Science.gov

Sample records for isotope-coded affinity tags

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

    E-print Network

    Craik, Charles S.

    Isotope-Coded and Affinity-Tagged Cross-Linking (ICATXL): An Efficient Strategy to Probe Protein, we present a novel cross-linking strategy termed ICATXL (isotope-coded and affinity-tagged cross-linking) that relies on the use of affinity-tagged cross-linkers and isotope coding on the cross

  2. Phosphoprotein Isotope-Coded Solid-Phase Tag Approach for Enrichment and Quantitative Analysis of Phosphopeptides from Complex Mixtures

    SciTech Connect

    Qian, Weijun ); Goshe, Michael B.; Camp, David G.); Yu, Li-Rong ); Tang, Keqi ); Smith, Richard D.)

    2003-10-15

    Many cellular processes are regulated by reversible protein phosphorylation and the ability to identify and quantify phosphoproteins from proteomes is essential for gaining a better understanding of these dynamic cellular processes. However, a sensitive, efficient and global method capable of addressing the phosphoproteome has yet to be developed. Here we describe an improved stable-isotope labeling method using a Phosphoprotein Isotope-coded Solid-phase Tag (PhIST) for isolating and measuring the relative abundance of phosphorylated peptides from complex peptide mixtures resulting from the enzymatic digestion of extracted proteins. The PhIST approach is an extension of the previously reported Phosphoprotein Isotope-coded Affinity Tag (PhIAT)approach developed by our laboratory1-2, where the O-phosphate moiety on phosphoseryl or phosphothreonyl residues were derivatized by hydroxide ion-medated B-elimination followed by the addition of 1,2-ethanedithiol (EDT). Instead of using the biotin affinity tag, peptides containing the EDT moiety were captured and labeled in one step using isotope-coded solid-phase reagents containing either light (12C6, 14N) or heavy (13C6, 15N) stable isotopes. The captured peptides labeled with the isotope-coded tags were released from the solid-phase support by UV photocleavage and analyzed by capillary LC-MS/MS. The efficiency and sensitivity of the PhIST labeling approach for identification of phosphopeptides from mixtures was demonstrated using casein phosphoproteins. Its utility for proteomic applications is demonstrated by the labeling of soluble proteins from human breast cancer cell line.

  3. Proteolytic Affinity Tag Cleavage.

    PubMed

    Block, Helena; Maertens, Barbara; Spriestersbach, Anne; Kubicek, Jan; Schäfer, Frank

    2015-01-01

    Here, we present protocols describing the use of the dipeptidyl-aminopeptidase-1 (DPP1, DAPase) exoprotease-based TAGZyme system and the endoprotease, Factor Xa. Both enable the recovery of proteins free of any amino acids encoded by the vector and/or protease recognition site. They also provide the possibility of removing the proteases from the preparation of the target protein by a simple subtractive chromatography step. TAGZyme enzymes contain an uncleavable His tag for removal by Immobilized Metal Ion Affinity Chromatography (IMAC). Factor Xa can be removed using Xa Removal Resin. PMID:26096504

  4. Affinity Chromatography GST-tagged Proteins

    E-print Network

    Lebendiker, Mario

    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

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

    SciTech Connect

    Giannone, Richard J; McDonald, W Hayes; Hurst, Gregory {Greg} B; Huang, Ying; Wu, Jun; Liu, Yie; Wang, Yisong

    2007-01-01

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

  6. Use of Dual Affinity Tags for Expression and Purification of Functional Peripheral Cannabinoid Receptor

    PubMed Central

    Yeliseev, Alexei; Zoubak, Lioudmila; Gawrisch, Klaus

    2007-01-01

    The human peripheral cannabinoid receptor (CB2) was expressed as a fusion with the maltose-binding protein (at the N-terminus), thioredoxin A (at the C-terminus) and two small affinity tags (a Strep-tag and a polyhistidine tag). Expression levels of the recombinant receptor in Escherichia coli BL21(DE3) cells were dependent on location and type of tags in the expression construct, and were as high as 1-2 mg per liter of bacterial culture. The recombinant receptor was ligand binding-competent, and activated cognate G-proteins in an in vitro coupled assay. The fusion CB2-125 protein was purified by immobilized metal affinity chromatography on a Ni-NTA resin. Maltose-binding protein, thioredoxin and a decahistidine tag were removed from the fusion by treatment with Tobacco etch virus (Tev) protease. Purification to over 90% homogeneity of the resulting CB2, containing an N-terminal Strep-tag was achieved by affinity chromatography on a StrepTactin resin. Circular dichroism spectroscopy indicated an ?-helical content of the purified recombinant protein of ?54%. The expression and purification protocol allows for production of large (milligram) quantities of functional peripheral cannabinoid receptor, suitable for subsequent structural characterization. Preliminary results of reconstitution experiments indicate that the CB2 has retained its ligand-binding properties. PMID:17223358

  7. Video Article Orthogonal Protein Purification Facilitated by a Small Bispecific Affinity Tag

    E-print Network

    Lebendiker, Mario

    Video Article Orthogonal Protein Purification Facilitated by a Small Bispecific Affinity Tag Johan of Technology Correspondence to: Sophia Hober at sophia.hober@biotech.kth.se URL: http://www.jove.com/video/3370 in combination1,7. Video Link The video component of this article can be found at http://www.jove.com/video/3370

  8. Yeast 3',5'-bisphosphate nucleotidase: an affinity tag for protein purification.

    PubMed

    Yang, Yang; Ma, Jianhui; Yang, Yilin; Zhang, Xiao; Wang, Yanxing; Yang, Ling; Sun, Meihao

    2014-05-01

    Affinity chromatography is one of the most popular methods for protein purification. Each tag method has its advantages and disadvantages, and combination of different tags and developing of new tags had been proposed and performed. Yeast 3',5'-bisphosphate nucleotidase, also known as HAL2, hydrolyzes 3'-phosphoadenosine 5'-phosphate (PAP) with submicromolar Km, which indicated the tight interactions between HAL2 and PAP. In order to explore the feasibility of HAL2 as a protein purification affinity tag, HAL2 was further characterized with PAP as substrate. Results demonstrated that KmPAP and kcatPAP were ?0.3?M and ?11s(-)(1), respectively. Kd for PAP was 0.008?M in the presence of Ca(2+). pH was also found to affect interactions between HAL2 and PAP, with tightest binding (Kd?8nM) at pH 7.5 and 8. The purification protocol was rationally designed based on nanomolar affinity to PAP agarose in the presence of Ca(2+), which could satisfy the metal requirement for PAP binding, prevent hydrolysis of immobilized PAP and could be chelated by ethylene glycol tetraacetic acid (EGTA) for elution. A series of expression vectors were further constructed and Escherichia coli adenosine 5'-phosphosulfate kinase (APSK) was prokaryotically expressed, purified and characterized. Ready to use expression vector with eight commonly used restriction enzyme recognition sites in multiple cloning site was subsequently constructed. By comparing with current popular tags, HAL2 was found to be an efficient and economical tag for prokaryotic protein expression and purification. PMID:24613729

  9. RNA complex purification using high-affinity fluorescent RNA aptamer tags.

    PubMed

    Panchapakesan, Shanker Shyam S; Jeng, Sunny C Y; Unrau, Peter J

    2015-04-01

    RNA plays important roles in cellular processes, but RNA-protein complexes are notoriously hard to isolate and study. We compare and contrast existing RNA- and protein-purification strategies with the potential of new RNA-tagging systems such as RNA Spinach and RNA Mango. Each RNA aptamer binds a small fluorophore, resulting in a highly fluorescent complex that is thousands of times brighter than the unbound fluorophore. Provided that the aptamer binding affinity is high enough, derivatized dyes can be used in conjunction with these aptamers to purify RNA complexes while simultaneously using their intrinsic fluorescence to track the complex of interest. The known strengths and weakness of these RNA tagging systems are discussed. PMID:25585661

  10. The elution of certain protein affinity tags with millimolar concentrations of diclofenac.

    PubMed

    Baliova, Martina; Juhasova, Anna; Jursky, Frantisek

    2015-12-01

    Diclofenac (2-[(2, 6-dichlorophenyl)amino] benzeneacetic acid) is a sparingly soluble, nonsteroidal anti-inflammatory drug therapeutically acting at low micromolar concentrations. In pH range from 8 to 11, its aqueous solubility can be increased up to 200 times by the presence of counter ions such as sodium. Our protein interaction studies revealed that a millimolar concentration of sodium diclofenac is able to elute glutathione S-transferase (GST), cellulose binding protein (CBD), and maltose binding protein (MBP) but not histidine-tagged or PDZ-tagged proteins from their affinity resins. The elution efficiency of diclofenac is comparable with the eluting agents normally used at similar concentrations. Native gel electrophoresis of sodium diclofenac-treated proteins showed that the interaction is non-covalent and non-denaturing. These results suggest that sodium diclofenac, in addition to its pharmaceutical applications, can also be exploited as a lead for the development of new proteomics reagents. PMID:26551210

  11. Robotic high-throughput purification of affinity-tagged recombinant proteins.

    PubMed

    Wiesler, Simone C; Weinzierl, Robert O J

    2015-01-01

    Affinity purification of recombinant proteins has become the method of choice to obtain good quantities and qualities of proteins for a variety of downstream biochemical applications. While manual or FPLC-assisted purification techniques are generally time-consuming and labor-intensive, the advent of high-throughput technologies and liquid handling robotics has simplified and accelerated this process significantly. Additionally, without the human factor as a potential source of error, automated purification protocols allow for the generation of large numbers of proteins simultaneously and under directly comparable conditions. The delivered material is ideal for activity comparisons of different variants of the same protein. Here, we present our strategy for the simultaneous purification of up to 24 affinity-tagged proteins for activity measurements in biochemical assays. The protocol described is suitable for the scale typically required in individual research laboratories. PMID:25749949

  12. Imidazole-free purification of His3-tagged recombinant proteins using ssDNA aptamer-based affinity chromatography.

    PubMed

    Bartnicki, Filip; Kowalska, Ewa; Pels, Katarzyna; Strzalka, Wojciech

    2015-10-30

    Immobilized metal ion affinity chromatography (IMAC) is widely used for the purification of many different His6-tagged recombinant proteins. On the one hand, it is a powerful technique but on the other hand it has its disadvantages. In this report, we present the development of a unique ssDNA aptamer for the purification of His3-tagged recombinant proteins. Our study shows that stability of the His3-tag/H3T aptamer complex can be controlled by the sodium ion concentration. Based on this feature, we demonstrate that H3T aptamer resin was successfully employed for the purification of three out of four tested His3-tagged recombinant proteins from an E. coli total protein extract using imidazole-free buffers. Finally, we show that the purity of His3-tagged proteins is superior when purified with the help of the H3T aptamer in comparison with Ni-NTA resin. PMID:26427325

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

    PubMed

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

    2014-11-01

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

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

    SciTech Connect

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

    2009-01-01

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

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

    PubMed

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

    2014-01-01

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

  16. Engineering Streptavidin and a Streptavidin-Binding Peptide with Infinite Binding Affinity and Reversible Binding Capability: Purification of a Tagged Recombinant Protein to High Purity via Affinity-Driven Thiol Coupling

    PubMed Central

    Fogen, Dawson; Wu, Sau-Ching; Ng, Kenneth Kai-Sing; Wong, Sui-Lam

    2015-01-01

    To extend and improve the utility of the streptavidin-binding peptide tag (SBP-tag) in applications ranging from affinity purification to the reversible immobilization of recombinant proteins, a cysteine residue was introduced to the streptavidin mutein SAVSBPM18 and the SBP-tag to generate SAVSBPM32 and SBP(A18C), respectively. This pair of derivatives is capable of forming a disulfide bond through the newly introduced cysteine residues. SAVSBPM32 binds SBP-tag and biotin with binding affinities (Kd ~ 10-8M) that are similar to SAVSBPM18. Although SBP(A18C) binds to SAVSBPM32 more weakly than SBP-tag, the binding affinity is sufficient to bring the two binding partners together efficiently before they are locked together via disulfide bond formation–a phenomenon we have named affinity-driven thiol coupling. Under the condition with SBP(A18C) tags in excess, two SBP(A18C) tags can be captured by a tetrameric SAVSBPM32. The stoichiometry of the disulfide-bonded SAVSBPM32-SBP(A18C) complex was determined using a novel two-dimensional electrophoresis method which has general applications for analyzing the composition of disulfide-bonded protein complexes. To illustrate the application of this reversible immobilization technology, optimized conditions were established to use the SAVSBPM32-affinity matrix for the purification of a SBP(A18C)-tagged reporter protein to high purity. Furthermore, we show that the SAVSBPM32-affinity matrix can also be applied to purify a biotinylated protein and a reporter protein tagged with the unmodified SBP-tag. The dual (covalent and non-covalent) binding modes possible in this system offer great flexibility to many different applications which need reversible immobilization capability. PMID:26406477

  17. High-affinity gold nanoparticle pin to label and localize histidine-tagged protein in macromolecular assemblies

    PubMed Central

    Anthony, Kelsey C.; You, Changjiang; Piehler, Jacob; Pomeranz Krummel, Daniel A.

    2014-01-01

    SUMMARY There is significant demand for experimental approaches to aid protein localization in electron microscopy micrographs and ultimately in three-dimensional reconstructions of macromolecular assemblies. We report preparation and use of a reagent consisting of tris-nitrilotriacetic acid (tris-NTA) conjugated with a monofunctional gold nanoparticle (AuNPtris-NTA) for site-specific, non-covalent labeling of protein termini fused to a histidine-tag (His-tag). Multivalent binding of tris-NTA to a His-tag via complexed Ni(II) ions results in subnanomolar affinity and a defined 1:1 stoichiometry. Precise localization of AuNPtris-NTA labeled proteins by electron microscopy is further ensured by the reagent’s short conformationally restricted linker. We have employed AuNPtris-NTA to localize His-tagged proteins in an oligomeric ATPase and in the bacterial 50S ribosomal subunit. AuNPtris-NTA can specifically bind to the target proteins in these assemblies and is clearly discernible. Our new labeling reagent should find broad application in non-covalent site-specific labeling of protein termini to pinpoint their location in macromolecular assemblies. PMID:24560806

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

    E-print Network

    Lebendiker, Mario

    The variable detergent sensitivity of proteases that are utilized for recombinant protein affinity online 24 April 2011 Keywords: Proteases Detergent stability Membrane proteins a b s t r a c for integral membrane proteins contain detergents, which are required to maintain protein solubility. We

  19. Synthesis of an azido-tagged low affinity ratiometric calcium sensor

    PubMed Central

    Caldwell, Stuart T.; Cairns, Andrew G.; Olson, Marnie; Chalmers, Susan; Sandison, Mairi; Mullen, William; McCarron, John G.; Hartley, Richard C.

    2015-01-01

    Changes in high localised concentrations of Ca2+ ions are fundamental to cell signalling. The synthesis of a dual excitation, ratiometric calcium ion sensor with a Kd of 90 ?M, is described. It is tagged with an azido group for bioconjugation, and absorbs in the blue/green and emits in the red region of the visible spectrum with a large Stokes shift. The binding modulating nitro group is introduced to the BAPTA core prior to construction of a benzofuran-2-yl carboxaldehyde by an allylation–oxidation–cyclisation sequence, which is followed by condensation with an azido-tagged thiohydantoin. The thiohydantoin unit has to be protected with an acetoxymethyl (AM) caging group to allow CuAAC click reaction and incorporation of the KDEL peptide endoplasmic reticulum (ER) retention sequence. PMID:26709317

  20. A New Versatile Immobilization Tag Based on the Ultra High Affinity and Reversibility of the Calmodulin-Calmodulin Binding Peptide Interaction.

    PubMed

    Mukherjee, Somnath; Ura, Marcin; Hoey, Robert J; Kossiakoff, Anthony A

    2015-08-14

    Reversible, high-affinity immobilization tags are critical tools for myriad biological applications. However, inherent issues are associated with a number of the current methods of immobilization. Particularly, a critical element in phage display sorting is functional immobilization of target proteins. To circumvent these problems, we have used a mutant (N5A) of calmodulin binding peptide (CBP) as an immobilization tag in phage display sorting. The immobilization relies on the ultra high affinity of calmodulin to N5A mutant CBP (RWKKNFIAVSAANRFKKIS) in presence of calcium (KD~2 pM), which can be reversed by EDTA allowing controlled "capture and release" of the specific binders. To evaluate the capabilities of this system, we chose eight targets, some of which were difficult to overexpress and purify with other tags and some had failed in sorting experiments. In all cases, specific binders were generated using a Fab phage display library with CBP-fused constructs. KD values of the Fabs were in subnanomolar to low nanomolar (nM) ranges and were successfully used to selectively recognize antigens in cell-based experiments. Some of these targets were problematic even without any tag; thus, the fact that all led to successful selection endpoints means that borderline cases can be worked on with a high probability of a positive outcome. Taken together with examples of successful case specific, high-level applications like generation of conformation-, epitope- and domain-specific Fabs, we feel that the CBP tag embodies all the attributes of covalent immobilization tags but does not suffer from some of their well-documented drawbacks. PMID:26159704

  1. A pair of ligation-independent Escherichia coli expression vectors for rapid addition of a polyhistidine affinity tag to the N- or C-termini of recombinant proteins.

    PubMed

    Dan, Hanhong; Balachandran, Aru; Lin, Min

    2009-12-01

    6x His tag is one of the most widely used affinity fusion tags that facilitates detection and purification of recombinant proteins. However, the location of this tag within a particular type of protein may influence the expression, solubility, and bioactivity of the protein, and the optimal location needs to be determined experimentally. To provide a tool for rapid generation of 6x His tags at the N- or C-terminus of any recombinant protein, we have constructed a pair of Escherichia coli expression vectors-pLIC-NHis and pLIC-CHis-based on the pET30a vector, for ligation-independent cloning (LIC). Construction of this new pair of LIC vectors was accomplished by replacement of the multiple cloning site of pET30a with two specifically designed LIC cloning sites. A target gene derived by PCR with a pair of predesigned primers can be inserted into the LIC site of pLIC-NHis for expression of recombinant proteins fused with the N-terminal sequence MHHHHHHG or into that of pLIC-CHis for expression of recombinant proteins with the C-terminal sequence THHHHHH. Successful expression of two normal mammalian prion proteins and five bacterial proteins in E. coli using this pair of LIC vectors reveals that these vectors are valuable tools for the production of recombinant His-tagged proteins in E. coli. PMID:19949695

  2. A modified metal-ion affinity chromatography procedure for the purification of histidine-tagged recombinant proteins expressed in Drosophila S2 cells.

    PubMed

    Lehr, R V; Elefante, L C; Kikly, K K; O'Brien, S P; Kirkpatrick, R B

    2000-08-01

    We have developed a modified method of immobilized metal-ion affinity chromatography (IMAC) that can be used for the purification of histidine-tagged proteins from conditioned medium containing free copper ions. Classical methods of IMAC purification, using resins such as Ni-NTA, have proven inefficient for this type of purification and require multiple steps due to the interference of divalent copper ions with the binding of His-tagged protein to the charged resin. In contrast, this modified IMAC procedure, using chelating Sepharose instead of Ni-NTA, enables efficient purification from copper-containing medium in a single step. This method appears to rely upon a preferential interaction of protein-copper complexes with immobilized chelating resin. We have utilized this method to purify active, His-tagged murine interleukin 12 from the conditioned medium of Drosophila S2 cells coexpressing recombinant p40 and His-tagged p35 subunits and for the purification of the extracellular domain of the erythropoietin receptor. This method should be applicable to the purification of a wide variety of His-tagged fusion proteins expressed in Drosophila cells and in other systems where free metal ions are present. PMID:10910726

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

    E-print Network

    Ghosh, Indraneel

    for the isolation and visualization of proteins under a particular set of conditions, but also for the bio- chemical and purification of recombinant proteins Thomas Gaj, Scott C. Meyer, Indraneel Ghosh * Department of Chemistry-established tools for recombinant protein immobilization and purification. More recently these tags have been

  4. An isotope-coded fluorogenic cross-linker for high-performance target identification based on photoaffinity labeling.

    PubMed

    Tomohiro, Takenori; Morimoto, Shota; Shima, Toshiya; Chiba, Junya; Hatanaka, Yasumaru

    2014-12-01

    A photoaffinity labeling (PAL)-based method for the rapid identification of target proteins is presented in which a high-performance chemical tag, an isotope-coded fluorescent tag (IsoFT), can be attached to the interacting site by irradiation. Labeled peptides can be easily distinguished among numerous proteolytic digests by sequential detection with highly sensitive fluorescence spectroscopy and mass spectrometry. Subsequent MS/MS analysis provides amino acid sequence information with a higher depth of coverage. The combination of PAL and heterogeneous target-selecting techniques significantly reduces the amount of time and protein required for identification. An additional photocleavable moiety successfully accelerated proteomic analysis using cell lysate. This method is a widely applicable approach for the rapid and accurate identification of interacting proteins. PMID:25382598

  5. Affinity of aptamers binding 33-mer gliadin peptide and gluten proteins: Influence of immobilization and labeling tags.

    PubMed

    Amaya-González, Sonia; López-López, Laura; Miranda-Castro, Rebeca; de-los-Santos-Álvarez, Noemí; Miranda-Ordieres, Arturo José; Lobo-Castañón, María Jesús

    2015-05-11

    Aptamers are starting to increase the reagents tool box to develop more sensitive and reliable methods for food allergens. In most of these assays, aptamers have to be modified for detection and/or immobilization purposes. To take full advantage of their affinity, which decisively influence the detectability, these modifications must be faced rationally. In this work, a recently developed aptamer for an immunotoxic peptide of gliadin associated to celiac disease is used in different configurations and modified with various markers and anchored groups to evaluate the influence of such modifications on the real affinity. The interaction in solution with the peptide is strong for a relatively small molecule (Kd = 45 ± 10 nM, 17 °C) and slightly stronger than that for the immobilized intact protein due to a cooperative binding effect. Comparatively, while only minor differences were found when the peptide or the aptamer were immobilized, labeling with a biotin resulted preferable over fluorescein (Kd = 102 ± 11 vs 208 ± 54 nM, 25 °C). These findings are of prime importance for the design of an aptamer-based analytical method for gluten quantification. PMID:25911431

  6. Metal Affinity Chromatography (MAC)

    E-print Network

    Lebendiker, Mario

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

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

    PubMed Central

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

    2014-01-01

    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

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

    PubMed Central

    Gretes, Michael C; Karplus, P Andrew

    2013-01-01

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

  9. On-line purification of His-tag enhanced green fluorescent protein taken directly from a bioreactor by continuous ultrasonic homogenization coupled with immobilized metal affinity expanded bed adsorption.

    PubMed

    Noubhani, A M; Dieryck, W; Chevalier, S; Santarelli, X

    2002-08-30

    In this report, we describe a new process for the on-line purification of His-tag EGFP (enhanced green fluorescent protein) taken directly from a bioreactor by continuous ultrasonic homogenization coupled with immobilized metal affinity expanded bed adsorption (IMAEBA). The use of proteins including a histidine-tag facilitates their subsequent purification after expression in many microorganisms. This meets the needs of scientific researchers as well as industrialists interested in purifying recombinant proteins. After evaluating the different flow-rates and ultrasonic probe sizes, the on-line purification was tested. After ultrasonic treatment, 70% of the cells were broken and 90% of free EGFP was recovered after IMAEBA. In our conditions, more than 450 mg of EGFP were obtained in 15 h. On-line bioreactor-ultrasonic probe-immobilized metal affinity expanded bed adsorption is a rapid automated technique for obtaining large quantities of pure EGFP. PMID:12236494

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

    PubMed Central

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

    2013-01-01

    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

  11. Yolk-shell nanostructured Fe3O4@NiSiO3 for selective affinity and magnetic separation of His-tagged proteins.

    PubMed

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

    2014-01-01

    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

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

    PubMed

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

    2006-04-13

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

  13. 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

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

    2015-01-01

    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

  14. 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 ...

  15. Epitope Discovery for a Synthetic Polymer Nanoparticle: A New Strategy for Developing a Peptide Tag

    PubMed Central

    2015-01-01

    We describe a novel epitope discovery strategy for creating an affinity agent/peptide tag pair. A synthetic polymer nanoparticle (NP) was used as the “bait” to catch an affinity peptide tag. Biotinylated peptide tag candidates of varied sequence and length were attached to an avidin platform and screened for affinity against the polymer NP. NP affinity for the avidin/peptide tag complexes was used to provide insight into factors that contribute NP/tag binding. The identified epitope sequence with an optimized length (tMel-tag) was fused to two recombinant proteins. The tagged proteins exhibited higher NP affinity than proteins without tags. The results establish that a fusion peptide tag consisting of optimized 15 amino acid residues can provide strong affinity to an abiotic polymer NP. The affinity and selectivity of NP/tMel-tag interactions were exploited for protein purification in conjunction with immobilized metal ion/His6-tag interactions to prepare highly purified recombinant proteins. This strategy makes available inexpensive, abiotic synthetic polymers as affinity agents for peptide tags and provides alternatives for important applications where more costly affinity agents are used. PMID:24410250

  16. Ligand affinity of the 67-kD elastin/laminin binding protein is modulated by the protein's lectin domain: visualization of elastin/laminin-receptor complexes with gold-tagged ligands

    PubMed Central

    1991-01-01

    Video-enhanced microscopy was used to examine the interaction of elastin- or laminin-coated gold particles with elastin binding proteins on the surface of live cells. By visualizing the binding events in real time, it was possible to determine the specificity and avidity of ligand binding as well as to analyze the motion of the receptor-ligand complex in the plane of the plasma membrane. Although it was difficult to interpret the rates of binding and release rigorously because of the possibility for multiple interactions between particles and the cell surface, relative changes in binding have revealed important aspects of the regulation of affinity of ligand-receptor interaction in situ. Both elastin and laminin were found to compete for binding to the cell surface and lactose dramatically decreased the affinity of the receptor(s) for both elastin and laminin. These findings were supported by in vitro studies of the detergent-solubilized receptor. Further, immobilization of the ligand-receptor complexes through binding to the cytoskeleton dramatically decreased the ability of bound particles to leave the receptor. The changes in the kinetics of ligand-coated gold binding to living cells suggest that both laminin and elastin binding is inhibited by lactose and that attachment of receptor to the cytoskeleton increases its affinity for the ligand. PMID:1848864

  17. Shark Tagging Activities.

    ERIC Educational Resources Information Center

    Current: The Journal of Marine Education, 1998

    1998-01-01

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

  18. Paramagnetic Ligand Tagging To Identify Protein Binding Sites

    PubMed Central

    2015-01-01

    Transient biomolecular interactions are the cornerstones of the cellular machinery. The identification of the binding sites for low affinity molecular encounters is essential for the development of high affinity pharmaceuticals from weakly binding leads but is hindered by the lack of robust methodologies for characterization of weakly binding complexes. We introduce a paramagnetic ligand tagging approach that enables localization of low affinity protein–ligand binding clefts by detection and analysis of intermolecular protein NMR pseudocontact shifts, which are invoked by the covalent attachment of a paramagnetic lanthanoid chelating tag to the ligand of interest. The methodology is corroborated by identification of the low millimolar volatile anesthetic interaction site of the calcium sensor protein calmodulin. It presents an efficient route to binding site localization for low affinity complexes and is applicable to rapid screening of protein–ligand systems with varying binding affinity. PMID:26289584

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

    PubMed Central

    Jing, Chaoran; Cornish, Virginia W.

    2013-01-01

    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

  20. Quantum Tagging with Cryptographically Secure Tags

    E-print Network

    Kent, Adrian

    2010-01-01

    Various authors have considered schemes for {\\it 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. This task raises some interesting new questions about cryptographic security assumptions, as relatively subtle details in the security model can dramatically affect the security attainable. We consider here the case in which the tag is cryptographically secure, and show how to implement tagging securely within this model.

  1. 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 ...

  2. Double Affine Bundles

    E-print Network

    Grabowski, Janusz; Urbanski, Pawel

    2009-01-01

    A theory of double affine and special double affine bundles, i.e. differential manifolds with two compatible (special) affine bundle structures, is developed as an affine counterpart of the theory of double vector bundles. The motivation and basic examples come from Analytical Mechanics, where double affine bundles have been recognized as a proper geometrical tool in a frame-independent description of many important systems. Different approaches to the (special) double affine bundles are compared and carefully studied together with the problems of double vector bundle models and hulls, duality, and relations to associated phase spaces, contact structures, and other canonical constructions.

  3. Double Affine Bundles

    E-print Network

    Janusz Grabowski; Mikolaj Rotkiewicz; Pawel Urbanski

    2010-01-26

    A theory of double affine and special double affine bundles, i.e. differential manifolds with two compatible (special) affine bundle structures, is developed as an affine counterpart of the theory of double vector bundles. The motivation and basic examples come from Analytical Mechanics, where double affine bundles have been recognized as a proper geometrical tool in a frame-independent description of many important systems. Different approaches to the (special) double affine bundles are compared and carefully studied together with the problems of double vector bundle models and hulls, duality, and relations to associated phase spaces, contact structures, and other canonical constructions.

  4. Extracting tag hierarchies.

    PubMed

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

    2013-01-01

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

  5. Extracting Tag Hierarchies

    PubMed Central

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

    2013-01-01

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

  6. HaloTag Technology: A Versatile Platform for Biomedical Applications

    PubMed Central

    2015-01-01

    Exploration of protein function and interaction is critical for discovering links among genomics, proteomics, and disease state; yet, the immense complexity of proteomics found in biological systems currently limits our investigational capacity. Although affinity and autofluorescent tags are widely employed for protein analysis, these methods have been met with limited success because they lack specificity and require multiple fusion tags and genetic constructs. As an alternative approach, the innovative HaloTag protein fusion platform allows protein function and interaction to be comprehensively analyzed using a single genetic construct with multiple capabilities. This is accomplished using a simplified process, in which a variable HaloTag ligand binds rapidly to the HaloTag protein (usually linked to the protein of interest) with high affinity and specificity. In this review, we examine all current applications of the HaloTag technology platform for biomedical applications, such as the study of protein isolation and purification, protein function, protein–protein and protein–DNA interactions, biological assays, in vitro cellular imaging, and in vivo molecular imaging. In addition, novel uses of the HaloTag platform are briefly discussed along with potential future applications. PMID:25974629

  7. Optimized E.coli expression strain LOBSTR eliminates common contaminants from His-tag purification

    E-print Network

    Andersen, Kasper R.

    His-tag affinity purification is one of the most commonly used methods to purify recombinant proteins expressed in E. coli. One drawback of using the His-tag is the co-purification of contaminating histidine-rich E. coli ...

  8. Sense Tagging: Semantic Tagging with a Lexicon

    E-print Network

    of this system has been implemented, correctly tagging 86% of polysemous word tokens in a small test set of this work include (Bruce and Guthrie, 1992), (Bruce and Wiebe, 1994), (McRoy, 1992). 2. WSD using

  9. Rapid analysis of biogenic amines from rice wine with isotope-coded derivatization followed by high performance liquid chromatography-tandem mass spectrometry.

    PubMed

    Cai, Yiping; Sun, Zhiwei; Chen, Guang; Liu, Xiaomei; You, Jinmao; Zhang, Caiqing

    2016-02-01

    A pair of isotope-coded derivatization reagents, d0-10-methyl-acridone-2-sulfonyl chloride (d0-MASC, light form) and d3-10-methyl-acridone-2-sulfonyl chloride (d3-MASC, heavy form), were used for labeling biogenic amines (BAs). On basis of the isotope-coded derivatization, a global isotope internal standard quantitative method for determining seven BAs by high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) was developed. The d0-MASC and d3-MASC can easily label BAs under mild conditions within 15 min at 50 °C. The obtained light and heavy labeled BAs were monitored by the transitions of [M+H](+) ? 208 and [M+H](+) ? 211, respectively. Relative quantification of BAs was achieved by calculation of the peak area ratios of d0-MASC/d3-MASC labeled derivatives. Excellent linear responses for relative quantification were observed in the range of 1/10-10/1. The developed method has been successfully applied to the quantification of BAs in Chinese rice wine with recoveries ranging from 94.9% to 104.5%. PMID:26304364

  10. Tagged Prairie Dog

    USGS Multimedia Gallery

    This wild prairie dog has been tagged by scientists in an effort to study the efficacy of a USGS-developed oral sylvatic plague vaccine (SPV) to help immunize prairie dogs against plague. It was released after being tagged and after scientists took hair, whisker, and blood samples. I...

  11. Dynamic optical tags

    NASA Astrophysics Data System (ADS)

    Griggs, Steven P.; Mark, Martin B.; Feldman, Barry J.

    2004-07-01

    The goal of the DARPA Dynamic Optical Tags (DOTs) program is to develop a small, robust, persistent, 2-way tagging, tracking and locating device that also supports communications at data rates greater than 100 kbps and can be interrogated at significant range. These tags will allow for two-way data exchange and tagging operations in friendly and denied areas. The DOTs will be passive and non-RF. To accomplish this, the DOTs program will develop small, thin, retro-reflecting modulators. The tags will operate for long periods of time (greater than two months) in real-world environmental conditions (-40° to +70° C) and allow for a wide interrogation angle (+/-60°). The tags will be passive (in the sleep mode) for most of the time and only become active when interrogated by a laser with the correct code. Once correctly interrogated, the tags will begin to modulate and retro-reflect the incoming beam. The program will also develop two tag specific transceiver systems that are eye-safe, employ automated scanning algorithms, and are capable of short search and interrogate times.

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

    PubMed Central

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

    2012-01-01

    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

  13. Quantitative analysis of aberrant fatty acid composition of zebrafish hepatic lipids induced by organochlorine pesticide using stable isotope-coded transmethylation and gas chromatography-mass spectrometry.

    PubMed

    Zhong, Hongying; Dong, Linjie; Dong, Qingjian; Ke, Changshu; Fu, Jieying; Wang, Xiaoli; Liu, Cong; Dai, Ling

    2012-07-01

    Organochlorine pesticides have been extensively used worldwide for agricultural purposes. Due to their resistance to metabolism, a major public health concern has been raised. Aberrant hepatic lipid composition has been a hallmark of many liver diseases associated with exposure to various toxins and chemicals. And thus lots of efforts have been focused on the development of analytical techniques that can rapidly and quantitatively determine the changes in fatty acid composition of hepatic lipids. In this work, changes in fatty acid composition of hepatic lipids in response to DDT (dichlorodiphenyltrichloroethane) exposure were quantitatively analyzed by a gas chromatography-mass spectrometric approach based on stable isotope-coded transmethylation. It has been quantitatively demonstrated that polyunsaturated fatty acids including C20:3n3, C20:4n6, and C22:6n3 decrease in response to DDT exposure. However, saturated long chain fatty acids including C16:0, C18:0, as well as monounsaturated long chain fatty acid C18:1n9 consistently increase in a DDT-concentration-dependent manner. In particular, much higher changes in the level of hepatic C16:0 and C18:0 for male fish were observed than that for female fish. These experimental results are in accordance with qualitative histopathological analysis that revealed liver morphological alterations. The stable isotope-coded mass spectrometric approach provides a reliable means for investigating hepatotoxicity associated with fatty acid synthesis, desaturation, mitochondrial beta-oxidation, and lipid mobilization. It should be useful in elucidation of hepatotoxic mechanisms and safety assessment of environmental toxins. PMID:22648165

  14. Ontologies and tag-statistics

    E-print Network

    Tibely, Gergely; Vicsek, Tamas; Palla, Gergely

    2012-01-01

    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 topic with great actuality 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 organisation 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 type of tagged networks available for research, where the tags are already organised 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 r...

  15. Facets: Ersatz, Resource and Tag

    ERIC Educational Resources Information Center

    Frické, Martin H.

    2013-01-01

    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…

  16. A dielectric affinity microbiosensor

    NASA Astrophysics Data System (ADS)

    Huang, Xian; Li, Siqi; Schultz, Jerome S.; Wang, Qian; Lin, Qiao

    2010-01-01

    We present an affinity biosensing approach that exploits changes in dielectric properties of a polymer due to its specific, reversible binding with an analyte. The approach is demonstrated using a microsensor comprising a pair of thin-film capacitive electrodes sandwiching a solution of poly(acrylamide-ran-3-acrylamidophenylboronic acid), a synthetic polymer with specific affinity to glucose. Binding with glucose induces changes in the permittivity of the polymer, which can be measured capacitively for specific glucose detection, as confirmed by experimental results at physiologically relevant concentrations. The dielectric affinity biosensing approach holds the potential for practical applications such as long-term continuous glucose monitoring.

  17. Protein-Protein Interactions of Tandem Affinity Purified Protein Kinases from Rice

    PubMed Central

    Rohila, Jai S.; Chen, Mei; Chen, Shuo; Chen, Johann; Cerny, Ronald L.; Dardick, Christopher; Canlas, Patrick; Fujii, Hiroaki; Gribskov, Michael; Kanrar, Siddhartha; Knoflicek, Lucas; Stevenson, Becky; Xie, Mingtang; Xu, Xia; Zheng, Xianwu; Zhu, Jian-Kang; Ronald, Pamela; Fromm, Michael E.

    2009-01-01

    Eighty-eight rice (Oryza sativa) cDNAs encoding rice leaf expressed protein kinases (PKs) were fused to a Tandem Affinity Purification tag (TAP-tag) and expressed in transgenic rice plants. The TAP-tagged PKs and interacting proteins were purified from the T1 progeny of the transgenic rice plants and identified by tandem mass spectrometry. Forty-five TAP-tagged PKs were recovered in this study and thirteen of these were found to interact with other rice proteins with a high probability score. In vivo phosphorylated sites were found for three of the PKs. A comparison of the TAP-tagged data from a combined analysis of 129 TAP-tagged rice protein kinases with a concurrent screen using yeast two hybrid methods identified an evolutionarily new rice protein that interacts with the well conserved cell division cycle 2 (CDC2) protein complex. PMID:19690613

  18. Comparative analysis of S-fatty acylation of gel-separated proteins by stable isotope-coded fatty acid transmethylation and mass spectrometry.

    PubMed

    Dong, Linjie; Li, Jianjian; Li, Lun; Li, Tingting; Zhong, Hongying

    2011-09-01

    Covalent attachment of palmitic acid or other fatty acids to the thiol groups of cysteine residues of proteins through reversible thioester bonds has an important role in the regulation of diverse biological processes. We describe here the development of a mass spectrometry protocol based on stable isotope-coded fatty acid transmethylation (iFAT) for qualitative and comparative analysis of protein S-fatty acylation under different experimental conditions. In this approach, cellular proteins extracted from different cell states are separated by SDS-PAGE and then the gel is stained with either Coomassie blue or Nile red for improved sensitivity. Protein bands are excised and then an in-gel stable iFAT procedure is performed. The fatty acid methyl esters resulting from derivatization with d0- and d3-methanol are identified by mass spectrometry. By measuring the intensities of labeled and unlabeled fragment ion pairs of fatty acid methyl esters, the levels of S-fatty acylation in different cells or tissues can be compared. This approach has been applied to monitor the changes of S-fatty acylation of zebrafish liver proteome in response to environmental dichlorodiphenyltrichloroethane exposure. Compared with the approach using metabolic incorporation of radioactive fatty acid analogs, it is not only simple and effective but also eliminates the hazards of handling radioactive isotopes. PMID:21886103

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

    PubMed Central

    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

    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

  20. 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...

  1. Application of Screening Experimental Designs to Assess Chromatographic Isotope Effect upon Isotope-Coded Derivatization for Quantitative Liquid Chromatography–Mass Spectrometry

    PubMed Central

    2015-01-01

    Isotope effect may cause partial chromatographic separation of labeled (heavy) and unlabeled (light) isotopologue pairs. Together with a simultaneous matrix effect, this could lead to unacceptable accuracy in quantitative liquid chromatography–mass spectrometry assays, especially when electrospray ionization is used. Four biologically relevant reactive aldehydes (acrolein, malondialdehyde, 4-hydroxy-2-nonenal, and 4-oxo-2-nonenal) were derivatized with light or heavy (d3-, 13C6-, 15N2-, or 15N4-labeled) 2,4-dinitrophenylhydrazine and used as model compounds to evaluate chromatographic isotope effects. For comprehensive assessment of retention time differences between light/heavy pairs under various gradient reversed-phase liquid chromatography conditions, major chromatographic parameters (stationary phase, mobile phase pH, temperature, organic solvent, and gradient slope) and different isotope labelings were addressed by multiple-factor screening using experimental designs that included both asymmetrical (Addelman) and Plackett–Burman schemes followed by statistical evaluations. Results confirmed that the most effective approach to avoid chromatographic isotope effect is the use of 15N or 13C labeling instead of deuterium labeling, while chromatographic parameters had no general influence. Comparison of the alternate isotope-coded derivatization assay (AIDA) using deuterium versus 15N labeling gave unacceptable differences (>15%) upon quantifying some of the model aldehydes from biological matrixes. On the basis of our results, we recommend the modification of the AIDA protocol by replacing d3-2,4-dinitrophenylhydrazine with 15N- or 13C-labeled derivatizing reagent to avoid possible unfavorable consequences of chromatographic isotope effects. PMID:24922593

  2. Methods for differential and quantitative analyses of brain neurosteroid levels by LC/MS/MS with ESI-enhancing and isotope-coded derivatization.

    PubMed

    Higashi, Tatsuya; Aiba, Naoto; Tanaka, Tomoya; Yoshizawa, Kazumi; Ogawa, Shoujiro

    2016-01-01

    The analysis of changes in the brain neurosteroid (NS) levels due to various stimuli can contribute to the elucidation of their physiological roles, and the discovery and development of new antipsychotic agents targeting neurosteroidogenesis. We developed methods for the differential and quantitative analyses of the brain levels of allopregnanolene (AP) and its precursor, pregnenolone (PREG), using liquid chromatography/electrospray ionization-tandem mass spectrometry (LC/ESI-MS/MS) combined with derivatization using 2-hydrazino-1-methylpyridine (HMP) and its isotope-coded analogue, (2)H3-HMP (d-HMP). For the differential analysis, the brain sample of an untreated rat was derivatized with HMP, while the brain sample of a treated (stressed or drug-administered) rat was derivatized with d-HMP. The two derivatives were mixed and then subjected to LC/ESI-MS/MS. The stress- and drug (clozapine and fluoxetine)-evoked increases in the brain AP and PREG levels were accurately analyzed by the developed method. It was also possible to determine the absolute concentrations of the brain steroids when a deuterium-coded moiety was introduced to the standard steroids of known amounts by the derivatization and the resulting derivatives were used as internal standards. The HMP-derivatization enabled the highly sensitive detection and the use of d-HMP significantly improved the assay precision [the intra- (n=5) and inter-assay (n=5) relative standard deviations did not exceed 13.7%] and accuracy (analytical recovery ranged from 98.7 to 106.7%). PMID:26355769

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

    E-print Network

    Snider, Michelle

    2010-01-01

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

  4. Social Tagging of Mission Data

    NASA Technical Reports Server (NTRS)

    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

    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.

  5. Antenna for passive RFID tags

    NASA Astrophysics Data System (ADS)

    Schiopu, Paul; Manea, Adrian; Cristea, Ionica; Grosu, Neculai; Vladescu, Marian; Craciun, Anca-Ileana; Craciun, Alexandru

    2015-02-01

    Minuscule devices, called RFID tags are attached to objects and persons and emit information which positioned readers may capture wirelessly. Many methods of identification have been used, but that of most common is to use a unique serial number for identification of person or object. RFID tags can be characterized as either active or passive [1,2]. Traditional passive tags are typically in "sleep" state until awakened by the reader's emitted field. In passive tags, the reader's field acts to charge the capacitor that powers the badge and this can be a combination of antenna and barcodes obtained with SAW( Surface Acoustic Wave) devices [1,2,3] . The antenna in an RFID tag is a conductive element that permits the tag to exchange data with the reader. The paper contribution are targeted to antenna for passive RFID tags. The electromagnetic field generated by the reader is somehow oriented by the reader antenna and power is induced in the tag only if the orientation of the tag antenna is appropriate. A tag placed orthogonal to the reader yield field will not be read. This is the reason that guided manufacturers to build circular polarized antenna capable of propagating a field that is alternatively polarized on all planes passing on the diffusion axis. Passive RFID tags are operated at the UHF frequencies of 868MHz (Europe) and 915MHz (USA) and at the microwave frequencies of 2,45 GHz and 5,8 GHz . Because the tags are small dimensions, in paper, we present the possibility to use circular polarization microstrip antenna with fractal edge [2].

  6. Top Tagging at ATLAS

    E-print Network

    Caudron, Julien; The ATLAS collaboration

    2015-01-01

    Top quark particles play an important role in many beyond-the-standard-model scenarios. When produced by a massive new particle, the top quark will have a very high transverse momentum, and will be referred to as boosted top. In this regime, the study of the substructure of the large radius jet that fully contains the hadronic decay products is more efficient than the resolved reconstruction. The algorithms that identify these decays are called top-taggers. This poster presents the different top-tagging techniques used in ATLAS.

  7. Analysis of Interrogator-tag Communication Protocols

    E-print Network

    Sekerinski, Emil

    and parameters for active RFID (Radio Frequency IDentification) air interface communication at the 433MHz ISM (In using radio waves. There are three types of RFID tags: active tags (with battery), passive tags (without battery), and battery assisted tags. Battery assisted tags are usually off, but when excited by some

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

    PubMed Central

    2015-01-01

    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

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

    PubMed

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

    2014-01-28

    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

  10. TASA: Tag-Free Activity Sensing Using RFID Tag Arrays

    E-print Network

    Guo, Minyi

    trend is to employ Radio Frequency IDentification (RFID), which is characterized by low cost, general availability, and automatic identification [9], [10], [11], [12]. So far, RFID has achieved widespread successTASA: Tag-Free Activity Sensing Using RFID Tag Arrays Daqiang Zhang, Jingyu Zhou, Minyi Guo, Senior

  11. Epitope tagging of endogenous proteins

    E-print Network

    Cai, Long

    -in'. The tagging method is straightforward, can be applied to many loci and several human somatic cell lines contains two multiple cloning sites, sequences that encode a triple Flag epitope tag (3ÂFlag), a neomycin respective cloning sites, and packaged the resulting vector into recombinant adeno-associated virus (r

  12. 50 CFR 635.33 - Archival tags.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... § 635.33 Archival tags. (a) Implantation report. Any person affixing or implanting an archival tag into a regulated species...Persons so authorized to conduct archival tag implantation must provide a written report to...

  13. 50 CFR 635.33 - Archival tags.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... § 635.33 Archival tags. (a) Implantation report. Any person affixing or implanting an archival tag into a regulated species...Persons so authorized to conduct archival tag implantation must provide a written report to...

  14. The affine matched filter

    NASA Astrophysics Data System (ADS)

    Schaum, A.; Priest, Richard

    2009-05-01

    The hyperspectral matched filter (MF) is a popular tool in remote sensing problems for locating objects that extend over several pixels. However, it is ideally suited only for the detection of sub-pixel targets with known mean signature in radiance space. Here we develop an alternative affine matched filter (AMF) that is more appropriate for detecting extended targets, and which accommodates practical uncertainties in target signature knowledge. In particular, AMF is ideal when used in conjunction with another new method we develop, called Virtual Relative Calibration (VRC), for generating a radiance space representation of a laboratory reflectance signature. VRC is related to the QUick Atmospheric Correction(QuAC) method but is much simpler. We also devise and test an extension of AMF that is meant to reduce false alarms caused by dark pixels. This Joint AMF (JAMF) expands the standard statistical model of hyperspectral backgrounds to accommodate variable illumination levels, analogously to how AMF treats target level uncertainty.

  15. LHCb Tag Collector

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

    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.

  17. Electron Affinity Calculations for Thioethers

    NASA Technical Reports Server (NTRS)

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

    1997-01-01

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

  18. Taking down the FLAG! How Insect Cell Expression Challenges an Established Tag-System

    PubMed Central

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

    2012-01-01

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

  19. Construction of a Chimeric Thermostable Pyrophosphatase To Facilitate Its Purification and Immobilization by Using the Choline-Binding Tag

    PubMed Central

    Moldes, Cristina; García, José L.; García, Pedro

    2004-01-01

    The thermophilic inorganic pyrophosphatase (Pyr) from Thermus thermophilus has been produced in Escherichia coli fused to the C terminus of the choline-binding tag (ChB tag) derived from the choline-binding domain (ChBD) of pneumococcal LytA autolysin. The chimeric ChBD-Pyr protein retains its thermostable activity and can be purified in a single step by DEAE-cellulose affinity chromatography. Pyr can be further released from the ChBD by thrombin, using the specific protease recognition site incorporated in the C terminus of this tag. Remarkably, the ChB tag provides a selective and very strong thermostable noncovalent immobilization of ChBD-Pyr in the DEAE-cellulose matrix. The binding of choline or choline analogues, such as DEAE, confers a high thermal stability to this tag; therefore, the immobilized chimeric enzyme can be assayed at high temperature without protein leakage, demonstrating the usefulness of the ChB tag for noncovalent immobilization of thermophilic proteins. Moreover, ChBD-Pyr can be purified and immobilized in a single step on commercial DEAE-cellulose paper. The affinity of the ChB tag for this versatile solid support can be very helpful in developing many biotechnological applications. PMID:15294797

  20. Quantum tagging for tags containing secret classical data

    SciTech Connect

    Kent, Adrian

    2011-08-15

    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.

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

    NASA Astrophysics Data System (ADS)

    Sekine-Aizawa, Yoko; Huganir, Richard L.

    2004-12-01

    -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

  2. Tagging insulin in microgravity

    NASA Technical Reports Server (NTRS)

    Dobeck, Michael; Nelson, Ronald S.

    1992-01-01

    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.

  3. Do Tags Work? Cathy Marshall

    E-print Network

    Marshall, Cathy

    of knowledge will be calmed; its power will light a billion tiny "aha!" light bulbs over a billion tiny avatar the vivid funeral scene in that so-bad-it's-good Peter Fonda movie The Wild Angels (1966). Tags

  4. Named entity tagged language models. 

    E-print Network

    Gotoh, Yoshihiko; Renals, Steve; Williams, Gethin

    1999-01-01

    We introduce Named Entity (NE) Language Modelling, a stochastic finite state machine approach to identifying both words and NE categories from a stream of spoken data. We provide an overview of our approach to NE tagged ...

  5. Distributed RFID Tag Storage Infrastructures Technical Report

    E-print Network

    Vaidya, Nitin

    Distributed RFID Tag Storage Infrastructures Technical Report May 11, 2009 Victor K. Y. Wu , Mirko, mmontan2, nhv, rhc,}@illinois.edu Abstract. We leverage increasing passive RFID tag memory to pro- pose distributed RFID tag storage infrastructures (D-RFID stores). A D-RFID store is a large set of tags

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

    E-print Network

    International Association for Cryptologic Research (IACR)

    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

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

    ERIC Educational Resources Information Center

    Bailey, Cheryl P.

    2009-01-01

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

  8. AFFINE ALGEBRAIC GEOMETRY pp. 287292

    E-print Network

    Kumar, N. Mohan

    AFFINE ALGEBRAIC GEOMETRY pp. 287­292 Some Remarks on Prill's Problem N. Mohan Kumar Abstract. If f for numerous discussions on the topic while I was preparing this paper. #12;288 N. Mohan Kumar Theorem 1. Let f

  9. Vaccine Efficacy and Affinity Maturation

    NASA Astrophysics Data System (ADS)

    Lee, Hayoun; Deem, Michael W.

    2002-03-01

    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.

  10. TagAssist: Automatic Tag Suggestion for Blog Posts Sanjay C. Sood

    E-print Network

    Bustamante, Fabián E.

    and incorporate novel concepts and changes in terminology without having to rely on a standardized tag corpus to evaluate the quality of a potential tag suggestion. Coupled with the ability for users to manually add tags

  11. Collaborative Video Annotation by Sharing Tag Clouds

    NASA Astrophysics Data System (ADS)

    Yamamoto, Daisuke; Masuda, Tomoki; Ohira, Shigeki; Nagao, Katashi

    In this paper, we propose a video scene annotation method based on tag clouds. First, user comments associated with a video are collected from existing video sharing services. Next, a tag cloud is generated from these user comments. The tag cloud is displayed on the video window of the Web browser. When users click on a tag included in the tag cloud while watching the video, the tag gets associated with the time point of the video. Users can share the information on the tags that have already been clicked. We confirmed that the coverage of annotations generated by this method is higher than that of the existing methods, and users are motivated to add tags by sharing tag clouds. This method will contribute to advanced video applications.

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

    USGS Publications Warehouse

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

    2015-01-01

    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.

  13. Expressivity tag: a novel tool for increased expression in Escherichia coli.

    PubMed

    Hansted, Jon Gade; Pietikäinen, Laura; Hög, Friederike; Sperling-Petersen, Hans Uffe; Mortensen, Kim Kusk

    2011-09-20

    Protein expression in Escherichia coli is rarely trivial as low expression and insolubility are common problems. In this work we define a fusion partner, which increases expression levels similarly to the distinct function of solubility and affinity tags. This type of fusion tag we term an expressivity tag. Our work is based on earlier observations where 3' deletions of the InfB gene displays strongly increased expression levels. We have constructed progressively shortened fragments of the InfB(1-471) gene and fused gene fragments to a gfp reporter gene. A 5-fold increase in GFP expression was seen for an optimal 21 nucleotide InfB(1-21) sequence compared to gfp independently. We defined the InfB(1-21) sequence as an expressivity tag. The tag was tested for improved expression of two biotechnological important proteins streptavidin and a single chain antibody (scFv). Expression of both streptavidin and scFv(L32) was improved as evaluated by SDS-PAGE. Calculation of folding energies in the translation initiation region gave higher free energies for gfp, L32 and streptavidin when linked to InfB(1-21) than independently. InfB(1-21) did however not improve the codon usage or codon adaptation index. The expressivity tag is an important addition to the box of tools available for optimizing heterologous protein expression. PMID:21801766

  14. Virtual colon tagging for electronic cleansing in dual-energy fecal-tagging CT colonography.

    PubMed

    Cai, Wenli; Kim, Se Hyung; Lee, June-Goo; Yoshida, Hiroyuki

    2012-01-01

    Partial volume effect (PVE) and tagging inhomogeneity are two major causes of artifacts in electronic cleansing (EC) for fecal-tagging CT colonography (CTC). Our purpose was to develop a novel method called "virtual tagging" for electronic cleansing in dual-energy fecal-tagging CTC. A three-material decomposition scheme was first applied in dual-energy CTC to decompose each voxel into a mixture of air, soft tissue, and iodine-tagged fecal material. The entire colonic lumen was then marked by virtually tagging the mixture portion of luminal air at each voxel. As a result, colon lumen including air and tagged materials was segmented and subtracted by their high values in virtually tagged images. Our virtual tagging scheme provides a cleansed colon that is free from artifacts caused by the PVE at air-tagging mixture and inhomogeneous tagging. PMID:23366740

  15. WebTag: Web Browsing into Sensor Tags over NFC

    PubMed Central

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

    2012-01-01

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

  16. Fish Tagging Forum Draft Compilation of Tagging Infrastructure

    E-print Network

    arrays N/A Genetic Sample collection equipment, lab processing Sample collection equipment, surface trawls, lab processing Sample collection equipment, lab processing Sample collection equipment, lab processing CWT Tags, trailers, marking machines, handheld injectors N/A N/A N/A Snout collection equipment

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

    PubMed

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

    2012-01-01

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

  18. Fish Tagging Forum Draft Compilation of Tagging Information

    E-print Network

    in the information gathered todate that warrants further communication with subject matter experts; 2. Provide, if you have any input prior to then please send it along. Here are a few notes to keep in mind.g., 2009 tagging report, followup conversations with subject matter experts, further FTF discussions, etc

  19. The structure of the SBP-Tag–streptavidin complex reveals a novel helical scaffold bridging binding pockets on separate subunits

    SciTech Connect

    Barrette-Ng, Isabelle H.; Wu, Sau-Ching; Tjia, Wai-Mui; Wong, Sui-Lam; Ng, Kenneth K. S.

    2013-05-01

    The structure of the SBP-Tag–streptavidin complex reveals a novel mode of peptide recognition in which a single peptide binds simultaneously to biotin-binding pockets from adjacent subunits of streptavidin. The molecular details of peptide recognition suggest how the SBP-Tag can be further modified to become an even more useful tag for a wider range of biotechnological applications. The 38-residue SBP-Tag binds to streptavidin more tightly (K{sub d} ? 2.5–4.9 nM) than most if not all other known peptide sequences. Crystallographic analysis at 1.75 Å resolution shows that the SBP-Tag binds to streptavidin in an unprecedented manner by simultaneously interacting with biotin-binding pockets from two separate subunits. An N-terminal HVV peptide sequence (residues 12–14) and a C-terminal HPQ sequence (residues 31–33) form the bulk of the direct interactions between the SBP-Tag and the two biotin-binding pockets. Surprisingly, most of the peptide spanning these two sites (residues 17–28) adopts a regular ?-helical structure that projects three leucine side chains into a groove formed at the interface between two streptavidin protomers. The crystal structure shows that residues 1–10 and 35–38 of the original SBP-Tag identified through in vitro selection and deletion analysis do not appear to contact streptavidin and thus may not be important for binding. A 25-residue peptide comprising residues 11–34 (SBP-Tag2) was synthesized and shown using surface plasmon resonance to bind streptavidin with very similar affinity and kinetics when compared with the SBP-Tag. The SBP-Tag2 was also added to the C-terminus of ?-lactamase and was shown to be just as effective as the full-length SBP-Tag in affinity purification. These results validate the molecular structure of the SBP-Tag–streptavidin complex and establish a minimal bivalent streptavidin-binding tag from which further rational design and optimization can proceed.

  20. OpenTag: Privacy protection for RFID

    E-print Network

    Holtzman, Henry N.

    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 ...

  1. 50 CFR 20.81 - Tagging requirement.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 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 migratory game birds unless such birds are tagged as required by § 20.36....

  2. 50 CFR 20.81 - Tagging requirement.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 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 migratory game birds unless such birds are tagged as required by § 20.36....

  3. 50 CFR 20.81 - Tagging requirement.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 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 migratory game birds unless such birds are tagged as required by § 20.36....

  4. 50 CFR 20.81 - Tagging requirement.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 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 migratory game birds unless such birds are tagged as required by § 20.36....

  5. 50 CFR 20.81 - Tagging requirement.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 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 migratory game birds unless such birds are tagged as required by § 20.36....

  6. HCI gesture tracking using wearable passive tags

    E-print Network

    Bainbridge, Rachel M

    2010-01-01

    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 ...

  7. Resolving Tag Ambiguity Kilian Weinberger

    E-print Network

    Weinberger, Kilian

    ­31, 2008, Vancouver, British Columbia, Canada. Copyright 2008 ACM 978-1-60558-303-7/08/10 ...$5.00. jaguar specification Figure 1: An example of how different expansion of one tag ("jaguar") can lead to very different (e.g. "jaguar" can be a car or an animal), geographic ambiguity (e.g. "Cambridge" as in MA or UK

  8. Vibrationally excited hydroxyl tagging velocimetry.

    PubMed

    Grady, Nathan; Pitz, Robert W

    2014-11-01

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

  9. RFID RFID RFID (tag) (reader)

    E-print Network

    Kovintavewat, Piya

    LF atmosphere RFID RFID (access control), (animal and personnel tracking), vehicle control), (item-level tracking), 13.56 MHz RFID 7.2.3 (UHF) 300 MHz 3 GHz RFID 344 MHz 7 RFID RFID RFID RFID (tag) (reader) RFID , RFID , RFID

  10. Supporting Information Tagged Simulation Regions

    E-print Network

    Jacob, Daniel J.

    1 Supporting Information Tagged Simulation Regions SI Figure 1 Definition of source and receptor regulation targeted specifically at mercury emission, FGD may be installed to limit emission of other air pollutants and will capture mercury as a co-benefit. SI Table 1 (next page) Present and future (2050) global

  11. NOT ALL TAGS ARE CREATED EQUAL: LEARNING FLICKR TAG SEMANTICS FOR GLOBAL ANNOTATION

    E-print Network

    California at Santa Barbara, University of

    NOT ALL TAGS ARE CREATED EQUAL: LEARNING FLICKR TAG SEMANTICS FOR GLOBAL ANNOTATION Emily Moxley in the presence of noisy data. In this work we explore the ability to automatically learn tag semantics by mining of noise in the labels and semantic uncertainty. A better understanding of tag semantics would benefit many

  12. The Blocker Tag: Selective Blocking of RFID Tags for Consumer Privacy

    E-print Network

    Rivest, Ronald L.

    An RFID (Radio-Frequency IDentification) tag consists of a small integrated circuit attached to a small such as clothing, and the small dashboard devices for automating toll payments. The cost of simple RFID tagsThe Blocker Tag: Selective Blocking of RFID Tags for Consumer Privacy Ari Juels RSA Laboratories

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

    E-print Network

    405 Recent advances in conventional tag- ging and ultrasonic telemetry meth- ods have substantially found along the Gulf and Atlantic coasts, conventional tagging and ultrasonic telemetry have been of conventional tags and the tracking of red drum tagged with ultrasonic transmitters have pro- vided important

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

    E-print Network

    Cortes, Corinna

    Discriminative Tag Learning on YouTube Videos with Latent Sub-tags Weilong Yang Simon Fraser semantic varia- tions (sub-tags) of the tag. Each video in the training set is assumed to be associated-scale testing video set which contains about 50 million YouTube videos. 1. Introduction On the Internet

  15. Estimates of tag-reporting and tag-shedding rates in a large-scale

    E-print Network

    - quired for an estimation of fishing and natural mortality rates from tagging data. For this purpose significant. Tag seeding car- ried out on board purse seiners by ob- servers resulted in 342 returns used to estimate mortality rates is to fit a tag-attrition model to a time series of tag-return data

  16. 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

  17. RFID Performance Tag Analysis Dan Deavours,

    E-print Network

    Kansas, University of

    a number of experiments aimed at evaluating the performance of item-level (small) UHF RFID tagsRFID 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

  18. Ultralightweight RFID Reader-Tag Mutual Authentication

    E-print Network

    Jiang, Jehn-Ruey

    to attacks, leading to privacy and security weakness. Typical attacks include the forged-tag, forged latent attacks. Typical attacks include the forged-tag, forged-server, denial of service (DoS), replay-14] of them use heavy-weight operations on tags; they are thus unsuitable for EPC C1G2 RFID systems. The other

  19. Implanting Telemetry Tag in Pallid Sturgeon

    USGS Multimedia Gallery

    Acoustic telemetry tags have to be fairly small to fit inside a five to fifteen pound pallid sturgeon.  The average tag is about the size of your ring finger (60-90 mm long and 16 mm diameter).  That means the battery that powers the acoustic tag is small, too.  A small battery means ...

  20. High capacity tagging using nanostructured diffraction barcodes

    E-print Network

    Zheludev, Nikolay

    High capacity tagging using nanostructured diffraction barcodes G. S. Galitonov, S. W. Birtwell capacity optical tagging technique based on the use of nanostructured barcodes. The tags are generated from peaks into barcodes," Spectrochim. Acta A (to be published). 3. X. Su, J. Zhang, L. Sun, T. Koo, S. Chan

  1. Affine toric SL(2)-embeddings

    NASA Astrophysics Data System (ADS)

    Gaifullin, S. A.

    2008-04-01

    In the theory of affine SL(2)-embeddings, which was constructed in 1973 by Popov, a locally transitive action of the group SL(2) on a normal affine three-dimensional variety X is determined by a pair (p/q,r), where 0 is a rational number written as an irreducible fraction and called the height of the action, while r is a positive integer that is the order of the stabilizer of a generic point. In the present paper it is shown that the variety X is toric, that is, it admits a locally transitive action of an algebraic torus if and only if the number r is divisible by q-p. For that, the following criterion for an affine G/H-embedding to be toric is proved. Let X be a normal affine variety, G a simply connected semisimple group acting regularly on X, and H\\subset G a closed subgroup such that the character group \\mathfrak{X}(H) of the group H is finite. If an open equivariant embedding G/H\\hookrightarrow X is defined, then X is toric if and only if there exist a quasitorus \\widehat T and a (G\\times\\widehat T)-module V such that X\\stackrel G\\cong V/\\!/\\widehat T. In the substantiation of this result a key role is played by Cox's construction in toric geometry. Bibliography: 12 titles.

  2. Affine Contractions on the Plane

    ERIC Educational Resources Information Center

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

    2007-01-01

    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.…

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

    E-print Network

    Robins, Gabriel

    Radio--Frequency Identification (RFID)Frequency Identification (RFID) Assumptions Tags are passive Tags have limited computational-Frequency Identification (RFID) tag RFID reader starting / closing tags · Develop new RFID "yoking-proofs" where tagsThree types of RFID tags · Passive / Active / Semi-Active · up to 19m range for UHF Computer

  4. To Tag or Not to Tag Harvesting Adjacent Metadata in Large-Scale Tagging Systems *

    E-print Network

    .lastname@epfl.ch pcm@csail.mit.edu ABSTRACT We present HAMLET, a suite of principles, scoring models and algorithms of our knowl- edge, HAMLET is the first system to promote an efficient and precise reuse of shared existing tags from one document to similar documents. We put for- ward HAMLET (Harvesting Adjacent Metadata

  5. 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

    ... 49 Transportation 4 2010-10-01 2010-10-01 false Tagging of wires and interference of wires or tags... Tagging of wires and interference of wires or tags with signal apparatus. Each wire shall be tagged or... be made of insulating material and so arranged that tags and wires do not interfere with moving...

  6. 49 CFR 234.239 - Tagging of wires and interference of wires or tags with signal apparatus.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 4 2011-10-01 2011-10-01 false Tagging of wires and interference of wires or tags... Tagging of wires and interference of wires or tags with signal apparatus. Each wire shall be tagged or... be made of insulating material and so arranged that tags and wires do not interfere with moving...

  7. Infrared tag and track technique

    DOEpatents

    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

    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.

  8. Electronic Tag and Position Sensor

    SciTech Connect

    Not Available

    1992-01-20

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

  9. Phase modulation in RF tag

    DOEpatents

    Carrender, Curtis Lee; Gilbert, Ronald W.

    2007-02-20

    A radio frequency (RF) communication system employs phase-modulated backscatter signals for RF communication from an RF tag to an interrogator. The interrogator transmits a continuous wave interrogation signal to the RF tag, which based on an information code stored in a memory, phase-modulates the interrogation signal to produce a backscatter response signal that is transmitted back to the interrogator. A phase modulator structure in the RF tag may include a switch coupled between an antenna and a quarter-wavelength stub; and a driver coupled between the memory and a control terminal of the switch. The driver is structured to produce a modulating signal corresponding to the information code, the modulating signal alternately opening and closing the switch to respectively decrease and increase the transmission path taken by the interrogation signal and thereby modulate the phase of the response signal. Alternatively, the phase modulator may include a diode coupled between the antenna and driver. The modulating signal from the driver modulates the capacitance of the diode, which modulates the phase of the response signal reflected by the diode and antenna.

  10. Tag retention, growth, and survival of red swamp crayfish marked with a visible implant tag

    USGS Publications Warehouse

    Isely, J.J.; Stockett, P.E.

    2001-01-01

    Eighty juvenile (means: 42.4 mm total length, 1.6 g) red swamp crayfish Procambarus clarkii were implanted with sequentially numbered visible implant tags and held in the laboratory. Tags were injected transversely into the musculature just beneath the exoskeleton of the third abdominal segment from the cephalothorax; tags were visible upon inspection. An additional 20 crayfish were left untagged and served as controls. After 150 d, tag retention was 80% and all tags were readable. No tagged crayfish died during the study, and no differences in total length or weight were detected between tagged and control crayfish. All individuals molted at least three times during the 150-d study, and some individuals molted up to six times, suggesting that most tags would be permanently retained. The readability in the field without specialized equipment makes the visible implant tag ideal for studies of crayfish ecology, management, and culture.

  11. Extended affine Lie algebras Erhard Neher1

    E-print Network

    Neher, Erhard

    . In particular, one can find there a detailed study of the root systems appearing in extended affine Lie algebrasExtended affine Lie algebras Erhard Neher1 Department of Mathematics and Statistics University describe the structure of an extended affine Lie algebra in terms of its centreless core. 0. Introduction

  12. Lectin affinity chromatography of glycolipids

    SciTech Connect

    Torres, B.V.; Smith, D.F.

    1987-05-01

    Since glycolipids (GLs) are either insoluble or form mixed micelles in water, lectin affinity chromatography in aqueous systems has not been applied to their separation. They have overcome this problem by using tetrahydrofuran (THF) in the mobile phase during chromatography. Affinity columns prepared with the GalNAc-specific Helix pomatia agglutinin (HPA) and equilibrated in THF specifically bind the (/sup 3/H)oligosaccharide derived from Forssman GL indicating that the immobilized HPA retained its carbohydrate-binding specificity in this solvent. Intact Forssman GL was bound by the HPA-column equilibrated in THF and was specifically eluted with 0.1 mg/ml GalNAc in THF. Purification of the Forssman GL was achieved when a crude lipid extract of sheep erythrocyte membranes was applied to the HPA-column in THF. Non-specifically bound GLs were eluted from the column using a step gradient of aqueous buffer in THF, while the addition of GalNAc was required to elute the specifically bound GLs. Using this procedure the A-active GLs were purified from a crude lipid extract of type A human erythrocytes in a single chromatographic step. The use of solvents that maintain carbohydrate-binding specificity and lipid solubility will permit the application of affinity chromatography on immobilized carbohydrate-binding proteins to intact GLs.

  13. Directional Radio-Frequency Identification Tag Reader

    NASA Technical Reports Server (NTRS)

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

    2004-01-01

    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).

  14. 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

    Tykvart, J.; Sacha, P.; Barinka, C.; Knedlik, T.; Starkova, J.; Lubkowski, J.; Konvalinka, J.

    2012-02-07

    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.

  15. Expression and affinity purification of recombinant proteins from plants

    NASA Technical Reports Server (NTRS)

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

    2002-01-01

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

  16. Use of the Nanofitin Alternative Scaffold as a GFP-Ready Fusion Tag.

    PubMed

    Huet, Simon; Gorre, Harmony; Perrocheau, Anaëlle; Picot, Justine; Cinier, Mathieu

    2015-01-01

    With the continuous diversification of recombinant DNA technologies, the possibilities for new tailor-made protein engineering have extended on an on-going basis. Among these strategies, the use of the green fluorescent protein (GFP) as a fusion domain has been widely adopted for cellular imaging and protein localization. Following the lead of the direct head-to-tail fusion of GFP, we proposed to provide additional features to recombinant proteins by genetic fusion of artificially derived binders. Thus, we reported a GFP-ready fusion tag consisting of a small and robust fusion-friendly anti-GFP Nanofitin binding domain as a proof-of-concept. While limiting steric effects on the carrier, the GFP-ready tag allows the capture of GFP or its blue (BFP), cyan (CFP) and yellow (YFP) alternatives. Here, we described the generation of the GFP-ready tag from the selection of a Nanofitin variant binding to the GFP and its spectral variants with a nanomolar affinity, while displaying a remarkable folding stability, as demonstrated by its full resistance upon thermal sterilization process or the full chemical synthesis of Nanofitins. To illustrate the potential of the Nanofitin-based tag as a fusion partner, we compared the expression level in Escherichia coli and activity profile of recombinant human tumor necrosis factor alpha (TNF?) constructs, fused to a SUMO or GFP-ready tag. Very similar expression levels were found with the two fusion technologies. Both domains of the GFP-ready tagged TNF? were proved fully active in ELISA and interferometry binding assays, allowing the simultaneous capture by an anti-TNF? antibody and binding to the GFP, and its spectral mutants. The GFP-ready tag was also shown inert in a L929 cell based assay, demonstrating the potent TNF? mediated apoptosis induction by the GFP-ready tagged TNF?. Eventually, we proposed the GFP-ready tag as a versatile capture and labeling system in addition to expected applications of anti-GFP Nanofitins (as illustrated with previously described state-of-the-art anti-GFP binders applied to living cells and in vitro applications). Through a single fusion domain, the GFP-ready tagged proteins benefit from subsequent customization within a wide range of fluorescence spectra upon indirect binding of a chosen GFP variant. PMID:26539718

  17. Use of the Nanofitin Alternative Scaffold as a GFP-Ready Fusion Tag

    PubMed Central

    Huet, Simon; Gorre, Harmony; Perrocheau, Anaëlle; Picot, Justine; Cinier, Mathieu

    2015-01-01

    With the continuous diversification of recombinant DNA technologies, the possibilities for new tailor-made protein engineering have extended on an on-going basis. Among these strategies, the use of the green fluorescent protein (GFP) as a fusion domain has been widely adopted for cellular imaging and protein localization. Following the lead of the direct head-to-tail fusion of GFP, we proposed to provide additional features to recombinant proteins by genetic fusion of artificially derived binders. Thus, we reported a GFP-ready fusion tag consisting of a small and robust fusion-friendly anti-GFP Nanofitin binding domain as a proof-of-concept. While limiting steric effects on the carrier, the GFP-ready tag allows the capture of GFP or its blue (BFP), cyan (CFP) and yellow (YFP) alternatives. Here, we described the generation of the GFP-ready tag from the selection of a Nanofitin variant binding to the GFP and its spectral variants with a nanomolar affinity, while displaying a remarkable folding stability, as demonstrated by its full resistance upon thermal sterilization process or the full chemical synthesis of Nanofitins. To illustrate the potential of the Nanofitin-based tag as a fusion partner, we compared the expression level in Escherichia coli and activity profile of recombinant human tumor necrosis factor alpha (TNF?) constructs, fused to a SUMO or GFP-ready tag. Very similar expression levels were found with the two fusion technologies. Both domains of the GFP-ready tagged TNF? were proved fully active in ELISA and interferometry binding assays, allowing the simultaneous capture by an anti-TNF? antibody and binding to the GFP, and its spectral mutants. The GFP-ready tag was also shown inert in a L929 cell based assay, demonstrating the potent TNF? mediated apoptosis induction by the GFP-ready tagged TNF?. Eventually, we proposed the GFP-ready tag as a versatile capture and labeling system in addition to expected applications of anti-GFP Nanofitins (as illustrated with previously described state-of-the-art anti-GFP binders applied to living cells and in vitro applications). Through a single fusion domain, the GFP-ready tagged proteins benefit from subsequent customization within a wide range of fluorescence spectra upon indirect binding of a chosen GFP variant. PMID:26539718

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

    PubMed Central

    Faircloth, Brant C.; Glenn, Travis C.

    2012-01-01

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

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

    PubMed Central

    Zhou, Weibin; Baneyx, François

    2013-01-01

    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 Zn2+ 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

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

    PubMed Central

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

    2014-01-01

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

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

    E-print Network

    Chen, Wilfred

    cycles. Although tunable polymers such as poly(N-isopropylacrylamide) (poly-NIPAM) have been used from straightforward. Typically, controlled copolymeriza- tion of NIPAM with either vinylimidazole. They behave very similar to poly-NIPAM polymers and have been shown to undergo reversible phase transitio

  2. Enrichment of Phosphorylated Proteins from Cell Lysate -Phosphate Affinity Chromatography using Phos-tagTM Agarose -

    E-print Network

    Lebendiker, Mario

    # distilled water 70 mL # 3.0 mol/L aqueous CH3COOH for pH adjustment at 7.5 a proper quantity # distilled # distilled water 80 mL # 3.0 mol/L aqueous CH3COOH for pH adjustment at 7.5 a proper quantity # distilledOH buffer (pH 7.5, 100 mL) # NaH2PO4 2.4 g # distilled water 80 mL # 1.0 mol/L aqueous NaOH for pH

  3. Crystal structures of fusion proteins with large-affinity tags DOUGLAS R. SMYTH,1

    E-print Network

    Lebendiker, Mario

    . MROZKIEWICZ,1 WILLIAM J. MCGRATH,1,3 PAWEL LISTWAN,1,2 AND BOSTJAN KOBE1,2 1 Department of Biochemistry, protein therapies, vaccine development, functional genomics, analysis of pro- tein trafficking, Department of Biochemistry and Molecular Biology, University of Queensland, Brisbane, Queensland 4072

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

    E-print Network

    Xie, Lexing

    , 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

  5. Sensor-based material tagging system

    SciTech Connect

    Vercellotti, L.C.; Cox, R.W.; Ravas, R.J.; Schlotterer, J.C. . Science and Technology Center)

    1991-01-01

    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.

  6. Sensor-based material tagging system

    SciTech Connect

    Vercellotti, L.C.; Cox, R.W.; Ravas, R.J.; Schlotterer, J.C.

    1991-12-31

    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.

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

    PubMed

    Hohn, Claudia; Petrie-Hanson, Lora

    2013-01-01

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

  8. Stochastic modeling of affinity adsorption.

    PubMed

    Hubble, J

    2001-01-01

    A stochastic model is described that allows surface proximity and packing effects to be incorporated into predictions of adsorption kinetics and equilibrium of affinity adsorption. Equilibrium predictions show that, depending on conditions chosen, the results obtained for equilibrium conditions can exhibit either a Freundlich- or a Langmuir-type relationship. Under conditions of surface density imposed adsorption constraints, the time taken for equilibrium to be reached increases as the "off" constant is decreased. This suggests that for resins having a high immobilized ligand density binding kinetics may be more highly limited by the "off" constant than by mass transfer limitations. PMID:11386880

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

    NASA Astrophysics Data System (ADS)

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

    2011-10-01

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

  10. 49 CFR 236.76 - Tagging of wires and interference of wires or tags with signal apparatus.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 4 2010-10-01 2010-10-01 false Tagging of wires and interference of wires or tags... SYSTEMS, DEVICES, AND APPLIANCES Rules and Instructions: All Systems Wires and Cables § 236.76 Tagging of wires and interference of wires or tags with signal apparatus. Each wire shall be tagged or otherwise...

  11. 49 CFR 236.76 - Tagging of wires and interference of wires or tags with signal apparatus.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 4 2011-10-01 2011-10-01 false Tagging of wires and interference of wires or tags... SYSTEMS, DEVICES, AND APPLIANCES Rules and Instructions: All Systems Wires and Cables § 236.76 Tagging of wires and interference of wires or tags with signal apparatus. Each wire shall be tagged or otherwise...

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

    SciTech Connect

    Cooke, Steven J.; Nguyen, Vivian M.; Murchie, Karen J.; Thiem, Jason D.; Donaldson, Michael R.; Hinch, Scott G.; Brown, Richard S.; Fisk, Aaron

    2013-11-01

    The advent and widespread adoption of electronic tags (including biotelemetry and biologging devices) for tracking animals has provided unprecedented information on the biology, management, and conservation of fish in the world’s oceans and inland waters. However, use of these tools is not without controversy. Even when scientific and management objectives may best be achieved using electronic tags, it is increasingly important to further consider other factors such as the welfare of tagged animals (i.e., the role of training and science-based surgical guidelines, anesthetic use, inability to maintain sterile conditions in field environments), the ethics of tagging threatened species vs. using surrogates, stakeholder perspectives on tagging (including aboriginals), as well as use of data emanating from such studies (e.g., by fishers to facilitate exploitation). Failure to do so will have the potential to create conflict and undermine scientific, management and public confidence in the use of this powerful tool. Indeed, there are already a number of examples of where tracking studies using electronic tags have been halted based on concerns raised by researchers, authorities, or stakeholders. Here we present a candid evaluation of several factors that should be considered when determining when to tag or not to tag fish with electronic devices. It is not our objective to judge the merit of previous studies. Rather, we hope to stimulate debate and discussion regarding the use of electronic tags to study fish. Relatedly, there is a need for more research to address these questions (e.g., what level of cleanliness is needed when conducting surgeries, what type of training should be required for fish surgery) including human dimensions studies to understand perspectives of different actors including society as a whole with respect to tagging and tracking studies.

  13. Maximin affinity learning of image segmentation

    E-print Network

    Turaga, Srinivas C; Helmstaedter, Moritz; Denk, Winfried; Seung, H Sebastian

    2009-01-01

    Images can be segmented by first using a classifier to predict an affinity graph that reflects the degree to which image pixels must be grouped together and then partitioning the graph to yield a segmentation. Machine learning has been applied to the affinity classifier to produce affinity graphs that are good in the sense of minimizing edge misclassification rates. However, this error measure is only indirectly related to the quality of segmentations produced by ultimately partitioning the affinity graph. We present the first machine learning algorithm for training a classifier to produce affinity graphs that are good in the sense of producing segmentations that directly minimize the Rand index, a well known segmentation performance measure. The Rand index measures segmentation performance by quantifying the classification of the connectivity of image pixel pairs after segmentation. By using the simple graph partitioning algorithm of finding the connected components of the thresholded affinity graph, we are ...

  14. Conformal field theory on affine Lie groups

    SciTech Connect

    Clubok, K.S.

    1996-04-01

    Working directly on affine Lie groups, we construct several new formulations of the WZW model, the gauged WZW model, and the generic affine-Virasoro action. In one formulation each of these conformal field theories (CFTs) is expressed as a one-dimensional mechanical system whose variables are coordinates on the affine Lie group. When written in terms of the affine group element, this formulation exhibits a two-dimensional WZW term. In another formulation each CFT is written as a two-dimensional field theory, with a three- dimensional WZW term, whose fields are coordinates on the affine group. On the basis of these equivalent formulations, we develop a translation dictionary in which the new formulations on the affine Lie group are understood as mode formulations of the conventional formulations on the Lie group. Using this dictionary, we also express each CFT as a three-dimensional field theory on the Lie group with a four-dimensional WZW term. 36 refs.

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

    PubMed

    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

    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

  16. 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

  17. Page 1 of 1 Fish Tagging Forum

    E-print Network

    Page 1 of 1 AGENDA Fish Tagging Forum Northwest Power and Conservation Council Meeting Date Spring Chinook Salmon Curt Knudsen, Oncorh Consulting LUNCH 1:15 to 2:00 Review of FTF Scope and Future for a second pass at each of the specific tagging technologies presented to date. 4:15 to 5:00 Recap and Plan

  18. Method and apparatus for manufacturing gas tags

    DOEpatents

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

    1996-01-01

    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.

  19. Method and apparatus for manufacturing gas tags

    DOEpatents

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

    1996-12-17

    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.

  20. In Brief .. Fish Tag Returns, Salmon

    E-print Network

    enhancement appropriation.... ....Texas anglers who don't know the value of tagged fish are throwing away goodIn Brief .. Fish Tag Returns, Salmon Facilities, and Brown Shrimp ....California has enacted a new {cohol salmon. the Department of Fish and Game reports. The law is aimed at preventing com· mercial

  1. Fish Tagging Forum February 12, 2013

    E-print Network

    ,800,000 Acoustic $ 18,000,000 Others $ 1,200,000 TOTAL $ 58,100,000 #12;CWT, $7,000,000 , 12% PIT, $24,500,000 , 42Fish Tagging Forum Update February 12, 2013 #12;Significance of Tagging/Marking · Roughly $50M decision making ­ Hydro, Habitat, Harvest, Hatchery, Predation, Population Status & Recovery 2 #12;Purpose

  2. A Radio Tag for Big Whales

    ERIC Educational Resources Information Center

    Watkins, William A.

    1978-01-01

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

  3. Non-Elimination Tag: A Multidisciplinary Approach

    ERIC Educational Resources Information Center

    Townsend, J. Scott; Mohr, Derek J.; Waronsky, Clint; Grana, Mario M.

    2006-01-01

    The activity of tag may be one of the most widely played games in elementary physical education programs. It comes in many shapes and sizes and can be morphed to meet many needs. For example, tag is used as a general body warm-up for young children (Rosengard, Mckenzie, & Short, 2000), to teach chasing, dodging, and fleeing skills (Graham,…

  4. Harnessing Collective Knowledge Inherent in Tag Clouds

    ERIC Educational Resources Information Center

    Cress, U.; Held, C.

    2013-01-01

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

  5. Available Tagging Products www.beeworks.com

    E-print Network

    Mayes, Keith

    tags into tissue Needles ­ for the syringe implanters Rapid Implant Gun ­ a more effective and no doubt syringe and gun implanters #12;Basically, other than aesthetic differences, the companies provide almost into a needle and injected into an individual all by the machine Handheld multi-shot tag injector ­ a more

  6. Notes on SAW Tag Interrogation Techniques

    NASA Technical Reports Server (NTRS)

    Barton, Richard J.

    2010-01-01

    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.

  7. Maxwell-affine gauge theory of gravity

    NASA Astrophysics Data System (ADS)

    Cebecio?lu, O.; Kibaro?lu, S.

    2015-12-01

    The Maxwell extension of the affine algebra in four dimensions with additional tensor generator is given. Using the methods of nonlinear realizations, we find the transformation rules for the group parameters and the corresponding generators. Gauging the Maxwell-affine algebra we present two possible invariant actions for gravity: one is first order and the other one is second order in the affine curvature. We notice that equations of motion for the action, second order in the affine curvature, lead to the generalized Bianchi identities on the choice of appropriate coefficients for a particular solution of the constraint equation.

  8. A Novel Vertex Affinity for Community Detection

    SciTech Connect

    Yoo, Andy; Sanders, Geoffrey; Henson, Van; Vassilevski, Panayot

    2015-10-05

    We propose a novel vertex affinity measure in this paper. The new vertex affinity quantifies the proximity between two vertices in terms of their clustering strength and is ideal for such graph analytics applications as community detection. We also developed a framework that combines simple graph searches and resistance circuit formulas to compute the vertex affinity efficiently. We study the properties of the new affinity measure empirically in comparison to those of other popular vertex proximity metrics. Our results show that the existing metrics are ill-suited for community detection due to their lack of fundamental properties that are essential for correctly capturing inter- and intra-cluster vertex proximity.

  9. Structural determinants of sigma receptor affinity

    SciTech Connect

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

    1987-12-01

    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.

  10. Deciphering the Cellular Targets of Bioactive Compounds Using a Chloroalkane Capture Tag.

    PubMed

    Friedman Ohana, Rachel; Kirkland, Thomas A; Woodroofe, Carolyn C; Levin, Sergiy; Uyeda, H Tetsuo; Otto, Paul; Hurst, Robin; Robers, Matthew B; Zimmerman, Kris; Encell, Lance P; Wood, Keith V

    2015-10-16

    Phenotypic screening of compound libraries is a significant trend in drug discovery, yet success can be hindered by difficulties in identifying the underlying cellular targets. Current approaches rely on tethering bioactive compounds to a capture tag or surface to allow selective enrichment of interacting proteins for subsequent identification by mass spectrometry. Such methods are often constrained by ineffective capture of low affinity and low abundance targets. In addition, these methods are often not compatible with living cells and therefore cannot be used to verify the pharmacological activity of the tethered compounds. We have developed a novel chloroalkane capture tag that minimally affects compound potency in cultured cells, allowing binding interactions with the targets to occur under conditions relevant to the desired cellular phenotype. Subsequent isolation of the interacting targets is achieved through rapid lysis and capture onto immobilized HaloTag protein. Exchanging the chloroalkane tag for a fluorophore, the putative targets identified by mass spectrometry can be verified for direct binding to the compound through resonance energy transfer. Using the interaction between histone deacetylases (HDACs) and the inhibitor, Vorinostat (SAHA), as a model system, we were able to identify and verify all the known HDAC targets of SAHA as well as two previously undescribed targets, ADO and CPPED1. The discovery of ADO as a target may provide mechanistic insight into a reported connection between SAHA and Huntington's disease. PMID:26162280

  11. HaloTag is an effective expression and solubilisation fusion partner for a range of fibroblast growth factors

    PubMed Central

    Taylor, Sarah E.; Mao, Xianqing; Wilkinson, Mark C.

    2015-01-01

    The production of recombinant proteins such as the fibroblast growth factors (FGFs) is the key to establishing their function in cell communication. The production of recombinant FGFs in E. coli is limited, however, due to expression and solubility problems. HaloTag has been used as a fusion protein to introduce a genetically-encoded means for chemical conjugation of probes. We have expressed 11 FGF proteins with an N-terminal HaloTag, followed by a tobacco etch virus (TEV) protease cleavage site to allow release of the FGF protein. These were purified by heparin-affinity chromatography, and in some instances by further ion-exchange chromatography. It was found that HaloTag did not adversely affect the expression of FGF1 and FGF10, both of which expressed well as soluble proteins. The N-terminal HaloTag fusion was found to enhance the expression and yield of FGF2, FGF3 and FGF7. Moreover, whereas FGF6, FGF8, FGF16, FGF17, FGF20 and FGF22 were only expressed as insoluble proteins, their N-terminal HaloTag fusion counterparts (Halo-FGFs) were soluble, and could be successfully purified. However, cleavage of Halo-FGF6, -FGF8 and -FGF22 with TEV resulted in aggregation of the FGF protein. Measurement of phosphorylation of p42/44 mitogen-activated protein kinase and of cell growth demonstrated that the HaloTag fusion proteins were biologically active. Thus, HaloTag provides a means to enhance the expression of soluble recombinant proteins, in addition to providing a chemical genetics route for covalent tagging of proteins. PMID:26137434

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

    E-print Network

    Eisen, Herman N.

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

  13. Engineering the ATLAS TAG Browser

    NASA Astrophysics Data System (ADS)

    Zhang, Qizhi; ATLAS Collaboration

    2011-12-01

    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.

  14. Photodissociation of Charge Tagged Peptides

    NASA Astrophysics Data System (ADS)

    He, Yi; Parthasarathi, Ramakrishnan; Raghavachari, Krishnan; Reilly, James P.

    2012-07-01

    Tris(2,4,6-trimethoxyphenyl) phosphonium acetyl (TMPP-Ac) was previously introduced to improve the mass spectrometric sequence analysis of peptides by fixing a permanent charge at the N-termini. However, peptides containing arginine residues did not fragment efficiently after TMPP-Ac modification. In this work, we combine charge derivatization with photodissociation. The fragmentation of TMPP-derivatized peptides is greatly improved and a series of N-terminal fragments is generated with complete sequence information. Arginine has a special effect on the fragmentation of the TMPP tagged peptides when it is the N-terminal peptide residue. Theoretical and experimental results suggest that this is due to hydrogen transfer from the charged N-terminus to the hydrogen-deficient peptide sequence.

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

    PubMed Central

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

    2013-01-01

    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

  16. Tandem affinity purification to identify cytosolic and nuclear g??-interacting proteins.

    PubMed

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

    2015-01-01

    It has become clear in recent years that the G?? subunits of heterotrimeric proteins serve broad roles in the regulation of cellular activity and interact with many proteins in different subcellular locations including the nucleus. Protein affinity purification is a common method to identify and confirm protein interactions. When used in conjugation with mass spectrometry it can be used to identify novel protein interactions with a given bait protein. The tandem affinity purification (TAP) technique identifies partner proteins bound to tagged protein bait. Combined with protocols to enrich the nuclear fraction of whole cell lysate through sucrose cushions, TAP allows for purification of interacting proteins found specifically in the nucleus. Here we describe the use of the TAP technique on cytosolic and nuclear lysates to identify candidate proteins, through mass spectrometry, that bind to G?1 subunits. PMID:25304356

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

    DOEpatents

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

    2008-04-22

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

  18. Double affine Hecke algebras and noncommutative geometry

    E-print Network

    Oblomkov, Alexei

    2005-01-01

    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, ...

  19. Affine Constellations Without Mutually Unbiased Counterparts

    E-print Network

    Stefan Weigert; Thomas Durt

    2010-07-22

    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.

  20. SWITCHING ADAPTIVE CONTROL OF AFFINE NONLINEAR SYSTEM

    E-print Network

    SWITCHING ADAPTIVE CONTROL OF AFFINE NONLINEAR SYSTEM D.V. Efimov Control of Complex Systems Russia efde@mail.rcom.ru Keywords: adaptive control, disturbances, switching, nonlin- ear systems of adaptive state feedback stabilisation of affine linearly parameterised system with ex- ternal disturbances

  1. A General Affine Earnings Valuation Model

    E-print Network

    A General Affine Earnings Valuation Model Andrew Ang Columbia University and NBER Jun Liu ¡ UCLA: stock valuation, earnings, residual income model, asset-pricing, affine model, linear information of Stock Valuation". We thank Geert Bekaert, Michael Brennan, Ron Kasznik, Charles Lee, Jing Liu, Stephen

  2. Projective and affine planes 1 Projective planes

    E-print Network

    Queen Mary, University of London

    plane. A projective plane of order q is a square 2-(q2 + q + 1,q + 1,1) design (a symmetric BIBD, the unique Steiner triple system of order 7. The Encyclopaedia of Design Theory Projective and affine planes. A 2-(q2,q,1) design is called an affine plane of order q. We've seen that any projective plane

  3. Loop realizations of quantum affine algebras

    SciTech Connect

    Cautis, Sabin; Licata, Anthony

    2012-12-15

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

  4. Perfect tag identification protocol in RFID networks

    E-print Network

    Bonuccelli, Maurizio A; Martelli, Francesca

    2008-01-01

    Radio Frequency IDentification (RFID) systems are becoming more and more popular in the field of ubiquitous computing, in particular for objects identification. An RFID system is composed by one or more readers and a number of tags. One of the main issues in an RFID network is the fast and reliable identification of all tags in the reader range. The reader issues some queries, and tags properly answer. Then, the reader must identify the tags from such answers. This is crucial for most applications. Since the transmission medium is shared, the typical problem to be faced is a MAC-like one, i.e. to avoid or limit the number of tags transmission collisions. We propose a protocol which, under some assumptions about transmission techniques, always achieves a 100% perfomance. It is based on a proper recursive splitting of the concurrent tags sets, until all tags have been identified. The other approaches present in literature have performances of about 42% in the average at most. The counterpart is a more sophistic...

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

    PubMed Central

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

    2015-01-01

    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

  6. Improving image segmentation by learning region affinities

    SciTech Connect

    Prasad, Lakshman; Yang, Xingwei; Latecki, Longin J

    2010-11-03

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

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

    SciTech Connect

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

    2008-02-01

    Numerous research tools and technologies are currently being used to evaluate fish passage and survival to determine the impacts of the Federal Columbia River Power System (FCRPS) on endangered and threatened juvenile salmonids, including PIT tags, balloon tags, hydroacoustic evaluations, radio telemetry, and acoustic telemetry. Each has advantages and disadvantages, but options are restricted in some situations because of limited capabilities of a specific technology, lack of detection capability downstream, or availability of adequate numbers of fish. However, there remains concern about the comparative effects of the tag or the tagging procedure on fish performance. The recently developed Juvenile Salmonid Acoustic Telemetry System (JSATS) acoustic transmitter is the smallest active acoustic tag currently available. The goal of this study was to determine whether fish tagged with the JSATS acoustic-telemetry tag can provide unbiased estimates of passage behavior and survival within the performance life of the tag. We conducted both field and laboratory studies to assess tag effects. For the field evaluation we released a total of 996 acoustic-tagged fish in conjunction with 21,026 PIT-tagged fish into the tailrace of Lower Granite Dam on 6 and 13 May. Travel times between release and downstream dams were not significantly different for the majority of the reaches between acoustic-tagged and PIT-tagged fish. In addition to the field evaluation, a series of laboratory experiments were conducted to determine if growth and survival of juvenile Chinook salmon surgically implanted with acoustic transmitters is different than untagged or PIT tagged juvenile Chinook salmon. Only yearling fish with integrated and non-integrated transmitters experienced mortalities, and these were low (<4.5%). Mortality among sub-yearling control and PIT-tag treatments ranged up to 7.7% while integrated and non-integrated treatments had slightly higher rates (up to 8.3% and 7.9% 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.

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

    USGS Publications Warehouse

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

    2003-01-01

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

  9. Time-Tag Generation Script

    NASA Technical Reports Server (NTRS)

    Jackson, Dan E.

    2010-01-01

    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.

  10. Lanthanide-tagged proteins – An illuminating partnership

    E-print Network

    Imperiali, Barbara

    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 ...

  11. Mass-producible micro-holographic tags

    SciTech Connect

    Sweatt, W.C.; Ray-Chaudhuri, A.K.; Kravitz, S.H.; Warren, M.E.; Stulen, R.H.; Tichenor, D.A.; Krenz, K.D. |; Descour, M.R.; Underwood, J.H.

    1996-06-01

    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.

  12. User Interface Program for secure electronic tags

    SciTech Connect

    Cai, Y.; Koehl, E.R.; Carlson, R.D.; Raptis, A.C.

    1995-05-01

    This report summarizes and documents the efforts of Argonne National Laboratory (ANL) in developing a secure tag communication user interface program comprising a tag monitor and a communication tool. This program can perform the same functions as the software that was developed at the Lawrence Livermore National Laboratory (LLNL), but it is enhanced with a user-friendly screen. It represents the first step in updating the TRANSCOM Tracking System (TRANSCOM) by incorporating a tag communication screen menu into the main menu of the TRANSCOM user program. A working version of TRANSCOM, enhanced with ANL secure-tag graphics, will strongly support the Department of Energy Warhead Dismantlement/Special Nuclear Materials Control initiatives. It will allow commercial satellite tracking of the movements and operational activities of treaty-limited items and transportation vehicles throughout Europe and the former USSR, as well as the continental US.

  13. Magnetic vector field tag and seal

    DOEpatents

    Johnston, Roger G.; Garcia, Anthony R.

    2004-08-31

    One or more magnets are placed in a container (preferably on objects inside the container) and the magnetic field strength and vector direction are measured with a magnetometer from at least one location near the container to provide the container with a magnetic vector field tag and seal. The location(s) of the magnetometer relative to the container are also noted. If the position of any magnet inside the container changes, then the measured vector fields at the these locations also change, indicating that the tag has been removed, the seal has broken, and therefore that the container and objects inside may have been tampered with. A hollow wheel with magnets inside may also provide a similar magnetic vector field tag and seal. As the wheel turns, the magnets tumble randomly inside, removing the tag and breaking the seal.

  14. 50 CFR 20.81 - Tagging requirement.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ...Wildlife and Fisheries UNITED STATES FISH AND WILDLIFE SERVICE, DEPARTMENT...MIGRATORY BIRD HUNTING Migratory Bird Preservation Facilities § 20.81 Tagging requirement. No migratory bird preservation facility shall receive or have...

  15. Untraceable RFID Tags via Insubvertible Encryption Giuseppe Ateniese

    E-print Network

    Ateniese, Giuseppe

    , in substitution of, or in addition to, barcode tags. However, unlike barcodes and other consumer labeling tech- niques, RFID tags record a sufficiently long bitstring to uniquely identify specific product units. For instance, RFID tags can be read faster than barcode tags Permission to make digital or hard copies of all

  16. Theory and Measurement of Backscattering from RFID Tags

    E-print Network

    Hannaford, Blake

    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

  17. Improved Approximation Algorithms for the Freeze-Tag Problem

    E-print Network

    Mitchell, Joseph S.B.

    Improved Approximation Algorithms for the Freeze-Tag Problem Esther M. Arkin Applied Math In the Freeze-Tag Problem, the objective is to awaken a set of "asleep" robots, starting with only one "awake resemblance to the children's game of freeze-tag, this problem has been called Freeze-Tag Problem (FTP

  18. Posting Act Tagging Using Transformation-Based Learning

    E-print Network

    Pottenger, William M.

    -based learning (TBL) [1] to the task of assigning tags to postings in online chat conversations. We define a list of posting tags that have proven useful in chat-conversation analysis. We describe the templates used-of-speech tagging and dialogue act tagging by incorporating regular expressions into our templates. We close

  19. MUSIC TAG ANNOTATION AND CLUSTERING USING LATENT MUSIC SEMANTIC ANALYSIS

    E-print Network

    Wang, Hsin-Min

    - occurs with hip-hop; synth and drum-machine often give electronic and techno tags. The tags co and predict the tag co-occurrence pattern of a song. The LMSA-based approach jointly models two types of features, namely, auditory music features and tag-based text features. We employ a Gaussian mixture model

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

    USGS Publications Warehouse

    Dixon, Christopher J.; Mesa, Matthew G.

    2011-01-01

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

  1. A Study on Exploring People’s Affinity for Solitude 

    E-print Network

    Lee, Sunwoo

    2013-01-09

    This study sought to investigate solitude as a phenomenon. People’s affinity for solitude and the antecedents of affinity for solitude were of crucial interest to the study because affinity for solitude has been considered ...

  2. Solid tags for identifying failed reactor components

    DOEpatents

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

    1987-01-01

    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.

  3. b-tagging at D0

    SciTech Connect

    Hanagaki, K.; /Fermilab

    2005-07-01

    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.

  4. Neural net controlled tag gas sampling system for nuclear reactors

    DOEpatents

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

    1997-01-01

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

  5. Neural net controlled tag gas sampling system for nuclear reactors

    DOEpatents

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

    1997-02-11

    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.

  6. Effective algorithms for tag SNP selection.

    PubMed

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

    2005-10-01

    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

  7. Harvesting Intelligence in Multimedia Social Tagging Systems

    NASA Astrophysics Data System (ADS)

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

    As more people adopt tagging practices, social tagging systems tend to form rich knowledge repositories that enable the extraction of patterns reflecting the way content semantics is perceived by the web users. This is of particular importance, especially in the case of multimedia content, since the availability of such content in the web is very high and its efficient retrieval using textual annotations or content-based automatically extracted metadata still remains a challenge. It is argued that complementing multimedia analysis techniques with knowledge drawn from web social annotations may facilitate multimedia content management. This chapter focuses on analyzing tagging patterns and combining them with content feature extraction methods, generating, thus, intelligence from multimedia social tagging systems. Emphasis is placed on using all available "tracks" of knowledge, that is tag co-occurrence together with semantic relations among tags and low-level features of the content. Towards this direction, a survey on the theoretical background and the adopted practices for analysis of multimedia social content are presented. A case study from Flickr illustrates the efficiency of the proposed approach.

  8. Self affine Delone sets and deviation phenomena

    E-print Network

    Scott Schmieding; Rodrigo Treviño

    2015-11-24

    We study the growth of norms of ergodic integrals for the translation action on spaces coming from expansive, self-affine Delone sets. The linear map giving the self-affinity induces a renormalization map on the pattern space and we show that the rate of growth of ergodic integrals is controlled by the induced action of the renormalizing map on the cohomology of the pattern space up to boundary errors. We explore the consequences for the diffraction of such Delone sets, and explore in detail what the picture is for substitution tilings as well as for cut and project sets which are self-affine. We also explicitly compute some examples.

  9. Molecules with a High Electron Affinity

    NASA Astrophysics Data System (ADS)

    Sidorov, Lev N.

    1982-04-01

    Experimental values of the electron affinity of inorganic compounds reported between 1975 and 1980 are systematically examined. The following methods of measuring electron affinity are briefly reviewed: photo-extraction and photo-electron spectroscopy, electron impact, ion-molecule reactions, ionisation by alkali metal atoms, ion-molecule equilibria, and methods based on measuring the frequency for intramolecular charge transfer in the absorption spectra of complexes and on calculations using a thermochemical cycle. Classes of compounds having an electron affinity greater than that of halogen atoms are identified by analysing published data. 166 references.

  10. Combinatorics in affine flag varieties James Parkinson

    E-print Network

    Ram, Arun

    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

  11. PRINCIPLES OF AFFINITY-BASED BIOSENSORS

    EPA Science Inventory

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

  12. Vertex representations of quantum affine algebras.

    PubMed

    Frenkel, I B; Jing, N

    1988-12-01

    We construct vertex representations of quantum affine algebras of ADE type, which were first introduced in greater generality by Drinfeld and Jimbo. The limiting special case of our construction is the untwisted vertex representation of affine Lie algebras of Frenkel-Kac and Segal. Our representation is given by means of a new type of vertex operator corresponding to the simple roots and satisfying the defining relations. In the case of the quantum affine algebra of type A, we introduce vertex operators corresponding to all the roots and determine their commutation relations. This provides an analogue of a Chevalley basis of the affine Lie algebra [unk](n) in the basic representation. PMID:16594004

  13. Vertex representations of quantum affine algebras

    PubMed Central

    Frenkel, Igor B.; Jing, Naihuan

    1988-01-01

    We construct vertex representations of quantum affine algebras of ADE type, which were first introduced in greater generality by Drinfeld and Jimbo. The limiting special case of our construction is the untwisted vertex representation of affine Lie algebras of Frenkel-Kac and Segal. Our representation is given by means of a new type of vertex operator corresponding to the simple roots and satisfying the defining relations. In the case of the quantum affine algebra of type A, we introduce vertex operators corresponding to all the roots and determine their commutation relations. This provides an analogue of a Chevalley basis of the affine Lie algebra [unk](n) in the basic representation. PMID:16594004

  14. Hylleraas hydride binding energy: diatomic electron affinities.

    PubMed

    Chen, Edward S; Keith, Herman; Lim, Tristan; Pham, Dang; Rosenthal, Reece; Herder, Charles; Pai, Sunil; Flores, R A; Chen, Edward C M

    2015-04-01

    Theoretical adiabatic electron affinities are often considered inaccurate because they are referenced to only a single value. Ground state electron affinities for all the main group elements and homonuclear diatomics were identified recently using the normalized binding energy of the hydrogen atom: [0.75420375(3)/2?=?0.37710187(1) eV]. Here we revisit experimental values and extend the identifications to diatomics in the G2-1 set. We assign new ground state electron affinities: (eV) Cl2, 3.2(2); Br2, 2.87(14); CH, 2.1(2); H2, 0.6 ; NH, 1.1, SiH, 1.90. Anion Morse potentials are calculated for H2 and N2 from positive electron affinities and for hyperfine superoxide states for the first time. PMID:25758340

  15. Associated Particle Tagging (APT) in Magnetic Spectrometers

    SciTech Connect

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

    2012-10-16

    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.

  16. Affinity Electrophoresis Using Ligands Attached To Polymers

    NASA Technical Reports Server (NTRS)

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

    1990-01-01

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

  17. A brief examination of optical tagging technologies.

    SciTech Connect

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

    2003-07-01

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

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

    E-print Network

    Greenberg, Saul

    Visible and Controllable RFID Tags Abstract Radio frequency identification (RFID) tags containing;Introduction and Motivation Since its invention in the early 20th century, radio frequency identification (RFID associated with RFID, likely because the technology remains largely invisible and uncontrollable

  19. TagFusion: A System for Integration and Leveraging of Collaborative Tags

    NASA Astrophysics Data System (ADS)

    Stankovi?, Milan; Jovanovi?, Jelena

    An ever increasing number of Web sites that allow users to easily collaborate, produce, and share content and interact have turned the Web into a more dynamic social place often referred to as Social Web. One form of Social Web sites is collaborative tagging systems that allow their users to annotate Web resources using tags, thus intuitively organizing them and making them easily findable. Tags would have been much more useful if collaborative tagging systems had been collaborating and allowing for integration of their tagging metadata. In this paper we address this issue of lack of collaboration by suggesting an approach for achieving that collaboration. We also present a concrete system called TagFusion that we developed to test the feasibility of the suggested approach. Special attention has been given to the strategies for attracting collaborative tagging systems to integrate using TagFusion, as well as to the possibility of involving artificial entities in the annotation process in accordance with the Semantic Web vision.

  20. Regulation of integrin affinity on cell surfaces

    PubMed Central

    Schürpf, Thomas; Springer, Timothy A

    2011-01-01

    Lymphocyte activation triggers adhesiveness of lymphocyte function-associated antigen-1 (LFA-1; integrin ?L?2) for intercellular adhesion molecules (ICAMs) on endothelia or antigen-presenting cells. Whether the activation signal, after transmission through multiple domains to the ligand-binding ?I domain, results in affinity changes for ligand has been hotly debated. Here, we present the first comprehensive measurements of LFA-1 affinities on T lymphocytes for ICAM-1 under a broad array of activating conditions. Only a modest increase in affinity for soluble ligand was detected after activation by chemokine or T-cell receptor ligation, conditions that primed LFA-1 and robustly induced lymphocyte adhesion to ICAM-1 substrates. By stabilizing well-defined LFA-1 conformations by Fab, we demonstrate the absolute requirement of the open LFA-1 headpiece for adhesiveness and high affinity. Interaction of primed LFA-1 with immobilized but not soluble ICAM-1 triggers energy-dependent affinity maturation of LFA-1 to an adhesive, high affinity state. Our results lend support to the traction or translational motion dependence of integrin activation. PMID:21946563

  1. Different endothelin receptor affinities in dog tissues

    SciTech Connect

    Loeffler, B.M.L.; Loehrer, W. )

    1991-01-01

    Endothelin (ET) is a long-lasting potent vasoconstrictor-peptide. Here the authors report different binding affinities of endothelin-1 (ET-1) to ET-receptors of various dog tissues. Crude microsomal fractions were prepared after homogenisation of dog tissues in 50 mM Tris/HCl, 20 mM MnCl2, 1 mM EDTA, pH 7.4 by differential centrifugation. Aliquots of microsomal fractions (70 micrograms of protein) were incubated at 25 degrees C for 180 min in the presence of 20 pM 125I-ET-1 and various concentrations of cold ET-1. Four different ET-1 receptor binding affinities were found: adrenals, cerebrum, liver, heart, skeletal muscle and stomach microsomal membranes contained high affinity binding sites (Kd 50 - 80 pM, Bmax 60 - 250 fmol/mg). In cerebellum and spleen medium affinity ET-1 receptors (Kd 350 pM, Bmax 880 and 1200 fmol/mg respectively) were present. In comparison lung and kidney microsomes contained a low affinity ET-1 receptor (Kd 800 and 880 pM, Bmax 1600 and 350 fmol/mg). Receptors of even lower affinity were present in heart, intestine and liver microsomes with Kd values of 3 - 6 nM.

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

    SciTech Connect

    Lee, Byung-Kwon; Jung, Kyung-Sik; Son, Cagdas D; Kim, Heejung; Verberkmoes, Nathan C; Arshava, Boris; Naider, Fred; Becker, Jeffrey Marvin

    2007-01-01

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

  3. The affinity purification and characterization of ATP synthase complexes from mitochondria

    PubMed Central

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

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

    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.

  5. Expression and purification of recombinant proteins in Escherichia coli tagged with a small metal-binding protein from Nitrosomonas europaea.

    PubMed

    Vargas-Cortez, Teresa; Morones-Ramirez, Jose Ruben; Balderas-Renteria, Isaias; Zarate, Xristo

    2016-02-01

    Escherichia coli is still the preferred organism for large-scale production of recombinant proteins. The use of fusion proteins has helped considerably in enhancing the solubility of heterologous proteins and their purification with affinity chromatography. Here, the use of a small metal-binding protein (SmbP) from Nitrosomonas europaea is described as a new fusion protein for protein expression and purification in E. coli. Fluorescent proteins tagged at the N-terminal with SmbP showed high levels of solubility, compared with those of maltose-binding protein and glutathione S-transferase, and low formation of inclusion bodies. Using commercially available IMAC resins charged with Ni(II), highly pure recombinant proteins were obtained after just one chromatography step. Proteins may be purified from the periplasm of E. coli if SmbP contains the signal sequence at the N-terminal. After removal of the SmbP tag from the protein of interest, high-yields are obtained since SmbP is a protein of just 9.9 kDa. The results here obtained suggest that SmbP is a good alternative as a fusion protein/affinity tag for the production of soluble recombinant proteins in E. coli. PMID:26494603

  6. Measurement of tag confidence in user generated contents retrieval

    NASA Astrophysics Data System (ADS)

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

    2009-01-01

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

  7. Social Tagging for Personalized Web Search

    NASA Astrophysics Data System (ADS)

    Biancalana, Claudio

    Social networks and collaborative tagging systems are rapidly gaining popularity as primary means for sorting and sharing data: users tag their bookmarks in order to simplify information dissemination and later lookup. Social Bookmarking services are useful in two important respects: first, they can allow an individual to remember the visited URLs, and second, tags can be made by the community to guide users towards valuable content. In this paper we focus on the latter use: we present a novel approach for personalized web search using query expansion. We further extend the family of well-known co-occurence matrix technique models by using a new way of exploring social tagging services. Our approach shows its strength particularly in the case of disambiguation of word contexts. We show how to design and implement such a system in practice and conduct several experiments. To the best of our knowledge this is the first study centered on using social bookmarking and tagging techniques for personalization of web search and its evaluation in a real-world scenario.

  8. Tags to Track Illicit Uranium and Plutonium

    SciTech Connect

    Haire, M. Jonathan; Forsberg, Charles W.

    2007-07-01

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

  9. Electronic tagging and integrated product intelligence

    NASA Astrophysics Data System (ADS)

    Swerdlow, Martin; Weeks, Brian

    1996-03-01

    The advent of 'intelligent,' electronic data bearing tags is set to revolutionize the way industrial and retail products are identified and tracked throughout their life cycles. The dominant system for unique identification today is the bar code, which is based on printed symbology and regulated by the International Article Numbering Association. Bar codes provide users with significant operational advantages and generate considerable added value to packaging companies, product manufacturers, distributors and retailers, across supply chains in many different sectors, from retailing, to baggage handling and industrial components, e.g., for vehicles or aircraft. Electronic tags offer the potential to: (1) record and store more complex data about the product or any modifications which occur during its life cycle; (2) access (and up-date) stored data in real time in a way which does not involve contact with the product or article; (3) overcome the limitations imposed by systems which rely on line-of-sight access to stored data. Companies are now beginning to consider how electronic data tags can be used, not only to improve the efficiency of their supply chain processes, but also to revolutionize the way they do business. This paper reviews the applications and business opportunities for electronic tags and outlines CEST's strategy for achieving an 'open' standard which will ensure that tags from different vendors can co-exist on an international basis.

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

    PubMed

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

    2015-02-01

    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 Escherichia coli and purified using immobilised metal ion affinity and size exclusion chromatography - yielding approximately 1.8 mg 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

  11. Single step purification of recombinant proteins using the metal ion-inducible autocleavage (MIIA) domain as linker for tag removal.

    PubMed

    Ibe, Susan; Schirrmeister, Jana; Zehner, Susanne

    2015-08-20

    For fast and easy purification, proteins are typically fused with an affinity tag, which often needs to be removed after purification. Here, we present a method for the removal of the affinity tag from the target protein in a single step protocol. The protein VIC_001052 of the coral pathogen Vibrio coralliilyticus ATCC BAA-450 contains a metal ion-inducible autocatalytic cleavage (MIIA) domain. Its coding sequence was inserted into an expression vector for the production of recombinant fusion proteins. Following, the target proteins MalE and mCherry were produced as MIIA-Strep fusion proteins in Escherichia coli. The target proteins could be separated from the MIIA-Strep part simply by the addition of calcium or manganese(II) ions within minutes. The cleavage is not affected in the pH range from 5.0 to 9.0 or at low temperatures (6°C). Autocleavage was also observed with immobilized protein on an affinity column. The protein yield was similar to that achieved with a conventional purification protocol. PMID:26026704

  12. High-throughput T7 LIC vector for introducing C-terminal poly-histidine tags with variable lengths without extra sequences.

    PubMed

    Lee, Jonas; Kim, Sung-Hou

    2009-01-01

    Immobilized metal ion affinity chromatography (IMAC) has become one of the most popular protein purification methods for recombinant proteins with a hexa-histidine tag (His-tag) placed at the C- or N-terminus of proteins. Nevertheless, there are always difficult proteins that show weak binding to the metal chelating resin and thus low purity. These difficulties are often overcome by increasing the His-tag to 8 or 10 histidines. Despite their success, there are only few expression vectors available to easily clone and test different His-tag lengths. Therefore, we have modified Escherichia coli T7 expression vector pET21a to accommodate ligation-independent cloning (LIC) that will allow easy and efficient parallel cloning of target genes with different His-tag lengths using a single insert. Unlike most LIC vectors available commercially, our vectors will not translate unwanted extra sequences by engineering the N-terminal linker to anneal before the open reading frame, and the C-terminal linker to anneal as a His-tag. PMID:18824233

  13. university-logo Affine space forms and hyperbolic geometry

    E-print Network

    Goldman, William

    university-logo Affine space forms and hyperbolic geometry 3-dimensional affine space forms Mathematics Department Colloquium University of Illinois, Chicago #12;university-logo Affine space forms one commensurability class. #12;university-logo Affine space forms and hyperbolic geometry Euclidean

  14. university-logo Affine space forms and hyperbolic geometry

    E-print Network

    Goldman, William

    university-logo Affine space forms and hyperbolic geometry 3-dimensional affine space forms University of Singapore #12;university-logo Affine space forms and hyperbolic geometry Euclidean manifolds. #12;university-logo Affine space forms and hyperbolic geometry Euclidean manifolds When can a group G

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

    PubMed Central

    2014-01-01

    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

  16. Ultrafast tissue staining with chemical tags

    PubMed Central

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

    2014-01-01

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

  17. Photon-tagged and B-meson-tagged b-jet production at the LHC

    NASA Astrophysics Data System (ADS)

    Huang, Jinrui; Kang, Zhong-Bo; Vitev, Ivan; Xing, Hongxi

    2015-11-01

    Tagged jet measurements in high energy hadronic and nuclear reactions provide constraints on the energy and parton flavor origin of the parton shower that recoils against the tagging particle. Such additional insight can be especially beneficial in illuminating the mechanisms of heavy flavor production in proton-proton collisions at the LHC and their modification in the heavy ion environment, which are not fully understood. With this motivation, we present theoretical results for isolated-photon-tagged and B-meson-tagged b-jet production at ?{sNN} = 5.1 TeV for comparison to the upcoming lead-lead data. We find that photon-tagged b-jets exhibit smaller momentum imbalance shift in nuclear matter, and correspondingly smaller energy loss, than photon-tagged light flavor jets. Our results show that B-meson tagging is most effective in ensuring that the dominant fraction of recoiling jets originate from prompt b-quarks. Interestingly, in this channel the large suppression of the cross section is not accompanied by a significant momentum imbalance shift.

  18. Photon-tagged and B-meson-tagged b-jet production at the LHC

    E-print Network

    Huang, Jinrui; Vitev, Ivan; Xing, Hongxi

    2015-01-01

    Tagged jet measurements in high energy hadronic and nuclear reactions provide constraints on the energy and parton flavor origin of the parton shower that recoils against the tagging particle. Such additional insight can be especially beneficial in illuminating the mechanisms of heavy flavor production in proton-proton collisions at the LHC and their modification in the heavy ion environment, which are not fully understood. With this motivation, we present theoretical results for isolated-photon-tagged and B-meson-tagged b-jet production at center-of-mass energy 5.1 TeV for comparison to the upcoming lead-lead data. We find that photon-tagged b-jets exhibit smaller momentum imbalance shift in nuclear matter, and correspondingly smaller energy loss, than photon-tagged light flavor jets. Our results show that B-meson tagging is most effective in ensuring that the dominant fraction of recoiling jets originate from prompt b-quarks. Interestingly, in this channel the large suppression of the cross section is not a...

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

    PubMed Central

    2010-01-01

    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

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

    E-print Network

    Springer, Timothy A.

    The connection between metal ion affinity and ligand affinity in integrin I domains Thomas Vorup Abstract Integrins are cell-surface heterodimeric proteins that mediate cell­cell, cell­matrix, and cell­pathogen interactions. Half of the known integrin subunits contain inserted domains (I domains) that coordinate ligand

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

    ERIC Educational Resources Information Center

    Parsons, Julie; Ridley, Kimberly

    2012-01-01

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

  2. B mixing and flavor tagging at CDF

    SciTech Connect

    Russ, James S.; /Carnegie Mellon U.

    2004-12-01

    The CDF Collaboration has made a preliminary measurement of B{sub d} mixing as a first step toward measuring mixing in the B{sub s} system. Flavor tagging using opposite-side jets and muons as well as same-side tagging schemes have been applied. Results agree well with precise results from the B-factories. They use these results to estimate CDF's B{sub s} mixing range using the present data set ({approx} 250 pb{sup -1}) and extrapolate to the potential from larger data sets in future running.

  3. Tags to Track Illicit Uranium and Plutonium

    SciTech Connect

    Haire, Marvin Jonathan

    2007-01-01

    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.

  4. Classification of neocortical interneurons using affinity propagation

    PubMed Central

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

    2013-01-01

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

  5. Classification of neocortical interneurons using affinity propagation.

    PubMed

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

    2013-01-01

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

  6. Evaluation of Intercontinental Transport of Ozone Using Full-tagged, Tagged-N and Sensitivity Methods

    NASA Astrophysics Data System (ADS)

    Guo, Y.; Liu, J.; Mauzerall, D. L.; Emmons, L. K.; Horowitz, L. W.; Fan, S.; Li, X.; Tao, S.

    2014-12-01

    Long-range transport of ozone is of great concern, yet the source-receptor relationships derived previously depend strongly on the source attribution techniques used. Here we describe a new tagged ozone mechanism (full-tagged), the design of which seeks to take into account the combined effects of emissions of ozone precursors, CO, NOx and VOCs, from a particular source, while keeping the current state of chemical equilibrium unchanged. We label emissions from the target source (A) and background (B). When two species from A and B sources react with each other, half of the resulting products are labeled A, and half B. Thus the impact of a given source on downwind regions is recorded through tagged chemistry. We then incorporate this mechanism into the Model for Ozone and Related chemical Tracers (MOZART-4) to examine the impact of anthropogenic emissions within North America, Europe, East Asia and South Asia on ground-level ozone downwind of source regions during 1999-2000. We compare our results with two previously used methods -- the sensitivity and tagged-N approaches. The ozone attributed to a given source by the full-tagged method is more widely distributed spatially, but has weaker seasonal variability than that estimated by the other methods. On a seasonal basis, for most source/receptor pairs, the full-tagged method estimates the largest amount of tagged ozone, followed by the sensitivity and tagged-N methods. In terms of trans-Pacific influence of ozone pollution, the full-tagged method estimates the strongest impact of East Asian (EA) emissions on the western U.S. (WUS) in MAM and JJA (~3 ppbv), which is substantially different in magnitude and seasonality from tagged-N and sensitivity studies. This difference results from the full-tagged method accounting for the maintenance of peroxy radicals (e.g., CH3O2, CH3CO3, and HO2), in addition to NOy, as effective reservoirs of EA source impact across the Pacific, allowing for a significant contribution to ozone formation over WUS (particularly in summer). Thus, the full-tagged method, with its clear discrimination of source and background contributions on a per-reaction basis, provides unique insights into the critical role of VOCs (and additional reactive nitrogen species) in determining the nonlinear inter-continental influence of ozone pollution.

  7. claMP Tag: A Versatile Inline Metal-Binding Platform Based on the Metal Abstraction Peptide

    PubMed Central

    2015-01-01

    Molecularly targeted research and diagnostic tools are essential to advancing understanding and detection of many diseases. Metals often impart the desired functionality to these tools, and conjugation of high-affinity chelators to proteins is carried out to enable targeted delivery of the metal. This approach has been much more effective with large lanthanide series metals than smaller transition metals. Because chemical conjugation requires additional processing and purification steps and yields a heterogeneous mixture of products, inline incorporation of a peptide tag capable of metal binding is a highly preferable alternative. Development of a transition metal binding tag would provide opportunity to greatly expand metal-based analyses. The metal abstraction peptide (MAP) sequence was genetically engineered into recombinant protein to generate the claMP Tag. The effects of this tag on recombinant epidermal growth factor (EGF) protein expression, disulfide bond formation, tertiary structural integrity, and transition metal incorporation using nickel were examined to confirm the viability of utilizing the MAP sequence to generate linker-less metal conjugates. PMID:24807049

  8. OpenTag : privacy control methods in RFID

    E-print Network

    Shen, Daniel Z

    2006-01-01

    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 ...

  9. II-A METHOD FOR TAGGING IMMATURE HERRING

    E-print Network

    -shaped nylon plug. A hypodermic needle is used to insert the tag through the anterior dorsal musculature in a legible manner. NYLON PLUG CODED VINYL TUBING ASSEMBLED TAG Nontoxic yellow polyvinyl chloride tubing

  10. Facette : using facets to improve tag-based bookmarking

    E-print Network

    Lai, Peter (Peter J.)

    2009-01-01

    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 ...

  11. Low-cost electromagnetic tagging : design and implementation

    E-print Network

    Fletcher, Richard R. (Richard Ribon)

    2002-01-01

    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 ...

  12. Tagging Summary of American Shad, Alosa Sapidissima (Wilson) and

    E-print Network

    Tagging Summary of American Shad, Alosa Sapidissima (Wilson) and Striped Bass, Roccus Saxatilis Tagging Summary of American Shad, Alosa Sapidissima (Wilson) and Striped Bass, Roccus Saxatilis (Walbaum of American Shad, Alosa Sapidissima (Wilson) and Striped Bass, Roccus Saxatilis (Walbaum), Bureau

  13. Displacement Phenomena in Lectin Affinity Chromatography.

    PubMed

    Cho, Wonryeon

    2015-10-01

    The work described here examines displacement phenomena that play a role in lectin affinity chromatography and their potential to impact reproducibility. This was achieved using Lycopersicon esculentum lectin (LEL), a lectin widely used in monitoring cancer. Four small identical LEL columns were coupled in series to form a single affinity chromatography system with the last in the series connected to an absorbance detector. The serial affinity column set (SACS) was then loaded with human plasma proteins. At the completion of loading, the column set was disassembled, the four columns were eluted individually, the captured proteins were trypsin digested, the peptides were deglycosylated with PNGase F, and the parent proteins were identified through mass spectral analyses. Significantly different sets of glycoproteins were selected by each column, some proteins appearing to be exclusively bound to the first column while others were bound further along in the series. Clearly, sample displacement chromatography (SDC) occurs. Glycoproteins were bound at different places in the column train, identifying the presence of glycoforms with different affinity on a single glycoprotein. It is not possible to see these phenomena in the single column mode of chromatography. Moreover, low abundance proteins were enriched, which facilitates detection. The great advantage of this method is that it differentiates between glycoproteins on the basis of their binding affinity. Displacement phenomena are concluded to be a significant component of the separation mechanism in heavily loaded lectin affinity chromatography columns. This further suggests that care must be exercised in sample loading of lectin columns to prevent analyte displacement with nonretained proteins. PMID:26348026

  14. Genetic affinities of the Shetland islanders.

    PubMed

    Roberts, D F

    1990-01-01

    Phenotype and gene frequencies in blood group, red cell enzyme, and serum protein polymorphisms in a sample of Shetland islanders are reported. Analyses of genetic distance and relationship indicate that Shetland affinities are closer to nearby populations bordering the North Sea rather than to those of the North Atlantic. The closest affinities seem to be with populations in north Britain with a similar history of Norse influence. There is evidence that the Shetlanders retain an element of an ultra-European population extreme in some gene frequencies and so, like the Orcadians, may be regarded as much diluted relict of an ancient population. PMID:2334107

  15. Satake diagrams of affine Kac Moody algebras

    NASA Astrophysics Data System (ADS)

    Tripathy, L. K.; Pati, K. C.

    2006-02-01

    Satake diagrams of affine Kac-Moody algebras (untwisted and twisted) are obtained from their Dynkin diagrams. These diagrams give a classification of restricted root systems associated with these algebras. In the case of simple Lie algebras, these root systems and Satake diagrams correspond to symmetric spaces which have recently found many physical applications in quantum integrable systems, quantum transport problems, random matrix theories etc. We hope these types of root systems may have similar applications in theoretical physics in future and may correspond to symmetric spaces analogue of affine Kac-Moody algebras if they exist.

  16. New unitary affine-Virasoro constructions

    SciTech Connect

    Halpern, M.B.; Kiritsis, E.; Obers, N.A.; Poratti, M. ); Yamron, J.P. )

    1990-06-20

    This paper reports on a quasi-systematic investigation of the Virasoro master equation. The space of all affine-Virasoro constructions is organized by K-conjugation into affine-Virasoro nests, and an estimate of the dimension of the space shows that most solutions await discovery. With consistent ansatze for the master equation, large classes of new unitary nests are constructed, including quadratic deformation nests with continuous conformal weights, and unitary irrational central charge nests, which may dominate unitary rational central charge on compact g.

  17. Structure and electron affinity of platinum fluorides.

    PubMed

    Wesendrup, R; Schwerdtfeger, P

    2001-07-01

    The structure, stability, and electron affinity of the even numbered molecular platinum fluorides PtF(2)(n) (n = 1-4) were studied by scalar relativistic density functional and coupled cluster methods. The di, tetra, and hexafluorides possess triplet ground states, while PtF(8) is a singlet. Formation of the latter from PtF(6) and F(2) is found to be endothermic. Differences between adiabiatic and vertical electron affinities are only significant for PtF(2). PMID:11421679

  18. Negative Electron Affinity Mechanism for Diamond Surfaces

    NASA Technical Reports Server (NTRS)

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

    1998-01-01

    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.

  19. Imaging mass spectrometer with mass tags

    DOEpatents

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

    2013-01-29

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

  20. Imaging mass spectrometer with mass tags

    DOEpatents

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

    2010-06-01

    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.

  1. Novel and efficient tag SNPs selection algorithms.

    PubMed

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

    2014-01-01

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

  2. Muon B Flavor Tagging A Likelihood Approach

    E-print Network

    Fermilab

    Muon B Flavor Tagging A Likelihood Approach Text for the blessed web page { CDF note 7043 The CDF Collaboration July 29, 2004 Abstract We describe a muon identi#12;cation algorithm to be used for opposite side in a likelihood function which estimates the probability that a muon object is a real muon. The tagger performance

  3. Beliefs and Uses of Tagging among Undergraduates

    ERIC Educational Resources Information Center

    Kramer-Duffield, Jacob

    2010-01-01

    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. …

  4. Efficient Object Identification with Passive RFID Tags

    E-print Network

    application is the "RFID Chef"2 , a kitchen assistant that recognizes food items, e.g. in a shopping bagEfficient Object Identification with Passive RFID Tags Harald Vogt Department of Computer Science identification (RFID) promises to be an unobtrusive, practical, cheap, yet flexible technology for identification

  5. GHRSST-14 DAS-TAG Report

    NASA Technical Reports Server (NTRS)

    Armstrong, Edward; Piolle, Jean Francois

    2013-01-01

    The DAS-TAG provides the informatics and data management expertise in emerging information technologies for the GHRSST community. It provides expertise in data and metadata formats and standards, fosters improvements for GHRSST data curation, experiments with new data processing paradigms, and evaluates services and tools for data usage. It provides a forum for producer and distributor data management issues and coordination.

  6. Semantic Enhancement of Social Tagging Systems

    NASA Astrophysics Data System (ADS)

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

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

  7. Krypton tagging velocimetry of an underexpanded jet.

    PubMed

    Parziale, N J; Smith, M S; Marineau, E C

    2015-06-01

    In this work, we present the excitation/emission strategy, experimental setup, and results of an implementation of krypton tagging velocimetry (KTV). KTV is performed as follows: (i) seed a base flow with krypton; (ii) photosynthesize metastable krypton atoms with a frequency-doubled dye laser to form the tagged tracer; (iii) record the translation of the tagged metastable krypton by imaging the laser-induced fluorescence (LIF) that is produced with an additional dye laser. The principle strength of KTV, relative to other tagging velocimetry techniques, is the use of a chemically inert tracer. KTV results are presented for an underexpanded jet of three mixtures of varying Kr/N2 concentration. It is demonstrated that KTV can be used in gas mixtures of relatively low krypton mole fraction (0.5% Kr/99.5% N2), and the KTV data from that experiment are found to be in good agreement with an empirical fit found in the literature. We find that KTV is useful to perform instantaneous velocity measurements with metastable krypton as a chemically inert, dilute, long-lifetime tracer in gas-phase flows. PMID:26192670

  8. 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

  9. 50 CFR 635.33 - Archival tags.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ...possess, retain, and land an Atlantic HMS in which an archival... Persons that retain an Atlantic HMS that has an archival...available for inspection and recovery of the tag by a NMFS scientist...Quota monitoring. If an Atlantic HMS landed under the...

  10. 50 CFR 635.33 - Archival tags.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ...possess, retain, and land an Atlantic HMS in which an archival... Persons that retain an Atlantic HMS that has an archival...available for inspection and recovery of the tag by a NMFS scientist...Quota monitoring. If an Atlantic HMS landed under the...

  11. Satellite Tagging and Cardiac Physiology Reveal Niche

    E-print Network

    Block, Barbara A.

    Satellite Tagging and Cardiac Physiology Reveal Niche Expansion in Salmon Sharks Kevin C. Weng,1 to track salmon sharks (Lamna ditropis) for up to 3.2 years. Here we show that salmon sharks have-contraction coupling proteins is en- hanced in salmon shark hearts, which may underlie the shark's ability to maintain

  12. Multiple Object Identification with Passive RFID Tags Harald Vogt

    E-print Network

    Multiple Object Identification with Passive RFID Tags Harald Vogt Department of Computer Science investigate the applicability of pas- sive RFID systems to the task of identifying multi- ple tagged objects on the performance of an implementation are presented. Keywords-- RFID, collision-resolution, tagging, combinatorics

  13. 29 CFR 1926.417 - Lockout and tagging of circuits.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 29 Labor 8 2010-07-01 2010-07-01 false Lockout and tagging of circuits. 1926.417 Section 1926.417... Practices § 1926.417 Lockout and tagging of circuits. (a) Controls. Controls that are to be deactivated during the course of work on energized or deenergized equipment or circuits shall be tagged....

  14. 29 CFR 1926.417 - Lockout and tagging of circuits.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 29 Labor 8 2014-07-01 2014-07-01 false Lockout and tagging of circuits. 1926.417 Section 1926.417... Practices § 1926.417 Lockout and tagging of circuits. (a) Controls. Controls that are to be deactivated during the course of work on energized or deenergized equipment or circuits shall be tagged....

  15. 29 CFR 1926.417 - Lockout and tagging of circuits.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 29 Labor 8 2012-07-01 2012-07-01 false Lockout and tagging of circuits. 1926.417 Section 1926.417... Practices § 1926.417 Lockout and tagging of circuits. (a) Controls. Controls that are to be deactivated during the course of work on energized or deenergized equipment or circuits shall be tagged....

  16. 29 CFR 1926.417 - Lockout and tagging of circuits.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 29 Labor 8 2011-07-01 2011-07-01 false Lockout and tagging of circuits. 1926.417 Section 1926.417... Practices § 1926.417 Lockout and tagging of circuits. (a) Controls. Controls that are to be deactivated during the course of work on energized or deenergized equipment or circuits shall be tagged....

  17. 29 CFR 1926.417 - Lockout and tagging of circuits.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 29 Labor 8 2013-07-01 2013-07-01 false Lockout and tagging of circuits. 1926.417 Section 1926.417... Practices § 1926.417 Lockout and tagging of circuits. (a) Controls. Controls that are to be deactivated during the course of work on energized or deenergized equipment or circuits shall be tagged....

  18. Doctoral Thesis A Study on Cryptographic Protocols for RFID Tags

    E-print Network

    Kim, Kwangjo

    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

  19. Fast Tag Searching Protocol for Large-Scale RFID Systems

    E-print Network

    Liu, Wenyin

    Fast Tag Searching Protocol for Large-Scale RFID Systems Yuanqing Zheng, Mo Li School of Computer--Fast searching a particular subset in a large number of products attached with RFID tags is of practical be highly inefficient. To address the tag searching efficiency in large-scale RFID systems, this paper

  20. An Improved Proof for RFID Tags Thiti Nuamcherm1

    E-print Network

    Kovintavewat, Piya

    all the tags. I. INTRODUCTION Radio Frequency Identification (RFID) is a technology for automated identification. An RFID system typically consists of servers, RFID readers, and RFID tags, where the readersAn Improved Proof for RFID Tags Thiti Nuamcherm1 , Piya Kovintavewat2 , Charturong Tantibundhit3

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

    ERIC Educational Resources Information Center

    Papper, Marc; Kempter, Richard; Leibold, Christian

    2011-01-01

    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…

  2. Probabilistic Network Formation through Coverage and Freeze-Tag

    E-print Network

    Isler, Ibrahim Volkan

    Probabilistic Network Formation through Coverage and Freeze-Tag Eric Meisner1 , Wei Yang1 formation problem and other fundamental problems such as rendezvous, coverage and freeze-tag. 1.1 Related is closely related to the Freeze-Tag problem [4]. In fr

  3. Tag Shedding by Southern Bluefin Tuna Thunnus maccoyii

    E-print Network

    Tag Shedding by Southern Bluefin Tuna Thunnus maccoyii John Hampton Geoffrey P. Kirkwood CSIRO.-Models are formu- lated for estimating tag-shedding rates from recapture records for eight dou- ble incorporate either a constant or time-varying rate of tag shedding and allow for the possibil- ity

  4. Linear Reduction Method for Predictive and Informative Tag SNP Selection

    E-print Network

    Zelikovsky, Alexander

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

  5. Disambiguating Main POS tags for Turkish Razieh Ehsani

    E-print Network

    [ Disambiguating Main POS tags for Turkish Razieh Ehsani Istanbul Technical University Faculty adali@itu.edu.tr ] Abstract This paper presents the results of main part-of-speech tagging of Turkish for part-of-speech (POS) tagging, Turkish poses interesting challenges to be modeled with them

  6. Meme Tags and Community Mirrors: Moving from Conferences to Collaboration

    E-print Network

    Meme Tags and Community Mirrors: Moving from Conferences to Collaboration Richard Borovoy, Fred}@media.mit.edu ABSTRACT Meme Tags are part of a body of research on Group- Wear: a wearable technology that supports people in the formative stages of cooperative work. Conference participants wear Meme Tags that allow

  7. 2012 UEC Tokyo. Visual Analysis of Tag Co-occurrence

    E-print Network

    Yanai, Keiji

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

  8. Streamlining the Pipeline for Generation of Recombinant Affinity Reagents by Integrating the Affinity Maturation Step

    PubMed Central

    Huang, Renhua; Gorman, Kevin T.; Vinci, Chris R.; Dobrovetsky, Elena; Gräslund, Susanne; Kay, Brian K.

    2015-01-01

    Often when generating recombinant affinity reagents to a target, one singles out an individual binder, constructs a secondary library of variants, and affinity selects a tighter or more specific binder. To enhance the throughput of this general approach, we have developed a more integrated strategy where the “affinity maturation” step is part of the phage-display pipeline, rather than a follow-on process. In our new schema, we perform two rounds of affinity selection, followed by error-prone PCR on the pools of recovered clones, generation of secondary libraries, and three additional rounds of affinity selection, under conditions of off-rate competition. We demonstrate the utility of this approach by generating low nanomolar fibronectin type III (FN3) monobodies to five human proteins: ubiquitin-conjugating enzyme E2 R1 (CDC34), COP9 signalosome complex subunit 5 (COPS5), mitogen-activated protein kinase kinase 5 (MAP2K5), Splicing factor 3A subunit 1 (SF3A1) and ubiquitin carboxyl-terminal hydrolase 11 (USP11). The affinities of the resulting monobodies are typically in the single-digit nanomolar range. We demonstrate the utility of two binders by pulling down the targets from a spiked lysate of HeLa cells. This integrated approach should be applicable to directed evolution of any phage-displayed affinity reagent scaffold. PMID:26437402

  9. Streamlining the Pipeline for Generation of Recombinant Affinity Reagents by Integrating the Affinity Maturation Step.

    PubMed

    Huang, Renhua; Gorman, Kevin T; Vinci, Chris R; Dobrovetsky, Elena; Gräslund, Susanne; Kay, Brian K

    2015-01-01

    Often when generating recombinant affinity reagents to a target, one singles out an individual binder, constructs a secondary library of variants, and affinity selects a tighter or more specific binder. To enhance the throughput of this general approach, we have developed a more integrated strategy where the "affinity maturation" step is part of the phage-display pipeline, rather than a follow-on process. In our new schema, we perform two rounds of affinity selection, followed by error-prone PCR on the pools of recovered clones, generation of secondary libraries, and three additional rounds of affinity selection, under conditions of off-rate competition. We demonstrate the utility of this approach by generating low nanomolar fibronectin type III (FN3) monobodies to five human proteins: ubiquitin-conjugating enzyme E2 R1 (CDC34), COP9 signalosome complex subunit 5 (COPS5), mitogen-activated protein kinase kinase 5 (MAP2K5), Splicing factor 3A subunit 1 (SF3A1) and ubiquitin carboxyl-terminal hydrolase 11 (USP11). The affinities of the resulting monobodies are typically in the single-digit nanomolar range. We demonstrate the utility of two binders by pulling down the targets from a spiked lysate of HeLa cells. This integrated approach should be applicable to directed evolution of any phage-displayed affinity reagent scaffold. PMID:26437402

  10. Survival, growth, and tag retention in age-0 Chinook Salmon implanted with 8-, 9-, and 12-mm PIT tags

    USGS Publications Warehouse

    Tiffan, Kenneth F.; Perry, Russell W.; Connor, William P.; Mullins, Frank L; Rabe, Craig; Nelson, Doug D

    2015-01-01

    The ability to represent a population of migratory juvenile fish with PIT tags becomes difficult when the minimum tagging size is larger than the average size at which fish begin to move downstream. Tags that are smaller (e.g., 8 and 9 mm) than the commonly used 12-mm PIT tags are currently available, but their effects on survival, growth, and tag retention in small salmonid juveniles have received little study. We evaluated growth, survival, and tag retention in age-0 Chinook Salmon Oncorhynchus tshawytscha of three size-groups: 40–49-mm fish were implanted with 8- and 9-mm tags, and 50– 59-mm and 60–69-mm fish were implanted with 8-, 9-, and 12-mm tags. Survival 28 d after tagging ranged from 97.8% to 100% across all trials, providing no strong evidence for a fish-size-related tagging effect or a tag size effect. No biologically significant effects of tagging on growth in FL (mm/d) or weight (g/d) were observed. Although FL growth in tagged fish was significantly reduced for the 40–49-mm and 50–59-mm groups over the first 7 d, growth rates were not different thereafter, and all fish were similar in size by the end of the trials (day 28). Tag retention across all tests ranged from 93% to 99%. We acknowledge that actual implantation of 8- or 9-mm tags into small fish in the field will pose additional challenges (e.g., capture and handling stress) beyond those observed in our laboratory. However, we conclude that experimental use of the smaller tags for small fish in the field is supported by our findings.

  11. Modern affinity reagents: Recombinant antibodies and aptamers.

    PubMed

    Groff, Katherine; Brown, Jeffrey; Clippinger, Amy J

    2015-12-01

    Affinity reagents are essential tools in both basic and applied research; however, there is a growing concern about the reproducibility of animal-derived monoclonal antibodies. The need for higher quality affinity reagents has prompted the development of methods that provide scientific, economic, and time-saving advantages and do not require the use of animals. This review describes two types of affinity reagents, recombinant antibodies and aptamers, which are non-animal technologies that can replace the use of animal-derived monoclonal antibodies. Recombinant antibodies are protein-based reagents, while aptamers are nucleic-acid-based. In light of the scientific advantages of these technologies, this review also discusses ways to gain momentum in the use of modern affinity reagents, including an update to the 1999 National Academy of Sciences monoclonal antibody production report and federal incentives for recombinant antibody and aptamer efforts. In the long-term, these efforts have the potential to improve the overall quality and decrease the cost of scientific research. PMID:26482034

  12. Affinity Chromatography Media CellufineTM Sulfate

    E-print Network

    Lebendiker, Mario

    been found to bind to the gel, including Influenza, Hepatitis B, Enchephalitis (Japanese), Herpes Sulfur: >700µg/g dry Protein Binding Capacity Lysozyme: >3mg/ml Hepatitis B Surface Antigen: 7mg and Depyrogenation of Virus, Viral/Microbial Antigens, Heparin Binding Proteins D A T A S H E E T FEATURES · Affinity

  13. On affine extension of splint root systems

    NASA Astrophysics Data System (ADS)

    Lyakhovsky, V. D.; Nazarov, A. A.

    2012-09-01

    Splint of root system of simple Lie algebra appears naturally in the study of (regular) embeddings of reductive subalgebras. It can be used to derive branching rules. Application of splint properties drastically simplifies calculations of branching coefficients. We study affine extension of splint root system of simple Lie algebra and obtain relations on theta and branching functions.

  14. Fan Affinity Laws from a Collision Model

    ERIC Educational Resources Information Center

    Bhattacharjee, Shayak

    2012-01-01

    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…

  15. SET AND AFFINE CAPS ELLEN MCCULLAGH

    E-print Network

    May, J. Peter

    SET AND AFFINE CAPS ELLEN MCCULLAGH Abstract. This paper begins by discussing the game SET. Contents 1. Introduction Marsha Falco created the game SET while doing genetics research on epilepsy with the two squiggles. Here straight lines do not necessarily determine SETs. Well this brings up the second

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

    ERIC Educational Resources Information Center

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

    2010-01-01

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

  17. Lightweight Distance bound Protocol for Low Cost RFID Tags

    E-print Network

    Ahmed, Eslam Gamal; Hashem, Mohamed

    2010-01-01

    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.

  18. Vulnerability Analysis of PAP for RFID Tags

    E-print Network

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

    2010-01-01

    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.

  19. Localization and tracking of passive RFID tags

    NASA Astrophysics Data System (ADS)

    Zhang, Yimin; Amin, Moeness G.

    2006-05-01

    Radio frequency identification (RFID) is poised for growth as businesses and governments explore applications implementing RFID. The RFID technology will continue to evolve to meet new demands for human and target location and tracking. In particular, there are increasing needs to find and track the positions of multiple RFID tagged items that are closely spaced. As a result, localization and tracking techniques with higher accuracy, yet low implementation complexity are required. This paper examines the applicability of direction-of-arrival (DOA) estimation methods to the localization and tracking problems of passive RFID tags. Different scenarios of stationary and moving targets are considered. It is shown through performance analysis and simulations that simple DOA estimation methods can be used to provide satisfactory localization performance.

  20. His-tagged norovirus-like particles: A versatile platform for cellular delivery and surface display.

    PubMed

    Koho, Tiia; Ihalainen, Teemu O; Stark, Marie; Uusi-Kerttula, Hanni; Wieneke, Ralph; Rahikainen, Rolle; Blazevic, Vesna; Marjomäki, Varpu; Tampé, Robert; Kulomaa, Markku S; Hytönen, Vesa P

    2015-10-01

    In addition to vaccines, noninfectious virus-like particles (VLPs) that mimic the viral capsid show an attractive possibility of presenting immunogenic epitopes or targeting molecules on their surface. Here, functionalization of norovirus-derived VLPs by simple non-covalent conjugation of various molecules is shown. By using the affinity between a surface-exposed polyhistidine-tag and multivalent tris-nitrilotriacetic acid (trisNTA), fluorescent dye molecules and streptavidin-biotin conjugated to trisNTA are displayed on the VLPs to demonstrate the use of these VLPs as easily modifiable nanocarriers as well as a versatile vaccine platform. The VLPs are able to enter and deliver surface-displayed fluorescent dye into HEK293T cells via a surface-attached cell internalization peptide (VSV-G). The ease of manufacturing, the robust structure of these VLPs, and the straightforward conjugation provide a technology, which can be adapted to various applications in biomedicine. PMID:26170162

  1. Scanning Cargo Containers with Tagged Neutrons

    SciTech Connect

    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.

    2007-10-26

    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.

  2. Scanning Cargo Containers with Tagged Neutrons

    NASA Astrophysics Data System (ADS)

    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

    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.

  3. A fractal circular polarized RFID tag antenna

    NASA Astrophysics Data System (ADS)

    Chaouki, Guesmi; Ferchichi, Abdelhak; Gharsallah, Ali

    2013-09-01

    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.

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

    USGS Publications Warehouse

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

    1999-01-01

    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.

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

    USGS Publications Warehouse

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

    1999-01-01

    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.

  6. An approach to sequence DNA without tagging

    NASA Astrophysics Data System (ADS)

    Niu, Sanjun; Saraf, Ravi F.

    2002-10-01

    Microarray technology is playing an increasingly important role in biology and medicine and its application to genomics for gene expression analysis has already reached the market with a variety of commercially available instruments. In these combinatorial analysis methods, known probe single-strand DNA (ssDNA) 'primers' are attached in clusters of typically 100 µm × 100 µm pixels. Each pixel of the array has a slightly different sequence. On exposure to 'unknown' target ssDNA, the pixels with the right complementary probe ssDNA sequence convert to double-stranded DNA (dsDNA) by a hybridization reaction. To transduct the conversion of the pixel to dsDNA, the target ssDNA is labelled with a photoluminescent tag during the polymerase chain reaction (PCR) amplification process. Due to the statistical distribution of the tags in the target ssDNA, it becomes significantly difficult to implement these methods as a diagnostic tool in a pathology laboratory. A method to sequence DNA without tagging the molecule is developed. The fabrication process is compatible with current microelectronics and (emerging) soft-material fabrication technologies, allowing the method to be integrable with micro-electromechanical systems (MEMS) and lab-on-a-chip devices. An estimated sensitivity of 10-12 g on a 1 cm2 device area is obtained.

  7. university-logo Complete affine 3-manifolds and hyperbolic

    E-print Network

    Goldman, William

    university-logo Complete affine 3-manifolds and hyperbolic surfaces Dedicated to Bill Thurston and hyperbolic surfaces #12;university-logo Three-dimensional affine space forms When can a group G act;university-logo Three-dimensional affine space forms When can a group G act on Euclidean space with quotient

  8. Representations of toroidal extended affine Lie algebras. Yuly Billig *

    E-print Network

    Billig,Yuly

    of an extended affine Lie algebra is that it is graded by a finite root system and possesses a nonRepresentations of toroidal extended affine Lie algebras. Yuly Billig * School of Mathematics@math.carleton.ca Abstract. We show that the representation theory for the toroidal extended affine Lie algebra is controlled

  9. Affinely infinitely divisible distributions and the embedding problem

    E-print Network

    Dani, S.G.

    Affinely infinitely divisible distributions and the embedding problem S.G. Dani and Klaus Schmidt (the identity trans- formation) and () 2() · · · k-1() = µ, and µ is affinely infinitely divisible if it has affine k-th roots for all orders. Clearly every infinitely di- visible probability measure

  10. Affine Hybrid Systems Aaron D. Ames and Shankar Sastry

    E-print Network

    Sastry, S. Shankar

    to a hybrid sys- tem Hid in which all the transition maps are the identity. An explicit and computable construction for Hid is given. 1 Introduction This paper introduces affine hybrid systems. Affine hybrid system Hid such that all of the transition maps are the identity. We also would like this affine hybrid

  11. Aalborg Universitet Algorithm-Architecture Affinity -Parallelism Changes the Picture

    E-print Network

    Berning, Torsten

    Aalborg Universitet Algorithm-Architecture Affinity - Parallelism Changes the Picture Abildgren, P., & Le Moullec, Y. (2007). Algorithm-Architecture Affinity - Parallelism Changes the Picture from vbn.aau.dk on: juli 06, 2015 #12;Algorithm-Architecture Affinity ­ Parallelism Changes the Picture

  12. Smooth big bounce from affine quantization

    NASA Astrophysics Data System (ADS)

    Bergeron, Hervé; Dapor, Andrea; Gazeau, Jean Pierre; Ma?kiewicz, Przemys?aw

    2014-04-01

    We examine the possibility of dealing with gravitational singularities on a quantum level through the use of coherent state or wavelet quantization instead of canonical quantization. We consider the Robertson-Walker metric coupled to a perfect fluid. It is the simplest model of a gravitational collapse, and the results obtained here may serve as a useful starting point for more complex investigations in the future. We follow a quantization procedure based on affine coherent states or wavelets built from the unitary irreducible representation of the affine group of the real line with positive dilation. The main issue of our approach is the appearance of a quantum centrifugal potential allowing for regularization of the singularity, essential self-adjointness of the Hamiltonian, and unambiguous quantum dynamical evolution.

  13. Smooth Big Bounce from Affine Quantization

    E-print Network

    Herve Bergeron; Andrea Dapor; Jean Pierre Gazeau; Przemyslaw Malkiewicz

    2014-01-28

    We examine the possibility of dealing with gravitational singularities on a quantum level through the use of coherent state or wavelet quantization instead of canonical quantization. We consider the Robertson-Walker metric coupled to a perfect fluid. It is the simplest model of a gravitational collapse and the results obtained here may serve as a useful starting point for more complex investigations in future. We follow a quantization procedure based on affine coherent states or wavelets built from the unitary irreducible representation of the affine group of the real line with positive dilation. The main issue of our approach is the appearance of a quantum centrifugal potential allowing for regularization of the singularity, essential self-adjointness of the Hamiltonian, and unambiguous quantum dynamical evolution.

  14. Artificial Affinity Proteins as Ligands of Immunoglobulins

    PubMed Central

    Mouratou, Barbara; Béhar, Ghislaine; Pecorari, Frédéric

    2015-01-01

    A number of natural proteins are known to have affinity and specificity for immunoglobulins. Some of them are widely used as reagents for detection or capture applications, such as Protein G and Protein A. However, these natural proteins have a defined spectrum of recognition that may not fit specific needs. With the development of combinatorial protein engineering and selection techniques, it has become possible to design artificial affinity proteins with the desired properties. These proteins, termed alternative scaffold proteins, are most often chosen for their stability, ease of engineering and cost-efficient recombinant production in bacteria. In this review, we focus on alternative scaffold proteins for which immunoglobulin binders have been identified and characterized. PMID:25647098

  15. Affinity Chromatography in Nonionic Detergent Solutions

    NASA Astrophysics Data System (ADS)

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

    1980-10-01

    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.

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

    PubMed

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

    2015-02-01

    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

  17. Negative affinity X-ray photocathodes

    NASA Technical Reports Server (NTRS)

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

    1974-01-01

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

  18. Recombinant Passenger Proteins Can Be Conveniently Purified by One-Step Affinity Chromatography

    PubMed Central

    Wang, Hua-zhen; Chu, Zhi-zhan; Chen, Chang-chao; Cao, Ao-cheng; Tong, Xin; Ouyang, Can-bin; Yuan, Qi-hang; Wang, Mi-nan; Wu, Zhong-kun; Wang, Hai-hong; Wang, Sheng-bin

    2015-01-01

    Fusion tag is one of the best available tools to date for enhancement of the solubility or improvement of the expression level of recombinant proteins in Escherichia coli. Typically, two consecutive affinity purification steps are often necessitated for the purification of passenger proteins. As a fusion tag, acyl carrier protein (ACP) could greatly increase the soluble expression level of Glucokinase (GlcK), ?-Amylase (Amy) and GFP. When fusion protein ACP-G2-GlcK-Histag and ACP-G2-Amy-Histag, in which a protease TEV recognition site was inserted between the fusion tag and passenger protein, were coexpressed with protease TEV respectively in E. coli, the efficient intracellular processing of fusion proteins was achieved. The resulting passenger protein GlcK-Histag and Amy-Histag accumulated predominantly in a soluble form, and could be conveniently purified by one-step Ni-chelating chromatography. However, the fusion protein ACP-GFP-Histag was processed incompletely by the protease TEV coexpressed in vivo, and a large portion of the resulting target protein GFP-Histag aggregated in insoluble form, indicating that the intracellular processing may affect the solubility of cleaved passenger protein. In this context, the soluble fusion protein ACP-GFP-Histag, contained in the supernatant of E. coli cell lysate, was directly subjected to cleavage in vitro by mixing it with the clarified cell lysate of E. coli overexpressing protease TEV. Consequently, the resulting target protein GFP-Histag could accumulate predominantly in a soluble form, and be purified conveniently by one-step Ni-chelating chromatography. The approaches presented here greatly simplify the purification process of passenger proteins, and eliminate the use of large amounts of pure site-specific proteases. PMID:26641240

  19. Integrated Management and Visualization of Electronic Tag Data with Tagbase

    PubMed Central

    Lam, Chi Hin; Tsontos, Vardis M.

    2011-01-01

    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

  20. Development of techniques for tagging precursor and essential chemicals

    SciTech Connect

    Swansiger, W.A.; Shepodd, T.J.; Phillips, M.L.F.

    1994-01-01

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

  1. Learning to rank image tags with limited training examples.

    PubMed

    Songhe Feng; Zheyun Feng; Rong Jin

    2015-04-01

    With an increasing number of images that are available in social media, image annotation has emerged as an important research topic due to its application in image matching and retrieval. Most studies cast image annotation into a multilabel classification problem. The main shortcoming of this approach is that it requires a large number of training images with clean and complete annotations in order to learn a reliable model for tag prediction. We address this limitation by developing a novel approach that combines the strength of tag ranking with the power of matrix recovery. Instead of having to make a binary decision for each tag, our approach ranks tags in the descending order of their relevance to the given image, significantly simplifying the problem. In addition, the proposed method aggregates the prediction models for different tags into a matrix, and casts tag ranking into a matrix recovery problem. It introduces the matrix trace norm to explicitly control the model complexity, so that a reliable prediction model can be learned for tag ranking even when the tag space is large and the number of training images is limited. Experiments on multiple well-known image data sets demonstrate the effectiveness of the proposed framework for tag ranking compared with the state-of-the-art approaches for image annotation and tag ranking. PMID:25622318

  2. Calculation of protein-ligand binding affinities.

    PubMed

    Gilson, Michael K; Zhou, Huan-Xiang

    2007-01-01

    Accurate methods of computing the affinity of a small molecule with a protein are needed to speed the discovery of new medications and biological probes. This paper reviews physics-based models of binding, beginning with a summary of the changes in potential energy, solvation energy, and configurational entropy that influence affinity, and a theoretical overview to frame the discussion of specific computational approaches. Important advances are reported in modeling protein-ligand energetics, such as the incorporation of electronic polarization and the use of quantum mechanical methods. Recent calculations suggest that changes in configurational entropy strongly oppose binding and must be included if accurate affinities are to be obtained. The linear interaction energy (LIE) and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) methods are analyzed, as are free energy pathway methods, which show promise and may be ready for more extensive testing. Ultimately, major improvements in modeling accuracy will likely require advances on multiple fronts, as well as continued validation against experiment. PMID:17201676

  3. Phosphopeptide Enrichment by Immobilized Metal Affinity Chromatography.

    PubMed

    Thingholm, Tine E; Larsen, Martin R

    2016-01-01

    Immobilized metal affinity chromatography (IMAC) has been the method of choice for phosphopeptide enrichment prior to mass spectrometric analysis for many years and it is still used extensively in many laboratories. Using the affinity of negatively charged phosphate groups towards positively charged metal ions such as Fe(3+), Ga(3+), Al(3+), Zr(4+), and Ti(4+) has made it possible to enrich phosphorylated peptides from peptide samples. However, the selectivity of most of the metal ions is limited, when working with highly complex samples, e.g., whole-cell extracts, resulting in contamination from nonspecific binding of non-phosphorylated peptides. This problem is mainly caused by highly acidic peptides that also share high binding affinity towards these metal ions. By lowering the pH of the loading buffer nonspecific binding can be reduced significantly, however with the risk of reducing specific binding capacity. After binding, the enriched phosphopeptides are released from the metal ions using alkaline buffers of pH 10-11, EDTA, or phosphate-containing buffers.Here we describe a protocol for IMAC using Fe(3+) for phosphopeptide enrichment. The principles are illustrated on a semi-complex peptide mixture. PMID:26584922

  4. A New Approach to Tagging Data in the Astronomical Literature

    NASA Astrophysics Data System (ADS)

    Alexov, A.; Good, J. C.

    2007-10-01

    Data Tags are strings used in journals to indicate the origin of the archival data and to enable the reader to recover the data. The NASA/IPAC Infrared Science Archive (IRSA) has recently introduced a new approach to production of data tags and recovery of data from them. Many of the data access services at the IRSA return filtered data sets (such as subsets of source catalogs) and dynamically created products (such as image cutouts); these dynamically created products are not saved permanently at the archive. Rather than tag the data sets from which the query result sets are drawn, the archive tags the query that generates the results. A single tag can, then, encode a complex dynamic data set and simplifies the embedding of tags in manuscripts and journals. By logging user queries and all the parameters for those query as Data Tags, IRSA can re-create the query and rerun the IRSA service using the same search parameters used when the Data Tag was created. At the same time, the logs give a simple count of the actual numbers of queries made to the archive, a powerful metric of archive usage unobtainable from the Apache web server logs. Currently, IRSA creates tags for queries to more than 20 data sets, including the Infrared Astronomical Satellite (IRAS), Cosmic Evolution Survey (COSMOS) and Spitzer Space Telescope Legacy Data Sets. These tags are returned by the spatial query engine, Atlas {http://irsa.ipac.caltech.edu/applications/Atlas/}. IRSA plans to create tags for queries to the rest of its services in late Spring 2007. The archive provides a simple web interface {http://irsa.ipac.caltech.edu/applications/DataTag/} which recovers a data set that corresponds to the input data tag. Archived data sets may evolve in time due to improved calibrations or augmentations to the data set. IRSA's query based approach guarantees that users always receive the best available data sets.

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

    DOEpatents

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

    2006-09-12

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

  6. Integrated development of up- and downstream processes supported by the Cherry-Tag™ for real-time tracking of stability and solubility of proteins.

    PubMed

    Baumann, Pascal; Bluthardt, Nicolai; Renner, Sarah; Burghardt, Hannah; Osberghaus, Anna; Hubbuch, Jürgen

    2015-04-20

    Product analytics is the bottleneck of most processes in bioprocess engineering, as it is rather time-consuming. Real-time and in-line product tracing without sample pre-treatment is only possible for few products. The Cherry-Tag™ (Delphi Genetics, Belgium) which can be fused to any target protein allows for straightforward product analytics by VIS absorption measurements. When the fused protein becomes unstable or insoluble, the chromophore function of the group is lost, which makes this technology an ideal screening tool for solubility and stability in up- and downstream process development. The Cherry-Tag™ technology will be presented for the tagged enzyme glutathione-S-transferase (GST) from Escherichia coli in a combined up- and downstream process development study. High-throughput cultivations were carried out in a 48-well format in a BioLector system (m2p-Labs, Germany). The best cultivation setup of highest product titer was scaled up to a 2.5L shake flask culture, followed by a selective affinity chromatography product capturing step. In upstream applications the tag was capable of identifying conditions where insoluble and non-native inclusion bodies were formed. In downstream applications the red-colored product was found to be bound effectively to a GST affinity column. Thus, it was identified to be a native and active protein, as the binding mechanism relies on catalytic activity of the enzyme. The Cherry-Tag™ was found to be a reliable and quantitative tool for real-time tracking of stable and soluble proteins in up- and downstream processing applications. Denaturation and aggregation of the product can be detected in-line at any stage of the process. Critical stages can be identified and subsequently changed or replaced. PMID:25747171

  7. Engineering, purification and applications of His-tagged recombinant antibody fragments with specificity for the major birch pollen allergen, bet v1.

    PubMed

    Flicker, S; Laffer, S; Steinberger, P; Alhani, B; Zhu, Y; Laukkanen, M L; Keinänen, K; Kraft, D; Valenta, R

    2000-01-01

    Type I allergy, an immunodisorder affecting almost 20% of the population worldwide, is based on the production of IgE antibodies against per se harmless allergens. We report the expression of hexahistidine-tagged antibody fragments (Fabs) with specificity for Bet v1, the major birch pollen allergen, in Escherichia coli. The cDNA coding for the heavy chain fragment of a mouse monoclonal anti-Bet v1 antibody, Bip 1, was engineered by PCR to contain a hexahistidine-encoding 3' end. The modified Bip1 heavy chain cDNA was co-expressed in E. coli XL-1 Blue with the Bip 1 light chain cDNA using the combinatorial plasmid pComb3H. His-tagged recombinant (r) Bip 1 Fabs were isolated by nickel affinity chromatography and rBip 1 Fabs without His-tag were purified via affinity to rBet v1. rBip 1 Fabs with and without His-tag bound specifically to rBet v1 and, like Bet v1 -specific human serum IgE and rabbit-anti rBet v1 antibodies, cross-reacted with Bet v1-related allergens in other plant-species (alder, oak, hazelnut). We demonstrate the usefulness of His-tagged rBip 1 Fabs (1) for the identification of pollen samples containing Bet v 1 by particle blotting, (2) forthe detection of Bet v1-specific IgE antibodies in human serum samples by sandwich ELISA and (3) for the quantification of Bet v1 in solution. Based on these examples we suggest to use rBip 1 Fabs for the detection of Bet v1 and Bet v1-related allergens in natural allergen sources for allergy prevention, as well as for the standardization of natural allergen extracts produced for diagnosis and immunotherapy of birch pollen allergy. PMID:10722049

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

    NASA Astrophysics Data System (ADS)

    Aygar, Gülfem; Kaya, Murat; Özkan, Necati; Kocab?y?k, Semra; Volkan, Mürvet

    2015-12-01

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

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

    NASA Technical Reports Server (NTRS)

    Barton, Richard J.

    2013-01-01

    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

  10. Purification of the proprotein convertase furin by affinity chromatography based on PC-specific inhibitors.

    PubMed

    Kuester, Miriam; Becker, Gero L; Hardes, Kornelia; Lindberg, Iris; Steinmetzer, Torsten; Than, Manuel E

    2011-11-01

    In eucaryotes, many secreted proteins and peptides are proteolytically excised from larger precursor proteins by a specific class of serine proteases, the proprotein/prohormone convertases (PCs). This cleavage is essential for substrate activation, making the PCs very interesting pharmacological targets in cancer and infectious disease research. Correspondingly, their structure, function and inhibition are intensely studied - studies that require the respective target proteins in large amounts and at high purity. Here we describe the development of a novel purification protocol of furin, the best-studied member of the PC family. We combined the heterologous expression of furin from CHO cells with a novel purification scheme employing an affinity step that efficiently extracts only active furin from the conditioned medium by using furin-specific inhibitor moieties as bait. Several potential affinity tags were synthesized and their binding to furin characterized. The best compound, Biotin-(Adoa)(2)-Arg-Pro-Arg-4-Amba coupled to streptavidin-Sepharose beads, was used in a three-step chromatographic protocol and routinely resulted in a high yield of a homogeneous furin preparation with a specific activity of ~60 units/mg protein. This purification and the general strategy can easily be adapted to the efficient purification of other PC family members. PMID:21875402

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

    PubMed Central

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

    2015-01-01

    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

  12. TRAP-rc, Translating Ribosome Affinity Purification from Rare Cell Populations of Drosophila Embryos.

    PubMed

    Bertin, Benjamin; Renaud, Yoan; Aradhya, Rajaguru; Jagla, Krzysztof; Junion, Guillaume

    2015-01-01

    Measuring levels of mRNAs in the process of translation in individual cells provides information on the proteins involved in cellular functions at a given point in time. The protocol dubbed Translating Ribosome Affinity Purification (TRAP) is able to capture this mRNA translation process in a cell-type-specific manner. Based on the affinity purification of polysomes carrying a tagged ribosomal subunit, TRAP can be applied to translatome analyses in individual cells, making it possible to compare cell types during the course of developmental processes or to track disease development progress and the impact of potential therapies at molecular level. Here we report an optimized version of the TRAP protocol, called TRAP-rc (rare cells), dedicated to identifying engaged-in-translation RNAs from rare cell populations. TRAP-rc was validated using the Gal4/UAS targeting system in a restricted population of muscle cells in Drosophila embryos. This novel protocol allows the recovery of cell-type-specific RNA in sufficient quantities for global gene expression analytics such as microarrays or RNA-seq. The robustness of the protocol and the large collections of Gal4 drivers make TRAP-rc a highly versatile approach with potential applications in cell-specific genome-wide studies. PMID:26381166

  13. TRAP-rc, Translating Ribosome Affinity Purification from Rare Cell Populations of Drosophila Embryos

    PubMed Central

    Bertin, Benjamin; Renaud, Yoan; Aradhya, Rajaguru; Jagla, Krzysztof; Junion, Guillaume

    2015-01-01

    Measuring levels of mRNAs in the process of translation in individual cells provides information on the proteins involved in cellular functions at a given point in time. The protocol dubbed Translating Ribosome Affinity Purification (TRAP) is able to capture this mRNA translation process in a cell-type-specific manner. Based on the affinity purification of polysomes carrying a tagged ribosomal subunit, TRAP can be applied to translatome analyses in individual cells, making it possible to compare cell types during the course of developmental processes or to track disease development progress and the impact of potential therapies at molecular level. Here we report an optimized version of the TRAP protocol, called TRAP-rc (rare cells), dedicated to identifying engaged-in-translation RNAs from rare cell populations. TRAP-rc was validated using the Gal4/UAS targeting system in a restricted population of muscle cells in Drosophila embryos. This novel protocol allows the recovery of cell-type-specific RNA in sufficient quantities for global gene expression analytics such as microarrays or RNA-seq. The robustness of the protocol and the large collections of Gal4 drivers make TRAP-rc a highly versatile approach with potential applications in cell-specific genome-wide studies. PMID:26381166

  14. Rapid large-scale purification of myofilament proteins using a cleavable His6-tag.

    PubMed

    Zhang, Mengjie; Martin, Jody L; Kumar, Mohit; Khairallah, Ramzi J; de Tombe, Pieter P

    2015-11-01

    With the advent of high-throughput DNA sequencing, the number of identified cardiomyopathy-causing mutations has increased tremendously. As the majority of these mutations affect myofilament proteins, there is a need to understand their functional consequence on contraction. Permeabilized myofilament preparations coupled with protein exchange protocols are a common method for examining into contractile mechanics. However, producing large quantities of myofilament proteins can be time consuming and requires different approaches for each protein of interest. In the present study, we describe a unified automated method to produce troponin C, troponin T, and troponin I as well as myosin light chain 2 fused to a His6-tag followed by a tobacco etch virus (TEV) protease site. TEV protease has the advantage of a relaxed P1' cleavage site specificity, allowing for no residues left after proteolysis and preservation of the native sequence of the protein of interest. After expression in Esherichia coli, cells were lysed by sonication in imidazole-containing buffer. The His6-tagged protein was then purified using a HisTrap nickel metal affinity column, and the His6-tag was removed by His6-TEV protease digestion for 4 h at 30°C. The protease was then removed using a HisTrap column, and complex assembly was performed via column-assisted sequential desalting. This mostly automated method allows for the purification of protein in 1 day and can be adapted to most soluble proteins. It has the advantage of greatly increasing yield while reducing the time and cost of purification. Therefore, production and purification of mutant proteins can be accelerated and functional data collected in a faster, less expensive manner. PMID:26386113

  15. Surface Plasmon Resonance Analysis of Histidine-Tagged F1-ATPase Surface Adsorption

    NASA Astrophysics Data System (ADS)

    Tucker, Jenifer K.; Richter, Mark L.; Berrie, Cindy L.

    2015-11-01

    Studies of the rotational activity of the enzymatic core (?3?3?) of the F1-ATPase motor protein have relied on binding the enzyme to NTA-coated glass surfaces via polyhistidine tags engineered into the C-termini of each of the three ? or ? subunits. Those studies revealed the rotational motion of the central ? subunit by monitoring the motion of attached micron-long actin filaments or spherical nanoparticles. However, only a small percentage of the attached filaments or particles were observed to rotate, likely due, at least in part, to non-uniform surface attachment of the motor proteins. In this study, we have applied surface plasmon resonance to monitor the kinetics and affinity of binding of the His-tagged motor protein to NTA-coated gold sensor surfaces. The binding data, when fit to a heterogeneous binding model, exhibit two sets of adsorption-desorption rate constants with two dissociation constants of 4.0 × 10-9 M and 8.6 × 10-11 M for 6His-?3?3? binding to the nickel ion-activated NTA surface. The data are consistent with mixed attachment of the protein via two (bimodal) and three (trimodal) NTA/Ni2+-His-tag interactions, respectively, with the less stable bimodal interaction dominating. The results provide a partial explanation for the low number of surface-attached F1 motors previously observed in rotation studies and suggest alternative approaches to uniform F1 motor surface attachment for future fabrication of motor-based nanobiodevices and materials.

  16. Measuring an antibody affinity distribution molecule by molecule

    SciTech Connect

    Bradbury, Andrew M; Werner, James H; Temirov, Jamshid

    2008-01-01

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

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

    PubMed Central

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

    2015-01-01

    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

  18. An overview of radio frequency identification (RFID) tags technology

    NASA Astrophysics Data System (ADS)

    Falinski, Wojciech

    2006-10-01

    RFID (Radio Frequency Identification) is the technology of wireless identification of tagged products. It is one of the fastest developing technologies in electronic market and it is predicted to replace soon the barcodes which are in common usage in today's economy. There are several advantages of RFID tags over barcode. The main are reading without must of scanning the product and the possibility to keep much more information on chip of the tag. In the article there are introduced the possible applications of RFID technology. There are also presented the classification of the RFID tags and the difference between working frequency. It is introduced every steps of manufacturing RFID tags with focus on the technology aspects (technologies of producing antenna, attaching the chip and creation of electrical connection between antenna and chip). Tele and Radio Research Institute is now starting to realize the project of manufacturing the RFID tags antenna. There is presented our guideline of the project.

  19. Method for nonlinear optimization for gas tagging and other systems

    DOEpatents

    Chen, T.; Gross, K.C.; Wegerich, S.

    1998-01-06

    A method and system are disclosed 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. 6 figs.

  20. Method for nonlinear optimization for gas tagging and other systems

    DOEpatents

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

    1998-01-01

    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.

  1. MFR PAPER 1070 Anchor tags show ment

    E-print Network

    hlllrdl. Demand of the marl-.lng program reqUired that the tag prOVide identiAcatlon of each crab. have\\l:nt:.-I\\\\P aJu l1 J...lng crah~ (in - LiuJ ing H, t.lggeJ anJ In cI' n trol ~) \\\\erc placcJ In 1\\\\11 (,- n-It 14- Inch J...lng crah pot\\. 1 hc pot. Ihelr tunncl entrance\\ c\\owJ With hanJ \\C\\\\ n n\\ Ion nell In g

  2. Estimating survival of radio-tagged birds

    USGS Publications Warehouse

    Bunck, C.M.; Pollock, K.H.

    1993-01-01

    Parametric and nonparametric methods for estimating survival of radio-tagged birds are described. The general assumptions of these methods are reviewed. An estimate based on the assumption of constant survival throughout the period is emphasized in the overview of parametric methods. Two nonparametric methods, the Kaplan-Meier estimate of the survival funcrion and the log rank test, are explained in detail The link between these nonparametric methods and traditional capture-recapture models is discussed aloag with considerations in designing studies that use telemetry techniques to estimate survival.

  3. Behavioral Tagging: A Translation of the Synaptic Tagging and Capture Hypothesis

    PubMed Central

    Moncada, Diego; Ballarini, Fabricio; Viola, Haydée

    2015-01-01

    Similar molecular machinery is activated in neurons following an electrical stimulus that induces synaptic changes and after learning sessions that trigger memory formation. Then, to achieve perdurability of these processes protein synthesis is required for the reinforcement of the changes induced in the network. The synaptic tagging and capture theory provided a strong framework to explain synaptic specificity and persistence of electrophysiological induced plastic changes. Ten years later, the behavioral tagging hypothesis (BT) made use of the same argument, applying it to learning and memory models. The hypothesis postulates that the formation of lasting memories relies on at least two processes: the setting of a learning tag and the synthesis of plasticity related proteins, which once captured at tagged sites allow memory consolidation. BT explains how weak events, only capable of inducing transient forms of memories, can result in lasting memories when occurring close in time with other behaviorally relevant experiences that provide proteins. In this review, we detail the findings supporting the existence of BT process in rodents, leading to the consolidation, persistence, and interference of a memory. We focus on the molecular machinery taking place in these processes and describe the experimental data supporting the BT in humans. PMID:26380117

  4. Affinity purification of proteins using expanded beds.

    PubMed

    Chase, H A; Draeger, N M

    1992-04-24

    The use of expanded beds of affinity adsorbents for the purification of proteins from feedstocks containing whole or broken cells is described. It is demonstrated that such feedstocks can be applied to the bed without prior removal of particulate material by centrifugation or filtration thus showing considerable potential for this approach in simplifying downstream processing flow-sheets. A stable, expanded bed can be obtained using simple equipment adapted from that used for conventional packed bed adsorption and chromatography processes. Circulation and mixing of the adsorbent particles is minimal and liquid flow through the expanded bed shows characteristics similar to those of plug flow. Frontal analysis performed with the highly selective affinity system involving the adsorption of human polyclonal immunoglobulin G onto Protein A Sepharose Fast Flow indicate that the adsorption performance of the expanded bed is similar to that achieved when the same amount of adsorbent is used in a packed configuration at the same volumetric flow-rate. The adsorption performance of the expanded bed was not diminished when adsorption was carried out in the presence of intact yeast cells. Batch adsorption experiments also indicated that the adsorption characteristics of the affinity system were not greatly altered in the presence of cells in contrast to results from a less selective ion-exchange system. An expanded bed of Cibacron Blue Sepharose Fast Flow was used to purify phosphofructokinase from feedstock of disrupted yeast prepared by high pressure homogenisation without the need for prior removal of particulate material. The potential for the use of expanded beds in large scale purification systems is discussed. PMID:1387651

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

    PubMed Central

    2014-01-01

    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

  6. Tag Retention and Survivorship of Hatchery Rainbow Trout Marked with Large-Format Visible Implant Alphanumeric Tags

    USGS Publications Warehouse

    Isely, J.J.; Trested, D.G.; Grabowski, T.B.

    2004-01-01

    Large-format visible implant alphanumeric (VIalpha) tags were implanted into 15,400 rainbow trout Oncorhynchus mykiss. Tag retention after 25 d was 82.6%, and survivorship was 92.8%. The results of this study compare favorably with those of similar studies on other species and suggest that large-format VIalpha tags are an appropriate choice for studies requiring the individual identification of larger rainbow trout.

  7. Affine Coherent States in Quantum Cosmology

    E-print Network

    Malkiewicz, Przemyslaw

    2015-01-01

    A brief summary of the application of coherent states in the examination of quantum dynamics of cosmological models is given. We discuss quantization maps, phase space probability distributions and semiclassical phase spaces. The implementation of coherent states based on the affine group resolves the hardest singularities, renders self-adjoint Hamiltonians without boundary conditions and provides a completely consistent semi-classical description of the involved quantum dynamics. We consider three examples: the closed Friedmann model, the anisotropic Bianchi Type I model and the deep quantum domain of the Bianchi Type IX model.

  8. Isolation of Endogenously Assembled RNA-Protein Complexes Using Affinity Purification Based on Streptavidin Aptamer S1

    PubMed Central

    Dong, Yangchao; Yang, Jing; Ye, Wei; Wang, Yuan; Ye, Chuantao; Weng, Daihui; Gao, Huan; Zhang, Fanglin; Xu, Zhikai; Lei, Yingfeng

    2015-01-01

    Efficient isolation of endogenously assembled viral RNA-protein complexes is essential for understanding virus replication mechanisms. We have developed an affinity purification strategy based on an RNA affinity tag that allows large-scale preparation of native viral RNA-binding proteins (RBPs). The streptavidin-binding aptamer S1 sequence was inserted into the 3? end of dengue virus (DENV) 5?–3? UTR RNA, and the DENV RNA UTR fused to the S1 RNA aptamer was expressed in living mammalian cells. This allowed endogenous viral ribonucleoprotein (RNP) assembly and isolation of RNPs from whole cell extract, through binding the S1 aptamer to streptavidin magnetic beads. Several novel host DENV RBPs were subsequently identified by liquid chromatography with tandem mass spectrometry (LC-MS/MS), including RPS8, which we further implicate in DENV replication. We proposed efficient S1 aptamer-based isolation of viral assembled RNPs from living mammalian cells will be generally applicable to the purification of high- and low-affinity RBPs and RNPs under endogenous conditions. PMID:26389898

  9. Single-Step Affinity Purification (ssAP) and Mass Spectrometry of Macromolecular Complexes in the Yeast S. cerevisiae.

    PubMed

    Trahan, Christian; Aguilar, Lisbeth-Carolina; Oeffinger, Marlene

    2016-01-01

    Cellular functions are mostly defined by the dynamic interactions of proteins within macromolecular networks. Deciphering the composition of macromolecular complexes and their dynamic rearrangements is the key to getting a comprehensive picture of cellular behavior and to understanding biological systems. In the last decade, affinity purification coupled to mass spectrometry has emerged as a powerful tool to comprehensively study interaction networks and their assemblies. However, the study of these interactomes has been hampered by severe methodological limitations. In particular, the affinity purification of intact complexes from cell lysates suffers from protein and RNA degradation, loss of transient interactors, and poor overall yields. In this chapter, we describe a rapid single-step affinity purification method for the efficient isolation of dynamic macromolecular complexes. The technique employs cell lysis by cryo-milling, which ensures nondegraded starting material in the submicron range, and magnetic beads, which allow for dense antibody-conjugation and thus rapid complex isolation, while avoiding loss of transient interactions. The method is epitope tag-independent, and overcomes many of the previous limitations to produce large interactomes with almost no contamination. The protocol described here has been optimized for the yeast S. cerevisiae. PMID:26483027

  10. Endogenous gene tagging with fluorescent proteins.

    PubMed

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

    2015-01-01

    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

  11. Heparin affinity purification of extracellular vesicles

    PubMed Central

    Balaj, Leonora; Atai, Nadia A.; Chen, Weilin; Mu, Dakai; Tannous, Bakhos A.; Breakefield, Xandra O.; Skog, Johan; Maguire, Casey A.

    2015-01-01

    Extracellular vesicles (EVs) are lipid membrane vesicles released by cells. They carry active biomolecules including DNA, RNA, and protein which can be transferred to recipient cells. Isolation and purification of EVs from culture cell media and biofluids is still a major challenge. The most widely used isolation method is ultracentrifugation (UC) which requires expensive equipment and only partially purifies EVs. Previously we have shown that heparin blocks EV uptake in cells, supporting a direct EV-heparin interaction. Here we show that EVs can be purified from cell culture media and human plasma using ultrafiltration (UF) followed by heparin-affinity beads. UF/heparin-purified EVs from cell culture displayed the EV marker Alix, contained a diverse RNA profile, had lower levels of protein contamination, and were functional at binding to and uptake into cells. RNA yield was similar for EVs isolated by UC. We were able to detect mRNAs in plasma samples with comparable levels to UC samples. In conclusion, we have discovered a simple, scalable, and effective method to purify EVs taking advantage of their heparin affinity. PMID:25988257

  12. Exploring Fluorous Affinity by Liquid Chromatography.

    PubMed

    Catani, Martina; Guzzinati, Roberta; Marchetti, Nicola; Pasti, Luisa; Cavazzini, Alberto

    2015-07-01

    Terms such as "fluorous affinity" and "fluorophilicity" have been used to describe the unique partition and sorption properties often exhibited by highly fluorinated organic compounds, that is molecules rich in sp(3) carbon-fluorine bonds. In this work, we made use of a highly fluorinated stationary phase and a series of benzene derivatives to study the effect of one single perfluorinated carbon on the chromatographic behavior and adsorption properties of molecules. For this purpose, the adsorption equilibria of ?,?,?-trifluorotoluene, toluene, and other alkylbenzenes have been studied by means of nonlinear chromatography in a variety of acetonitrile/water eluents. Our results reveal that one single perfluorinated carbon is already enough to induce a drastic change in the adsorption properties of molecules on the perfluorinated stationary phase. In particular, it has been found that adsorption is monolayer if the perfluoroalkyl carbon is present but that, when this unit is missing, molecules arrange as multilayer stack structures. These findings can contribute to the understanding of molecular mechanisms of fluorous affinity. PMID:26047527

  13. Affine Mirkovi\\'c-Vilonen polytopes

    E-print Network

    Baumann, Pierre; Tingley, Peter

    2011-01-01

    Each integrable lowest weight representation of a symmetrizable Kac-Moody Lie algebra g has a crystal in the sense of Kashiwara, which describes its combinatorial properties. For a given g, there is a limit crystal, usually denoted by B(-\\infty), which contains all the other crystals. When g is finite dimensional, a convex polytope, called the Mirkovi\\'c-Vilonen polytope, can be associated to each element in B(-\\infty). This polytope sits in the dual space of a Cartan subalgebra of g, and its edges are parallel to the roots of g. In this paper, we generalize this construction to the case where g is a symmetric affine Kac-Moody algebra. The datum of the polytope must however be complemented by partitions attached to the edges parallel to the imaginary root \\delta. We prove that these decorated polytopes are characterized by conditions on their normal fans and on their 2-faces. In addition, we discuss how our polytopes provide an analog of the notion of Lusztig datum for affine Kac-Moody algebras. Our main tool...

  14. Cyclage, catabolism, and the affine Hecke algebra

    E-print Network

    Blasiak, Jonah

    2010-01-01

    We identify a subalgebra \\pH_n of the extended affine Hecke algebra \\eH_n of type A. The subalgebra \\pH_n is a \\u-analogue of the monoid algebra of \\S_n \\ltimes \\ZZ_{\\geq 0}^n and inherits a canonical basis from that of \\eH_n. We show that its left cells are naturally labeled by tableaux filled with positive integer entries having distinct residues mod n, which we term \\emph{positive affine tableaux} (PAT). We then exhibit a cellular subquotient \\R_{1^n} of \\pH_n that is a \\u-analogue of the ring of coinvariants \\CC[y_1,...,y_n]/(e_1,...,e_n) with left cells labeled by PAT that are essentially standard Young tableaux with cocharge labels. Multiplying canonical basis elements by a certain element \\pi \\in \\pH_n corresponds to rotations of words, and on cells corresponds to cocyclage. We further show that \\R_{1^n} has cellular quotients \\R_\\lambda that are \\u-analogues of the Garsia-Procesi modules R_\\lambda with left cells labeled by (a PAT version of) the \\lambda-catabolizable tableaux. We give a conjectural d...

  15. Quantification of hydrophobic interaction affinity of colloids

    NASA Astrophysics Data System (ADS)

    Saini, G.; Nasholm, N.; Wood, B. D.

    2009-12-01

    Colloids play an important role in a wide variety of disciplines, including water and wastewater treatment, subsurface transport of metals and organic contaminants, migration of fines in oil reservoirs, biocolloid (virus and bacteria) transport in subsurface, and are integral to laboratory transport studies. Although the role of hydrophobicity in adhesion and transport of colloids, particularly bacteria, is well known; there is scarcity of literature regarding hydrophobicity measurement of non-bacterial colloids and other micron-sized particles. Here we detail an experimental approach based on differential partitioning of colloids between two liquid phases (hydrocarbon and buffer) as a measure of the hydrophobic interaction affinity of colloids. This assay, known as Microbial adhesion to hydrocarbons or MATH, is frequently used in microbiology and bacteriology for quantifying the hydrophobicity of microbes. Monodispersed colloids and particles, with sizes ranging from 1 micron to 33 micron, were used for the experiments. A range of hydrophobicity values were observed for different particles. The hydrophobicity results are also verified against water contact angle measurements of these particles. This liquid-liquid partitioning assay is quick, easy-to-perform and requires minimal instrumentation. Estimation of the hydrophobic interaction affinity of colloids would lead to a better understanding of their adhesion to different surfaces and subsequent transport in porous media.

  16. High-affinity Cyclic Peptide Matriptase Inhibitors*

    PubMed Central

    Quimbar, Pedro; Malik, Uru; Sommerhoff, Christian P.; Kaas, Quentin; Chan, Lai Y.; Huang, Yen-Hua; Grundhuber, Maresa; Dunse, Kerry; Craik, David J.; Anderson, Marilyn A.; Daly, Norelle L.

    2013-01-01

    The type II transmembrane serine protease matriptase is a key activator of multiple signaling pathways associated with cell proliferation and modification of the extracellular matrix. Deregulated matriptase activity correlates with a number of diseases, including cancer and hence highly selective matriptase inhibitors may have therapeutic potential. The plant-derived cyclic peptide, sunflower trypsin inhibitor-1 (SFTI-1), is a promising drug scaffold with potent matriptase inhibitory activity. In the current study we have analyzed the structure-activity relationships of SFTI-1 and Momordica cochinchinensis trypsin inhibitor-II (MCoTI-II), a structurally divergent trypsin inhibitor from Momordica cochinchinensis that also contains a cyclic backbone. We show that MCoTI-II is a significantly more potent matriptase inhibitor than SFTI-1 and that all alanine mutants of both peptides, generated using positional scanning mutagenesis, have decreased trypsin affinity, whereas several mutations either maintain or result in enhanced matriptase inhibitory activity. These intriguing results were used to design one of the most potent matriptase inhibitors known to date with a 290 pm equilibrium dissociation constant, and provide the first indication on how to modulate affinity for matriptase over trypsin in cyclic peptides. This information might be useful for the design of more selective and therapeutically relevant inhibitors of matriptase. PMID:23548907

  17. Neighborhood-based Tag Prediction* Adriana Budura1

    E-print Network

    . We put forward HAMLET, a novel approach to automatically propa- gate tags along the edges of a graph to related documents. We put forward HAMLET (Harvesting Adjacent Metadata in Large-ScalE Tagging Systems), a suite of principles, scoring models and algorithms for metadata prop- agation. HAMLET is based

  18. 48 CFR 908.7101-7 - Government license tags.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false Government license tags. 908.7101-7 Section 908.7101-7 Federal Acquisition Regulations System DEPARTMENT OF ENERGY COMPETITION ACQUISITION PLANNING REQUIRED SOURCES OF SUPPLIES AND SERVICES Acquisition of Special Items 908.7101-7 Government license tags. (a)...

  19. 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...

  20. Efficient Tag Detection in RFID Systems Bogdan Carbunar

    E-print Network

    Carbunar, Bogdan

    readers). RFID tags store information using a small integrated circuit and communicate using an antenna1 Efficient Tag Detection in RFID Systems Bogdan Carbunar , Murali Krishna Ramanathan ¡ , Mehmet:koyuturk@eecs.case.edu #12;2 Abstract Recent technological advances have motivated large-scale deployment of RFID systems

  1. 9 CFR 381.99 - Official retention and rejection tags.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 9 Animals and Animal Products 2 2011-01-01 2011-01-01 false Official retention and rejection tags. 381.99 Section 381.99 Animals and Animal Products FOOD SAFETY AND INSPECTION SERVICE, DEPARTMENT OF... Certificates; Export Certificates; Certification Procedures § 381.99 Official retention and rejection tags....

  2. 9 CFR 381.100 - Official detention tag.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 9 Animals and Animal Products 2 2011-01-01 2011-01-01 false Official detention tag. 381.100 Section 381.100 Animals and Animal Products FOOD SAFETY AND INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE... Certificates; Export Certificates; Certification Procedures § 381.100 Official detention tag. The detention...

  3. Fully printed flexible and disposable wireless cyclic voltammetry tag

    E-print Network

    Javey, Ali

    through a scalable gravure printing method. By proximity of 13.56 MHz RF reader, the printed CV tag wirelessly diagnose the presence of TMPD in the solution using the CV tag in the proximity of the 13.56 MHz and marks the path for the utilization of inexpensive and disposable wireless electrochemical sensor systems

  4. Fully printed flexible and disposable wireless cyclic voltammetry tag.

    PubMed

    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

    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

  5. Acoustic competition in the gulf toadfish Opsanus beta: Acoustic tagging

    NASA Astrophysics Data System (ADS)

    Thorson, Robert F.; Fine, Michael L.

    2002-05-01

    Nesting male gulf toadfish Opsanus beta produce a boatwhistle advertisement call used in male-male competition and to attract females and an agonistic grunt call. The grunt is a short-duration pulsatile call, and the boatwhistle is a complex call typically consisting of zero to three introductory grunts, a long tonal boop note, and zero to three shorter boops. The beginning of the boop note is also gruntlike. Anomalous boatwhistles contain a short-duration grunt embedded in the tonal portion of the boop or between an introductory grunt and the boop. Embedded grunts have sound-pressure levels and frequency spectra that correspond with those of recognized neighbors, suggesting that one fish is grunting during another's call, a phenomenon here termed acoustic tagging. Snaps of nearby pistol shrimp may also be tagged, and chains of tags involving more than two fish occur. The stimulus to tag is a relatively intense sound with a rapid rise time, and tags are generally produced within 100 ms of a trigger stimulus. Time between the trigger and the tag decreases with increased trigger amplitude. Tagging is distinct from increased calling in response to natural calls or stimulatory playbacks since calls rarely overlap other calls or playbacks. Tagging is not generally reciprocal between fish, suggesting parallels to dominance displays.

  6. 9 CFR 2.51 - Form of official tag.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 9 Animals and Animal Products 1 2013-01-01 2013-01-01 false Form of official tag. 2.51 Section 2.51 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE ANIMAL WELFARE REGULATIONS Identification of Animals § 2.51 Form of official tag. (a) The official...

  7. Automatic Image Tagging System Hsiao-Tung, Chen (hc847)

    E-print Network

    Afshari, Ehsan

    of searchable image databases Database · 160,000 images form Flickr · 150,000 for training · 10,000 for testing System Input Output animals zoo Leopard Wildlife cat system Framework How about generating tags the database and then extract relevant tags from them Linear Search K-Means Tree K-D Tree Failure Case Fail

  8. MARC/AACR2/Authority Control Tagging. Blitz Cataloging Workbook.

    ERIC Educational Resources Information Center

    Ferguson, Bobby

    This workbook is designed to help librarians learn the correct way of applying cataloging tools, identifying errors in both original and copy cataloging, and maintaining proper authority control for more complete access. Chapter 1, "MARC Format," includes: introduction; families of tags; families of tags exercises; 008 (header) information,…

  9. Tag Elimination and Jones-Optimality (Includes Proofs)

    E-print Network

    Taha, Walid

    for a specific family of tasks at hand. A popular and viable strategy for imple- menting domain specific language, which is a highly-valued feature of many typed functional programming languages. Tag elimination [15 taha@cs.yale.edu Abstract. Tag elimination is a program transformation for removing

  10. `YOU GOT TAGGED!': The city as a playground

    E-print Network

    Design, HP Labs, Bristol, 11-13 May 2004 `YOU GOT TAGGED!': THE CITY AS A PLAYGROUND YANNA VOGIAZOU 1`YOU GOT TAGGED!': The city as a playground Tech Report kmi-04-3 Yanna Vogiazou, Bas Raijmakers and Josephine Reid Accepted in Proceedings of 2AD: Second International Conference on Appliance Design, HP Labs

  11. A New Continuous Multimodal Musical Controller Using Wireless Magnetic Tags

    E-print Network

    interface based on magnetic tagging technology that can turn essentially any object into a continuousA New Continuous Multimodal Musical Controller Using Wireless Magnetic Tags Kai-Yuh Hsiao controller with both contact and noncontact degrees of freedom. Our system responds to magnetically

  12. Fully printed flexible and disposable wireless cyclic voltammetry tag

    PubMed Central

    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

    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

  13. Data Collection1 Associated with Fish Tagging/Marking Technologies

    E-print Network

    Data Collection1 Associated with Fish Tagging/Marking Technologies Tag/Mark & Release Juvenile fish application: automated Data collection: manual Data upload: manual Collection locations: mainstem, tributary Data collection: visual/manual Data upload: manual Data collection: visual/manual Data upload: manual

  14. Discovering Video Clusters from Visual Features and Noisy Tags

    E-print Network

    Mori, Greg

    develop a struc- tured model that considers the interaction between visual features, video tags and video consistency. In the end, videos are clustered from the refined tags as well as the visual features. We learn, bride, kids, cake kid, birthday Clustering outdoor, couple, wedding cake, party, candle church, groom

  15. On Tag Spell Checking Franco Maria Nardini2

    E-print Network

    the tagged object to be actually retrieved. Correcting "hip hop" as "hip- hop", when the latter is more for the concept "hip-hop"1 . By tagging a resource, a user wants that resource to be easily found. When query- ing

  16. 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...

  17. Improved gas tagging and cover gas combination for nuclear reactor

    DOEpatents

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

    1983-09-26

    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.

  18. Gas tagging and cover gas combination for nuclear reactor

    DOEpatents

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

    1985-01-01

    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.

  19. RFID Authentication Protocol for Low-cost Tags Boyeon Song

    E-print Network

    Mitchell, Chris

    tracking in a supply chain, passports, transport payments, livestock identification, au- tomated vehicle in a broad range of markets, including Point of Sale (POS), warehouse management and logistics, product supplied by them [9]. The reader queries tags by broadcasting an RF signal, and the tag responds

  20. Tagging fast neutrons from an (241)Am/(9)Be source.

    PubMed

    Scherzinger, J; Annand, J R M; Davatz, G; Fissum, K G; Gendotti, U; Hall-Wilton, R; Håkansson, E; Jebali, R; Kanaki, K; Lundin, M; Nilsson, B; Rosborge, A; Svensson, H

    2015-04-01

    Shielding, coincidence, and time-of-flight measurement techniques are employed to tag fast neutrons emitted from an (241)Am/(9)Be source resulting in a continuous polychromatic energy-tagged beam of neutrons with energies up to 7MeV. The measured energy structure of the beam agrees qualitatively with both previous measurements and theoretical calculations. PMID:25644080

  1. Fully printed flexible and disposable wireless cyclic voltammetry tag

    NASA Astrophysics Data System (ADS)

    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

    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.

  2. Exploring Tag-based Like Networks Author Keywords

    E-print Network

    Lee, Dongwon

    Exploring Tag-based Like Networks Author Keywords Instagram; Like network; social network; tags consisting of 51K photos posted by 36K users in Instagram, we present the structural and relational aspects and analysis, we chose Instagram, because Instagram is one of the most popular social network sites

  3. 76 FR 4634 - Proposed Information Collection; Comment Request; Implantation and Recovery of Archival Tags for...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-01-26

    ...Information Collection; Comment Request; Implantation and Recovery of Archival Tags for Highly...Administration (NOAA) allows scientists to implant archival tags in, or affix archival...Scientists outside of NOAA who affix or implant archival tags must obtain prior...

  4. 48 CFR 552.211-92 - Radio Frequency Identification (RFID) using passive tags.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ...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...

  5. Versatile vector suite for the extracytoplasmic production and purification of heterologous His-tagged proteins in Lactococcus lactis.

    PubMed

    Neef, Jolanda; Milder, Fin J; Koedijk, Danny G A M; Klaassens, Marindy; Heezius, Erik C; van Strijp, Jos A G; Otto, Andreas; Becher, Dörte; van Dijl, Jan Maarten; Buist, Girbe

    2015-11-01

    Recent studies have shown that the Gram-positive bacterium Lactococcus lactis can be exploited for the expression of heterologous proteins; however, a versatile set of vectors suitable for inducible extracellular protein production and subsequent purification of the expressed proteins by immobilized metal affinity chromatography was so far lacking. Here we describe three novel vectors that, respectively, facilitate the nisin-inducible production of N- or C-terminally hexa-histidine (His6)-tagged proteins in L. lactis. One of these vectors also encodes a tobacco etch virus (TEV) protease cleavage site allowing removal of the N-terminal His6-tag from expressed proteins. Successful application of the developed vectors for protein expression, purification and/or functional studies is exemplified with six different cell wall-bound or secreted proteins from Staphylococcus aureus. The results show that secretory production of S. aureus proteins is affected by the position, N- or C-terminal, of the His6-tag. This seems to be due to an influence of the His6-tag on protein stability. Intriguingly, the S. aureus IsdB protein, which is phosphorylated in S. aureus, was also found to be phosphorylated when heterologously produced in L. lactis, albeit not on the same Tyr residue. This implies that this particular post-translational protein modification is to some extent conserved in S. aureus and L. lactis. Altogether, we are confident that the present vector set combined with the L. lactis expression host has the potential to become a very useful tool in optimization of the expression, purification and functional analysis of extracytoplasmic bacterial proteins. PMID:26160391

  6. Multiple ant colony algorithm method for selecting tag SNPs.

    PubMed

    Liao, Bo; Li, Xiong; Zhu, Wen; Li, Renfa; Wang, Shulin

    2012-10-01

    The search for the association between complex disease and single nucleotide polymorphisms (SNPs) or haplotypes has recently received great attention. Finding a set of tag SNPs for haplotyping in a great number of samples is an important step to reduce cost for association study. Therefore, it is essential to select tag SNPs with more efficient algorithms. In this paper, we model problem of selection tag SNPs by MINIMUM TEST SET and use multiple ant colony algorithm (MACA) to search a smaller set of tag SNPs for haplotyping. The various experimental results on various datasets show that the running time of our method is less than GTagger and MLR. And MACA can find the most representative SNPs for haplotyping, so that MACA is more stable and the number of tag SNPs is also smaller than other evolutionary methods (like GTagger and NSGA-II). Our software is available upon request to the corresponding author. PMID:22480582

  7. Passive UHF RFID Tag with Multiple Sensing Capabilities

    PubMed Central

    Fernández-Salmerón, José; Rivadeneyra, Almudena; Martínez-Martí, Fernando; Capitán-Vallvey, Luis Fermín; Palma, Alberto J.; Carvajal, Miguel A.

    2015-01-01

    This work presents the design, fabrication, and characterization of a printed radio frequency identification tag in the ultra-high frequency band with multiple sensing capabilities. This passive tag is directly screen printed on a cardboard box with the aim of monitoring the packaging conditions during the different stages of the supply chain. This tag includes a commercial force sensor and a printed opening detector. Hence, the force applied to the package can be measured as well as the opening of the box can be detected. The architecture presented is a passive single-chip RFID tag. An electronic switch has been implemented to be able to measure both sensor magnitudes in the same access without including a microcontroller or battery. Moreover, the chip used here integrates a temperature sensor and, therefore, this tag provides three different parameters in every reading. PMID:26506353

  8. Passive UHF RFID Tag with Multiple Sensing Capabilities.

    PubMed

    Fernández-Salmerón, José; Rivadeneyra, Almudena; Martínez-Martí, Fernando; Capitán-Vallvey, Luis Fermín; Palma, Alberto J; Carvajal, Miguel A

    2015-01-01

    This work presents the design, fabrication, and characterization of a printed radio frequency identification tag in the ultra-high frequency band with multiple sensing capabilities. This passive tag is directly screen printed on a cardboard box with the aim of monitoring the packaging conditions during the different stages of the supply chain. This tag includes a commercial force sensor and a printed opening detector. Hence, the force applied to the package can be measured as well as the opening of the box can be detected. The architecture presented is a passive single-chip RFID tag. An electronic switch has been implemented to be able to measure both sensor magnitudes in the same access without including a microcontroller or battery. Moreover, the chip used here integrates a temperature sensor and, therefore, this tag provides three different parameters in every reading. PMID:26506353

  9. Lightweight Mutual Authentication Protocol for Low Cost RFID Tags

    E-print Network

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

    2010-01-01

    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.

  10. Flavor tagging TeV jets for BSM and QCD

    E-print Network

    Pedersen, Keith

    2015-01-01

    We present a new scheme for tagging high-$p_{T}$ bottom and charm jets using energetic muons. Contemporary track-based $b$ tags lose their ability to reject light jet background as jet $p_{T}\\rightarrow\\mathcal{O}(\\mathrm{TeV})$, where the massive boost exposes fundamental limits in tracking resolution. For our "$\\mu_{x}$" tag, the signal efficiency and light jet rejection is robust versus $p_{T}$. In the tested regime (jet $p_{T}\\in[\\mathrm{0.5,2.1}]$ TeV), $\\mu_{x}$ tags $\\sim14\\%$ of $b$ jets, $\\sim6.5\\%$ of $c$ jets and $\\sim0.65\\%$ of light jets. Since $\\mu_{x}$ tagging should be immediately useful in a searches for heavy resonances, we test it with a typical dijet search --- a heavy, leptophobic $Z^{\\prime}$.

  11. Flavor tagging TeV jets for BSM and QCD

    E-print Network

    Keith Pedersen; Zack Sullivan

    2015-09-24

    We present a new scheme for tagging high-$p_{T}$ bottom and charm jets using energetic muons. Contemporary track-based $b$ tags lose their ability to reject light jet background as jet $p_{T}\\rightarrow\\mathcal{O}(\\mathrm{TeV})$, where the massive boost exposes fundamental limits in tracking resolution. For our "$\\mu_{x}$" tag, the signal efficiency and light jet rejection is robust versus $p_{T}$. In the tested regime (jet $p_{T}\\in[\\mathrm{0.5,2.1}]$ TeV), $\\mu_{x}$ tags $\\sim14\\%$ of $b$ jets, $\\sim6.5\\%$ of $c$ jets and $\\sim0.65\\%$ of light jets. Since $\\mu_{x}$ tagging should be immediately useful in a searches for heavy resonances, we test it with a typical dijet search --- a heavy, leptophobic $Z^{\\prime}$.

  12. Comparison of three nonlinear models to describe long-term tag shedding by lake trout

    USGS Publications Warehouse

    Fabrizio, Mary C.; Swanson, Bruce L.; Schram, Stephen T.; Hoff, Michael H.

    1996-01-01

    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.

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

    PubMed Central

    Richard, Peter; Valkonen, Mari; Viljanen, Kaarina

    2014-01-01

    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

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

    PubMed Central

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

    2013-01-01

    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

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

    PubMed

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

    2013-01-01

    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

  16. NMFS Cooperative SharkTagging Program, 1962-93: An Atlas of SharkTag and Recapture Data

    E-print Network

    commercially valuable species. Several shark attacks along the New Jersey coast at that time gave rise; and tiger sharks, Galeocerdo cuvier, considered to be among the most dangerous species. When the detailsNMFS Cooperative SharkTagging Program, 1962-93: An Atlas of SharkTag and Recapture Data NANCY E

  17. QUANTITY: An Isobaric Tag for Quantitative Glycomics

    PubMed Central

    Yang, Shuang; Wang, Meiyao; Chen, Lijun; Yin, Bojiao; Song, Guoqiang; Turko, Illarion V.; Phinney, Karen W.; Betenbaugh, Michael J.; Zhang, Hui; Li, Shuwei

    2015-01-01

    Glycan is an important class of macromolecules that play numerous biological functions. Quantitative glycomics - analysis of glycans at global level - however, is far behind genomics and proteomics owing to technical challenges associated with their chemical properties and structural complexity. As a result, technologies that can facilitate global glycan analysis are highly sought after. Here, we present QUANTITY (Quaternary Amine Containing Isobaric Tag for Glycan), a quantitative approach that can not only enhance detection of glycans by mass spectrometry, but also allow high-throughput glycomic analysis from multiple biological samples. This robust tool enabled us to accomplish glycomic survey of bioengineered Chinese Hamster Ovary (CHO) cells with knock-in/out enzymes involved in protein glycosylation. Our results demonstrated QUANTITY is an invaluable technique for glycan analysis and bioengineering. PMID:26616285

  18. Reliable Food Traceability Using RFID Tagging

    NASA Astrophysics Data System (ADS)

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

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

  19. Reconciling Knowledge in Social Tagging Web Services

    NASA Astrophysics Data System (ADS)

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

    Sometimes we want to search for new information about topics but we can not find relevant results using our own knowledge (for example, our personal bookmarks). A potential solution could be the use of knowledge from other users to find what we are searching for. This solution implies that we can achieve some agreement on implicit semantics used by the other users. We call it Reconciliation of Knowledge. The aim of this paper is to show an agent-based method which lets us reconcile two different knowledge basis (associated with tagging systems) into a common language, obtaining a new one that allows the reconcilitiation of (part of) this knowledge. The agents use Formal Concept Analysis concepts and tools and it has been implemented on the JADE multiagent platform.

  20. The Fourth International Chinese Language Processing Bakeoff: Chinese Word Segmentation, Named Entity Recognition and Chinese POS Tagging

    E-print Network

    /University of Colorado (CTB) for WS and POS tagging, by Peking University for NER and POS tagging, by Shanxi University and delimiters. For test data, all tags removed except sentence end tags. Comparable XML format data was also

  1. Peptides with selective affinity for carbon nanotubes

    NASA Astrophysics Data System (ADS)

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

    2003-03-01

    Because of their extraordinary electronic and mechanical properties, carbon nanotubes have great potential as materials for applications ranging from molecular electronics to ultrasensitive biosensors. Biological molecules interacting with carbon nanotubes provide them with specific chemical handles that would make several of these applications possible. Here we use phage display to identify peptides with selective affinity for carbon nanotubes. Binding specificity has been confirmed by demonstrating direct attachment of nanotubes to phage and free peptides immobilized on microspheres. Consensus binding sequences show a motif rich in histidine and tryptophan, at specific locations. Our analysis of peptide conformations shows that the binding sequence is flexible and folds into a structure matching the geometry of carbon nanotubes. The hydrophobic structure of the peptide chains suggests that they act as symmetric detergents.

  2. Affine connection form of Regge calculus

    E-print Network

    Khatsymovsky, V M

    2015-01-01

    Regge action is represented analogously to how the Palatini action for general relativity (GR) as some functional of the metric and a general connection as independent variables represents the Einstein-Hilbert action. The piecewise flat (or simplicial) spacetime of Regge calculus is equipped with some world coordinates and some piecewise affine metric which is completely defined by the set of edge lengths and the world coordinates of the vertices. The conjugate variables are the general nondegenerate matrices on the 3-simplices which play a role of a general discrete connection. Our previous result on some representation of the Regge calculus action in terms of the local Euclidean (Minkowsky) frame vectors and orthogonal connection matrices as independent variables is somewhat modified for the considered case of the general linear group GL(4,R) of the connection matrices. As a result, we have some action invariant w. r. t. arbitrary change of coordinates of the vertices (and related GL(4,R) transformations in...

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

    NASA Astrophysics Data System (ADS)

    Schrammel, Johann; Deutsch, Stephanie; Tscheligi, Manfred

    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.

  4. Smooth surfaces from bilinear patches: discrete affine minimal surfaces

    E-print Network

    Pottmann, Helmut

    Smooth surfaces from bilinear patches: discrete affine minimal surfaces Florian K are composed of smoothly joined bilinear patches. These surfaces turn out to be discrete versions of negatively curved affine minimal surfaces and share many properties with their classical smooth counterparts. We

  5. PRESENTATION OF AFFINE KAC-MOODY GROUPS DANIEL ALLCOCK

    E-print Network

    Allcock, Daniel

    PRESENTATION OF AFFINE KAC-MOODY GROUPS OVER RINGS DANIEL ALLCOCK Abstract. Tits has defined a Curtis-Tits-style presentation for the Steinberg group St of any rank 3 irreducible affine root system of the Kac-Moody group is due to Tits [20]. He first constructed a group functor R StA(R) generalizing

  6. BOUNDING REFLECTION LENGTH IN AN AFFINE COXETER GROUP

    E-print Network

    Bigelow, Stephen

    BOUNDING REFLECTION LENGTH IN AN AFFINE COXETER GROUP JON MCCAMMOND AND T. KYLE PETERSEN Abstract reflections and the minimal number of reflections needed to factor a particular element is called its reflection length. In this article we prove that the reflection length function on an affine Coxeter group

  7. A MEMS AFFINITY GLUCOSE SENSOR USING PERMITTIVITY MEASUREMENTS

    E-print Network

    Lin, Qiao

    A MEMS AFFINITY GLUCOSE SENSOR USING PERMITTIVITY MEASUREMENTS Xian Huang1 , Siqi Li2 , Jerome of California, Riverside, CA, USA ABSTRACT We present a MEMS affinity glucose sensor using permittivity measurements. This device employs a biocompatible glucose-specific polymer as the sensing solu- tion

  8. Coordinated Transporter Activity Shapes High Affinity Iron Acquisition in Cyanobacteria

    E-print Network

    Einat, Aharonov

    Coordinated Transporter Activity Shapes High Affinity Iron Acquisition in Cyanobacteria C. Kranzler, Edmond J. Safra Campus, Givat Ram, Hebrew University of Jerusalem, Jerusalem, Israel. Cyanobacteria for a central high-affinity iron transport system in non-siderophore producing cyanobacteria. #12;#12;

  9. THE CENTROID OF EXTENDED AFFINE AND ROOT GRADED LIE ALGEBRAS

    E-print Network

    Neher, Erhard

    THE CENTROID OF EXTENDED AFFINE AND ROOT GRADED LIE ALGEBRAS GEORGIA BENKARTA,1 AND ERHARD NEHERB,2 algebras, and Lie algebras graded by finite root systems. 1. Introduction Our main focus.13), extended affine Lie algebras (Cor. 4.13), Lie algebras graded by finite root systems (Thm. 5.15 and Thm. 5

  10. LIE TORI --A SIMPLE CHARACTERIZATION OF EXTENDED AFFINE LIE ALGEBRAS

    E-print Network

    require that the Lie algebra be graded by both a finite irreducible root system (possibly nonreducedLIE TORI -- A SIMPLE CHARACTERIZATION OF EXTENDED AFFINE LIE ALGEBRAS Yoji Yoshii Department affine Lie algebra (EALA). Namely, the core of any EALA is a Lie torus, and any centreless Lie torus

  11. Tending to Change: Toward a Situated Model of Affinity Spaces

    ERIC Educational Resources Information Center

    Bommarito, Dan

    2014-01-01

    The concept of affinity spaces, a theoretical construct used to analyze literate activity from a spatial perspective, has gained popularity among scholars of literacy studies and, particularly, video-game studies. This article seeks to expand current notions of affinity spaces by identifying key assumptions that have limited researchers'…

  12. Frame-independent mechanics:geometry on affine bundles

    E-print Network

    K. Grabowska; J. Grabowski; P. Urbanski

    2005-10-06

    Main ideas of the differential geometry on affine bundles are presented. Affine counterparts of Lie algebroid and Poisson structures are introduced and discussed. The developed concepts are applied in a frame-independent formulation of the time-dependent and the Newtonian mechanics.

  13. Affine group formulation of the Standard Model coupled to gravity

    SciTech Connect

    Chou, Ching-Yi; Ita, Eyo; Soo, Chopin

    2014-04-15

    In this work we apply the affine group formalism for four dimensional gravity of Lorentzian signature, which is based on Klauder’s affine algebraic program, to the formulation of the Hamiltonian constraint of the interaction of matter and all forces, including gravity with non-vanishing cosmological constant ?, as an affine Lie algebra. We use the hermitian action of fermions coupled to gravitation and Yang–Mills theory to find the density weight one fermionic super-Hamiltonian constraint. This term, combined with the Yang–Mills and Higgs energy densities, are composed with York’s integrated time functional. The result, when combined with the imaginary part of the Chern–Simons functional Q, forms the affine commutation relation with the volume element V(x). Affine algebraic quantization of gravitation and matter on equal footing implies a fundamental uncertainty relation which is predicated upon a non-vanishing cosmological constant. -- Highlights: •Wheeler–DeWitt equation (WDW) quantized as affine algebra, realizing Klauder’s program. •WDW formulated for interaction of matter and all forces, including gravity, as affine algebra. •WDW features Hermitian generators in spite of fermionic content: Standard Model addressed. •Constructed a family of physical states for the full, coupled theory via affine coherent states. •Fundamental uncertainty relation, predicated on non-vanishing cosmological constant.

  14. AUTOMATA AND CELLS IN AFFINE WEYL GROUPS PAUL E. GUNNELLS

    E-print Network

    Gunnells, Paul

    conjugacy classes in simple complex algebraic groups [5,6]. The definition of cells is quite complicated (§2 combinatorial data. In particular from the definition it is not clear how "computable" cells are. For instanceAUTOMATA AND CELLS IN AFFINE WEYL GROUPS PAUL E. GUNNELLS Abstract. Let W be an affine Weyl group

  15. PIECEWISE AFFINE SYSTEMS CONTROLLABILITY AND HYBRID OPTIMAL CONTROL

    E-print Network

    Rondepierre, Aude

    PIECEWISE AFFINE SYSTEMS CONTROLLABILITY AND HYBRID OPTIMAL CONTROL Aude Rondepierre Laboratoire de.Rondepierre@imag.fr Keywords: Piecewise affine hybrid systems, polyhedral sets, controllability, optimal control synthesis-approximating the controllable domain under the given hybrid dynamic. Given an optimal sequence of states of the hybrid automaton

  16. The Study of Affinity-Seeking in an Organizational Setting.

    ERIC Educational Resources Information Center

    Flath, Dominic B.

    This study investigated the relationship between supervisors' use of Bell and Daly's affinity-seeking strategies and their impact on employee satisfaction. Results indicated that 16 of the 25 affinity-seeking strategies were positively correlated with a subordinate's perception of supervisor credibility. Results also indicated that a supervisor's…

  17. A wireless sensor tag platform for container security and integrity

    NASA Astrophysics Data System (ADS)

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

    2011-04-01

    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.

  18. A wireless sensor tag platform for container security and integrity

    SciTech Connect

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

    2011-05-06

    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.

  19. 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

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

    2003-01-01

    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.

  20. Hard Diffraction with Proton Tagging at the LHC

    E-print Network

    Maciej Trzebinski

    2015-08-07

    The main parts of the LHC diffractive physics programme possible to be measured using a proton tagging technique are presented. The geometric acceptance of the ATLAS forward proton detectors: ALFA and AFP for various LHC optics settings are shown. The probabilities of observing a proton originating from a minimum-bias event in ALFA and AFP stations are given. The main properties of single diffractive and double Pomeron exchange production of dijets, photon+jet, jet-gap-jet and W/Z bosons are discussed. The possibility of measuring the jet production in exclusive (double proton tag) and semi-exclusive (single tag) mode is evaluated.

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

    NASA Astrophysics Data System (ADS)

    Scott, Tyler D.

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

  2. Electronic cleansing in fecal-tagging dual-energy CT colonography based on material decomposition and virtual colon tagging.

    PubMed

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

    2015-02-01

    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 study. Our results demonstrated that our VCT-EC scheme may provide a significant reduction of EC artifacts. PMID:25350911

  3. High-productivity membrane adsorbers: Polymer surface-modification studies for ion-exchange and affinity bioseparations

    NASA Astrophysics Data System (ADS)

    Chenette, Heather C. S.

    This dissertation centers on the surface-modification of macroporous membranes to make them selective adsorbers for different proteins, and the analysis of the performance of these membranes relative to existing technology. The common approach used in these studies, which is using membrane technology for chromatographic applications and using atom transfer radical polymerization (ATRP) as a surface modification technique, will be introduced and supported by a brief review in Chapter 1. The specific approaches to address the unique challenges and motivations of each study system are given in the introduction sections of the respective dissertation chapters. Chapter 2 describes my work to develop cation-exchange membranes. I discuss the polymer growth kinetics and characterization of the membrane surface. I also present an analysis of productivity, which measures the mass of protein that can bind to the stationary phase per volume of stationary phase adsorbing material per time. Surprisingly and despite its importance, this performance measure was not described in previous literature. Because of the significantly shorter residence time necessary for binding to occur, the productivity of these cation-exchange membrane adsorbers (300 mg/mL/min) is nearly two orders of magnitude higher than the productivity of a commercial resin product (4 mg/mL/min). My work studying membrane adsorbers for affinity separations was built on the productivity potential of this approach, as articulated in the conclusion of Chapter 2. Chapter 3 focuses on the chemical formulation work to incorporate glycoligands into the backbone of polymer tentacles grown from the surface of the same membrane stationary phase. Emphasis is given to characterizing and testing the working formulation for ligand incorporation, and details about how I arrived at this formulation are given in Appendix B. The plant protein, or lectin, Concanavalin A (conA) was used as the target protein. The carbohydrate affinity membrane adsorbers were found to have a static binding capacity for con A (6.0 mg/mL) that is nearly the same as the typical dextran-based separation media used in practice. Binding under dynamic conditions was tested using flow rates of 0.1-1.0 mL/min. No bound lectin was observed for the higher flow rate. The first Damkohler number was used to assess whether adsorption kinetics or mass transport contributed the limitation to conA binding. Analyses indicate that this system is not limited by the accessibility of the binding sites, but by the inherently low rate of adsorption of conA onto the glycopolymer. The research described in Chapter 4 focuses on reaction chemistry experiments to incorporate a phosphonate-based polymer in the membrane platform to develop a new class of affinity adsorbers that function based on their affinity for Arginine (Arg) amino acid residues. The hypothesis was that benzyl phosphonate-containing functional polymers would form strong complexes with Arg-rich proteins as a result of multivalent binding. Introducing a new class of affinity membranes for purification of Arg-rich and Arg-tagged proteins may have an impact similar to the introduction of immobilized metal ion affinity chromatography (IMAC), which would be a significant achievement. Using Arg-tags would overcome some of the associated drawbacks of using metal ions in IMAC. Additionally, some cell penetrating peptides are said to be Arg-rich, and this would be a convenient feature to exploit for their isolation and purification. Lysozyme was used as a model Arg-rich protein. The affinity membranes show a static binding capacity of 3 mg/mL. (Abstract shortened by UMI.)

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

    PubMed

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

    2014-04-01

    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

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

    PubMed Central

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

    2014-01-01

    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

  6. Identification of proteins associated with the yeast mitochondrial RNA polymerase by tandem affinity purification

    PubMed Central

    Markov, Dmitriy A; Savkina, Maria; Anikin, Michael; Del Campo, Mark; Ecker, Karen; Lambowitz, Alan M; De Gnore, Jon P; McAllister, William T

    2009-01-01

    The abundance of mitochondrial (mt) transcripts varies under different conditions, and is thought to depend upon rates of transcription initiation, transcription termination/attenuation and RNA processing/degradation. The requirement to maintain the balance between RNA synthesis and processing may involve coordination between these processes; however, little is known about factors that regulate the activity of mtRNA polymerase (mtRNAP). Recent attempts to identify mtRNAP–protein interactions in yeast by means of a generalized tandem affinity purification (TAP) protocol were not successful, most likely because they involved a C-terminal mtRNAP–TAP fusion (which is incompatible with mtRNAP function) and because of the use of whole-cell solubilization protocols that did not preserve the integrity of mt protein complexes. Based upon the structure of T7 RNAP (to which mtRNAPs show high sequence similarity), we identified positions in yeast mtRNAP that allow insertion of a small affinity tag, confirmed the mature N-terminus, constructed a functional N-terminal TAP–mtRNAP fusion, pulled down associated proteins, and identified them by LC–MS–MS. Among the proteins found in the pull-down were a DEAD-box protein (Mss116p) and an RNA-binding protein (Pet127p). Previous genetic experiments suggested a role for these proteins in linking transcription and RNA degradation, in that a defect in the mt degradadosome could be suppressed by overexpression of either of these proteins or, independently, by mutations in either mtRNAP or its initiation factor Mtf1p. Further, we found that Mss116p inhibits transcription by mtRNAP in vitro in a steady-state reaction. Our results support the hypothesis that Mss116p and Pet127p are involved in modulation of mtRNAP activity. Copyright © 2009 John Wiley & Sons, Ltd. PMID:19536766

  7. Selectively promiscuous opioid ligands: discovery of high affinity/low efficacy opioid ligands with substantial nociceptin opioid peptide receptor affinity.

    PubMed

    Kumar, Vinod; Ridzwan, Irna E; Grivas, Konstantinos; Lewis, John W; Clark, Mary J; Meurice, Claire; Jimenez-Gomez, Corina; Pogozheva, Irina; Mosberg, Henry; Traynor, John R; Husbands, Stephen M

    2014-05-22

    Emerging clinical and preclinical evidence suggests that a compound displaying high affinity for ?, ?, and ? opioid (MOP, KOP, and DOP) receptors and antagonist activity at each, coupled with moderate affinity and efficacy at nociceptin opioid peptide (NOP) receptors will have utility as a relapse prevention agent for multiple types of drug abuse. Members of the orvinol family of opioid ligands have the desired affinity profile but have typically displayed substantial efficacy at MOP and or KOP receptors. In this study it is shown that a phenyl ring analogue (1d) of buprenorphine displays the desired profile in vitro with high, nonselective affinity for the MOP, KOP, and DOP receptors coupled with moderate affinity for NOP receptors. In vivo, 1d lacked any opioid agonist activity and was an antagonist of both the MOP receptor agonist morphine and the KOP receptor agonist ethylketocyclazocine, confirming the desired opioid receptor profile in vivo. PMID:24761755

  8. Reversible site-specific tagging of enzymatically synthesized RNAs using aldehyde–hydrazine chemistry and protease-cleavable linkers

    PubMed Central

    Pfander, Stephanie; Fiammengo, Roberto; Kirin, Sre?ko I.; Metzler-Nolte, Nils; Jäschke, Andres

    2007-01-01

    The investigation of RNA structure, dynamics and biological function often requires the site-specific incorporation of non-natural moieties. Here we describe the functionalization of RNA transcripts by aldehyde–hydrazine chemistry using a simple initiator nucleotide that carries an acetal-protected aldehyde function. This initiator nucleotide was efficiently incorporated into RNA, and the modified RNAs were quantitatively coupled to a peptide derivative displaying a hydrazine moiety at one end, a biotin tag at the other, and a trypsin-cleavable sequence in between. RNA conjugates could be easily isolated by affinity chromatography on streptavidin agarose and quantitatively cleaved off the support by trypsin treatment without detectable RNA degradation. The strategy described here may allow the incorporation of various new features into enzymatically synthesized RNA under mild conditions. PMID:17259220

  9. TAGGING, TRACKING AND LOCATING WITHOUT GPS

    SciTech Connect

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

    2012-07-08

    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.

  10. Ultrasound-tagged light assessment of osteoporosis

    NASA Astrophysics Data System (ADS)

    Lev, Aner; Rubanov, Evgeni; Sfez, Bruno; Shany, Shraga; Foldes, Joseph

    2005-04-01

    There have been several attempts to detect bone structural changes using optical techniques. H.G. Eberle et al. have used ultrafast optical techniques on the finger in trans-illumination and have shown an excellent correlation between their measurements of the scattering coefficient and bone mineral density obtained using dual X-ray absorption (DXA) imaging. Encouraged by these results, we have developed a system based on the combination of cw laser light and low-frequency ultrasound to probe the bone structure. The physical principle of this system is the detection of laser light diffusing in the bone tissue modulated ("tagged") by a low-frequency ultrasound pulse, which allows a local measurement of the attenuation coefficient. The basic assumption of the technique is that the main factor of attenuation changes in the bone of elderly patients is a scattering change due to osteoporosis, and therefore attenuation measurements directly reflect the scattering properties of the bone. We present a preliminary series of clinical experiments showing that this technique allows determining the bone scattering modification inside the trabecular bone. In this series of clinical experiments, the scattering coefficient determined using the optical technique is compared with the bone mineral density obtained using dual X-ray absorption in a group of 9 patients. A correlation of 0.84 (p=0.05) was found, showing the potential of this technique for the assessment of osteoporosis.

  11. Online b-jets tagging at CDF

    SciTech Connect

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

    2007-04-01

    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.

  12. Prospects for Barium Tagging in Gaseous Xenon

    SciTech Connect

    Sinclair, D.; Rollin, E.; Smith, J.; Mommers, A.; Ackerman, N.; Aharmim, B.; Auger, M.; Barbeau, P.S.; Benitez-Medina, C.; Breidenbach, M.; Burenkov, A.; Cook, S.; Coppens, A.; Daniels, T.; DeVoe, R.; Dobi, A.; Dolinski, M.J.; Donato, K.; Fairbank, W., Jr.; Farine, J.; Giroux, G.; /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

    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.

  13. Mixed orthogonal frequency coded SAW RFID tags.

    PubMed

    Gallagher, Mark W; Malocha, Donald C

    2013-03-01

    Orthogonal frequency coded (OFC) SAW radio-frequency identification (RFID) tags are currently being explored as a multi-sensor platform because of their passive spread-spectrum operation, low loss, and resilience in harsh environments. Ongoing research continues to search for robust device embodiments that increase the number of identifiable codes, in the presence of intersymbol interference, while maintaining reasonable device lengths. This paper presents a technique that shortens the SAW response length while preserving code diversity and bandwidth by utilizing a multi-track SAW configuration. These new devices allow the time response of multiple OFC chips to overlap and yield a mixed-frequency chip having the sum of the chip bandwidths but shorter overall time response. The theoretical development is presented and examples are discussed for these new mixed orthogonal frequency coded (MOFC) SAW devices. Experimental results for MOFC sensors, fabricated on YZ-LiNbO3, with a 7% fractional bandwidth and five chip frequencies in three cells, provide a good contrast to similar OFC designs. Experimental results are presented for the simultaneous operation of eight wireless temperature sensors--four OFC and four MOFC--in a 915-MHz wireless correlator receiver system, highlighting the ability of these devices to operate in the same system. PMID:23475925

  14. Fluorescent labeling of SNAP-tagged proteins in cells.

    PubMed

    Lukinavi?ius, Gražvydas; Reymond, Luc; Johnsson, Kai

    2015-01-01

    One of the most prominent self-labeling tags is SNAP-tag. It is an in vitro evolution product of the human DNA repair protein O (6)-alkylguanine-DNA alkyltransferase (hAGT) that reacts specifically with benzylguanine (BG) and benzylchloropyrimidine (CP) derivatives, leading to covalent labeling of SNAP-tag with a synthetic probe (Gronemeyer et al., Protein Eng Des Sel 19:309-316, 2006; Curr Opin Biotechnol 16:453-458, 2005; Keppler et al., Nat Biotechnol 21:86-89, 2003; Proc Natl Acad Sci U S A 101:9955-9959, 2004). SNAP-tag is well suited for the analysis and quantification of fused target protein using fluorescence microscopy techniques. It provides a simple, robust, and versatile approach to the imaging of fusion proteins under a wide range of experimental conditions. PMID:25560070

  15. Low-Cost, Ubiquitous RFID-Tag-Antenna-Based Sensing

    E-print Network

    Bhattacharyya, Rahul

    Radio-frequency identification (RFID) has been well established as an effective technology for track and trace applications. In this paper, we go beyond the ID in RFID, and discuss the potential for RFID tags to be used ...

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

    PubMed

    Foster, Kenneth R; Jaeger, Jan

    2008-08-01

    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

  17. Feasibility of Surgically Implanting Acoustic Tags into Pacific Herring

    USGS Publications Warehouse

    Hershberger, Paul K.; Gregg, Jacob L.; Seitz, A.C.; Norcross, B.L.; Payne, J.C.; Kagley, A.N.; Meloy, B

    2010-01-01

    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 g) in Pacific herring that had been held in captivity for nearly a year and that ranged from 165 to 215 mm in fork length (FL) and from 41.6 to 142.6 g. Relatively low mortality (4%) and tag shedding (4%), as well as growth similar to that observed in control fish after 135 d, indicate that, with proper handling, Pacific herring are amenable to surgical implantation of acoustic tags.

  18. Tailing RFID Tags for Clone Detection Davide Zanetti

    E-print Network

    Capkun, Srdjan

    Tailing RFID Tags for Clone Detection Davide Zanetti ETH Zurich, Switzerland zanettid, simply "wireless barcodes," themselves vulnerable to cloning and counterfeiting. While continuous monitoring can, in principle, detect cloning at- tacks, real-world supply chains often contain significant

  19. InkTag: Secure Applications on an Untrusted Operating System

    PubMed Central

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

    2014-01-01

    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

  20. Energy Calibration of the JLab Bremsstrahlung Tagging System

    SciTech Connect

    Stepan Stepanyan; S. Boyarinov; H. Egiyan; D. Dale; L. Guo; M. Gabrielyan; L. Gan; Ashot Gasparian; Bernhard Mecking; A. Teymurazyan; I. Nakagawa; Oleksandr Glamazdin; Michael Wood

    2007-03-01

    In this report, we present the energy calibration of the Hall B bremsstrahlung tagging system at the Thomas Jefferson National Accelerator Facility. The calibration was performed using a magnetic pair spectrometer. The tagged photon energy spectrum was measured in coincidence with e{sup +}e{sup -} pairs as a function of the pair spectrometer magnetic field. Taking advantage of the internal linearity of the pair spectrometer, the energy of the tagging system was calibrated at the level of {+-} 0.1% E{sub {gamma}}. The absolute energy scale was determined using the e{sup +}e{sup -} rate measurements close to the end-point of the photon spectrum. The energy variations across the full tagging range were found to be <3 MeV.

  1. Effect of Gen2 Protocol Parameters on RFID Tag Performance

    E-print Network

    Hochberg, Michael

    transmission is shown in Fig. 1. At first, the reader transmits to the tag a carrier wave (CW) unmodulated RF to installation. Those variations are mostly due to differences in RF environment and reader sensitivity

  2. Visual implant elastomer and anchor tag retention in largemouth bass

    USGS Publications Warehouse

    Hartman, K.J.; Janney, E.C.

    2006-01-01

    We double-marked largemouth bass Micropterus salmoides with Floy FD-68B anchor tags and visible implant elastomer (VIE) marks before stocking to compare retention of the two marks for age-0 (178 mm total length [TL]) and age-1 (273 mm TL) largemouth bass. In a short-term (31-d) evaluation, retention rate of anchor tags was over 94% for each age-class and retention of VIE marks was 98% in both age-classes. In a longer-term comparison of fish stocked into the Ohio River, retention was substantially higher for VIE marks (92.9%) than for anchor tags (42.9%) after 403 d (ages combined). Although anchor tags had high retention in two sizes of largemouth bass during the short-term experiment, they should not be used in situations where accurate identification of marked fish is required for periods longer than 123 d. ?? Copyright by the American Fisheries Society 2006.

  3. Methyl-CpG island-associated genome signature tags

    DOEpatents

    Dunn, John J

    2014-05-20

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

  4. A METHOD OF SIMULTANEOUSLY TAGGING LARGE OCEANIC FISH AND

    E-print Network

    A METHOD OF SIMULTANEOUSLY TAGGING LARGE OCEANIC FISH AND INJECTING THEM WITH TETRACYCLINE A simple with tetracycline of yellowfin tuna >45 kg from the deck of sport fish- ing vessels, is easily adaptable to other

  5. InkTag: Secure Applications on an Untrusted Operating System.

    PubMed

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

    2013-01-01

    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

  6. Keeping track. Barcodes and RFID tags make inroads in hospitals.

    PubMed

    Degaspari, John

    2011-03-01

    Barcodes are a proven technology for reducing medication administration errors, while RFID tags show promise for tracking of assets as well as personnel and patients. Yet implementation has been slow, as hospitals struggle with cost and complexity issues. PMID:21446265

  7. Cambrian trilobites with Siberian affinities, southwestern Alaska

    SciTech Connect

    Palmer, A.R.; Egbert, R.M.; Sullivan, R.; Knoth, J.S.

    1985-02-01

    Cambrian trilobites occur in two levels (about 7 m apart) in the core of a large, complex anticlinal structure in the area between the Taylor Mountains and the Hoholitna River in southwestern Alaska. The lower collection contains Erbia, Macannaia (a species close to Soviet forms described as Pagetia ferox Lermontova), two species of Kootenia (including one perhaps cospecific with forms from the central Brooks range), and several species of ptychoparioid trilobites. It is clear that biogeographic affinities are with the transitional facies of the eastern Siberian platform and the south Siberian foldbelt. In Soviet terms, the age of the collection falls in a disputed interval called latest Early Cambrian (Tojonian) by some authors, and earliest Middle Cambrian (Amgan) by others. In North American terms, Macannaia is known only from early Middle Cambrian beds. The younger collection contains abundant agnostids, a variety of conocoryphids, Paradoxides, and several species of ptychoparioid trilobites. This is an assemblage of undoubted late Middle Cambrian age, comparable to faunas described from the Maya State of the Siberian platform and the Paradoxides paradoxissimus Stage of the Baltic region. Both faunas are from ocean-facing or outer shelf environments. None of the key non-agnostid or non-pagetiid elements have been seen previously in deposits of Cambrian North America.

  8. Ligand Affinities Estimated by Quantum Chemical Calculations.

    PubMed

    Söderhjelm, Pär; Kongsted, Jacob; Ryde, Ulf

    2010-05-11

    We present quantum chemical estimates of ligand-binding affinities performed, for the first time, at a level of theory for which there is a hope that dispersion and polarization effects are properly accounted for (MP2/cc-pVTZ) and at the same time effects of solvation, entropy, and sampling are included. We have studied the binding of seven biotin analogues to the avidin tetramer. The calculations have been performed by the recently developed PMISP approach (polarizable multipole interactions with supermolecular pairs), which treats electrostatic interactions by multipoles up to quadrupoles, induction by anisotropic polarizabilities, and nonclassical interactions (dispersion, exchange repulsion, etc.) by explicit quantum chemical calculations, using a fragmentation approach, except for long-range interactions that are treated by standard molecular-mechanics Lennard-Jones terms. In order to include effects of sampling, 10 snapshots from a molecular dynamics simulation are studied for each biotin analogue. Solvation energies are estimated by the polarized continuum model (PCM), coupled to the multipole-polarizability model. Entropy effects are estimated from vibrational frequencies, calculated at the molecular mechanics level. We encounter several problems, not previously discussed, illustrating that we are first to apply such a method. For example, the PCM model is, in the present implementation, questionable for large molecules, owing to the use of a surface definition that gives numerous small cavities in a protein. PMID:26615702

  9. A differential dielectric affinity glucose sensor.

    PubMed

    Huang, Xian; Leduc, Charles; Ravussin, Yann; Li, Siqi; Davis, Erin; Song, Bing; Li, Dachao; Xu, Kexin; Accili, Domenico; Wang, Qian; Leibel, Rudolph; Lin, Qiao

    2014-01-21

    A continuous glucose monitor with a differential dielectric sensor implanted within the subcutaneous tissue that determines the glucose concentration in the interstitial fluid is presented. The device, created using microelectromechanical systems (MEMS) technology, consists of sensing and reference modules that are identical in design and placed in close proximity. Each module contains a microchamber housing a pair of capacitive electrodes residing on the device substrate and embedded in a suspended, perforated polymer diaphragm. The microchambers, enclosed in semi-permeable membranes, are filled with either a polymer solution that has specific affinity to glucose or a glucose-insensitive reference solution. To accurately determine the glucose concentration, changes in the permittivity of the sensing and the reference solutions induced by changes in glucose concentration are measured differentially. In vitro characterization demonstrated the sensor was capable of measuring glucose concentrations from 0 to 500 mg dL(-1) with resolution and accuracy of ~1.7 ?g dL(-1) and ~1.74 mg dL(-1), respectively. In addition, device drift was reduced to 1.4% (uncontrolled environment) and 11% (5 °C of temperature variation) of that from non-differential measurements, indicating significant stability improvements. Preliminary animal testing demonstrated that the differential sensor accurately tracks glucose concentration in blood. This sensor can potentially be used clinically as a subcutaneously implanted continuous monitoring device in diabetic patients. PMID:24220675

  10. Prostate Cancer and Bone: The Elective Affinities

    PubMed Central

    2014-01-01

    The onset of metastases dramatically changes the prognosis of prostate cancer patients, determining increased morbidity and a drastic fall in survival expectancy. Bone is a common site of metastases in few types of cancer, and it represents the most frequent metastatic site in prostate cancer. Of note, the prevalence of tumor relapse to the bone appears to be increasing over the years, likely due to a longer overall survival of prostate cancer patients. Bone tropism represents an intriguing challenge for researchers also because the preference of prostate cancer cells for the bone is the result of a sequential series of targetable molecular events. Many factors have been associated with the peculiar ability of prostate cancer cells to migrate in bone marrow and to determine mixed osteoblastic/osteolytic lesions. As anticipated by the success of current targeted therapy aimed to block bone resorption, a better understanding of molecular affinity between prostate cancer and bone microenvironment will permit us to cure bone metastasis and to improve prognosis of prostate cancer patients. PMID:24971315

  11. Affine connection form of Regge calculus

    E-print Network

    V. M. Khatsymovsky

    2015-09-16

    Regge action is represented analogously to how the Palatini action for general relativity (GR) as some functional of the metric and a general connection as independent variables represents the Einstein-Hilbert action. The piecewise flat (or simplicial) spacetime of Regge calculus is equipped with some world coordinates and some piecewise affine metric which is completely defined by the set of edge lengths and the world coordinates of the vertices. The conjugate variables are the general nondegenerate matrices on the 3-simplices which play a role of a general discrete connection. Our previous result on some representation of the Regge calculus action in terms of the local Euclidean (Minkowsky) frame vectors and orthogonal connection matrices as independent variables is somewhat modified for the considered case of the general linear group GL(4,R) of the connection matrices. As a result, we have some action invariant w. r. t. arbitrary change of coordinates of the vertices (and related GL(4,R) transformations in the 4-simplices). Excluding GL(4,R) connection from this action via the equations of motion we have exactly the Regge action for the considered spacetime.

  12. Affinity of guanosine derivatives for polycytidylate revisited

    NASA Technical Reports Server (NTRS)

    Kanavarioti, A.; Hurley, T. B.; Baird, E. E.

    1995-01-01

    Evidence is presented for complexation of guanosine 5'-monophosphate 2-methylimidazolide (2-MeImpG) with polycytidylate (poly(C)) at pH 8.0 and 23 degrees C in the presence of 1.0 M NaCl2 and 0.2 M MgCl2 in water. The association of 2-MeImpG with poly(C) was investigated using UV-vis spectroscopy as well as by monitoring the kinetics of the nucleophilic substitution reaction of the imidazole moiety by amines. The results of both methods are consistent with moderately strong poly(C) 2-MeImpG complexation and the spectrophotometric measurements allowed the construction of a binding isotherm with a concentration of 2-MeImpG equal to 5.55 +/- 0.15 mM at half occupancy. UV spectroscopy was employed to establish the binding of other guanosine derivatives on poly(C). These derivatives are guanosine 5'-monophosphate (5'GMP), guanosine 5'-monophosphate imidazolide (ImpG), and guanosine 5'-monophosphate morpholidate (morpG). Within experimental error these guanosine derivatives exhibit the same affinity for poly(C) as 2-MeImpG.

  13. The Use of Social Tags in Text and Image Searching on the Web

    ERIC Educational Resources Information Center

    Kim, Yong-Mi

    2011-01-01

    In recent years, tags have become a standard feature on a diverse range of sites on the Web, accompanying blog posts, photos, videos, and online news stories. Tags are descriptive terms attached to Internet resources. Despite the rapid adoption of tagging, how people use tags during the search process is not well understood. There is little…

  14. 77 FR 76367 - Availability of E-Tag Information to Commission Staff

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-28

    ...\\ 77 FR 12760 (Mar. 2, 2012). II. Discussion A. Legal Authority To Require E-Tag Access 1. E-Tag NOPR... Energy Regulatory Commission 18 CFR Part 366 Availability of E-Tag Information to Commission Staff AGENCY... and receive e-Tags addressed to the Commission. The information made available under this Final...

  15. MEASUREMENT OF BACKSCATTERING FROM RFID TAGS Pavel V. Nikitin and K. V. S. Rao

    E-print Network

    Hannaford, Blake

    signal backscattering from an RFID tag and calculating tag radar cross-section (RCS), which depends on the chip input impedance. We present a derivation of a theoretical formula for RFID tag radar cross-section presents a certain radar cross section (RCS). The tag sends the information back by varying its input

  16. Tagging methods to study the move-ment, growth, and exploitation rate

    E-print Network

    476 Tagging methods to study the move- ment, growth, and exploitation rate for the American lobster was the introduction of an insertion tag called the "sphyrion tag" that is anchored to muscle tissue (Scarratt providing information on long-term movement and more accurate data on growth. Tag loss could greatly bias

  17. Maximalist Cryptography and Computation on the WISP UHF RFID Tag

    E-print Network

    Hochberg, Michael

    Maximalist Cryptography and Computation on the WISP UHF RFID Tag Hee-Jin Chae1 , Daniel J. Yeager2}@cs.umass.edu 2 Intel Research Seattle, Seattle, WA, USA, yeagerd@ee.washington.edu, Joshua.r.smith@intel.com http://www.rfid-32/12/16 on the WISP UHF RFID tag shows that conventional cryptography is no longer beyond the reach of a general

  18. Affinity Inequality among Serum Antibodies That Originate in Lymphoid Germinal Centers

    E-print Network

    Eisen, Ellen A.

    Upon natural infection with pathogens or vaccination, antibodies are produced by a process called affinity maturation. As affinity maturation ensues, average affinity values between an antibody and ligand increase with ...

  19. Tailored amino acid diversity for the evolution of antibody affinity

    PubMed Central

    González-Muñoz, Andrea; Bokma, Evert; O’Shea, Desmond; Minton, Kevin; Strain, Martin; Vousden, Katherine; Rossant, Christine; Jermutus, Lutz; Minter, Ralph

    2012-01-01

    Antibodies are a unique class of proteins with the ability to adapt their binding sites for high affinity and high specificity to a multitude of antigens. Many analyses have been performed on antibody sequences and structures to elucidate which amino acids have a predominant role in antibody interactions with antigens. These studies have generally not distinguished between amino acids selected for broad antigen specificity in the primary immune response and those selected for high affinity in the secondary immune response. By studying a large data set of affinity matured antibodies derived from in vitro directed evolution experiments, we were able to specifically highlight a subset of amino acids associated with affinity improvements. In a comparison of affinity maturations using either tailored or full amino acid diversification, the tailored approach was found to be at least as effective at improving affinity while requiring fewer mutagenesis libraries than the traditional method. The resulting sequence data also highlight the potential for further reducing amino acid diversity for high affinity binding interactions. PMID:22926024

  20. Statistical modeling of transcription factor binding affinities predicts regulatory interactions.

    PubMed

    Manke, Thomas; Roider, Helge G; Vingron, Martin

    2008-03-01

    Recent experimental and theoretical efforts have highlighted the fact that binding of transcription factors to DNA can be more accurately described by continuous measures of their binding affinities, rather than a discrete description in terms of binding sites. While the binding affinities can be predicted from a physical model, it is often desirable to know the distribution of binding affinities for specific sequence backgrounds. In this paper, we present a statistical approach to derive the exact distribution for sequence models with fixed GC content. We demonstrate that the affinity distribution of almost all known transcription factors can be effectively parametrized by a class of generalized extreme value distributions. Moreover, this parameterization also describes the affinity distribution for sequence backgrounds with variable GC content, such as human promoter sequences. Our approach is applicable to arbitrary sequences and all transcription factors with known binding preferences that can be described in terms of a motif matrix. The statistical treatment also provides a proper framework to directly compare transcription factors with very different affinity distributions. This is illustrated by our analysis of human promoters with known binding sites, for many of which we could identify the known regulators as those with the highest affinity. The combination of physical model and statistical normalization provides a quantitative measure which ranks transcription factors for a given sequence, and which can be compared directly with large-scale binding data. Its successful application to human promoter sequences serves as an encouraging example of how the method can be applied to other sequences. PMID:18369429

  1. Trimmed strategy for affine registration of point sets

    NASA Astrophysics Data System (ADS)

    Peng, Yaxin; Ying, Shihui; Qin, Jing; Zeng, Tieyong

    2013-01-01

    We propose a trimmed strategy for affine registration of point sets using the Lie group parameterization. All affine transformations form an affine Lie group, thus finding an optimal transformation in registration is reduced to finding an optimal element in the affine group. Given two point sets (with outliers) and an initial element in the transformation group, we seek the optimal group element iteratively by minimizing an energy functional. This is conducted by sequentially finding the closest correspondence of two point sets, estimating the overlap rate of two sets, and finding the optimal affine transformation via the exponential map of the affine group. This method improves the trimmed iterative closest point algorithm (TrICP) in two aspects: (1) We use the Lie group parameterization to implement TrICP. (2) We also extend TrICP to the case of affine transformations. The performance of the proposed algorithm is demonstrated by using the LiDAR data acquired in the Mount St. Helens area. Both visual inspections and evaluation index (root mean trimmed squared distance) indicate that our algorithm performs consistently better than TrICP and other related algorithms, especially in the presence of outliers and missing points.

  2. Preening behavior of adult gyrfalcons tagged with backpack transmitters

    USGS Publications Warehouse

    Booms, T.L.; Schempf, P.F.; Fuller, M.R.

    2011-01-01

    Radio transmitters provide data that enhance understanding of raptor biology (Walls and Kenward 2007) and are now used to answer a multitude of research questions (Meyburg and Fuller 2007). However, transmitters affect the birds that carry them (Barron et al. 2010), and it is important to document and evaluate such effects (Casper 2009). For example, decreased survival has been documented in Prairie Falcons (Falco mexicanus; Steenhof et al. 2006), Northern Goshawks (Accipiter gentilis; Reynolds et al. 2004), and Spotted Owls (Strix occidentalis; Paton et al. 1991) tagged with radio transmitters. However, no such effects were reported for Peregrine Falcons (Falco peregrinus; Fuller et al. 1998, McGrady et al. 2002) and a number of other species (Kenward 2001). White and Garrott (1990) noted that in general, animals tagged with radio transmitters often altered their behaviors for 1–14 d after release during an adjustment period that included increased preening and grooming frequencies. Although more than 90 Gyrfalcons (Falco rusticolus) have been tagged with radio transmitters (e.g., Burnham 2007, McIntyre et al. 2009, T. Booms unpubl. data), the effects of transmitters on this species are not well documented. Anecdotal information suggests some Gyrfalcons might be negatively affected by radio-tagging (Booms et al. 2008). As part of a study investigating Gyrfalcon breeding biology, we conducted opportunistic, focused observations on two radio-tagged adult female Gyrfalcons and their unmarked mates. We here describe and quantify preening behavior of Gyrfalcons shortly after radio-tagging.

  3. Playing Tag with ANN: Boosted Top Identification with Pattern Recognition

    E-print Network

    Leandro G. Almeida; Mihailo Backovic; Mathieu Cliche; Seung J. Lee; Maxim Perelstein

    2015-01-23

    Many searches for physics beyond the Standard Model at the Large Hadron Collider (LHC) rely on top tagging algorithms, which discriminate between boosted hadronic top quarks and the much more common jets initiated by light quarks and gluons. We note that the hadronic calorimeter (HCAL) effectively takes a "digital image" of each jet, with pixel intensities given by energy deposits in individual HCAL cells. Viewed in this way, top tagging becomes a canonical pattern recognition problem. With this motivation, we present a novel top tagging algorithm based on an Artificial Neural Network (ANN), one of the most popular approaches to pattern recognition. The ANN is trained on a large sample of boosted tops and light quark/gluon jets, and is then applied to independent test samples. The ANN tagger demonstrated excellent performance in a Monte Carlo study: for example, for jets with p_T in the 1100-1200 GeV range, 60% top-tag efficiency can be achieved with a 4% mis-tag rate. We discuss the physical features of the jets identified by the ANN tagger as the most important for classification, as well as correlations between the ANN tagger and some of the familiar top-tagging observables and algorithms.

  4. Positional distribution of CLA in TAG of lamb tissues.

    PubMed

    Paterson, Lyn J; Weselake, Randall J; Mir, Priya S; Mir, Zahir

    2002-06-01

    The content and positional distribution of CLA in TAG fractions of lamb tissues was examined with either preformed CLA or the linoleic acid precursor of CLA in the diet as experimental treatments. The CLA content of phospholipid (PL) from these tissues was also examined. Thirteen lambs were randomized to the following dietary treatments: (i) control diet (no supplement); (ii) CLA supplementation (0.33 g d(-1) for 21 d prior to weaning) to milk-replacer of pre-ruminating lambs, or (iii) feeding linoleic acid-rich oil (6% safflower oil on a dry matter basis) to weaned ruminating lambs. At slaughter, tissue samples were procured from diaphragm, rib muscle, and subcutaneous (SC) adipose tissue. Safflower oil supplementation in the diet resulted in an increase in CLA content of the TAG from diaphragm, rib muscle, and SC adipose tissue by about threefold (P< 0.05) on a mol% basis. CLA was localized to the sn-1/3 positions of TAG. Animals that received pre-formed CLA, however, had increased proportions of CLA at the sn-2 position of TAG from SC adipose tissue, suggesting that there were tissue-specific dietary effects and possible age-related effects on the mode of FA incorporation into TAG. Safflower oil supplementation in the diet had no effect on the CLA content of PL from diaphragm, rib muscle, and SC adipose tissue, suggesting that CLA was preferentially incorporated into the TAG of these tissues. PMID:12120960

  5. Tags and seals to strengthen arms control verification

    SciTech Connect

    DeVolpi, A.

    1990-10-03

    Tags and seals have long been recognized as important tools in arms control. The trend in control of armaments is to limit militarily significant equipment that is capable of being verified through direct and cooperative means, chiefly on-site inspection or monitoring. Although this paper will focus on the CFE treaty, the role of tags and seals for other treaties will also be addressed. Published technology and concepts will be reviewed, based on open sources. Arms control verification tags are defined as unique identifiers designed to be tamper-revealing; in that respect, seals are similar, being used as indicators of unauthorized access. Tamper-revealing tags are intended as single-point markers, seals for two-point couplings, and nets for volume containment. Seals usually bind two separate components, such as a hatch or flange that provides access to a secure compartment or a valve that controls fluid flow. A tamper-revealing net might be comprised of a coupled fiberoptic bundle wrapped around an object. Sometimes the term ``seal`` is used to denote the tamper-revealing feature of a tag that is attached to a surface, but in this paper the tamper-indicating connection is considered to be part of the tag concept itself.

  6. Playing tag with ANN: boosted top identification with pattern recognition

    NASA Astrophysics Data System (ADS)

    Almeida, Leandro G.; Backovi?, Mihailo; Cliche, Mathieu; Lee, Seung J.; Perelstein, Maxim

    2015-07-01

    Many searches for physics beyond the Standard Model at the Large Hadron Collider (LHC) rely on top tagging algorithms, which discriminate between boosted hadronic top quarks and the much more common jets initiated by light quarks and gluons. We note that the hadronic calorimeter (HCAL) effectively takes a "digital image" of each jet, with pixel intensities given by energy deposits in individual HCAL cells. Viewed in this way, top tagging becomes a canonical pattern recognition problem. With this motivation, we present a novel top tagging algorithm based on an Artificial Neural Network (ANN), one of the most popular approaches to pattern recognition. The ANN is trained on a large sample of boosted tops and light quark/gluon jets, and is then applied to independent test samples. The ANN tagger demonstrated excellent performance in a Monte Carlo study: for example, for jets with p T in the 1100-1200 GeV range, 60% top-tag efficiency can be achieved with a 4% mis-tag rate. We discuss the physical features of the jets identified by the ANN tagger as the most important for classification, as well as correlations between the ANN tagger and some of the familiar top-tagging observables and algorithms.

  7. Affinity+: Semi-Structured Brainstorming on Large Displays

    SciTech Connect

    Burtner, Edwin R.; May, Richard A.; Scarberry, Randall E.; LaMothe, Ryan R.; Endert, Alexander

    2013-04-27

    Affinity diagraming is a powerful method for encouraging and capturing lateral thinking in a group environment. The Affinity+ Concept was designed to improve the collaborative brainstorm process through the use of large display surfaces in conjunction with mobile devices like smart phones and tablets. The system works by capturing the ideas digitally and allowing users to sort and group them on a large touch screen manually. Additionally, Affinity+ incorporates theme detection, topic clustering, and other processing algorithms that help bring structured analytic techniques to the process without requiring explicit leadership roles and other overhead typically involved in these activities.

  8. A constant affinity threshold for T cell tolerance

    PubMed Central

    Naeher, Dieter; Daniels, Mark A.; Hausmann, Barbara; Guillaume, Philippe; Luescher, Immanuel; Palmer, Ed

    2007-01-01

    T cell tolerance depends on the T cell receptor's affinity for peptide/major histocompatibility complex (MHC) ligand; this critical parameter determines whether a thymocyte will be included (positive selection) or excluded (negative selection) from the T cell repertoire. A quantitative analysis of ligand binding was performed using an experimental system permitting receptor–coreceptor interactions on live cells under physiological conditions. Using three transgenic mouse strains expressing distinct class I MHC–restricted T cell receptors, we determined the affinity that defines the threshold for negative selection. The affinity threshold for self-tolerance appears to be a constant for cytotoxic T lymphocytes. PMID:17938233

  9. Micro-structured peptide surfaces for the detection of high-affinity peptide-receptor interactions in living cells.

    PubMed

    Lipp, Anna-Maria; Ji, Bozhi; Hager, Roland; Haas, Sandra; Schweiggl, Simone; Sonnleitner, Alois; Haselgrübler, Thomas

    2015-12-15

    Peptide ligands have great potential as selective agents for diagnostic imaging and therapeutic targeting of human cancers. A number of high-throughput assays for screening potential candidate peptides have been developed. Although these screening assays are indispensable for the identification of peptide ligands at a large scale, it is crucial to validate peptide binding and selectivity for targeted receptors in a live-cell context. For testing high-affinity peptide-receptor interactions in the plasma membrane of living cells, we developed cell-resistant, micro-structured glass surfaces with high-density and high-contrast peptide features. Cell adhesion and recruitment of fluorescent receptors to micro-patterned peptides in the live-cell membrane were evaluated by reflection interference contrast (RIC) and total internal reflection (TIRF) microscopy, respectively. To demonstrate both the specificity and modularity of the assay, co-patterning of fluorescent receptors with three different immobilized micro-structured ligands was shown: first, interaction of green fluorescent protein (GFP)-tagged epidermal growth factor (EGF) receptor expressed in Jurkat cells with immobilized EGF was detected and quantified. Second, using Jurkat cells, we demonstrated specific interaction of yellow fluorescent protein (YFP)-tagged ?3 integrin with c(RGDfK) peptide. Third, we identified indirect recruitment of GFP-tagged ?5 integrin to an 11-mer peptide. In summary, our results show that the developed micro-structured surfaces are a useful tool for the validation and quantification of peptide-receptor interactions in their natural cellular environment. PMID:26210593

  10. ______ Number of people attending Please print your name(s) as you would like it/them to appear on your name tag(s).

    E-print Network

    Sheridan, Jennifer

    q ______ Number of people attending Please print your name(s) as you would like it/them to appear on your name tag(s). Name(s: ____ ____ ____ ____ ____ ____ ____ ____ ____ ____ ____ ____ ____ ____ ____ ____ Cardholder's Name (please print): ___________________________________________________________ Cardholder

  11. Aspects of affine Toda field theory

    SciTech Connect

    Corrigan, E. )

    1992-06-01

    This paper describes affine Toda field theory which is a theory of r scalar fields in two-dimensional Minkowski space-time, where r is the rank of a compact semi-simple Lie algebra g. The classical field theory is determined by the lagrangian density L = 1/2 {partial derivative}{sub {rho}}{phi}{sup a}{partial derivative}{sup {mu}}{phi}{sup a} {minus} V({phi}) where V({phi}) = m{sup 2}/{beta}{sup 2} {Sigma}{sub 0}{sup r}n{sub i}e{sup {beta}{alpha}{sub i} {center dot} {phi}}. m and {beta} are real, classically unimportant constants, {alpha}{sub i} i = 1, . . . ,r are the simple roots of the Lie algebra g, and {alpha}{sub 0} = {Sigma}{sub 1}{sup 4} n{alpha}{sub i} is a linear combination of the simple roots; it corresponds to the extra spot on an extended Dynkin diagram for g. A reasonable question to ask is whether the classical integrability survives into the quantum field theory and, if so, what is the spectrum and to what extent is it possible to calculate explicitly quantities of interest such as S-matrices and form factors. The recent discoveries leave no doubt that these relatively simple models have much structure and their study (even in the {beta}{sup 2} {gt} 0 regime) will be informative. In this short review, the ADE series of Lie algebras will be singled out for special attention.

  12. Jet Dipolarity: Top Tagging with Color Flow

    SciTech Connect

    Hook, Anson; Jankowiak, Martin; Wacker, Jay G.; /SLAC

    2011-08-12

    A new jet observable, dipolarity, is introduced that can distinguish whether a pair of subjets arises from a color singlet source. This observable is incorporated into the HEPTopTagger and is shown to improve discrimination between top jets and QCD jets for moderate to high p{sub T}. The impressive resolution of the ATLAS and CMS detectors means that a typical QCD jet at the LHC deposits energy in {Omicron}(10-100) calorimeter cells. Such fine-grained calorimetry allows for jets to be studied in much greater detail than previously, with sophisticated versions of current techniques making it possible to measure more than just the bulk properties of jets (e.g. event jet multiplicities or jet masses). One goal of the LHC is to employ these techniques to extend the amount of information available from each jet, allowing for a broader probe of the properties of QCD. The past several years have seen significant progress in developing such jet substructure techniques. A number of general purpose tools have been developed, including: (i) top-tagging algorithms designed for use at both lower and higher p{sub T} as well as (ii) jet grooming techniques such as filtering, pruning, and trimming, which are designed to improve jet mass resolution. Jet substructure techniques have also been studied in the context of specific particle searches, where they have been shown to substantially extend the reach of traditional search techniques in a wide variety of scenarios, including for example boosted Higgses, neutral spin-one resonances, searches for supersymmetry, and many others. Despite these many successes, however, there is every reason to expect that there remains room for refinement of jet substructure techniques.

  13. Measuring auditory selective attention using frequency tagging

    PubMed Central

    Bharadwaj, Hari M.; Lee, Adrian K. C.; Shinn-Cunningham, Barbara G.

    2014-01-01

    Frequency tagging of sensory inputs (presenting stimuli that fluctuate periodically at rates to which the cortex can phase lock) has been used to study attentional modulation of neural responses to inputs in different sensory modalities. For visual inputs, the visual steady-state response (VSSR) at the frequency modulating an attended object is enhanced, while the VSSR to a distracting object is suppressed. In contrast, the effect of attention on the auditory steady-state response (ASSR) is inconsistent across studies. However, most auditory studies analyzed results at the sensor level or used only a small number of equivalent current dipoles to fit cortical responses. In addition, most studies of auditory spatial attention used dichotic stimuli (independent signals at the ears) rather than more natural, binaural stimuli. Here, we asked whether these methodological choices help explain discrepant results. Listeners attended to one of two competing speech streams, one simulated from the left and one from the right, that were modulated at different frequencies. Using distributed source modeling of magnetoencephalography results, we estimate how spatially directed attention modulates the ASSR in neural regions across the whole brain. Attention enhances the ASSR power at the frequency of the attended stream in contralateral auditory cortex. The attended-stream modulation frequency also drives phase-locked responses in the left (but not right) precentral sulcus (lPCS), a region implicated in control of eye gaze and visual spatial attention. Importantly, this region shows no phase locking to the distracting stream. Results suggest that the lPCS in engaged in an attention-specific manner. Modeling results that take account of the geometry and phases of the cortical sources phase locked to the two streams (including hemispheric asymmetry of lPCS activity) help to explain why past ASSR studies of auditory spatial attention yield seemingly contradictory results. PMID:24550794

  14. Anchor and visible implant elastomer tag retention by hatchery rainbow trout stocked into an Ozark stream

    USGS Publications Warehouse

    Walsh, M.G.; Winkelman, D.L.

    2004-01-01

    As part of a study to evaluate the stocking of rainbow trout Oncorhynchus mykiss in an Oklahoma Ozark stream, we tagged 2,542 hatchery-reared rainbow trout (123-366 mm total length) with individually numbered Floy FD-68B anchor tags and visible implant fluorescent elastomer (VIE) tags. We experimentally stocked double-marked rainbow trout into a small northeastern Oklahoma stream from November 2001 to March 2002 and resampled them monthly from December 2001 to October 2002 by electrofishing. Anchor tag retention was 91% through 6 months, and VIE tag retention was 96% through 6 months despite extensive handling of fish within 24 h of tagging. Based on the ease of application, high visibility, and high retention observed in this study, we recommend the use of VIE tags as a batch mark in similarly sized, similarly pigmented fish. The retention of VIE tags was slightly higher than that of anchor tags, and cost per fish was less for VIE than for anchor tags. However, VIE tags would have limited utility if numerous individual tags are necessary; therefore, we recommend anchor tags as individual marks in similarly sized salmonids. Retention for both tag types was relatively high and could be corrected for when estimating population parameters from tagging data.

  15. Identifying Protein-Protein Interaction in Drosophila Adult Heads by Tandem Affinity Purification (TAP)

    PubMed Central

    Tian, Xiaolin; Zhu, Mingwei; Li, Long; Wu, Chunlai

    2014-01-01

    Genetic screens conducted using Drosophilamelanogaster (fruit fly) have made numerous milestone discoveries in the advance of biological sciences. However, the use of biochemical screens aimed at extending the knowledge gained from genetic analysis was explored only recently. Here we describe a method to purify the protein complex that associates with any protein of interest from adult fly heads. This method takes advantage of the Drosophila GAL4/UAS system to express a bait protein fused with a Tandem Affinity Purification (TAP) tag in fly neurons in vivo, and then implements two rounds of purification using a TAP procedure similar to the one originally established in yeast1 to purify the interacting protein complex. At the end of this procedure, a mixture of multiple protein complexes is obtained whose molecular identities can be determined by mass spectrometry. Validation of the candidate proteins will benefit from the resource and ease of performing loss-of-function studies in flies. Similar approaches can be applied to other fly tissues. We believe that the combination of genetic manipulations and this proteomic approach in the fly model system holds tremendous potential for tackling fundamental problems in the field of neurobiology and beyond. PMID:24335807

  16. Soluble prokaryotic expression and purification of crotamine using an N-terminal maltose-binding protein tag.

    PubMed

    Vu, Thu Trang Thi; Jeong, Boram; Yu, Jing; Koo, Bon-Kyung; Jo, Su-Hyun; Robinson, Robert Charles; Choe, Han

    2014-12-15

    Crotamine is a peptide toxin found in the venom of the rattlesnake Crotalus durissus terrificus. Interestingly, crotamine demonstrates promising anticancer, antimicrobial, and antifungal activities. The crotamine peptide can also deliver plasmids into rapidly dividing cells, such as cancer and stem cells, and demonstrates potent analgesic effects. Efficiently producing crotamine in mammalian cells is difficult because it is both cell-permeable and cytotoxic. Prokaryotic expression of this peptide is also difficult to maintain because it does not fold properly in the cytoplasm, resulting in aggregation and in the formation of inclusion bodies. In our current study, we show for the first time that N-terminal fusion with three protein tags-N-utilization substance protein A (NusA), protein disulfide isomerase b'a' domain (PDIb'a'), and maltose-binding protein (MBP)-enables the soluble overexpression of crotamine in the cytoplasm of Escherichia coli. MBP-tagged crotamine was purified using Ni affinity, anion exchange, and MBP chromatography. The tag was cleaved using TEV protease, and the final product was pure on a silver-stained gels. In total, 0.9 mg pure crotamine was obtained from each liter of bacterial culture with endotoxin level approximately 0.15 EU/?g, which is low enough to use in biomedical applications. The identity and intramolecular disulfide bonds were confirmed using MALDI-TOF MS analysis. Purified crotamine inhibited the hKv1.3 channel (but not hKv1.5) in a dose-dependent manner with IC50 value of 67.2 ± 44.7 nM (n = 10), indicating the correct protein folding. The crotamine product fused with MBP at its N-terminus also inhibited the hKv1.3 channel, suggesting that the N-terminus is not involved in the channel binding of the toxin. PMID:25448388

  17. An in vivo imaging-based assay for detecting protein interactions over a wide range of binding affinities

    SciTech Connect

    Fowlkes, Jason Davidson; Owens, Elizabeth T; Standaert, Robert F; Pelletier, Dale A; Hurst, Gregory {Greg} B; Doktycz, Mitchel John; Morrell-Falvey, Jennifer L; Billings, Amanda N

    2009-01-01

    Identifying and characterizing protein interactions are fundamental steps towards understanding and modeling biological networks. Methods that detect protein interactions in intact cells rather than buffered solutions are likely more relevant to natural systems since molecular crowding events in the cytosol can influence the diffusion and reactivity of individual proteins. One in vivo, imaging-based method relies on the co-localization of two proteins of interest fused to DivIVA, a cell division protein from Bacillus subtilis, and green fluorescent protein (GFP). We have modified this imaging-based assay to facilitate rapid cloning by constructing new vectors encoding N- and C-terminal DivIVA or GFP molecular tag fusions based on site-specific recombination technology. The sensitivity of the assay was defined using a well-characterized protein interaction system involving the eukaryotic nuclear import receptor subunit, Importin (Imp ) and variant nuclear localization signals (NLS) representing a range of binding affinities. These data demonstrate that the modified co-localization assay is sensitive enough to detect protein interactions with Kd values that span over four orders of magnitude (1nM to 15 M). Lastly, this assay was used to confirm numerous protein interactions identified from mass spectrometry-based analyses of affinity isolates as part of an interactome mapping project in Rhodopseudomonas palustris

  18. New tools for target identification by affinity chromatography 

    E-print Network

    Landi, Felicetta

    2011-06-27

    The recovery of the selected biological material in affinity-based separations relies on reversing the biological interaction responsible for the binding. General elution methods which are independent of the bioaffinity ...

  19. Vibrations of circular orthotropic plates in affine space

    NASA Technical Reports Server (NTRS)

    Oyibo, G. A.; Brunelle, E. J.

    1985-01-01

    The vibration of an initially compressed plate having a circular geometry and orthotropy is examined in an affine space. The classical linear plate theory and Hamilton's principle are employed. The equations of motion of the plate are particularly simple in the chosen affine space, permitting a free-vibration study of the entire spectrum of composite materials with polar orthotropy. Approximate but very accurate standing-wave-type mode shapes are used in solving the essentially double eigenvalue problem to determine the effects of midplane forces on the vibration frequencies of the plate. The results indicate that the affine-space frequency increases with increasing stiffness ratio but decreases with increasing midplane compression. It is also discovered that, contrary to the trends observed for rectangular geometry and orthotropy by Oyibo (1981), Brunelle (1982), and Brunelle and Oyibo (1983), the affine-space frequency increases with increasing generalized Poisson's ratio.

  20. Integrated affinity and electrophoresis systems for multiplexed biomarker analysis.

    PubMed

    Nge, Pamela N; Pagaduan, Jayson V; Yang, Weichun; Woolley, Adam T

    2013-01-01

    The integration of affinity columns in microfluidic devices generates a micro-total analysis system which has high value in applications such as analyte extraction and preconcentration. In this chapter we describe the preparation of affinity columns in situ by photopolymerization of acrylate monomers. The epoxy groups on the columns are further functionalized with antibodies to form affinity columns. We describe in detail the use of our affinity columns in extracting cancer biomarkers from model mixtures and blood serum. The purified biomarkers are then eluted from the column, separated by microchip capillary electrophoresis, and detected by laser-induced fluorescence. Our procedures allow efficient sample pretreatment and preconcentration, as well as simultaneous and rapid quantification of multiple biomarkers. PMID:22976102

  1. COMPARATIVE OXYGEN AFFINITY OF FISH AND MAMMALIAN MYOGLOBINS

    EPA Science Inventory

    Myoglobins from rat, coho salmon (Oncorhynchus kisutch), buffalo sculpin (Enophrys bison) hearts, and yellowfin tuna (Thunnus albacares) red skeletal muscle were partially purified and their O2 binding affinities determined. Commercially prepared sperm whale myoglobin was employe...

  2. Antibody Affinity Maturation in Fishes-Our Current Understanding.

    PubMed

    Magor, Brad G

    2015-01-01

    It has long been believed that fish lack antibody affinity maturation, in part because they were thought to lack germinal centers. Recent research done on sharks and bony fishes indicates that these early vertebrates are able to affinity mature their antibodies. This article reviews the functionality of the fish homologue of the immunoglobulin (Ig) mutator enzyme activation-induced cytidine deaminase (AID). We also consider the protein and molecular evidence for Ig somatic hypermutation and antibody affinity maturation. In the context of recent evidence for a putative proto-germinal center in fishes we propose some possible reasons that observed affinity maturation in fishes often seems lacking and propose future work that might shed further light on this process in fishes. PMID:26264036

  3. Antibody Affinity Maturation in Fishes—Our Current Understanding

    PubMed Central

    Magor, Brad G.

    2015-01-01

    It has long been believed that fish lack antibody affinity maturation, in part because they were thought to lack germinal centers. Recent research done on sharks and bony fishes indicates that these early vertebrates are able to affinity mature their antibodies. This article reviews the functionality of the fish homologue of the immunoglobulin (Ig) mutator enzyme activation-induced cytidine deaminase (AID). We also consider the protein and molecular evidence for Ig somatic hypermutation and antibody affinity maturation. In the context of recent evidence for a putative proto-germinal center in fishes we propose some possible reasons that observed affinity maturation in fishes often seems lacking and propose future work that might shed further light on this process in fishes. PMID:26264036

  4. A Tool for Conditions Tag Management in ATLAS

    NASA Astrophysics Data System (ADS)

    Sharmazanashvili, A.; Batiashvili, G.; Gvaberidze, G.; Shekriladze, L.; Formica, A.; Atlas Collaboration

    2014-06-01

    ATLAS Conditions data include about 2 TB in a relational database and 400 GB of files referenced from the database. Conditions data is entered and retrieved using COOL, the API for accessing data in the LCG Conditions Database infrastructure. It is managed using an ATLAS-customized python based tool set. Conditions data are required for every reconstruction and simulation job, so access to them is crucial for all aspects of ATLAS data taking and analysis, as well as by preceding tasks to derive optimal corrections to reconstruction. Optimized sets of conditions for processing are accomplished using strict version control on those conditions: a process which assigns COOL Tags to sets of conditions, and then unifies those conditions over data-taking intervals into a COOL Global Tag. This Global Tag identifies the set of conditions used to process data so that the underlying conditions can be uniquely identified with 100% reproducibility should the processing be executed again. Understanding shifts in the underlying conditions from one tag to another and ensuring interval completeness for all detectors for a set of runs to be processed is a complex task, requiring tools beyond the above mentioned python utilities. Therefore, a JavaScript /PHP based utility called the Conditions Tag Browser (CTB) has been developed. CTB gives detector and conditions experts the possibility to navigate through the different databases and COOL folders; explore the content of given tags and the differences between them, as well as their extent in time; visualize the content of channels associated with leaf tags. This report describes the structure and PHP/ JavaScript classes of functions of the CTB.

  5. Biological properties of purified recombinant HCV particles with an epitope-tagged envelope

    SciTech Connect

    Takahashi, Hitoshi; Akazawa, Daisuke; Toray Industries, Inc., Kanagawa ; Kato, Takanobu; Date, Tomoko; Shirakura, Masayuki; Toray Industries, Inc., Kanagawa ; Nakamura, Noriko; Mochizuki, Hidenori; Tanaka-Kaneko, Keiko; Sata, Tetsutaro; Tanaka, Yasuhito; Mizokami, Masashi; Suzuki, Tetsuro; Wakita, Takaji

    2010-05-14

    To establish a simple system for purification of recombinant infectious hepatitis C virus (HCV) particles, we designed a chimeric J6/JFH-1 virus with a FLAG (FL)-epitope-tagged sequence at the N-terminal region of the E2 hypervariable region-1 (HVR1) gene (J6/JFH-1/1FL). We found that introduction of an adaptive mutation at the potential N-glycosylation site (E2N151K) leads to efficient production of the chimeric virus. This finding suggests the involvement of glycosylation at Asn within the envelope protein(s) in HCV morphogenesis. To further analyze the biological properties of the purified recombinant HCV particles, we developed a strategy for large-scale production and purification of recombinant J6/JFH-1/1FL/E2N151K. Infectious particles were purified from the culture medium of J6/JFH-1/1FL/E2N151K-infected Huh-7 cells using anti-FLAG affinity chromatography in combination with ultrafiltration. Electron microscopy of the purified particles using negative staining showed spherical particle structures with a diameter of 40-60 nm and spike-like projections. Purified HCV particle-immunization induced both an anti-E2 and an anti-FLAG antibody response in immunized mice. This strategy may contribute to future detailed analysis of HCV particle structure and to HCV vaccine development.

  6. Novel affinity purification of xanthine oxidase from Arthrobacter M3.

    PubMed

    Zhang, Yuran; Xin, Yu; Yang, Hailin; Zhang, Ling; Xia, Xiaole; Tong, Yanjun; Chen, Yi; Ma, Li; Wang, Wu

    2012-10-01

    An affinity protocol for purification of xanthine oxidase (XOD) from Arthrobacter M3 was developed. The isolation procedure consisted of only three steps, ammonium sulfate precipitation, affinity extraction to exclude the major impurities, and the final refining procedure with DEAE ion-exchange chromatography for removal of minor contaminants. In this affinity preparation, guanine, an analogue of xanthine, was chosen as the affinity ligand, and was coupled with Sepharose 4B through spacers composed of epichlorohydrin and ethylenediamine. Crude protein has been run through ammonium sulfate precipitation and the affinity column, 99.1% of proteins were removed. After DEAE ion-exchange chromatography, the purity of the refined XOD was 97.5% by Native-PAGE analysis. The activity recovery of purified XOD (36.1%) was almost higher than that of other methods reported. Reducing SDS-PAGE analysis showed that the purified XOD (one band in Native-PAGE analysis) showed two polypeptides with the molecular weights ?35kDa and ?100kDa, respectively. The desorption constant K(d) and the theoretical maximum absorption Q(max) on the affinity medium were 3.0?g/ml and 2.2mg/g medium in absorption analysis. PMID:22954965

  7. Enhancing IHE XDS for federated clinical affinity domain support.

    PubMed

    Dogac, Asuman; Laleci, Gokce B; Aden, Thomas; Eichelberg, Marco

    2007-03-01

    One of the key problems in healthcare informatics is the inability to share patient records across enterprises. To address this problem, an important industry initiative called "integrating the healthcare enterprise (IHE)" specified the "cross enterprise document sharing (XDS)" profile. In the IHE XDS, healthcare enterprises that agree to work together form a "clinical affinity domain" and store healthcare documents in an ebXML registry/repository architecture to facilitate their sharing. The affinity domains also agree on a common set of policies such as coding lists to be used to annotate clinical documents in the registry/repository and the common schemes for patient identification. However, since patients expect their records to follow them as they move from one clinical affinity domain to another, there is a need for affinity domains to be federated to enable information exchange. In this paper, we describe how IHE XDS can be enhanced to support federated clinical affinity domains. We demonstrate that federation of affinity domains are facilitated when ontologies, rather than coding term lists, are used to annotate clinical documents. Furthermore, we describe a patient identification protocol that eliminates the need to keep a master patient index file for the federation. PMID:17390991

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

    PubMed Central

    2014-01-01

    With smartphone distribution becoming common and robotic applications on the rise, social tagging services for various applications including robotic domains have advanced significantly. Though social tagging plays an important role when users are finding the exact information through web search, reliability and semantic relation between web contents and tags are not considered. Spams are making ill use of this aspect and put irrelevant tags deliberately on contents and induce users to advertise contents when they click items of search results. Therefore, this study proposes a detection method for tag-ranking manipulation to solve the problem of the existing methods which cannot guarantee the reliability of tagging. Similarity is measured for ranking the grade of registered tag on the contents, and weighted values of each tag are measured by means of synonym relevance, frequency, and semantic distances between tags. Lastly, experimental evaluation results are provided and its efficiency and accuracy are verified through them. PMID:25114975

  9. Tag jumps illuminated - reducing sequence-to-sample misidentifications in metabarcoding studies.

    PubMed

    Schnell, Ida Baerholm; Bohmann, Kristine; Gilbert, M Thomas P

    2015-11-01

    Metabarcoding of environmental samples on second-generation sequencing platforms has rapidly become a valuable tool for ecological studies. A fundamental assumption of this approach is the reliance on being able to track tagged amplicons back to the samples from which they originated. In this study, we address the problem of sequences in metabarcoding sequencing outputs with false combinations of used tags (tag jumps). Unless these sequences can be identified and excluded from downstream analyses, tag jumps creating sequences with false, but already used tag combinations, can cause incorrect assignment of sequences to samples and artificially inflate diversity. In this study, we document and investigate tag jumping in metabarcoding studies on Illumina sequencing platforms by amplifying mixed-template extracts obtained from bat droppings and leech gut contents with tagged generic arthropod and mammal primers, respectively. We found that an average of 2.6% and 2.1% of sequences had tag combinations, which could be explained by tag jumping in the leech and bat diet study, respectively. We suggest that tag jumping can happen during blunt-ending of pools of tagged amplicons during library build and as a consequence of chimera formation during bulk amplification of tagged amplicons during library index PCR. We argue that tag jumping and contamination between libraries represents a considerable challenge for Illumina-based metabarcoding studies, and suggest measures to avoid false assignment of tag jumping-derived sequences to samples. PMID:25740652

  10. OSIRI-REx Touch and Go (TAG) Navigation Performance

    NASA Technical Reports Server (NTRS)

    Berry, Kevin; Antreasian, Peter; Moreau, Michael C.; May, Alex; Sutter, Brian

    2015-01-01

    The Origins Spectral Interpretation Resource Identification Security Regolith Explorer (OSIRIS-REx) mission is a NASA New Frontiers mission launching in 2016 to rendezvous with the near-Earth asteroid (101955) Bennu in late 2018. Following an extensive campaign of proximity operations activities to characterize the properties of Bennu and select a suitable sample site, OSIRIS-REx will fly a Touch-And-Go (TAG) trajectory to the asteroid's surface to obtain a regolith sample. The paper summarizes the mission design of the TAG sequence, the propulsive maneuvers required to achieve the trajectory, and the sequence of events leading up to the TAG event. The paper also summarizes the Monte-Carlo simulation of the TAG sequence and presents analysis results that demonstrate the ability to conduct the TAG within 25 meters of the selected sample site and 2 cm/s of the targeted contact velocity. The paper describes some of the challenges associated with conducting precision navigation operations and ultimately contacting a very small asteroid.

  11. OSIRIS-REx Touch-And-Go (TAG) Navigation Performance

    NASA Technical Reports Server (NTRS)

    Berry, Kevin; Antreasian, Peter; Moreau, Michael C.; May, Alex; Sutter, Brian

    2015-01-01

    The Origins Spectral Interpretation Resource identification Security Regolith Explorer (OSIRIS-REx) mission is a NASA New Frontiers mission launching in 2016 to rendezvous with the near-Earth asteroid (101955) Bennu in late 2018. Following an extensive campaign of proximity operations activities to characterize the properties of Bennu and select a suitable sample site, OSIRIES-REx will fly a Touch-And-Go (TAG) trajectory to the asteroid's surface to obtain a regolith sample. The paper summarizes the mission design of the TAG sequence, the propulsive required to achieve the trajectory, and the sequence of events leading up to the TAG event. The paper will summarize the Monte-Carlo simulation of the TAG sequence and present analysis results that demonstrate the ability to conduct the TAG within 25 meters of the selected sample site and +-2 cms of the targeted contact velocity. The paper will describe some of the challenges associated with conducting precision navigation operations and ultimately contacting a very small asteroid.

  12. Theory and experiments on Peano and Hilbert curve RFID tags

    NASA Astrophysics Data System (ADS)

    McVay, John; Hoorfar, Ahmad; Engheta, Nader

    2006-05-01

    Recently, there has been considerable interest in the area of Radio Frequency Identification (RFID) and Radio Frequency Tagging (RFTAG). This emerging area of interest can be applied for inventory control (commercial) as well as friend/foe identification (military) to name but a few. The current technology can be broken down into two main groups, namely passive and active RFID tags. Utilization of Space-Filling Curve (SFC) geometries, such as the Peano and Hilbert curves, has been recently investigated for use in completely passive RFID applications [1, 2]. In this work, we give an overview of our work on the space-filling curves and the potential for utilizing the electrically small, resonant characteristics of these curves for use in RFID technologies with an emphasis on the challenging issues involved when attempting to tag conductive objects. In particular, we investigate the possible use of these tags in conjunction with high impedance ground-planes made of Hilbert or Peano curve inclusions [3, 4] to develop electrically small RFID tags that may also radiate efficiently, within close proximity of large conductive objects [5].

  13. Reliable Identification of RFID Tags Using Multiple Independent Reader Sessions

    E-print Network

    Jacobsen, Rasmus; Popovski, Petar; Larsen, Torben

    2009-01-01

    Radio Frequency Identification (RFID) systems are gaining momentum in various applications of logistics, inventory, etc. A generic problem in such systems is to ensure that the RFID readers can reliably read a set of RFID tags, such that the probability of missing tags stays below an acceptable value. A tag may be missing (left unread) due to errors in the communication link towards the reader e.g. due to obstacles in the radio path. The present paper proposes techniques that use multiple reader sessions, during which the system of readers obtains a running estimate of the probability to have at least one tag missing. Based on such an estimate, it is decided whether an additional reader session is required. Two methods are proposed, they rely on the statistical independence of the tag reading errors across different reader sessions, which is a plausible assumption when e.g. each reader session is executed on different readers. The first method uses statistical relationships that are valid when the reader sess...

  14. Utility of biological sensor tags in animal conservation.

    PubMed

    Wilson, A D M; Wikelski, M; Wilson, R P; Cooke, S J

    2015-08-01

    Electronic tags (both biotelemetry and biologging platforms) have informed conservation and resource management policy and practice by providing vital information on the spatial ecology of animals and their environments. However, the extent of the contribution of biological sensors (within electronic tags) that measure an animal's state (e.g., heart rate, body temperature, and details of locomotion and energetics) is less clear. A literature review revealed that, despite a growing number of commercially available state sensor tags and enormous application potential for such devices in animal biology, there are relatively few examples of their application to conservation. Existing applications fell under 4 main themes: quantifying disturbance (e.g., ecotourism, vehicular and aircraft traffic), examining the effects of environmental change (e.g., climate change), understanding the consequences of habitat use and selection, and estimating energy expenditure. We also identified several other ways in which sensor tags could benefit conservation, such as determining the potential efficacy of management interventions. With increasing sensor diversity of commercially available platforms, less invasive attachment techniques, smaller device sizes, and more researchers embracing such technology, we suggest that biological sensor tags be considered a part of the necessary toolbox for conservation. This approach can measure (in real time) the state of free-ranging animals and thus provide managers with objective, timely, relevant, and accurate data to inform policy and decision making. PMID:25833384

  15. Electronic tagging and population structure of Atlantic bluefin tuna.

    PubMed

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

    2005-04-28

    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 of individual fish (n = 330). Geoposition data delineate two populations, one using spawning grounds in the Gulf of Mexico and another from the Mediterranean Sea. Transatlantic movements of western-tagged bluefin tuna reveal site fidelity to known spawning areas in the Mediterranean Sea. Bluefin tuna that occupy western spawning grounds move to central and eastern Atlantic foraging grounds. Our results are consistent with two populations of bluefin tuna with distinct spawning areas that overlap on North Atlantic foraging grounds. Electronic tagging locations, when combined with US pelagic longline observer and logbook catch data, identify hot spots for spawning bluefin tuna in the northern slope waters of the Gulf of Mexico. Restrictions on the time and area where longlining occurs would reduce incidental catch mortalities on western spawning grounds. PMID:15858572

  16. Estimating fishing mortality, natural mortality, and selectivity using recoveries from tagging young fish

    USGS Publications Warehouse

    Jiang, H.; Brownie, C.; Hightower, J.E.; Pollock, K.H.

    2007-01-01

    Current methods for estimation of age- and year-specific instantaneous mortality rates based on multiyear, multiple-age tagging studies assume that it is feasible to tag fish in a wide range of ages. For some species, however, only the youngest one or two age-classes are readily available for tagging. Given the practical advantages of tagging young fish only, an important question is whether such studies would provide the information needed for estimation of age-dependent mortality rates. We investigated three designs: tagging only the youngest available age-class, tagging the two youngest age-classes, and tagging the first five age-classes. We carried out simulation studies to assess estimator performance under these three designs, in each case assuming the same total number of tagged fish. Data were generated assuming fishing mortality rates to be age and year dependent and natural mortality rates to be constant or with limited age dependence. Estimator performance is best when fish are tagged in five age-classes, and tagging fish in the two youngest age-classes shows substantial improvement compared with tagging one age-class only. External information about the tag-reporting rate is necessary to obtain estimators with reasonable properties, especially in the case of models with age-dependent natural mortality. Such information can be obtained from auxiliary studies by means of high-reward tags or planted tags. Collecting recovery information for several additional years after the last release produces small improvements in precision and bias. If tagging fish in multiple age-classes is impractical, reasonable precision can be obtained by tagging one or preferably two age-classes and obtaining supplemental information on the reporting rate. For illustration, estimates of age-dependent fishing and natural mortality rates were obtained from tag returns on Chesapeake Bay striped bass Morone saxatilis tagged at ages 3 and 4 years. ?? Copyright by the American Fisheries Society 2007.

  17. Proton affinity of methyl nitrate - Less than proton affinity of nitric acid

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Rice, Julia E.

    1992-01-01

    Several state-of-the-art ab initio quantum mechanical methods were used to investigate the equilibrium structure, dipole moments, harmonic vibrational frequencies, and IR intensities of methyl nitrate, methanol, and several structures of protonated methyl nitrate, using the same theoretical methods as in an earlier study (Lee and Rice, 1992) of nitric acid. The ab initio results for methyl nitrate and methanol were found to be in good agreement with available experimental data. The proton affinity (PA) of methyl nitrate was calculated to be 176.9 +/-5 kcal/mol, in excellent agreement with the experimental value 176 kcal/mol obtained by Attina et al. (1987) and less than the PA value of nitric acid. An explanation of the discrepancy of the present results with those of an earlier study on protonated nitric acid is proposed.

  18. Indexing of Tagged Moving Objects over Localized Trajectory with Time Intervals in RFID Systems

    NASA Astrophysics Data System (ADS)

    Kim, Jongwan; Oh, Dukshin; Kim, Keecheon

    Since a radio frequency identification (RFID) transponder (tag) generates both location and time information when it enters and leaves a reader, the trajectory of a moving, tagged object can be traced. Due to the time intervals between entries to successive readers, during which tags are not tracked, accurate tracing of complete trajectories can be difficult. To overcome this problem, we propose a tag trajectory indexing scheme called TR-tree (R-tree-based tag trajectory index) that can trace tags by combining the local trajectories at each reader. In experiments, this scheme showed superior performance compared with other indices.

  19. Movements of striped mullet, Mugil cephalus, tagged in Everglades National Park, Florida

    USGS Publications Warehouse

    Funicelli, N.A.; Meineke, D.A.; Bryant, H.E.; Dewey, M.R.; Ludwig, G.M.; Mengel, L.S.

    1989-01-01

    The movements of striped mullet, Mugil cephalus, were studied from fish tagged in Everglades National Park. Florida. A total of 16,604 fish were tagged from March 1984 to September 1985. During the period December 1984 through February 1985 recaptured tagged fish moved significantly further and more northerly out of the Park's waters than they did the rest of the year. Tags were returned from 2.8% of the fish tagged along the west coast and from 0.3% of the fish tagged in Florida Bay and west coast mullet form a series of spatially overlapping stocks.

  20. $B$ flavour tagging using charm decays at the LHCb experiment

    E-print Network

    LHCb collaboration; R. Aaij; B. Adeva; M. Adinolfi; A. Affolder; Z. Ajaltouni; S. Akar; J. Albrecht; F. Alessio; M. Alexander; S. Ali; G. Alkhazov; P. Alvarez Cartelle; A. A. Alves Jr; S. Amato; S. Amerio; Y. Amhis; L. An; L. Anderlini; J. Anderson; G. Andreassi; M. Andreotti; J. E. Andrews; R. B. Appleby; O. Aquines Gutierrez; F. Archilli; P. d'Argent; A. Artamonov; M. Artuso; E. Aslanides; G. Auriemma; M. Baalouch; S. Bachmann; J. J. Back; A. Badalov; C. Baesso; W. Baldini; R. J. Barlow; C. Barschel; S. Barsuk; W. Barter; V. Batozskaya; V. Battista; A. Bay; L. Beaucourt; J. Beddow; F. Bedeschi; I. Bediaga; L. J. Bel; V. Bellee; N. Belloli; I. Belyaev; E. Ben-Haim; G. Bencivenni; S. Benson; J. Benton; A. Berezhnoy; R. Bernet; A. Bertolin; M. -O. Bettler; M. van Beuzekom; A. Bien; S. Bifani; P. Billoir; T. Bird; A. Birnkraut; A. Bizzeti; T. Blake; F. Blanc; J. Blouw; S. Blusk; V. Bocci; A. Bondar; N. Bondar; W. Bonivento; S. Borghi; M. Borsato; T. J. V. Bowcock; E. Bowen; C. Bozzi; S. Braun; M. Britsch; T. Britton; J. Brodzicka; N. H. Brook; E. Buchanan; A. Bursche; J. Buytaert; S. Cadeddu; R. Calabrese; M. Calvi; M. Calvo Gomez; P. Campana; D. Campora Perez; L. Capriotti; A. Carbone; G. Carboni; R. Cardinale; A. Cardini; P. Carniti; L. Carson; K. Carvalho Akiba; G. Casse; L. Cassina; L. Castillo Garcia; M. Cattaneo; Ch. Cauet; G. Cavallero; R. Cenci; M. Charles; Ph. Charpentier; M. Chefdeville; S. Chen; S. -F. Cheung; N. Chiapolini; M. Chrzaszcz; X. Cid Vidal; G. Ciezarek; P. E. L. Clarke; M. Clemencic; H. V. Cliff; J. Closier; V. Coco; J. Cogan; E. Cogneras; V. Cogoni; L. Cojocariu; G. Collazuol; P. Collins; A. Comerma-Montells; A. Contu; A. Cook; M. Coombes; S. Coquereau; G. Corti; M. Corvo; B. Couturier; G. A. Cowan; D. C. Craik; A. Crocombe; M. Cruz Torres; S. Cunliffe; R. Currie; C. D'Ambrosio; E. Dall'Occo; J. Dalseno; P. N. Y. David; A. Davis; K. De Bruyn; S. De Capua; M. De Cian; J. M. De Miranda; L. De Paula; P. De Simone; C. -T. Dean; D. Decamp; M. Deckenhoff; L. Del Buono; N. Déléage; M. Demmer; D. Derkach; O. Deschamps; F. Dettori; B. Dey; A. Di Canto; F. Di Ruscio; H. Dijkstra; S. Donleavy; F. Dordei; M. Dorigo; A. Dosil Suárez; D. Dossett; A. Dovbnya; K. Dreimanis; L. Dufour; G. Dujany; F. Dupertuis; P. Durante; R. Dzhelyadin; A. Dziurda; A. Dzyuba; S. Easo; U. Egede; V. Egorychev; S. Eidelman; S. Eisenhardt; U. Eitschberger; R. Ekelhof; L. Eklund; I. El Rifai; Ch. Elsasser; S. Ely; S. Esen; H. M. Evans; T. Evans; A. Falabella; C. Färber; C. Farinelli; N. Farley; S. Farry; R. Fay; D. Ferguson; V. Fernandez Albor; F. Ferrari; F. Ferreira Rodrigues; M. Ferro-Luzzi; S. Filippov; M. Fiore; M. Fiorini; M. Firlej; C. Fitzpatrick; T. Fiutowski; K. Fohl; P. Fol; M. Fontana; F. Fontanelli; R. Forty; O. Francisco; M. Frank; C. Frei; M. Frosini; J. Fu; E. Furfaro; A. Gallas Torreira; D. Galli; S. Gallorini; S. Gambetta; M. Gandelman; P. Gandini; Y. Gao; J. García Pardiñas; J. Garra Tico; L. Garrido; D. Gascon; C. Gaspar; R. Gauld; L. Gavardi; G. Gazzoni; D. Gerick; E. Gersabeck; M. Gersabeck; T. Gershon; Ph. Ghez; A. Gianelle; S. Gianì; V. Gibson; O. G. Girard; L. Giubega; V. V. Gligorov; C. Göbel; D. Golubkov; A. Golutvin; A. Gomes; C. Gotti; M. Grabalosa Gándara; R. Graciani Diaz; L. A. Granado Cardoso; E. Graugés; E. Graverini; G. Graziani; A. Grecu; E. Greening; S. Gregson; P. Griffith; L. Grillo; O. Grünberg; B. Gui; E. Gushchin; Yu. Guz; T. Gys; T. Hadavizadeh; C. Hadjivasiliou; G. Haefeli; C. Haen; S. C. Haines; S. Hall; B. Hamilton; X. Han; S. Hansmann-Menzemer; N. Harnew; S. T. Harnew; J. Harrison; J. He; T. Head; V. Heijne; K. Hennessy; P. Henrard; L. Henry; J. A. Hernando Morata; E. van Herwijnen; M. Heß; A. Hicheur; D. Hill; M. Hoballah; C. Hombach; W. Hulsbergen; T. Humair; N. Hussain; D. Hutchcroft; D. Hynds; M. Idzik; P. Ilten; R. Jacobsson; A. Jaeger; J. Jalocha; E. Jans; A. Jawahery; F. Jing; M. John; D. Johnson; C. R. Jones; C. Joram; B. Jost; N. Jurik; S. Kandybei; W. Kanso; M. Karacson; T. M. Karbach; S. Karodia; M. Kecke; M. Kelsey; I. R. Kenyon; M. Kenzie; T. Ketel; B. Khanji; C. Khurewathanakul; S. Klaver; K. Klimaszewski; O. Kochebina; M. Kolpin; I. Komarov; R. F. Koopman; P. Koppenburg; M. Kozeiha; L. Kravchuk; K. Kreplin; M. Kreps; G. Krocker; P. Krokovny; F. Kruse; W. Krzemien; W. Kucewicz; M. Kucharczyk; V. Kudryavtsev; A. K. Kuonen; K. Kurek; T. Kvaratskheliya; D. Lacarrere; G. Lafferty; A. Lai; D. Lambert; G. Lanfranchi; C. Langenbruch; B. Langhans; T. Latham; C. Lazzeroni; R. Le Gac; J. van Leerdam; J. -P. Lees; R. Lefèvre; A. Leflat; J. Lefrançois; O. Leroy; T. Lesiak; B. Leverington; Y. Li; T. Likhomanenko; M. Liles; R. Lindner; C. Linn; F. Lionetto; B. Liu; X. Liu; D. Loh; I. Longstaff; J. H. Lopes; D. Lucchesi; M. Lucio Martinez; H. Luo; A. Lupato; E. Luppi; O. Lupton; A. Lusiani; F. Machefert; F. Maciuc; O. Maev; K. Maguire

    2015-10-09

    An algorithm is described for tagging the flavour content at production of neutral $B$ mesons in the LHCb experiment. The algorithm exploits the correlation of the flavour of a $B$ meson with the charge of a reconstructed secondary charm hadron from the decay of the other $b$ hadron produced in the proton-proton collision. Charm hadron candidates are identified in a number of fully or partially reconstructed Cabibbo-favoured decay modes. The algorithm is calibrated on the self-tagged decay modes $B^+ \\to J/\\psi \\, K^+$ and $B^0 \\to J/\\psi \\, K^{*0}$ using $3.0\\mathrm{\\,fb}^{-1}$ of data collected by the LHCb experiment at $pp$ centre-of-mass energies of $7\\mathrm{\\,TeV}$ and $8\\mathrm{\\,TeV}$. Its tagging power on these samples of $B \\to J/\\psi \\, X$ decays is $(0.30 \\pm 0.01 \\pm 0.01) \\%$.