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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

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

3

Protein Profiling with Cleavable Isotope-coded Affinity Tag (cICAT) Reagents  

Microsoft Academic Search

Protein expression profiles in yeast cells, in response to salinity stress, were determined using the cleavable iso- tope-coded affinity tag (cICAT) labeling strategy. The analysis included separation of the mixed protein samples by SDS-PAGE, followed by excision of the entire gel lane, and division of the lane into 14 gel regions. Regions were subjected to in-gel digestion, biotin affinity chromatogra-

Jiaxu Li; Hanno Steen; Steven P. Gygi

4

Protein profiling with cleavable isotope-coded affinity tag (cICAT) reagents: the yeast salinity stress response.  

PubMed

Protein expression profiles in yeast cells, in response to salinity stress, were determined using the cleavable isotope-coded affinity tag (cICAT) labeling strategy. The analysis included separation of the mixed protein samples by SDS-PAGE, followed by excision of the entire gel lane, and division of the lane into 14 gel regions. Regions were subjected to in-gel digestion, biotin affinity chromatography, and analysis by nano-scale microcapillary liquid chromatography coupled to tandem mass spectrometry. The novel (13)C-labeled ICAT reagents have identical elution profiles for labeled peptide pairs and broadly spread the distribution of labeled peptides during reversed-phase chromatography. A total of 560 proteins were identified and quantified, with 51 displaying more than 2-fold expression differences. In addition to some known proteins involved in salt stress, four RNA-binding proteins were found to be up-regulated by high salinity, suggesting that selective RNA export from the nucleus is important for the salt-stress response. Some proteins involved in amino acid synthesis, which have been observed to be up-regulated by amino acid starvation, were also found to increase their abundance on salt stress. These results indicate that salt stress and amino acid starvation cause overlapping cellular responses and are likely to be physiologically linked. PMID:14506205

Li, Jiaxu; Steen, Hanno; Gygi, Steven P

2003-11-01

5

Element-coded affinity tags for peptides and proteins.  

PubMed

Isotope-coded affinity tags (ICAT) represent an important new tool for the analysis of complex mixtures of proteins in living systems [Aebersold, R., and Mann, M. (2003) Nature, 422, 198-207]. We envisage an alternative protein-labeling technique based on tagging with different element-coded metal chelates, which affords affinity chromatography, quantification, and identification of a tagged peptide from a complex mixture. As proof of concept, a synthetic peptide was modified at a cysteine side chain with either a carboxymethyl group or acetamidobenzyl-1,4,7,10-tetraazacyclododecane-N,N',N' ',N' "-tetraacetic acid (AcBD) chelates of terbium or yttrium. A mixture of the three modified peptides in a mole ratio of 100:1.0:0.83 carboxymethyl:AcBD-Tb:AcBD-Y was trypsinized, purified on a new affinity column that binds rare-earth DOTA chelates, and analyzed by LC-MS/MS. Chelate-tagged tryptic peptides eluted cleanly from the affinity column; the tagged peptides chromatographically coeluted during LC-MS analysis, were present in the expected ratio as indicated by MS ion intensity, and were sequence-identified by tandem mass spectrometry. DOTA-rare earth chelates have exceptional properties for use as affinity tags. They are highly polar and water-soluble. Many of the rare earth elements are naturally monoisotopic, providing a variety of simple choices for preparing mass tags. Further, the rare earths are heavy elements, whose mass defects give the masses of tagged peptides exact values not normally shared by molecules that contain only light elements. PMID:14733576

Whetstone, Paul A; Butlin, Nathaniel G; Corneillie, Todd M; Meares, Claude F

2004-01-01

6

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

7

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

8

Quantification of Tryptic Peptides in Quadrupole Ion Trap Using High-Mass Signals Derived from Isotope-Coded N-Acetyl Dipeptide Tags  

NASA Astrophysics Data System (ADS)

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.

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

2011-09-01

9

Mass spectrometric identification of N-linked glycopeptides using lectin-mediated affinity capture and glycosylation site–specific stable isotope tagging  

Microsoft Academic Search

Protein post-translational modifications (PTMs), such as glycosylation and phosphorylation, are crucial for various signaling and regulatory events, and are therefore an important objective of proteomics research. We describe here a protocol for isotope-coded glycosylation site–specific tagging (IGOT), a method for the large-scale identification of N-linked glycoproteins from complex biological samples. The steps of this approach are: (1) lectin column–mediated affinity

Hiroyuki Kaji; Yoshio Yamauchi; Nobuhiro Takahashi; Toshiaki Isobe

2007-01-01

10

Metal-coded affinity tag labeling: a demonstration of analytical robustness and suitability for biological applications.  

PubMed

Quantitative peptide and protein analysis is one of the most promising fields in modern life science. Besides stable isotope coded labeling, metal chelate complexes are an alternative tool for quantification. The development of metal-coded affinity tags (MeCAT) was aimed to provide a robust tool for the quantification of peptides and proteins by utilizing lanthanide-harboring metal tags. It was shown that MeCAT is suited for relative quantification of proteins via standard mass spectrometric methods. The approach of tagging biomolecules with MeCAT offers the unique advantage of absolute quantification via inductively coupled plasma mass spectrometry (ICPMS), a well-established technique for assessing concentrations down to low attomole ranges. This work investigates the compatibility of MeCAT labeling to analysis workflows such as nano liquid chromatography/electrospray ionization tandem mass spectrometry (nano-LC/ESI-MS(n)). Focus was given toward the separation behavior of labeled peptides and the dynamic range of detection and peptide charge distribution. Furthermore, the stability of MeCAT under harsh analytical conditions was investigated. With the application of the MeCAT technique to a standard analysis scheme in proteomics, such as the investigation of changes in an Escherichia coli proteome, we successfully addressed the suitability to utilize MeCAT on biological samples. Furthermore, we demonstrated that MeCAT complexes are stable under a variety of conditions and that by applying LC/ESI-MS it is possible to cover a dynamic range of 2 orders of magnitude down to the low femtomole range with an average standard deviation below 15%. Therefore, this technique is suitable to common proteomic workflows and enables relative as well as absolute differential peptide quantification. PMID:19228048

Ahrends, Robert; Pieper, Stefan; Neumann, Boris; Scheler, Christian; Linscheid, Michael W

2009-03-15

11

Tamavidin, a versatile affinity tag for protein purification and immobilization.  

PubMed

Tamavidin 2 is a fungal avidin-like protein that binds biotin with high affinity and is highly produced in soluble form in Escherichia coli. By contrast, widely used biotin-binding proteins avidin and streptavidin are rarely produced in soluble form in E. coli. In this study, we describe an efficient system for one-step purification and immobilization of recombinant proteins using tamavidin 2 as an affinity tag. A bacterial sialyltransferase and soybean agglutinin were fused to tamavidin 2 and expressed in E. coli and tobacco BY-2 cells, respectively. High-level expressions of the fusion proteins were detected (80 mg l(-1)E. coli culture for bacterial sialyltransferase-tamavidin 2 and 2 mg l(-1) BY-2 cell culture for soybean agglutinin-tamavidin 2). To immobilize and purify the fusion proteins, biotinylated magnetic microbeads were incubated with the soluble extract from each recombinant host producing the fusion protein and then washed thoroughly. As the result, both fusion proteins were immobilized tightly on the microbeads without substantial loss of activity and simultaneously highly purified (90-95% purity) on the microbeads. Biotin with a longer linker contributed to higher affinity between the fusion protein and biotin. These results suggest that tamavidin fusion technology is a powerful tool for production, purification, and immobilization of recombinant proteins. PMID:20026208

Takakura, Yoshimitsu; Oka, Naomi; Kajiwara, Hitomi; Tsunashima, Masako; Usami, Satoru; Tsukamoto, Hiroshi; Ishida, Yuji; Yamamoto, Takeshi

2010-02-15

12

Isotope-coded protein label.  

PubMed

A great variety of technologies using stable isotope labeling in combination with mass spectrometry have been described being tools to identify and relatively quantify proteins within complex mixtures. Here, we present a method, termed isotope-coded protein label (ICPL), which is capable of high-throughput quantitative proteome profiling on a global scale. Since ICPL is based on tagging stable isotope derivatives at the free amino groups of intact proteins, the method is applicable to any protein sample, including extracts from tissues or body fluids. All separation methods currently employed in proteome studies can be used to reduce complexity on the protein level. After enzymatic cleavage of the protein fractions, the ratios of peptides from different proteome states can be calculated by simple MS-based mass spectrometric analyses. Only peptides representing different expression levels in the different proteomic states are further analyzed by tandem-mass spectrometry to identify respective proteins. For quantification of proteins from multiplexed ICPL experiments, ICPLQuant was developed, a software package especially designed to cover the whole ICPL workflow. The ICPL method results in accurate and reproducible quantification of proteins and high sequence coverage, indispensable for a comprehensive detection of posttranslational modifications and discrimination of protein isoforms. PMID:22665300

Kellermann, Josef; Lottspeich, Friedrich

2012-01-01

13

PROTEIN-PROTEIN INTERACTIONS OF TANDEM AFFINITY PURIFICATION (TAP)-TAGGED PROTEIN KINASES IN RICE  

Technology Transfer Automated Retrieval System (TEKTRAN)

Forty-one rice cDNAs encoding protein kinases were fused to the tandem affinity purification (TAP) tag and expressed in transgenic rice plants. The TAP-tagged kinases and interacting proteins were purified from the T1 progeny of the transgenic rice plants and identified by mass spectrometry. Ninet...

14

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

15

A general affinity method to purify peroxidase-tagged antibodies  

Microsoft Academic Search

Antibodies tagged with enzymes, e.g. horseradish peroxidase (HRPO) are used extensively in a broad range of immunoassay, immunohistochemical, and prodrug-based immunotherapeutic applications. These antibodies may be polyclonal, monoclonal, bispecific or genetically engineered in origin. Often, purification of the antibody is the single greatest obstacle to obtaining immunoprobes with high specific activity [Milstein and Cuello, Nature 305 (1983) 537]. We have

Donald R Husereau; Mavanur R Suresh

2001-01-01

16

Affinity-tagged miniprion derivatives spontaneously adopt protease-resistant conformations.  

PubMed

An abridged PrP molecule of 106 amino acids designated PrP106 can form infectious miniprions in transgenic (Tg) mice (29). Addition of six-histidine (His(6)) affinity tags to selective sites within PrP106 resulted unexpectedly in new PrP proteins that spontaneously adopted protease-resistant conformations when expressed in neuroblastoma cells and Tg mice. Acquisition of protease resistance depended on the length, charge, and placement of the affinity tag. Introduction of the disease-linked mutation E200K into the sequence of PrP106(140/6His) increased the recovery of protease-resistant PrP fivefold, whereas introduction of the mutations C213A and Delta214-220 did not affect the recovery of protease-resistant PrP. Treatment of cultured cells expressing affinity-tagged PrP106 mutants with polypropyleneimine dendrimer rendered these proteins sensitive to protease digestion in a manner similar to wild-type PrP(Sc). We conclude that certain affinity-tagged PrP106 proteins spontaneously fold into conformations partially resembling, yet distinct from, wild-type PrP(Sc). These proteins might be useful tools in the identification of new disease-causing mutations as well as for screening compounds for therapeutic efficacy. PMID:11090193

Supattapone, S; Nguyen, H O; Muramoto, T; Cohen, F E; DeArmond, S J; Prusiner, S B; Scott, M

2000-12-01

17

A tandem affinity purification tag of TGA2 for isolation of interacting proteins in Arabidopsis thaliana.  

PubMed

Tandem affinity purification (TAP) tagging provides a powerful tool for isolating interacting proteins in vivo. TAP-tag purification offers particular advantages for the identification of stimulus-induced protein interactions. Type II bZIP transcription factors (TGA2, TGA5 and TGA6) play key roles in pathways that control salicylic acid, ethylene, xenobiotic and reactive oxylipin signaling. Although proteins interacting with these transcription factors have been identified through genetic and yeast 2-hybrid screening, others are still elusive. We have therefore generated a C-terminal TAP-tag of TGA2 to isolate additional proteins that interact with this transcription factor. Three lines most highly expressing TAP-tagged TGA2 were functional in that they partially complemented reactive oxylipin-responsive gene expression in a tga2 tga5 tga6 triple mutant. TAP-tagged TGA2 in the most strongly overexpressing line was proteolytically less stable than in the other 2 lines. Only this overexpressing line could be used in a 2-step purification process, resulting in isolation of co-purifying bands of larger molecular weight than TGA2. TAP-tagged TGA2 was used to pull down NPR1, a protein known to interact with this transcription factor. Mass spectrometry was used to identify peptides that co-purified with TAP-tagged TGA2. Having generated this TGA2 TAP-tag line will therefore be an asset to researchers interested in stimulus-induced signal transduction processes. PMID:25482810

Stotz, Henrik U; Findling, Simone; Nukarinen, Ella; Weckwerth, Wolfram; Mueller, Martin J; Berger, Susanne

2014-10-01

18

Systematic Uncovering of Multiple Pathways Underlying the Pathology of Huntington Disease by an Acid-cleavable Isotope-coded Affinity Tag Approach  

Microsoft Academic Search

Huntington disease (HD) is an autosomal dominant neuro- degenerative disease that results from a CAG (glutamine) trinucleotide expansion in exon 1 of huntingtin (Htt). The aggregation of mutant Htt has been implicated in the pro- gression of HD. The earliest degeneration occurs in the striatum. To identify proteins critical for the progression of HD, we applied acid-cleavable ICAT technology to

Ming-Chang Chiang; Chiun-Gung Juo; Hao-Hung Chang; Hui-Mei Chen; Eugene C. Yi; Yijuang Chern

2007-01-01

19

Purification of resistance protein complexes using a biotinylated affinity (HPB) tag.  

PubMed

Plant disease resistance (R) proteins confer strong resistance against pathogens by recognizing particular pathogen effectors. Identification of proteins associated with an R protein will provide insight into the mechanism of R protein function. Many R proteins are associated with the plasma membrane (PM) and expressed at low levels. Here, we describe a method to purify such low-abundance PM R protein -complexes from Arabidopsis using a biotinylated affinity tag, called the HPB tag. We have successfully applied this method to identify candidate components of the RPS2 resistance protein complex(es). This method should also be applicable to purification of other low-abundance PM protein complexes. PMID:21359797

Qi, Yiping; Katagiri, Fumiaki

2011-01-01

20

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

Schäffer, Ursula; Schlosser, Andreas; Müller, Kristian M.; Schäfer, Angelika; Katava, Nenad; Baumeister, Ralf; Schulze, Ekkehard

2010-01-01

21

Generation of Affinity-Tagged Fluoromycobacteriophages by Mixed Assembly of Phage Capsids  

PubMed Central

Addition of affinity tags to bacteriophage particles facilitates a variety of applications, including vaccine construction and diagnosis of bacterial infections. Addition of tags to phage capsids is desirable, as modification of the tails can lead to poor adsorption and loss of infectivity. Although tags can readily be included as fusions to head decoration proteins, many phages do not have decoration proteins as virion components. The addition of a small (10-amino-acid) Strep-tag II (STAG II) to the mycobacteriophage TM4 capsid subunit, gp9, was not tolerated as a genetically homogenous recombinant phage but could be incorporated into the head by growth of wild-type phage on a host expressing the capsid-STAG fusion. Particles with capsids composed of wild-type and STAG-tagged subunit mixtures could be grown to high titers, showed good infectivities, and could be used to isolate phage-bacterium complexes. Preparation of a STAG-labeled fluoromycobacteriophage enabled capture of bacterial complexes and identification of infected bacteria by fluorescence. PMID:23851082

Piuri, Mariana; Rondón, Liliana; Urdániz, Estefanía

2013-01-01

22

A novel gigaporous GSH affinity medium for high-speed affinity chromatography of GST-tagged proteins.  

PubMed

Novel GSH-AP (phenoxyl agarose coated gigaporous polystyrene, Agap-co-PSt) microspheres were successfully prepared by introducing GSH ligand into hydrophilic AP microspheres pre-activated with 1,4-butanediol diglycidyl ether. The gigaporous structure and chromatographic properties of GSH-AP medium were evaluated and compared with commercial GSH Sepharose FF (GSH-FF) medium. The macropores (100-500nm) of gigaporous PSt microspheres were well maintained after coating with agarose and functionalized with GSH ligand. Hydrodynamic experiments showed that GSH-AP column had less backpressure and plate height than those of GSH-FF column at high flow velocity, which was beneficial for its use in high-speed chromatography. The presence of flow-through pores in GSH-AP microspheres also accelerated the mass transfer rate of biomolecules induced by convective flow, leading to high protein resolution and high dynamic binding capacity (DBC) of glutathione S-transferase (GST) at high flow velocity. High purity of GST and GST-tagged recombinant human interleukin-1 receptor antagonist (rhIL-1RA) were obtained from crude extract with an acceptable recovery yield within 1.5min at a velocity up to 1400cm/h. GSH-AP medium is promising for high-speed affinity chromatography for the purification of GST and GST-tagged proteins. PMID:24269760

Huang, Yongdong; Zhang, Rongyue; Li, Juan; Li, Qiang; Su, Zhiguo; Ma, Guanghui

2014-03-01

23

Enhancement of phosphoprotein analysis using a fluorescent affinity tag and mass spectrometry.  

PubMed

A fluorescent affinity tag (FAT) was synthesized and was utilized to selectively modify phosphorylated serine and threonine residues via beta-elimination and Michael addition chemistries in a 'one-step' reaction. This labeling technique was used for covalent modification of both phosphoproteins and phosphopeptides, allowing identification of these molecular species by fluorescence imaging after solution- or gel-based separation methods. In addition to the strong fluorescence of the rhodamine tag, a commercially available antibody can be used to enrich low-abundance post-labeled phosphopeptides present in complex mixtures. Application of this methodology to phosphorylation-site mapping has been evaluated for a phosphoprotein standard, bovine beta-casein. Initial results demonstrated low femtomole detection limits after fluorescence image analysis of FAT-labeled proteins or peptides. PMID:15988732

Stevens, Stanley M; Chung, Alfred Y; Chow, Marjorie C; McClung, Scott H; Strachan, Camille N; Harmon, Alice C; Denslow, Nancy D; Prokai, Laszlo

2005-01-01

24

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

PubMed Central

Background Functional Genomics, the systematic characterisation of the functions of an organism's genes, includes the study of the gene products, the proteins. Such studies require methods to express and purify these proteins in a parallel, time and cost effective manner. Results We developed a method for parallel expression and purification of recombinant proteins with a hexahistidine tag (His-tag) or glutathione S-transferase (GST)-tag from bacterial expression systems. Proteins are expressed in 96-well microplates and are purified by a fully automated procedure on a pipetting robot. Up to 90 microgram purified protein can be obtained from 1 ml microplate cultures. The procedure is readily reproducible and 96 proteins can be purified in approximately three hours. It avoids clearing of crude cellular lysates and the use of magnetic affinity beads and is therefore less expensive than comparable commercial systems. We have used this method to compare purification of a set of human proteins via His-tag or GST-tag. Proteins were expressed as fusions to an N-terminal tandem His- and GST-tag and were purified by metal chelating or glutathione affinity chromatography. The purity of the obtained protein samples was similar, yet His-tag purification resulted in higher yields for some proteins. Conclusion A fully automated, robust and cost effective method was developed for the purification of proteins that can be used to quickly characterise expression clones in high throughput and to produce large numbers of proteins for functional studies. His-tag affinity purification was found to be more efficient than purification via GST-tag for some proteins. PMID:12885298

Scheich, Christoph; Sievert, Volker; Büssow, Konrad

2003-01-01

25

Application of Ni(II)-Assisted Peptide Bond Hydrolysis to Non-Enzymatic Affinity Tag Removal  

PubMed Central

In this study, we demonstrate a non-enzymatic method for hydrolytic peptide bond cleavage, applied to the removal of an affinity tag from a recombinant fusion protein, SPI2-SRHWAP-His6. This method is based on a highly specific Ni(II) reaction with (S/T)XHZ peptide sequences. It can be applied for the protein attached to an affinity column or to the unbound protein in solution. We studied the effect of pH, temperature and Ni(II) concentration on the efficacy of cleavage and developed an analytical protocol, which provides active protein with a 90% yield and ?100% purity. The method works well in the presence of non-ionic detergents, DTT and GuHCl, therefore providing a viable alternative for currently used techniques. PMID:22574150

Kopera, Edyta; Belczyk-Ciesielska, Agnieszka; Bal, Wojciech

2012-01-01

26

A new peptide-affinity tag for the detection and affinity purification of recombinant proteins with a monoclonal antibody.  

PubMed

A monoclonal anti-peptide antibody (2E11) was raised against the synthetic peptide 38 (C-L-D-K-S-G-L-P-S-D-R-F-F-A) representing a part of the variable region of the Vbeta 6.2 T-cell receptor. This mAb (IgG(1), kappa light chain) bound very specifically to peptide 38 as shown by ELISA but did not recognize the corresponding native Vbeta 6.2 T-cell receptor on T-cells. For epitope analysis, overlapping peptides of 4-10 amino acids in length corresponding to the sequence of peptide 38 were synthesized and assayed by SPOT synthesis on cellulose sheets. The shortest peptide recognized was L-P-S-D-R. The specificity of mAb 2E11 was examined with 100 different peptides comprising other parts of the different variable Vbeta domains of the human T-cell receptor that do not include the epitope region L-P-S-D-R. None of these peptides were recognized. The chemical synthesis of a peptide with the sequence L-P-S-D-R on Sepharose beads allowed to efficiently purify the mAb 2E11 in a single step by affinity chromatography. An equilibrium binding constant of 4.9x10(6) l/mol was determined for mAb 2E11 by using rhodamine-green-labelled peptide 38 in fluorescence correlation spectroscopy. In order to demonstrate that peptide 38 can be used as an affinity-tag, it was fused to the carboxyl-terminus of interferon regulatory factor-1 (IRF-1). It could be shown that in vitro translated peptide 38 tagged IRF-1 was immunoprecipitated by the mAb 2E11 and that the fusion protein could be purified by immunoaffinity chromatography. Additionally peptide 38 was fused to the amino-terminus of the Taq polymerase. This recombinant protein was expressed in E. coli and specifically detected in a Dot blot and Western blot using mAb 2E11. PMID:10854611

Böldicke, T; Struck, F; Schaper, F; Tegge, W; Sobek, H; Villbrandt, B; Lankenau, P; Böcher, M

2000-06-23

27

Quantitative Proteomics Isotope Coding Proteomics  

E-print Network

Smaller final tag ­ more informative MS/MS spectra Coefficient-of-variation in test system ­ 10% #12 side chains) - isomeric/isobaric labels (MS/MS based readout) Reporter Balance PRG Peptide 145 amu Facilitates quantitation of PTMs #12;control test 1 test 2 test 3 reduce, alkylate, digest label combine

Richardson, David

28

Optimizing the bioavailability of small molecular optical imaging probes by conjugation to an albumin affinity tag.  

PubMed

Small molecular imaging probes are often found to be rapidly cleared from the circulation. In order to improve signal to noise ratio (SNR) by high probe accumulation in the target tissue we intended to prolong the presence of the probes in the circulation by exploiting inherent transport mechanisms. Human serum albumin (HSA) is playing an increasingly important role as a drug carrier in clinical settings and drugs directly bound to albumin or attached to albumin binding moieties have been successfully developed for treatment approaches. To optimize the bioavailability of existing fluorescent probes, a hydrophobic affinity tag is installed, which enhances albumin binding. In a first experiment an endothelin-A receptor (ETAR) probe is modified by inserting a trivalent linker, attaching an albumin affinity tag and labeling the conjugate with the fluorescent dye Cy 5.5. The spectroscopic properties of the conjugate are examined by photometer- and fluorometer measurements in comparison to a probe without albumin binding tag. Albumin binding was proven by agarose gel electrophoresis. The affinity towards ETAR was confirmed in vitro by cell binding assays on human fibrosarcoma cells (HT-1080) and in vivo by murine xenograft imaging studies. In vitro, the modified probe retains high target binding in the absence and presence of albumin. Binding could be blocked by predosing with ETAR antagonist atrasentan, proving specificity. The in vivo examinations in comparison to the established probe showed a reduced renal elimination and a prolonged circulation of the tracer resulting in significantly higher signal intensity (SI) at the target and a higher signal-to-noise ratio (SNR) between 3h and 96 h after injection. In summary, we designed a small molecular, non-peptidic fluorescent probe which targets ETAR and reversibly binds to serum albumins. The reversible binding to albumin enhances the biological half-life of the probe substantially and enables near infrared optical imaging of subcutaneous tumors for several days. This approach of reversibly attaching probes to serum albumin may serve as a tool to optimize tracer distribution for more precise target characterization in molecular imaging experiments. PMID:24815420

Hahnenkamp, Anke; Alsibai, Wael; Bremer, Christoph; Höltke, Carsten

2014-07-28

29

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

30

Probing the Mechanism of Electron Capture and Electron Transfer Dissociation Using Tags with Variable Electron Affinity  

PubMed Central

Electron capture dissociation (ECD) and electron transfer dissociation (ETD) of doubly protonated electron affinity (EA)-tuned peptides were studied to further illuminate the mechanism of these processes. The model peptide FQpSEEQQQTEDELQDK, containing a phosphoserine residue, was converted to EA-tuned peptides via ?-elimination and Michael addition of various thiol compounds. These include propanyl, benzyl, 4-cyanobenzyl, perfluorobenzyl, 3,5-dicyanobenzyl, 3-nitrobenzyl and 3,5-dinitrobenzyl structural moieties, having a range of EA from -1.15 to 1.65 eV, excluding the propanyl group. Typical ECD or ETD backbone fragmentations are completely inhibited in peptides with substituent tags having EA over 1.00 eV, which are referred to as electron predators in this work. Nearly identical rates of electron capture by the dications substituted by the benzyl (EA = -1.15 eV) and 3-nitrobenzyl (EA = 1.00 eV) moieties are observed, which indicates the similarity of electron capture cross sections for the two derivatized peptides. This observation leads to the inference that electron capture kinetics are governed by the long range electron-dication interaction and are not affected by side chain derivatives with positive EA. Once an electron is captured to high-n Rydberg states, however, through-space or through-bond electron transfer to the EA-tuning tags or low-n Rydberg states via potential curve crossing occurs in competition with transfer to the amide ?* orbital. The energetics of these processes are evaluated using time-dependent density functional theory with a series of reduced model systems. The intramolecular electron transfer process is modulated by structure-dependent hydrogen bonds and is heavily affected by the presence and type of electron withdrawing groups in the EA-tuning tag. The anion radicals formed by electron predators have high proton affinities (approximately 1400 kJ/mol for the 3-nitrobenzyl anion radical) in comparison to other basic sites in the model peptide dication, facilitating exothermic proton transfer from one of the two sites of protonation. This interrupts the normal sequence of events in ECD or ETD leading to backbone fragmentation by forming a stable radical intermediate. The implications which these results have for previously proposed ECD and ETD mechanisms are discussed. PMID:19331417

Sohn, Chang Ho; Chung, Cheol K.; Yin, Sheng; Ramachandran, Prasanna; Loo, Joseph A.; Beauchamp, J. L.

2009-01-01

31

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

32

A carboxy-terminal affinity tag for the purification and mass spectrometric characterization of integral membrane proteins  

PubMed Central

G-protein-coupled receptors (GPCRs) and other, structurally and functionally related membrane proteins represent particularly attractive targets for drug discovery. Integral membrane proteins are often difficult to purify from native contexts, and lack of sufficient quantities hampers subsequent structural and functional proteomic studies. We describe here the implementation of an optimized enrichment strategy involving a membrane protein-compatible 1D4 affinity tag that is derived from the carboxy-terminal nine amino residues of bovine rhodopsin, and its corresponding tag-specific, high-affinity monoclonal antibody. Expressing two GPCRs as well as two related ATP binding cassette (ABC) transporters in their functional forms in human cell lines, we have shown that a single detergent and wash condition can be employed for the purification of all said membrane proteins. Subsequent in-gel digestion with trypsin and mass spectrometric peptide analysis resulted in high sequence coverage for the ABC transporters ABCA1-1D4 and ABCA4-1D4. In contrast, digestion by various enzymatic combinations was necessary to obtain the best sequence coverage for affinity-enriched GPCRs CXCR4-1D4 and CCR5-1D4 in an annotated spectrum library, and to identify the N-glycosylation sites for CXCR4. Our results demonstrate that the 1D4-tag enrichment strategy is a versatile tool for the characterization of integral membrane proteins that can be employed for functional proteomic studies. PMID:19236039

Wong, Julie P.; Reboul, Emmanuelle; Molday, Robert S.; Kast, Juergen

2014-01-01

33

Vectors for expression of proteins with single or combinatorial fluorescent protein and tandem affinity purification tags in Dictyostelium.  

PubMed

We constructed a series of expression vectors for purification of native proteins and protein complexes in Dictyostelium. Protein purification is achieved by either a C-terminal or N-terminal fusion of the protein of choice to the tandem affinity purification (TAP) tag. The TAP tag consists of a protein A tag and a calmodulin binding peptide (CBP) and has been successfully used for purification of native protein complexes from yeast and animal cells. Protein expression is driven by the constitutive actin 15 promoter and the vectors optionally carry additional green- or yellow fluorescent protein (GFP or YFP) tags for fusion at either a C- or N-terminal location. Tandem affinity purification of native Dictyostelium protein complexes was tested by using pArc-34, one of the members of the well characterized Dictyostelium Arp2/3 complex, as bait. After denaturation and SDS-PAGE separation of the pArc-34 associated proteins all members of the Arp2/3 complex could be identified. PMID:17296313

Meima, Marcel E; Weening, Karin E; Schaap, Pauline

2007-06-01

34

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

E-print Network

rhinovirus 3C protease, SUMOstar, tobacco etch virus protease, and thrombin) by use of a panel of 94 tag removal. Common proteases include entero- kinase [1], factor Xa [2], human rhinovirus 3C protease

Lebendiker, Mario

35

Affinity chromatography of native SUMO proteins using His-tagged recombinant UBC9 bound to Co2+-charged talon resin.  

PubMed

Four small ubiquitin-related modifier (SUMO) genes have been identified in humans. The recently identified SUMO4 was detected in mRNA transcripts from HEK293 cells, and human kidney and spleen tissue and may be involved in regulation of NF-kappaB and susceptibility to autoimmune diseases. However, identification and characterization of a native SUMO4 protein has not yet been reported. Here, we analyzed for the presence of native SUMO proteins in HEK293 cells and human kidney tissue using an affinity purification procedure using a UBC9 matrix followed by mass spectroscopy analyses for SUMO-specific peptides. Identification by mass spectroscopy of peptides generated by Trypsin and Lys-C digestion did reveal peptides unique to SUMO1 and SUMO2/3, but not SUMO4. In control experiments, SUMO4 prepared by recombinant methods was isolated and even enriched by our UBC9 affinity purification. Thus, SUMO4 protein appears to be either in extremely low abundance in human kidney or HEK293 cells or it is not present at all. It remains possible that SUMO4 protein is more abundant in other cell types or can be induced by hormonal or environmental challenges and the procedures reported here should be extremely useful for detecting native SUMO4. Furthermore, using His-tagged recombinant proteins bound to Co(2+)-charged Talon resin has general applicability to isolate native proteins that have strong non-covalent interactions with the resin-bound His-tagged proteins. PMID:17459725

Bohren, Kurt M; Gabbay, Kenneth H; Owerbach, David

2007-08-01

36

The structure of an orthorhombic crystal form of a 'forced reduced' thiol peroxidase reveals lattice formation aided by the presence of the affinity tag.  

PubMed

Thiol peroxidase (Tpx) is an atypical 2-Cys peroxiredoxin, which has been suggested to be important for cell survival and virulence in Gram-negative pathogens. The structure of a catalytically inactive version of this protein in an orthorhombic crystal form has been determined by molecular replacement. Structural alignments revealed that Tpx is conserved. Analysis of the crystal packing shows that the linker region of the affinity tag is important for formation of the crystal lattice. PMID:22691780

Beckham, Katherine S H; Byron, Olwyn; Roe, Andrew J; Gabrielsen, Mads

2012-05-01

37

Isolation of centromeric-tandem repetitive DNA sequences by chromatin affinity purification using a HaloTag7-fused centromere-specific histone H3 in tobacco.  

PubMed

The centromere is a multi-functional complex comprising centromeric DNA and a number of proteins. To isolate unidentified centromeric DNA sequences, centromere-specific histone H3 variants (CENH3) and chromatin immunoprecipitation (ChIP) have been utilized in some plant species. However, anti-CENH3 antibody for ChIP must be raised in each species because of its species specificity. Production of the antibodies is time-consuming and costly, and it is not easy to produce ChIP-grade antibodies. In this study, we applied a HaloTag7-based chromatin affinity purification system to isolate centromeric DNA sequences in tobacco. This system required no specific antibody, and made it possible to apply a highly stringent wash to remove contaminated DNA. As a result, we succeeded in isolating five tandem repetitive DNA sequences in addition to the centromeric retrotransposons that were previously identified by ChIP. Three of the tandem repeats were centromere-specific sequences located on different chromosomes. These results confirm the validity of the HaloTag7-based chromatin affinity purification system as an alternative method to ChIP for isolating unknown centromeric DNA sequences. The discovery of more than two chromosome-specific centromeric DNA sequences indicates the mosaic structure of tobacco centromeres. PMID:22147136

Nagaki, Kiyotaka; Shibata, Fukashi; Kanatani, Asaka; Kashihara, Kazunari; Murata, Minoru

2012-04-01

38

PCR-based cloning of the full-length Neurospora eukaryotic initiation factor 5A cDNA: polyhistidine-tagging and overexpression for protein affinity binding.  

PubMed

Eukaryotic initiation factor 5A (eIF-5A) is the only cellular protein known to contain a hypusine residue that is formed by transferring the aminobutyl moiety from spermidine to a specific lysine residue, followed by hydroxylation at the aminobutyl group. A simple PCR-based strategy was developed to obtain a full-length cDNA of Neurospora crassa eIF-5A. The strategy consists of (i) the design of a pair of key primers (21-mer) based on the highly conserved eIF-5A cDNA domains known in other species, (ii) PCR amplification of Neurospora cDNA using the two key primers to obtain the core sequence for the design of core primers, and (iii) combined use of the key primers, core primers and the universal primers, T3 and T7, to amplify the target sequence in a Neurospora cDNA library. The longest cDNA obtained was cloned into pBlueScript phagemid, and sequence analysis indicated that it encodes a polypeptide of 163 amino acid residues with a codon usage preference characteristic of abundant Neurospora genes. The Neurospora polypeptide showed 59% and 67% identity with human and yeast eIF-5A precursor protein respectively. We subcloned the Neurospora eIF-5A cDNA into pQE-30, which introduces six adjacent histidine residues to the N-terminus of the recombinant protein. The resulting plasmid, pQTy21, was overexpressed in Escherichia coli, and the soluble polyhistidine-tagged protein was purified by metal chelation chromatography. We obtained about 60 mg of purified eIF-5A precursor from 1 litre of culture in a single step using a Ni(II)-nitrilotriacetic acid (NTA)-agarose column. The histidine-tagged eIF-5A precursor protein could be recognized by anti-Neurospora crassa 21 kDa protein serum raised against wild-type eIF-5A precursor and could serve as the substrate protein for deoxyhypusine synthase. Using the histidine-tagged recombinant protein and the Ni(II)-NTA-agarose column, we constructed a protein affinity column and demonstrated an affinity binding between eIF-5A precursor and deoxyhypusine synthase in the presence of NAD+. One-step eIF-5A precursor affinity-column chromatography could lead to a 30-fold purification of deoxyhypusine synthase. PMID:8093005

Tao, Y; Chen, K Y

1994-09-01

39

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, Víctor; Sanz, Jesús M.

2014-01-01

40

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

41

Isotope Coded Protein Labeling Coupled Immunoprecipitation (ICPL-IP): A Novel Approach for Quantitative Protein Complex Analysis From Native Tissue*  

PubMed Central

High confidence definition of protein interactions is an important objective toward the understanding of biological systems. Isotope labeling in combination with affinity-based isolation of protein complexes has increased in accuracy and reproducibility, yet, larger organisms—including humans—are hardly accessible to metabolic labeling and thus, a major limitation has been its restriction to small animals, cell lines, and yeast. As composition as well as the stoichiometry of protein complexes can significantly differ in primary tissues, there is a great demand for methods capable to combine the selectivity of affinity-based isolation as well as the accuracy and reproducibility of isotope-based labeling with its application toward analysis of protein interactions from intact tissue. Toward this goal, we combined isotope coded protein labeling (ICPL)1 with immunoprecipitation (IP) and quantitative mass spectrometry (MS). ICPL-IP allows sensitive and accurate analysis of protein interactions from primary tissue. We applied ICPL-IP to immuno-isolate protein complexes from bovine retinal tissue. Protein complexes of immunoprecipitated ?-tubulin, a highly abundant protein with known interactors as well as the lowly expressed small GTPase RhoA were analyzed. The results of both analyses demonstrate sensitive and selective identification of known as well as new protein interactions by our method. PMID:23268931

Vogt, Andreas; Fuerholzner, Bettina; Kinkl, Norbert; Boldt, Karsten; Ueffing, Marius

2013-01-01

42

Expression of the functional mature chloroplast triose phosphate translocator in yeast internal membranes and purification of the histidine-tagged protein by a single metal-affinity chromatography step.  

PubMed Central

The mature part of the chloroplast triose phosphate-phosphate translocator was cloned into the yeast expression vector pEVP11. This construct was used to transform cells from both Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. The chloroplast translocator protein was functionally expressed in the transformed yeast cells and represented about 1-2% of the Sch. pombe cell membrane protein. It was localized to mitochondrial membranes and/or membranes of the rough endoplasmic reticulum. In order to purify the recombinant translocator protein, a sequence encoding a C-terminal tag of six histidine residues was introduced into the corresponding cDNA. The expressed histidine-tagged translocator protein was purified from the transformed yeast cells under nondenaturing conditions to apparent homogeneity by a single-step affinity chromatography using a Ni2+. nitrilotriacetic acid resin. Both the expressed triose phosphate translocator and the recombinant histidine-tagged protein possess substrate specificities identical to those of the authentic chloroplast protein, providing definitive evidence for its identity as the triose phosphate translocator and further disproving its assignment as the receptor for chloroplast protein import. The yeast expression system in combination with the Ni2+. nitrilotriacetic acid chromatography thus provides a valuable tool for the production of purified membrane proteins in a functional state. Images Fig. 1 Fig. 4 PMID:11607374

Loddenkötter, B; Kammerer, B; Fischer, K; Flügge, U I

1993-01-01

43

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

44

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

45

Automated solid-phase synthesis of high capacity oligo-dT cellulose for affinity purification of poly-A tagged biomolecules.  

PubMed

Affinity purification of poly-adenylated biomolecules using solid supports that are derivatized with poly-thymidine oligonucleotides provides a powerful method for isolating cellular mRNA. These systems have also been used to purify mRNA-peptide fusions generated by RNA-display. However, the commercial source for high capacity oligo-dT cellulose was recently discontinued. To overcome this problem, we have developed a low cost solid-phase synthesis protocol to generate oligo-dT cellulose. Comparative binding studies indicate that chemically synthesized oligo-dT cellulose functions with superior loading capacity when compared to the discontinued product. We suggest that this method could be used to synthesize oligo-dT resin for routine purification of poly-adenylated biomolecules. PMID:25467163

Sau, Sujay P; Larsen, Andrew C; Chaput, John C

2014-12-15

46

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

PubMed

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

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

2015-01-01

47

Tagging Walruses  

USGS Multimedia Gallery

A transmitter tag (left) is being deployed by a USGS Wildlife Biologist (far right). Transmitter tags are deployed on the back of walruses where their skin is thickest and where their data transmissions may be received from passing satellites. Tag deployment happens in the blink of an eye with the ...

48

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

49

Affinity Chromatography  

NSDL National Science Digital Library

Using exposition, graphics, and commercial videos, this module teaches the theory and application of affinity chromatography in the characterization of proteins, nucleic acids, and other biochemical/biomedical systems. Problems and application examples support the tutorial material.

50

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

51

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

52

Deciphering systemic wound responses of the pumpkin extrafascicular phloem by metabolomics and stable isotope-coded protein labeling.  

PubMed

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, Jörg

2012-12-01

53

New cobalt resin for optimal purification of His-tagged proteins  

Microsoft Academic Search

The expression and purification of recombinant proteins is central to protein regulation, structure and function studies. The majority of recombinant proteins are expressed as fusions with short affinity tags, the most popular being the polyhistidine (6xHis) tag. The method used to purify these recombinant His-tagged proteins is immobilized metal affinity chromatography (IMAC) consisting of chelating resins charged with either nickel

Michael Major; Marty Wilkes; Martin Bremmer; Navid Haghdoost; Barbara Kaboord; Thermo Fisher

54

The utility of isotope-coded protein labeling for prioritization of proteins found in ovarian cancer patient urine.  

PubMed

Urine offers a number of attractive features as a sample type for biomarker discovery, including noninvasive sampling, quantity and availability, stability, and a narrow dynamic range. In this study we report the first application of isotope coded protein labeling (ICPL), coupled with in-solution isoelectric fractionation and LC-MALDI-TOF/TOF, to examine and prioritize urinary proteins from ovarian cancer patients. Following the definition of stringent exclusion criteria a total of 579 proteins were identified with 43% providing quantitation data. Protein abundance changes were validated for selected proteins by ESI-Qq-TOF MS, following which Western blot and immunohistochemical analysis by tissue microarray was used to explore the biological relevance of the proteins identified. Several established markers (e.g., HE4, osteopontin) were identified at increased levels in ovarian cancer patient urine, validating the approach used; we also identified a number of potential marker candidates (e.g., phosphatidylethanolamine binding protein 1, cell-adhesion molecule 1) previously unreported in the context of ovarian cancer. We conclude that the ICPL strategy for identification and relative quantitation of urine proteins is an appropriate tool for biomarker discovery studies, and can be applied for the selection of potential biomarker candidates for further characterization. PMID:23952987

Rainczuk, Adam; Condina, Mark; Pelzing, Matthias; Dolman, Sebastiaan; Rao, Jyothsna; Fairweather, Nicole; Jobling, Tom; Stephens, Andrew N

2013-09-01

55

Isotopically-coded short-range hetero-bifunctional photo-reactive crosslinkers for studying protein structure.  

PubMed

The resolution and the fidelity of a protein structural model, constructed using crosslinking data, is dependent on the crosslinking distance constraints. Most of the popular amine-reactive NHS-ester crosslinkers are limited in their capacity to provide short distance constraints because of the rarity of lysine residues occurring in close proximity in the protein structure. To solve this problem, hetero-bifunctional crosslinkers containing both a photo-reactive functional group and an NHS-ester group can be used to enable non-specific crosslinking within the proximity of these lysine residues. Here we develop three such isotopically-coded hetero-bifunctional photo-reactive crosslinkers, bearing azido, diazirine or benzophenone photo-reactive groups (azido-benzoic-acid-succinimide (ABAS)-(12)C6/(13)C6, succinimidyl-diazirine (SDA)-(12)C5/(13)C5, and carboxy-benzophenone-succinimide (CBS)-(12)C6/(13)C6, respectively). These crosslinkers were validated using several model proteins/peptides and were then applied to study the structure of the native ?-synuclein protein. In that case the ABAS crosslinker proved to be the most suitable, with 10 crosslinks being found in the native ?-synuclein structure. PMID:25192908

Brodie, Nicholas I; Makepeace, Karl A T; Petrotchenko, Evgeniy V; Borchers, Christoph H

2014-09-01

56

DXMSMS Match Program for Automated Analysis of LC-MS/MS Data Obtained Using Isotopically Coded CID-Cleavable Cross-Linking Reagents.  

PubMed

Cross-linking combined with mass spectrometry for the study of proteins and protein complexes is greatly facilitated by the use of isotopically coded cleavable cross-linking reagents. The isotopic coding of the cross-linker enables confident detection of the cross-link signals, while cleavage of the cross-linker provides masses of the individual peptides composing the cross-link and, therefore, facilitates unambiguous assignment of the cross-links. Here, we describe the DXMSMS Match program, designed for automatic analysis of LC-MS/MS mass spectrometric data obtained with isotopically coded CID-cleavable cross-linkers. The program verifies the assignments of the cross-links by precursor mass and by inspection of the MS/MS spectra for the fragments and the cleavage products of the cross-linked peptides. The program produces nonprobabilistic scores for matching the spectra to the theoretical fragmentation of the cross-links and a visual interface for the validation of the mass spectral matches. © 2014 by John Wiley & Sons, Inc. PMID:25501944

Petrotchenko, Evgeniy V; Makepeace, Karl A T; Borchers, Christoph H

2014-01-01

57

DESIGN, SYNTHESIS, AND APPLICATION OF THE TRIMETHOPRIM-BASED CHEMICAL TAG FOR LIVE CELL IMAGING  

PubMed Central

Over the past decade chemical tags have been developed to complement the use of fluorescent proteins in live cell imaging. Chemical tags retain the specificity of protein labeling achieved with fluorescent proteins through genetic encoding, but provide smaller, more robust tags and modular use of organic fluorophores with high photon-output and tailored functionalities. The trimethoprim-based chemical tag (TMP-tag) was initially developed based on the high affinity interaction between E.coli dihydrofolatereductase and the antibiotic trimethoprim and subsequently rendered covalent and fluorogenic via proximity-induced protein labeling reactions. To date, the TMP-tag is one of the few chemical tags that enable intracellular protein labeling and high-resolution live cell imaging. Here we describe the general design, chemical synthesis, and application of TMP-tag for live cell imaging. Alternative protocols for synthesizing and using the covalent and the fluorogenic TMP-tags are also included. PMID:23839994

Jing, Chaoran; Cornish, Virginia W.

2013-01-01

58

Donor Tag Game  

MedlinePLUS

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

59

Hierarchical Tag Visualization and Application for Tag Recommendations  

E-print Network

One Microsoft Way Redmond, WA 98052, USA yangsong@microsoft.com Baojun Qiu Computer Science sites typically visualize user-generated tags as tag clouds. While tag clouds effectively show the rel) the similarity between tags, and (2) the abstractness of tags. We suggest an alternative to tag clouds known

60

Cutaneous skin tag  

MedlinePLUS

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

61

Extracting tag hierarchies.  

PubMed

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

Tibély, Gergely; Pollner, Péter; Vicsek, Tamás; Palla, Gergely

2013-01-01

62

A peptide tag system for facile purification and single-molecule immobilization.  

PubMed

A peptide fusion tag and accompanying recombinant capture reagents have been developed on the basis of the peptide-PDZ domain interaction and affinity clamps, a new class of affinity reagent. This system allows for single-step purification under mild conditions and stable capture of a tagged protein. The subnanomolar affinity, high force resistance (>30 pN), small size ( approximately 25 kDa, approximately one-sixth of the size of IgG), and monomeric nature of the affinity clamp are all superior features for many applications, in particular single-molecule measurements. PMID:19928925

Huang, Jin; Nagy, Stanislav S; Koide, Akiko; Rock, Ronald S; Koide, Shohei

2009-12-22

63

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

PubMed

We introduce a new method for purifying recombinant proteins expressed in bacteria using a highly specific, inducible, self-cleaving protease tag. This tag is comprised of the Vibrio cholerae MARTX toxin cysteine protease domain (CPD), an autoprocessing enzyme that cleaves exclusively after a leucine residue within the target protein-CPD junction. Importantly, V. cholerae CPD is specifically activated by inositol hexakisphosphate (InsP(6)), a eukaryotic-specific small molecule that is absent from the bacterial cytosol. As a result, when His(6)-tagged CPD is fused to the C-terminus of target proteins and expressed in Escherichia coli, the full-length fusion protein can be purified from bacterial lysates using metal ion affinity chromatography. Subsequent addition of InsP(6) to the immobilized fusion protein induces CPD-mediated cleavage at the target protein-CPD junction, releasing untagged target protein into the supernatant. This method condenses affinity chromatography and fusion tag cleavage into a single step, obviating the need for exogenous protease addition to remove the fusion tag(s) and increasing the efficiency of tag separation. Furthermore, in addition to being timesaving, versatile, and inexpensive, our results indicate that the CPD purification system can enhance the expression, integrity, and solubility of intractable proteins from diverse organisms. PMID:19956581

Shen, Aimee; Lupardus, Patrick J; Morell, Montse; Ponder, Elizabeth L; Sadaghiani, A Masoud; Garcia, K Christopher; Bogyo, Matthew

2009-01-01

64

Protein-protein interactions of TAP-tagged protein kinases in rice  

Technology Transfer Automated Retrieval System (TEKTRAN)

Eighty-eight rice (Oryza sativa) cDNAs encoding leaf expressed protein kinases (RLePKs) were fused to a Tandem Affinity Purification tag (TAPtag) and expressed in transgenic rice plants. The TAP-tagged RLePKs and interacting proteins were purified from the T1 progeny of the transgenic rice plants a...

65

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

66

Passive optoelectronic tag  

NASA Astrophysics Data System (ADS)

In response to a pressing demand for tagging systems and technologies developing, Physical Optics Corporation (POC) proposes a novel Passive Optoelectronical (POET) Tag system. The POET tag is an omnidirectional (360° in azimuth), with up to 180° field-of-view in elevation, retroreflection optical system with a high frequency multiple quantum well (MQW) light intensity modulator for free space IR optical communication. The POET tag optical scheme is a compact, high quality generalized fish-eye lens with telecentric arrangement in image space. The telecentric arrangement in image space provides perfect omnidirectional retroreflection of a recall beam and an optimum divergent of light at the MQW providing maximum modulation contrast ratios. The important POET tag features are low power consumption, zero probability of jamming and intercepting (high security of communication,) because it operates in a passive retroreflection mode with a highly-directed optical beam.

Agurok, Il'ya P.; Jannson, Tomasz P.; Savant, Gajendra D.

2003-09-01

67

Affine and degenerate affine BMW algebras: Actions on tensor space  

E-print Network

Affine and degenerate affine BMW algebras: Actions on tensor space Zajj Daugherty Department Actions of classical type tantalizers 8 2.1 The degenerate affine BMW algebra action . . . . . . . . . . . . . . . . . . . . . 13 2.2 The affine BMW algebra action . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16 3

Ram, Arun

68

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, Jörg

2012-01-01

69

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.

2012-06-26

70

Facets: Ersatz, Resource and Tag  

ERIC Educational Resources Information Center

Introduction: Faceted classification appears to be of utmost importance. Ersatz facets, resource faceting and tag faceting: The distinctions are drawn between facets and ersatz facets, and between faceted resources and faceted tags. Single tag resource faceting and multiple tag information object faceting: The basic features are explored of single…

Frické, Martin H.

2013-01-01

71

Affine Defects and Gravitation  

E-print Network

We argue that the structure general relativity (GR) as a theory of affine defects is deeper than the standard interpretation as a metric theory of gravitation. Einstein-Cartan theory (EC), with its inhomogenous affine symmetry, should be the standard-bearer for GR-like theories. A discrete affine interpretation of EC (and gauge theory) yields topological definitions of momentum and spin (and Yang Mills current), and their conservation laws become discrete topological identities. Considerations from quantum theory provide evidence that discrete affine defects are the physical foundation for gravitation.

Petti, R J

2014-01-01

72

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

73

Discourse Tagging Tool and Discourse-Tagged Multilingual Corpora  

Microsoft Academic Search

As a part of our on-going research on multilingual anaphora resolution (cf. Aone and McKee [3],Aone [1]), we have built a graphical tool to tag texts with antecedent-anaphor relations and havecreated corpora tagged with such relations. The tool, called the Discourse Tagging Tool (DTTool),has been used to manually tag Japanese, Spanish and English texts with anaphora, their types (suchas pronouns

Chinatsu Aone; Scott W. Bennett

1994-01-01

74

Ontologies and tag-statistics  

NASA Astrophysics Data System (ADS)

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

Tibély, Gergely; Pollner, Péter; Vicsek, Tamás; Palla, Gergely

2012-05-01

75

On the Selection of Tags for Tag Clouds Petros Venetis  

E-print Network

On the Selection of Tags for Tag Clouds Petros Venetis Computer Science Dept. Stanford University-Molina Computer Science Dept. Stanford University hector@cs.stanford.edu ABSTRACT We examine the creation of a tag cloud for exploring and under- standing a set of objects (e.g., web pages, documents). In the first part

Chang, Edward Y.

76

Collaborative Tagging as Information Foraging  

Microsoft Academic Search

Collaborative tagging has become a very popular feature on many websites, such as Flickr and Del.icio.us. Tag collections are known to display strong regularities such as power-law distributions. The term \\

Samarth Swarup

2008-01-01

77

Prairie Dog Tagging  

USGS Multimedia Gallery

An anaesthetized prairie dog is tagged in Wind Cave National Park.  Over 30 organizations and agencies are testing a USGS-developed oral vaccine to prevent the spread of plague in prairie dogs. If successful, the sylvatic plague vaccine could help protect endangered black-f...

78

Project 8 Tags  

ERIC Educational Resources Information Center

In this article, the author describes 8 Tags, a project that she used with her eighth-grade studio art students to encourage them to come up with original and creative solutions to an assignment. She also wanted to incorporate their knowledge of the elements of art and principles of design. In this project, students were challenged to create an…

Ramos-Burrows, Michele

2010-01-01

79

Towards Social Semantic Suggestive Tagging  

Microsoft Academic Search

The organization of the knowledge on the web is increasingly becoming a social task performed by online communities whose members share a common interest in classifying different types of information for a later retrieval. Collaborative tagging systems allow people to organize a set of resources of interest through unconstrained annotations based on free keywords commonly named tags. Suggestive tagging techniques

Fabio Calefato; Domenico Gendarmi; Filippo Lanubile

2007-01-01

80

Semiotic Dynamics and Collaborative Tagging  

Microsoft Academic Search

Collaborative tagging has been quickly gaining ground because of its ability to recruit the activity of web users into effectively organizing and sharing vast amounts of information. Here we collect data from a popular system and investigate the statistical properties of tag cooccurrence. We introduce a stochastic model of user behavior embodying two main aspects of collaborative tagging: (i) a

Ciro Cattuto; Vittorio Loreto; Luciano Pietronero

2007-01-01

81

Quantitative isomer-specific N-glycan fingerprinting using isotope coded labeling and high performance liquid chromatography-electrospray ionization-mass spectrometry with graphitic carbon stationary phase.  

PubMed

Glycan reductive isotope labeling (GRIL) using (12)C6-/(13)C6-aniline as labeling reagent is reported with the aim of quantitative N-glycan fingerprinting. Porous graphitized carbon (PGC) as stationary phase in capillary scale HPLC coupled to electrospray mass spectrometry with time of flight analyzer was applied for the determination of labeled N-glycans released from glycoproteins. The main benefit of using stable isotope-coding in the context of comparative glycomics lies in the improved accuracy and precision of the quantitative analysis in combined samples and in the potential of correcting for structure-dependent incomplete enzymatic release of oligosaccharides when comparing identical target proteins. The method was validated with respect to mobile phase parameters, reproducibility, accuracy, linearity and limit of detection/quantification (LOD/LOQ) using test glycoproteins. It is shown that the developed method is capable of determining relative amounts of N-glycans (including isomers) comparing two samples in one single HPLC-MS run. The analytical potential and usefulness of GRIL in combination with PGC-ESI-TOF-MS is demonstrated comparing glycosylation in human monoclonal antibodies produced in Chinese hamster ovary cells (CHO) and hybridoma cell lines. PMID:25638265

Michael, Claudia; Rizzi, Andreas M

2015-02-27

82

Separation and detection of large phosphoproteins using Phos-tag SDS-PAGE  

Microsoft Academic Search

We provide a standard phosphate-affinity SDS-PAGE (Mn2+–Phos-tag SDS-PAGE) protocol, in which Phos-tag is used to analyze large phosphoproteins with molecular masses of more than 200 kDa. A previous protocol required a long electrophoresis time of 12 h for separation of phosphoisotypes of large proteins (?150 kDa). This protocol, which uses a 3% (wt\\/vol) polyacrylamide gel strengthened with 0.5% (wt\\/vol) agarose,

Emiko Kinoshita-Kikuta; Tohru Koike

2009-01-01

83

Affine and degenerate affine BMW algebras: Actions on tensor space  

E-print Network

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

Daugherty, Zajj; Virk, Rahbar

2012-01-01

84

TagMyDoc  

NSDL National Science Digital Library

Do you need to share documents quickly with a number of different users? You may want to give TagMyDoc a look. Visitors can choose their documents, and upload them so they can be scanned and retrieved as virtual copies. Additionally, users can sign up for free accounts for enhanced functionality and there's an explanatory video here as well. This version is compatible with all operating systems.

2012-01-01

85

Fast and Complete Unknown Tag Identification in Large  

E-print Network

tags in large RFID systems Unknown tag Known tag Reader #12;7 Motivation A continuous scanning scheme singleton expected collision known tags unknown tags #12;12 BUIP: Basic Unknown tag Identification Protocol expected collision known tags unknown tags #12;13 Known Tag Acknowledgment Not all known tags can

Xiao, Bin

86

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

87

A Highly Efficient Multifunctional Tandem Affinity Purification Approach Applicable to Diverse Organisms*  

PubMed Central

Determining the localization, binding partners, and secondary modifications of individual proteins is crucial for understanding protein function. Several tags have been constructed for protein localization or purification under either native or denaturing conditions, but few tags permit all three simultaneously. Here, we describe a multifunctional tandem affinity purification (MAP) method that is both highly efficient and enables protein visualization. The MAP tag utilizes affinity tags inserted into an exposed surface loop of mVenus offering two advantages: (1) mVenus fluorescence can be used for protein localization or FACS-based selection of cell lines; and (2) spatial separation of the affinity tags from the protein results in high recovery and reduced variability between proteins. MAP purification was highly efficient in multiple organisms for all proteins tested. As a test case, MAP combined with liquid chromatography-tandem MS identified known and new candidate binding partners and modifications of the kinase Plk1. Thus the MAP tag is a new powerful tool for determining protein modification, localization, and interactions. PMID:22474084

Ma, Hanhui; McLean, Janel R.; Chao, Lucy Fang-I; Mana-Capelli, Sebastian; Paramasivam, Murugan; Hagstrom, Kirsten A.; Gould, Kathleen L.; McCollum, Dannel

2012-01-01

88

Fluorescence: Molecular Tagging  

NSDL National Science Digital Library

In this activity, by the Concord Consortium's Molecular Literacy project, students will be introduced to the concept of fluorescence and how this method allows scientists to better analyze objects at a molecular level. The site is interactive and allows students to interact with virtual cells and tag them just as a scientist would. The focus of the topic can be applied to many different fields, such as: mineralogy, biochemistry, medicine, forensics and biotechnology. The activity itself is a java-based interactive resource built upon the free, open source Molecular Workbench software. In addition, visitors will find an overview of the activity, assessments, and concepts and their correlation to AAAS and NSES standards.

2008-10-17

89

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

NASA Astrophysics Data System (ADS)

Li and Zhang (2014) studied affine hypersurfaces of R n + 1 with parallel difference tensor relative to the affine ?-connection ? (?), and characterized the generalized Cayley hypersurfaces by K n - 1 ? 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

90

Analysis of tag within online social networks  

Microsoft Academic Search

In recent years, tagging systems have been paid increasing attentions from both research communities and system designers. Most popular online social networking sites harness tag for managing and locating contents, for organizing and connecting users, and for recommending and sharing resources. We believe that tag acts like bridge between people and resources. Research on tag and tagging behavior will provide

Chao Wu; Bo Zhou

2009-01-01

91

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, Hélène 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

92

Affine Structure and Photometry  

Microsoft Academic Search

Motion of an observer relative to objects in a scene provides information about the structure of the scene. Changing patterns of shading due to motion relative to the light source provide information about surface structure, albedos, and light sources. One can stratify this photometric information into affine, unitary, and metric structure, much like the stratification of structure from motion. For

Ruth Rosenholtz; Jan J. Koenderink

1996-01-01

93

Free-tagging methods for opinion analysis of online news comments  

Microsoft Academic Search

To overcome challenges of processing timeliness and changeful topics when analyzing opinions of online news comments, free-tagging methods including two steps, object identification and polarity analysis, are proposed in this paper. In the first step, from news text, we employ the Affinity Propagation Cluster (APC) to extract key sentences whose name entities will be identified and their specified types will

Changwei Zhao; Heng Liu; Qinke Peng; Ying Yang

2010-01-01

94

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

95

Affine and degenerate affine BMW algebras: The center  

E-print Network

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

Daugherty, Zajj; Virk, Rahbar

2011-01-01

96

Genetic tagging of humpback whales  

Microsoft Academic Search

The ability to recognize individual animals has substantially increased our knowledge of the biology and behaviour of many taxa. However, not all species lend themselves to this approach, either because of insufficient phenotypic variation or because tag attachment is not feasible. The use of genetic markers (`tags') represents a viable alternative to traditional methods of individual recognition, as they are

Per J. Palsbøll; Judith Allen; Martine Bérubé; Phillip J. Clapham; Tonnie P. Feddersen; Philip S. Hammond; Richard R. Hudson; Hanne Jørgensen; Steve Katona; Anja Holm Larsen; Jon Lien; David K. Mattila; Jóhann Sigurjónsson; Richard Sears; Tim Smith; Renate Sponer; Peter Stevick; Nils Øien

1997-01-01

97

Fish Tagging Forum Meeting Notes  

E-print Network

Attendees: see list on the Fish Tagging Forum website http://www.nwcouncil.org/fw/tag/ Introductions fashion but may expand in future; and `f' for it may be used in the future. Nancy went over the major, "future use" means 1-5 years into the future. Also, the group agreed to add "adult reach survival

98

Semiotic dynamics and collaborative tagging  

PubMed Central

Collaborative tagging has been quickly gaining ground because of its ability to recruit the activity of web users into effectively organizing and sharing vast amounts of information. Here we collect data from a popular system and investigate the statistical properties of tag cooccurrence. We introduce a stochastic model of user behavior embodying two main aspects of collaborative tagging: (i) a frequency-bias mechanism related to the idea that users are exposed to each other's tagging activity; (ii) a notion of memory, or aging of resources, in the form of a heavy-tailed access to the past state of the system. Remarkably, our simple modeling is able to account quantitatively for the observed experimental features with a surprisingly high accuracy. This points in the direction of a universal behavior of users who, despite the complexity of their own cognitive processes and the uncoordinated and selfish nature of their tagging activity, appear to follow simple activity patterns. PMID:17244704

Cattuto, Ciro; Loreto, Vittorio; Pietronero, Luciano

2007-01-01

99

LHCb Tag Collector  

NASA Astrophysics Data System (ADS)

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

Fuente Fernández, Paloma; Clemencic, Marco; Cousin, Nicolas; LHCb Collaboration

2011-12-01

100

Expression of a translationally fused TAP-tagged plasma membrane proton pump in Arabidopsis thaliana.  

PubMed

The Arabidopsis thaliana plasma membrane proton ATPase genes, AHA1 and AHA2, are the two most highly expressed isoforms of an 11 gene family and are collectively essential for embryo development. We report the translational fusion of a tandem affinity-purification tag to the 5' end of the AHA1 open reading frame in a genomic clone. Stable expression of TAP-tagged AHA1 in Arabidopsis rescues the embryonic lethal phenotype of endogenous double aha1/aha2 knockdowns. Western blots of SDS-PAGE and Blue Native gels show enrichment of AHA1 in plasma membrane fractions and indicate a hexameric quaternary structure. TAP-tagged AHA1 rescue lines exhibited reduced vertical root growth. Analysis of the plasma membrane and soluble proteomes identified several plasma membrane-localized proteins with alterred abundance in TAP-tagged AHA1 rescue lines compared to wild type. Using affinity-purification mass spectrometry, we uniquely identified two additional AHA isoforms, AHA9 and AHA11, which copurified with TAP-tagged AHA1. In conclusion, we have generated transgenic Arabidopsis lines in which a TAP-tagged AHA1 transgene has complemented all essential endogenous AHA1 and AHA2 functions and have shown that these plants can be used to purify AHA1 protein and to identify in planta interacting proteins by mass spectrometry. PMID:24397334

Rodrigues, Rachel B; Sabat, Gregorz; Minkoff, Benjamin B; Burch, Heather L; Nguyen, Thao T; Sussman, Michael R

2014-01-28

101

Expression of a Translationally Fused TAP-Tagged Plasma Membrane Proton Pump in Arabidopsis thaliana  

PubMed Central

The Arabidopsis thaliana plasma membrane proton ATPase genes, AHA1 and AHA2, are the two most highly expressed isoforms of an 11 gene family and are collectively essential for embryo development. We report the translational fusion of a tandem affinity-purification tag to the 5? end of the AHA1 open reading frame in a genomic clone. Stable expression of TAP-tagged AHA1 in Arabidopsis rescues the embryonic lethal phenotype of endogenous double aha1/aha2 knockdowns. Western blots of SDS-PAGE and Blue Native gels show enrichment of AHA1 in plasma membrane fractions and indicate a hexameric quaternary structure. TAP-tagged AHA1 rescue lines exhibited reduced vertical root growth. Analysis of the plasma membrane and soluble proteomes identified several plasma membrane-localized proteins with alterred abundance in TAP-tagged AHA1 rescue lines compared to wild type. Using affinity-purification mass spectrometry, we uniquely identified two additional AHA isoforms, AHA9 and AHA11, which copurified with TAP-tagged AHA1. In conclusion, we have generated transgenic Arabidopsis lines in which a TAP-tagged AHA1 transgene has complemented all essential endogenous AHA1 and AHA2 functions and have shown that these plants can be used to purify AHA1 protein and to identify in planta interacting proteins by mass spectrometry. PMID:24397334

2015-01-01

102

Affinity driven social networks  

NASA Astrophysics Data System (ADS)

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

Ruyú, B.; Kuperman, M. N.

2007-04-01

103

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

104

Tunable Charge Tags for Electron-Based Methods of Peptide Sequencing: Design and Applications  

NASA Astrophysics Data System (ADS)

Charge tags using basic auxiliary functional groups 6-aminoquinolinylcarboxamido, 4-aminopyrimidyl-1-methylcarboxamido, 2-aminobenzoimidazolyl-1-methylcarboxamido, and the fixed-charge 4-(dimethylamino)pyridyl-1-carboxamido moiety are evaluated as to their properties in electron transfer dissociation mass spectra of arginine C-terminated peptides. The neutral tags have proton affinities that are competitive with those of amino acid residues in peptides. Charge reduction by electron transfer from fluoranthene anion-radicals results in peptide backbone dissociations that improve sequence coverage by providing extensive series of N-terminal c-type fragments without impeding the formation of C-terminal z fragments. Comparison of ETD mass spectra of free and tagged peptides allows one to resolve ambiguities in fragment ion assignment through mass shifts of c ions. Simple chemical procedures are reported for N-terminal tagging of Arg-containing tryptic peptides.

Zimnicka, Magdalena; Moss, Christopher L.; Chung, Thomas W.; Hui, Renjie; Ture?ek, František

2012-04-01

105

Cost-effective isobaric tagging for quantitative phosphoproteomics using DiART reagents.  

PubMed

We describe the use of an isobaric tagging reagent, Deuterium isobaric Amine Reactive Tag (DiART), for quantitative phosphoproteomic experiments. Using DiART tagged custom mixtures of two phosphorylated peptides from alpha casein and their non-phosphorylated counterparts, we demonstrate the compatibility of DiART with TiO2 affinity purification of phosphorylated peptides. Comparison of theoretical vs. experimental reporter ion ratios reveals accurate quantification of phosphorylated peptides over a dynamic range of more than 15-fold. Using DiART labelling and TiO2 enrichment (DiART-TiO2) with large quantities of proteins (8 mg) from the cell lysate of model fungus Aspergillus nidulans, we quantified 744 unique phosphopeptides. Overlap of median values of TiO2 enriched phosphopeptides with theoretical values indicates accurate trends. Altogether these findings confirm the feasibility of performing quantitative phosphoproteomic experiments in a cost-effective manner using isobaric tagging reagents, DiART. PMID:24129742

Ramsubramaniam, Nikhil; Tao, Feng; Li, Shuwei; Marten, Mark R

2013-12-01

106

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

107

Tagging insulin in microgravity  

NASA Technical Reports Server (NTRS)

Knowing the exact subcellular sites of action of insulin in the body has the potential to give basic science investigators a basis from which a cause and cure for this disease can be approached. The goal of this project is to create a test reagent that can be used to visualize these subcellular sites. The unique microgravity environment of the Shuttle will allow the creation of a reagent that has the possibility of elucidating the subcellular sites of action of insulin. Several techniques have been used in an attempt to isolate the sites of action of items such as insulin. One of these is autoradiography in which the test item is obtained from animals fed radioactive materials. What is clearly needed is to visualize individual insulin molecules at their sites of action. The insulin tagging process to be used on G-399 involves the conjugation of insulin molecules with ferritin molecules to create a reagent that will be used back on Earth in an attempt to elucidate the sites of action of insulin.

Dobeck, Michael; Nelson, Ronald S.

1992-01-01

108

Collaborative Tagging and Semiotic Dynamics  

Microsoft Academic Search

Collaborative tagging has been quickly gaining ground because of its ability\\u000ato recruit the activity of web users into effectively organizing and sharing\\u000avast amounts of information. Here we collect data from a popular system and\\u000ainvestigate the statistical properties of tag co-occurrence. We introduce a\\u000astochastic model of user behavior embodying two main aspects of collaborative\\u000atagging: (i) a

Ciro Cattuto; Vittorio Loreto; Luciano Pietronero

2006-01-01

109

Compiled April 2010 Clam Bag Identification Tags  

E-print Network

Compiled April 2010 Clam Bag Identification Tags PermaTag Aluminum tags, 1" x 3-1/2". Write or emboss on one side. To attach, bend attached strip around, insert in hole and crimp. Box of 500. Price: $26.95 per box, $22.75 for 5+ boxes Comments: Inexpensive but may not be very durable. Aluminum Tags

Florida, University of

110

Herpetological PIT Tag Migration in Seaturtle Flippers  

E-print Network

is common and decreases the rate at which previously tagged indi- viduals are identified (Balazs 1982 Integrated Transponder (PIT) tags, also termed Radio Frequency Identification tags, has increased (Balazs and increase the reliability of re-identifying tagged animals (Balazs 1999; Braun-McNeill et al. 2003; Dutton

Wyneken, Wyneken Jeanette

111

BPA Tagging Cost Estimates Tag Types Funded in FY 12 By BPA  

E-print Network

BPA Tagging Cost Estimates FY 2012 #12;Tag Types Funded in FY 12 By BPA · Coded wire tags · PIT, and data analysis. #12;Task # Projects Annually* FY 12 Estimated Cost** Contractors Species Tag Insertion Tasks and Costs Task # Projects Annually FY 12 Estimated Cost* Contractors Species Tag Insertion 69 $9

112

Scalable Grouping-proof Protocol for RFID Tags Grouping-Proof Protocol for RFID Tags  

E-print Network

Scalable Grouping-proof Protocol for RFID Tags Grouping-Proof Protocol for RFID Tags: Security-proof protocol for RFID tags based on secret sharing. Our proposed protocol addresses the scalability issue of the previous protocols by removing the need for an RFID reader to relay messages from one tag to another tag

113

Biotin tagging coupled with amino acid-coded mass tagging (BioCAT) for efficient and precise screening of interaction proteome in mammalian cells  

PubMed Central

In mammalian cells, when tandem affinity purification (TAP) approach is employed, the existence of untagged endogenous target protein and repetitive washing steps together result in overall low yield of purified/stable complexes and the loss of weakly and transiently interacting partners of biological significance. To avoid the trade-offs involving in methodological sensitivity, precision, and throughput here we introduce an integrated method, biotin tagging coupled with amino acid-coded mass tagging (BioCAT) for highly sensitive and accurate screening of mammalian protein-protein interactions (PPIs). Without the need of establishing a stable cell line, using a short peptide tag which could be specifically biotinylated in vivo, the biotin-tagged target/bait protein was then isolated along with its associates efficiently by streptavidin magnetic microbeads in a single step. In a pulled-down complex amino acid-coded mass tagging (AACT) serves as ‘in-spectra’ quantitative markers to distinguish those bait-specific interactors from non-specific background proteins under stringent criteria. Applying this BioCAT approach, we first biotin-tagged in vivo a multi-functional protein family member, 14-3-3?, which was expressed at close to endogenous level. Starting with approximately 20 millions of 293T cells which were significantly less than what needed for a TAP run, 266 specific interactors of 14-3-3? were identified in high confidence. PMID:19834888

He, Yu-Fei; Bao, Hui-Min; Xiao, Xiao-Feng; Zuo, Shuai; Du, Ru-Yun; Tang, Si-Wei; Yang, Peng-Yuan; Chen, Xian

2013-01-01

114

Learning to Tag Multilingual Texts Through Observation  

Microsoft Academic Search

This paper describes RoboTag, an ad- vanced prototype for a machine learning- based multilingual information extraction system. First, we describe a general client\\/server architecture used in learning from observation. Then we give a detailed description of our novel decision-tree tag- ging approach. RoboTag performance for the proper noun tagging task in English and Japanese is compared against human- tagged keys

Scott W. Bennett; Chinatsu Aone; Craig Lovell

1997-01-01

115

From the Cover: Imaging of receptor trafficking by using -bungarotoxin-binding-site-tagged receptors  

NASA Astrophysics Data System (ADS)

-Amino-3-hydroxy-5-methyl-4-isoxazole-propionate (AMPA) receptors mediate excitatory synaptic transmission and are dynamically regulated during synaptic plasticity in the CNS. The membrane trafficking of AMPA receptors to synapses is critical for the regulation of the efficacy of excitatory synaptic transmission. Direct imaging of AMPA receptors in various cell compartments is important to dissecting the regulation of distinct steps in receptor membrane trafficking. In this study, we have developed an approach for the imaging of receptor trafficking with subunits tagged with a 13-aa -bungarotoxin (BTX)-binding site (BBS). The small polypeptide neurotoxin BTX has been used for decades to study the nicotinic acetylcholine receptor. Similar high-affinity ligands are rarely available for most receptors. Engineering the BBS tag into receptor subunits allowed the high-affinity binding of fluorescent, radioactive, and biotinylated BTX to the tagged receptor subunits. By using this approach, the total receptor expression, surface expression, internalization, and insertion of receptors into the plasma membrane could be visualized and quantified in fixed or live cells including cultured neurons. The BBS tag is a flexible approach for labeling membrane proteins and studying their dynamic trafficking. GFP | glutamate receptor | live imaging | synapses | tag

Sekine-Aizawa, Yoko; Huganir, Richard L.

2004-12-01

116

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

E-print Network

Visible and Controllable RFID Tags Abstract Radio frequency identification (RFID) tags containing associated with RFID, likely because the technology remains largely invisible and uncontrollable alternative tag designs to make RFID visible and controllable. This video and demonstration illustrates

Greenberg, Saul

117

Quantum Reduction for Affine Superalgebras  

Microsoft Academic Search

We extend the homological method of quantization of generalized Drinfeld–Sokolov reductions to affine superalgebras. This leads, in particular, to a unified representation theory of superconformal algebras.

Victor G. Kac; Shi-Shyr Roan; Minoru Wakimoto

2003-01-01

118

Removal of the Tag from His-tagged ILYd4, a Human CD59 Inhibitor, Significantly Improves its Physical Properties and its Activity  

PubMed Central

Complement dependent cytotoxicity (CDC) significantly contributes to Rituximab (RTX) and Ofatumumab (OFA) efficacies in the treatment of B-cell non-Hodgkin’s lymphoma (NHL) and chronic lymphocytic leukemia (CLL). Human CD59 (hCD59) is a key complement regulatory protein that restricts the formation of the membrane attack complex and thereby inhibits CDC. hCD59 is an important determinant of the sensitivity of NHL and CLL to RTX and OFA treatment. Recently, we developed a specific and potent hCD59 inhibitor, His-tagged ILYd4, which consists of 30 amino acid sequences extending from the N-terminus of ILYd4. Our previously published results indicate that His-tagged ILYd4 can be used as a lead candidate to further develop a potential therapeutic adjuvant for RTX and OFA treatment of RTX-resistant NHL and CLL. However, these studies were conducted using ILYd4 tagged on the N-terminus with 30 additional amino acids (AA) containing 6 X His used for immobilized metal affinity chromatograph. As a further step towards the development of ILYd4-based therapeutics, we investigated the impact of the removal of this extraneous sequence on the anti-hCD59 activity. In this paper, we report the generation and characterization of tag-free ILYd4. We demonstrate that tag-free ILYd4 has over three-fold higher anti-hCD59 activities than the His-tagged ILYd4. The enhanced RTX-mediated CDC effect on B-cell malignant cells comes from tag-free ILYd4’s improved functionality and physical properties including better solubility, reduced tendency to aggregation, and greater thermal stability. Therefore, tag-free ILYd4 is a better candidate for the further development for the clinical application. PMID:22642361

Wu, Lin; Su, Sanbao; Liu, Fengming; Xu, Tao; Wang, Xiaoxiao; Huang, Yan; Sun, Xinlu; Ge, Xiaowen; Chen, Ting; Liu, Huixia; Wang, Chun; Chorev, Michael; Xu, Ting; Qin, Xuebin

2014-01-01

119

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

120

A laboratory evaluation of tagging-related mortality and tag loss in juvenile humpback chub  

USGS Publications Warehouse

We quantified tag retention, survival, and growth in juvenile, captive-reared Humpback Chub Gila cypha marked with three different tag types: (1) Biomark 12.5-mm, 134.2-kHz, full duplex PIT tags injected into the body cavity with a 12-gauge needle; (2) Biomark 8.4-mm, 134.2-kHz, full duplex PIT tags injected with a 16-gauge needle; and (3) Northwest Marine Technology visible implant elastomer (VIE) tags injected under the skin with a 29-gauge needle. Estimates of tag loss, tagging-induced mortality, and growth were evaluated for 60 d with each tag type for four different size-groups of fish: 40–49 mm, 50–59 mm, 60–69 mm, and 70–79 mm TL. Total length was a significant predictor of the probability of PIT tag retention and mortality for both 8-mm and 12-mm PIT tags, and the smallest fish had the highest rates of tag loss (12.5–30.0%) and mortality (7.5–20.0%). Humpback Chub of sizes 40–49 mm TL and tagged with VIE tags had no mortality but did have a 17.5% tag loss. Growth rates of all tagged fish were similar to controls. Our data indicate Humpback Chub can be effectively tagged using either 8-mm or 12-mm PIT tags with little tag loss or mortality at sizes as low as 65 mm TL.

Ward, David L.; Persons, William R.; Young, Kirk; Stone, Dennis M.; Van Haverbeke, Randy; Knight, William R.

2015-01-01

121

Vaccine Efficacy and Affinity Maturation  

Microsoft Academic Search

We propose macroscopic equations to describe variable vaccine efficacy between repeated vaccinee and first time vaccinee. The main ingredients are antigenic distance between epidemic strain and vaccne strain, and affinity maturation dynamics which differs in primary and second response. Increase of affinity by repeated vaccine leads to localization in immune space. This localization decreases the ability of the immune system

Hayoun Lee; Michael W. Deem

2002-01-01

122

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

123

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

124

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; Álvarez, Maite; Ayerbe, Ana; Vazquez, Juan Ignacio

2012-01-01

125

Monodisperse, "Highly" Positively Charged Protein Polymer Drag-Tags Generated in an Intein-Mediated Purification System Used in  

E-print Network

, a one-step purification method that combines affinity chromatography and on-column tag cleavage sieving polymer network to separate Sanger fragments1 by length by electrophoresis. To date, the only is achieved by separating Sanger fragments with single- base resolution. FSCE is ideal for implementation

Barron, Annelise E.

126

Broad host range vectors for expression of proteins with (Twin-) Strep-tag, His-tag and engineered, export optimized yellow fluorescent protein  

PubMed Central

Background In current protein research, a limitation still is the production of active recombinant proteins or native protein associations to assess their function. Especially the localization and analysis of protein-complexes or the identification of modifications and small molecule interaction partners by co-purification experiments requires a controllable expression of affinity- and/or fluorescence tagged variants of a protein of interest in its native cellular background. Advantages of periplasmic and/or homologous expressions can frequently not be realized due to a lack of suitable tools. Instead, experiments are often limited to the heterologous production in one of the few well established expression strains. Results Here, we introduce a series of new RK2 based broad host range expression plasmids for inducible production of affinity- and fluorescence tagged proteins in the cytoplasm and periplasm of a wide range of Gram negative hosts which are designed to match the recently suggested modular Standard European Vector Architecture and database. The vectors are equipped with a yellow fluorescent protein variant which is engineered to fold and brightly fluoresce in the bacterial periplasm following Sec-mediated export, as shown from fractionation and imaging studies. Expression of Strep-tag®II and Twin-Strep-tag® fusion proteins in Pseudomonas putida KT2440 is demonstrated for various ORFs. Conclusion The broad host range constructs we have produced enable good and controlled expression of affinity tagged protein variants for single-step purification and qualify for complex co-purification experiments. Periplasmic export variants enable production of affinity tagged proteins and generation of fusion proteins with a novel engineered Aequorea-based yellow fluorescent reporter protein variant with activity in the periplasm of the tested Gram-negative model bacteria Pseudomonas putida KT2440 and Escherichia coli K12 for production, localization or co-localization studies. In addition, the new tools facilitate metabolic engineering and yield assessment for cytoplasmic or periplasmic protein production in a number of different expression hosts when yields in one initially selected are insufficient. PMID:23687945

2013-01-01

127

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

PubMed Central

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

128

Site-specific immobilization of a (His)6-tagged acetylcholinesterase on nickel nanoparticles for highly sensitive toxicity biosensors.  

PubMed

This paper reports site-specific affinity immobilization of (His)6-tagged acetylcholinesterase (AChE) onto Ni/NiO nanoparticles for the development of an electrochemical screen-printed biosensor for the detection of organophosphate pesticides. The method is based on the specific affinity binding of the His-tagged enzyme to oxidized nickel nanoparticle surfaces in the absence of metal chelators. This approach allows stable and oriented attachment of the enzyme onto the oxidized nickel through the external His residue in one-step procedure, allowing for fast and sensitive detection of paraoxon in the concentration range from 10(-8) to 10(-13) M. A detection limit of 10(-12) M for paraoxon was obtained after 20 min incubation. This method can be used as a generic approach for the immobilization of other His-tagged enzymes for the development of biosensors. PMID:21937214

Ganesana, Mallikarjunarao; Istarnboulie, Georges; Marty, Jean-Louis; Noguer, Thierry; Andreescu, Silvana

2011-12-15

129

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

130

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.

131

Genetic tagging of humpback whales.  

PubMed

The ability to recognize individual animals has substantially increased our knowledge of the biology and behaviour of many taxa. However, not all species lend themselves to this approach, either because of insufficient phenotypic variation or because tag attachment is not feasible. The use of genetic markers ('tags') represents a viable alternative to traditional methods of individual recognition, as they are permanent and exist in all individuals. We tested the use of genetic markers as the primary means of identifying individuals in a study of humpback whales in the North Atlantic Ocean. Analysis of six microsatellite loci among 3,060 skin samples collected throughout this ocean allowed the unequivocal identification of individuals. Analysis of 692 'recaptures', identified by their genotype, revealed individual local and migratory movements of up to 10,000 km, limited exchange among summer feeding grounds, and mixing in winter breeding areas, and also allowed the first estimates of animal abundance based solely on genotypic data. Our study demonstrates that genetic tagging is not only feasible, but generates data (for example, on sex) that can be valuable when interpreting the results of tagging experiments. PMID:9285587

Palsbøll, P J; Allen, J; Bérubé, M; Clapham, P J; Feddersen, T P; Hammond, P S; Hudson, R R; Jørgensen, H; Katona, S; Larsen, A H; Larsen, F; Lien, J; Mattila, D K; Sigurjónsson, J; Sears, R; Smith, T; Sponer, R; Stevick, P; Oien, N

1997-08-21

132

A Survey of RFID Tags  

Microsoft Academic Search

The Radio Frequency Identification System (RFID) has become a popular system and its applications has reached in most of the fields like toll bridge, supply chain management and defense sector (8). The RFID has also entered into the field of medical sciences (4, 7). Everyday, RFID tags are becoming very small and their dimensions are also reducing to 0.002 inches

M Ayoub Khan; Manoj Sharma; Brahmanandha Prabhu R

2009-01-01

133

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.

134

pAUL: A Gateway-Based Vector System for Adaptive Expression and Flexible Tagging of Proteins in Arabidopsis  

PubMed Central

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

135

PPS-Tags: Physical, Perceptual and Semantic Tags for Autonomous Mobile Manipulation  

Microsoft Academic Search

For many promising application areas, au- tonomous mobile manipulators do not yet exhibit sufficiently robust performance. We propose the use of tags applied to task-relevant locations in human environments in order to help autonomous mobile manipulators physically interact with the location, perceive the location, and understand the location's semantics. We call these tags physical, perceptual and semantic tags (PPS-tags). We

Hai Nguyen; Travis Deyle; Matt Reynolds; Charles C. Kemp

136

Document recommendation in social tagging services  

Microsoft Academic Search

Social tagging services allow users to annotate various online resources with freely chosen keywords (tags). They not only facilitate the users in finding and organizing online resources, but also provide meaningful collaborative semantic data which can potentially be exploited by recommender systems. Traditional studies on recommender systems focused on user rating data, while recently social tagging data is becoming more

Ziyu Guan; Can Wang; Jiajun Bu; Chun Chen; Kun Yang; Deng Cai; Xiaofei He

2010-01-01

137

AMERICAN LOBSTERS TAGGED BY MAINE COMMERCIAL FISHERMEN,  

E-print Network

AMERICAN LOBSTERS TAGGED BY MAINE COMMERCIAL FISHERMEN, 1957-59 In 1957 at the suggestion of C. Owen Smith, then editor of the "Maine Coast Fisherman," several commercial lobster fishermen volunteered to tag illegal American lobster, Homarus ameri- canus, with tags furnished by the Maine Depart

138

Fish Tagging Forum February 12, 2013  

E-print Network

· Life-cycle Infrastructure and Data Management Schematics · BPA and USACE Cost Information · Management) · "Take Away" Scenario Analysis · Indicator & Tag Prioritization Spreadsheet · Basic Cost and Tagging Data to $60M spent in 2012 on tagging/marking related activities ­ Labor and infrastructure for application

139

Multiple object identification with passive RFID tags  

Microsoft Academic Search

We investigate the applicability of passive RFID systems to the task of identifying multiple tagged objects simultaneously, assuming that the number of tags is not known in advance. We present a combinatorial model of the communication mechanism between the reader device and the tags, and use this model to derive the optimal parameter setting for the reading process, based on

Harald Vogt

2002-01-01

140

RFID Performance Tag Analysis Dan Deavours,  

E-print Network

RFID Performance Tag Analysis Dan Deavours, Karthik Moncombu Ramakrishnan, and Afzal Syed ITTC This report describes efforts to measure performance of item-level EPC-based passive UHF RFID tags on cell phones. The intended application is to use RFID tags to keep unauthorized cell phones from restricted

Kansas, University of

141

Requesting Pervasive Services by Touching RFID Tags  

Microsoft Academic Search

We suggest a general framework for requesting pervasive services by touching RFID tags. The tags conne ct the physical and digital environments. Visual symbols c ommunicate to users the objects that can be touched and the services that can be activated. When a user touches such a symbol with a mobile phone, the data stored in the tag and other

Jukka Riekki; Timo Salminen; Ismo Alakärppä

2006-01-01

142

Efficient Object Identification with Passive RFID Tags  

Microsoft Academic Search

Radio frequency identification systems with passive tags are power- ful tools for object identification. However, if multiple tags are to be identified simultaneously, messages from the tags can collide and cancel each other out. Therefore, multiple read cycles have to be performed in order to achieve a high recognition rate. For a typical stochastic anti-collision scheme, we show how to

Harald Vogt

2002-01-01

143

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

144

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 #1. Lattice locations of tag nodes in multi-dimensional space are then used in calculating the compositions of a node #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.

Gross, Kenny C. (1433 Carriage La., Bolingbrook, IL 60440)

1995-01-01

145

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

PubMed Central

The advent of protein display systems has provided access to tailor-made protein binders by directed evolution. We introduce a new in vitro display system, bead surface display (BeSD), in which a gene is mounted on a bead via strong non-covalent (streptavidin/biotin) interactions and the corresponding protein is displayed via a covalent thioether bond on the DNA. In contrast to previous monovalent or low-copy bead display systems, multiple copies of the DNA and the protein or peptide of interest are displayed in defined quantities (up to 106 of each), so that flow cytometry can be used to obtain a measure of binding affinity. The utility of the BeSD in directed evolution is validated by library selections of randomized peptide sequences for binding to the anti-hemagglutinin (HA) antibody that proceed with enrichments in excess of 103 and lead to the isolation of high-affinity HA-tags within one round of flow cytometric screening. On-bead Kd measurements suggest that the selected tags have affinities in the low nanomolar range. In contrast to other display systems (such as ribosome, mRNA and phage display) that are limited to affinity panning selections, BeSD possesses the ability to screen and rank binders by their affinity in vitro, a feature that hitherto has been exclusive to in vivo multivalent cell display systems (such as yeast display). PMID:23980186

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

2013-01-01

146

Dual tagging as an approach to isolate endogenous chromatin remodeling complexes from Saccharomyces cerevisiae.  

PubMed

Affinity isolation has been an essential technique for molecular studies of cellular assemblies, such as the switch/sucrose non-fermentable (SWI/SNF) family of ATP-dependent chromatin remodeling complexes. However, even biochemically pure isolates can contain heterogeneous mixtures of complexes and their components. In particular, purification strategies that rely on affinity tags fused to only one component of a complex may be susceptible to this phenomenon. This study demonstrates that fusing purification tags to two different proteins enables the isolation of intact complexes of remodels the structure of chromatin (RSC). A Protein A tag was fused to one of the RSC proteins and a Twin-Strep tag to another protein of the complex. By mass spectrometry, we demonstrate the enrichment of the RSC complexes. The complexes had an apparent Svedberg value of about 20S, as shown by glycerol gradient ultracentrifugation. Additionally, purified complexes were demonstrated to be functional. Electron microscopy and single-particle analyses revealed a conformational rearrangement of RSC upon interaction with acetylated histone H3 peptides. This purification method is useful to purify functionally active, structurally well-defined macromolecular assemblies. PMID:25486077

Lin, Tzong-Yuan; Voronovsky, Andriy; Raabe, Monika; Urlaub, Henning; Sander, Bjoern; Golas, Monika M

2015-03-01

147

Three types of RFID tags Passive / Active / Semi-Active  

E-print Network

Three types of RFID tags · Passive / Active / Semi-Active · up to 19m range for UHF Computer GeneralizedGeneralized ""YokingYoking--ProofsProofs"" for a Group of RFID Tagsfor a Group of RFID Tags RFID TagRFID Tag ""YokingYoking--ProofsProofs"" Generalized Tag GroupGeneralized Tag Group ""Yoking

Robins, Gabriel

148

Adaptive binary splitting for efficient RFID tag anti-collision  

Microsoft Academic Search

Tag collision arbitration for passive RFID tags is a significant issue for fast tag identification. This letter presents a novel tag anti-collision scheme called adaptive binary splitting (ABS). For reducing collisions, ABS assigns distinct timeslots to tags by using information obtained from the last identification process. Our performance evaluation shows that ABS outperforms other tree based tag anti-collision protocols.

Jihoon Myung; Wonjun Lee; J. Srivastava

2006-01-01

149

Exotic affinities under Debye plasma  

SciTech Connect

Muonic affinities of the exotic system {pi}{sup +}{mu}{sup -} have been calculated variationally using a general three-body formalism. The system is found to be stable in the ground state under Coulomb coupling. The stability of this system under an external plasma environment has been analyzed using multiterm correlated basis sets of Hylleraas type. The effect of external plasma has been incorporated using the standard Debye screening model. The system tends toward gradual instability under the increased strength of the plasma, and the affinities have been found to decrease gradually and systematically. The effect of correlation on the exotic affinities has been analyzed in detail. The effect of angular correlation on exotic affinities is found to be around 40-80%.

Bhattacharyya, S.; Sil, A. N.; Mukherjee, T. K.; Mukherjee, P. K. [Kandi Raj College, Kandi, Murshidabad, West Bengal 742 137 (India); Department of Spectroscopy, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032 (India); Narula Institute of Technology, Agarpara, Kolkata 700 109 (India); Department of Spectroscopy, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032 (India)

2007-02-15

150

BONCAT: Metabolic Labeling, Click Chemistry, and Affinity Purification of Newly Synthesized Proteomes.  

PubMed

Metabolic labeling of proteins using classical radioisotope-labeled amino acids has enabled the analysis and function of protein synthesis for many biological processes but cannot be combined with modern high-throughput mass spectrometry analysis. This chapter describes the unbiased identification of a whole de novo synthesized proteome of cultured cells or of a translationally active subcellular fraction of the mammalian brain. This technique relies on the introduction of a small bioorthogonal reactive group by metabolic labeling accomplished by replacing the amino acid methionine by the azide-bearing methionine surrogate azidohomoalanine (AHA) or the amino acid homopropargylglycine (HPG). Subsequently an alkyne- or azide-bearing affinity tag is covalently attached to the group by "click chemistry"-a copper(I)-catalyzed [3+2] azide-alkyne cycloaddition. Affinity tag-labeled proteins can be analyzed in candidate-based approaches by conventional biochemical methods or with high-throughput mass spectrometry. PMID:25560077

Landgraf, Peter; Antileo, Elmer R; Schuman, Erin M; Dieterich, Daniela C

2015-01-01

151

Vaccine Efficacy and Affinity Maturation  

NASA Astrophysics Data System (ADS)

We propose macroscopic equations to describe variable vaccine efficacy between repeated vaccinee and first time vaccinee. The main ingredients are antigenic distance between epidemic strain and vaccne strain, and affinity maturation dynamics which differs in primary and second response. Increase of affinity by repeated vaccine leads to localization in immune space. This localization decreases the ability of the immune system to response to distant, but related epidemic strains.

Lee, Hayoun; Deem, Michael W.

2002-03-01

152

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

153

Directional Radio-Frequency Identification Tag Reader  

NASA Technical Reports Server (NTRS)

A directional radio-frequency identification (RFID) tag reader has been designed to facilitate finding a specific object among many objects in a crowded room. The device could be an adjunct to an electronic inventory system that tracks RFID-tagged objects as they move through reader-equipped doorways. Whereas commercial RFID-tag readers do not measure directions to tagged objects, the device is equipped with a phased-array antenna and a received signal-strength indicator (RSSI) circuit for measuring direction. At the beginning of operation, it is set to address only the RFID tag of interest. It then continuously transmits a signal to interrogate that tag while varying the radiation pattern of the antenna. It identifies the direction to the tag as the radiation pattern direction of peak strength of the signal returned by the tag. An approximate distance to the tag is calculated from the peak signal strength. The direction and distance can be displayed on a screen. A prototype containing a Yagi antenna was found to be capable of detecting a 915.5-MHz tag at a distance of approximately equal to 15 ft (approximately equal to 4.6 m).

Medelius, Pedro J.; Taylor, John D.; Henderson, John J.

2004-01-01

154

BIACORE analysis of histidine-tagged proteins using a chelating NTA sensor chip.  

PubMed

While BIACORE instruments are routinely used for kinetic measurements and for the determination of binding constants, the immobilization of a ligand onto the sensor chip surface has to be individually optimized for every system. We show here that the histidine (His) tag, routinely used in protein purification and in detection is an ideal tag for immobilization, despite the intrinsically low affinity between an immobilized metal ion and the His tag. This is due to strong rebinding effects caused by the high surface density of immobilized Ni2+-nitrilotriacetic acid (NTA) on the chips used here. The immobilization of the ligand can be adjusted to a low level using the same chip, such that mass transport limitation and rebinding of the analyte to the immobilized ligand is minimal. Nine different proteins with different numbers of His tags were tested for stable binding to the Ni2+-NTA surface. Most proteins with one His tag dissociate very rapidly from the Ni2+-NTA surface, and the KD for the interaction between His tag and Ni2+-NTA was estimated to about 10(-6) m at neutral pH. In contrast, two His tags are usually found to be sufficient for stable binding. The kinetics of the chaperonin system of Escherichia coli GroEL and GroES were analyzed as a model using this system and found to be very similar to those obtained with covalently immobilized ligands. The sensor chip can be reused many times, because of the powerful regeneration methods. The ligand can be freshly immobilized after each cycle, thus eliminating potential denaturation upon regeneration as a source of error. PMID:9344407

Nieba, L; Nieba-Axmann, S E; Persson, A; Hämäläinen, M; Edebratt, F; Hansson, A; Lidholm, J; Magnusson, K; Karlsson, A F; Plückthun, A

1997-10-15

155

Protonation effect on drug affinity.  

PubMed

Pharmacologic ligand-macromolecule interactions are commonly characterized by affinity (dissociation) constants such as K(d) or K(i) without regard to the protonation effect of the buffer used in the measurement. The protonation effect is demonstrated here using isothermal titration microcalorimetry measurements of the competitive inhibitor binding of cytidine 2'-monophosphate (2'-CMP) to RNase-A as a model system in buffers of different ionization Delta H(buffer). The results demonstrate the importance of protonation in measures of affinity. PMID:14729124

Raffa, Robert B; Stagliano, Gregory W; Spencer, Shawn D

2004-01-12

156

Design of supported membranes tethered via metal-affinity ligand-receptor pairs.  

PubMed Central

Model lipid layers are very promising in investigating the complex network of recognition, transport and signaling processes at membranes. We have developed a novel and generic approach to create supported lipid membranes tethered by metal-affinity binding. By self-assembly we have generated various interfaces that display histidine sequences (6xHis) via polymer spacers. These histidine-functionalized interfaces are designed to allow specific docking and fusion of vesicles containing metal-chelating lipids. By means of surface plasmon resonance and atomic force microscopy we analyzed the formation and subsequently the structure of these solid-supported membranes. Although the affinity constant of single ligand-receptor pairs is only in the micromolar range, very stable immobilization of these membranes was observed. This behavior can be explained by multivalent interactions resembling many features of cell adhesion. The process is highly specific, because vesicle docking and bilayer formation are strictly dependent on the presence of metal-affinity ligand-receptor pairs. The surface accessibility and geometry of these tethered membranes were probed by binding of histidine-tagged polypeptides. The supported membranes show adsorption kinetics and values similar to planar supported monolayers. Using various combinations of metal-chelating and histidine-tagged lipids or thiols these metal-affinity-tethered membranes should make a great impact on probing and eventually understanding the dynamic dialog of reconstituted membrane proteins. PMID:11106619

Rädler, U; Mack, J; Persike, N; Jung, G; Tampé, R

2000-01-01

157

Picture Tags and World Knowledge learning tag rela4ons from visual seman4c sources  

E-print Network

, shark atlanta, georgia atlanta, hammerhead shark, underwater fish, waterons? · Image tagging evalua4ons #12;Which tags are related? aquarium, shark aquarium, hammerhead aquarium, georgia aquarium, fish aquarium, atlanta atlanta

Xie, Lexing

158

Sensor-based material tagging system  

SciTech Connect

Electronic identification tags are being developed for tracking material and personnel. In applying electronic identification tags to radioactive materials safeguards, it is important to measure attributes of the material to ensure that the tag remains with the material. The addition of a microcontroller with an on-board analog-to-digital converter to an electronic identification tag application-specific integrated-circuit has been demonstrated as means to provide the tag with sensor data. Each tag is assembled into a housing, which serves as a scale for measuring the weight of a paint-can-sized container and its contents. Temperature rise of the can above ambient is also measured, and a piezoelectric detector detects disturbances and immediately puts the tag into its alarm and beacon mode. Radiation measurement was also considered, but the background from nearby containers was found to be excessive. The sensor-based tagging system allows tracking of the material in cans as it is stored in vaults or is moved through the manufacturing process. The paper presents details of the sensor-based material tagging system and describes a demonstration system.

Vercellotti, L.C.; Cox, R.W.; Ravas, R.J.; Schlotterer, J.C. (Westinghouse Electric Corp., Churchill, PA (United States). Science and Technology Center)

1991-01-01

159

Sensor-based material tagging system  

SciTech Connect

Electronic identification tags are being developed for tracking material and personnel. In applying electronic identification tags to radioactive materials safeguards, it is important to measure attributes of the material to ensure that the tag remains with the material. The addition of a microcontroller with an on-board analog-to-digital converter to an electronic identification tag application-specific integrated-circuit has been demonstrated as means to provide the tag with sensor data. Each tag is assembled into a housing, which serves as a scale for measuring the weight of a paint-can-sized container and its contents. Temperature rise of the can above ambient is also measured, and a piezoelectric detector detects disturbances and immediately puts the tag into its alarm and beacon mode. Radiation measurement was also considered, but the background from nearby containers was found to be excessive. The sensor-based tagging system allows tracking of the material in cans as it is stored in vaults or is moved through the manufacturing process. The paper presents details of the sensor-based material tagging system and describes a demonstration system.

Vercellotti, L.C.; Cox, R.W.; Ravas, R.J.; Schlotterer, J.C. [Westinghouse Electric Corp., Churchill, PA (United States). Science and Technology Center

1991-12-31

160

A novel approach for separating bacteriophages from other bacteriophages using affinity chromatography and phage display  

PubMed Central

Practical applications of bacteriophages in medicine and biotechnology induce a great need for technologies of phage purification. None of the popular methods offer solutions for separation of a phage from another similar phage. We used affinity chromatography combined with competitive phage display (i) to purify T4 bacteriophage from bacterial debris and (ii) to separate T4 from other contaminating bacteriophages. In ‘competitive phage display’ bacterial cells produced both wild types of the proteins (expression from the phage genome) and the protein fusions with affinity tags (expression from the expression vectors). Fusion proteins were competitively incorporated into the phage capsid. It allowed effective separation of T4 from a contaminating phage on standard affinity resins. PMID:24225840

Ceglarek, Izabela; Piotrowicz, Agnieszka; Lecion, Dorota; Miernikiewicz, Paulina; Owczarek, Barbara; Hodyra, Katarzyna; Harhala, Marek; Górski, Andrzej; D?browska, Krystyna

2013-01-01

161

Programmare sul Web 2.0 Tagging systems and tag clouds  

E-print Network

1 MODULO 2 PARTE 5.a Programmare sul Web 2.0 Tagging systems and tag clouds Goy - a.a. 2012/2013 Programmazione Web 1 Tagging systems and tag clouds Cos'è il Web 2.0 - I · Web 2.0 = termine introdotto per la serie di concetti emergenti Goy - a.a. 2012/2013 Programmazione Web 2 · La maggior parte dei siti

Goy, Anna

162

Programmare sul Web 2.0 Tagging systems and tag clouds  

E-print Network

1 MODULO 2 PARTE 5.a Programmare sul Web 2.0 Tagging systems and tag clouds Goy - a.a. 2011/2012 Programmazione Web 1 Tagging systems and tag clouds Cos'è il Web 2.0 - I · Web 2.0 = termine introdotto per la serie di concetti emergenti Goy - a.a. 2011/2012 Programmazione Web 2 · La maggior parte dei siti

Goy, Anna

163

Programmare sul Web 2.0 Tagging systems and tag clouds  

E-print Network

1 MODULO 2 PARTE 5.a Programmare sul Web 2.0 Tagging systems and tag clouds a.a. 2009/2010 Programmazione Web 1 Tagging systems and tag clouds Cos'è il Web 2.0 - I · Web 2.0 = termine introdotto per la serie di concetti emergenti Goy - a.a. 2009/2010 Programmazione Web 2 · La maggior parte dei siti

Goy, Anna

164

Programmare sul Web 2.0 Tagging systems and tag clouds  

E-print Network

1 MODULO 2 PARTE 5.a Programmare sul Web 2.0 Tagging systems and tag clouds Goy - a.a. 2010/2011 Programmazione Web 1 Tagging systems and tag clouds Cos'è il Web 2.0 - I · Web 2.0 = termine introdotto per la serie di concetti emergenti Goy - a.a. 2010/2011 Programmazione Web 2 · La maggior parte dei siti

Goy, Anna

165

Biofabrication of ZnS:Mn luminescent nanocrystals using histidine, hexahistidine, and His-tagged proteins: a comparison study.  

PubMed

The ubiquitous hexahistidine purification tag has been used to conjugate proteins to the shell of CdSe:ZnS quantum dots (QDs) due to its affinity for surface-exposed Zn(2+) ions but little attention has been paid to the potential of His-tagged proteins for mineralizing luminescent ZnS nanocrystals. Here, we compare the ability of free histidine, a His tag peptide, His-tagged thioredoxin (TrxA, a monomeric protein), and N- and C-terminally His-tagged versions of Hsp31 (a homodimeric protein) to support the synthesis of Mn-doped ZnS nanocrystals from aqueous precursors under mild conditions of pH (8.2) and temperature (37°C). We find that: (1) it is possible to produce poor quality QDs when histidine is used at high (8 mM) concentration; (2) an increase in local histidine concentration through repetition of the amino acid as a His tag decreases the amount of needed reagent ?10-fold and improves optical properties; (3) fusion of the same His tag to TrxA allows for ZnS:Mn QDs mineralization at micromolar concentrations; and (4) doubling the local hexahistidine concentration by exploiting Hsp31 dimerization further improves nanocrystal luminescence with the brightest particles obtained when His tags are spatially co-localized at the Hsp31 N-termini. Although hexahistidine tracts are not as efficient as combinatorially selected ZnS binding peptides at QD synthesis, it should be possible to use the large number of available His-tagged proteins and the synthesis approach described herein to produce luminescent nanoparticles whose protein shell carries a broad range of functions. PMID:25013361

Zhou, Weibin; Baneyx, François

2014-08-15

166

Discriminative Tag Learning on YouTube Videos with Latent Sub-tags Weilong Yang  

E-print Network

Discriminative Tag Learning on YouTube Videos with Latent Sub-tags Weilong Yang Simon Fraser-scale testing video set which contains about 50 million YouTube videos. 1. Introduction On the Internet of social sharing websites (i.e., Flickr, Picasa, and YouTube), the tags help organize, browse and search

Tomkins, Andrew

167

Models for tagging data that allow for incomplete mixing of newly tagged animals  

E-print Network

Models for tagging data that allow for incomplete mixing of newly tagged animals John M. Hoenig previously tagged animals because of lack of complete mixing. We develop a model that allows for the animals developed a model for which it is assumed that animals become fully mixed (recruited) after a portion

Newman, Michael C.

168

Partial Year Tagging Models: Accounting for Changing Tag Visibility and Delayed Mixing  

E-print Network

Partial Year Tagging Models: Accounting for Changing Tag Visibility and Delayed Mixing Acknowledgments References 36 37 37 38 38 39 42 43 CHAPTER 3: TAGGING MODELS ALLOWING FOR DELAYED MIXING OF NEWLY mixed case Delayed mixing lasting a full year Delayed mixing lasting part of the year New Model: partial

Newman, Michael C.

169

Affine Contractions on the Plane  

ERIC Educational Resources Information Center

Contractions play a considerable role in the theory of fractals. However, it is not easy to find contractions which are not similitudes. In this study, it is shown by counter examples that an affine transformation of the plane carrying a given triangle onto another triangle may not be a contraction even if it contracts edges, heights or medians.…

Celik, D.; Ozdemir, Y.; Ureyen, M.

2007-01-01

170

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

171

Quantifying Affinity among Chinese Dialects.  

ERIC Educational Resources Information Center

A study of the relationships between Chinese dialects based on a quantitative measure of dialect affinity is summarized. First, tone values in all the dialect localities available in the early 1970s were used to calculate the dialectal differences in terms of tone height with respect to the "yin and yang" split. In the late 1970s, calculations of…

Cheng, Chin-Chuan

172

A Microfluidic Affinity Cocaine Sensor  

Microsoft Academic Search

We present a novel microfluidic sensor that is capable of detecting trace cocaine concentrations and is fully regenerable at modest temperatures. The sensor exploits affinity aptamers (synthetic DNA\\/RNA oligonucleotides), labeled with a fluorophore and immobilized onto polymer microbeads as a highly sensitive cocaine receptor medium. The device demonstrates the capability of detecting native cocaine concentrations as low as 100 pM,

J. P. Hilton; ThaiHuu Nguyen; Renjun Pei; M. Stojanovic; Qiao Lin

2009-01-01

173

An overview of enzymatic reagents for the removal of affinity tags David S. Waugh  

E-print Network

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 00 Rhinovirus 3C protease

Lebendiker, Mario

174

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

175

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

176

Theoretical proton affinity and fluoride affinity of nerve agent VX.  

PubMed

Proton affinity and fluoride affinity of nerve agent VX at all of its possible sites were calculated at the RI-MP2/cc-pVTZ//B3LYP/6-31G* and RI-MP2/aug-cc-pVTZ//B3LYP/6-31+G* levels, respectively. The protonation leads to various unique structures, with H(+) attached to oxygen, nitrogen, and sulfur atoms; among which the nitrogen site possesses the highest proton affinity of -?E ? 251 kcal/mol, suggesting that this is likely to be the major product. In addition some H(2), CH(4) dissociation as well as destruction channels have been found, among which the CH(4) + [Et-O-P(?O)(Me)-S-(CH(2))(2)-N(+)(iPr)?CHMe] product and the destruction product forming Et-O-P(?O)(Me)-SMe + CH(2)?N(+)(iPr)(2) are only 9 kcal/mol less stable than the most stable N-protonated product. For fluoridization, the S-P destruction channel to give Et-O-P(?O)(Me)(F) + [S-(CH(2))(2)-N-(iPr)(2)](-) is energetically the most favorable, with a fluoride affinity of -?E ? 44 kcal. Various F(-) ion-molecule complexes are also found, with the one having F(-) interacting with two hydrogen atoms in different alkyl groups to be only 9 kcal/mol higher than the above destruction product. These results suggest VX behaves quite differently from surrogate systems. PMID:21117653

Bera, Narayan C; Maeda, Satoshi; Morokuma, Keiji; Viggiano, Al A

2010-12-23

177

A Radio Tag for Big Whales  

ERIC Educational Resources Information Center

Radio tags to track wildlife have been used for years. However, such tagging of whales has been more complicated and less successful. This article explores the latest technology that is designed to give information over a long period of time. (MA)

Watkins, William A.

1978-01-01

178

Towards the Semantic Web: Collaborative Tag Suggestions  

Microsoft Academic Search

Content organization over the Internet went through several interesting phases of evolution: from structured di rectories to unstructured Web search engines and more recently, to tagging as a way for aggregating information, a step toward s the semantic web vision. Tagging allows ranking and dat a organization to directly utilize inputs from end us ers, enabling machine processing of Web

Zhichen Xu; Yun Fu; Jianchang Mao; Difu Su

2006-01-01

179

Virtual Tagging: Numerical Considerations and Phantom Validation  

Microsoft Academic Search

This paper presents a virtual tagging framework for measuring, as well as visualising, myocardial deformation using magnetic resonance (MR) velocity imaging. Tagging grids are allocated artificially according to the deformation gradient with varying shapes and densities. The control points are then de- formed such that the difference between the induced deformation velocity and that of actually measured MR data is

Sharmeen Masood; Jianxin Gao; Guang-zhong Yang

2002-01-01

180

CORROSION RESISTANCE OF FISH TAGGING PINS  

E-print Network

CORROSION RESISTANCE OF FISH TAGGING PINS [Marine Biological Laboratoryj WOODS HOLE, MASS. SPECIAL A, Seaton, Secretary Fish and Wildlife Service, Arnie J. Suoraela, Commissioner CORROSION RESISTANCE were tagged with nickel and Type 304 stainless steel pins to compare the corrosion resistance

181

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

182

Environmental effects on RFID tag antennas  

Microsoft Academic Search

We have studied the effects of nearby objects on the read range of several types of RFID tags, and the impedance, pattern, and radiative efficiency of antennas that closely emulate the tag structures, using measurements and simulations. We find that the main reason for the decrease in read range at perpendicular incidence in close proximity to metals or dielectrics (such

Daniel M. Dobkin; Steven M. Weigand

2005-01-01

183

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

184

Tagging English Text with a Probabilistic Model  

Microsoft Academic Search

In this paper we present some experiments on the use of a probabilistic model to tag English text, i.e. to assign to each word the correct tag (part of speech) in the context of the sentence. The main novelty of these experiments is the use of untagged text in the training of the model. We have used a simple triclass

Bernard Merialdo

1994-01-01

185

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

186

50 CFR 20.36 - Tagging requirement.  

Code of Federal Regulations, 2013 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...

2013-10-01

187

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

188

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

189

Notes on SAW Tag Interrogation Techniques  

NASA Technical Reports Server (NTRS)

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 with geometric power-decay constant alpha >/= 2. (2) The interfering tag IDs are unknown but well approximated as independent, identically distributed random samples from a probability distribution of tag ID waveforms with known second-order properties, and the tag of interest is drawn independently from the same distribution. (3) The ranges of the interfering tags are unknown but well approximated as independent, identically distributed realizations of a random variable rho with a known probability distribution f(sub rho) , and the tag ranges are independent of the tag ID waveforms. In particular, we model the tag waveforms as random impulse responses from a wide-sense-stationary, uncorrelated-scattering (WSSUS) fading channel with known bandwidth and scattering function. A brief discussion of the properties of such channels and the notation used to describe them in this document is given in the Appendix. Under these assumptions, we derive the expression for the output signal-to-noise ratio (SNR) for an arbitrary combination of transmitted interrogation signal and linear receiver filter. Based on this expression, we derive the optimal interrogator configuration (i.e., transmitted signal/receiver filter combination) in the two extreme noise/interference regimes, i.e., noise-limited and interference-limited, under the additional assumption that the coherence bandwidth of the tags is much smaller than the total tag bandwidth. Finally, we evaluate the performance of both optimal interrogators over a broad range of operating scenarios using both numerical simulation based on the assumed model and Monte Carlo simulation based on a small sample of measured tag waveforms. The performance evaluation results not only provide guidelines for proper interrogator design, but also provide some insight on the validity of the assumed signal model. It should be noted that the assumption that the impulse response of the tag of interest is known precisely implies that the temperature and range of the tag are also known precisely, which is generally not the case in practice. However, analyzing interrogator performance under this simplifying assumption is much more straightforward and still provides a great deal of insight into the nature of the problem.

Barton, Richard J.

2010-01-01

190

Collaborative Topic Regression with Social Regularization for Tag Recommendation  

E-print Network

and organize photos, Last.fm2 adopts tags to categorize artists and music, and CiteULike3 allows users to tag proposed by researchers. Existing tag recommendation methods can be roughly cat- egorized into three

Li, Wu-Jun

191

29 CFR 1926.200 - Accident prevention signs and tags.  

Code of Federal Regulations, 2011 CFR

...2011-07-01 2011-07-01 false Accident prevention signs and tags. 1926...Signals, and Barricades § 1926.200 Accident prevention signs and tags. (a) General...regulations/ibr_locations.html. (h) Accident prevention tags. (1)...

2011-07-01

192

29 CFR 1926.200 - Accident prevention signs and tags.  

Code of Federal Regulations, 2013 CFR

...2013-07-01 2013-07-01 false Accident prevention signs and tags. 1926...Signals, and Barricades § 1926.200 Accident prevention signs and tags. (a) General...regulations/ibr_locations.html. (h) Accident prevention tags. (1)...

2013-07-01

193

29 CFR 1926.200 - Accident prevention signs and tags.  

...2014-07-01 2014-07-01 false Accident prevention signs and tags. 1926...Signals, and Barricades § 1926.200 Accident prevention signs and tags. (a) General...by reference in § 1926.6. (h) Accident prevention tags. (1)...

2014-07-01

194

29 CFR 1926.200 - Accident prevention signs and tags.  

Code of Federal Regulations, 2012 CFR

...2012-07-01 2012-07-01 false Accident prevention signs and tags. 1926...Signals, and Barricades § 1926.200 Accident prevention signs and tags. (a) General...regulations/ibr_locations.html. (h) Accident prevention tags. (1)...

2012-07-01

195

29 CFR 1926.417 - Lockout and tagging of circuits.  

Code of Federal Regulations, 2013 CFR

...2013-07-01 false Lockout and tagging of circuits. 1926.417 Section 1926.417...1926.417 Lockout and tagging of circuits. (a) Controls. Controls that...energized or deenergized equipment or circuits shall be tagged. (b) Equipment...

2013-07-01

196

29 CFR 1926.417 - Lockout and tagging of circuits.  

Code of Federal Regulations, 2010 CFR

...2010-07-01 false Lockout and tagging of circuits. 1926.417 Section 1926.417...1926.417 Lockout and tagging of circuits. (a) Controls. Controls that...energized or deenergized equipment or circuits shall be tagged. (b) Equipment...

2010-07-01

197

29 CFR 1926.417 - Lockout and tagging of circuits.  

...2014-07-01 false Lockout and tagging of circuits. 1926.417 Section 1926.417...1926.417 Lockout and tagging of circuits. (a) Controls. Controls that...energized or deenergized equipment or circuits shall be tagged. (b) Equipment...

2014-07-01

198

29 CFR 1926.417 - Lockout and tagging of circuits.  

Code of Federal Regulations, 2012 CFR

...2012-07-01 false Lockout and tagging of circuits. 1926.417 Section 1926.417...1926.417 Lockout and tagging of circuits. (a) Controls. Controls that...energized or deenergized equipment or circuits shall be tagged. (b) Equipment...

2012-07-01

199

29 CFR 1926.417 - Lockout and tagging of circuits.  

Code of Federal Regulations, 2011 CFR

...2011-07-01 false Lockout and tagging of circuits. 1926.417 Section 1926.417...1926.417 Lockout and tagging of circuits. (a) Controls. Controls that...energized or deenergized equipment or circuits shall be tagged. (b) Equipment...

2011-07-01

200

Intrinsic-surface-tag image authentication  

SciTech Connect

The objective of this work is to further the development of a unique treaty limited item (TLI) intrinsic surface tag for arms control applications. This tag`s unique feature is the ability to capture the sub-micron scale topography of the TLI surface. The surface topography is captured by plastic castings of the surface as digitally imaged by an electron microscope. Tag authentication is accomplished by comparing digital castings images obtained in two different inspections. Surface replication experiments are described, as these experiments from the basis for the authentication algorithm. Both the experiments and the authentication algorithm are analyzed using the modulation transfer function. Recommendations for future improvements in tag authentication are also suggested by the modulation transfer function analysis. 4 refs.

Palm, R.G.; DeVolpi, A.

1991-12-01

201

Definite affine spheres and loop groups  

NASA Astrophysics Data System (ADS)

We obtain the Weierstrass-type representation and the dressing transformation for definite affine spheres in this paper. As an application of the Weierstrass-type representation, we construct the entire family of finite-Symes type affine spheres.

Liang, Mingheng; Ji, Qingchun

2010-05-01

202

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

203

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

204

Advances in Phos-tag-based methodologies for separation and detection of the phosphoproteome.  

PubMed

This review article describes analytical techniques based on the phosphate-binding tag molecule "Phos-tag", which is an alkoxide-bridged dinuclear metal complex with 1,3-bis(pyridin-2-ylmethylamino)propan-2-olate, for studying the protein phosphorylome. The dinuclear zinc(II) complex forms a stable 1:1 complex with a phosphate monoester dianion in an aqueous solution under conditions of neutral pH. By using a series of functional Phos-tag derivatives, our group has developed novel techniques that are useful in studies on kinomics and phosphoproteomics. Among the derivatives, a series of biotinylated Phos-tag derivatives have been used as molecular tools in applications such as Western blotting for comprehensive detection of phosphorylated proteins and in highly sensitive peptide microarray-based techniques for the detection of kinase activities in biological samples. The review also gives an outline of phosphate affinity electrophoresis, in which immobilized Phos-tag molecules in a general polyacrylamide gel are used to separate proteins and detect differences in their phosphorylation status. This technique permits quantitative analyses of multiple phosphorylation statuses of individual cellular proteins and their time-dependent changes. Conventional mass spectrometry-based shotgun techniques used in phosphoproteomics detect the phosphorylation modification of proteins in peptide fragments, whereas the Phos-tag electrophoresis technique permits the direct analysis of the phosphorylation status of full-length proteins. The technique therefore provides a greater understanding of the detailed properties of particular proteins involved in specific physiological and pathological events. This article is part of a Special Issue entitled: Medical Proteomics. PMID:25315852

Kinoshita, Eiji; Kinoshita-Kikuta, Emiko; Koike, Tohru

2014-10-12

205

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

206

Construction, Verification and Experimental Use of Two Epitope-Tagged Collections of Budding Yeast Strains  

PubMed Central

A major challenge in the post-genomic era is the development of experimental approaches to monitor the properties of proteins on a proteome-wide level. It would be particularly useful to systematically assay protein subcellular localization, post-translational modifications and protein–protein interactions, both at steady state and in response to environmental stimuli. Development of new reagents and methods will enhance our ability to do so efficiently and systematically. Here we describe the construction of two collections of budding yeast strains that facilitate proteome-wide measurements of protein properties. These collections consist of strains with an epitope tag integrated at the C-terminus of essentially every open reading frame (ORF), one with the tandem affinity purification (TAP) tag, and one with the green fluorescent protein (GFP) tag. We show that in both of these collections we have accurately tagged a high proportion of all ORFs (approximately 75% of the proteome) by confirming expression of the fusion proteins. Furthermore, we demonstrate the use of the TAP collection in performing high-throughput immunoprecipitation experiments. Building on these collections and the methods described in this paper, we hope that the yeast community will expand both the quantity and type of proteome level data available. PMID:18629296

Howson, Russell; Huh, Won-Ki; Ghaemmaghami, Sina; Falvo, James V.; Bower, Kiowa; Belle, Archana; Dephoure, Noah; Wykoff, Dennis D.; Weissman, Jonathan S.

2005-01-01

207

Site-specific dual labeling of proteins by using small orthogonal tags at neutral pH.  

PubMed

To expand the utility of proteinaceous FRET biosensors, we have developed a dual-labeling approach based on two small bio-orthogonal tags: pyrroline-carboxy-lysine (Pcl) and the S6 peptide. The lack of cross-reactivity between those tags enables site-specific two-color protein conjugation in a one-pot reaction. Moreover, Pcl/S6 dual-tagged proteins can be produced in both bacterial and mammalian expression systems, as demonstrated for Z domain and IgE-Fc, respectively. Both proteins could be efficiently dual-labeled with FRET-compatible fluorescent dyes at neutral pH. In the case of IgE-Fc, the resulting conjugate enabled the monitoring of IgE binding to its high-affinity receptor Fc?RI, which is a key event in allergic disease. PMID:25044133

Grünewald, Jan; Jones, David H; Brock, Ansgar; Chiu, Hsien-Po; Bursulaya, Badry; Ng, Kenneth; Vo, Todd; Patterson, Paula; Uno, Tetsuo; Hunt, James; Spraggon, Glen; Geierstanger, Bernhard H

2014-08-18

208

Fabrication process for a flexible tag microlab  

NASA Astrophysics Data System (ADS)

The aim of this paper is to present an integrated process flow for a smart tag with integrated sensors and RFID communication, a Flexible Tag Microlab (FTM). The heart of the designed container tracing system is an RFID system (Reader + Tag) with gas sensing capabilities on board. In the former prototypes, the chemical sensors were integrated on the reader, whereas the tags where addressed like conventional RFID-tags containing also physical (temperature, humidity and light) sensors. However, this paper will show how the gas sensing reader functionalities are being transferred to the tag, reaching a flexible tag microlab, which represents a real innovation in the field of flexible labels. Key issues for the realisation of the FTM, such us flexible substrates and gas sensor integration technologies will be presented. The process flow employed for the two metal levels interconnect fabrication will be described in detail. The material used is the DuPont TM Pyralux (R) AP 8525R double-sided copper-clad laminate, formed by a Kapton foil with a copper layer on each side. The vias and windows openings are performed by femtosecond laser ablation. The copper interconnections are realized by photolithography and wet chemical etching. The MOX sensors hotplates specially developed to fulfil the FTM constrains in terms of low power consumption has been used to prove two integration technologies into the flexible substrates: Chip on Flex (COF) wire bonding and Anisotropic Conductive Adhesive (ACA) flip chip bonding. Both technologies will be compared and benchmarked for future product developments.

Abad, E.; Mazzolai, B.; Juarros, A.; Gómez, D.; Mondini, A.; Sayhan, I.; Krenkow, A.; Becker, Th.

2007-05-01

209

Enhanced UHF RFID tags for drug tracing.  

PubMed

Radio Frequency Identification (RFID) technology is playing a crucial role for item-level tracing systems in healthcare scenarios. The pharmaceutical supply chain is a fascinating application context, where RFID can guarantee transparency in the drug flow, supporting both suppliers and consumers against the growing counterfeiting problem. In such a context, the choice of the most adequate RFID tag, in terms of shape, frequency, size and reading range, is crucial. The potential presence of items containing materials hostile to the electromagnetic propagation exasperates the problem. In addition, the peculiarities of the different RFID-based checkpoints make even more stringent the requirements for the tag. In this work, the performance of several commercial UHF RFID tags in each step of the pharmaceutical supply chain has been evaluated, confirming the expected criticality. On such basis, a guideline for the electromagnetic design of new high-performance tags capable to overcome such criticalities has been defined. Finally, driven by such guidelines, a new enhanced tag has been designed, realized and tested. Due to patent pending issues, the antenna shape is not shown. Nevertheless, the optimal obtained results do not lose their validity. Indeed, on the one hand they demonstrate that high performance item level tracing systems can actually be implemented also in critical operating conditions. On the other hand, they encourage the tag designer to follow the identified guidelines so to realize enhanced UHF tags. PMID:22048779

Catarinucci, Luca; Colella, Riccardo; De Blasi, Mario; Patrono, Luigi; Tarricone, Luciano

2012-12-01

210

Influence of material properties upon immobilization of histidine-tagged protein on Ni-Co coated chip.  

PubMed

In protein research, protein microarray facilitates high-throughput study of protein abundance and function. An appropriate microarray surface that can be used to immobilize protein samples is a prerequisite for the investigation of molecular interactions. Ni-Co alloy coated protein microarray chip has been found to adsorb histidine-tagged proteins effectively based on the method of immobilized metal affinity chromatography. Due to the ingredient of bi-metallic elements, different electroplating conditions resulted in distinct binding affinities. Therefore, the influence of Ni-Co material properties on the immobilization of histidine-tagged protein was systematically investigated in this study. In the experiments, the contact angle measurement suggested that no strong relationship can be established between the wettability of chip surface and its corresponding protein immobilization. ESCA test demonstrated that the major ingredients of the Ni-Co alloy coated protein microarray chip were Ni and Co. In addition, the XRD test concluded that a Ni-Co protein chip that consists mostly of hcp lattice has better binding capability. SEM micrographs provide direct image evidence. These material tests summarize that the Ni-Co alloy coated protein microarray chip adsorbs His-tagged proteins through its surface morphology. Therefore, it can provide specific binding due to the affinity adsorption between the intermediate metals and the protein. PMID:24582262

Chang, Yaw-Jen; Ho, Ching-Yuan; Chang, Cheng-Hao

2014-04-01

211

A liquid phase affinity capture assay using magnetic beads to study protein-protein interaction: the poliovirus-nanobody example.  

PubMed

In this article, a simple, quantitative, liquid phase affinity capture assay is presented. Provided that one protein can be tagged and another protein labeled, this method can be implemented for the investigation of protein-protein interactions. It is based on one hand on the recognition of the tagged protein by cobalt coated magnetic beads and on the other hand on the interaction between the tagged protein and a second specific protein that is labeled. First, the labeled and tagged proteins are mixed and incubated at room temperature. The magnetic beads, that recognize the tag, are added and the bound fraction of labeled protein is separated from the unbound fraction using magnets. The amount of labeled protein that is captured can be determined in an indirect way by measuring the signal of the labeled protein remained in the unbound fraction. The described liquid phase affinity assay is extremely useful when conformational conversion sensitive proteins are assayed. The development and application of the assay is demonstrated for the interaction between poliovirus and poliovirus recognizing nanobodies(1). Since poliovirus is sensitive to conformational conversion(2) when attached to a solid surface (unpublished results), the use of ELISA is limited and a liquid phase based system should therefore be preferred. An example of a liquid phase based system often used in polioresearch(3,4) is the micro protein A-immunoprecipitation test(5). Even though this test has proven its applicability, it requires an Fc-structure, which is absent in the nanobodies(6,7). However, as another opportunity, these interesting and stable single-domain antibodies(8) can be easily engineered with different tags. The widely used (His)(6)-tag shows affinity for bivalent ions such as nickel or cobalt, which can on their turn be easily coated on magnetic beads. We therefore developed this simple quantitative affinity capture assay based on cobalt coated magnetic beads. Poliovirus was labeled with (35)S to enable unhindered interaction with the nanobodies and to make a quantitative detection feasible. The method is easy to perform and can be established with a low cost, which is further supported by the possibility of effectively regenerating the magnetic beads. PMID:22688388

Schotte, Lise; Rombaut, Bart; Thys, Bert

2012-01-01

212

Comparative Performance of Acoustic-tagged and PIT-tagged Juvenile Salmonids  

SciTech Connect

Numerous research tools and technologies are currently being used to evaluate fish passage and survival to determine the impacts of the Federal Columbia River Power System (FCRPS) on endangered and threatened juvenile salmonids, including PIT tags, balloon tags, hydroacoustic evaluations, radio telemetry, and acoustic telemetry. Each has advantages and disadvantages, but options are restricted in some situations because of limited capabilities of a specific technology, lack of detection capability downstream, or availability of adequate numbers of fish. However, there remains concern about the comparative effects of the tag or the tagging procedure on fish performance. The recently developed Juvenile Salmonid Acoustic Telemetry System (JSATS) acoustic transmitter is the smallest active acoustic tag currently available. The goal of this study was to determine whether fish tagged with the JSATS acoustic-telemetry tag can provide unbiased estimates of passage behavior and survival within the performance life of the tag. We conducted both field and laboratory studies to assess tag effects. For the field evaluation we released a total of 996 acoustic-tagged fish in conjunction with 21,026 PIT-tagged fish into the tailrace of Lower Granite Dam on 6 and 13 May. Travel times between release and downstream dams were not significantly different for the majority of the reaches between acoustic-tagged and PIT-tagged fish. In addition to the field evaluation, a series of laboratory experiments were conducted to determine if growth and survival of juvenile Chinook salmon surgically implanted with acoustic transmitters is different than untagged or PIT tagged juvenile Chinook salmon. Only yearling fish with integrated and non-integrated transmitters experienced mortalities, and these were low (<4.5%). Mortality among sub-yearling control and PIT-tag treatments ranged up to 7.7% while integrated and non-integrated treatments had slightly higher rates (up to 8.3% and 7.9% respectively). No acoustic transmitters were shed by yearling fish during the course of the 90 day study. Up to 7.8% of subyearling fish expelled transmitters. Tags were expelled from 5 to 63 days post-surgery. The average time to expulsion was 27 days; few fish expelled transmitters within 14 days of implantation or less. Histological results suggest that inflammation associated with implantation of an acoustic transmitter can produce fibrous tissue which can invade and possibly damage internal organs soon after implantation. Reactions severe enough to damage organs however, were limited to only ~20% of subyearling Chinook salmon, all of which were under 101mm and 12g at tagging. The infiltration of the fibrous tissue into organs was observed most often in fish held for 21 days and appeared to decrease in subsequent holding times.

Hockersmith, Eric E.; Brown, Richard S.; Liedtke, Theresa L.

2008-02-01

213

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

214

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

215

Intrinsic-surface-tag image authentication  

SciTech Connect

The objective of this work is to further the development of a unique treaty limited item (TLI) intrinsic surface tag for arms control applications. This tag's unique feature is the ability to capture the sub-micron scale topography of the TLI surface. The surface topography is captured by plastic castings of the surface as digitally imaged by an electron microscope. Tag authentication is accomplished by comparing digital castings images obtained in two different inspections. Surface replication experiments are described, as these experiments from the basis for the authentication algorithm. Both the experiments and the authentication algorithm are analyzed using the modulation transfer function. Recommendations for future improvements in tag authentication are also suggested by the modulation transfer function analysis. 4 refs.

Palm, R.G.; DeVolpi, A.

1991-12-01

216

50 CFR 20.81 - Tagging requirement.  

Code of Federal Regulations, 2011 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...

2011-10-01

217

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

218

50 CFR 20.81 - Tagging requirement.  

Code of Federal Regulations, 2013 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...

2013-10-01

219

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

220

Survival and tag retention of Pacific lamprey larvae and macrophthalmia marked with coded wire tags  

USGS Publications Warehouse

We examined the survival, tag retention, and growth of Pacific lamprey Lampetra tridentata larvae and macrophthalmia marked with standard-length decimal coded wire tags and exposed to two levels of handling stress. The survival of marked individuals did not differ from that of unmarked individuals at either life stage for the duration of the experiment (56 d). Tag retention was 100% for all treatment combinations except larvae that were handled frequently (93 ?? 3%). The majority of tag loss occurred within 28 d of marking, and no tag loss was observed between 42 and 56 d after marking. The individuals that lost tags were among the smallest marked, and a logistic regression model indicated a relationship between larva length and the probability of tag retention. Size of larvae (length and mass) and macrophthalmia (mass) decreased over the duration of the experiment; however, changes in size were systematic among treatment combinations, indicating that factors other than tagging or handling affected growth. These data indicate that coded wire tags may be useful for field-based studies of Pacific lamprey larvae and macrophthalmia.

Meeuwig, M.H.; Puls, A.L.; Bayer, J.M.

2007-01-01

221

Solid tags for identifying failed reactor components  

DOEpatents

A solid tag material which generates stable detectable, identifiable, and measurable isotopic gases on exposure to a neutron flux to be placed in a nuclear reactor component, particularly a fuel element, in order to identify the reactor component in event of its failure. Several tag materials consisting of salts which generate a multiplicity of gaseous isotopes in predetermined ratios are used to identify different reactor components.

Bunch, Wilbur L. (Richland, WA); Schenter, Robert E. (Richland, WA)

1987-01-01

222

b-tagging at D0  

SciTech Connect

Many high p{sub T} physics analyses at the Tevatron contain a b-quark and hence a b-jet in the final states. We report on the b-jet identification methods in D0 and their performance. For 0.5% of light jet tagging rate, 40 or 45% of b-jet tagging efficiency is achieved for jets with 35 < E{sub T} < 55 GeV and |{eta}| < 1.2.

Hanagaki, K.; /Fermilab

2005-07-01

223

Smart-tag based data dissemination  

Microsoft Academic Search

Monitoring wide, hostile areas requires disseminating data between fixed, disconnected clusters of sensor nodes. It is not always possible to install long-range radios in order to cover the whole area. We propose to leverage the movement of mobile individuals, equipped with smart-tags, to disseminate data across disconnected static nodes spread across a wide area. Static nodes and mobile smart-tags exchange

Allan Beaufour; Martin Leopold; Philippe Bonnet

2002-01-01

224

Programmable reflectors for SAW-ID-tags  

Microsoft Academic Search

Surface acoustic wave devices for identification systems (SAW-ID-tags or SAW wireless labels) have a large potential for future applications. We concentrate in this paper on reflective SAW-ID-tags with amplitude modulation. We use splitfinger interdigital transducers as reflecting structures. If the transducers are short circuited or capacitively loaded the reflection disappears almost entirely. On the other hand, if an open circuit

L. Reindl; W. Ruile

1993-01-01

225

Lysosomal Degradation of Ubiquitin-Tagged Receptors  

NSDL National Science Digital Library

Access to the article is free, however registration and sign-in are required. Cytosolic proteins are tagged with the polypeptide ubiquitin for eventual destruction by the proteasome. A recent paper in Cell (L. Hicke and H. Riezman, vol. 84, p. 277) shows that in yeast ubiquitin also serves to tag membrane proteins for degradation by proteases in the vacuole, the yeast equivalent of the lysosome.

Stella M. Hurtley (AAAS; Science Magazine, Europe Office)

1996-02-02

226

Lock-Out / Tag-Out  

NSDL National Science Digital Library

Tags and locks can be the last line of defense against machinery accidents. This MATEC module leaves your learners solidly grounded in OSHA's six-step lockout/tagout procedures for preventing unexpected start-ups of equipment. They learn how to use energy-isolating devices and how to safely remove locks and tags. They can demonstrate their facility with the OHSA standards using a machine on the manufacturing floor.

227

Lightweight Authentication Protocols for Low-Cost RFID Tags  

Microsoft Academic Search

Providing security in low-cost RFID tags is a challenging task because tags are highly resource con- strained and cannot support strong cryptography. Special lightweight algorithms and protocols need to be designed that take into account the limitations of the tags. In this paper, we propose a set of extremely lightweight tag authentication protocols. We also provide an analysis of the

Istvan Vajda

2003-01-01

228

Theory and measurement of backscattering from RFID tags  

Microsoft Academic Search

This paper presents a method for measuring signal backscattering from RFID tags, and for calculating a tag's radar cross section (RCS). We derive a theoretical formula for the RCS of an RFID tag with a minimum-scattering antenna. We describe an experimental measurement technique, which involves using a network analyzer connected to an anechoic chamber with and without the tag. The

Pavel V. Nikitin; K. V. S. Rao

2006-01-01

229

Theory and Measurement of Backscattering from RFID Tags  

E-print Network

Theory and Measurement of Backscattering from RFID Tags Pavel V. Nikitin and K. V. S. Rao Intermec backscattering from RFID tags and for calculating a tag radar cross-section (RCS). We derive a theoretical formula for RCS of an RFID tag with a minimum scattering antenna and describe an experimental measurement

Hochberg, Michael

230

Quantifying tag representativeness of visual content of social images  

Microsoft Academic Search

Social tags describe images from many aspects including the visual content observable from the images, the context and usage of images, user opinions and others. Not all tags are therefore useful for image search and are appropriate for tag recommendation with respect to visual content of images. However, the relationship between a given tag and the visual content of its

Aixin Sun; Sourav S. Bhowmick

2010-01-01

231

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

232

Effective algorithms for tag SNP selection.  

PubMed

Single nucleotide polymorphisms (SNPs), due to their abundance and low mutation rate, are very useful genetic markers for genetic association studies. However, the current genotyping technology cannot afford to genotype all common SNPs in all the genes. By making use of linkage disequilibrium, we can reduce the experiment cost by genotyping a subset of SNPs, called Tag SNPs, which have a strong association with the ungenotyped SNPs, while are as independent from each other as possible. The problem of selecting Tag SNPs is NP-complete; when there are large number of SNPs, in order to avoid extremely long computational time, most of the existing Tag SNP selection methods first partition the SNPs into blocks based on certain block definitions, then Tag SNPs are selected in each block by brute-force search. The size of the Tag SNP set obtained in this way may usually be reduced further due to the inter-dependency among blocks. This paper proposes two algorithms, TSSA and TSSD, to tackle the block-independent Tag SNP selection problem. TSSA is based on A* search algorithm, and TSSD is a heuristic algorithm. Experiments show that TSSA can find the optimal solutions for medium-sized problems in reasonable time, while TSSD can handle very large problems and report approximate solutions very close to the optimal ones. PMID:16278949

Liu, Tie-Fei; Sung, Wing-Kin; Li, Yi; Liu, Jian-Jun; Mittal, Ankush; Mao, Pei-Lin

2005-10-01

233

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

234

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

235

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

236

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

237

Tag-based Web Photo Retrieval Improved by Batch Mode Re-Tagging Lin Chen Dong Xu Ivor W. Tsang  

E-print Network

Tag-based Web Photo Retrieval Improved by Batch Mode Re-Tagging Lin Chen Dong Xu Ivor W. Tsang 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

Tsang Wai Hung "Ivor"

238

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

Code of Federal Regulations, 2013 CFR

...2013-10-01 2013-10-01 false Tagging of wires and interference of wires or tags with signal apparatus. 236.76 Section...Systems Wires and Cables § 236.76 Tagging of wires and interference of wires or tags with signal apparatus. Each...

2013-10-01

239

49 CFR 234.239 - Tagging of wires and interference of wires or tags with signal apparatus.  

Code of Federal Regulations, 2010 CFR

...2010-10-01 2010-10-01 false Tagging of wires and interference of wires or tags with signal apparatus. 234.239 Section...Maintenance Standards § 234.239 Tagging of wires and interference of wires or tags with signal apparatus. Each wire...

2010-10-01

240

A prototype passive UHF RFID transfer tattoo tag  

Microsoft Academic Search

A novel temporary transfer tattoo based RFID tag is presented providing a non-optimised read range of 50cm. The transfer based tag is proposed for security and personnel tagging applications where the injection of a sub-skin tag is not desirable. With some refinement the tag could have a life span of a day or more, but could not be transferred to

M. A. Ziai; J. C. Batchelor

2011-01-01

241

Positive-negative epitope-tagging of beta amyloid precursor protein to identify inhibitors of A beta processing.  

PubMed

In this report, a novel positive-negative epitope tagging approach was developed to study the cellular processing of beta amyloid precursor protein (beta APP). Amino acids centered around the alpha-secretase cleavage site within the A beta sequence were replaced with residues comprising an epitope for which high-affinity monoclonal antibodies are commercially available. The resulting mutant beta APP cDNAs were expressed in human embryonic kidney cells (HEK 293). Cleavage of labeled beta APP by beta- and gamma-secretase(s) results in the release of an epitope-tagged A beta peptide, whereas cleavage by alpha-secretase results in destruction of the epitope. Highly sensitive and specific immunoassays were developed to study processing of this labeled beta APP via the amyloidogenic pathway. Secretion of epitope-tagged A beta was prevented by MDL 28170, a previously described gamma-secretase inhibitor. Confocal microscopic studies revealed that processing and cellular trafficking of epitope-tagged beta APP was not different from wild-type beta APP. These results suggest that positive-negative epitope-tagged beta APP is normally processed within the cell and may be used to identify secretase inhibitors as therapeutics for Alzheimer's disease. PMID:11113538

Seiffert, D; Mitchell, T; Stern, A M; Roach, A; Zhan, Y; Grzanna, R

2000-12-01

242

Proteomic Studies of Syk-Interacting Proteins Using a Novel Amine-Specific Isotope Tag and GFP Nanotrap  

NASA Astrophysics Data System (ADS)

Green fluorescent protein (GFP) and variants have become powerful tools to study protein localization, interactions, and dynamics. We present here a mass spectrometry-based proteomics strategy to examine protein-protein interactions using anti-GFP single-chain antibody VHH in a combination with a novel stable isotopic labeling reagent, isotope tag on amino groups (iTAG). We demonstrate that the single-chain VHH (GFP nanotrap) allows us to identify interacting partners of the Syk protein-tyrosine kinase bearing a GFP epitope tag with high efficiency and high specificity. Interacting proteins identified include CrkL, BLNK, ?- and ?-tubulin, Csk, RanBP5 and DJ-1. The iTAG reagents were prepared with simple procedures and characterized with high accuracy in the determination of peptides in model peptide mixtures and as well as in complex mixture. Applications of the iTAG method and GFP nanotrap to an analysis of the nucleocytoplasmic trafficking of Syk led to the identification of location-specific associations between Syk and multiple proteins. While the results reveal that the new quantitative proteomic strategy is generally applicable to integrate protein interaction data with subcellular localization, extra caution should be taken in evaluating the results obtained by such affinity purification strategies as many interactions appear to occur following cell lysis.

Galan, Jacob A.; Paris, Leela L.; Zhang, Hua-jie; Adler, Jacob; Geahlen, Robert L.; Tao, W. Andy

2011-02-01

243

The automorphisms of affine fusion rings  

E-print Network

The fusion rings associated to affine Kac-Moody algebras appear in several different contexts in math and mathematical physics. In this paper we find all automorphisms of all affine fusion rings, or equivalently the symmetries of the corresponding fusion coefficients. Most of these are directly related to symmetries of the corresponding Coxeter-Dynkin diagram. We also find all pairs of isomorphic affine fusion rings.

T. Gannon

2000-02-07

244

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

245

Structural determinants of sigma receptor affinity  

SciTech Connect

The structural determinants of sigma receptor affinity have been evaluated by examining a wide range of compounds related to opioids, neuroleptics, and phenylpiperidine dopaminergic structures for affinity at sigma receptor-binding sites labeled with (+)-(/sup 3/H)3-PPP. Among opioid compounds, requirements for sigma receptor affinity differ strikingly from the determinants of affinity for conventional opiate receptors. Sigma sites display reverse stereoselectivity to classical opiate receptors. Multi-ringed opiate-related compounds such as morphine and naloxone have negligible affinity for sigma sites, with the highest sigma receptor affinity apparent for benzomorphans which lack the C ring of opioids. Highest affinity among opioids and other compounds occurs with more lipophilic N-substituents. This feature is particularly striking among the 3-PPP derivatives as well as the opioids. The butyrophenone haloperidol is the most potent drug at sigma receptors we have detected. Among the series of butyrophenones, receptor affinity is primarily associated with the 4-phenylpiperidine moiety. Conformational calculations for various compounds indicate a fairly wide range of tolerance for distances between the aromatic ring and the amine nitrogen, which may account for the potency at sigma receptors of structures of considerable diversity. Among the wide range of structures that bind to sigma receptor-binding sites, the common pharmacophore associated with high receptor affinity is a phenylpiperidine with a lipophilic N-substituent.

Largent, B.L.; Wikstroem, H.G.; Gundlach, A.L.; Snyder, S.H.

1987-12-01

246

A brief examination of optical tagging technologies.  

SciTech Connect

Presented within this report are the results of a brief examination of optical tagging technologies funded by the Laboratory Directed Research and Development (LDRD) program at Sandia National Laboratories. The work was performed during the summer months of 2002 with total funding of $65k. The intent of the project was to briefly examine a broad range of approaches to optical tagging concentrating on the wavelength range between ultraviolet (UV) and the short wavelength infrared (SWIR, {lambda} < 2{micro}m). Tagging approaches considered include such things as simple combinations of reflective and absorptive materials closely spaced in wavelength to give a high contrast over a short range of wavelengths, rare-earth oxides in transparent binders to produce a narrow absorption line hyperspectral tag, and fluorescing materials such as phosphors, dies and chemically precipitated particles. One technical approach examined in slightly greater detail was the use of fluorescing nano particles of metals and semiconductor materials. The idea was to embed such nano particles in an oily film or transparent paint binder. When pumped with a SWIR laser such as that produced by laser diodes at {lambda}=1.54{micro}m, the particles would fluoresce at slightly longer wavelengths, thereby giving a unique signal. While it is believed that optical tags are important for military, intelligence and even law enforcement applications, as a business area, tags do not appear to represent a high on return investment. Other government agencies frequently shop for existing or mature tag technologies but rarely are interested enough to pay for development of an untried technical approach. It was hoped that through a relatively small investment of laboratory R&D funds, enough technologies could be identified that a potential customers requirements could be met with a minimum of additional development work. Only time will tell if this proves to be correct.

Ackermann, Mark R.; Cahill, Paul A. (Aspecular Optics, Dayton, OH); Drummond, Timothy J.; Wilcoxon, Jess Patrick

2003-07-01

247

Synthesis of poly(N-isopropylacrylamide) particles for metal affinity binding of peptides.  

PubMed

Temperature-sensitive poly(N-isopropylacrylamide) (PNIPAM) microgel particles with metal affinity ligands were prepared for selective binding of peptides containing the His6-tag (six consecutive histidine residues). The PNIPAM particles were copolymerized with the functional ligand vinylbenzyl iminodiacetic acid (VBIDA) through a two-stage dispersion polymerization using poly(N-vinyl pyrrolidone) (PVP) as a steric stabilizer. The resulting particles were monodisperse in size and colloidally stable over a wide range of temperature and ionic strength due to chemically grafted PVP chains. The particle size was also found to be sensitive to ionic strength and pH of the aqueous environment, likely due to the electrostatic repulsion between ionized VBIDA groups. Divalent nickel ions were chelated to the VBIDA groups, allowing selective metal affinity attachment of a His6-Cys peptide. The peptide was released upon the addition of the competitive ligand imidazole, demonstrating that the peptide attachment to the particles is reversible and selective. PMID:24176889

Tsai, Hsin-Yi; Lee, Alexander; Peng, Wei; Yates, Matthew Z

2014-02-01

248

Synthesis of poly(N-isopropylacrylamide) particles for metal affinity binding of peptides  

PubMed Central

Temperature-sensitive poly(N-isopropylacrylamide) (PNIPAM) microgel particles with metal affinity ligands were prepared for selective binding of peptides containing the His6-tag (six consecutive histidine residues). The PNIPAM particles were copolymerized with the functional ligand vinylbenzyl iminodiacetic acid (VBIDA) through a two-stage dispersion polymerization using poly(N-vinyl pyrrolidone) (PVP) as a steric stabilizer. The resulting particles were monodisperse in size and colloidally stable over a wide range of temperature and ionic strength due to chemically grafted PVP chains. The particle size was also found to be sensitive to ionic strength and pH of the aqueous environment, likely due to the electrostatic repulsion between ionized VBIDA groups. Divalent nickel ions were chelated to the VBIDA groups, allowing selective metal affinity attachment of a His6-Cys peptide. The peptide was released upon the addition of the competitive ligand imidazole, demonstrating that the peptide attachment to the particles is reversible and selective. PMID:24176889

Tsai, Hsin-Yi; Lee, Alexander; Peng, Wei; Yates, Matthew Z.

2013-01-01

249

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

E-print Network

being used in cards and documents containing privacy- sensitive personal information, e.g., in passports, credit cards, and enhanced drivers' licences [5,7] (e.g., Figure 3). People, however, are often unaware on communications between tags and readers, and cloning and misuse of data stored on tags (e.g., [4,7,8]). While

Hunt, Galen

250

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

251

Fast and scalable image auto-tagging  

E-print Network

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

Frejaville, Camille; Lepetit, Vincent

252

Double trouble-Buffer selection and His-tag presence may be responsible for nonreproducibility of biomedical experiments.  

PubMed

The availability of purified and active protein is the starting point for the majority of in vitro biomedical, biochemical, and drug discovery experiments. The use of polyhistidine affinity tags has resulted in great increases of the efficiency of the protein purification process, but can negatively affect structure and/or activity measurements. Similarly, buffer molecules may perturb the conformational stability of a protein or its activity. During the determination of the structure of a Gcn5-related N-acetyltransferase (GNAT) from Pseudomonas aeruginosa (PA4794), we found that both HEPES and the polyhistidine affinity tag bind (separately) in the substrate-binding site. In the case of HEPES, the molecule induces conformational changes in the active site, but does not significantly affect enzyme activity. In contrast, the uncleaved His-tag does not induce major conformational changes but acts as a weak competitive inhibitor of peptide substrate. In two other GNAT enzymes, we observed that the presence of the His-tag had a strong influence on the activity of these proteins. The influence of protein preparation on functional studies may affect the reproducibility of experiments in other laboratories, even when changes between protocols seem at first glance to be insignificant. Moreover, the results presented here show how critical it is to adjust the experimental conditions for each protein or family of proteins, and investigate the influence of these factors on protein activity and structure, as they may significantly alter the effectiveness of functional characterization and screening methods. Thus, we show that a polyhistidine tag and the buffer molecule HEPES bind in the substrate-binding site and influence the conformation of the active site and the activity of GNAT acetyltransferases. We believe that such discrepancies can influence the reproducibility of some experiments and therefore could have a significant "ripple effect" on subsequent studies. PMID:25044180

Majorek, Karolina A; Kuhn, Misty L; Chruszcz, Maksymilian; Anderson, Wayne F; Minor, Wladek

2014-10-01

253

Accurate Protein Complex Retrieval by Affinity Enrichment Mass Spectrometry (AE-MS) Rather than Affinity Purification Mass Spectrometry (AP-MS).  

PubMed

Protein-protein interactions are fundamental to the understanding of biological processes. Affinity purification coupled to mass spectrometry (AP-MS) is one of the most promising methods for their investigation. Previously, complexes were purified as much as possible, frequently followed by identification of individual gel bands. However, todays mass spectrometers are highly sensitive, and powerful quantitative proteomics strategies are available to distinguish true interactors from background binders. Here we describe a high performance affinity enrichment-mass spectrometry method for investigating protein-protein interactions, in which no attempt at purifying complexes to homogeneity is made. Instead, we developed analysis methods that take advantage of specific enrichment of interactors in the context of a large amount of unspecific background binders. We perform single-step affinity enrichment of endogenously expressed GFP-tagged proteins and their interactors in budding yeast, followed by single-run, intensity-based label-free quantitative LC-MS/MS analysis. Each pull-down contains around 2000 background binders, which are reinterpreted from troubling contaminants to crucial elements in a novel data analysis strategy. First the background serves for accurate normalization. Second, interacting proteins are not identified by comparison to a single untagged control strain, but instead to the other tagged strains. Third, potential interactors are further validated by their intensity profiles across all samples. We demonstrate the power of our AE-MS method using several well-known and challenging yeast complexes of various abundances. AE-MS is not only highly efficient and robust, but also cost effective, broadly applicable, and can be performed in any laboratory with access to high-resolution mass spectrometers. PMID:25363814

Keilhauer, Eva C; Hein, Marco Y; Mann, Matthias

2015-01-01

254

Accurate Protein Complex Retrieval by Affinity Enrichment Mass Spectrometry (AE-MS) Rather than Affinity Purification Mass Spectrometry (AP-MS)*  

PubMed Central

Protein–protein interactions are fundamental to the understanding of biological processes. Affinity purification coupled to mass spectrometry (AP-MS) is one of the most promising methods for their investigation. Previously, complexes were purified as much as possible, frequently followed by identification of individual gel bands. However, todays mass spectrometers are highly sensitive, and powerful quantitative proteomics strategies are available to distinguish true interactors from background binders. Here we describe a high performance affinity enrichment-mass spectrometry method for investigating protein–protein interactions, in which no attempt at purifying complexes to homogeneity is made. Instead, we developed analysis methods that take advantage of specific enrichment of interactors in the context of a large amount of unspecific background binders. We perform single-step affinity enrichment of endogenously expressed GFP-tagged proteins and their interactors in budding yeast, followed by single-run, intensity-based label-free quantitative LC-MS/MS analysis. Each pull-down contains around 2000 background binders, which are reinterpreted from troubling contaminants to crucial elements in a novel data analysis strategy. First the background serves for accurate normalization. Second, interacting proteins are not identified by comparison to a single untagged control strain, but instead to the other tagged strains. Third, potential interactors are further validated by their intensity profiles across all samples. We demonstrate the power of our AE-MS method using several well-known and challenging yeast complexes of various abundances. AE-MS is not only highly efficient and robust, but also cost effective, broadly applicable, and can be performed in any laboratory with access to high-resolution mass spectrometers. PMID:25363814

Keilhauer, Eva C.; Hein, Marco Y.; Mann, Matthias

2015-01-01

255

Recursive Turtle Programs and Iterated Affine Transformations  

E-print Network

Recursive Turtle Programs and Iterated Affine Transformations Tao Ju*, Scott Schaefer, Ron Goldman of equivalence between the class of fractals created by Recursive Turtle Programs (RTP) and Iterated Affine, turtle graphics 1 Introduction In computer graphics, there are several different methods for generating 2

Schaefer, Scott

256

Double affine Hecke algebras and noncommutative geometry  

E-print Network

In the first part we study Double Affine Hecke algebra of type An-1 which is important tool in the theory of orthogonal polynomials. We prove that the spherical subalgebra eH(t, 1)e of the Double Affine Hecke algebra H(t, ...

Oblomkov, Alexei

2005-01-01

257

Affine Constellations Without Mutually Unbiased Counterparts  

E-print Network

It has been conjectured that a complete set of mutually unbiased bases in a space of dimension d exists if and only if there is an affine plane of order d. We introduce affine constellations and compare their existence properties with those of mutually unbiased constellations, mostly in dimension six. The observed discrepancies make a deeper relation between the two existence problems unlikely.

Stefan Weigert; Thomas Durt

2010-07-22

258

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

259

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

PubMed

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-Ni(2+) column. PMID:24270901

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

2013-12-20

260

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

261

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

PubMed Central

Background Sequencing metagenomes that were pre-amplified with primer-based methods requires the removal of the additional tag sequences from the datasets. The sequenced reads can contain deletions or insertions due to sequencing limitations, and the primer sequence may contain ambiguous bases. Furthermore, the tag sequence may be unavailable or incorrectly reported. Because of the potential for downstream inaccuracies introduced by unwanted sequence contaminations, it is important to use reliable tools for pre-processing sequence data. Results TagCleaner is a web application developed to automatically identify and remove known or unknown tag sequences allowing insertions and deletions in the dataset. TagCleaner is designed to filter the trimmed reads for duplicates, short reads, and reads with high rates of ambiguous sequences. An additional screening for and splitting of fragment-to-fragment concatenations that gave rise to artificial concatenated sequences can increase the quality of the dataset. Users may modify the different filter parameters according to their own preferences. Conclusions TagCleaner is a publicly available web application that is able to automatically detect and efficiently remove tag sequences from metagenomic datasets. It is easily configurable and provides a user-friendly interface. The interactive web interface facilitates export functionality for subsequent data processing, and is available at http://edwards.sdsu.edu/tagcleaner. PMID:20573248

2010-01-01

262

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

263

Electron neutrino tagging through tertiary lepton detection  

E-print Network

We discuss an experimental technique aimed at tagging electron neutrinos in multi-GeV artificial sources on an event-by-event basis. It exploits in a novel manner calorimetric and tracking technologies developed in the framework of the LHC experiments and of rare kaon decay searches. The setup is suited for slow-extraction, moderate power beams and it is based on an instrumented decay tunnel equipped with tagging units that intercept secondary and tertiary leptons from the bulk of undecayed \\pi^+ and protons. We show that the taggers are able to reduce the \

L. Ludovici; F. Terranova

2010-07-27

264

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

265

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

266

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

267

48 CFR 908.7101-7 - Government license tags.  

Code of Federal Regulations, 2010 CFR

...Assignments of specific “blocks” of tag numbers and the...Assignments of additional “blocks” of tag numbers will be made...Transportation, Motor Vehicles Services Branch, District of Columbia, for...exempt for security purposes) based or housed in the...

2010-10-01

268

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

269

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

270

Improved expression and purification of the Helicobacter pylori adhesin BabA through the incorporation of a hexa-lysine tag.  

PubMed

Helicobacter pylori is a pathogenic bacterium that has the remarkable ability to withstand the harsh conditions of the stomach for decades. This is achieved through unique evolutionary adaptations, which include binding Lewis(b) antigens found on the gastric epithelium using the outer membrane protein BabA. We show here the yield of a recombinant form of BabA, comprising its putative extracellular binding domain, can be significantly increased through the addition of a hexa-lysine tag to the C-terminus of the protein. BabA was expressed in the periplasmic space of Escherichiacoli and purified using immobilised metal ion affinity and size exclusion chromatography - yielding approximately 1.8mg of protein per litre of culture. The hexa-lysine tag does not inhibit the binding activity of BabA as the recombinant protein was found to possess affinity towards HSA-Lewis(b) glycoconjugates. PMID:25448827

Hage, Naim; Renshaw, Jonathan G; Winkler, G Sebastiaan; Gellert, Paul; Stolnik, Snow; Falcone, Franco H

2015-02-01

271

Myocardial tissue tagging with cardiovascular magnetic resonance  

Microsoft Academic Search

Cardiovascular magnetic resonance (CMR) is currently the gold standard for assessing both global and regional myocardial function. New tools for quantifying regional function have been recently developed to characterize early myocardial dysfunction in order to improve the identification and management of individuals at risk for heart failure. Of particular interest is CMR myocardial tagging, a non-invasive technique for assessing regional

Monda L Shehata; Susan Cheng; Nael F Osman; David A Bluemke; João AC Lima

2009-01-01

272

Altruism "For Free" using Tags David Hales  

E-print Network

of Bologna dave@davidhales.com Keywords: Altruism, Evolution of cooperation, Tags, Prisoner's Dilemma a simpler approach in which individuals play the single round Prisoner's Dilemma (PD) game. Contrary in the population the quicker altruism emerges) and robust to noise. This "altruism for free" property has already

Hales, David

273

Imaging mass spectrometer with mass tags  

DOEpatents

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

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

2013-01-29

274

Beliefs and Uses of Tagging among Undergraduates  

ERIC Educational Resources Information Center

Context: This dissertation examines beliefs and uses regarding tagging among current undergraduate students, and examines the ecology of communications practice and implications for formation and maintenance of identity within the population. Currently enrolled undergraduate students at UNC-Chapel Hill formed the population for examination. …

Kramer-Duffield, Jacob

2010-01-01

275

Chemical Address Tags of Fluorescent Bioimaging Probes  

PubMed Central

Chemical address tags can be defined as specific structural features shared by a set of bioimaging probes having a predictable influence on cell-associated visual signals obtained from these probes. Here, using a large image dataset acquired with a high content screening instrument, machine vision and cheminformatics analysis have been applied to reveal chemical address tags. With a combinatorial library of fluorescent molecules, fluorescence signal intensity, spectral, and spatial features characterizing each one of the probes' visual signals were extracted from images acquired with the three different excitation and emission channels of the imaging instrument. With multivariate regression, the additive contribution from each one of the different building blocks of the bioimaging probes towards each measured, cell-associated image-based feature was calculated. In this manner, variations in the chemical features of the molecules were associated with the resulting staining patterns, facilitating quantitative, objective analysis of chemical address tags. Hierarchical clustering and paired image-cheminformatics analysis revealed key structure-property relationships amongst many building blocks of the fluorescent molecules. The results point to different chemical modifications of the bioimaging probes that can exert similar (or different) effects on the probes' visual signals. Inspection of the clustered structures suggests intramolecular charge migration or partial charge distribution as potential mechanistic determinants of chemical address tag behavior. PMID:20104576

Shedden, Kerby; Rosania, Gus R.

2010-01-01

276

Automated tag reading system for material tracking  

NASA Astrophysics Data System (ADS)

An automated product tag reading system based on CCD cameras and computer image processing has been developed by West Virginia University, and demonstrated at the Weirton Steel Corporation. The system was developed to read painted steel identification tags which are fastened to the ends of steel slabs. The prototype was mounted on a slab hauler and tested in a steel mill environment. It demonstrated the ability to survey a wide-angle image of a scene, locate the target tags in the image, pan and zoom on each one in turn, and read the contents of the tag -- both bar code and alphanumeric code. The system could communicate via radio modem to a stationary computer which could be interfaced to the plant's inventory management database. We are aware of no other system which can both point and read a bar code scanner. The pointing function is important, in that it allows operation in bright sunlight or at long distances: two conditions where humans encounter difficulties in aiming. Our system can read 50-mil bar codes at distances of 30 feet without the use of retro reflective targets. This paper provides an overview of the technical approach used, and the results of stem testing.

Banta, Larry E.; Rosenberry-Friend, Kimberly A.; Pertl, Franz A.

1997-09-01

277

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

278

RFID-Tags for Anti-counterfeiting  

Microsoft Academic Search

RFID-tags are becoming very popular tools for identiflcation of products. As they have a small microchip on board, they ofier func- tionality that can be used for security purposes. This chip functionality makes it possible to verify the authenticity of a product and hence to detect and prevent counterfeiting. In order to be successful for these secu- rity purposes too,

Pim Tuyls; Lejla Batina

2006-01-01

279

Untraceable RFID tags via insubvertible encryption  

Microsoft Academic Search

We introduce a new cryptographic primitive, called insubvertible encryption, that produces ciphertexts which can be randomized without the need of any key material. Unlike plain universal re-encryption schemes, insubvertible encryption prevents against adversarial exploitation of hidden channels, by including certificates proving that the ciphertext can only be decrypted by authorized parties.The scheme can be applied to RFID tags, providing strong

Giuseppe Ateniese; Jan Camenisch; Breno de Medeiros

2005-01-01

280

TagSense RFID Communications Mikyle Bengtson  

E-print Network

TagSense RFID Communications Mikyle Bengtson Faculty Mentor: Professor Russell Tessier This project focuses on the communications between an RFID reader and several RFID transmitters. Once complete so that response times in mass-casualty incidents can be reduced. At the heart of this system is RFID

Mountziaris, T. J.

281

Novel and efficient tag SNPs selection algorithms.  

PubMed

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

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

2014-01-01

282

Marine Fisheries On the cover: A tagged  

E-print Network

Marine Fisheries ~@WD@W Articles On the cover: A tagged striped marlin ready for release. See Crab Gunnar Finne, and Debra J. Hopson 38 Incidental Catch of Marine Mammals by Foreign Fishing Vessels. Gordon, Assistant Administrator for Fisheries National Marine Fisheries Service Editor: W. Hobart

283

Affine braids, Markov traces and the category O Rosa Orellana  

E-print Network

, affine BMW algebras, cyclotomic BMW algebras, Markov traces, Jacobi-Trudi type identities, dual pairs [Ze of affine braid groups of type A, (d) We define the affine BMW algebra (Birman-Murakami-Wenzl) and show

Ram, Arun

284

Development of Translating Ribosome Affinity Purification for Zebrafish  

PubMed Central

Summary The regulation of transcription and translation by specific cell types is essential to generate the cellular diversity that typifies complex multicellular organisms. Tagging and purification of ribosomal proteins has been shown to be an innovative and effective means of characterizing the ribosome bound transcriptome of highly specific cell populations in vivo. To test the feasibility of using translating ribosome affinity purification (TRAP) in zebrafish, we have generated both a ubiquitous TRAP line and a melanocyte-specific TRAP line using the native zebrafish rpl10a ribosomal protein. We have demonstrated the capacity to capture mRNA transcripts bound to ribosomes, and confirmed the expected enrichment of melanocyte specific genes and depletion of non-melanocyte genes when expressing the TRAP construct with a cell specific promoter. We have also generated a generic EGFP-rpl10a Tol2 plasmid construct (Tol2-zTRAP) that can be readily modified to target any additional cell populations with characterized promoters in zebrafish. PMID:23281262

Tryon, Robert C.; Pisat, Nilambari; Johnson, Stephen L.; Dougherty, Joseph D.

2013-01-01

285

Comparison of cation binding affinities of quinones  

NASA Astrophysics Data System (ADS)

The relative gas-phase basicity scale and the relative dimethoxy borinium ion affinity scale of various quinones were determined by the ligand exchange method to investigate the structural factors which influence the binding properties of the quinones. The relative gas-phase basicity scale and dimethoxy borinium ion affinity scale were similar, and were proved to correlate with the extent of favorable functional group interactions and counteractive electron-withdrawing effects of certain substituents. For 1,2-naphthoquinone and lawsone the order of affinities was reversed, presumably because of a secondary hydrogen-bonding interaction active for lawsone that particularly enhanced the stability of its borinium adduct.

Hall, Brad J.; Brodbelt, Jennifer S.

1996-11-01

286

Affinity purification of long noncoding RNA-protein complexes from formaldehyde cross-linked mammalian cells.  

PubMed

Long noncoding RNAs (lncRNAs) are a class of recently identified untranslated RNA molecules that have been shown to function in diverse cellular processes. The purification and analysis of lncRNA-protein (lncRNP) complexes is critical toward understanding the normal physiological function of these molecules. Here, we describe the purification of lncRNP complexes from human cells using a FLAG-tagged MS2-phage coat protein (MS2 CP) that binds in sequence-specific fashion to MS2-phage coat protein-binding sites (MS2bs) with high affinity. In these experiments, a FLAG-tagged MS2 CP is transiently co-expressed with a version of the lncRNA into which 12 copies of the MS2bs have been inserted near its 3'-end. The lncRNA-FLAG-tagged MS2 CP complex is then isolated using an anti-FLAG antibody, allowing for characterization of associated cellular proteins and RNAs. PMID:25240888

Gong, Chenguang; Maquat, Lynne E

2015-01-01

287

CTSC: Core-Tag Oriented Spectral Clustering Algorithm on Web2.0 Tags  

Microsoft Academic Search

With the rapid development of the Web2.0 communities, many researchers have been attracted by the concept of folksonomy from the field of data mining and information retrieval. Finding out semantic correlation of tags is avid requirement for Web2.0 application. However, no proper algorithm can tackle this task very well. This paper proposes a core-tag oriented clustering method to handle the

Yexi Jiang; Changjie Tang; Kaikuo Xu; Yu Chen; Jie Gong; Liang Tang

2009-01-01

288

Accurate Visual Features for Automatic Tag Correction in Videos  

E-print Network

Accurate Visual Features for Automatic Tag Correction in Videos Hoang-Tung Tran, Elisa Fromont-Etienne, Fr Abstract. We present a new system for video auto tagging which aims at correcting the tags provided by users for videos uploaded on the In- ternet. Unlike most existing systems, in our proposal, we

Paris-Sud XI, Université de

289

A global SAW ID tag with large data capacity  

Microsoft Academic Search

The Global SAW Tag uses a recently-invented digital modulation based on simultaneous time position and phase shifting. A unique feature of this tag is that it satisfies global RFID requirements using the international 2.44 GHz ISM band. Precision amplitude and phase weighting of reflectors and accurate control of parasitic effects is critical to implementing this device. This tag has significantly

Clinton S. Hartmann

2002-01-01

290

Electronic tagging and population structure of Atlantic bluefin tuna  

Microsoft Academic Search

Electronic tags that archive or transmit stored data to satellites have advanced the mapping of habitats used by highly migratory fish in pelagic ecosystems. Here we report on the electronic tagging of 772 Atlantic bluefin tuna in the western Atlantic Ocean in an effort to identify population structure. Reporting electronic tags provided accurate location data that show the extensive migrations

Barbara A. Block; Steven L. H. Teo; Andreas Walli; Andre Boustany; Michael J. W. Stokesbury; Charles J. Farwell; Kevin C. Weng; Heidi Dewar; Thomas D. Williams

2005-01-01

291

Change Your Tags Fast! A necessary condition for cooperation?  

E-print Network

of high mutation applied to tags. In order to import MABS techniques into engineering of MAS these kinds models discussed here tags are modeled using some number (either a binary bit string, a real number using a real number, there are many possible unique tags rather than just 3 colors) however, the basic

Hales, David

292

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

E-print Network

of high mutation applied to tags. In order to import MABS techniques into engineering of MAS these kinds models discussed here tags are modeled using some number (either a binary bit string, a real number using a real number, there are many possible unique tags rather than just 3 colors) however, the basic

Hales, David

293

Authentication for RFID Tags: Observations on the HB Protocols  

E-print Network

Authentication for RFID Tags: Observations on the HB Protocols Erik Zenner Technical University Mathematics) Authentication for RFID Tags Aalborg, April 23, 2009 1 / 20 #12;1 RFID Basics 2 The Original HB) Authentication for RFID Tags Aalborg, April 23, 2009 2 / 20 #12;RFID Basics Outline 1 RFID Basics 2 The Original

Zenner, Erik

294

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 be constructed with a commercial passive UHF RFID IC. The temperature sensor tag's measurement range spans from

Elsherbeni, Atef Z.

295

Doctoral Thesis A Study on Cryptographic Protocols for RFID Tags  

E-print Network

Doctoral Thesis RFID A Study on Cryptographic Protocols for RFID Tags ( Dang, Nguyen Duc 2010 #12;RFID A Study on Cryptographic Protocols for RFID Tags #12;A Study on Cryptographic Protocols for RFID Tags Advisor : Professor Kim, Kwangjo by Dang, Nguyen Duc Department of Information

Kim, Kwangjo

296

Synaptic Tagging, Evaluation of Memories, and the Distal Reward Problem  

ERIC Educational Resources Information Center

Long-term synaptic plasticity exhibits distinct phases. The synaptic tagging hypothesis suggests an early phase in which synapses are prepared, or "tagged," for protein capture, and a late phase in which those proteins are integrated into the synapses to achieve memory consolidation. The synapse specificity of the tags is consistent with…

Papper, Marc; Kempter, Richard; Leibold, Christian

2011-01-01

297

Soft Lepton Flavor Tagging at CDF using Run 2 Data  

NASA Astrophysics Data System (ADS)

An overview of soft lepton tagging at CDF is presented. Flavour tagging is needed to determine the flavour of a B(B_0/B_S) meson at production. Making such a decision is called flavour tagging the B meson. This is required to make precision measurements of B mixing and CP violation. Soft Lepton tagging is an opposite side tagging which exploits the sign of the lepton in the decays, b arrow X l^- compared to barb arrow X l^+, where l is an electron or muon, to tag the B. The effectiveness of the tagging is characterised by the effective tagging efficiency, ? D^2, where ? is the tagging efficiency and the dilution D is a measure of the wrong sign tags. In Run 2, CDF expects to improve the effective tagging efficiency, due to an extended lepton coverage with the muon extension systems and the plug calorimeter. Details on the soft lepton tagging studies and results using the latest data sample at CDF are presented.

Moulik, Tania

2003-04-01

298

Lightweight Authentication Protocols for Low-Cost RFID Tags  

E-print Network

Lightweight Authentication Protocols for Low-Cost RFID Tags Istv´an Vajda and Levente Butty of Technology and Economics, Hungary http://www.crysys.hu/ August 5, 2003 Abstract Providing security in low-cost identification numbers to user written data or data computed by the tag. In the near future, low-cost RFID tags

Levente, Buttyán

299

Integrated Management and Visualization of Electronic Tag Data with Tagbase  

Microsoft Academic Search

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,

Chi Hin Lam; Vardis M. Tsontos

2011-01-01

300

Bootstrapping Large Sense Tagged Corpora Rada F. MIHALCEA  

E-print Network

of a bootstrapping algorithm. We start with a set of seeds that are used (1) to extract text snippets from the WebNet. Seeds may also be extracted from additional sense tagged examples, as for instance the training data that can be accurately sense tagged. The newly tagged words are added to the set of seeds

Mihalcea, Rada

301

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

PubMed

Tandem affinity purification coupled to mass spectrometry (TAP-MS) is one of the most advanced methods to characterize protein complexes in plants, giving a comprehensive view on the protein-protein interactions (PPIs) of a certain protein of interest (bait). The bait protein is fused to a double affinity tag, which consists of a protein G tag and a streptavidin-binding peptide separated by a very specific protease cleavage site, allowing highly specific protein complex isolation under near-physiological conditions. Implementation of this optimized TAP tag, combined with ultrasensitive MS, means that these experiments can be performed on small amounts (25 mg of total protein) of protein extracts from Arabidopsis cell suspension cultures. It is also possible to use this approach to isolate low abundant protein complexes from Arabidopsis seedlings, thus opening perspectives for the exploration of protein complexes in a plant developmental context. Next to protocols for efficient biomass generation of seedlings (?7.5 months), we provide detailed protocols for TAP (1 d), and for sample preparation and liquid chromatography-tandem MS (LC-MS/MS; ?5 d), either from Arabidopsis seedlings or from cell cultures. For the identification of specific co-purifying proteins, we use an extended protein database and filter against a list of nonspecific proteins on the basis of the occurrence of a co-purified protein among 543 TAP experiments. The value of the provided protocols is illustrated through numerous applications described in recent literature. PMID:25521792

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

2015-01-01

302

Facile purification of Escherichia coli expressed tag-free recombinant human tumor necrosis factor alpha from supernatant.  

PubMed

Fusing affinity tag at N-terminus was reported to decrease the biological activity of the recombinant human tumor necrosis factor alpha. Although preparation of tag-free rhTNF-? has already been achieved, the processes were yet laborious, especially in large scale. In this paper, tag-free rhTNF-? was almost equally synthesized by Escherichia coli in both soluble and insoluble forms. A two-step ion exchange chromatography, DEAE-Sepharose combined with CM-Sepharose, was developed to purify the soluble specie from supernatant after cell lysis. Native PAGE and HP-SEC showed the rhTNF-? extracted from supernatant existed in a homogeneous form. HP-SAX and SDS-PAGE analysis demonstrated the purity of the final fraction was over 98% with a very high recovery of 75%. Circular dichroism spectrum demonstrated that ?-sheet structure was dominant and fluorescence analysis suggested no dramatic exposure of aromatic amino acid residues on the protein surface. Bioassay indicated that purified rhTNF-? was biologically active with a specific activity of approximately 2.0×10(7)U/mg. All these results suggested that this two-step ion exchange chromatography is efficient for preparation of biologically active tag-free rhTNF-? from supernatant. PMID:24412132

Zhang, Chun; Liu, Yongdong; Zhao, Dawei; Li, Xiunan; Yu, Rong; Su, Zhiguo

2014-03-01

303

Tag Retention and Survival of Age0 Atlantic Salmon following Surgical Implantation with Passive Integrated Transponder Tags  

Microsoft Academic Search

We evaluated an alternative to using hypodermic needles to implant passive integrated transponder (PIT) tags in the body cavities of juvenile salmonids. We used surgical techniques to place PIT tags into the body cavities of 3,037 age-0 Atlantic salmon Salmo salar and then held fish under hatchery conditions for 9 months. Tag retention was 99.8% (six fish lost tags), and

G. Gries; B. H. Letcher

2002-01-01

304

Combinatorics in affine flag varieties James Parkinson  

E-print Network

Combinatorics in affine flag varieties James Parkinson Institut f¨ur Mathematische Strukturtheorie Technische Universit¨at Graz Steyrergasse 30/III, A-8010 Graz Austria parkinson@weyl.math.tu-graz.ac.at Arun

Ram, Arun

305

Growth, Mortality, and Mark Retention of Hatchery Brook Trout Marked with Visible Implant Tags, Jaw Tags, and Adipose Fin Clips  

Microsoft Academic Search

Growth, mortality, mark retention, and mark readability were compared among control and treatment groups of 197–265-mm hatchery brook trout Salvelinus fonitinalis marked with visible implant (VI) tags, adipose tin (AD) clips, or stainless steel circularstrap jaw tags. Based on growth rates calculated for individual fish after 90 d, brook trout marked with VI tags grew faster than those with jaw

Adam Zerrenner; Daniel C. Josephson; Charles C. Krueger

1997-01-01

306

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

307

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

PubMed Central

We present an example of expression and purification of a biologically active G protein coupled receptor (GPCR) from yeast. An expression 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. Ligand binding and signaling assays of the epitope-tagged, mutated receptor showed it maintained the full wild-type 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 MALDI-TOF 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. PMID:17646109

Lee, Byung-Kwon; Jung, Kyung-Sik; Son, Cagdas; Kim, Heejung; VerBerkmoes, Nathan C.; Arshava, Boris; Naider, Fred; Becker, Jeffrey M.

2007-01-01

308

His-tag truncated butyrylcholinesterase as a useful construct for in vitro characterization of wild-type and variant butyrylcholinesterases.  

PubMed

Human butyrylcholinesterase (BChE) can scavenge and thereby provide protection against various toxic esters, including organophosphate-based chemical warfare agents and the recreational drug cocaine. It is currently being used in molecular evolution studies to generate novel enzymes with improved ability to hydrolyze toxic ester compounds. Currently, the most commonly used purification strategies for recombinant BChE enzymes involve using affinity resins based on small molecule interactions with the enzyme's substrate binding site. However, as BChE variants are discovered and developed, a generic purification protocol that is insensitive to amino acid substitutions is necessary. In the current manuscript, an expression vector encoding a C-terminal truncation and a His?-tag was designed for BChE and used to express recombinant "wild-type" enzyme and two variants (i.e., G117H BChE and G117H/E197Q BChE). All the three His?-tagged enzymes were successfully purified via metal-affinity columns using similar procedures with good recovery. Steady-state kinetic parameters were determined for each enzyme, and values were compared to those obtained with the corresponding non-truncated non-His?-tagged enzymes. Rates of inhibition by echothiophate, a model compound for organophosphate-based pesticides, and rates of oxime-mediated reactivation after inhibition with a nerve agent model compound were also determined for selected enzymes. Rates of spontaneous reactivation from ETP inhibition were determined for the G117H variants. In all instances examined, truncation of the C-terminus of BChE and introduction of a His?-tag had no significant effects on the observed kinetic parameters, making this a highly useful construct for in vitro characterization of wild-type and variant BChEs. PMID:21802514

Ralph, Erik C; Xiang, Longkuan; Cashman, John R; Zhang, Jun

2011-11-01

309

Design and establishment of a vector system that enables production of multifusion proteins and easy purification by a two-step affinity chromatography approach.  

PubMed

The LE (LguI/Eco81I)-cloning procedure allows a step-wise, directional fusion of multiple DNA-fragments into a vector by utilizing two restriction enzymes generating identical non-palindromic overhangs. This strategy was applied to produce heat-stable cellulase-fusion proteins containing up to five single moieties. Terminal affinity tags enable efficient purification using a simple two-step approach. PMID:25026273

Marquardt, Tabea; von der Heyde, Amélie; Elleuche, Skander

2014-10-01

310

Online magnetic bead based dynamic protein affinity selection coupled to LC–MS for the screening of acetylcholine binding protein ligands  

Microsoft Academic Search

A magnetic beads based affinity-selection methodology towards the screening of acetylcholine binding protein (AChBP) binders in mixtures and pure compound libraries was developed. The methodology works as follows: after in solution incubation of His-tagged AChBP with potential ligands, and subsequent addition of cobalt (II)-coated paramagnetic beads, the formed bead-AChBP-ligand complexes are fetched out of solution by injection and trapping in

Lionel Pochet; Ferry Heus; Niels Jonker; Henk Lingeman; August B. Smit; Wilfried M. A. Niessen; Jeroen Kool

2011-01-01

311

Uncertainty of exploitation estimates made from tag returns  

USGS Publications Warehouse

Over 6,000 crappies Pomoxis spp. were tagged in five water bodies to estimate exploitation rates by anglers. Exploitation rates were computed as the percentage of tags returned after adjustment for three sources of uncertainty: postrelease mortality due to the tagging process, tag loss, and the reporting rate of tagged fish. Confidence intervals around exploitation rates were estimated by resampling from the probability distributions of tagging mortality, tag loss, and reporting rate. Estimates of exploitation rates ranged from 17% to 54% among the five study systems. Uncertainty around estimates of tagging mortality, tag loss, and reporting resulted in 90% confidence intervals around the median exploitation rate as narrow as 15 percentage points and as broad as 46 percentage points. The greatest source of estimation error was uncertainty about tag reporting. Because the large investments required by tagging and reward operations produce imprecise estimates of the exploitation rate, it may be worth considering other approaches to estimating it or simply circumventing the exploitation question altogether.

Miranda, L.E.; Brock, R.E.; Dorr, B.S.

2002-01-01

312

Lightweight Distance bound Protocol for Low Cost RFID Tags  

E-print Network

Almost all existing RFID authentication schemes (tag/reader) are vulnerable to relay attacks, because of their inability to estimate the distance to the tag. These attacks are very serious since it can be mounted without the notice of neither the reader nor the tag and cannot be prevented by cryptographic protocols that operate at the application layer. Distance bounding protocols represent a promising way to thwart relay attacks, by measuring the round trip time of short authenticated messages. All the existing distance bounding protocols use random number generator and hash functions at the tag side which make them inapplicable at low cost RFID tags. This paper proposes a lightweight distance bound protocol for low cost RFID tags. The proposed protocol based on modified version of Gossamer mutual authentication protocol. The implementation of the proposed protocol meets the limited abilities of low-cost RFID tags.

Ahmed, Eslam Gamal; Hashem, Mohamed

2010-01-01

313

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

314

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

315

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

316

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

317

The CRAPome: a Contaminant Repository for Affinity Purification Mass Spectrometry Data  

PubMed Central

Affinity purification coupled with mass spectrometry (AP-MS) is now a widely used approach for the identification of protein-protein interactions. However, for any given protein of interest, determining which of the identified polypeptides represent bona fide interactors versus those that are background contaminants (e.g. proteins that interact with the solid-phase support, affinity reagent or epitope tag) is a challenging task. While the standard approach is to identify nonspecific interactions using one or more negative controls, most small-scale AP-MS studies do not capture a complete, accurate background protein set. Fortunately, negative controls are largely bait-independent. Hence, aggregating negative controls from multiple AP-MS studies can increase coverage and improve the characterization of background associated with a given experimental protocol. Here we present the Contaminant Repository for Affinity Purification (the CRAPome) and describe the use of this resource to score protein-protein interactions. The repository (currently available for Homo sapiens and Saccharomyces cerevisiae) and computational tools are freely available online at www.crapome.org. PMID:23921808

Mellacheruvu, Dattatreya; Wright, Zachary; Couzens, Amber L.; Lambert, Jean-Philippe; St-Denis, Nicole; Li, Tuo; Miteva, Yana V.; Hauri, Simon; Sardiu, Mihaela E.; Low, Teck Yew; Halim, Vincentius A.; Bagshaw, Richard D.; Hubner, Nina C.; al-Hakim, Abdallah; Bouchard, Annie; Faubert, Denis; Fermin, Damian; Dunham, Wade H.; Goudreault, Marilyn; Lin, Zhen-Yuan; Badillo, Beatriz Gonzalez; Pawson, Tony; Durocher, Daniel; Coulombe, Benoit; Aebersold, Ruedi; Superti-Furga, Giulio; Colinge, Jacques; Heck, Albert J. R.; Choi, Hyungwon; Gstaiger, Matthias; Mohammed, Shabaz; Cristea, Ileana M.; Bennett, Keiryn L.; Washburn, Mike P.; Raught, Brian; Ewing, Rob M.; Gingras, Anne-Claude; Nesvizhskii, Alexey I.

2013-01-01

318

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

319

The CRAPome: a contaminant repository for affinity purification-mass spectrometry data.  

PubMed

Affinity purification coupled with mass spectrometry (AP-MS) is a widely used approach for the identification of protein-protein interactions. However, for any given protein of interest, determining which of the identified polypeptides represent bona fide interactors versus those that are background contaminants (for example, proteins that interact with the solid-phase support, affinity reagent or epitope tag) is a challenging task. The standard approach is to identify nonspecific interactions using one or more negative-control purifications, but many small-scale AP-MS studies do not capture a complete, accurate background protein set when available controls are limited. Fortunately, negative controls are largely bait independent. Hence, aggregating negative controls from multiple AP-MS studies can increase coverage and improve the characterization of background associated with a given experimental protocol. Here we present the contaminant repository for affinity purification (the CRAPome) and describe its use for scoring protein-protein interactions. The repository (currently available for Homo sapiens and Saccharomyces cerevisiae) and computational tools are freely accessible at http://www.crapome.org/. PMID:23921808

Mellacheruvu, Dattatreya; Wright, Zachary; Couzens, Amber L; Lambert, Jean-Philippe; St-Denis, Nicole A; Li, Tuo; Miteva, Yana V; Hauri, Simon; Sardiu, Mihaela E; Low, Teck Yew; Halim, Vincentius A; Bagshaw, Richard D; Hubner, Nina C; Al-Hakim, Abdallah; Bouchard, Annie; Faubert, Denis; Fermin, Damian; Dunham, Wade H; Goudreault, Marilyn; Lin, Zhen-Yuan; Badillo, Beatriz Gonzalez; Pawson, Tony; Durocher, Daniel; Coulombe, Benoit; Aebersold, Ruedi; Superti-Furga, Giulio; Colinge, Jacques; Heck, Albert J R; Choi, Hyungwon; Gstaiger, Matthias; Mohammed, Shabaz; Cristea, Ileana M; Bennett, Keiryn L; Washburn, Mike P; Raught, Brian; Ewing, Rob M; Gingras, Anne-Claude; Nesvizhskii, Alexey I

2013-08-01

320

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

321

MFR PAPER 1069 Coded wire tagging  

E-print Network

ucce - fully operated in fish ladder on the Snake River at Ice Harbor and Little Goose Dam from 1970MFR PAPER 1069 Coded wire tagging is excellent for automatic identification. Marking Fishes.I\\I!d Geller£ll delcnp/lo//.I oj Ihe lIlI{(/ll/(lIic /(II{ delecfOr and adllil fish sep£lrlllOr (Ire gil ell

322

Semantic Enhancement of Social Tagging Systems  

Microsoft Academic Search

\\u000a Social tagging systems have shown an impressive potential for information discovery and exploration. Enriched with Semantic\\u000a Web technologies, they enable to tap valuable metadata about Web resources and to detect hidden relations, thus, to capture\\u000a information about both content and context of the resources. In this article, we propose a novel way to combine semantic technologies\\u000a with Web 2.0 paradigms.

Fabian Abel; Nicola Henze; Daniel Krause; Matthias Kriesell

2009-01-01

323

Scanning Cargo Containers with Tagged Neutrons  

SciTech Connect

A new Tagged Neutron Inspection System (TNIS) able to detect illicit materials such as explosives and narcotics in cargo containers has been developed within the EURopean Illicit TRAfficing Countermeasures Kit (EURITRACK) project. After the R and D phase, the inspection portal has been installed and commissioned at the Rijeka seaport in Croatia, where it has been operated in connection with the existing X-ray scanner for a first two-month demonstration campaign. Results obtained are presented and discussed in this paper.

Viesti, G.; Botosso, C.; Fabris, D.; Lunardon, M.; Moretto, S.; Nebbia, G.; Pesente, S. [INFN and Universita di Padova, Via Marzolo 8, I-35131 Padova (Italy); Zenoni, A.; Donzella, A. [INFN and Universita di Brescia, 38 Via Branze 25123 Brescia (Italy); Perot, B.; Carasco, C.; Bernard, S.; Mariani, A. [Commissariat a l'Energie Atomique, 13108 St Paul-lez-Durance (France); Szabo, J.-L.; Sannie, G. [Commissariat a l'Energie Atomique, 91191 Gif-Sur-Yvette (France); Valkovic, V.; Sudac, D.; Nad, K. [Institute Ruder Boskovic, 54 Bijenicka c. 10000 Zagreb (Croatia); Peerani, P.; Sequeira, V. [European Commission, Joint Research Centre, I-21020 Ispra (Italy)] (and others)

2007-10-26

324

Scanning Cargo Containers with Tagged Neutrons  

NASA Astrophysics Data System (ADS)

A new Tagged Neutron Inspection System (TNIS) able to detect illicit materials such as explosives and narcotics in cargo containers has been developed within the EURopean Illicit TRAfficing Countermeasures Kit (EURITRACK) project. After the R&D phase, the inspection portal has been installed and commissioned at the Rijeka seaport in Croatia, where it has been operated in connection with the existing X-ray scanner for a first two-month demonstration campaign. Results obtained are presented and discussed in this paper.

Viesti, G.; Botosso, C.; Fabris, D.; Lunardon, M.; Moretto, S.; Nebbia, G.; Pesente, S.; Zenoni, A.; Donzella, A.; Perot, B.; Carasco, C.; Bernard, S.; Mariani, A.; Szabo, J.-L.; Sannie, G.; Valkovic, V.; Sudac, D.; Nad, K.; Peerani, P.; Sequeira, V.; Salvato, M.; Moszynski, M.; Gierlik, M.; Klamra, W.; Le Tourneur, P.; Lhuissier, M.; Colonna, A.; Tintori, C.

2007-10-01

325

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

326

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

327

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

328

TagRecon: High-Throughput Mutation Identification through Sequence Tagging  

PubMed Central

Shotgun proteomics produces collections of tandem mass spectra that contain all the data needed to identify mutated peptides from clinical samples. Identifying these sequence variations, however, has not been feasible with conventional database search strategies, which require exact matches between observed and expected sequences. Searching for mutations as mass shifts on specified residues through database search can incur significant performance penalties and generate substantial false positive rates. Here we describe TagRecon, an algorithm that leverages inferred sequence tags to identify unanticipated mutations in clinical proteomic data sets. TagRecon identifies unmodified peptides as sensitively as the related MyriMatch database search engine. In both LTQ and Orbitrap data sets, TagRecon outperformed state of the art software in recognizing sequence mismatches from data sets with known variants. We developed guidelines for filtering putative mutations from clinical samples, and we applied them in an analysis of cancer cell lines and an examination of colon tissue. Mutations were found in up to 6% of identified peptides, and only a small fraction corresponded to dbSNP entries. The RKO cell line, which is DNA mismatch repair deficient, yielded more mutant peptides than the mismatch repair proficient SW480 line. Analysis of colon cancer tumor and adjacent tissue revealed hydroxyproline modifications associated with extracellular matrix degradation. These results demonstrate the value of using sequence tagging algorithms to fully interrogate clinical proteomic data sets. PMID:20131910

Dasari, Surendra; Chambers, Matthew C.; Slebos, Robbert J.; Zimmerman, Lisa J.; Ham, Amy-Joan L.; Tabb, David L.

2010-01-01

329

Transitive Closures of Affine Integer Tuple Relations and their Overapproximations  

E-print Network

Transitive Closures of Affine Integer Tuple Relations and their Overapproximations Sven Verdoolaege to the transi- tive closure of the relation representing the graph. Relations described using only affine. Unfortunately, the transitive closure of such a quasi-affine relation may not be quasi-affine and so

Paris-Sud XI, Université de

330

AFFINE JACQUET FUNCTORS AND HARISH-CHANDRA CATEGORIES  

E-print Network

AFFINE JACQUET FUNCTORS AND HARISH-CHANDRA CATEGORIES MILEN YAKIMOV Abstract. We define an affine Jacquet functor and use it to describe the structure of induced affine Harish-Chandra modules for certain extension groups to construct a block decomposition of the categories of affine Harish-Chandra

Bigelow, Stephen

331

Single-step antibody-based affinity cryo-electron microscopy for imaging and structural analysis of macromolecular assemblies.  

PubMed

Single particle cryo-electron microscopy (cryo-EM) is an emerging powerful tool for structural studies of macromolecular assemblies (i.e., protein complexes and viruses). Although single particle cryo-EM requires less concentrated and smaller amounts of samples than X-ray crystallography, it remains challenging to study specimens that are low-abundance, low-yield, or short-lived. The recent development of affinity grid techniques can potentially further extend single particle cryo-EM to these challenging samples by combining sample purification and cryo-EM grid preparation into a single step. Here we report a new design of affinity cryo-EM approach, cryo-SPIEM, that applies a traditional pathogen diagnosis tool Solid Phase Immune Electron Microscopy (SPIEM) to the single particle cryo-EM method. This approach provides an alternative, largely simplified and easier to use affinity grid that directly works with most native macromolecular complexes with established antibodies, and enables cryo-EM studies of native samples directly from cell cultures. In the present work, we extensively tested the feasibility of cryo-SPIEM with multiple samples including those of high or low molecular weight, macromolecules with low or high symmetry, His-tagged or native particles, and high- or low-yield macromolecules. Results for all these samples (non-purified His-tagged bacteriophage T7, His-tagged Escherichiacoli ribosomes, native Sindbis virus, and purified but low-concentration native Tulane virus) demonstrated the capability of cryo-SPIEM approach in specifically trapping and concentrating target particles on TEM grids with minimal view constraints for cryo-EM imaging and determination of 3D structures. PMID:24780590

Yu, Guimei; Vago, Frank; Zhang, Dongsheng; Snyder, Jonathan E; Yan, Rui; Zhang, Ci; Benjamin, Christopher; Jiang, Xi; Kuhn, Richard J; Serwer, Philip; Thompson, David H; Jiang, Wen

2014-07-01

332

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; Larrañaga, Pedro; Yuste, Rafael

2013-01-01

333

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

334

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

335

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

336

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

337

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

338

Extraction of haemoglobin from human blood by affinity precipitation using a haptoglobin-based stimuli–responsive affinity macroligand  

Microsoft Academic Search

Affinity precipitation was compared to affinity chromatography and batch adsorption as the final purification step in a protocol for the isolation of haemoglobin from human blood. Haptoglobin was the affinity ligand. The first steps on the process were realized by traditional methods (lyses of red blood cells followed by ammonium sulphate precipitation). For affinity chromatography (and batch adsorption) the ligand

Gisela Stocker-Majd; Frank Hilbrig; Ruth Freitag

2008-01-01

339

Mass spectrum patterns of 18O-tagged peptides labeled by enzyme-catalyzed oxygen exchange.  

PubMed

(18)O-labeling of peptides is a technique widely and routinely applied in the protein chemistry laboratories. The rate of (18)O incorporation at the carboxyl terminus of peptides via enzyme-catalyzed oxygen exchange fluctuates from peptide to peptide. This fluctuation is mostly attributed to enzyme-substrate different affinity. The final distributions of the (18)O(0)-, (18)O(1)-, and (18)O(2)-tagged peptides remain unpredictable though usually constrained to binomial proportions. It is proved here that this constraint can sometimes be a poor model. A more general model is then derived which predicts linear paths for digestion in H(2)(18)O-enriched water while confining binomial proportions to postdigestion labeling. Both subderived models are simple in structure and relevant for the current software development in the analysis of quantitative shotgun proteomics data. Accuracy and time dependency are examined and compared with actual labeled-digest data. PMID:21417365

Fernandez-de-Cossio, Jorge

2011-04-15

340

Some Fundamental Limits on SAW RFID Tag Information Capacity and Collision Resolution  

NASA Technical Reports Server (NTRS)

In this paper, we apply results from multi-user information theory to study the limits of information capacity and collision resolution for SAW RFID tags. In particular, we derive bounds on the achievable data rate per tag as a function of fundamental parameters such as tag time-bandwidth product, tag signal-to-noise ratio (SNR), and number of tags in the environment. We also discuss the implications of these bounds for tag waveform design and tag interrogation efficiency

Barton, Richard J.

2013-01-01

341

Affinity biosensors for tumor-marker analysis.  

PubMed

The use of cancer biomarkers is emerging as one of the most promising strategies for early detection and management of cancer. Biosensors can provide advanced platforms for biomarker analysis with the advantages of being easy to use, inexpensive, rapid and offering multi-analyte testing capability. The intention of this article is to discuss recent advances and trends in affinity biosensors for cancer diagnosis, prognosis and even theragnosis. The different types of affinity biosensors will be reviewed in terms of molecular recognition element. Current challenges and trends for this technology will be also discussed, with a particular emphasis on recent developments in miRNA detection. PMID:25534795

Palchetti, Ilaria

2014-12-01

342

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

343

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

344

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

345

Tag-based approaches for deep transcriptome analysis in plants  

Microsoft Academic Search

Serial analysis of gene expression (SAGE) has pioneered the use of short-tag sequences derived from the 3?-ends of cDNAs for transcriptome research. Many new tag-based technologies, capitalizing on the success of SAGE, have been developed in the last decade greatly improving the tag length, cloning efficacy and the depth of transcriptome analysis in targeted genomes. Moreover, the recent introduction of

Miguel E. Vega-Sánchez; Malali Gowda; Guo-Liang Wang

2007-01-01

346

Minimalist Cryptography for Low-Cost RFID Tags  

Microsoft Academic Search

A radio-frequency identification (RFID) tag is a small, inexpensive microchip that emits an identifier in response to a query from a nearby reader. The price of these tags promises to drop to the range of $0.05 per unit in the next several years, oering a viable and powerful replacement for barcodes. The challenge in providing security for low-cost RFID tags

Ari Juels

2004-01-01

347

Bifunctional redox tagging of carbon nanoparticles  

NASA Astrophysics Data System (ADS)

Despite extensive work on the controlled surface modification of carbon with redox moieties, to date almost all available methodologies involve complex chemistry and are prone to the formation of polymerized multi-layer surface structures. Herein, the facile bifunctional redox tagging of carbon nanoparticles (diameter 27 nm) and its characterization is undertaken using the industrial dye Reactive Blue 2. The modification route is demonstrated to be via exceptionally strong physisorption. The modified carbon is found to exhibit both well-defined oxidative and reductive voltammetric redox features which are quantitatively interpreted. The method provides a generic approach to monolayer modifications of carbon and carbon nanoparticle surfaces.

Poon, Jeffrey; Batchelor-McAuley, Christopher; Tschulik, Kristina; Palgrave, Robert G.; Compton, Richard G.

2015-01-01

348

Proteomic profiling of cardiac tissue by isolation of nuclei tagged in specific cell types (INTACT)  

PubMed Central

The proper dissection of the molecular mechanisms governing the specification and differentiation of specific cell types requires isolation of pure cell populations from heterogeneous tissues and whole organisms. Here, we describe a method for purification of nuclei from defined cell or tissue types in vertebrate embryos using INTACT (isolation of nuclei tagged in specific cell types). This method, previously developed in plants, flies and worms, utilizes in vivo tagging of the nuclear envelope with biotin and the subsequent affinity purification of the labeled nuclei. In this study we successfully purified nuclei of cardiac and skeletal muscle from Xenopus using this strategy. We went on to demonstrate the utility of this approach by coupling the INTACT approach with liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomic methodologies to profile proteins expressed in the nuclei of developing hearts. From these studies we have identified the Xenopus orthologs of 12 human proteins encoded by genes, which when mutated in human lead to congenital heart disease. Thus, by combining these technologies we are able to identify tissue-specific proteins that are expressed and required for normal vertebrate organ development. PMID:24496632

Amin, Nirav M.; Greco, Todd M.; Kuchenbrod, Lauren M.; Rigney, Maggie M.; Chung, Mei-I; Wallingford, John B.; Cristea, Ileana M.; Conlon, Frank L.

2014-01-01

349

Optimized immobilization of lectins using self-assembled monolayers on polysilicon encoded materials for cell tagging.  

PubMed

Self-assembled monolayers (SAMs) have been used for the preparation of functional microtools consisting of encoded polysilicon barcodes biofunctionalized with proteins of the lectin family. These hybrid microtools exploit the lectins ability for recognizing specific carbohydrates of the cell membrane to give an efficient system for cell tagging. This work describes how the control of the methodology for SAM formation on polysilicon surfaces followed by lectin immobilization has a crucial influence on the microtool biofunction. Several parameters (silanization time, silane molar concentration, type of solvent or deposition methodology) have been studied to establish optimal function. Furthermore, silanes incorporating different terminal groups, such as aldehyde, activated ester or epoxide groups were tested in order to analyze their chemical coupling with the biomolecules, as well as their influence on the biofunctionality of the immobilized protein. Two different lectins - wheat germ agglutinin (WGA) and phytohemagglutinin (PHA-L) - were immobilized, because they have different and specific cell recognition behaviour and exhibit different cell toxicity. In this way we can assess the effect of intrinsic bulk toxicity with that of the cell compatibility once immobilized as well as the importance of cell affinity. A variety of nanometrical techniques were used to characterize the active surfaces, and lectin immobilization was quantified using ultraviolet-visible absorption spectroscopy (UV-vis) and optical waveguide light mode spectroscopy (OWLS). Once the best protocol was found, WGA and PHA were immobilized on polysilicon coded barcodes, and these microtools showed excellent cell tagging on living mouse embryos when WGA was used. PMID:24462779

Penon, Oriol; Siapkas, Dimitrios; Novo, Sergi; Durán, Sara; Oncins, Gerard; Errachid, Abdelhamid; Barrios, Lleonard; Nogués, Carme; Duch, Marta; Plaza, José Antonio; Pérez-García, Lluïsa

2014-04-01

350

Comparing the Properties of Electrochemical-Based DNA Sensors Employing Different Redox Tags  

PubMed Central

Many electrochemical biosensor approaches developed in recent years utilize redox labeled (most commonly methylene blue or ferrocene) oligonucleotide probes site-specifically attached to an interrogating electrode. Sensors in this class have been reported employing a range of probe architectures, including single- and double-stranded DNA, more complex DNA structures, DNA and RNA aptamers and, most recently, DNA-small molecule chimeras. Signaling in this class of sensors is generally predicated on binding-induced changes in the efficiency with which the covalently attached redox label transfers electrons with the interrogating electrode. Here we have investigated how the properties of the redox tag affect the performance of such sensors. Specifically, we compare the differences in signaling and stability of electrochemical DNA sensors (E-DNA sensors) fabricated using either ferrocene or methylene blue as the signaling redox moiety. We find that while both tags support efficient E-DNA signaling, ferrocene produces slightly improved signal gain and target affinity. These small advantages, however, come at a potentially significant price: the ferrocene-based sensors are far less stable than their methylene blue counterparts, particularly with regards to stability to long-term storage, repeated electrochemical interrogations, repeated sensing/regeneration iterations, and employment in complex sample matrices such as blood serum. PMID:19810694

Kang, Di; Zuo, Xiaolei; Yang, Renqiang; Xia, Fan; Plaxco, Kevin W.; White, Ryan J.

2009-01-01

351

Improved Strains and Plasmid Vectors for Conditional Overexpression of His-Tagged Proteins in Haloferax volcanii?  

PubMed Central

Research into archaea will not achieve its full potential until systems are in place to carry out genetics and biochemistry in the same species. Haloferax volcanii is widely regarded as the best-equipped organism for archaeal genetics, but the development of tools for the expression and purification of H. volcanii proteins has been neglected. We have developed a series of plasmid vectors and host strains for conditional overexpression of halophilic proteins in H. volcanii. The plasmids feature the tryptophan-inducible p.tnaA promoter and a 6×His tag for protein purification by metal affinity chromatography. Purification is facilitated by host strains, where pitA is replaced by the ortholog from Natronomonas pharaonis. The latter lacks the histidine-rich linker region found in H. volcanii PitA and does not copurify with His-tagged recombinant proteins. We also deleted the mrr restriction endonuclease gene, thereby allowing direct transformation without the need to passage DNA through an Escherichia coli dam mutant. PMID:20097827

Allers, Thorsten; Barak, Shahar; Liddell, Susan; Wardell, Kayleigh; Mevarech, Moshe

2010-01-01

352

Crouching Dirichlet, Hidden Markov Model: Unsupervised POS Tagging with Context Local Tag Generation  

Microsoft Academic Search

We define the crouching Dirichlet, hidden Markov model (CDHMM), an HMM for part- of-speech tagging which draws state prior dis- tributions for each local document context. This simple modification of the HMM takes advantage of the dichotomy in natural lan- guage between content and function words. In contrast, a standard HMM draws all prior dis- tributions once over all states

Taesun Moon; Katrin Erk; Jason Baldridge

2010-01-01

353

Power Margin Reduction in Linear passive UHF RFID tag arrays  

E-print Network

Power Margin Reduction in Linear passive UHF RFID tag arrays Qi Zhang, Michael Crisp, Ian H. White and Richard V.Penty Centre for Photonic Systems, Electrical Division, Department of Engineering, University of Cambridge, 9 JJ Thomson Avenue... , Cambridge, CB3 0FA, U.K. Abstract—This paper studies the power margin reduction in linear passive UHF RFID tag arrays due to proximity effects. It is shown experimentally that a 40% reduction in tag power margin occurs when two tags are placed with a...

Zhang, Qi; Crisp, Michael; White, Ian H.; Penty, Richard V.

2014-07-17

354

Current test results for the Athena radar responsive tag  

NASA Astrophysics Data System (ADS)

Sandia National Laboratories has teamed with General Atomics and Sierra Monolithics to develop the Athena tag for the Army's Radar Tag Engagement (RaTE) program. The radar-responsive Athena tag can be used for Blue Force tracking and Combat Identification (CID) as well as data collection, identification, and geolocation applications. The Athena tag is small (~4.5" x 2.4" x 4.2"), battery-powered, and has an integral antenna. Once remotely activated by a Synthetic Aperture Radar (SAR) or Moving Target Indicator (MTI) radar, the tag transponds modulated pulses to the radar at a low transmit power. The Athena tag can operate Ku-band and X-band airborne SAR and MTI radars. This paper presents results from current tag development testing activities. Topics covered include recent field tests results from the AN/APY-8 Lynx, F16/APG-66, and F15E/APG-63 V(1) radars and other Fire Control radars. Results show that the Athena tag successfully works with multiple radar platforms, in multiple radar modes, and for multiple applications. Radar-responsive tags such as Athena have numerous applications in military and government arenas. Military applications include battlefield situational awareness, combat identification, targeting, personnel recovery, and unattended ground sensors. Government applications exist in nonproliferation, counter-drug, search-and-rescue, and land-mapping activities.

Ormesher, Richard C.; Martinez, Ana; Plummer, Kenneth W.; Erlandson, David; Delaware, Sheri; Clark, David R.

2006-05-01

355

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

356

State estimation for affine LPV systems  

Microsoft Academic Search

The design of a scheduled observer which allows us to estimate the state of an affine LPV (linear parameter varying) system is investigated. The state and the gain matrices of the observer are scheduled by using an interpolation method which is linear according to each parameter but which is nonlinear according to the parameter vector. The stability of the estimation

G. Iulia Bara; Jamal Daafouz; José Ragot; Frédéric Kratz

2000-01-01

357

An euclidean affine invariant of quadrilaterals  

E-print Network

A certain real number, depending on two neighbouring sides of a quadrilateral and the diagonal meeting these two sides at their common point, is shown to be invariant under affinity. As an application we demonstrate a nice formula for the area of a finite sector at centre of a planar quadric with point symmetry.

Helmut Kahl

2010-07-02

358

Gait Recognition using Dynamic Affine Invariants  

Microsoft Academic Search

We present a method for recognizing classes of human gaits from video sequences. We propose a novel image based representation for human gaits. At any instance of time a gait is represented by a vector of affine invariant moments. The invariants are computed on the binary silhouettes cor- responding to the moving body. We represent the time tra- jectories of

Alessandro Bissacco; Payam Saisan; Stefano Soatto

2004-01-01

359

Affinity gradients drive copper to cellular destinations.  

PubMed

Copper is an essential trace element for eukaryotes and most prokaryotes. However, intracellular free copper must be strictly limited because of its toxic side effects. Complex systems for copper trafficking evolved to satisfy cellular requirements while minimizing toxicity. The factors driving the copper transfer between protein partners along cellular copper routes are, however, not fully rationalized. Until now, inconsistent, scattered and incomparable data on the copper-binding affinities of copper proteins have been reported. Here we determine, through a unified electrospray ionization mass spectrometry (ESI-MS)-based strategy, in an environment that mimics the cellular redox milieu, the apparent Cu(I)-binding affinities for a representative set of intracellular copper proteins involved in enzymatic redox catalysis, in copper trafficking to and within various cellular compartments, and in copper storage. The resulting thermodynamic data show that copper is drawn to the enzymes that require it by passing from one copper protein site to another, exploiting gradients of increasing copper-binding affinity. This result complements the finding that fast copper-transfer pathways require metal-mediated protein-protein interactions and therefore protein-protein specific recognition. Together with Cu,Zn-SOD1, metallothioneins have the highest affinity for copper(I), and may play special roles in the regulation of cellular copper distribution; however, for kinetic reasons they cannot demetallate copper enzymes. Our study provides the thermodynamic basis for the kinetic processes that lead to the distribution of cellular copper. PMID:20463663

Banci, Lucia; Bertini, Ivano; Ciofi-Baffoni, Simone; Kozyreva, Tatiana; Zovo, Kairit; Palumaa, Peep

2010-06-01

360

Algorithms for affine Kac-Moody algebras  

E-print Network

Weyl groups are ubiquitous, and efficient algorithms for them -- especially for the exceptional algebras -- are clearly desirable. In this paper we provide several of these, addressing practical concerns arising naturally for instance in computational aspects of the study of affine algebras or Wess-Zumino-Witten conformal field theories. We also discuss the efficiency and numerical accuracy of these algorithms.

Terry Gannon

2002-02-12

361

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

362

Tracking foveated corner clusters using affine structure  

Microsoft Academic Search

The authors describe a novel method of obtaining a fixation point on a moving object for a real-time gaze control system. The method makes use of a real-time implementation of a corner detector and tracker and reconstructs the image position of the desired fixation point from a cluster of corners detected on the object using the affine structure available from

I. D. Reid; D. W. Murray

1993-01-01

363

Calculations of Hf -electron affinity and  

E-print Network

Calculations of Hf - electron affinity and photodetachment partial cross sections Lin Pan Abstract. Relativistic configuration interaction calculations show Hf - has only one bound state, 5d2 6s2 6V (532 nm), the partial cross sections to energetically accessible neutral thresholds are calculated

Beck, Donald R.

364

Affinity-Based Purification of Dehydrogenase Subproteomes  

PubMed Central

Summary The high cost of drug discovery and development requires more efficient approaches to the identification and inhibition of tractable protein targets. One strategy is to pursue families of proteins that already possess affinity for a drug lead scaffold, where that scaffold plays the dual role of serving: (a) when tethered to a resin, as a ligand to purify a subproteome of interest, and (b) as a lead molecule that has the potential for optimization for a given member of the subproteome. Here, we describe the former application, the purification of a subproteome using a scaffold tailored to the dehydrogenase family of enzymes. Combined with modern LC-MS/MS and subsequent searching of proteome databases, such affinity chromatography strategies can be used to purify and identify any proteins with affinity for the scaffold molecule. The method is exemplified using the CRAA (Catechol Rhodanine Acetic Acid) privileged scaffold, which is tailored to dehydrogenases. CRAA affinity column chromatography, combined with LC-MS/MS, is described as a method for profiling dehydrogenase subproteomes. PMID:22065224

Ge, Xia; Sem, Daniel S.

2014-01-01

365

Superior triacylglycerol (TAG) accumulation in starchless mutants of Scenedesmus obliquus: (II) evaluation of TAG yield and productivity in controlled photobioreactors  

PubMed Central

Background Many microalgae accumulate carbohydrates simultaneously with triacylglycerol (TAG) upon nitrogen starvation, and these products compete for photosynthetic products and metabolites from the central carbon metabolism. As shown for starchless mutants of the non-oleaginous model alga Chlamydomonas reinhardtii, reduced carbohydrate synthesis can enhance TAG production. However, these mutants still have a lower TAG productivity than wild-type oleaginous microalgae. Recently, several starchless mutants of the oleaginous microalga Scenedesmus obliquus were obtained which showed improved TAG content and productivity. Results The most promising mutant, slm1, is compared in detail to wild-type S. obliquus in controlled photobioreactors. In the slm1 mutant, the maximum TAG content increased to 57?±?0.2% of dry weight versus 45?±?1% in the wild type. In the wild type, TAG and starch were accumulated simultaneously during initial nitrogen starvation, and starch was subsequently degraded and likely converted into TAG. The starchless mutant did not produce starch and the liberated photosynthetic capacity was directed towards TAG synthesis. This increased the maximum yield of TAG on light by 51%, from 0.144?±?0.004 in the wild type to 0.217?±?0.011 g TAG/mol photon in the slm1 mutant. No differences in photosynthetic efficiency between the slm1 mutant and the wild type were observed, indicating that the mutation specifically altered carbon partitioning while leaving the photosynthetic capacity unaffected. Conclusions The yield of TAG on light can be improved by 51% by using the slm1 starchless mutant of S. obliquus, and a similar improvement seems realistic for the areal productivity in outdoor cultivation. The photosynthetic performance is not negatively affected in the slm1 and the main difference with the wild type is an improved carbon partitioning towards TAG. PMID:24883102

2014-01-01

366

HERRING TAGGING EXPERIMENTS IN SOUTHEASTERN ALASKA By BERNARD EINAR SKUD, Fishery Biologist  

E-print Network

and procedures used in tagging and recovery. Internal metal tags were found to be superior to external tags, both conditions. An electromagnet was designed to provide a mechanical means of recov- , ering metal tags from electromagnets. Dahlgren (1936) emphasized the limitations of the magnet recoveries. The allocation of tags

367

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

368

Endogenous gene tagging with fluorescent proteins.  

PubMed

Human genome manipulation has become a powerful tool for understanding the mechanisms of numerous diseases including cancer. Inserting reporter sequences in the desired locations in the genome of a cell can allow monitoring of endogenous activities of disease related genes. Native gene expression and regulation is preserved in these knock-in cells in contrast to cell lines with target overexpression under an exogenous promoter as in the case of transient transfection or stable cell lines with random integration. The fusion proteins created using the modern genome editing tools are expressed at their physiological level and thus are more likely to retain the characteristic expression profile of the endogenous proteins in the cell. Unlike biochemical assays or immunostaining, using a tagged protein under endogenous regulation avoids fixation artifacts and allows detection of the target's activity in live cells. Multiple gene targets could be tagged in a single cell line allowing for the creation of effective cell-based assays for compound screening to discover novel drugs. PMID:25408409

Fetter, John; Samsonov, Andrey; Zenser, Nathan; Zhang, Fan; Zhang, Hongyi; Malkov, Dmitry

2015-01-01

369

Chemical Tags for Labeling Proteins Inside Living Cells  

PubMed Central

Conspectus To build on the last century's tremendous strides in understanding the workings of individual proteins in the test tube, we now face the challenge of understanding how macromolecular machines, signaling pathways, and other biological networks operate in the complex environment of the living cell. The fluorescent proteins (FPs) revolutionized our ability to study protein function directly in the cell by enabling individual proteins to be selectively labeled through genetic encoding of a fluorescent tag. Although FPs continue to be invaluable tools for cell biology, they show limitations in the face of the increasingly sophisticated dynamic measurements of protein interactions now called for to unravel cellular mechanisms. Therefore, just as chemical methods for selectively labeling proteins in the test tube significantly impacted in vitro biophysics in the last century, chemical tagging technologies are now poised to provide a breakthrough to meet this century's challenge of understanding protein function in the living cell. With chemical tags, the protein of interest is attached to a polypeptide rather than an FP. The polypeptide is subsequently modified with an organic fluorophore or another probe. The FlAsH peptide tag was first reported in 1998. Since then, more refined protein tags, exemplified by the TMP- and SNAP-tag, have improved selectivity and enabled imaging of intracellular proteins with high signal-to-noise ratios. Further improvement is still required to achieve direct incorporation of powerful fluorophores, but enzyme-mediated chemical tags show promise for overcoming the difficulty of selectively labeling a short peptide tag. In this Account, we focus on the development and application of chemical tags for studying protein function within living cells. Thus, in our overview of different chemical tagging strategies and technologies, we emphasize the challenge of rendering the labeling reaction sufficiently selective and the fluorophore probe sufficiently well behaved to image intracellular proteins with high signal-to-noise ratios. We highlight recent applications in which the chemical tags have enabled sophisticated biophysical measurements that would be difficult or even impossible with FPs. Finally, we conclude by looking forward to (i) the development of high-photon-output chemical tags compatible with living cells to enable high-resolution imaging, (ii) the realization of the potential of the chemical tags to significantly reduce tag size, and (iii) the exploitation of the modular chemical tag label to go beyond fluorescent imaging. PMID:21879706

Jing, Chaoran; Cornish, Virginia W.

2011-01-01

370

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 0.024 pg mL(-1) and 0.032 pg mL(-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

371

Interaction of lactate dehydrogenase with structurally related triazine dyes using affinity partitioning and affinity chromatography.  

PubMed

Affinity partitioning in aqueous two-phase systems consisting of dextran and dye-liganded polyethylene glycol was employed to study the interaction of lactate dehydrogenase (LDH) from rabbit muscle (E.C. 1.1.1.27) with Procion Red HE-3B and four structurally related derivatives of this dye in order to follow the significance of the terminal rings of Procion Red HE-3B for the strength of interaction. The study revealed that the arrangement of the two 1-amino-8-naphthol-3,6-disulphonic acid rings seems to be a prerequisite for the interaction of azonaphthol dyes with LDH. The negatively charged sulfonic acid group at the terminal rings of Procion Red HE-3B enhances the affinity of the ligand for LDH significantly. The removal of this sulphonic acid group or splitting off the complete terminal rings decreases the affinity to LDH and improves the competitive effect of NAD+. The results of affinity partitioning are compared with those of affinity chromatography and kinetic data. The usefulness and the choice of parameters of affinity partitioning as an analytical tool to predict the chromatographic behaviour of dye ligands are discussed. PMID:2625437

Kirchberger, J; Cadelis, F; Kopperschläger, G; Vijayalakshmi, M A

1989-12-01

372

Dissection of an old protein reveals a novel application: domain D of Staphylococcus aureus Protein A (sSpAD) as a secretion - tag  

PubMed Central

Background Escherichia coli as a frequently utilized host organism for recombinant protein production offers different cellular locations with distinct qualities. The periplasmic space is often favored for the production of complex proteins due to enhanced disulfide bond formation, increased target product stability and simplified downstream processing. To direct proteins to the periplasmic space rather small proteinaceus tags that can be used for affinity purification would be advantageous. Results We discovered that domain D of the Staphylococcus aureus protein A was sufficient for the secretion of various target proteins into the periplasmic space of E. coli. Our experiments indicated the Sec pathway as the mode of secretion, although N-terminal processing was not observed. Furthermore, the solubility of recombinant fusion proteins was improved for proteins prone to aggregation. The tag allowed a straightforward affinity purification of recombinant fusion protein via an IgG column, which was exemplified for the target protein human superoxide dismutase 1 (SOD). Conclusions In this work we present a new secretion tag that combines several advantages for the production of recombinant proteins in E. coli. Domain D of S. aureus protein A protects the protein of interest against N-terminal degradation, increases target protein solubility and enables a straight-forward purification of the recombinant protein using of IgG columns. PMID:21092285

2010-01-01

373

QUANTITATION OF MAST CELLS AND COLLAGEN FIBERS IN SKIN TAGS  

PubMed Central

Background: Skin tags are common benign skin tumors usually occurring on the neck and major flexors of elder people. Aims: The aim of this study is to perform quantitation of mast cells and collagen fibers in skin tags and normal skin in diabetics and nondiabetics, to find a possible correlation between mast cells and collagen fibers in the pathogenesis of skin tags. Methods: Thirty participants with skin tags were divided into two groups (15 diabetic and 15 nondiabetic). Three biopsies were obtained from one anatomical site: A large skin tag, a small skin tag, and adjacent normal skin. Mast cells stained with Bismarck brown were counted manually in ten different fields of each section with magnification ×1000 and the average count was correlated with the percentage of mean collagen area in five fields done by the image analyzer. Results: A statistically significant correlation between mast cell count and percentage of collagen mean area was detected in both studied groups (except in large skin tags of the nondiabetic group). Conclusion: The positive correlation between mast cell count and percentage of collagen mean area suggests the critical role of mast cells in the etiogenesis of skin tags through its interaction with fibroblasts. PMID:20101330

El Safoury, Omar Soliman; Fawzy, Marwa M; El Maadawa, Zeinab M; Mohamed, Dalia H

2009-01-01

374

Tagging Makes Secrecy Decidable with Unbounded Nonces as Well  

Microsoft Academic Search

Tagging schemes have been used in security protocols to ensure that the analysis of such protocols can work with messages of bounded length. When the set of nonces is bounded, this leads to decid- ability of secrecy. In this paper, we show that tagging schemes can be used to obtain decidability of secrecy even in the presence of unbound- edly

Ramaswamy Ramanujam; S. P. Suresh

2003-01-01

375

Increasing Design Space of the Instruction Queue with Tag Coding  

E-print Network

Increasing Design Space of the Instruction Queue with Tag Coding Junwei Zhou Department of ECE for instruction wakeup from the tags for physical register access, thus increasing the design space, Michigan State University East Lansing, MI 48824 mason@egr.msu.edu ABSTRACT The instruction queue

Mason, Andrew

376

Fully printed flexible and disposable wireless cyclic voltammetry tag.  

PubMed

A disposable cyclic voltammetry (CV) tag is printed on a plastic film by integrating wireless power transmitter, polarized triangle wave generator, electrochemical cell and signage through a scalable gravure printing method. By proximity of 13.56?MHz RF reader, the printed CV tag generates 320?mHz of triangular sweep wave from +500?mV to -500?mV which enable to scan a printed electrochemical cell in the CV tag. By simply dropping any specimen solution on the electrochemical cell in the CV tag, the presence of solutes in the solution can be detected and shown on the signage of the CV tag in five sec. 10?mM of N,N,N',N'-tetramethyl-p-phenylenediamine (TMPD) was used as a standard solute to prove the working concept of fully printed disposable wireless CV tag. Within five seconds, we can wirelessly diagnose the presence of TMPD in the solution using the CV tag in the proximity of the 13.56?MHz RF reader. This fully printed and wirelessly operated flexible CV tag is the first of its kind and marks the path for the utilization of inexpensive and disposable wireless electrochemical sensor systems for initial diagnose hazardous chemicals and biological molecules to improve public hygiene and health. PMID:25630250

Jung, Younsu; Park, Hyejin; Park, Jin-Ah; Noh, Jinsoo; Choi, Yunchang; Jung, Minhoon; Jung, Kyunghwan; Pyo, Myungho; Chen, Kevin; Javey, Ali; Cho, Gyoujin

2015-01-01

377

Radio Tagged Adult Female Walrus on Ice Floe  

USGS Multimedia Gallery

Adult female walrus on ice floe photographed shortly after receiving a behavior monitoring satellite-linked radio tag from USGS researchers.  Data acquired from such radio-tags are providing insights on the distribution and behavior of Pacific walruses during a time when their summer sea ice h...

378

The Recurrence Dynamics of Social Tagging Birkbeck, University of London  

E-print Network

before individually and about 90% of tags have been used before collectively. 0 100k 200k 300k 400k 500k total number 0 100k 200k 300k 400k 500k recurrencenumber individual collective Figure 1: The rate of tag

Zhang, Dell

379

Preparing Research Boats to Track Tagged Pallid Sturgeon  

USGS Multimedia Gallery

Biologist, Dave Combs prepares a tracking boat (foreground) and a DIDSON survey boat (background) to search the Yellowstone River for tagged pallid sturgeon, Near Fairview, Montana.  Pallid sturgeon in Montana are tagged with radio telemetry transmitters that are detected with large antennas mo...

380

Evaluating the Impact of Attacks In Collaborative Tagging Environments  

E-print Network

behavior by inserting erroneous or misleading annotations, thus altering the way in which informationEvaluating the Impact of Attacks In Collaborative Tagging Environments Maryam Ramezani and J. J,jsandvig,tschimoler,jgemmell,mobasher,rburke}@cs.depaul.edu Abstract--The proliferation of social web technologies such as collaborative tagging has led

Burke, Robin

381

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

382

Improved gas tagging and cover gas combination for nuclear reactor  

DOEpatents

The invention discloses the use of stable isotopes of neon and argon, sealed as tags in different cladding nuclear fuel elements to be used in a liquid metal fast breeder reactor. Cladding failure allows fission gases and these tag isotopes to escape and to combine with the cover gas. The isotopes are Ne/sup 20/, Ne/sup 21/ and Ne/sup 22/ and Ar/sup 36/, Ar/sup 38/ and Ar/sup 40/, and the cover gas is He. 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 0 and -25/sup 0/C to remove the fission gases from the cover gas and tags, and the second or tag recovery system bed between -170 and -185/sup 0/C to isolate the tags from the cover gas. Spectrometric analysis 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 determined.

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

1983-09-26

383

Identifying the missing tags in a large RFID system  

Microsoft Academic Search

Comparing with the classical barcode system, RFID extends the operational distance from inches to a number of feet (passive RFID tags) or even hundreds of feet (active RFID tags). Their wireless transmission, processing and storage capabilities enable them to support the full automation of many inventory management functions in the industry. This paper studies the practically important problem of monitoring

Tao Li; Shigang Chen; Yibei Ling

2010-01-01

384

Fully printed flexible and disposable wireless cyclic voltammetry tag  

PubMed Central

A disposable cyclic voltammetry (CV) tag is printed on a plastic film by integrating wireless power transmitter, polarized triangle wave generator, electrochemical cell and signage through a scalable gravure printing method. By proximity of 13.56?MHz RF reader, the printed CV tag generates 320?mHz of triangular sweep wave from +500?mV to ?500?mV which enable to scan a printed electrochemical cell in the CV tag. By simply dropping any specimen solution on the electrochemical cell in the CV tag, the presence of solutes in the solution can be detected and shown on the signage of the CV tag in five sec. 10?mM of N,N,N?,N?-tetramethyl-p-phenylenediamine (TMPD) was used as a standard solute to prove the working concept of fully printed disposable wireless CV tag. Within five seconds, we can wirelessly diagnose the presence of TMPD in the solution using the CV tag in the proximity of the 13.56?MHz RF reader. This fully printed and wirelessly operated flexible CV tag is the first of its kind and marks the path for the utilization of inexpensive and disposable wireless electrochemical sensor systems for initial diagnose hazardous chemicals and biological molecules to improve public hygiene and health. PMID:25630250

Jung, Younsu; Park, Hyejin; Park, Jin-Ah; Noh, Jinsoo; Choi, Yunchang; Jung, Minhoon; Jung, Kyunghwan; Pyo, Myungho; Chen, Kevin; Javey, Ali; Cho, Gyoujin

2015-01-01

385

Contribution ID : 133 The TAG Collector -A Tool for Atlas  

E-print Network

management. The tool is tightly coupled to CVS, and also to CMT, the configuration management tool. Developers can interactively select the CVS tags to be included in a build, and the complete build commands; communicating the correct CVS code repository version tag of their respective packages. This was subject to all

Paris-Sud XI, Université de

386

Inventory Management using Passive RFID Tags: A Survey  

Microsoft Academic Search

Radio Frequency Identification (RFID) systems have emerged as an affordable solution for object identification. They are a cheap and error proof alternative to traditional object identification techniques such as bar codes and visual recognition. The problem is to identify objects attached with passive tags. If there are multiple objects within the range of the tag reader, then all objects send

Cherian Abraham; Vinay Ahuja; Arnab Kumar Ghosh; Praveen Pakanati

387

RFID Tag Antenna Based Temperature Sensing in the Frequency Domain  

E-print Network

RFID Tag Antenna Based Temperature Sensing in the Frequency Domain R. Bhattacharyya, C of a low-cost, single-use RFID based temperature threshold sensor that is capable of relating the violation to the tag IC. This shift is detectable by commercial UHF RFID readers operating in the 902-928 MHz frequency

Entekhabi, Dara

388

Scalable RFID Security Protocols supporting Tag Ownership Transfer  

E-print Network

Scalable RFID Security Protocols supporting Tag Ownership Transfer Boyeon Songa,1 , Chris J Abstract We identify privacy, security and performance requirements for RFID protocols, as well. In support of scalability, some RFID protocols, however, only require constant time for tag identification

Sheldon, Nathan D.

389

Tailing RFID Tags for Clone Detection Davide Zanetti  

E-print Network

Tailing RFID Tags for Clone Detection Davide Zanetti ETH Zurich, Switzerland zanettid ajuels@rsa.com Abstract RFID (Radio-Frequency IDentification) is a key emerg- ing technology for supply-chain monitoring and detection of counterfeit and grey-market goods. The most preva- lent RFID tags are, however

Capkun, Srdjan

390

Identification of RFID Tags in Dynamic Framed Slotted ALOHA  

E-print Network

Identification of RFID Tags in Dynamic Framed Slotted ALOHA Okkyeong Bang, Sunghyun Kim, Korea E-mail: {railmery, boofunky, and hjlee}@icu.ac.kr Abstract--Passive RFID tags, which have no self. INTRODUCTION A radio frequency identification (RFID) system has attracted considerable attention in supply

Kim, Yong Jung

391

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

392

An Approach to Proper Name Tagging for German  

Microsoft Academic Search

This paper presents an incremental method for the tagging of proper names in German newspaper texts. The tagging is performed by the analysis of the syntactic and textual contexts of proper names together with a morphological analysis. The proper names selected by this process supply new contexts which can be used for finding new proper names, and so on. This

Christine Thielen

1995-01-01

393

Identification-Free Batch Authentication for RFID Tags  

E-print Network

are typically low-cost and pervasive devices, being attached to products or targets to enable the identification) systems. While there exist both per-tag and probabilistic approaches for the cardinality estimation tag sequentially, incurring large volume of authentication data and huge communication cost. We study

Liu, Yunhao

394

Multiplexed immunoassay based on micromotors and microscale tags.  

PubMed

This work reports on the coupling of antibody-functionalized micromotors and microwire-tagged proteins for rapid and multiplexed immunoassays. While micromotor-induced mixing accelerates the immunoreaction, tagging the proteins with microscopic particles of different sizes and shapes allows for their multiplexed discrimination, alerting of the presence of a biological threat. PMID:25017813

Vilela, D; Orozco, J; Cheng, G; Sattayasamitsathit, S; Galarnyk, M; Kan, C; Wang, J; Escarpa, A

2014-09-21

395

Why meaningful automatic tagging of images is very hard  

Microsoft Academic Search

The paper points out that while automatic image tagging is often studied in connection with content-based image retrieval (CBIR), it is actually a much harder problem. Given the difficulty of the latter, the prospects for automatic image tagging do not appear promising. A brief survey of the current state of the art confirms that conclusion. Then the paper discusses an

Theo Pavlidis

2009-01-01

396

Jet Charge Tagging at CDF using Run II Data  

NASA Astrophysics Data System (ADS)

We present a study of the jet charge tagging in Run II CDF. The jet charge tagging method is applied to determine the b/barb-quark flavor of B hadrons at the time of production in a sample of b arrow ? ? X decays collected in 2002-2003.

Paus, Christoph

2004-05-01

397

TagCaptcha: Annotating images with CAPTCHAs Donn Morrison  

E-print Network

TagCaptcha: Annotating images with CAPTCHAs Donn Morrison Viper Group University of Geneva Geneva setting by exploiting the need for CAPTCHAs (Com- pletely Automated Public Turing test to tell Computers and Humans Apart) online. Our system, called TagCaptcha, presents the user with a number of images that must

Genève, Université de

398

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

399

NE Pacific Basin --Tagging Data Kate Myers, Ph.D.  

E-print Network

Ocean B: NE Pacific Basin --Tagging Data Kate Myers, Ph.D. Principal Investigator, High Seas Salmon Research Program University of Washington School of Aquatic and Fishery Sciences Box 355020, Seattle, WA tagging data: Biodiversity in freshwater and ocean life histories makes Columbia R. salmon resilient

400

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

401

Peptide nucleic acid probe for protein affinity purification based on biotin-streptavidin interaction and peptide nucleic acid strand hybridization.  

PubMed

We describe a new method for protein affinity purification that capitalizes on the high affinity of streptavidin for biotin but does not require dissociation of the biotin-streptavidin complex for protein retrieval. Conventional reagents place both the selectively reacting group (the "warhead") and the biotin on the same molecule. We place the warhead and the biotin on separate molecules, each linked to a short strand of peptide nucleic acid (PNA), synthetic polymers that use the same bases as DNA but attached to a backbone that is resistant to attack by proteases and nucleases. As in DNA, PNA strands with complementary base sequences hybridize. In conditions that favor PNA duplex formation, the warhead strand (carrying the tagged protein) and the biotin strand form a complex that is held onto immobilized streptavidin. As in DNA, the PNA duplex dissociates at moderately elevated temperature; therefore, retrieval of the tagged protein is accomplished by a brief exposure to heat. Using iodoacetate as the warhead, 8-base PNA strands, biotin, and streptavidin-coated magnetic beads, we demonstrate retrieval of the cysteine protease papain. We were also able to use our iodoacetyl-PNA:PNA-biotin probe for retrieval and identification of a thiol reductase and a glutathione transferase from soybean seedling cotyledons. PMID:25447466

Tse, Jenny; Wang, Yuanyuan; Zengeya, Thomas; Rozners, Eriks; Tan-Wilson, Anna

2015-02-01

402

48 CFR 552.211-92 - Radio Frequency Identification (RFID) using passive tags.  

Code of Federal Regulations, 2011 CFR

...false Radio Frequency Identification (RFID) using passive tags. 552.211-92...211-92 Radio Frequency Identification (RFID) using passive tags. As prescribed...clause: Radio Frequency Identification (RFID) Using Passive Tags (JAN...

2011-10-01

403

48 CFR 552.211-92 - Radio Frequency Identification (RFID) using passive tags.  

Code of Federal Regulations, 2010 CFR

...false Radio Frequency Identification (RFID) using passive tags. 552.211-92...211-92 Radio Frequency Identification (RFID) using passive tags. As prescribed...clause: Radio Frequency Identification (RFID) Using Passive Tags (JAN...

2010-10-01

404

48 CFR 552.211-92 - Radio Frequency Identification (RFID) using passive tags.  

Code of Federal Regulations, 2013 CFR

...false Radio Frequency Identification (RFID) using passive tags. 552.211-92...211-92 Radio Frequency Identification (RFID) using passive tags. As prescribed...clause: Radio Frequency Identification (RFID) Using Passive Tags (JAN...

2013-10-01

405

48 CFR 552.211-92 - Radio Frequency Identification (RFID) using passive tags.  

...false Radio Frequency Identification (RFID) using passive tags. 552.211-92...211-92 Radio Frequency Identification (RFID) using passive tags. As prescribed...clause: Radio Frequency Identification (RFID) Using Passive Tags (JAN...

2014-10-01

406

48 CFR 552.211-92 - Radio Frequency Identification (RFID) using passive tags.  

Code of Federal Regulations, 2012 CFR

...false Radio Frequency Identification (RFID) using passive tags. 552.211-92...211-92 Radio Frequency Identification (RFID) using passive tags. As prescribed...clause: Radio Frequency Identification (RFID) Using Passive Tags (JAN...

2012-10-01

407

78 FR 66641 - Incorporation by Reference; Accident Prevention Signs and Tags; Correction  

Federal Register 2010, 2011, 2012, 2013

...1218-AC77 Incorporation by Reference; Accident Prevention Signs and Tags; Correction...ANSI) standards on specifications for accident prevention signs and tags. DATES: Effective...and affect employers required to use accident prevention signs and tags under the...

2013-11-06

408

Lightweight Mutual Authentication Protocol for Low Cost RFID Tags  

E-print Network

Radio Frequency Identification (RFID) technology one of the most promising technologies in the field of ubiquitous computing. Indeed, RFID technology may well replace barcode technology. Although it offers many advantages over other identification systems, there are also associated security risks that are not easy to be addressed. When designing a real lightweight authentication protocol for low cost RFID tags, a number of challenges arise due to the extremely limited computational, storage and communication abilities of Low-cost RFID tags. This paper proposes a real mutual authentication protocol for low cost RFID tags. The proposed protocol prevents passive attacks as active attacks are discounted when designing a protocol to meet the requirements of low cost RFID tags. However the implementation of the protocol meets the limited abilities of low cost RFID tags.

Ahmed, Eslam Gamal; Hashem, Mohamed; 10.5121/ijnsa.2010.2203

2010-01-01

409

Integral self-affine sets with positive Lebesgue measures  

Microsoft Academic Search

.  A self-affine region is an integral self-affine set with positive Lebesgue measure. In this note we give two criteria for\\u000a integral self-affine sets being self-affine regions. As their applications we study the L\\u000a 1-solutions of refinement equations, which play an important role in constructing wavelets, and we give several interesting\\u000a examples.

Guo-Tai Deng; Xing-Gang He

2008-01-01

410

Affinity Chromatography in Nonionic Detergent Solutions  

NASA Astrophysics Data System (ADS)

Anionic dye affinity chromatography is commonly unproductive in the presence of nonionic detergents used to extract particulate proteins. Using lactate dehydrogenase as a model protein, Cibacron blue F3GA as a model dye, and Triton X-100 as a model detergent, we find that the dye is encapsulated in nonionic detergent micelles, rendering the dye incapable of ligation with the enzyme. However, the dye can be liberated from the micelles without altering the nonionic detergent concentration by addition of an anionic detergent, such as deoxycholate or sodium dodecyl sulfate, forming mixed anionic/nonionic micelles that displace the anionic dye. Encapsulation of the anionic detergents prevents their activity as protein denaturants. These observations have been successfully translated to the dye affinity chromatography of a detergent extract of brain particulate cyclic nucleotide phosphodiesterase.

Robinson, Jack B.; Strottmann, James M.; Wick, Donald G.; Stellwagen, Earle

1980-10-01

411

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

412

Community Detection from Location-Tagged Networks  

E-print Network

Many real world systems or web services can be represented as a network such as social networks and transportation networks. In the past decade, many algorithms have been developed to detect the communities in a network using connections between nodes. However in many real world networks, the locations of nodes have great influence on the community structure. For example, in a social network, more connections are established between geographically proximate users. The impact of locations on community has not been fully investigated by the research literature. In this paper, we propose a community detection method which takes locations of nodes into consideration. The goal is to detect communities with both geographic proximity and network closeness. We analyze the distribution of the distances between connected and unconnected nodes to measure the influence of location on the network structure on two real location-tagged social networks. We propose a method to determine if a location-based community detection...

Liu, Zhi

2015-01-01

413

TagGD: Fast and Accurate Software for DNA Tag Generation and Demultiplexing  

PubMed Central

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

414

Avoiding degenerate coframes in an affine gauge approach to quantum gravity  

SciTech Connect

This report discusses the following concepts on quantum gravity: The affine gauge approach; affine gauge transformations versus active differomorphisms; affine gauge approach to quantum gravity with topology change.

Mielke, E.W.; McCrea, J.D.; Ne`eman, Y.; Hehl, F.W.

1993-04-01

415

Global equisingularity of families of affine hypersurfaces  

Microsoft Academic Search

We consider an equisingularity problem for polynomial families of affine hypersurfaces $X_\\\\tau \\\\subset \\\\bC^n$. We show that the constancy of the global polar invariants $\\\\gamma^* (X_\\\\tau)$ is equivalent to the $t$-equisingularity at infinity, an asymptotic-type equisingularity that we introduce. We prove that $\\\\gamma^*$-constancy implies C$^\\\\ity$-triviality in the neighbourhood of infinity. We show how the invariants $\\\\gamma^*$ enter in the description

Mihai Tibar

1998-01-01

416

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

417

THE AFFINE INVARIANT OF GENERALIZED SEMITORIC SYSTEMS  

E-print Network

THE AFFINE INVARIANT OF GENERALIZED SEMITORIC SYSTEMS ´ALVARO PELAYO TUDOR S. RATIU SAN V~U NGO. C these vertical lines, and generalizes a construction of V~u Ngo.c. The set := f(F(M)) R2 is a symplectic PELAYO TUDOR S. RATIU SAN V~U NGO. C . Figure 1.1. The singular Lagrangian fibration F : M R2

Pelayo, Alvaro

418

On Affine Invariant Clustering and Automatic Cast Listing in Movies  

Microsoft Academic Search

We develop a distance metric for clustering and classification algo- rithms which is invariant to affine transformations and includes priors on the transformation parameters. Such clustering requirements are generic to a num- ber of problems in computer vision. We extend existing techniques for affine-invariant clustering, and show that the new distance metric outperforms existing approximations to affine invariant dis- tance

Andrew W. Fitzgibbon; Andrew Zisserman

2002-01-01

419

Affine configurations of 4 lines in R R R 3  

Microsoft Academic Search

We prove that affine configurations of 4 lines in R 3 are topologically and combina- torially homeomorphic to affine configurations of 6 points in R4. 1. Introduction. Consider four lines ? 1 ,? 2 ,? 3 ,? 4 in 3-dimensional space R 3 ; their affineconfiguration is their equivalence class under the natural (diagonal) action of the affine group Aff(3).

Jorge L. Arocha; Javier Bracho; Chaim Goodman-Strauss; Luis Montejano

420

On the Affine Connection Structure Charged Symplectic 2-Form  

E-print Network

in an electromagnetic field in spacetime. The more familiar method uses standard Poisson brackets (i.e. the canonical in electromagnetic fields defines a generalized affine connection on an affine frame bundle associated with spacetime. Conversely, a generalized affine connection can be used to construct a symplectic 2-form if the associated

Norris, Larry K.

421

Metal chelate affinity chromatography, a new approach to protein fractionation  

Microsoft Academic Search

CONVENTIONAL nonspecific precipitation methods sometimes depend on affinities which can be used in a more selective fashion by modern chromatographic techniques. The affinity of proteins for heavy metal ions, for example, may provide a basis for their purification and analysis. A highly flexible method based on such affinities is described here.

Jerker Porath; Jan Carlsson; Ingmar Olsson; Greta Belfrage

1975-01-01

422

Retention of passive integrated transponder tags in largemouth bass brood fish  

SciTech Connect

Passive integrated transponder (PIT) tags were injected into 22 largemouth bass (Micropterus salmoides) brood fish to determine the retention rate of the tags, the effect on spawning success, and the utility of the tags as a means of individual fish identification. Fish were evaluated 12, 17, and 24 months after implantation. All tags were retained and all tagged fish were recognized. Tag injection and retention had no discernible effect on spawning success.

Harvey, W.D.; Campbell, D.L. (Texas Parks and Wildlife Dept., Austin (USA))

1989-07-01

423

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

424

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

425

A MEMS Dielectric Affinity Glucose Biosensor  

PubMed Central

Continuous glucose monitoring (CGM) sensors based on affinity detection are desirable for long-term and stable glucose management. However, most affinity sensors contain mechanical moving structures and complex design in sensor actuation and signal readout, limiting their reliability in subcutaneously implantable glucose detection. We have previously demonstrated a proof-of-concept dielectric glucose sensor that measured pre-mixed glucose-sensitive polymer solutions at various glucose concentrations. This sensor features simplicity in sensor design, and possesses high specificity and accuracy in glucose detection. However, lack of glucose diffusion passage, this device is unable to fulfill real-time in-vivo monitoring. As a major improvement to this device, we present in this paper a fully implantable MEMS dielectric affinity glucose biosensor that contains a perforated electrode embedded in a suspended diaphragm. This capacitive-based sensor contains no moving parts, and enables glucose diffusion and real-time monitoring. The experimental results indicate that this sensor can detect glucose solutions at physiological concentrations and possesses good reversibility and reliability. This sensor has a time constant to glucose concentration change at approximately 3 min, which is comparable to commercial systems. The sensor has potential applications in fully implantable CGM that require excellent long-term stability and reliability. PMID:24511215

Huang, Xian; Li, Siqi; Davis, Erin; Li, Dachao; Wang, Qian; Lin, Qiao

2013-01-01

426

Non-Contrast Renal MR Angiography: Value of Subtraction of Tagging and Non-Tagging Technique  

PubMed Central

Purpose: The aim of this study was to examine the usefulness of the subtraction technique of non-contrast renal magnetic resonance angiography (MRA) between tagged and non-tagged data collection. Material and Methods: We performed renal MRA on eleven healthy volunteers using a 3T MRI unit. For renal MRA, a three dimensional balanced type steady-state free precession (SSFP) sequence (True FISP, Siemens) was used with diaphragmatic navigator gating. We tried to acquire selective arterial images by subtracting black-blood images (tagged images, on which arterial longitudinal magnetization was nearly zero by selective inversion of upper-stream aortic flow) from bright-blood images (non-tagged images, on which arterial flow is bright due to inflow effect). For analysis, two radiologists independently evaluated the visual quality of the axial and coronal targeted maximum intensity projection images (MIP) of original bright-blood MRA and subtraction MRA. Results: Visualization of the main stem of the renal arteries and their 1st branches were satisfactory on both techniques, and there was no statistically significant difference. The score of 2nd branch appeared superior with the subtraction method, but only the right side showed a statistically significant difference (P <0.01). Visualization of small intraparenchymal arteries was significantly superior with subtraction method on both sides. Conclusion: We tried to improve selective demonstration of renal arterial branches using subtraction technique. Although full sequence optimization was not performed, this pilot study showed this technique to be slightly time-consuming but superior in visualization of peripheral branches and possibly more sensitive in detecting small vessel abnormalities. PMID:23555505

Amanuma, Makoto; Takahashi, Ayako; Tsushima, Yoshito

2012-01-01

427

SILAC-iPAC: A quantitative method for distinguishing genuine from non-specific components of protein complexes by parallel affinity capture.  

PubMed

Pull-down assays can identify members of protein complexes but suffer from co-isolation of contaminants. The problem is particularly acute when the specifically interacting partners are of low-abundance and/or bind transiently with low affinity. To differentiate true interacting partners from contaminants, we have combined SILAC labelling with a proteomic method called "Interactomes by Parallel Affinity Capture" (iPAC). In our method, a cell-line stably expressing a doubly tagged target endogenous protein and its tag-less control cell-line are differentially SILAC labelled. Lysates from the two cell-lines are mixed and the tagged protein is independently purified for MS analysis using multiple affinity resins in parallel. This allows the quantitative identification of tagged proteins and their binding partners. SILAC-iPAC provides a rigorous and sensitive approach that can discriminate between genuine binding partners and contaminants, even when the contaminants in the pull-down are in large excess. We employed our method to examine the interacting partners of phosphatidyl inositol 5-phosphate 4-kinase 2? subunit (PI5P4K2?) and the Fanconi anaemia core complex in the chicken pre-B cell-line DT40. We confirmed known components of these two complexes, and we have identified new potential binding partners. Combining the iPAC approach with SILAC labelling provides a sensitive and fully quantitative method for the discrimination of specific interactions under conditions where low signal to noise ratios are unavoidable. In addition, our work provides the first characterisation of the most abundant proteins within the DT40 proteome and the non-specific DT40 'beadomes' (non-specific proteins binding to beads) for common epitope tags. Given the importance and widespread use of the DT40 cell-line, these will be important resources for the cell biology and immunology communities. Biological significance SILAC-iPAC provides an improved method for the analysis of low-affinity and/or low abundance protein-protein interactions. We use it to clarify two examples where the nature of the protein complexes are known, or are currently unclear. The method is simple and quantitative and will be applicable to many problems in cell and molecular biology. We also report the first chicken beadomes. PMID:25534881

Rees, Johanna S; Lilley, Kathryn S; Jackson, Antony P

2015-02-01

428

PLAYING WITH TAGGING: A REAL-TIME TAGGING MUSIC PLAYER Ju-Chiang Wang1,2  

E-print Network

PLAYING 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 or incomprehensible displays to users. In this paper, we present an intelligent music player called the Playing

Wang, Hsin-Min

429

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

430

LOBSTER TRAP TAG REPLACEMENT FORM Your request for the replacement of trap tags in an amount exceeding 10 % of your  

E-print Network

LOBSTER TRAP TAG REPLACEMENT FORM Your request for the replacement of trap tags in an amount lobster fishery by helping to restrict the number of traps fished by an individual permit holder and thus enforce that provision of the effort reduction program for the American Lobster Fishery. Public reporting

431

Electronic Cleansing in Dual-energy Fecal-tagging CT Colonography Based on Material Decomposition and Virtual Colon Tagging.  

PubMed

Dual-energy CT provides a promising solution to identify tagged fecal materials in electronic cleansing (EC) for fecal-tagging CT colonography (CTC). In this study, we developed a new EC method based on virtual colon tagging (VCT) for minimizing EC artifacts by use of the material decomposition ability in dual-energy CTC images. In our approach, a localized three-material decomposition model decomposes each voxel into a material mixture vector and the first partial derivatives of three base materials: luminal air, soft tissue, and iodine-tagged fecal material. A Poisson-based derivative smoothing algorithm smoothes the derivatives and implicitly smoothes the associated material mixture fields. VCT is a means for marking the entire colonic lumen by virtually elevating the CT value of luminal air as high as that of the tagged fecal materials to differentiate effectively soft-tissue structures from air-tagging mixtures. A dual-energy EC scheme based on VCT method, denoted as VCT-EC, was developed, in which the colonic lumen was first virtually tagged and then segmented by its high values in VCT images. The performance of the VCT-EC scheme was evaluated in a phantom study and a clinical dual-energy fecal-tagging CTC study. Our results demonstrated that our VCT-EC scheme may provide a significant reduction of EC artifacts. PMID:25350911

Cai, Wenli; Lee, June-Goo; Zhang, Da; Kim, Se Hyung; Zalis, Michael; Yoshida, Hiroyuki

2014-10-24

432

Performance of Passive Integrated Transponder Tags and Radio Tags in Determining Dam Passage Behavior of Adult Chinook Salmon and Steelhead  

Microsoft Academic Search

Passage of adult Pacific salmon Oncorhynchus spp. and steelhead O. mykiss at dams in the Columbia River basin has historically been determined by visual fish counts and radiotelemetry. Increasingly, however, passive integrated transponder (PIT) tags are being used for adult salmonid research and monitoring. Although both radiotelemetry and PIT tag technology provide accurate and cost-effective data under certain circumstances, neither

Brian J. Burke; Michael A. Jepson

2006-01-01

433

Conversion of Low-Affinity Peptides to High-Affinity Peptide Binders by Using a ?-Hairpin Scaffold-Assisted Approach.  

PubMed

Affinity maturation of protein-targeting peptides is generally accomplished by homo- or heterodimerization of known peptides. However, applying a heterodimerization approach is difficult because it is not clear a priori what length or type of linker is required for cooperative binding to a target. Thus, an efficient and simple affinity maturation method for converting low-affinity peptides into high-affinity peptides would clearly be advantageous for advancing peptide-based therapeutics. Here, we describe the development of a novel affinity maturation method based on a robust ?-hairpin scaffold and combinatorial phage-display technology. With this strategy, we were able to increase the affinity of existing peptides by more than four orders of magnitude. Taken together, our data demonstrate that this scaffold-assisted approach is highly efficient and effective in generating high-affinity peptides from their low-affinity counterparts. PMID:25371172

Kim, Sunghyun; Kim, Daejin; Lee, Yonghyun; Jeon, Hyungsu; Lee, Byung-Heon; Jon, Sangyong

2015-01-01

434

Engineering of Bispecific Affinity Proteins with High Affinity for ERBB2 and Adaptable Binding to Albumin  

PubMed Central

The epidermal growth factor receptor 2, ERBB2, is a well-validated target for cancer diagnostics and therapy. Recent studies suggest that the over-expression of this receptor in various cancers might also be exploited for antibody-based payload delivery, e.g. antibody drug conjugates. In such strategies, the full-length antibody format is probably not required for therapeutic effect and smaller tumor-specific affinity proteins might be an alternative. However, small proteins and peptides generally suffer from fast excretion through the kidneys, and thereby require frequent administration in order to maintain a therapeutic concentration. In an attempt aimed at combining ERBB2-targeting with antibody-like pharmacokinetic properties in a small protein format, we have engineered bispecific ERBB2-binding proteins that are based on a small albumin-binding domain. Phage display selection against ERBB2 was used for identification of a lead candidate, followed by affinity maturation using second-generation libraries. Cell surface display and flow-cytometric sorting allowed stringent selection of top candidates from pools pre-enriched by phage display. Several affinity-matured molecules were shown to bind human ERBB2 with sub-nanomolar affinity while retaining the interaction with human serum albumin. Moreover, parallel selections against ERBB2 in the presence of human serum albumin identified several amino acid substitutions that dramatically modulate the albumin affinity, which could provide a convenient means to control the pharmacokinetics. The new affinity proteins competed for ERBB2-binding with the monoclonal antibody trastuzumab and recognized the native receptor on a human cancer cell line. Hence, high affinity tumor targeting and tunable albumin binding were combined in one small adaptable protein. PMID:25089830

Nilvebrant, Johan; Åstrand, Mikael; Georgieva-Kotseva, Maria; Björnmalm, Mattias; Löfblom, John; Hober, Sophia

2014-01-01

435

Removal of PCR Error Products and Unincorporated Primers by Metal-Chelate Affinity Chromatography  

PubMed Central

Immobilized Metal Affinity Chromatography (IMAC) has been used for decades to purify proteins on the basis of amino acid content, especially surface-exposed histidines and “histidine tags” genetically added to recombinant proteins. We and others have extended the use of IMAC to purification of nucleic acids via interactions with the nucleotide bases, especially purines, of single-stranded RNA and DNA. We also have demonstrated the purification of plasmid DNA from contaminating genomic DNA by IMAC capture of selectively-denatured genomic DNA. Here we describe an efficient method of purifying PCR products by specifically removing error products, excess primers, and unincorporated dNTPs from PCR product mixtures using flow-through metal-chelate affinity adsorption. By flowing a PCR product mixture through a Cu2+-iminodiacetic acid (IDA) agarose spin column, 94–99% of the dNTPs and nearly all the primers can be removed. Many of the error products commonly formed by Taq polymerase also are removed. Sequencing of the IMAC-processed PCR product gave base-calling accuracy comparable to that obtained with a commercial PCR product purification method. The results show that IMAC matrices (specifically Cu2+-IDA agarose) can be used for the purification of PCR products. Due to the generality of the base-specific mechanism of adsorption, IMAC matrices may also be used in the purification of oligonucleotides, cDNA, mRNA and micro RNAs. PMID:21264292

Kanakaraj, Indhu; Jewell, David L.; Murphy, Jason C.; Fox, George E.; Willson, Richard C.

2011-01-01

436

Affinity purification–mass spectrometry and network analysis to understand protein-protein interactions  

PubMed Central

By determining protein-protein interactions in normal, diseased and infected cells, we can improve our understanding of cellular systems and their reaction to various perturbations. In this protocol, we discuss how to use data obtained in affinity purification–mass spectrometry (AP-MS) experiments to generate meaningful interaction networks and effective figures. We begin with an overview of common epitope tagging, expression and AP practices, followed by liquid chromatography–MS (LC-MS) data collection. We then provide a detailed procedure covering a pipeline approach to (i) pre-processing the data by filtering against contaminant lists such as the Contaminant Repository for Affinity Purification (CRAPome) and normalization using the spectral index (SIN) or normalized spectral abundance factor (NSAF); (ii) scoring via methods such as MiST, SAInt and CompPASS; and (iii) testing the resulting scores. Data formats familiar to MS practitioners are then transformed to those most useful for network-based analyses. The protocol also explores methods available in Cytoscape to visualize and analyze these types of interaction data. The scoring pipeline can take anywhere from 1 d to 1 week, depending on one’s familiarity with the tools and data peculiarities. Similarly, the network analysis and visualization protocol in Cytoscape takes 2–4 h to complete with the provided sample data, but we recommend taking days or even weeks to explore one’s data and find the right questions. PMID:25275790

Morris, John H; Knudsen, Giselle M; Verschueren, Erik; Johnson, Jeffrey R; Cimermancic, Peter; Greninger, Alexander L; Pico, Alexander R

2015-01-01

437

GST-tagged mouse estrogen receptor alpha-transactivation domain fusion protein is specifically degraded during its over-expression in E. coli and purification.  

PubMed

Escherichia coli BL21 (DE3) is commonly used for the overproduction of fusion proteins. Using this system, we recently reported the overproduction of histidine-tagged mouse estrogen receptor (ER) alpha-ligand binding domain as an intact 30 kD protein and its inhibitory effect on the growth of bacteria. However, when GST-tagged mouse ERalpha transactivation domain (TAD) was overproduced using this system, it showed no effect on the growth of bacteria but was specifically degraded during its expression and purification. Here we report the expression of 47 kD GST-tagged mouse ERalpha-TAD protein, which was degraded partially and specifically into 46 and 43 kD fragments. This fusion protein was further degraded into 37, 31, 29 and 26 kD fragments during its purification by affinity chromatography. Such specific degradation of GST-tagged mouse ERalpha-TAD during its overproduction in E. coli and purification indicates the induction of specific protease and suggests the modification of expression system. PMID:19319663

Thakur, M K; Ghosh, Swati

2010-03-01

438

Novel peptide VIP-TAT with higher affinity for PAC1 inhibited scopolamine induced amnesia.  

PubMed

A novel peptide VIP-TAT with a cell penetrating peptide TAT at the C-terminus of VIP was constructed and prepared using intein mediated purification with an affinity chitin-binding tag (IMPACT) system to enhance the brain uptake efficiency for the medical application in central nervous system. It was found by labeling VIP-TAT and VIP with fluorescein isothiocyanate (FITC) that the extension with TAT increased the brain uptake efficiency of VIP-TAT significantly. Then short-term and long-term treatment with scopolamine (Scop) was used to evaluate the effect of VIP-TAT or VIP on Scop induced amnesia. Both short-term and long-term administration of VIP-TAT inhibited the latent time reduction in step-through test induced by Scop significantly, but long-term administration of VIP aggravated the Scop induced amnesia. Long-term i.p. injection of VIP-TAT was shown to have positive effect by inhibiting the oxidative damage, apoptosis and the cholinergic system activity reduction that induced by Scop, while VIP exerted negative effect in brain opposite to that in periphery system. The in vitro data showed that VIP-TAT had not only protective but also proliferative effect on Neuro2a cells which was inhibited by PAC1 antagonist PACAP(6-38). Competition binding assay and cAMP assay confirmed that VIP-TAT had higher affinity and activation for PAC1 than VIP. So it was concluded that the significantly stronger protective effect of VIP-TAT against Scop induced amnesia than VIP was due to (1) the enhanced brain uptake efficiency of VIP-TAT and (2) the increased affinity and activation of VIP-TAT for receptor PAC1. PMID:25086267

Yu, Rongjie; Yang, Yanxu; Cui, Zekai; Zheng, Lijun; Zeng, Zhixing; Zhang, Huahua

2014-10-01

439

Applying thiouracil (TU)-tagging for mouse transcriptome analysis  

PubMed Central

Transcriptional profiling is a powerful approach to study mouse development, physiology, and disease models. Here, we describe a protocol for mouse thiouracil-tagging (TU-tagging), a transcriptome analysis technology that includes in vivo covalent labeling, purification, and analysis of cell type-specific RNA. TU-tagging enables 1) the isolation of RNA from a given cell population of a complex tissue, avoiding transcriptional changes induced by cell isolation trauma, and 2) the identification of actively transcribed RNAs and not pre-existing transcripts. Therefore, in contrast to other cell-specific transcriptional profiling methods based on purification of tagged ribosomes or nuclei, TU-tagging provides a direct examination of transcriptional regulation. We describe how to: 1) deliver 4-thiouracil to transgenic mice to thio-label cell lineage-specific transcripts, 2) purify TU-tagged RNA and prepare libraries for Illumina sequencing, and 3) follow a straight-forward bioinformatics workflow to identify cell type-enriched or differentially expressed genes. Tissue containing TU-tagged RNA can be obtained in one day, RNA-Seq libraries generated within two days, and, following sequencing, an initial bioinformatics analysis completed in one additional day. PMID:24457332

Gay, Leslie; Karfilis, Kate V.; Miller, Michael R.; Doe, Chris Q.; Stankunas, Kryn

2014-01-01

440

Site-Specific Protein Labeling with SNAP-Tags  

PubMed Central

Site-specific labeling of cellular proteins with chemical probes is a powerful tool for studying proteins function in living cells. A number of small peptide and protein tags have been developed that can be labeled with synthetic probes with high efficiencies and specificities and provide flexibility not available with fluorescent proteins (FPs). The SNAP-tag is a modified form of the DNA repair enzyme, human O6-alkylguanine-DNA-alkyltransferase (AGT), and undergoes a self-labeling reaction to form a covalent bond with O6-benzylguanine (BG) derivatives. BG can be modified with a wide variety of fluorophores and other reporter compounds generally without affecting the reaction with the SNAP-tag. In this unit, basic strategies for labeling SNAP-tag fusion proteins, both for live cell imaging and for in vitro analysis, will be described. This includes a description of a releasable SNAP-tag probe that allows the user to chemically cleave the fluorophore from the labeled SNAP-tag fusion. In vitro labeling of purified SNAP-tag fusions is briefly described. PMID:24510614

Cole, Nelson B.

2013-01-01

441

abFASP-MS: Affinity-Based Filter-Aided Sample Preparation Mass Spectrometry for Quantitative Analysis of Chemically Labeled Protein Complexes  

PubMed Central

Affinity purification coupled to 1-D gel-free liquid chromatography mass spectrometry (LC–MS) is a well-established and widespread approach for the analyses of noncovalently interacting protein complexes. In this study, two proteins conjugated to a streptavidin-binding peptide and hemagglutinin double tag were expressed in the respective Flp-In HEK293 cell lines: green fluorescent protein (SH-GFP) and TANK binding kinase 1 (SH-TBK1_MOUSE). Fluorescent anti-HA immunoblots revealed that the expression level of SH-GFP was ?50% lower than that of SH-TBK1_MOUSE. Subsequently, the input material was normalized to obtain a similar quantity of purified SH-tagged proteins. Optimization of the release of protein complexes from the anti-HA-agarose with different eluting agents was then assessed. With respect to the total number of protein groups identified in the purified complexes, elution with 2% SDS surpassed both 100 mM glycine and 100 mM formic acid. Relative quantitation of the purified protein complexes using TMT 6-plex reagents confirmed the higher efficiency of the 2% SDS elution followed by filter-aided sample preparation (FASP). The data presented in this study provide a new application of FASP to quantitative MS analysis of affinity-purified protein complexes. We have termed the approach abFASP-MS, or affinity-based filter-aided sample preparation mass spectrometry. PMID:24400740

2014-01-01

442

A wireless sensor tag platform for container security and integrity  

NASA Astrophysics Data System (ADS)

Cargo containers onboard ships are widely used in the global supply chain. The need for container security is evidenced by the Container Security Initiative launched by the U.S. Bureau of Customs and Border Protection (CBP). One method of monitoring cargo containers is using low power wireless sensor tags. The wireless sensor tags are used to set up a network that is comprised of tags internal to the container and a central device. The sensor network reports alarms and other anomalies to a central device, which then relays the message to an outside network upon arrival at the destination port. This allows the port authorities to have knowledge of potential security or integrity issues before physically examining the container. Challenges of using wireless sensor tag networks for container security include battery life, size, environmental conditions, information security, and cost among others. PNNL developed an active wireless sensor tag platform capable of reporting data wirelessly to a central node as well as logging data to nonvolatile memory. The tags, operate at 2.4 GHz over an IEEE 802.15.4 protocol, and were designed to be distributed throughout the inside of a shipping container in the upper support frame. The tags are mounted in a housing that allows for simple and efficient installation or removal prior to, during, or after shipment. The distributed tags monitor the entire container volume. The sensor tag platform utilizes low power electronics and provides an extensible sensor interface for incorporating a wide range of sensors including chemical, biological, and environmental sensors.

Amaya, Ivan A.; Cree, Johnathan V.; Mauss, Fredrick J.

2011-04-01

443

A wireless sensor tag platform for container security and integrity  

SciTech Connect

Cargo containers onboard ships are widely used in the global supply chain. The need for container security is evidenced by the Container Security Initiative launched by the U.S. Bureau of Customs and Border Protection (CBP). One method of monitoring cargo containers is using low power wireless sensor tags. The wireless sensor tags are used to set up a network that is comprised of tags internal to the container and a central device. The sensor network reports alarms and other anomalies to a central device, which then relays the message to an outside network upon arrival at the destination port. This allows the port authorities to have knowledge of potential security or integrity issues before physically examining the container. Challenges of using wireless sensor tag networks for container security include battery life, size, environmental conditions, information security, and cost among others. PNNL developed an active wireless sensor tag platform capable of reporting data wirelessly to a central node as well as logging data to nonvolatile memory. The tags, operate at 2.4 GHz over an IEEE 802.15.4 protocol, and were designed to be distributed throughout the inside of a shipping container in the upper support frame. The tags are mounted in a housing that allows for simple and efficient installation or removal prior to, during, or after shipment. The distributed tags monitor the entire container volume. The sensor tag platform utilizes low power electronics and provides an extensible sensor interface for incorporating a wide range of sensors including chemical, biological, and environmental sensors.

Amaya, Ivan A.; Cree, Johnathan V.; Mauss, Fredrick J.

2011-05-06

444

Tag loss can bias Jolly-Seber capture-recapture estimates  

USGS Publications Warehouse

We identified cases where the Jolly-Seber estimator of population size is biased under tag loss and tag-induced mortality by examining the mathematical arguments and performing computer simulations. We found that, except under certain tag-loss models and high sample sizes, the population size estimators (uncorrected for tag loss) are severely biased high when tag loss or tag-induced mortality occurs. Our findings verify that this misconception about effects of tag loss and tag-induced mortality could have serious consequences for field biologists interested in population size. Reiterating common sense, we encourage those engaged in capture-recapture studies to be careful and humane when handling animals during tagging, to use tags with high retention rates, to double-tag animals when possible, and to strive for the highest capture probabilities possible.

McDonald, T.L.; Amstrup, Steven C.; Manly, B.F.J.

2003-01-01

445

Visual Search Strategies of Tag Clouds - Results from an Eyetracking Study  

NASA Astrophysics Data System (ADS)

Tag clouds have become a frequently used interaction technique in the web in the past couple of years. Research has shown the influence of variables such as tag size and location on the perception of tag clouds. However, several questions remain unclear. First, little is know on how tag clouds are perceived visually and which search strategies users apply when looking for tags in a tag cloud. Second, there are variables, especially tag location, were prior work comes to conflicting results. Third, several approaches to present tag clouds with the tags semantically clustered have been proposed recently. However, it remains unclear which effects these new approaches have on the perception of tag clouds. In this paper we report the results of an extensive study on the perception of tag clouds using eye tracking technology that allows answering these questions.

Schrammel, Johann; Deutsch, Stephanie; Tscheligi, Manfred

446

Affine A3(1) N = 2 Monopole as the D Module and Affine ADHMN Sheaf  

NASA Astrophysics Data System (ADS)

A Higgs Yang Mills monopole scattering spherical symmetrically along light cones is given. The left incoming anti-self-dual a plane fields are holomorphic, but the right outgoing SD ? plane fields are antiholomorphic, meanwhile the diffeomorphism symmetry is preserved with mutual inverse affine rapidity parameters ? and ?-1. The Dirac wave function scattering in this background also factorized respectively into the (anti)holomorphic amplitudes. The holomorphic anomaly is realized by the center term of a quasi Hopf algebra corresponding to an integrable conformal affine massive field. We find explicit Nahm transformation matrix (Fourier-Mukai transformation) between the Higgs YM BPS (flat) bundles (D modules) and the affinized blow up ADHMN twistors (perverse sheafs). Thus we establish the algebra for the 't Hooft Hecke operators in the Hecke correspondence of the geometric Langlands program.

Hou, Bo-Yu; Hou, Bo-Yuan

2008-02-01

447

Affinity purification of influenza virus ribonucleoprotein complexes from the chromatin of infected cells.  

PubMed

Like all negative-strand RNA viruses, the genome of influenza viruses is packaged in the form of viral ribonucleoprotein complexes (vRNP), in which the single-stranded genome is encapsidated by the nucleoprotein (NP), and associated with the trimeric polymerase complex consisting of the PA, PB1, and PB2 subunits. However, in contrast to most RNA viruses, influenza viruses perform viral RNA synthesis in the nuclei of infected cells. Interestingly, viral mRNA synthesis uses cellular pre-mRNAs as primers, and it has been proposed that this process takes place on chromatin. Interactions between the viral polymerase and the host RNA polymerase II, as well as between NP and host nucleosomes have also been characterized. Recently, the generation of recombinant influenza viruses encoding a One-Strep-Tag genetically fused to the C-terminus of the PB2 subunit of the viral polymerase (rWSN-PB2-Strep) has been described. These recombinant viruses allow the purification of PB2-containing complexes, including vRNPs, from infected cells. To obtain purified vRNPs, cell cultures are infected, and vRNPs are affinity purified from lysates derived from these cells. However, the lysis procedures used to date have been based on one-step detergent lysis, which, despite the presence of a general nuclease, often extract chromatin-bound material only inefficiently. Our preliminary work suggested that a large portion of nuclear vRNPs were not extracted during traditional cell lysis, and therefore could not be affinity purified. To increase this extraction efficiency, and to separate chromatin-bound from non-chromatin-bound nuclear vRNPs, we adapted a step-wise subcellular extraction protocol to influenza virus-infected cells. Briefly, this procedure first separates the nuclei from the cell and then extracts soluble nuclear proteins (here termed the "nucleoplasmic" fraction). The remaining insoluble nuclear material is then digested with Benzonase, an unspecific DNA/RNA nuclease, followed by two salt extraction steps: first using 150 mM NaCl (termed "ch150"), then 500 mM NaCl ("ch500") (Fig. 1). These salt extraction steps were chosen based on our observation that 500 mM NaCl was sufficient to solubilize over 85% of nuclear vRNPs yet still allow binding of tagged vRNPs to the affinity matrix. After subcellular fractionation of infected cells, it is possible to affinity purify PB2-tagged vRNPs from each individual fraction and analyze their protein and RNA components using Western Blot and primer extension, respectively. Recently, we utilized this method to discover that vRNP export complexes form during late points after infection on the chromatin fraction extracted with 500 mM NaCl (ch500). PMID:22688655

Chase, Geoffrey P; Schwemmle, Martin

2012-01-01

448

Passive microwave tags : LDRD 52709, FY04 final report.  

SciTech Connect

This report describes both a general methodology and specific examples of completely passive microwave tags. Surface acoustic wave (SAW) devices were used to make tags for both identification and sensing applications at different frequencies. SAW correlators were optimized for wireless identification, and SAW filters were developed to enable wireless remote sensing of physical properties. Identification tag applications and wireless remote measurement applications are discussed. Significant effort went into optimizing the SAW devices used for this work, and the lessons learned from that effort are reviewed.

Brocato, Robert Wesley

2004-10-01

449

Edible oils from microalgae: insights in TAG accumulation.  

PubMed

Microalgae are a promising future source for sustainable edible oils. To make microalgal oil a cost-effective alternative for common vegetable oils, increasing TAG productivity and TAG content are of high importance. Fulfilling these targets requires proper understanding of lipid metabolism in microalgae. Here, we provide an overview of our current knowledge on the biology of TAG accumulation as well as the latest developments and future directions for increasing oil production in microalgae, considering both metabolic engineering techniques and cultivation strategies. PMID:25168414

Klok, A J; Lamers, P P; Martens, D E; Draaisma, R B; Wijffels, R H

2014-10-01

450

Flavor Tagging at CDF using Run II Data  

NASA Astrophysics Data System (ADS)

An overview on soft lepton tagging at CDF is presented. Determine the b flavor at production is required for B mixing and CP asymmetry measurements. At Tevatron, we produce bbarb pairs and so the flavor of the B is strongly correlated with the flavor of the B decay on the opposite side. One can then tag the B, using a semileptonic decay of the b quark into a lepton (b(barb) ? ?^-(?^+)bar?(?)X) on the opposite side where ? stands for electrons or muons. We study the performance of the soft lepton tagging using a sample of semileptonic b arrow ? ? X decays .

Paus, Christoph

2004-05-01

451

Using Geotags to Derive Rich Tag-Clouds for Image Annotation  

NASA Astrophysics Data System (ADS)

Geotagging has become popular for many multimedia applications. In this chapter, we present an integrated and intuitive system for location-driven tag suggestion, in the form of tag-clouds, for geotagged photos. Potential tags from multiple sources are extracted and weighted. Sources include points of interest (POI) tags from a public Geographic Names Information System (GNIS) database, community tags from Flickr® pictures, and personal tags shared through users' own, family, and friends' photo collections. To increase the effectiveness of GNIS POI tags, bags of place-name tags are first retrieved, clustered, and then re-ranked using a combined tf-idf and spatial distance criteria. The community tags from photos taken in the vicinity of the input geotagged photo are ranked according to distance and visual similarity to the input photo. Personal tags from other personally related photos inherently carry a significant weight due more to their high relevance than to both the generic place-name tags and community tags, and are ranked by weights that decay over time and distance differences. Finally, a rich set of the most relevant location-driven tags is presented to the user in the form of individual tag clouds under the three mentioned source categories. The tag clouds act as intuitive suggestions for tagging an input image. We also discuss quantitative and qualitative findings from a user study that we conducted. Evaluation has revealed the respective benefits of the three categories toward the effectiveness of the integrated tag suggestion system.

Joshi, Dhiraj; Luo, Jiebo; Yu, Jie; Lei, Phoury; Gallagher, Andrew

452

In situ fabrication of a microfluidic device for immobilised metal affinity sensing.  

PubMed

In this work a novel microfluidic device was constructed in situ containing the smallest microscopic co-polymeric immobilised metal affinity (IMA) adsorbent yet documented. This device has for the first time allowed the microlitre scale chromatographic assay of histidine-tagged proteins in a biological sample. To enable this approach, rather than using a high capacity commercial packed bed column which requires large sample volumes and would be susceptible to occlusion by cell debris, a microgram capacity co-polymeric chromatographic substrate suitable for analytical applications was fabricated within a microfluidic channel. This porous co-polymeric IMA micro-chromatographic element, only 27?l in volume, was assessed for the analytical capture of two different histidine-tagged recombinant fusion proteins. The micro-chromatographic adsorber was fabricated in situ by photo-polymerising an iminodiacetic acid (IDA) functionalised polymer matrix around a template of fused 100?m diameter NH(4)Cl particles entirely within the microfluidic channel and then etching away the salt with water to form a network of interconnected voids. The surface of the micro-chromatographic adsorber was chemically functionalised with a chelating agent and loaded with Cu(2+) ions. FTIR and NMR analysis verified the presence of the chelating agent on the adsorbent surface and its Cu(2+) ion binding capacity was determined to be 2.4?mol Cu(2+) (ml of adsorbent)(-1). Micro-scale equilibrium adsorption studies using the two different histidine-tagged proteins, LacI-His(6)-GFP and ?-Synuclein-His(8)-YFP, were carried out and the protein binding capacity of the adsorbent was determined to be 0.370 and 0.802mg(g of adsorbent)(-1), respectively. The dynamic binding capacity was determined at four different flow rates and found to be comparable to the equilibrium binding capacity at low flow rates. The sensing platform was also used to adsorb LacI-His(6)-GFP protein from crude cell lysate. During adsorption, laser scanning confocal microscopy identified locations within the adsorbent where protein adsorption and desorption occurred. The findings indicate that minimal channelling, selective product capture and near quantitative elution of the captured (adsorbed) product could be achieved, supporting the application of this new device as a high-throughput process analytical tool (PAT) for the in-process monitoring of histidine-tagged proteins in manufacturing. PMID:22341688

Deshpande, Abhishek G; Darton, Nicholas J; Yunus, Kamran; Fisher, Adrian C; Slater, Nigel K H

2012-05-15

453

Effect of C-terminal protein tags on pentitol and L-arabinose transport by Ambrosiozyma monospora Lat1 and Lat2 transporters in Saccharomyces cerevisiae.  

PubMed

Functional expression in heterologous hosts is often less successful for integral membrane proteins than for soluble proteins. Here, two Ambrosiozyma monospora transporters were successfully expressed in Saccharomyces cerevisiae as tagged proteins. Growth of A. monospora on l-arabinose instead of glucose caused transport activities of l-arabinose, l-arabitol, and ribitol, measured using l-[1-(3)H]arabinose, l-[(14)C]arabitol, and [(14)C]ribitol of demonstrated purity. A. monospora LAT1 and LAT2 genes were cloned earlier by using their ability to improve the growth of genetically engineered Saccharomyces cerevisiae on l-arabinose. However, the l-arabinose and pentitol transport activities of S. cerevisiae carrying LAT1 or LAT2 are only slightly greater than those of control strains. S. cerevisiae carrying the LAT1 or LAT2 gene fused in frame to the genes for green fluorescent protein (GFP) or red fluorescent protein (mCherry) or adenylate kinase (AK) exhibited large (>3-fold for LAT1; >20-fold for LAT2) increases in transport activities. Lat1-mCherry transported l-arabinose with high affinity (Km ? 0.03 mM) and l-arabitol and ribitol with very low affinity (Km ? 75 mM). The Lat2-GFP, Lat2-mCherry, and Lat2-AK fusion proteins could not transport l-arabinose but were high-affinity pentitol transporters (Kms ? 0.2 mM). The l-arabinose and pentitol transport activities of A. monospora could not be completely explained by any combination of the observed properties of tagged Lat1 and Lat2, suggesting either that tagging and expression in a foreign membrane alters the transport kinetics of Lat1 and/or Lat2 or that A. monospora contains at least one more l-arabinose transporter. PMID:24561586

Londesborough, John; Richard, Peter; Valkonen, Mari; Viljanen, Kaarina

2014-05-01

454

Effect of C-Terminal Protein Tags on Pentitol and l-Arabinose Transport by Ambrosiozyma monospora Lat1 and Lat2 Transporters in Saccharomyces cerevisiae  

PubMed Central

Functional expression in heterologous hosts is often less successful for integral membrane proteins than for soluble proteins. Here, two Ambrosiozyma monospora transporters were successfully expressed in Saccharomyces cerevisiae as tagged proteins. Growth of A. monospora on l-arabinose instead of glucose caused transport activities of l-arabinose, l-arabitol, and ribitol, measured using l-[1-3H]arabinose, l-[14C]arabitol, and [14C]ribitol of demonstrated purity. A. monospora LAT1 and LAT2 genes were cloned earlier by using their ability to improve the growth of genetically engineered Saccharomyces cerevisiae on l-arabinose. However, the l-arabinose and pentitol transport activities of S. cerevisiae carrying LAT1 or LAT2 are only slightly greater than those of control strains. S. cerevisiae carrying the LAT1 or LAT2 gene fused in frame to the genes for green fluorescent protein (GFP) or red fluorescent protein (mCherry) or adenylate kinase (AK) exhibited large (>3-fold for LAT1; >20-fold for LAT2) increases in transport activities. Lat1-mCherry transported l-arabinose with high affinity (Km ? 0.03 mM) and l-arabitol and ribitol with very low affinity (Km ? 75 mM). The Lat2-GFP, Lat2-mCherry, and Lat2-AK fusion proteins could not transport l-arabinose but were high-affinity pentitol transporters (Kms ? 0.2 mM). The l-arabinose and pentitol transport activities of A. monospora could not be completely explained by any combination of the observed properties of tagged Lat1 and Lat2, suggesting either that tagging and expression in a foreign membrane alters the transport kinetics of Lat1 and/or Lat2 or that A. monospora contains at least one more l-arabinose transporter. PMID:24561586

Richard, Peter; Valkonen, Mari; Viljanen, Kaarina

2014-01-01

455

Comparison of migration rate and survival between radio-tagged and PIT-tagged migrant yearling chinook salmon in the Snake and Columbia rivers  

USGS Publications Warehouse

A study was conducted to compare the travel times, detection probabilities, and survival of migrant hatchery-reared yearling chinook salmon Oncorhynchus tshawytscha tagged with either gastrically or surgically implanted sham radio tags (with an imbedded passive integrated transponder [PIT] tag) with those of their cohorts tagged only with PIT tags in the Snake and Columbia rivers. Juvenile chinook salmon with gastrically implanted radio tags migrated significantly faster than either surgically radio-tagged or PIT-tagged fish, while migration rates were similar among surgically radio-tagged and PIT-tagged fish. The probabilities of PIT tag detection at downstream dams varied by less than 5% and were not significantly different among the three groups. Survival was similar among treatments for median travel times of less than approximately 6 d (migration distance of 106 km). However, for both gastrically and surgically radio-tagged fish, survival was significantly less than for PIT-tagged fish, for which median travel times exceeded approximately 10 d (migration distance of 225 km). The results of this study support the use of radio tags to estimate the survival of juvenile chinook salmon having a median fork length of approximately 150 mm (range, 127-285 mm) and a median travel time of migration of less than approximately 6 d.

Hockersmith, E.E.; Muir, W.D.; Smith, S.G.; Sandford, B.P.; Perry, R.W.; Adams, N.S.; Rondorf, D.W.

2003-01-01

456

Latest European coelacanth shows Gondwanan affinities  

PubMed Central

The last European fossil occurrence of a coelacanth is from the Mid-Cretaceous of the English Chalk (Turonian, 90 million years ago). Here, we report the discovery of a coelacanth from Late Cretaceous non-marine rocks in southern France. It consists of a left angular bone showing structures that imply close phylogenetic affinities with some extinct Mawsoniidae. The closest relatives are otherwise known from Cretaceous continental deposits of southern continents and suggest that the dispersal of freshwater organisms from Africa to Europe occurred in the Late Cretaceous. PMID:17148159

Cavin, Lionel; Forey, Peter L; Buffetaut, Eric; Tong, Haiyan

2005-01-01

457

Accounting for tagging-to-harvest mortality in a Brownie tag-recovery model by incorporating radio-telemetry data.  

PubMed

The Brownie tag-recovery model is useful for estimating harvest rates but assumes all tagged individuals survive to the first hunting season; otherwise, mortality between time of tagging and the hunting season will cause the Brownie estimator to be negatively biased. Alternatively, fitting animals with radio transmitters can be used to accurately estimate harvest rate but may be more costly. We developed a joint model to estimate harvest and annual survival rates that combines known-fate data from animals fitted with transmitters to estimate the probability of surviving the period from capture to the first hunting season, and data from reward-tagged animals in a Brownie tag-recovery model. We evaluated bias and precision of the joint estimator, and how to optimally allocate effort between animals fitted with radio transmitters and inexpensive ear tags or leg bands. Tagging-to-harvest survival rates from >20 individuals with radio transmitters combined with 50-100 reward tags resulted in an unbiased and precise estimator of harvest rates. In addition, the joint model can test whether transmitters affect an individual's probability of being harvested. We illustrate application of the model using data from wild turkey, Meleagris gallapavo, to estimate harvest rates, and data from white-tailed deer, Odocoileus virginianus, to evaluate whether the presence of a visible radio transmitter is related to the probability of a deer being harvested. The joint known-fate tag-recovery model eliminates the requirement to capture and mark animals immediately prior to the hunting season to obtain accurate and precise estimates of harvest rate. In addition, the joint model can assess whether marking animals with radio transmitters affects the individual's probability of being harvested, caused by hunter selectivity or changes in a marked animal's behavior. PMID:24834339

Buderman, Frances E; Diefenbach, Duane R; Casalena, Mary Jo; Rosenberry, Christopher S; Wallingford, Bret D

2014-04-01

458

Prospects for Barium Tagging in Gaseous Xenon  

SciTech Connect

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. It is clear from this study that electrospray is a convenient mechanism for producing Ba++ is gas at atmospheric pressure. It is likely that the source will perform just as effectively at higher pressures. Even though the source region has water vapour and methanol vapour at the 0.3% level, there is no evidence for molecular formation. The use of TEA offers an effective method to achieve the charge state conversion. The overall design of the ion extraction from high pressure to vacuum is very similar to the scheme proposed for the final detector and this appears to work well although the efficiency is not yet determined.

Sinclair, D.; /Carleton U. /TRIUMF; Rollin, E.; /Carleton U.; Smith, J.; /Carleton U.; Mommers, A.; /Ottawa U.; Ackerman, N.; /SLAC; Aharmim, B.; /Laurentian U.; Auger, M.; /Bern U., LHEP; Barbeau, P.S.; /Stanford U., Phys. Dept.; Benitez-Medina, C.; /Colorado State U.; Breidenbach, M.; /SLAC; Burenkov, A.; /Moscow, ITEP; Cook, S.; /SLAC; Coppens, A.; /Carleton U.; Daniels, T.; /Massachusetts U., Amherst; DeVoe, R.; /Stanford U., Phys. Dept.; Dobi, A.; /Maryland U.; Dolinski, M.J.; Donato, K.; /Stanford U., Phys. Dept.; Fairbank, W., Jr.; /Colorado State U.; Farine, J.; /Laurentian U.; Giroux, G.; /Bern U., LHEP /Carleton U. /Stanford U., Phys. Dept. /Carleton U. /Laurentian U. /Carleton U. /SLAC /Indiana U. /Indiana U., CEEM /Korea U. /Stanford U., Phys. Dept. /SLAC /Alabama U. /Colorado State U. /Stanford U., Phys. Dept. /Alabama U. /SLAC /Stanford U., Phys. Dept. /Alabama U. /Massachusetts U., Amherst /SLAC /Alabama U. /SLAC /Maryland U. /Moscow, ITEP /Stanford U., Phys. Dept. /Maryland U. /Bern U., LHEP /Laurentian U. /SLAC /Maryland U.

2012-05-03

459

TAGGING, TRACKING AND LOCATING WITHOUT GPS  

SciTech Connect

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 (GPS), could communicate back to the owner, and worked where normal cell phone communications did not work or were unreliable. SRNL brought together multiple technologies in a demonstration that was held in in various Alaska venues, including metropolitan, wilderness, and at-sea that met the working group's requirements. Using prototypical technologies from Boeing, On Ramp, and Fortress, SRNL was able to demonstrate the ability to track personnel and material in all scenarios including indoors, in heavily wooden areas, canyons, and in parking garages. In all cases GPS signals were too weak to measure. Bi-directional communication was achieved in areas that Wi-Fi, cell towers, or traditional radios would not perform. The results of the exercise will be presented. These technologies are considered ideal for tracking high value material such has nuclear material with a platform that allows seamless tracking anywhere in the world, indoors or outdoors.

Cordaro, J.; Coleman, T.; Shull, D.

2012-07-08

460

Online b-jets tagging at CDF  

SciTech Connect

We propose a method to identify b-quark jets at trigger level which exploits recently increased CDF trigger system capabilities. b-quark jets identification is of central interest for the CDF high-P{sub T} physics program, and the possibility to select online b-jets enriched samples can extend the physics reaches especially for light Higgs boson searches where the H {yields} b{bar b} decay mode is dominant. Exploiting new trigger primitives provided by two recent trigger upgrades, the Level2 XFT stereo tracking and the improved Level2 cluster-finder, in conjunction with the existing Silicon Vertex Tracker (SVT), we design an online trigger algorithm aimed at selecting good purity b-jets samples useful for many physics measurements, the most important being inclusive H {yields} b{bar b} searches. We discuss the performances of the proposed b-tagging algorithm which must guarantee reasonable trigger rates at luminosity greater than 2 x 10{sup 32} cm{sup -2}s{sup -1} and provide high efficiency on H {yields} b{bar b} events.

Casarsa, M.; /Fermilab; Ristori, L.; /INFN, Pisa; Amerio, S.; Lucchesi, D.; Pagan Griso, S.; /INFN, Padua; Torre, S.T.; /Frascati; Cortiana, G.; /Padua U., Astron. Dept.

2007-04-01

461

Chemical tagging of stellar kinematic groups  

NASA Astrophysics Data System (ADS)

Stellar Kinematic Groups are kinematical coherent groups of stars which might share a common origin. These groups spread through the Galaxy over time due to tidal effects caused by galactic rotation and disc heating, however the chemical information survives. The aim of chemical tagging is to show that abundances of every chemical element must be homogeneus among candidate members. We have studied the case of the Hyades Supercluster and the Ursa Major Moving Group for kinematically selected FGK stars, based on high-resolution spectroscopic observations obtained at the 1.2 m Mercator Telescope with the HERMES Spectrograph. Stellar atmospheric parameters (T_{eff}, log{g}, ? and [Fe/H]) have been determined using an own-implemented automatic code (StePar) which makes use of the sensibility from iron EWs measured in the spectra. We have derived the chemical abundances of several elements and their [X/Fe] ratios. Thus, we finally perform a careful differential abundance analysis using a known member of each cluster as a reference star, with the aim to clarify the origin of these kinematical groups.

Tabernero, H. M.; Montes, D.; González Hernández, J. I.

2013-05-01

462

Have tag, will travel Send us your business card --or  

E-print Network

16 1 Have tag, will travel Send us your business card -- or just your business information to the College of Arts & Sciences at IU and will improve our alumni database. Mail your card or information __________________________________ State ____________________ Zip_______________________________ Business title

Indiana University

463

Methyl-CpG island-associated genome signature tags  

DOEpatents

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

Dunn, John J

2014-05-20

464

Ethical implications of implantable radiofrequency identification (RFID) tags in humans.  

PubMed

This article reviews the use of implantable radiofrequency identification (RFID) tags in humans, focusing on the VeriChip (VeriChip Corporation, Delray Beach, FL) and the associated VeriMed patient identification system. In addition, various nonmedical applications for implanted RFID tags in humans have been proposed. The technology offers important health and nonhealth benefits, but raises ethical concerns, including privacy and the potential for coercive implantation of RFID tags in individuals. A national discussion is needed to identify the limits of acceptable use of implantable RFID tags in humans before their use becomes widespread and it becomes too late to prevent misuse of this useful but ethically problematic technology. PMID:18802863

Foster, Kenneth R; Jaeger, Jan

2008-08-01

465

48 CFR 952.208-7 - Tagging of leased vehicles.  

Code of Federal Regulations, 2010 CFR

...leased vehicles. 952.208-7 Section 952.208-7 Federal Acquisition Regulations System DEPARTMENT OF ENERGY CLAUSES AND FORMS SOLICITATION PROVISIONS AND CONTRACT CLAUSES Text of Provisions and Clauses 952.208-7 Tagging...

2010-10-01

466

48 CFR 952.208-7 - Tagging of leased vehicles.  

Code of Federal Regulations, 2012 CFR

...leased vehicles. 952.208-7 Section 952.208-7 Federal Acquisition Regulations System DEPARTMENT OF ENERGY CLAUSES AND FORMS SOLICITATION PROVISIONS AND CONTRACT CLAUSES Text of Provisions and Clauses 952.208-7 Tagging...

2012-10-01

467

48 CFR 952.208-7 - Tagging of leased vehicles.  

Code of Federal Regulations, 2011 CFR

...leased vehicles. 952.208-7 Section 952.208-7 Federal Acquisition Regulations System DEPARTMENT OF ENERGY CLAUSES AND FORMS SOLICITATION PROVISIONS AND CONTRACT CLAUSES Text of Provisions and Clauses 952.208-7 Tagging...

2011-10-01

468

48 CFR 952.208-7 - Tagging of leased vehicles.  

Code of Federal Regulations, 2013 CFR

...leased vehicles. 952.208-7 Section 952.208-7 Federal Acquisition Regulations System DEPARTMENT OF ENERGY CLAUSES AND FORMS SOLICITATION PROVISIONS AND CONTRACT CLAUSES Text of Provisions and Clauses 952.208-7 Tagging...

2013-10-01

469

InkTag: Secure Applications on an Untrusted Operating System  

PubMed Central

InkTag is a virtualization-based architecture that gives strong safety guarantees to high-assurance processes even in the presence of a malicious operating system. InkTag advances the state of the art in untrusted operating systems in both the design of its hypervisor and in the ability to run useful applications without trusting the operating system. We introduce paraverification, a technique that simplifies the InkTag hypervisor by forcing the untrusted operating system to participate in its own verification. Attribute-based access control allows trusted applications to create decentralized access control policies. InkTag is also the first system of its kind to ensure consistency between secure data and metadata, ensuring recoverability in the face of system crashes. PMID:24429939

Hofmann, Owen S.; Kim, Sangman; Dunn, Alan M.; Lee, Michael Z.; Witchel, Emmett

2014-01-01

470

Unsupervised mining of frequent tags for clinical eligibility text indexing.  

PubMed

Clinical text, such as clinical trial eligibility criteria, is largely underused in state-of-the-art medical search engines due to difficulties of accurate parsing. This paper proposes a novel methodology to derive a semantic index for clinical eligibility documents based on a controlled vocabulary of frequent tags, which are automatically mined from the text. We applied this method to eligibility criteria on ClinicalTrials.gov and report that frequent tags (1) define an effective and efficient index of clinical trials and (2) are unlikely to grow radically when the repository increases. We proposed to apply the semantic index to filter clinical trial search results and we concluded that frequent tags reduce the result space more efficiently than an uncontrolled set of UMLS concepts. Overall, unsupervised mining of frequent tags from clinical text leads to an effective semantic index for the clinical eligibility documents and promotes their computational reuse. PMID:24036004

Miotto, Riccardo; Weng, Chunhua

2013-12-01

471

Feasibility of Surgically Implanting Acoustic Tags into Pacific Herring  

USGS Publications Warehouse

Internally implanted acoustic tags represent a potentially valuable approach to assessing the seasonal migration and distribution patterns of Pacific herring Clupea palasii. We examined the feasibility of implanting two sizes of dummy acoustic tags (9 mm in diameter × 21 mm long, 1.6 g; and 7 mm in diameter × 18 mm long, 0.7