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Sample records for affinity tagging method

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

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    Büssow Konrad

    2003-07-01

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

  2. Several Affinity Tags Commonly Used in Chromatographic Purification

    OpenAIRE

    Xinyu Zhao; Guoshun Li; Shufang Liang

    2013-01-01

    Affinity tags have become powerful tools from basic biological research to structural and functional proteomics. They were widely used to facilitate the purification and detection of proteins of interest, as well as the separation of protein complexes. Here, we mainly discuss the benefits and drawbacks of several affinity or epitope tags frequently used, including hexahistidine tag, FLAG tag, Strep II tag, streptavidin-binding peptide (SBP) tag, calmodulin-binding peptide (CBP), glutathione S...

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

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    Young Ah Goo

    2008-01-01

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

  4. Several Affinity Tags Commonly Used in Chromatographic Purification

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    Xinyu Zhao

    2013-01-01

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

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

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

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

    2016-10-01

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

  7. Crystal structures of fusion proteins with large-affinity tags.

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    Smyth, Douglas R; Mrozkiewicz, Marek K; McGrath, William J; Listwan, Pawel; Kobe, Bostjan

    2003-07-01

    The fusion of a protein of interest to a large-affinity tag, such as the maltose-binding protein (MBP), thioredoxin (TRX), or glutathione-S-transferase (GST), can be advantageous in terms of increased expression, enhanced solubility, protection from proteolysis, improved folding, and protein purification via affinity chromatography. Unfortunately, crystal growth is hindered by the conformational heterogeneity induced by the fusion tag, requiring that the tag is removed by a potentially problematic cleavage step. The first three crystal structures of fusion proteins with large-affinity tags have been reported recently. All three structures used a novel strategy to rigidly fuse the protein of interest to MBP via a short three- to five-amino acid spacer. This strategy has the potential to aid structure determination of proteins that present particular experimental challenges and are not conducive to more conventional crystallization strategies (e.g., membrane proteins). Structural genomics initiatives may also benefit from this approach as a way to crystallize problematic proteins of significant interest. PMID:12824478

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

    OpenAIRE

    Vergis, James M.; Michael C. Wiener

    2011-01-01

    Recombinant proteins typically include one or more affinity tags to facilitate purification and/or detection. Expression constructs with affinity tags often include an engineered protease site for tag removal. Like other enzymes, the activities of proteases can be affected by buffer conditions. The buffers used for integral membrane proteins contain detergents, which are required to maintain protein solubility. We examined the detergent sensitivity of six commonly-used proteases (Enterokinase...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2005-08-25

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

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

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    Edyta Kopera

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

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

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    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. Identification of Thioredoxin Target Disulfides Using Isotope-Coded Affinity Tags

    DEFF Research Database (Denmark)

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

    extracts is described. The procedure utilizes the isotope-coded affinity tag (ICAT) reagents containing a thiol reactive iodoacetamide group and a biotin affinity tag to target peptides containing reduced cysteine residues. The identification of substrates for Trx and the extent of target disulfide......Thioredoxins (Trx) are small redox proteins that reduce disulfide bonds in various target proteins and maintain cellular thiol redox control. Here, a thiol-specific labeling and affinity enrichment approach for identification and relative quantification of Trx target disulfides in complex protein...

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

    OpenAIRE

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

    2016-01-01

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

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

    OpenAIRE

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

    2014-01-01

    Tandem affinity purification (TAP) tagging provides a powerful tool for isolating interacting proteins in vivo. TAP-tag purification offers particular advantages for the identification of stimulus-induced protein interactions. Type II bZIP transcription factors (TGA2, TGA5 and TGA6) play key roles in pathways that control salicylic acid, ethylene, xenobiotic and reactive oxylipin signaling. Although proteins interacting with these transcription factors have been identified through genetic and...

  15. A novel phosphate-affinity bead with immobilized Phos-tag for separation and enrichment of phosphopeptides and phosphoproteins

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    Chika Inoue

    2011-01-01

    Full Text Available A simple and efficient method was developed for separating and enriching phosphoproteins from crude biological samples containing solubil-ized cellular proteins by immobilized zinc(II affinity chromatography. The phosphate-binding site of the affinity gel is an alkoxide-bridged dinuclear zinc(II complex, Phos-tag, which is linked to a hydrophilic vinylic polymer bead. A novel phosphate-affinity bead (Phos-tag Toyopearl was prepared by reaction of N-hydroxysuccinimide-activated Toyopearl AF-Carboxy-650M gel with a 2-aminoethylcarbamoyl de-rivative of Phos-tag. Phosphopeptides were retrieved quantitatively and selectively on a µL-scale column at room temperature. The column was stable for long-term storage and could be reused many times. The technique was used to separate and enrich phosphoproteins from an epider-mal growth factor-stimulated human epidermoid carcinoma A431 cell lysate. The operations necessary for 1-mL-scale open-column chroma-tography were conducted at a physiological pH during 1 h. The strong enrichment of the phosphoproteins into the eluted fraction was evaluat-ed by gel electrophoresis, followed by Western blotting with Phos-tag Biotin and several antibodies, Pro-Q Diamond phosphoprotein gel stain-ing, and mass spectrometry.

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

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

    2014-01-01

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

  17. Single-step affinity and cost-effective purification of recombinant proteins using the Sepharose-binding lectin-tag from the mushroom Laetiporus sulphureus as fusion partner.

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    Li, Xiao-Jing; Liu, Jin-Ling; Gao, Dong-Sheng; Wan, Wen-Yan; Yang, Xia; Li, Yong-Tao; Chang, Hong-Tao; Chen, Lu; Wang, Chuan-Qing; Zhao, Jun

    2016-03-01

    Previous research showed that a lectin from the mushroom Laetiporus sulphureus, designed LSL, bound to Sepharose and could be eluted by lactose. In this study, by taking advantage of the strong affinity of LSL-tag for Sepharose, we developed a single-step purification method for LSL-tagged fusion proteins. We utilized unmodified Sepharose-4B as a specific adsorbent and 0.2 M lactose solution as an elution buffer. Fusion proteins of LSL-tag and porcine circovirus capsid protein, designated LSL-Cap was recovered with purity of 90 ± 4%, and yield of 87 ± 3% from crude extract of recombinant Escherichia coli. To enable the remove of LSL-tag, tobacco etch virus (TEV) protease recognition sequence was placed downstream of LSL-tag in the expression vector, and LSL-tagged TEV protease, designated LSL-TEV, was also expressed in E. coli., and was recovered with purity of 82 ± 5%, and yield of 85 ± 2% from crude extract of recombinant E. coli. After digestion of LSL-tagged recombinant proteins with LSL-TEV, the LSL tag and LSL-TEV can be easily removed by passing the digested products through the Sepharose column. It is of worthy noting that the Sepharose can be reused after washing with PBS. The LSL affinity purification method enables rapid and inexpensive purification of LSL-tagged fusion proteins and scale-up production of native proteins. PMID:26616099

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

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    Buhrman Jason S

    2012-09-01

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

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

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    Janine Schulte-Zweckel

    2016-06-01

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

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

    Science.gov (United States)

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

    2004-01-01

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

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

    Science.gov (United States)

    Scott; Jeff W. , Pratt; Richard M.

    2006-09-12

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

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

    Science.gov (United States)

    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

  3. Hybrid Method for Tagging Arabic Text

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    Yamina Tlili-Guiassa

    2006-01-01

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

  4. Evaluation of immobilized metal affinity chromatography kits for the purification of histidine-tagged recombinant CagA protein.

    Science.gov (United States)

    Karakus, Cebrail; Uslu, Merve; Yazici, Duygu; Salih, Barik A

    2016-05-15

    Immobilized metal affinity chromatography (IMAC) technique is used for fast and reliable purification of histidine(His)-tagged recombinant proteins. The technique provides purification under native and denaturing conditions. The aim of this study is to evaluate three commercially available IMAC kits (Thermo Scientific, GE Healthcare and Qiagen) for the purification of a 6xHis-tagged recombinant CagA (cytotoxin-associated gene A) protein from IPTG-induced Escherichia coli BL21(DE3) culture. The kits were tested according to the manufacturer instructions and the protein was purified with only GE Healthcare and Qiagen kits under denaturing conditions. 1% (w/v) SDS was used as denaturing agent in PBS instead of extraction reagent of Thermo Scientific kit to lyse bacterial cells from 100ml culture. The 6xHis-tagged recombinant protein was purified by the three kits equally. PMID:26657801

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

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    Kimberly A Kelly

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

  6. Methods for Improving Aptamer Binding Affinity

    OpenAIRE

    Hijiri Hasegawa; Nasa Savory; Koichi Abe; Kazunori Ikebukuro

    2016-01-01

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

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

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    Colin P De Souza

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

  8. Affine Moment Invariants Generated by Graph Method

    Czech Academy of Sciences Publication Activity Database

    Suk, Tomáš; Flusser, Jan

    2011-01-01

    Roč. 44, č. 9 (2011), 2047 – 2056. ISSN 0031-3203 R&D Projects: GA ČR(CZ) GA102/08/1593 Institutional research plan: CEZ:AV0Z10750506 Keywords : Image moments * Object recognition * Affine transformation * Affine moment invariants * Pseudoinvariants * Graph representation * Irreducibility * Independence Subject RIV: IN - Informatics, Computer Science Impact factor: 2.292, year: 2011 http://library.utia.cas.cz/separaty/2011/ZOI/suk-0359752.pdf

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

    DEFF Research Database (Denmark)

    Prentø, Jannick Cornelius; Bukh, Jens

    2011-01-01

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

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

    OpenAIRE

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

    2009-01-01

    Electron capture dissociation (ECD) and electron transfer dissociation (ETD) of doubly protonated electron affinity (EA)-tuned peptides were studied to further illuminate the mechanism of these processes. The model peptide FQpSEEQQQTEDELQDK, containing a phosphoserine residue, was converted to EA-tuned peptides via β-elimination and Michael addition of various thiol compounds. These include propanyl, benzyl, 4-cyanobenzyl, perfluorobenzyl, 3,5-dicyanobenzyl, 3-nitrobenzyl, and 3,5-dinitrobenz...

  11. Image analysis methods for tagged MRI cardiac studies

    International Nuclear Information System (INIS)

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

  12. Image analysis methods for tagged MRI cardiac studies

    Science.gov (United States)

    Guttman, Michael A.; Prince, Jerry L.

    1990-07-01

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

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

    NARCIS (Netherlands)

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

    2001-01-01

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

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

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

    Burghard, Brion J.; Skorpik, James R.

    2008-04-22

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

  16. Top-tagging: A Method for Identifying Boosted Hadronic Tops

    CERN Document Server

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

    2008-01-01

    A method is introduced for distinguishing top jets -- boosted, hadronically decaying top quarks -- from standard model backgrounds using jet substructure. The procedure involves parsing the jet cluster to resolve features such as three light quark subjets, and then imposing angular and kinematic constraints. This method is much more efficient than simple invariant mass cuts or jet clustering with fixed angular size. With top-tagging, high pT dijets can be rejected with an efficiency of around 99% while retaining 20-40% of the tops. This allows us to reach into the all-hadronic channel for new-physics signals, such as new heavy t-tbar resonances, which ordinarily would be overwhelmed by the enormous dijet background. In addition, it will improve the reach for cases when one of the tops decays semi-leptonically, and may also have applications to single-top searches and studies of b-tagging efficiency at high pT.

  17. Flavour tagging methods used in the ATLAS B physics program

    International Nuclear Information System (INIS)

    Full text: Major tasks of the ATLAS B-physics program are the measurement of the B0s oscillations and the weak mixing phase Φs. The B0s oscillation parameter δms will be measured by using the hadronic decay channels B0s → Ds(φ, π)π and B0s → Ds(φ, π)a1, while the weak mixing phase Ψs uses the channel B0s → J/ψ(μ+, μ-)φ, with φ → K+K-. For an accurate measurement the determination of the B0s flavour at production time is crucial. Various methods for flavour tagging like e.g. opposite side soft muon tagging or same side jet charge tagging are studied and possible calibration channels are explored. Also the combination of different kinematic observables in order to receive event-by-event mistag rates using a multivariate analysis will be presented. (author)

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

    Science.gov (United States)

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

    2014-07-18

    This study describes the determination of the adsorption isotherms and binding kinetics of tagged recombinant proteins using a recently developed IMAC cassette system and employing automated robotic liquid handling procedures for IMAC resin screening. These results confirm that these new IMAC resins, generated from a variety of different metal-charged binuclear 1,4,7-triaza-cyclononane (tacn) ligands, interact with recombinant proteins containing a novel N-terminal metal binding tag, NT1A, with static binding capacities similar to those obtained with conventional hexa-His tagged proteins, but with significantly increased association constants. In addition, higher kinetic binding rates were observed with these new IMAC systems, an attribute that can be positively exploited to increase process productivity. The results from this investigation demonstrate that enhancements in binding capacities and affinities were achieved with these new IMAC resins and chosen NT1A tagged protein. Further, differences in the binding performances of the bis(tacn) xylenyl-bridged ligands were consistent with the distance between the metal binding centres of the two tacn moieties, the flexibility of the ligand and the potential contribution from the aromatic ring of the xylenyl group to undergo π/π stacking interactions with the tagged proteins. PMID:24891160

  19. Method of tagging excipients with /sup 99m/Tc

    Energy Technology Data Exchange (ETDEWEB)

    Bardy, A.; Beydon, J.; Gobin, R.; Hegesippe, M.

    1977-11-08

    A method of using /sup 99m/technetium for tagging excipients in medical diagnosis by scintigraphy comprises mixing, in an aqueous solution of alkali-metal pertechnetate, an excipient and a reducing agent in the form of a complex, which complex is such that the association constant of the anion with reduced techetium is less than the association constant of the excipient with reduced technetium, thereby forming a radio-pharmaceutical substance which is a complex between the excipient and /sup 99m/technetium.

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

    Science.gov (United States)

    Kollmar, Martin

    2006-08-15

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

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

    Directory of Open Access Journals (Sweden)

    XIAO Xiongwu

    2015-04-01

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

  2. Studying protein–protein affinity and immobilized ligand–protein affinity interactions using MS-based methods

    OpenAIRE

    Kool, J.; N. Jonker; Irth, H.; Niessen, W.M.A.

    2011-01-01

    This review discusses the most important current methods employing mass spectrometry (MS) analysis for the study of protein affinity interactions. The methods are discussed in depth with particular reference to MS-based approaches for analyzing protein–protein and protein–immobilized ligand interactions, analyzed either directly or indirectly. First, we introduce MS methods for the study of intact protein complexes in the gas phase. Next, pull-down methods for affinity-based analysis of prote...

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

    CERN Document Server

    Jiang, Chenfanfu; Teran, Joseph

    2016-01-01

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

  4. Parameters of explosives detection through tagged neutron method

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-06-01

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

  5. Parameters of explosives detection through tagged neutron method

    International Nuclear Information System (INIS)

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

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

    International Nuclear Information System (INIS)

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

  7. Synthesis of an artificial cell surface receptor that enables oligohistidine affinity tags to function as metal-dependent cell-penetrating peptides.

    Science.gov (United States)

    Boonyarattanakalin, Siwarutt; Athavankar, Sonalee; Sun, Qi; Peterson, Blake R

    2006-01-18

    Cell-penetrating peptides and proteins (CPPs) are important tools for the delivery of impermeable molecules into living mammalian cells. To enable these cells to internalize proteins fused to common oligohistidine affinity tags, we synthesized an artificial cell surface receptor comprising an N-alkyl derivative of 3beta-cholesterylamine linked to the metal chelator nitrilotriacetic acid (NTA). This synthetic receptor inserts into cellular plasma membranes, projects NTA headgroups from the cell surface, and rapidly cycles between the plasma membrane and intracellular endosomes. Jurkat lymphocytes treated with the synthetic receptor (10 microM) for 1 h displayed approximately 8,400,000 [corrected]NTA groups on the cell surface. Subsequent addition of the green fluorescent protein AcGFP fused to hexahistidine or decahistidine peptides (3 microM) and Ni(OAc)(2) (100 microM) enhanced the endocytosis of AcGFP by 150-fold (hexahistidine fusion protein) or 600-fold (decahistidine fusion protein) within 4 h at 37 degrees C. No adverse effects on cellular proliferation or morphology were observed under these conditions. By enabling common oligohistidine affinity tags to function as cell-penetrating peptides, this metal-chelating cell surface receptor provides a useful tool for studies of cellular biology [corrected] PMID:16402806

  8. Overexpression of (His)6-tagged human arginase I in Saccharomyces cerevisiae and enzyme purification using metal affinity chromatography

    Czech Academy of Sciences Publication Activity Database

    Zakalskiy, A. E.; Zakalska, O. M.; Rzhepetskyy, Y. A.; Potocka, N.; Stasyk, O. V.; Horák, Daniel; Gonchar, M. V.

    2012-01-01

    Roč. 81, č. 1 (2012), s. 63-68. ISSN 1046-5928 R&D Projects: GA ČR GA203/09/1242 Institutional research plan: CEZ:AV0Z40500505 Keywords : human arginase I * (His)6-tag * Saccharomyces cerevisiae Subject RIV: CD - Macromolecular Chemistry Impact factor: 1.429, year: 2012

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

    Institute of Scientific and Technical Information of China (English)

    朱松豪; 邹黎明

    2013-01-01

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

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

    OpenAIRE

    Korndörfer, Ingo P.; Skerra, Arne

    2002-01-01

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

  11. Methods for determining the genetic affinity of microorganisms and viruses

    Science.gov (United States)

    Fox, George E. (Inventor); Willson, III, Richard C. (Inventor); Zhang, Zhengdong (Inventor)

    2012-01-01

    Selecting which sub-sequences in a database of nucleic acid such as 16S rRNA are highly characteristic of particular groupings of bacteria, microorganisms, fungi, etc. on a substantially phylogenetic tree. Also applicable to viruses comprising viral genomic RNA or DNA. A catalogue of highly characteristic sequences identified by this method is assembled to establish the genetic identity of an unknown organism. The characteristic sequences are used to design nucleic acid hybridization probes that include the characteristic sequence or its complement, or are derived from one or more characteristic sequences. A plurality of these characteristic sequences is used in hybridization to determine the phylogenetic tree position of the organism(s) in a sample. Those target organisms represented in the original sequence database and sufficient characteristic sequences can identify to the species or subspecies level. Oligonucleotide arrays of many probes are especially preferred. A hybridization signal can comprise fluorescence, chemiluminescence, or isotopic labeling, etc.; or sequences in a sample can be detected by direct means, e.g. mass spectrometry. The method's characteristic sequences can also be used to design specific PCR primers. The method uniquely identifies the phylogenetic affinity of an unknown organism without requiring prior knowledge of what is present in the sample. Even if the organism has not been previously encountered, the method still provides useful information about which phylogenetic tree bifurcation nodes encompass the organism.

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

    Directory of Open Access Journals (Sweden)

    Przemysław Płociński

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

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

    CERN Document Server

    Kuribayashi, Shin-ichi

    2010-01-01

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

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

    CERN Document Server

    Takeuchi, Tomoki; Murase, Kenya

    2016-01-01

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

  15. Extended Range Passive Wireless Tag System and Method

    Science.gov (United States)

    Fink, Patrick W. (Inventor); Kennedy, Timothy F. (Inventor); Lin, Gregory Y. (Inventor)

    2013-01-01

    A passive wireless tag assembly comprises a plurality of antennas and transmission lines interconnected with circuitry and constructed and arranged in a Van Atta array or configuration to reflect an interrogator signal in the direction from where it came. The circuitry may comprise at least one surface acoustic wave (SAW)-based circuit that functions as a signal reflector and is operatively connected with an information circuit. In another embodiment, at least one delay circuit and/or at least one passive modulation circuit(s) are utilized. In yet another embodiment, antennas connected to SAW-based devices are mounted to at least one of the orthogonal surfaces of a corner reflector.

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

    Science.gov (United States)

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

    2012-05-29

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

  17. Development of multiphasic tagging method and its application for visualization and quantification of descending aortic flow

    International Nuclear Information System (INIS)

    Conventional single phasic tagging (SPT) method is neither available for the evaluation of high speed blood flow nor for long time investigation such as whole cardiac cycle, because the tag becomes unclear due to proton spin relaxation and diffusion in those situation. To overcome those difficulties, we developed the multiphasic tagging (MPT) method, and estimated the utility of this method in flow phantom and in clinical patients. Cine MR imaging was performed with a 0.5 T MRT-50A (TOSHIBA). The MPT pulse sequence was composed of continuous many (9-16) frame units for each R-R interval, and this each frame unit consisted of an initial presaturation 180deg RF pulse followed by one unit of conventional field echo pulse sequence (TR=50ms, TE=22ms, FA=30deg). The flow phantom was composed of polyvinyl chloride tube, electric motor and pulse generator. The SPT and MPT cine MR imagings were performed with the flow phantom. The fresh tags by MTP kept a sharpness for one (cardiac) cycle, but the tag by SPT became unclear. The velocity calculated by measuring the distance of tag from baseline on MPT cine MR images was significantly correlated with that measured by a cylinder. The MPT cine MR imaging of descending aorta was performed in five healthy volunteers and 12 pts with various heart diseases. The tag on blood intra descending aorta by the MPT was also sharply imaged for one cardiac cycle in human. Severe backward shift of tag was observed in early diastolic phase in a patient with severe aortic regurgitation. The descending aortic flow volume by MPT significantly (p<0.01) correlated (r=0.86) with LV stroke volume, except for two patients with severe mitral regurgitation. The MPT is useful for visualization and quantification of the descending aortic flow. (author)

  18. Affine Correlation Method for Direct Vorticity, Skew and Displacement Estimation

    Czech Academy of Sciences Publication Activity Database

    Gronát, Petr

    Praha : Ústav termomechaniky, AV ČR, v. v. i., 2010 - (Příhoda, J.; Kozel, K.), s. 59-62 ISBN 978-80-87012-25-3. [Topical Problems of Fluid Mechanics 2010. Praha (CZ), 10.02.2010-11.02.2010] R&D Projects: GA ČR GA101/08/1112 Institutional research plan: CEZ:AV0Z20760514 Keywords : normalized cross correlation * affine correlation Subject RIV: BK - Fluid Dynamics

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

    Science.gov (United States)

    Mayer-Cumblidge, M. Uljana; Cao, Haishi

    2013-01-15

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

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

    DEFF Research Database (Denmark)

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

    1990-01-01

    affinity-purify anti-peptide antibodies. To test our system, rabbits were immunized with model peptides representing sequences of the putative rabbit growth hormone receptor and several HLA-DQ beta-chain molecules. Polystyrene plastic beads were coated with peptides. Immune serum was incubated with the...... beads and after a wash step the bound antibodies were eluted in 1 M acetic acid. The eluted material was composed predominantly of intact immunoglobulin as evidenced by the presence of heavy and light chain bands in SDS-PAGE. The eluted antibodies were peptide specific in ELISA and bound only to intact......, antigenic protein in immunoblot analyses. The sequence-specific nature of the eluted antibodies was confirmed since binding to the antigenic proteins could be displaced by the immunizing but not by unrelated peptides....

  1. Paired-end genomic signature tags: a method for the functional analysis of genomes and epigenomes.

    Science.gov (United States)

    Dunn, John J; McCorkle, Sean R; Everett, Logan; Anderson, Carl W

    2007-01-01

    Because paired-end genomic signature tags are sequenced-based, they have the potential to become an alternate tool to tiled microarray hybridization as a method for genome-wide localization of transcription factors and other sequence-specific DNA binding proteins. As outlined here the method also can be used for global analysis of DNA methylation. One advantage of this approach is the ability to easily switch between different genome types without having to fabricate a new microarray for each and every DNA type. However, the method does have some disadvantages. Among the most rate-limiting steps of our PE-GST protocol are the need to concatemerize the diTAGs, size fractionate them and then clone them prior to sequencing. This is usually followed by additional steps to amplify and size select for long (> or = 500) concatemer inserts prior to sequencing. These time-consuming steps are important for standard DNA sequencing as they increase efficiency approximately 20-30-fold since each amplified concatemer can now provide information on multiple tags; the limitation on data acqui- sition is read length during sequencing. However, the development of new sequencing methods such as Life Sciences' 454 new nanotechnology-based sequencing instrument (41) could increase tag sequencing efficiency by several orders of magnitude (> or = 100,000 diTAG reads/run), which is sufficient to provide in-depth global analysis of all ChIP PE-GSTs in a single run. This is because the lengths of our paired-end diTAGs (approximately 60 bp) fall well within the region of high accuracy for read lengths on this instrument. In principle, sequence analysis of diTAGs could begin as soon as they are generated, thereby completely bypassing the need for the concatemerization, sizing, downstream cloning steps and sequencing template purification. In addition, our protocol places any one of several unique four-base long nucleotide sequences, such as GATC, between each and every diTAG pair, which could

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

    CERN Document Server

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

    2008-01-01

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

  3. Further development of multiplex single nucleotide polymorphism typing method, the DigiTag2 assay.

    Science.gov (United States)

    Nishida, Nao; Tanabe, Tetsuya; Takasu, Miwa; Suyama, Akira; Tokunaga, Katsushi

    2007-05-01

    A number of single nucleotide polymorphisms (SNPs) are considered to be candidate susceptibility or resistance genetic factors for multifactorial disease. Genome-wide searches for disease susceptibility regions followed by high-resolution mapping of primary genes require cost-effective and highly reliable technology. To accomplish successful and low-cost typing for candidate SNPs, new technologies must be developed. We previously reported a multiplex SNP typing method, designated the DigiTag assay, that has the potential to analyze nearly any SNP with high accuracy and reproducibility. However, the DigiTag assay requires multiple washing steps in manipulation and uses genotyping probes modified with biotin for each target SNP. Here we describe the next version of the assay, DigiTag2, which works with simple protocols and uses unmodified genotyping probes. We investigated the feasibility of the DigiTag2 assay by genotyping 96 target SNPs spanning a 610-kb region of human chromosome 5. The DigiTag2 assay is suitable for genotyping an intermediate number of SNPs (tens to hundreds of sites) with a high conversion rate (>90%), high accuracy, and low cost. PMID:17359929

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

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

    Korndörfer, Ingo P.; Skerra, Arne

    2002-01-01

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

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

    OpenAIRE

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

    2014-01-01

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

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

    DEFF Research Database (Denmark)

    Østergaard, Jesper; Jensen, Henrik; Holm, Rene

    2012-01-01

    influence on the ionic strength of the background electrolyte when the cyclodextrin is used in capillary electrophoresis. Mobility-shift affinity capillary methods for investigation of the complexation of taurocholate and taurochenodeoxycholate with the negatively charged cyclodextrin derivative applying...... constant power and ionic strength conditions as well as constant voltage and varying ionic strength were investigated. A new approach for the correction of background electrolyte ionic strength was developed. Mobility-shift affinity capillary electrophoresis experiments obtained at constant voltage and...

  8. A method to measure prompt fission neutron spectrum using gamma multiplicity tagging

    Science.gov (United States)

    Blain, E.; Daskalakis, A.; Block, R. C.; Barry, D.; Danon, Y.

    2016-01-01

    In order to improve on current prompt fission neutron spectrum measurements, a gamma multiplicity tagging method was developed at the Rensselaer Polytechnic Institute Gearttner Linear Accelerator Center. This method involves using a coincidence requirement on an array of BaF2 gamma detectors to determine the timing of a fission event. This allows for much larger fission samples to be used due to the higher penetrability of gammas compared to fission fragments. Additionally, since the method relies on gammas as opposed to fission fragments, the effects of the low level discriminator, used in fission chambers to eliminate alpha events, are not seen. A 252Cf fission chamber was constructed in order to determine the viability of this method as well as the efficiency when compared to a fission chamber. The implemented multiple gamma tagging method was found to accurately reproduce the prompt fission neutron spectrum for the spontaneous fission of 252Cf and to detect 30% of fission events.

  9. Development of chelate tagging method of protein at low temperature

    International Nuclear Information System (INIS)

    This study aimed at development of a protein labelling method at a low temperature, available for functional proteins, such as antibodies and enzymes mostly unstable at high temperatures. A solution of anti-mouse IgG antibody added with EDTA was incubated with 51CrCl3 at 4degC for 24 hours. After stopping the reaction with 100-fold amount of EDTA-2Na, the solution was fractionated into antibody fraction and metal fraction by HPLC. After incubation, non-specific Cr adsorption on the antibody in no relation to the chelate reagent was chased with 10-fold amount of CrCl3. To remove free Cr, the sample solution was incubated with 10 to 50-fold ICB-EDTA solution containing N,N-dimethyl-formamide. Then, the amount of Cr-labelling on the antibody was determined. In Western-blotting, chick actin was applied onto SDS-polyacrylamide gel electrophoresis. One part of the lane was stained with brilliant-blue and the other was transferred on nitrocellulose membrane by semi-dry method and stained with panceau-S. Anti-actin monoclonal antibody and anti-mouse IgG antibody were used as the first antibody and the second one, respectively. When incubated with ICB-EDTA for 3 days, labelling reached the maximum level. Although labelling of the second antibody was performed with maleimido-C3-benzyl EDTA and 45Ca as a substitute for 51Cr, the rate of labelling was lower than the rate for a combination of ICB-EDTA and 51Cr. Autoradiography of the anti-mouse IgG preparation after SDS-acrylamide gel electrophoresis revealed that radioactivity was detected on the site of H-chain but not L-chain. This indicates that 51Cr labelling of protein is stable even under the conditions of SDS denaturation. (M.N.)

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

    OpenAIRE

    Andberg, Tor Arne Heim

    2011-01-01

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

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

    DEFF Research Database (Denmark)

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

    2015-01-01

    studies using external tagging has increased, especially with the development of archival tags (data storage tags, DSTs), pop-up satellite archival tags (PSATs) and other environment-sensing tags. Scientific evaluations of the tagging method are rather scarce for most species. We identified 89...

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

    OpenAIRE

    Meslet-Cladière Laurence; Vallon Olivier

    2012-01-01

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

  13. Multivariate analysis methods to tag b-quark events at LEP/SLC

    International Nuclear Information System (INIS)

    Multivariate analyses are applied to tag Z→banti b events at LEP/SLC. They are based on the specific b-event shape caused by the large b-quark mass. Discriminant analyses, classification trees and neural networks are presented and their performances are compared. It is shown that the neural network approach, due to its nonlinearity, copes best with the complexity of the problem. As an example for an application of the developed methods the measurement of Γ(Z→banti b) is discussed. The usefulness of methods based on the global event shape is limited by the uncertainties introduced by the necessity of event simulation. As a solution we present a double tag method which can be applied to many tasks of LEP/SLC heavy flavour physics. (orig.)

  14. Multivariate analysis methods to tag b quark events at LEP/SLC

    International Nuclear Information System (INIS)

    Multivariate analyses are applied to tag Z → bb-bar events at LEP/SLC. They are based on the specific b-event shape caused by the large b-quark mass. Discriminant analyses, classification trees and neural networks are presented and their performances are compared. It is shown that the neural network approach, due to its non-linearity, copes best with the complexity of the problem. As an example for an application of the developed methods the measurement of Γ(Z → bb-bar) is discussed. The usefulness of methods based on the global event shape is limited by the uncertainties introduced by the necessity of event simulation. As solution a double tag method is presented which can be applied to many tasks of LEP/SLC heavy flavour physics. (author) 29 refs.; 6 figs.; 1 tab

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

    DEFF Research Database (Denmark)

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

    2016-01-01

    be used for functionalization of other nanoparticles or solid surfaces. The method exploits a synergistic effect of having both affinity and covalent anchoring tags on the surface of the liposome. This was achieved by synthesizing a peptide linker system that uses Cu-free strain-promoted click...... chemistry in combination with histidine affinity tags. The investigation of post-functionalization of PEGylated liposomes was performed with a cyclic RGDfE peptide. By exploring both affinity and covalent tags a 98 ± 2.0% coupling efficiency was achieved, even a diluted system showed a coupling efficiency...

  16. Top Tagging: A Method for Identifying Boosted Hadronically Decaying Top Quarks

    International Nuclear Information System (INIS)

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

  17. Immobilized Metal Affinity Electrophoresis: A Novel Method of Capturing Phosphoproteins by Electrophoresis

    OpenAIRE

    Lee, Bao-Shiang; Lasanthi, G.D.; Jayathilaka, P.; Huang, Jin-Sheng; Gupta, Shalini

    2008-01-01

    An immobilized metal affinity electrophoresis (IMAEP) method is described here. In this method, metal ions are immobilized in a native polyacrylamide gel to capture phosphoproteins. The capture of phosphoproteins by IMAEP is demonstrated with immobilized metals like iron, aluminum, manganese, or titanium. In the case studies, phosphoproteins α-casein, β-casein, and phosvitin are successfully extracted from a protein mixture by IMAEP.

  18. Interpolation method for accurate affinity ranking of arrayed ligand-analyte interactions.

    Science.gov (United States)

    Schasfoort, Richard B M; Andree, Kiki C; van der Velde, Niels; van der Kooi, Alex; Stojanović, Ivan; Terstappen, Leon W M M

    2016-05-01

    The values of the affinity constants (kd, ka, and KD) that are determined by label-free interaction analysis methods are affected by the ligand density. This article outlines a surface plasmon resonance (SPR) imaging method that yields high-throughput globally fitted affinity ranking values using a 96-plex array. A kinetic titration experiment without a regeneration step has been applied for various coupled antibodies binding to a single antigen. Globally fitted rate (kd and ka) and dissociation equilibrium (KD) constants for various ligand densities and analyte concentrations are exponentially interpolated to the KD at Rmax = 100 RU response level (KD(R100)). PMID:26878776

  19. Novel method for digital subtraction of tagged stool in virtual colonoscopy

    Science.gov (United States)

    Guendel, Lutz; Suehling, Michael; Eckert, Helmut

    2008-03-01

    Colon cancer is one of the most frequent causes of death. CT colonography is a novel method for the detection of polyps and early cancer. The general principle of CT colonography includes a cathartic bowel preparation. The resulting discomfort for patients leads to limited patient acceptance and therefore to limited cancer detection rates. Reduced bowel preparation, techniques for stool tagging, and electronic cleansing, however, improve the acceptance rates. Hereby, the high density of oral contrast material highlights residual stool and can be digitally removed. Known subtraction methods cause artifacts: additional 3D objects are introduced and small bowel folds are perforated. We propose a new algorithm that is based on the 2 nd derivative of the image data using the Hessian matrix and the following principal axis transform to detect tiny folds which shall not be subtracted together with tagged stool found by a thresholding method. Since the stool is usually not homogenously tagged with contrast media a detection algorithm for island-like structures is incorporated. The interfaces of air-stool level and colon wall are detected by a 3-dimensional difference of Gaussian module. A 3-dimensional filter smoothes the transitions between removed stool and colon tissue. We evaluated the efficacy of the new algorithm with 10 patient data sets. The results showed no introduced artificial objects and no perforated folds. The artifacts at the air-stool and colon tissue-stool transitions are considerably reduced compared to those known from the literature.

  20. Extracting Tag Hierarchies

    OpenAIRE

    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 o...

  1. A pseudo wavelet-based method for accurate tagline tracing on tagged MR images of the tongue

    Science.gov (United States)

    Yuan, Xiaohui; Ozturk, Cengizhan; Chi-Fishman, Gloria

    2006-03-01

    In this paper, we present a pseudo wavelet-based tagline detection method. The tagged MR image is transformed to the wavelet domain, and the prominent tagline coefficients are retained while others are eliminated. Significant stripes are extracted via segmentation, which are mixtures of tags and anatomical boundary that resembles line. A refinement step follows such that broken lines or isolated points are grouped or eliminated. Without assumption on tag models, our method extracts taglines automatically regardless their width and spacing. In addition, founded on the multi-resolution wavelet analysis, our method reconstructs taglines precisely and shows great robustness to various types of taglines.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-07-15

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

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

    OpenAIRE

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

    2015-01-01

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

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

    Science.gov (United States)

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

    2016-02-01

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

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

    Science.gov (United States)

    Wu, Zhenyu; Zou, Ming

    2014-10-01

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

  6. 08391 Working Group Summary -- Analyzing Tag Semantics Across Tagging Systems

    OpenAIRE

    Benz, Dominik; Grobelnik, Marko; Hotho, Andreas; Jäschke, Robert; Mladenic, Dunja; Vito D P Servedio; Sizov, Sergej; Szomszor, Martin

    2008-01-01

    The objective of our group was to exploit state-of-the-art Information Retrieval methods for finding associations and dependencies between tags, capturing and representing differences in tagging behavior and vocabulary of various folksonomies, with the overall aim to better understand the semantics of tags and the tagging process. Therefore we analyze the semantic content of tags in the Flickr and Delicious folksonomies. We find that: tag context similarity leads to meani...

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

    DEFF Research Database (Denmark)

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

    2014-01-01

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

  8. Social Tagging in Bibliotheken

    OpenAIRE

    Mitis-Stanzel, Irene

    2008-01-01

    This thesis deals with social tagging used for indexing of library holdings. Social tagging is the process by which users add metadata in form of free keywords to resources. The emerging pool of tags is called folksonomy. This paper describes how folksonomies work and illustrates potential features of social tagging in libraries. It becomes clear that folksonomies cannot keep up with traditional cataloguing methods in some respects, but allow various new possibilities. Therefore social taggin...

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

    Science.gov (United States)

    Harr, Jennifer C; Reddy, Karen L

    2016-01-01

    The three-dimensional (3D) organization of the genome is important for chromatin regulation. This organization is nonrandom and appears to be tightly correlated with or regulated by chromatin state and scaffolding proteins. To understand how specific DNA and chromatin elements contribute to the functional organization of the genome, we developed a new tool-the tagged chromosomal insertion site (TCIS) system-to identify and study minimal DNA sequences that drive nuclear compartmentalization and applied this system to specifically study the role of cis elements in targeting DNA to the nuclear lamina. The TCIS system allows Cre-recombinase-mediated site-directed integration of any DNA fragment into a locus tagged with lacO arrays, thus enabling both functional molecular studies and positional analysis of the altered locus. This system can be used to study the minimal DNA sequences that target the nuclear periphery (or other nuclear compartments), allowing researchers to understand how genome-wide results obtained, for example, by DNA adenine methyltransferase identification, chromosome conformation capture (HiC), or related methods, connect to the actual organization of DNA and chromosomes at the single-cell level. Finally, TCIS allows one to test roles for specific proteins in chromatin reorganization and to determine how changes in nuclear environment affect chromatin state and gene regulation at a single locus. PMID:26778570

  10. Improved native affinity purification of RNA.

    Science.gov (United States)

    Batey, Robert T; Kieft, Jeffrey S

    2007-08-01

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

  11. Billfish Tagging

    Data.gov (United States)

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

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

    Directory of Open Access Journals (Sweden)

    Aimee Shen

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

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

    OpenAIRE

    Jepsen, Niels; Thorstad, Eva Bonsak; Havn, Torgeir Børresen; Lucas, Martyn C.

    2015-01-01

    External tagging of fish with electronic tags has been used for decades for a wide range of marine and freshwater species. In the early years of fish telemetry research, it was the most commonly used attachment method, but later internal implants became preferred. Recently, the number of telemetry studies using external tagging has increased, especially with the development of archival tags (data storage tags, DSTs), pop-up satellite archival tags (PSATs) and other environment-sen...

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

    OpenAIRE

    Yoshimatsu, Keiichi; Yamazaki, Tomohiko; Hoshino, Yu; Rose, Paul E.; Epstein, Linda F.; Miranda, Les P.; Tagari, Philip; Beierle, John M.; Yonamine, Yusuke; Shea, Kenneth J

    2014-01-01

    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 ...

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

    Science.gov (United States)

    Mayer-Cumblidge, M. Uljana; Cao, Haishi

    2010-08-17

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

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

    Directory of Open Access Journals (Sweden)

    Yu. B. Gimpilevich

    2013-12-01

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

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

    International Nuclear Information System (INIS)

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

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

    Directory of Open Access Journals (Sweden)

    Meslet-Cladière Laurence

    2012-06-01

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

  19. Extracting tag hierarchies.

    Science.gov (United States)

    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

  20. Extracting tag hierarchies.

    Directory of Open Access Journals (Sweden)

    Gergely Tibély

    Full Text Available 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

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

    International Nuclear Information System (INIS)

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

  2. Binding affinity prediction of novel estrogen receptor ligands using receptor-based 3-D QSAR methods.

    Science.gov (United States)

    Sippl, Wolfgang

    2002-12-01

    We have recently reported the development of a 3-D QSAR model for estrogen receptor ligands showing a significant correlation between calculated molecular interaction fields and experimentally measured binding affinity. The ligand alignment obtained from docking simulations was taken as basis for a comparative field analysis applying the GRID/GOLPE program. Using the interaction field derived with a water probe and applying the smart region definition (SRD) variable selection procedure, a significant and robust model was obtained (q(2)(LOO)=0.921, SDEP=0.345). To further analyze the robustness and the predictivity of the established model several recently developed estrogen receptor ligands were selected as external test set. An excellent agreement between predicted and experimental binding data was obtained indicated by an external SDEP of 0.531. Two other traditionally used prediction techniques were applied in order to check the performance of the receptor-based 3-D QSAR procedure. The interaction energies calculated on the basis of receptor-ligand complexes were correlated with experimentally observed affinities. Also ligand-based 3-D QSAR models were generated using program FlexS. The interaction energy-based model, as well as the ligand-based 3-D QSAR models yielded models with lower predictivity. The comparison with the interaction energy-based model and with the ligand-based 3-D QSAR models, respectively, indicates that the combination of receptor-based and 3-D QSAR methods is able to improve the quality of prediction. PMID:12413831

  3. Learning Mixed Membership Community Models in Social Tagging Networks through Tensor Methods

    OpenAIRE

    Anandkumar, Anima; Sedghi, Hanie

    2015-01-01

    Community detection in graphs has been extensively studied both in theory and in applications. However, detecting communities in hypergraphs is more challenging. In this paper, we propose a tensor decomposition approach for guaranteed learning of communities in a special class of hypergraphs modeling social tagging systems or folksonomies. A folksonomy is a tripartite 3-uniform hypergraph consisting of (user, tag, resource) hyperedges. We posit a probabilistic mixed membership community model...

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

    Directory of Open Access Journals (Sweden)

    Wikström Lilian

    2005-04-01

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

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

    Science.gov (United States)

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

    2015-01-01

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

  6. Application of isotope coded affinity tag (ICAT) analysis for the identification of differentially expressed proteins following infection of atlantic salmon (Salmo salar) with infectious hematopoietic necrosis virus (IHNV) or Renibacterium salmoninarum (BKD).

    Science.gov (United States)

    Booy, A T; Haddow, J D; Ohlund, L B; Hardie, D B; Olafson, R W

    2005-01-01

    Aquaculture and commercial fisheries worldwide suffer from significant economic loss due to diseases of net-pen reared fish. In British Columbia, infectious hematopoietic necrosis (IHN) and bacterial kidney disease (BKD) epidemics occur because there are currently no commercially available drugs or fully licensed vaccines to treat these diseases. With a better understanding of the molecular mechanisms underlying these diseases, this circumstance might be significantly improved. In the present study, we have used a proteomics approach in an effort to identify and quantitate differentially expressed proteins in the liver and kidneys of diseased and healthy Atlantic salmon (Salmo salar). Isotope coded affinity tagging (ICAT), 2D gel electrophoresis, and multidimensional liquid chromatography coupled to tandem mass spectrometry (2D-LC MS/MS) were used to identify hundreds of differentially expressed proteins. While the direct significance of changes in expression levels of many proteins remains to be elucidated, others appear to be more clearly related to the infectious process. Examples of the latter are discussed here and include, a natural killer cell enhancement factor (NKEF), procathepsin L, superoxide-producing NADPH oxidase and interferon-induced viral resistance protein Mx (IFI-Mx). PMID:15822907

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

    Directory of Open Access Journals (Sweden)

    Hössjer Ola

    2006-03-01

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

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

    Directory of Open Access Journals (Sweden)

    Xiafu Peng

    2015-01-01

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

  9. Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods.

    Science.gov (United States)

    Ryde, Ulf; Söderhjelm, Pär

    2016-05-11

    One of the largest challenges of computational chemistry is calculation of accurate free energies for the binding of a small molecule to a biological macromolecule, which has immense implications in drug development. It is well-known that standard molecular-mechanics force fields used in most such calculations have a limited accuracy. Therefore, there has been a great interest in improving the estimates using quantum-mechanical (QM) methods. We review here approaches involving explicit QM energies to calculate binding affinities, with an emphasis on the methods, rather than on specific applications. Many different QM methods have been employed, ranging from semiempirical QM calculations, via density-functional theory, to strict coupled-cluster calculations. Dispersion and other empirical corrections are mandatory for the approximate methods, as well as large basis sets for the stricter methods. QM has been used for the ligand, for a few crucial groups around the ligand, for all the closest atoms (200-1000 atoms), or for the full receptor-ligand complex, but it is likely that with a proper embedding it might be enough to include all groups within ∼6 Å of the ligand. Approaches involving minimized structures, simulations of the end states of the binding reaction, or full free-energy simulations have been tested. PMID:27077817

  10. Extracting tag hierarchies

    CERN Document Server

    Tibély, Gergely; Vicsek, Tamás; Palla, Gergely

    2014-01-01

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

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

    DEFF Research Database (Denmark)

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

    2001-01-01

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

  12. Accurate Ionization Potentials and Electron Affinities of Acceptor Molecules III: A Benchmark of GW Methods.

    Science.gov (United States)

    Knight, Joseph W; Wang, Xiaopeng; Gallandi, Lukas; Dolgounitcheva, Olga; Ren, Xinguo; Ortiz, J Vincent; Rinke, Patrick; Körzdörfer, Thomas; Marom, Noa

    2016-02-01

    The performance of different GW methods is assessed for a set of 24 organic acceptors. Errors are evaluated with respect to coupled cluster singles, doubles, and perturbative triples [CCSD(T)] reference data for the vertical ionization potentials (IPs) and electron affinities (EAs), extrapolated to the complete basis set limit. Additional comparisons are made to experimental data, where available. We consider fully self-consistent GW (scGW), partial self-consistency in the Green's function (scGW0), non-self-consistent G0W0 based on several mean-field starting points, and a "beyond GW" second-order screened exchange (SOSEX) correction to G0W0. We also describe the implementation of the self-consistent Coulomb hole with screened exchange method (COHSEX), which serves as one of the mean-field starting points. The best performers overall are G0W0+SOSEX and G0W0 based on an IP-tuned long-range corrected hybrid functional with the former being more accurate for EAs and the latter for IPs. Both provide a balanced treatment of localized vs delocalized states and valence spectra in good agreement with photoemission spectroscopy (PES) experiments. PMID:26731609

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

    Science.gov (United States)

    Guo, Wei-Feng; Zhang, Shao-Wu

    2016-04-01

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

  14. 可伸缩TAGS%Scalable TAGS

    Institute of Scientific and Technical Information of China (English)

    闵帆; 张君雁; 杨国纬

    2003-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Maren Lönne

    2015-12-01

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

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

    International Nuclear Information System (INIS)

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

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

    NARCIS (Netherlands)

    Xiao, ZS; Jansen, PA; Zhang, ZB

    2006-01-01

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

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

    NARCIS (Netherlands)

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

    2006-01-01

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

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

    International Nuclear Information System (INIS)

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-01-01

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

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

    DEFF Research Database (Denmark)

    Durao, Frederico; Dolog, Peter

    2009-01-01

    Tagging activity has been recently identified as a potential source of knowledge about personal interests, preferences, goals, and other attributes known from user models. Tags themselves can be therefore used for finding personalized recommendations of items. In this paper, we present a tag......-based recommender system which suggests similar Web pages based on the similarity of their tags from a Web 2.0 tagging application. The proposed approach extends the basic similarity calculus with external factors such as tag popularity, tag representativeness and the affinity between user and tag. In order to...

  2. Spectral Tagging

    International Nuclear Information System (INIS)

    This research examines the feasibility of spectral tagging, which involves modifying the spectral signature of a target, e.g. by mixing an additive with the target's paint. The target is unchanged to the human eye, but the tag is revealed when viewed with a spectrometer. This project investigates a layer of security that is not obvious, and therefore easy to conceal. The result is a tagging mechanism that is difficult to counterfeit. Uniquely tagging an item is an area of need in safeguards and security and non-proliferation. The powdered forms of the minerals lapis lazuli and olivine were selected as the initial test tags due to their availability and uniqueness in the visible to near-infrared spectral region. They were mixed with paints and applied to steel. In order to verify the presence of the tags quantitatively, the data from the spectrometer was input into unmixing models and signal detection algorithms. The mixture with the best results was blue paint mixed with lapis lazuli and olivine. The tag had a 0% probability of false alarm and a 100% probability of detection. The research proved that spectral tagging is feasible, although certain tag/paint mixtures are more detectable than others

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

    CERN Document Server

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

    1999-01-01

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

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

    DEFF Research Database (Denmark)

    Nielsen, Morten; Lundegaard, Claus; Lund, Ole

    2007-01-01

    correct alignment of a peptide in the binding groove a crucial part of identifying the core of an MHC class II binding motif. Here, we present a novel stabilization matrix alignment method, SMM-align, that allows for direct prediction of peptide:MHC binding affinities. The predictive performance of the...

  5. High-affinity RNA aptamers to C-reactive protein (CRP): newly developed pre-elution methods for aptamer selection

    International Nuclear Information System (INIS)

    We have developed a modified SELEX (systematic evolution of ligands by exponential enrichment) method to obtain RNA aptamers with high affinity to C-reactive protein (CRP). CRP is a clinical biomarker present in plasma, the level of which increases in response to infections and noninfectious inflammation. The CRP level is also an important prognostic indicator in patients with several syndromes. At present, CRP content in blood is measured immunochemically using antibodies. To develop a more sensitive method using RNA aptamers, we have attempted to obtain high-affinity RNA aptamers to CRP. We succeeded in obtaining an RNA aptamer with high affinity to CRP using a CRP-immobilized Sepharose column and pre-elution procedure. Pre-elution is a method that removes the weak binding portion from a selected RNA population by washing for a short time with buffer containing CRP. By surface plasmon-resonance (SPR) analysis, the affinity constant of this aptamer for CRP was calculated to be KD = 2.25x10-9 (M). The secondary structure, contact sites with CRP protein, and application of this aptamer will be described.

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

    DEFF Research Database (Denmark)

    Durao, Frederico; Dolog, Peter

    2009-01-01

    second takes into account external factors such as tag popularity, tag representativeness and the affinity between user and tag and the third approach recommends pages in grouped by tag. The experiment evaluates the wiki performance in different scenarios regarding the amount of pages, tags and users...

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

    OpenAIRE

    Fujiwara, Shin-ichi; Amisaki, Takashi

    2007-01-01

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

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

    DEFF Research Database (Denmark)

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

    2010-01-01

    objective function is linear, we have investigated a global algorithm based upon a branch-and-bound procedure. The algorithm uses Lagrangian bound coupling with a simplicial bisection in the criteria space. Preliminary computational results show that the global algorithm is promising.......Both the efficient and weakly efficient sets of an affine fractional vector optimization problem, in general, are neither convex nor given explicitly. Optimization problems over one of these sets are thus nonconvex. We propose two methods for optimizing a real-valued function over the efficient and...... weakly efficient sets of an affine fractional vector optimization problem. The first method is a local one. By using a regularization function, we reformulate the problem into a standard smooth mathematical programming problem that allows applying available methods for smooth programming. In case the...

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

    Science.gov (United States)

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

    2016-01-01

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

  10. Flavour Tagging at LHCb

    CERN Multimedia

    Grabalosa Gandara, M

    2009-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Durrett, Timothy; Ohlrogge, John; Pollard, Michael

    2016-05-03

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

  12. A sensitive and selective resonance Rayleigh scattering method for quick detection of avidin using affinity labeling Au nanoparticles.

    Science.gov (United States)

    Wang, Qi; Huang, Xi; Fu, Xuan; Deng, Huan; Ma, Meihu; Cai, Zhaoxia

    2016-06-01

    Avidin is a glycoprotein with antinutritional property, which should be limited in daily food. We developed an affinity biosensor system based on resonance Rayleigh scattering (RRS) and using affinity biotin labeling Au nanoparticles (AuNPs). This method was selective and sensitive for quick avidin detection due to the avidin-biotin affinitive interaction. Under optimal conditions, RRS intensity of biotin-AuNPs increase linearly with an increasing concentration of avidin from 5 to 160ng/mL. The lower limit of detection was 0.59ng/mL. This rapid and selective avidin detection method was used in synthetic samples and egg products with recoveries of between 102.97 and 107.92%, thereby demonstrating the feasible and practical application of this assay. PMID:26978788

  13. A sensitive and selective resonance Rayleigh scattering method for quick detection of avidin using affinity labeling Au nanoparticles

    Science.gov (United States)

    Wang, Qi; Huang, Xi; Fu, Xuan; Deng, Huan; Ma, Meihu; Cai, Zhaoxia

    2016-06-01

    Avidin is a glycoprotein with antinutritional property, which should be limited in daily food. We developed an affinity biosensor system based on resonance Rayleigh scattering (RRS) and using affinity biotin labeling Au nanoparticles (AuNPs). This method was selective and sensitive for quick avidin detection due to the avidin-biotin affinitive interaction. Under optimal conditions, RRS intensity of biotin-AuNPs increase linearly with an increasing concentration of avidin from 5 to 160 ng/mL. The lower limit of detection was 0.59 ng/mL. This rapid and selective avidin detection method was used in synthetic samples and egg products with recoveries of between 102.97 and 107.92%, thereby demonstrating the feasible and practical application of this assay.

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

    OpenAIRE

    Gallicchio, Emilio; Ronald M Levy

    2012-01-01

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

  15. High-Quality Vector Field and Direct Vorticity Estimation Uusing the Affine Correlation Method

    Czech Academy of Sciences Publication Activity Database

    Gronát, Petr

    Prague : Institute of Thermomechanics AS CR, v. v. i., 2010 - (Zolotarev, I.), s. 35-36 ISBN 978-80-87012-26-0. [ENGINEERING MECHANICS 2010. Svratka (CZ), 10.05.2010-13.05.2010] R&D Projects: GA ČR GA101/08/1112; GA ČR GAP101/10/1230 Institutional research plan: CEZ:AV0Z20760514 Keywords : PIV * normalized cross correlation * affine correlation * vortex detection Subject RIV: BK - Fluid Dynamics

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

    Institute of Scientific and Technical Information of China (English)

    Peihua GUO; Detong ZHU

    2008-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

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

  18. Tagging of MADS domain proteins for chromatin immunoprecipitation

    Directory of Open Access Journals (Sweden)

    van Zuijlen Lisette GC

    2007-09-01

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

  19. Identification on Membrane and Characterization of Phosphoproteins Using an Alkoxide-Bridged Dinuclear Metal Complex as a Phosphate-Binding Tag Molecule

    OpenAIRE

    Nakanishi, Tsuyoshi; ANDO, EIJI; Furuta, Masaru; Kinoshita, Eiji; Kinoshita-Kikuta, Emiko; Koike, Tohru; Tsunasawa, Susumu; Nishimura, Osamu

    2007-01-01

    We have developed a method for on-membrane direct identification of phosphoproteins, which are detected by a phosphate-binding tag (Phos-tag) that has an affinity to phosphate groups with a chelated Zn2+ ion. This rapid profiling approach for phosphoproteins combines chemical inkjet technology for microdispensing of reagents onto a tiny region of target proteins with mass spectrometry for on-membrane digested peptides. Using this method, we analyzed human epidermoid carcinoma cell lysates of ...

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

    DEFF Research Database (Denmark)

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

    2012-01-01

    An efficient and reliable procedure for the capture of affinity-tagged proteins and associated complexes from human cell lines is reported. Through multiple optimizations, high yield and low background affinity-purifications are achieved from modest quantities of human cells expressing endogenous......-level tagged proteins. Isolations of triple-FLAG and GFP-tagged fusion proteins involved in RNA metabolism are presented....

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

    OpenAIRE

    Cattuto, Ciro; Benz, Dominik; Hotho, Andreas; Stumme, Gerd

    2008-01-01

    Social bookmarking systems allow users to organise collections of resources on the Web in a collaborative fashion. The increasing popularity of these systems as well as first insights into their emergent semantics have made them relevant to disciplines like knowledge extraction and ontology learning. The problem of devising methods to measure the semantic relatedness between tags and characterizing it semantically is still largely open. Here we analyze three measures of tag relatedness: tag c...

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

    Directory of Open Access Journals (Sweden)

    Nikola Štambuk

    2014-05-01

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

  3. Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags

    Directory of Open Access Journals (Sweden)

    Hwang Jennifer

    2010-07-01

    Full Text Available Abstract Intense interest centers on the role of the human gut microbiome in health and disease, but optimal methods for analysis are still under development. Here we present a study of methods for surveying bacterial communities in human feces using 454/Roche pyrosequencing of 16S rRNA gene tags. We analyzed fecal samples from 10 individuals and compared methods for storage, DNA purification and sequence acquisition. To assess reproducibility, we compared samples one cm apart on a single stool specimen for each individual. To analyze storage methods, we compared 1 immediate freezing at -80°C, 2 storage on ice for 24 or 3 48 hours. For DNA purification methods, we tested three commercial kits and bead beating in hot phenol. Variations due to the different methodologies were compared to variation among individuals using two approaches--one based on presence-absence information for bacterial taxa (unweighted UniFrac and the other taking into account their relative abundance (weighted UniFrac. In the unweighted analysis relatively little variation was associated with the different analytical procedures, and variation between individuals predominated. In the weighted analysis considerable variation was associated with the purification methods. Particularly notable was improved recovery of Firmicutes sequences using the hot phenol method. We also carried out surveys of the effects of different 454 sequencing methods (FLX versus Titanium and amplification of different 16S rRNA variable gene segments. Based on our findings we present recommendations for protocols to collect, process and sequence bacterial 16S rDNA from fecal samples--some major points are 1 if feasible, bead-beating in hot phenol or use of the PSP kit improves recovery; 2 storage methods can be adjusted based on experimental convenience; 3 unweighted (presence-absence comparisons are less affected by lysis method.

  4. Top Tagging with New Approaches

    CERN Document Server

    CMS Collaboration

    2016-01-01

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

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

    Science.gov (United States)

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

    2016-07-15

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

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

    Directory of Open Access Journals (Sweden)

    Lund Ole

    2007-07-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-04-15

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

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

    International Nuclear Information System (INIS)

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

  9. Antenna for passive RFID tags

    Science.gov (United States)

    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].

  10. Review on SAW RFID tags.

    Science.gov (United States)

    Plessky, Victor P; Reindl, Leonhard M

    2010-03-01

    SAW tags were invented more than 30 years ago, but only today are the conditions united for mass application of this technology. The devices in the 2.4-GHz ISM band can be routinely produced with optical lithography, high-resolution radar systems can be built up using highly sophisticated, but low-cost RF-chips, and the Internet is available for global access to the tag databases. The "Internet of Things," or I-o-T, will demand trillions of cheap tags and sensors. The SAW tags can overcome semiconductor-based analogs in many aspects: they can be read at a distance of a few meters with readers radiating power levels 2 to 3 orders lower, they are cheap, and they can operate in robust environments. Passive SAW tags are easily combined with sensors. Even the "anti-collision" problem (i.e., the simultaneous reading of many nearby tags) has adequate solutions for many practical applications. In this paper, we discuss the state-of-the-art in the development of SAW tags. The design approaches will be reviewed and optimal tag designs, as well as encoding methods, will be demonstrated. We discuss ways to reduce the size and cost of these devices. A few practical examples of tags using a time-position coding with 10(6) different codes will be demonstrated. Phase-coded devices can additionally increase the number of codes at the expense of a reduction of reading distance. We also discuss new and exciting perspectives of using ultra wide band (UWB) technology for SAW-tag systems. The wide frequency band available for this standard provides a great opportunity for SAW tags to be radically reduced in size to about 1 x 1 mm(2) while keeping a practically infinite number of possible different codes. Finally, the reader technology will be discussed, as well as detailed comparison made between SAW tags and IC-based semiconductor device. PMID:20211785

  11. Protein Complex Purification by Affinity Capture.

    Science.gov (United States)

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

    2016-01-01

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

  12. Convergence and divergence in tagging systems: An examination of tagging practices over a four year period

    OpenAIRE

    Kipp, Margaret E.I.

    2010-01-01

    This paper analyses the tagging patterns on delicious.com for a set of documents (URLs) over a 4 year period using informetrics methods to assess how collaborative tagging supports and enhances traditional document indexing. Results of the study show that there is still a mix of consensus and divergence in tagging term use and tagging patterns. While some of the chosen URLs maintained or even increased their popularity, others experienced a severe drop in popularity. Tag usage showed some mea...

  13. iTag: Incentive-Based Tagging

    OpenAIRE

    Maniu, S; Lei, S.; Yang, X.; Mo, L; Cheng, CK

    2014-01-01

    In social tagging systems, such as Delicious1 and Flickr2, users are allowed to annotate resources (e.g., Web URLs and images) with textual descriptions called tags. Tags have proven to be invaluable building blocks in algorithms for searching, mining and recommending resources. In practice, however, not all resources receive the same attention from users, and as a result, most tags are added to the few highly-popular resources, while most of the resources receive few tags. Crucially, this in...

  14. A Review on Chipless RFID Tag Design

    Directory of Open Access Journals (Sweden)

    Ali Hashemi

    2013-06-01

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

  15. The Abundance of Nonphosphorylated Tau in Mouse and Human Tauopathy Brains Revealed by the Use of Phos-Tag Method.

    Science.gov (United States)

    Kimura, Taeko; Hatsuta, Hiroyuki; Masuda-Suzukake, Masami; Hosokawa, Masato; Ishiguro, Koichi; Akiyama, Haruhiko; Murayama, Shigeo; Hasegawa, Masato; Hisanaga, Shin-ichi

    2016-02-01

    Tauopathies are neurodegenerative diseases characterized by aggregates of hyperphosphorylated tau. Previous studies have identified many disease-related phosphorylation sites on tau. However, it is not understood how tau is hyperphosphorylated and what extent these sites are phosphorylated in both diseased and normal brains. Most previous studies have used phospho-specific antibodies to analyze tau phosphorylation. These results are useful but do not provide information about nonphosphorylated tau. Here, we applied the method of Phos-tag SDS-PAGE, in which phosphorylated tau was separated from nonphosphorylated tau in vivo. Among heterogeneously phosphorylated tau species in adult mouse brains, the nonphosphorylated 0N4R isoform was detected most abundantly. In contrast, perinatal tau and tau in cold water-stressed mice were all phosphorylated with a similar extent of phosphorylation. In normal elderly human brains, nonphosphorylated 0N3R and 0N4R tau were most abundant. A slightly higher phosphorylation of tau, which may represent the early step of hyperphosphorylation, was increased in Alzheimer disease patients at Braak stage V. Tau with this phosphorylation state was pelleted by centrifugation, and sarkosyl-soluble tau in either Alzheimer disease or corticobasal degeneration brains showed phosphorylation profiles similar to tau in normal human brain, suggesting that hyperphosphorylation occurs in aggregated tau. These results indicate that tau molecules are present in multiple phosphorylation states in vivo, and nonphosphorylated forms are highly expressed among them. PMID:26687814

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

    DEFF Research Database (Denmark)

    2015-01-01

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

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

    DEFF Research Database (Denmark)

    Rudolf, Amalie Frederikke; Skovgaard, Tine; Knapp, Stefan; Jensen, Lars Juhl; Berthelsen, Jens

    2014-01-01

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

  18. Critical evaluation of sequential extraction and sink-float methods used for the determination of Ga and Ge affinity in lignite

    Energy Technology Data Exchange (ETDEWEB)

    Zdenek Klika; Lenka Ambruzova; Ivana Sykorova; Jana Seidlerova; Ivan Kolomaznik [VSB-Technical University Ostrava, Ostrava (Czech Republic)

    2009-10-15

    The affinities of Ga and Ge in lignite were determined using sequential extraction (SE) and element affinity calculation (EAC) based on sink-float data. For this study a bulk lignite sample was fractioned into two sets. The first set of samples (A) consisted of the different grain sizes fractions; the second one set (B) was prepared by density fractionation. Sequential extractions (1) were performed on both sets of fractions with very good agreement between determined organic elements affinities (OEA of Ga evaluated from A data is 32%, from B data 35%; OEA of Ge evaluated from A data is 31% and from B data 26%). The data of B lignite fractions were evaluated using two element affinity calculations: (a) EAC (I) of Klika and Kolomaznk (2) and (b) newly prepared subroutine EAC (II) based on quantitative contents of lignite macerals and minerals. There was also good agreement between both methods obtained (OEA of Ga calculated by EAC (I) is 83% and by EAC (II) 77%; OEA of Ge calculated by EAC (I) is 89% and by EAC (II) 97%). The significant differences of organic elements affinities of Ga and Ge evaluated by sequential extraction and by element affinity calculation based on sink-float data are discussed. 34 refs., 7 figs., 6 tabs.

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

    Directory of Open Access Journals (Sweden)

    Mehfuza Holia

    2009-11-01

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

  20. Yellowtail Tagging Data (MRDBS)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Yellowtail Flounder Tagging Program began in 2003 and works with commercial fishermen to tag and release yellowtaiI flounder with pink and yellow disc tags or...

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

    Directory of Open Access Journals (Sweden)

    Jiabing Ji

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2007-11-05

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

  3. Providing affinity

    DEFF Research Database (Denmark)

    Guglielmi, Michel; Johannesen, Hl

    , Essex, Hertfordshire, Norfolk and Suffolk. Research found that there was a lack of identity or sense of belonging and nothing anchoring people to the region as a whole. Common affinity is somehow forced to the people of East England and thereby we came to the conclusion that a single landmark or a...... a sense of belonging to people sharing deterritorialized synchronic experiences. But at the same time, the immersion experience is highly low tech and desperately analog, mainly based on fabulation, cartoons, and mushrooms growing in local forests. It ultimately appeals to the experienced sense of...

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

    OpenAIRE

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

    2014-01-01

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

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

    Science.gov (United States)

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

    2015-01-01

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

  6. Identification of pyrazosulfuron-ethyl binding affinity and binding site subdomain IIA in human serum albumin by spectroscopic methods

    Science.gov (United States)

    Ding, Fei; Liu, Wei; Zhang, Xi; Wu, Li-Jun; Zhang, Li; Sun, Ying

    2010-03-01

    Pyrazosulfuron-ethyl (PY) is a sulfonylurea herbicide developed by DuPont which has been widely used for weed control in cereals. The determination of PY binding affinity and binding site in human serum albumin (HSA) by spectroscopic methods is the subject of this work. From the fluorescence emission, circular dichroism and three-dimensional fluorescence results, the interaction of PY with HSA caused secondary structure changes in the protein. Fluorescence data demonstrated that the quenching of HSA fluorescence by PY was the result of the formation of HSA-PY complex at 1:1 molar ratio, a static mechanism was confirmed to lead to the fluorescence quenching. Hydrophobic probe 8-anilino-1-naphthalenesulfonic acid (ANS) displacement results show that hydrophobic patches are the major sites for PY binding on HSA. The thermodynamic parameters Δ H° and Δ S° were calculated to be -36.32 kJ mol -1 and -35.91 J mol -1 K -1, which illustrated van der Waals forces and hydrogen bonds interactions were the dominant intermolecular force in stabilizing the complex. Also, site marker competitive experiments showed that the binding of PY to HSA took place primarily in subdomain IIA (Sudlow's site I). What presented in this paper binding research enriches our knowledge of the interaction between sulfonylurea herbicides and the physiologically important protein HSA.

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

    Science.gov (United States)

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

    2016-01-11

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

  8. b-tagging in DELPHI at LEP

    CERN Document Server

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

    2004-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Lee Wah

    2008-09-01

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

  10. Affinity purification of proteins binding to GST fusion proteins.

    Science.gov (United States)

    Swaffield, J C; Johnston, S A

    2001-05-01

    This unit describes the use of proteins fused to glutathione-S-transferase (GST fusion proteins) to affinity purify other proteins, a technique also known as GST pulldown purification. The describes a strategy in which a GST fusion protein is bound to agarose affinity beads and the complex is then used to assay the binding of a specific test protein that has been labeled with [35S]methionine by in vitro translation. However, this method can be adapted for use with other types of fusion proteins; for example, His6, biotin tags, or maltose-binding protein fusions (MBP), and these may offer particular advantages. A describes preparation of an E. coli extract that is added to the reaction mixture with purified test protein to reduce nonspecific binding. PMID:18265191

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

    Science.gov (United States)

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

    2009-08-15

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

  12. Implicit Human Centered Tagging

    OpenAIRE

    Pantic, Maja; Vinciarelli, Alessandro

    2009-01-01

    Tagging is the annotation of multimedia data with userspecified keywords known as tags, with the aim of facilitating fast and accurate data retrieval based on these tags. In contrast to this process, also referred to as explicit tagging, implicit human-centered tagging (IHCT) refers to exploiting the information on user's nonverbal reactions (e.g., facial expressions like smiles or head gestures like shakes) to multimedia data, with which he or she interacts, to assign new or improve the exis...

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

    Science.gov (United States)

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

    2016-07-20

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

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

    Science.gov (United States)

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

    2016-01-01

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

  15. Gas tagging system development in Japan

    International Nuclear Information System (INIS)

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

  16. Gaussian Affine Feature Detector

    OpenAIRE

    Xu, Xiaopeng; Zhang, Xiaochun

    2011-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    刘跃亮; 曾照芳

    2011-01-01

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

  18. A simple nonradioactive method for the determination of the binding affinities of antibodies induced by hapten bioconjugates for drugs of abuse

    OpenAIRE

    Torres, Oscar B.; Antoline, Joshua F. G.; Li, Fuying; Jalah, Rashmi; Jacobson, Arthur E; Rice, Kenner C.; Alving, Carl R.; Matyas, Gary R.

    2015-01-01

    The accurate analytical measurement of binding affinities of polyclonal antibody in sera to heroin, 6-acetylmorphine (6-AM), and morphine has been a challenging task. A simple nonradioactive method that uses deuterium-labeled drug tracers and equilibrium dialysis (ED) combined with ultra performance liquid chromatography/tandem mass spectrometry (UPLC/MS/MS) to measure the apparent dissociation constant (K d) of antibodies to 6-AM and morphine is described. The method can readily detect antib...

  19. Dot-ELISA affinity test: an easy, low-cost method to estimate binding activity of monoclonal antibodies

    Czech Academy of Sciences Publication Activity Database

    Svobodová, Z.; Jankovičová, B.; Horák, Daniel; Bílková, Z.

    2013-01-01

    Roč. 4, č. 3 (2013), 1000168_1-1000168_5. ISSN 2155-9872 R&D Projects: GA MŠk 7E12053; GA MŠk 7E09109 EU Projects: European Commission(XE) 246513 - NADINE; European Commission(XE) 228980 - CAMINEMS Institutional support: RVO:61389013 Keywords : dot-ELISA * affinity * monoclonal antibody Subject RIV: CD - Macromolecular Chemistry

  20. Methodologies for Improved Tag Cloud Generation with Clustering

    DEFF Research Database (Denmark)

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

    2012-01-01

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

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

    Science.gov (United States)

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

    2012-07-01

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

  2. Preserving Privacy in Social Tagging

    Directory of Open Access Journals (Sweden)

    Pradnya M. Deshmane

    2015-12-01

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

  3. Tag Meaning Disambiguation through Analysis of Tripartite Structure of Folksonomies

    OpenAIRE

    Au Yeung, Ching Man; Gibbins, Nicholas; Shadbolt, Nigel

    2007-01-01

    Collaborative tagging systems are becoming very popular recently. Web users use freely-chosen tags to describe shared resources, resulting in a folksonomy. One problem of folksonomies is that tags which appear in the same form may carry multiple meanings and represent different concepts. As this kind of tags are ambiguous, the precisions in both description and retrieval of the shared resources are reduced. We attempt to develop effective methods to disambiguate tags by studying the tripartit...

  4. Nickel(II)-immobilized sulfhydryl cotton fiber for selective binding and rapid separation of histidine-tagged proteins.

    Science.gov (United States)

    He, Xiao-Mei; Zhu, Gang-Tian; Lu, Wei; Yuan, Bi-Feng; Wang, Hong; Feng, Yu-Qi

    2015-07-31

    In the current study, a novel nickel(II)-immobilized sulfhydryl cotton fiber (SCF-Ni(2+)) was prepared in a simple way based on the coordination effect between Ni(2+) and thiol group on the surface of SCF. The composition and element mapping of SCF-Ni(2+) fibers were demonstrated by energy-dispersive X-ray (EDX) spectroscopy. Based on the high affinity of Ni(2+) to 6×His on histidine-tagged (His-tagged) proteins, SCF-Ni(2+) fibers were then further used as an immobilized metal ion affinity chromatography (IMAC) adsorbent for selective binding and rapid separation of His-tagged proteins using an in- pipette-tip SPE format. Our results showed that SCF-Ni(2+) adsorbent can selectively capture His-tagged proteins from protein mixture and Escherichia coli cell lysates. Taken together, the developed method provides a rapid, convenient and efficient approach for the purification of His-tagged proteins. PMID:26087962

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

    Science.gov (United States)

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

    2015-03-01

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

  6. Hierarchical Affinity Propagation

    CERN Document Server

    Givoni, Inmar; Frey, Brendan J

    2012-01-01

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

  7. Gillnet Tag Program

    Data.gov (United States)

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

  8. North Pacific Albacore Tagging

    Data.gov (United States)

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

  9. Satellite Tags- Hawaii EEZ

    Data.gov (United States)

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

  10. Cooperative Tagging Center (CTC)

    Data.gov (United States)

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

  11. Measurement of B- -> tau- nu_tau-bar with a Hadronic Tagging Method Using the Full Data Sample of Belle

    CERN Document Server

    Adachi, I; Aihara, H; Arinstein, K; Arita, Y; Asner, D M; Aso, T; Aulchenko, V; Aushev, T; Aziz, T; Bakich, A M; Ban, Y; Barberio, E; Barrett, M; Bay, A; Bedny, I; Belhorn, M; Belous, K; Bhardwaj, V; Bhuyan, B; Bischofberger, M; Blyth, S; Bondar, A; Bonvicini, G; Bozek, A; Bracko, M; Brodzicka, J; Brovchenko, O; Browder, T E; Chang, M -C; Chang, P; Chao, Y; Chekelian, V; Chen, A; Chen, K -F; Chen, P; Cheon, B G; Chilikin, K; Chistov, R; Cho, I -S; Cho, K; Choi, K -S; Choi, S -K; Choi, Y; Crnkovic, J; Dalseno, J; Danilov, M; Dingfelder, J; Dolezal, Z; Drásal, Z; Drutskoy, A; Dungel, W; Dutta, D; Eidelman, S; Epifanov, D; Esen, S; Fast, J E; Feindt, M; Frey, A; Fujikawa, M; Gaur, V; Gabyshev, N; Garmash, A; Goh, Y M; Golob, B; GrossePerdekamp, M; Guo, H; Haba, J; Hamer, P; Han, Y L; Hara, K; Hara, T; Hasegawa, Y; Hayasaka, K; Hayashii, H; Heffernan, D; Higuchi, T; Horii, Y; Hoshi, Y; Hoshina, K; Hou, W -S; Hsiung, Y B; Hyun, H J; Igarashi, Y; Iijima, T; Imamura, M; Inami, K; Ishikawa, A; Itoh, R; Iwabuchi, M; Iwasaki, M; Iwasaki, Y; Iwashita, T; Iwata, S; Jaegle, I; Jones, M; Julius, T; Kah, D H; Kakuno, H; Kang, J H; Kapusta, P; Kataoka, S U; Katayama, N; Kawai, H; Kawasaki, T; Kichimi, H; Kiesling, C; Kim, B H; Kim, H J; Kim, H O; Kim, J B; Kim, J H; Kim, K T; Kim, M J; Kim, S K; Kim, Y J; Kinoshita, K; Klucar, J; Ko, B R; Kobayashi, N; Koblitz, S; Kodys, P; Koga, Y; Korpar, S; Kouzes, R T; Kreps, M; Krizan, P; Krokovny, P; Kronenbitter, B; Kuhr, T; Kumar, R; Kumita, T; Kurihara, E; Kuroki, Y; Kuzmin, A; Kvasnicka, P; Kwon, Y -J; Kyeong, S -H; Lange, J S; Lee, M J; Lee, S -H; Leitgab, M; Leitner, R; Li, J; Li, X; Li, Y; Libby, J; Lim, C -L; Limosani, A; Liu, C; Liu, Y; Liu, Z Q; Liventsev, D; Louvot, R; MacNaughton, J; Marlow, D; Matvienko, D; Matyja, A; McOnie, S; Mikami, Y; Miyabayashi, K; Miyachi, Y; Miyata, H; Miyazaki, Y; Mizuk, R; Mohanty, G B; Mohapatra, D; Moll, A; Mori, T; Müller, T; Muramatsu, N; Mussa, R; Nagamine, T; Nagasaka, Y; Nakahama, Y; Nakamura, I; Nakano, E; Nakano, T; Nakao, M; Nakayama, H; Nakazawa, H; Natkaniec, Z; Nayak, M; Nedelkovska, E; Negishi, K; Neichi, K; Neubauer, S; Ng, C; Niiyama, M; Nishida, S; Nishimura, K; Nitoh, O; Nozaki, T; Ogawa, A; Ogawa, S; Ohshima, T; Okuno, S; Olsen, S L; Onuki, Y; Ostrowicz, W; Ozaki, H; Pakhlov, P; Pakhlova, G; Palka, H; Panzenböck, E; Park, C W; Park, H; Park, H K; Park, K S; Peak, L S; Pedlar, T K; Peng, T; Pestotnik, R; Peters, M; Petric, M; Piilonen, L E; Poluektov, A; Prim, M; Prothmann, K; Reisert, B; Ritter, M; Röhrken, M; Rorie, J; Rozanska, M; Ryu, S; Sahoo, H; Sakai, K; Sakai, Y; Sandilya, S; Santel, D; Santelj, L; Sanuki, T; Sasao, N; Sato, Y; Schneider, O; Schnell, G; Schönmeier, P; Schwanda, C; Schwartz, A J; Schwenker, B; Seidl, R; Sekiya, A; Senyo, K; Seon, O; Sevior, M E; Shang, L; Shapkin, M; Shebalin, V; Shen, C P; Shibata, T -A; Shibuya, H; Shinomiya, S; Shiu, J -G; Shwartz, B; Sibidanov, A; Simon, F; Singh, J B; Sinha, R; Smerkol, P; Sohn, Y -S; Sokolov, A; Solovieva, E; Stanic, S; Staric, M; Stypula, J; Sugihara, S; Sugiyama, A; Sumihama, M; Sumisawa, K; Sumiyoshi, T; Suzuki, K; Suzuki, S; Suzuki, S Y; Takeichi, H; Tamponi, U; Tanaka, M; Tanaka, S; Tanida, K; Taniguchi, N; Tatishvili, G; Taylor, G N; Teramoto, Y; Thorne, F; Tikhomirov, I; Trabelsi, K; Tse, Y F; Tsuboyama, T; Uchida, M; Uchida, T; Uchida, Y; Uehara, S; Ueno, K; Uglov, T; Unno, Y; Uno, S; Urquijo, P; Ushiroda, Y; Usov, Y; Vahsen, S E; Vanhoefer, P; VanHulse, C; Varner, G; Varvell, K E; Vervink, K; Vinokurova, A; Vorobyev, V; Vossen, A; Wang, C H; Wang, J; Wang, M -Z; Wang, P; Wang, X L; Watanabe, M; Watanabe, Y; Wedd, R; White, E; Wicht, J; Widhalm, L; Wiechczynski, J; Williams, K M; Won, E; Yabsley, B D; Yamamoto, H; Yamaoka, J; Yamashita, Y; Yamauchi, M; Yuan, C Z; Yusa, Y; Zander, D; Zhang, C C; Zhang, L M; Zhang, Z P; Zhao, L; Zhilich, V; Zhou, P; Zhulanov, V; Zivko, T; Zupanc, A; Zwahlen, N; Zyukova, O

    2012-01-01

    We measure the branching fraction of B- -> tau- nu_tau-bar using the full Upsilon(4S) data sample containing 772*10^6 BBbar pairs collected with the Belle detector at the KEKB asymmetric-energy e+e- collider. Events with BBbar pairs are tagged by reconstructing one of the B mesons decaying into hadronic final states, and B- -> tau- nu_tau-bar candidates are detected in the recoil. We find evidence of B- -> tau- nu_tau-bar with a branching fraction of B(B- -> tau- nu_tau-bar) = [0.72^{+0.27}_{-0.25}(stat) +/- 0.11(syst)] * 10^-4, and a significance of 3.0 standard deviations including systematic uncertainties.

  12. Cardiac MRI tagging

    International Nuclear Information System (INIS)

    Cardiac MRI tagging is an original technique based upon the perturbation of the magnetization of determined regions of the myocardium (tags). The motion of the tags accurately reflects the deformation of the underlying tissue. Data analysis requires special techniques to reconstruct the 3D motion of the heart, and to evaluate the myocardial strain, locally and throughout the whole heart. (authors)

  13. Cutaneous skin tag

    Science.gov (United States)

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

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

    Institute of Scientific and Technical Information of China (English)

    樊新; 高曙

    2015-01-01

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

  15. GST-His purification: a two-step affinity purification protocol yielding full-length purified proteins.

    Science.gov (United States)

    Maity, Ranjan; Pauty, Joris; Krietsch, Jana; Buisson, Rémi; Genois, Marie-Michelle; Masson, Jean-Yves

    2013-01-01

    Key assays in enzymology for the biochemical characterization of proteins in vitro necessitate high concentrations of the purified protein of interest. Protein purification protocols should combine efficiency, simplicity and cost effectiveness. Here, we describe the GST-His method as a new small-scale affinity purification system for recombinant proteins, based on a N-terminal Glutathione Sepharose Tag (GST) and a C-terminal 10xHis tag, which are both fused to the protein of interest. The latter construct is used to generate baculoviruses, for infection of Sf9 infected cells for protein expression. GST is a rather long tag (29 kDa) which serves to ensure purification efficiency. However, it might influence physiological properties of the protein. Hence, it is subsequently cleaved off the protein using the PreScission enzyme. In order to ensure maximum purity and to remove the cleaved GST, we added a second affinity purification step based on the comparatively small His-Tag. Importantly, our technique is based on two different tags flanking the two ends of the protein, which is an efficient tool to remove degraded proteins and, therefore, enriches full-length proteins. The method presented here does not require an expensive instrumental setup, such as FPLC. Additionally, we incorporated MgCl2 and ATP washes to remove heat shock protein impurities and nuclease treatment to abolish contaminating nucleic acids. In summary, the combination of two different tags flanking the N- and the C-terminal and the capability to cleave off one of the tags, guaranties the recovery of a highly purified and full-length protein of interest. PMID:24193370

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

    OpenAIRE

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

    2012-01-01

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

  17. Monitoring Arthrobacter protophormiae RKJ100 in a 'tag and chase' method during p-nitrophenol bio-remediation in soil microcosms.

    Science.gov (United States)

    Pandey, Gunjan; Pandey, Janmejay; Jain, Rakesh K

    2006-05-01

    Monitoring of micro-organisms released deliberately into the environment is essential to assess their movement during the bio-remediation process. During the last few years, DNA-based genetic methods have emerged as the preferred method for such monitoring; however, their use is restricted in cases where organisms used for bio-remediation are not well characterized or where the public domain databases do not provide sufficient information regarding their sequence. For monitoring of such micro-organisms, alternate approaches have to be undertaken. In this study, we have specifically monitored a p-nitrophenol (PNP)-degrading organism, Arthrobacter protophormiae RKJ100, using molecular methods during PNP degradation in soil microcosm. Cells were tagged with a transposon-based foreign DNA sequence prior to their introduction into PNP-contaminated microcosms. Later, this artificially introduced DNA sequence was PCR-amplified to distinguish the bio-augmented organism from the indigenous microflora during PNP bio-remediation. PMID:16205921

  18. FTR tag burnup

    International Nuclear Information System (INIS)

    The gas tag burnup changes investigated were limited to the three tags (Kr-78/Kr-80, Xe-126/Xe-129 and Kr-82/Kr-80) currently accepted as being the most desirable. Control rod tag burnup was significantly greater than fuel rod tag burnup. This occurs because control rods stay in the reactor longer and occupy positions of greater low-energy flux. Thus, minimum tag spacings were set by the control rods as 1.079 for Kr-78/Kr-80, 1.189 for Xe-126/Xe-129 and 1.134 for Kr-82/Kr-80

  19. Gaussian Affine Feature Detector

    CERN Document Server

    Xu, Xiaopeng

    2011-01-01

    A new method is proposed to get image features' geometric information. Using Gaussian as an input signal, a theoretical optimal solution to calculate feature's affine shape is proposed. Based on analytic result of a feature model, the method is different from conventional iterative approaches. From the model, feature's parameters such as position, orientation, background luminance, contrast, area and aspect ratio can be extracted. Tested with synthesized and benchmark data, the method achieves or outperforms existing approaches in term of accuracy, speed and stability. The method can detect small, long or thin objects precisely, and works well under general conditions, such as for low contrast, blurred or noisy images.

  20. Social Tags: Meaning and Suggestions

    OpenAIRE

    Suchanek, Fabian; Vojnovic, Milan; Gunawardena, Dinan

    2008-01-01

    This paper aims to quantify two common assumptions about social tagging: (1) that tags are ``meaningful" and (2) that the tagging process is influenced by tag suggestions. For (1), we analyze the semantic properties of tags and the relationship between the tags and the content of the tagged page. Our analysis is based on a corpus of search keywords, contents, titles, and tags applied to several thousand popular Web pages. Among other results, we find that the more popu...

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

    CERN Document Server

    Cattuto, Ciro; Hotho, Andreas; Stumme, Gerd

    2008-01-01

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

  2. Graph based techniques for tag cloud generation

    DEFF Research Database (Denmark)

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

    2013-01-01

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

  3. Measurement of tag confidence in user generated contents retrieval

    Science.gov (United States)

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

    2009-01-01

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

  4. A New Method for Navigating Optimal Direction for Pulling Ligand from Binding Pocket: Application to Ranking Binding Affinity by Steered Molecular Dynamics.

    Science.gov (United States)

    Vuong, Quan Van; Nguyen, Tin Trung; Li, Mai Suan

    2015-12-28

    In this paper we present a new method for finding the optimal path for pulling a ligand from the binding pocket using steered molecular dynamics (SMD). Scoring function is defined as the steric hindrance caused by a receptor to ligand movement. Then the optimal path corresponds to the minimum of this scoring function. We call the new method MSH (Minimal Steric Hindrance). Contrary to existing navigation methods, our approach takes into account the geometry of the ligand while other methods including CAVER only consider the ligand as a sphere with a given radius. Using three different target + receptor sets, we have shown that the rupture force Fmax and nonequilibrium work Wpull obtained based on the MSH method show a much higher correlation with experimental data on binding free energies compared to CAVER. Furthermore, Wpull was found to be a better indicator for binding affinity than Fmax. Thus, the new MSH method is a reliable tool for obtaining the best direction for ligand exiting from the binding site. Its combination with the standard SMD technique can provide reasonable results for ranking binding affinities using Wpull as a scoring function. PMID:26595261

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

    Directory of Open Access Journals (Sweden)

    Junfeng Gu

    2015-10-01

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

  6. Tag Based Audio Search Engine

    Directory of Open Access Journals (Sweden)

    Parameswaran Vellachu

    2012-03-01

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

  7. Using Interference to Block RFID Tags

    DEFF Research Database (Denmark)

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

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

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

    International Nuclear Information System (INIS)

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-10-01

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

  10. Internally readable identifying tag

    International Nuclear Information System (INIS)

    A method of identifying non-metallic objects by means of X-ray equipment is described in detail. A small metal pin with a number of grooves cut in a pre-determined equi-spaced pattern is implanted into the non-metallic object and by decoding the groove patterns using X-ray equipment, the object is uniquely identified. A specific example of such an application is in studying the migratory habits of fish. The pin inserted into the snout of the fish is 0.010 inch in diameter, 0.040 inch in length with 8 possible positions for grooves if spaced 0.005 inch apart. With 6 of the groove positions available for data, the capacity is 26 or 64 combinations; clearly longer pins would increase the data capacity. This method of identification is a major advance over previous techniques which necessitated destruction of the fish in order to recover the identification tag. (UK)

  11. Affine functors and duality

    OpenAIRE

    J. Navarro; Sancho, C.; Sancho, P.

    2009-01-01

    A functor of sets $\\mathbb X$ over the category of $K$-commutative algebras is said to be an affine functor if its functor of functions, $\\mathbb A_{\\mathbb X}$, is reflexive and $\\mathbb X=\\Spec \\mathbb A_{\\mathbb X}$. We prove that affine functors are equal to a direct limit of affine schemes and that affine schemes, formal schemes, the completion of affine schemes along a closed subscheme, etc., are affine functors. Endowing an affine functor $\\mathbb X$ with a functor of monoids structure...

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

    Directory of Open Access Journals (Sweden)

    Afaz Uddin Ahmed

    2014-01-01

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

  13. Studying Social Tagging and Folksonomy: A Review and Framework

    OpenAIRE

    Trant, J.

    2009-01-01

    This paper reviews research into social tagging and folksonomy (as reflected in about 180 sources published through December 2007). Methods of researching the contribution of social tagging and folksonomy are described, and outstanding research questions are presented. This is a new area of research, where theoretical perspectives and relevant research methods are only now being defined. This paper provides a framework for the study of folksonomy, tagging and social tagging systems. Three bro...

  14. Multilabel Learning for Automatic Web Services Tagging

    Directory of Open Access Journals (Sweden)

    Mustapha AZNAG

    2014-08-01

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

  15. Personalization of tagging systems

    OpenAIRE

    Wang, Jun; Clements, Maarten; J. Yang(Department of Physics, Ewha Womans University, Seoul, Republic of Korea); De, Vries, J.A.; Reinders, M.J.T.

    2010-01-01

    Social media systems have encouraged end user participation in the Internet, for the purpose of storing and distributing Internet content, sharing opinions and maintaining relationships. Collaborative tagging allows users to annotate the resulting user-generated content, and enables effective retrieval of otherwise uncategorised data. However, compared to professional web content production, collaborative tagging systems face the challenge that end-users assign tags in an uncontrolled manner,...

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

    CERN Document Server

    Tibély, Gergely; Palla, Gergely

    2015-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-10-29

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

  18. Friction induced skin tags.

    Science.gov (United States)

    Allegue, Francisco; Fachal, Carmen; Pérez-Pérez, Lidia

    2008-01-01

    Skin tags are common benign neoplasm located predominantly in intertriginous skin. Generally of cosmetic concern, they can be easily treated with cryotherapy, electrodessication or snip-excision. Despite their high incidence data about their etiopathogenesis are scarce in the medical literature. We describe a patient who developed multiple skin tags arranged in a linear fashion suggesting an etiopathogenic role for friction. PMID:18627719

  19. Tag Starvation and Tag Collisions in RFID System- A Solution

    Directory of Open Access Journals (Sweden)

    Prof. Nithya S

    2013-06-01

    Full Text Available Radio Frequency Identification (RFID is entirely based on tag identification. Reader identifies a tag by its ID. Collisions occur frequently while reading the passive tags and reader fails to identify the tags sometimes. This will lead to tag-starvation problem. Therefore, an algorithm is developed to address both collisions and tag-starvation problem. This paper uses Query Tree protocol and ALOHA to develop the algorithm. Query Tree protocol is used to address tag-starvation problem and ALOHA to reduce the collisions of passive tags.

  20. Unexploded Ordnance identification-A gamma-ray spectral analysis method for Carbon, Nitrogen and Oxygen signals following tagged neutron interrogation

    Energy Technology Data Exchange (ETDEWEB)

    Mitra, S., E-mail: sudeepmitra@hotmail.com [Environmental Sciences Department, Brookhaven National Laboratory, Bell Avenue, Upton, NY 11973 (United States); Dioszegi, I. [Nonproliferation and National Security Department, Brookhaven National Laboratory, Upton, NY 11973 (United States)

    2012-11-21

    A novel gamma-ray spectral analysis method has been demonstrated to optimally extract the signals of the signature elements of explosives, carbon (C), nitrogen (N) and oxygen (O) from 57-155 mm projectiles following tagged neutron interrogation with 14 MeV neutrons. The method was implemented on Monte Carlo simulated, synthetic spectra of Unexploded Ordnance (UXO) that contained high explosive fillers (Composition B, TNT or Explosive D) within steel casings of appropriate thicknesses. The analysis technique defined three broad regions-of-interest (ROI) between 4-7.5 MeV of a spectrum and from a system of three equations for the three unknowns namely C, N and O, the maximum counts from each of these elements were extracted. Unlike conventional spectral analysis techniques, the present method included the Compton continuum under a spectrum. For a neutron output of {approx}2 Multiplication-Sign 10{sup 7} ns{sup -1} and using four 12.7 cm diameter Multiplication-Sign 12.7 cm NaI(Tl) detectors, the C/N and C/O gamma-ray counts ratios of the explosive fillers were vastly different from that of an inert substance like sand. Conversion of the counts ratios to elemental ratios could further discriminate the different types of explosive fillers. The interrogation time was kept at ten minutes for each projectile.

  1. Unexploded Ordnance identification—A gamma-ray spectral analysis method for Carbon, Nitrogen and Oxygen signals following tagged neutron interrogation

    International Nuclear Information System (INIS)

    A novel gamma-ray spectral analysis method has been demonstrated to optimally extract the signals of the signature elements of explosives, carbon (C), nitrogen (N) and oxygen (O) from 57–155 mm projectiles following tagged neutron interrogation with 14 MeV neutrons. The method was implemented on Monte Carlo simulated, synthetic spectra of Unexploded Ordnance (UXO) that contained high explosive fillers (Composition B, TNT or Explosive D) within steel casings of appropriate thicknesses. The analysis technique defined three broad regions-of-interest (ROI) between 4–7.5 MeV of a spectrum and from a system of three equations for the three unknowns namely C, N and O, the maximum counts from each of these elements were extracted. Unlike conventional spectral analysis techniques, the present method included the Compton continuum under a spectrum. For a neutron output of ∼2×107 ns−1 and using four 12.7 cm diameter×12.7 cm NaI(Tl) detectors, the C/N and C/O gamma-ray counts ratios of the explosive fillers were vastly different from that of an inert substance like sand. Conversion of the counts ratios to elemental ratios could further discriminate the different types of explosive fillers. The interrogation time was kept at ten minutes for each projectile.

  2. Detection of uranium with a wireless sensing method by using salophen as receptor and magnetic nanoparticles as signal-amplifying tags

    International Nuclear Information System (INIS)

    A new wireless sensing method for the detection of uranium in water samples has been reported in this paper. The method is based on a sandwich-type detection strategy. Salophen, a tetradentate ligand of uranyl ion, was immobilized on the surface of the polyurethane-protected magnetoelastic sensor as receptor for the capture of uranyl ion. The phosphorylated polyvinyl alcohol coated magnetic Fe3O4 nanoparticles were used as signal-amplifying tags of uranyl ion. In a procedure of determining uranium, firstly uranyl ion in sample solution was captured on the sensor surface. Then the captured uranyl bound the nanoparticle through its coordination with the phosphate group. The amount of uranium was detected through the measure of the resonance frequency shift caused by the enhanced mass loading on the sensor surface. A linear range was found to be 0.2-20.0 μg/L under optimal conditions with a detection limit of 0.11 μg/L. The method has been applied to determine uranium in environmental water samples with the relative standard deviations of 2.1-3.6 % and the recoveries of 98.0-101.5 %. The present technique is one of the most suitable techniques for assay of uranium at trace level in environmental water samples collected from different sources. (author)

  3. Semantic Stability in Social Tagging Streams

    CERN Document Server

    Wagner, Claudia; Strohmaier, Markus; Huberman, Bernardo A

    2013-01-01

    One potential disadvantage of social tagging systems is that due to the lack of a centralized vocabulary, a crowd of users may never manage to reach a consensus on the description of resources (e.g., books, users or songs) on the Web. Yet, previous research has provided interesting evidence that the tag distributions of resources may become semantically stable over time as more and more users tag them. At the same time, previous work has raised an array of new questions such as: (i) How can we assess the semantic stability of social tagging systems in a robust and methodical way? (ii) Does semantic stabilization of tags vary across different social tagging systems and ultimately, (iii) what are the factors that can explain semantic stabilization in such systems? In this work we tackle these questions by (i) presenting a novel and robust method which overcomes a number of limitations in existing methods, (ii) empirically investigating semantic stabilization processes in a wide range of social tagging systems w...

  4. Hydroxyl Tagging Velocimetry for Rocket Plumes Project

    Data.gov (United States)

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

  5. Mass-producible micro-holographic tags

    Energy Technology Data Exchange (ETDEWEB)

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

    1996-06-01

    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.

  6. On incentive-based tagging

    OpenAIRE

    Yang, XS; Mo, L; Cheng, R; Kao, B; Cheung, DWL

    2013-01-01

    A social tagging system, such as del.icio.us and Flickr, allows users to annotate resources (e.g., web pages and photos) with text descriptions called tags. Tags have proven to be invaluable information for searching, mining, and recommending resources. In practice, however, not all resources receive the same attention from users. As a result, while some highly-popular resources are over-tagged, most of the resources are under-tagged. Incomplete tagging on resources severely affects the effec...

  7. RFID Label Tag Design for Metallic Surface Environments

    Science.gov (United States)

    Park, Chong Ryol; Eom, Ki Hwan

    2011-01-01

    This paper describes a metal mount RFID tag that works reliably on metallic surfaces. The method proposes the use of commercial label type RFID tags with 2.5 mm thick Styrofoam103.7 with a relative permittivity of 1.03 attached on the back of the tag. In order to verify the performance of the proposed method, we performed experiments on an electric transformer supply chain system. The experimental results showed that the proposed tags can communicate with readers from a distance of 2 m. The recognition rates are comparable to those of commercial metallic mountable tags. PMID:22346612

  8. A simple nonradioactive method for the determination of the binding affinities of antibodies induced by hapten bioconjugates for drugs of abuse.

    Science.gov (United States)

    Torres, Oscar B; Antoline, Joshua F G; Li, Fuying; Jalah, Rashmi; Jacobson, Arthur E; Rice, Kenner C; Alving, Carl R; Matyas, Gary R

    2016-02-01

    The accurate analytical measurement of binding affinities of polyclonal antibody in sera to heroin, 6-acetylmorphine (6-AM), and morphine has been a challenging task. A simple nonradioactive method that uses deuterium-labeled drug tracers and equilibrium dialysis (ED) combined with ultra performance liquid chromatography/tandem mass spectrometry (UPLC/MS/MS) to measure the apparent dissociation constant (K d) of antibodies to 6-AM and morphine is described. The method can readily detect antibodies with K d in the low nanomolar range. Since heroin is rapidly degraded in sera, esterase inhibitors were included in the assay, greatly reducing heroin hydrolysis. MS/MS detection directly measured the heroin in the assay after overnight ED, thereby allowing the quantitation of % bound heroin in lieu of K d as an alternative measurement to assess heroin binding to polyclonal antibody sera. This is the first report that utilizes a solution-based assay to quantify heroin-antibody binding without being confounded by the presence of 6-AM and morphine and to measure K d of polyclonal antibody to 6-AM. Hapten surrogates 6-AcMorHap, 6-PrOxyHap, MorHap, DiAmHap, and DiPrOxyHap coupled to tetanus toxoid (TT) were used to generate high affinity antibodies to heroin, 6-AM, and morphine. In comparison to competition ED-UPLC/MS/MS which gave K d values in the nanomolar range, the commonly used competition enzyme-linked immunosorbent assay (ELISA) measured the 50% inhibition concentration (IC50) values in the micromolar range. Despite the differences in K d and IC50 values, similar trends in affinities of hapten antibodies to heroin, 6-AM, and morphine were observed by both methods. Competition ED-UPLC/MS/MS revealed that among the five TT-hapten bioconjugates, TT-6-AcMorHap and TT-6-PrOxyHap induced antibodies that bound heroin, 6-AM, and morphine. In contrast, TT-MorHap induced antibodies that poorly bound heroin, while TT-DiAmHap and TT-DiPrOxyHap induced antibodies either did not

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

    OpenAIRE

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

    2016-01-01

    Isolation of endogenous proteins from Saccharomyces cerevisiae has been facilitated by inserting encoding polypeptide affinity tags at the C-termini of chromosomal open reading frames (ORFs) using homologous recombination of DNA fragments. Tagged protein isolation is limited by a number of factors, including high cost of affinity resins for bulk isolation and low concentration of ligands on the resin surface, leading to low isolation efficiencies and trapping of contaminants. To address this,...

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

    Institute of Scientific and Technical Information of China (English)

    李方楼; 姬小明; 魏跃伟; 杨永锋; 刘国顺

    2011-01-01

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

  11. Tagging vs. Controlled Vocabulary

    DEFF Research Database (Denmark)

    Bogers, Toine; Petras, Vivien

    2015-01-01

    The popularity of social tagging has sparked a great deal of debate on whether tags could replace or improve upon professional metadata as descriptors of books and other information objects. In this paper we present a large-scale empirical comparison of the contributions of individual information...... elements like core bibliographic data, controlled vocabulary terms, reviews, and tags to the retrieval performance. Our comparison is done using a test collection of over 2 million book records with information elements from Amazon, the British Library, the Library of Congress, and LibraryThing. We find...

  12. Spiral MR myocardial tagging.

    Science.gov (United States)

    Ryf, Salome; Kissinger, Kraig V; Spiegel, Marcus A; Börnert, Peter; Manning, Warren J; Boesiger, Peter; Stuber, Matthias

    2004-02-01

    In the present study, complementary spatial modulation of magnetization (CSPAMM) myocardial tagging was extended with an interleaved spiral imaging sequence. The use of a spiral sequence enables the acquisition of grid-tagged images with a tagline distance as low as 4 mm in a single breath-hold. Alternatively, a high temporal resolution of 77 frames per second was obtained with 8-mm grid spacing. Ten healthy adult subjects were studied. With this new approach, high-quality images can be obtained and the tags persist throughout the entire cardiac cycle. PMID:14755646

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

    Science.gov (United States)

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

    2003-06-01

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

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

    Science.gov (United States)

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

    2011-02-01

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

  15. Dual Affine invariant points

    OpenAIRE

    Meyer, Mathieu; Schuett, Carsten; Werner, Elisabeth M.

    2013-01-01

    An affine invariant point on the class of convex bodies in R^n, endowed with the Hausdorff metric, is a continuous map p which is invariant under one-to-one affine transformations A on R^n, that is, p(A(K))=A(p(K)). We define here the new notion of dual affine point q of an affine invariant point p by the formula q(K^{p(K)})=p(K) for every convex body K, where K^{p(K)} denotes the polar of K with respect to p(K). We investigate which affine invariant points do have a dual point, whether this ...

  16. Ontologies and tag-statistics

    CERN Document Server

    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...

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

    Directory of Open Access Journals (Sweden)

    Gianluca Petris

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

  18. TAG Advertisement Hardware

    Science.gov (United States)

    1994-01-01

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

  19. Tagged Vector Contour (TVC)

    Data.gov (United States)

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

  20. Transcriptome annotation using tandem SAGE tags

    Science.gov (United States)

    Rivals, Eric; Boureux, Anthony; Lejeune, Mireille; Ottones, Florence; Pecharromàn Pérez, Oscar; Tarhio, Jorma; Pierrat, Fabien; Ruffle, Florence; Commes, Thérèse; Marti, Jacques

    2007-01-01

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

  1. APPECT: An Approximate Backbone-Based Clustering Algorithm for Tags

    DEFF Research Database (Denmark)

    Zong, Yu; Xu, Guandong; Jin, Pin;

    2011-01-01

    resulting from the severe difficulty of ambiguity, redundancy and less semantic nature of tags. Clustering method is a useful tool to address the aforementioned difficulties. Most of the researches on tag clustering are directly using traditional clustering algorithms such as K-means or Hierarchical...... algorithm for Tags (APPECT). The main steps of APPECT are: (1) we execute the K-means algorithm on a tag similarity matrix for M times and collect a set of tag clustering results Z={C1,C2,…,Cm}; (2) we form the approximate backbone of Z by executing a greedy search; (3) we fix the approximate backbone as...

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

    Science.gov (United States)

    Burdick, Summer M.

    2011-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-07-15

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

  4. Personalized Tag Recommendation Using Social Influence

    Institute of Scientific and Technical Information of China (English)

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

    2012-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Yonghua Wang

    2010-09-01

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

  6. Affine Grassmann codes

    DEFF Research Database (Denmark)

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

    2010-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    郑杰; 茅于杭

    2001-01-01

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

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

    OpenAIRE

    Tonn, Timo

    2012-01-01

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

  9. Tagging of Explosives for Detection

    Directory of Open Access Journals (Sweden)

    J. S. Gharia

    2000-01-01

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

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

    Science.gov (United States)

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

    2016-05-01

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

  11. Forward physics in CMS: Simulation of PMT hits in HF and Higgs mass reconstruction methods with a focus on forward jet tagging

    Science.gov (United States)

    Moeller, Anthony Richard

    Abnormally high energy events were seen in the Hadronic Forward (HF) calorimeter for pion and muon data during testbeam in 2004. Analysis of testbeam data suggested that such events were caused by particles traveling the entire length of HF and striking the photomultiplier (PMT) windows in the readout box behind HF. Charged particles traversing the window of the PMT emit cerenkov radiation, which creates abnormally high energy events in the data. To further study these events, a modification of the existing official CMS HF simulation was created that added the PMT windows to the simulation as sensitive detectors. In agreement with testbeam data, abnormally high energy events in the PMTs were seen in the simulation for muons and pions. The simulation was then extended to jets simulated with Pythia, and then for collision like events as well. PMT hits were seen in both of these cases. Energy sharing between PMTs for long and short fibers in HF as well as timing differences between normal HF events and PMT events were investigated as methods to tag such abnormal events. While both methods were somewhat successful, it was determined that they were not sufficient. The simulation was also modified to use thinner PMT windows. Reducing the thickness of the window reduced the number of PMT hits, and drastically reduced the energy of these hits, bringing most of them below standard jet energy thresholds. These results led to the replacement of the existing PMTs with new PMTs with a smaller, thinner window. Higgs mass reconstruction methods were applied to Monte Carlo datasets for 115 and 130 GeV Higgs produced through vector boson fusion. In these datasets, the Higgs boson decayed to two tau particles, each of which decayed leptonically. The mass reconstruction methods successfully created a peak at the proper mass for both datasets. In addition to creating a Higgs, the vector boson fusion signal also has two forward jets. These jets are not found in the signal of the

  12. Coenzyme- and His-tag-induced crystallization of octopine dehydrogenase

    International Nuclear Information System (INIS)

    The crystal structure of octopine dehydrogenase revealed a specific role of the His5 tag in inducing the crystal contacts required for successful crystallization. Over the last decade, protein purification has become more efficient and standardized through the introduction of affinity tags. The choice and position of the tag, however, can directly influence the process of protein crystallization. Octopine dehydrogenase (OcDH) without a His tag and tagged protein constructs such as OcDH-His5 and OcDH-LEHis6 have been investigated for their crystallizability. Only OcDH-His5 yielded crystals; however, they were multiple. To improve crystal quality, the cofactor NADH was added, resulting in single crystals that were suitable for structure determination. As shown by the structure, the His5 tag protrudes into the cleft between the NADH and l-arginine-binding domains and is mainly fixed in place by water molecules. The protein is thereby stabilized to such an extent that the formation of crystal contacts can proceed. Together with NADH, the His5 tag obviously locks the enzyme into a specific conformation which induces crystal growth

  13. Speech acts meets tagging : NiceTag ontology.

    OpenAIRE

    Monnin, Alexandre; Limpens, Freddy; Gandon, Fabien; Laniado, David

    2010-01-01

    Current tag models do not fully take into account the rich and diverse nature of tags. Each model makes different partial assumptions as to the definition and attributes a tag should receive. In this paper we propose an ontology, NiceTag, whose primitives are " tag actions " modeled with RDF named graphs. This mechanism allows us to type, describe and thus ensure the traceability of each single act of tagging. Our named graphs contain at least a resource linked to a " sign " , which can be an...

  14. The tagged photon beam polarization of the jet target experiment

    International Nuclear Information System (INIS)

    The applicability of the residual electron selection method to the tagging method of the jet target laboratory has been studied. With this end in view the behaviour of the polarized bremsstrahlung cross section in the range considered has been analysed, while the polarization increase by means of the RES has been evaluated. The vertical conditions of the focusing of the tagging spectrometer as a function of energy have been determined. Finally the gamma beam density and the tagging efficiency have been calculated

  15. Analysis of tag-position bias in MPSS technology

    Directory of Open Access Journals (Sweden)

    Rattray Magnus

    2006-04-01

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

  16. TagPad

    DEFF Research Database (Denmark)

    Bornoe, Nis; Barkhuus, Louise

    2013-01-01

    The area of cyberinfrastructures has looked extensively at research within the natural sciences, however, the social sciences have been largely overlooked in terms of novel data collection and analysis systems. We developed a probe tool, TagPad, to look at the process for social science data...... collection through interviews and surveys. Our research participants found that TagPad facilitated structuring of interviews but we also found that the setting in which the interview takes place is essential to the success of using this particular tool. We conclude suggesting future designs of social science...

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

    Science.gov (United States)

    Balabanov, Nikolai B.; Peterson, Kirk A.

    2006-08-01

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

  18. Single step surface modification of highly stable magnetic nanoparticles for purification of His-tag proteins

    Energy Technology Data Exchange (ETDEWEB)

    Sahu, Sumanta Kumar [Indian Institute of Technology Kharagpur, Department of Chemistry (India); Chakrabarty, Arindam [Indian Institute of Technology Kharagpur, Department of Biotechnology (India); Bhattacharya, Dipsikha [Indian Institute of Technology Kharagpur, Department of Chemistry (India); Ghosh, Sudip K. [Indian Institute of Technology Kharagpur, Department of Biotechnology (India); Pramanik, Panchanan, E-mail: chandrasourov@gmail.com [Indian Institute of Technology Kharagpur, Department of Chemistry (India)

    2011-06-15

    The aim of this study was to develop a simple, cheap, and rapid method for purification of His-tag recombinant proteins with high yields. The new immobilized metal ion affinity adsorbent containing superparamagnetic nanoparticles and hydrophilic resins are proposed here to improve the purification of His-tagged recombinant proteins. In this report, we have described the preparation of nanosized superparamagnetic nanoparticles (Fe{sub 3}O{sub 4}) which were prepared by chemical precipitation method followed by surface modification using phosphonomethyl iminodiacetic acid. The stable surface functionalized nanoparticles were further linked with Ni{sup 2+} for purification of 6 Multiplication-Sign His-tagged proteins. The phosphonate group of the N-phosphonomethyl iminodiacetic acid ligand acts as a surface anchoring agent on magnetite nanoparticles and the remaining free -COOH groups outside for binding with Ni{sup 2+} ions. The nanoparticles were approximately 6-8 nm in size and were stable and had negligible non-specific binding for protein. The proteins were purified within 1 h and observed on sodium dodecyl sulfate-polyacrylamide electrophoresis gel.

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

    Science.gov (United States)

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

    2016-08-01

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

  20. Rapid screening method for quinolone residues in livestock and fishery products using immobilised metal chelate affinity chromatographic clean-up and liquid chromatography-fluorescence detection.

    Science.gov (United States)

    Takeda, N; Gotoh, M; Matsuoka, T

    2011-09-01

    An efficient LC method was developed for screening the presence of quinolones (QLs)--comprising fluoroquinolones (FQs) and acidic quinolones (AQs)--residues in various livestock and fishery products. Targeted analytes were for nine FQs of marbofloxacin (MAR), ofloxacin (OFL), norfloxacin (NOR), ciprofloxacin (CIP), enrofloxacin (ENR), danofloxacin (DAN), orbifloxacin (ORB), difloxacin (DIF) and sarafloxacin (SAR), and three AQs of oxolinic acid (OXA), nalidixic acid (NAL) and flumequine (FMQ). Samples comprised ten different food products covering five matrices: muscle (cattle, swine and chicken), liver (chicken), raw fish (shrimp and salmon), egg (chicken), and processed food (ham, sausage and fish sausage). This method involved a simple extraction with (1:1) acetonitrile-methanol, a highly selective clean-up with an immobilised metal chelate affinity column charged with Fe(3+), a fast isocratic LC analysis using a short column (20 mm × 4.6 mm, 3 µm) with a mobile phase of (15:85:0.1) methanol/water/formic acid, and fluorescence detection (excitation/emission wavelengths of 295 nm/455 nm for FQs (495 nm for MAR), and 320 nm/365 nm for AQs). Among FQs, pairs of NOR/OFL, ORB/DIF and ENR/DAN were incompletely resolved. A confirmatory LC run with a Mg(2+) containing methanolic mobile phase was also proposed for the samples suspected of being positive. The optimised method gave satisfactory recoveries of 88.5% (56.1-108.6%) and 78.7% (44.1-99.5%) for intra- and inter-day assays with relative standard deviations of 7.2% (0.7-18.4%) and 6.8% (1.4-16.6%), respectively. Limits of quantitation ranged from 0.8 µg kg(-1) (DAN) to 6.5 µg kg(-1) (SAR). This method was successfully employed to analyse 113 real samples and two positive samples were found: fish sausage (CIP 990 µg kg(-1)) and shrimp (ENR 20 µg kg(-1)). PMID:21749230

  1. RichTags: A Social Semantic Tagging System

    OpenAIRE

    Fountopoulos, Georgios I.

    2007-01-01

    Social tagging systems allow users associating arbitrary keywords (or tags, or labels) to resources they want to save for future recall. Such saved items are called posts or bookmarks and usually constitute shared information in social tagging systems (although access control mechanisms might be applied as well). This means that users of a social tagging system can save and share their bookmarks with each other. The term social stresses the fact that much of the usefulness of the system relie...

  2. Tag Completion for Image Retrieval.

    Science.gov (United States)

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

    2013-03-01

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

  3. Der erste Tag

    Institute of Scientific and Technical Information of China (English)

    HugoLoetscher

    2004-01-01

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

  4. Tagging Grammatical Functions

    CERN Document Server

    Brants, T; Krenn, B; Brants, Thorsten; Skut, Wojciech; Krenn, Brigitte

    1997-01-01

    This paper addresses issues in automated treebank construction. We show how standard part-of-speech tagging techniques extend to the more general problem of structural annotation, especially for determining grammatical functions and syntactic categories. Annotation is viewed as an interactive process where manual and automatic processing alternate. Efficiency and accuracy results are presented. We also discuss further automation steps.

  5. Ontologies and tag-statistics

    International Nuclear Information System (INIS)

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

  6. Affine and Projective Geometry

    CERN Document Server

    Bennett, M K

    1995-01-01

    An important new perspective on AFFINE AND PROJECTIVE GEOMETRY. This innovative book treats math majors and math education students to a fresh look at affine and projective geometry from algebraic, synthetic, and lattice theoretic points of view. Affine and Projective Geometry comes complete with ninety illustrations, and numerous examples and exercises, covering material for two semesters of upper-level undergraduate mathematics. The first part of the book deals with the correlation between synthetic geometry and linear algebra. In the second part, geometry is used to introduce lattice theory

  7. Associated Particle Tagging (APT) in Magnetic Spectrometers

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-10-16

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

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

    Science.gov (United States)

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

    2016-01-01

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

  9. Software Engineering for Tagging Software

    OpenAIRE

    Karan Gupta; Anita Goel

    2013-01-01

    Tagging is integrated into web application to ease maintenance of large amount of information stored in aweb application. With no mention of requirement specification or design document for tagging software,academically or otherwise, integrating tagging software in a web application is a tedious task. In thispaper, a framework has been created for integration of tagging software in a web application. Theframework follows the software development life cycle paradigms and is to be used during i...

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

    Directory of Open Access Journals (Sweden)

    Lim Yan

    2010-06-01

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

  11. Folksonomic Tag Clouds as an Aid to Content Indexing

    OpenAIRE

    Harvey, M.; Baillie, M.; Ruthven, I.; Elsweiler, David

    2009-01-01

    Social tagging systems have recently developed as a popular method of data organisation on the Internet. These systems allow users to organise their content in a way that makes sense to them, rather than forcing them to use a pre-determined and rigid set of categorisations. These folksonomies provide well populated sources of unstructured tags describing web resources which could potentially be used as semantic index terms for these resources. However getting people to agree on what tags best...

  12. Tagging, Folksonomy and Art Museums: Early Experiments and Ongoing Research

    OpenAIRE

    Trant, J.

    2009-01-01

    Tagging has proven attractive to art museums as a means of enhancing the indexing of online collections. This paper examines the state of the art in tagging within museums and introduces the steve.museum research project, and its study of tagging behaviour and the relationship of the resulting folksonomy to professionally created museum documentation. A variety of research questions are proposed and methods for answering them discussed. Experiments implemented in the steve.museum research col...

  13. Development of techniques for tagging precursor and essential chemicals

    Energy Technology Data Exchange (ETDEWEB)

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

    1994-01-01

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

  14. Tag-Aware Recommender Systems: A State-of-the-art Survey

    CERN Document Server

    Zhang, Zi-Ke; Zhang, Yi-Cheng; 10.1007/s11390-011-0176-1

    2012-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Qian, Weijun (BATTELLE (PACIFIC NW LAB)); Goshe, Michael B.(North Carolina State University); Camp, David G.(BATTELLE (PACIFIC NW LAB)); Yu, Li-Rong (BATTELLE (PACIFIC NW LAB)); Tang, Keqi (BATTELLE (PACIFIC NW LAB)); Smith, Richard D.(BATTELLE (PACIFIC NW LAB))

    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.

  16. An audio file tagging mobile game, mTagATune

    OpenAIRE

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

    2011-01-01

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

  17. Affine dynamics with torsion

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-03-15

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

  18. A Hybrid Probabilistic Model for Unified Collaborative and Content-Based Image Tagging.

    Science.gov (United States)

    Zhou, Ning; Cheung, William K; Qiu, Guoping; Xue, Xiangyang

    2011-07-01

    The increasing availability of large quantities of user contributed images with labels has provided opportunities to develop automatic tools to tag images to facilitate image search and retrieval. In this paper, we present a novel hybrid probabilistic model (HPM) which integrates low-level image features and high-level user provided tags to automatically tag images. For images without any tags, HPM predicts new tags based solely on the low-level image features. For images with user provided tags, HPM jointly exploits both the image features and the tags in a unified probabilistic framework to recommend additional tags to label the images. The HPM framework makes use of the tag-image association matrix (TIAM). However, since the number of images is usually very large and user-provided tags are diverse, TIAM is very sparse, thus making it difficult to reliably estimate tag-to-tag co-occurrence probabilities. We developed a collaborative filtering method based on nonnegative matrix factorization (NMF) for tackling this data sparsity issue. Also, an L1 norm kernel method is used to estimate the correlations between image features and semantic concepts. The effectiveness of the proposed approach has been evaluated using three databases containing 5,000 images with 371 tags, 31,695 images with 5,587 tags, and 269,648 images with 5,018 tags, respectively. PMID:21079279

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

    CERN Document Server

    Daugherty, Zajj; Virk, Rahbar

    2012-01-01

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

  20. Improving image segmentation by learning region affinities

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-11-03

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

  1. Software for tag single nucleotide polymorphism selection

    Directory of Open Access Journals (Sweden)

    Stram Daniel O

    2005-06-01

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

  2. Affinity Proteomics in the mountains: Alpbach 2015.

    Science.gov (United States)

    Taussig, Michael J

    2016-09-25

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

  3. Protein isolation using affinity chromatography

    OpenAIRE

    Besselink, T.

    2012-01-01

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

  4. Tagging with leisure needs

    OpenAIRE

    PESTIEAU, Pierre; Racionero, Maria

    2015-01-01

    We study optimal redistributive taxes when individuals differ in two characteristics - earning ability and leisure needs - assumed to be imperfectly correlated. Individuals have private information about their abilities but needs are observable. With two different levels of observable needs the population can be separated into two groups and needs may be used as a tag. We first assume that the social planner considers individuals should be compensated for their leisure needs and characterize ...

  5. Tag cloud generation for results of multiple keywords queries

    DEFF Research Database (Denmark)

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

    2013-01-01

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

  6. Versatile protein tagging in cells with split fluorescent protein

    OpenAIRE

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

    2016-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Okkyung Choi

    2014-01-01

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

  8. Tag-elese or The Language of Tags

    Directory of Open Access Journals (Sweden)

    Jan Simons

    2008-01-01

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

  9. Fast and scalable image auto-tagging

    CERN Document Server

    Frejaville, Camille; Lepetit, Vincent

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

  10. A multiscale framework for affine invariant pattern recognition and registration

    OpenAIRE

    Rahtu, E. (Esa)

    2007-01-01

    Abstract This thesis presents a multiscale framework for the construction of affine invariant pattern recognition and registration methods. The idea in the introduced approach is to extend the given pattern to a set of affine covariant versions, each carrying slightly different information, and then to apply known affine invariants to each of them separately. The key part of the framework is the construction of the affine covariant set, and this is done by combining several scaled represen...

  11. Identifying Nuclear Materials Using Tagged Muons

    CERN Document Server

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

    2014-01-01

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

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

    CERN Document Server

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

    2010-01-01

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

  13. Spectral affinity in protein networks

    Directory of Open Access Journals (Sweden)

    Teng Shang-Hua

    2009-11-01

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

  14. Optimized Affinity Capture of Yeast Protein Complexes.

    Science.gov (United States)

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

    2016-01-01

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

  15. A new strategy for the on-column exopeptidase cleavage of poly-histidine tagged proteins.

    Science.gov (United States)

    Kuo, Wen-Hui K; Chase, Howard A

    2011-10-15

    This paper describes a new strategy, which aims to make on-column poly-histidine tag removal more useful in the production of recombinant proteins by improving the yield and efficiency of on-column exopeptidase cleavage. This involves improvement of the on-column cleavage condition by using imidazole concentrations in the range of 100-500 mM in the cleavage buffer. At 300 mM imidazole, maximum on-column cleavage yield (in excess of 99%) was achieved in 3h of incubation. However, as a result of the increased imidazole concentration, this new strategy of on-column cleavage results in some residual uncleaved poly-histidine tagged proteins (~0.1%) and the production of cleaved dipeptides, both of which need to be further removed in a subsequent step. A method involving the recirculation of recovered proteins and peptides through the immobilized metal affinity chromatography (IMAC) column (same-column recirculation) was found to be superior to subtractive IMAC for the purpose of contaminant clearance. Recovery of the detagged target proteins was achieved using 10 column volumes of recovery buffer, which had the effect of diluting the imidazole concentration to a suitably low level for contaminant removal by same-column recirculation. This strategy was also applicable at a higher adsorbent loading of 10 mg protein/mL adsorbent with an optimal ratio of 200 mU of DAPase per mg of adsorbed tagged maltose binding protein (MBP), giving a cleavage yield of 99.1% in 3 h. Finally, on-column cleavage conditions including the effect of protease concentration and incubation time on the new strategy have been investigated and comparisons are made for different tag removal strategies. PMID:21925974

  16. Histidine-tag-directed chromophores for tracer analyses in the analytical ultracentrifuge

    OpenAIRE

    Hellman, Lance M.; Zhao, Chunxia; Melikishvili, Manana; Tao, Xiaorong; Hopper, James E.; Whiteheart, Sidney W.; Fried, Michael G.

    2010-01-01

    Many recombinant proteins carry an oligohistidine (HisX)-tag that allows their purification by immobilized metal affinity chromatography (IMAC). This tag can be exploited for the site-specific attachment of chromophores and fluorophores, using the same metal ion–nitrilotriacetic acid (NTA) coordination chemistry that forms the basis of popular versions of IMAC. Labeling proteins in this way can allow their detection at wavelengths outside of the absorption envelopes of un-modified proteins an...

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

    Institute of Scientific and Technical Information of China (English)

    Peng Li; Bin Wang; Wei Jin

    2012-01-01

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

  18. Extended Social Tags: Identity Tags Meet Social Networks

    OpenAIRE

    Lajmi, Sonia; Stan, Johann; Hacid, Hakim; Egyed-Zsigmond, Elod; Maret, Pierre

    2009-01-01

    This paper proposes a new approach that uses social networks and common sense deduction rules to adapt the description tags of the photos for the current viewer. We exploit social graphs to enrich the tags associated to the concerned persons in the photo by following the different links between people (i.e. viewer and captured people in the photos). The main contributions of our work are: (i) addition of a more meaningful tagging layer for photos, making tags dynamic and auto-adaptable thanks...

  19. Imaging mass spectrometer with mass tags

    Science.gov (United States)

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

    2013-01-29

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

  20. Nanocrystal and noble gas tagging for monitoring defective CANDU fuel bundles

    International Nuclear Information System (INIS)

    The purpose of this paper is to discuss two possible defective fuel bundle tagging techniques that have been suggested for CANDU-6 nuclear reactors. The general design of a CANDU-6 reactor and fuel bundle is reviewed. Nanocrystal tagging is introduced. A current production method for CdTe nanocrystals and future experimental goals are outlined and noble gas tagging is reviewed. Considerations for the future implementation of these tagging methods for fuel in a CANDU-6 reactor is also discussed. (author)

  1. Antibody affinity maturation

    DEFF Research Database (Denmark)

    Skjødt, Mette Louise

    Yeast surface display is an effective tool for antibody affinity maturation because yeast can be used as an all-in-one workhorse to assemble, display and screen diversified antibody libraries. By employing the natural ability of yeast Saccharomyces cerevisiae to efficiently recombine multiple DNA...

  2. Buddy Tag CONOPS and Requirements.

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-12-01

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

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

    Science.gov (United States)

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

    2014-11-01

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

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

    Institute of Scientific and Technical Information of China (English)

    李晓静; 林海伦; 贾岩涛; 王元卓; 程学旗

    2015-01-01

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

  5. Study of mast cell count in skin tags

    Directory of Open Access Journals (Sweden)

    Zaher Hesham

    2007-01-01

    Full Text Available Background: Skin tags or acrochordons are common tumors of middle-aged and elderly subjects. They consist of loose fibrous tissue and occur mainly on the neck and major flexures as small, soft, pedunculated protrusions. Objectives: The aim was to compare the mast cells count in skin tags to adjacent normal skin in diabetic and nondiabetic participants in an attempt to elucidate the possible role of mast cells in the pathogenesis of skin tags. Participants and Methods: Thirty participants with skin tags were divided into group I (15 nondiabetic participants and group II (15 diabetic participants. Three biopsies were obtained from each participant: a large skin tag, a small skin tag and adjacent normal skin. Mast cell count from all the obtained sections was carried out, and the mast cell density was expressed as the average mast cell count/high power field (HPF. Results: A statistically significant increase in mast cells count in skin tags in comparison to normal skin was detected in group I and group II. There was no statistically significant difference between mast cell counts in skin tags of both the groups. Conclusion: Both the mast cell mediators and hyperinsulinemia are capable of inducing fibroblast proliferation and epidermal hyperplasia that are the main pathologic abnormalities seen in all types of skin tags. However, the presence of mast cells in all examined skin tags regardless of diabetes and obesity may point to the possible crucial role of mast cells in the etiogenesis of skin tags through its interaction with fibroblasts and keratinocytes.

  6. Novel and efficient tag SNPs selection algorithms.

    Science.gov (United States)

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

    2014-01-01

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

  7. Tag Gardening for Folksonomy Enrichment and Maintenance

    Directory of Open Access Journals (Sweden)

    Katrin Weller

    2008-09-01

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

  8. Methyl-CpG island-associated genome signature tags

    Science.gov (United States)

    Dunn, John J

    2014-05-20

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

  9. Affine and degenerate affine BMW algebras: The center

    CERN Document Server

    Daugherty, Zajj; Virk, Rahbar

    2011-01-01

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

  10. LHCb Tag Collector

    CERN Document Server

    Fuente Fernàndez, P; Cousin, N

    2011-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Skalski, John

    2007-02-01

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

  12. Tagging, Encoding, and Jones Optimality

    DEFF Research Database (Denmark)

    Danvy, Olivier; López, Pablo Ernesto Martínes

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

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

    OpenAIRE

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

    2014-01-01

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

  14. Affinity driven social networks

    Science.gov (United States)

    Ruyú, B.; Kuperman, M. N.

    2007-04-01

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

  15. Affine General Equilibrium Models

    OpenAIRE

    Bjørn Eraker

    2008-01-01

    No-arbitrage models are extremely flexible modelling tools but often lack economic motivation. This paper describes an equilibrium consumption-based CAPM framework based on Epstein-Zin preferences, which produces analytic pricing formulas for stocks and bonds under the assumption that macro growth rates follow affine processes. This allows the construction of equilibrium pricing formulas while maintaining the same flexibility of state dynamics as in no-arbitrage models. In demonstrating the a...

  16. Folksonomic Tag Clouds as an Aid to Content Indexing

    CERN Document Server

    Harvey, Morgan; Ruthven, Ian; Elsweiler, David

    2009-01-01

    Social tagging systems have recently developed as a popular method of data organisation on the Internet. These systems allow users to organise their content in a way that makes sense to them, rather than forcing them to use a pre-determined and rigid set of categorisations. These folksonomies provide well populated sources of unstructured tags describing web resources which could potentially be used as semantic index terms for these resources. However getting people to agree on what tags best describe a resource is a difficult problem, therefore any feature which increases the consistency and stability of terms chosen would be extremely beneficial. We investigate how the provision of a tag cloud, a weighted list of terms commonly used to assist in browsing a folksonomy, during the tagging process itself influences the tags produced and how difficult the user perceived the task to be. We show that illustrating the most popular tags to users assists in the tagging process and encourages a stable and consistent ...

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

    Science.gov (United States)

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

    2016-01-01

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

  18. Engineering the ATLAS TAG Browser

    CERN Document Server

    Zhang, Q; The ATLAS collaboration

    2011-01-01

    ELSSI is a web-based event metadata (TAG) browser and event-level selection service for ATLAS. TAGs from all ATLAS physics and Monte Carlo data sets are routinely loaded into Oracle databases as an integral part of event processing. As data volumes increase, more and more sites are joining the distributed TAG data hosting topology. Meanwhile, TAG content and database schemata continue to evolve as new user requirements and additional sources of metadata emerge. All of this has posed many challenges to the development of ELSSI, which must support vast amounts of TAG data while source, content, geographic locations, and user query patterns may change over time. 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 a...

  19. Development of partial-filling affinity capillary electrophoresis method for chiral separations using helical extended diquats (helquats) as new chiral selectors

    Czech Academy of Sciences Publication Activity Database

    Růžička, Martin; Jirásek, Michael; Reyes Gutierrez, Paul Eduardo; Teplý, Filip; Koval, Dušan; Kašička, Václav

    Natal: -, 2014. s. 174. [ITP & LACE 2014. International Symposium on Electro- and Liquid Phase-Separation Techniques /21./ and Latin-American Symposium on Biotechnology, Biomedical, Biopharmaceutical, and Industrial Applications of Capillary Electrophoresis and Microchip Technology /20./. 04.10.2014-08.10.2014, Natal] R&D Projects: GA ČR(CZ) GA13-17224S; GA ČR GA13-32974S; GA ČR(CZ) GAP206/12/0453 Institutional support: RVO:61388963 Keywords : affinity capillary electrophoresis * helquats * chiral separation Subject RIV: CB - Analytical Chemistry, Separation

  20. On the Affine Isoperimetric Inequalities

    Indian Academy of Sciences (India)

    Wuyang Yu; Gangsong Leng

    2011-11-01

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

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

    Science.gov (United States)

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

    2016-04-01

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

  2. Overexpression of Soluble Recombinant Human Lysyl Oxidase by Using Solubility Tags: Effects on Activity and Solubility

    Science.gov (United States)

    Smith, Madison A.; Gonzalez, Jesica; Hussain, Anjum; Oldfield, Rachel N.; Johnston, Kathryn A.; Lopez, Karlo M.

    2016-01-01

    Lysyl oxidase is an important extracellular matrix enzyme that has not been fully characterized due to its low solubility. In order to circumvent the low solubility of this enzyme, three solubility tags (Nus-A, Thioredoxin (Trx), and Glutathione-S-Transferase (GST)) were engineered on the N-terminus of mature lysyl oxidase. Total enzyme yields were determined to be 1.5 mg for the Nus-A tagged enzyme (0.75 mg/L of media), 7.84 mg for the Trx tagged enzyme (3.92 mg/L of media), and 9.33 mg for the GST tagged enzyme (4.67 mg/L of media). Enzymatic activity was calculated to be 0.11 U/mg for the Nus-A tagged enzyme and 0.032 U/mg for the Trx tagged enzyme, and no enzymatic activity was detected for the GST tagged enzyme. All three solubility-tagged forms of the enzyme incorporated copper; however, the GST tagged enzyme appears to bind adventitious copper with greater affinity than the other two forms. The catalytic cofactor, lysyl tyrosyl quinone (LTQ), was determined to be 92% for the Nus-A and Trx tagged lysyl oxidase using the previously reported extinction coefficient of 15.4 mM−1 cm−1. No LTQ was detected for the GST tagged lysyl oxidase. Given these data, it appears that Nus-A is the most suitable tag for obtaining soluble and active recombinant lysyl oxidase from E. coli culture. PMID:26942005

  3. Adjoint affine fusion and tadpoles

    OpenAIRE

    Urichuk, Andrew; Walton, Mark A.

    2016-01-01

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

  4. Aptamer Affinity Maturation by Resampling and Microarray Selection.

    Science.gov (United States)

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

    2016-07-19

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

  5. Social Tagging to Enhance Collaborative Learning

    OpenAIRE

    Lavoué, Elise

    2011-01-01

    In this paper, we investigate how social tagging could be used in Education as a support for learning processes. We first summarize the results of recent works on the effect of the use of social tagging for knowledge building and learning. We show that few educational tag-based systems intentionally use tagging to enhance learning. We then describe a Tag-based Collaborative System (TaCS), meant for supporting social and collaborative learning thanks to tagging, and detail the learning process...

  6. The Structure of Collaborative Tagging Systems

    OpenAIRE

    Golder, Scott; Huberman, Bernardo A.

    2005-01-01

    Collaborative tagging describes the process by which many users add metadata in the form of keywords to shared content. Recently, collaborative tagging has grown in popularity on the web, on sites that allow users to tag bookmarks, photographs and other content. In this paper we analyze the structure of collaborative tagging systems as well as their dynamical aspects. Specifically, we discovered regularities in user activity, tag frequencies, kinds of tags used, bursts of popularity in bookma...

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

    Science.gov (United States)

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

    2016-01-01

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

  8. The affine quantum gravity programme

    International Nuclear Information System (INIS)

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

  9. Tagging behaviour with support from controlled vocabulary

    DEFF Research Database (Denmark)

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

    2011-01-01

    The paper investigates how knowledge structures from a controlled vocabulary affect tagging. The study is a comparative analysis of tags assigned in two tagging systems, a simple tagging system (control system) that provides suggestions from two tag clouds (all users tags and my tags) and an enha....... Furthermore, controlled vocabularies might be useful for automatic spell checking. Future study should explore in what direction the different kinds of suggestions lead the tagger and whether it is possible to identify scope or patterns between related tags from the two systems....

  10. Regional assessment of left ventricular torsion by CMR tagging

    OpenAIRE

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

    2008-01-01

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

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

    Science.gov (United States)

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

    2015-01-01

    Isolation of endogenous proteins from Saccharomyces cerevisiae has been facilitated by inserting encoding polypeptide affinity tags at the C-termini of chromosomal open reading frames (ORFs) using homologous recombination of DNA fragments. Tagged protein isolation is limited by a number of factors, including high cost of affinity resins for bulk isolation and low concentration of ligands on the resin surface, leading to low isolation efficiencies and trapping of contaminants. To address this, we have created a recombinant "CelTag" DNA construct from which PCR fragments can be created to easily tag C-termini of S. cerevisiae ORFs using selection for a nat1 marker. The tag has a C-terminal cellulose binding module to be used in the first affinity step. Microgranular cellulose is very inexpensive and has an effectively continuous ligand on its surface, allowing rapid, highly efficient purification with minimal background. Cellulose-bound proteins are released by specific cleavage of an included site for TEV protease, giving nearly pure product. The tag can be lifted from the recombinant DNA construct either with or without a 13x myc epitope tag between the target ORF and the TEV protease site. Binding of CelTag protein fusions to cellulose is stable to high salt, nonionic detergents, and 1 M urea, allowing stringent washing conditions to remove loosely associated components, as needed, before specific elution. It is anticipated that this reagent could allow isolation of protein complexes from large quantities of yeast extract, including soluble, membrane-bound, or nucleic acid-associated assemblies. PMID:26715090

  12. Social Tagging: Exploring the Image, the Tags, and the Game

    OpenAIRE

    Konkova, E.; Goker, A.S.; Butterworth, R.; MacFarlane, A.

    2014-01-01

    An increasing amount of images are being uploaded, shared, and retrieved on the Web. These large image collections need to be properly stored, organized and easily retrieved. Tags have a key role in image retrieval but it is difficult for those who upload the images to also undertake the quality tag assignment for potential future retrieval by others. Relying on professional keyword assignment is not a practical option for large image collections due to resource constraints. Although a number...

  13. DVM meeting 2000: Materials and methods in competition - lightweight construction in vehicle construction. Lectures; DVM-Tag 2000: Werkstoffe und Verfahren im Wettbewerb - Leichtbau im Fahrzeugbau. Vortraege

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2000-07-01

    The DVM 2000 meeting focused on lightweight construction in motor car engineering. There is a conflict in this industry between the developers' goals of long life and high safety on the one hand and the users' demand for high comfort on the other hand, while both parties agree on the importance of low cost. The meeting was accompanied by an exhibition of lightweight components. The programme comprised five sections: Lightweight construction in transportation systems, lightweight construction materials, construction principles and processes, and selected examples to illustrate the many available synergy options from an application-oriented point of view. The meeting addressed managers of the vehicle and component industries, universities and development institutes as well as materials experts. [German] Der DVM-Tag im Jahre 2000 befasst sich erneut mit dem Thema 'Leichtbau', diesmal unter dem neuen Motto 'Werkstoffe und Verfahren im Wettbewerb', und richtet sich gezielt an den Fahrzeugbau. Gerade in diesem Industriezweig sind fuer die Entwickler der Zielkonflikt zwischen Lebensdauer und Sicherheit auf der einen, fuer den Kunden besonders der Komfort auf der anderen und fuer alle Beteiligten die Kostenseite von grosser Bedeutung. Es findet gleichzeitig eine Praesentation 'Leichtbau-Bauteile' statt. Das Programm umfasst fuenf Abschnitte: Leichtbau in Verkehrssystemen, Leichtbauwerkstoffe, Konstruktionsprinzipien und Verfahren, anschliessend werden ausgewaehlte Beispiele vorgetragen, die anwendungsorientiert eine Fuelle von Synergiemoeglichkeiten aufzeigen. Zielgruppen des DVM-Tages 2000 sind das untere und mittlere Management der Fahrzeugindustrie (Fahrzeughersteller und Zulieferer), Hochschulen und Institute, die sich mit Forschungs- und Entwicklungsprojekten im Vorstadium einer Produktionsreife befassen und natuerlich aller Werkstoffler, die 'ihren' Werkstoff im Wettbwerb mit anderen Werkstoffen innerhalb des Themas

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-09-30

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

  15. Ranked Tag Recommendation Systems Based on Logistic Regression

    Science.gov (United States)

    Quevedo, J. R.; Montañés, E.; Ranilla, J.; Díaz, I.

    This work proposes an approach to tag recommendation based on a logistic regression based system. The goal of the method is to support users of current social network systems by providing a rank of new meaningful tags for a resource. This system provides a ranked tag set and it feeds on different posts depending on the resource for which the user requests the recommendation. The performance of this approach is tested according to several evaluation measures, one of them proposed in this paper (F_1^+). The experiments show that this learning system outperforms certain benchmark recommenders.

  16. Device-free object tracking using passive tags

    CERN Document Server

    Han, Jinsong; Zhao, Kun; Jiang, Zhiping

    2014-01-01

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

  17. Rational self-affine tiles

    CERN Document Server

    Steiner, Wolfgang

    2012-01-01

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

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

    Science.gov (United States)

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

    2015-12-01

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

  19. Behavioral tagging of extinction learning.

    Science.gov (United States)

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

    2013-01-15

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

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

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

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

  1. An affine framework for analytical mechanics

    OpenAIRE

    Urbanski, Pawel

    2003-01-01

    An affine Cartan calculus is developed. The concepts of special affine bundles and special affine duality are introduced. The canonical isomorphisms, fundamental for Lagrangian and Hamiltonian formulations of the dynamics in the affine setting are proved.

  2. Optimization of MR imaging tagging patterns for the measurement of strain in the myocardium

    International Nuclear Information System (INIS)

    MR imaging tagging techniques provide a method for the measurement of strain in the myocardium; it is possible to generate a wide variety of tagging patterns. The purpose of this paper is to develop a method for determination of the optimal tagging pattern for measuring strain and gradients in the strain. Programs were written to simulate the signal intensity of tagging patterns, the image noise, and the pixel sampling of the tagging patterns. Monte-Carlo simulations were performed to evaluate the accuracy and precision of point tracking and strain calculation as a function of the image resolution and the tagging pattern. The precision of the detection of the center of a gaussian-shaped tag line (sigma = 1 mm) has been shown to be between 0.1 and 0.2 mm for images with an in-plane resolution of 0.625 x 1.25 mm. It has also been shown that the tag width must be greater than the pixel dimension (ie, sigma > one pixel) in order to avoid large variations in the precision of the estimate of the tag center with changing position of the tag. A method has been developed to evaluate various tag pattern/image resolution combinations to measure strain

  3. TAG Based Skimming In ATLAS

    CERN Document Server

    Doherty, T; The ATLAS collaboration; Hrivnac, J; Slater, M; Nowak, M; Quilty, D; Zhang, Q

    2012-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Indhu Kanakaraj

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

  5. Understanding the Usage and Requirements of the Photo Tagging System

    OpenAIRE

    Malik, Aqdas; Marko, Nieminen

    2014-01-01

    The amount of personal photos is massively increasing and managing them effectively and efficiently requires new approaches and practices. This study analyses the users’ needs and their behaviour towards photo tagging in the context of a personal photo repository. Our results are from a qualitative study with 15 users. Study methods include a questionnaire and a task analy-sis approach in which we analyse and evaluate practices around semi-automated photo tagging. In the task analysis, we des...

  6. Part-of-Speech Tagging with Neural Networks

    CERN Document Server

    Schmid, H

    1994-01-01

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

  7. Adjoint affine fusion and tadpoles

    Science.gov (United States)

    Urichuk, Andrew; Walton, Mark A.

    2016-06-01

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

  8. Adjoint affine fusion and tadpoles

    CERN Document Server

    Urichuk, Andrew

    2016-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Mark Melenhorst

    2010-01-01

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

  10. A Mobile Picture Tagging System Using Tree-Structured Layered Bayesian Networks

    OpenAIRE

    Young-Seol Lee; Sung-Bae Cho

    2013-01-01

    Advances in digital media technology have increased in multimedia content. Tagging is one of the most effective methods to manage a great volume of multimedia content. However, manual tagging has limitations such as human fatigue and subjective and ambiguous keywords. In this paper, we present an automatic tagging method to generate semantic annotation on a mobile phone. In order to overcome the constraints of the mobile environment, the method uses two layered Bayesian networks. In contrast ...

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

    OpenAIRE

    Cao, Heping; Lin, Rui

    2009-01-01

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

  12. Tag Gardening for Folksonomy Enrichment and Maintenance

    OpenAIRE

    Katrin Weller; Isabella Peters

    2008-01-01

    As social tagging applications continuously gain in popularity, it becomes more and more accepted that models and tools for (re-)organizing tags are needed. Some first approaches are already practically implemented. Recently, activities to edit and organize tags have been described as "tag gardening". We discuss different ways to subsequently revise and reedit tags and thus introduce different "gardening activities"; among them models that allow gradually adding semantic structures to folkson...

  13. Tag trails: Navigating with context and history

    OpenAIRE

    Gwizdka, Jacek; Bakelaar, Philip

    2009-01-01

    We describe a technique for preserving and presenting context and history while navigating web resources described by keywords. We use tagging and tag clouds as an application area for our technique. The technique is illustrated by employing it in a prototype that interfaces data from a social tagging website used to bookmark academic articles. The prototype displays a “tag trail” which can reveal contextual connections between web resources and the associated tags. We argue that the user’s u...

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

    Directory of Open Access Journals (Sweden)

    Brian H. Carrick

    2016-03-01

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

  15. Dynamic three-dimensional tagged imaging of left ventricular contraction

    International Nuclear Information System (INIS)

    This paper reports on a method, cardiac tagging with MR imaging, used to assess ventricular deformation during the cardiac cycle. Twenty human volunteers were examined. Six short-axis images of the left ventricle placed to encompass the entire left ventricle were acquired with six radially distributed linear tags generated at the R wave of the electrocardiogram. A series of six images in the long axis of left ventricle with six equidistant tags extending from apex to base parallel to the short axis of the ventricle were also obtained to determine the amount of apex-to-base translation. An inhouse computer program was used to determine automatically the epicardial, endocardial, and tag contours. A three-dimensional wire frame construct was then generated to serve as the data base for a dynamic three-dimensional display of the contracting ventricle as well as to measure the main components of strain

  16. Tag-elese or The Language of Tags

    OpenAIRE

    Jan Simons

    2008-01-01

    The core "meme" of Web 2.0 from which almost all other memes radiated was: 'You control your own data' (O'Reilly, 2005, 3). Key instruments for this user control are tagging systems that allow users to freely assign keywords of their own choosing to Internet resources of their own making as well as to documents produced by others. Of course, freely chosen keywords tags do not necessarily follow prefixed taxonomies or classification systems. But going by the maxim that interaction creates simi...

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

    Directory of Open Access Journals (Sweden)

    Kate Koles

    2016-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Saeed Shahrivari

    2015-07-01

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

  19. Neutral B meson flavor tagging

    CERN Document Server

    Wilson, R J

    2001-01-01

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

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

    DEFF Research Database (Denmark)

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

    2008-01-01

    be linked by UV light irradiation onto a plain, unmodified glass surface. Probes immobilized onto unmodified glass microscope slides performed similarly to probes bound to commercial amino-silane-coated slides and had comparable detection limits. The TC-tagged probes linked to unmodified glass did...... improved the hybridization performance of the immobilized probes on the amino-silane surface, indicating a general benefit of adding a TC tag to DNA probes. In conclusion, our results show that using TC-tagged DNA probes immobilized on an unmodified glass surface is a robust, heat-stable, very simple, and...

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

    Science.gov (United States)

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

    2005-04-01

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

  2. WebTag: Web Browsing into Sensor Tags over NFC

    Science.gov (United States)

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

    2012-01-01

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

  3. WebTag: Web Browsing into Sensor Tags over NFC

    Directory of Open Access Journals (Sweden)

    Juan Jose Echevarria

    2012-06-01

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

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

    Science.gov (United States)

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

    2012-01-01

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

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

    Science.gov (United States)

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

    2014-10-01

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

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

    Institute of Scientific and Technical Information of China (English)

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

    2011-01-01

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

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

    DEFF Research Database (Denmark)

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

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

  8. SKIN TAGS AND ITS ASSOCIATION WITH SYSTEMIC ILLNESSES

    Directory of Open Access Journals (Sweden)

    Ramya

    2015-05-01

    Full Text Available BACKGROUND AND OBJECTIVES: Skin tags (Acrochordons are very common benign tumor of the skin. It is seen in 25% of population, particularly in women in advancing age and in pregnancy. Skin tags are small, soft, pedunculated and papillomatous lesions usually seen on eyelids and major flexures of the body. Skin tags are enti rely asymptomatic and diagnosis is unmistakable. Many cutaneous lesions have been well established to be associated with some systemic diseases and this has been proven beneficial as it helps in early diagnosis. METHODS: A total no of 50 patients with skin tags were included in the study. Detailed history, thorough physical examination and relevant investigations were done to confirm the systemic manifestations when present. RESULTS: In the study the patient’s age ranged from 18 – 65 yrs with female - male ratio 1:1.17. The number of skin tags among the 50 patients ranged from 1 – 74. In our study we found that 74% of our patients with skin tags were either obese or overweight, 24% of our patients fulfilled the criteria of metabolic syndrome, 36% of the patients were diabetics & 4 of our patients had evidence of thyroid disorder. INTERPRETATION & CONCLUSION: Presence of multiple, hyper pigmented skin tags at more than one site can be a marker for diabetes, obesity and metabolic syndrome. All such patients should be evaluated thoroughly for detecting such illnesses. This study thus emphasizes the need for systemic evaluation of all patients with skin tags for early management and improve d quality of life by life style modification.

  9. EXPLOITING SOCIAL TAGS TO OVERCOME COLD START RECOMMENDATION PROBLEM

    Directory of Open Access Journals (Sweden)

    A. S. Ghabayen

    2014-01-01

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

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

    DEFF Research Database (Denmark)

    Achiam, M.P.; Chabanova, E.; Logager, V.B.; Thomsen, H.S.; Rosenberg, J.

    2008-01-01

    . Materials and Methods. Twenty patients referred to CC underwent dark lumen MRC prior to the colonoscopy. Two groups of patients received two different oral contrast agents (barium sulfate and barium sulfate/ferumoxsil) as a laxative-free fecal tagging prior to the MRC. After MRC, the contrast agent was...... rated qualitatively (with the standard method using contrast-to-wall ratio) and subjectively (using a visual analog scale [VAS]) by three different blinded observers. Results. Evaluated both qualitatively and subjectively, the tagging efficiency of barium sulfate/ferumoxsil was significantly better (P...... <.05) than barium sulfate alone. The VAS method for evaluating the tagging efficiency of contrast agents showed a high correlation (observer 11, r = 0.91) to the standard method using contrast-to-wall ratio and also a high interclass correlation (observer 11 and III = 0.89/0.85). MRC found I of 22 (5...

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

    OpenAIRE

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

    2012-01-01

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

  12. Classification of neocortical interneurons using affinity propagation

    Directory of Open Access Journals (Sweden)

    Roberto eSantana

    2013-12-01

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

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

    International Nuclear Information System (INIS)

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

  14. Popular Computational Methods to Assess Multiprotein Complexes Derived From Label-Free Affinity Purification and Mass Spectrometry (AP-MS) Experiments*

    OpenAIRE

    Armean, I. M.; Lilley, K.S.; Trotter, M. W. B.

    2012-01-01

    Advances in sensitivity, resolution, mass accuracy, and throughput have considerably increased the number of protein identifications made via mass spectrometry. Despite these advances, state-of-the-art experimental methods for the study of protein-protein interactions yield more candidate interactions than may be expected biologically owing to biases and limitations in the experimental methodology. In silico methods, which distinguish between true and false interactions, have been developed a...

  15. Satellite Tags- Guam/CNMI EEZ

    Data.gov (United States)

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

  16. AFSC/ABL: Satellite tagging data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set captures the tag release and timeseries of tracking locations and sensor data associated with each satellite tag that has released. Sablefish, spiny...

  17. HMSRP Hawaiian Monk Seal Tag Data

    Data.gov (United States)

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2000-06-01

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

  19. Popular computational methods to assess multiprotein complexes derived from label-free affinity purification and mass spectrometry (AP-MS) experiments.

    Science.gov (United States)

    Armean, Irina M; Lilley, Kathryn S; Trotter, Matthew W B

    2013-01-01

    Advances in sensitivity, resolution, mass accuracy, and throughput have considerably increased the number of protein identifications made via mass spectrometry. Despite these advances, state-of-the-art experimental methods for the study of protein-protein interactions yield more candidate interactions than may be expected biologically owing to biases and limitations in the experimental methodology. In silico methods, which distinguish between true and false interactions, have been developed and applied successfully to reduce the number of false positive results yielded by physical interaction assays. Such methods may be grouped according to: (1) the type of data used: methods based on experiment-specific measurements (e.g., spectral counts or identification scores) versus methods that extract knowledge encoded in external annotations (e.g., public interaction and functional categorisation databases); (2) the type of algorithm applied: the statistical description and estimation of physical protein properties versus predictive supervised machine learning or text-mining algorithms; (3) the type of protein relation evaluated: direct (binary) interaction of two proteins in a cocomplex versus probability of any functional relationship between two proteins (e.g., co-occurrence in a pathway, sub cellular compartment); and (4) initial motivation: elucidation of experimental data by evaluation versus prediction of novel protein-protein interaction, to be experimentally validated a posteriori. This work reviews several popular computational scoring methods and software platforms for protein-protein interactions evaluation according to their methodology, comparative strengths and weaknesses, data representation, accessibility, and availability. The scoring methods and platforms described include: CompPASS, SAINT, Decontaminator, MINT, IntAct, STRING, and FunCoup. References to related work are provided throughout in order to provide a concise but thorough introduction to a

  20. EMERGENT COMMUNITY STRUCTURE IN SOCIAL TAGGING SYSTEMS

    OpenAIRE

    CIRO CATTUTO; ANDREA BALDASSARRI; Vito D P Servedio; VITTORIO LORETO

    2008-01-01

    A distributed classification paradigm known as collaborative tagging has been widely adopted in new Web applications designed to manage and share online resources. Users of these applications organize resources (Web pages, digital photographs, academic papers) by associating with them freely chosen text labels, or tags. Here we leverage the social aspects of collaborative tagging and introduce a notion of resource distance based on the collective tagging activity of users. We collect data fro...

  1. FRAMEWORK FOR TAGGING SOFTWARE IN WEB APPLICATION

    OpenAIRE

    Karan Gupta; Anita Goel

    2013-01-01

    Tagging is included in web application to ease maintenance of large amount of information stored in a web application. With no mention of requirement specification or design document for tagging software, academically or otherwise, integrating tagging software in a web application is a tedious task. In this paper, a framework is presented for integrating tagging software into a web application. The framework is for use during different stages of software development life cycle....

  2. Social tagging versus Expert created subject headings

    OpenAIRE

    Rahman, A. I. M. Jakaria

    2012-01-01

    The purpose of the study was to investigate social tagging practice in science book context. In addition, it identified the usefulness of social tags as supplementary of controlled vocabulary to enhance the use of library resources. More specifically, this study examined to know to what extent the social tags match with controlled vocabulary, and whether or not any additional perception is provided by social tags to improve the accessibility and information retrieval in a digital environment....

  3. Optimal Tagging with Markov Chain Optimization

    OpenAIRE

    Rosenfeld, Nir; Globerson, Amir

    2016-01-01

    Many information systems use tags and keywords to describe and annotate content. These allow for efficient organization and categorization of items, as well as facilitate relevant search queries. As such, the selected set of tags for an item can have a considerable effect on the volume of traffic that eventually reaches an item. In settings where tags are chosen by an item's creator, who in turn is interested in maximizing traffic, a principled approach for choosing tags can prove valuable. I...

  4. Tagging, Folksonomy & Co - Renaissance of Manual Indexing?

    OpenAIRE

    Voß, Jakob

    2007-01-01

    This paper gives an overview of current trends in manual indexing on the Web. Along with a general rise of user generated content there are more and more tagging systems that allow users to annotate digital resources with tags (keywords) and share their annotations with other users. Tagging is frequently seen in contrast to traditional knowledge organization systems or as something completely new. This paper shows that tagging should better be seen as a popular form of manual indexing on the ...

  5. Exploiting tag correlations to improve multilabel learning

    OpenAIRE

    Payne, Brent

    2011-01-01

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

  6. Infinite transitivity on affine varieties

    OpenAIRE

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

    2012-01-01

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

  7. Representations of affine Hecke algebras

    CERN Document Server

    Xi, Nanhua

    1994-01-01

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

  8. Affine toric SL(2)-embeddings

    International Nuclear Information System (INIS)

    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 0GV//T-hat. In the substantiation of this result a key role is played by Cox's construction in toric geometry. Bibliography: 12 titles

  9. Tagging for Health Information Organization and Retrieval

    OpenAIRE

    Kipp, Margaret E.I.

    2007-01-01

    This paper examines the tagging practices evident on CiteULike, a research oriented social bookmarking site for journal articles. Articles selected for this study were health information and medicine related. Tagging practices were examined using standard informetric measures for analysis of bibliographic information and analysis of term use. Additionally, tags were compared to descriptors assigned to the same article.

  10. Towards EPC compatible plastic RFID tags

    NARCIS (Netherlands)

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

    2010-01-01

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

  11. 50 CFR 635.33 - Archival tags.

    Science.gov (United States)

    2010-10-01

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

  12. Tagging and Findability: Do Tags Help Users Find Things?

    OpenAIRE

    Kipp, Margaret E.I.

    2007-01-01

    Background The question of findability is an old one and led directly to the creation of cataloguing and classification systems for the organisation of knowledge. However, such systems have not proven to be truly scalable when dealing with digital information and especially information on the web. Can the user created categories and classification schemes of tagging be used to enhance findability in these new environments? Much speculation has been advanced on the subject but so far no emp...

  13. Tagging Tagging: Analysing user keywords in scientific bibliography management systems

    OpenAIRE

    Heckner, Markus; Mühlbacher, Susanne; Wolff, Christian

    2008-01-01

    1. Research Context and previous work Recently, a growing amount of systems that allow personal content annotation (tagging) are being created, ranging from personal sites for organising bookmarks (del.icio.us), photos (flickr.com) or videos (video.google.com, youtube.com) to systems for managing bibliographies for scientific research projects (citeulike.org, connotea.org). Simultaneously, a debate on the pro and cons of allowing users to add personal keywords to digital conten...

  14. Searching with Tags: Do Tags Help Users Find Things?

    OpenAIRE

    Kipp, Margaret E.I.

    2008-01-01

    In traditional library indexing systems, the indexer was an individual trained in the rules of information organisation to assign keywords for important information about the physical media and the subject matter of the content. While other groups have been involved in creating index terms (for example, journal article authors who are asked to provide keywords with their submitted articles), these keywords generally have a small circulation and are not widely used. Collaborative tagging syst...

  15. P174-T Affinity Protein Purification by Automation Using a Magtration Robotic System

    OpenAIRE

    Patel, S.; Duan, X.; TerBush, D.; Yang, Q.; Obata, K.

    2007-01-01

    Affinity purification is a powerful tool for protein enrichment in proteomics studies. We here present a fully automated system for purification of His-tag proteins and IgG using Ni2+/Co2+ and Protein A magnetic beads, respectively. Reagents for His-tag protein or IgG purification are pre-dispensed in a sealed cartridge for automated runs on a Magtration 12GC robot. The automated purification is based on Magtration technology to perform magnetic bead separation similar to a filtration process...

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

    Science.gov (United States)

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

    2007-02-01

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

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

    OpenAIRE

    Bieberich, Erhard

    2011-01-01

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

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

    OpenAIRE

    Eftang, Jens Lohne

    2008-01-01

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

  19. Noisy Tags: A Pretty Good Key Exchange Protocol for RFID Tags

    OpenAIRE

    Avoine, Gildas; Castelluccia, Claude

    2006-01-01

    We propose a protocol that can be used between an RFID tag and a reader to exchange a secret without performing any expensive computation. Similarly to the famous blocker tag suggested by Juels, Rivest, and Szydlo, our scheme makes use of special tags that we call "noisy tags". Noisy tags are owned by the reader's manager and set out within the reader's field. They are regular RFID tags that generate noise on the public channel between the reader and the queried tag, such that an eavesdropper...

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

    Science.gov (United States)

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

    2015-01-01

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

  1. A Novel Multilayered RFID Tagged Cargo Integrity Assurance Scheme

    Directory of Open Access Journals (Sweden)

    Ming Hour Yang

    2015-10-01

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

  2. Tagging b quark events in ALEPH with neural networks

    International Nuclear Information System (INIS)

    Comparison of different methods to tag b quark events are presented: multilayered perceptron (MLP), Learning Vector Quantization (LVQ), discriminant analysis, combination of any two of the above methods. The sample events come from the ALEPH Monte Carlo and data, from the 1990 ALEPH runs. (authors) 12 refs., 16 figs., 5 tabs

  3. AFFINE TRANSFORMATION IN RANDOM ITERATED FUNCTION SYSTEMS

    Institute of Scientific and Technical Information of China (English)

    熊勇; 史定华

    2001-01-01

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

  4. Soft lepton tagging for Bd mixing at CDF

    International Nuclear Information System (INIS)

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

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

    International Nuclear Information System (INIS)

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

  6. mu_x boosted-bottom-jet tagging and Z-prime boson searches

    CERN Document Server

    Pedersen, Keith

    2015-01-01

    We present a new technique for tagging heavy-flavor jets with p_T > 500 GeV called "mu_x tagging." Current track-based methods of b-jet tagging lose efficiency and experience a large rise in fake rate in the boosted regime. Using muons from B hadron decay, we combine angular information and jet substructure to tag b jets, c jets, light jets, and "light-heavy" jets (those containing B hadrons from gluon splitting). We find tagging efficiencies of epsilon_b = 14%, epsilon_c = 6.5%, epsilon_{light-light} = 0.14%, and epsilon_{light-heavy} = 0.5%, respectively, that are nearly independent of transverse momentum at high energy. We demonstrate the usefulness of this new scheme by examining the discovery potential for multi-TeV leptophobic Z-prime bosons in the boosted-b-tagged dijet channel at the Large Hadron Collider.

  7. μx boosted-bottom-jet tagging and Z' boson searches

    Science.gov (United States)

    Pedersen, Keith; Sullivan, Zack

    2016-01-01

    We present a new technique for tagging heavy-flavor jets with pT>500 GeV called "μx tagging." Current track-based methods of b -jet tagging lose efficiency and experience a large rise in fake rate in the boosted regime. Using muons from B hadron decay, we combine angular information and jet substructure to tag b jets, c jets, light jets, and "light-heavy" jets (those containing B hadrons from gluon splitting). We find tagging efficiencies of ɛb=14 %, ɛc=6.5 %, ɛlight-light=0.14 % , and ɛlight-heavy=0.5 %, respectively, that are nearly independent of transverse momentum at high energy. We demonstrate the usefulness of this new scheme by examining the discovery potential for multi-TeV leptophobic Z' bosons in the boosted-b -tagged dijet channel at the Large Hadron Collider.

  8. ATLAS boosted object tagging 2

    CERN Document Server

    Caudron, Julien; The ATLAS collaboration

    2015-01-01

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

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

    Science.gov (United States)

    Ramírez, David; Caballero, Julio

    2016-01-01

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

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

    Science.gov (United States)

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

    2003-12-15

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

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

    International Nuclear Information System (INIS)

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

  12. B-tagging in CMS

    International Nuclear Information System (INIS)

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

  13. Approximation properties of haplotype tagging

    Directory of Open Access Journals (Sweden)

    Dreiseitl Stephan

    2006-01-01

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

  14. Enhancing Navigation on Wikipedia with Social Tags

    CERN Document Server

    Zubiaga, Arkaitz

    2012-01-01

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

  15. Phos-tag beads as an immunoblotting enhancer for selective detection of phosphoproteins in cell lysates

    OpenAIRE

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

    2009-01-01

    The low specificity of anti-phosphoprotein antibodies is often a problem in immunoblotting analyses. We introduce a simple pretreatment procedure for cell lysates to give more-specific detection of phosphoproteins in immunoblotting. Cellular phosphoproteins were preferentially trapped on Phos-tag agarose phosphate-affinity beads in a homemade spin-centrifuge microtube unit, and nonphosphorylated proteins were excluded in the filtrate. The phosphoprotein-bound beads suspended in a sample-loadi...

  16. Simultaneous purification and refolding of proteins by affinity precipitation and macro (affinity ligand)-facilitated three phase partitioning (MLFTPP).

    Science.gov (United States)

    Roy, Ipsita; Mondal, Kalyani; Gupta, Munishwar N

    2014-01-01

    This chapter describes two simple interrelated non-chromatographic methods of protein purification. In the first method, called affinity precipitation, inherent affinity of reversibly soluble-insoluble polymers (also called stimuli-sensitive or smart polymers) is exploited to form an affinity complex in free solution with target protein. The affinity complex is precipitated by a suitable change in the medium. The desired protein is dissociated from the smart polymer. In the second method called macro (affinity ligand)-facilitated three phase partitioning (MLFTPP), the affinity complex is precipitated at an interface between upper t-butanol-rich phase and lower aqueous phase. These three phases are achieved by adding appropriate amounts of ammonium sulfate and t-butanol to the initial crude extract. In the first protocol, sequential MLFTPP is used with two different smart polymers to purify pectinase and cellulase from a single crude preparation. The second protocol illustrates the application of the affinity precipitation in simultaneous purification and refolding of a urea-denatured xylanase. PMID:24648072

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

    Science.gov (United States)

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

    2016-05-01

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

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

    Science.gov (United States)

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

    2009-11-03

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

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

    OpenAIRE

    Wood, David W.; Camarero, Julio A.

    2014-01-01

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

  20. Phosphopeptide enrichment by immobilized metal affinity chromatography

    DEFF Research Database (Denmark)

    Thingholm, Tine E.; Larsen, Martin R.

    2016-01-01

    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......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 Fe3+, Ga3+, Al3+, Zr4+, and Ti4+ 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...

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

    Science.gov (United States)

    Scott, Tyler D.

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

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

    Science.gov (United States)

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

    2016-03-16

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

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

    Directory of Open Access Journals (Sweden)

    Yuxing Mao

    2014-06-01

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

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

    Directory of Open Access Journals (Sweden)

    Chen Nansheng

    2010-12-01

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

  5. Measuring γ Cleanly with CP -Tagged Bs and Bd Decays

    International Nuclear Information System (INIS)

    We propose a new method for measuring the Cabibbo-Kobayashi-Maskawa phase γ using the partial rates for CP -tagged Bs decays. Such an experiment could be performed at a very high luminosity symmetric e+e- collider operating at the Υ(5S) resonance, where the BsBs pair is produced in a state of definite CP . We also discuss CP tagging in the Bd system at the Υ(4S) , where a time-dependent analysis is required to compensate for the anticipated large CP violation in Bd-Bd mixing. (c) 2000 The American Physical Society

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

    CERN Document Server

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

    1998-01-01

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

  7. Multiple tagging of flow boil with MR imaging

    International Nuclear Information System (INIS)

    Because the determination of the hemodynamic significance of a vascular lesion is facilitated by both imaging the vascular flow channel and measuring flow velocities in the vessel, the authors investigated specific tagging strategies designed to improve the reliability and range of applicability of MR velocity measurements. The authors found that the ability to determine velocities was critically dependent on the radiofrequency (RF) pulse shapes. Appropriately tailored RF pulses were investigated, and optimum characteristics for velocity quantitation were determined. A multiple tagging sequence was developed and generated a steady state in which the interbolus distance provided a more reliable velocity measurement than did single-bolus tagging methods. The strategy also allowed the simultaneous determination of velocities at multiple sites along a vessel and were used to determine peak systolic regions to be avoided during acquisition of long-echo-time angiographic images of vessels in peripheral vascular disease

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

    CERN Document Server

    Mullins, Matt; 10.1109/WI-IAT.2010.289

    2011-01-01

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

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

    International Nuclear Information System (INIS)

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

  10. Scalable, high-performance magnetoelastic tags using frame-suspended hexagonal resonators

    International Nuclear Information System (INIS)

    This paper presents the analysis, design and experimental evaluation of miniaturized magnetoelastic tags using frame-suspended hexagonal resonators. Magnetoelastic tags—also known as acousto-magnetic or magnetomechanical tags-–are used in wireless detection systems—for example, electronic article surveillance and location mapping systems—that electromagnetically query the resonant response of the tags. In order to obtain a strong resonant response for miniaturized tags, a frame-suspended configuration is utilized to diminish the interaction between the vibrating portion of the tag and the substrate. The signal strength can be boosted by utilizing signal superposition with arrayed or clustered magnetoelastic tags. The hexagonal tags with a diameter of 1.3 mm are batch fabricated by photochemical machining from 27 µm thick Metglas™ 2826 MB, which is an amorphous NiFeMoB alloy. A preferred dc magnetic field bias for these tags is experimentally determined to be ≈31.5 Oe. A single frame-suspended magnetoelastic tag shows quality factors of 100–200. This design provides ≈75X improvement in signal amplitude compared to the non-suspended disc tag with similar size and resonant frequency. Across ten individual frame-suspended tags, the average resonant frequency is 2.13 MHz with a standard deviation of 0.44%, illustrating that this fabrication method provides repeatability. Linear signal superposition of the response has been experimentally measured for sets of frame-suspended tags that include as many as 500 units. (paper)

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

    Science.gov (United States)

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

    2013-01-01

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

  12. "Flavour Tagging and Systematics for Bs→J/ψϕ Measurement in ATLAS"

    CERN Document Server

    "Agatonovic Jovin, T; The ATLAS collaboration

    2013-01-01

    Poster for the Beauty 2013 Conference in Bologna. Flavour tagging methods and the tagging informaton used in the mass-lifetime angular fit to perform the measurement of the CP-violating phase in the channel Bs→J/ψϕ, are presented. Study of systematic uncertainties is also shown by considering several effect that are not accounted for in the likelihood fit.

  13. Affine Toda Field Theory

    International Nuclear Information System (INIS)

    We have given several pieces of evidence that perturbation theory manages to reproduce various salient features of the conjectured exact S-matrices of ATFT. At present, we do not see how to use perturbation theory to provide an efficient description of the quantum field theory; an alternative formulation may well be required in order to find a proper understanding of the conjectured S-matrices and other features such as the mass-renormalization and the Clebsch-Gordan property. Certainly, the knowledge from other approaches, for example, the Quantum Group approach to imaginary coupling ATFT, investigations of the Bethe-Salpeter equations for the bound states in ATFT and the algebraic Bethe ansatz method advocated for many years by Faddeev and others would be helpful in the search for such a re-formulation. (J.P.N.)

  14. Stability of the Neurotensin Receptor NTS1 Free in Detergent Solution and Immobilized to Affinity Resin

    OpenAIRE

    White, Jim F.; Reinhard Grisshammer

    2010-01-01

    BACKGROUND: Purification of recombinant membrane receptors is commonly achieved by use of an affinity tag followed by an additional chromatography step if required. This second step may exploit specific receptor properties such as ligand binding. However, the effects of multiple purification steps on protein yield and integrity are often poorly documented. We have previously reported a robust two-step purification procedure for the recombinant rat neurotensin receptor NTS1 to give milligram q...

  15. Stability of the Neurotensin Receptor NTS1 Free in Detergent Solution and Immobilized to Affinity Resin

    OpenAIRE

    White, Jim F.; Grisshammer, Reinhard

    2010-01-01

    Background Purification of recombinant membrane receptors is commonly achieved by use of an affinity tag followed by an additional chromatography step if required. This second step may exploit specific receptor properties such as ligand binding. However, the effects of multiple purification steps on protein yield and integrity are often poorly documented. We have previously reported a robust two-step purification procedure for the recombinant rat neurotensin receptor NTS1 to give milligram qu...

  16. Phosphopeptide Enrichment by Immobilized Metal Affinity Chromatography.

    Science.gov (United States)

    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

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

    OpenAIRE

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

    2006-01-01

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

  18. Aptamers and Capillary Electrophoresis: physico-chemical characterization of free aptamers in solution or grafted on nanoparticles, and study of their affinity towards a proteic target in view of their use in sensitive diagnosis methods

    OpenAIRE

    Girardot, Marie

    2010-01-01

    Aptamers are short oligonucleotides selected by SELEX (systematic evolution of ligands by exponential enrichment) and showing great affinity and specificity towards their target. This work deals with the physico-chemical characterization of aptamers and the study of their affinity towards their target, using capillary electrophoresis, through the example of an aptamer selected against a highly basic protein, lysozyme. After having evaluated several modifications of the capillary surface, the ...

  19. Using sutures to attach miniature tracking tags to small bats for multimonth movement and behavioral studies.

    Science.gov (United States)

    Castle, Kevin T; Weller, Theodore J; Cryan, Paul M; Hein, Cris D; Schirmacher, Michael R

    2015-07-01

    Determining the detailed movements of individual animals often requires them to carry tracking devices, but tracking broad-scale movement of small bats (bat dispersal and migration, particularly in the context of emerging conservation issues such as fatalities at wind turbines and diseases. We tested a novel method of attaching lightweight global positioning system (GPS) tags and geolocating data loggers to small bats. We used monofilament, synthetic, absorbable sutures to secure GPS tags and data loggers to the skin of anesthetized big brown bats (Eptesicus fuscus) in Colorado and hoary bats (Lasiurus cinereus) in California. GPS tags and data loggers were sutured to 17 bats in this study. Three tagged bats were recaptured 7 months after initial deployment, with tags still attached; none of these bats showed ill effects from the tag. No severe injuries were apparent upon recapture of 6 additional bats that carried tags up to 26 days after attachment; however, one of the bats exhibited skin chafing. Use of absorbable sutures to affix small tracking devices seems to be a safe, effective method for studying movements of bats over multiple months, although additional testing is warranted. This new attachment method has the potential to quickly advance our understanding of small bats, particularly as more sophisticated miniature tracking devices (e.g., satellite tags) become available. PMID:26306181

  20. Trinity:Walking on a User-Ob ject-Tag Heterogeneous Network for Personalised Recommendations

    Institute of Scientific and Technical Information of China (English)

    Ming-Xin Gan; Lily Sun; Rui Jiang

    2016-01-01

    The rapid evolution of the Internet has been appealing for effective recommender systems to pinpoint useful information from online resources. Although historical rating data has been widely used as the most important information in recommendation methods, recent advancements have been demonstrating the improvement in recommendation performance with the incorporation of tag information. Furthermore, the availability of tag annotations has been well addressed by such fruitful online social tagging applications as CiteULike, MovieLens and BibSonomy, which allow users to express their preferences, upload resources and assign their own tags. Nevertheless, most existing tag-aware recommendation approaches model relationships among users, objects and tags using a tripartite graph, and hence overlook relationships within the same types of nodes. To overcome this limitation, we propose a novel approach, Trinity, to integrate historical data and tag information towards personalised recommendation. Trinity constructs a three-layered object-user-tag network that considers not only interconnections between different types of nodes but also relationships within the same types of nodes. Based on this heterogeneous network, Trinity adopts a random walk with restart model to assign the strength of associations to candidate objects, thereby providing a means of prioritizing the objects for a query user. We validate our approach via a series of large-scale 10-fold cross-validation experiments and evaluate its performance using three comprehensive criteria. Results show that our method outperforms several existing methods, including supervised random walk with restart, simulation of resource allocating processes, and traditional collaborative filtering.

  1. Affinity tagging & purification of the fucose binding LecB protein

    OpenAIRE

    Creavin, Aileen; O'Connor, Brendan

    2007-01-01

    The fucose binding LecB protein is one of two identified lectins produced by the opportunistic pathogen Pseudomonas aeruginosa (PA01) and is implicated in contributing to its virulence. A large number of homologous proteins have been identified in other bacterial species that exhibit extremely high sequence identity and similarity to LecB. However, key amino acid residues known to participate in fucose binding in LecB are altered in many of these proteins. Some of these proteins have been sho...

  2. Peculiarities of Matter Motion in Metric-Affine Gravitational Theory

    OpenAIRE

    Babourova, O. V.; Frolov, B. N.; Koroliov, M. Yu.

    1995-01-01

    On the basis of the Lie derivative method in a metric-affine space-time it is shown that in the metric-affine gravitational theory the energy-momentum conservation law and therefore the equations of the matter motion are the consequence (as in the GR) of the gravitational field equations. The possi- bility of the detection of the space-time non-metric properties is discussed.

  3. Affine invariant texture analysis based on structural properties

    OpenAIRE

    Zhang, Jianguo; Tan, Tieniu

    2002-01-01

    This paper presents a new texture analysis method based on structural properties. The texture features extracted using this algorithm are invariant to affine transform (including rotation, translation, scaling, and skewing). Affine invariant structural properties are derived based on texel areas. An area-ratio map utilizing these properties is introduced to characterize texture images. Histogram based on this map is constructed for texture classification. Efficiency of this algorithm for affi...

  4. Hypergraph model of social tagging networks

    CERN Document Server

    Zhang, Zi-Ke

    2010-01-01

    The past few years have witnessed the great success of a new family of paradigms, so-called folksonomy, which allows users to freely associate tags to resources and efficiently manage them. In order to uncover the underlying structures and user behaviors in folksonomy, in this paper, we propose an evolutionary hypergrah model to explain the emerging statistical properties. The present model introduces a novel mechanism that one can not only assign tags to resources, but also retrieve resources via collaborative tags. We then compare the model with a real-world dataset: \\emph{Del.icio.us}. Indeed, the present model shows considerable agreement with the empirical data in following aspects: power-law hyperdegree distributions, negtive correlation between clustering coefficients and hyperdegrees, and small average distances. Furthermore, the model indicates that most tagging behaviors are motivated by labeling tags to resources, and tags play a significant role in effectively retrieving interesting resources and ...

  5. Building Tag Clouds in Perl and PHP

    CERN Document Server

    Bumgardner, Jim

    2006-01-01

    Tag clouds are everywhere on the web these days. First popularized by the web sites Flickr, Technorati, and del.icio.us, these amorphous clumps of words now appear on a slew of web sites as visual evidence of their membership in the elite corps of "Web 2.0." This PDF analyzes what is and isn't a tag cloud, offers design tips for using them effectively, and then goes on to show how to collect tags and display them in the tag cloud format. Scripts are provided in Perl and PHP. Yes, some have said tag clouds are a fad. But as you will see, tag clouds, when used properly, have real merits. More

  6. Tracking User Attention in Collaborative Tagging Communities

    CERN Document Server

    Santos-Neto, Elizeu; Ripeanu, Matei

    2007-01-01

    Collaborative tagging has recently attracted the attention of both industry and academia due to the popularity of content-sharing systems such as CiteULike, del.icio.us, and Flickr. These systems give users the opportunity to add data items and to attach their own metadata (or tags) to stored data. The result is an effective content management tool for individual users. Recent studies, however, suggest that, as tagging communities grow, the added content and the metadata become harder to manage due to an ease in content diversity. Thus, mechanisms that cope with increase of diversity are fundamental to improve the scalability and usability of collaborative tagging systems. This paper analyzes whether usage patterns can be harnessed to improve navigability in a growing knowledge space. To this end, it presents a characterization of two collaborative tagging communities that target scientific literature: CiteULike and Bibsonomy. We explore three main directions: First, we analyze the tagging activity distributi...

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

    Science.gov (United States)

    Strohmaier, Markus; Körner, Christian; Kern, Roman

    2012-01-01

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

  8. Monodisperse REPO4 (RE = Yb, Gd, Y) hollow microspheres covered with nanothorns as affinity probes for selectively capturing and labeling phosphopeptides.

    Science.gov (United States)

    Cheng, Gong; Zhang, Ji-Lin; Liu, Yan-Lin; Sun, De-Hui; Ni, Jia-Zuan

    2012-02-13

    Rare-earth phosphate microspheres with unique structures were developed as affinity probes for the selective capture and tagging of phosphopeptides. Prickly REPO(4) (RE = Yb, Gd, Y) monodisperse microspheres, that have hollow structures, low densities, high specific surface areas, and large adsorptive capacities were prepared by an ion-exchange method. The elemental compositions and crystal structures of these affinity probes were confirmed by energy-dispersive spectroscopy (EDS), powder X-ray diffraction (XRD), and Fourier-transform infrared (FTIR) spectroscopy. The morphologies of these compounds were investigated using scanning electron microscopy (SEM), transmission electron microscopy (TEM), and nitrogen-adsorption isotherms. The potential ability of these microspheres for selectively capturing and labeling target biological molecules was evaluated by using protein-digestion analysis and a real sample as well as by comparison with the widely used TiO(2) affinity microspheres. These results show that these porous rare-earth phosphate microspheres are highly promising probes for the rapid purification and recognition of phosphopeptides. PMID:22241661

  9. Optimization of tagged MRI for quantification of liver stiffness using computer simulated data.

    Directory of Open Access Journals (Sweden)

    Serena Monti

    Full Text Available The heartbeat has been proposed as an intrinsic source of motion that can be used in combination with tagged Magnetic Resonance Imaging (MRI to measure displacements induced in the liver as an index of liver stiffness. Optimizing a tagged MRI acquisition protocol in terms of sensitivity to these displacements, which are in the order of pixel size, is necessary to develop the method as a quantification tool for staging fibrosis. We reproduced a study of cardiac-induced strain in the liver at 3T and simulated tagged MR images with different grid tag patterns to evaluate the performance of the Harmonic Phase (HARP image analysis method and its dependence on the parameters of tag spacing and grid angle. The Partial Volume Effect (PVE, T1 relaxation, and different levels of noise were taken into account. Four displacement fields of increasing intensity were created and applied to the tagged MR images of the liver. These fields simulated the deformation at different liver stiffnesses. An Error Index (EI was calculated to evaluate the estimation accuracy for various parameter values. In the absence of noise, the estimation accuracy of the displacement fields increased as tag spacings decreased. EIs for each of the four displacement fields were lower at 0° and the local minima of the EI were found to correspond to multiples of pixel size. The accuracy of the estimation decreased for increasing levels of added noise; as the level increased, the improved estimation caused by decreasing the tag spacing tended to zero. The optimal tag spacing turned out to be a compromise between the smallest tag period that is a multiple of the pixel size and is achievable in a real acquisition and the tag spacing that guarantees an accurate liver displacement measure in the presence of realistic levels of noise.

  10. Self-organization in social tagging systems

    OpenAIRE

    Liu C; Yeung C.H.; Zhang Z.-K.

    2011-01-01

    Individuals often imitate each other to fall into the typical group, leading to a self-organized state of typical behaviors in a community. In this paper, we model self-organization in social tagging systems and illustrate the underlying interaction and dynamics. Specifically, we introduce a model in which individuals adjust their own tagging tendency to imitate the average tagging tendency. We found that when users are of low confidence, they tend to imitate others and lead to a self-organiz...

  11. Spam Fighting in Social Tagging Systems

    OpenAIRE

    Yazdani, Sasan; Ivanov, Ivan; Analoui, Morteza; Berangi, Reza; Ebrahimi, Touradj

    2012-01-01

    Tagging in online social networks is very popular these days, as it facilitates search and retrieval of diverse resources available online. However, noisy and spam annotations often make it difficult to perform an efficient search. Users may make mistakes in tagging and irrelevant tags and resources may be maliciously added for advertisement or self-promotion. Since filtering spam annotations and spammers is time-consuming if it is done manually, machine learning approaches can be employed to...

  12. Circularly Polarized Broadband RFID Microstrip Tag Antenna

    OpenAIRE

    B. Rajini; G. V. Subrahmanyam

    2014-01-01

    In recent years, the application of radio frequency identification (RFID) operating in the ultra-high frequency (UHF) band (860-960MHz) are expanding exponentially, due to the advantages such as long reading distance, high data transfer rate, and small tag size. So the design of a CP tag antenna with broadband characteristic is presently one of the most challenging topics. This project presents a square patch passive RFID tag antenna designed for UHF band. To a...

  13. Tagging diversity in personal learning environments

    OpenAIRE

    Cao, Yiwei; Kovachev, Dejan; Klamma, Ralf; Jarke, Matthias; Lau, Rynson W. H.

    2015-01-01

    Tagging is a prevalent practice in the Web 2.0. It has been widely usedto annotate different media like video. However, in personal learning environments(PLEs), tagging is supporting not only content indexing but also the self-regulatedlearning process consisting of different phases like planning, learning, and reflecting.In particular, in the reflection phase, tags support the organization of learningoutcomes. We have researched the interrelations of learning content, learningprocesses, and ...

  14. Tracking User Attention in Collaborative Tagging Communities

    OpenAIRE

    Santos-Neto, Elizeu; Ripeanu, Matei; Iamnitchi, Adriana

    2007-01-01

    Collaborative tagging has recently attracted the attention of both industry and academia due to the popularity of content-sharing systems such as CiteULike, del.icio.us, and Flickr. These systems give users the opportunity to add data items and to attach their own metadata (or tags) to stored data. The result is an effective content management tool for individual users. Recent studies, however, suggest that, as tagging communities grow, the added content and the metadata become harder to mana...

  15. Transcriptome Annotation using Tandem SAGE Tags

    OpenAIRE

    Rivals, Eric; Boureux, Anthony; Lejeune, Mireille; Ottones, Florence; Pecharromàn Pérez, Oscar; Tarhio, Jorma; Pierrat, Fabien; Ruffle, Florence; Commes, Thérèse; Marti, Jacques

    2007-01-01

    Analysis of several million expressed gene signatures (tags) revealed an increasing number of different sequences, largely exceeding that of annotated genes in mammalian genomes. Serial Analysis of Gene Expression (SAGE) can reveal new polyadenylated RNAs transcribed from previously unrecognized chromosomal regions. However, conventional SAGE tags are too short to identify unambiguously unique sites in large genomes. Here, we design a novel strategy with tags anchored on two different restric...

  16. Learner Corpora without Error Tagging

    Directory of Open Access Journals (Sweden)

    Rastelli, Stefano

    2009-01-01

    Full Text Available The article explores the possibility of adopting a form-to-function perspective when annotating learner corpora in order to get deeper insights about systematic features of interlanguage. A split between forms and functions (or categories is desirable in order to avoid the "comparative fallacy" and because – especially in basic varieties – forms may precede functions (e.g., what resembles to a "noun" might have a different function or a function may show up in unexpected forms. In the computer-aided error analysis tradition, all items produced by learners are traced to a grid of error tags which is based on the categories of the target language. Differently, we believe it is possible to record and make retrievable both words and sequence of characters independently from their functional-grammatical label in the target language. For this purpose at the University of Pavia we adapted a probabilistic POS tagger designed for L1 on L2 data. Despite the criticism that this operation can raise, we found that it is better to work with "virtual categories" rather than with errors. The article outlines the theoretical background of the project and shows some examples in which some potential of SLA-oriented (non error-based tagging will be possibly made clearer.

  17. Tagging: An Organization Scheme for the Internet

    OpenAIRE

    Visser, Marijke A.

    2010-01-01

    How should the information on the Internet be organized? This question and the possible solutions spark debates among people concerned with how we identify, classify, and retrieve Internet content. This paper discusses the benefits and the controversies of using a tagging system to organize Internet resources. Tagging refers to a classification system where individual Internet users apply labels, or tags, to digital resources. Tagging increased in popularity with the advent of Web 2.0 applica...

  18. Modeling Consensus Semantics in Social Tagging Systems

    Institute of Scientific and Technical Information of China (English)

    Bin Zhang; Yin Zhang; Ke-Ning Gao

    2011-01-01

    In social tagging systems,people can annotate arbitrary tags to online data to categorize and index them.However,the lack of the "a priori" set of words makes it difficult for people to reach consensus about the semantics of tags and how to categorize data.Ontologies based approaches can help reaching such consensus,but they are still facing problems such as inability of model ambiguous and new concepts properly.For tags that are used very few times,since they can only be used in very specific contexts,their semantics are very clear and detailed.Although people have no consensus on these tags,it is still possible to leverage these detailed semantics to model the other tags.In this paper we introduce a random walk and spreading activation like model to represent the semantics of tags using semantics of unpopular tags.By comparing the proposed model to the classic Latent Semantic Analysis approach in a concept clustering task,we show that the proposed model can properly capture the semantics of tags.

  19. External tagging does not affect the feeding behavior of a coral reef fish, Chaetodon vagabundus (Pisces: Chaetodontidae)

    KAUST Repository

    Berumen, Michael L.

    2009-11-10

    Increasingly, the ability to recognize individual fishes is important for studies of population dynamics, ecology, and behavior. Although a variety of methods exist, external tags remain one of the most widely applied because they are both effective and cost efficient. However, a key assumption is that neither the tagging procedure nor the presence of a tag negatively affects the individual. While this has been demonstrated for relatively coarse metrics such as growth and survival, few studies have examined the impact of tags and tagging on more subtle aspects of behavior. We tagged adult vagabond butterflyfish (Chaetodon vagabundus) occupying a 30-ha insular reef in Kimbe Bay, Papua New Guinea, using a commonly-utilized t-bar anchor tag. We quantified and compared feeding behavior (bite rate), which is sensitive to stress, of tagged and untagged individuals over four separate sampling periods spanning 4 months post-tagging. Bite rates did not differ between tagged and untagged individuals at each sampling period and, combined with additional anecdotal observations of normal pairing behavior and successful reproduction, suggest that tagging did not adversely affect individuals. © Springer Science+Business Media B.V. 2009.

  20. Extending birthday paradox theory to estimate the number of tags in RFID systems.

    Science.gov (United States)

    Shakiba, Masoud; Singh, Mandeep Jit; Sundararajan, Elankovan; Zavvari, Azam; Islam, Mohammad Tariqul

    2014-01-01

    The main objective of Radio Frequency Identification systems is to provide fast identification for tagged objects. However, there is always a chance of collision, when tags transmit their data to the reader simultaneously. Collision is a time-consuming event that reduces the performance of RFID systems. Consequently, several anti-collision algorithms have been proposed in the literature. Dynamic Framed Slotted ALOHA (DFSA) is one of the most popular of these algorithms. DFSA dynamically modifies the frame size based on the number of tags. Since the real number of tags is unknown, it needs to be estimated. Therefore, an accurate tag estimation method has an important role in increasing the efficiency and overall performance of the tag identification process. In this paper, we propose a novel estimation technique for DFSA anti-collision algorithms that applies birthday paradox theory to estimate the number of tags accurately. The analytical discussion and simulation results prove that the proposed method increases the accuracy of tag estimation and, consequently, outperforms previous schemes. PMID:24752285

  1. Extending birthday paradox theory to estimate the number of tags in RFID systems.

    Directory of Open Access Journals (Sweden)

    Masoud Shakiba

    Full Text Available The main objective of Radio Frequency Identification systems is to provide fast identification for tagged objects. However, there is always a chance of collision, when tags transmit their data to the reader simultaneously. Collision is a time-consuming event that reduces the performance of RFID systems. Consequently, several anti-collision algorithms have been proposed in the literature. Dynamic Framed Slotted ALOHA (DFSA is one of the most popular of these algorithms. DFSA dynamically modifies the frame size based on the number of tags. Since the real number of tags is unknown, it needs to be estimated. Therefore, an accurate tag estimation method has an important role in increasing the efficiency and overall performance of the tag identification process. In this paper, we propose a novel estimation technique for DFSA anti-collision algorithms that applies birthday paradox theory to estimate the number of tags accurately. The analytical discussion and simulation results prove that the proposed method increases the accuracy of tag estimation and, consequently, outperforms previous schemes.

  2. Rekomendasi Tag Pada Berita Online Menggunakan Tf-Idf Dan Collaborative Tagging

    OpenAIRE

    Farizi, Salman All

    2015-01-01

    The rapid development of internet technology leads to increase the flow of information and further increase the amount of published news online. Social tagging techonology exists to simplyfy the search process of news online and news archive settings based on tag infomation similarity. To facilitate tagging process, autotag system is developed. In this study, the autotag system is developed by using TF-IDF and Collaborative Tagging where the process begins with text preprocessing until featur...

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

    OpenAIRE

    Strohmaier, Markus; Körner, Christian; Kern, Roman

    2012-01-01

    While recent progress has been achieved in understanding the structure and dynamics of social tagging systems, we know little about the underlying user motivations for tagging, and how they influence resulting folksonomies and tags. This paper addresses three issues related to this question. (1) What distinctions of user motivations are identified by previous research, and in what ways are the motivations of users amenable to quantitative analysis? (2) To what extent does tagging motivation v...

  4. In Tags We Trust: Trust modeling in social tagging of multimedia content

    OpenAIRE

    Ivanov, Ivan; Vajda, Péter; Lee, Jong Seok; Ebrahimi, Touradj

    2012-01-01

    Tagging in online social networks is very popular these days, as it facilitates search and retrieval of multimedia content. However, noisy and spam annotations often make it difficult to perform an efficient search. Users may make mistakes in tagging and irrelevant tags and content may be maliciously added for advertisement or self-promotion. This article surveys recent advances in techniques for combatting such noise and spam in social tagging. We classify the state-of-the-art approaches int...

  5. Nitric oxide flow tagging in unseeded air.

    Science.gov (United States)

    Dam, N; Klein-Douwel, R J; Sijtsema, N M; Meulen, J J

    2001-01-01

    A scheme for molecular tagging velocimetry is presented that can be used in air flows without any kind of seeding. The method is based on the local and instantaneous creation of nitric oxide (NO) molecules from N(2) and O(2) in the waist region of a focused ArF excimer laser beam. This NO distribution is advected by the flow and can be visualized any time later by laser-induced fluorescence in the gamma bands. The creation of NO is confirmed by use of an excitation spectrum. Two examples of the application of the new scheme for air-flow velocimetry are given in which single laser pulses are used for creation and visualization of NO. PMID:18033499

  6. Improving Recommendations in Tag-based Systems with Spectral Clustering of Tag Neighbors

    DEFF Research Database (Denmark)

    Pan, Rong; Xu, Guandong; Dolog, Peter

    2012-01-01

    Tag as a useful metadata reflects the collaborative and conceptual features of documents in social collaborative annotation systems. In this paper, we propose a collaborative approach for expanding tag neighbors and investigate the spectral clustering algorithm to filter out noisy tag neighbors i...

  7. SERS-active nanoparticle aggregate technology for tags and seals

    Energy Technology Data Exchange (ETDEWEB)

    Brown, Leif O [Los Alamos National Laboratory; Montoya, Velma M [Los Alamos National Laboratory; Havrilla, George J [Los Alamos National Laboratory; Doorn, Stephen K [Los Alamos National Laboratory

    2010-06-03

    In this paper, we describe our efforts to create a modern tagging and sealing technology for international safeguards application. Our passive tagging methods are based on SANAs (SERS-Active Nanoparticle Aggregates; SERS: Surface Enhanced Raman Scattering). These SANAs offer robust spectral barcoding capability in an inexpensive tag/seal, with the possibility of rapid in-field verification that requires no human input. At INMM 2009, we introduced SANAs, and showed approaches to integrating our technology with tags under development at Sandia National Laboratories (SNL). Here, we will focus on recent LANL development work, as well as adding additional dimensionality to the barcoding technique. The field of international safeguards employs a broad array of tags, seals, and tamper-indicating devices to assist with identification, tracking, and verification of components and materials. These devices each have unique strengths suited to specific applications, and span a range of technologies from passive metal cup seals and adhesive seals to active, remotely monitored fiber optic seals. Regardless of the technology employed, essential characteristics center around security, environmental and temporal stability, ease of use, and the ability to provide confidence to all parties. Here, we present a new inexpensive tagging technology that will deliver these attributes, while forming the basis of either a new seal, or as a secure layer added to many existing devices. Our approach uses the Surface Enhanced Raman Scattering (SERS) response from SANAs (SERS-Active Nanoparticle Aggregates, Figure 1) to provide a unique identifier or signature for tagging applications. SANAs are formed from gold or silver nanoparticles in the 40-80 nm size range. A chemical dye is installed on the nanoparticle surface, and the nanoparticles are then aggregated into ensembles of {approx}100 to 500 nm diameter, prior to being coated with silica. The silica shell protects the finished SANA from

  8. Quantum affine symmetry in vertex models

    CERN Document Server

    Idzumi, M; Jimbo, M; Miwa, T; Nakashima, T; Tokihiro, T; Idzumi, Makoto; Iohara, Kenji; Jimbo, Michio; Miwa, Tetsuji; Nakashima, Toshiki; Tokihiro, Tetsuji

    1993-01-01

    We study the higher spin anologs of the six vertex model on the basis of its symmetry under the quantum affine algebra $U_q(\\slth)$. Using the method developed recently for the XXZ spin chain, we formulate the space of states, transfer matrix, vacuum, creation/annihilation operators of particles, and local operators, purely in the language of representation theory. We find that, regardless of the level of the representation involved, the particles have spin $1/2$, and that the $n$-particle space has an RSOS-type structure rather than a simple tensor product of the $1$-particle space. This agrees with the picture proposed earlier by Reshetikhin.

  9. Reducing fungal infections and testing tag loss in juvenile Pacific lampreys implanted with passive integrated transponders.

    Science.gov (United States)

    Christiansen, H.E.; Gee, L.P.; Mesa, M.G.

    2012-01-01

    Pacific lamprey Entosphenus tridentatus are facing severe population declines, yet little is known about juvenile lamprey passage, life history, or adult return rates because until now, these small fish could not be tagged for unique identification of live individuals. Previously, we developed a simple and effective method for tagging juvenile lampreys with passive integrated transponder (PIT) tags and showed that tagging per se did not affect survival. Mortality in tagged and untagged control fish, however, was frequently associated with fungal infection. In this study, we addressed two outstanding issues related to handling and tagging juvenile lampreys. First, we tried to mitigate freshwater fungal infections by reducing irritation and stress from anesthesia and by treating tagged fish briefly with a prophylactic immediately after tagging. We tested four anesthetics at three concentrations each and determined that 100 mg/L MS-222 and 60 mg/L BENZOAK® (benzocaine) were the most effective for anesthetizing juvenile lampreys to handleable while minimizing irritation. We also showed that fish anesthetized with BENZOAK® may have lower rates of fungal infection than those anesthetized with MS-222 or AQUI-S® 20E (eugenol). When fish anesthetized with MS-222 or BENZOAK® were given a 30 min prophylactic treatment with Stress Coat®, hydrogen peroxide, or salt immediately after tagging, few fish presented with fungal infections. However, untreated, tagged control fish also showed few fungal infections, making it difficult to determine if the prophylactic treatments were successful. The second question we addressed was whether activity would increase tag loss in PIT-tagged lampreys. We found that active swimming did not cause tag loss if fish were first held for 20–24 h after tagging. Therefore, we recommend anesthesia with MS-222 or BENZOAK® and then tagging with a 20–24 h recovery period followed by immediate release. If field studies show that lampreys are not

  10. CT colonography with rectal iodine tagging: Feasibility and comparison with oral tagging in a colorectal cancer screening population

    International Nuclear Information System (INIS)

    Highlights: • In the group receiving rectal tagging, mean per-polyp sensitivity, specificity were 96.1% and 95.3%; while in the group receiving oral tagging, mean per-polyp sensitivity, specificity were 89.4% and 95.8%. The difference between the two groups was not statistically significant (p = 0.549). • Rectal tagging can be an effective alternative to oral tagging. • Rectal tagging allowed greater patient acceptance and lower overall examination time. - Abstract: Purpose: To evaluate feasibility, diagnostic performance, patient acceptance, and overall examination time of CT colonography (CTC) performed through rectal administration of iodinated contrast material. Materials and methods: Six-hundred asymptomatic subjects (male:female = 270:330; mean 63 years) undergoing CTC for colorectal cancer screening on an individual basis were consecutively enrolled in the study. Out of them, 503 patients (group 1) underwent CTC with rectal tagging, of which 55 had a total of 77 colonic lesions. The remaining 97 patients (group 2) were randomly selected to receive CTC with oral tagging of which 15 had a total of 20 colonic lesions. CTC findings were compared with optical colonoscopy, and per-segment image quality was visually assessed using a semi-quantitative score (1 = poor, 2 = adequate, 3 = excellent). In 70/600 patients (11.7%), CTC was performed twice with both types of tagging over a 5-year follow-up cancer screening program. In this subgroup, patient acceptance was rated via phone interview two weeks after CTC using a semi-quantitative scale (1 = poor, 2 = fair, 3 = average, 4 = good, 5 = excellent). Results: Mean per-polyp sensitivity, specificity, positive and negative predictive values of CTC with rectal vs oral tagging were 96.1% (CI95% 85.4 ÷ 99.3%) vs 89.4% (CI95% 65.4 ÷ 98.1%), 95.3% (CI95% 90.7 ÷ 97.8%) vs 95.8% (CI95% 87.6 ÷ 98.9%), 86.0% (CI95% 73.6 ÷ 93.3) vs 85.0% (CI95% 61.1 ÷ 96.0%), and 98.8% (CI95% 95.3 ÷ 99.8%) vs 97.2% (CI95% 89.4 ÷ 99

  11. CT colonography with rectal iodine tagging: Feasibility and comparison with oral tagging in a colorectal cancer screening population

    Energy Technology Data Exchange (ETDEWEB)

    Neri, Emanuele, E-mail: emanuele.neri@med.unipi.it [Diagnostic and Interventional Radiology – Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa (Italy); Mantarro, Annalisa; Faggioni, Lorenzo; Scalise, Paola; Bemi, Pietro; Pancrazi, Francesca [Diagnostic and Interventional Radiology – Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa (Italy); D’Ippolito, Giuseppe [Federal University of São Paulo – Sena Madureira 1500 – Vila Mariana, UNIFESP, São Paulo, SP (Brazil); Bartolozzi, Carlo [Diagnostic and Interventional Radiology – Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa (Italy)

    2015-09-15

    Highlights: • In the group receiving rectal tagging, mean per-polyp sensitivity, specificity were 96.1% and 95.3%; while in the group receiving oral tagging, mean per-polyp sensitivity, specificity were 89.4% and 95.8%. The difference between the two groups was not statistically significant (p = 0.549). • Rectal tagging can be an effective alternative to oral tagging. • Rectal tagging allowed greater patient acceptance and lower overall examination time. - Abstract: Purpose: To evaluate feasibility, diagnostic performance, patient acceptance, and overall examination time of CT colonography (CTC) performed through rectal administration of iodinated contrast material. Materials and methods: Six-hundred asymptomatic subjects (male:female = 270:330; mean 63 years) undergoing CTC for colorectal cancer screening on an individual basis were consecutively enrolled in the study. Out of them, 503 patients (group 1) underwent CTC with rectal tagging, of which 55 had a total of 77 colonic lesions. The remaining 97 patients (group 2) were randomly selected to receive CTC with oral tagging of which 15 had a total of 20 colonic lesions. CTC findings were compared with optical colonoscopy, and per-segment image quality was visually assessed using a semi-quantitative score (1 = poor, 2 = adequate, 3 = excellent). In 70/600 patients (11.7%), CTC was performed twice with both types of tagging over a 5-year follow-up cancer screening program. In this subgroup, patient acceptance was rated via phone interview two weeks after CTC using a semi-quantitative scale (1 = poor, 2 = fair, 3 = average, 4 = good, 5 = excellent). Results: Mean per-polyp sensitivity, specificity, positive and negative predictive values of CTC with rectal vs oral tagging were 96.1% (CI{sub 95%} 85.4 ÷ 99.3%) vs 89.4% (CI{sub 95%} 65.4 ÷ 98.1%), 95.3% (CI{sub 95%} 90.7 ÷ 97.8%) vs 95.8% (CI{sub 95%} 87.6 ÷ 98.9%), 86.0% (CI{sub 95%} 73.6 ÷ 93.3) vs 85.0% (CI{sub 95%} 61.1 ÷ 96.0%), and 98.8% (CI{sub 95

  12. Affine density in wavelet analysis

    CERN Document Server

    Kutyniok, Gitta

    2007-01-01

    In wavelet analysis, irregular wavelet frames have recently come to the forefront of current research due to questions concerning the robustness and stability of wavelet algorithms. A major difficulty in the study of these systems is the highly sensitive interplay between geometric properties of a sequence of time-scale indices and frame properties of the associated wavelet systems. This volume provides the first thorough and comprehensive treatment of irregular wavelet frames by introducing and employing a new notion of affine density as a highly effective tool for examining the geometry of sequences of time-scale indices. Many of the results are new and published for the first time. Topics include: qualitative and quantitative density conditions for existence of irregular wavelet frames, non-existence of irregular co-affine frames, the Nyquist phenomenon for wavelet systems, and approximation properties of irregular wavelet frames.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-11-01

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

  14. Inhomogeneous self-affine carpets

    OpenAIRE

    Fraser, Jonathan M.

    2013-01-01

    We investigate the dimension theory of inhomogeneous self-affine carpets. Through the work of Olsen, Snigireva and Fraser, the dimension theory of inhomogeneous self-similar sets is now relatively well-understood, however, almost no progress has been made concerning more general non-conformal inhomogeneous attractors. If a dimension is countably stable, then the results are immediate and so we focus on the upper and lower box dimensions and compute these explicitly for large classes of inhomo...

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

    Directory of Open Access Journals (Sweden)

    Miriam S. Goyder

    2012-04-01

    Full Text Available We present a top down separation platform for yeast ribosomalproteins using affinity chromatography and capillary electrophoresiswhich is designed to allow deposition of proteins ontoa substrate. FLAG tagged ribosomes were affinity purified, andrRNA acid precipitation was performed on the ribosomes followedby capillary electrophoresis to separate the ribosomalproteins. Over 26 peaks were detected with excellent reproducibility(<0.5% RSD migration time. This is the first reportedseparation of eukaryotic ribosomal proteins using capillaryelectrophoresis. The two stages in this workflow, affinity chromatographyand capillary electrophoresis, share the advantagesthat they are fast, flexible and have small sample requirementsin comparison to more commonly used techniques. This methodis a remarkably quick route from cell to separation that hasthe potential to be coupled to high throughput readout platformsfor studies of the ribosomal proteome. [BMB reports2012; 45(4: 233-238

  16. Transposon tagging in diploid strawberry.

    Science.gov (United States)

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

    2012-10-01

    Fragaria vesca was transformed with a transposon tagging construct harbouring amino terminally deleted maize transposase and EGFP (Ac element), NPTII, CaMV 35S promoter (P35S) driving transposase and mannopine synthase promoter (Pmas) driving EGFP (Ds element). Of 180 primary transgenics, 48 were potential launch pads, 72 were multiple insertions or chimaeras, and 60 exhibited somatic transposition. T₁ progeny of 32 putative launch pads were screened by multiplex PCR for transposition. Evidence of germ-line transposition occurred in 13 putative launch pads; however, the transposition frequency was too low in three for efficient recovery of transposants. The transposition frequency in the remaining launch pads ranged from 16% to 40%. After self-pollination of the T₀ launch pads, putative transposants in the T₁ generation were identified by multiplex PCR. Sequencing of hiTAIL-PCR products derived from nested primers within the Ds end sequences (either P35S at the left border or the inverted repeat at the right border) of T₁ plants revealed transposition of the Ds element to distant sites in the strawberry genome. From more than 2400 T₁ plants screened, 103 unique transposants have been identified, among which 17 were somatic transpositions observed in the T₀ generation. Ds insertion sites were dispersed among various gene elements [exons (15%), introns (23%), promoters (30%), 3' UTRs (17%) as well as intergenically (15%)]. Three-primer (one on either side of the Ds insertion and one within the Ds T-DNA) PCR could be used to identify homozygous T₂ transposon-tagged plants. The mutant collection has been catalogued in an on-line database. PMID:22845757

  17. Flavor tagging TeV jets for physics beyond the Standard Model

    Science.gov (United States)

    Sullivan, Zack; Pedersen, Keith

    2016-07-01

    We present a new scheme for tagging boosted heavy flavor jets called "µx tagging." At the LHC, the primary method to tag b-jets relies on tracking their charged constituents. However, when highly boosted, track-based b-tags lose efficiency, and the probability to mistag light jets rises dramatically. Using muons from B hadron decay and defining a particular combination "x" of angular information and boost estimation, we find fairly flat efficiencies to tag b-jets, c-jets, light-quark jets, and light-heavy jets (containing B hadrons from gluon splitting) of ɛb = 14%, ɛc = 6:5%, ɛlight-light = 0:1%, and ɛlight-heavy = 0:5%, respectively. We demonstrate the usefulness of this new scheme by showing the reach for discovery of a leptophobic Z' → bb¯ in the dijet channel.

  18. Sex identification and PIT-tagging: tools and prospects for studying intersexual differences in freshwater fishes

    DEFF Research Database (Denmark)

    Hulthén, K.; Chapman, B.B.; Nilsson, P.A.;

    2014-01-01

    This study evaluated a technique to allow the long-term monitoring of individual fishes of known sex in the wild using sex confirmation in close proximity to the reproductive period combined with individual tagging. Hundreds of partially migratory roach Rutilus rutilus were tagged with passive...... integrated transponders (PIT) following sex determination in spring and various performance measures were compared with fish tagged outside the reproductive period in autumn. Short-term survival was >95% for R. rutilus sexed and tagged under natural field conditions. Total length (LT) did not affect the...... observed sex ratio of recaptured fish did not differ from the expected values of equal recapture rates between males and females. Hence, there is no observable evidence for an adverse effect of tagging close to the reproductive period and therefore this method is suitable for studying intersexual...

  19. TAG (Teaching Active Games) for the Holidays

    Science.gov (United States)

    Erwin, Heather E.; Bachtel, Amy

    2007-01-01

    Holidays present the perfect opportunity for physical educators to utilize creative TAG (Teaching Active Games) games to offer maximum physical activity opportunities for their students. The TAG ideas in this article offer physical education teachers quick, instant activities that involve very little equipment, time management, or instruction. At…

  20. Evaluation of PIT-tagging in cyprinids

    DEFF Research Database (Denmark)

    Skov, Christian; Brodersen, J.; Brönmark, C.;

    2005-01-01

    Laboratory and field experiments were used to investigate how different marking procedures, with 23 mm PIT (passive integrated transponders) - tags. affected mortality, body condition and tag expulsion in small roach Rutilus rutilus and rudd Scardinus erythrophthalmus (117 to 163 mm total length)...

  1. A Radio Tag for Big Whales

    Science.gov (United States)

    Watkins, William A.

    1978-01-01

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

  2. A versatile PCR-based tandem epitope tagging system for Streptomyces coelicolor genome.

    Science.gov (United States)

    Kim, Ji-Nu; Yi, Jeong Sang; Lee, Bo-Rahm; Kim, Eun-Jung; Kim, Min Woo; Song, Yoseb; Cho, Byung-Kwan; Kim, Byung-Gee

    2012-07-20

    Epitope tagging approaches have been widely used for the analysis of functions, interactions and subcellular distributions of proteins. However, incorporating epitope sequence into protein loci in Streptomyces is time-consuming procedure due to the absence of the versatile tagging methods. Here, we developed a versatile PCR-based tandem epitope tagging tool for the Streptomyces genome engineering. We constructed a series of template plasmids that carry repeated sequence of c-myc epitope, Flp recombinase target (FRT) sites, and apramycin resistance marker to insert epitope tags into any desired spot of the chromosomal loci. A DNA module which includes the tandem epitope-encoding sequence and a selectable marker was amplified by PCR with primers that carry homologous extensions to the last portion and downstream region of the targeted gene. We fused the epitope tags at the 3' region of global transcription factors of Streptomyces coelicolor to test the validity of this system. The proper insertion of the epitope tag was confirmed by PCR and western blot analysis. The recombinants showed the identical phenotype to the wild-type that proved the conservation of in vivo function of the tagged proteins. Finally, the direct binding targets were successfully detected by chromatin immunoprecipitation with the increase in the signal-to-noise ratio. The epitope tagging system describes here would provide wide applications to study the protein functions in S. coelicolor. PMID:22704935

  3. Array processing for RFID tag localization exploiting multi-frequency signals

    Science.gov (United States)

    Zhang, Yimin; Li, Xin; Amin, Moeness G.

    2009-05-01

    RFID is an increasingly valuable business and technology tool for electronically identifying, locating, and tracking products, assets, and personnel. As a result, precise positioning and tracking of RFID tags and readers have received considerable attention from both academic and industrial communities. Finding the position of RFID tags is considered an important task in various real-time locating systems (RTLS). As such, numerous RFID localization products have been developed for various applications. The majority of RFID positioning systems is based on the fusion of pieces of relevant information, such as the range and the direction-of-arrival (DOA). For example, trilateration can determine the tag position by using the range information of the tag estimated from three or more spatially separated reader antennas. Triangulation is another method to locate RFID tags that use the direction-of-arrival (DOA) information estimated at multiple spatially separated locations. The RFID tag positions can also be determined through hybrid techniques that combine the range and DOA information. The focus of this paper to study the design and performance of the localization of passive RFID tags using array processing techniques in a multipath environment, and exploiting multi-frequency CW signals. The latter are used to decorrelate the coherent multipath signals for effective DOA estimation and for the purpose of accurate range estimation. Accordingly, the spatial and frequency dimensionalities are fully utilized for robust and accurate positioning of RFID tags.

  4. Direct Labeling of Polyphosphate at the Ultrastructural Level in Saccharomyces cerevisiae by Using the Affinity of the Polyphosphate Binding Domain of Escherichia coli Exopolyphosphatase

    OpenAIRE

    Saito, Katsuharu; Ohtomo, Ryo; Kuga-Uetake, Yukari; Aono, Toshihiro; Saito, Masanori

    2005-01-01

    Inorganic polyphosphate (polyP) is a linear polymer of orthophosphate and has many biological functions in prokaryotic and eukaryotic organisms. To investigate polyP localization, we developed a novel technique using the affinity of the recombinant polyphosphate binding domain (PPBD) of Escherichia coli exopolyphosphatase to polyP. An epitope-tagged PPBD was expressed and purified from E. coli. Equilibrium binding assay of PPBD revealed its high affinity for long-chain polyP and its weak affi...

  5. Alternative affinity tools: more attractive than antibodies?

    NARCIS (Netherlands)

    Ruigrok, V.J.B.; Levisson, M.; Eppink, M.H.M.; Smidt, H.; Oost, van der J.

    2011-01-01

    Antibodies are the most successful affinity tools used today, in both fundamental and applied research (diagnostics, purification and therapeutics). Nonetheless, antibodies do have their limitations, including high production costs and low stability. Alternative affinity tools based on nucleic acids

  6. Self-organization in social tagging systems

    CERN Document Server

    Liu, Chuang; Zhang, Zi-Ke

    2011-01-01

    Individuals often imitate each other to fall into the typical group, leading to a self-organized state of typical behaviors in a community. In this paper, we model self-organization in social tagging systems and illustrate the underlying interaction and dynamics. Specifically, we introduce a model in which individuals adjust their own tagging tendency to imitate the average tagging tendency. We found that when users are of low confidence, they tend to imitate others and lead to a self-organized state with active tagging. On the other hand, when users are of high confidence and are stubborn for changes, tagging becomes inactive. We observe a phase transition at a critical level of user confidence when the system changes from one regime to the other. The distributions of post length obtained from the model are compared to real data which show good agreements.

  7. Emergent Community Structure in Social Tagging Systems

    CERN Document Server

    Cattuto, Ciro; Servedio, Vito D P; Loreto, Vittorio

    2008-01-01

    A distributed classification paradigm known as collaborative tagging has been widely adopted in new Web applications designed to manage and share online resources. Users of these applications organize resources (Web pages, digital photographs, academic papers) by associating with them freely chosen text labels, or tags. Here we leverage the social aspects of collaborative tagging and introduce a notion of resource distance based on the collective tagging activity of users. We collect data from a popular system and perform experiments showing that our definition of distance can be used to build a weighted network of resources with a detectable community structure. We show that this community structure clearly exposes the semantic relations among resources. The communities of resources that we observe are a genuinely emergent feature, resulting from the uncoordinated activity of a large number of users, and their detection paves the way for mapping emergent semantics in social tagging systems.

  8. Using DEDICOM for completely unsupervised part-of-speech tagging.

    Energy Technology Data Exchange (ETDEWEB)

    Chew, Peter A.; Bader, Brett William; Rozovskaya, Alla (University of Illinois, Urbana, IL)

    2009-02-01

    A standard and widespread approach to part-of-speech tagging is based on Hidden Markov Models (HMMs). An alternative approach, pioneered by Schuetze (1993), induces parts of speech from scratch using singular value decomposition (SVD). We introduce DEDICOM as an alternative to SVD for part-of-speech induction. DEDICOM retains the advantages of SVD in that it is completely unsupervised: no prior knowledge is required to induce either the tagset or the associations of terms with tags. However, unlike SVD, it is also fully compatible with the HMM framework, in that it can be used to estimate emission- and transition-probability matrices which can then be used as the input for an HMM. We apply the DEDICOM method to the CONLL corpus (CONLL 2000) and compare the output of DEDICOM to the part-of-speech tags given in the corpus, and find that the correlation (almost 0.5) is quite high. Using DEDICOM, we also estimate part-of-speech ambiguity for each term, and find that these estimates correlate highly with part-of-speech ambiguity as measured in the original corpus (around 0.88). Finally, we show how the output of DEDICOM can be evaluated and compared against the more familiar output of supervised HMM-based tagging.

  9. Geographical Topics Learning of Geo-Tagged Social Images.

    Science.gov (United States)

    Zhang, Xiaoming; Ji, Shufan; Wang, Senzhang; Li, Zhoujun; Lv, Xueqiang

    2016-03-01

    With the availability of cheap location sensors, geotagging of images in online social media is very popular. With a large amount of geo-tagged social images, it is interesting to study how these images are shared across geographical regions and how the geographical language characteristics and vision patterns are distributed across different regions. Unlike textual document, geo-tagged social image contains multiple types of content, i.e., textual description, visual content, and geographical information. Existing approaches usually mine geographical characteristics using a subset of multiple types of image contents or combining those contents linearly, which ignore correlations between different types of contents, and their geographical distributions. Therefore, in this paper, we propose a novel method to discover geographical characteristics of geo-tagged social images using a geographical topic model called geographical topic model of social images (GTMSIs). GTMSI integrates multiple types of social image contents as well as the geographical distributions, in which image topics are modeled based on both vocabulary and visual features. In GTMSI, each region of the image would have its own topic distribution, and hence have its own language model and vision pattern. Experimental results show that our GTMSI could identify interesting topics and vision patterns, as well as provide location prediction and image tagging. PMID:25861092

  10. Query-Driven Approach to Face Clustering and Tagging.

    Science.gov (United States)

    Zhang, Liyan; Wang, Xikui; Kalashnikov, Dmitri V; Mehrotra, Sharad; Ramanan, Deva

    2016-10-01

    In the era of big data, a traditional offline setting to processing image data is simply not tenable. We simply do not have the computational power to process every image with every possible tag; moreover, we will not have the manpower to clean up the potentially noisy results. In this paper, we introduce a query-driven approach to visual tagging, focusing on the application of face tagging and clustering. We integrate active learning with query-driven probabilistic databases. Rather than asking a user to provide manual labels so as to minimize the uncertainty of labels (face tags) across the entire data set, we ask the user to provide labels that minimize the uncertainty of his/her query result (e.g., "How many times did Bob and Jim appear together?"). We use a data-driven Gaussian process model of facial appearance to write the probabilistic estimates of facial identity into a probabilistic database, which can then support inference through query answering. Importantly, the database is augmented with contextual constraints (faces in the same image cannot be the same identity, while faces in the same track must be identical). Experiments on the real-world photo collections demonstrate the effectiveness of the proposed method. PMID:27448352

  11. Job optimization in ATLAS TAG-based distributed analysis

    International Nuclear Information System (INIS)

    The ATLAS experiment is projected to collect over one billion events/year during the first few years of operation. The efficient selection of events for various physics analyses across all appropriate samples presents a significant technical challenge. ATLAS computing infrastructure leverages the Grid to tackle the analysis across large samples by organizing data into a hierarchical structure and exploiting distributed computing to churn through the computations. This includes events at different stages of processing: RAW, ESD (Event Summary Data), AOD (Analysis Object Data), DPD (Derived Physics Data). Event Level Metadata Tags (TAGs) contain information about each event stored using multiple technologies accessible by POOL and various web services. This allows users to apply selection cuts on quantities of interest across the entire sample to compile a subset of events that are appropriate for their analysis. This paper describes new methods for organizing jobs using the TAGs criteria to analyze ATLAS data. It further compares different access patterns to the event data and explores ways to partition the workload for event selection and analysis. Here analysis is defined as a broader set of event processing tasks including event selection and reduction operations ('skimming', 'slimming' and 'thinning') as well as DPD making. Specifically it compares analysis with direct access to the events (AOD and ESD data) to access mediated by different TAG-based event selections. We then compare different ways of splitting the processing to maximize performance.

  12. Manifolds with integrable affine shape operator

    Directory of Open Access Journals (Sweden)

    Daniel A. Joaquín

    2005-05-01

    Full Text Available This work establishes the conditions for the existence of vector fields with the property that theirs covariant derivative, with respect to the affine normal connection, be the affine shape operatorS in hypersurfaces. Some results are obtained from this property and, in particular, for some kind of affine decomposable hypersurfaces we explicitely get the actual vector fields.

  13. Production of N-acetyl-D-neuraminic acid using two sequential enzymes overexpressed as double-tagged fusion proteins

    Directory of Open Access Journals (Sweden)

    Cheng Chung-Hsien

    2009-07-01

    Full Text Available Abstract Background Two sequential enzymes in the production of sialic acids, N-acetyl-D-glucosamine 2-epimerase (GlcNAc 2-epimerase and N-acetyl-D-neuraminic acid aldolase (Neu5Ac aldolase, were overexpressed as double-tagged gene fusions. Both were tagged with glutathione S-transferase (GST at the N-terminus, but at the C-terminus, one was tagged with five contiguous aspartate residues (5D, and the other with five contiguous arginine residues (5R. Results Both fusion proteins were overexpressed in Escherichia coli and retained enzymatic activity. The fusions were designed so their surfaces were charged under enzyme reaction conditions, which allowed isolation and immobilization in a single step, through a simple capture with either an anionic or a cationic exchanger (Sepharose Q or Sepharose SP that electrostatically bound the 5D or 5R tag. The introduction of double tags only marginally altered the affinity of the enzymes for their substrates, and the double-tagged proteins were enzymatically active in both soluble and immobilized forms. Combined use of the fusion proteins led to the production of N-acetyl-D-neuraminic acid (Neu5Ac from N-acetyl-D-glucosamine (GlcNAc. Conclusion Double-tagged gene fusions were overexpressed to yield two enzymes that perform sequential steps in sialic acid synthesis. The proteins were easily immobilized via ionic tags onto ionic exchange resins and could thus be purified by direct capture from crude protein extracts. The immobilized, double-tagged proteins were effective for one-pot enzymatic production of sialic acid.

  14. Pop-up Archival Transmitting (PAT) fish tag data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The cooperative tagging center (CTC) began deploying electronic tags in 2002. To date over 300 tags have been deployed. The following species have been monitored:...

  15. Evolutionary Optimization of Network Structures using Informative Genotype Tag

    Science.gov (United States)

    Ando, Shin; Iba, Hitoshi

    Evolutionary computation has been applied to numerous design tasks, including design of electric circuits, neural networks, and genetic circuits. Though it is a very effective solution for optimizing network structures, genetic algorithm faces many difficulties, often referred to as the permutation problems, when both topologies and the weights of the network are the target of optimization. We propose a new crossover method used in conjunction with a genotype with information tags. The information tags allow GA to recognize and preserve the common structure of parent chromosomes during genetic crossover. The method is implemented along with subpopulating strategies to make the parallel evolution of network topology and weights feasible and efficient. The proposed method is evaluated on a few typical and practical problems, and shows improvement from conventional methodologies and genotypes.

  16. Analyzing Tag Distributions in Folksonomies for Resource Classification

    OpenAIRE

    Zubiaga, Arkaitz; Martínez, Raquel; Fresno, Víctor

    2012-01-01

    Recent research has shown the usefulness of social tags as a data source to feed resource classification. Little is known about the effect of settings on folksonomies created on social tagging systems. In this work, we consider the settings of social tagging systems to further understand tag distributions in folksonomies. We analyze in depth the tag distributions on three large-scale social tagging datasets, and analyze the effect on a resource classification task. To this end, we study the a...

  17. The Influences of Online Cultural Capital on Social Tagging Behavior

    OpenAIRE

    Yi-Fan Chen; Chi-Shiou Lin

    2012-01-01

    This study examines the influences of online cultural capital on social tagging behavior in Delicious.com. The researchers identified three online cultural capital-related variables (understanding of social tagging, understanding of Delicious’ social functionalities, and quantity of tags and bookmarks) via factor analysis of a survey dataset and analyzed their influences on tagging motivations (information organization-oriented vs. social-oriented) and tagging strategies (object-based tagging...

  18. Folksonomy-based tag recommendation for online audio clip sharing

    OpenAIRE

    Font, Frederic; Serr?? Juli??, Joan; Serra, Xavier

    2012-01-01

    Collaborative tagging has emerged as an efficient way to semantically describe online resources shared by a community of users. However, tag descriptions present some drawbacks such as tag scarcity or concept inconsistencies. In these situations, tag recommendation strategies can help users in adding meaningful tags to the resources being described. Freesound is an online audio clip sharing site that uses collaborative tagging to describe a collection of more than 140,...

  19. Satellite tagging and biopsy sampling of killer whales at subantarctic Marion Island: effectiveness, immediate reactions and long-term responses.

    Directory of Open Access Journals (Sweden)

    Ryan R Reisinger

    Full Text Available Remote tissue biopsy sampling and satellite tagging are becoming widely used in large marine vertebrate studies because they allow the collection of a diverse suite of otherwise difficult-to-obtain data which are critical in understanding the ecology of these species and to their conservation and management. Researchers must carefully consider their methods not only from an animal welfare perspective, but also to ensure the scientific rigour and validity of their results. We report methods for shore-based, remote biopsy sampling and satellite tagging of killer whales Orcinus orca at Subantarctic Marion Island. The performance of these methods is critically assessed using 1 the attachment duration of low-impact minimally percutaneous satellite tags; 2 the immediate behavioural reactions of animals to biopsy sampling and satellite tagging; 3 the effect of researcher experience on biopsy sampling and satellite tagging; and 4 the mid- (1 month and long- (24 month term behavioural consequences. To study mid- and long-term behavioural changes we used multievent capture-recapture models that accommodate imperfect detection and individual heterogeneity. We made 72 biopsy sampling attempts (resulting in 32 tissue samples and 37 satellite tagging attempts (deploying 19 tags. Biopsy sampling success rates were low (43%, but tagging rates were high with improved tag designs (86%. The improved tags remained attached for 26±14 days (mean ± SD. Individuals most often showed no reaction when attempts missed (66% and a slight reaction-defined as a slight flinch, slight shake, short acceleration, or immediate dive-when hit (54%. Severe immediate reactions were never observed. Hit or miss and age-sex class were important predictors of the reaction, but the method (tag or biopsy was unimportant. Multievent trap-dependence modelling revealed considerable variation in individual sighting patterns; however, there were no significant mid- or long-term changes

  20. Novel Use of PIT Tags in Sea Cucumbers: Promising Results with the Commercial Species Cucumaria frondosa.

    Science.gov (United States)

    Gianasi, Bruno L; Verkaik, Katie; Hamel, Jean-François; Mercier, Annie

    2015-01-01

    The lack of a reliable and innocuous mark-recapture method has limited studies that would provide essential information for the management of commercial sea cucumbers. Tagging sea cucumbers is notoriously difficult because of their plastic nature and autolysis capacities. The markers that have so far been tested, mainly on or through the body wall, were either lost rapidly or had major drawbacks (e.g. suitable only for batch identification, requiring complex analysis, causing infections, necrosis, behavioural changes and mortality). The present study explored the efficacy of passive integrated transponder (PIT) tags for individually marking sea cucumbers by assessing retention rates and long-term side effects of tags inserted in previously unstudied tissues/organs. Individuals of the species Cucumaria frondosa were tagged in the body wall, aquapharyngeal bulb and at the base of the oral tentacles. They were monitored closely for evidence of stress, infection, change in feeding and spawning behaviour and tag retention rate. Implanting the tag in an oral tentacle to reach the hydrovascular system of the aquapharyngeal bulb achieved the best retention rates in full-size individuals: from a maximum of 92% after 30 days to 68% at the end of the experimental period (300 days). Efficacy was lower in smaller individuals (84% after 30 d and 42% after 300 d). Following a slight increase in cloacal movements for 15 h post tagging, no side effect was noted in sea cucumbers tagged in the aquapharyngeal bulb via the tentacles. Feeding and spawning behaviours were not affected and no signs of infections or abnormal cell development in the vicinity of the tags were observed. This study indicates that marking sea cucumbers with 8.2 mm long PIT tags implanted via the oral tentacle is an effective technique, yielding relatively high retention rates over long periods without any detectable physiological or behavioural effects. PMID:26011165