart, independent, sensor command, and control units has greatly expanded the applications domain. In the past four years, Pacific Northwest National Laboratory (PNNL) scientists and engineers have developed smart sensor tags (health tags) for the Army to monitor environmental conditions of high value assets over their lifetime (10 yrs). These field tested health tags uniquely identify individual assets, record and store data, run diagnostic and prognostic protocols, identify asset performance status (GO, CAUTION, NO-GO), and provide all this information over a wireless RF link to a portable, hand held reader. Leveraging the innovation achieved for health monitoring tags, the next generation active sensor tag has been developed (FlexiTag) providing reduced tag size and manufacturing cost, greater sensor interface capabilities, and a flexible substrate for surface mount conformity. The design has a greatly reduced part count due to the use of newly available, highly integrated RF chip sets. In addition to asset health monitoring, the new tag platform opens up additional application areas such as TTL (tagging, tracking, and locating), real-time machine fault monitoring, and ad-hoc sensor networking. This paper will compare and contrast the FlexiTag to its predecessors and discuss the current application areas it is being applied to.

Burghard, B. J.; Silvers, K. L.; Skorpik, J. R.

2005-05-01

369

Integrated Management and Visualization of Electronic Tag Data with Tagbase  

PubMed Central

Electronic tags have been used widely for more than a decade in studies of diverse marine species. However, despite significant investment in tagging programs and hardware, data management aspects have received insufficient attention, leaving researchers without a comprehensive toolset to manage their data easily. The growing volume of these data holdings, the large diversity of tag types and data formats, and the general lack of data management resources are not only complicating integration and synthesis of electronic tagging data in support of resource management applications but potentially threatening the integrity and longer-term access to these valuable datasets. To address this critical gap, Tagbase has been developed as a well-rounded, yet accessible data management solution for electronic tagging applications. It is based on a unified relational model that accommodates a suite of manufacturer tag data formats in addition to deployment metadata and reprocessed geopositions. Tagbase includes an integrated set of tools for importing tag datasets into the system effortlessly, and provides reporting utilities to interactively view standard outputs in graphical and tabular form. Data from the system can also be easily exported or dynamically coupled to GIS and other analysis packages. Tagbase is scalable and has been ported to a range of database management systems to support the needs of the tagging community, from individual investigators to large scale tagging programs. Tagbase represents a mature initiative with users at several institutions involved in marine electronic tagging research. PMID:21750734

Lam, Chi Hin; Tsontos, Vardis M.

2011-01-01

370

Development of techniques for tagging precursor and essential chemicals  

SciTech Connect

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.

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

371

Identity, Affinity, Reality: Making the Case for Affinity Groups in Elementary School  

ERIC Educational Resources Information Center

Affinity groups are places where students build connections and process "ouch" moments from their classes. Children talk about the isolation they sometimes feel. The relationships students gain through race-based affinity groups enable them to feel less alone with their emotions and help them build a stronger sense of self. At the same time,…

Parsons, Julie; Ridley, Kimberly

2012-01-01

372

Integrin avidity regulation: are changes in affinity and conformation underemphasized?  

E-print Network

Integrin avidity regulation: are changes in affinity and conformation underemphasized? Opinion their adhesiveness through both affinity- and valency-based mechanisms. Recent advances have shed light on the structural basis for affinity regulation and on the signaling mechanisms responsible for both affinity

Springer, Timothy A.

373

On Characterizing Affinity and Its Impact on Network Performance  

E-print Network

On Characterizing Affinity and Its Impact on Network Performance Gabriel Lucas School for generating member groups with different degrees of affinity (clusteredness) and show that affinity can have the algorithm's input parameter as a method for classifying and comparing affinity groups. In this paper, we

Chuang, John C.-I.

374

Use of Affinity Diagrams as Instructional Tools in Inclusive Classrooms.  

ERIC Educational Resources Information Center

This article describes how the affinity diagram, a tool for gathering information and organizing it into natural groupings, can be used in inclusive classrooms. It discusses how students can be taught to use an affinity diagram, how affinity diagrams can be used to reflect many voices, and how affinity diagrams can be used to plan class projects.…

Haselden, Polly G.

2003-01-01

375

Maximin affinity learning of image segmentation Srinivas C. Turaga  

E-print Network

Maximin affinity learning of image segmentation Srinivas C. Turaga MIT Kevin L. Briggman Max by first using a classifier to predict an affinity graph that reflects the degree to which image pixels been applied to the affinity classifier to produce affinity graphs that are good in the sense

Seung, Sebastian

376

On Affinity Measures for Artificial Immune System Movie Recommenders  

E-print Network

On Affinity Measures for Artificial Immune System Movie Recommenders Proceedings RASC-2004, The 5th the effect of different affinity measure algorithms for the AIS. Two different affinity measures, Kendall and that, as long as a suitable affinity measure is chosen, results are good. Keywords: Artificial Immune

Aickelin, Uwe

377

AR-quiver approach to affine canonical basis elements  

Microsoft Academic Search

This is the continuation of [Y. Li, Affine quivers of type A˜n and canonical bases, math.QA\\/0501175]. We describe the affine canonical basis elements in the case when the affine quiver has arbitrary orientation. This generalizes the description in [G. Lusztig, Affine quivers and canonical bases, Publ. Math. Inst. Hautes Études Sci. 76 (1992) 111–163].

Yiqiang Li; Zongzhu Lin

2007-01-01

378

Affine coherent states and Toeplitz operators  

NASA Astrophysics Data System (ADS)

We study a parameterized family of Toeplitz operators in the context of affine coherent states based on the Calderón reproducing formula (=?resolution of unity on L_2( {R})) and the specific admissible wavelets (=?affine coherent states in L_2( {R})) related to Laguerre functions. Symbols of such Calderón-Toeplitz operators as individual coordinates of the affine group (=?upper half-plane with the hyperbolic geometry) are considered. In this case, a certain class of pseudo-differential operators, their properties and their operator algebras are investigated. As a result of this study, the Fredholm symbol algebras of the Calderón-Toeplitz operator algebras for these particular cases of symbols are described. This article is part of a special issue of Journal of Physics A: Mathematical and Theoretical devoted to ‘Coherent states: mathematical and physical aspects’.

Hutníková, Mária; Hutník, Ondrej

2012-06-01

379

Affinity selection using filamentous phage display.  

PubMed

Display of peptides on filamentous phage, phage display, is an in vitro selection technique well suited for identification of therapeutic peptide binders for a huge variety of protein targets. The peptides are identified in a process where phage libraries are subjected to affinity selection towards a particular protein target. A successful outcome of an affinity selection is dependent on proper surveillance of the phage life cycle, to make sure that the selection is based on affinity for the target, not on bias in phage propagation rate. In this chapter we present two approaches for protein target presentation and a protocol for phage rescue and propagation, which includes several controls to ensure that all phages initially eluted from the protein target are given equal conditions during the following amplification and selection steps. PMID:24146397

Kulseth, Mari Ann; Fagerlund, Annette; Myrset, Astrid Hilde

2014-01-01

380

The dynamics of metric-affine gravity  

SciTech Connect

Highlights: > The role and the dynamics of the connection in metric-affine theories is explored. > The most general second order action does not lead to a dynamical connection. > Including higher order invariants excites new degrees of freedom in the connection. > f(R) actions are also discussed and shown to be a non- representative class. - Abstract: Metric-affine theories of gravity provide an interesting alternative to general relativity: in such an approach, the metric and the affine (not necessarily symmetric) connection are independent quantities. Furthermore, the action should include covariant derivatives of the matter fields, with the covariant derivative naturally defined using the independent connection. As a result, in metric-affine theories a direct coupling involving matter and connection is also present. The role and the dynamics of the connection in such theories is explored. We employ power counting in order to construct the action and search for the minimal requirements it should satisfy for the connection to be dynamical. We find that for the most general action containing lower order invariants of the curvature and the torsion the independent connection does not carry any dynamics. It actually reduces to the role of an auxiliary field and can be completely eliminated algebraically in favour of the metric and the matter field, introducing extra interactions with respect to general relativity. However, we also show that including higher order terms in the action radically changes this picture and excites new degrees of freedom in the connection, making it (or parts of it) dynamical. Constructing actions that constitute exceptions to this rule requires significant fine tuned and/or extra a priori constraints on the connection. We also consider f(R) actions as a particular example in order to show that they constitute a distinct class of metric-affine theories with special properties, and as such they cannot be used as representative toy theories to study the properties of metric-affine gravity.

Vitagliano, Vincenzo, E-mail: vitaglia@sissa.it [SISSA-International School for Advanced Studies, Via Bonomea 265, 34136 Trieste (Italy); INFN, Sez. di Trieste, Via Valerio 2, 34127 Trieste (Italy); Sotiriou, Thomas P., E-mail: T.Sotiriou@damtp.cam.ac.uk [Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Wilberforce Road, Cambridge, CB3 0WA (United Kingdom); Liberati, Stefano, E-mail: liberati@sissa.it [SISSA-International School for Advanced Studies, Via Bonomea 265, 34136 Trieste (Italy); INFN, Sez. di Trieste, Via Valerio 2, 34127 Trieste (Italy)

2011-05-15

381

N2O molecular tagging velocimetry  

NASA Astrophysics Data System (ADS)

A new seeded velocity measurement technique, N2O molecular tagging velocimetry (MTV), is developed to measure velocity in wind tunnels by photochemically creating an NO tag line. Nitrous oxide "laughing gas" is seeded into the air flow. A 193 nm ArF excimer laser dissociates the N2O to O(1D) that subsequently reacts with N2O to form NO. O2 fluorescence induced by the ArF laser "writes" the original position of the NO line. After a time delay, the shifted NO line is "read" by a 226-nm laser sheet and the velocity is determined by time-of-flight. At standard atmospheric conditions with 4% N2O in air, ˜1000 ppm of NO is photochemically created in an air jet based on experiment and simulation. Chemical kinetic simulations predict 800-1200 ppm of NO for 190-750 K at 1 atm and 850-1000 ppm of NO for 0.25-1 atm at 190 K. Decreasing the gas pressure (or increasing the temperature) increases the NO ppm level. The presence of humid air has no significant effect on NO formation. The very short NO formation time (<10 ns) makes the N2O MTV method amenable to low- and high-speed air flow measurements. The N2O MTV technique is demonstrated in air jet to measure its velocity profile. The N2O MTV method should work in other gas flows as well (e.g., helium) since the NO tag line is created by chemical reaction of N2O with O(1D) from N2O photodissociation and thus does not depend on the bulk gas composition.

ElBaz, A. M.; Pitz, R. W.

2012-03-01

382

Affinity chromatography purification of Clostridium perfringens enterotoxin.  

PubMed Central

Anti-enterotoxin immunoglobulins immobilized on CH-Sepharose or CNBr-Sepharose were used for affinity chromatography purification of Clostridium perfringens enterotoxin. Cell extracts containing enterotoxin or partially purified toxin preparations were applied to the column and nonspecifically-bound protein was eluted. NaOH was used to elute specifically bound toxin. The purity of enterotoxin purified by Sephadex G-100 chromatography followed by affinity chromatography appears similar to toxin highly purified by conventional means. The procedure can be used successfully for the rapid (less than 2 h) purification of small amounts of enterotoxin. Images PMID:170205

Scott, V N; Duncan, C L

1975-01-01

383

Affine Invariant Character Recognition by Progressive Removing  

NASA Astrophysics Data System (ADS)

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.

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

384

Cation affinity numbers of Lewis bases  

PubMed Central

Summary Using selected theoretical methods the affinity of a large range of Lewis bases towards model cations has been quantified. The range of model cations includes the methyl cation as the smallest carbon-centered electrophile, the benzhydryl and trityl cations as models for electrophilic substrates encountered in Lewis base-catalyzed synthetic procedures, and the acetyl cation as a substrate model for acyl-transfer reactions. Affinities towards these cationic electrophiles are complemented by data for Lewis-base addition to Michael acceptors as prototypical neutral electrophiles. PMID:23019478

Lindner, Christoph; Tandon, Raman; Maryasin, Boris; Larionov, Evgeny

2012-01-01

385

Adsorption affinity of anions on metal oxyhydroxides  

NASA Astrophysics Data System (ADS)

The dependences of anion (phosphate, carbonate, sulfate, chromate, oxalate, tartrate, and citrate) adsorption affinity anions from geometric characteristics, acid-base properties, and complex forming ability are generalized. It is shown that adsorption depends on the nature of both the anions and the ionic medium and adsorbent. It is established that anions are generally grouped into the following series of adsorption affinity reduction: PO{4/3-}, CO{3/2-} > C2O{4/2-}, C(OH)(CH2)2(COO){3/3-}, (CHOH)2(COO){2/2-} > CrO{4/2-} ? SO{4/2-}.

Pechenyuk, S. I.; Semushina, Yu. P.; Kuz'mich, L. F.

2013-03-01

386

On the electron affinity of B2  

SciTech Connect

We present the results of high-level ab initio calculations on the electron affinity of B2. Our new best estimate of 1.93±0.03 eV is in agreement with previous calculations as well as the sole existing experimental estimate of 1.8 eV, as derived from quantities with an uncertainty of 0.4 eV. The electron affinity of atomic boron, which is much smaller, is also calculated for comparison, and again found to be in good agreement with experiment. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.

Glezakou, Vanda A.; Taylor, Peter

2009-02-02

387

Negative Electron Affinity Mechanism for Diamond Surfaces  

NASA Technical Reports Server (NTRS)

The energy distribution of the secondary electrons for chemical vacuum deposited diamond films with Negative Electron Affinity (NEA) was investigated. It was found that while for completely hydrogenated diamond surfaces the negative electron affinity peak in the energy spectrum of the secondary electrons is present for any energy of the primary electrons, for partially hydrogenated diamond surfaces there is a critical energy above which the peak is present in the spectrum. This critical energy increases sharply when hydrogen coverage of the diamond surface diminishes. This effect was explained by the change of the NEA from the true type for the completely hydrogenated surface to the effective type for the partially hydrogenated surfaces.

Krainsky, I. L.; Asnin, V. M.

1998-01-01

388

Elusive electron affinity of ClF  

NASA Astrophysics Data System (ADS)

Highly correlated methods were used to obtain the optimized bond lengths and vibrational frequencies of ClF and ClF-. With convergent quantum mechanical methods, the anion is much more difficult to treat than neutral ClF. Adiabatic electron affinities (EAad), vertical electron affinities, and vertical detachment energies have been evaluated and compared to the controversial experimental values reported in the literature. Our best prediction for the zero-point vibrationally corrected EAad is 2.25+/-0.1 eV.

Horný, ?uboš; Sattelmeyer, Kurt W.; Schaefer, Henry F.

2003-12-01

389

Method for nonlinear optimization for gas tagging and other systems  

DOEpatents

A method and system for providing nuclear fuel rods with a configuration of isotopic gas tags. The method includes selecting a true location of a first gas tag node, selecting initial locations for the remaining n-1 nodes using target gas tag compositions, generating a set of random gene pools with L nodes, applying a Hopfield network for computing on energy, or cost, for each of the L gene pools and using selected constraints to establish minimum energy states to identify optimal gas tag nodes with each energy compared to a convergence threshold and then upon identifying the gas tag node continuing this procedure until establishing the next gas tag node until all remaining n nodes have been established.

Chen, Ting (Chicago, IL); Gross, Kenny C. (Bolingbrook, IL); Wegerich, Stephan (Glendale Heights, IL)

1998-01-01

390

Tags Help Make Libraries Del.icio.us: Social Bookmarking and Tagging Boost Participation  

ERIC Educational Resources Information Center

Traditional library web products, whether online public access catalogs, library databases, or even library web sites, have long been rigidly controlled and difficult to use. Patrons regularly prefer Google's simple interface. Now social bookmarking and tagging tools help librarians bridge the gap between the library's need to offer authoritative,…

Rethlefsen, Melissa L.

2007-01-01

391

TAG composition of ewe's milk fat. Detection of foreign fats  

Microsoft Academic Search

The TAG composition of 45 samples of ewe's milk, collected throughout the year from five Spanish breeds, was analyzed according\\u000a to their carbon number by using short capillary column GC. The TAG content had a bimodal distribution with maxima at C38 (12.8%) and C52 (8.4%). The TAG composition did not vary significantly with respect to the time of year of

Hanane Goudjil; Javier Fontecha; Ma Jesús Fraga; Manuela Juárez

2003-01-01

392

SERS-active nanoparticle aggregate technology for tags and seals  

Microsoft Academic Search

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

Leif O Brown; Velma M Montoya; George J Havrillia; Stephen K Doorn

2010-01-01

393

HTML Tags as Extraction Cues for Web Page Description Construction  

Microsoft Academic Search

Using four previously identified samples of Web pages containing meta-tagged descriptions, the value of meta-tagged keywords, the first 200 characters of the body, and text marked with common HTML tags as extracts helpful for writing summaries was estimated by applying two measures: density of de- scription words and density of two-word description phrases. Generally, titles and keywords showed the highest

Timothy C. Craven

2003-01-01

394

The Jolly-Seber model with tag loss.  

PubMed

Tag loss in mark-recapture experiments is a violation of one of the Jolly-Seber model assumptions. It causes bias in parameter estimates and has only been dealt with in an ad hoc manner. We develop methodology to estimate tag retention and abundance in double-tagging mark-recapture experiments. We apply this methodology to walleyes (Stizostedion vitreum) in Mille Lacs, Minnesota. PMID:16984310

Cowen, Laura; Schwarz, Carl J

2006-09-01

395

Public-Key Cryptography for RFID-Tags  

Microsoft Academic Search

RFID-tags are a new generation of bar-codes with added functionality. They are becom- ing very popular tools for identication of products in various applications like e.g. supply-chain management. An emerging application is the use of RFID-tags for anti-counterfeiting by embedding them into a product. However, there is a risk related to naively using those tags for several applica- tions. In

Lejla Batina; Jorge Guajardo; Tim Kerins; Nele Mentens; Pim Tuyls; Ingrid Verbauwhede

2007-01-01

396

Remote object authentication using distortion-invariant ID tags  

NASA Astrophysics Data System (ADS)

A number of applications in security or inventory control may benefit from an authentication system able to identify a remote object viewed from different perspectives or distances. Object identification can be accomplished by using optical ID tags, which include relevant information of the target and are located on a visible part of the object under surveillance. Encryption of the information codified in the ID tag allows increasing security and deters from unauthorized usage of optical tags. The identification process encompasses several steps such as detection, information decoding and verification which are all detailed in this work. Design of distortion-invariant ID tags has to be taken into account to achieve a correct object authentication even if the ID tag is detected and captured at different distances (i.e. different scales) or from different views (i.e. rotated versions of the original ID tag). Description of diverse distortion-invariant ID tags and authentication results using the proposed ID tags are provided. We show that distortion-tolerance is achieved by the described identification system. Information encrypted on the tested ID tags is correctly decoded and verified even if variations in scale and rotations are considered. The effects of environmental degradation are taken into account in the recognition process.

Perez-Cabre, Elisabet; Millan, Maria S.; Javidi, Bahram

2005-09-01

397

Optimum Performance of UHF RFID Tags in Dielectric Environment  

E-print Network

homogeneous medium based on the frequency- dielectric transformation. We validate the “immersed Uda model” in Section. 3.2.1. 3.1 Tag on Slab Model Consider a tag placed on a large “cardboard” (corrugated fiberboard) box, with contents in the box having... their supply chains to better control their inventory. Thus, the UHF RFID tags need to work effectively in complex dielectric environments like some of the commercial products shown in Figure. 1.1. For example, a tag can be placed on a “cardboard” (corrugated...

Kosuru, Lakshmi Anusha

2011-09-08

398

Conic Epipolar Constraints from Affine Correspondences  

E-print Network

relations constrain the location of the epipole to a conic section. Therefore, the location of the epipoleConic Epipolar Constraints from Affine Correspondences Jacob Bentolilaa , and Joseph M. Francosb can be extracted from 3 regions by intersecting conics. The result is further employed to derive

Francos, Joseph M.

399

Localization of Affine W-Algebras  

NASA Astrophysics Data System (ADS)

We introduce the notion of an asymptotic algebra of chiral differential operators. We then construct, via a chiral Hamiltonian reduction, one such algebra over a resolution of the intersection of the Slodowy slice with the nilpotent cone. We compute the space of global sections of this algebra, thereby proving a localization theorem for affine W-algebras at the critical level.

Arakawa, T.; Kuwabara, T.; Malikov, F.

2014-10-01

400

Peptides with selective affinity for carbon nanotubes  

Microsoft Academic Search

Because of their extraordinary electronic and mechanical properties, carbon nanotubes have great potential as materials for applications ranging from molecular electronics to ultrasensitive biosensors. Biological molecules interacting with carbon nanotubes provide them with specific chemical handles that would make several of these applications possible. Here we use phage display to identify peptides with selective affinity for carbon nanotubes. Binding specificity

Siqun Wang; Elen S. Humphreys; Sung-Yoon Chung; Daniel F. Delduco; Steven R. Lustig; Hong Wang; Kimberley N. Parker; Nancy W. Rizzo; Shekhar Subramoney; Yet-Ming Chiang; Anand Jagota

2003-01-01

401

Fan Affinity Laws from a Collision Model  

ERIC Educational Resources Information Center

The performance of a fan is usually estimated using hydrodynamical considerations. The calculations are long and involved and the results are expressed in terms of three affinity laws. In this paper we use kinetic theory to attack this problem. A hard sphere collision model is used, and subsequently a correction to account for the flow behaviour…

Bhattacharjee, Shayak

2012-01-01

402

Navigation using Affine Structure from Motion  

Microsoft Academic Search

A structure from motion algorithm is described which recovers structure and camera position, modulo a projective ambiguity. Camera calibration is not required, and camera parameters such as focal length can be altered freely during motion. Unlike recent schemes which compute projective or affine structure using a batch process, the structure is updated sequentially over an image sequence. A specialisation of

Paul A. Beardsley; Andrew Zisserman; David W. Murray

1994-01-01

403

Vygotsky's and Buber's Pedagogical Perspectives: Some Affinities  

ERIC Educational Resources Information Center

The purpose of this paper is to examine the dialogical and creative character of pedagogic work by analyzing the affinities between Martin Buber's "I-Thou relation" and Lev Semenovich Vygotsky's "Zone of Proximal Development". Backed up by empirical studies on the teacher-student relation, we understand that education can only result in students'…

Bartholo, Roberto; Tunes, Elizabeth; Tacca, Maria Carmen Villela Rosa

2010-01-01

404

Specification Analysis of Affine Term Structure Models  

Microsoft Academic Search

This paper explores the structural differences and relative goodness-of-fits of affine term structure models (ATSMs). Within the family of ATSMs there is a trade-off between flexibility in modeling the conditional correlations and volatilities of the risk factors. This trade-off is formalized by our classification of \\

Qiang Dai; Kenneth J. Singleton

2000-01-01

405

Multiple Affinity Removal System Another Breakthrough  

E-print Network

Visit www.agilent.com/chem/proteomics for the latest in proteomics technology Don't miss out! YourStay current Stay current Multiple Affinity Removal System Another Breakthrough Technology from colleagues are using this technology now. H H H HH H H H L L L L L L L L L L L L L L HL H Crude Human

Lebendiker, Mario

406

A Self-Affine Fractal Multiband Antenna  

Microsoft Academic Search

The design of a new fractal multiband antenna based on the self-affinity property is presented in this letter. Experimental return loss has been compared with that obtained using the method of moments and the fractal antenna is found to possess predictable multiband characteristics

Sachendra N. Sinha; Manish Jain

2007-01-01

407

Structure-Guided Design of an Engineered Streptavidin with Reusability to Purify Streptavidin-Binding Peptide Tagged Proteins or Biotinylated Proteins  

PubMed Central

Development of a high-affinity streptavidin-binding peptide (SBP) tag allows the tagged recombinant proteins to be affinity purified using the streptavidin matrix without the need of biotinylation. The major limitation of this powerful technology is the requirement to use biotin to elute the SBP-tagged proteins from the streptavidin matrix. Tight biotin binding by streptavidin essentially allows the matrix to be used only once. To address this problem, differences in interactions of biotin and SBP with streptavidin were explored. Loop3–4 which serves as a mobile lid for the biotin binding pocket in streptavidin is in the closed state with biotin binding. In contrast, this loop is in the open state with SBP binding. Replacement of glycine-48 with a bulkier residue (threonine) in this loop selectively reduces the biotin binding affinity (Kd) from 4×10?14 M to 4.45×10?10 M without affecting the SBP binding affinity. Introduction of a second mutation (S27A) to the first mutein (G48T) results in the development of a novel engineered streptavidin SAVSBPM18 which could be recombinantly produced in the functional form from Bacillus subtilis via secretion. To form an intact binding pocket for tight binding of SBP, two diagonally oriented subunits in a tetrameric streptavidin are required. It is vital for SAVSBPM18 to be stably in the tetrameric state in solution. This was confirmed using an HPLC/Laser light scattering system. SAVSBPM18 retains high binding affinity to SBP but has reversible biotin binding capability. The SAVSBPM18 matrix can be applied to affinity purify SBP-tagged proteins or biotinylated molecules to homogeneity with high recovery in a reusable manner. A mild washing step is sufficient to regenerate the matrix which can be reused for multiple rounds. Other applications including development of automated protein purification systems, lab-on-a-chip micro-devices, reusable biosensors, bioreactors and microarrays, and strippable detection agents for various blots are possible. PMID:23874971

Wu, Sau-Ching; Wong, Sui-Lam

2013-01-01

408

Characterization of C-terminal histidine-tagged human recombinant lecithin:cholesterol acyltransferase.  

PubMed

Lecithin:cholesterol acyltransferase (LCAT) is the plasma enzyme that catalyzes esterification of the sn-2 fatty acid of phospholipid to cholesterol. To facilitate the isolation of large quantities of LCAT and to assist in future structure;-function studies, LCAT containing a carboxy-terminal histidine-tag (H6) was expressed in Chinese hamster ovary cells (CHO). A high level of CHO-hLCATH6 expression ( approximately 15 mg L(-1)) was achieved over a 72-h period using 10 mm sodium butyrate to enhance transcription and PFX-CHO protein-free medium. The pure enzyme ( approximately 96%) was isolated by cobalt metal affinity chromatography with an activity yield of 82 +/- 26%. CHO-hLCATH6 and CHO-hLCAT species had identical specific activities (26 +/- 6 and 26 +/- 3 nmol CE formed microg(-1) h(-1), respectively). The enzymatic activity of CHO-hLCATH6 was stable at 4 degrees C in excess of 60 days. Substrate saturation studies, using rHDL composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), cholesterol, and apolipoprotein A-I (80:5:1) indicated that the appK(m) for CHO-hLCATH6, CHO-hLCAT, and purified plasma LCAT were nearly identical at approximately 2 microm substrate cholesterol. We conclude that carboxy-terminal histidine-tagged LCAT is a suitable replacement for both plasma LCAT and CHO-hLCAT. PMID:10428989

Chisholm, J W; Gebre, A K; Parks, J S

1999-08-01

409

Generation and analysis of recombinant Bunyamwera orthobunyaviruses expressing V5 epitope-tagged L proteins  

PubMed Central

The L protein of Bunyamwera virus (BUNV; family Bunyaviridae) is an RNA-dependent RNA polymerase, 2238?aa in length, that catalyses transcription and replication of the negative-sense, tripartite RNA genome. To learn more about the molecular interactions of the L protein and to monitor its intracellular distribution we inserted a 14?aa V5 epitope derived from parainfluenza virus type 5, against which high-affinity antibodies are available, into different regions of the protein. Insertion of the epitope at positions 1935 or 2046 resulted in recombinant L proteins that retained functionality in a minireplicon assay. Two viable recombinant viruses, rBUNL4V5 and rBUNL5V5, expressing the tagged L protein were rescued by reverse genetics, and characterized with respect to their plaque size, growth kinetics and protein synthesis profile. The recombinant viruses behaved similarly to wild-type (wt) BUNV in BHK-21 cells, but formed smaller plaques and grew to lower titres in Vero E6 cells compared with wt BUNV. Immunofluorescent staining of infected cells showed the L protein to have a punctate to reticular distribution in the cytoplasm, and cell fractionation studies indicated that the L protein was present in both soluble and microsomal fractions. Co-immunoprecipitation and confocal microscopic assays confirmed an interaction between BUNV L and N proteins. The recombinant viruses expressing tagged L protein will be highly valuable reagents for the detailed dissection of the role of the BUNV L protein in virus replication. PMID:19141438

Shi, Xiaohong; Elliott, Richard M.

2009-01-01

410

Management and Ecological Note Long-term anchor tag retention in yellow perch,  

E-print Network

Management and Ecological Note Long-term anchor tag retention in yellow perch, Perca flavescens, Perca flavescens, tag loss, tag retention, yellow perch. Tagging and marking techniques are frequently of yellow perch, Perca flavescens (Mitchill), information was needed on long-term tag retention

411

Evaluations of Tag Retention and a Device for Releasing Discarded Hawaiian Spiny Lobsters Panulirus marginatus  

Microsoft Academic Search

Tag loss and mortality that results directly from the tagging process are a concern to all tagging programs because they reduce sample sizes and can bias population and survival estimates. The purposes of this study were to estimate streamer tag loss in Hawaiian spiny lobsters Panulirus marginatus, evaluate the use of passive integrated transponder (PIT) tags in these lobsters, and

Joseph M. OMalley

2008-01-01

412

Passive Integrated Transponder Tag Retention Rates in Headwater Populations of Coastal Cutthroat Trout  

Microsoft Academic Search

Passive integrated transponder (PIT) tags have desirable qualities (e.g., unique identification, indefinite tag life, and capacity for remote detection) that make them useful for evaluating survival, growth, and movement of fish, but low tag retention rates can confound data interpretation. Although the effects of PIT tags on short-term growth and survival have been minimal and tag retention rates in laboratory

Douglas S. Bateman; Robert E. Gresswell; Aaron M. Berger

2009-01-01

413

A low-power CMOS integrated circuit for field-powered radio frequency identification tags  

Microsoft Academic Search

Cheap, compact radio frequency identification (RFID) tags will make a wide range of new applications cost-effective. Minimum cost can be achieved only in a passive tag (that acquires operating power from the interrogating RF field). A compact tag form factor demands a small tag antenna, that in turn demands either external components or a high-frequency RF carrier for effective tag

D. Friedman; H. Heinreich; D.-W. Duan

1997-01-01

414

Identification of protein complexes in Escherichia coli using sequential peptide affinity purification in combination with tandem mass spectrometry.  

PubMed

Since most cellular processes are mediated by macromolecular assemblies, the systematic identification of protein-protein interactions (PPI) and the identification of the subunit composition of multi-protein complexes can provide insight into gene function and enhance understanding of biological systems(1, 2). Physical interactions can be mapped with high confidence vialarge-scale isolation and characterization of endogenous protein complexes under near-physiological conditions based on affinity purification of chromosomally-tagged proteins in combination with mass spectrometry (APMS). This approach has been successfully applied in evolutionarily diverse organisms, including yeast, flies, worms, mammalian cells, and bacteria(1-6). In particular, we have generated a carboxy-terminal Sequential Peptide Affinity (SPA) dual tagging system for affinity-purifying native protein complexes from cultured gram-negative Escherichia coli, using genetically-tractable host laboratory strains that are well-suited for genome-wide investigations of the fundamental biology and conserved processes of prokaryotes(1, 2, 7). Our SPA-tagging system is analogous to the tandem affinity purification method developed originally for yeast(8, 9), and consists of a calmodulin binding peptide (CBP) followed by the cleavage site for the highly specific tobacco etch virus (TEV) protease and three copies of the FLAG epitope (3X FLAG), allowing for two consecutive rounds of affinity enrichment. After cassette amplification, sequence-specific linear PCR products encoding the SPA-tag and a selectable marker are integrated and expressed in frame as carboxy-terminal fusions in a DY330 background that is induced to transiently express a highly efficient heterologous bacteriophage lambda recombination system(10). Subsequent dual-step purification using calmodulin and anti-FLAG affinity beads enables the highly selective and efficient recovery of even low abundance protein complexes from large-scale cultures. Tandem mass spectrometry is then used to identify the stably co-purifying proteins with high sensitivity (low nanogram detection limits). Here, we describe detailed step-by-step procedures we commonly use for systematic protein tagging, purification and mass spectrometry-based analysis of soluble protein complexes from E. coli, which can be scaled up and potentially tailored to other bacterial species, including certain opportunistic pathogens that are amenable to recombineering. The resulting physical interactions can often reveal interesting unexpected components and connections suggesting novel mechanistic links. Integration of the PPI data with alternate molecular association data such as genetic (gene-gene) interactions and genomic-context (GC) predictions can facilitate elucidation of the global molecular organization of multi-protein complexes within biological pathways. The networks generated for E. coli can be used to gain insight into the functional architecture of orthologous gene products in other microbes for which functional annotations are currently lacking. PMID:23168686

Babu, Mohan; Kagan, Olga; Guo, Hongbo; Greenblatt, Jack; Emili, Andrew

2012-01-01

415

Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry  

PubMed Central

Since most cellular processes are mediated by macromolecular assemblies, the systematic identification of protein-protein interactions (PPI) and the identification of the subunit composition of multi-protein complexes can provide insight into gene function and enhance understanding of biological systems1, 2. Physical interactions can be mapped with high confidence vialarge-scale isolation and characterization of endogenous protein complexes under near-physiological conditions based on affinity purification of chromosomally-tagged proteins in combination with mass spectrometry (APMS). This approach has been successfully applied in evolutionarily diverse organisms, including yeast, flies, worms, mammalian cells, and bacteria1-6. In particular, we have generated a carboxy-terminal Sequential Peptide Affinity (SPA) dual tagging system for affinity-purifying native protein complexes from cultured gram-negative Escherichia coli, using genetically-tractable host laboratory strains that are well-suited for genome-wide investigations of the fundamental biology and conserved processes of prokaryotes1, 2, 7. Our SPA-tagging system is analogous to the tandem affinity purification method developed originally for yeast8, 9, and consists of a calmodulin binding peptide (CBP) followed by the cleavage site for the highly specific tobacco etch virus (TEV) protease and three copies of the FLAG epitope (3X FLAG), allowing for two consecutive rounds of affinity enrichment. After cassette amplification, sequence-specific linear PCR products encoding the SPA-tag and a selectable marker are integrated and expressed in frame as carboxy-terminal fusions in a DY330 background that is induced to transiently express a highly efficient heterologous bacteriophage lambda recombination system10. Subsequent dual-step purification using calmodulin and anti-FLAG affinity beads enables the highly selective and efficient recovery of even low abundance protein complexes from large-scale cultures. Tandem mass spectrometry is then used to identify the stably co-purifying proteins with high sensitivity (low nanogram detection limits). Here, we describe detailed step-by-step procedures we commonly use for systematic protein tagging, purification and mass spectrometry-based analysis of soluble protein complexes from E. coli, which can be scaled up and potentially tailored to other bacterial species, including certain opportunistic pathogens that are amenable to recombineering. The resulting physical interactions can often reveal interesting unexpected components and connections suggesting novel mechanistic links. Integration of the PPI data with alternate molecular association data such as genetic (gene-gene) interactions and genomic-context (GC) predictions can facilitate elucidation of the global molecular organization of multi-protein complexes within biological pathways. The networks generated for E. coli can be used to gain insight into the functional architecture of orthologous gene products in other microbes for which functional annotations are currently lacking. PMID:23168686

Babu, Mohan; Kagan, Olga; Guo, Hongbo; Greenblatt, Jack; Emili, Andrew

2012-01-01

416

Lightweight Cryptographic Authentication in Passive RFID-Tagged Systems  

Microsoft Academic Search

The explosion in recent interest in radio-frequency identification (RFID) tags stems primarily from advances in information processing in supply chain management. Given their processing power and memory capabilities, RFID tags can be used in a wide range of applications including those where barcodes can and cannot be used. Although the potential exists, it is hampered by the relatively high unit

Selwyn Piramuthu

2008-01-01

417

Gas tagging and cover gas combination for nuclear reactor  

DOEpatents

The invention discloses the use of stable isotopes of neon and argon, that are grouped in preselected different ratios one to the other and are then sealed as tags in different cladded nuclear fuel elements to be used in a liquid metal fast breeder reactor. Failure of the cladding of any fuel element allows fission gases generated in the reaction and these tag isotopes to escape and to combine with the cover gas held in the reactor over the fuel elements. The isotopes specifically are Ne.sup.20, Ne.sup.21 and Ne.sup.22 of neon and Ar.sup.36, Ar.sup.38 and Ar.sup.40 of argon, and the cover gas is helium. Serially connected cryogenically operated charcoal beds are used to clean the cover gas and to separate out the tags. The first or cover gas cleanup bed is held between approximately 0.degree. and -25.degree. C. operable to remove the fission gases from the cover gas and tags and the second or tag recovery system bed is held between approximately -170.degree. and -185.degree. C. operable to isolate the tags from the cover gas. Spectrometric analysis further is used to identify the specific tags that are recovered, and thus the specific leaking fuel element. By cataloging the fuel element tags to the location of the fuel elements in the reactor, the location of the leaking fuel element can then be specifically determined.

Gross, Kenny C. (Lemont, IL); Laug, Matthew T. (Idaho Falls, ID)

1985-01-01

418

Towards tag antenna based sensing - An RFID displacement sensor  

Microsoft Academic Search

Displacements can be used as indicators of structural health and are measured by commercially available sensors that need to be accurate and cost effective. In this paper, we examine a technique to utilize a UHF RFID tag antenna as a displacement sensor by mapping structural deformation to a change in RFID tag characteristics. We evaluate how changes in two different

Rahul Bhattacharyya; Christian Floerkemeier; Sanjay Sarma

2009-01-01

419

HIP-tags architecture implementation for the Internet of things  

Microsoft Academic Search

This paper describes a possible implementation for the innovative and highly secure networking architecture dedicated to the Internet of Things (IoT). We propose an infrastructure that works with a new type of tags, supporting the upcoming standard Host Identity Protocol (HIP). Our main concern is to ensure RFID tags privacy, while enabling things to things communications.

Pascal Urien; Simon Elrharbi; Dorice Nyamy; Hervé Chabanne; Thomas Icart; François Lecocq; Cyrille Pépin; Khalifa Toumi; Mathieu Bouet; Guy Pujolle; Patrice Krzanik; Jean-Ferdinand Susini

2009-01-01

420

Continuous Recording of Bird Nesting Visits using Radioactive Tagging  

Microsoft Academic Search

IN view of the successful application of radioactive tagging in entomology in Central Africa, I have investigated the potentiality of the method as a tagging technique in ornithology. Because the detection range of small amounts of radioactive material is only of the order of feet, the method requires the close proximity of the labelled bird and the radiation detector. It

P. R. B. Ward

1967-01-01

421

A viable technique for tagging earthworms using visible implant elastomer  

Microsoft Academic Search

Earthworms perform many ecosystem services. However, due to their body shape, mucus covering, and subterranean behaviour, it has been very difficult to successfully tag individual animals for experimental purposes. This paper examines the potential use of commercially available visible implant elastomer (VIE) tags to mark earthworms. Two laboratory experiments were conducted employing four temperate earthworm species by injection of the

Kevin R. Butt; Christopher N. Lowe

2007-01-01

422

Categorising social tags to improve folksonomy-based recommendations  

Microsoft Academic Search

In social tagging systems, users have different purposes when they annotate items. Tags not only depict the content of the annotated items, for example by listing the objects that appear in a photo, or express contextual information about the items, for example by providing the location or the time in which a photo was taken, but also describe subjective qualities

Iván Cantador; Ioannis Konstas; Joemon M. Jose

2011-01-01

423

MUSIC TAG ANNOTATION AND CLUSTERING USING LATENT MUSIC SEMANTIC ANALYSIS  

E-print Network

can include different types of musical information, such as genre, mood, instrumentation, personalMUSIC TAG ANNOTATION AND CLUSTERING USING LATENT MUSIC SEMANTIC ANALYSIS Ju-Chiang Wang1,2 , Meng-mail: {asriver, wums, whm}@iis.sinica.edu.tw, skjeng@cc.ee.ntu.edu.tw ABSTRACT Music tags include different types

Wang, Hsin-Min

424

Social media recommendation based on people and tags  

Microsoft Academic Search

We study personalized item recommendation within an enterprise social media application suite that includes blogs, bookmarks, communities, wikis, and shared files. Recommendations are based on two of the core elements of social media - people and tags. Relationship information among people, tags, and items, is collected and aggregated across different sources within the enterprise. Based on these aggregated relationships, the

Ido Guy; Naama Zwerdling; Inbal Ronen; David Carmel; Erel Uziel

2010-01-01

425

Techniques for Feral Pigeon Trapping, Tagging and Nest Monitoring  

Microsoft Academic Search

We describe here techniques used to capture, tag, and check nests of feral Rock Doves (or pigeons, Columba livia) on upstate New York farms. In- cluded are designs for patagium tags, drop-win- dow covers, catch windows, and pigeon stuffers. Climbing on structures and technical climbing were the most efficient methods to get to pigeons and their nests, and we describe

J. Edward Kautz; Thomas W. Seamans

426

ACCIDENT PREVENTION SIGNS, TAGS, LABELS, SIGNALS, PIPING SYSTEM IDENTIFICATION AND  

E-print Network

EM 385-1-1 XX Sep 13 i Section 8 ACCIDENT PREVENTION SIGNS, TAGS, LABELS, SIGNALS, PIPING SYSTEM............................................................8-13 Tables: 8-1 Accident Prevention Sign Requirements..........................8-17 8-2 Accident.......................................8-24 8-9 Accident Prevention Tags.............................................8-25 #12;EM 385-1-1 XX

US Army Corps of Engineers

427

Secured Ownership Transfer Scheme for Low-Cost RFID Tags  

Microsoft Academic Search

Although widely used in various applications, the current RFID (Radio Frequency Identification) systems lack efficiently enforcement of security and privacy. Furthermore, considering that the bearer of a RFID tag might be changed, the ownership transferring of the tags also becomes an issue. Some schemes have been suggested, but they are lack of participation of people. In this paper, we propose

Tongliang Li; Zhigang Jin; Chaoyi Pang

2010-01-01

428

Tagged magnetic resonance imaging of the heart: a survey  

Microsoft Academic Search

Magnetic resonance imaging (MRI) of the heart with magnetization tagging provides a potentially useful new way to assess car-diac mechanical function, through revealing the local motion of otherwise indistinguishable portions of the heart wall. While still an evolving area, tagged cardiac MRI is already able to provide novel quantitative information on cardiac function. Exploiting this potential requires developing tailored methods

Leon Axel; Albert Montillo; Daniel Kim

2005-01-01

429

Distortion-invariant ID tags for object identification  

NASA Astrophysics Data System (ADS)

Active and passive optical identification (ID) tags and readers for remote identification and verification of objects are described. We focus our attention on the design of passive ID tags to achieve distortion-invariant authentication of the information included in the optical tag. A passive ID tag will consist of an optical phase code which can be placed in a visible part of an object for remote detection. We aim to authenticate the object even if the reader captures a distorted version of the code due to in-plane rotations. Distortion-invariance is achieved by both multiplexing the information included in the ID tag and the topology of the tag. For security purposes, double-phase encryption has already been shown as an appropriate technique to encode information. By using double-phase encryption, a signature is hidden in a phase-encoded ID tag not visible by visual inspection. Once the ID tag is captured by the reader and is decrypted, a correlation-based processor verifies the decoded information with a previously stored reference signal. The proposed system may have broad applications in transportation, homeland security, and inventory control.

Perez-Cabre, Elisabet; Javidi, Bahram

2004-11-01

430

Tags and Image Scoring for Robust Cooperation Nathan Griffiths  

E-print Network

Tags and Image Scoring for Robust Cooperation Nathan Griffiths Department of Computer Science University of Warwick Coventry, CV4 7AL, UK nathan@dcs.warwick.ac.uk ABSTRACT Establishing and maintaining approaches exist for some environments, Cite as: Tags and Image Scoring for Robust Cooperation, Nathan Grif

Griffiths, Nathan

431

CT colonography with fecal tagging after incomplete colonoscopy  

Microsoft Academic Search

The objective of this study was to evaluate dietary fecal tagging (FT) as a cleansing method prior to CT colonography (CTC) in patients with incomplete conventional colonoscopy (CC). After written informed consent was obtained, 24 patients had standard colonoscopic preparation (ScCl), and 25 patients had FT as cleansing method. Segmental distention, fluid levels, fecal residues, tagged appearance of fluid levels,

S. Gryspeerdt; P. Lefere; M. Herman; R. Deman; L. Rutgeerts; G. Ghillebert; F. Baert; M. Baekelandt; B. Van Holsbeeck

2005-01-01

432

Animal Population Survey: Tag and Recapture. Grades 5-12.  

ERIC Educational Resources Information Center

This brochure contains two activities for upper elementary, middle school, and high school students that focuses on the method of "tag and recapture" used to estimate wildlife populations. The first activity involves students in tagging and recapturing animal shaped cookies and building a data table used to estimate the total number of an "animal"…

HAZWRAP, The Hazardous Waste Remedial Actions Program.

433

ORIGINAL ARTICLE Simple conjugation and outgrowth procedures for tagging  

E-print Network

cultured and transformed with the gfp gene. This methodology is necessarily limited to cultura- bleORIGINAL ARTICLE Simple conjugation and outgrowth procedures for tagging vibrios with GFP, and factors affecting the stable expression of the gfp tag T. Sawabe1 , Y. Fukui1 and E.V. Stabb2 1 Faculty

McFall-Ngai, Margaret

434

Multiobjective Genetic Programming for Natural Language Parsing and Tagging  

E-print Network

Multiobjective Genetic Programming for Natural Language Parsing and Tagging L. Araujo Dpto@sip.ucm.es Abstract. Parsing and Tagging are very important tasks in Natural Language Processing. Parsing amounts belong to more than one lexical class, it turns out to be a disambiguation task. Because parsing

Fernandez, Thomas

435

Template matching for improved accuracy in molecular tagging velocimetry  

Microsoft Academic Search

In 2D molecular tagging velocimetry (MTV), tags are written into a fluid flow with a laser grid and imaged at discrete times. These images are analyzed to calculate Lagrangian displacement vectors, often by direct cross correlation. The cross correlation method is inherited from particle imaging velocimetry, where the correlated images contain a random pattern of particles. A template matching method

Marc C. Ramsey; Robert W. Pitz

2011-01-01

436

Change Your Tags Fast! --A necessary condition for cooperation? 1  

E-print Network

Change Your Tags Fast! -- A necessary condition for cooperation? 1 David Hales Department to individuals (agents) and are observable by others (Holland 1993). They evolve like any other trait in a given evolutionary model. The key point is that the tags have no direct behavioral implication for the agents

Hales, David

437

Change Your Tags Fast! A necessary condition for cooperation?  

E-print Network

Change Your Tags Fast! ­ A necessary condition for cooperation? 1 David Hales Department to individuals (agents) and are observable by others (Holland 1993). They evolve like any other trait in a given evolutionary model. The key point is that the tags have no direct behavioral implication for the agents

Hales, David

438

Creating tag hierarchies for effective navigation in social media  

Microsoft Academic Search

In social media, such as blogs, since the content naturally evolves over time, it is hard or in many cases impossible to organize the content for effective navigation. Thus, one commonly has to resort to simple tools, such as tags and tag clouds, for presenting frequently used keywords to users to provide them at least some high level idea about

K. Selçuk Candan; Luigi Di Caro; Maria Luisa Sapino

2008-01-01

439

Socially Distributed Perception: GRACE plays social tag at AAAI 2005  

Microsoft Academic Search

This paper presents a robot search task (social tag) that uses social interaction, in the form of asking for help, as an integral component of task completion. Socially distributed perception is defined as a robot's ability to aug- ment its limited sensory capacities through social interaction. We describe the task of social tag and its implementation on the robot GRACE

Marek P. Michalowski; Selma Sabanovic; Carl F. Disalvo; Dídac Busquets; Laura M. Hiatt; Nik A. Melchior; Reid G. Simmons

2007-01-01

440

Organizing Resources on Tagging Systems using T-ORG  

Microsoft Academic Search

Tagging systems (or folksonomies) like Flickr or Delicious are expanding tremendously. More and more resources are being added to them. As the resources present on these system increase in amount, it becomes difficult to explore these resources. For this purpose, we present a system T-ORG, which provides a mechanism to organize these resources by classifying the tags (or keywords) attached

Rabeeh Abbasi; Steffen Staab; Philipp Cimiano

441

Development of stereoscopic molecular tagging velocimetry  

NASA Astrophysics Data System (ADS)

This paper describes the development of a stereoscopic molecular tagging velocimetry (sMTV) technique for measuring the instantaneous three-component velocity field over a plane in a flow. The calibration technique employed allows the stereo imaging parameters to be determined directly from a target image without the direct physical measurement of those parameters. Effects of index of refraction variations are accounted for approximately in the calibration method. Sensitivity analysis and target test experiments for a typical optical setup indicate maximum error levels for the in-plane components to be nominally the same as two-component MTV measurements. The error in the out-of-plane velocity component can be one to three times larger, depending on the stereo viewing angle. Experimental results are presented to validate the sMTV technique against other known measured results, along with an application to the highly three-dimensional flow field near the tip of a model propeller.

Bohl, D. G.; Koochesfahani, M. M.; Olson, B. J.

442

Reliable Food Traceability Using RFID Tagging  

NASA Astrophysics Data System (ADS)

Radio Frequency IDentification (RFID) technology has numerous potential applications in various industries. One important use is for complete traceability of a specific product with the added advantage of being able to verify that quality controls have been passed, with all the necessary steps complied with and for the time required. The aim of this work is to present a food traceability system using RFID tags with contents guaranteed secure by the use of public-key cryptography and at an affordable cost without the need for substantial investment in infrastructure. Aggregate signatures are used so that all the steps can be signed in a reduced memory space. This type of signature is a cryptographic primitive that "consolidates" several signatures into one in such a way that if n users sign n messages, all the signatures can be grouped into one single signature.

Azuara, Guillermo; Salazar, José L.; Tornos, José L.; Piles, Joan J.

443

Reconciling Knowledge in Social Tagging Web Services  

NASA Astrophysics Data System (ADS)

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.

Aranda-Corral, Gonzalo A.; Borrego-Díaz, Joaquín

444

Development of a flexible tag microlab  

NASA Astrophysics Data System (ADS)

The objective of this ongoing work is the development of a microlab on flexible tag, capable to monitor the quality of the food, during transport, storage and vending. The idea is to bring together different sensor technologies that will be integrated into a data communication environment for online food monitoring during the logistics chain. The proposed solution is the concept of silicon chips and microcomponents assembled and integrated on top of a flexible substrate acting mainly as a passive interconnect structure. Three technologies have been identified as necessary to get the final integration: a) Substrate technology. This technology refers to the realisation of the flexible substrate with the metallic interconnections. b) Assembly technology to integrate the discrete components on the flexible substrate. The conventional processes are wire bonding, flip chip, and adhesive bonding. c) Encapsulation technology and windows opening over the gas sensitive areas. The first flexible tag prototype integrates two different metal oxide sensor arrays with a commercial microprocessor. The dimensions are 43 mm long, 22 mm wide and about 2 mm thick and two metal levels are necessary for the interconnect. The strategy undertaken by the groups involved in this work, consists in the evaluation of different approaches, that combine diverse process sequences and materials, with the final aim of identifying the best solution. Regarding the substrate technology, the approach realized using Pyralux copper-clad laminated composites, constructed of DuPont Kapton polyimide film with copper foil on both sides, as flexible substrate will be described in this paper. The cupper interconnections are generated by standard photolithography and wet etching and the vias definition in Kapton is performed by femtosecond laser ablation. On the other hand, the assembly technology based on the use of anisotropically conductive adhesives will be also illustrated.

Abad, Estefania; Raffa, Vittoria Simona; Mazzolai, Barbara; Marco, Santiago; Krenkow, Angelika; Becker, Thomas

2005-07-01

445

Multiplexed electrochemical immunoassay using streptavidin/nanogold/carbon nanohorn as a signal tag to induce silver deposition.  

PubMed

An ultrasensitive multiplexed immunoassay method was developed by using streptavidin/nanogold/carbon nanohorn (SA/Au/CNH) as a novel signal tag to induce silver enhancement for signal amplification. The Au/CNH was prepared by in situ growth of nanogold on carboxylated CNH and functionalized with streptavidin. The SA/Au/CNH showed well dispersibility in physiological buffer and could sever as a common tracing tag to recognize biotinylated signal antibody. The immunosensor array was prepared on disposable screen-printed electrodes. Through sandwich-type immunoreaction and biotin-streptavidin affinity reaction, the SA/Au/CNH tag was captured on the immunoconjugates to induce silver deposition and amplify the electrochemical stripping signals. Using ?-fetoprotein and carcinoembryonic antigen as model analytes, the proposed method showed wide linear ranges with the detection limits down to 0.024pgmL(-1) and 0.032pgmL(-1), respectively, and eliminated completely signal cross-talk between adjacent immunosensors. It provided a convenient, high-efficient and ultrasensitive electrochemical detection route for biological analytes, showing great potential in clinical application. PMID:25261898

Zhao, Changrong; Wu, Jie; Ju, Huangxian; Yan, Feng

2014-10-17

446

TagGD: fast and accurate software for DNA Tag generation and demultiplexing.  

PubMed

Multiplexing is of vital importance for utilizing the full potential of next generation sequencing technologies. We here report TagGD (DNA-based Tag Generator and Demultiplexor), a fully-customisable, fast and accurate software package that can generate thousands of barcodes satisfying user-defined constraints and can guarantee full demultiplexing accuracy. The barcodes are designed to minimise their interference with the experiment. Insertion, deletion and substitution events are considered when designing and demultiplexing barcodes. 20,000 barcodes of length 18 were designed in 5 minutes and 2 million barcoded Illumina HiSeq-like reads generated with an error rate of 2% were demultiplexed with full accuracy in 5 minutes. We believe that our software meets a central demand in the current high-throughput biology and can be utilised in any field with ample sample abundance. The software is available on GitHub (https://github.com/pelinakan/UBD.git). PMID:23469199

Costea, Paul Igor; Lundeberg, Joakim; Akan, Pelin

2013-01-01

447

SNAP-tag as a tool for surface immobilization.  

PubMed

SNAP-tag technology has been an important tool for protein study for more than a decade and in the meanwhile has found a number of applications beyond the field of molecular biology and protein purification. Based on covalent interaction of SNAP-tag, 20 kDA mutant of DNA repair protein and benzylguanine, it enables irreversible and controllable protein modification. In this mini review, recent developments in the use of SNAP-tag for the design of protein arrays and nanoparticle biofunctionalization are presented and discussed. A short overview of other applications that paved the way to surface modifications is also given with emphasis on fluorescent labeling through the use of SNAP-tag fusion proteins. Finally, the future of the SNAP-tag methodology for surface patterning and 3D structural scaffolding is addressed. PMID:23431987

Engin, Sinem; Fichtner, Dagmar; Wedlich, Doris; Fruk, Ljiljana

2013-01-01

448

Perfluoro(Methylcyclohexane) Tracer Tagging Test and Demonstration  

SciTech Connect

On February 14 and 15, 2000, a demonstration of current perfluorocarbon tagging technology and the future potential of these methods was held at Oak Ridge National Laboratory (ORNL). The demonstration consisted of a brief technical discussion followed by a laboratory demonstration. The laboratory demonstrations included the detection of letters, parcels, briefcases and lockers containing perfluorocarbon-tagged papers. Discrimination between tagged and non-tagged items and between three perfluorocarbon tags was demonstrated along with the detection of perfluorocarbon in a background of non-fluorinated volatile organic solvent. All demonstrations involved real-time detection using a direct sampling ion trap mass spectrometer. The technical results obtained at ORNL during and in preparation for the demonstration are presented in Appendix 1 to assist Tracer Detection Technology Corp. in further evaluating their position on development and marketing of perfluorocarbon tracer technology.

Sigman, M.E.

2000-09-26

449

A Novel Tag Removal Technique for Tagged Cardiac Mri and Its Applications  

Microsoft Academic Search

Inthispaperwepresentanoveltagremovalmethodfortagged cardiac MR images. This method is based on a 2D band- stop filtering technique, which selectively attenuates the tag pattern's frequency components in the spatial-frequency do- main. To automatically design the band-stop filter, we de- veloped a mean shift-based clustering method to partition the power spectrum image into several harmonic regions. Then a principal component analysis-based multivariate fitting pro-

Zhen Qian; Rui Huang; Dimitris N. Metaxas; Leon Axel

2007-01-01

450

Tagging Data In The Network Stack: mbuf tags Angelos D. Keromytis  

E-print Network

. Originally introduced in OpenBSD, mbuf tags were initially in- tended for use by the IPsec stack. The API has to the packet, e.g., the fact that a packet was encrypted under a particular IPsec [5] secu- rity association) or by a user-level process (e.g., exposing to a net- work daemon some IPsec-related information, indicat- ing

Keromytis, Angelos D.

451

Integrating Structured Metadata with Relational Affinity Propagation  

E-print Network

Structured and semi-structured data describing entities, taxonomies and ontologies appears in many domains. There is a huge interest in integrating structured information from multiple sources; however integrating structured data to infer complex common structures is a difficult task because the integration must aggregate similar structures while avoiding structural inconsistencies that may appear when the data is combined. In this work, we study the integration of structured social metadata: shallow personal hierarchies specified by many individual users on the SocialWeb, and focus on inferring a collection of integrated, consistent taxonomies. We frame this task as an optimization problem with structural constraints. We propose a new inference algorithm, which we refer to as Relational Affinity Propagation (RAP) that extends affinity propagation (Frey and Dueck 2007) by introducing structural constraints. We validate the approach on a real-world social media dataset, collected from the photosharing website ...

Plangprasopchok, Anon; Getoor, Lise

2010-01-01

452

High electron affinity polymers for LEDs  

Microsoft Academic Search

Several high electron affinity cyano derivatives based on poly(phenylenevinylene) (PPV) have been synthesised via a Knoevenagel condensation reaction. The HOMO-LUMO gap and hence the electro-optical properties of the polymers can be altered by judicious choice of the monomer units or the solubilising groups. The construction of efficient polymer LEDs on both glass and silicon substrates using air stable aluminium negative

S. C. Moratti; R. Cervini; A. B. Holmes; D. R. Baigent; R. H. Friend; N. C. Greenham; J. Grüner; P. J. Hamer

1995-01-01

453

Object recognition by affine invariant matching  

Microsoft Academic Search

Novel techniques are described for model-based recognition of 3-D objects from unknown viewpoints using single-gray-scale images. The objects in the scene may be overlapping and partially occluded. Efficient matching algorithms, which assume affine approximation to the perspective viewing transformation, are proposed. The study is currently restricted to flat rigid 3-D objects. Point, line and curve matching algorithms are presented. The

Yehezkel Lamdan; J. T. Schwartz; H. J. Wolfson

1988-01-01

454

Negative affinity X-ray photocathodes  

NASA Technical Reports Server (NTRS)

A new X-ray image intensifier is described. The device should eventually have a quantum efficiency which is an order of magnitude greater than that of presently available high spatial resolution X-ray detectors, such as microchannel plates. The new intesifier is based upon a GaAs crystal photocathode which is activated to achieve negative electron affinity. Details concerning the detector concept are discussed together with the theoretical relations involved, X-ray data, and optical data.

Vanspeybroeck, L.; Kellogg, E.; Murray, S.; Duckett, S.

1974-01-01

455

Affine invariant model-based object recognition  

Microsoft Academic Search

New techniques are described for model-based recognition of the objects in 3-D space. The recognition is performed from single gray-scale images taken from unknown viewpoints. The objects in the scene may be overlapping and partially occluded. An efficient matching algorithm, which assumes affine approximation to the prospective viewing transformation, is proposed. The algorithm has an offline model preprocessing (shape representation)

Y. Lamdan; J. T. Schwartz; H. J. Wolfson

1990-01-01

456

Discovering High-Affinity Ligands for Proteins  

NSDL National Science Digital Library

This article reports on development of a method for producing high-affinity ligands in which small molecules that bind to proximal subsites of a protein are identified in an NMR-based screen and then linked together in their experimentally determined bound orientations. The method is called âÂÂSAR by NMR,â which stands for âÂÂstructure-activity relationships by nuclear magnetic resonance.âÂÂ

Philip J Hajduk (Abbott Laboratories;); Robert P. Meadows (Abbott Laboratories;); Stephen Fesik (Abbott Laboratories;)

1997-10-17

457

Aptamers in Affinity Separations:Capillary Electrophoresis  

Microsoft Academic Search

Assays employing aptamers in capillary electrophoresis (CE), including competitive and noncompetitive assays, fluorescence polarization (FP) assays, nonequilibrium capillary electrophoresis of equilibrium mixtures, and affinity-polymerase chain reaction-CE assays, are summarized. These assays can be used to estimate dissociation rate and equilibrium binding constants, determine binding stoichiometries, study molecular interactions, and quantitatively determine specific analytes (e.g., proteins) in complex media. They can

Jeffrey W. Guthrie; Yuanhua Shao; X. Chris Le

2009-01-01

458

A Simple and Cost-effective RFID Tag-Reader Mutual Authentication Scheme  

E-print Network

to corporate espionage. Such readers can also corrupt and modify the tag's data. Therefore, a tag must be able-effective, light-weight, and practical RFID tag-reader mutual authentication scheme. Our scheme adheres to two

Kim, Kwangjo

459

Direct Visualization of Spruce Budworm Antifreeze Protein Interacting with Ice Crystals: Basal Plane Affinity Confers Hyperactivity  

PubMed Central

Antifreeze proteins (AFPs) protect certain organisms from freezing by adhering to ice crystals, thereby preventing their growth. All AFPs depress the nonequilibrium freezing temperature below the melting point; however AFPs from overwintering insects, such as the spruce budworm (sbw) are 10–100 times more effective than most fish AFPs. It has been proposed that the exceptional activity of these AFPs depends on their ability to prevent ice growth at the basal plane. To test the hypothesis that the hyperactivity of sbwAFP results from direct affinity to the basal plane, we fluorescently tagged sbwAFP and visualized it on the surface of ice crystals using fluorescence microscopy. SbwAFP accumulated at the six prism plane corners and the two basal planes of hexagonal ice crystals. In contrast, fluorescently tagged fish type III AFP did not adhere to the basal planes of a single-crystal ice hemisphere. When ice crystals were grown in the presence of a mixture of type III AFP and sbwAFP, a hybrid crystal shape was produced with sbwAFP bound to the basal planes of truncated bipyramidal crystals. These observations are consistent with the blockage of c-axial growth of ice as a result of direct interaction of sbwAFP with the basal planes. PMID:18339740

Pertaya, Natalya; Marshall, Christopher B.; Celik, Yeliz; Davies, Peter L.; Braslavsky, Ido

2008-01-01

460

ENCOUNTER HISTORY MODELING OF JOINT MARK RECAPTURE, TAG-RESIGHTING AND TAG-RECOVERY DATA UNDER TEMPORARY EMIGRATION  

Microsoft Academic Search

We describe a joint analysis of mark-recapture, tag-resight and tag- recovery data that directly models the encounter history of an animal. The proba- bility of the encounter history for each animal is partitioned into survival, recapture, resighting, and recovery components, and a component for the probability that the animal is never encountered again. Temporary migration enters into the likelihood through

Richard J. Barker; Kenneth P. Burnham; Gary C. White

461

PLAYING WITH TAGGING: A REAL-TIME TAGGING MUSIC PLAYER Ju-Chiang Wang1,2  

E-print Network

may provide different facets of informa- tion about the music, such as genre, mood, instrumentationPLAYING WITH TAGGING: A REAL-TIME TAGGING MUSIC PLAYER Ju-Chiang Wang1,2 , Hsin-Min Wang2 and Shyh@cc.ee.ntu.edu.tw ABSTRACT Visualizing audio signals during playback has long been a fundamental function of music players

Wang, Hsin-Min

462

A discrete Fourier transform associated with the affine Hecke algebra  

E-print Network

We introduce an explicit representation of the double affine Hecke algebra (of type $A_1$) at $q=1$ that gives rise to a periodic counterpart of a well-known Fourier transform associated with the affine Hecke algebra.

J. F. van Diejen; E. Emsiz

2012-09-14

463

Coordinated Transporter Activity Shapes High Affinity Iron Acquisition in Cyanobacteria  

E-print Network

Coordinated Transporter Activity Shapes High Affinity Iron Acquisition in Cyanobacteria C. Kranzler for a central high-affinity iron transport system in non-siderophore producing cyanobacteria. #12;#12;

Simon, Emmanuel

464

01-ERD-111-The Development of Synthetic High Affinity Ligands.  

National Technical Information Service (NTIS)

The aim of this project was to develop Synthetic High-Affinity Ligands (SHALs), which bind with high affinity and specificity to proteins of interest for national security and cancer therapy applications. The aim of producing synthetic ligands for sensory...

J. Perkins, R. Balhorn, M. Cosman, F. Lightstone, L. Zeller

2004-01-01

465

Overview of affinity biosensors in food analysis.  

PubMed

The 4 major driving forces that are expected to lead to increased use of affinity biosensors that meet crucial industrial test specifications, e.g., fast, reliable, cost-effective, and use of low-skilled personnel, are (1) strict legislative framework, e.g., recent changes proposed to the European food safety and hygiene legislation, EC No. 178/2002; (2) industrial shift from quality control to quality assurance procedures, e.g., Hazard Analysis Critical Control Point, ensuring effective positioning in the global competitive trade; (3) just-in-time production resulting in 'right' product every time; and (4) consumer demand for safe and wholesome products. The affinity biosensors field has expanded significantly over the past decade, with a projected global biosensors market growth from $6.1 billion in 2004 to $8.2 billion in 2009, representing major industrial sectors (e.g., Pharma, Medicare, and Food). This brief review is targeted to affinity biosensors developed for the food industry and includes research and development leading to biosensors for microbiological and chemical analytes of industrial concern, commercial biosensors products on the market, and examples of future prospects in this diagnostic field. PMID:16792079

Patel, Pradip D

2006-01-01

466

Notch and Integrin Affinity: A Sticky Situation  

NSDL National Science Digital Library

The Notch pathway is a conserved signal transduction system that mediates intercellular signaling to regulate cell fate decisions in various tissues. Dysregulation of Notch activity results in various disorders, including cardiovascular diseases and cancer. Notch regulates cell fate through a number of mechanisms that include control of cell proliferation, survival, migration, and differentiation. Notch activation increases vascular endothelial cell adhesion through the enhancement of β1 integrin affinity for fibronectin, collagens I and IV, and vitronectin without altering the abundance of β1 integrin at the cell surface. A study now suggests that this Notch-dependent increase in β1 integrin affinity occurs through the activation of the small guanosine triphosphate (GTP)–binding protein, R-Ras. It is proposed that Notch-dependent activation of R-Ras reverses H-Ras–mediated suppression of integrin affinity. Activation of R-Ras by Notch may be triggered by a noncanonical CSL (CBF1 or RBP-Jκ in vertebrates, Suppressor of Hairless in Drosophila, Lag-1 in Caenorhabditis elegans)–independent pathway. Because R-Ras is selectively distributed in vascular cells, these findings are of particular importance in understanding the effector functions of Notch in the vascular system.

Aly Karsan (Vancouver;British Columbia Cancer Agency and University of British Columbia REV)

2008-01-15

467

Affine Invariant Detection: Edges, Active Contours, and Segments  

Microsoft Academic Search

In this paper we undertake a systematic investigationof affine invariant object detection. Edge detectionis first presented from the point of view ofthe affine invariant scale-space obtained by curvaturebased motion of the image level-sets. In this case,affine invariant edges are obtained as a weighted differenceof images at different scales. We then introducethe affine gradient as the simplest possibleaffine invariant differential function

Peter J. Olver; Guillermo Sapiro; Allen Tannenbaum

1996-01-01

468

Evaluation of VI-alpha and PIT-tagging of the seahorse Hippocampus abdominalis  

Microsoft Academic Search

.  The suitability of visible implant alphanumeric (VI-alpha) and passive integrated transponder (PIT)-tagging to individually identify seahorses (Hippocampus abdominalis) was assessed in two trials. For each trial, 24 seahorses were tagged and mortality, growth, tag retention and tag visibility\\/readability assessed, together with 24 control seahorses, over a period of 3 months. For VI-alpha tagging, a single tag was inserted under the skin between the

Chris M. C. Woods

2005-01-01

469

Long-Term PIT and T-Bar Anchor Tag Retention Rates in Adult Muskellunge  

Microsoft Academic Search

Mark–recapture studies require knowledge of tag retention rates specific to the tag types, fish species and size, and study duration. We determined the probability of tag loss for passive integrated transponder (PIT) tags implanted into dorsal musculature, T-bar anchor tags attached to dorsal pterygiophores, and both tags in relation to years posttagging for double-marked adult muskellunge Esox masquinongy over a

Neil P. Rude; Gregory W. Whitledge; Quinton E. Phelps; Shawn Hirst

2011-01-01

470

Comparison of three nonlinear models to describe long-term tag shedding by lake trout  

USGS Publications Warehouse

We estimated long-term tag-shedding rates for lake trout Salvelinus namaycush using two existing models and a model we developed to account for the observed permanence of some tags. Because tag design changed over the course of the study, we examined the tag-shedding rates for three types of numbered anchor tags (Floy tags FD-67, FD-67C, and FD-68BC) and an unprinted anchor tag (FD-67F). Lake trout from the Gull Island Shoal region, Lake Superior, were double-tagged and subsequent recaptures were monitored in annual surveys conducted from 1974 to 1992. We modeled tag-shedding rates, using time at liberty and probabilities of tag shedding estimated from fish released in 1974 and 1978-1983 and later recaptured. Long-term shedding of numbered anchor tags in lake trout was best described by a nonlinear model with two parameters: an instantaneous tag-shedding rate and a constant representing the proportion of tags that were never shed. Although our estimates of annual shedding rates varied with tag type (0.300 for FD-67, 0.441 for FD-67C, and 0.656 for FD-68BC), differences were not significant. About 36% of tags remained permanently affixed to the fish. Of the numbered tags that were shed (about 64%), two mechanisms contributed to tag loss: disintegration and dislodgment. Tags from about 11% of recaptured fish had disintegrated, but most tags were dislodged. Unprinted tags were shed at a significant but low rate immediately after release, but the long-term annual shedding rate of these tags was only 0.013. Compared with unprinted tags, numbered tags dislodged at higher annual rates; we hypothesized that this was due to the greater frictional drag associated with the larger cross-sectional area of numbered tags.

Fabrizio, Mary C.; Swanson, Bruce L.; Schram, Stephen T.; Hoff, Michael H.

1996-01-01

471

Cancer profiles by Affinity Propagation Federico Ambrogi2  

E-print Network

Cancer profiles by Affinity Propagation Federico Ambrogi2 , Elena Raimondi1 , Daniele Soria3, Wollaton Road, Nottingham, NG8 1BB, UK E-mail: federico.ambrogi@unimi.it Abstract The affinity propagation cancer case series was used to compare the results of the affinity propagation with the results obtained