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Sample records for determine cleavage-site recognition

  1. Analysis of eukaryotic topoisomerase II cleavage sites in the presence of the quinolone CP-115,953 reveals drug-dependent and -independent recognition elements.

    PubMed

    Spitzner, J R; Chung, I K; Gootz, T D; McGuirk, P R; Muller, M T

    1995-08-01

    The quinolone derivative CP-115,953 [6,8-difluoro-7-(4-hydroxyphenyl)-1-cyclopropyl-4-quinolone-3-carboxylic acid] has been shown to induce eukaryotic topoisomerase II-mediated breaks in DNA, producing cleavage patterns that are distinct from those induced by the anticancer drugs amsacrine, etoposide, and teniposide. High levels of the quinolone have been found to inhibit topoisomerase II activity via an interaction with the enzyme and not by DNA unwinding. Topoisomerase II cleavage sites were analyzed on nine DNA fragments, and 85 quinolone-induced sites were sequenced, as well as 86 amsacrine and 134 teniposide sites. A consensus sequence was derived for the quinolone sites that is different from those reported for other drugs; however, because topoisomerase II cleavage sites are double-stranded but not palindromic, different consensus sequences are not easily compared. For this reason, a new, double-stranded, consensus sequence method, the "unique-base analysis," was developed; this was applied to the quinolone sites as well as six other large sets of topoisomerase II sites determined in the absence or presence of drugs. For each of the seven sets of sites, conserved bases were found in the 16-base region spanning positions -6 to +10, relative to the enzyme cleavage site (DNA breakage between -1 and +1). The conserved bases were virtually identical in the regions flanking the cleavage site for all seven data sets. In contrast, the base preferences identified proximal to the cleavage sites were unique to the drug tested. These observations suggest that the selection of cleavage sites by topoisomerase II involves both enzyme-dependent and drug-dependent recognition elements. The single most preferred base in the quinolone sites was a cytosine at -1; the same preference was found with teniposide, and 60 of the 85 quinolone sites co-localized with teniposide sites.

  2. The recognition of DNA cleavage sites by porcine spleen topoisomerase II.

    PubMed

    Huang, H W; Juang, J K; Liu, H J

    1992-02-11

    The cutting sites specificity of topoisomerase II from porcine spleen were determined by a modified Sanger's DNA sequencing method. The topoisomerase II prefers to cut DNA at the 3' side of A and leave 5' protruding end with two staggering bases. Through the free energy analysis for DNA duplex, we also found that the topoisomerase II seemed cut DNA preferably at energetically unstable regions. So it is concluded that the specific DNA cutting by porcine spleen topoisomerase II has two structural recognition factors: one is to localize around the energetically unstable region and another is to act at the 3' side of A base.

  3. Determination of the Proteolytic Cleavage Sites of the Amyloid Precursor-Like Protein 2 by the Proteases ADAM10, BACE1 and γ-Secretase

    PubMed Central

    Hogl, Sebastian; Kuhn, Peer-Hendrik; Colombo, Alessio; Lichtenthaler, Stefan F.

    2011-01-01

    Regulated intramembrane proteolysis of the amyloid precursor protein (APP) by the protease activities α-, β- and γ-secretase controls the generation of the neurotoxic amyloid β peptide. APLP2, the amyloid precursor-like protein 2, is a homolog of APP, which shows functional overlap with APP, but lacks an amyloid β domain. Compared to APP, less is known about the proteolytic processing of APLP2, in particular in neurons, and the cleavage sites have not yet been determined. APLP2 is cleaved by the β-secretase BACE1 and additionally by an α-secretase activity. The two metalloproteases ADAM10 and ADAM17 have been suggested as candidate APLP2 α-secretases in cell lines. Here, we used RNA interference and found that ADAM10, but not ADAM17, is required for the constitutive α-secretase cleavage of APLP2 in HEK293 and SH-SY5Y cells. Likewise, in primary murine neurons knock-down of ADAM10 suppressed APLP2 α-secretase cleavage. Using mass spectrometry we determined the proteolytic cleavage sites in the APLP2 sequence. ADAM10 was found to cleave APLP2 after arginine 670, whereas BACE1 cleaves after leucine 659. Both cleavage sites are located in close proximity to the membrane. γ-secretase cleavage was found to occur at different peptide bonds between alanine 694 and valine 700, which is close to the N-terminus of the predicted APLP2 transmembrane domain. Determination of the APLP2 cleavage sites enables functional studies of the different APLP2 ectodomain fragments and the production of cleavage-site specific antibodies for APLP2, which may be used for biomarker development. PMID:21695060

  4. Predictions of Cleavability of Calpain Proteolysis by Quantitative Structure-Activity Relationship Analysis Using Newly Determined Cleavage Sites and Catalytic Efficiencies of an Oligopeptide Array*

    PubMed Central

    Shinkai-Ouchi, Fumiko; Koyama, Suguru; Ono, Yasuko; Hata, Shoji; Ojima, Koichi; Shindo, Mayumi; duVerle, David; Ueno, Mika; Kitamura, Fujiko; Doi, Naoko; Takigawa, Ichigaku; Mamitsuka, Hiroshi; Sorimachi, Hiroyuki

    2016-01-01

    Calpains are intracellular Ca2+-regulated cysteine proteases that are essential for various cellular functions. Mammalian conventional calpains (calpain-1 and calpain-2) modulate the structure and function of their substrates by limited proteolysis. Thus, it is critically important to determine the site(s) in proteins at which calpains cleave. However, the calpains' substrate specificity remains unclear, because the amino acid (aa) sequences around their cleavage sites are very diverse. To clarify calpains' substrate specificities, 84 20-mer oligopeptides, corresponding to P10-P10′ of reported cleavage site sequences, were proteolyzed by calpains, and the catalytic efficiencies (kcat/Km) were globally determined by LC/MS. This analysis revealed 483 cleavage site sequences, including 360 novel ones. The kcat/Kms for 119 sites ranged from 12.5–1,710 M−1s−1. Although most sites were cleaved by both calpain-1 and −2 with a similar kcat/Km, sequence comparisons revealed distinct aa preferences at P9-P7/P2/P5′. The aa compositions of the novel sites were not statistically different from those of previously reported sites as a whole, suggesting calpains have a strict implicit rule for sequence specificity, and that the limited proteolysis of intact substrates is because of substrates' higher-order structures. Cleavage position frequencies indicated that longer sequences N-terminal to the cleavage site (P-sites) were preferred for proteolysis over C-terminal (P′-sites). Quantitative structure-activity relationship (QSAR) analyses using partial least-squares regression and >1,300 aa descriptors achieved kcat/Km prediction with r = 0.834, and binary-QSAR modeling attained an 87.5% positive prediction value for 132 reported calpain cleavage sites independent of our model construction. These results outperformed previous calpain cleavage predictors, and revealed the importance of the P2, P3′, and P4′ sites, and P1-P2 cooperativity. Furthermore, using our

  5. Determination of the protease cleavage site repertoire—The RNase H but not the RT domain is essential for foamy viral protease activity

    SciTech Connect

    Spannaus, Ralf; Bodem, Jochen

    2014-04-15

    In contrast to orthoretroviruses, the foamy virus protease is only active as a protease-reverse transcriptase fusion protein and requires viral RNA for activation. Maturation of foamy viral proteins seems to be restricted to a single cleavage site in Gag and Pol. We provide evidence that unprocessed Gag is required for optimal infectivity, which is unique among retroviruses. Analyses of the cleavage site sequences of the Gag and Pol cleavage sites revealed a high similarity compared to those of Lentiviruses. We show that positions P2' and P2 are invariant and that Gag and Pol cleavage sites are processed with similar efficiencies. The RNase H domain is essential for protease activity, but can functionally be substituted by RNase H domains of other retroviruses. Thus, the RNase H domain might be involved in the stabilization of the protease dimer, while the RT domain is essential for RNA dependent protease activation. - Highlights: • Unprocessed Gag is required for optimal infectivity of foamy viruses. • Positions P2 and P2' are invariant in the foamy viral cleavage sites. • The RNaseH domain is essential for protease activity. • The RNaseH domains of other retroviruses support foamy viral protease activity.

  6. Fluorescence Based Primer Extension Technique to Determine Transcriptional Starting Points and Cleavage Sites of RNases In Vivo

    PubMed Central

    Schuster, Christopher F.; Bertram, Ralph

    2014-01-01

    Fluorescence based primer extension (FPE) is a molecular method to determine transcriptional starting points or processing sites of RNA molecules. This is achieved by reverse transcription of the RNA of interest using specific fluorescently labeled primers and subsequent analysis of the resulting cDNA fragments by denaturing polyacrylamide gel electrophoresis. Simultaneously, a traditional Sanger sequencing reaction is run on the gel to map the ends of the cDNA fragments to their exact corresponding bases. In contrast to 5'-RACE (Rapid Amplification of cDNA Ends), where the product must be cloned and multiple candidates sequenced, the bulk of cDNA fragments generated by primer extension can be simultaneously detected in one gel run. In addition, the whole procedure (from reverse transcription to final analysis of the results) can be completed in one working day. By using fluorescently labeled primers, the use of hazardous radioactive isotope labeled reagents can be avoided and processing times are reduced as products can be detected during the electrophoresis procedure. In the following protocol, we describe an in vivo fluorescent primer extension method to reliably and rapidly detect the 5' ends of RNAs to deduce transcriptional starting points and RNA processing sites (e.g., by toxin-antitoxin system components) in S. aureus, E. coli and other bacteria. PMID:25406941

  7. Peptide bond cleavage site determination of novel proteolytic enzymes found in ROS 17/2.8 cell lysates.

    PubMed

    Guidon, P T; Perrin, D; Harrison, P

    1996-02-01

    We have identified proteolytic activities in the rat osteoblastic osteosarcoma cell line ROS 17/2.8 which are capable of cleaving a peptide substrate for protein kinase C-mediated phosphorylation (PSPKC, Pro-Leu-Ser-Arg-Thr-Leu-Ser-Val-Ala-Ala-Lys). Using polyacrylamide gel electrophoresis conditions similar to those used to resolve small molecular weight proteins, the peptide bonds of PSPKC which are cleaved by the proteolytic activities present in ROS 17/2.8 cell lysates have been determined. These activities cleave the Ser-Arg, Thr-Leu, and Ser-Val peptide bonds. To date, no proteolytic activities present in osteoblast cell lysates have been described with the aforementioned peptide bond specificities, suggesting that these activities are novel. The PSPKC-cleaved peptide fragment pattern generated was similar for several different osteoblast cell lysates. Lysates generated from different rat tissues were also able to cleave PSPKC, but the peptide fragment pattern generated by ROS 17/2.8 cell lysates appeared to be unique amongst these tissues.

  8. GPS-CCD: A Novel Computational Program for the Prediction of Calpain Cleavage Sites

    PubMed Central

    Gao, Xinjiao; Ma, Qian; Ren, Jian; Xue, Yu

    2011-01-01

    As one of the most essential post-translational modifications (PTMs) of proteins, proteolysis, especially calpain-mediated cleavage, plays an important role in many biological processes, including cell death/apoptosis, cytoskeletal remodeling, and the cell cycle. Experimental identification of calpain targets with bona fide cleavage sites is fundamental for dissecting the molecular mechanisms and biological roles of calpain cleavage. In contrast to time-consuming and labor-intensive experimental approaches, computational prediction of calpain cleavage sites might more cheaply and readily provide useful information for further experimental investigation. In this work, we constructed a novel software package of GPS-CCD (Calpain Cleavage Detector) for the prediction of calpain cleavage sites, with an accuracy of 89.98%, sensitivity of 60.87% and specificity of 90.07%. With this software, we annotated potential calpain cleavage sites for hundreds of calpain substrates, for which the exact cleavage sites had not been previously determined. In this regard, GPS-CCD 1.0 is considered to be a useful tool for experimentalists. The online service and local packages of GPS-CCD 1.0 were implemented in JAVA and are freely available at: http://ccd.biocuckoo.org/. PMID:21533053

  9. Signal peptide prediction based on analysis of experimentally verified cleavage sites

    PubMed Central

    Zhang, Zemin; Henzel, William J.

    2004-01-01

    A number of computational tools are available for detecting signal peptides, but their abilities to locate the signal peptide cleavage sites vary significantly and are often less than satisfactory. We characterized a set of 270 secreted recombinant human proteins by automated Edman analysis and used the verified cleavage sites to evaluate the success rate of a number of computational prediction programs. An examination of the frequency of amino acid in the N-terminal region of the data set showed a preference of proline and glutamine but a bias against tyrosine. The data set was compared to the SWISS-PROT database and revealed a high percentage of discrepancies with cleavage site annotations that were computationally generated. The best program for predicting signal sequences was found to be SignalP 2.0-NN with an accuracy of 78.1% for cleavage site recognition. The new data set can be utilized for refining prediction algorithms, and we have built an improved version of profile hidden Markov model for signal peptides based on the new data. PMID:15340161

  10. Proteomic identification of protease cleavage sites characterizes prime and non-prime specificity of cysteine cathepsins B, L, and S.

    PubMed

    Biniossek, Martin L; Nägler, Dorit K; Becker-Pauly, Christoph; Schilling, Oliver

    2011-12-02

    Cysteine cathepsins mediate proteome homeostasis and have pivotal functions in diseases such as cancer. To better understand substrate recognition by cathepsins B, L, and S, we applied proteomic identification of protease cleavage sites (PICS) for simultaneous profiling of prime and non-prime specificity. PICS profiling of cathepsin B endopeptidase specificity highlights strong selectivity for glycine in P3' due to an occluding loop blocking access to the primed subsites. In P1', cathepsin B has a partial preference for phenylalanine, which is not found for cathepsins L and S. Occurrence of P1' phenylalanine often coincides with aromatic residues in P2. For cathepsin L, PICS identifies 845 cleavage sites, representing the most comprehensive PICS profile to date. Cathepsin L specificity is dominated by the canonical preference for aromatic residues in P2 with limited contribution of prime-site selectivity determinants. Profiling of cathepsins B and L with a shorter incubation time (4 h instead of 16 h) did not reveal time-dependency of individual specificity determinants. Cathepsin S specificity was profiled at pH 6.0 and 7.5. The PICS profiles at both pH values display a high degree of similarity. Cathepsin S specificity is primarily guided by aliphatic residues in P2 with limited importance of prime-site residues.

  11. The VHSE-based prediction of proteasomal cleavage sites.

    PubMed

    Xie, Jiangan; Xu, Zhiling; Zhou, Shangbo; Pan, Xianchao; Cai, Shaoxi; Yang, Li; Mei, Hu

    2013-01-01

    Prediction of proteasomal cleavage sites has been a focus of computational biology. Up to date, the predictive methods are mostly based on nonlinear classifiers and variables with little physicochemical meanings. In this paper, the physicochemical properties of 14 residues both upstream and downstream of a cleavage site are characterized by VHSE (principal component score vector of hydrophobic, steric, and electronic properties) descriptors. Then, the resulting VHSE descriptors are employed to construct prediction models by support vector machine (SVM). For both in vivo and in vitro datasets, the performance of VHSE-based method is comparatively better than that of the well-known PAProC, MAPPP, and NetChop methods. The results reveal that the hydrophobic property of 10 residues both upstream and downstream of the cleavage site is a dominant factor affecting in vivo and in vitro cleavage specificities, followed by residue's electronic and steric properties. Furthermore, the difference in hydrophobic potential between residues flanking the cleavage site is proposed to favor substrate cleavages. Overall, the interpretable VHSE-based method provides a preferable way to predict proteasomal cleavage sites.

  12. Specific anti-integrase abzymes from HIV-infected patients: a comparison of the cleavage sites of intact globular HIV integrase and two 20-mer oligopeptides corresponding to its antigenic determinants.

    PubMed

    Odintsova, Elena S; Dmitrenok, Pavel S; Buneva, Valentina N; Nevinsky, Georgy A

    2013-03-01

    HIV-infected patients possess anti-integrase (IN) IgGs and IgMs that, after isolation by chromatography on IN-Sepharose, unlike canonical proteases, specifically hydrolyze only IN but not many other tested proteins. Hydrolysis of intact globular IN first leads to formation of many long fragments of protein, while its long incubation with anti-IN antibodies, especially in the case of abzymes (Abzs) with a high proteolytic activity, results in the formation of short and very short oligopeptides (OPs). To identify all sites of IgG-mediated proteolysis corresponding to known AGDs of integrase, we have used a combination of reverse-phase chromatography, matrix-assisted laser desorption/ionization spectrometry, and thin-layer chromatography to analyze the cleavage products of two 20-mer OPs corresponding to these AGDs. Both OPs contained 9-10 mainly clustered major, medium, and minor sites of cleavage. The main superficial cleavage sites of the AGDs in the intact IN and sites of partial or deep hydrolysis of the peptides analyzed do not coincide. The active sites of anti-IN Abzs are localized on their light chains, whereas the heavy chains are responsible for the affinity of protein substrates. Interactions of intact globular proteins with both light and heavy chains of Abzs provide high specificity of IN hydrolysis. The affinity of anti-IN Abzs for intact integrase was ~1000-fold higher than for the OPs. The data suggest that both OPs interact mainly with the light chains of different monoclonal Abzs of the total pool of IgGs, which possesses lower affinity for substrates; and therefore, depending on the oligopeptide sequences, their hydrolysis may be less specific and remarkably different in comparison with the cleavage of intact globular IN.

  13. Characterization of a Non-Canonical Signal Peptidase Cleavage Site in a Replication Protein from Tomato Ringspot Virus

    PubMed Central

    Wei, Ting; Chisholm, Joan

    2016-01-01

    The NTB-VPg polyprotein from tomato ringspot virus is an integral membrane replication protein associated with endoplasmic reticulum membranes. A signal peptidase (SPase) cleavage was previously detected in the C-terminal region of NTB-VPg downstream of a 14 amino acid (aa)-long hydrophobic region (termed TM2). However, the exact location of the cleavage site was not determined. Using in vitro translation assays, we show that the SPase cleavage site is conserved in the NTB-VPg protein from various ToRSV isolates, although the rate of cleavage varies from one isolate to another. Systematic site-directed mutagenesis of the NTB-VPg SPase cleavage sites of two ToRSV isolates allowed the identification of sequences that affect cleavage efficiency. We also present evidence that SPase cleavage in the ToRSV-Rasp2 isolate occurs within a GAAGG sequence likely after the AAG (GAAG/G). Mutation of a downstream MAAV sequence to AAAV resulted in SPase cleavage at both the natural GAAG/G and the mutated AAA/V sequences. Given that there is a distance of seven aa between the two cleavage sites, this indicates that there is flexibility in the positioning of the cleavage sites relative to the inner surface of the membrane and the SPase active site. SPase cleavage sites are typically located 3–7 aa downstream of the hydrophobic region. However, the NTB-VPg GAAG/G cleavage site is located 17 aa downstream of the TM2 hydrophobic region, highlighting unusual features of the NTB-VPg SPase cleavage site. A putative 11 aa-long amphipathic helix was identified immediately downstream of the TM2 region and five aa upstream of the GAAG/G cleavage site. Based on these results, we present an updated topology model in which the hydrophobic and amphipathic domains form a long tilted helix or a bent helix in the membrane lipid bilayer, with the downstream cleavage site(s) oriented parallel to the membrane inner surface. PMID:27589230

  14. 3C-like protease of rabbit hemorrhagic disease virus: identification of cleavage sites in the ORF1 polyprotein and analysis of cleavage specificity.

    PubMed Central

    Wirblich, C; Sibilia, M; Boniotti, M B; Rossi, C; Thiel, H J; Meyers, G

    1995-01-01

    Rabbit hemorrhagic disease virus, a positive-stranded RNA virus of the family Caliciviridae, encodes a trypsin-like cysteine protease as part of a large polyprotein. Upon expression in Escherichia coli, the protease releases itself from larger precursors by proteolytic cleavages at its N and C termini. Both cleavage sites were determined by N-terminal sequence analysis of the cleavage products. Cleavage at the N terminus of the protease occurred with high efficiency at an EG dipeptide at positions 1108 and 1109. Cleavage at the C terminus of the protease occurred with low efficiency at an ET dipeptide at positions 1251 and 1252. To study the cleavage specificity of the protease, amino acid substitutions were introduced at the P2, P1, and P1' positions at the cleavage site at the N-terminal boundary of the protease. This analysis showed that the amino acid at the P1 position is the most important determinant for substrate recognition. Only glutamic acid, glutamine, and aspartic acid were tolerated at this position. At the P1' position, glycine, serine, and alanine were the preferred substrates of the protease, but a number of amino acids with larger side chains were also tolerated. Substitutions at the P2 position had only little effect on the cleavage efficiency. Cell-free expression of the C-terminal half of the ORF1 polyprotein showed that the protease catalyzes cleavage at the junction of the RNA polymerase and the capsid protein. An EG dipeptide at positions 1767 and 1768 was identified as the putative cleavage site. Our data show that rabbit hemorrhagic disease virus encodes a trypsin-like cysteine protease that is similar to 3C proteases with regard to function and specificity but is more similar to 2A proteases with regard to size. PMID:7474137

  15. DNA translocation blockage, a general mechanism of cleavage site selection by type I restriction enzymes.

    PubMed Central

    Janscak, P; MacWilliams, M P; Sandmeier, U; Nagaraja, V; Bickle, T A

    1999-01-01

    Type I restriction enzymes bind to a specific DNA sequence and subsequently translocate DNA past the complex to reach a non-specific cleavage site. We have examined several potential blocks to DNA translocation, such as positive supercoiling or a Holliday junction, for their ability to trigger DNA cleavage by type I restriction enzymes. Introduction of positive supercoiling into plasmid DNA did not have a significant effect on the rate of DNA cleavage by EcoAI endonuclease nor on the enzyme's ability to select cleavage sites randomly throughout the DNA molecule. Thus, positive supercoiling does not prevent DNA translocation. EcoR124II endonuclease cleaved DNA at Holliday junctions present on both linear and negatively supercoiled substrates. The latter substrate was cleaved by a single enzyme molecule at two sites, one on either side of the junction, consistent with a bi-directional translocation model. Linear DNA molecules with two recognition sites for endonucleases from different type I families were cut between the sites when both enzymes were added simultaneously but not when a single enzyme was added. We propose that type I restriction enzymes can track along a DNA substrate irrespective of its topology and cleave DNA at any barrier that is able to halt the translocation process. PMID:10228175

  16. Identification of TMPRSS6 cleavage sites of hemojuvelin

    PubMed Central

    Rausa, Marco; Ghitti, Michela; Pagani, Alessia; Nai, Antonella; Campanella, Alessandro; Musco, Giovanna; Camaschella, Clara; Silvestri, Laura

    2015-01-01

    Hemojuvelin (HJV), the coreceptor of the BMP-SMAD pathway that up-regulates hepcidin transcription, is a repulsive guidance molecule (RGMc) which undergoes a complex intracellular processing. Following autoproteolysis, it is exported to the cell surface both as a full-length and a heterodimeric protein. In vitro membrane HJV (m-HJV) is cleaved by the transmembrane serine protease TMPRSS6 to attenuate signalling and to inhibit hepcidin expression. In this study, we investigated the number and position of HJV cleavage sites by mutagenizing arginine residues (R), potential TMPRSS6 targets, to alanine (A). We analysed translation and membrane expression of HJV R mutants and the pattern of fragments they release in the culture media in the presence of TMPRSS6. Abnormal fragments were observed for mutants at arginine 121, 176, 218, 288 and 326. Considering that all variants, except HJVR121A, lack autoproteolytic activity and some (HJVR176A and HJVR288A) are expressed at reduced levels on cell surface, we identified the fragments originating from either full-length or heterodimeric proteins and defined the residues 121 and 326 as the TMPRSS6 cleavage sites in both isoforms. Using the N-terminal FLAG-tagged HJV, we showed that residue 121 is critical also in the rearrangement of the N-terminal heterodimeric HJV. Exploiting the recently reported RGMb crystallographic structure, we generated a model of HJV that was used as input structure for all-atoms molecular dynamics simulation in explicit solvent. As assessed by in silico studies, we concluded that some arginines in the von Willebrand domain appear TMPRSS6 insensitive, likely because of partial protein structure destabilization. PMID:25704252

  17. GraBCas: a bioinformatics tool for score-based prediction of Caspase- and Granzyme B-cleavage sites in protein sequences

    PubMed Central

    Backes, Christina; Kuentzer, Jan; Lenhof, Hans-Peter; Comtesse, Nicole; Meese, Eckart

    2005-01-01

    Caspases and granzyme B are proteases that share the primary specificity to cleave at the carboxyl terminal of aspartate residues in their substrates. Both, caspases and granzyme B are enzymes that are involved in fundamental cellular processes and play a central role in apoptotic cell death. Although various targets are described, many substrates still await identification and many cleavage sites of known substrates are not identified or experimentally verified. A more comprehensive knowledge of caspase and granzyme B substrates is essential to understand the biological roles of these enzymes in more detail. The relatively high variability in cleavage site recognition sequence often complicates the identification of cleavage sites. As of yet there is no software available that allows identification of caspase and/or granzyme with cleavage sites differing from the consensus sequence. Here, we present a bioinformatics tool ‘GraBCas’ that provides score-based prediction of potential cleavage sites for the caspases 1–9 and granzyme B including an estimation of the fragment size. We tested GraBCas on already known substrates and showed its usefulness for protein sequence analysis. GraBCas is available at . PMID:15980455

  18. Predicting caspase substrate cleavage sites based on a hybrid SVM-PSSM method.

    PubMed

    Li, Dandan; Jiang, Zhenran; Yu, Weiming; Du, Lei

    2010-12-01

    Caspases play an important role in many critical non-apoptosis processes by cleaving relevant substrates at cleavage sites. Identification of caspase substrate cleavage sites is the key to understand these processes. This paper proposes a hybrid method using support vector machine (SVM) in conjunction with position specific scoring matrices (PSSM) for caspase substrate cleavage sites prediction. Three encoding schemes including orthonormal binary encoding, BLOSUM62 matrix profile and PSSM profile of neighborhood surrounding the substrate cleavage sites were regarded as the input of SVM. The 10-fold cross validation results demonstrate that the SVM-PSSM method performs well with an overall accuracy of 97.619% on a larger dataset.

  19. Simulative and experimental investigation on the cleavage site that generates the soluble human LOX-1.

    PubMed

    Biocca, Silvia; Arcangeli, Tania; Tagliaferri, Elisa; Testa, Barbara; Vindigni, Giulia; Oteri, Francesco; Giorgi, Alessandra; Iacovelli, Federico; Novelli, Giuseppe; Desideri, Alessandro; Falconi, Mattia

    2013-12-01

    Lectin-like oxidized low-density lipoprotein receptor-1 (LOX-1) is a scavenger receptor that mediates the recognition, the binding and internalization of ox-LDL. A truncated soluble form of LOX-1 (sLOX-1) has been identified that, at elevated levels, has been associated to acute coronary syndrome. Human sLOX-1 is the extracellular part of membrane LOX-1 which is cleaved in the NECK domain with a mechanism that has not yet been identified. Purification of human sLOX-1 has been carried out to experimentally identify the cleavage site region within the NECK domain. Molecular modelling and classical molecular dynamics simulation techniques have been used to characterize the structural and dynamical properties of the LOX-1 NECK domain in the presence and absence of the CTLD recognition region, taking into account the obtained proteolysis results. The simulative data indicate that the NECK domain is stabilized by the coiled-coil heptad repeat motif along the simulations, shows a definite flexibility pattern and is characterized by specific electrostatic potentials. The detection of a mobile inter-helix space suggests an explanation for the in vivo susceptibility of the NECK domain to the proteolytic cleavage, validating the assumption that the NECK domain sequence is composed of a coiled-coil motif destabilized in specific regions of functional significance.

  20. Evolutionarily distinct bacteriophage endolysins featuring conserved peptidoglycan cleavage sites protect mice from MRSA infection

    PubMed Central

    Schmelcher, Mathias; Shen, Yang; Nelson, Daniel C.; Eugster, Marcel R.; Eichenseher, Fritz; Hanke, Daniela C.; Loessner, Martin J.; Dong, Shengli; Pritchard, David G.; Lee, Jean C.; Becker, Stephen C.; Foster-Frey, Juli; Donovan, David M.

    2015-01-01

    Objectives In the light of increasing drug resistance in Staphylococcus aureus, bacteriophage endolysins [peptidoglycan hydrolases (PGHs)] have been suggested as promising antimicrobial agents. The aim of this study was to determine the antimicrobial activity of nine enzymes representing unique homology groups within a diverse class of staphylococcal PGHs. Methods PGHs were recombinantly expressed, purified and tested for staphylolytic activity in multiple in vitro assays (zymogram, turbidity reduction assay and plate lysis) and against a comprehensive set of strains (S. aureus and CoNS). PGH cut sites in the staphylococcal peptidoglycan were determined by biochemical assays (Park–Johnson and Ghuysen procedures) and MS analysis. The enzymes were tested for their ability to eradicate static S. aureus biofilms and compared for their efficacy against systemic MRSA infection in a mouse model. Results Despite similar modular architectures and unexpectedly conserved cleavage sites in the peptidoglycan (conferred by evolutionarily divergent catalytic domains), the enzymes displayed varying degrees of in vitro lytic activity against numerous staphylococcal strains, including cell surface mutants and drug-resistant strains, and proved effective against static biofilms. In a mouse model of systemic MRSA infection, six PGHs provided 100% protection from death, with animals being free of clinical signs at the end of the experiment. Conclusions Our results corroborate the high potential of PGHs for treatment of S. aureus infections and reveal unique antimicrobial and biochemical properties of the different enzymes, suggesting a high diversity of potential applications despite highly conserved peptidoglycan target sites. PMID:25630640

  1. Cleavage Site Localization Differentially Controls Interleukin-6 Receptor Proteolysis by ADAM10 and ADAM17

    PubMed Central

    Riethmueller, Steffen; Ehlers, Johanna C.; Lokau, Juliane; Düsterhöft, Stefan; Knittler, Katharina; Dombrowsky, Gregor; Grötzinger, Joachim; Rabe, Björn; Rose-John, Stefan; Garbers, Christoph

    2016-01-01

    Limited proteolysis of the Interleukin-6 Receptor (IL-6R) leads to the release of the IL-6R ectodomain. Binding of the cytokine IL-6 to the soluble IL-6R (sIL-6R) results in an agonistic IL-6/sIL-6R complex, which activates cells via gp130 irrespective of whether the cells express the IL-6R itself. This signaling pathway has been termed trans-signaling and is thought to mainly account for the pro-inflammatory properties of IL-6. A Disintegrin And Metalloprotease 10 (ADAM10) and ADAM17 are the major proteases that cleave the IL-6R. We have previously shown that deletion of a ten amino acid long stretch within the stalk region including the cleavage site prevents ADAM17-mediated cleavage, whereas the receptor retained its full biological activity. In the present study, we show that deletion of a triple serine (3S) motif (Ser-359 to Ser-361) adjacent to the cleavage site is sufficient to prevent IL-6R cleavage by ADAM17, but not ADAM10. We find that the impaired shedding is caused by the reduced distance between the cleavage site and the plasma membrane. Positioning of the cleavage site in greater distance towards the plasma membrane abrogates ADAM17-mediated shedding and reveals a novel cleavage site of ADAM10. Our findings underline functional differences in IL-6R proteolysis by ADAM10 and ADAM17. PMID:27151651

  2. Genetic Predisposition To Acquire a Polybasic Cleavage Site for Highly Pathogenic Avian Influenza Virus Hemagglutinin

    PubMed Central

    Nao, Naganori; Yamagishi, Junya; Miyamoto, Hiroko; Igarashi, Manabu; Manzoor, Rashid; Ohnuma, Aiko; Tsuda, Yoshimi; Furuyama, Wakako; Shigeno, Asako; Kajihara, Masahiro; Kishida, Noriko; Yoshida, Reiko

    2017-01-01

    ABSTRACT Highly pathogenic avian influenza viruses with H5 and H7 hemagglutinin (HA) subtypes evolve from low-pathogenic precursors through the acquisition of multiple basic amino acid residues at the HA cleavage site. Although this mechanism has been observed to occur naturally only in these HA subtypes, little is known about the genetic basis for the acquisition of the polybasic HA cleavage site. Here we show that consecutive adenine residues and a stem-loop structure, which are frequently found in the viral RNA region encoding amino acids around the cleavage site of low-pathogenic H5 and H7 viruses isolated from waterfowl reservoirs, are important for nucleotide insertions into this RNA region. A reporter assay to detect nontemplated nucleotide insertions and deep-sequencing analysis of viral RNAs revealed that an increased number of adenine residues and enlarged stem-loop structure in the RNA region accelerated the multiple adenine and/or guanine insertions required to create codons for basic amino acids. Interestingly, nucleotide insertions associated with the HA cleavage site motif were not observed principally in the viral RNA of other subtypes tested (H1, H2, H3, and H4). Our findings suggest that the RNA editing-like activity is the key mechanism for nucleotide insertions, providing a clue as to why the acquisition of the polybasic HA cleavage site is restricted to the particular HA subtypes. PMID:28196963

  3. Amino acid substitutions in the poliovirus maturation cleavage site affect assembly and result in accumulation of provirions.

    PubMed Central

    Ansardi, D C; Morrow, C D

    1995-01-01

    The assembly of infectious poliovirus virions requires a proteolytic cleavage between an asparagine-serine amino acid pair (the maturation cleavage site) in VP0 after encapsidation of the genomic RNA. In this study, we have investigated the effects that mutations in the maturation cleavage site have on P1 polyprotein processing, assembly of subviral intermediates, and encapsidation of the viral genomic RNA. We have made mutations in the maturation cleavage site which change the asparagine-serine amino acid pair to either glutamine-glycine or threonine-serine. The mutations were created by site-directed mutagenesis of P1 cDNAs which were recombined into wild-type vaccinia virus to generate recombinant vaccinia viruses. The P1 polyproteins expressed from the recombinant vaccinia viruses were analyzed for proteolytic processing and assembly defects in cells coinfected with a recombinant vaccinia virus (VV-P3) that expresses the poliovirus 3CD protease. A trans complementation system using a defective poliovirus genome was utilized to assess the capacity of the mutant P1 proteins to encapsidate genomic RNA (D. C. Ansardi, D. C. Porter, and C. D. Morrow, J. Virol. 67:3684-3690, 1993). The mutant P1 proteins containing the glutamine-glycine amino acid pair (VP4-QG) and the threonine-serine pair (VP4-TS) were processed by 3CD provided in trans from VV-P3. The processed capsid proteins VP0, VP3, and VP1 derived from the mutant precursor VP4-QG were unstable and failed to assemble into subviral structures in cells coinfected with VV-P3. However, the capsid proteins derived from VP4-QG did assemble into empty-capsid-like structures in the presence of the defective poliovirus genome. In contrast, the capsid proteins derived from processing of the VP4-TS mutant assembled into subviral intermediates both in the presence and in the absence of the defective genome RNA. By a sedimentation analysis, we determined that the capsid proteins derived from the VP4-TS precursor

  4. Molecular pathogenesis of H5 highly pathogenic avian influenza: the role of the haemagglutinin cleavage site motif

    PubMed Central

    Luczo, Jasmina M.; Stambas, John; Durr, Peter A.; Michalski, Wojtek P.

    2015-01-01

    Summary The emergence of H5N1 highly pathogenic avian influenza has caused a heavy socio‐economic burden through culling of poultry to minimise human and livestock infection. Although human infections with H5N1 have to date been limited, concerns for the pandemic potential of this zoonotic virus have been greatly intensified following experimental evidence of aerosol transmission of H5N1 viruses in a mammalian infection model. In this review, we discuss the dominance of the haemagglutinin cleavage site motif as a pathogenicity determinant, the host‐pathogen molecular interactions driving cleavage activation, reverse genetics manipulations and identification of residues key to haemagglutinin cleavage site functionality and the mechanisms of cell and tissue damage during H5N1 infection. We specifically focus on the disease in chickens, as it is in this species that high pathogenicity frequently evolves and from which transmission to the human population occurs. With >75% of emerging infectious diseases being of zoonotic origin, it is necessary to understand pathogenesis in the primary host to explain spillover events into the human population. © 2015 The Authors. Reviews in Medical Virology published by John Wiley & Sons Ltd. PMID:26467906

  5. Genetic Predisposition To Acquire a Polybasic Cleavage Site for Highly Pathogenic Avian Influenza Virus Hemagglutinin.

    PubMed

    Nao, Naganori; Yamagishi, Junya; Miyamoto, Hiroko; Igarashi, Manabu; Manzoor, Rashid; Ohnuma, Aiko; Tsuda, Yoshimi; Furuyama, Wakako; Shigeno, Asako; Kajihara, Masahiro; Kishida, Noriko; Yoshida, Reiko; Takada, Ayato

    2017-02-14

    Highly pathogenic avian influenza viruses with H5 and H7 hemagglutinin (HA) subtypes evolve from low-pathogenic precursors through the acquisition of multiple basic amino acid residues at the HA cleavage site. Although this mechanism has been observed to occur naturally only in these HA subtypes, little is known about the genetic basis for the acquisition of the polybasic HA cleavage site. Here we show that consecutive adenine residues and a stem-loop structure, which are frequently found in the viral RNA region encoding amino acids around the cleavage site of low-pathogenic H5 and H7 viruses isolated from waterfowl reservoirs, are important for nucleotide insertions into this RNA region. A reporter assay to detect nontemplated nucleotide insertions and deep-sequencing analysis of viral RNAs revealed that an increased number of adenine residues and enlarged stem-loop structure in the RNA region accelerated the multiple adenine and/or guanine insertions required to create codons for basic amino acids. Interestingly, nucleotide insertions associated with the HA cleavage site motif were not observed principally in the viral RNA of other subtypes tested (H1, H2, H3, and H4). Our findings suggest that the RNA editing-like activity is the key mechanism for nucleotide insertions, providing a clue as to why the acquisition of the polybasic HA cleavage site is restricted to the particular HA subtypes.IMPORTANCE Influenza A viruses are divided into subtypes based on the antigenicity of the viral surface glycoproteins hemagglutinin (HA) and neuraminidase. Of the 16 HA subtypes (H1 to -16) maintained in waterfowl reservoirs of influenza A viruses, H5 and H7 viruses often become highly pathogenic through the acquisition of multiple basic amino acid residues at the HA cleavage site. Although this mechanism has been known since the 1980s, the genetic basis for nucleotide insertions has remained unclear. This study shows the potential role of the viral RNA secondary structure for

  6. PROSPER: An Integrated Feature-Based Tool for Predicting Protease Substrate Cleavage Sites

    PubMed Central

    Perry, Andrew J.; Akutsu, Tatsuya; Webb, Geoffrey I.; Whisstock, James C.; Pike, Robert N.

    2012-01-01

    The ability to catalytically cleave protein substrates after synthesis is fundamental for all forms of life. Accordingly, site-specific proteolysis is one of the most important post-translational modifications. The key to understanding the physiological role of a protease is to identify its natural substrate(s). Knowledge of the substrate specificity of a protease can dramatically improve our ability to predict its target protein substrates, but this information must be utilized in an effective manner in order to efficiently identify protein substrates by in silico approaches. To address this problem, we present PROSPER, an integrated feature-based server for in silico identification of protease substrates and their cleavage sites for twenty-four different proteases. PROSPER utilizes established specificity information for these proteases (derived from the MEROPS database) with a machine learning approach to predict protease cleavage sites by using different, but complementary sequence and structure characteristics. Features used by PROSPER include local amino acid sequence profile, predicted secondary structure, solvent accessibility and predicted native disorder. Thus, for proteases with known amino acid specificity, PROSPER provides a convenient, pre-prepared tool for use in identifying protein substrates for the enzymes. Systematic prediction analysis for the twenty-four proteases thus far included in the database revealed that the features we have included in the tool strongly improve performance in terms of cleavage site prediction, as evidenced by their contribution to performance improvement in terms of identifying known cleavage sites in substrates for these enzymes. In comparison with two state-of-the-art prediction tools, PoPS and SitePrediction, PROSPER achieves greater accuracy and coverage. To our knowledge, PROSPER is the first comprehensive server capable of predicting cleavage sites of multiple proteases within a single substrate sequence using

  7. Evaluation of fusion protein cleavage site sequences of Newcastle disease virus in genotype matched vaccines

    PubMed Central

    Kim, Shin-Hee; Chen, Zongyan; Yoshida, Asuka; Paldurai, Anandan; Xiao, Sa; Samal, Siba K.

    2017-01-01

    Newcastle disease virus (NDV) causes a devastating poultry disease worldwide. Frequent outbreaks of NDV in chickens vaccinated with conventional live vaccines suggest a need to develop new vaccines that are genetically matched against circulating NDV strains, such as the genotype V virulent strains currently circulating in Mexico and Central America. In this study, a reverse genetics system was developed for the virulent NDV strain Mexico/01/10 strain and used to generate highly attenuated vaccine candidates by individually modifying the cleavage site sequence of fusion (F) protein. The cleavage site sequence of parental virus was individually changed to those of the avirulent NDV strain LaSota and other serotypes of avian paramyxoviruses (APMV serotype-2, -3, -4, -6, -7, -8, and -9). In general, these mutations affected cell-to-cell fusion activity in vitro and the efficiency of the F protein cleavage and made recombinant Mexico/01/10 (rMex) virus highly attenuated in chickens. When chickens were immunized with the rMex mutant viruses and challenged with the virulent parent virus, there was reduced challenge virus shedding compared to birds immunized with the heterologous vaccine strain LaSota. Among the vaccine candidates, rMex containing the cleavage site sequence of APMV-2 induced the highest neutralizing antibody titer and completely protected chickens from challenge virus shedding. These results show the role of the F protein cleavage site sequence of each APMV type in generating genotype V-matched vaccines and the efficacy of matched vaccine strains to provide better protection against NDV strains currently circulating in Mexico. PMID:28339499

  8. Signal peptide discrimination and cleavage site identification using SVM and NN.

    PubMed

    Kazemian, H B; Yusuf, S A; White, K

    2014-02-01

    About 15% of all proteins in a genome contain a signal peptide (SP) sequence, at the N-terminus, that targets the protein to intracellular secretory pathways. Once the protein is targeted correctly in the cell, the SP is cleaved, releasing the mature protein. Accurate prediction of the presence of these short amino-acid SP chains is crucial for modelling the topology of membrane proteins, since SP sequences can be confused with transmembrane domains due to similar composition of hydrophobic amino acids. This paper presents a cascaded Support Vector Machine (SVM)-Neural Network (NN) classification methodology for SP discrimination and cleavage site identification. The proposed method utilises a dual phase classification approach using SVM as a primary classifier to discriminate SP sequences from Non-SP. The methodology further employs NNs to predict the most suitable cleavage site candidates. In phase one, a SVM classification utilises hydrophobic propensities as a primary feature vector extraction using symmetric sliding window amino-acid sequence analysis for discrimination of SP and Non-SP. In phase two, a NN classification uses asymmetric sliding window sequence analysis for prediction of cleavage site identification. The proposed SVM-NN method was tested using Uni-Prot non-redundant datasets of eukaryotic and prokaryotic proteins with SP and Non-SP N-termini. Computer simulation results demonstrate an overall accuracy of 0.90 for SP and Non-SP discrimination based on Matthews Correlation Coefficient (MCC) tests using SVM. For SP cleavage site prediction, the overall accuracy is 91.5% based on cross-validation tests using the novel SVM-NN model.

  9. MitoFates: improved prediction of mitochondrial targeting sequences and their cleavage sites.

    PubMed

    Fukasawa, Yoshinori; Tsuji, Junko; Fu, Szu-Chin; Tomii, Kentaro; Horton, Paul; Imai, Kenichiro

    2015-04-01

    Mitochondria provide numerous essential functions for cells and their dysfunction leads to a variety of diseases. Thus, obtaining a complete mitochondrial proteome should be a crucial step toward understanding the roles of mitochondria. Many mitochondrial proteins have been identified experimentally but a complete list is not yet available. To fill this gap, methods to computationally predict mitochondrial proteins from amino acid sequence have been developed and are widely used, but unfortunately, their accuracy is far from perfect. Here we describe MitoFates, an improved prediction method for cleavable N-terminal mitochondrial targeting signals (presequences) and their cleavage sites. MitoFates introduces novel sequence features including positively charged amphiphilicity, presequence motifs, and position weight matrices modeling the presequence cleavage sites. These features are combined with classical ones such as amino acid composition and physico-chemical properties as input to a standard support vector machine classifier. On independent test data, MitoFates attains better performance than existing predictors in both detection of presequences and in predicting their cleavage sites. We used MitoFates to look for undiscovered mitochondrial proteins from 42,217 human proteins (including isoforms such as alternative splicing or translation initiation variants). MitoFates predicts 1167 genes to have at least one isoform with a presequence. Five-hundred and eighty of these genes were not annotated as mitochondrial in either UniProt or Gene Ontology. Interestingly, these include candidate regulators of parkin translocation to damaged mitochondria, and also many genes with known disease mutations, suggesting that careful investigation of MitoFates predictions may be helpful in elucidating the role of mitochondria in health and disease. MitoFates is open source with a convenient web server publicly available.

  10. Studies on the preferred uracil-adenine base pair at the cleavage site of 10-23 DNAzyme by functional group modifications on adenine.

    PubMed

    Zhu, Junfei; Li, Zhiwen; Yang, Zhenjun; He, Junlin

    2015-08-01

    10-23 DNAzyme is capable of catalytically cleaving RNA substrates with the preferred cleavage sites rAU and rGU, in which the common base pair U-dA0 forms between the substrate and the DNAzyme in the cleavage reaction. Here its conservation was studied with base modifications on dA and extra functional groups introduced. The nitrogen atom at 7- or 8-position of adenine was demonstrated to be equally important for the cleavage reaction, although it is not related to the thermal stability of the base pair. Deletion of 6-amino group led to decreased stability of the base pair and a slight slower reaction rate. Extra functional groups through 6-amino group were not favorably accommodated in the cleavage site. From these modifications at the level of functional groups, it demonstrated that the base pair U-dA0 not only contributes to the recognition and binding stability, but also it is involved in the active catalytic center by its functional groups and base stacking. This kind of chemical modifications with 7-substituted 8-aza-7-deaza-2'-deoxyadenosine at dA0 is favorable for the introduction of signal molecules for mechanistic studies and biological applications, without significant loss of the catalytic function and structural destruction.

  11. Nucleotide sequence of miRNA precursor contributes to cleavage site selection by Dicer.

    PubMed

    Starega-Roslan, Julia; Galka-Marciniak, Paulina; Krzyzosiak, Wlodzimierz J

    2015-12-15

    The ribonuclease Dicer excises mature miRNAs from a diverse group of precursors (pre-miRNAs), most of which contain various secondary structure motifs in their hairpin stem. In this study, we analyzed Dicer cleavage in hairpin substrates deprived of such motifs. We searched for the factors other than the secondary structure, which may influence the length diversity and heterogeneity of miRNAs. We found that the nucleotide sequence at the Dicer cleavage site influences both of these miRNA characteristics. With regard to cleavage mechanism, we demonstrate that the Dicer RNase IIIA domain that cleaves within the 3' arm of the pre-miRNA is more sensitive to the nucleotide sequence of its substrate than is the RNase IIIB domain. The RNase IIIA domain avoids releasing miRNAs with G nucleotide and prefers to generate miRNAs with a U nucleotide at the 5' end. We also propose that the sequence restrictions at the Dicer cleavage site might be the factor that contributes to the generation of miRNA duplexes with 3' overhangs of atypical lengths. This finding implies that the two RNase III domains forming the single processing center of Dicer may exhibit some degree of flexibility, which allows for the formation of these non-standard 3' overhangs.

  12. Nucleotide sequence of miRNA precursor contributes to cleavage site selection by Dicer

    PubMed Central

    Starega-Roslan, Julia; Galka-Marciniak, Paulina; Krzyzosiak, Wlodzimierz J.

    2015-01-01

    The ribonuclease Dicer excises mature miRNAs from a diverse group of precursors (pre-miRNAs), most of which contain various secondary structure motifs in their hairpin stem. In this study, we analyzed Dicer cleavage in hairpin substrates deprived of such motifs. We searched for the factors other than the secondary structure, which may influence the length diversity and heterogeneity of miRNAs. We found that the nucleotide sequence at the Dicer cleavage site influences both of these miRNA characteristics. With regard to cleavage mechanism, we demonstrate that the Dicer RNase IIIA domain that cleaves within the 3′ arm of the pre-miRNA is more sensitive to the nucleotide sequence of its substrate than is the RNase IIIB domain. The RNase IIIA domain avoids releasing miRNAs with G nucleotide and prefers to generate miRNAs with a U nucleotide at the 5′ end. We also propose that the sequence restrictions at the Dicer cleavage site might be the factor that contributes to the generation of miRNA duplexes with 3′ overhangs of atypical lengths. This finding implies that the two RNase III domains forming the single processing center of Dicer may exhibit some degree of flexibility, which allows for the formation of these non-standard 3′ overhangs. PMID:26424848

  13. DNA cleavage site selection by Type III restriction enzymes provides evidence for head-on protein collisions following 1D bidirectional motion.

    PubMed

    Schwarz, Friedrich W; van Aelst, Kara; Tóth, Júlia; Seidel, Ralf; Szczelkun, Mark D

    2011-10-01

    DNA cleavage by the Type III Restriction-Modification enzymes requires communication in 1D between two distant indirectly-repeated recognitions sites, yet results in non-specific dsDNA cleavage close to only one of the two sites. To test a recently proposed ATP-triggered DNA sliding model, we addressed why one site is selected over another during cleavage. We examined the relative cleavage of a pair of identical sites on DNA substrates with different distances to a free or protein blocked end, and on a DNA substrate using different relative concentrations of protein. Under these conditions a bias can be induced in the cleavage of one site over the other. Monte-Carlo simulations based on the sliding model reproduce the experimentally observed behaviour. This suggests that cleavage site selection simply reflects the dynamics of the preceding stochastic enzyme events that are consistent with bidirectional motion in 1D and DNA cleavage following head-on protein collision.

  14. A new approach to an influenza live vaccine: modification of the cleavage site of hemagglutinin.

    PubMed

    Stech, J; Garn, H; Wegmann, M; Wagner, R; Klenk, H-D

    2005-06-01

    A promising approach to reduce the impact of influenza is the use of an attenuated, live virus as a vaccine. Using reverse genetics, we generated a mutant of strain A/WSN/33 with a modified cleavage site within its hemagglutinin, which depends on proteolytic activation by elastase. Unlike the wild-type, which requires trypsin, this mutant is strictly dependent on elastase. Both viruses grow equally well in cell culture. In contrast to the lethal wild-type virus, the mutant is entirely attenuated in mice. At a dose of 10(5) plaque-forming units, it induced complete protection against lethal challenge. This approach allows the conversion of any epidemic strain into a genetically homologous attenuated virus.

  15. Modification of the Hemagglutinin Cleavage Site Allows Indirect Activation of Avian Influenza Virus H9N2 by Bacterial Staphylokinase

    PubMed Central

    Tse, Longping V.; Whittaker, Gary R.

    2015-01-01

    Influenza H9N2 is considered to be a low pathogenicity avian influenza (LPAI) virus that commonly infects avian species and can also infect humans. In 1996, the influenza virus, A/chicken/Korea/MS96-CE6/1996/H9N2 (MS96) was isolated from an outbreak in multiple farms in South Korea that resulted in upwards of 30% mortality in infected chickens, with the virus infecting a number of extrapulmonary tissues, indicating internal spread. However, in experimental infections, complete recovery of specific pathogen free (SPF) chickens occurred. Such a discrepancy indicated an alternative pathway for MS96 virus to gain virulence in farmed chickens. A key determinant of influenza pathogenesis is the susceptibility of the viral hemagglutinin (HA) to proteolytic cleavage/activation. Here, we identified that an amino acid substitution, Ser to Tyr found at the P2 position of the MS96 HA cleavage site optimizes cleavage by the protease plasmin (Pm). Importantly, we identified that certain Staphylococcus sp. are able to cleave and activate MS96 HA by activating plasminogen (Plg) to plasmin by use of a virulence factor, staphylokinase. Overall, these studies provide an in-vitro mechanism for bacterially mediated enhancement of influenza activation, and allow insight into the microbiological mechanisms underlying the avian influenza H9N2 outbreak in Korea in1996. PMID:25841078

  16. Mutagenesis and computer modelling approach to study determinants for recognition of signal peptides by the mitochondrial processing peptidase.

    PubMed

    Zhang, X P; Sjöling, S; Tanudji, M; Somogyi, L; Andreu, D; Eriksson, L E; Gräslund, A; Whelan, J; Glaser, E

    2001-09-01

    Determinants for the recognition of a mitochondrial presequence by the mitochondrial processing peptidase (MPP) have been investigated using mutagenesis and bioinformatics approaches. All plant mitochondrial presequences with a cleavage site that was confirmed by experimental studies can be grouped into three classes. Two major classes contain an arginine residue at position -2 or -3, and the third class does not have any conserved arginines. Sequence logos revealed loosely conserved cleavage motifs for the first two classes but no significant amino acid conservation for the third class. Investigation of processing determinants for a class III precursor, Nicotiana plumbaginifolia F1beta precursor of ATP synthase (pF1beta), was performed using a series of pF1beta presequence mutants and mutant presequence peptides derived from the C-terminal portion of the presequence. Replacement of -2 Gln by Arg inhibited processing, whereas replacement of either the most proximally located -5 Arg or -15 Arg by Leu had only a low inhibitory effect. The C-terminal portion of the pF1beta presequence forms a helix-turn-helix structure. Mutations disturbing or prolonging the helical element upstream of the cleavage site inhibited processing significantly. Structural models of potato MPP and the C-terminal pF1beta presequence peptide were built by homology modelling and empirical conformational energy search methods, respectively. Molecular docking of the pF1beta presequence peptide to the MPP model suggested binding of the peptide to the negatively charged binding cleft formed by the alpha-MPP and beta-MPP subunits in close proximity to the H111XXE114H115X(116-190)E191 proteolytic active site on beta-MPP. Our results show for the first time that the amino acid at the -2 position, even if not an arginine, as well as structural properties of the C-terminal portion of the presequence are important determinants for the processing of a class III precursor by MPP.

  17. Identification of the cleavage sites of the RNA2-encoded polyproteins for two members of the genus Torradovirus by N-terminal sequencing of the virion capsid proteins.

    PubMed

    Ferriol, I; Silva Junior, D M; Nigg, J C; Zamora-Macorra, E J; Falk, B W

    2016-11-01

    Torradoviruses, family Secoviridae, are emergent bipartite RNA plant viruses. RNA1 is ca. 7kb and has one open reading frame (ORF) encoding for the protease, helicase and RNA-dependent RNA polymerase (RdRp). RNA2 is ca. 5kb and has two ORFs. RNA2-ORF1 encodes for a putative protein with unknown function(s). RNA2-ORF2 encodes for a putative movement protein and three capsid proteins. Little is known about the replication and polyprotein processing strategies of torradoviruses. Here, the cleavage sites in the RNA2-ORF2-encoded polyproteins of two torradoviruses, Tomato marchitez virus isolate M (ToMarV-M) and tomato chocolate spot virus, were determined by N-terminal sequencing, revealing that the amino acid (aa) at the -1 position of the cleavage sites is a glutamine. Multiple aa sequence comparison confirmed that this glutamine is conserved among other torradoviruses. Finally, site-directed mutagenesis of conserved aas in the ToMarV-M RdRp and protease prevented substantial accumulation of viral coat proteins or RNAs.

  18. A Single Maturation Cleavage Site in Adenovirus Impacts Cell Entry and Capsid Assembly

    PubMed Central

    Moyer, Crystal L.; Besser, Eli S.

    2015-01-01

    ABSTRACT Proteolytic maturation drives the conversion of stable, immature virus particles to a mature, metastable state primed for cell infection. In the case of human adenovirus, this proteolytic cleavage is mediated by the virally encoded protease AVP. Protein VI, an internal capsid cement protein and substrate for AVP, is cleaved at two sites, one of which is near the N terminus of the protein. In mature capsids, the 33 residues at the N terminus of protein VI (pVIn) are sequestered inside the cavity formed by peripentonal hexon trimers at the 5-fold vertex. Here, we describe a glycine-to-alanine mutation in the N-terminal cleavage site of protein VI that profoundly impacts proteolytic processing, the generation of infectious particles, and cell entry. The phenotypic effects associated with this mutant provide a mechanistic framework for understanding the multifunctional nature of protein VI. Based on our findings, we propose that the primary function of the pVIn peptide is to mediate interactions between protein VI and hexon during virus replication, driving hexon nuclear accumulation and particle assembly. Once particles are assembled, AVP-mediated cleavage facilitates the release of the membrane lytic region at the amino terminus of mature VI, allowing it to lyse the endosome during cell infection. These findings highlight the importance of a single maturation cleavage site for both infectious particle production and cell entry and emphasize the exquisite spatiotemporal regulation governing adenovirus assembly and disassembly. IMPORTANCE Postassembly virus maturation is a cornerstone principle in virology. However, a mechanistic understanding of how icosahedral viruses utilize this process to transform immature capsids into infection-competent particles is largely lacking. Adenovirus maturation involves proteolytic processing of seven precursor proteins. There is currently no information for the role of each independent cleavage event in the generation of

  19. Avian paramyxovirus serotype 1 strains of low virulence with unusual fusion protein cleavage sites isolated from poultry species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Avian paramyxo-serotype-1 viruses (APMV1) with fusion cleavage sites containing two basic amino acids and a phenylalanine (F) at position 117 have been isolated from poultry species in two states from 2007-2009. The intracerebral pathogenicity indices for these viruses are of low virulence at 0.00 ...

  20. The Identity of the Nucleophile Substitution may Influence Metal Interactions with the Cleavage Site of the Minimal Hammerhead Ribozyme

    PubMed Central

    Osborne, Edith M.; Ward, W. Luke; Ruehle, Max Z.; DeRose, Victoria J.

    2010-01-01

    Potential metal interactions with the cleavage site of a minimal hammerhead ribozyme (mHHRz) were probed using 31P NMR-detected Cd2+ titration studies of HHRz constructs containing a phosphorothioate (PS) modification at the cleavage site. The mHHRz nucleophile position was replaced by either a 2′-F or a 2′-NH2 in order to block cleavage activity during the study. The 2′-F/PS cleavage site mHHRz construct, in which the 2′-F should closely imitate the atom size and electronegativity of a 2′OH, demonstrates low levels of metal ion association (<1 ppm 31P chemical shift changes). This observation indicates that having an atom size and electrostatic properties that are similar to the 2′-OH are not the governing factors in allowing metal interactions with the scissile phosphate of the mHHRz. With a 2′-NH2 substitution, a large upfield change in 31P NMR chemical shift of the phosphorothioate peak (Δ~3 ppm with 6 equivalents added Cd2+) indicates observable Cd2+ interactions with the substituted site. Since a 2′-NH2, but not a 2′-F, can serve as a metal ligand, these data suggest that a metal ion interaction with the HHRz cleavage site may include both the scissile phosphate and the 2′ nucleophile. Control samples in which the 2′-NH2/PS unit is placed either next to the mHHRz cleavage site (at U16.1), in a duplex, or in a amUPSU dinucleotide, show much weaker interactions with Cd2+. Results with these control samples indicate that simply the presence of a 2′-NH2/PS unit does not create a strong metal binding site, reinforcing the possibility that the 2′-NH2-moderated Cd-PS interaction is specific to the mHHRz cleavage site. Upfield chemical shifts of both 31P and H2′ 1H resonances in amUPSU are observed with addition of Cd2+, consistent with the predicted metal coordination to both 2′-NH2 and phosphorothioate ligands. These data suggest that metal ion association with the HHRz cleavage site may include an interaction with the 2

  1. COL1 C-propeptide Cleavage Site Mutations Cause High Bone Mass Osteogenesis Imperfecta

    PubMed Central

    Lindahl, Katarina; Barnes, Aileen M.; Fratzl-Zelman, Nadja; Whyte, Michael P.; Hefferan, Theresa E.; Makareeva, Elena; Brusel, Marina; Yaszemski, Michael J.; Rubin, Carl-Johan; Kindmark, Andreas; Roschger, Paul; Klaushofer, Klaus; McAlister, William H.; Mumm, Steven; Leikin, Sergey; Kessler, Efrat; Boskey, Adele L.; Ljunggren, Östen; Marini, Joan C.

    2011-01-01

    Osteogenesis imperfecta (OI) is most often caused by mutations in the type I procollagen genes (COL1A1/COL1A2). We identified two children with substitutions in the type I procollagen C-propeptide cleavage site, which disrupt a unique processing step in collagen maturation and define a novel phenotype within OI. The patients have mild OI caused by mutations in COL1A1 (Patient 1: p.Asp1219Asn) or COL1A2 (Patient 2: p.Ala1119Thr), respectively. Patient 1 L1-L4 DXA z-score was +3.9 and pQCT vBMD was +3.1; Patient 2 had L1-L4 DXA z-score of 0.0 and pQCT vBMD of −1.8. Patient BMD contrasts with radiographic osteopenia and histomorphometry without osteosclerosis. Mutant procollagen processing is impaired in pericellular and in vitro assays. Patient dermal collagen fibrils have irregular borders. Incorporation of pC-collagen into matrix leads to increased bone mineralization. FT-IR imaging confirms elevated mineral/matrix ratios in both patients, along with increased collagen maturation in trabecular bone, compared to normal or OI controls. Bone mineralization density distribution revealed a marked shift toward increased mineralization density for both patients. Patient 1 has areas of higher and lower bone mineralization than controls; Patient 2’s bone matrix has a mineral content exceeding even classical OI bone. These patients define a new phenotype of high BMD OI and demonstrate that procollagen C-propeptide cleavage is crucial to normal bone mineralization. PMID:21344539

  2. Evolution of the R2 Retrotransposon Ribozyme and Its Self-Cleavage Site

    PubMed Central

    Eickbush, Danna G.; Burke, William D.; Eickbush, Thomas H.

    2013-01-01

    R2 is a non-long terminal repeat retrotransposon that inserts site-specifically in the tandem 28S rRNA genes of many animals. Previously, R2 RNA from various species of Drosophila was shown to self-cleave from the 28S rRNA/R2 co-transcript by a hepatitis D virus (HDV)-like ribozyme encoded at its 5' end. RNA cleavage was at the precise 5' junction of the element with the 28S gene. Here we report that RNAs encompassing the 5' ends of R2 elements from throughout its species range fold into HDV-like ribozymes. In vitro assays of RNA self-cleavage conducted in many R2 lineages confirmed activity. For many R2s, RNA self-cleavage was not at the 5' end of the element but at 28S rRNA sequences up to 36 nucleotides upstream of the junction. The location of cleavage correlated well with the types of endogenous R2 5' junctions from different species. R2 5' junctions were uniform for most R2s in which RNA cleavage was upstream in the rRNA sequences. The 28S sequences remaining on the first DNA strand synthesized during retrotransposition are postulated to anneal to the target site and uniformly prime second strand DNA synthesis. In species where RNA cleavage occurred at the R2 5' end, the 5' junctions were variable. This junction variation is postulated to result from the priming of second strand DNA synthesis by chance microhomologies between the target site and the first DNA strand. Finally, features of R2 ribozyme evolution, especially changes in cleavage site and convergence on the same active site sequences, are discussed. PMID:24066021

  3. Rice tungro spherical virus polyprotein processing: identification of a virus-encoded protease and mutational analysis of putative cleavage sites.

    PubMed

    Thole, V; Hull, R

    1998-07-20

    Rice tungro spherical virus encodes a large polyprotein containing motifs with sequence similarity to viral serine-like proteases and RNA polymerases. Polyclonal antisera raised against domains of the putative protease and polymerase in fusion with glutathione S-transferase detected a protein of about 35 kDa and, in very low amounts, a protein of about 70 kDa, respectively, in extracts from infected plants. In in vitro transcription/translation systems and in Escherichia coli we demonstrated a proteolytic activity in the C-terminal region of the polyprotein. This protease rapidly cleaved its polyprotein precursors in vitro. Mutating a potential cleavage site located N-terminal to the protease domain, Gln2526-Asp2527, diminished processing. The transversion mutation at the putative C-terminal cleavage site of the protease, at Gln2852-Ala2853, led to a delayed and partial processing.

  4. Design of protease-resistant myelin basic protein-derived peptides by cleavage site directed amino acid substitutions.

    PubMed

    Burster, Timo; Marin-Esteban, Viviana; Boehm, Bernhard O; Dunn, Shannon; Rotzschke, Olaf; Falk, Kirsten; Weber, Ekkehard; Verhelst, Steven H L; Kalbacher, Hubert; Driessen, Christoph

    2007-11-15

    Multiple Sclerosis (MS) is considered to be a T cell-mediated autoimmune disease. An attractive strategy to prevent activation of autoaggressive T cells in MS, is the use of altered peptide ligands (APL), which bind to major histocompatibility complex class II (MHC II) molecules. To be of clinical use, APL must be capable of resisting hostile environments including the proteolytic machinery of antigen presenting cells (APC). The current design of APL relies on cost- and labour-intensive strategies. To overcome these major drawbacks, we used a deductive approach which involved modifying proteolytic cleavage sites in APL. Cleavage site-directed amino acid substitution of the autoantigen myelin basic protein (MBP) resulted in lysosomal protease-resistant, high-affinity binding peptides. In addition, these peptides mitigated T cell activation in a similar fashion as conventional APL. The strategy outlined allows the development of protease-resistant APL and provides a universal design strategy to improve peptide-based immunotherapeutics.

  5. Fusion expression and purification of four disulfide-rich peptides reveals enterokinase secondary cleavage sites in animal toxins.

    PubMed

    Chen, Zongyun; Han, Song; Cao, Zhijian; Wu, Yingliang; Zhuo, Renxi; Li, Wenxin

    2013-01-01

    Animal toxins are powerful tools for testing the pharmacological, physiological, and structural characteristics of ion channels, proteases, and other receptors. However, most animal toxins are disulfide-rich peptides that are difficult to produce functionally. Here, a glutathione S-transferase (GST) fusion expression strategy was used to produce four recombinant animal toxin peptides, ChTX, StKTx23, BmP01, and ImKTx1, with different isoelectric points from 4.7 to 9.2. GST tags were removed by enterokinase, a widely used and effective commercial protease that cleaves after lysine at the cleavage site DDDDK. Using this strategy, two disulfide-rich animal toxins ChTX and StKTx23 were obtained successfully with a yield of approximately 1-2 mg/l culture. Electrophysiological experiments further showed that these two recombinant toxins showed good bioactivities, indicating that our method was effective in producing large amounts of functional disulfide-rich animal toxins. Interestingly, by analyzing the separated fractions of BmP01, StKTx23, and ImKTx1 using matrix-assisted laser desorption ionization time-of-flight mass spectrometry, four new enterokinase secondary cleavage sites were found, consisting of the sequences "WEYR," "EDK," "QNAR," and "DNDK." To our knowledge, this is the first report of the presence of secondary cleavage sites for commercial enterokinase in animal toxins. These findings will help us use commercial enterokinase appropriately as a cleavage tool in the production of animal toxins.

  6. New strategy for specific activation of recombinant microbial pro-transglutaminase by introducing an enterokinase cleavage site.

    PubMed

    Wang, Kun; Wang, Bin; Yang, Hui-Lin; Pan, Li

    2013-03-01

    Recombinant microbial transglutaminase (rMTG) is usually expressed as a soluble zymogen (pro-rMTG) in heterologous expression systems but proteolytic activation of the inactive pro-rMTG is essential. Instead of screening proteases for activating pro-rMTG, we examined an alternative method by introducing a specific cleavage site of enterokinase between the pro-peptide and mature rMTG, generating three pro-rMTG variants (Pro-mrMTG, Pro-m-rMTG and mPro-rMTG). Pro-mrMTG and Pro-m-rMTG were activated by enterokinase without degrading mature rMTG. The activation productivity of Pro-m-rMTG by enterokinase reached 92 % after 22 h activation, while the activation productivity of Pro-rMTG activated by trypsin was 47 %. MALDI-MS analysis revealed that the pro-peptide including the cleavage site was specifically removed from Pro-m-rMTG after activation. This methodology has the potential to be applied in rMTG production by incorporating highly specific cleavage sites of other proteases.

  7. Characterization of an H4N2 influenza virus from Quails with a multibasic motif in the hemagglutinin cleavage site.

    PubMed

    Wong, Sook-San; Yoon, Sun-Woo; Zanin, Mark; Song, Min-Suk; Oshansky, Christine; Zaraket, Hassan; Sonnberg, Stephanie; Rubrum, Adam; Seiler, Patrick; Ferguson, Angela; Krauss, Scott; Cardona, Carol; Webby, Richard J; Crossley, Beate

    2014-11-01

    The cleavage motif in the hemagglutinin (HA) protein of highly pathogenic H5 and H7 subtypes of avian influenza viruses is characterized by a peptide insertion or a multibasic cleavage site (MBCS). Here, we isolated an H4N2 virus from quails (Quail/CA12) with two additional arginines in the HA cleavage site, PEKRRTR/G, forming an MBCS-like motif. Quail/CA12 is a reassortant virus with the HA and neuraminidase (NA) gene most similar to a duck-isolated H4N2 virus, PD/CA06 with a monobasic HA cleavage site. Quail/CA12 required exogenous trypsin for efficient growth in culture and caused no clinical illness in infected chickens. Quail/CA12 had high binding preference for α2,6-linked sialic acids and showed higher replication and transmission ability in chickens and quails than PD/CA06. Although the H4N2 virus remained low pathogenic, these data suggests that the acquisition of MBCS in the field is not restricted to H5 or H7 subtypes.

  8. A motivational determinant of facial emotion recognition: regulatory focus affects recognition of emotions in faces.

    PubMed

    Sassenrath, Claudia; Sassenberg, Kai; Ray, Devin G; Scheiter, Katharina; Jarodzka, Halszka

    2014-01-01

    Two studies examined an unexplored motivational determinant of facial emotion recognition: observer regulatory focus. It was predicted that a promotion focus would enhance facial emotion recognition relative to a prevention focus because the attentional strategies associated with promotion focus enhance performance on well-learned or innate tasks - such as facial emotion recognition. In Study 1, a promotion or a prevention focus was experimentally induced and better facial emotion recognition was observed in a promotion focus compared to a prevention focus. In Study 2, individual differences in chronic regulatory focus were assessed and attention allocation was measured using eye tracking during the facial emotion recognition task. Results indicated that the positive relation between a promotion focus and facial emotion recognition is mediated by shorter fixation duration on the face which reflects a pattern of attention allocation matched to the eager strategy in a promotion focus (i.e., striving to make hits). A prevention focus did not have an impact neither on perceptual processing nor on facial emotion recognition. Taken together, these findings demonstrate important mechanisms and consequences of observer motivational orientation for facial emotion recognition.

  9. A Motivational Determinant of Facial Emotion Recognition: Regulatory Focus Affects Recognition of Emotions in Faces

    PubMed Central

    Sassenrath, Claudia; Sassenberg, Kai; Ray, Devin G.; Scheiter, Katharina; Jarodzka, Halszka

    2014-01-01

    Two studies examined an unexplored motivational determinant of facial emotion recognition: observer regulatory focus. It was predicted that a promotion focus would enhance facial emotion recognition relative to a prevention focus because the attentional strategies associated with promotion focus enhance performance on well-learned or innate tasks - such as facial emotion recognition. In Study 1, a promotion or a prevention focus was experimentally induced and better facial emotion recognition was observed in a promotion focus compared to a prevention focus. In Study 2, individual differences in chronic regulatory focus were assessed and attention allocation was measured using eye tracking during the facial emotion recognition task. Results indicated that the positive relation between a promotion focus and facial emotion recognition is mediated by shorter fixation duration on the face which reflects a pattern of attention allocation matched to the eager strategy in a promotion focus (i.e., striving to make hits). A prevention focus did not have an impact neither on perceptual processing nor on facial emotion recognition. Taken together, these findings demonstrate important mechanisms and consequences of observer motivational orientation for facial emotion recognition. PMID:25380247

  10. Characterization of clade 2.3.4.4 H5N8 highly pathogenic avian influenza viruses from wild birds possessing atypical hemagglutinin polybasic cleavage sites.

    PubMed

    Usui, Tatsufumi; Soda, Kosuke; Tomioka, Yukiko; Ito, Hiroshi; Yabuta, Toshiyo; Takakuwa, Hiroki; Otsuki, Koichi; Ito, Toshihiro; Yamaguchi, Tsuyoshi

    2017-02-01

    Since 2014, clade 2.3.4.4 H5 subtype highly pathogenic avian influenza viruses (HPAIVs) have been distributed worldwide. These viruses, which were reported to be highly virulent in chickens by intravenous inoculation, have a consensus HPAI motif PLRERRRKR at the HA cleavage site. However, two-clade 2.3.4.4 H5N8 viruses which we isolated from wild migratory birds in late 2014 in Japan possessed atypical HA cleavage sequences. A swan isolate, Tottori/C6, had a novel polybasic cleavage sequence, PLGERRRKR, and another isolate from a dead mandarin duck, Gifu/01, had a heterogeneous mixture of consensus PLRERRRKR and variant PLRERRRRKR sequences. The polybasic HA cleavage site is the prime virulence determinant of AIVs. Therefore, in the present study, we examined the pathogenicity of these H5N8 isolates in chickens by intravenous inoculation. When 10(6) EID50 of these viruses were intravenously inoculated into chickens, the mean death time associated with Tottori/C6 was substantially longer (>6.1 days) than that associated with Gifu/01 (2.5 days). These viruses had comparable abilities to replicate in tissue culture cells in the presence and absence of exogenous trypsin, but the growth of Tottori/C6 was hampered. These results indicate that the novel cleavage motif of Tottori/C6 did not directly affect the infectivity of the virus, but Tottori/C6 caused attenuated pathogenicity in chickens because of hampered replication efficiency. It is important to test for the emergence of diversified HPAIVs, because introduction of HPAIVs with a lower virulence like Tottori/C6 might hinder early detection of affected birds in poultry farms.

  11. Mapping sequence differences between thimet oligopeptidase and neurolysin implicates key residues in substrate recognition.

    PubMed

    Ray, Kallol; Hines, Christina S; Rodgers, David W

    2002-09-01

    The highly homologous endopeptidases thimet oligopeptidase and neurolysin are both restricted to short peptide substrates and share many of the same cleavage sites on bioactive and synthetic peptides. They sometimes target different sites on the same peptide, however, and defining the determinants of differential recognition will help us to understand how both enzymes specifically target a wide variety of cleavage site sequences. We have mapped the positions of the 224 surface residues that differ in sequence between the two enzymes onto the surface of the neurolysin crystal structure. Although the deep active site channel accounts for about one quarter of the total surface area, only 11% of the residue differences map to this region. Four isolated sequence changes (R470/E469, R491/M490, N496/H495, and T499/R498; neurolysin residues given first) are well positioned to affect recognition of substrate peptides, and differences in cleavage site specificity can be largely rationalized on the basis of these changes. We also mapped the positions of three cysteine residues believed to be responsible for multimerization of thimet oligopeptidase, a process that inactivates the enzyme. These residues are clustered on the outside of one channel wall, where multimerization via disulfide formation is unlikely to block the substrate-binding site. Finally, we mapped the regulatory phosphorylation site in thimet oligopeptidase to a location on the outside of the molecule well away from the active site, which indicates this modification has an indirect effect on activity.

  12. CaspNeuroD: a knowledgebase of predicted caspase cleavage sites in human proteins related to neurodegenerative diseases

    PubMed Central

    Kumar, Sonu; Cieplak, Piotr

    2016-01-01

    Background: A variety of neurodegenerative diseases (NDs) have been associated with deregulated caspase activation that leads to neuronal death. Caspases appear to be involved in the molecular pathology of NDs by directly cleaving important proteins. For instance, several proteins involved in Alzheimer’s disease, including β-amyloid precursor protein (APP) and presenilins, are known to be cleaved by caspases. Therefore, cell death pathway may play a central role in many neurological diseases, and targeting the important proteins that control the cell survival and death may potentially represent a therapeutic approach for chronic neurodegenerative disorders. Findings: We developed CaspNeuroD, a relational database of in silico predicted caspase cleavage sites in human proteins associated with NDs. The prediction has been done on collection of 249 human proteins reported in clinical studies of NDs using the recently published CaspDB Random Forest machine-learning model. This database could be used for identifying new caspase substrates and further our understanding of the caspase-mediated substrate cleavage in NDs. Conclusion: Our database provides information about potential caspase cleavage sites in a verified set of human proteins involved in NDs. It provides also information about the conservation of cleavage positions in corresponding orthologs, and information about the positions of single nucleotide polymorphisms and posttranslational modifications (PTMs) that may modulate the caspase cleavage efficiency. Database URL: caspdb.sanfordburnham.org/caspneurod.php . PMID:28025335

  13. In-line alignment and Mg2+ coordination at the cleavage site of the env22 twister ribozyme

    PubMed Central

    Ren, Aiming; Košutić, Marija; Rajashankar, Kanagalaghatta R.; Frener, Marina; Santner, Tobias; Westhof, Eric; Micura, Ronald; Patel, Dinshaw J.

    2015-01-01

    Small self-cleaving nucleolytic ribozymes contain catalytic domains that accelerate site-specific cleavage/ligation of phosphodiester backbones. We report on the 2.9-Å crystal structure of the env22 twister ribozyme, which adopts a compact tertiary fold stabilized by co-helical stacking, double-pseudoknot formation and long-range pairing interactions. The U-A cleavage site adopts a splayed-apart conformation with the modeled 2′-O of U positioned for in-line attack on the adjacent to-be-cleaved P-O5′ bond. Both an invariant guanosine and a Mg2+ are directly coordinated to the non-bridging phosphate oxygens at the U-A cleavage step, with the former positioned to contribute to catalysis and the latter to structural integrity. The impact of key mutations on cleavage activity identified an invariant guanosine that contributes to catalysis. Our structure of the in-line aligned env22 twister ribozyme is compared with two recently-reported twister ribozymes structures, which adopt similar global folds, but differ in conformational features around the cleavage site. PMID:25410397

  14. Different cleavage sites are aligned differently in the active site of M1 RNA, the catalytic subunit of Escherichia coli RNase P.

    PubMed Central

    Kufel, J; Kirsebom, L A

    1996-01-01

    We have studied RNase P RNA (M1 RNA) cleavage of model tRNA precursors that are cleaved at two independent positions. Here we present data demonstrating that cleavage at both sites depends on the 2'-OH immediately 5' of the respective cleavage site. However, we show that the 2-amino group of a guanosine at the cleavage site plays a significant role in cleavage at one of these sites but not at the other. These data suggest that these two cleavage sites are handled differently by the ribozyme. This theory is supported by our finding that the cross-linking pattern between Ml RNA and tRNA precursors carrying 4-thioU showed distinct differences, depending on the location of the 4-thioU relative to the respective cleavage site. These findings lead us to suggest that different cleavage sites are aligned differently in the active site, possibly as a result of different binding modes of a substrate to M1 RNA. We discuss a model in which the interaction between the 3'-terminal "RCCA" motif (first three residues interact) of a tRNA precursor and M1 RNA plays a significant role in this process. Images Fig. 2 Fig. 3 Fig. 4 PMID:8650223

  15. The T210M Substitution in the HLA-a*02:01 gp100 Epitope Strongly Affects Overall Proteasomal Cleavage Site Usage and Antigen Processing*

    PubMed Central

    Textoris-Taube, Kathrin; Keller, Christin; Liepe, Juliane; Henklein, Petra; Sidney, John; Sette, Alessandro; Kloetzel, Peter M.; Mishto, Michele

    2015-01-01

    MHC class I-restricted epitopes, which carry a tumor-specific mutation resulting in improved MHC binding affinity, are preferred T cell receptor targets in innovative adoptive T cell therapies. However, T cell therapy requires efficient generation of the selected epitope. How such mutations may affect proteasome-mediated antigen processing has so far not been studied. Therefore, we analyzed by in vitro experiments the effect on antigen processing and recognition of a T210M exchange, which previously had been introduced into the melanoma gp100209–217tumor epitope to improve the HLA-A*02:01 binding and its immunogenicity. A quantitative analysis of the main steps of antigen processing shows that the T210M exchange affects proteasomal cleavage site usage within the mutgp100201–230 polypeptide, leading to the generation of an unique set of cleavage products. The T210M substitution qualitatively affects the proteasome-catalyzed generation of spliced and non-spliced peptides predicted to bind HLA-A or -B complexes. The T210M substitution also induces an enhanced production of the mutgp100209–217 epitope and its N-terminally extended peptides. The T210M exchange revealed no effect on ERAP1-mediated N-terminal trimming of the precursor peptides. However, mutant N-terminally extended peptides exhibited significantly increased HLA-A*02:01 binding affinity and elicited CD8+ T cell stimulation in vitro similar to the wtgp100209–217 epitope. Thus, our experiments demonstrate that amino acid exchanges within an epitope can result in the generation of an altered peptide pool with new antigenic peptides and in a wider CD8+ T cell response also towards N-terminally extended versions of the minimal epitope. PMID:26507656

  16. The mechanism behind the selection of two different cleavage sites in NAG-NAM polymers

    PubMed Central

    Mihelič, Marko; Vlahoviček-Kahlina, Kristina; Renko, Miha; Mesnage, Stephane; Doberšek, Andreja; Taler-Verčič, Ajda; Jakas, Andreja; Turk, Dušan

    2017-01-01

    Peptidoglycan is a giant molecule that forms the cell wall that surrounds bacterial cells. It is composed of alternating N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) residues connected by β-(1,4)-glycosidic bonds and cross-linked with short polypeptide chains. Owing to the increasing antibiotic resistance against drugs targeting peptidoglycan synthesis, studies of enzymes involved in the degradation of peptidoglycan, such as N-acetylglucos­aminidases, may expose new, valuable drug targets. The scientific challenge addressed here is how lysozymes, muramidases which are likely to be the most studied enzymes ever, and bacterial N-acetylglucosaminidases discriminate between two glycosidic bonds that are different in sequence yet chemically equivalent in the same NAG-NAM polymers. In spite of more than fifty years of structural studies of lysozyme, it is still not known how the enzyme selects the bond to be cleaved. Using macromolecular crystallography, chemical synthesis and molecular modelling, this study explains how these two groups of enzymes based on an equivalent structural core exhibit a difference in selectivity. The crystal structures of Staphylococcus aureus N-acetylglucosaminidase autolysin E (AtlE) alone and in complex with fragments of peptidoglycan revealed that N-acetylglucosaminidases and muramidases approach the substrate at alternate glycosidic bond positions from opposite sides. The recognition pocket for NAM residues in the active site of N-acetylglucosaminidases may make them a suitable drug target. PMID:28250957

  17. The mechanism behind the selection of two different cleavage sites in NAG-NAM polymers.

    PubMed

    Mihelič, Marko; Vlahoviček-Kahlina, Kristina; Renko, Miha; Mesnage, Stephane; Doberšek, Andreja; Taler-Verčič, Ajda; Jakas, Andreja; Turk, Dušan

    2017-03-01

    Peptidoglycan is a giant molecule that forms the cell wall that surrounds bacterial cells. It is composed of alternating N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) residues connected by β-(1,4)-glycosidic bonds and cross-linked with short polypeptide chains. Owing to the increasing antibiotic resistance against drugs targeting peptidoglycan synthesis, studies of enzymes involved in the degradation of peptidoglycan, such as N-acetylglucos-aminidases, may expose new, valuable drug targets. The scientific challenge addressed here is how lysozymes, muramidases which are likely to be the most studied enzymes ever, and bacterial N-acetylglucosaminidases discriminate between two glycosidic bonds that are different in sequence yet chemically equivalent in the same NAG-NAM polymers. In spite of more than fifty years of structural studies of lysozyme, it is still not known how the enzyme selects the bond to be cleaved. Using macromolecular crystallography, chemical synthesis and molecular modelling, this study explains how these two groups of enzymes based on an equivalent structural core exhibit a difference in selectivity. The crystal structures of Staphylococcus aureusN-acetylglucosaminidase autolysin E (AtlE) alone and in complex with fragments of peptidoglycan revealed that N-acetylglucosaminidases and muramidases approach the substrate at alternate glycosidic bond positions from opposite sides. The recognition pocket for NAM residues in the active site of N-acetylglucosaminidases may make them a suitable drug target.

  18. Determination of candidate subjects for better recognition of faces

    NASA Astrophysics Data System (ADS)

    Wang, Xuansheng; Chen, Zhen; Teng, Zhongming

    2016-05-01

    In order to improve the accuracy of face recognition and to solve the problem of various poses, we present an improved collaborative representation classification (CRC) algorithm using original training samples and the corresponding mirror images. First, the mirror images are generated from the original training samples. Second, both original training samples and their mirror images are simultaneously used to represent the test sample via improved collaborative representation. Then, some classes which are "close" to the test sample are coarsely selected as candidate classes. At last, the candidate classes are used to represent the test sample again, and then the class most similar to the test sample can be determined finely. The experimental results show our proposed algorithm has more robustness than the original CRC algorithm and can effectively improve the accuracy of face recognition.

  19. Preparation of recombinant thioredoxin fused N-terminal proCNP: Analysis of enterokinase cleavage products reveals new enterokinase cleavage sites.

    PubMed

    Liew, Oi Wah; Ching Chong, Jenny Pek; Yandle, Tim G; Brennan, Stephen O

    2005-06-01

    C-type natriuretic peptide (CNP) acts as a paracrine hormone to dilate blood vessels and is also required for the growth of long bones. In vivo, CNP is produced by cleavage from the C-terminal end of a larger proCNP peptide. The remaining N-terminal proCNP fragment (NT-proCNP) escapes into the circulation where its concentration is much higher than that of CNP due presumably to a lower clearance rate. Our strategy to obtain large quantities of pure NT-proCNP for further physiological investigations was to express it as a fusion protein with His(6)-tagged thioredoxin followed by cleavage using enterokinase to yield NT-proCNP alone. We have successfully designed and artificially synthesized the coding sequence specifying both mouse and human NT-proCNP with built-in codon bias towards Escherichia coli codon preference. An enterokinase recognition sequence was incorporated immediately upstream of the NT-proCNP coding sequence to allow the fusion protein to be cleaved without leaving any extra residues on the NT-proCNP peptide. High levels of fusion proteins were obtained, constituting 50-58% of total bacterial proteins. Greater than 90% of recombinant thioredoxin/NT-proCNP was expressed in the soluble form and purified to near homogeneity in a single chromatographic step using nickel as the metal ion in IMAC. A time course analysis of the products released from enterokinase cleavage of the recombinant proteins by ESI-MS revealed three sensitive secondary cleavage sites: two were located on vector-associated sequences linking the thioredoxin moiety and NT-proCNP, and one at the C-terminal end of NT-proCNP. Clearly, substrate specificity of both the native and recombinant forms of enterokinase for the recognition sequence DDDDK was by no means exclusive. Hydrolysis at the unexpected LKGDR site located towards the carboxyl end on NT-proCNP was significantly more efficient than at the internally sited DDDDK target sequence. However, when this same sequence was sited

  20. Identification of E-cadherin signature motifs functioning as cleavage sites for Helicobacter pylori HtrA

    NASA Astrophysics Data System (ADS)

    Schmidt, Thomas P.; Perna, Anna M.; Fugmann, Tim; Böhm, Manja; Jan Hiss; Haller, Sarah; Götz, Camilla; Tegtmeyer, Nicole; Hoy, Benjamin; Rau, Tilman T.; Neri, Dario; Backert, Steffen; Schneider, Gisbert; Wessler, Silja

    2016-03-01

    The cell adhesion protein and tumour suppressor E-cadherin exhibits important functions in the prevention of gastric cancer. As a class-I carcinogen, Helicobacter pylori (H. pylori) has developed a unique strategy to interfere with E-cadherin functions. In previous studies, we have demonstrated that H. pylori secretes the protease high temperature requirement A (HtrA) which cleaves off the E-cadherin ectodomain (NTF) on epithelial cells. This opens cell-to-cell junctions, allowing bacterial transmigration across the polarised epithelium. Here, we investigated the molecular mechanism of the HtrA-E-cadherin interaction and identified E-cadherin cleavage sites for HtrA. Mass-spectrometry-based proteomics and Edman degradation revealed three signature motifs containing the [VITA]-[VITA]-x-x-D-[DN] sequence pattern, which were preferentially cleaved by HtrA. Based on these sites, we developed a substrate-derived peptide inhibitor that selectively bound and inhibited HtrA, thereby blocking transmigration of H. pylori. The discovery of HtrA-targeted signature sites might further explain why we detected a stable 90 kDa NTF fragment during H. pylori infection, but also additional E-cadherin fragments ranging from 105 kDa to 48 kDa in in vitro cleavage experiments. In conclusion, HtrA targets E-cadherin signature sites that are accessible in in vitro reactions, but might be partially masked on epithelial cells through functional homophilic E-cadherin interactions.

  1. A camel-derived MERS-CoV with a variant spike protein cleavage site and distinct fusion activation properties

    PubMed Central

    Millet, Jean Kaoru; Goldstein, Monty E; Labitt, Rachael N; Hsu, Hung-Lun; Daniel, Susan; Whittaker, Gary R

    2016-01-01

    Middle East respiratory syndrome coronavirus (MERS-CoV) continues to circulate in both humans and camels, and the origin and evolution of the virus remain unclear. Here we characterize the spike protein of a camel-derived MERS-CoV (NRCE-HKU205) identified in 2013, early in the MERS outbreak. NRCE-HKU205 spike protein has a variant cleavage motif with regard to the S2′ fusion activation site—notably, a novel substitution of isoleucine for the otherwise invariant serine at the critical P1′ cleavage site position. The substitutions resulted in a loss of furin-mediated cleavage, as shown by fluorogenic peptide cleavage and western blot assays. Cell–cell fusion and pseudotyped virus infectivity assays demonstrated that the S2′ substitutions decreased spike-mediated fusion and viral entry. However, cathepsin and trypsin-like protease activation were retained, albeit with much reduced efficiency compared with the prototypical EMC/2012 human strain. We show that NRCE-HKU205 has more limited fusion activation properties possibly resulting in more restricted viral tropism and may represent an intermediate in the complex pattern of MERS-CoV ecology and evolution. PMID:27999426

  2. Engineering D-Amino Acid Containing Collagen Like Peptide at the Cleavage Site of Clostridium histolyticum Collagenase for Its Inhibition

    PubMed Central

    Velmurugan, Punitha; Jonnalagadda, Raghava Rao; Unni Nair, Balachandran

    2015-01-01

    Collagenase is an important enzyme which plays an important role in degradation of collagen in wound healing, cancer metastasis and even in embryonic development. However, the mechanism of this degradation has not yet been completely understood. In the field of biomedical and protein engineering, the design and development of new peptide based materials is of main concern. In the present work an attempt has been made to study the effect of DAla in collagen like peptide (imino-poor region of type I collagen) on the structure and stability of peptide against enzyme hydrolysis. Effect of replacement of DAla in the collagen like peptide has been studied using circular dichroic spectroscopy (CD). Our findings suggest that, DAla substitution leads to conformational changes in the secondary structure and favours the formation of polyproline II conformation than its L-counterpart in the imino-poor region of collagen like peptides. Change in the chirality of alanine at the cleavage site of collagenase in the imino-poor region inhibits collagenolytic activity. This may find application in design of peptides and peptidomimics for enzyme-substrate interaction, specifically with reference to collagen and other extra cellular matrix proteins. PMID:25973613

  3. Genetic determinants of mate recognition in Brachionus manjavacas (Rotifera)

    PubMed Central

    Snell, Terry W; Shearer, Tonya L; Smith, Hilary A; Kubanek, Julia; Gribble, Kristin E; Welch, David B Mark

    2009-01-01

    Background Mate choice is of central importance to most animals, influencing population structure, speciation, and ultimately the survival of a species. Mating behavior of male brachionid rotifers is triggered by the product of a chemosensory gene, a glycoprotein on the body surface of females called the mate recognition pheromone. The mate recognition pheromone has been biochemically characterized, but little was known about the gene(s). We describe the isolation and characterization of the mate recognition pheromone gene through protein purification, N-terminal amino acid sequence determination, identification of the mate recognition pheromone gene from a cDNA library, sequencing, and RNAi knockdown to confirm the functional role of the mate recognition pheromone gene in rotifer mating. Results A 29 kD protein capable of eliciting rotifer male circling was isolated by high-performance liquid chromatography. Two transcript types containing the N-terminal sequence were identified in a cDNA library; further characterization by screening a genomic library and by polymerase chain reaction revealed two genes belonging to each type. Each gene begins with a signal peptide region followed by nearly perfect repeats of an 87 to 92 codon motif with no codons between repeats and the final motif prematurely terminated by the stop codon. The two Type A genes contain four and seven repeats and the two Type B genes contain three and five repeats, respectively. Only the Type B gene with three repeats encodes a peptide with a molecular weight of 29 kD. Each repeat of the Type B gene products contains three asparagines as potential sites for N-glycosylation; there are no asparagines in the Type A genes. RNAi with Type A double-stranded RNA did not result in less circling than in the phosphate-buffered saline control, but transfection with Type B double-stranded RNA significantly reduced male circling by 17%. The very low divergence between repeat units, even at synonymous positions

  4. Sequence diversity and associated pathogenicity of the hemagglutinin cleavage site of H5N2 avian influenza viruses isolated from chickens in Taiwan during 2013–2015

    PubMed Central

    LI, Kuang-Po; CHANG, Poa-Chun; CHENG, Ming-Chu; TAN, Duen-Huey; CHEN, Li-Hsuan; LIU, Yu-Pin; LIN, Yu-Ju; TSAI, Hsiang-Jung; SHIEN, Jui-Hung

    2016-01-01

    The sequence at the hemagglutinin (HA) cleavage site (CS) plays a key role in determining the pathogenicity of avian influenza viruses. Three types of HA CS sequences, QREKR/GL, QRKKR/GL and QRRKR/GL, were previously reported in Taiwanese H5N2 viruses that were isolated from chickens from 2003 to 2013. However, no HA CS sequence was reported for viruses isolated after 2013. This article presents the HA CS sequences and pathogenicity of H5N2 viruses that were isolated from chickens in Taiwan during 2013–2015. Two novel HA CS sequences, QKEKR/GL and KREKREKR/GL, were found in the viruses isolated in 2013 and 2014, and pathogenicity tests showed that the viruses with these novel HA CS sequences are low and high pathogenic viruses, respectively. In contrast, the HA CS sequence QREKR/GL was found in all viruses that were isolated in 2015, and all of these viruses were low pathogenic viruses. After 10 passages in embryonated chicken eggs, a virus strain that was isolated in 2003 evolved into a viral quasispecies that contained at least four distinct types of HA CS sequences. These results highlight the potential of Taiwanese H5N2 viruses to change their pathogenicity and HA CS sequences via mutations. Furthermore, viruses with the HA CS sequence QREKR/GL were more prevalent than others in 2015. These findings are useful for understanding the mechanism of sequence changes at the HA CS and for refining H5N2 virus control measures in Taiwan. PMID:27725416

  5. Limited proteolysis and sequence analysis of the 2-oxo acid dehydrogenase complexes from Escherichia coli. Cleavage sites and domains in the dihydrolipoamide acyltransferase components.

    PubMed Central

    Packman, L C; Perham, R N

    1987-01-01

    The structures of the dihydrolipoamide acyltransferase (E2) components of the 2-oxo acid dehydrogenase complexes from Escherichia coli were investigated by limited proteolysis. Trypsin and Staphylococcus aureus V8 proteinase were used to excise the three lipoyl domains from the E2p component of the pyruvate dehydrogenase complex and the single lipoyl domain from the E2o component of the 2-oxoglutarate dehydrogenase complex. The principal sites of action of these enzymes on each E2 chain were determined by sequence analysis of the isolated lipoyl fragments and of the truncated E2p and E2o chains. Each of the numerous cleavage sites (12 in E2p, six in E2o) fell within similar segments of the E2 chains, namely stretches of polypeptide rich in alanine, proline and/or charged amino acids. These regions are clearly accessible to proteinases of Mr 24,000-28,000 and, on the basis of n.m.r. spectroscopy, some of them have previously been implicated in facilitating domain movements by virtue of their conformational flexibility. The limited proteolysis data suggest that E2p and E2o possess closer architectural similarities than would be predicted from inspection of their amino acid sequences. As a result of this work, an error was detected in the sequence of E2o inferred from the previously published sequence of the encoding gene, sucB. The relevant peptides from E2o were purified and sequenced by direct means; an amended sequence is presented. Images Fig. 1. Fig. 2. PMID:3297046

  6. Perceptual Organization as a Determinant of Visual Recognition Memory

    ERIC Educational Resources Information Center

    Wiseman, Sandor; Neisser, Ulric

    1974-01-01

    Ambiguous pictures that could be seen as faces or as meaningless patterns were the stimuli in two recognition-memory experiments. Recognition was far more accurate when the stimuli were seen as faces. (Editor)

  7. DNA bending is a determinant of calicheamicin target recognition.

    PubMed

    Salzberg, A A; Dedon, P C

    2000-06-27

    Calicheamicin is a hydrophobic enediyne antibiotic that binds noncovalently to DNA and causes sequence-selective oxidation of deoxyribose. While the drug makes several base contacts along the minor groove, the diversity of binding-site sequences and the effects of DNA conformation on calicheamicin-induced DNA cleavage suggest that sequence recognition per se is not the primary determinant of target selection. We now present evidence that calicheamicin bends its DNA targets. Using a gel mobility assay, we observed that polymers of oligonucleotide constructs containing AGGA and ACAA binding sites for calicheamicin did not possess intrinsic curvature. Binding of calicheamicin epsilon, the aromatized form of the parent calicheamicin gamma(1)(I), to oligonucleotide constructs containing binding sites in phase with the helical repeat caused a shift to smaller circle sizes in T4 ligase-mediated circle formation assays, with a much smaller shift observed with constructs containing out-of-phase binding sites. It was also observed that binding of calicheamicin epsilon to a 273 bp construct with phased binding sites caused an increase in the molar cyclization factor, J, from 8 x 10(-8) to 9 x 10(-6) M. These results are consistent with DNA bending as part of an induced-fit mechanism of DNA target recognition and with the hypothesis that the preferred targets of calicheamicin, the 3' ends of oligopurine tracts, are characterized by unique conformational properties.

  8. Peptidase specificity from the substrate cleavage collection in the MEROPS database and a tool to measure cleavage site conservation

    PubMed Central

    Rawlings, Neil D.

    2016-01-01

    One peptidase can usually be distinguished from another biochemically by its action on proteins, peptides and synthetic substrates. Since 1996, the MEROPS database (http://merops.sanger.ac.uk) has accumulated a collection of cleavages in substrates that now amounts to 66,615 cleavages. The total number of peptidases for which at least one cleavage is known is 1700 out of a total of 2457 different peptidases. This paper describes how the cleavages are obtained from the scientific literature, how they are annotated and how cleavages in peptides and proteins are cross-referenced to entries in the UniProt protein sequence database. The specificity profiles of 556 peptidases are shown for which ten or more substrate cleavages are known. However, it has been proposed that at least 40 cleavages in disparate proteins are required for specificity analysis to be meaningful, and only 163 peptidases (6.6%) fulfil this criterion. Also described are the various displays shown on the website to aid with the understanding of peptidase specificity, which are derived from the substrate cleavage collection. These displays include a logo, distribution matrix, and tables to summarize which amino acids or groups of amino acids are acceptable (or not acceptable) in each substrate binding pocket. For each protein substrate, there is a display to show how it is processed and degraded. Also described are tools on the website to help with the assessment of the physiological relevance of cleavages in a substrate. These tools rely on the hypothesis that a cleavage site that is conserved in orthologues is likely to be physiologically relevant, and alignments of substrate protein sequences are made utilizing the UniRef50 database, in which in each entry sequences are 50% or more identical. Conservation in this case means substitutions are permitted only if the amino acid is known to occupy the same substrate binding pocket from at least one other substrate cleaved by the same peptidase. PMID

  9. Linear models of ovine IgG1 and IgG2 subclasses and predicted pepsin cleavage sites.

    PubMed

    Jones, Russell G A; Martino, Angela

    2016-01-05

    Highly purified specific Fab antibody fragments derived from sheep have a long history of therapeutic use as safe and effective emergency medicines. In more recent years simple low-cost methods have been developed, which take advantage of the ability of pepsin under optimally controlled conditions to preferentially digest ovine IgG within the Fc region to produce F(ab')2 and easy to remove low MW Fc sub-fragments. Despite these developments no information is currently available on the pepsin digestion of ovine IgG at the amino acid level hindering the development of improved F(ab')2 processing methods. To gain knowledge of the fragments properties we have constructed linear models of ovine IgG1 and IgG2 subclasses, starting from the gamma-1 and gamma-2 chain amino acid sequences, which also incorporate the inter- and intra-chain disulphide bonds. Any potential pepsin cleavage site was initially predicted in silico, then high probability points identified for each of the molecules and mapped onto the individual models. A theoretical order of digestion was subsequently constructed, which appeared to agree with the experimental data, suggesting an accurate prediction model for ovine IgG1 and IgG2 subclasses. These findings lay the foundations for a more detailed analysis of pepsin cleavage fragments in the future. Additionally, the F(ab')2 generated following pepsin digestion were predicted to contain subclass unique C-terminal octapeptide neoepitopes, despite the high 89% sequence identity of the intact gamma-1 and gamma-2 chain constant regions. These neoepitopes have the potential to be utilised for identification purposes once confirmed experimentally.

  10. Effects of Recognition on Subsequent Recall: Comments on "Determinants of Recognition and Recall: Accessibility and Generation"

    ERIC Educational Resources Information Center

    Broadbent, Donald E.; Broadbent, Margaret H. P.

    1977-01-01

    Attempts have been made by Rabinowitz, Mandler, and Patterson (AA 527 084) to show that both recall and recognition involve the accessibility of individual words. Their recall tests preceded recognition tests, or vice versa, thus contaminating each other; a fresh experiment is presented to confirm that this is so. (Editor)

  11. RNA Sequencing Identifies New RNase III Cleavage Sites in Escherichia coli and Reveals Increased Regulation of mRNA.

    PubMed

    Gordon, Gina C; Cameron, Jeffrey C; Pfleger, Brian F

    2017-03-28

    predictions of transcript half-life and to design synthetic transcripts with optimal stability. RNase III does not have a conserved target sequence but instead recognizes RNA secondary structure. Prior to this study, only a few RNase III target sites in E. coli were known, so we used RNA sequencing to provide a more comprehensive list of cleavage sites and to examine the impact of RNase III on transcript degradation. With this added information on how RNase III participates in transcript regulation and recycling, a more complete picture of RNA turnover can be developed for E. coli Similar approaches could be used to augment our understanding of RNA turnover in other bacteria.

  12. New Findings in Cleavage Sites Variability across Groups, Subtypes and Recombinants of Human Immunodeficiency Virus Type 1

    PubMed Central

    Torrecilla, Esther; Llácer Delicado, Teresa; Holguín, África

    2014-01-01

    Background Polymorphisms at cleavage sites (CS) can influence Gag and Pol proteins processing by the viral protease (PR), restore viral fitness and influence the virological outcome of specific antiretroviral drugs. However, data of HIV-1 variant-associated CS variability is scarce. Methods In this descriptive research, we examine the effect of HIV-1 variants on CS conservation using all 9,028 gag and 3,906 pol HIV-1 sequences deposited in GenBank, focusing on the 110 residues (10 per site) involved at 11 CS: P17/P24, P24/P2, P2/P7, P7/P1, P1/P6gag, NC/TFP, TFP/P6pol, P6pol/PR, PR/RTp51, RTp51/RTp66 and RTp66/IN. CS consensus amino acid sequences across HIV-1 groups (M, O, N, P), group M 9 subtypes and 51 circulating recombinant forms (CRF) were inferred from our alignments and compared to the HIV-1 consensus-of-consensuses sequence provided by GenBank. Results In all HIV-1 variants, the most conserved CS were PR/RTp51, RTp51/RTp66, P24/P2 and RTp66/IN and the least P2/P7 and P6pol/PR. Conservation was significantly lower in subtypes vs. recombinants in P2/P7 and TFP/P6pol and higher in P17/P24. We found a significantly higher conservation rate among Group M vs. non-M Groups HIV-1. The late processing sites at Gag (P7/P1) and GagPol precursors (PR/RTp51) presented a significantly higher conservation vs. the first CS (P2/P7) in the 4 HIV-1 groups. Here we show 52 highly conserved residues across HIV-1 variants in 11 CS and the amino acid consensus sequence in each HIV-1 group and HIV-1 group M variant for each 11 CS. Conclusions This is the first study to describe the CS conservation level across all HIV-1 variants and 11 sites in one of the largest available sequence HIV-1 dataset. These results could help other researchers for the future design of both novel antiretroviral agents acting as maturation inhibitors as well as for vaccine targeting CS. PMID:24516589

  13. Recognition determinants of broadly neutralizing human antibodies against dengue viruses.

    PubMed

    Rouvinski, Alexander; Guardado-Calvo, Pablo; Barba-Spaeth, Giovanna; Duquerroy, Stéphane; Vaney, Marie-Christine; Kikuti, Carlos M; Navarro Sanchez, M Erika; Dejnirattisai, Wanwisa; Wongwiwat, Wiyada; Haouz, Ahmed; Girard-Blanc, Christine; Petres, Stéphane; Shepard, William E; Desprès, Philippe; Arenzana-Seisdedos, Fernando; Dussart, Philippe; Mongkolsapaya, Juthathip; Screaton, Gavin R; Rey, Félix A

    2015-04-02

    Dengue disease is caused by four different flavivirus serotypes, which infect 390 million people yearly with 25% symptomatic cases and for which no licensed vaccine is available. Recent phase III vaccine trials showed partial protection, and in particular no protection for dengue virus serotype 2 (refs 3, 4). Structural studies so far have characterized only epitopes recognized by serotype-specific human antibodies. We recently isolated human antibodies potently neutralizing all four dengue virus serotypes. Here we describe the X-ray structures of four of these broadly neutralizing antibodies in complex with the envelope glycoprotein E from dengue virus serotype 2, revealing that the recognition determinants are at a serotype-invariant site at the E-dimer interface, including the exposed main chain of the E fusion loop and the two conserved glycan chains. This 'E-dimer-dependent epitope' is also the binding site for the viral glycoprotein prM during virus maturation in the secretory pathway of the infected cell, explaining its conservation across serotypes and highlighting an Achilles' heel of the virus with respect to antibody neutralization. These findings will be instrumental for devising novel immunogens to protect simultaneously against all four serotypes of dengue virus.

  14. Optimization of a multi-stage, multi-subunit malaria vaccine candidate for the production in Pichia pastoris by the identification and removal of protease cleavage sites.

    PubMed

    Spiegel, Holger; Schinkel, Helga; Kastilan, Robin; Dahm, Pia; Boes, Alexander; Scheuermayer, Matthias; Chudobová, Ivana; Maskus, Dominika; Fendel, Rolf; Schillberg, Stefan; Reimann, Andreas; Fischer, Rainer

    2015-04-01

    We demonstrated the successful optimization of a recombinant multi-subunit malaria vaccine candidate protein for production in the methylotrophic yeast Pichia pastoris by the identification and subsequent removal of two protease cleavage sites. After observing protein degradation in the culture supernatant of a fed-batch fermentation, the predominant proteolytic fragment of the secreted recombinant protein was analyzed by mass spectrometry. The MS data indicated the cleavage of an amino acid sequence matching the yeast KEX2-protease consensus motif EKRE. The cleavage in this region was completely abolished by the deletion of the EKRE motif in a modified variant. This modified variant was produced, purified, and used for immunization of rabbits, inducing high antigen specific antibody titers (2 × 10(6) ). Total IgG from rabbit immune sera recognized different stages of Plasmodium falciparum parasites in immunofluorescence assays, indicating native folding of the vaccine candidate. However, the modified variant was still degraded, albeit into different fragments. Further analysis by mass spectrometry and N-terminal sequencing revealed a second cleavage site downstream of the motif PEVK. We therefore removed a 17-amino-acid stretch including the PEVK motif, resulting in the subsequent production of the full-length recombinant vaccine candidate protein without significant degradation, with a yield of 53 mg per liter culture volume. We clearly demonstrate that the proteolytic degradation of recombinant proteins by endogenous P. pastoris proteases can be prevented by the identification and removal of such cleavage sites. This strategy is particularly relevant for the production of recombinant subunit vaccines, where product yield and stability play a more important role than for the production of a stringently-defined native sequence which is necessary for most therapeutic molecules.

  15. Visual Flight Feedback as a Determiner of Motor Response Recognition

    ERIC Educational Resources Information Center

    Newell, K. M.

    1975-01-01

    In this study, over a series of learning trials of projecting a ball a criterion distance, the hypotheses were tested and confirmed that withdrawal of visual feedback of the flight of the ball would produce a decrement in response recognition but not recall. (JS)

  16. Transcriptome-Wide Cleavage Site Mapping on Cellular mRNAs Reveals Features Underlying Sequence-Specific Cleavage by the Viral Ribonuclease SOX

    PubMed Central

    Gaglia, Marta Maria; Rycroft, Chris H.; Glaunsinger, Britt A.

    2015-01-01

    Many viruses express factors that reduce host gene expression through widespread degradation of cellular mRNA. An example of this class of proteins is the mRNA-targeting endoribonuclease SOX from the gamma-herpesvirus Kaposi’s sarcoma-associated herpesvirus (KSHV). Previous studies indicated that cleavage of messenger RNAs (mRNA) by SOX occurs at specific locations defined by the sequence of the target RNA, which is at odds with the down-regulation of a large portion of cellular transcripts. In this study, we address this paradox by using high-throughput sequencing of cleavage intermediates combined with a custom bioinformatics-based analysis pipeline to identify SOX cleavage sites across the mRNA transcriptome. These data, coupled with targeted mutagenesis, reveal that while cleavage sites are specific and reproducible, they are defined by a degenerate sequence motif containing a small number of conserved residues rather than a strong consensus sequence. This degenerate element is well represented in both human and KSHV mRNA, and its presence correlates with RNA destabilization by SOX. This represents a new endonuclease targeting strategy, in which use of a degenerate targeting element enables RNA cleavage at specific locations without restricting the range of targets. Furthermore, it shows that strong target selectivity can be achieved without a high degree of sequence specificity. PMID:26646420

  17. sgRNAcas9: a software package for designing CRISPR sgRNA and evaluating potential off-target cleavage sites.

    PubMed

    Xie, Shengsong; Shen, Bin; Zhang, Chaobao; Huang, Xingxu; Zhang, Yonglian

    2014-01-01

    Although the CRISPR/Cas9/sgRNA system efficiently cleaves intracellular DNA at desired target sites, major concerns remain on potential "off-target" cleavage that may occur throughout the whole genome. In order to improve CRISPR-Cas9 specificity for targeted genome editing and transcriptional control, we describe a bioinformatics tool "sgRNAcas9", which is a software package developed for fast design of CRISPR sgRNA with minimized off-target effects. This package consists of programs to perform a search for CRISPR target sites (protospacers) with user-defined parameters, predict genome-wide Cas9 potential off-target cleavage sites (POT), classify the POT into three categories, batch-design oligonucleotides for constructing 20-nt (nucleotides) or truncated sgRNA expression vectors, extract desired length nucleotide sequences flanking the on- or off-target cleavage sites for designing PCR primer pairs to validate the mutations by T7E1 cleavage assay. Importantly, by identifying potential off-target sites in silico, the sgRNAcas9 allows the selection of more specific target sites and aids the identification of bona fide off-target sites, significantly facilitating the design of sgRNA for genome editing applications. sgRNAcas9 software package is publicly available at BiooTools website (www.biootools.com) under the terms of the GNU General Public License.

  18. Development of a novel anti-HIV-1 agent from within: Effect of chimeric Vpr-containing protease cleavage site residues on virus replication

    PubMed Central

    Serio, D.; Rizvi, T. A.; Cartas, M.; Kalyanaraman, V. S.; Weber, I. T.; Koprowski, H.; Srinivasan, A.

    1997-01-01

    Effective antiviral agents will be of great value in controlling virus replication and delaying the onset of HIV-1-related disease symptoms. Current therapy involves the use of antiviral agents that target the enzymatic functions of the virus, resulting in the emergence of resistant viruses to these agents, thus lowering their effectiveness. To overcome this problem, we have considered the idea of developing novel agents from within HIV-1 as inhibitors of virus replication. The specificity of the Vpr protein for the HIV-1 virus particle makes it an attractive molecule for the development of antiviral agents targeting the events associated with virus maturation. We have generated chimeric Vpr proteins containing HIV-1-specific sequences added to the C terminus of Vpr. These sequences correspond to nine cleavage sites of the Gag and Gag–Pol precursors of HIV-1. The chimeric Vpr constructs were introduced into HIV-1 proviral DNA to assess their effect on virus infectivity using single- and multiple-round replication assays. The virus particles generated exhibited a variable replication pattern depending on the protease cleavage site used as a fusion partner. Interestingly, the chimeric Vpr containing the cleavage sequences from the junction of p24 and p2, 24/2, completely abolished virus infectivity. These results show that chimeric proteins generated from within HIV-1 have the ability to suppress HIV-1 replication and make ideal agents for gene therapy or intracellular immunization to treat HIV-1 infection. PMID:9096396

  19. The cleavage sites and localization of genes encoding the restriction endonucleases Eco1831I and EcoHI.

    PubMed

    Kravetz, A N; Zakharova, M V; Beletskaya, I V; Sineva, E V; Denjmuchametov, M M; Petrov, S I; Glatman, L I; Solonin, A S

    1993-07-15

    The restriction endonucleases Eco1831I and EcoHI cleave before the first 5'-cytosine in the recognition sequence 5'-decreases CCSGG--3'/3'--GGSCC increases-5' (where S = G or C), generate 5-base 5' cohesive ends, and are encoded by homologous plasmids that are restricted in McrA+ hosts. Thus, they differ in their cleavage specificity from that of the BcnI isoschizomer, which cleaves after the second 5' cytosine.

  20. Structural determinants of RNA recognition and cleavage by Dicer.

    PubMed

    MacRae, Ian J; Zhou, Kaihong; Doudna, Jennifer A

    2007-10-01

    A hallmark of RNA interference is the production of short double-stranded RNA (dsRNA) molecules 21-28 nucleotides in length by the specialized RNase III protein Dicer. Dicer enzymes uniquely generate RNA products of specific lengths by mechanisms that have not been fully elucidated. Here we show that the PAZ domain responsible for dsRNA end recognition confers this measuring ability through both its structural position and RNA-binding specificity. Point mutations define the dsRNA-binding surface and reveal a protein loop important for cleavage of substrates containing perfect or imperfect base pairing. On the basis of these results, we reengineered Dicer with a U1A RNA-binding domain in place of the PAZ domain to create an enzyme with altered end-recognition specificity and RNA product length. These results explain how Dicer functions as a molecular ruler and provide a structural basis for modifying its activity in cells.

  1. Genetic determinants of self identity and social recognition in bacteria.

    PubMed

    Gibbs, Karine A; Urbanowski, Mark L; Greenberg, E Peter

    2008-07-11

    The bacterium Proteus mirabilis is capable of movement on solid surfaces by a type of motility called swarming. Boundaries form between swarming colonies of different P. mirabilis strains but not between colonies of a single strain. A fundamental requirement for boundary formation is the ability to discriminate between self and nonself. We have isolated mutants that form boundaries with their parent. The mutations map within a six-gene locus that we term ids for identification of self. Five of the genes in the ids locus are required for recognition of the parent strain as self. Three of the ids genes are interchangeable between strains, and two encode specific molecular identifiers.

  2. Determinants of novel object and location recognition during development.

    PubMed

    Jablonski, S A; Schreiber, W B; Westbrook, S R; Brennan, L E; Stanton, M E

    2013-11-01

    In the novel object recognition (OR) paradigm, rats are placed in an arena where they encounter two sample objects during a familiarization phase. A few minutes later, they are returned to the same arena and are presented with a familiar object and a novel object. The object location recognition (OL) variant involves the same familiarization procedure but during testing one of the familiar objects is placed in a novel location. Normal adult rats are able to perform both the OR and OL tasks, as indicated by enhanced exploration of the novel vs. the familiar test item. Rats with hippocampal lesions perform the OR but not OL task indicating a role of spatial memory in OL. Recently, these tasks have been used to study the ontogeny of spatial memory but the literature has yielded conflicting results. The current experiments add to this literature by: (1) behaviorally characterizing these paradigms in postnatal day (PD) 21, 26 and 31-day-old rats; (2) examining the role of NMDA systems in OR vs. OL; and (3) investigating the effects of neonatal alcohol exposure on both tasks. Results indicate that normal-developing rats are able to perform OR and OL by PD21, with greater novelty exploration in the OR task at each age. Second, memory acquisition in the OL but not OR task requires NMDA receptor function in juvenile rats [corrected]. Lastly, neonatal alcohol exposure does not disrupt performance in either task. Implications for the ontogeny of incidental spatial learning and its disruption by developmental alcohol exposure are discussed.

  3. Probing the Specificity Determinants of Amino Acid Recognition by Arginase

    SciTech Connect

    Shishova, E.; Di Costanzo, L; Emig, F; Ash, D; Christianson, D

    2009-01-01

    Arginase is a binuclear manganese metalloenzyme that serves as a therapeutic target for the treatment of asthma, erectile dysfunction, and atherosclerosis. In order to better understand the molecular basis of inhibitor affinity, we have employed site-directed mutagenesis, enzyme kinetics, and X-ray crystallography to probe the molecular recognition of the amino acid moiety (i.e., the ?-amino and ?-carboxylate groups) of substrate l-arginine and inhibitors in the active site of arginase I. Specifically, we focus on (1) a water-mediated hydrogen bond between the substrate ?-carboxylate and T135, (2) a direct hydrogen bond between the substrate ?-carboxylate and N130, and (3) a direct charged hydrogen bond between the substrate ?-amino group and D183. Amino acid substitutions for T135, N130, and D183 generally compromise substrate affinity as reflected by increased KM values but have less pronounced effects on catalytic function as reflected by minimal variations of kcat. As with substrate KM values, inhibitor Kd values increase for binding to enzyme mutants and suggest that the relative contribution of intermolecular interactions to amino acid affinity in the arginase active site is water-mediated hydrogen bond < direct hydrogen bond < direct charged hydrogen bond. Structural comparisons of arginase with the related binuclear manganese metalloenzymes agmatinase and proclavaminic acid amidinohydrolase suggest that the evolution of substrate recognition in the arginase fold occurs by mutation of residues contained in specificity loops flanking the mouth of the active site (especially loops 4 and 5), thereby allowing diverse guanidinium substrates to be accommodated for catalysis.

  4. A strategy for fusion expression and preparation of functional glucagon-like peptide-1 (GLP-1) analogue by introducing an enterokinase cleavage site.

    PubMed

    Liu, Yang; Ren, Limei; Ge, Lingmiao; Cui, Qingxin; Cao, Xiaofang; Hou, Yuanyuan; Bai, Fang; Bai, Gang

    2014-08-01

    KGLP-1, a 31-amino acid glucagon-like peptide-1 (GLP-1) analogue, has a great therapeutic potential for anti-diabetes. In this work, a strategy for expression and purification of functional KGLP-1 peptide has been established. KGLP-1 cDNA was fused with glutathione S-transferase (GST), with an enterokinase cleavage site in the fusion junction. The recombinant fusion protein GST-KGLP-1 was affinity purified via the GST-tag, and then digested with enterokinase. The resulting GST part as well as the enzymes were eliminated by ultra-filtration followed by size exclusion chromatograph. The yield of purified KGLP-1 was approximately 12.1 mg/L, with purity of 96.18 %. The recombinant KGLP-1 was shown to have similar bioactivity as native GLP-1 when evaluated in a Chinese hamster ovary cell line expressing a GLP-1 receptor-egfp reporter gene.

  5. Identification of the cleavage sites in the alpha6A integrin subunit: structural requirements for cleavage and functional analysis of the uncleaved alpha6Abeta1 integrin.

    PubMed Central

    Delwel, G O; Kuikman, I; van der Schors, R C; de Melker, A A; Sonnenberg, A

    1997-01-01

    The alpha6A and alpha6B integrin subunits are proteolytically cleaved during biosynthesis into a heavy chain (120 kDa) that is disulphide-linked to one of two light chains (31 or 30 kDa). Analysis of the structure of the alpha6A subunit on the carcinoma cell line T24 and human platelets demonstrated that the two light chains of alpha6 are not differentially glycosylated products of one polypeptide. Rather they possess different polypeptide backbones, which presumably result from proteolytic cleavage at distinct sites in the alpha6 precursor. Mutations were introduced in the codons for the R876KKR879, E883K884, R890K891 and R898K899 sequences, the potential proteolytic cleavage sites, and wild-type and mutant alpha6A cDNAs were transfected into K562 cells. The mutant alpha6A integrin subunits were expressed in association with endogenous beta1 at levels comparable to that of wild-type alpha6Abeta1. A single alpha6 polypeptide chain (150 kDa) was precipitated from transfectants expressing alpha6A with mutations or deletions in the RKKR sequence. Mutations in the EK sequence yielded alpha6A subunits that were cleaved once into a heavy and a light chain, whereas alpha6A subunits with mutations in one of the two RK sequences were, like wild-type alpha6A, cleaved into one heavy and two light chains. Thus a change in the RKKR sequence prevents the cleavage of alpha6. The EK site is the secondary cleavage site, which is used only when the primary site (RKKR) is intact. Microsequencing of the N-termini of the two alpha6A light chains from platelets demonstrated that cleavage occurs after Arg879 and Lys884. Because alpha6(RKKG), alpha6(GKKR) and alpha6(RGGR) subunits were not cleaved it seems that both the arginine residues and the lysine residues are essential for cleavage of RKKR. alpha6A mutants with the RKKR sequence shifted to the EK site, in such a way that the position of the arginine residue after which cleavage occurs corresponds exactly to Lys884, were partly

  6. A peptide-based approach to evaluate the adaptability of influenza A virus to humans based on its hemagglutinin proteolytic cleavage site

    PubMed Central

    Straus, Marco R.; Whittaker, Gary R.

    2017-01-01

    Cleavage activation of the hemagglutinin (HA) protein by host proteases is a crucial step in the infection process of influenza A viruses (IAV). However, IAV exists in eighteen different HA subtypes in nature and their cleavage sites vary considerably. There is uncertainty regarding which specific proteases activate a given HA in the human respiratory tract. Understanding the relationship between different HA subtypes and human-specific proteases will be valuable in assessing the pandemic potential of circulating viruses. Here we utilized fluorogenic peptides mimicking the HA cleavage motif of representative IAV strains causing disease in humans or of zoonotic/pandemic potential and tested them with a range of proteases known to be present in the human respiratory tract. Our results show that peptides from the H1, H2 and H3 subtypes are cleaved efficiently by a wide range of proteases including trypsin, matriptase, human airway tryptase (HAT), kallikrein-related peptidases 5 (KLK5) and 12 (KLK12) and plasmin. Regarding IAVs currently of concern for human adaptation, cleavage site peptides from H10 viruses showed very limited cleavage by respiratory tract proteases. Peptide mimics from H6 viruses showed broader cleavage by respiratory tract proteases, while H5, H7 and H9 subtypes showed variable cleavage; particularly matriptase appeared to be a key protease capable of activating IAVs. We also tested HA substrate specificity of Factor Xa, a protease required for HA cleavage in chicken embryos and relevant for influenza virus production in eggs. Overall our data provide novel tool allowing the assessment of human adaptation of IAV HA subtypes. PMID:28358853

  7. Requirement of helix P2.2 and nucleotide G1 for positioning the cleavage site and cofactor of the glmS ribozyme.

    PubMed

    Klein, Daniel J; Wilkinson, Sara R; Been, Michael D; Ferré-D'Amaré, Adrian R

    2007-10-12

    The glmS ribozyme is a catalytic RNA that self-cleaves at its 5'-end in the presence of glucosamine 6-phosphate (GlcN6P). We present structures of the glmS ribozyme from Thermoanaerobacter tengcongensis that are bound with the cofactor GlcN6P or the inhibitor glucose 6-phosphate (Glc6P) at 1.7 A and 2.2 A resolution, respectively. The two structures are indistinguishable in the conformations of the small molecules and of the RNA. GlcN6P binding becomes apparent crystallographically when the pH is raised to 8.5, where the ribozyme conformation is identical with that observed previously at pH 5.5. A key structural feature of this ribozyme is a short duplex (P2.2) that is formed between sequences just 3' of the cleavage site and within the core domain, and which introduces a pseudoknot into the active site. Mutagenesis indicates that P2.2 is required for activity in cis-acting and trans-acting forms of the ribozyme. P2.2 formation in a trans-acting ribozyme was exploited to demonstrate that N1 of the guanine at position 1 contributes to GlcN6P binding by interacting with the phosphate of the cofactor. At neutral pH, RNAs with adenine, 2-aminopurine, dimethyladenine or purine substitutions at position 1 cleave faster with glucosamine than with GlcN6P. This altered cofactor preference provides biochemical support for the orientation of the cofactor within the active site. Our results establish two features of the glmS ribozyme that are important for its activity: a sequence within the core domain that selects and positions the cleavage-site sequence, and a nucleobase at position 1 that helps position GlcN6P.

  8. Amylose recognition and ring-size determination of amylomaltase

    PubMed Central

    Roth, Christian; Weizenmann, Nicole; Bexten, Nicola; Saenger, Wolfram; Zimmermann, Wolfgang; Maier, Timm; Sträter, Norbert

    2017-01-01

    Starch is a major carbon and energy source throughout all kingdoms of life. It consists of two carbohydrate polymers, branched amylopectin and linear amylose, which are sparingly soluble in water. Hence, the enzymatic breakdown by glycoside hydrolases (GHs) is of great biological and societal importance. Amylomaltases (AMs) are GHs specialized in the hydrolysis of α-1,4–linked sugar chains such as amylose. They are able to catalyze an intramolecular transglycosylation of a bound sugar chain yielding polymeric sugar rings, the cycloamyloses (CAs), consisting of 20 to 100 glucose units. Despite a wealth of data on short oligosaccharide binding to GHs, no structural evidence is available for their interaction with polymeric substrates that better represent the natural polysaccharide. We have determined the crystal structure of Thermus aquaticus AM in complex with a 34-meric CA—one of the largest carbohydrates resolved by x-ray crystallography and a mimic of the natural polymeric amylose substrate. In total, 15 glucose residues interact with the protein in an extended crevice with a length of more than 40 Å. A modified succinimide, derived from aspartate, mediates protein-sugar interactions, suggesting a biological role for this nonstandard amino acid. The structure, together with functional assays, provides unique insights into the interaction of GHs with their polymeric substrate and reveals a molecular ruler mechanism for minimal ring-size determination of CA products. PMID:28097217

  9. Recognition and Specificity Determinants of the Human Cbx Chromodomains

    SciTech Connect

    Kaustov, Lilia; Ouyang, Hui; Amaya, Maria; Lemak, Alexander; Nady, Nataliya; Duan, Shili; Wasney, Gregory A.; Li, Zhihong; Vedadi, Masoud; Schapira, Matthieu; Min, Jinrong; Arrowsmith, Cheryl H.

    2011-08-17

    The eight mammalian Cbx proteins are chromodomain-containing proteins involved in regulation of heterochromatin, gene expression, and developmental programs. They are evolutionarily related to the Drosophila HP1 (dHP1) and Pc (dPc) proteins that are key components of chromatin-associated complexes capable of recognizing repressive marks such as trimethylated Lys-9 and Lys-27, respectively, on histone H3. However, the binding specificity and function of the human homologs, Cbx1-8, remain unclear. To this end we employed structural, biophysical, and mutagenic approaches to characterize the molecular determinants of sequence contextual methyllysine binding to human Cbx1-8 proteins. Although all three human HP1 homologs (Cbx1, -3, -5) replicate the structural and binding features of their dHP counterparts, the five Pc homologs (Cbx2, -4, -6, -7, -8) bind with lower affinity to H3K9me3 or H3K27me3 peptides and are unable to distinguish between these two marks. Additionally, peptide permutation arrays revealed a greater sequence tolerance within the Pc family and suggest alternative nonhistone sequences as potential binding targets for this class of chromodomains. Our structures explain the divergence of peptide binding selectivity in the Pc subfamily and highlight previously unrecognized features of the chromodomain that influence binding and specificity.

  10. Systematic Design of Trypsin Cleavage Site Mutated Exendin4-Cysteine 1, an Orally Bioavailable Glucagon-Like Peptide-1 Receptor Agonist

    PubMed Central

    Sai, Wenbo; Tian, Hong; Yang, Kangmin; Tang, Daoqi; Bao, Jinxiao; Ge, Yang; Song, Xiaoda; Zhang, Yu; Luo, Cheng; Gao, Xiangdong; Yao, Wenbing

    2017-01-01

    Exendin-4 is a strong therapeutic candidate for the treatment of metabolic syndrome. Related receptor agonist drugs have been on the market since 2005. However, technical limitations and the pain caused by subcutaneous injection have severely limited patient compliance. The goal of the study is to investigate a biologically active exendin-4 analog could be administered orally. Using intraperitoneal glucose tolerance tests, we discovered that exendin4-cysteine administered by oral gavage had a distinct hypoglycemic effect in C57BL/6J mice. Using Rosetta Design and Amber, we designed and screened a series of exendin4-cysteine analogs to identify those that retained biological activity while resisting trypsin digestion. Trypsin Cleavage Site Mutated Exendin4-cysteine 1 (TSME-1), an analog whose bioactivity was similar to exendin-4 and was almost completely resistant to trypsin, was screened out. In addition, TSME-1 significantly normalized the blood glucose levels and the availability of TSME-1 was significantly higher than that of exendin-4 and exendin4-cysteine. Collectively orally administered TSME-1, a trypsin-resistant exendin-4 analog obtained by the system, is a strong candidate for future treatments of type 2 diabetes. PMID:28282854

  11. Albumin Redhill (-1 Arg, 320 Ala yields Thr): A glycoprotein variant of human serum albumin whose precursor has an aberrant signal peptidase cleavage site

    SciTech Connect

    Brennan, S.O.; Myles, T.; Peach, R.J.; George, P.M. ); Donaldson, D. )

    1990-01-01

    Albumin Redhill is an electrophoretically slow genetic variant of human serum albumin that does not bind {sup 63}Ni{sup 2+} and has a molecular mass 2.5 kDa higher than normal albumin. Its inability to bind Ni{sup 2+} was explained by the finding of an additional residue of Arg at position -1. This did not explain the molecular basis of the genetic variation or the increase in apparent molecular mass. Fractionation of tryptic digests on concanavalin A-Sepharose followed by peptide mapping of the bound and unbound fractions and sequence analysis of the glycopeptides identified a mutation of 320 Ala {yields} Thr. This introduces as Asn-Tyr-Thr oligosaccharide attachment sequence centered on Asn-318 and explains the increase in molecular mass. This, however, did not satisfactorily explain the presence of the additional Arg residue at position -1. DNA sequencing of polymerase chain reaction-amplified genomic DNA encoding the prepro sequence of albumin indicated an additional mutation of -2 Arg {yields} Cys. The authors propose that the new Phe-Cys-Arg sequence in the propeptide is an aberrant signal peptidase cleavage site and that the signal peptidase cleaves the propeptide of albumin Redhill in the lumen of the endoplasmic reticulum before it reaches the Golgi vesicles, the site of the diarginyl-specific proalbumin convertase.

  12. APASdb: a database describing alternative poly(A) sites and selection of heterogeneous cleavage sites downstream of poly(A) signals.

    PubMed

    You, Leiming; Wu, Jiexin; Feng, Yuchao; Fu, Yonggui; Guo, Yanan; Long, Liyuan; Zhang, Hui; Luan, Yijie; Tian, Peng; Chen, Liangfu; Huang, Guangrui; Huang, Shengfeng; Li, Yuxin; Li, Jie; Chen, Chengyong; Zhang, Yaqing; Chen, Shangwu; Xu, Anlong

    2015-01-01

    Increasing amounts of genes have been shown to utilize alternative polyadenylation (APA) 3'-processing sites depending on the cell and tissue type and/or physiological and pathological conditions at the time of processing, and the construction of genome-wide database regarding APA is urgently needed for better understanding poly(A) site selection and APA-directed gene expression regulation for a given biology. Here we present a web-accessible database, named APASdb (http://mosas.sysu.edu.cn/utr), which can visualize the precise map and usage quantification of different APA isoforms for all genes. The datasets are deeply profiled by the sequencing alternative polyadenylation sites (SAPAS) method capable of high-throughput sequencing 3'-ends of polyadenylated transcripts. Thus, APASdb details all the heterogeneous cleavage sites downstream of poly(A) signals, and maintains near complete coverage for APA sites, much better than the previous databases using conventional methods. Furthermore, APASdb provides the quantification of a given APA variant among transcripts with different APA sites by computing their corresponding normalized-reads, making our database more useful. In addition, APASdb supports URL-based retrieval, browsing and display of exon-intron structure, poly(A) signals, poly(A) sites location and usage reads, and 3'-untranslated regions (3'-UTRs). Currently, APASdb involves APA in various biological processes and diseases in human, mouse and zebrafish.

  13. Substrate recognition by ribonucleoprotein ribonuclease MRP.

    PubMed

    Esakova, Olga; Perederina, Anna; Quan, Chao; Berezin, Igor; Krasilnikov, Andrey S

    2011-02-01

    The ribonucleoprotein complex ribonuclease (RNase) MRP is a site-specific endoribonuclease essential for the survival of the eukaryotic cell. RNase MRP closely resembles RNase P (a universal endoribonuclease responsible for the maturation of the 5' ends of tRNA) but recognizes distinct substrates including pre-rRNA and mRNA. Here we report the results of an in vitro selection of Saccharomyces cerevisiae RNase MRP substrates starting from a pool of random sequences. The results indicate that RNase MRP cleaves single-stranded RNA and is sensitive to sequences in the immediate vicinity of the cleavage site requiring a cytosine at the position +4 relative to the cleavage site. Structural implications of the differences in substrate recognition by RNases P and MRP are discussed.

  14. Differential DNA sequence recognition is a determinant of specificity in homeotic gene action.

    PubMed Central

    Ekker, S C; von Kessler, D P; Beachy, P A

    1992-01-01

    The homeotic genes of Drosophila encode transcriptional regulatory proteins that specify distinct segment identities. Previous studies have implicated the homeodomain as a major determinant of biological specificity within these proteins, but have not established the physical basis of this specificity. We show here that the homeodomains encoded by the Ultrabithorax and Deformed homeotic genes bind optimally to distinct DNA sequences and have mapped the determinants responsible for differential recognition. We further show that relative transactivation by these two proteins in a simple in vivo system can differ by nearly two orders of magnitude. Such differences in DNA sequence recognition and target activation provide a biochemical basis for at least part of the biological specificity of homeotic gene action. Images PMID:1356765

  15. Human cytomegalovirus maturational proteinase: expression in Escherichia coli, purification, and enzymatic characterization by using peptide substrate mimics of natural cleavage sites.

    PubMed Central

    Burck, P J; Berg, D H; Luk, T P; Sassmannshausen, L M; Wakulchik, M; Smith, D P; Hsiung, H M; Becker, G W; Gibson, W; Villarreal, E C

    1994-01-01

    The proteolytic processing of the human cytomegalovirus (HCMV) assembly protein, resulting in truncation of its C terminus, is an essential step in virion maturation. The proteinase responsible for this cleavage is the amino-terminal half of the protein encoded by the UL80a open reading fame. We have obtained high expression levels of this 256-amino-acid HCMV proteinase, assemblin, in Escherichia coli. In addition to the 28-kDa proteinase, a 15-kDa protein comprising the first 143 amino acids and a 13-kDa protein comprising the last 113 amino acids of the 28-kDa HCMV proteinase were present. Both the 28-kDa proteinase and the 15-kDa protein were purified by a two-step chromatographic procedure utilizing anion exchange in urea and dithiothreitol and size exclusion in NaSCN and dithiothreitol. Activation of the purified 28-kDa proteinase required denaturation in urea as well as complete reduction of all five cysteine residues in the molecule. Removal of the urea by dialysis with retention of the reducing agent yielded an active proteinase. Addition of glycerol to 50% enhanced the activity. The HCMV proteinase cleaved the peptides RGVVNASSRLAK and SYVKASVSPE, which are mimics of the maturational (M)- and release (R)-site sequences, respectively, in the UL80a-encoded protein. The cleavage site in the peptides was at the same Ala-Ser scissile bond as observed in the UL80a protein. The Km value for the cleavage of RGVVNASSRLAK (M-site mimic) by the proteinase was similar to that for SYVKASVSPE (R-site mimic), but the turnover (kcat) of the M-site peptide mimic substrate by the proteinase was six to eight times faster. The peptide homologs of the herpes simplex virus type 1 M- and R-site sequences in the UL26-encoded protein were also cleaved by the HCMV proteinase, although at rates slower than those for the HCMV substrates. The HCMV proteinase was inhibited by Zn2+ and by alkylating agents, but only at very high inhibitor concentrations. The purified 15-kDa protein

  16. Determinants of tRNA Recognition by the Radical SAM Enzyme RlmN

    PubMed Central

    Fitzsimmons, Christina M.; Fujimori, Danica Galonić

    2016-01-01

    RlmN, a bacterial radical SAM methylating enzyme, has the unusual ability to modify two distinct types of RNA: 23S rRNA and tRNA. In rRNA, RlmN installs a methyl group at the C2 position of A2503 of 23S rRNA, while in tRNA the modification occurs at nucleotide A37, immediately adjacent to the anticodon triplet. Intriguingly, only a subset of tRNAs that contain an adenosine at position 37 are substrates for RlmN, suggesting that the enzyme carefully probes the highly conserved tRNA fold and sequence features to identify its targets. Over the past several years, multiple studies have addressed rRNA modification by RlmN, while relatively few investigations have focused on the ability of this enzyme to modify tRNAs. In this study, we utilized in vitro transcribed tRNAs as model substrates to interrogate RNA recognition by RlmN. Using chimeras and point mutations, we probed how the structure and sequence of RNA influences methylation, identifying position 38 of tRNAs as a critical determinant of substrate recognition. We further demonstrate that, analogous to previous mechanistic studies with fragments of 23S rRNA, tRNA methylation requirements are consistent with radical SAM reactivity. Together, our findings provide detailed insight into tRNA recognition by a radical SAM methylating enzyme. PMID:27902775

  17. Neutrophil proteinase cathepsin G is proteolytically active on the human platelet glycoprotein Ib-IX receptor: characterization of the cleavage sites within the glycoprotein Ib alpha subunit.

    PubMed Central

    Pidard, D; Renesto, P; Berndt, M C; Rabhi, S; Clemetson, K J; Chignard, M

    1994-01-01

    The proteolytic activity of the neutrophil serine-proteinase cathepsin G (CG) on platelet adherence receptors, the glycoprotein (GP) Ib-IX complex and the integrin alpha IIb beta 3, has been investigated. In the range 50 to 200 nmol/l, CG is a potent platelet agonist which induces shape change, granule exocytosis and aggregation. Investigation of the proteolysis of the receptors' subunits during the course of platelet activation by CG was performed by immunoblot analysis of platelet proteins using a panel of specific antibodies. Exposure of platelets for 3 min at 37 degrees C to CG at a concentration that induces full cell activation resulted in an extensive cleavage of the N-terminal region of the extracellular domain of GPIb alpha, the largest (relative molecular mass, M(r), 143,000) of the three subunits constituting the GPIb-IX complex. In contrast, no detectable proteolytic modification of the two other subunits, GPIb beta and GPIX, was detected. Similarly, we observed that neither of the two subunits of the alpha IIb beta 3 receptor were proteolytically modified by CG. Cleavage of GPIb alpha by CG leaves a remnant of the polypeptide chain with M(r) approx. 106,000 in the plasma membrane, while releasing into the extracellular milieu the N-terminal domain with M(r) in the range 40,000 to 46,000. N-terminal sequencing of the CG-derived fragments of GPIb alpha indicated that the Leu275-Tyr276 peptide bond was the primary cleavage site for this proteinase. Proteolysis of GPIb alpha was already detectable at concentrations of CG as low as 25 nmol/l, while with 200 nmol/l the cleavage was detected as soon as 10 s after exposure of platelets to the proteinase. Comparison of the kinetics and concentration dependency for the proteolysis of GPIb alpha and for the activation of platelets by CG showed that cleavage of the GPIb-IX receptor is an early event that accompanies exocytosis and aggregation. Quantitative evaluation of the conversion of GPIb alpha into its

  18. Mutation of the f-protein cleavage site of avian paramyxovirus type 7 results in furin cleavage, fusion promotion, and increased replication in vitro but not increased replication, tissue tropism, or virulence in chickens.

    PubMed

    Xiao, Sa; Khattar, Sunil K; Subbiah, Madhuri; Collins, Peter L; Samal, Siba K

    2012-04-01

    We constructed a reverse genetics system for avian paramyxovirus serotype 7 (APMV-7) to investigate the role of the fusion F glycoprotein in tissue tropism and virulence. The AMPV-7 F protein has a single basic residue arginine (R) at position -1 in the F cleavage site sequence and also is unusual in having alanine at position +2 (LPSSR↓FA) (underlining indicates the basic amino acids at the F protein cleavage site, and the arrow indicates the site of cleavage.). APMV-7 does not form syncytia or plaques in cell culture, but its replication in vitro does not depend on, and is not increased by, added protease. Two mutants were successfully recovered in which the cleavage site was modified to mimic sites that are found in virulent Newcastle disease virus isolates and to contain 4 or 5 basic residues as well as isoleucine in the +2 position: (RRQKR↓FI) or (RRKKR↓FI), named Fcs-4B or Fcs-5B, respectively. In cell culture, one of the mutants, Fcs-5B, formed protease-independent syncytia and grew to 10-fold-higher titers compared to the parent and Fcs-4B viruses. This indicated the importance of the single additional basic residue (K) at position -3. Syncytium formation and virus yield of the Fcs-5B virus was impaired by the furin inhibitor decanoyl-RVKR-CMK, whereas parental APMV-7 was not affected. APMV-7 is avirulent in chickens and is limited in tropism to the upper respiratory tract of 1-day-old and 2-week-old chickens, and these characteristics were unchanged for the two mutant viruses. Thus, the acquisition of furin cleavability by APMV-7 resulted in syncytium formation and increased virus yield in vitro but did not alter virus yield, tropism, or virulence in chickens.

  19. On the Psychology of the Recognition Heuristic: Retrieval Primacy as a Key Determinant of Its Use

    ERIC Educational Resources Information Center

    Pachur, Thorsten; Hertwig, Ralph

    2006-01-01

    The recognition heuristic is a prime example of a boundedly rational mind tool that rests on an evolved capacity, recognition, and exploits environmental structures. When originally proposed, it was conjectured that no other probabilistic cue reverses the recognition-based inference (D. G. Goldstein & G. Gigerenzer, 2002). More recent studies…

  20. Chiral recognition and determination of enantiomeric excess by mass spectrometry: A review.

    PubMed

    Yu, Xiangying; Yao, Zhong-Ping

    2017-05-22

    Chiral analysis is of great importance to fundamental and applied research in chemical, biological and pharmaceutical sciences. Due to the superiority of mass spectrometry (MS) over other analytical methods in terms of speed, specificity and sensitivity, chiral analysis by MS has attracted much interest in recent years. Chiral analysis by MS typically involves introduction of a chiral selector to form diastereomers with analyte enantiomers, and comparison of the behaviors of diastereomers in MS. Chiral differentiation can be achieved by comparing the relative abundances of diastereomers, the thermodynamic or kinetic constants of ion-molecule reactions of diastereomers in the gas phase, the dissociation of diastereomers in MS/MS, or the mobility of diastereomers in ion mobility mass spectrometry. In this review, chiral recognition and determination of enantiomeric excess by these chiral MS methods were summarized, and the prospects of chiral analysis by MS were discussed.

  1. In Vivo Recognition of Ovalbumin Expressed by Transgenic Leishmania Is Determined by Its Subcellular Localization1

    PubMed Central

    Prickett, Sara; Gray, Peter M.; Colpitts, Sara L.; Scott, Phillip; Kaye, Paul M.; Smith, Deborah F.

    2009-01-01

    The importance of the site of Ag localization within microbial pathogens for the effective generation of CD8+ T cells has been studied extensively, generally supporting the view that Ag secretion within infected target cells is required for optimal MHC class I-restricted Ag presentation. In contrast, relatively little is known about the importance of pathogen Ag localization for the activation of MHC class II-restricted CD4+ T cells, despite their clear importance for host protection. We have used the N-terminal targeting sequence of Leishmania major hydrophilic acylated surface protein B to generate stable transgenic lines expressing physiologically relevant levels of full-length OVA on the surface of metacyclic promastigotes and amastigotes. In addition, we have mutated the hydrophilic acylated surface protein B N-terminal acylation sequence to generate control transgenic lines in which OVA expression is restricted to the parasite cytosol. In vitro, splenic dendritic cells are able to present membrane-localized, but not cytosolic, OVA to OVA-specific DO.11 T cells. Strikingly and unexpectedly, surface localization of OVA is also a strict requirement for recognition by OVA-specific T cells (DO.11 and OT-II) and for the development of OVA-specific Ab responses in vivo. However, recognition of cytosolic OVA could be observed with increasing doses of infection. These data suggest that, even under in vivo conditions, where varied pathways of Ag processing are likely to operate, the site of Leishmania Ag localization is an important determinant of immunogenicity and hence an important factor when considering the likely candidacy of vaccine Ags for inducing CD4+ T cell-dependent immunity. PMID:16585577

  2. Evolution of CRISPR RNA recognition and processing by Cas6 endonucleases.

    PubMed

    Niewoehner, Ole; Jinek, Martin; Doudna, Jennifer A

    2014-01-01

    In many bacteria and archaea, small RNAs derived from clustered regularly interspaced short palindromic repeats (CRISPRs) associate with CRISPR-associated (Cas) proteins to target foreign DNA for destruction. In Type I and III CRISPR/Cas systems, the Cas6 family of endoribonucleases generates functional CRISPR-derived RNAs by site-specific cleavage of repeat sequences in precursor transcripts. CRISPR repeats differ widely in both sequence and structure, with varying propensity to form hairpin folds immediately preceding the cleavage site. To investigate the evolution of distinct mechanisms for the recognition of diverse CRISPR repeats by Cas6 enzymes, we determined crystal structures of two Thermus thermophilus Cas6 enzymes both alone and bound to substrate and product RNAs. These structures show how the scaffold common to all Cas6 endonucleases has evolved two binding sites with distinct modes of RNA recognition: one specific for a hairpin fold and the other for a single-stranded 5'-terminal segment preceding the hairpin. These findings explain how divergent Cas6 enzymes have emerged to mediate highly selective pre-CRISPR-derived RNA processing across diverse CRISPR systems.

  3. D-Isonucleotide (isoNA) incorporation around cleavage site of passenger strand promotes the vibration of Ago2-PAZ domain and enhances in vitro potency of siRNA.

    PubMed

    Huang, Ye; Tian, Miao; Zhang, Yichao; Sheng, Gang; Chen, Zhuo; Ma, Yuan; Chen, Yue; Peng, Yihong; Zhao, Yi-Lei; Wang, Yanli; Zhang, Lihe; Yang, Zhenjun

    2015-11-28

    It has been demonstrated that passenger strand cleavage is important for the activation of RNA-induced silencing complex (RISC), which is a crucial step for siRNA-mediated gene silencing. Herein, we report that isonucleotide (isoNA) modification around the cleavage site of the passenger strand would affect the in vitro potency of modified siRNAs by altering the motion pattern of the Ago2-PAZ domain. According to western blotting, q-PCR and antiviral test results, we proved that D-isonucleotide (isoNA) modification at the position 8 of the passenger strand (siMek1-S08D), which is adjacent to the cleavage site, markedly improved the in vitro potency of the modified siRNA, whereas siRNAs with D-isoNA incorporation at position 9 (siMek1-S09D) or L-isoNA incorporation at positions 8 and 9 (siMek1-S08L, siMek1-S09L) displayed lower activity compared to native siRNA. Kinetics evaluation of passenger strand cleavage induced by T. thermophilus Ago (Tt-Ago) showed that D-isoNA modification at position 8 of the passenger strand had no significant influence on the cleavage rate, but L-isoNA modification at position 8 slowed the cleavage rate markedly. Moreover, the results of molecular dynamics simulations showed that D-isoNA modification at position 8 affected the open-close motion of the PAZ domain in the Ago/siRNA complex, which may promote the loading of RISC and release of a passenger strand cleavage product, and consequently accelerate the activation of RISC and enhance silencing activity. However, D-isoNA modification at position 9 or L-isoNA modification at position 8 or 9 exerted opposite influences on the motion of the Ago-PAZ domain.

  4. N-Glycosylation Improves the Pepsin Resistance of Histidine Acid Phosphatase Phytases by Enhancing Their Stability at Acidic pHs and Reducing Pepsin's Accessibility to Its Cleavage Sites.

    PubMed

    Niu, Canfang; Luo, Huiying; Shi, Pengjun; Huang, Huoqing; Wang, Yaru; Yang, Peilong; Yao, Bin

    2015-12-04

    N-Glycosylation can modulate enzyme structure and function. In this study, we identified two pepsin-resistant histidine acid phosphatase (HAP) phytases from Yersinia kristensenii (YkAPPA) and Yersinia rohdei (YrAPPA), each having an N-glycosylation motif, and one pepsin-sensitive HAP phytase from Yersinia enterocolitica (YeAPPA) that lacked an N-glycosylation site. Site-directed mutagenesis was employed to construct mutants by altering the N-glycosylation status of each enzyme, and the mutant and wild-type enzymes were expressed in Pichia pastoris for biochemical characterization. Compared with those of the N-glycosylation site deletion mutants and N-deglycosylated enzymes, all N-glycosylated counterparts exhibited enhanced pepsin resistance. Introduction of the N-glycosylation site into YeAPPA as YkAPPA and YrAPPA conferred pepsin resistance, shifted the pH optimum (0.5 and 1.5 pH units downward, respectively) and improved stability at acidic pH (83.2 and 98.8% residual activities at pH 2.0 for 1 h). Replacing the pepsin cleavage sites L197 and L396 in the immediate vicinity of the N-glycosylation motifs of YkAPPA and YrAPPA with V promoted their resistance to pepsin digestion when produced in Escherichia coli but had no effect on the pepsin resistance of N-glycosylated enzymes produced in P. pastoris. Thus, N-glycosylation may improve pepsin resistance by enhancing the stability at acidic pH and reducing pepsin's accessibility to peptic cleavage sites. This study provides a strategy, namely, the manipulation of N-glycosylation, for improvement of phytase properties for use in animal feed.

  5. N-Glycosylation Improves the Pepsin Resistance of Histidine Acid Phosphatase Phytases by Enhancing Their Stability at Acidic pHs and Reducing Pepsin's Accessibility to Its Cleavage Sites

    PubMed Central

    Niu, Canfang; Luo, Huiying; Shi, Pengjun; Huang, Huoqing; Wang, Yaru; Yang, Peilong

    2015-01-01

    N-Glycosylation can modulate enzyme structure and function. In this study, we identified two pepsin-resistant histidine acid phosphatase (HAP) phytases from Yersinia kristensenii (YkAPPA) and Yersinia rohdei (YrAPPA), each having an N-glycosylation motif, and one pepsin-sensitive HAP phytase from Yersinia enterocolitica (YeAPPA) that lacked an N-glycosylation site. Site-directed mutagenesis was employed to construct mutants by altering the N-glycosylation status of each enzyme, and the mutant and wild-type enzymes were expressed in Pichia pastoris for biochemical characterization. Compared with those of the N-glycosylation site deletion mutants and N-deglycosylated enzymes, all N-glycosylated counterparts exhibited enhanced pepsin resistance. Introduction of the N-glycosylation site into YeAPPA as YkAPPA and YrAPPA conferred pepsin resistance, shifted the pH optimum (0.5 and 1.5 pH units downward, respectively) and improved stability at acidic pH (83.2 and 98.8% residual activities at pH 2.0 for 1 h). Replacing the pepsin cleavage sites L197 and L396 in the immediate vicinity of the N-glycosylation motifs of YkAPPA and YrAPPA with V promoted their resistance to pepsin digestion when produced in Escherichia coli but had no effect on the pepsin resistance of N-glycosylated enzymes produced in P. pastoris. Thus, N-glycosylation may improve pepsin resistance by enhancing the stability at acidic pH and reducing pepsin's accessibility to peptic cleavage sites. This study provides a strategy, namely, the manipulation of N-glycosylation, for improvement of phytase properties for use in animal feed. PMID:26637601

  6. Deformability in the cleavage site of primary microRNA is not sensed by the double-stranded RNA binding domains in the microprocessor component DGCR8.

    PubMed

    Quarles, Kaycee A; Chadalavada, Durga; Showalter, Scott A

    2015-06-01

    The prevalence of double-stranded RNA (dsRNA) in eukaryotic cells has only recently been appreciated. Of interest here, RNA silencing begins with dsRNA substrates that are bound by the dsRNA-binding domains (dsRBDs) of their processing proteins. Specifically, processing of microRNA (miRNA) in the nucleus minimally requires the enzyme Drosha and its dsRBD-containing cofactor protein, DGCR8. The smallest recombinant construct of DGCR8 that is sufficient for in vitro dsRNA binding, referred to as DGCR8-Core, consists of its two dsRBDs and a C-terminal tail. As dsRBDs rarely recognize the nucleotide sequence of dsRNA, it is reasonable to hypothesize that DGCR8 function is dependent on the recognition of specific structural features in the miRNA precursor. Previously, we demonstrated that noncanonical structural elements that promote RNA flexibility within the stem of miRNA precursors are necessary for efficient in vitro cleavage by reconstituted Microprocessor complexes. Here, we combine gel shift assays with in vitro processing assays to demonstrate that neither the N-terminal dsRBD of DGCR8 in isolation nor the DGCR8-Core construct is sensitive to the presence of noncanonical structural elements within the stem of miRNA precursors, or to single-stranded segments flanking the stem. Extending DGCR8-Core to include an N-terminal heme-binding region does not change our conclusions. Thus, our data suggest that although the DGCR8-Core region is necessary for dsRNA binding and recruitment to the Microprocessor, it is not sufficient to establish the previously observed connection between RNA flexibility and processing efficiency.

  7. Size determines whether specialized expert processes are engaged for recognition of faces.

    PubMed

    Yang, Nan; Shafai, Fakhri; Oruc, Ipek

    2014-07-22

    Many influential models of face recognition postulate specialized expert processes that are engaged when viewing upright, own-race faces, as opposed to a general-purpose recognition route used for nonface objects and inverted or other-race faces. In contrast, others have argued that empirical differences do not stem from qualitatively distinct processing. We offer a potential resolution to this ongoing controversy. We hypothesize that faces engage specialized processes at large sizes only. To test this, we measured recognition efficiencies for a wide range of sizes. Upright face recognition efficiency increased with size. This was not due to better visibility of basic image features at large sizes. We ensured this by calculating efficiency relative to a specialized ideal observer unique to each individual that incorporated size-related changes in visibility and by measuring inverted efficiencies across the same range of face sizes. Inverted face recognition efficiencies did not change with size. A qualitative face inversion effect, defined as the ratio of relative upright and inverted efficiencies, showed a complete lack of inversion effects for small sizes up to 6°. In contrast, significant face inversion effects were found for all larger sizes. Size effects may stem from predominance of larger faces in the overall exposure to faces, which occur at closer viewing distances typical of social interaction. Our results offer a potential explanation for the contradictory findings in the literature regarding the special status of faces.

  8. An Efficient and Robust Singular Value Method for Star Pattern Recognition and Attitude Determination

    NASA Technical Reports Server (NTRS)

    Juang, Jer-Nan; Kim, Hye-Young; Junkins, John L.

    2003-01-01

    A new star pattern recognition method is developed using singular value decomposition of a measured unit column vector matrix in a measurement frame and the corresponding cataloged vector matrix in a reference frame. It is shown that singular values and right singular vectors are invariant with respect to coordinate transformation and robust under uncertainty. One advantage of singular value comparison is that a pairing process for individual measured and cataloged stars is not necessary, and the attitude estimation and pattern recognition process are not separated. An associated method for mission catalog design is introduced and simulation results are presented.

  9. Specificity of the hepatitis C virus NS3 serine protease: effects of substitutions at the 3/4A, 4A/4B, 4B/5A, and 5A/5B cleavage sites on polyprotein processing.

    PubMed Central

    Kolykhalov, A A; Agapov, E V; Rice, C M

    1994-01-01

    Cleavage at four sites (3/4A, 4A/4B, 4B/5A, and 5A/5B) in the hepatitis C virus polyprotein requires a viral serine protease activity residing in the N-terminal one-third of the NS3 protein. Sequence comparison of the residues flanking these cleavage sites reveals conserved features including an acidic residue (Asp or Glu) at the P6 position, a Cys or Thr residue at the P1 position, and a Ser or Ala residue at the P1' position. In this study, we used site-directed mutagenesis to assess the importance of these and other residues for NS3 protease-dependent cleavages. Substitutions at the P7 to P2' positions of the 4A/4B site had varied effects on cleavage efficiency. Only Arg at the P1 position or Pro at P1' substantially blocked processing at this site. Leu was tolerated at the P1 position, whereas five other substitutions allowed various degrees of cleavage. Substitutions with positively charged or other hydrophilic residues at the P7, P3, P2, and P2' positions did not reduce cleavage efficiency. Five substitutions examined at the P6 position allowed complete cleavage, demonstrating that an acidic residue at this position is not essential. Parallel results were obtained with substrates containing an active NS3 protease domain in cis or when the protease domain was supplied in trans. Selected substitutions blocking or inhibiting cleavage at the 4A/4B site were also examined at the 3/4A, 4B/5A, and 5A/5B sites. For a given substitution, a site-dependent gradient in the degree of inhibition was observed, with a 3/4A site being least sensitive to mutagenesis, followed by the 4A/4B, 4B/5A, and 5A/5B sites. In most cases, mutations abolishing cleavage at one site did not affect processing at the other serine protease-dependent sites. However, mutations at the 3/4A site which inhibited cleavage also interfered with processing at the 4B/5A site. Finally, during the course of these studies an additional NS3 protease-dependent cleavage site has been identified in the NS4B

  10. Coiled coil miniprotein randomization on phage leads to charge pattern mimicry of the receptor recognition determinant of interleukin 5.

    PubMed

    Li, Chuanzhao; Plugariu, Carmela G; Bajgier, Joanna; White, John R; Liefer, Kristin M; Wu, Sheng-Jiun; Chaiken, Irwin

    2002-01-01

    Phage display was used to identify sequences that mimic structural determinants in interleukin5 (IL5) for IL5 receptor recognition. A coiled coil stem loop (CCSL) miniprotein scaffold library was constructed with its turn region randomized and panned for binding variants against human IL5 receptor alpha chain (IL5Ralpha). Competition enzyme-linked immunosorbent assays identified CCSL-phage selectants for which binding to IL5Ralpha was competed by IL5. The most frequently selected and IL5-competed CCSL-phage contain charged residues Arg and Glu in their turn sequences, in this regard resembling a beta strand sequence in the 'CD turn' region, of IL5, that has been proposed to present a key determinant for IL5 receptor alpha chain recognition. The most dominant CCSL-phage selectant sequence, PVEGRV, contains a negative/positive charge pattern similar to that seen in the original CD turn. To test the relatedness of CCSL-phage selectant sequences to the IL5 receptor recognition epitope, PVEGRV was grafted into the sequence 87--92 of a monomeric IL5. The resulting IL5 variant, [(87)PVEGRV(92)]GM1, was able to bind to IL5Ralpha in biosensor assays, to elicit TF-1 cell proliferation and to induce STAT5 phosphorylation in TF-1 cells. The results help discern sequence patterns in the IL5 CD turn region which are key in driving receptor recognition and demonstrate the utility of CCSL miniprotein scaffold phage display to identify local IL5 mimetic sequence arrangements that may ultimately lead to IL5 antagonists.

  11. Development of a Pattern Recognition Methodology for Determining Operationally Optimal Heat Balance Instrumentation Calibration Schedules

    SciTech Connect

    Kurt Beran; John Christenson; Dragos Nica; Kenny Gross

    2002-12-15

    The goal of the project is to enable plant operators to detect with high sensitivity and reliability the onset of decalibration drifts in all of the instrumentation used as input to the reactor heat balance calculations. To achieve this objective, the collaborators developed and implemented at DBNPS an extension of the Multivariate State Estimation Technique (MSET) pattern recognition methodology pioneered by ANAL. The extension was implemented during the second phase of the project and fully achieved the project goal.

  12. Degradation pattern of photosystem II reaction center protein D1 in intact leaves. The major photoinhibition-induced cleavage site in D1 polypeptide is located amino terminally of the DE loop.

    PubMed Central

    Kettunen, R; Tyystjärvi, E; Aro, E M

    1996-01-01

    Photoinhibition-induced degradation of the D1 protein of the photosystem II reaction center was studied in intact pumpkin (Cucurbita pepo L.) leaves. Photoinhibition was observed to cause the cleavage of the D1 protein at two distinct sites. The main cleavage generated an 18-kD N-terminal and a 20-kD C-terminal degradation fragment of the D1 protein. this cleavage site was mapped to be located clearly N terminally of the DE loop. The other, less-frequent cleavage occurred at the DE loop and produced the well-documented 23-kD, N-terminal D1 degradation product. Furthermore, the 23-kD, N-terminal D1 fragment appears to be phosphorylated and can be detected only under severe photoinhibition in vivo. Comparison of the D1 degradation pattern after in vivo photoinhibition to that after in vitro acceptor-side and donor-side photoinhibition, performed with isolated photosystem II core particles, gives indirect evidence in support of donor-side photoinhibition in intact leaves. PMID:8756500

  13. Acquisition of a novel eleven amino acid insertion directly N-terminal to a tetrabasic cleavage site confers intracellular cleavage of an H7N7 influenza virus hemagglutinin

    SciTech Connect

    Hamilton, Brian S.; Sun, Xiangjie; Chung, Changik; Whittaker, Gary R.

    2012-12-05

    A critical feature of highly pathogenic avian influenza viruses (H5N1 and H7N7) is the efficient intracellular cleavage of the hemagglutinin (HA) protein. H7N7 viruses also exist in equine species, and a unique feature of the equine H7N7 HA is the presence of an eleven amino acid insertion directly N-terminal to a tetrabasic cleavage site. Here, we show that three histidine residues within the unique insertion of the equine H7N7 HA are essential for intracellular cleavage. An asparagine residue within the insertion-derived glycosylation site was also found to be essential for intracellular cleavage. The presence of the histidine residues also appear to be involved in triggering fusion, since mutation of the histidine residues resulted in a destabilizing effect. Importantly, the addition of a tetrabasic site and the eleven amino acid insertion conferred efficient intracellular cleavage to the HA of an H7N3 low pathogenicity avian influenza virus. Our studies show that acquisition of the eleven amino acid insertion offers an alternative mechanism for intracellular cleavage of influenza HA.

  14. Use of a recombinant fluorescent substrate with cleavage sites for all botulinum neurotoxins in high-throughput screening of natural product extracts for inhibitors of serotypes A, B, and E.

    PubMed

    Hines, Harry B; Kim, Alexander D; Stafford, Robert G; Badie, Shirin S; Brueggeman, Ernst E; Newman, David J; Schmidt, James J

    2008-02-01

    The seven serotypes of botulinum neurotoxin (BoNTs) are zinc metalloproteases that cleave and inactivate proteins critical for neurotransmission. The synaptosomal protein of 25 kDa (SNAP-25) is cleaved by BoNTs A, C, and E, while vesicle-associated membrane protein (VAMP) is the substrate for BoNTs B, D, F, and G. BoNTs not only are medically useful drugs but also are potential bioterrorist and biowarfare threat agents. Because BoNT protease activity is required for toxicity, inhibitors of that activity might be effective for antibotulinum therapy. To expedite inhibitor discovery, we constructed a hybrid gene encoding (from the N terminus to the C terminus, with respect to the expressed product) green fluorescent protein, then a SNAP-25 fragment encompassing residues Met-127 to Gly-206, and then VAMP residues Met-1 to Lys-94. Cysteine was added as the C terminus. The expressed product, which contained the protease cleavage sites for all seven botulinum serotypes, was purified and coupled covalently through the C-terminal sulfhydryl group to maleimide-activated 96-well plates. The substrate was readily cleaved by BoNTs A, B, D, E, and F. Using this assay and an automated 96-well pipettor, we screened 528 natural product extracts for inhibitors of BoNT A, B, and E protease activities. Serotype-specific inhibition was found in 30 extracts, while 5 others inhibited two serotypes.

  15. Origin recognition specificity in pT181 plasmids is determined by a functionally asymmetric palindromic DNA element.

    PubMed Central

    Wang, P Z; Projan, S J; Henriquez, V; Novick, R P

    1993-01-01

    The leading strand replication origin of pT181 plasmids consists of two adjacent inverted repeat elements (IR-II and IR-III), which are involved in origin recognition by the initiator (Rep) protein. The conserved core element, IR-II, which contains the initiation nick site, is induced by Rep to form a cruciform structure, probably the primary substrate for the initiation of rolling circle replication. The divergent repeat, IR-III, constitutes the determinant of origin recognition specificity. We show here that the distal arm of IR-III is not required for sequence-specific recognition, whereas the proximal arm and central region are required. Since the initiator is dimeric, we presume that it binds symmetrically to IR-III. A unique type of DNA-protein interaction is proposed, in which the lack of sequence requirement for the distal arm is a consequence of binding to the adjacent IR-II, which thereby polarizes the stringency of binding to the two arms of IR-III. In addition, genetic evidence indicates that both the spacing and the phasing of IR-II to IR-III are crucial for function and that the central segment of IR-III may serve to position the two flanking half-sites for optimal interaction of Rep with IR-III. Images PMID:8428593

  16. Study to determine potential flight applications and human factors design guidelines for voice recognition and synthesis systems

    NASA Technical Reports Server (NTRS)

    White, R. W.; Parks, D. L.

    1985-01-01

    A study was conducted to determine potential commercial aircraft flight deck applications and implementation guidelines for voice recognition and synthesis. At first, a survey of voice recognition and synthesis technology was undertaken to develop a working knowledge base. Then, numerous potential aircraft and simulator flight deck voice applications were identified and each proposed application was rated on a number of criteria in order to achieve an overall payoff rating. The potential voice recognition applications fell into five general categories: programming, interrogation, data entry, switch and mode selection, and continuous/time-critical action control. The ratings of the first three categories showed the most promise of being beneficial to flight deck operations. Possible applications of voice synthesis systems were categorized as automatic or pilot selectable and many were rated as being potentially beneficial. In addition, voice system implementation guidelines and pertinent performance criteria are proposed. Finally, the findings of this study are compared with those made in a recent NASA study of a 1995 transport concept.

  17. A microflow chemiluminescence sensor for indirect determination of dibutyl phthalate by hydrolyzing based on biological recognition materials.

    PubMed

    Qiu, Huamin; Fan, Lulu; Li, Xiangjun; Li, Leilei; Sun, Min; Luo, Chuannan

    2013-03-05

    A microflow chemiluminescence (CL) sensor for determination of dibutyl phthalate (DBP) based on magnetic molecularly imprinted polymer (MMIP) as recognition element was fabricated. Briefly, a hydrophilic molecularly imprinted polymer layer was produced at the surface of Fe₃O₄@SiO₂ magnetic nanoparticles (MNPs) via combination of molecular imprinting and reversible stimuli responsive hydrogel. In this protocol, the initial step involved co-precipitation of Fe²⁺ and Fe³⁺ in an ammonia solution. Silica was then coated on the Fe₃O₄ nanoparticles using a sol-gel method to obtain silica shell magnetic nanoparticles. The MMIP was synthesized using methacrylic acid (MAA) as functional monomer and ethylene glycol dimethacrylate (EGDMA) as cross-linker and 2,2-azobisisobutyronitrile (AIBN) as initiator in chloroform. Then the synthesized MMIP and magnetic non-molecular imprinted polymers (MNIP) were employed as recognition by packing into lab-made straight shape tubes, connected in CL analyzer for establishing the novel sensor with a single channel syringe pump. And a mixer for hydrolyzing of DBP was followed. Based on this experiment principle, DBP was determined indirectly. And the MMIP showed satisfactory recognition capacity to DBP, resulting to the wide linear range of 3.84 × 10⁻⁸ to 2.08 × 10⁻⁵ M and the low detection limit of 2.09 × 10⁻⁹ M (3σ) for DBP. The relative standard deviation (RSD) for DBP (3.20 × 10⁻⁶ M) was 1.40% (n=11). Besides improving sensitivity and selectivity, the sensor was reusable. The proposed DBP-MMIP-CL sensor has been successfully applied to determine DBP in drink samples.

  18. The determination of tRNALeu recognition nucleotides for Escherichia coli L/F transferase

    PubMed Central

    Fung, Angela Wai Shan; Leung, Charles Chung Yun; Fahlman, Richard Peter

    2014-01-01

    Escherichia coli leucyl/phenylalanyl-tRNA protein transferase catalyzes the tRNA-dependent post-translational addition of amino acids onto the N-terminus of a protein polypeptide substrate. Based on biochemical and structural studies, the current tRNA recognition model by L/F transferase involves the identity of the 3′ aminoacyl adenosine and the sequence-independent docking of the D-stem of an aminoacyl-tRNA to the positively charged cluster on L/F transferase. However, this model does not explain the isoacceptor preference observed 40 yr ago. Using in vitro-transcribed tRNA and quantitative MALDI-ToF MS enzyme activity assays, we have confirmed that, indeed, there is a strong preference for the most abundant leucyl-tRNA, tRNALeu (anticodon 5′-CAG-3′) isoacceptor for L/F transferase activity. We further investigate the molecular mechanism for this preference using hybrid tRNA constructs. We identified two independent sequence elements in the acceptor stem of tRNALeu (CAG)—a G3:C70 base pair and a set of 4 nt (C72, A4:U69, C68)—that are important for the optimal binding and catalysis by L/F transferase. This maps a more specific, sequence-dependent tRNA recognition model of L/F transferase than previously proposed. PMID:24935875

  19. Timing of presentation and nature of stimuli determine retroactive interference with social recognition memory in mice.

    PubMed

    Perna, Judith Camats; Wotjak, Carsten T; Stork, Oliver; Engelmann, Mario

    2015-05-01

    The present study was designed to further investigate the nature of stimuli and the timing of their presentation, which can induce retroactive interference with social recognition memory in mice. In accordance with our previous observations, confrontation with an unfamiliar conspecific juvenile 3h and 6h, but not 22 h, after the initial learning session resulted in retroactive interference. The same effect was observed with the exposure to both enantiomers of the monomolecular odour carvone, and with a novel object. Exposure to a loud tone (12 KHz, 90 dB) caused retroactive interference at 6h, but not 3h and 22 h, after sampling. Our data show that retroactive interference of social recognition memory can be induced by exposing the experimental subjects to the defined stimuli presented <22 h after learning in their home cage. The distinct interference triggered by the tone presentation at 6h after sampling may be linked to the intrinsic aversiveness of the loud tone and suggests that at this time point memory consolidation is particularly sensitive to stress.

  20. Vγ2Vδ2 T Cell Receptor Recognition of Prenyl Pyrophosphates is Dependent on all Complementarity Determining Regions1

    PubMed Central

    Wang, Hong; Fang, Zhimei; Morita, Craig T.

    2010-01-01

    γδ T cells differ from αβ T cells in the antigens they recognize and their functions in immunity. While most αβ T cell receptors (TCR) recognize peptides presented by MHC class I or II, human γδ T cells expressing Vγ2Vδ2 TCRs recognize nonpeptide prenyl pyrophosphates. To define the molecular basis for this recognition, the effect of mutations in the TCR complementarity-determining regions (CDR) was assessed. Mutations in all CDR loops altered recognition and cover a large footprint. Unlike murine γδ TCR recognition of the MHC class Ib T22 protein, there was no CDR3δ motif required for recognition because only 1 residue is required. Instead, the length and sequence of CDR3γ was key. Although a potential prenyl pyrophosphate-binding site was defined by Lys109 in Jγ1.2 and Arg51 in CDR2δ, the area outlined by critical mutations is much larger. These results show that prenyl pyrophosphate recognition is primarily by germline-encoded regions of the γδ TCR, allowing a high proportion of Vγ2Vδ2 TCRs to respond. This underscores its parallels to innate immune receptors. Our results also provide strong evidence for the existence of an antigen-presenting molecule for prenyl pyrophosphates. This is an author-produced version of a manuscript accepted for publication in The Journal of Immunology (The JI). The American Association of Immunologists, Inc. (AAI), publisher of The JI, holds the copyright to this manuscript. This version of the manuscript has not yet been copyedited or subjected to editorial proofreading by The JI; hence, it may differ from the final version published in The JI (online and in print). AAI (The JI) is not liable for errors or omissions in this author-produced version of the manuscript or in any version derived from it by the U.S. National Institutes of Health or any other third party. The final, citable version of record can be found at www.jimmunol.org. PMID:20483784

  1. Determining and improving the fault tolerance of multilayer perceptrons in a pattern-recognition application.

    PubMed

    Emmerson, M D; Damper, R I

    1993-01-01

    We investigate empirically the performance under damage conditions of single- and multilayer perceptrons (MLP's), with various numbers of hidden units, in a representative pattern-recognition task. While some degree of graceful degradation was observed, the single-layer perceptron was considerably less fault tolerant than any of the multilayer perceptrons, including one with fewer adjustable weights. Our initial hypothesis that fault tolerance would be significantly improved for multilayer nets with larger numbers of hidden units proved incorrect. Indeed, there appeared to be a liability to having excess hidden units. A simple technique (called augmentation) is described, which was successful in translating excess hidden units into improved fault tolerance. Finally, our results were supported by applying singular value decomposition (SVD) analysis to the MLP's internal representations.

  2. Recognition of protein-linked glycans as a determinant of peptidase activity.

    PubMed

    Noach, Ilit; Ficko-Blean, Elizabeth; Pluvinage, Benjamin; Stuart, Christopher; Jenkins, Meredith L; Brochu, Denis; Buenbrazo, Nakita; Wakarchuk, Warren; Burke, John E; Gilbert, Michel; Boraston, Alisdair B

    2017-01-31

    The vast majority of proteins are posttranslationally altered, with the addition of covalently linked sugars (glycosylation) being one of the most abundant modifications. However, despite the hydrolysis of protein peptide bonds by peptidases being a process essential to all life on Earth, the fundamental details of how peptidases accommodate posttranslational modifications, including glycosylation, has not been addressed. Through biochemical analyses and X-ray crystallographic structures we show that to hydrolyze their substrates, three structurally related metallopeptidases require the specific recognition of O-linked glycan modifications via carbohydrate-specific subsites immediately adjacent to their peptidase catalytic machinery. The three peptidases showed selectivity for different glycans, revealing protein-specific adaptations to particular glycan modifications, yet always cleaved the peptide bond immediately preceding the glycosylated residue. This insight builds upon the paradigm of how peptidases recognize substrates and provides a molecular understanding of glycoprotein degradation.

  3. Cleavage of the NR2B subunit amino terminus of N-methyl-D-aspartate (NMDA) receptor by tissue plasminogen activator: identification of the cleavage site and characterization of ifenprodil and glycine affinities on truncated NMDA receptor.

    PubMed

    Ng, Kay-Siong; Leung, How-Wing; Wong, Peter T-H; Low, Chian-Ming

    2012-07-20

    Thrombolysis using tissue plasminogen activator (tPA) has been the key treatment for patients with acute ischemic stroke for the past decade. Recent studies, however, suggest that this clot-busting protease also plays various roles in brain physiological and pathophysiological glutamatergic-dependent processes, such as synaptic plasticity and neurodegeneration. In addition, increasing evidence implicates tPA as an important neuromodulator of the N-methyl-d-aspartate (NMDA) receptors. Here, we demonstrate that recombinant human tPA cleaves the NR2B subunit of NMDA receptor. Analysis of NR2B in rat brain lysates and cortical neurons treated with tPA revealed concentration- and time-dependent degradation of NR2B proteins. Peptide sequencing studies performed on the cleaved-off products obtained from the tPA treatment on a recombinant fusion protein of the amino-terminal domain of NR2B revealed that tPA-mediated cleavage occurred at arginine 67 (Arg(67)). This cleavage is tPA-specific, plasmin-independent, and removes a predicted ~4-kDa fragment (Arg(27)-Arg(67)) from the amino-terminal domain of the NR2B protein. Site-directed mutagenesis of putative cleavage site Arg(67) to Ala(67) impeded tPA-mediated degradation of recombinant protein. This analysis revealed that NR2B is a novel substrate of tPA and suggested that an Arg(27)-Arg(67)-truncated NR2B-containing NMDA receptor could be formed. Heterologous expression of NR2B with Gln(29)-Arg(67) deleted is functional but exhibits reduced ifenprodil inhibition and increased glycine EC(50) with no change in glutamate EC(50). Our results confirmed NR2B as a novel proteolytic substrate of tPA, where tPA may directly interact with NR2B subunits leading to a change in pharmacological properties of NR2B-containing NMDA receptors.

  4. Pattern-Based Recognition for the Rapid Determination of Identity, Concentration, and Enantiomeric Excess of Subtly Different Threo Diols

    PubMed Central

    Shabbir, Shagufta H.; Joyce, Leo A.; da Cruz, Gabriella M.; Lynch, Vincent M.; Sorey, Steven; Anslyn, Eric V.

    2009-01-01

    A pattern based recognition approach was developed for the rapid determination of identity, concentration, and enantiomeric excess of chiral vicinal diols, specifically threo diols. A diverse enantioselective sensor array was generated using three chiral boronic acid receptors and three pH indicators. The optical response produced by the sensor array was analyzed by two pattern recognition algorithms: principal component analysis and artificial neural networks. Principle component analysis demonstrated good chemoselective and enantioselective separation of the analytes, and an artificial neural network was used to accurately determine the concentration and enantiomeric excess of five unknown samples with an average absolute error of ± 0.08 mM in concentration and 3.6% in enantiomeric excess. The speed of the analysis was enhanced by using a 96-well plate format, which portents to applications in high-throughput screening for asymmetric catalyst discovery. X-ray crystallography and 11B NMR was utilized to study the enantioselective nature of boronic acid host-2. PMID:19691315

  5. Determination of association constant of host-guest supramolecular complex (molecular recognition of carbamazepine, antiseizure drug, with calix(4)arene).

    PubMed

    Meenakshi, C; Jayabal, P; Ramakrishnan, V

    2015-12-05

    The thermodynamic property of the host-guest, inclusion complex formed between p-t-butyl calix(4)arene which is a supramolecule, and the antiseizure drug, carbamazepine was studied. p-t-Butyl calix(4)arene has been used as a host molecule and carbamazepine as a guest molecule. Optical absorption spectral studies were carried out to investigate the molecular recognition properties of p-t-butyl calix(4)arene with carbamazepine. The stochiometry of the host-guest complexes formed and the association constant were determined. An interesting 1:2 stochiometric host-guest complex was formed. Job's continuous method of variation and Benesi-Hildebrand expression were used for the determination of binding constant and the stochiometry of the host-guest complex formed. Molecular dimension of the host molecule plays a vital role in the formation of the host-guest stochiometric complexes.

  6. Determination of CFTR densities in erythrocyte plasma membranes using recognition imaging

    NASA Astrophysics Data System (ADS)

    Ebner, Andreas; Nikova, Dessy; Lange, Tobias; Häberle, Johannes; Falk, Sabine; Dübbers, Angelika; Bruns, Reimer; Hinterdorfer, Peter; Oberleithner, Hans; Schillers, Hermann

    2008-09-01

    CFTR (cystic fibrosis transmembrane conductance regulator) is a cAMP-regulated chloride (Cl-) channel that plays an important role in salt and fluid movement across epithelia. Cystic fibrosis (CF), the most common genetic disease among Caucasians, is caused by mutations in the gene encoding CFTR. The most predominant mutation, F508del, disturbs CFTR protein trafficking, resulting in a reduced number of CFTR in the plasma membrane. Recent studies indicate that CFTR is not only found in epithelia but also in human erythrocytes. Although considerable attempts have been made to quantify CFTR in cells, conclusions on numbers of CFTR molecules localized in the plasma membrane have been drawn indirectly. AFM has the power to provide the needed information, since both sub-molecular spatial resolution and direct protein recognition via antibody-antigen interaction can be observed. We performed a quantification study of the CFTR copies in erythrocyte membranes at the single molecule level, and compared the difference between healthy donors and CF patients. We detected that the number of CFTR molecules is reduced by 70% in erythrocytes of cystic fibrosis patients.

  7. Environmental Determinants of Chronic Disease and Medical Approaches: Recognition, Avoidance, Supportive Therapy, and Detoxification

    PubMed Central

    Sears, Margaret E.; Genuis, Stephen J.

    2012-01-01

    The World Health Organization warns that chronic, noncommunicable diseases are rapidly becoming epidemic worldwide. Escalating rates of neurocognitive, metabolic, autoimmune and cardiovascular diseases cannot be ascribed only to genetics, lifestyle, and nutrition; early life and ongoing exposures, and bioaccumulated toxicants may also cause chronic disease. Contributors to ill health are summarized from multiple perspectives—biological effects of classes of toxicants, mechanisms of toxicity, and a synthesis of toxic contributors to major diseases. Healthcare practitioners have wide-ranging roles in addressing environmental factors in policy and public health and clinical practice. Public health initiatives include risk recognition and chemical assessment then exposure reduction, remediation, monitoring, and avoidance. The complex web of disease and environmental contributors is amenable to some straightforward clinical approaches addressing multiple toxicants. Widely applicable strategies include nutrition and supplements to counter toxic effects and to support metabolism; as well as exercise and sweating, and possibly medication to enhance excretion. Addressing environmental health and contributors to chronic disease has broad implications for society, with large potential benefits from improved health and productivity. PMID:22315626

  8. Structure-function analysis of Staphylococcus aureus amidase reveals the determinants of peptidoglycan recognition and cleavage.

    PubMed

    Büttner, Felix Michael; Zoll, Sebastian; Nega, Mulugeta; Götz, Friedrich; Stehle, Thilo

    2014-04-18

    The bifunctional major autolysin AtlA of Staphylococcus aureus cleaves the bacterium's peptidoglycan network (PGN) at two distinct sites during cell division. Deletion of the enzyme results in large cell clusters with disordered division patterns, indicating that AtlA could be a promising target for the development of new antibiotics. One of the two functions of AtlA is performed by the N-acetylmuramyl-l-alanine amidase AmiA, which cleaves the bond between the carbohydrate and the peptide moieties of PGN. To establish the structural requirements of PGN recognition and the enzymatic mechanism of cleavage, we solved the crystal structure of the catalytic domain of AmiA (AmiA-cat) in complex with a peptidoglycan-derived ligand at 1.55 Å resolution. The peptide stem is clearly visible in the structure, forming extensive contacts with protein residues by docking into an elongated groove. Less well defined electron density and the analysis of surface features indicate likely positions of the carbohydrate backbone and the pentaglycine bridge. Substrate specificity analysis supports the importance of the pentaglycine bridge for fitting into the binding cleft of AmiA-cat. PGN of S. aureus with l-lysine tethered with d-alanine via a pentaglycine bridge is completely hydrolyzed, whereas PGN of Bacillus subtilis with meso-diaminopimelic acid directly tethered with d-alanine is not hydrolyzed. An active site mutant, H370A, of AmiA-cat was completely inactive, providing further support for the proposed catalytic mechanism of AmiA. The structure reported here is not only the first of any bacterial amidase in which both the PGN component and the water molecule that carries out the nucleophilic attack on the carbonyl carbon of the scissile bond are present; it is also the first peptidoglycan amidase complex structure of an important human pathogen.

  9. Alternative Selection of β-Site APP-Cleaving Enzyme 1 (BACE1) Cleavage Sites in Amyloid β-Protein Precursor (APP) Harboring Protective and Pathogenic Mutations within the Aβ Sequence.

    PubMed

    Kimura, Ayano; Hata, Saori; Suzuki, Toshiharu

    2016-11-11

    β-Site APP-cleaving enzyme 1 (BACE1) cleaves amyloid β-protein precursor (APP) at the bond between Met(671) and Asp(672) (β-site) to generate the carboxyl-terminal fragment (CTFβ/C99). BACE1 also cleaves APP at another bond between Thr(681) and Gln(682) (β'-site), yielding CTFβ'/C89. Cleavage of CTFβ/C99 by γ-secretase generates Aβ(1-XX), whereas cleavage of CTFβ'/C89 generates Aβ(11-XX). Thus, β'-site cleavage by BACE1 is amyloidolytic rather than amyloidogenic. β' cleavage of mouse APP is more common than the corresponding cleavage of human APP. We found that the H684R substitution within human Aβ, which replaces the histidine in the human protein with the arginine found at the corresponding position in mouse, facilitated β' cleavage irrespective of the species origin of BACE1, thereby significantly increasing the level of Aβ(11-XX) and decreasing the level of Aβ(1-XX). Thus, amino acid substitutions within the Aβ sequence influenced the selectivity of alternative β- or β'-site cleavage of APP by BACE1. In familial Alzheimer's disease (FAD), the APP gene harbors pathogenic variations such as the Swedish (K670N/M671L), Leuven (E682K), and A673V mutations, all of which decrease Aβ(11-40) generation, whereas the protective Icelandic mutation (A673T) increases generation of Aβ(11-40). Thus, A673T promotes β' cleavage of APP and protects subjects against AD. In addition, CTFβ/C99 was cleaved by excess BACE1 activity to generate CTFβ'/C89, followed by Aβ(11-40), even if APP harbored pathogenic mutations. The resultant Aβ(11-40) was more metabolically labile in vivo than Aβ(1-40). Our analysis suggests that some FAD mutations in APP are amyloidogenic and/or amyloidolytic via selection of alternative BACE1 cleavage sites.

  10. BCL::contact-low confidence fold recognition hits boost protein contact prediction and de novo structure determination.

    PubMed

    Karakaş, Mert; Woetzel, Nils; Meiler, Jens

    2010-02-01

    Knowledge of all residue-residue contacts within a protein allows determination of the protein fold. Accurate prediction of even a subset of long-range contacts (contacts between amino acids far apart in sequence) can be instrumental for determining tertiary structure. Here we present BCL::Contact, a novel contact prediction method that utilizes artificial neural networks (ANNs) and specializes in the prediction of medium to long-range contacts. BCL::Contact comes in two modes: sequence-based and structure-based. The sequence-based mode uses only sequence information and has individual ANNs specialized for helix-helix, helix-strand, strand-helix, strand-strand, and sheet-sheet contacts. The structure-based mode combines results from 32-fold recognition methods with sequence information to a consensus prediction. The two methods were presented in the 6(th) and 7(th) Critical Assessment of Techniques for Protein Structure Prediction (CASP) experiments. The present work focuses on elucidating the impact of fold recognition results onto contact prediction via a direct comparison of both methods on a joined benchmark set of proteins. The sequence-based mode predicted contacts with 42% accuracy (7% false positive rate), while the structure-based mode achieved 45% accuracy (2% false positive rate). Predictions by both modes of BCL::Contact were supplied as input to the protein tertiary structure prediction program Rosetta for a benchmark of 17 proteins with no close sequence homologs in the protein data bank (PDB). Rosetta created higher accuracy models, signified by an improvement of 1.3 A on average root mean square deviation (RMSD), when driven by the predicted contacts. Further, filtering Rosetta models by agreement with the predicted contacts enriches for native-like fold topologies.

  11. Novel Protein–Protein Contacts Facilitate mRNA 3'-Processing Signal Recognition by Rna15 and Hrp1

    SciTech Connect

    Leeper, Thomas C.; Qu, Xiangping; Lu, Connie; Moore, Claire; Varani, Gabriele

    2010-08-01

    Precise 3'-end processing of mRNA is essential for correct gene expression, yet in yeast, 3'-processing signals consist of multiple ambiguous sequence elements. Two neighboring elements upstream of the cleavage site are particularly important for the accuracy (positioning element) and efficiency (efficiency element) of 3'-processing and are recognized by the RNA-binding proteins Rna15 and Hrp1, respectively. In vivo, these interactions are strengthened by the scaffolding protein Rna14 that stabilizes their association. The NMR structure of the 34 -kDa ternary complex of the RNA recognition motif (RRM) domains of Hrp1 and Rna15 bound to this pair of RNA elements was determined by residual dipolar coupling and paramagnetic relaxation experiments. It reveals how each of the proteins binds to RNA and introduces a novel class of protein–protein contact in regions of previously unknown function. These interdomain contacts had previously been overlooked in other multi-RRM structures, although a careful analysis suggests that they may be frequently present. Mutations in the regions of these contacts disrupt 3'-end processing, suggesting that they may structurally organize the ribonucleoprotein complexes responsible for RNA processing.

  12. Novel Protein-Protein Contacts Facilitate mRNA 3'-Processing Signal Recognition by Rna15 and Hrp1.

    SciTech Connect

    Leeper, Thomas C; Qu, Xiangping; Lu, Connie; Moore, Claire; Varani, Gabriele

    2010-06-19

    Precise 3'-end processing of mRNA is essential for correct gene expression, yet in yeast, 3'-processing signals consist of multiple ambiguous sequence elements. Two neighboring elements upstream of the cleavage site are particularly important for the accuracy (positioning element) and efficiency (efficiency element) of 3'-processing and are recognized by the RNAbinding proteins Rna15 and Hrp1, respectively. In vivo, these interactions are strengthened by the scaffolding protein Rna14 that stabilizes their association. The NMR structure of the 34 -kDa ternary complex of the RNA recognition motif (RRM) domains of Hrp1 and Rna15 bound to this pair of RNA elements was determined by residual dipolar coupling and paramagnetic relaxation experiments. It reveals how each of the proteins binds to RNA and introduces a novel class of protein–protein contact in regions of previously unknown function. These interdomain contacts had previously been overlooked in other multi-RRM structures, although a careful analysis suggests that they may be frequently present. Mutations in the regions of these contacts disrupt 3'-end processing, suggesting that they may structurally organize the ribonucleoprotein complexes responsible for RNA processing.

  13. Molecular Mechanisms of Viral and Host Cell Substrate Recognition by Hepatitis C Virus NS3/4A Protease

    SciTech Connect

    Romano, Keith P.; Laine, Jennifer M.; Deveau, Laura M.; Cao, Hong; Massi, Francesca; Schiffer, Celia A.

    2011-08-16

    Hepatitis C NS3/4A protease is a prime therapeutic target that is responsible for cleaving the viral polyprotein at junctions 3-4A, 4A4B, 4B5A, and 5A5B and two host cell adaptor proteins of the innate immune response, TRIF and MAVS. In this study, NS3/4A crystal structures of both host cell cleavage sites were determined and compared to the crystal structures of viral substrates. Two distinct protease conformations were observed and correlated with substrate specificity: (i) 3-4A, 4A4B, 5A5B, and MAVS, which are processed more efficiently by the protease, form extensive electrostatic networks when in complex with the protease, and (ii) TRIF and 4B5A, which contain polyproline motifs in their full-length sequences, do not form electrostatic networks in their crystal complexes. These findings provide mechanistic insights into NS3/4A substrate recognition, which may assist in a more rational approach to inhibitor design in the face of the rapid acquisition of resistance.

  14. Molecular Mechanisms of Viral and Host Cell Substrate Recognition by Hepatitis C Virus NS3/4A Protease▿

    PubMed Central

    Romano, Keith P.; Laine, Jennifer M.; Deveau, Laura M.; Cao, Hong; Massi, Francesca; Schiffer, Celia A.

    2011-01-01

    Hepatitis C NS3/4A protease is a prime therapeutic target that is responsible for cleaving the viral polyprotein at junctions 3-4A, 4A4B, 4B5A, and 5A5B and two host cell adaptor proteins of the innate immune response, TRIF and MAVS. In this study, NS3/4A crystal structures of both host cell cleavage sites were determined and compared to the crystal structures of viral substrates. Two distinct protease conformations were observed and correlated with substrate specificity: (i) 3-4A, 4A4B, 5A5B, and MAVS, which are processed more efficiently by the protease, form extensive electrostatic networks when in complex with the protease, and (ii) TRIF and 4B5A, which contain polyproline motifs in their full-length sequences, do not form electrostatic networks in their crystal complexes. These findings provide mechanistic insights into NS3/4A substrate recognition, which may assist in a more rational approach to inhibitor design in the face of the rapid acquisition of resistance. PMID:21507982

  15. Nanosilica-based molecularly imprinted polymer nanoshell for specific recognition and determination of rhodamine B in red wine and beverages.

    PubMed

    Long, Zerong; Xu, Weiwei; Lu, Yi; Qiu, Hongdeng

    2016-09-01

    A new and facile rhodamine B (RhB)-imprinted polymer nanoshell coating for SiO2 nanoparticles was readily prepared by a combination of silica gel modification and molecular surface imprinting. The RhB-imprinted polymers (RhB-MIPs) were characterized by Fourier transform infrared spectroscopy, scanning electron microscopy, and UV-vis spectroscopy; the binding properties and selectivity of these MIPs were investigated in detail. The uniformly imprinted nanoparticles displayed a rather thin shell thickness (23nm) with highly effective recognition sites, showing homogenous distribution and monolayer adsorption. The maximum MIP adsorption capacity (Qm) was as high as 45.2mgg(-1), with an adsorption equilibrium time of about 15min at ambient temperature. Dynamic rebinding experiments showed that chemical adsorption is crucial for RhB binding to RhB-MIPs. The adsorption isotherm for RhB-MIPs binding could also be described by the Langmuir equation at different temperatures and pH values. Increasing temperature led to an enhanced Qm, a decreased dissociation constant (K'd), and a more negative free energy (ΔG), indicating that adsorption is favored at higher temperatures. Moreover, the adsorption capacity of RhB was remarkably affected by pH. At pH>7, the adsorption of RhB was driven by hydrogen bonding interactions, while at pH<7 electrostatic forces were dominant. Additionally, the MIPs also showed specific recognition of RhB from the standard mixture solution containing five structurally analogs. This method was also successfully employed to determine RhB content in red wine and beverages using three levels of spiking, with recoveries in the range of 91.6-93.1% and relative standard deviations lower than 4.1%.

  16. Research progress in radiation detectors, pattern recognition programs, and radiation damage determination in DNA

    NASA Technical Reports Server (NTRS)

    Baily, N. A.

    1973-01-01

    The radiological implications of statistical variations in energy deposition by ionizing radiation were investigated in the conduct of the following experiments: (1) study of the production of secondary particles generated by the passage of the primary radiation through bone and muscle; (2) the study of the ratio of nonreparable to reparable damage in DNA as a function of different energy deposition patterns generated by X rays versus heavy fast charged particles; (3) the use of electronic radiography systems for direct fluoroscopic tomography and for the synthesis of multiple planes and; (4) the determination of the characteristics of systems response to split fields having different contrast levels, and of minimum detectable contrast levels between the halves under realistic clinical situations.

  17. Echocardiographic evaluation of left ventricular diastolic function in cats: Hemodynamic determinants and pattern recognition.

    PubMed

    Schober, Karsten E; Chetboul, Valérie

    2015-12-01

    Left ventricular (LV) diastolic dysfunction is highly prevalent in cats and is a functional hallmark of feline cardiomyopathy. The majority of cats with hypertrophic, restrictive, and dilated cardiomyopathy have echocardiographic evidence of abnormal LV filling, even during the occult (preclinical) phase. Moderate and severe diastolic dysfunction is an indicator of advanced myocardial disease, is associated with clinical signs including exercise intolerance and congestive heart failure, affects outcome, and influences therapeutic decisions. Therefore, identification and quantification of LV diastolic dysfunction are clinically important. Surrogate measures of diastolic function determined by transthoracic two-dimensional, M-mode, and Doppler echocardiographic (DE) methods have been used widely for such purpose. Major functional characteristics of LV diastole, including global function, relaxation and untwist, chamber compliance, filling volume, and the resultant filling pressures can be semi-quantified by echocardiographic methods, and variables retrieved from transmitral flow, pulmonary vein flow, and tissue Doppler recordings are most frequently used. Although there is still a critical lack of well-designed studies in the field, knowledge has steadily accumulated over the past 20 years, reference ranges of diastolic echocardiographic variables have been determined, epidemiological studies have been conducted, and new treatments of diastolic dysfunction in cats have been evaluated. This report will give the reader a summary of the current status in the field of feline diastology with focus on the noninvasive diagnostic methods and interpretation of echocardiographic surrogate measures of LV diastolic function. Lastly, a grading system using a composite of left atrial size and various DE variables potentially useful in the functional classification of LV diastole in cats is introduced.

  18. Visual determination of aliphatic diamines based on host-guest recognition of calix[4]arene derivatives capped gold nanoparticles.

    PubMed

    Chen, Yangyang; Zhang, Jiangjiang; Gao, Yanmin; Lee, Jaebeom; Chen, Hongxia; Yin, Yongmei

    2015-10-15

    Since amine compounds have been widespread pollutants in nature and they are extensively used in pharmaceutical industries and dye manufacturing, it is highly desirable to develop simple, effective and naked-eye available analytical methods for such aliphatic diamines determination. Calixarenes as macrocycles have drawn intensive interests for fields such as biomedicine, supramolecular chemistry and smart materials. Here, instead of the normal complicated modification strategy, a facile and efficient method for one-pot synthesis of calix[4]arene crown ether (CCE4) capped gold nanoparticles (AuNPs) is proposed. The as-prepared CCE4-AuNPs are not only high water dispersity and stability even after storage for 3 months, but also capable of host-guest recognition of diamines in aqueous systems. Size-selective encapsulation of amine group between CCE4 and diamines carry out the aggregation of CCE4-AuNPs. The determination of diamines such as hexamethylenediamine or spermine can be realized by the UV-vis absorbance change and visual color difference.

  19. Rationalization and Design of the Complementarity Determining Region Sequences in an Antibody-Antigen Recognition Interface

    PubMed Central

    Chen, Ing-Chien; Lee, Yu-Ching; Chen, Jun-Bo; Tsai, Keng-Chang; Chen, Ching-Tai; Chang, Jeng-Yih; Yang, Ei-Wen; Hsu, Po-Chiang; Jian, Jhih-Wei; Hsu, Hung-Ju; Chang, Hung-Ju; Hsu, Wen-Lian; Huang, Kai-Fa; Ma, Alex Che; Yang, An-Suei

    2012-01-01

    Protein-protein interactions are critical determinants in biological systems. Engineered proteins binding to specific areas on protein surfaces could lead to therapeutics or diagnostics for treating diseases in humans. But designing epitope-specific protein-protein interactions with computational atomistic interaction free energy remains a difficult challenge. Here we show that, with the antibody-VEGF (vascular endothelial growth factor) interaction as a model system, the experimentally observed amino acid preferences in the antibody-antigen interface can be rationalized with 3-dimensional distributions of interacting atoms derived from the database of protein structures. Machine learning models established on the rationalization can be generalized to design amino acid preferences in antibody-antigen interfaces, for which the experimental validations are tractable with current high throughput synthetic antibody display technologies. Leave-one-out cross validation on the benchmark system yielded the accuracy, precision, recall (sensitivity) and specificity of the overall binary predictions to be 0.69, 0.45, 0.63, and 0.71 respectively, and the overall Matthews correlation coefficient of the 20 amino acid types in the 24 interface CDR positions was 0.312. The structure-based computational antibody design methodology was further tested with other antibodies binding to VEGF. The results indicate that the methodology could provide alternatives to the current antibody technologies based on animal immune systems in engineering therapeutic and diagnostic antibodies against predetermined antigen epitopes. PMID:22457753

  20. RNA recognition by the Caenorhabditis elegans oocyte maturation determinant OMA-1.

    PubMed

    Kaymak, Ebru; Ryder, Sean P

    2013-10-18

    Maternally supplied mRNAs encode proteins that pattern early embryos in many species. In the nematode Caenorhabditis elegans, a suite of RNA-binding proteins regulates expression of maternal mRNAs during oogenesis, the oocyte to embryo transition, and early embryogenesis. To understand how these RNA-binding proteins contribute to development, it is necessary to determine how they select specific mRNA targets for regulation. OMA-1 and OMA-2 are redundant proteins required for oocyte maturation--an essential part of meiosis that prepares oocytes for fertilization. Both proteins have CCCH type tandem zinc finger RNA-binding domains. Here, we define the RNA binding specificity of OMA-1 and demonstrate that OMA-1/2 are required to repress the expression of a glp-1 3'-UTR reporter in developing oocytes. OMA-1 binds with high affinity to a conserved region of the glp-1 3'-UTR previously shown to interact with POS-1 and GLD-1, RNA-binding proteins required for glp-1 reporter repression in the posterior of fertilized embryos. Our results reveal that OMA-1 is a sequence-specific RNA-binding protein required to repress expression of maternal transcripts during oogenesis and suggest that interplay between OMA-1 and other factors for overlapping binding sites helps to coordinate the transition from oocyte to embryo.

  1. Flow injection chemiluminescence sensor using core-shell molecularly imprinted polymers as recognition element for determination of dapsone.

    PubMed

    Lu, Fuguang; Yang, Jinlong; Sun, Min; Fan, Lulu; Qiu, Huamin; Li, Xiangjun; Luo, Chuannan

    2012-07-01

    This paper reports the preparation of dapsone (DDS) imprinted polymer layer-coated silica submicron particles (SiO(2)) combined with chemiluminescence (CL) toward analysis of tracing DDS in practical samples. To induce the selective occurrence of surface polymerization, the amino groups were first grafted at the surface of SiO(2) by the (3-aminopropyl)triethoxysilane (APTES). The molecularly imprinted polymers (MIP) were coated at the surface of modified SiO(2) by the graft copolymerization. After the removal of templates, recognition sites of DDS were exposed in the polymer layers. The DDS-imprinted products were characterized by FT-IR, SEM, TEM, dynamic adsorption, and static adsorption tests. The proximity between the thickness of MIP layer and the spatial size of DDS indicated that the imprinted sites almost situated at the surface of MIP, leading to rapid adsorption saturation within 90 min. The apparent maximum binding amount of MIP toward DDS was evaluated as 14.98 mg·g(-1), which was much higher than that of non-molecularly imprinted polymers. The CL sensor provided a wide linear range for DDS within 1.0 × 10(-6) to 1.0 × 10(-4) mol·L(-1) with a detection limit of 5.27 × 10(-7) mol·L(-1) and the relative standard deviation of 1.8 % (n = 11) by determinations of 5.0 × 10(-6) mol·L(-1) DDS. This method was applied to determine DDS in urine samples and satisfactory results were obtained.

  2. Crystal structure of pentapeptide-independent chemotaxis receptor methyltransferase (CheR) reveals idiosyncratic structural determinants for receptor recognition.

    PubMed

    Batra, Monu; Sharma, Rajesh; Malik, Anjali; Dhindwal, Sonali; Kumar, Pravindra; Tomar, Shailly

    2016-12-01

    Chemotactic methyltransferase, CheR catalyse methylation of specific glutamate residues in the cytoplasmic domain of methyl-accepting chemotactic protein receptors (MCPRs). The methylation of MCPRs is essential for the chemical sensing and chemotactic bacterial mobility towards favorable chemicals or away from unfavorable ones. In this study, crystal structure of B. subtilis CheR (BsCheR) in complex with S-adenosyl-l-homocysteine (SAH) has been determined to 1.8Å resolution. This is the first report of crystal structure belonging to the pentapeptide-independent CheR (PICheR) class. Till date, only one crystal structure of CheR from S. typhimurium (StCheR) belonging to pentapeptide-dependent CheR (PDCheR) class is available. Structural analysis of BsCheR reveals a helix-X-helix motif (HXH) with Asp53 as the linker residue in the N-terminal domain. The key structural features of the PDCheR β-subdomain involved in the formation of a tight complex with the pentapeptide binding motif in MCPRs were found to be absent in the structure of BsCheR. Additionally, isothermal titration calorimetry (ITC) experiments were performed to investigate S-adenosyl-(l)-methionine (SAM) binding affinity and KD was determined to be 0.32mM. The structure of BsCheR reveals that mostly residues of the large C-terminal domain contribute to SAH binding, with contributions of few residues from the linker region and the N-terminal domain. Structural investigations and sequence analysis carried out in this study provide critical insights into the distinct receptor recognition mechanism of the PDCheR and PICheR methyltransferase classes.

  3. Proposed study to determine potential flight applications and human factors design guidelines of voice recognition/synthesis systems

    NASA Technical Reports Server (NTRS)

    Bergeron, H. P.

    1983-01-01

    An effort to evaluate the human factors aspects and potential of voice recognition/synthesis techniques and the application of present and near-future (5 years) voice recognition/synthesis systems as a pilot/aircraft cockpit interface capability in an operational environment is discussed. The analysis will emphasize applications for single pilot instrument flight rules operations but will also include applications for other categories of aircraft with various levels of complexity.

  4. Calicheamicin-DNA complexes: warhead alignment and saccharide recognition of the minor groove.

    PubMed

    Ikemoto, N; Kumar, R A; Ling, T T; Ellestad, G A; Danishefsky, S J; Patel, D J

    1995-11-07

    The solution structures of calicheamicin gamma 1I, its cycloaromatized analog (calicheamicin epsilon), and its aryl tetrasaccharide complexed to a common DNA hairpin duplex have been determined by NMR and distance-refined molecular dynamics computations. Sequence specificity is associated with carbohydrate-DNA recognition that places the aryl tetrasaccharide component of all three ligands in similar orientations in the minor groove at the d(T-C-C-T).d(A-G-G-A) segment. The complementary fit of the ligands and the DNA minor groove binding site creates numerous van der Waals contacts as well as hydrogen bonding interactions. Notable are the iodine and sulfur atoms of calicheamicin that hydrogen bond with the exposed amino proton of the 5'- and 3'-guanines, respectively, of the d(A-G-G-A) segment. The sequence-specific carbohydrate binding orients the enediyne aglycone of calicheamicin gamma 1I such that its C3 and C6 proradical centers are adjacent to the cleavage sites. While the enediyne aglycone of calicheamicin gamma 1I is tilted relative to the helix axis and spans the minor groove, the cycloaromatized aglycone is aligned approximately parallel to the helix axis in the respective complexes. Specific localized conformational perturbations in the DNA have been identified from imino proton complexation shifts and changes in specific sugar pucker patterns on complex formation. The helical parameters for the carbohydrate binding site are comparable with corresponding values in B-DNA fibers while a widening of the groove is observed at the adjacent aglycone binding site.

  5. Recognition sequences of restriction endonucleases and methylases--a review.

    PubMed

    Kessler, C; Neumaier, P S; Wolf, W

    1985-01-01

    The properties and sources of all known endonucleases and methylases acting site-specifically on DNA are listed. The enzymes are crossindexed (Table I), classified according to homologies within their recognition sequences (Table II), and characterized within Table II by the cleavage and methylation positions, the number of recognition sites on the DNA of the bacteriophages lambda, phi X174 and M13mp7, the viruses Ad2 and SV40, the plasmids pBR322 and pBR328 and the microorganisms from which they originate. Other tabulated properties of the restriction endonucleases include relaxed specificities (Table III), the structure of the restriction fragment ends (Table IV), and the sensitivity to different kinds of DNA methylation (Table V). Table VI classifies the methylases according to the nature of the methylated base(s) within their recognition sequences. This table also comprises those restriction endonucleases, which are known to be inhibited by the modified nucleotides. Furthermore, this review includes a restriction map of bacteriophage lambda DNA based on sequence data. Table VII lists the exact nucleotide positions of the cleavage sites, the length of the generated fragments ordered according to size, and the effects of the Escherichia coli dam- and dcmI-coded methylases M X Eco dam and M X Eco dcmI on the particular recognition sites.

  6. Trend recognition and failure prediction of the attitude determination and control system of the Space Station Freedom

    NASA Astrophysics Data System (ADS)

    Nelson, Kyle S.; Hadden, George D.

    An approach to automated trend recognition and failure prediction in the health parameter data of spacecraft is described. The approach, State-Based Feature Recognition (SBER), combines intelligent data filtering with state machines to detect the presence of features (trends and impending failures) in the health parameter data of spacecraft. SBFR, when implemented in a space-based or ground-based monitoring system, can increase spacecraft autonomy and decrease technician workload. An implemented, prototype Space Station Freedom (SSF) Maintenance and Diagnostic System (SSFMDS) that demonstrates the applicability of SBFR to trend detection and failure prediction will be described. SBFR allows features to be tracked, using specialized state machines, as they develop in a time-independent manner, allowing both short term and long term features to be detected. Each state machine operates independently of the other machines, making simultaneous feature tracking possible.

  7. Structure of the propeptide of prothrombin containing the. gamma. -carboxylation recognition site determined by two-dimensional NMR spectroscopy

    SciTech Connect

    Sanford, D.G.; Sudmeier, J.L.; Bachovchin, W.W.; Kanagy, C.; Furie, B.C.; Furie, B. )

    1991-10-15

    The propeptides of the vitamin K dependent blood clotting and regulatory proteins contain a {gamma}-carboxylation recognition site that directs precursor forms of these proteins for posttranslational {gamma}-carboxylation. Peptides corresponding to the propeptide of prothrombin were synthesized and examined by circular dichroism (CD) and nuclear magnetic resonance spectroscopy (NMR). CD spectra indicate that these peptides have little or no secondary structure in aqueous solutions but that the addition of trifluoroethanol induces or stabilizes a structure containing {alpha}-helical character. The maximum helical content occurs at 35-40% trifluoroethanol. This trifluoroethanol-stabilized structure was solved by two-dimensional NMR spectroscopy. The NMR results demonstrate that residues {minus}13 to {minus}3 form an amphipathic {alpha}-helix. NMR spectra indicate that a similar structure is present at 5C, in the absence of trifluoroethanol. Of the residues previously implicated in defining the {gamma}-carboxylation recognition site, four residues ({minus}18, {minus}17, {minus}16, and {minus}15) are adjacent to the helical region and one residue ({minus}10) is located within the helix. The potential role of the amphipathic {alpha}-helix in the {gamma}-carboxylation recognition site is discussed.

  8. Large domain motions in Ago protein controlled by the guide DNA-strand seed region determine the Ago-DNA-mRNA complex recognition process.

    PubMed

    Xia, Zhen; Huynh, Tien; Ren, Pengyu; Zhou, Ruhong

    2013-01-01

    The recognition mechanism and cleavage activity of argonaute (Ago), miRNA, and mRNA complexes are the core processes to the small non-coding RNA world. The 5' nucleation at the 'seed' region (position 2-8) of miRNA was believed to play a significant role in guiding the recognition of target mRNAs to the given miRNA family. In this paper, we have performed all-atom molecular dynamics simulations of the related and recently revealed Ago-DNA:mRNA ternary complexes to study the dynamics of the guide-target recognition and the effect of mutations by introducing "damaging" C·C mismatches at different positions in the seed region of the DNA-RNA duplex. Our simulations show that the A-form-like helix duplex gradually distorts as the number of seed mismatches increases and the complex can survive no more than two such mismatches. Severe distortions of the guide-target heteroduplex are observed in the ruinous 4-sites mismatch mutant, which give rise to a bending motion of the PAZ domain along the L1/L2 "hinge-like" connection segment, resulting in the opening of the nucleic-acid-binding channel. These long-range interactions between the seed region and PAZ domain, moderated by the L1/L2 segments, reveal the central role of the seed region in the guide-target strands recognition: it not only determines the guide-target heteroduplex's nucleation and propagation, but also regulates the dynamic motions of Ago domains around the nucleic-acid-binding channel.

  9. Molecular Determinants of Antibiotic Recognition and Resistance by Aminoglycoside Phosphotransferase (3′)-IIIa: A Calorimetric and Mutational Analysis

    PubMed Central

    Kaul, Malvika; Barbieri, Christopher M.; Srinivasan, Annankoil R.; Pilch, Daniel S.

    2007-01-01

    Summary The growing threat from the emergence of multidrug resistant pathogens highlight a critical need to expand our currently available arsenal of broad-spectrum antibiotics. In this connection, new antibiotics must be developed that exhibit the abilities to circumvent known resistance pathways. An important step toward achieving this goal is to define the key molecular interactions that govern antibiotic resistance. Here, we use site-specific mutagenesis, coupled with calorimetric, NMR, and enzymological techniques, to define the key interactions that govern the binding of the aminoglycoside antibiotics neomycin and kanamycin B to APH(3′)-IIIa (an antibiotic phosphorylating enzyme that produces resistance). Our mutational analyses identify the D261, E262, and C-terminal F264 residues of the enzyme as being critical for recognition of the two drugs as well as the manifestation of the resistance phenotype. In addition, the E160 residue is more important for recognition of kanamycin B than neomycin, with mutation of this residue partially restoring sensitivity to kanamycin B but not to neomycin. By contrast, the D193 residue partially restores sensitivity to neomycin but not to kanamycin B, with the origins of this differential effect being due to the importance of D193 for catalyzing the phosphorylation of neomycin. These collective mutational results, coupled with 15N NMR-derived pKa and calorimetrically-derived binding-linked drug protonation data, identify the 1-, 3-, and 2′-amino groups of both neomycin and kanamycin B as being critical functionalities for binding to APH(3′)-IIIa. These drug amino functionalities represent potential sites of modification in the design of next-generation compounds that can overcome APH(3′)-IIIa-induced resistance. PMID:17418235

  10. Molecular determinants of antibiotic recognition and resistance by aminoglycoside phosphotransferase (3')-IIIa: a calorimetric and mutational analysis.

    PubMed

    Kaul, Malvika; Barbieri, Christopher M; Srinivasan, Annankoil R; Pilch, Daniel S

    2007-05-25

    The growing threat from the emergence of multidrug resistant pathogens highlights a critical need to expand our currently available arsenal of broad-spectrum antibiotics. In this connection, new antibiotics must be developed that exhibit the abilities to circumvent known resistance pathways. An important step toward achieving this goal is to define the key molecular interactions that govern antibiotic resistance. Here, we use site-specific mutagenesis, coupled with calorimetric, NMR, and enzymological techniques, to define the key interactions that govern the binding of the aminoglycoside antibiotics neomycin and kanamycin B to APH(3')-IIIa (an antibiotic phosphorylating enzyme that confers resistance). Our mutational analyses identify the D261, E262, and C-terminal F264 residues of the enzyme as being critical for recognition of the two drugs as well as for the manifestation of the resistance phenotype. In addition, the E160 residue is more important for recognition of kanamycin B than neomycin, with mutation of this residue partially restoring sensitivity to kanamycin B but not to neomycin. By contrast, the D193 residue partially restores sensitivity to neomycin but not to kanamycin B, with the origins of this differential effect being due to the importance of D193 for catalyzing the phosphorylation of neomycin. These collective mutational results, coupled with (15)N NMR-derived pK(a) and calorimetrically derived binding-linked drug protonation data, identify the 1-, 3-, and 2'-amino groups of both neomycin and kanamycin B as being critical functionalities for binding to APH(3')-IIIa. These drug amino functionalities represent potential sites of modification in the design of next-generation compounds that can overcome APH(3')-IIIa-induced resistance.

  11. Nicotine, cotinine, and myosmine determination using polymer films of tailor-designed zinc porphyrins as recognition units for piezoelectric microgravimetry chemosensors.

    PubMed

    Noworyta, Krzysztof; Kutner, Wlodzimierz; Wijesinghe, Channa A; Srour, Serge G; D'Souza, Francis

    2012-03-06

    Two electropolymerizable zinc porphyrins with receptor sites tailor-designed for selective recognition of the nicotine, cotinine, or myosmine alkaloids were synthesized. These were 5-(2-phenoxyacetamide)-10,15,20-tris(triphenylamino)porphyrinato zinc(II) 1 and 5-(2,5-phenylene-bis(oxy)diacetamide)-10,15,20-tris(triphenylamino)porphyrinato zinc(II) 2 featuring one and two pendant amide side "pincers", respectively, and three triphenylamine substituents at the meso positions of the porphyrin macrocycles capable of electrochemical polymerization. Thin polymerfilms of these porphyrins served for recognition and the piezoelectric microgravimetry (PM) for analytical signal transduction of a new chemical sensor devised for determination of these alkaloids. The films were deposited by potentiodynamic electropolymerization on the 10 MHz quartz resonators of the electrochemical quartz crystal microbalance (EQCM) without affecting the electronic structure of the porphyrin macrocycles. Under favorable flow injection analysis (FIA) conditions, the alkaloid analytes were determined at the concentration level of 0.1 mM with high sensitivity and selectivity. Affinity toward the analytes of the polymer of 2 was higher than that of 1 due to the higher binding ability offered by two pendant pincers of the former. Because of the selective receptors and PM applied under FIA conditions, the developed procedure offered an alternative to the time-consuming and relatively expensive high-performance liquid chromatography (HPLC), capillary electrophoresis (CE), and gas chromatography mass spectrometry (GC-MS) methods of detection and quantification of these alkaloids.

  12. Structural and Functional Analysis of Murine Polyomavirus Capsid Proteins Establish the Determinants of Ligand Recognition and Pathogenicity

    PubMed Central

    O’Hara, Samantha D.; Garcea, Robert L.; Neu, Ursula; Stehle, Thilo

    2015-01-01

    Murine polyomavirus (MuPyV) causes tumors of various origins in newborn mice and hamsters. Infection is initiated by attachment of the virus to ganglioside receptors at the cell surface. Single amino acid exchanges in the receptor-binding pocket of the major capsid protein VP1 are known to drastically alter tumorigenicity and spread in closely related MuPyV strains. The virus represents a rare example of differential receptor recognition directly influencing viral pathogenicity, although the factors underlying these differences remain unclear. We performed structural and functional analyses of three MuPyV strains with strikingly different pathogenicities: the low-tumorigenicity strain RA, the high-pathogenicity strain PTA, and the rapidly growing, lethal laboratory isolate strain LID. Using ganglioside deficient mouse embryo fibroblasts, we show that addition of specific gangliosides restores infectability for all strains, and we uncover a complex relationship between virus attachment and infection. We identify a new infectious ganglioside receptor that carries an additional linear [α-2,8]-linked sialic acid. Crystal structures of all three strains complexed with representative oligosaccharides from the three main pathways of ganglioside biosynthesis provide the molecular basis of receptor recognition. All strains bind to a range of sialylated glycans featuring the central [α-2,3]-linked sialic acid present in the established receptors GD1a and GT1b, but the presence of additional sialic acids modulates binding. An extra [α-2,8]-linked sialic acid engages a protein pocket that is conserved among the three strains, while another, [α-2,6]-linked branching sialic acid lies near the strain-defining amino acids but can be accommodated by all strains. By comparing electron density of the oligosaccharides within the binding pockets at various concentrations, we show that the [α-2,8]-linked sialic acid increases the strength of binding. Moreover, the amino acid

  13. Structural and Functional Analysis of Murine Polyomavirus Capsid Proteins Establish the Determinants of Ligand Recognition and Pathogenicity.

    PubMed

    Buch, Michael H C; Liaci, A Manuel; O'Hara, Samantha D; Garcea, Robert L; Neu, Ursula; Stehle, Thilo

    2015-10-01

    Murine polyomavirus (MuPyV) causes tumors of various origins in newborn mice and hamsters. Infection is initiated by attachment of the virus to ganglioside receptors at the cell surface. Single amino acid exchanges in the receptor-binding pocket of the major capsid protein VP1 are known to drastically alter tumorigenicity and spread in closely related MuPyV strains. The virus represents a rare example of differential receptor recognition directly influencing viral pathogenicity, although the factors underlying these differences remain unclear. We performed structural and functional analyses of three MuPyV strains with strikingly different pathogenicities: the low-tumorigenicity strain RA, the high-pathogenicity strain PTA, and the rapidly growing, lethal laboratory isolate strain LID. Using ganglioside deficient mouse embryo fibroblasts, we show that addition of specific gangliosides restores infectability for all strains, and we uncover a complex relationship between virus attachment and infection. We identify a new infectious ganglioside receptor that carries an additional linear [α-2,8]-linked sialic acid. Crystal structures of all three strains complexed with representative oligosaccharides from the three main pathways of ganglioside biosynthesis provide the molecular basis of receptor recognition. All strains bind to a range of sialylated glycans featuring the central [α-2,3]-linked sialic acid present in the established receptors GD1a and GT1b, but the presence of additional sialic acids modulates binding. An extra [α-2,8]-linked sialic acid engages a protein pocket that is conserved among the three strains, while another, [α-2,6]-linked branching sialic acid lies near the strain-defining amino acids but can be accommodated by all strains. By comparing electron density of the oligosaccharides within the binding pockets at various concentrations, we show that the [α-2,8]-linked sialic acid increases the strength of binding. Moreover, the amino acid

  14. Structural Determinants of Substrate Recognition in the HAD Superfamily Member D-glycero-D-manno-Heptose-1,7-bisphosphate Phosphatase (GmhB)

    SciTech Connect

    Nguyen, H.; Wang, L; Huang, H; Peisach, E; Dunaway-Mariano, D; Allen, K

    2010-01-01

    The haloalkanoic acid dehalogenase (HAD) enzyme superfamily is the largest family of phosphohydrolases. In HAD members, the structural elements that provide the binding interactions that support substrate specificity are separated from those that orchestrate catalysis. For most HAD phosphatases, a cap domain functions in substrate recognition. However, for the HAD phosphatases that lack a cap domain, an alternate strategy for substrate selection must be operative. One such HAD phosphatase, GmhB of the HisB subfamily, was selected for structure-function analysis. Herein, the X-ray crystallographic structures of Escherichia coli GmhB in the apo form (1.6 {angstrom} resolution), in a complex with Mg{sup 2+} and orthophosphate (1.8 {angstrom} resolution), and in a complex with Mg{sup 2+} and D-glycero-D-manno-heptose 1{beta},7-bisphosphate (2.2 {angstrom} resolution) were determined, in addition to the structure of Bordetella bronchiseptica GmhB bound to Mg{sup 2+} and orthophosphate (1.7 {angstrom} resolution). The structures show that in place of a cap domain, the GmhB catalytic site is elaborated by three peptide inserts or loops that pack to form a concave, semicircular surface around the substrate leaving group. Structure-guided kinetic analysis of site-directed mutants was conducted in parallel with a bioinformatics study of sequence diversification within the HisB subfamily to identify loop residues that serve as substrate recognition elements and that distinguish GmhB from its subfamily counterpart, the histidinol-phosphate phosphatase domain of HisB. We show that GmhB and the histidinol-phosphate phosphatase domain use the same design of three substrate recognition loops inserted into the cap domain yet, through selective residue usage on the loops, have achieved unique substrate specificity and thus novel biochemical function.

  15. Structural determinants of substrate recognition in the HAD superfamily member D-glycero-D-manno-heptose-1,7-bisphosphate phosphatase (GmhB) .

    PubMed

    Nguyen, Henry H; Wang, Liangbing; Huang, Hua; Peisach, Ezra; Dunaway-Mariano, Debra; Allen, Karen N

    2010-02-16

    The haloalkanoic acid dehalogenase (HAD) enzyme superfamily is the largest family of phosphohydrolases. In HAD members, the structural elements that provide the binding interactions that support substrate specificity are separated from those that orchestrate catalysis. For most HAD phosphatases, a cap domain functions in substrate recognition. However, for the HAD phosphatases that lack a cap domain, an alternate strategy for substrate selection must be operative. One such HAD phosphatase, GmhB of the HisB subfamily, was selected for structure-function analysis. Herein, the X-ray crystallographic structures of Escherichia coli GmhB in the apo form (1.6 A resolution), in a complex with Mg(2+) and orthophosphate (1.8 A resolution), and in a complex with Mg(2+) and d-glycero-d-manno-heptose 1beta,7-bisphosphate (2.2 A resolution) were determined, in addition to the structure of Bordetella bronchiseptica GmhB bound to Mg(2+) and orthophosphate (1.7 A resolution). The structures show that in place of a cap domain, the GmhB catalytic site is elaborated by three peptide inserts or loops that pack to form a concave, semicircular surface around the substrate leaving group. Structure-guided kinetic analysis of site-directed mutants was conducted in parallel with a bioinformatics study of sequence diversification within the HisB subfamily to identify loop residues that serve as substrate recognition elements and that distinguish GmhB from its subfamily counterpart, the histidinol-phosphate phosphatase domain of HisB. We show that GmhB and the histidinol-phosphate phosphatase domain use the same design of three substrate recognition loops inserted into the cap domain yet, through selective residue usage on the loops, have achieved unique substrate specificity and thus novel biochemical function.

  16. A conserved motif in JNK/p38-specific MAPK phosphatases as a determinant for JNK1 recognition and inactivation

    PubMed Central

    Liu, Xin; Zhang, Chen-Song; Lu, Chang; Lin, Sheng-Cai; Wu, Jia-Wei; Wang, Zhi-Xin

    2016-01-01

    Mitogen-activated protein kinases (MAPKs), important in a large array of signalling pathways, are tightly controlled by a cascade of protein kinases and by MAPK phosphatases (MKPs). MAPK signalling efficiency and specificity is modulated by protein–protein interactions between individual MAPKs and the docking motifs in cognate binding partners. Two types of docking interactions have been identified: D-motif-mediated interaction and FXF-docking interaction. Here we report the crystal structure of JNK1 bound to the catalytic domain of MKP7 at 2.4-Å resolution, providing high-resolution structural insight into the FXF-docking interaction. The 285FNFL288 segment in MKP7 directly binds to a hydrophobic site on JNK1 that is near the MAPK insertion and helix αG. Biochemical studies further reveal that this highly conserved structural motif is present in all members of the MKP family, and the interaction mode is universal and critical for the MKP-MAPK recognition and biological function. PMID:26988444

  17. Unraveling a Hotspot for TCR Recognition on HLA-A2: Evidence Against the Existence of Peptide-independent TCR Binding Determinants

    SciTech Connect

    Gagnon, Susan J.; Borbulevych, Oleg Y.; Davis-Harrison, Rebecca L.; Baxter, Tiffany K.; Clemens, John R.; Armstrong, Kathryn M.; Turner, Richard V.; Damirjian, Marale; Biddison, William E.; Baker, Brian M.

    2010-07-19

    T cell receptor (TCR) recognition of peptide takes place in the context of the major histocompatibility complex (MHC) molecule, which accounts for approximately two-thirds of the peptide/MHC buried surface. Using the class I MHC HLA-A2 and a large panel of mutants, we have previously shown that surface mutations that disrupt TCR recognition vary with the identity of the peptide. The single exception is Lys66 on the HLA-A2 {alpha}1 helix, which when mutated to alanine disrupts recognition for 93% of over 250 different T cell clones or lines, independent of which peptide is bound. Thus, Lys66 could serve as a peptide-independent TCR binding determinant. Here, we have examined the role of Lys66 in TCR recognition of HLA-A2 in detail. The structure of a peptide/HLA-A2 molecule with the K66A mutation indicates that although the mutation induces no major structural changes, it results in the exposure of a negatively charged glutamate (Glu63) underneath Lys66. Concurrent replacement of Glu63 with glutamine restores TCR binding and function for T cells specific for five different peptides presented by HLA-A2. Thus, the positive charge on Lys66 does not serve to guide all TCRs onto the HLA-A2 molecule in a manner required for productive signaling. Furthermore, electrostatic calculations indicate that Lys66 does not contribute to the stability of two TCR-peptide/HLA-A2 complexes. Our findings are consistent with the notion that each TCR arrives at a unique solution of how to bind a peptide/MHC, most strongly influenced by the chemical and structural features of the bound peptide. This would not rule out an intrinsic affinity of TCRs for MHC molecules achieved through multiple weak interactions, but for HLA-A2 the collective mutational data place limits on the role of any single MHC amino acid side-chain in driving TCR binding in a peptide-independent fashion.

  18. Chemical cross-linking of HIV-1 Env for direct TLR7/8 ligand conjugation compromises recognition of conserved antigenic determinants

    PubMed Central

    Feng, Yu; Forsell, Mattias N. E.; Flynn, Barbara; Adams, William; Loré, Karin; Seder, Robert; Wyatt, Richard T.; Karlsson Hedestam, Gunilla B.

    2013-01-01

    Covalent conjugation of immune-stimulatory compounds to protein antigens is a potential means to self-adjuvant non-replicating subunit vaccines. Previously, it was demonstrated that covalent coupling of a Toll-like receptor (TLR) ligand to the exterior HIV-1 envelope glycoprotein, gp120, enhanced its immunogenicity. However, the consequences of chemical conjugation to gp120 on broadly neutralizing antibody (bNAb) epitopes were so far not examined. Here, we conjugated a TLR7/8 ligand to lysine residues on gp120 using NHS-PEO8-maleimide linkers and investigated if this affected Ab recognition of the CD4 binding site (CD4bs), a highly conserved target for bNAbs. We demonstrate that the recognition of the CD4bs was reduced following coupling, especially at a higher coupling ratio. These results have implications for the coupling of ligands to vaccine antigens where elicitation of humoral immune responses to specific neutralizing determinants is desired. PMID:24074567

  19. A Combined NMR and Computational Approach to Determine the RGDechi-hCit-αv β3 Integrin Recognition Mode in Isolated Cell Membranes.

    PubMed

    Farina, Biancamaria; de Paola, Ivan; Russo, Luigi; Capasso, Domenica; Liguoro, Annamaria; Gatto, Annarita Del; Saviano, Michele; Pedone, Paolo V; Di Gaetano, Sonia; Malgieri, Gaetano; Zaccaro, Laura; Fattorusso, Roberto

    2016-01-11

    The critical role of integrins in tumor progression and metastasis has stimulated intense efforts to identify pharmacological agents that can modulate integrin function. In recent years, αv β3 and αv β5 integrin antagonists were demonstrated to be effective in blocking tumor progression. RGDechi-hCit, a chimeric peptide containing a cyclic RGD motif linked to an echistatin C-terminal fragment, is able to recognize selectively αv β3 integrin both in vitro and in vivo. High-resolution molecular details of the selective αv β3 recognition of the peptide are certainly required, nonetheless RGDechi-hCit internalization limited the use of classical in cell NMR experiments. To overcome such limitations, we used WM266 isolated cellular membranes to accomplish a detailed NMR interaction study that, combined with a computational analysis, provides significant structural insights into αv β3 molecular recognition by RGDechi-hCit. Remarkably, on the basis of the identified molecular determinants, we design a RGDechi-hCit mutant that is selective for αv β5 integrin.

  20. Critical determinants for substrate recognition and catalysis in the M. tuberculosis class II AP-endonuclease/3'-5' exonuclease III.

    PubMed

    Khanam, Taran; Shukla, Ankita; Rai, Niyati; Ramachandran, Ravishankar

    2015-05-01

    The Mycobacterium tuberculosis AP-endonuclease/3'-5' exodeoxyribonuclease (MtbXthA) is an important player in DNA base excision repair (BER). We demonstrate that the enzyme has robust apurinic/apyrimidinic (AP) endonuclease activity, 3'-5' exonuclease, phosphatase, and phosphodiesterase activities. The enzyme functions as an AP-endonuclease at high ionic environments, while the 3'-5'-exonuclease activity is predominant at low ionic environments. Our molecular modelling and mutational experiments show that E57 and D251 are critical for catalysis. Although nicked DNA and gapped DNA are fair substrates of MtbXthA, the gap-size did not affect the excision activity and furthermore, a substrate with a recessed 3'-end is preferred. To understand the determinants of abasic-site recognition, we examined the possible roles of (i) the base opposite the abasic site, (ii) the abasic ribose ring itself, (iii) local distortions in the AP-site, and (iv) conserved residues located near the active site. Our experiments demonstrate that the first three determinants do not play a role in MtbXthA, and in fact the enzyme exhibits robust endonucleolytic activity against single-stranded AP DNA also. Regarding the fourth determinant, it is known that the catalytic-site of AP endonucleases is surrounded by conserved aromatic residues and intriguingly, the exact residues that are directly involved in abasic site recognition vary with the individual proteins. We therefore, used a combination of mutational analysis, kinetic assays, and structure-based modelling, to identify that Y237, supported by Y137, mediates the formation of the MtbXthA-AP-DNA complex and AP-site incision.

  1. Latent ClpX-recognition signals ensure LexA destruction after DNA damage

    PubMed Central

    Neher, Saskia B.; Flynn, Julia M.; Sauer, Robert T.; Baker, Tania A.

    2003-01-01

    The DNA-damage response genes in bacteria are up-regulated when LexA repressor undergoes autocatalytic cleavage stimulated by activated RecA protein. Intact LexA is stable to intracellular degradation but its auto-cleavage fragments are degraded rapidly. Here, both fragments of LexA are shown to be substrates for the ClpXP protease. ClpXP recognizes these fragments using sequence motifs that flank the auto-cleavage site but are dormant in intact LexA. Furthermore, ClpXP degradation of the LexA-DNA-binding fragment is important to cell survival after DNA damage. These results demonstrate how one protein-processing event can activate latent protease recognition signals, triggering a cascade of protein turnover in response to environmental stress. PMID:12730132

  2. Molecular recognition in a propazine-imprinted polymer and its application to the determination of triazines in environmental samples.

    PubMed

    Turiel, E; Martin-Esteban, A; Fernández, P; Pérez-Conde, C; Cámara, C

    2001-11-01

    An analytical methodology for the determination of triazines in environmental samples incorporating a molecularly imprinted solid-phase extraction (MISPE) process using a propazine-imprinted polymer was developed. Two different polymers were prepared using acetonitrile or toluene as porogen, and their optimum loading, washing, and elution conditions were established. Although both polymers were able to recognize several chlorotriazines (propazine, atrazine, simazine, desethylatrazine, and desisopropylatrazine), the polymer prepared in toluene showed the best performance and was also capable of recognizing a methylthiotriazine (prometryn). A binding study carried out in this polymer demonstrated that it possesses heterogeneous binding sites with different binding abilities. From this study, it was also concluded that desethylatrazine and desisopropylatrazine displace the other triazines at high concentrations, including the template molecule. The accuracy and selectivity of the MISPE process developed was verified using a certified reference material for drinking water containing atrazine and simazine among other commonly used pesticides. Finally, the MISPE procedure was successfully applied to the cleanup of drinking and groundwater, soil, and corn sample extracts, and the triazines were determined by micellar electrokinetic chromatography.

  3. Cleavage sites within the poliovirus capsid protein precursors

    SciTech Connect

    Larsen, G.R.; Anderson, C.W.; Dorner, A.J.; Semler, B.L.; Wimmer, E.

    1982-01-01

    Partial amino-terminal sequence analysis was performed on radiolabeled poliovirus capsid proteins VP1, VP2, and VP3. A computer-assisted comparison of the amino acid sequences obtained with that predicted by the nucleotide sequence of the poliovirus genome allows assignment of the amino terminus of each capsid protein to a unique position within the virus polyprotein. Sequence analysis of trypsin-digested VP4, which has a blocked amino terminus, demonstrates that VP4 is encoded at or very near to the amino terminus of the polyprotein. The gene order of the capsid proteins is VP4-VP2-VP3-VP1. Cleavage of VP0 to VP4 and VP2 is shown to occur between asparagine and serine, whereas the cleavages that separate VP2/VP3 and VP3/VP1 occur between glutamine and glycine residues. This finding supports the hypothesis that the cleavage of VP0, which occurs during virion morphogenesis, is distinct from the cleavages that separate functional regions of the polyprotein.

  4. von Willebrand factor storage requires intact prosequence cleavage site.

    PubMed

    Journet, A M; Saffaripour, S; Cramer, E M; Tenza, D; Wagner, D D

    1993-02-01

    Large multimers of the adhesive glycoprotein von Willebrand factor (vWf) are stored in endothelial cells in rod-shaped granules called Weibel-Palade bodies, while small multimers are secreted constitutively. Expression of pro-vWf in other cells with a regulated pathway of secretion, results in formation of vWf-containing storage granules that have a morphology similar to Weibel-Palade bodies. vWf expressed without its prosequence is not stored. To evaluate the importance of prosequence cleavage in vWf storage, the Arg at position -1, known to be necessary for cleavage, was mutated to Gly. Transfection of this cleavage mutant into two cell lines with a regulated pathway of secretion (RIN 5F and AtT-20 cells) led to the formation of large multimers. However, treatment of the cell lysates by the enzyme endoglycosidase H (Endo-H) did not reveal significant amounts of intracellular Endo-H-resistant vWf, which indicates the absence of a pool of stored processed vWf. In addition, no Weibel-Palade body-like structure was detected in these cells by immunofluorescence labeling with anti-vWf antiserum. Electron microscopy and immunocytochemistry of RIN 5F cells expressing the pro-vWf mutant confirmed the absence of Weibel-Palade body-like structures. In addition, anti-vWf-linked gold particles were found in the ER, occasionally in rounded granules and particularly in lysosomal structures which were abundant. We conclude that the formation of large aggregates is not sufficient to induce efficient vWf storage, and that the lack of cleavage of the prosequence may direct the mutant pro-vWf molecule to a degradative pathway. Therefore, the prosequence cleavage is a requirement for vWf storage.

  5. [Structural regularities in activated cleavage sites of thrombin receptors].

    PubMed

    Mikhaĭlik, I V; Verevka, S V

    1999-01-01

    Comparison of thrombin receptors activation splitting sites sequences testifies to their similarity both in activation splitting sites of protein precursors and protein proteinase inhibitors reactive sites. In all these sites corresponded to effectory sites P2'-positions are placed by hydrophobic amino-acids only. The regularity defined conforms with previous thesis about the role of effectory S2'-site in regulation of the processes mediated by serine proteinases.

  6. Structural determinants of species-selective substrate recognition in human and Drosophila serotonin transporters revealed through computational docking studies.

    PubMed

    Kaufmann, Kristian W; Dawson, Eric S; Henry, L Keith; Field, Julie R; Blakely, Randy D; Meiler, Jens

    2009-02-15

    To identify potential determinants of substrate selectivity in serotonin (5-HT) transporters (SERT), models of human and Drosophila serotonin transporters (hSERT, dSERT) were built based on the leucine transporter (LeuT(Aa)) structure reported by Yamashita et al. (Nature 2005;437:215-223), PBDID 2A65. Although the overall amino acid identity between SERTs and the LeuT(Aa) is only 17%, it increases to above 50% in the first shell of the putative 5-HT binding site, allowing de novo computational docking of tryptamine derivatives in atomic detail. Comparison of hSERT and dSERT complexed with substrates pinpoints likely structural determinants for substrate binding. Forgoing the use of experimental transport and binding data of tryptamine derivatives for construction of these models enables us to critically assess and validate their predictive power: A single 5-HT binding mode was identified that retains the amine placement observed in the LeuT(Aa) structure, matches site-directed mutagenesis and substituted cysteine accessibility method (SCAM) data, complies with support vector machine derived relations activity relations, and predicts computational binding energies for 5-HT analogs with a significant correlation coefficient (R = 0.72). This binding mode places 5-HT deep in the binding pocket of the SERT with the 5-position near residue hSERT A169/dSERT D164 in transmembrane helix 3, the indole nitrogen next to residue Y176/Y171, and the ethylamine tail under residues F335/F327 and S336/S328 within 4 A of residue D98. Our studies identify a number of potential contacts whose contribution to substrate binding and transport was previously unsuspected.

  7. Genetic specificity of face recognition.

    PubMed

    Shakeshaft, Nicholas G; Plomin, Robert

    2015-10-13

    Specific cognitive abilities in diverse domains are typically found to be highly heritable and substantially correlated with general cognitive ability (g), both phenotypically and genetically. Recent twin studies have found the ability to memorize and recognize faces to be an exception, being similarly heritable but phenotypically substantially uncorrelated both with g and with general object recognition. However, the genetic relationships between face recognition and other abilities (the extent to which they share a common genetic etiology) cannot be determined from phenotypic associations. In this, to our knowledge, first study of the genetic associations between face recognition and other domains, 2,000 18- and 19-year-old United Kingdom twins completed tests assessing their face recognition, object recognition, and general cognitive abilities. Results confirmed the substantial heritability of face recognition (61%), and multivariate genetic analyses found that most of this genetic influence is unique and not shared with other cognitive abilities.

  8. Conjoint Recognition.

    ERIC Educational Resources Information Center

    Brainerd, C. J.; Reyna, V. F.; Mojardin, A. H.

    1999-01-01

    Reviews some limiting properties of the process-dissociation model as it applies to the study of dual-process conceptions of memory. A second-generation model (conjoint recognition) is proposed to address these limitations and supply additional capabilities. Worked applications to data are provided. (Author/GCP)

  9. Androgenic control of male-typical behavior, morphology and sex recognition is independent of the mode of sex determination: A case study on Lichtenfelder's gecko (Eublepharidae: Goniurosaurus lichtenfelderi).

    PubMed

    Golinski, Alison; Kubička, Lukáš; John-Alder, Henry; Kratochvíl, Lukáš

    2015-06-01

    Previous work on lizards has shown that many sexually dimorphic traits depend on testosterone (T), but the details of this control can vary among species. Here, we tested the role of T on the expression of morphological, physiological, and behavioral traits in Lichtenfelder's gecko (Goniurosaurus lichtenfelderi), from the lizard family Eublepharidae notable for interspecific variation in sexually dimorphic traits and the mode of sex determination. Experiments included three groups of males (intact control, surgically castrated, castrated with T replacement) and two groups of females (intact control, T supplemented). In males, castration caused reductions in 1) the size of hemipenes, 2) offensive aggression, 3) male sexual behavior in a neutral arena, 4) activity of precloacal glands, and 5) loss of male chemical cues for sex recognition. These reductions were not observed in castrated males with T replacement. Interestingly, castrated males performed sexual behavior in their home cages, which shows that the effect of T depends on the environmental context. Notably, tail vibration, previously reported as a courtship behavior in other eublepharids, is displayed by males of G. lichtenfelderi during interactions with conspecifics of both sexes, suggesting an evolutionary shift in the meaning of this signal. In females, T induced growth of hemipenes and male-typical courtship but did not induce precloacal pore activity, aggression, or mounting. In comparison to previous reports on Eublepharis macularius, our results indicate that effects of T do not depend on the mode of sex determination. Further, our results extend our understanding of the complexity of control of male traits and illustrate how lability in the effects of T can be a general mechanism causing evolutionary changes in the components of suites of functionally correlated traits.

  10. Nine Crystal Structures Determine the Substrate Envelope of the MDR HIV-1 Protease

    SciTech Connect

    Liu, Zhigang; Wang, Yong; Brunzelle, Joseph; Kovari, Iulia A.; Kovari, Ladislau C.

    2012-03-27

    Under drug selection pressure, emerging mutations render HIV-1 protease drug resistant, leading to the therapy failure in anti-HIV treatment. It is known that nine substrate cleavage site peptides bind to wild type (WT) HIV-1 protease in a conserved pattern. However, how the multidrug-resistant (MDR) HIV-1 protease binds to the substrate cleavage site peptides is yet to be determined. MDR769 HIV-1 protease (resistant mutations at residues 10, 36, 46, 54, 62, 63, 71, 82, 84, and 90) was selected for present study to understand the binding to its natural substrates. MDR769 HIV-1 protease was co-crystallized with nine substrate cleavage site hepta-peptides. Crystallographic studies show that MDR769 HIV-1 protease has an expanded substrate envelope with wide open flaps. Furthermore, ligand binding energy calculations indicate weaker binding in MDR769 HIV-1 protease-substrate complexes. These results help in designing the next generation of HIV-1 protease inhibitors by targeting the MDR HIV-1 protease.

  11. Pocket 4 of the HLA-DR(alpha,beta 1*0401) molecule is a major determinant of T cells recognition of peptide

    PubMed Central

    1995-01-01

    To investigate the functional roles of individual HLA-DR residues in T cell recognition, transfectants expressing wild-type or mutant DR(alpha,beta 1*0401) molecules with single amino acid substitutions at 14 polymorphic positions of the DR beta 1*0401 chain or 19 positions of the DR alpha chain were used as antigen-presenting cells for five T cell clones specific for the influenza hemagglutinin peptide, HA307-19. Of the six polymorphic positions in the DR beta floor that were examined, mutations at only two positions eliminated T cell recognition: positions 13 (four clones) and 28 (one clone). In contrast, individual mutations at DR beta positions 70, 71, 78, and 86 on the alpha helix eliminated recognition by each of the clones, and mutations at positions 74 and 67 eliminated recognition by four and two clones, respectively. Most of the DR alpha mutations had minimal or no effect on most of the clones, although one clone was very sensitive to changes in the DR alpha chain, with loss of recognition in response to 10 mutants. Mutants that abrogated recognition by all of the clones were assessed for peptide binding, and only the beta 86 mutation drastically decreased peptide binding. Single amino acid substitutions at polymorphic positions in the central part of the DR beta alpha helix disrupted T cell recognition much more frequently than substitutions in the floor, suggesting that DR beta residues on the alpha helix make relatively greater contributions than those in the floor to the ability of the DR(alpha,beta 1*0401) molecule to present HA307-19. The data indicate that DR beta residues 13, 70, 71, 74, and 78, which are located in pocket 4 of the peptide binding site in the crystal structure of the DR1 molecule, exert a major and disproportionate influence on the outcome of T cell recognition, compared with other polymorphic residues. PMID:7869051

  12. Graphene sheet-starch platform based on the groove recognition for the sensitive and highly selective determination of iodide in seafood samples.

    PubMed

    Liu, Shou-Qing; Hu, Feng-Tian; Liu, Cheng-Bao; Chen, Feng; Wu, Zheng-Ying; Liang, Zuo-Qin; Xu, Nan; Chen, Zhi-Gang

    2013-09-15

    The functionalization of graphene nanosheets was realized using a simple starch mixture to achieve a highly selective recognition of iodide, thereby surmounting the complicated reactions possibly leading to low yield during functionalization. The groove recognition for starch to iodide, a novel recognition model, was established. The starch-to-graphene nanosheet mass ratio of 3:2 produced an optimal current signal. The recognition and measurement procedures were conducted in different cells, respectively. These procedures improved the selectivity and sensitivity, and overcame the possibility of interference from coexisting ions. Under optimal conditions, the graphene sheet-starch electrode was immersed in a recognition cell at pH 2.0 for 10min, afterward, in a measurement cell at pH 1.0 for quantitative analysis, resulting in the highest current signals obtained. The quantitative electrochemical measurements yielded a mean value of 214.6mg/kg in actual samples of commercially available seafood sample, whereas the spectrophotometric measurements produced a mean value of 226.7mg/kg. If the spectrophotometric value for the seafood sample is accurate, the percentage error for the electrochemical method is only 5.3%. Therefore, the electrochemical method is reliable for qualitative iodide measurements. The groove recognition was highlighted to elucidate the specific selectivity.

  13. Conjoint recognition.

    PubMed

    Brainerd, C J; Reyna, V F; Mojardin, A H

    1999-01-01

    The process-dissociation model has stimulated important advances in the study of dual-process conceptions of memory. The authors review some limiting properties of that model and consider the degree of support for its parent theory (the recollection-familiarity distinction). A 2nd-generation model (conjoint recognition) is proposed that addresses these limitations and supplies additional capabilities, such as goodness-of-fit tests, the ability to measure dual processes for false-memory responses, and statistical procedures for testing within- and between-conditions hypotheses about its parameters. The conjoint-recognition model also implements an alternative theoretical interpretation (the identity-similarity distinction of fuzzy-trace theory). Worked applications to data are provided.

  14. Structural Insights into Substrate Recognition by Clostridium difficile Sortase

    PubMed Central

    Yin, Jui-Chieh; Fei, Chun-Hsien; Lo, Yen-Chen; Hsiao, Yu-Yuan; Chang, Jyun-Cyuan; Nix, Jay C.; Chang, Yuan-Yu; Yang, Lee-Wei; Huang, I-Hsiu; Wang, Shuying

    2016-01-01

    Sortases function as cysteine transpeptidases that catalyze the covalent attachment of virulence-associated surface proteins into the cell wall peptidoglycan in Gram-positive bacteria. The substrate proteins targeted by sortase enzymes have a cell wall sorting signal (CWSS) located at the C-terminus. Up to date, it is still not well understood how sortases with structural resemblance among different classes and diverse species of bacteria achieve substrate specificity. In this study, we focus on elucidating the molecular basis for specific recognition of peptide substrate PPKTG by Clostridium difficile sortase B (Cd-SrtB). Combining structural studies, biochemical assays and molecular dynamics simulations, we have constructed a computational model of Cd-SrtBΔN26–PPKTG complex and have validated the model by site-directed mutagensis studies and fluorescence resonance energy transfer (FRET)-based assay. Furthermore, we have revealed that the fourth amino acid in the N-terminal direction from cleavage site of PPKTG forms specific interaction with Cd-SrtB and plays an essential role in configuring the peptide to allow more efficient substrate-specific cleavage by Cd-SrtB. PMID:27921010

  15. Andes virus recognition of human and Syrian hamster beta3 integrins is determined by an L33P substitution in the PSI domain.

    PubMed

    Matthys, Valery S; Gorbunova, Elena E; Gavrilovskaya, Irina N; Mackow, Erich R

    2010-01-01

    Andes virus (ANDV) causes a fatal hantavirus pulmonary syndrome (HPS) in humans and Syrian hamsters. Human alpha(v)beta(3) integrins are receptors for several pathogenic hantaviruses, and the function of alpha(v)beta(3) integrins on endothelial cells suggests a role for alpha(v)beta(3) in hantavirus directed vascular permeability. We determined here that ANDV infection of human endothelial cells or Syrian hamster-derived BHK-21 cells was selectively inhibited by the high-affinity alpha(v)beta(3) integrin ligand vitronectin and by antibodies to alpha(v)beta(3) integrins. Further, antibodies to the beta(3) integrin PSI domain, as well as PSI domain polypeptides derived from human and Syrian hamster beta(3) subunits, but not murine or bovine beta(3), inhibited ANDV infection of both BHK-21 and human endothelial cells. These findings suggest that ANDV interacts with beta(3) subunits through PSI domain residues conserved in both Syrian hamster and human beta(3) integrins. Sequencing the Syrian hamster beta(3) integrin PSI domain revealed eight differences between Syrian hamster and human beta(3) integrins. Analysis of residues within the PSI domains of human, Syrian hamster, murine, and bovine beta(3) integrins identified unique proline substitutions at residues 32 and 33 of murine and bovine PSI domains that could determine ANDV recognition. Mutagenizing the human beta(3) PSI domain to contain the L33P substitution present in bovine beta(3) integrin abolished the ability of the PSI domain to inhibit ANDV infectivity. Conversely, mutagenizing either the bovine PSI domain, P33L, or the murine PSI domain, S32P, to the residue present human beta(3) permitted PSI mutants to inhibit ANDV infection. Similarly, CHO cells transfected with the full-length bovine beta(3) integrin containing the P33L mutation permitted infection by ANDV. These findings indicate that human and Syrian hamster alpha(v)beta(3) integrins are key receptors for ANDV and that specific residues within the

  16. Determination of the Processing Sites of an Arabidopsis 2S Albumin and Characterization of the Complete Gene Family.

    PubMed

    Krebbers, E; Herdies, L; De Clercq, A; Seurinck, J; Leemans, J; Van Damme, J; Segura, M; Gheysen, G; Van Montagu, M; Vandekerckhove, J

    1988-08-01

    The most abundant isoform of the 2S albumin present in seeds of Arabidopsis thaliana has been sequenced and the corresponding gene isolated. Examination of the protein and DNA sequences allows the determination of the exact proteolytic cleavage sites during posttranslational processing. Like other 2S albumins, that of Arabidopsis is made as a prepropeptide. After removal of the signal peptide, the propeptide is cleaved at four other points, giving two subunits linked by a disulfide bridge(s). Comparison of these cleavage sites with those of 2S albumins of Brassica napus and Bertholletia excelsa suggests that while individual cleavage sites between species are conserved, the four processing sites within a species are not similar, suggesting that up to four different proteases may be involved in processing 2S albumins. The Arabidopsis 2S albumin gene was used to isolate the entire gene family. There are four genes, tightly linked in a tandem array. None of the genes contains an intron. Comparison of the predicted protein sequences shows that only one of the genes can encode the isoform determined by protein analysis to be the most abundant, and therefore this gene is certain to be expressed. It is possible that some or all of the other three genes are also active.

  17. Individual recognition between mother and infant bats (Myotis)

    NASA Technical Reports Server (NTRS)

    Turner, D.; Shaughnessy, A.; Gould, E.

    1972-01-01

    The recognition process and the basis for that recognition, in brown bats, between mother and infant are analyzed. Two parameters, ultrasonic communication and olfactory stimuli, are investigated. The test animals were not allowed any visual contact. It was concluded that individual recognition between mother and infant occurred. However, it could not be determined if the recognition was based on ultrasonic signals or olfactory stimuli.

  18. Highly conserved regions within the spike proteins of human coronaviruses 229E and NL63 determine recognition of their respective cellular receptors.

    PubMed

    Hofmann, Heike; Simmons, Graham; Rennekamp, Andrew J; Chaipan, Chawaree; Gramberg, Thomas; Heck, Elke; Geier, Martina; Wegele, Anja; Marzi, Andrea; Bates, Paul; Pöhlmann, Stefan

    2006-09-01

    We have recently demonstrated that the severe acute respiratory syndrome coronavirus (SARS-CoV) receptor angiotensin converting enzyme 2 (ACE2) also mediates cellular entry of the newly discovered human coronavirus (hCoV) NL63. Here, we show that expression of DC-SIGN augments NL63 spike (S)-protein-driven infection of susceptible cells, while only expression of ACE2 but not DC-SIGN is sufficient for entry into nonpermissive cells, indicating that ACE2 fulfills the criteria of a bona fide hCoV-NL63 receptor. As for SARS-CoV, murine ACE2 is used less efficiently by NL63-S for entry than human ACE2. In contrast, several amino acid exchanges in human ACE2 which diminish SARS-S-driven entry do not interfere with NL63-S-mediated infection, suggesting that SARS-S and NL63-S might engage human ACE2 differentially. Moreover, we observed that NL63-S-driven entry was less dependent on a low-pH environment and activity of endosomal proteases compared to infection mediated by SARS-S, further suggesting differences in hCoV-NL63 and SARS-CoV cellular entry. NL63-S does not exhibit significant homology to SARS-S but is highly related to the S-protein of hCoV-229E, which enters target cells by engaging CD13. Employing mutagenic analyses, we found that the N-terminal unique domain in NL63-S, which is absent in 229E-S, does not confer binding to ACE2. In contrast, the highly homologous C-terminal parts of the NL63-S1 and 229E-S1 subunits in conjunction with distinct amino acids in the central regions of these proteins confer recognition of ACE2 and CD13, respectively. Therefore, despite the high homology of these sequences, they likely form sufficiently distinct surfaces, thus determining receptor specificity.

  19. Recognition Tunneling

    PubMed Central

    Lindsay, Stuart; He, Jin; Sankey, Otto; Hapala, Prokop; Jelinek, Pavel; Zhang, Peiming; Chang, Shuai; Huang, Shuo

    2010-01-01

    Single molecules in a tunnel junction can now be interrogated reliably using chemically-functionalized electrodes. Monitoring stochastic bonding fluctuations between a ligand bound to one electrode and its target bound to a second electrode (“tethered molecule-pair” configuration) gives insight into the nature of the intermolecular bonding at a single molecule-pair level, and defines the requirements for reproducible tunneling data. Simulations show that there is an instability in the tunnel gap at large currents, and this results in a multiplicity of contacts with a corresponding spread in the measured currents. At small currents (i.e. large gaps) the gap is stable, and functionalizing a pair of electrodes with recognition reagents (the “free analyte” configuration) can generate a distinct tunneling signal when an analyte molecule is trapped in the gap. This opens up a new interface between chemistry and electronics with immediate implications for rapid sequencing of single DNA molecules. PMID:20522930

  20. Recognition of teaching excellence.

    PubMed

    Hammer, Dana; Piascik, Peggy; Medina, Melissa; Pittenger, Amy; Rose, Renee; Creekmore, Freddy; Soltis, Robert; Bouldin, Alicia; Schwarz, Lindsay; Scott, Steven

    2010-11-10

    The 2008-2009 Task Force for the Recognition of Teaching Excellence was charged by the AACP Council of Faculties Leadership to examine teaching excellence by collecting best practices from colleges and schools of pharmacy, evaluating the literature to identify evidence-based criteria for excellent teaching, and recommending appropriate means to acknowledge and reward teaching excellence. This report defines teaching excellence and discusses a variety of ways to assess it, including student, alumni, peer, and self-assessment. The task force identifies important considerations that colleges and schools must address when establishing teaching recognition programs including the purpose, criteria, number and mix of awards, frequency, type of award, and method of nominating and determining awardees. The report concludes with recommendations for the academy to consider when establishing and revising teaching award programs.

  1. Proteolytic Characteristics of Cathepsin D Related to the Recognition and Cleavage of Its Target Proteins

    PubMed Central

    Sun, Huiying; Lou, Xiaomin; Shan, Qiang; Zhang, Ju; Zhu, Xu; Zhang, Jia; Wang, Yang; Xie, Yingying; Xu, Ningzhi; Liu, Siqi

    2013-01-01

    Cathepsin D (CD) plays an important role in both biological and pathological processes, although the cleavage characteristics and substrate selection of CD have yet to be fully explored. We employed liquid chromatography-tandem mass spectrometry (LC-MS/MS) to identify the CD cleavage sites in bovine serum albumin (BSA). We found that the hydrophobic residues at P1 were not only a preferential factor for CD cleavage but that the hydrophobicity at P1’ also contributed to CD recognition. The concept of hydrophobic scores of neighbors (HSN) was proposed to describe the hydrophobic microenvironment of CD recognition sites. The survey of CD cleavage characteristics in several proteins suggested that the HSN was a sensitive indicator for judging the favorable sites in peptides for CD cleavage, with HSN values of 0.5–1.0 representing a likely threshold. Ovalbumin (OVA), a protein resistant to CD cleavage in its native state, was easily cleaved by CD after denaturation, and the features of the cleaved peptides were quite similar to those found in BSA, where a higher HSN value indicated greater cleavability. We further conducted two-dimensional gel electrophoresis (2DE) to find more proteins that were insensitive to CD cleavage in CD-knockdown cells. Based on an analysis of secondary and three-dimensional structures, we postulated that intact proteins with a structure consisting of all α-helices would be relatively accessible to CD cleavage. PMID:23840360

  2. Base-pair opening dynamics of primary miR156a using NMR elucidates structural determinants important for its processing level and leaf number phenotype in Arabidopsis

    PubMed Central

    Kim, Wanhui; Kim, Hee-Eun; Lee, Ae-Ree; Jun, A Rim; Jung, Myeong Gyo; Ahn, Ji Hoon; Lee, Joon-Hwa

    2017-01-01

    MicroRNAs originate from primary transcripts containing hairpin structures. The levels of mature miR156 influence the leaf number prior to flowering in the life cycle of plants. To understand the molecular mechanism of biogenesis of primary miR156a (pri-miR156a) to mature miR156, a base-pair opening dynamics study was performed using model RNAs mimicking the cleavage site of wild type and B5 bulge-stabilizing mutant pri-miR156a constructs. We also determined the mature miR156 levels and measured leaf numbers at flowering of plants overexpressing the wild type and mutant constructs. Our results suggest that the stabilities and/or opening dynamics of the C15·G98 and U16·A97 base-pairs at the cleavage site are essential for formation of the active conformation and for efficient processing of pri-miR156a, and that mutations of the B5 bulge can modulate mature miR156 levels as well as miR156-driven leaf number phenotypes via changes in the base-pair stability of the cleavage site. PMID:27574118

  3. Information Security: Securing Smart Cards With IRIS Recognition

    DTIC Science & Technology

    2001-03-01

    recognition code was examined. It was necessary to determine the time necessary to break the iris recognition code should the smart card be...are excessive. Additionally, smart card technology was examined to determine if existing technology could store the necessary iris recognition

  4. Structural requirements for recognition of the HLA-Dw14 class II epitope: A key HLA determinant associated with rheumatoid arthritis

    SciTech Connect

    Hiraiwa, Akikazu; Yamanaka, Katsuo; Kwok, W.W.; Nepom, G.T. ); Mickelson, E.M.; Masewicz, S.; Hansen, J.A. ); Radka, S.F. )

    1990-10-01

    Although HLA genes have been shown to be associated with certain diseases, the basis for this association is unknown. Recent studies, however, have documented patterns of nucleotide sequence variation among some HLA genes associated with a particular disease. For rheumatoid arthritis, HLA genes in most patients have a shared nucleotide sequence encoding a key structural element of an HLA class II polypeptide; this sequence element is critical for the interaction of the HLA molecule with antigenic peptides and with responding T cells, suggestive of a direct role for this sequence element in disease susceptibility. The authors describe the serological and cellular immunologic characteristics encoded by this rheumatoid arthritis-associated sequence element. Site-directed mutagenesis of the DRB1 gene was used to define amino acids critical for antibody and T-cell recognition of this structural element, focusing on residues that distinguish the rheumatoid arthritis-associated alleles Dw4 and Dw14 from a closely related allele, Dw10, not associated with disease. Both the gain and loss of rheumatoid arthritis-associated epitopes were highly dependent on three residues within a discrete domain of the HLA-DR molecule. Recognition was most strongly influenced by the following amino acids (in order): 70 > 71 > 67. Some alloreactive T-cell clones were also influenced by amino acid variation in portions of the DR molecule lying outside the shared sequence element.

  5. Early development of visual recognition.

    PubMed

    Plebe, Alessio; Domenella, Rosaria Grazia

    2006-01-01

    The most important ability of the human vision is object recognition, yet it is exactly the less understood aspect of the vision system. Computational models have been helpful in progressing towards an explanation of this obscure cognitive ability, and today it is possible to conceive more refined models, thanks to the new availability of neuroscientific data about the human visual cortex. This work proposes a model of the development of the object recognition capability, under a different perspective with respect to the most common approaches, with a precise theoretical epistemology. It is assumed that the main processing functions involved in recognition are not genetically determined and hardwired in the neural circuits, but are the result of interactions between epigenetic influences and the basic neural plasticity mechanisms. The model is organized in modules related with the main visual biological areas, and is implemented mainly using the LISSOM architecture, a recent self-organizing algorithm closely reflecting the essential behavior of cortical circuits.

  6. A comparison of iron extraction methods for the determination of degree of pyritisation and the recognition of iron-limited pyrite formation

    NASA Technical Reports Server (NTRS)

    Raiswell, R.; Canfield, D. E.; Berner, R. A.

    1994-01-01

    Measurements of degree of pyritisation require an estimate of sediment iron which is capable of reaction with dissolved sulphide to form pyrite, either directly or indirectly via iron monosulphide precursors. Three dissolution techniques (buffered dithionite, cold 1 M HCl, boiling 12 M HCl) were examined for their capacity to extract iron from a variety of iron minerals, and iron-bearing sediments, as a function of different extraction times and different grain sizes. All the iron oxides studied are quantitatively extracted by dithionite and boiling HCl (but not by cold HCl). Both HCl techniques extract more iron from silicates than does dithionite but probably about the same amounts as are potentially capable of sulphidation. Modern sediment studies indicate that most sedimentary pyrite is formed rapidly from iron oxides, with smaller amounts formed more slowly from iron silicates (if sufficient geologic time is available). It is therefore recommended that the degree of pyritisation be defined with respect to the dithionite-extractable (mainly iron oxide) pool and/or the boiling HCl-extractable pool (which includes some silicate iron) for the recognition of iron-limited pyritisation.

  7. Computational analysis of siRNA recognition by the Ago2 PAZ domain and identification of the determinants of RNA-induced gene silencing.

    PubMed

    Kandeel, Mahmoud; Kitade, Yukio

    2013-01-01

    RNA interference (RNAi) is a highly specialized process of protein-siRNA interaction that results in the regulation of gene expression and cleavage of target mRNA. The PAZ domain of the Argonaute proteins binds to the 3' end of siRNA, and during RNAi the attaching end of the siRNA switches between binding and release from its binding pocket. This biphasic interaction of the 3' end of siRNA with the PAZ domain is essential for RNAi activity; however, it remains unclear whether stronger or weaker binding with PAZ domain will facilitate or hinder the overall RNAi process. Here we report the correlation between the binding of modified siRNA 3' overhang analogues and their in vivo RNAi efficacy. We found that higher RNAi efficacy was associated with the parameters of lower Ki value, lower total intermolecular energy, lower free energy, higher hydrogen bonding, smaller total surface of interaction and fewer van der Waals interactions. Electrostatic interaction was a minor contributor to compounds recognition, underscoring the presence of phosphate groups in the modified analogues. Thus, compounds with lower binding affinity are associated with better gene silencing. Lower binding strength along with the smaller interaction surface, higher hydrogen bonding and fewer van der Waals interactions were among the markers for favorable RNAi activity. Within the measured parameters, the interaction surface, van der Waals interactions and inhibition constant showed a statistically significant correlation with measured RNAi efficacy. The considerations provided in this report will be helpful in the design of new compounds with better gene silencing ability.

  8. Global identification of target recognition and cleavage by the Microprocessor in human ES cells.

    PubMed

    Seong, Youngmo; Lim, Do-Hwan; Kim, Augustine; Seo, Jae Hong; Lee, Young Sik; Song, Hoseok; Kwon, Young-Soo

    2014-11-10

    The Microprocessor plays an essential role in canonical miRNA biogenesis by facilitating cleavage of stem-loop structures in primary transcripts to yield pre-miRNAs. Although miRNA biogenesis has been extensively studied through biochemical and molecular genetic approaches, it has yet to be addressed to what extent the current miRNA biogenesis models hold true in intact cells. To address the issues of in vivo recognition and cleavage by the Microprocessor, we investigate RNAs that are associated with DGCR8 and Drosha by using immunoprecipitation coupled with next-generation sequencing. Here, we present global protein-RNA interactions with unprecedented sensitivity and specificity. Our data indicate that precursors of canonical miRNAs and miRNA-like hairpins are the major substrates of the Microprocessor. As a result of specific enrichment of nascent cleavage products, we are able to pinpoint the Microprocessor-mediated cleavage sites per se at single-nucleotide resolution. Unexpectedly, a 2-nt 3' overhang invariably exists at the ends of cleaved bases instead of nascent pre-miRNAs. Besides canonical miRNA precursors, we find that two novel miRNA-like structures embedded in mRNAs are cleaved to yield pre-miRNA-like hairpins, uncoupled from miRNA maturation. Our data provide a framework for in vivo Microprocessor-mediated cleavage and a foundation for experimental and computational studies on miRNA biogenesis in living cells.

  9. Molecular dynamics investigations of ozone on an ab initio potential energy surface with the utilization of pattern-recognition neural network for accurate determination of product formation.

    PubMed

    Le, Hung M; Dinh, Thach S; Le, Hieu V

    2011-10-13

    The singlet-triplet transformation and molecular dissociation of ozone (O(3)) gas is investigated by performing quasi-classical molecular dynamics (MD) simulations on an ab initio potential energy surface (PES) with visible and near-infrared excitations. MP4(SDQ) level of theory with the 6-311g(2d,2p) basis set is executed for three different electronic spin states (singlet, triplet, and quintet). In order to simplify the potential energy function, an approximation is adopted by ignoring the spin-orbit coupling and allowing the molecule to switch favorably and instantaneously to the spin state that is more energetically stable (lowest in energy among the three spin states). This assumption has previously been utilized to study the SiO(2) system as reported by Agrawal et al. (J. Chem. Phys. 2006, 124 (13), 134306). The use of such assumption in this study probably makes the upper limits of computed rate coefficients the true rate coefficients. The global PES for ozone is constructed by fitting 5906 ab initio data points using a 60-neuron two-layer feed-forward neural network. The mean-absolute error and root-mean-squared error of this fit are 0.0446 eV (1.03 kcal/mol) and 0.0756 eV (1.74 kcal/mol), respectively, which reveal very good fitting accuracy. The parameter coefficients of the global PES are reported in this paper. In order to identify the spin state with high confidence, we propose the use of a pattern-recognition neural network, which is trained to predict the spin state of a given configuration (with a prediction accuracy being 95.6% on a set of testing data points). To enhance the prediction effectiveness, a buffer series of five points are validated to confirm the spin state during the MD process to gain better confidence. Quasi-classical MD simulations from 1.2 to 2.4 eV of total internal energy (including zero-point energy) result in rate coefficients of singlet-triplet transformation in the range of 0.027 ps(-1) to 1.21 ps(-1). Also, we find very

  10. Image Recognition Based on Biometric Pattern Recognition

    NASA Astrophysics Data System (ADS)

    Sun, Shuliang; Chen, Zhong; Liu, Chenglian; Guo, Yongning; Lin, Xueyun

    2011-09-01

    A new method, biomimetric pattern recognition, is mentioned to recognize images. At first, the image is pretreatment and feature extraction, then a high vector is got. A biomimetric pattern recognition model is designed. The judgment function is used to discriminate the classification of the samples. It is showed that the method is effective for little samples by experiment. It would be useful in many fields in future.

  11. Optical Pattern Recognition

    NASA Astrophysics Data System (ADS)

    Yu, Francis T. S.; Jutamulia, Suganda

    2008-10-01

    Contributors; Preface; 1. Pattern recognition with optics Francis T. S. Yu and Don A. Gregory; 2. Hybrid neural networks for nonlinear pattern recognition Taiwei Lu; 3. Wavelets, optics, and pattern recognition Yao Li and Yunglong Sheng; 4. Applications of the fractional Fourier transform to optical pattern recognition David Mendlovic, Zeev Zalesky and Haldum M. Oxaktas; 5. Optical implementation of mathematical morphology Tien-Hsin Chao; 6. Nonlinear optical correlators with improved discrimination capability for object location and recognition Leonid P. Yaroslavsky; 7. Distortion-invariant quadratic filters Gregory Gheen; 8. Composite filter synthesis as applied to pattern recognition Shizhou Yin and Guowen Lu; 9. Iterative procedures in electro-optical pattern recognition Joseph Shamir; 10. Optoelectronic hybrid system for three-dimensional object pattern recognition Guoguang Mu, Mingzhe Lu and Ying Sun; 11. Applications of photrefractive devices in optical pattern recognition Ziangyang Yang; 12. Optical pattern recognition with microlasers Eung-Gi Paek; 13. Optical properties and applications of bacteriorhodopsin Q. Wang Song and Yu-He Zhang; 14. Liquid-crystal spatial light modulators Aris Tanone and Suganda Jutamulia; 15. Representations of fully complex functions on real-time spatial light modulators Robert W. Cohn and Laurence G. Hassbrook; Index.

  12. Study on Information Fusion Based Check Recognition System

    NASA Astrophysics Data System (ADS)

    Wang, Dong

    Automatic check recognition techniques play an important role in financial systems, especially in risk management. This paper presents a novel check recognition system based on multi-cue information fusion theory. For Chinese bank check, the amount can be independently determined by legal amount, courtesy amount, or E13B code. The check recognition algorithm consists of four steps: preprocessing, check layout analysis, segmentation and recognition, and information fusion. For layout analysis, an adaptive template matching algorithm is presented to locate the target recognition regions on the check. The hidden markov model is used to segment and recognize legal amount. Courtesy and E13B code are recognized by artificial neural network method, respectively. Finally, D-S evidence theory is then introduced to fuse above three recognition results for better recognition performance. Experimental results demonstrate that the system can robustly recognize checks and the information fusion based algorithm improves the recognition rate by 5~10 percent.

  13. On three dimensional object recognition and pose-determination: An abstraction based approach. Ph.D. Thesis - Michigan Univ. Final Report

    NASA Technical Reports Server (NTRS)

    Quek, Kok How Francis

    1990-01-01

    A method of computing reliable Gaussian and mean curvature sign-map descriptors from the polynomial approximation of surfaces was demonstrated. Such descriptors which are invariant under perspective variation are suitable for hypothesis generation. A means for determining the pose of constructed geometric forms whose algebraic surface descriptors are nonlinear in terms of their orienting parameters was developed. This was done by means of linear functions which are capable of approximating nonlinear forms and determining their parameters. It was shown that biquadratic surfaces are suitable companion linear forms for cylindrical approximation and parameter estimation. The estimates provided the initial parametric approximations necessary for a nonlinear regression stage to fine tune the estimates by fitting the actual nonlinear form to the data. A hypothesis-based split-merge algorithm for extraction and pose determination of cylinders and planes which merge smoothly into other surfaces was developed. It was shown that all split-merge algorithms are hypothesis-based. A finite-state algorithm for the extraction of the boundaries of run-length regions was developed. The computation takes advantage of the run list topology and boundary direction constraints implicit in the run-length encoding.

  14. Kin Recognition in Bacteria.

    PubMed

    Wall, Daniel

    2016-09-08

    The ability of bacteria to recognize kin provides a means to form social groups. In turn these groups can lead to cooperative behaviors that surpass the ability of the individual. Kin recognition involves specific biochemical interactions between a receptor(s) and an identification molecule(s). Recognition specificity, ensuring that nonkin are excluded and kin are included, is critical and depends on the number of loci and polymorphisms involved. After recognition and biochemical perception, the common ensuing cooperative behaviors include biofilm formation, quorum responses, development, and swarming motility. Although kin recognition is a fundamental mechanism through which cells might interact, microbiologists are only beginning to explore the topic. This review considers both molecular and theoretical aspects of bacterial kin recognition. Consideration is also given to bacterial diversity, genetic relatedness, kin selection theory, and mechanisms of recognition.

  15. Multimodal eye recognition

    NASA Astrophysics Data System (ADS)

    Zhou, Zhi; Du, Yingzi; Thomas, N. L.; Delp, Edward J., III

    2010-04-01

    Multimodal biometrics use more than one means of biometric identification to achieve higher recognition accuracy, since sometimes a unimodal biometric is not good enough used to do identification and classification. In this paper, we proposed a multimodal eye recognition system, which can obtain both iris and sclera patterns from one color eye image. Gabor filter and 1-D Log-Gabor filter algorithms have been applied as the iris recognition algorithms. In sclera recognition, we introduced automatic sclera segmentation, sclera pattern enhancement, sclera pattern template generation, and sclera pattern matching. We applied kernelbased matching score fusion to improve the performance of the eye recognition system. The experimental results show that the proposed eye recognition method can achieve better performance compared to unimodal biometric identification, and the accuracy of our proposed kernel-based matching score fusion method is higher than two classic linear matching score fusion methods: Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA).

  16. Reconstruction of LPS Transfer Cascade Reveals Structural Determinants within LBP, CD14, and TLR4-MD2 for Efficient LPS Recognition and Transfer.

    PubMed

    Ryu, Je-Kyung; Kim, Soo Jin; Rah, Sang-Hyun; Kang, Ji In; Jung, Hi Eun; Lee, Dongsun; Lee, Heung Kyu; Lee, Jie-Oh; Park, Beom Seok; Yoon, Tae-Young; Kim, Ho Min

    2017-01-17

    Lipopolysaccharide (LPS), the major component of the outer membrane of Gram-negative bacteria, binds Toll-like receptor 4 (TLR4)-MD2 complex and activates innate immune responses. LPS transfer to TLR4-MD2 is catalyzed by both LPS binding protein (LBP) and CD14. To define the sequential molecular interactions underlying this transfer, we reconstituted in vitro the entire LPS transfer process from LPS micelles to TLR4-MD2. Using electron microscopy and single-molecule approaches, we characterized the dynamic intermediate complexes for LPS transfer: LBP-LPS micelles, CD14-LBP-LPS micelle, and CD14-LPS-TLR4-MD2 complex. A single LBP molecule bound longitudinally to LPS micelles catalyzed multi-rounds of LPS transfer to CD14s that rapidly dissociated from LPB-LPS complex upon LPS transfer via electrostatic interactions. Subsequently, the single LPS molecule bound to CD14 was transferred to TLR4-MD2 in a TLR4-dependent manner. The definition of the structural determinants of the LPS transfer cascade to TLR4 may enable the development of targeted therapeutics for intervention in LPS-induced sepsis.

  17. Moreland Recognition Program.

    ERIC Educational Resources Information Center

    Moreland Elementary School District, San Jose, CA.

    THE FOLLOWING IS THE FULL TEXT OF THIS DOCUMENT: Recognition for special effort and achievement has been noted as a component of effective schools. Schools in the Moreland School District have effectively improved standards of discipline and achievement by providing forty-six different ways for children to receive positive recognition. Good…

  18. Collagen binding specificity of the discoidin domain receptors: binding sites on collagens II and III and molecular determinants for collagen IV recognition by DDR1.

    PubMed

    Xu, Huifang; Raynal, Nicolas; Stathopoulos, Stavros; Myllyharju, Johanna; Farndale, Richard W; Leitinger, Birgit

    2011-01-01

    The discoidin domain receptors, DDR1 and DDR2 are cell surface receptor tyrosine kinases that are activated by triple-helical collagen. While normal DDR signalling regulates fundamental cellular processes, aberrant DDR signalling is associated with several human diseases. We previously identified GVMGFO (O is hydroxyproline) as a major DDR2 binding site in collagens I-III, and located two additional DDR2 binding sites in collagen II. Here we extend these studies to the homologous DDR1 and the identification of DDR binding sites on collagen III. Using sets of overlapping triple-helical peptides, the Collagen II and Collagen III Toolkits, we located several DDR2 binding sites on both collagens. The interaction of DDR1 with Toolkit peptides was more restricted, with DDR1 mainly binding to peptides containing the GVMGFO motif. Triple-helical peptides containing the GVMGFO motif induced DDR1 transmembrane signalling, and DDR1 binding and receptor activation occurred with the same amino acid requirements as previously defined for DDR2. While both DDRs exhibit the same specificity for binding the GVMGFO motif, which is present only in fibrillar collagens, the two receptors display distinct preferences for certain non-fibrillar collagens, with the basement membrane collagen IV being exclusively recognised by DDR1. Based on our recent crystal structure of a DDR2-collagen complex, we designed mutations to identify the molecular determinants for DDR1 binding to collagen IV. By replacing five amino acids in DDR2 with the corresponding DDR1 residues we were able to create a DDR2 construct that could function as a collagen IV receptor.

  19. Molecular Recognition and Ligand Association

    NASA Astrophysics Data System (ADS)

    Baron, Riccardo; McCammon, J. Andrew

    2013-04-01

    We review recent developments in our understanding of molecular recognition and ligand association, focusing on two major viewpoints: (a) studies that highlight new physical insight into the molecular recognition process and the driving forces determining thermodynamic signatures of binding and (b) recent methodological advances in applications to protein-ligand binding. In particular, we highlight the challenges posed by compensating enthalpic and entropic terms, competing solute and solvent contributions, and the relevance of complex configurational ensembles comprising multiple protein, ligand, and solvent intermediate states. As more complete physics is taken into account, computational approaches increase their ability to complement experimental measurements, by providing a microscopic, dynamic view of ensemble-averaged experimental observables. Physics-based approaches are increasingly expanding their power in pharmacology applications.

  20. Face and body recognition show similar improvement during childhood.

    PubMed

    Bank, Samantha; Rhodes, Gillian; Read, Ainsley; Jeffery, Linda

    2015-09-01

    Adults are proficient in extracting identity cues from faces. This proficiency develops slowly during childhood, with performance not reaching adult levels until adolescence. Bodies are similar to faces in that they convey identity cues and rely on specialized perceptual mechanisms. However, it is currently unclear whether body recognition mirrors the slow development of face recognition during childhood. Recent evidence suggests that body recognition develops faster than face recognition. Here we measured body and face recognition in 6- and 10-year-old children and adults to determine whether these two skills show different amounts of improvement during childhood. We found no evidence that they do. Face and body recognition showed similar improvement with age, and children, like adults, were better at recognizing faces than bodies. These results suggest that the mechanisms of face and body memory mature at a similar rate or that improvement of more general cognitive and perceptual skills underlies improvement of both face and body recognition.

  1. Recognition of the Protein Kinase AVRPPHB SUSCEPTIBLE1 by the Disease Resistance Protein RESISTANCE TO PSEUDOMONAS SYRINGAE5 Is Dependent on S-Acylation and an Exposed Loop in AVRPPHB SUSCEPTIBLE11[W][OPEN

    PubMed Central

    Qi, Dong; Dubiella, Ullrich; Kim, Sang Hee; Sloss, D. Isaiah; Dowen, Robert H.; Dixon, Jack E.; Innes, Roger W.

    2014-01-01

    The recognition of pathogen effector proteins by plants is typically mediated by intracellular receptors belonging to the nucleotide-binding leucine-rich repeat (NLR) family. NLR proteins often detect pathogen effector proteins indirectly by detecting modification of their targets. How NLR proteins detect such modifications is poorly understood. To address these questions, we have been investigating the Arabidopsis (Arabidopsis thaliana) NLR protein RESISTANCE TO PSEUDOMONAS SYRINGAE5 (RPS5), which detects the Pseudomonas syringae effector protein Avirulence protein Pseudomonas phaseolicolaB (AvrPphB). AvrPphB is a cysteine protease that specifically targets a subfamily of receptor-like cytoplasmic kinases, including the Arabidopsis protein kinase AVRPPHB Susceptible1 (PBS1). RPS5 is activated by the cleavage of PBS1 at the apex of its activation loop. Here, we show that RPS5 activation requires that PBS1 be localized to the plasma membrane and that plasma membrane localization of PBS1 is mediated by amino-terminal S-acylation. We also describe the development of a high-throughput screen for mutations in PBS1 that block RPS5 activation, which uncovered four new pbs1 alleles, two of which blocked cleavage by AvrPphB. Lastly, we show that RPS5 distinguishes among closely related kinases by the amino acid sequence (SEMPH) within an exposed loop in the C-terminal one-third of PBS1. The SEMPH loop is located on the opposite side of PBS1 from the AvrPphB cleavage site, suggesting that RPS5 associates with the SEMPH loop while leaving the AvrPphB cleavage site exposed. These findings provide support for a model of NLR activation in which NLR proteins form a preactivation complex with effector targets and then sense a conformational change in the target induced by effector modification. PMID:24225654

  2. Pattern recognition technique

    NASA Technical Reports Server (NTRS)

    Hong, J. P.

    1971-01-01

    Technique operates regardless of pattern rotation, translation or magnification and successfully detects out-of-register patterns. It improves accuracy and reduces cost of various optical character recognition devices and page readers and provides data input to computer.

  3. Mechanistic insights into ectodomain shedding: susceptibility of CADM1 adhesion molecule is determined by alternative splicing and O-glycosylation

    PubMed Central

    Shirakabe, Kyoko; Omura, Takuya; Shibagaki, Yoshio; Mihara, Emiko; Homma, Keiichi; Kato, Yukinari; Yoshimura, Akihiko; Murakami, Yoshinori; Takagi, Junichi; Hattori, Seisuke; Ogawa, Yoshihiro

    2017-01-01

    Ectodomain shedding (shedding) is a post-translational modification, which liberates the extracellular domain of membrane proteins through juxtamembrane processing executed mainly by the ADAM (a disintegrin and metalloprotease) family of metalloproteases. Because shedding alters characteristics of cells in a rapid and irreversible manner, it should be strictly regulated. However, the molecular mechanisms determining membrane protein susceptibility to shedding (shedding susceptibility) are largely unknown. Here we report that alternative splicing can give rise to both shedding-susceptible and shedding-resistant CADM1 (cell adhesion molecule 1) variant proteins. We further show that O-glycans adjacent to the shedding cleavage site interfere with CADM1 shedding, and the only 33-bp alternative exon confers shedding susceptibility to CADM1 by inserting five non-glycosylatable amino acids between interfering O-glycans and the shedding cleavage site. These results demonstrate that shedding susceptibility of membrane protein can be determined at two different levels of its biosynthesis pathway, alternative splicing and O-glycosylation. PMID:28393893

  4. Object recognition by artificial cortical maps.

    PubMed

    Plebe, Alessio; Domenella, Rosaria Grazia

    2007-09-01

    Object recognition is one of the most important functions of the human visual system, yet one of the least understood, this despite the fact that vision is certainly the most studied function of the brain. We understand relatively well how several processes in the cortical visual areas that support recognition capabilities take place, such as orientation discrimination and color constancy. This paper proposes a model of the development of object recognition capability, based on two main theoretical principles. The first is that recognition does not imply any sort of geometrical reconstruction, it is instead fully driven by the two dimensional view captured by the retina. The second assumption is that all the processing functions involved in recognition are not genetically determined or hardwired in neural circuits, but are the result of interactions between epigenetic influences and basic neural plasticity mechanisms. The model is organized in modules roughly related to the main visual biological areas, and is implemented mainly using the LISSOM architecture, a recent neural self-organizing map model that simulates the effects of intercortical lateral connections. This paper shows how recognition capabilities, similar to those found in brain ventral visual areas, can develop spontaneously by exposure to natural images in an artificial cortical model.

  5. Neonatal Recognition Processes and Attachment: The Masking Experiment.

    ERIC Educational Resources Information Center

    Cassel, Thomas Z. K.; Sander, Louis W.

    This research project was designed to determine whether 1-week-old neonates would indicate biological recognition of their mothers. Biological recognition is defined as the particular configuration of sensory, kinesthetic, and motor cues and the temporal patterning of these cues which characterizes infants' exchange processes with their…

  6. Macrophage pattern recognition receptors in immunity, homeostasis and self tolerance.

    PubMed

    Mukhopadhyay, Subhankar; Plüddemann, Annette; Gordon, Siamon

    2009-01-01

    Macrophages, a major component of innate immune defence, express a large repertoire of different classes of pattern recognition receptors and other surface antigens which determine the immunologic and homeostatic potential of these versatile cells. In the light of present knowledge ofmacrophage surface antigens, we discuss self versus nonself recognition, microbicidal effector functions and self tolerance in the innate immune system.

  7. Sequence divergence and loss-of-function phenotypes of S locus F-box brothers genes are consistent with non-self recognition by multiple pollen determinants in self-incompatibility of Japanese pear (Pyrus pyrifolia).

    PubMed

    Kakui, Hiroyuki; Kato, Masaki; Ushijima, Koichiro; Kitaguchi, Miyoko; Kato, Shu; Sassa, Hidenori

    2011-12-01

    The S-RNase-based gametophytic self-incompatibility (SI) of Rosaceae, Solanaceae, and Plantaginaceae is controlled by at least two tightly linked genes located at the complex S locus; the highly polymorphic S-RNase for pistil specificity and the F-box gene (SFB/SLF) for pollen. Self-incompatibility in Prunus (Rosaceae) is considered to represent a 'self recognition by a single factor' system, because loss-of-function of SFB is associated with self-compatibility, and allelic divergence of SFB is high and comparable to that of S-RNase. In contrast, Petunia (Solanaceae) exhibits 'non-self recognition by multiple factors'. However, the distribution of 'self recognition' and 'non-self recognition' SI systems in different taxa is not clear. In addition, in 'non-self recognition' systems, a loss-of-function phenotype of pollen S is unknown. Here we analyze the divergence of SFBB genes, the multiple pollen S candidates, of a rosaceous plant Japanese pear (Pyrus pyrifolia) and show that intrahaplotypic divergence is high and comparable to the allelic diversity of S-RNase while interhaplotypic divergence is very low. Next, we analyzed loss-of-function of the SFBB1 type gene. Genetic analysis showed that pollen with the mutant haplotype S(4sm) lacking SFBB1-S(4) is rejected by pistils with an otherwise compatible S(1) while it is accepted by other non-self pistils. We found that the S(5) haplotype encodes a truncated SFBB1 protein, even though S(5) pollen is accepted normally by pistils with S(1) and other non-self haplotypes. These findings suggest that Japanese pear has a 'non-self recognition by multiple factors' SI system, although it is a species of Rosaceae to which Prunus also belongs.

  8. Risk Recognition and Intimate Partner Violence

    ERIC Educational Resources Information Center

    Witte, Tricia H.; Kendra, Rachel

    2010-01-01

    The objective of this study was to determine whether female victims of physical forms of intimate partner violence (IPV) displayed deficits in risk recognition, or the ability to detect danger, in physically violent dating encounters. A total of 182 women watched a video depicting a psychologically and physically aggressive encounter between…

  9. Molecular Basis for the Recognition and Cleavages of IGF-II, TGF-[alpha], and Amylin by Human Insulin-Degrading Enzyme

    SciTech Connect

    Guo, Qing; Manolopoulou, Marika; Bian, Yao; Schilling, Alexander B.; Tang, Wei-Jen

    2010-02-11

    Insulin-degrading enzyme (IDE) is involved in the clearance of many bioactive peptide substrates, including insulin and amyloid-{beta}, peptides vital to the development of diabetes and Alzheimer's disease, respectively. IDE can also rapidly degrade hormones that are held together by intramolecular disulfide bond(s) without their reduction. Furthermore, IDE exhibits a remarkable ability to preferentially degrade structurally similar peptides such as the selective degradation of insulin-like growth factor (IGF)-II and transforming growth factor-{alpha} (TGF-{alpha}) over IGF-I and epidermal growth factor, respectively. Here, we used high-accuracy mass spectrometry to identify the cleavage sites of human IGF-II, TGF-{alpha}, amylin, reduced amylin, and amyloid-{beta} by human IDE. We also determined the structures of human IDE-IGF-II and IDE-TGF-{alpha} at 2.3 {angstrom} and IDE-amylin at 2.9 {angstrom}. We found that IDE cleaves its substrates at multiple sites in a biased stochastic manner. Furthermore, the presence of a disulfide bond in amylin allows IDE to cut at an additional site in the middle of the peptide (amino acids 18-19). Our amylin-bound IDE structure offers insight into how the structural constraint from a disulfide bond in amylin can alter IDE cleavage sites. Together with NMR structures of amylin and the IGF and epidermal growth factor families, our work also reveals the structural basis of how the high dipole moment of substrates complements the charge distribution of the IDE catalytic chamber for the substrate selectivity. In addition, we show how the ability of substrates to properly anchor their N-terminus to the exosite of IDE and undergo a conformational switch upon binding to the catalytic chamber of IDE can also contribute to the selective degradation of structurally related growth factors.

  10. [Prosopagnosia and facial expression recognition].

    PubMed

    Koyama, Shinichi

    2014-04-01

    This paper reviews clinical neuropsychological studies that have indicated that the recognition of a person's identity and the recognition of facial expressions are processed by different cortical and subcortical areas of the brain. The fusiform gyrus, especially the right fusiform gyrus, plays an important role in the recognition of identity. The superior temporal sulcus, amygdala, and medial frontal cortex play important roles in facial-expression recognition. Both facial recognition and facial-expression recognition are highly intellectual processes that involve several regions of the brain.

  11. Segmental Rescoring in Text Recognition

    DTIC Science & Technology

    2014-02-04

    ttm № tes/m, m* tmvr mowm* a Smyrna Of l δrtA£ACf02S’ A w m - y i p m AmiKSiS € f № ) C № № m .. sg6#?«rA fiθN ; Atφ h Sft№’·’Spxn mm m fim f№b t&m&mm...applying a Hidden Markov Model (HMM) recognition approach. Generating the plurality text hypotheses for the image forming includes generating a first...image. Applying segmental analysis to a segmentation determined by a first OCR engine, such as a segmentation determined by a Hidden Markov Model (HMM

  12. Recognition of caudal regression syndrome.

    PubMed

    Boulas, Mari M

    2009-04-01

    Caudal regression syndrome, also referred to as caudal dysplasia and sacral agenesis syndrome, is a rare congenital malformation characterized by varying degrees of developmental failure early in gestation. It involves the lower extremities, the lumbar and coccygeal vertebrae, and corresponding segments of the spinal cord. This is a rare disorder, and true pathogenesis is unclear. The etiology is thought to be related to maternal diabetes, genetic predisposition, and vascular hypoperfusion, but no true causative factor has been determined. Fetal diagnostic tools allow for early recognition of the syndrome, and careful examination of the newborn is essential to determine the extent of the disorder. Associated organ system dysfunction depends on the severity of the disease. Related defects are structural, and systematic problems including respiratory, cardiac, gastrointestinal, urinary, orthopedic, and neurologic can be present in varying degrees of severity and in different combinations. A multidisciplinary approach to management is crucial. Because the primary pathology is irreversible, treatment is only supportive.

  13. Pattern recognition systems and procedures

    NASA Technical Reports Server (NTRS)

    Nelson, G. D.; Serreyn, D. V.

    1972-01-01

    The objectives of the pattern recognition tasks are to develop (1) a man-machine interactive data processing system; and (2) procedures to determine effective features as a function of time for crops and soils. The signal analysis and dissemination equipment, SADE, is being developed as a man-machine interactive data processing system. SADE will provide imagery and multi-channel analog tape inputs for digitation and a color display of the data. SADE is an essential tool to aid in the investigation to determine useful features as a function of time for crops and soils. Four related studies are: (1) reliability of the multivariate Gaussian assumption; (2) usefulness of transforming features with regard to the classifier probability of error; (3) advantage of selecting quantizer parameters to minimize the classifier probability of error; and (4) advantage of using contextual data. The study of transformation of variables (features), especially those experimental studies which can be completed with the SADE system, will be done.

  14. Automatic object recognition

    NASA Technical Reports Server (NTRS)

    Ranganath, H. S.; Mcingvale, Pat; Sage, Heinz

    1988-01-01

    Geometric and intensity features are very useful in object recognition. An intensity feature is a measure of contrast between object pixels and background pixels. Geometric features provide shape and size information. A model based approach is presented for computing geometric features. Knowledge about objects and imaging system is used to estimate orientation of objects with respect to the line of sight.

  15. Units of Word Recognition.

    ERIC Educational Resources Information Center

    Santa, Carol M.; And Others

    Both psychologists and reading specialists have been interested in whether words are processed letter by letter or in larger units. A reaction time paradigm was used to evaluate these options with interest focused on potential units of word recognition which might be functional within single syllable words. The basic paradigm involved presenting…

  16. Optical Character Recognition.

    ERIC Educational Resources Information Center

    Converso, L.; Hocek, S.

    1990-01-01

    This paper describes computer-based optical character recognition (OCR) systems, focusing on their components (the computer, the scanner, the OCR, and the output device); how the systems work; and features to consider in selecting a system. A list of 26 questions to ask to evaluate systems for potential purchase is included. (JDD)

  17. Automated Optical Target Recognition.

    DTIC Science & Technology

    1994-12-01

    A multi-resolution signal processing approach to object recognition is presented using an optical correlator for generating a wavelet transform . The...This report presents an overview of continuous and discrete wavelet transforms. Both digital and optical implementations of the discrete wavelet ... transform are discussed. Examples of typical wavelet basis functions are compared and the constraints imposed by optical implementations are discussed

  18. Teaching Word Recognition Skills.

    ERIC Educational Resources Information Center

    Dawson, Mildred A., Comp.

    A series of articles with the chief emphasis on phonics as a means of analyzing words is presented. Various articles pertain to elementary, secondary, and college level instruction. The first of the five parts into which the volume is divided is comprised of a single article which gives an excellent overview of the field of word recognition. Part…

  19. View Invariant Gait Recognition

    NASA Astrophysics Data System (ADS)

    Seely, Richard D.; Goffredo, Michela; Carter, John N.; Nixon, Mark S.

    Recognition by gait is of particular interest since it is the biometric that is available at the lowest resolution, or when other biometrics are (intentionally) obscured. Gait as a biometric has now shown increasing recognition capability. There are many approaches and these show that recognition can achieve excellent performance on current large databases. The majority of these approaches are planar 2D, largely since the early large databases featured subjects walking in a plane normal to the camera view. To extend deployment capability, we need viewpoint invariant gait biometrics. We describe approaches where viewpoint invariance is achieved by 3D approaches or in 2D. In the first group, the identification relies on parameters extracted from the 3D body deformation during walking. These methods use several video cameras and the 3D reconstruction is achieved after a camera calibration process. On the other hand, the 2D gait biometric approaches use a single camera, usually positioned perpendicular to the subject’s walking direction. Because in real surveillance scenarios a system that operates in an unconstrained environment is necessary, many of the recent gait analysis approaches are orientated toward view-invariant gait recognition.

  20. Automatic aircraft recognition

    NASA Astrophysics Data System (ADS)

    Hmam, Hatem; Kim, Jijoong

    2002-08-01

    Automatic aircraft recognition is very complex because of clutter, shadows, clouds, self-occlusion and degraded imaging conditions. This paper presents an aircraft recognition system, which assumes from the start that the image is possibly degraded, and implements a number of strategies to overcome edge fragmentation and distortion. The current vision system employs a bottom up approach, where recognition begins by locating image primitives (e.g., lines and corners), which are then combined in an incremental fashion into larger sets of line groupings using knowledge about aircraft, as viewed from a generic viewpoint. Knowledge about aircraft is represented in the form of whole/part shape description and the connectedness property, and is embedded in production rules, which primarily aim at finding instances of the aircraft parts in the image and checking the connectedness property between the parts. Once a match is found, a confidence score is assigned and as evidence in support of an aircraft interpretation is accumulated, the score is increased proportionally. Finally a selection of the resulting image interpretations with the highest scores, is subjected to competition tests, and only non-ambiguous interpretations are allowed to survive. Experimental results demonstrating the effectiveness of the current recognition system are given.

  1. Anticipatory coarticulation facilitates word recognition in toddlers.

    PubMed

    Mahr, Tristan; McMillan, Brianna T M; Saffran, Jenny R; Ellis Weismer, Susan; Edwards, Jan

    2015-09-01

    Children learn from their environments and their caregivers. To capitalize on learning opportunities, young children have to recognize familiar words efficiently by integrating contextual cues across word boundaries. Previous research has shown that adults can use phonetic cues from anticipatory coarticulation during word recognition. We asked whether 18-24 month-olds (n=29) used coarticulatory cues on the word "the" when recognizing the following noun. We performed a looking-while-listening eyetracking experiment to examine word recognition in neutral vs. facilitating coarticulatory conditions. Participants looked to the target image significantly sooner when the determiner contained facilitating coarticulatory cues. These results provide the first evidence that novice word-learners can take advantage of anticipatory sub-phonemic cues during word recognition.

  2. School IPM Recognition and Certification

    EPA Pesticide Factsheets

    Schools and school districts can get support and recognition for implementation of school IPM. EPA is developing a program to provide recognition for school districts that are working towards or have achieved a level of success with school IPM programs.

  3. Automatic testing of speech recognition.

    PubMed

    Francart, Tom; Moonen, Marc; Wouters, Jan

    2009-02-01

    Speech reception tests are commonly administered by manually scoring the oral response of the subject. This requires a test supervisor to be continuously present. To avoid this, a subject can type the response, after which it can be scored automatically. However, spelling errors may then be counted as recognition errors, influencing the test results. We demonstrate an autocorrection approach based on two scoring algorithms to cope with spelling errors. The first algorithm deals with sentences and is based on word scores. The second algorithm deals with single words and is based on phoneme scores. Both algorithms were evaluated with a corpus of typed answers based on three different Dutch speech materials. The percentage of differences between automatic and manual scoring was determined, in addition to the mean difference in speech recognition threshold. The sentence correction algorithm performed at a higher accuracy than commonly obtained with these speech materials. The word correction algorithm performed better than the human operator. Both algorithms can be used in practice and allow speech reception tests with open set speech materials over the internet.

  4. Visual Recognition Memory across Contexts

    ERIC Educational Resources Information Center

    Jones, Emily J. H.; Pascalis, Olivier; Eacott, Madeline J.; Herbert, Jane S.

    2011-01-01

    In two experiments, we investigated the development of representational flexibility in visual recognition memory during infancy using the Visual Paired Comparison (VPC) task. In Experiment 1, 6- and 9-month-old infants exhibited recognition when familiarization and test occurred in the same room, but showed no evidence of recognition when…

  5. International Recognition of Vocational Qualifications.

    ERIC Educational Resources Information Center

    Imrie, Bradford W.

    Certain issues are relevant to the international recognition of vocational qualifications: (1) the assumption that each country does or should value vocational education and training; (2) the quality of the national system and the implications for international recognition of qualifications, including recognition of the accrediting and awarding…

  6. Word Recognition in Auditory Cortex

    ERIC Educational Resources Information Center

    DeWitt, Iain D. J.

    2013-01-01

    Although spoken word recognition is more fundamental to human communication than text recognition, knowledge of word-processing in auditory cortex is comparatively impoverished. This dissertation synthesizes current models of auditory cortex, models of cortical pattern recognition, models of single-word reading, results in phonetics and results in…

  7. Speech Recognition: A General Overview.

    ERIC Educational Resources Information Center

    de Sopena, Luis

    Speech recognition is one of five main areas in the field of speech processing. Difficulties in speech recognition include variability in sound within and across speakers, in channel, in background noise, and of speech production. Speech recognition can be used in a variety of situations: to perform query operations and phone call transfers; for…

  8. Age of Acquisition and Sensitivity to Gender in Spanish Word Recognition

    ERIC Educational Resources Information Center

    Foote, Rebecca

    2014-01-01

    Speakers of gender-agreement languages use gender-marked elements of the noun phrase in spoken-word recognition: A congruent marking on a determiner or adjective facilitates the recognition of a subsequent noun, while an incongruent marking inhibits its recognition. However, while monolinguals and early language learners evidence this…

  9. Cleavage sites in the polypeptide precursors of poliovirus protein P2-X

    SciTech Connect

    Selmer, B.L.; Hanecak, R.; Anderson, C.W.; Wimmer, E.

    1981-01-01

    Partial amino-terminal sequence analysis has been performed on the three major polypeptide products (P2-3b, P2-5b, and P2-X) from the central region (P2) of the poliovirus polyprotein, and this analysis precisely locates the amino termini of these products with respect to the nucleotide sequence of the poliovirus RNA genome. Like most of the products of the replicase region (P3), the amino termini of P2-5b and P2-X are generated by cleavage between glutamine and glycine residues. Thus, P2-5b and P2-X are probably both produced by the action of a singly (virus-encoded.) proteinase. The amino terminus of P2-3b, on the other hand, is produced by a cleavage between the carboxy-terminal tyrosine of VP1 and the glycine encoded by nucleotides 3381-3383. This result may suggest that more than one proteolytic activity is required for the complete processing of the poliovirus polyprotein.

  10. Peptide substrate specificities and protein cleavage sites of human endometase/matrilysin-2/matrix metalloproteinase-26.

    PubMed

    Park, Hyun I; Turk, Benjamin E; Gerkema, Ferry E; Cantley, Lewis C; Sang, Qing-Xiang Amy

    2002-09-20

    Human endometase/matrilysin-2/matrix metalloproteinase-26 (MMP-26) is a novel epithelial and cancer-specific metalloproteinase. Peptide libraries were used to profile the substrate specificity of MMP-26 from the P4-P4' sites. The optimal cleavage motifs for MMP-26 were Lys-Pro-Ile/Leu-Ser(P1)-Leu/Met(P1')-Ile/Thr-Ser/Ala-Ser. The strongest preference was observed at the P1' and P2 sites where hydrophobic residues were favored. Proline was preferred at P3, and Serine was preferred at P1. The overall specificity was similar to that of other MMPs with the exception that more flexibility was observed at P1, P2', and P3'. Accordingly, synthetic inhibitors of gelatinases and collagenases inhibited MMP-26 with similar efficacy. A pair of stereoisomers had only a 40-fold difference in K(i)(app) values against MMP-26 compared with a 250-fold difference against neutrophil collagenase, indicating that MMP-26 is less stereoselective for its inhibitors. MMP-26 autodigested itself during the folding process. Two of the major autolytic sites were Leu(49)-Thr(50) and Ala(75)-Leu(76), which still left the cysteine switch sequence (PHC(82)GVPD) intact. This suggests that Cys(82) may not play a role in the latency of the zymogen. Interestingly, inhibitor titration studies revealed that only approximately 5% of the total MMP-26 molecules was catalytically active, indicating that the thiol groups of Cys(82) in the active molecules may be dissociated or removed from the active site zinc ions. MMP-26 cleaved Phe(352)-Leu(353) and Pro(357)-Met(358) in the reactive loop of alpha(1)-proteinase inhibitor and His(140)-Val(141) in insulin-like growth factor-binding protein-1, probably rendering these substrates inactive. Among the fluorescent peptide substrates analyzed, Mca-Pro-Leu-Ala-Nva-Dpa-Ala-Arg-NH(2) displayed the highest specificity constant (30,000/molar second) with MMP-26. This report proposes a working model for the future studies of pro-MMP-26 activation, the design of inhibitors, and the identification of optimal physiological and pathological substrates of MMP-26 in vivo.

  11. Evolutionarily distinct bacteriophage endolysins featuring conserved peptidoglycan cleavage sites protect mice from MRSA infection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Staphylococcus aureus is a Gram-positive pathogen relevant for both human and animal health. With multi-drug resistant S. aureus strains becoming increasingly prevalent, alternative therapeutics are urgently needed. Bacteriophage endolysins (peptidoglycan hydrolases, PGH) are capable of killing Gra...

  12. Exploring the DNA-recognition potential of homeodomains.

    PubMed

    Chu, Stephanie W; Noyes, Marcus B; Christensen, Ryan G; Pierce, Brian G; Zhu, Lihua J; Weng, Zhiping; Stormo, Gary D; Wolfe, Scot A

    2012-10-01

    The recognition potential of most families of DNA-binding domains (DBDs) remains relatively unexplored. Homeodomains (HDs), like many other families of DBDs, display limited diversity in their preferred recognition sequences. To explore the recognition potential of HDs, we utilized a bacterial selection system to isolate HD variants, from a randomized library, that are compatible with each of the 64 possible 3' triplet sites (i.e., TAANNN). The majority of these selections yielded sets of HDs with overrepresented residues at specific recognition positions, implying the selection of specific binders. The DNA-binding specificity of 151 representative HD variants was subsequently characterized, identifying HDs that preferentially recognize 44 of these target sites. Many of these variants contain novel combinations of specificity determinants that are uncommon or absent in extant HDs. These novel determinants, when grafted into different HD backbones, produce a corresponding alteration in specificity. This information was used to create more explicit HD recognition models, which can inform the prediction of transcriptional regulatory networks for extant HDs or the engineering of HDs with novel DNA-recognition potential. The diversity of recovered HD recognition sequences raises important questions about the fitness barrier that restricts the evolution of alternate recognition modalities in natural systems.

  13. Audio-visual gender recognition

    NASA Astrophysics Data System (ADS)

    Liu, Ming; Xu, Xun; Huang, Thomas S.

    2007-11-01

    Combining different modalities for pattern recognition task is a very promising field. Basically, human always fuse information from different modalities to recognize object and perform inference, etc. Audio-Visual gender recognition is one of the most common task in human social communication. Human can identify the gender by facial appearance, by speech and also by body gait. Indeed, human gender recognition is a multi-modal data acquisition and processing procedure. However, computational multimodal gender recognition has not been extensively investigated in the literature. In this paper, speech and facial image are fused to perform a mutli-modal gender recognition for exploring the improvement of combining different modalities.

  14. Homology recognition funnel

    NASA Astrophysics Data System (ADS)

    Lee, Dominic; Kornyshev, Alexei A.

    2009-10-01

    The recognition of homologous sequences of DNA before strand exchange is considered to be the most puzzling stage of homologous recombination. A mechanism for two homologous dsDNAs to recognize each other from a distance in electrolytic solution without unzipping had been proposed in an earlier paper [A. A. Kornyshev and S. Leikin, Phys. Rev. Lett. 86, 366 (2001)]. In that work, the difference in the electrostatic interaction energy between homologous duplexes and between nonhomologous duplexes, termed the recognition energy, has been calculated. That calculation was later extended in a series of papers to account for torsional elasticity of the molecules. A recent paper [A. A. Kornyshev and A. Wynveen, Proc. Natl. Acad. Sci. U.S.A. 106, 4683 (2009)] investigated the form of the potential well that homologous DNA molecules may feel when sliding along each other. A simple formula for the shape of the well was obtained. However, this latter study was performed under the approximation that the sliding molecules are torsionally rigid. Following on from this work, in the present article we investigate the effect of torsional flexibility of the molecules on the shape of the well. A variational approach to this problem results in a transcendental equation that is easily solved numerically. Its solutions show that at large interaxial separations the recognition well becomes wider and shallower, whereas at closer distances further unexpected features arise related to an abrupt change in the mean azimuthal alignment of the molecules. The energy surface as a function of interaxial separation and the axial shift defines what we call the recognition funnel. We show that it depends dramatically on the patterns of adsorption of counterions on DNA.

  15. Metamorphopsia and letter recognition.

    PubMed

    Wiecek, Emily; Dakin, Steven C; Bex, Peter

    2014-12-01

    Acuity is the most commonly used measure of visual function, and reductions in acuity are associated with most eye diseases. Metamorphopsia--a perceived distortion of visual space--is another common symptom of visual impairment and is currently assessed qualitatively using Amsler (1953) charts. In order to quantify the impact of metamorphopsia on acuity, we measured the effect of physical spatial distortion on letter recognition. Following earlier work showing that letter recognition is tuned to specific spatial frequency (SF) channels, we hypothesized that the effect of distortion might depend on the spatial scale of visual distortion just as it depends on the spatial scale of masking noise. Six normally sighted observers completed a 26 alternate forced choice (AFC) Sloan letter identification task at five different viewing distances, and the letters underwent different levels of spatial distortion. Distortion was controlled using spatially band-pass filtered noise that spatially remapped pixel locations. Noise was varied over five spatial frequencies and five magnitudes. Performance was modeled with logistic regression and worsened linearly with increasing distortion magnitude and decreasing letter size. We found that retinal SF affects distortion at midrange frequencies and can be explained with the tuning of a basic contrast sensitivity function, while object-centered distortion SF follows a similar pattern of letter object recognition sensitivity and is tuned to approximately three cycles per letter (CPL). The interaction between letter size and distortion makes acuity an unreliable outcome for metamorphopsia assessment.

  16. Metamorphopsia and letter recognition

    PubMed Central

    Wiecek, Emily; Dakin, Steven C.; Bex, Peter

    2014-01-01

    Acuity is the most commonly used measure of visual function, and reductions in acuity are associated with most eye diseases. Metamorphopsia—a perceived distortion of visual space—is another common symptom of visual impairment and is currently assessed qualitatively using Amsler (1953) charts. In order to quantify the impact of metamorphopsia on acuity, we measured the effect of physical spatial distortion on letter recognition. Following earlier work showing that letter recognition is tuned to specific spatial frequency (SF) channels, we hypothesized that the effect of distortion might depend on the spatial scale of visual distortion just as it depends on the spatial scale of masking noise. Six normally sighted observers completed a 26 alternate forced choice (AFC) Sloan letter identification task at five different viewing distances, and the letters underwent different levels of spatial distortion. Distortion was controlled using spatially band-pass filtered noise that spatially remapped pixel locations. Noise was varied over five spatial frequencies and five magnitudes. Performance was modeled with logistic regression and worsened linearly with increasing distortion magnitude and decreasing letter size. We found that retinal SF affects distortion at midrange frequencies and can be explained with the tuning of a basic contrast sensitivity function, while object-centered distortion SF follows a similar pattern of letter object recognition sensitivity and is tuned to approximately three cycles per letter (CPL). The interaction between letter size and distortion makes acuity an unreliable outcome for metamorphopsia assessment. PMID:25453116

  17. Human motion recognition based on features and models selected HMM

    NASA Astrophysics Data System (ADS)

    Lu, Haixiang; Zhou, Hongjun

    2015-03-01

    This paper research on the motion recognition based on HMM with Kinect. Kinect provides skeletal data consist of 3D body joints with its lower price and convenience. In this work, several methods are used to determine the optimal subset of features among Cartesian coordinates, distance to hip center, velocity, angle and angular velocity, in order to improve the recognition rate. K-means is used for vector quantization and HMM is used as recognition method. HMM is an effective signal processing method which contains time calibration, provides a learning mechanism and recognition ability. Cluster numbers of K-means, structure and state numbers of HMM are optimized as well. The proposed methods are applied to the MSR Action3D dataset. Results show that the proposed methods obtain better recognition accuracy than the state of the art methods.

  18. Laptop Computer - Based Facial Recognition System Assessment

    SciTech Connect

    R. A. Cain; G. B. Singleton

    2001-03-01

    The objective of this project was to assess the performance of the leading commercial-off-the-shelf (COTS) facial recognition software package when used as a laptop application. We performed the assessment to determine the system's usefulness for enrolling facial images in a database from remote locations and conducting real-time searches against a database of previously enrolled images. The assessment involved creating a database of 40 images and conducting 2 series of tests to determine the product's ability to recognize and match subject faces under varying conditions. This report describes the test results and includes a description of the factors affecting the results. After an extensive market survey, we selected Visionics' FaceIt{reg_sign} software package for evaluation and a review of the Facial Recognition Vendor Test 2000 (FRVT 2000). This test was co-sponsored by the US Department of Defense (DOD) Counterdrug Technology Development Program Office, the National Institute of Justice, and the Defense Advanced Research Projects Agency (DARPA). Administered in May-June 2000, the FRVT 2000 assessed the capabilities of facial recognition systems that were currently available for purchase on the US market. Our selection of this Visionics product does not indicate that it is the ''best'' facial recognition software package for all uses. It was the most appropriate package based on the specific applications and requirements for this specific application. In this assessment, the system configuration was evaluated for effectiveness in identifying individuals by searching for facial images captured from video displays against those stored in a facial image database. An additional criterion was that the system be capable of operating discretely. For this application, an operational facial recognition system would consist of one central computer hosting the master image database with multiple standalone systems configured with duplicates of the master operating in

  19. NMR-based analysis of aminoglycoside recognition by the resistance enzyme ANT(4'): the pattern of OH/NH3(+) substitution determines the preferred antibiotic binding mode and is critical for drug inactivation.

    PubMed

    Revuelta, Julia; Vacas, Tatiana; Torrado, Mario; Corzana, Francisco; Gonzalez, Carlos; Jiménez-Barbero, Jesús; Menendez, Margarita; Bastida, Agatha; Asensio, Juan Luis

    2008-04-16

    The most significant mechanism of bacterial resistance to aminoglycosides is the enzymatic inactivation of the drug. Herein, we analyze several key aspects of the aminoglycoside recognition by the resistance enzyme ANT(4') from Staphylococcus aureus, employing NMR complemented with site-directed mutagenesis experiments and measurements of the enzymatic activity on newly synthesized kanamycin derivatives. From a methodological perspective, this analysis provides the first example reported for the use of transferred NOE (trNOE) experiments in the analysis of complex molecular recognition processes, characterized by the existence of simultaneous binding events of the ligand to different regions of a protein receptor. The obtained results show that, in favorable cases, these overlapping binding processes can be isolated employing site-directed mutagenesis and then independently analyzed. From a molecular recognition perspective, this work conclusively shows that the enzyme ANT(4') displays a wide tolerance to conformational variations in the drug. Thus, according to the NMR data, kanamycin-A I/II linkage exhibits an unusual anti-Psi orientation in the ternary complex, which is in qualitative agreement with the previously reported crystallographic complex. In contrast, closely related, kanamycin-B is recognized by the enzyme in the syn-type arrangement for both glycosidic bonds. This observation together with the enzymatic activity displayed by ANT(4') against several synthetic kanamycin derivatives strongly suggests that the spatial distribution of positive charges within the aminoglycoside scaffold is the key feature that governs its preferred binding mode to the protein catalytic region and also the regioselectivity of the adenylation reaction. In contrast, the global shape of the antibiotic does not seem to be a critical factor. This feature represents a qualitative difference between the target A-site RNA and the resistance enzyme ANT(4') as aminoglycoside

  20. Determination of polychlorinated biphenyl levels in the serum of residents and in the homogenates of seafood from the New Bedford, Massachusetts Area: A comparison of exposure sources through pattern recognition techniques

    SciTech Connect

    Burse, V.W.; Groce, D.F.; Caudill, S.P.; Korver, M.P.; Phillips, D.L.

    1994-01-01

    Gas chromatographic patterns of polychlorinated biophenyls (PCBs) found in the serum of New Bedford, MA residents with high serum PCBs were compared to patterns found in lobsters and bluefish taken from local waters, and goats fed selected technical Aroclors (e.g., Aroclors 1016, 1242, 1254, or 1260) using Jaccard measures of similarity and Principal Component Analysis. Pattern in humans were silimar to patterns in lobsters and both were more similar to those in the goat fed Aroclor 1254 as demonstrated by both pattern recognition techniques. However, patterns observed in humans, lobsters and bluefish all exhibited some presence of PCBs more characteristic of Aroclors 1016 and/or 1242 or 1260.

  1. Sequence determinants for DNA packaging specificity in the S. aureus pathogenicity island SaPI1.

    PubMed

    Bento, Joana C; Lane, Kristin D; Read, Erik K; Cerca, Nuno; Christie, Gail E

    2014-01-01

    The SaPIs and their relatives are a family of genomic islands that exploit helper phages for high frequency horizontal transfer. One of the mechanisms used by SaPIs to accomplish this molecular piracy is the redirection of the helper phage DNA packaging machinery. SaPIs encode a small terminase subunit that can be substituted for that of the phage. In this study we have determined the initial packaging cleavage sites for helper phage 80α, which uses the phage-encoded small terminase subunit, and for SaPI1, which uses the SaPI-encoded small terminase subunit. We have identified a 19nt SaPI1 sequence that is necessary and sufficient to allow high frequency 80α transduction of a plasmid by a terminase carrying the SaPI1-encoded small subunit. We also show that the hybrid enzyme with the SaPI1 small terminase subunit is capable of generalized transduction.

  2. Automatic Speech Recognition

    NASA Astrophysics Data System (ADS)

    Potamianos, Gerasimos; Lamel, Lori; Wölfel, Matthias; Huang, Jing; Marcheret, Etienne; Barras, Claude; Zhu, Xuan; McDonough, John; Hernando, Javier; Macho, Dusan; Nadeu, Climent

    Automatic speech recognition (ASR) is a critical component for CHIL services. For example, it provides the input to higher-level technologies, such as summarization and question answering, as discussed in Chapter 8. In the spirit of ubiquitous computing, the goal of ASR in CHIL is to achieve a high performance using far-field sensors (networks of microphone arrays and distributed far-field microphones). However, close-talking microphones are also of interest, as they are used to benchmark ASR system development by providing a best-case acoustic channel scenario to compare against.

  3. [Comparative studies of face recognition].

    PubMed

    Kawai, Nobuyuki

    2012-07-01

    Every human being is proficient in face recognition. However, the reason for and the manner in which humans have attained such an ability remain unknown. These questions can be best answered-through comparative studies of face recognition in non-human animals. Studies in both primates and non-primates show that not only primates, but also non-primates possess the ability to extract information from their conspecifics and from human experimenters. Neural specialization for face recognition is shared with mammals in distant taxa, suggesting that face recognition evolved earlier than the emergence of mammals. A recent study indicated that a social insect, the golden paper wasp, can distinguish their conspecific faces, whereas a closely related species, which has a less complex social lifestyle with just one queen ruling a nest of underlings, did not show strong face recognition for their conspecifics. Social complexity and the need to differentiate between one another likely led humans to evolve their face recognition abilities.

  4. Image recognition and consistency of response

    NASA Astrophysics Data System (ADS)

    Haygood, Tamara M.; Ryan, John; Liu, Qing Mary A.; Bassett, Roland; Brennan, Patrick C.

    2012-02-01

    Purpose: To investigate the connection between conscious recognition of an image previously encountered in an experimental setting and consistency of response to the experimental question.
    Materials and Methods: Twenty-four radiologists viewed 40 frontal chest radiographs and gave their opinion as to the position of a central venous catheter. One-to-three days later they again viewed 40 frontal chest radiographs and again gave their opinion as to the position of the central venous catheter. Half of the radiographs in the second set were repeated images from the first set and half were new. The radiologists were asked of each image whether it had been included in the first set. For this study, we are evaluating only the 20 repeated images. We used the Kruskal-Wallis test and Fisher's exact test to determine the relationship between conscious recognition of a previously interpreted image and consistency in interpretation of the image.
    Results. There was no significant correlation between recognition of the image and consistency in response regarding the position of the central venous catheter. In fact, there was a trend in the opposite direction, with radiologists being slightly more likely to give a consistent response with respect to images they did not recognize than with respect to those they did recognize.
    Conclusion: Radiologists' recognition of previously-encountered images in an observer-performance study does not noticeably color their interpretation on the second encounter.

  5. A Fuzzy Aproach For Facial Emotion Recognition

    NASA Astrophysics Data System (ADS)

    Gîlcă, Gheorghe; Bîzdoacă, Nicu-George

    2015-09-01

    This article deals with an emotion recognition system based on the fuzzy sets. Human faces are detected in images with the Viola - Jones algorithm and for its tracking in video sequences we used the Camshift algorithm. The detected human faces are transferred to the decisional fuzzy system, which is based on the variable fuzzyfication measurements of the face: eyebrow, eyelid and mouth. The system can easily determine the emotional state of a person.

  6. New FASB standard addresses revenue recognition considerations.

    PubMed

    McKee, Thomas E

    2015-12-01

    Healthcare organizations are expected to apply the following steps in revenue recognition under the new standard issued in May 2014 by the Financial Accounting Standards Board: Identify the customer contract. Identify the performance obligations in the contract. Determine the transaction price. Allocate the transaction price to the performance obligations in the contract. Recognize revenue when--or in some circumstances, as--the entity satisfies the performance obligation.

  7. Sparsity Motivated Automated Target Recognition

    DTIC Science & Technology

    2010-09-29

    been suggested for tasks such as face and iris recognition . In this project, we evaluated the effectiveness of such methods for automatic target...Sparsity-based methods have recently been suggested for tasks such as face and iris recognition . In this project, we evaluated the effectiveness of...have recently been suggested for tasks such as face and iris recognition . In this project, we evaluated the effectiveness of such methods for

  8. Sudden Event Recognition: A Survey

    PubMed Central

    Suriani, Nor Surayahani; Hussain, Aini; Zulkifley, Mohd Asyraf

    2013-01-01

    Event recognition is one of the most active research areas in video surveillance fields. Advancement in event recognition systems mainly aims to provide convenience, safety and an efficient lifestyle for humanity. A precise, accurate and robust approach is necessary to enable event recognition systems to respond to sudden changes in various uncontrolled environments, such as the case of an emergency, physical threat and a fire or bomb alert. The performance of sudden event recognition systems depends heavily on the accuracy of low level processing, like detection, recognition, tracking and machine learning algorithms. This survey aims to detect and characterize a sudden event, which is a subset of an abnormal event in several video surveillance applications. This paper discusses the following in detail: (1) the importance of a sudden event over a general anomalous event; (2) frameworks used in sudden event recognition; (3) the requirements and comparative studies of a sudden event recognition system and (4) various decision-making approaches for sudden event recognition. The advantages and drawbacks of using 3D images from multiple cameras for real-time application are also discussed. The paper concludes with suggestions for future research directions in sudden event recognition. PMID:23921828

  9. Radically enhanced molecular recognition

    NASA Astrophysics Data System (ADS)

    Trabolsi, Ali; Khashab, Niveen; Fahrenbach, Albert C.; Friedman, Douglas C.; Colvin, Michael T.; Cotí, Karla K.; Benítez, Diego; Tkatchouk, Ekaterina; Olsen, John-Carl; Belowich, Matthew E.; Carmielli, Raanan; Khatib, Hussam A.; Goddard, William A.; Wasielewski, Michael R.; Stoddart, J. Fraser

    2010-01-01

    The tendency for viologen radical cations to dimerize has been harnessed to establish a recognition motif based on their ability to form extremely strong inclusion complexes with cyclobis(paraquat-p-phenylene) in its diradical dicationic redox state. This previously unreported complex involving three bipyridinium cation radicals increases the versatility of host-guest chemistry, extending its practice beyond the traditional reliance on neutral and charged guests and hosts. In particular, transporting the concept of radical dimerization into the field of mechanically interlocked molecules introduces a higher level of control within molecular switches and machines. Herein, we report that bistable and tristable [2]rotaxanes can be switched by altering electrochemical potentials. In a tristable [2]rotaxane composed of a cyclobis(paraquat-p-phenylene) ring and a dumbbell with tetrathiafulvalene, dioxynaphthalene and bipyridinium recognition sites, the position of the ring can be switched. On oxidation, it moves from the tetrathiafulvalene to the dioxynaphthalene, and on reduction, to the bipyridinium radical cation, provided the ring is also reduced simultaneously to the diradical dication.

  10. Complex Event Recognition Architecture

    NASA Technical Reports Server (NTRS)

    Fitzgerald, William A.; Firby, R. James

    2009-01-01

    Complex Event Recognition Architecture (CERA) is the name of a computational architecture, and software that implements the architecture, for recognizing complex event patterns that may be spread across multiple streams of input data. One of the main components of CERA is an intuitive event pattern language that simplifies what would otherwise be the complex, difficult tasks of creating logical descriptions of combinations of temporal events and defining rules for combining information from different sources over time. In this language, recognition patterns are defined in simple, declarative statements that combine point events from given input streams with those from other streams, using conjunction, disjunction, and negation. Patterns can be built on one another recursively to describe very rich, temporally extended combinations of events. Thereafter, a run-time matching algorithm in CERA efficiently matches these patterns against input data and signals when patterns are recognized. CERA can be used to monitor complex systems and to signal operators or initiate corrective actions when anomalous conditions are recognized. CERA can be run as a stand-alone monitoring system, or it can be integrated into a larger system to automatically trigger responses to changing environments or problematic situations.

  11. The neural correlates of visual self-recognition.

    PubMed

    Devue, Christel; Brédart, Serge

    2011-03-01

    This paper presents a review of studies that were aimed at determining which brain regions are recruited during visual self-recognition, with a particular focus on self-face recognition. A complex bilateral network, involving frontal, parietal and occipital areas, appears to be associated with self-face recognition, with a particularly high implication of the right hemisphere. Results indicate that it remains difficult to determine which specific cognitive operation is reflected by each recruited brain area, in part due to the variability of used control stimuli and experimental tasks. A synthesis of the interpretations provided by previous studies is presented. The relevance of using self-recognition as an indicator of self-awareness is discussed. We argue that a major aim of future research in the field should be to identify more clearly the cognitive operations induced by the perception of the self-face, and search for dissociations between neural correlates and cognitive components.

  12. Defining protein electrostatic recognition processes

    NASA Astrophysics Data System (ADS)

    Getzoff, Elizabeth D.; Roberts, Victoria A.

    The objective is to elucidate the nature of electrostatic forces controlling protein recognition processes by using a tightly coupled computational and interactive computer graphics approach. The TURNIP program was developed to determine the most favorable precollision orientations for two molecules by systematic search of all orientations and evaluation of the resulting electrostatic interactions. TURNIP was applied to the transient interaction between two electron transfer metalloproteins, plastocyanin and cytochrome c. The results suggest that the productive electron-transfer complex involves interaction of the positive region of cytochrome c with the negative patch of plastocyanin, consistent with experimental data. Application of TURNIP to the formation of the stable complex between the HyHEL-5 antibody and its protein antigen lysozyme showed that long-distance electrostatic forces guide lysozyme toward the HyHEL-5 binding site, but do not fine tune its orientation. Determination of docked antigen/antibody complexes requires including steric as well as electrostatic interactions, as was done for the U10 mutant of the anti-phosphorylcholine antibody S107. The graphics program Flex, a convenient desktop workstation program for visualizing molecular dynamics and normal mode motions, was enhanced. Flex now has a user interface and was rewritten to use standard graphics libraries, so as to run on most desktop workstations.

  13. Chemical recognition of gases and gas mixtures with terahertz waves

    NASA Astrophysics Data System (ADS)

    Jacobsen, R. H.; Mittleman, D. M.; Nuss, M. C.

    1996-12-01

    A time-domain chemical-recognition system for classifying gases and analyzing gas mixtures is presented. We analyze the free induction decay exhibited by gases excited by far-infrared (terahertz) pulses in the time domain, using digital signal-processing techniques. A simple geometric picture is used for the classification of the waveforms measured for unknown gas species. We demonstrate how the recognition system can be used to determine the partial pressures of an ammonia-water gas mixture.

  14. Amygdala damage impairs emotion recognition from music.

    PubMed

    Gosselin, Nathalie; Peretz, Isabelle; Johnsen, Erica; Adolphs, Ralph

    2007-01-28

    The role of the amygdala in recognition of danger is well established for visual stimuli such as faces. A similar role in another class of emotionally potent stimuli -- music -- has been recently suggested by the study of epileptic patients with unilateral resection of the anteromedian part of the temporal lobe [Gosselin, N., Peretz, I., Noulhiane, M., Hasboun, D., Beckett, C., & Baulac, M., et al. (2005). Impaired recognition of scary music following unilateral temporal lobe excision. Brain, 128(Pt 3), 628-640]. The goal of the present study was to assess the specific role of the amygdala in the recognition of fear from music. To this aim, we investigated a rare subject, S.M., who has complete bilateral damage relatively restricted to the amygdala and not encompassing other sectors of the temporal lobe. In Experiment 1, S.M. and four matched controls were asked to rate the intensity of fear, peacefulness, happiness, and sadness from computer-generated instrumental music purposely created to express those emotions. Subjects also rated the arousal and valence of each musical stimulus. An error detection task assessed basic auditory perceptual function. S.M. performed normally in this perceptual task, but was selectively impaired in the recognition of scary and sad music. In contrast, her recognition of happy music was normal. Furthermore, S.M. judged the scary music to be less arousing and the peaceful music less relaxing than did the controls. Overall, the pattern of impairment in S.M. is similar to that previously reported in patients with unilateral anteromedial temporal lobe damage. S.M.'s impaired emotional judgments occur in the face of otherwise intact processing of musical features that are emotionally determinant. The use of tempo and mode cues in distinguishing happy from sad music was also spared in S.M. Thus, the amygdala appears to be necessary for emotional processing of music rather than the perceptual processing itself.

  15. The Legal Recognition of Sign Languages

    ERIC Educational Resources Information Center

    De Meulder, Maartje

    2015-01-01

    This article provides an analytical overview of the different types of explicit legal recognition of sign languages. Five categories are distinguished: constitutional recognition, recognition by means of general language legislation, recognition by means of a sign language law or act, recognition by means of a sign language law or act including…

  16. Automatic speech recognition

    NASA Astrophysics Data System (ADS)

    Espy-Wilson, Carol

    2005-04-01

    Great strides have been made in the development of automatic speech recognition (ASR) technology over the past thirty years. Most of this effort has been centered around the extension and improvement of Hidden Markov Model (HMM) approaches to ASR. Current commercially-available and industry systems based on HMMs can perform well for certain situational tasks that restrict variability such as phone dialing or limited voice commands. However, the holy grail of ASR systems is performance comparable to humans-in other words, the ability to automatically transcribe unrestricted conversational speech spoken by an infinite number of speakers under varying acoustic environments. This goal is far from being reached. Key to the success of ASR is effective modeling of variability in the speech signal. This tutorial will review the basics of ASR and the various ways in which our current knowledge of speech production, speech perception and prosody can be exploited to improve robustness at every level of the system.

  17. Chemical recognition software

    SciTech Connect

    Wagner, J.S.; Trahan, M.W.; Nelson, W.E.; Hargis, P.H. Jr.; Tisone, G.C.

    1994-06-01

    We have developed a capability to make real time concentration measurements of individual chemicals in a complex mixture using a multispectral laser remote sensing system. Our chemical recognition and analysis software consists of three parts: (1) a rigorous multivariate analysis package for quantitative concentration and uncertainty estimates, (2) a genetic optimizer which customizes and tailors the multivariate algorithm for a particular application, and (3) an intelligent neural net chemical filter which pre-selects from the chemical database to find the appropriate candidate chemicals for quantitative analyses by the multivariate algorithms, as well as providing a quick-look concentration estimate and consistency check. Detailed simulations using both laboratory fluorescence data and computer synthesized spectra indicate that our software can make accurate concentration estimates from complex multicomponent mixtures, even when the mixture is noisy and contaminated with unknowns.

  18. Chemical recognition software

    SciTech Connect

    Wagner, J.S.; Trahan, M.W.; Nelson, W.E.; Hargis, P.J. Jr.; Tisone, G.C.

    1994-12-01

    We have developed a capability to make real time concentration measurements of individual chemicals in a complex mixture using a multispectral laser remote sensing system. Our chemical recognition and analysis software consists of three parts: (1) a rigorous multivariate analysis package for quantitative concentration and uncertainty estimates, (2) a genetic optimizer which customizes and tailors the multivariate algorithm for a particular application, and (3) an intelligent neural net chemical filter which pre-selects from the chemical database to find the appropriate candidate chemicals for quantitative analyses by the multivariate algorithms, as well as providing a quick-look concentration estimate and consistency check. Detailed simulations using both laboratory fluorescence data and computer synthesized spectra indicate that our software can make accurate concentration estimates from complex multicomponent mixtures. even when the mixture is noisy and contaminated with unknowns.

  19. Recognition Using Hybrid Classifiers.

    PubMed

    Osadchy, Margarita; Keren, Daniel; Raviv, Dolev

    2016-04-01

    A canonical problem in computer vision is category recognition (e.g., find all instances of human faces, cars etc., in an image). Typically, the input for training a binary classifier is a relatively small sample of positive examples, and a huge sample of negative examples, which can be very diverse, consisting of images from a large number of categories. The difficulty of the problem sharply increases with the dimension and size of the negative example set. We propose to alleviate this problem by applying a "hybrid" classifier, which replaces the negative samples by a prior, and then finds a hyperplane which separates the positive samples from this prior. The method is extended to kernel space and to an ensemble-based approach. The resulting binary classifiers achieve an identical or better classification rate than SVM, while requiring far smaller memory and lower computational complexity to train and apply.

  20. Early recognition of speech

    PubMed Central

    Remez, Robert E; Thomas, Emily F

    2013-01-01

    Classic research on the perception of speech sought to identify minimal acoustic correlates of each consonant and vowel. In explaining perception, this view designated momentary components of an acoustic spectrum as cues to the recognition of elementary phonemes. This conceptualization of speech perception is untenable given the findings of phonetic sensitivity to modulation independent of the acoustic and auditory form of the carrier. The empirical key is provided by studies of the perceptual organization of speech, a low-level integrative function that finds and follows the sensory effects of speech amid concurrent events. These projects have shown that the perceptual organization of speech is keyed to modulation; fast; unlearned; nonsymbolic; indifferent to short-term auditory properties; and organization requires attention. The ineluctably multisensory nature of speech perception also imposes conditions that distinguish language among cognitive systems. WIREs Cogn Sci 2013, 4:213–223. doi: 10.1002/wcs.1213 PMID:23926454

  1. Coordinate Transformations in Object Recognition

    ERIC Educational Resources Information Center

    Graf, Markus

    2006-01-01

    A basic problem of visual perception is how human beings recognize objects after spatial transformations. Three central classes of findings have to be accounted for: (a) Recognition performance varies systematically with orientation, size, and position; (b) recognition latencies are sequentially additive, suggesting analogue transformation…

  2. Automatic Recognition of Deaf Speech.

    ERIC Educational Resources Information Center

    Abdelhamied, Kadry; And Others

    1990-01-01

    This paper describes a speech perception system for automatic recognition of deaf speech. Using a 2-step segmentation approach for 468 utterances by 2 hearing-impaired men and 2 normal-hearing men, rates as high as 93.01 percent and 81.81 percent recognition were obtained in recognizing from deaf speech isolated words and connected speech,…

  3. Computer image processing and recognition

    NASA Technical Reports Server (NTRS)

    Hall, E. L.

    1979-01-01

    A systematic introduction to the concepts and techniques of computer image processing and recognition is presented. Consideration is given to such topics as image formation and perception; computer representation of images; image enhancement and restoration; reconstruction from projections; digital television, encoding, and data compression; scene understanding; scene matching and recognition; and processing techniques for linear systems.

  4. Conjoint recognition and phantom recollection.

    PubMed

    Brainerd, C J; Wright, R; Reyna, V F; Mojardin, A H

    2001-03-01

    A new methodology for measuring illusory conscious experience of the "presentation" of unstudied material (phantom recollection) is evaluated that extracts measurements directly from recognition responses, rather than indirectly from introspective reports. Application of this methodology in the Deese-Roediger-McDermott (DRM) paradigm (Experiments 1 and 2) and in a more conventional paradigm (Experiment 3) showed that 2 processes (phantom recollection and familiarity) contribute to false recognition of semantically related distractors. Phantom recollection was the larger contributor to false recognition of critical distractors in the DRM paradigm, but surprisingly, it was also the larger contributor to false recognition of other types of distractors. Variability in false recognition was tied to variability in phantom recollection. Experimental control of phantom recollection was achieved with manipulations that were motivated by fuzzy-trace theory's hypothesis that the phenomenon is gist-based.

  5. Recognition memory impairments caused by false recognition of novel objects.

    PubMed

    Yeung, Lok-Kin; Ryan, Jennifer D; Cowell, Rosemary A; Barense, Morgan D

    2013-11-01

    A fundamental assumption underlying most current theories of amnesia is that memory impairments arise because previously studied information either is lost rapidly or is made inaccessible (i.e., the old information appears to be new). Recent studies in rodents have challenged this view, suggesting instead that under conditions of high interference, recognition memory impairments following medial temporal lobe damage arise because novel information appears as though it has been previously seen. Here, we developed a new object recognition memory paradigm that distinguished whether object recognition memory impairments were driven by previously viewed objects being treated as if they were novel or by novel objects falsely recognized as though they were previously seen. In this indirect, eyetracking-based passive viewing task, older adults at risk for mild cognitive impairment showed false recognition to high-interference novel items (with a significant degree of feature overlap with previously studied items) but normal novelty responses to low-interference novel items (with a lower degree of feature overlap). The indirect nature of the task minimized the effects of response bias and other memory-based decision processes, suggesting that these factors cannot solely account for false recognition. These findings support the counterintuitive notion that recognition memory impairments in this memory-impaired population are not characterized by forgetting but rather are driven by the failure to differentiate perceptually similar objects, leading to the false recognition of novel objects as having been seen before.

  6. Probabilistic view clustering in object recognition

    NASA Astrophysics Data System (ADS)

    Camps, Octavia I.; Christoffel, Douglas W.; Pathak, Anjali

    1992-11-01

    To recognize objects and to determine their poses in a scene we need to find correspondences between the features extracted from the image and those of the object models. Models are commonly represented by describing a few characteristic views of the object representing groups of views with similar properties. Most feature-based matching schemes assume that all the features that are potentially visible in a view will appear with equal probability, and the resulting matching algorithms have to allow for 'errors' without really understanding what they mean. PREMIO is an object recognition system that uses CAD models of 3D objects and knowledge of surface reflectance properties, light sources, sensor characteristics, and feature detector algorithms to estimate the probability of the features being detectable and correctly matched. The purpose of this paper is to describe the predictions generated by PREMIO, how they are combined into a single probabilistic model, and illustrative examples showing its use in object recognition.

  7. Photonics: From target recognition to lesion detection

    NASA Technical Reports Server (NTRS)

    Henry, E. Michael

    1994-01-01

    Since 1989, Martin Marietta has invested in the development of an innovative concept for robust real-time pattern recognition for any two-dimensioanal sensor. This concept has been tested in simulation, and in laboratory and field hardware, for a number of DOD and commercial uses from automatic target recognition to manufacturing inspection. We have now joined Rose Health Care Systems in developing its use for medical diagnostics. The concept is based on determining regions of interest by using optical Fourier bandpassing as a scene segmentation technique, enhancing those regions using wavelet filters, passing the enhanced regions to a neural network for analysis and initial pattern identification, and following this initial identification with confirmation by optical correlation. The optical scene segmentation and pattern confirmation are performed by the same optical module. The neural network is a recursive error minimization network with a small number of connections and nodes that rapidly converges to a global minimum.

  8. Determining bacteriophage endopeptidase activity using either fluorophore-quencher labeled peptides combined with liquid chromatography-mass spectrometry (LC-MS) or Förster resonance energy transfer (FRET) assays

    PubMed Central

    Molina, Henrik; Fischetti, Vincent A.

    2017-01-01

    The necessity of identifying novel methods to combat infections caused by antibiotic resistant bacteria is increasing each year. Recent advancements in the development of peptidoglycan hydrolases (e.g. lysins) from bacterial viruses (bacteriophages) have revealed the efficiency of this class of enzymes in treating serious bacterial infections. Though promising results have been obtained regarding the lethal action of lysin on bacterial pathogens both in vitro and in vivo, an often-overlooked factor in these studies is precisely identifying their peptidoglycan cleavage site. This knowledge would be useful for following the activity of the enzyme during development, without the need for whole-organism lytic assays. However, more importantly, it would enable the selection of lysins with different cleavage activities that would act synergistically for enhanced efficacy. Here, we have developed two new methods to accurately identify the cleavage site of lysins using liquid chromatography mass spectrometry (LC-MS) on peptidoglycan-like fluorophore-quencher modified synthetic peptides, as well as determining the enzymatic action and kinetics of the enzymes on modified peptides in a Förster resonance energy transfer (FRET) assay. These methods should facilitate progress within the lysin field, accelerating the development of therapeutic lysins to combat antibiotic resistant bacterial infections. PMID:28296948

  9. Long-range Electrostatic Complementarity Governs Substrate Recognition by Human Chymotrypsin C, a Key Regulator of Digestive Enzyme Activation*

    PubMed Central

    Batra, Jyotica; Szabó, András; Caulfield, Thomas R.; Soares, Alexei S.; Sahin-Tóth, Miklós; Radisky, Evette S.

    2013-01-01

    Human chymotrypsin C (CTRC) is a pancreatic serine protease that regulates activation and degradation of trypsinogens and procarboxypeptidases by targeting specific cleavage sites within their zymogen precursors. In cleaving these regulatory sites, which are characterized by multiple flanking acidic residues, CTRC shows substrate specificity that is distinct from that of other isoforms of chymotrypsin and elastase. Here, we report the first crystal structure of active CTRC, determined at 1.9-Å resolution, revealing the structural basis for binding specificity. The structure shows human CTRC bound to the small protein protease inhibitor eglin c, which binds in a substrate-like manner filling the S6-S5′ subsites of the substrate binding cleft. Significant binding affinity derives from burial of preferred hydrophobic residues at the P1, P4, and P2′ positions of CTRC, although acidic P2′ residues can also be accommodated by formation of an interfacial salt bridge. Acidic residues may also be specifically accommodated in the P6 position. The most unique structural feature of CTRC is a ring of intense positive electrostatic surface potential surrounding the primarily hydrophobic substrate binding site. Our results indicate that long-range electrostatic attraction toward substrates of concentrated negative charge governs substrate discrimination, which explains CTRC selectivity in regulating active digestive enzyme levels. PMID:23430245

  10. Building Hierarchical Representations for Oracle Character and Sketch Recognition.

    PubMed

    Jun Guo; Changhu Wang; Roman-Rangel, Edgar; Hongyang Chao; Yong Rui

    2016-01-01

    In this paper, we study oracle character recognition and general sketch recognition. First, a data set of oracle characters, which are the oldest hieroglyphs in China yet remain a part of modern Chinese characters, is collected for analysis. Second, typical visual representations in shape- and sketch-related works are evaluated. We analyze the problems suffered when addressing these representations and determine several representation design criteria. Based on the analysis, we propose a novel hierarchical representation that combines a Gabor-related low-level representation and a sparse-encoder-related mid-level representation. Extensive experiments show the effectiveness of the proposed representation in both oracle character recognition and general sketch recognition. The proposed representation is also complementary to convolutional neural network (CNN)-based models. We introduce a solution to combine the proposed representation with CNN-based models, and achieve better performances over both approaches. This solution has beaten humans at recognizing general sketches.

  11. Macromolecular recognition: Recognition of polymer side chains by cyclodextrin

    NASA Astrophysics Data System (ADS)

    Hashidzume, Akihito; Harada, Akira

    2015-12-01

    The interaction of cyclodextrins (CD) with water soluble polymers possessing guest residues has been investigated as model systems in biological molecular recognition. The selectivity of interaction of CD with polymer-carrying guest residues is controlled by polymer chains, i.e., the steric effect of polymer main chain, the conformational effect of polymer main chain, and multi-site interaction. Macroscopic assemblies have been also realized based on molecular recognition using polyacrylamide-based gels possessing CD and guest residues.

  12. Protospacer recognition motifs

    PubMed Central

    Shah, Shiraz A.; Erdmann, Susanne; Mojica, Francisco J.M.; Garrett, Roger A.

    2013-01-01

    Protospacer adjacent motifs (PAMs) were originally characterized for CRISPR-Cas systems that were classified on the basis of their CRISPR repeat sequences. A few short 2–5 bp sequences were identified adjacent to one end of the protospacers. Experimental and bioinformatical results linked the motif to the excision of protospacers and their insertion into CRISPR loci. Subsequently, evidence accumulated from different virus- and plasmid-targeting assays, suggesting that these motifs were also recognized during DNA interference, at least for the recently classified type I and type II CRISPR-based systems. The two processes, spacer acquisition and protospacer interference, employ different molecular mechanisms, and there is increasing evidence to suggest that the sequence motifs that are recognized, while overlapping, are unlikely to be identical. In this article, we consider the properties of PAM sequences and summarize the evidence for their dual functional roles. It is proposed to use the terms protospacer associated motif (PAM) for the conserved DNA sequence and to employ spacer acqusition motif (SAM) and target interference motif (TIM), respectively, for acquisition and interference recognition sites. PMID:23403393

  13. Recognition of speech spectrograms.

    PubMed

    Greene, B G; Pisoni, D B; Carrell, T D

    1984-07-01

    The performance of eight naive observers in learning to identify speech spectrograms was studied over a 2-month period. Single tokens from a 50-word phonetically balanced (PB) list were recorded by several talkers and displayed on a Spectraphonics Speech Spectrographic Display system. Identification testing occurred immediately after daily training sessions. After approximately 20 h of training, naive subjects correctly identified the 50 PB words from a single talker over 95% of the time. Generalization tests with the same words were then carried out with different tokens from the original talker, new tokens from another male talker, a female talker, and finally, a synthetic talker. The generalization results for these talkers showed recognition performance at 91%, 76%, 76%, and 48%, respectively. Finally, generalization tests with a novel set of PB words produced by the original talker were also carried out to examine in detail the perceptual strategies and visual features that subjects abstracted from the training set. Our results demonstrate that even without formal training in phonetics or acoustics naive observers can learn to identify visual displays of speech at very high levels of accuracy. Analysis of subjects' performance in a verbal protocol task demonstrated that they rely on salient visual correlates of many phonetic features in speech.

  14. Structural Target Analysis And Recognition System

    NASA Astrophysics Data System (ADS)

    Lee, Harry C.

    1984-06-01

    The structural target analysis and recognition system (STARS) is a pyramid and syntactical based vision system that uniquely classifies targets, using their viewable internal structure. Being a totally structural approach, STARS uses a resolution sequence to develop a hierarchical pyramid organized segmentation and formal language to perform the recognition function. Global structure of the target is derived by the segment connectivity of the inter-resolution levels, while local structure is based on the local relationship of segments at a single level. The relationships of both the global and local structures form a resolution syntax tree (RST). Two targets are said to be structurally similar if they have similar RSTs. The matching process of the RSTs proceeds from the root to the leaves of the tree. The depth to which the match progresses before failure or completion determines the degree of patch in a resolution sense. RSTs from various views of a target are grouped together to form a formal language. The underlying grammar is transformed into a stochastic grammar so as to accommodate segmentation and environmental variations. Recognition metrics are a function of the resolution structure and posterior probability at each resolution level. Because of the inherent resolution sequence, STARS can accommodate both candidate and reference targets from various resolutions.

  15. Gait recognition and walking exercise intensity estimation.

    PubMed

    Lin, Bor-Shing; Liu, Yu-Ting; Yu, Chu; Jan, Gene Eu; Hsiao, Bo-Tang

    2014-04-04

    Cardiovascular patients consult doctors for advice regarding regular exercise, whereas obese patients must self-manage their weight. Because a system for permanently monitoring and tracking patients' exercise intensities and workouts is necessary, a system for recognizing gait and estimating walking exercise intensity was proposed. For gait recognition analysis, αβ filters were used to improve the recognition of athletic attitude. Furthermore, empirical mode decomposition (EMD) was used to filter the noise of patients' attitude to acquire the Fourier transform energy spectrum. Linear discriminant analysis was then applied to this energy spectrum for training and recognition. When the gait or motion was recognized, the walking exercise intensity was estimated. In addition, this study addressed the correlation between inertia and exercise intensity by using the residual function of the EMD and quadratic approximation to filter the effect of the baseline drift integral of the acceleration sensor. The increase in the determination coefficient of the regression equation from 0.55 to 0.81 proved that the accuracy of the method for estimating walking exercise intensity proposed by Kurihara was improved in this study.

  16. 77 FR 64799 - Notice of Submission for OMB Review; Office of Postsecondary Education; Secretary's Recognition...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-10-23

    ...The information collected is required to determine if an accrediting agency complies with the Secretary of Education's Criteria for Recognition and is used to allow the Secretary to make determinations on extending and/or continuing...

  17. A two-stage exon recognition model based on synergetic neural network.

    PubMed

    Huang, Zhehuang; Chen, Yidong

    2014-01-01

    Exon recognition is a fundamental task in bioinformatics to identify the exons of DNA sequence. Currently, exon recognition algorithms based on digital signal processing techniques have been widely used. Unfortunately, these methods require many calculations, resulting in low recognition efficiency. In order to overcome this limitation, a two-stage exon recognition model is proposed and implemented in this paper. There are three main works. Firstly, we use synergetic neural network to rapidly determine initial exon intervals. Secondly, adaptive sliding window is used to accurately discriminate the final exon intervals. Finally, parameter optimization based on artificial fish swarm algorithm is used to determine different species thresholds and corresponding adjustment parameters of adaptive windows. Experimental results show that the proposed model has better performance for exon recognition and provides a practical solution and a promising future for other recognition tasks.

  18. Emotion recognition from physiological signals.

    PubMed

    Gouizi, K; Bereksi Reguig, F; Maaoui, C

    2011-01-01

    Emotion recognition is one of the great challenges in human-human and human-computer interaction. Accurate emotion recognition would allow computers to recognize human emotions and therefore react accordingly. In this paper, an approach for emotion recognition based on physiological signals is proposed. Six basic emotions: joy, sadness, fear, disgust, neutrality and amusement are analysed using physiological signals. These emotions are induced through the presentation of International Affecting Picture System (IAPS) pictures to the subjects. The physiological signals of interest in this analysis are: electromyogram signal (EMG), respiratory volume (RV), skin temperature (SKT), skin conductance (SKC), blood volume pulse (BVP) and heart rate (HR). These are selected to extract characteristic parameters, which will be used for classifying the emotions. The SVM (support vector machine) technique is used for classifying these parameters. The experimental results show that the proposed methodology provides in general a recognition rate of 85% for different emotional states.

  19. Gesture recognition on smart cameras

    NASA Astrophysics Data System (ADS)

    Dziri, Aziz; Chevobbe, Stephane; Darouich, Mehdi

    2013-02-01

    Gesture recognition is a feature in human-machine interaction that allows more natural interaction without the use of complex devices. For this reason, several methods of gesture recognition have been developed in recent years. However, most real time methods are designed to operate on a Personal Computer with high computing resources and memory. In this paper, we analyze relevant methods found in the literature in order to investigate the ability of smart camera to execute gesture recognition algorithms. We elaborate two hand gesture recognition pipelines. The first method is based on invariant moments extraction and the second on finger tips detection. The hand detection method used for both pipeline is based on skin color segmentation. The results obtained show that the un-optimized versions of invariant moments method and finger tips detection method can reach 10 fps on embedded processor and use about 200 kB of memory.

  20. Effective indexing for face recognition

    NASA Astrophysics Data System (ADS)

    Sochenkov, I.; Sochenkova, A.; Vokhmintsev, A.; Makovetskii, A.; Melnikov, A.

    2016-09-01

    Face recognition is one of the most important tasks in computer vision and pattern recognition. Face recognition is useful for security systems to provide safety. In some situations it is necessary to identify the person among many others. In this case this work presents new approach in data indexing, which provides fast retrieval in big image collections. Data indexing in this research consists of five steps. First, we detect the area containing face, second we align face, and then we detect areas containing eyes and eyebrows, nose, mouth. After that we find key points of each area using different descriptors and finally index these descriptors with help of quantization procedure. The experimental analysis of this method is performed. This paper shows that performing method has results at the level of state-of-the-art face recognition methods, but it is also gives results fast that is important for the systems that provide safety.

  1. Applications of chaotic neurodynamics in pattern recognition

    NASA Astrophysics Data System (ADS)

    Baird, Bill; Freeman, Walter J.; Eeckman, Frank H.; Yao, Yong

    1991-08-01

    Network algorithms and architectures for pattern recognition derived from neural models of the olfactory system are reviewed. These span a range from highly abstract to physiologically detailed, and employ the kind of dynamical complexity observed in olfactory cortex, ranging from oscillation to chaos. A simple architecture and algorithm for analytically guaranteed associative memory storage of analog patterns, continuous sequences, and chaotic attractors in the same network is described. A matrix inversion determines network weights, given prototype patterns to be stored. There are N units of capacity in an N node network with 3N2 weights. It costs one unit per static attractor, two per Fourier component of each sequence, and three to four per chaotic attractor. There are no spurious attractors, and for sequences there is a Liapunov function in a special coordinate system which governs the approach of transient states to stored trajectories. Unsupervised or supervised incremental learning algorithms for pattern classification, such as competitive learning or bootstrap Widrow-Hoff can easily be implemented. The architecture can be ''folded'' into a recurrent network with higher order weights that can be used as a model of cortex that stores oscillatory and chaotic attractors by a Hebb rule. Network performance is demonstrated by application to the problem of real-time handwritten digit recognition. An effective system with on-line learning has been written by Eeckman and Baird for the Macintosh. It utilizes static, oscillatory, and/or chaotic attractors of two kinds--Lorenze attractors, or attractors resulting from chaotically interacting oscillatory modes. The successful application to an industrial pattern recognition problem of a network architecture of considerable physiological and dynamical complexity, developed by Freeman and Yao, is described. The data sets of the problem come in three classes of difficulty, and performance of the biological network is

  2. Thermal to Visible Face Recognition

    DTIC Science & Technology

    2012-04-01

    recognition has been an active area of research for the past two decades due its wide range of applications in law enforcement and verification...an ideal modality for nighttime tasks, but the large disparateness between the thermal IR and visible spectrums results in a wide modality gap that...CONCLUSION AND FUTURE WORK In this study, we investigated the thermal-to-visible face recognition problem, which has a wide modality gap. We showed

  3. [Neurological disease and facial recognition].

    PubMed

    Kawamura, Mitsuru; Sugimoto, Azusa; Kobayakawa, Mutsutaka; Tsuruya, Natsuko

    2012-07-01

    To discuss the neurological basis of facial recognition, we present our case reports of impaired recognition and a review of previous literature. First, we present a case of infarction and discuss prosopagnosia, which has had a large impact on face recognition research. From a study of patient symptoms, we assume that prosopagnosia may be caused by unilateral right occipitotemporal lesion and right cerebral dominance of facial recognition. Further, circumscribed lesion and degenerative disease may also cause progressive prosopagnosia. Apperceptive prosopagnosia is observed in patients with posterior cortical atrophy (PCA), pathologically considered as Alzheimer's disease, and associative prosopagnosia in frontotemporal lobar degeneration (FTLD). Second, we discuss face recognition as part of communication. Patients with Parkinson disease show social cognitive impairments, such as difficulty in facial expression recognition and deficits in theory of mind as detected by the reading the mind in the eyes test. Pathological and functional imaging studies indicate that social cognitive impairment in Parkinson disease is possibly related to damages in the amygdalae and surrounding limbic system. The social cognitive deficits can be observed in the early stages of Parkinson disease, and even in the prodromal stage, for example, patients with rapid eye movement (REM) sleep behavior disorder (RBD) show impairment in facial expression recognition. Further, patients with myotonic dystrophy type 1 (DM 1), which is a multisystem disease that mainly affects the muscles, show social cognitive impairment similar to that of Parkinson disease. Our previous study showed that facial expression recognition impairment of DM 1 patients is associated with lesion in the amygdalae and insulae. Our study results indicate that behaviors and personality traits in DM 1 patients, which are revealed by social cognitive impairment, are attributable to dysfunction of the limbic system.

  4. Computer Recognition of Facial Profiles

    DTIC Science & Technology

    1974-08-01

    effective in identifying those feature vectors which are of most importance in the recognition process . Thus the training procedure generally produces...ga Ente#lodI- i COMPUTER RECOGNITTON OF FACIAL PROFILES iU A Thesis i Presented in Partial Fulfillment of the Requirements for the Degree Master of... thesis , the suggestion that the state of the art in pattern recognition was sufficient to enable a machine capable of recognizing human faces to be built

  5. Holistic processing predicts face recognition.

    PubMed

    Richler, Jennifer J; Cheung, Olivia S; Gauthier, Isabel

    2011-04-01

    The concept of holistic processing is a cornerstone of face-recognition research. In the study reported here, we demonstrated that holistic processing predicts face-recognition abilities on the Cambridge Face Memory Test and on a perceptual face-identification task. Our findings validate a large body of work that relies on the assumption that holistic processing is related to face recognition. These findings also reconcile the study of face recognition with the perceptual-expertise work it inspired; such work links holistic processing of objects with people's ability to individuate them. Our results differ from those of a recent study showing no link between holistic processing and face recognition. This discrepancy can be attributed to the use in prior research of a popular but flawed measure of holistic processing. Our findings salvage the central role of holistic processing in face recognition and cast doubt on a subset of the face-perception literature that relies on a problematic measure of holistic processing.

  6. Pattern recognition characterizations of micromechanical and morphological materials states via analytical quantitative ultrasonics

    NASA Technical Reports Server (NTRS)

    Williams, J. H., Jr.; Lee, S. S.

    1986-01-01

    One potential approach to the quantitative acquisition of discriminatory information that can isolate a single structural state is pattern recognition. The pattern recognition characterizations of micromechanical and morphological materials states via analytical quantiative ultrasonics are outlined. The concepts, terminology, and techniques of statistical pattern recognition are reviewed. Feature extraction and classification and states of the structure can be determined via a program of ultrasonic data generation.

  7. Recognition Failure: Another Case of Retrieval Failure

    ERIC Educational Resources Information Center

    Rabinowitz, Jan; And Others

    1977-01-01

    A theoretical explanation of the phenomenon of recognition failure and a presentation of seven experiments investigating performance. Recognition failure is reduced when a more stringent recognition criterion is used, essentially eliminated when the proper access test is used and significantly reduced when variability in recognition performance is…

  8. Document Form and Character Recognition using SVM

    NASA Astrophysics Data System (ADS)

    Park, Sang-Sung; Shin, Young-Geun; Jung, Won-Kyo; Ahn, Dong-Kyu; Jang, Dong-Sik

    2009-08-01

    Because of development of computer and information communication, EDI (Electronic Data Interchange) has been developing. There is OCR (Optical Character Recognition) of Pattern recognition technology for EDI. OCR contributed to changing many manual in the past into automation. But for the more perfect database of document, much manual is needed for excluding unnecessary recognition. To resolve this problem, we propose document form based character recognition method in this study. Proposed method is divided into document form recognition part and character recognition part. Especially, in character recognition, change character into binarization by using SVM algorithm and extract more correct feature value.

  9. Pattern recognition monitoring of PEM fuel cell

    DOEpatents

    Meltser, Mark Alexander

    1999-01-01

    The CO-concentration in the H.sub.2 feed stream to a PEM fuel cell stack is monitored by measuring current and voltage behavior patterns from an auxiliary cell attached to the end of the stack. The auxiliary cell is connected to the same oxygen and hydrogen feed manifolds that supply the stack, and discharges through a constant load. Pattern recognition software compares the current and voltage patterns from the auxiliary cell to current and voltage signature determined from a reference cell similar to the auxiliary cell and operated under controlled conditions over a wide range of CO-concentrations in the H.sub.2 fuel stream.

  10. Pattern recognition monitoring of PEM fuel cell

    DOEpatents

    Meltser, M.A.

    1999-08-31

    The CO-concentration in the H{sub 2} feed stream to a PEM fuel cell stack is monitored by measuring current and voltage behavior patterns from an auxiliary cell attached to the end of the stack. The auxiliary cell is connected to the same oxygen and hydrogen feed manifolds that supply the stack, and discharges through a constant load. Pattern recognition software compares the current and voltage patterns from the auxiliary cell to current and voltage signature determined from a reference cell similar to the auxiliary cell and operated under controlled conditions over a wide range of CO-concentrations in the H{sub 2} fuel stream. 4 figs.

  11. Statistical pattern recognition algorithms for autofluorescence imaging

    NASA Astrophysics Data System (ADS)

    Kulas, Zbigniew; Bereś-Pawlik, Elżbieta; Wierzbicki, Jarosław

    2009-02-01

    In cancer diagnostics the most important problems are the early identification and estimation of the tumor growth and spread in order to determine the area to be operated. The aim of the work was to design of statistical algorithms helping doctors to objectively estimate pathologically changed areas and to assess the disease advancement. In the research, algorithms for classifying endoscopic autofluorescence images of larynx and intestine were used. The results show that the statistical pattern recognition offers new possibilities for endoscopic diagnostics and can be of a tremendous help in assessing the area of the pathological changes.

  12. Alzheimer’s disease-associated mutations increase amyloid precursor protein resistance to γ-secretase cleavage and the Aβ42/Aβ40 ratio

    PubMed Central

    Xu, Ting-Hai; Yan, Yan; Kang, Yanyong; Jiang, Yi; Melcher, Karsten; Xu, H Eric

    2016-01-01

    Mutations in the amyloid precursor protein (APP) gene and the aberrant cleavage of APP by γ-secretase are associated with Alzheimer’s disease (AD). Here we have developed a simple and sensitive cell-based assay to detect APP cleavage by γ-secretase. Unexpectedly, most familial AD (FAD)-linked APP mutations make APP partially resistant to γ-secretase. Mutations that alter residues N terminal to the γ-secretase cleavage site Aβ42 have subtle effects on cleavage efficiency and cleavage-site selectivity. In contrast, mutations that alter residues C terminal to the Aβ42 site reduce cleavage efficiency and dramatically shift cleavage-site specificity toward the aggregation-prone Aβ42. Moreover, mutations that remove positive charge at residue 53 greatly reduce the APP cleavage by γ-secretase. These results suggest a model of γ-secretase substrate recognition, in which the APP region C terminal to the Aβ42 site and the positively charged residue at position 53 are the primary determinants for substrate binding and cleavage-site selectivity. We further demonstrate that this model can be extended to γ-secretase processing of notch receptors, a family of highly conserved cell-surface signaling proteins. PMID:27625790

  13. Two new restriction endonucleases DraII and DraIII from Deinococcus radiophilus.

    PubMed Central

    Grosskopf, R; Wolf, W; Kessler, C

    1985-01-01

    In addition to recently characterized DraI (1), two new Type II restriction endonucleases, DraII and DraIII, with novel site-specificities were isolated and purified from Deinococcus radiophilus ATCC 27603. DraII and DraIII recognize the hepta- and nonanucleotide sequences (sequence in text) The cleavage sites within both strands are indicated by arrows. The recognition sequences were established by mapping of the cleavage sites on pBR322 (DraII) and fd109 RF DNA (DraIII). The sequence specifities were confirmed by computer-assisted restriction analyses of the generated fragment patterns of the sequenced DNA's of the bacteriophages lambda, phi X174 RF, M13mp8 RF and fd109 RF, the viruses Adeno2 and SV40, and the plasmids pBR322 and pBR328. The cleavage positions within the recognition sequences were determined by sequencing experiments. Images PMID:2987827

  14. Bidirectional Modulation of Recognition Memory.

    PubMed

    Ho, Jonathan W; Poeta, Devon L; Jacobson, Tara K; Zolnik, Timothy A; Neske, Garrett T; Connors, Barry W; Burwell, Rebecca D

    2015-09-30

    Perirhinal cortex (PER) has a well established role in the familiarity-based recognition of individual items and objects. For example, animals and humans with perirhinal damage are unable to distinguish familiar from novel objects in recognition memory tasks. In the normal brain, perirhinal neurons respond to novelty and familiarity by increasing or decreasing firing rates. Recent work also implicates oscillatory activity in the low-beta and low-gamma frequency bands in sensory detection, perception, and recognition. Using optogenetic methods in a spontaneous object exploration (SOR) task, we altered recognition memory performance in rats. In the SOR task, normal rats preferentially explore novel images over familiar ones. We modulated exploratory behavior in this task by optically stimulating channelrhodopsin-expressing perirhinal neurons at various frequencies while rats looked at novel or familiar 2D images. Stimulation at 30-40 Hz during looking caused rats to treat a familiar image as if it were novel by increasing time looking at the image. Stimulation at 30-40 Hz was not effective in increasing exploration of novel images. Stimulation at 10-15 Hz caused animals to treat a novel image as familiar by decreasing time looking at the image, but did not affect looking times for images that were already familiar. We conclude that optical stimulation of PER at different frequencies can alter visual recognition memory bidirectionally. Significance statement: Recognition of novelty and familiarity are important for learning, memory, and decision making. Perirhinal cortex (PER) has a well established role in the familiarity-based recognition of individual items and objects, but how novelty and familiarity are encoded and transmitted in the brain is not known. Perirhinal neurons respond to novelty and familiarity by changing firing rates, but recent work suggests that brain oscillations may also be important for recognition. In this study, we showed that stimulation of

  15. Kazakh Traditional Dance Gesture Recognition

    NASA Astrophysics Data System (ADS)

    Nussipbekov, A. K.; Amirgaliyev, E. N.; Hahn, Minsoo

    2014-04-01

    Full body gesture recognition is an important and interdisciplinary research field which is widely used in many application spheres including dance gesture recognition. The rapid growth of technology in recent years brought a lot of contribution in this domain. However it is still challenging task. In this paper we implement Kazakh traditional dance gesture recognition. We use Microsoft Kinect camera to obtain human skeleton and depth information. Then we apply tree-structured Bayesian network and Expectation Maximization algorithm with K-means clustering to calculate conditional linear Gaussians for classifying poses. And finally we use Hidden Markov Model to detect dance gestures. Our main contribution is that we extend Kinect skeleton by adding headwear as a new skeleton joint which is calculated from depth image. This novelty allows us to significantly improve the accuracy of head gesture recognition of a dancer which in turn plays considerable role in whole body gesture recognition. Experimental results show the efficiency of the proposed method and that its performance is comparable to the state-of-the-art system performances.

  16. Cognitive object recognition system (CORS)

    NASA Astrophysics Data System (ADS)

    Raju, Chaitanya; Varadarajan, Karthik Mahesh; Krishnamurthi, Niyant; Xu, Shuli; Biederman, Irving; Kelley, Troy

    2010-04-01

    We have developed a framework, Cognitive Object Recognition System (CORS), inspired by current neurocomputational models and psychophysical research in which multiple recognition algorithms (shape based geometric primitives, 'geons,' and non-geometric feature-based algorithms) are integrated to provide a comprehensive solution to object recognition and landmarking. Objects are defined as a combination of geons, corresponding to their simple parts, and the relations among the parts. However, those objects that are not easily decomposable into geons, such as bushes and trees, are recognized by CORS using "feature-based" algorithms. The unique interaction between these algorithms is a novel approach that combines the effectiveness of both algorithms and takes us closer to a generalized approach to object recognition. CORS allows recognition of objects through a larger range of poses using geometric primitives and performs well under heavy occlusion - about 35% of object surface is sufficient. Furthermore, geon composition of an object allows image understanding and reasoning even with novel objects. With reliable landmarking capability, the system improves vision-based robot navigation in GPS-denied environments. Feasibility of the CORS system was demonstrated with real stereo images captured from a Pioneer robot. The system can currently identify doors, door handles, staircases, trashcans and other relevant landmarks in the indoor environment.

  17. An audiovisual emotion recognition system

    NASA Astrophysics Data System (ADS)

    Han, Yi; Wang, Guoyin; Yang, Yong; He, Kun

    2007-12-01

    Human emotions could be expressed by many bio-symbols. Speech and facial expression are two of them. They are both regarded as emotional information which is playing an important role in human-computer interaction. Based on our previous studies on emotion recognition, an audiovisual emotion recognition system is developed and represented in this paper. The system is designed for real-time practice, and is guaranteed by some integrated modules. These modules include speech enhancement for eliminating noises, rapid face detection for locating face from background image, example based shape learning for facial feature alignment, and optical flow based tracking algorithm for facial feature tracking. It is known that irrelevant features and high dimensionality of the data can hurt the performance of classifier. Rough set-based feature selection is a good method for dimension reduction. So 13 speech features out of 37 ones and 10 facial features out of 33 ones are selected to represent emotional information, and 52 audiovisual features are selected due to the synchronization when speech and video fused together. The experiment results have demonstrated that this system performs well in real-time practice and has high recognition rate. Our results also show that the work in multimodules fused recognition will become the trend of emotion recognition in the future.

  18. Speech recognition in dental software systems: features and functionality.

    PubMed

    Yuhaniak Irwin, Jeannie; Fernando, Shawn; Schleyer, Titus; Spallek, Heiko

    2007-01-01

    Speech recognition allows clinicians a hands-free option for interacting with computers, which is important for dentists who have difficulty using a keyboard and a mouse when working with patients. While roughly 13% of all general dentists with computers at chairside use speech recognition for data entry, 16% have tried and discontinued using this technology. In this study, researches explored the speech recognition features and functionality of four dental software applications. For each system, the documentation as well as the working program was evaluated to determine speech recognition capabilities. A comparison checklist was created to highlight each program's speech functionality. Next, after the development of charting scripts, feasibility user tests were conducted to determine if performance comparisons could be made across systems. While four systems were evaluated in the feature comparison, only two of the systems were reviewed during the feasibility user tests. Results show that current speech functionality, instead of being intuitive, is directly comparable to using a mouse. Further, systems require memorizing an enormous amount of specific terminology opposed to using natural language. User testing is a feasible way to measure the performance of speech recognition across systems and will be conducted in the near future. Overall, limited speech functionality reduces the ability of clinicians to interact directly with the computer during clinical care. This can hinder the benefits of electronic patient records and clinical decision support systems.

  19. Ignorance- versus Evidence-Based Decision Making: A Decision Time Analysis of the Recognition Heuristic

    ERIC Educational Resources Information Center

    Hilbig, Benjamin E.; Pohl, Rudiger F.

    2009-01-01

    According to part of the adaptive toolbox notion of decision making known as the recognition heuristic (RH), the decision process in comparative judgments--and its duration--is determined by whether recognition discriminates between objects. By contrast, some recently proposed alternative models predict that choices largely depend on the amount of…

  20. 10 CFR 431.19 - Department of Energy recognition of accreditation bodies.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 10 Energy 3 2010-01-01 2010-01-01 false Department of Energy recognition of accreditation bodies. 431.19 Section 431.19 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY EFFICIENCY PROGRAM FOR... Methods of Determining Efficiency § 431.19 Department of Energy recognition of accreditation bodies....

  1. 10 CFR 431.19 - Department of Energy recognition of accreditation bodies.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 10 Energy 3 2011-01-01 2011-01-01 false Department of Energy recognition of accreditation bodies. 431.19 Section 431.19 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY EFFICIENCY PROGRAM FOR... Methods of Determining Efficiency § 431.19 Department of Energy recognition of accreditation bodies....

  2. Relations among Linguistic and Cognitive Skills and Spoken Word Recognition in Adults with Cochlear Implants

    ERIC Educational Resources Information Center

    Collison, Elizabeth A.; Munson, Benjamin; Carney, Arlene Earley

    2004-01-01

    This study examined spoken word recognition in adults with cochlear implants (CIs) to determine the extent to which linguistic and cognitive abilities predict variability in speech-perception performance. Both a traditional consonant-vowel-consonant (CVC)-repetition measure and a gated-word recognition measure (F. Grosjean, 1996) were used.…

  3. 10 CFR 431.19 - Department of Energy recognition of accreditation bodies.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 10 Energy 3 2014-01-01 2014-01-01 false Department of Energy recognition of accreditation bodies. 431.19 Section 431.19 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY EFFICIENCY PROGRAM FOR... Methods of Determining Efficiency § 431.19 Department of Energy recognition of accreditation bodies....

  4. 10 CFR 431.19 - Department of Energy recognition of accreditation bodies.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 10 Energy 3 2012-01-01 2012-01-01 false Department of Energy recognition of accreditation bodies. 431.19 Section 431.19 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY EFFICIENCY PROGRAM FOR... Methods of Determining Efficiency § 431.19 Department of Energy recognition of accreditation bodies....

  5. 10 CFR 431.19 - Department of Energy recognition of accreditation bodies.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 10 Energy 3 2013-01-01 2013-01-01 false Department of Energy recognition of accreditation bodies. 431.19 Section 431.19 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY EFFICIENCY PROGRAM FOR... Methods of Determining Efficiency § 431.19 Department of Energy recognition of accreditation bodies....

  6. Emotion Recognition in Fathers and Mothers at High-Risk for Child Physical Abuse

    ERIC Educational Resources Information Center

    Asla, Nagore; de Paul, Joaquin; Perez-Albeniz, Alicia

    2011-01-01

    Objective: The present study was designed to determine whether parents at high risk for physical child abuse, in comparison with parents at low risk, show deficits in emotion recognition, as well as to examine the moderator effect of gender and stress on the relationship between risk for physical child abuse and emotion recognition. Methods: Based…

  7. The Effect of Asymmetrical Signal Degradation on Binaural Speech Recognition in Children and Adults.

    ERIC Educational Resources Information Center

    Rothpletz, Ann M.; Tharpe, Anne Marie; Grantham, D. Wesley

    2004-01-01

    To determine the effect of asymmetrical signal degradation on binaural speech recognition, 28 children and 14 adults were administered a sentence recognition task amidst multitalker babble. There were 3 listening conditions: (a) monaural, with mild degradation in 1 ear; (b) binaural, with mild degradation in both ears (symmetric degradation); and…

  8. Mandarin recognition over the telephone

    NASA Astrophysics Data System (ADS)

    Kao, Yuhung

    1996-06-01

    Mandarin Chinese is the official language in China and Taiwan, it is the native language of a quarter of the world population. As the services enabled by speech recognition technology (e.g. telephone voice dialing, information query) become more popular in English, we would like to extend this capability to other languages. Mandarin is one of the major languages under research in our laboratory. This paper describes how we extend our work in English speech recognition into Mandarin. We will described the corpus: Voice Across Taiwan, the training of a complete set of Mandarin syllable models, preliminary performance results and error analysis. A fast prototyping system was built, where a user can write any context free grammar with no restriction of vocabulary, then the grammar can be compiled into recognition models. It enables user to quickly test the performance of a new vocabulary.

  9. Lesion Recognition and Cleavage by Endonuclease V

    PubMed Central

    Lin, Jun; Gao, Honghai; Schallhorn, Kathryn A.; Harris, Rebecca M.; Cao, Weiguo; Ke, Pu Chun

    2008-01-01

    Endonuclease V (endo V) recognizes and cleaves deoxyinosine in deaminated DNA. These enzymatic activities are precursors of DNA repair and are fueled by metal ions such as Ca2+ and Mg2+, with the former being associated with protein binding and the latter with DNA cleavage. Using the technique of fluorescence resonance energy transfer (FRET) we determined the single-molecule kinetics of endo V in a catalytic cycle using a substrate of deoxyinosine-containing single-stranded DNA (ssDNA). The ssDNA was labeled with TAMRA, a fluorescence donor, while the endo V was labeled with Cy5, a fluorescence acceptor. The time lapses of FRET, resulting from the sequential association, recognition, and dissociation of the deoxyinosine by the endo V, were determined at 5.9 s, 14.5 s, and 9.1 s, respectively, in the presence of Mg2+. In contrast, the process of deoxyinosine recognition appeared little affected by the metal type. The prolonged association and dissociation events in the presence of the Ca2+-Mg2+ combination, as compared to that of Mg2+ alone, support the hypothesis that endo V has two metal binding sites to regulate its enzymatic activities. PMID:17521169

  10. Syntactic neural network for character recognition

    NASA Astrophysics Data System (ADS)

    Jaravine, Viktor A.

    1992-08-01

    This article presents a synergism of syntactic 2-D parsing of images and multilayered, feed- forward network techniques. This approach makes it possible to build a written text reading system with absolute recognition rate for unambiguous text strings. The Syntactic Neural Network (SNN) is created during image parsing process by capturing the higher order statistical structure in the ensemble of input image examples. Acquired knowledge is stored in the form of hierarchical image elements dictionary and syntactic network. The number of hidden layers and neuron units is not fixed and is determined by the structural complexity of the teaching set. A proposed syntactic neuron differs from conventional numerical neuron by its symbolic input/output and usage of the dictionary for determining the output. This approach guarantees exact recognition of an image that is a combinatorial variation of the images from the training set. The system is taught to generalize and to make stochastic parsing of distorted and shifted patterns. The generalizations enables the system to perform continuous incremental optimization of its work. New image data learned by SNN doesn''t interfere with previously stored knowledge, thus leading to unlimited storage capacity of the network.

  11. Developing Signal-Pattern-Recognition Programs

    NASA Technical Reports Server (NTRS)

    Shelton, Robert O.; Hammen, David

    2006-01-01

    Pattern Interpretation and Recognition Application Toolkit Environment (PIRATE) is a block-oriented software system that aids the development of application programs that analyze signals in real time in order to recognize signal patterns that are indicative of conditions or events of interest. PIRATE was originally intended for use in writing application programs to recognize patterns in space-shuttle telemetry signals received at Johnson Space Center's Mission Control Center: application programs were sought to (1) monitor electric currents on shuttle ac power busses to recognize activations of specific power-consuming devices, (2) monitor various pressures and infer the states of affected systems by applying a Kalman filter to the pressure signals, (3) determine fuel-leak rates from sensor data, (4) detect faults in gyroscopes through analysis of system measurements in the frequency domain, and (5) determine drift rates in inertial measurement units by regressing measurements against time. PIRATE can also be used to develop signal-pattern-recognition software for different purposes -- for example, to monitor and control manufacturing processes.

  12. Familiar Person Recognition: Is Autonoetic Consciousness More Likely to Accompany Face Recognition Than Voice Recognition?

    NASA Astrophysics Data System (ADS)

    Barsics, Catherine; Brédart, Serge

    2010-11-01

    Autonoetic consciousness is a fundamental property of human memory, enabling us to experience mental time travel, to recollect past events with a feeling of self-involvement, and to project ourselves in the future. Autonoetic consciousness is a characteristic of episodic memory. By contrast, awareness of the past associated with a mere feeling of familiarity or knowing relies on noetic consciousness, depending on semantic memory integrity. Present research was aimed at evaluating whether conscious recollection of episodic memories is more likely to occur following the recognition of a familiar face than following the recognition of a familiar voice. Recall of semantic information (biographical information) was also assessed. Previous studies that investigated the recall of biographical information following person recognition used faces and voices of famous people as stimuli. In this study, the participants were presented with personally familiar people's voices and faces, thus avoiding the presence of identity cues in the spoken extracts and allowing a stricter control of frequency exposure with both types of stimuli (voices and faces). In the present study, the rate of retrieved episodic memories, associated with autonoetic awareness, was significantly higher from familiar faces than familiar voices even though the level of overall recognition was similar for both these stimuli domains. The same pattern was observed regarding semantic information retrieval. These results and their implications for current Interactive Activation and Competition person recognition models are discussed.

  13. Iris Recognition for Human Identification

    NASA Astrophysics Data System (ADS)

    Alandkar, Lajari; Gengaje, Sachin

    2010-11-01

    Iris recognition system is the biometric identification system. Iris has an intricate structure, uniqueness, stability, and natural protection. Due to these features of the iris it can be used for biometric identification. This system gives better performance than other biometric identification systems. A novel eyelash removal method for preprocessing of human iris images in a human iris recognition system is presented.. Discrete cosine transform (DCT) method is used for feature extraction. For matching of two-iris code Hamming distance calculation is used. EER value must be less for the optimum performance of the system.

  14. 31 CFR 223.12 - Recognition as reinsurer.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ..., and (5) Such other evidence as the Secretary of the Treasury may determine necessary to establish that.... branch of an alien company applying for such recognition shall file the following data with the Assistant... above all liabilities, and (2) Evidence satisfactory to the Secretary of the Treasury to establish...

  15. Video Educational Intervention Improves Reporting of Concussion and Symptom Recognition

    ERIC Educational Resources Information Center

    Hunt, Tamerah N.

    2015-01-01

    Context: Concussion management is potentially complicated by the lack of reporting due to poor educational intervention in youth athletics. Objective: Determine if a concussion-education video developed for high school athletes will increase the reporting of concussive injuries and symptom recognition in this group. Design: Cross-sectional,…

  16. Evolutionary-Rough Feature Selection for Face Recognition

    NASA Astrophysics Data System (ADS)

    Mazumdar, Debasis; Mitra, Soma; Mitra, Sushmita

    Elastic Bunch Graph Matching is a feature-based face recognition algorithm which has been used to determine facial attributes from an image. However the dimension of the feature vectors, in case of EBGM, is quite high. Feature selection is a useful preprocessing step for reducing dimensionality, removing irrelevant data, improving learning accuracy and enhancing output comprehensibility.

  17. Recognition of Emotions in Autism: A Formal Meta-Analysis

    ERIC Educational Resources Information Center

    Uljarevic, Mirko; Hamilton, Antonia

    2013-01-01

    Determining the integrity of emotion recognition in autistic spectrum disorder is important to our theoretical understanding of autism and to teaching social skills. Previous studies have reported both positive and negative results. Here, we take a formal meta-analytic approach, bringing together data from 48 papers testing over 980 participants…

  18. Guide to Prior Learning Assessment and Recognition at SIAST.

    ERIC Educational Resources Information Center

    Saskatchewan Inst. of Applied Science and Technology, Saskatoon.

    This guide describes the Saskatchewan Institute of Applied Science and Technology's (SIAST's) (Canada) Prior Learning Assessment and Recognition (PLAR) program. PLAR is an evaluation through a valid and reliable process of the knowledge and skills a student has learned through previous education, training, or experience, to determine the…

  19. Neural Correlates of Music Recognition in Down Syndrome

    ERIC Educational Resources Information Center

    Virji-Babul, N.; Moiseev, A.; Sun, W.; Feng, T.; Moiseeva, N.; Watt, K. J.; Huotilainen, M.

    2013-01-01

    The brain mechanisms that subserve music recognition remain unclear despite increasing interest in this process. Here we report the results of a magnetoencephalography experiment to determine the temporal dynamics and spatial distribution of brain regions activated during listening to a familiar and unfamiliar instrumental melody in control adults…

  20. Evaluating a county-based Healthy nail Salon Recognition Program

    EPA Science Inventory

    To determine whether nail solons that participate in the SF recognition program have reduced measured levels of toluene, methyl methacrylate (MMA), and total volatile organic compounds (TVOC)as compared to nail salons that do not participate. We also evaluated changes in worker ...

  1. Elements of the Word Recognition Process: A Two Part Study.

    ERIC Educational Resources Information Center

    Marzano, Robert J.; DiStefano, Philip

    There are basically two different models for the word recognition process. One model postulates that a reader primarily uses sound/symbol cues to recognize a word; a second model states that a reader focuses mainly on whole-word characteristics. To determine which model best fits beginning and adult readers, a multiple regression analysis was…

  2. Binary optical filters for scale invariant pattern recognition

    NASA Technical Reports Server (NTRS)

    Reid, Max B.; Downie, John D.; Hine, Butler P.

    1992-01-01

    Binary synthetic discriminant function (BSDF) optical filters which are invariant to scale changes in the target object of more than 50 percent are demonstrated in simulation and experiment. Efficient databases of scale invariant BSDF filters can be designed which discriminate between two very similar objects at any view scaled over a factor of 2 or more. The BSDF technique has considerable advantages over other methods for achieving scale invariant object recognition, as it also allows determination of the object's scale. In addition to scale, the technique can be used to design recognition systems invariant to other geometric distortions.

  3. Comparison of emotion recognition from facial expression and music.

    PubMed

    Gaspar, Tina; Labor, Marina; Jurić, Iva; Dumancić, Dijana; Ilakovac, Vesna; Heffer, Marija

    2011-01-01

    The recognition of basic emotions in everyday communication involves interpretation of different visual and auditory clues. The ability to recognize emotions is not clearly determined as their presentation is usually very short (micro expressions), whereas the recognition itself does not have to be a conscious process. We assumed that the recognition from facial expressions is selected over the recognition of emotions communicated through music. In order to compare the success rate in recognizing emotions presented as facial expressions or in classical music works we conducted a survey which included 90 elementary school and 87 high school students from Osijek (Croatia). The participants had to match 8 photographs of different emotions expressed on the face and 8 pieces of classical music works with 8 offered emotions. The recognition of emotions expressed through classical music pieces was significantly less successful than the recognition of emotional facial expressions. The high school students were significantly better at recognizing facial emotions than the elementary school students, whereas girls were better than boys. The success rate in recognizing emotions from music pieces was associated with higher grades in mathematics. Basic emotions are far better recognized if presented on human faces than in music, possibly because the understanding of facial emotions is one of the oldest communication skills in human society. Female advantage in emotion recognition was selected due to the necessity of their communication with the newborns during early development. The proficiency in recognizing emotional content of music and mathematical skills probably share some general cognitive skills like attention, memory and motivation. Music pieces were differently processed in brain than facial expressions and consequently, probably differently evaluated as relevant emotional clues.

  4. Enduring voice recognition in bonobos

    PubMed Central

    Keenan, Sumir; Mathevon, Nicolas; Stevens, Jeroen MG; Guéry, Jean Pascal; Zuberbühler, Klaus; Levréro, Florence

    2016-01-01

    Long-term social recognition is vital for species with complex social networks, where familiar individuals can encounter one another after long periods of separation. For non-human primates who live in dense forest environments, visual access to one another is often limited, and recognition of social partners over distances largely depends on vocal communication. Vocal recognition after years of separation has never been reported in any great ape species, despite their complex societies and advanced social intelligence. Here we show that bonobos, Pan paniscus, demonstrate reliable vocal recognition of social partners, even if they have been separated for five years. We experimentally tested bonobos’ responses to the calls of previous group members that had been transferred between captive groups. Despite long separations, subjects responded more intensely to familiar voices than to calls from unknown individuals - the first experimental evidence that bonobos can identify individuals utilising vocalisations even years after their last encounter. Our study also suggests that bonobos may cease to discriminate between familiar and unfamiliar individuals after a period of eight years, indicating that voice representations or interest could be limited in time in this species. PMID:26911199

  5. Interval Recognition in Minimal Context.

    ERIC Educational Resources Information Center

    Shatzkin, Merton

    1984-01-01

    Music majors were asked to identify interval when it was either preceded or followed by a tone moving in the same direction. Difficulties in interval recognition in context appear to be an effect not just of placement within the context or of tonality, but of particular combinations of these aspects. (RM)

  6. Response Reversals in Recognition Memory

    ERIC Educational Resources Information Center

    Van Zandt, Trisha; Maldonado-Molina, Mildred M.

    2004-01-01

    Using a dynamic sequential sampling model and a recently proposed model for confidence judgments in recognition memory (T. Van Zandt, 2000b), the authors examine the tendency for rememberers to reverse their responses after a primary decision. In 4 experiments, speeded "old"-"new" decisions were made under bias followed by a 2nd response', either…

  7. Letter Recognition and Sound Identification.

    ERIC Educational Resources Information Center

    Prior, Jennifer

    This lesson, which is most appropriate for kindergartners, reviews letter names and their sounds through a group letter recognition activity, a picture book activity, and alphabet practice with several online activities. During three 30-minute sessions, students will: identify the letters of the alphabet; identify the sounds of letters; identify…

  8. Intelligent Scene Analysis and Recognition

    DTIC Science & Technology

    2010-03-30

    in IEEE Conference on Computer Vision and Pattern Recognition, 2005, pp. 688–695. [15] J. Vogel and B. Schiele , “A semantic typicality measure for...Computer Vision, vol. 60, pp. 63–86, 2004. [54] M. Stark, M. Goesele, and B. Schiele , “A shape-based object class model for knowledge trans- fer,” in In

  9. Output Interference in Recognition Memory

    ERIC Educational Resources Information Center

    Criss, Amy H.; Malmberg, Kenneth J.; Shiffrin, Richard M.

    2011-01-01

    Dennis and Humphreys (2001) proposed that interference in recognition memory arises solely from the prior contexts of the test word: Interference does not arise from memory traces of other words (from events prior to the study list or on the study list, and regardless of similarity to the test item). We evaluate this model using output…

  10. Enduring voice recognition in bonobos.

    PubMed

    Keenan, Sumir; Mathevon, Nicolas; Stevens, Jeroen M G; Guéry, Jean Pascal; Zuberbühler, Klaus; Levréro, Florence

    2016-02-25

    Long-term social recognition is vital for species with complex social networks, where familiar individuals can encounter one another after long periods of separation. For non-human primates who live in dense forest environments, visual access to one another is often limited, and recognition of social partners over distances largely depends on vocal communication. Vocal recognition after years of separation has never been reported in any great ape species, despite their complex societies and advanced social intelligence. Here we show that bonobos, Pan paniscus, demonstrate reliable vocal recognition of social partners, even if they have been separated for five years. We experimentally tested bonobos' responses to the calls of previous group members that had been transferred between captive groups. Despite long separations, subjects responded more intensely to familiar voices than to calls from unknown individuals - the first experimental evidence that bonobos can identify individuals utilising vocalisations even years after their last encounter. Our study also suggests that bonobos may cease to discriminate between familiar and unfamiliar individuals after a period of eight years, indicating that voice representations or interest could be limited in time in this species.

  11. Kin recognition in Drosophila: the importance of ecology and gut microbiota.

    PubMed

    Lizé, Anne; McKay, Raegan; Lewis, Zenobia

    2014-02-01

    The animal gut commonly contains a large reservoir of symbiotic microbes. Although these microbes have obvious functions in digestion and immune defence, gut microbes can also affect behaviour. Here, we explore whether gut microbiota has a role in kin recognition. We assessed whether relatedness, familiarity and food eaten during development altered copulation investment in three species of Drosophila with diverse ecologies. We found that a monandrous species exhibited true kin recognition, whereas familiarity determined kin recognition in a species living in dense aggregations. Finally, in a food generalist species, food eaten during development masked kin recognition. The effect of food type on copulation duration, in addition to the removal of this effect via antibiotic treatment, suggests the influence of bacteria associated with the gut. Our results provide the first evidence that varied ecologically determined mechanisms of kin recognition occur in Drosophila, and that gut bacteria are likely to have a key role in these mechanisms.

  12. Low Energy Physical Activity Recognition System on Smartphones

    PubMed Central

    Morillo, Luis Miguel Soria; Gonzalez-Abril, Luis; Ramirez, Juan Antonio Ortega; de la Concepcion, Miguel Angel Alvarez

    2015-01-01

    An innovative approach to physical activity recognition based on the use of discrete variables obtained from accelerometer sensors is presented. The system first performs a discretization process for each variable, which allows efficient recognition of activities performed by users using as little energy as possible. To this end, an innovative discretization and classification technique is presented based on the χ2 distribution. Furthermore, the entire recognition process is executed on the smartphone, which determines not only the activity performed, but also the frequency at which it is carried out. These techniques and the new classification system presented reduce energy consumption caused by the activity monitoring system. The energy saved increases smartphone usage time to more than 27 h without recharging while maintaining accuracy. PMID:25742171

  13. A Taxonomy of 3D Occluded Objects Recognition Techniques

    NASA Astrophysics Data System (ADS)

    Soleimanizadeh, Shiva; Mohamad, Dzulkifli; Saba, Tanzila; Al-ghamdi, Jarallah Saleh

    2016-03-01

    The overall performances of object recognition techniques under different condition (e.g., occlusion, viewpoint, and illumination) have been improved significantly in recent years. New applications and hardware are shifted towards digital photography, and digital media. This faces an increase in Internet usage requiring object recognition for certain applications; particularly occulded objects. However occlusion is still an issue unhandled, interlacing the relations between extracted feature points through image, research is going on to develop efficient techniques and easy to use algorithms that would help users to source images; this need to overcome problems and issues regarding occlusion. The aim of this research is to review recognition occluded objects algorithms and figure out their pros and cons to solve the occlusion problem features, which are extracted from occluded object to distinguish objects from other co-existing objects by determining the new techniques, which could differentiate the occluded fragment and sections inside an image.

  14. Face recognition under variable illumination via sparse representation of patches

    NASA Astrophysics Data System (ADS)

    Fan, Shouke; Liu, Rui; Feng, Weiguo; Zhu, Ming

    2013-10-01

    The objective of this work is to recognize faces under variations in illumination. Previous works have indicated that the variations in illumination can dramatically reduce the performance of face recognition. To this end - ;an efficient method for face recognition which is robust under variable illumination is proposed in this paper. First of all, a discrete cosine transform(DCT) in the logarithm domain is employed to preprocess the images, removing the illumination variations by discarding an appropriate number of low-frequency DCT coefficients. Then, a face image is partitioned into several patches, and we classify the patches using Sparse Representation-based Classification, respectively. At last, the identity of a test image can be determined by the classification results of its patches. Experimental results on the Yale B database and the CMU PIE database show that excellent recognition rates can be achieved by the proposed method.

  15. DWT features performance analysis for automatic speech recognition of Urdu.

    PubMed

    Ali, Hazrat; Ahmad, Nasir; Zhou, Xianwei; Iqbal, Khalid; Ali, Sahibzada Muhammad

    2014-01-01

    This paper presents the work on Automatic Speech Recognition of Urdu language, using a comparative analysis for Discrete Wavelets Transform (DWT) based features and Mel Frequency Cepstral Coefficients (MFCC). These features have been extracted for one hundred isolated words of Urdu, each word uttered by ten different speakers. The words have been selected from the most frequently used words of Urdu. A variety of age and dialect has been covered by using a balanced corpus approach. After extraction of features, the classification has been achieved by using Linear Discriminant Analysis. After the classification task, the confusion matrix obtained for the DWT features has been compared with the one obtained for Mel-Frequency Cepstral Coefficients based speech recognition. The framework has been trained and tested for speech data recorded under controlled environments. The experimental results are useful in determination of the optimum features for speech recognition task.

  16. Object recognition memory in zebrafish.

    PubMed

    May, Zacnicte; Morrill, Adam; Holcombe, Adam; Johnston, Travis; Gallup, Joshua; Fouad, Karim; Schalomon, Melike; Hamilton, Trevor James

    2016-01-01

    The novel object recognition, or novel-object preference (NOP) test is employed to assess recognition memory in a variety of organisms. The subject is exposed to two identical objects, then after a delay, it is placed back in the original environment containing one of the original objects and a novel object. If the subject spends more time exploring one object, this can be interpreted as memory retention. To date, this test has not been fully explored in zebrafish (Danio rerio). Zebrafish possess recognition memory for simple 2- and 3-dimensional geometrical shapes, yet it is unknown if this translates to complex 3-dimensional objects. In this study we evaluated recognition memory in zebrafish using complex objects of different sizes. Contrary to rodents, zebrafish preferentially explored familiar over novel objects. Familiarity preference disappeared after delays of 5 mins. Leopard danios, another strain of D. rerio, also preferred the familiar object after a 1 min delay. Object preference could be re-established in zebra danios by administration of nicotine tartrate salt (50mg/L) prior to stimuli presentation, suggesting a memory-enhancing effect of nicotine. Additionally, exploration biases were present only when the objects were of intermediate size (2 × 5 cm). Our results demonstrate zebra and leopard danios have recognition memory, and that low nicotine doses can improve this memory type in zebra danios. However, exploration biases, from which memory is inferred, depend on object size. These findings suggest zebrafish ecology might influence object preference, as zebrafish neophobia could reflect natural anti-predatory behaviour.

  17. Hand Gesture Recognition Using Neural Networks.

    DTIC Science & Technology

    1996-05-01

    inherent in the model. The high gesture recognition rates and quick network retraining times found in the present study suggest that a neural network approach to gesture recognition be further evaluated.

  18. Method and System for Object Recognition Search

    NASA Technical Reports Server (NTRS)

    Duong, Tuan A. (Inventor); Duong, Vu A. (Inventor); Stubberud, Allen R. (Inventor)

    2012-01-01

    A method for object recognition using shape and color features of the object to be recognized. An adaptive architecture is used to recognize and adapt the shape and color features for moving objects to enable object recognition.

  19. Voice Recognition in Face-Blind Patients.

    PubMed

    Liu, Ran R; Pancaroglu, Raika; Hills, Charlotte S; Duchaine, Brad; Barton, Jason J S

    2016-04-01

    Right or bilateral anterior temporal damage can impair face recognition, but whether this is an associative variant of prosopagnosia or part of a multimodal disorder of person recognition is an unsettled question, with implications for cognitive and neuroanatomic models of person recognition. We assessed voice perception and short-term recognition of recently heard voices in 10 subjects with impaired face recognition acquired after cerebral lesions. All 4 subjects with apperceptive prosopagnosia due to lesions limited to fusiform cortex had intact voice discrimination and recognition. One subject with bilateral fusiform and anterior temporal lesions had a combined apperceptive prosopagnosia and apperceptive phonagnosia, the first such described case. Deficits indicating a multimodal syndrome of person recognition were found only in 2 subjects with bilateral anterior temporal lesions. All 3 subjects with right anterior temporal lesions had normal voice perception and recognition, 2 of whom performed normally on perceptual discrimination of faces. This confirms that such lesions can cause a modality-specific associative prosopagnosia.

  20. Educational interventions to improve recognition of delirium: a systematic review.

    PubMed

    Yanamadala, Mamata; Wieland, Darryl; Heflin, Mitchell T

    2013-11-01

    Delirium is a common and serious condition that is underrecognized in older adults in a variety of healthcare settings. It is poorly recognized because of deficiencies in provider knowledge and its atypical presentation. Early recognition of delirium is warranted to better manage the disease and prevent the adverse outcomes associated with it. The purpose of this article is to review the literature concerning educational interventions focusing on recognition of delirium. The Medline and Cumulative Index to Nursing and Allied Health Literature (CINHAL) databases were searched for studies with specific educational focus in the recognition of delirium, and 26 studies with various designs were identified. The types of interventions used were classified according to the Predisposing, Reinforcing and Enabling Constructs in Educational Diagnosis and Evaluation (PRECEDE) model, and outcomes were sorted according to Kirkpatrick's hierarchy. Educational strategies combining predisposing, enabling, and reinforcing factors achieved better results than strategies that included one or two of these components. Studies using predisposing, enabling, and reinforcing strategies together were more often effective in producing changes in staff behavior and participant outcomes. Based on this review, improvements in knowledge and skill alone seem insufficient to favorably influence recognition of delirium. Educational interventions to recognize delirium are most effective when formal teaching is interactive and is combined with strategies including engaging leadership and using clinical pathways and assessment tools. The goal of the current study was to systematically review the published literature to determine the effect of educational interventions on recognition of delirium.

  1. Dynamics of alpha oscillations elucidate facial affect recognition in schizophrenia.

    PubMed

    Popov, Tzvetan G; Rockstroh, Brigitte S; Popova, Petia; Carolus, Almut M; Miller, Gregory A

    2014-03-01

    Impaired facial affect recognition is characteristic of schizophrenia and has been related to impaired social function, but the relevant neural mechanisms have not been fully identified. The present study sought to identify the role of oscillatory alpha activity in that deficit during the process of facial emotion recognition. Neuromagnetic brain activity was monitored while 44 schizophrenia patients and 44 healthy controls viewed 5-s videos showing human faces gradually changing from neutral to fearful or happy expressions or from the neutral face of one poser to the neutral face of another. Recognition performance was determined separately by self-report. Relative to prestimulus baseline, controls exhibited a 10- to 15-Hz power increase prior to full recognition and a 10- to 15-Hz power decrease during the postrecognition phase. These results support recent proposals about the function of alpha-band oscillations in normal stimulus evaluation. The patients failed to show this sequence of alpha power increase and decrease and also showed low 10- to 15-Hz power and high 10- to 15-Hz connectivity during the prestimulus baseline. In light of the proposal that a combination of alpha power increase and functional disconnection facilitates information intake and processing, the finding of an abnormal association of low baseline alpha power and high connectivity in schizophrenia suggests a state of impaired readiness that fosters abnormal dynamics during facial affect recognition.

  2. Receptor recognition mechanisms of coronaviruses: a decade of structural studies.

    PubMed

    Li, Fang

    2015-02-01

    Receptor recognition by viruses is the first and essential step of viral infections of host cells. It is an important determinant of viral host range and cross-species infection and a primary target for antiviral intervention. Coronaviruses recognize a variety of host receptors, infect many hosts, and are health threats to humans and animals. The receptor-binding S1 subunit of coronavirus spike proteins contains two distinctive domains, the N-terminal domain (S1-NTD) and the C-terminal domain (S1-CTD), both of which can function as receptor-binding domains (RBDs). S1-NTDs and S1-CTDs from three major coronavirus genera recognize at least four protein receptors and three sugar receptors and demonstrate a complex receptor recognition pattern. For example, highly similar coronavirus S1-CTDs within the same genus can recognize different receptors, whereas very different coronavirus S1-CTDs from different genera can recognize the same receptor. Moreover, coronavirus S1-NTDs can recognize either protein or sugar receptors. Structural studies in the past decade have elucidated many of the puzzles associated with coronavirus-receptor interactions. This article reviews the latest knowledge on the receptor recognition mechanisms of coronaviruses and discusses how coronaviruses have evolved their complex receptor recognition pattern. It also summarizes important principles that govern receptor recognition by viruses in general.

  3. Tone recognition in continuous Cantonese speech using supratone models.

    PubMed

    Qian, Yao; Lee, Tan; Soong, Frank K

    2007-05-01

    This paper studies automatic tone recognition in continuous Cantonese speech. Cantonese is a major Chinese dialect that is known for being rich in tones. Tone information serves as a useful knowledge source for automatic speech recognition of Cantonese. Cantonese tone recognition is difficult because the tones have similar shapes of pitch contours. The tones are differentiated mainly by their relative pitch heights. In natural speech, the pitch level of a tone may shift up and down and the F0 ranges of different tones overlap with each other, making them acoustically indistinguishable within the domain of a syllable. Our study shows that the relative pitch heights are largely preserved between neighboring tones. A novel method of supratone modeling is proposed for Cantonese tone recognition. Each supratone model characterizes the F0 contour of two or three tones in succession. The tone sequence of a continuous utterance is formed as an overlapped concatenation of supratone units. The most likely tone sequence is determined under phonological constraints on syllable-tone combinations. The proposed method attains an accuracy of 74.68% in speaker-independent tone recognition experiments. In particular, the confusion among the tones with similar contour shapes is greatly resolved.

  4. Interaction of new sulfaphenazole derivatives with human liver cytochrome p450 2Cs: structural determinants required for selective recognition by CYP 2C9 and for inhibition of human CYP 2Cs.

    PubMed

    Ha-Duong, N T; Marques-Soares, C; Dijols, S; Sari, M A; Dansette, P M; Mansuy, D

    2001-10-15

    A series of new derivatives of sulfaphenazole (SPA), in which the NH(2) and phenyl substituents of SPA are replaced by various groups or in which the sulfonamide function of SPA is N-alkylated, were synthesized in order to further explore CYP 2C9 active site and to determine the structural factors explaining the selectivity of SPA for CYP 2C9 within the human P450 2C subfamily. Compounds in which the NH(2) group of SPA was replaced with R(1) = CH(3), Br, CH = CH(2), CH(2)CH = CH(2), and CH(2)CH(2)OH exhibited a high affinity for CYP 2C9, as shown by the dissociation constant of their CYP 2C9 complexes, K(s), which was determined by difference visible spectroscopy (K(s) between 0.1 and 0.4 microM) and their constant of CYP 2C9 inhibition (K(i) between 0.3 and 0.6 microM). This indicates that the CYP 2C9-iron(III)-NH(2)R bond previously described to exist in the CYP 2C9-SPA complex does not play a key role in the high affinity of SPA for CYP 2C9. Compounds in which the phenyl group of SPA was replaced with various aryl or alkyl R(2) substituents only exhibited a high affinity for CYP 2C9 if R(2) is a freely rotating and sufficiently electron-rich aryl substituent. Finally, compounds resulting from a N-alkylation of the SPA sulfonamide function (R(3) = CH(3), C(2)H(5), or C(3)H(7)) did not retain the selective inhibitory properties of SPA toward CYP 2C9. However, they are reasonably good inhibitors of CYP 2C8 and CYP 2C18 (IC(50) approximately 20 microM). These data allow one to better understand the structural factors that are important for selective binding in the CYP 2C9 active site. They also provide us with clues towards new selective inhibitors of CYP 2C8 and CYP 2C18.

  5. Determination of the utility of remote sensing data for land use/cover analysis in the lower Appalachia region: Assessing the utility of remote sensing data for archeological site recognition

    NASA Technical Reports Server (NTRS)

    Weber, N. V.

    1983-01-01

    Thematic Mapper Simulator (TMS) data were gathered by NASA/ERL over a portion of the lower Ohio River and the middle Mississippi River valleys on April 11, 1982. CIR imagery accompanied the 10 and 30 meter resolution TMS data sets. This area is somewhat unique archeologically as there exists a concentration of sites with major features such as mounds, earthworks, and villages. It was the primary purpose of this study to determine the utility of TMS data in identifying signatures which are distinctly archeological. TMS data were processed using the NASA/ERL software package ELAS. No signatures that were distinctly archeological were detected, due in large part to the complexity of the land cover and land use practices. However, as more sophisticated classification techniques were employed, the classes which were related to archeological features were narrowed. TMS data could certainly be of assistance to a trained archeologist/interpreter in narrowing an area which has to be field-surveyed as anomalous features can be recognized within a particular environmental context.

  6. Face age and sex modulate the other-race effect in face recognition.

    PubMed

    Wallis, Jennifer; Lipp, Ottmar V; Vanman, Eric J

    2012-11-01

    Faces convey a variety of socially relevant cues that have been shown to affect recognition, such as age, sex, and race, but few studies have examined the interactive effect of these cues. White participants of two distinct age groups were presented with faces that differed in race, age, and sex in a face recognition paradigm. Replicating the other-race effect, young participants recognized young own-race faces better than young other-race faces. However, recognition performance did not differ across old faces of different races (Experiments 1, 2A). In addition, participants showed an other-age effect, recognizing White young faces better than White old faces. Sex affected recognition performance only when age was not varied (Experiment 2B). Overall, older participants showed a similar recognition pattern (Experiment 3) as young participants, displaying an other-race effect for young, but not old, faces. However, they recognized young and old White faces on a similar level. These findings indicate that face cues interact to affect recognition performance such that age and sex information reliably modulate the effect of race cues. These results extend accounts of face recognition that explain recognition biases (such as the other-race effect) as a function of dichotomous ingroup/outgroup categorization, in that outgroup characteristics are not simply additive but interactively determine recognition performance.

  7. Automatic semantic feedback during visual word recognition.

    PubMed

    Reimer, Jason F; Lorsbach, Thomas C; Bleakney, Dana M

    2008-04-01

    Four experiments were conducted to determine whether semantic feedback spreads to orthographic and/or phonological representations during visual word recognition and whether such feedback occurs automatically. Three types of prime-target word pairs were used within the mediated-priming paradigm: (1) homophonically mediated (e.g.,frog-[toad]-towed), (2) orthographically mediated (e.g.,frog-[toad]-told), and (3) associatively related (e.g.,frog-toad). Using both brief (53 msec; Experiment 1) and long (413 msec; Experiment 3) prime exposure durations, significant facilitatory-priming effects were found in the response time data with orthographically, but not homophonically, mediated prime-target word pairs. When the prime exposure duration was shortened to 33 msec in Experiment 4, however, facilitatory priming was absent with both orthographically and homophonically mediated word pairs. In addition, with a brief (53-msec) prime exposure duration, direct-priming effects were found with associatively (e.g.,frog-toad), orthographically (e.g., toad-told), and homophonically (e.g., toad-towed) related word pairs in Experiment 2. Taken together, these results indicate that following the initial activation of semantic representations, activation automatically feeds back to orthographic, but not phonological, representations during the early stages of word processing. These findings were discussed in the context of current accounts of visual word recognition.

  8. Continuous speech recognition for clinicians.

    PubMed

    Zafar, A; Overhage, J M; McDonald, C J

    1999-01-01

    The current generation of continuous speech recognition systems claims to offer high accuracy (greater than 95 percent) speech recognition at natural speech rates (150 words per minute) on low-cost (under $2000) platforms. This paper presents a state-of-the-technology summary, along with insights the authors have gained through testing one such product extensively and other products superficially. The authors have identified a number of issues that are important in managing accuracy and usability. First, for efficient recognition users must start with a dictionary containing the phonetic spellings of all words they anticipate using. The authors dictated 50 discharge summaries using one inexpensive internal medicine dictionary ($30) and found that they needed to add an additional 400 terms to get recognition rates of 98 percent. However, if they used either of two more expensive and extensive commercial medical vocabularies ($349 and $695), they did not need to add terms to get a 98 percent recognition rate. Second, users must speak clearly and continuously, distinctly pronouncing all syllables. Users must also correct errors as they occur, because accuracy improves with error correction by at least 5 percent over two weeks. Users may find it difficult to train the system to recognize certain terms, regardless of the amount of training, and appropriate substitutions must be created. For example, the authors had to substitute "twice a day" for "bid" when using the less expensive dictionary, but not when using the other two dictionaries. From trials they conducted in settings ranging from an emergency room to hospital wards and clinicians' offices, they learned that ambient noise has minimal effect. Finally, they found that a minimal "usable" hardware configuration (which keeps up with dictation) comprises a 300-MHz Pentium processor with 128 MB of RAM and a "speech quality" sound card (e.g., SoundBlaster, $99). Anything less powerful will result in the system lagging

  9. Continuous Speech Recognition for Clinicians

    PubMed Central

    Zafar, Atif; Overhage, J. Marc; McDonald, Clement J.

    1999-01-01

    The current generation of continuous speech recognition systems claims to offer high accuracy (greater than 95 percent) speech recognition at natural speech rates (150 words per minute) on low-cost (under $2000) platforms. This paper presents a state-of-the-technology summary, along with insights the authors have gained through testing one such product extensively and other products superficially. The authors have identified a number of issues that are important in managing accuracy and usability. First, for efficient recognition users must start with a dictionary containing the phonetic spellings of all words they anticipate using. The authors dictated 50 discharge summaries using one inexpensive internal medicine dictionary ($30) and found that they needed to add an additional 400 terms to get recognition rates of 98 percent. However, if they used either of two more expensive and extensive commercial medical vocabularies ($349 and $695), they did not need to add terms to get a 98 percent recognition rate. Second, users must speak clearly and continuously, distinctly pronouncing all syllables. Users must also correct errors as they occur, because accuracy improves with error correction by at least 5 percent over two weeks. Users may find it difficult to train the system to recognize certain terms, regardless of the amount of training, and appropriate substitutions must be created. For example, the authors had to substitute “twice a day” for “bid” when using the less expensive dictionary, but not when using the other two dictionaries. From trials they conducted in settings ranging from an emergency room to hospital wards and clinicians' offices, they learned that ambient noise has minimal effect. Finally, they found that a minimal “usable” hardware configuration (which keeps up with dictation) comprises a 300-MHz Pentium processor with 128 MB of RAM and a “speech quality” sound card (e.g., SoundBlaster, $99). Anything less powerful will result in

  10. Famous face recognition, face matching, and extraversion.

    PubMed

    Lander, Karen; Poyarekar, Siddhi

    2015-01-01

    It has been previously established that extraverts who are skilled at interpersonal interaction perform significantly better than introverts on a face-specific recognition memory task. In our experiment we further investigate the relationship between extraversion and face recognition, focusing on famous face recognition and face matching. Results indicate that more extraverted individuals perform significantly better on an upright famous face recognition task and show significantly larger face inversion effects. However, our results did not find an effect of extraversion on face matching or inverted famous face recognition.

  11. Quantum-Limited Image Recognition

    DTIC Science & Technology

    1989-12-01

    middle of the range, as was done here. This accounts for the majority of the error between thoery and experiment shown in Figs. 5.5 and 5.6. Note that even... USERS Unclassified 22a. NAME OF RESPONSIBLE INDIVIDUAL 22b. TELEPHONE (Include Area Code) 22c. OFFICE SYMBOL G. Michael Morris 716-275-5140 D0 FORM...utilized in a cluttered environment. iv The estimation of moment invariants for image recognition is also considered. Experiments are performed that

  12. Speech Recognition in 7 Languages

    DTIC Science & Technology

    2000-08-01

    best monolingual cross-lingual [10] F. Weng, H. Bratt, L. Neumeyer, and A. Stol- recognizers could not always be tested. cke. A Study of Multilingual ...are r the same tm the proaches, namely portation, cross-lingual and simul- two languages are recognized at the same time, the taneous multilingual ...in cross-lingual will present experiments and results for different ap- recognition for different baseline systems and found proaches of multilingual

  13. Receptive Field Structures for Recognition

    DTIC Science & Technology

    2005-03-01

    that such statistics might be useful for pattern recognition is not new, indeed Julesz (Julesz 1975) suggested that ‘ needle statistics’ could be useful...Gaussians to be manipulated independently of either one’s spatial constant (Figure 4) In so doing, we lose the ability to create ‘ steerable ’ filters...the goal of sensory coding?" Neural Computation 6: 559-601. Freeman, W. T. and E. H. Adelson (1991). "The design and use of steerable filters

  14. Immune recognition of protein antigens

    SciTech Connect

    Laver, W.G.; Air, G.M.

    1985-01-01

    This book contains 33 papers. Some of the titles are: Antigenic Structure of Influenze Virus Hemagglutinin; Germ-line and Somatic Diversity in the Antibody Response to the Influenza Virus A/PR/8/34 Hemagglutinin; Recognition of Cloned Influenza A Virus Gene Products by Cytotoxic T Lymphocytes; Antigenic Structure of the Influenza Virus N2 Neuraminidase; and The Molecular and Genetic Basis of Antigenic Variation in Gonococcal Pillin.

  15. Perceptual Organization and Visual Recognition

    DTIC Science & Technology

    1984-09-01

    spatial relations are detected directly amtong two-dimensional image features. A basic requirement of the recognition process is that perceptual organi... excellent facilities that made this work possible, and made many important contributions to the content of this thesis. Chapter 5 is based largely on his...Mackworth, who gave me an excellent grounding in computer vision while I was an undergraduatc at the University of British Columbia and has continued

  16. A novel fingerprint recognition algorithm based on VK-LLE

    NASA Astrophysics Data System (ADS)

    Luo, Jing; Lin, Shu-zhong; Ni, Jian-yun; Song, Li-mei

    2009-07-01

    It is a challenging problem to overcome shift and rotation and nonlinearity in fingerprint images. By analyzing the shortcoming of fingerprint recognition algorithm on shift or rotation images at present, manifold learning algorithm is introduced. A fingerprint recognition algorithm has been proposed based on locally linear embedding of variable neighbourhood k (VK-LLE). Firstly, approximate geodesic distance between any two points is computed by ISOMAP ( isometric feature mapping) and then the neighborhood is determined for each point by the relationship between its local estimated geodesic distance matrix and local Euclidean distance matrix. Secondly, the dimension of fingerprint image is reduced by nonlinear dimension-reduction method. And the best projected features of original fingerprint data of large dimension are acquired. By analyzing the changes of recognition accuracy with the neighborhood and embedding dimension, the neighborhood and embedding dimension is determined at last. Finally, fingerprint recognition is accomplished by Euclidean distance Classifier. The experimental results based on standard fingerprint datasets have verified the proposed algorithm had a better robustness to those fingerprint images of shift or rotation or nonlinearity than the algorithm using LLE, thus this method has some values in practice.

  17. Gender recognition from vocal source

    NASA Astrophysics Data System (ADS)

    Sorokin, V. N.; Makarov, I. S.

    2008-07-01

    Efficiency of automatic recognition of male and female voices based on solving the inverse problem for glottis area dynamics and for waveform of the glottal airflow volume velocity pulse is studied. The inverse problem is regularized through the use of analytical models of the voice excitation pulse and of the dynamics of the glottis area, as well as the model of one-dimensional glottal airflow. Parameters of these models and spectral parameters of the volume velocity pulse are considered. The following parameters are found to be most promising: the instant of maximum glottis area, the maximum derivative of the area, the slope of the spectrum of the glottal airflow volume velocity pulse, the amplitude ratios of harmonics of this spectrum, and the pitch. On the plane of the first two main components in the space of these parameters, an almost twofold decrease in the classification error relative to that for the pitch alone is attained. The male voice recognition probability is found to be 94.7%, and the female voice recognition probability is 95.9%.

  18. Face Recognition Incorporating Ancillary Information

    NASA Astrophysics Data System (ADS)

    Kim, Sang-Ki; Toh, Kar-Ann; Lee, Sangyoun

    2007-12-01

    Due to vast variations of extrinsic and intrinsic imaging conditions, face recognition remained to be a challenging computer vision problem even today. This is particularly true when the passive imaging approach is considered for robust applications. To advance existing recognition systems for face, numerous techniques and methods have been proposed to overcome the almost inevitable performance degradation due to external factors such as pose, expression, occlusion, and illumination. In particular, the recent part-based method has provided noticeable room for verification performance improvement based on the localized features which have good tolerance to variation of external conditions. The part-based method, however, does not really stretch the performance without incorporation of global information from the holistic method. In view of the need to fuse the local information and the global information in an adaptive manner for reliable recognition, in this paper we investigate whether such external factors can be explicitly estimated and be used to boost the verification performance during fusion of the holistic and part-based methods. Our empirical evaluations show noticeable performance improvement adopting the proposed method.

  19. Fingerprint recognition using image processing

    NASA Astrophysics Data System (ADS)

    Dholay, Surekha; Mishra, Akassh A.

    2011-06-01

    Finger Print Recognition is concerned with the difficult task of matching the images of finger print of a person with the finger print present in the database efficiently. Finger print Recognition is used in forensic science which helps in finding the criminals and also used in authentication of a particular person. Since, Finger print is the only thing which is unique among the people and changes from person to person. The present paper describes finger print recognition methods using various edge detection techniques and also how to detect correct finger print using a camera images. The present paper describes the method that does not require a special device but a simple camera can be used for its processes. Hence, the describe technique can also be using in a simple camera mobile phone. The various factors affecting the process will be poor illumination, noise disturbance, viewpoint-dependence, Climate factors, and Imaging conditions. The described factor has to be considered so we have to perform various image enhancement techniques so as to increase the quality and remove noise disturbance of image. The present paper describe the technique of using contour tracking on the finger print image then using edge detection on the contour and after that matching the edges inside the contour.

  20. Automatic speech recognition technology development at ITT Defense Communications Division

    NASA Technical Reports Server (NTRS)

    White, George M.

    1977-01-01

    An assessment of the applications of automatic speech recognition to defense communication systems is presented. Future research efforts include investigations into the following areas: (1) dynamic programming; (2) recognition of speech degraded by noise; (3) speaker independent recognition; (4) large vocabulary recognition; (5) word spotting and continuous speech recognition; and (6) isolated word recognition.

  1. Infant visual attention and object recognition.

    PubMed

    Reynolds, Greg D

    2015-05-15

    This paper explores the role visual attention plays in the recognition of objects in infancy. Research and theory on the development of infant attention and recognition memory are reviewed in three major sections. The first section reviews some of the major findings and theory emerging from a rich tradition of behavioral research utilizing preferential looking tasks to examine visual attention and recognition memory in infancy. The second section examines research utilizing neural measures of attention and object recognition in infancy as well as research on brain-behavior relations in the early development of attention and recognition memory. The third section addresses potential areas of the brain involved in infant object recognition and visual attention. An integrated synthesis of some of the existing models of the development of visual attention is presented which may account for the observed changes in behavioral and neural measures of visual attention and object recognition that occur across infancy.

  2. Fragrant pear sexuality recognition with machine vision

    NASA Astrophysics Data System (ADS)

    Ma, Benxue; Ying, Yibin

    2006-10-01

    In this research, a method to identify Kuler fragrant pear's sexuality with machine vision was developed. Kuler fragrant pear has male pear and female pear. They have an obvious difference in favor. To detect the sexuality of Kuler fragrant pear, images of fragrant pear were acquired by CCD color camera. Before feature extraction, some preprocessing is conducted on the acquired images to remove noise and unnecessary contents. Color feature, perimeter feature and area feature of fragrant pear bottom image were extracted by digital image processing technique. And the fragrant pear sexuality was determined by complexity obtained from perimeter and area. In this research, using 128 Kurle fragrant pears as samples, good recognition rate between the male pear and the female pear was obtained for Kurle pear's sexuality detection (82.8%). Result shows this method could detect male pear and female pear with a good accuracy.

  3. Acquired prosopagnosia without word recognition deficits.

    PubMed

    Susilo, Tirta; Wright, Victoria; Tree, Jeremy J; Duchaine, Bradley

    2015-01-01

    It has long been suggested that face recognition relies on specialized mechanisms that are not involved in visual recognition of other object categories, including those that require expert, fine-grained discrimination at the exemplar level such as written words. But according to the recently proposed many-to-many theory of object recognition (MTMT), visual recognition of faces and words are carried out by common mechanisms [Behrmann, M., & Plaut, D. C. ( 2013 ). Distributed circuits, not circumscribed centers, mediate visual recognition. Trends in Cognitive Sciences, 17, 210-219]. MTMT acknowledges that face and word recognition are lateralized, but posits that the mechanisms that predominantly carry out face recognition still contribute to word recognition and vice versa. MTMT makes a key prediction, namely that acquired prosopagnosics should exhibit some measure of word recognition deficits. We tested this prediction by assessing written word recognition in five acquired prosopagnosic patients. Four patients had lesions limited to the right hemisphere while one had bilateral lesions with more pronounced lesions in the right hemisphere. The patients completed a total of seven word recognition tasks: two lexical decision tasks and five reading aloud tasks totalling more than 1200 trials. The performances of the four older patients (3 female, age range 50-64 years) were compared to those of 12 older controls (8 female, age range 56-66 years), while the performances of the younger prosopagnosic (male, 31 years) were compared to those of 14 younger controls (9 female, age range 20-33 years). We analysed all results at the single-patient level using Crawford's t-test. Across seven tasks, four prosopagnosics performed as quickly and accurately as controls. Our results demonstrate that acquired prosopagnosia can exist without word recognition deficits. These findings are inconsistent with a key prediction of MTMT. They instead support the hypothesis that face

  4. Breaking Object Correspondence Across Saccadic Eye Movements Deteriorates Object Recognition.

    PubMed

    Poth, Christian H; Herwig, Arvid; Schneider, Werner X

    2015-01-01

    Visual perception is based on information processing during periods of eye fixations that are interrupted by fast saccadic eye movements. The ability to sample and relate information on task-relevant objects across fixations implies that correspondence between presaccadic and postsaccadic objects is established. Postsaccadic object information usually updates and overwrites information on the corresponding presaccadic object. The presaccadic object representation is then lost. In contrast, the presaccadic object is conserved when object correspondence is broken. This helps transsaccadic memory but it may impose attentional costs on object recognition. Therefore, we investigated how breaking object correspondence across the saccade affects postsaccadic object recognition. In Experiment 1, object correspondence was broken by a brief postsaccadic blank screen. Observers made a saccade to a peripheral object which was displaced during the saccade. This object reappeared either immediately after the saccade or after the blank screen. Within the postsaccadic object, a letter was briefly presented (terminated by a mask). Observers reported displacement direction and letter identity in different blocks. Breaking object correspondence by blanking improved displacement identification but deteriorated postsaccadic letter recognition. In Experiment 2, object correspondence was broken by changing the object's contrast-polarity. There were no object displacements and observers only reported letter identity. Again, breaking object correspondence deteriorated postsaccadic letter recognition. These findings identify transsaccadic object correspondence as a key determinant of object recognition across the saccade. This is in line with the recent hypothesis that breaking object correspondence results in separate representations of presaccadic and postsaccadic objects which then compete for limited attentional processing resources (Schneider, 2013). Postsaccadic object recognition is

  5. Definition of the extended substrate specificity determinants for beta-tryptases I and II.

    PubMed

    Harris, J L; Niles, A; Burdick, K; Maffitt, M; Backes, B J; Ellman, J A; Kuntz, I; Haak-Frendscho, M; Craik, C S

    2001-09-14

    Tryptases betaI and betaII were heterologously expressed and purified in yeast to functionally characterize the substrate specificity of each enzyme. Three positional scanning combinatorial tetrapeptide substrate libraries were used to determine the primary and extended substrate specificity of the proteases. Both enzymes have a strict primary preference for cleavage after the basic amino acids, lysine and arginine, with only a slight preference for lysine over arginine. betaI and betaII tryptase share similar extended substrate specificity, with preference for proline at P4, preference for arginine or lysine at P3, and P2 showing a slight preference for asparagine. Measurement of kinetic constants with multiple substrates designed for beta-tryptases reveal that selectivity is highly dependent on ground state substrate binding. Coupled with the functional determinants, structural determinants of tryptase substrate specificity were identified. Molecular docking of the preferred substrate sequence to the three-dimensional tetrameric tryptase structure reveals a novel extended substrate binding mode that involves interactions from two adjacent protomers, including P4 Thr-96', P3 Asp-60B' and Glu-217, and P1 Asp-189. Based on the determined substrate information, a mechanism-based tetrapeptide-chloromethylketone inhibitor was designed and shown to be a potent tryptase inhibitor. Finally, the cleavage sites of several physiologically relevant substrates of beta-tryptases show consistency with the specificity data presented here.

  6. Emotion recognition deficits in eating disorders are explained by co-occurring alexithymia

    PubMed Central

    Brewer, Rebecca; Cook, Richard; Cardi, Valentina; Treasure, Janet; Bird, Geoffrey

    2015-01-01

    Previous research has yielded inconsistent findings regarding the ability of individuals with eating disorders (EDs) to recognize facial emotion, making the clinical features of this population hard to determine. This study tested the hypothesis that where observed, emotion recognition deficits exhibited by patients with EDs are due to alexithymia, a co-occurring condition also associated with emotion recognition difficulties. Ability to recognize facial emotion was investigated in a sample of individuals with EDs and varying degrees of co-occurring alexithymia, and an alexithymia-matched control group. Alexithymia, but not ED symptomology, was predictive of individuals' emotion recognition ability, inferred from tolerance to high-frequency visual noise. This relationship was specific to emotion recognition, as neither alexithymia nor ED symptomology was associated with ability to recognize facial identity. These findings suggest that emotion recognition difficulties exhibited by patients with ED are attributable to alexithymia, and may not be a feature of EDs per se. PMID:26064585

  7. A study on target recognition fusion algorithm based on fuzzy theory

    NASA Astrophysics Data System (ADS)

    Han, Feng; Yang, WanHai

    2008-03-01

    In the process of the multi-sensors target recognition fusion, focused on the problem that it is difficult to determine the reliability of each sensor and how the data measured by different sensors are fused, a multi-sensor target recognition fusion method based on fuzzy theory is proposed. The mutual supportability of multiple sensors is obtained from the correlation function. Then by the membership function, the reliability of information provide by each sensor is gained. Finally, the supposed fusion result of multi-sensors target recognition can be produced on the basis of fuzzy integration function. The method is simple computationally and can objectively reflect the reliability of each sensor and interrelationship between these sensors. By applying the method to the target recognition, the simulation experiment shows that it can identify the target accurately and is an effective and feasible multi-sensors target recognition fusion method.

  8. Identification of off-target cleavage sites of zinc finger nucleases and TAL effector nucleases using predictive models.

    PubMed

    Fine, Eli J; Cradick, Thomas J; Bao, Gang

    2014-01-01

    Using engineered nucleases, such as Zinc Finger Nucleases (ZFNs) or Transcription Activator-Like Effector Nucleases (TALENs), to make targeted genomic modifications has become a common technique to create new model organisms and custom cell lines, and has shown great promise for disease treatment. However, these nucleases have the potential for off-target cleavage that could confound interpretation of experimental results and be detrimental for therapeutic use. Here, we describe a method to test for nuclease cleavage at potential off-target sites predicted by bioinformatics models.

  9. A targeted mutation at the known collagenase cleavage site in mouse type I collagen impairs tissue remodeling

    PubMed Central

    1995-01-01

    Degradation of type I collagen, the most abundant collagen, is initiated by collagenase cleavage at a highly conserved site between Gly775 and Ile776 of the alpha 1 (I) chain. Mutations at or around this site render type I collagen resistant to collagenase digestion in vitro. We show here that mice carrying a collagenase-resistant mutant Col1a-1 transgene die late in embryo-genesis, ascribable to overexpression of the transgene, since the same mutation introduced into the endogenous Col1a-1 gene by gene targeting permitted normal development of mutant mice to young adulthood. With increasing age, animals carrying the targeted mutation developed marked fibrosis of the dermis similar to that in human scleroderma. Postpartum involution of the uterus in the mutant mice was also impaired, with persistence of collagenous nodules in the uterine wall. Although type I collagen from the homozygous mutant mice was resistant to cleavage by human or rat fibroblast collagenases at the helical site, only the rat collagenase cleaved collagen trimers at an additional, novel site in the nonhelical N-telopeptide domain. Our results suggest that cleavage by murine collagenase at the N-telopeptide site could account for resorption of type I collagen during embryonic and early adult life. During intense collagen resorption, however, such as in the immediate postpartum uterus and in the dermis later in life, cleavage at the helical site is essential for normal collagen turnover. Thus, type I collagen is degraded by at least two differentially controlled mechanisms involving collagenases with distinct, but overlapping, substrate specificities. PMID:7790374

  10. The first crystal structure of human RNase 6 reveals a novel substrate-binding and cleavage site arrangement

    PubMed Central

    Prats-Ejarque, Guillem; Arranz-Trullén, Javier; Blanco, Jose A.; Pulido, David; Nogués, M. Victòria; Moussaoui, Mohammed; Boix, Ester

    2016-01-01

    Human RNase 6 is a cationic secreted protein that belongs to the RNase A superfamily. Its expression is induced in neutrophils and monocytes upon bacterial infection, suggesting a role in host defence. We present here the crystal structure of RNase 6 obtained at 1.72 Å (1 Å=0.1 nm) resolution, which is the first report for the protein 3D structure and thereby setting the basis for functional studies. The structure shows an overall kidney-shaped globular fold shared with the other known family members. Three sulfate anions bound to RNase 6 were found, interacting with residues at the main active site (His15, His122 and Gln14) and cationic surface-exposed residues (His36, His39, Arg66 and His67). Kinetic characterization, together with prediction of protein–nucleotide complexes by molecular dynamics, was applied to analyse the RNase 6 substrate nitrogenous base and phosphate selectivity. Our results reveal that, although RNase 6 is a moderate catalyst in comparison with the pancreatic RNase type, its structure includes lineage-specific features that facilitate its activity towards polymeric nucleotide substrates. In particular, enzyme interactions at the substrate 5′ end can provide an endonuclease-type cleavage pattern. Interestingly, the RNase 6 crystal structure revealed a novel secondary active site conformed by the His36–His39 dyad that facilitates the polynucleotide substrate catalysis. PMID:27013146

  11. Expression of heterologous proteins flanked by NS3-4A cleavage sites within the hepatitis C virus polyprotein.

    PubMed

    Horwitz, Joshua A; Dorner, Marcus; Friling, Tamar; Donovan, Bridget M; Vogt, Alexander; Loureiro, Joana; Oh, Thomas; Rice, Charles M; Ploss, Alexander

    2013-04-25

    Hepatitis C virus (HCV) contributes substantially to human morbidity and mortality world-wide. The development of HCV genomes expressing heterologous proteins has enhanced the ability to study viral infection, but existing systems have drawbacks. Recombinant viruses often require adaptive mutations to compensate for reduced viral titers, or rely on an artificial genomic organization that uncouples viral protein expression from recombinant gene expression. Here, we sought to exploit the viral polyprotein processing machinery to express heterologous proteins within the context of the HCV polyprotein. We show that HCV genotypes 2a and 1b permit insertion of reporter proteins between NS5A and NS5B with minimal impact on viral fitness. Using this strategy we constructed reporter genomes exhibiting a wide dynamic range, simplifying analysis of HCV infection in primary hepatocytes. Expression of heterologous proteins within the HCV genome offers new opportunities to analyze HCV infection in experimental systems without perturbing functions of individual viral proteins.

  12. RNA Sequencing Identifies New RNase III Cleavage Sites in Escherichia coli and Reveals Increased Regulation of mRNA

    PubMed Central

    Gordon, Gina C.; Cameron, Jeffrey C.

    2017-01-01

    ABSTRACT Ribonucleases facilitate rapid turnover of RNA, providing cells with another mechanism to adjust transcript and protein levels in response to environmental conditions. While many examples have been documented, a comprehensive list of RNase targets is not available. To address this knowledge gap, we compared levels of RNA sequencing coverage of Escherichia coli and a corresponding RNase III mutant to expand the list of known RNase III targets. RNase III is a widespread endoribonuclease that binds and cleaves double-stranded RNA in many critical transcripts. RNase III cleavage at novel sites found in aceEF, proP, tnaC, dctA, pheM, sdhC, yhhQ, glpT, aceK, and gluQ accelerated RNA decay, consistent with previously described targets wherein RNase III cleavage initiates rapid degradation of secondary messages by other RNases. In contrast, cleavage at three novel sites in the ahpF, pflB, and yajQ transcripts led to stabilized secondary transcripts. Two other novel sites in hisL and pheM overlapped with transcriptional attenuators that likely serve to ensure turnover of these highly structured RNAs. Many of the new RNase III target sites are located on transcripts encoding metabolic enzymes. For instance, two novel RNase III sites are located within transcripts encoding enzymes near a key metabolic node connecting glycolysis and the tricarboxylic acid (TCA) cycle. Pyruvate dehydrogenase activity was increased in an rnc deletion mutant compared to the wild-type (WT) strain in early stationary phase, confirming the novel link between RNA turnover and regulation of pathway activity. Identification of these novel sites suggests that mRNA turnover may be an underappreciated mode of regulating metabolism. PMID:28351917

  13. Familial Alzheimer’s mutations within APPTM increase Aβ42 production by enhancing accessibility of ɛ-cleavage site

    NASA Astrophysics Data System (ADS)

    Chen, Wen; Gamache, Eric; Rosenman, David J.; Xie, Jian; Lopez, Maria M.; Li, Yue-Ming; Wang, Chunyu

    2014-01-01

    The high Aβ42/Aβ40 production ratio is a hallmark of familial Alzheimer’s disease, which can be caused by mutations in the amyloid precursor protein (APP). The C-terminus of Aβ is generated by γ-secretase cleavage within the transmembrane domain of APP (APPTM), a process that is primed by an initial ɛ-cleavage at either T48 or L49, resulting in subsequent production of Aβ42 or Aβ40, respectively. Here we solve the dimer structures of wild-type APPTM (AAPTM WT) and mutant APPTM (FAD mutants V44M) with solution NMR. The right-handed APPTM helical dimer is mediated by GXXXA motif. From the NMR structural and dynamic data, we show that the V44M and V44A mutations can selectively expose the T48 site by weakening helical hydrogen bonds and increasing hydrogen-deuterium exchange rate (kex). We propose a structural model in which FAD mutations (V44M and V44A) can open the T48 site γ-secretase for the initial ɛ-cleavage, and consequently shift cleavage preference towards Aβ42.

  14. Different cleavage site for high molecular weight kininogen in vivo following intravenous injection of dextran sulfate in the rabbit

    SciTech Connect

    Wiggins, R.C.

    1986-04-01

    Purified radiolabeled rabbit Hageman factor, prekallikrein, and high molecular weight kininogen were used to examine Hageman factor system molecular dynamics after the intravenous injection of heparin-like dextran sulfate polymer in the rabbit. Hageman factor system proteins rapidly disappeared from the circulation following dextran sulfate injection, as measured by radial immunodiffusion, by kaolin-releasable kinin formation, and by measuring circulating levels of radiolabeled Hageman factor, prekallikrein, and high molecular weight kininogen. /sup 125/I-Hageman factor was distributed mainly to lung, liver, and spleen following dextran sulfate injection. Proteolysis of circulating /sup 125/I-Hageman factor occurred at a site within a disulfide loop into fragments of 50,000 and 30,000 molecular weight. Proteolysis of /sup 125/I-prekallikrein also occurred with visualization of a 50,000 molecular weight fragment. Although extensive proteolysis of /sup 131/I-high molecular weight kininogen was observed, the cleavage fragments were not the same as those generated during contact activation in vitro. The major fragment of high molecular weight kininogen observed in vivo was at 80,000 molecular weight, in contrast to the 65,000 molecular weight fragment generated by kallikrein in vitro. These results indicate that high molecular weight kininogen can undergo proteolysis in vivo into fragments not known to be associated with kinin release.

  15. Novel factor VIII variants with a modified furin cleavage site improve the efficacy of gene therapy for hemophilia A.

    PubMed

    Nguyen, G N; George, L A; Siner, J I; Davidson, R J; Zander, C B; Zheng, X L; Arruda, V R; Camire, R M; Sabatino, D E

    2017-01-01

    Essentials Factor (F) VIII is an inefficiently expressed protein. Furin deletion FVIII variants were purified and characterized using in vitro and in vivo assays. These minimally modified novel FVIII variants have enhanced function. These variants provide a strategy for increasing FVIII expression in hemophilia A gene therapy.

  16. Molecular determinants of pathogen recognition and defense elicitation in potato

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The potato late blight pathogen, Phytophthora infestans, is able to rapidly evolve to overcome resistance genes. The pathogen accomplishes this by secreting an arsenal of proteins, termed effectors, that function to modify host cells. Although hundreds of candidate effectors have been identified in ...

  17. Recognition.

    ERIC Educational Resources Information Center

    Bowen, John; Wildasin, Michael; Chaltain, Sam

    2002-01-01

    Tells about schools rewarded for upholding First Amendment protections. Discusses the Let Freedom Ring Award. Considers how even the prestige and honor associated with winning national awards for freedom in the schools does not guarantee success in the ongoing fight to practice what the United States Constitution guarantees and educational logic…

  18. Training industrial robots with gesture recognition techniques

    NASA Astrophysics Data System (ADS)

    Piane, Jennifer; Raicu, Daniela; Furst, Jacob

    2013-01-01

    In this paper we propose to use gesture recognition approaches to track a human hand in 3D space and, without the use of special clothing or markers, be able to accurately generate code for training an industrial robot to perform the same motion. The proposed hand tracking component includes three methods: a color-thresholding model, naïve Bayes analysis and Support Vector Machine (SVM) to detect the human hand. Next, it performs stereo matching on the region where the hand was detected to find relative 3D coordinates. The list of coordinates returned is expectedly noisy due to the way the human hand can alter its apparent shape while moving, the inconsistencies in human motion and detection failures in the cluttered environment. Therefore, the system analyzes the list of coordinates to determine a path for the robot to move, by smoothing the data to reduce noise and looking for significant points used to determine the path the robot will ultimately take. The proposed system was applied to pairs of videos recording the motion of a human hand in a „real‟ environment to move the end-affector of a SCARA robot along the same path as the hand of the person in the video. The correctness of the robot motion was determined by observers indicating that motion of the robot appeared to match the motion of the video.

  19. Optimal wavelength band clustering for multispectral iris recognition.

    PubMed

    Gong, Yazhuo; Zhang, David; Shi, Pengfei; Yan, Jingqi

    2012-07-01

    This work explores the possibility of clustering spectral wavelengths based on the maximum dissimilarity of iris textures. The eventual goal is to determine how many bands of spectral wavelengths will be enough for iris multispectral fusion and to find these bands that will provide higher performance of iris multispectral recognition. A multispectral acquisition system was first designed for imaging the iris at narrow spectral bands in the range of 420 to 940 nm. Next, a set of 60 human iris images that correspond to the right and left eyes of 30 different subjects were acquired for an analysis. Finally, we determined that 3 clusters were enough to represent the 10 feature bands of spectral wavelengths using the agglomerative clustering based on two-dimensional principal component analysis. The experimental results suggest (1) the number, center, and composition of clusters of spectral wavelengths and (2) the higher performance of iris multispectral recognition based on a three wavelengths-bands fusion.

  20. Alexithymia, not autism, predicts poor recognition of emotional facial expressions.

    PubMed

    Cook, Richard; Brewer, Rebecca; Shah, Punit; Bird, Geoffrey

    2013-05-01

    Despite considerable research into whether face perception is impaired in autistic individuals, clear answers have proved elusive. In the present study, we sought to determine whether co-occurring alexithymia (characterized by difficulties interpreting emotional states) may be responsible for face-perception deficits previously attributed to autism. Two experiments were conducted using psychophysical procedures to determine the relative contributions of alexithymia and autism to identity and expression recognition. Experiment 1 showed that alexithymia correlates strongly with the precision of expression attributions, whereas autism severity was unrelated to expression-recognition ability. Experiment 2 confirmed that alexithymia is not associated with impaired ability to detect expression variation; instead, results suggested that alexithymia is associated with difficulties interpreting intact sensory descriptions. Neither alexithymia nor autism was associated with biased or imprecise identity attributions. These findings accord with the hypothesis that the emotional symptoms of autism are in fact due to co-occurring alexithymia and that existing diagnostic criteria may need to be revised.

  1. Speech recognition technology: a critique.

    PubMed Central

    Levinson, S E

    1995-01-01

    This paper introduces the session on advanced speech recognition technology. The two papers comprising this session argue that current technology yields a performance that is only an order of magnitude in error rate away from human performance and that incremental improvements will bring us to that desired level. I argue that, to the contrary, present performance is far removed from human performance and a revolution in our thinking is required to achieve the goal. It is further asserted that to bring about the revolution more effort should be expended on basic research and less on trying to prematurely commercialize a deficient technology. PMID:7479808

  2. Document recognition serving people with disabilities

    NASA Astrophysics Data System (ADS)

    Fruchterman, James R.

    2007-01-01

    Document recognition advances have improved the lives of people with print disabilities, by providing accessible documents. This invited paper provides perspectives on the author's career progression from document recognition professional to social entrepreneur applying this technology to help people with disabilities. Starting with initial thoughts about optical character recognition in college, it continues with the creation of accurate omnifont character recognition that did not require training. It was difficult to make a reading machine for the blind in a commercial setting, which led to the creation of a nonprofit social enterprise to deliver these devices around the world. This network of people with disabilities scanning books drove the creation of Bookshare.org, an online library of scanned books. Looking forward, the needs for improved document recognition technology to further lower the barriers to reading are discussed. Document recognition professionals should be proud of the positive impact their work has had on some of society's most disadvantaged communities.

  3. Speech recognition with amplitude and frequency modulations

    NASA Astrophysics Data System (ADS)

    Zeng, Fan-Gang; Nie, Kaibao; Stickney, Ginger S.; Kong, Ying-Yee; Vongphoe, Michael; Bhargave, Ashish; Wei, Chaogang; Cao, Keli

    2005-02-01

    Amplitude modulation (AM) and frequency modulation (FM) are commonly used in communication, but their relative contributions to speech recognition have not been fully explored. To bridge this gap, we derived slowly varying AM and FM from speech sounds and conducted listening tests using stimuli with different modulations in normal-hearing and cochlear-implant subjects. We found that although AM from a limited number of spectral bands may be sufficient for speech recognition in quiet, FM significantly enhances speech recognition in noise, as well as speaker and tone recognition. Additional speech reception threshold measures revealed that FM is particularly critical for speech recognition with a competing voice and is independent of spectral resolution and similarity. These results suggest that AM and FM provide independent yet complementary contributions to support robust speech recognition under realistic listening situations. Encoding FM may improve auditory scene analysis, cochlear-implant, and audiocoding performance. auditory analysis | cochlear implant | neural code | phase | scene analysis

  4. Automatic face recognition in HDR imaging

    NASA Astrophysics Data System (ADS)

    Pereira, Manuela; Moreno, Juan-Carlos; Proença, Hugo; Pinheiro, António M. G.

    2014-05-01

    The gaining popularity of the new High Dynamic Range (HDR) imaging systems is raising new privacy issues caused by the methods used for visualization. HDR images require tone mapping methods for an appropriate visualization on conventional and non-expensive LDR displays. These visualization methods might result in completely different visualization raising several issues on privacy intrusion. In fact, some visualization methods result in a perceptual recognition of the individuals, while others do not even show any identity. Although perceptual recognition might be possible, a natural question that can rise is how computer based recognition will perform using tone mapping generated images? In this paper, a study where automatic face recognition using sparse representation is tested with images that result from common tone mapping operators applied to HDR images. Its ability for the face identity recognition is described. Furthermore, typical LDR images are used for the face recognition training.

  5. Shape Recognition Of Complex Objects By Syntactical Primitives

    NASA Astrophysics Data System (ADS)

    Lenger, D.; Cipovic, H.

    1985-04-01

    The paper describes a pattern recognition method based on syntactic image analysis applicable in autonomous systems of robot vision for the purpose of pattern detection or classification. The discrimination of syntactic elements is realized by polygonal approximation of contours employing a very fast algorithm based upon coding, local pixel logic and methods of choice instead of numerical methods. Semantic information is derived from attributes calculated from the filtered shape vector. No a priori information on image objects is required, and the choice of starting point is determined by finding the significant directions on the shape vector. The radius of recognition sphere is minimum Euclidian distance, i.e. maximum similarity between the unknown model and each individual grammar created in the learning phase. By keeping information on derivations of individual syntactic elements, an alternative of parsing recognition is left. The analysis is very flexible, and permits the recognition of highly distorted or even partially visible objects. The output from syntactic analyzer is the measure of irregularity, and the method is thus applicable in any application where sample deformation is being examined.

  6. A unified framework for gesture recognition and spatiotemporal gesture segmentation.

    PubMed

    Alon, Jonathan; Athitsos, Vassilis; Yuan, Quan; Sclaroff, Stan

    2009-09-01

    Within the context of hand gesture recognition, spatiotemporal gesture segmentation is the task of determining, in a video sequence, where the gesturing hand is located and when the gesture starts and ends. Existing gesture recognition methods typically assume either known spatial segmentation or known temporal segmentation, or both. This paper introduces a unified framework for simultaneously performing spatial segmentation, temporal segmentation, and recognition. In the proposed framework, information flows both bottom-up and top-down. A gesture can be recognized even when the hand location is highly ambiguous and when information about when the gesture begins and ends is unavailable. Thus, the method can be applied to continuous image streams where gestures are performed in front of moving, cluttered backgrounds. The proposed method consists of three novel contributions: a spatiotemporal matching algorithm that can accommodate multiple candidate hand detections in every frame, a classifier-based pruning framework that enables accurate and early rejection of poor matches to gesture models, and a subgesture reasoning algorithm that learns which gesture models can falsely match parts of other longer gestures. The performance of the approach is evaluated on two challenging applications: recognition of hand-signed digits gestured by users wearing short-sleeved shirts, in front of a cluttered background, and retrieval of occurrences of signs of interest in a video database containing continuous, unsegmented signing in American Sign Language (ASL).

  7. The Effect of Set Size on Color Recognition

    DTIC Science & Technology

    1985-01-25

    affects recognition. This was done by measuring the time required to recall whether or not a test object belonged to the memory set. Sternberg...subject, whose task it was to determine if that test digit belonged to the set in memory or not. Sternberg found that as the length of the list...this set were designated as the negative set. The task o-f the subject was to memorize the positive set and then on a subsequent test presentation

  8. Temporal identity in axonal target layer recognition.

    PubMed

    Petrovic, Milan; Hummel, Thomas

    2008-12-11

    The segregation of axon and dendrite projections into distinct synaptic layers is a fundamental principle of nervous system organization and the structural basis for information processing in the brain. Layer-specific recognition molecules that allow projecting neurons to stabilize transient contacts and initiate synaptogenesis have been identified. However, most of the neuronal cell-surface molecules critical for layer organization are expressed broadly in the developing nervous system, raising the question of how these so-called permissive adhesion molecules support synaptic specificity. Here we show that the temporal expression dynamics of the zinc-finger protein sequoia is the major determinant of Drosophila photoreceptor connectivity into distinct synaptic layers. Neighbouring R8 and R7 photoreceptors show consecutive peaks of elevated sequoia expression, which correspond to their sequential target-layer innervation. Loss of sequoia in R7 leads to a projection switch into the R8 recipient layer, whereas a prolonged expression in R8 induces a redirection of their axons into the R7 layer. The sequoia-induced axon targeting is mediated through the ubiquitously expressed Cadherin-N cell adhesion molecule. Our data support a model in which recognition specificity during synaptic layer formation is generated through a temporally restricted axonal competence to respond to broadly expressed adhesion molecules. Because developing neurons innervating the same target area often project in a distinct, birth-order-dependent sequence, temporal identity seems to contain crucial information in generating not only cell type diversity during neuronal division but also connection diversity of projecting neurons.

  9. [Recognition and identification of unknown infectious agents].

    PubMed

    Berche, P

    1994-04-01

    The recognition and the identification of previously unrecognized infectious agents require a multidisciplinary approach to specify the nosologic entity of the disease and the epidemiological data, especially the modes of transmission and the risk factors, as well as to discover the microorganism in the laboratory. In the past 20 years, significant breakthroughs have been achieved in cellular cultures (growth factors), in immunology (monoclonal antibodies), and moreover in molecular biology, which have been widely used in the field of infectious diseases. Whereas the classical methods used to grow microorganisms remain of major interest in many cases, innovating strategies have been recently designed to identify previously unknown pathogens. The genomic amplification by polymerase chain reaction (PCR) of highly conserved bacterial genes (as those coding for ribosomal RNA), from tissue biopsies for example, allow to recognize unknown bacteria. The evolutionary distance between a newly recognized pathogen and known microorganisms can be calculated through sequencing of these genes, as described for Rochalimaea henselae or Tropheryma whipplelii. The constitution of cDNA banks from infected tissues is also a novel approach allowing to clone and sequence viral genes, such as those from hepatitis C or from hepatitis E. In the near future, noteworthy improvements will be achieved to rapidly detect microorganisms with highly sensitive and specific tests using monoclonal antibodies, molecular probes (including branched DNA) and with PCR (including Q beta replicase and ligase chain reaction), and to determine the genetic diversity of microbial pathogens by new methods as pulse field gel electrophoresis or arbitrarily primed PCR. This will result in a better knowledge of the pathophysiology of infectious diseases, in a better recognition of a typical, previously unrecognized clinical expression of pathogenicity, and also in a more precise assessment of the actual impact of a

  10. Effect of spectral resolution on pattern recognition analysis using passive fourier transform infrared sensor data

    SciTech Connect

    Bangalore, Arjun S.; Demirgian, Jack C.; Boparai, Amrit S.; Small, Gary W.

    1999-11-01

    The Fourier transform infrared (FT-IR) spectral data of two nerve agent simulants, diisopropyl methyl phosphonate (DIMP) and dimethyl methyl phosphonate (DMMP), are used as test cases to determine the spectral resolution that gives optimal pattern recognition performance. DIMP is used as the target analyte for detection, while DMMP is used to test the ability of the automated pattern recognition methodology to detect the analyte selectively. Interferogram data are collected by using a Midac passive FT-IR instrument. The methodology is based on the application of pattern recognition techniques to short segments of single-beam spectra obtained by Fourier processing the collected interferogram data. The work described in this article evaluates the effect of varying spectral resolution on the pattern recognition results. The objective is to determine the optimal spectral resolution to be used for data collection. The results of this study indicate that the data with a nominal spectral resolution of 16 cm{sup -1} provide sufficient selectivity to give pattern recognition results comparable to that obtained by using higher resolution data. We found that, while higher resolution does not increase selectivity sufficiently to provide better pattern recognition results, lower resolution decreases selectivity and degrades the pattern recognition results. These results can be used as guidelines to maximize detection sensitivity, to minimize the time needed for data collection, and to reduce data storage requirements. (c) 2000 Society for Applied Spectroscopy.

  11. Foreign Language Analysis and Recognition (FLARE) Progress

    DTIC Science & Technology

    2015-02-01

    Cleared 29 April 2015 14. ABSTRACT This interim report provides research results in the areas of automatic speech recognition (ASR) and information...retrieval (IR). 15. SUBJECT TERMS Automatic speech recognition (ASR), information retrieval (IR). 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF...period 1 October 2012 to 30 November 2014 under contract FA8650-09-D-6939. The following tasks were completed on Automatic Speech Recognition (ASR

  12. Gesture Recognition Development for the Interactive Datawall

    DTIC Science & Technology

    2008-01-01

    AFRL-RI-RS-TR-2007-280 Final Technical Report January 2008 GESTURE RECOGNITION DEVELOPMENT FOR THE INTERACTIVE DATAWALL...DATES COVERED (From - To) Sep 05 – Sep 07 5a. CONTRACT NUMBER FA8750-05-C-0257 5b. GRANT NUMBER 4. TITLE AND SUBTITLE GESTURE RECOGNITION DEVELOPMENT... gesture recognition technology. Also, due to the large screen size (12’ x 3’) of the DataWall, oftentimes, it is difficult to precisely identify what

  13. Performance Improvements of the Phoneme Recognition Algorithm.

    DTIC Science & Technology

    1984-06-01

    present time, there are commercially available speech recognition machines that perform limited speech recognition. There are still major drawbacks to...to recognize. Even though the training period has been made fairly painless to the user, it still severely limits the vocabulary the machine can...this information to perform the recognition routines. 47 ..- 7f Alterations to the templates’ spectrum file was limited to changing values in the

  14. Face Recognition Performance: Role of Demographic Information

    DTIC Science & Technology

    2012-01-01

    BTAS). His other research interests include pattern recognition and computer vision . Mark J. Burge is a scientist with The MITRE Corporation, McLean... Pattern Anal. Mach. Intell., vol. 28, no. 12, pp. 2037–2041, 2006. [23] X. Tan and B. Triggs, “Enhanced local texture feature sets for face recognition ...wavelets for face recognition ,” Pattern Analysis & Applications, vol. 9, pp. 273–292, 2006. [25] M. Riesenhuber and T. Poggio, “Hierarchical models of

  15. Sparsity-motivated automatic target recognition.

    PubMed

    Patel, Vishal M; Nasrabadi, Nasser M; Chellappa, Rama

    2011-04-01

    We present an automatic target recognition algorithm using the recently developed theory of sparse representations and compressive sensing. We show how sparsity can be helpful for efficient utilization of data for target recognition. We verify the efficacy of the proposed algorithm in terms of the recognition rate and confusion matrices on the well known Comanche (Boeing-Sikorsky, USA) forward-looking IR data set consisting of ten different military targets at different orientations.

  16. Domain swapping between homologous bacterial small RNAs dissects processing and Hfq binding determinants and uncovers an aptamer for conditional RNase E cleavage

    PubMed Central

    Göpel, Yvonne; Khan, Muna Ayesha; Görke, Boris

    2016-01-01

    In E. coli, small RNA GlmZ activates the glmS mRNA by base-pairing in an Hfq dependent manner. When not required, GlmZ is bound by adaptor protein RapZ and recruited to RNase E, which cleaves GlmZ in its base-pairing sequence. Small RNA GlmY counteracts cleavage of GlmZ by sequestration of RapZ. Although both sRNAs are highly homologous, only GlmZ specifically binds Hfq and undergoes cleavage by RNase E. We used domain swapping to identify the responsible modules. Two elements, the 3′ terminal oligo(U) stretch and the base-pairing region enable GlmZ to interact with Hfq. Accordingly, Hfq inhibits cleavage of GlmZ, directing it to base-pairing. Intriguingly, the central stem loop of GlmZ is decisive for cleavage, whereas the sequence comprising the actual cleavage site is dispensable. Assisted by RapZ, RNase E cleaves any RNA fused to the 3′ end of this module. These results suggest a novel mode for RNase E recognition, in which one of the required handholds in the substrate is replaced by an RNA binding protein. This device can generate RNAs of interest in their 5′ monophosphorylated form on demand. As these species are rapidly degraded, this tool allows to regulate gene expression post-transcriptionally by modulation of RapZ levels. PMID:26531825

  17. Characterization of molecular recognition in gas sensors

    SciTech Connect

    Hierlemann, A.; Ricco, A.J.; Bodenhoefer, K.; Goepel, W.

    1998-08-01

    Molecular recognition is an important topic when searching for new, selective coating materials for chemical sensing. Recently, the general idea of molecular recognition in the gas phase was challenged by Grate et al. However, in earlier thickness-shear mode resonator (TSMR) investigations, convincing evidence was presented for specific recognition of particular analyte target molecules. In this study, the authors systematically investigated coatings previously shown to be highly selective, such as the bucket-like cyclodextrins for chiral recognition, Ni-camphorates for the specific detection of the bases pyridine and DMMP (dimethylmethylphosphonate), and phthalocyanines to specifically detect benzene, toluene, and xylene (BTX).

  18. Toward the ultimate synthesis/recognition system.

    PubMed

    Furui, S

    1995-10-24

    This paper predicts speech synthesis, speech recognition, and speaker recognition technology for the year 2001, and it describes the most important research problems to be solved in order to arrive at these ultimate synthesis and recognition systems. The problems for speech synthesis include natural and intelligible voice production, prosody control based on meaning, capability of controlling synthesized voice quality and choosing individual speaking style, multilingual and multidialectal synthesis, choice of application-oriented speaking styles, capability of adding emotion, and synthesis from concepts. The problems for speech recognition include robust recognition against speech variations, adaptation/normalization to variations due to environmental conditions and speakers, automatic knowledge acquisition for acoustic and linguistic modeling, spontaneous speech recognition, naturalness and ease of human-machine interaction, and recognition of emotion. The problems for speaker recognition are similar to those for speech recognition. The research topics related to all these techniques include the use of articulatory and perceptual constraints and evaluation methods for measuring the quality of technology and systems.

  19. Rank Pooling for Action Recognition.

    PubMed

    Fernando, Basura; Gavves, Efstratios; Oramas M, Jose Oramas; Ghodrati, Amir; Tuytelaars, Tinne

    2017-04-01

    We propose a function-based temporal pooling method that captures the latent structure of the video sequence data - e.g., how frame-level features evolve over time in a video. We show how the parameters of a function that has been fit to the video data can serve as a robust new video representation. As a specific example, we learn a pooling function via ranking machines. By learning to rank the frame-level features of a video in chronological order, we obtain a new representation that captures the video-wide temporal dynamics of a video, suitable for action recognition. Other than ranking functions, we explore different parametric models that could also explain the temporal changes in videos. The proposed functional pooling methods, and rank pooling in particular, is easy to interpret and implement, fast to compute and effective in recognizing a wide variety of actions. We evaluate our method on various benchmarks for generic action, fine-grained action and gesture recognition. Results show that rank pooling brings an absolute improvement of 7-10 average pooling baseline. At the same time, rank pooling is compatible with and complementary to several appearance and local motion based methods and features, such as improved trajectories and deep learning features.

  20. Ordinal measures for iris recognition.

    PubMed

    Sun, Zhenan; Tan, Tieniu

    2009-12-01

    Images of a human iris contain rich texture information useful for identity authentication. A key and still open issue in iris recognition is how best to represent such textural information using a compact set of features (iris features). In this paper, we propose using ordinal measures for iris feature representation with the objective of characterizing qualitative relationships between iris regions rather than precise measurements of iris image structures. Such a representation may lose some image-specific information, but it achieves a good trade-off between distinctiveness and robustness. We show that ordinal measures are intrinsic features of iris patterns and largely invariant to illumination changes. Moreover, compactness and low computational complexity of ordinal measures enable highly efficient iris recognition. Ordinal measures are a general concept useful for image analysis and many variants can be derived for ordinal feature extraction. In this paper, we develop multilobe differential filters to compute ordinal measures with flexible intralobe and interlobe parameters such as location, scale, orientation, and distance. Experimental results on three public iris image databases demonstrate the effectiveness of the proposed ordinal feature models.

  1. Dynamic Features for Iris Recognition.

    PubMed

    da Costa, R M; Gonzaga, A

    2012-08-01

    The human eye is sensitive to visible light. Increasing illumination on the eye causes the pupil of the eye to contract, while decreasing illumination causes the pupil to dilate. Visible light causes specular reflections inside the iris ring. On the other hand, the human retina is less sensitive to near infra-red (NIR) radiation in the wavelength range from 800 nm to 1400 nm, but iris detail can still be imaged with NIR illumination. In order to measure the dynamic movement of the human pupil and iris while keeping the light-induced reflexes from affecting the quality of the digitalized image, this paper describes a device based on the consensual reflex. This biological phenomenon contracts and dilates the two pupils synchronously when illuminating one of the eyes by visible light. In this paper, we propose to capture images of the pupil of one eye using NIR illumination while illuminating the other eye using a visible-light pulse. This new approach extracts iris features called "dynamic features (DFs)." This innovative methodology proposes the extraction of information about the way the human eye reacts to light, and to use such information for biometric recognition purposes. The results demonstrate that these features are discriminating features, and, even using the Euclidean distance measure, an average accuracy of recognition of 99.1% was obtained. The proposed methodology has the potential to be "fraud-proof," because these DFs can only be extracted from living irises.

  2. Longitudinal study of fingerprint recognition.

    PubMed

    Yoon, Soweon; Jain, Anil K

    2015-07-14

    Human identification by fingerprints is based on the fundamental premise that ridge patterns from distinct fingers are different (uniqueness) and a fingerprint pattern does not change over time (persistence). Although the uniqueness of fingerprints has been investigated by developing statistical models to estimate the probability of error in comparing two random samples of fingerprints, the persistence of fingerprints has remained a general belief based on only a few case studies. In this study, fingerprint match (similarity) scores are analyzed by multilevel statistical models with covariates such as time interval between two fingerprints in comparison, subject's age, and fingerprint image quality. Longitudinal fingerprint records of 15,597 subjects are sampled from an operational fingerprint database such that each individual has at least five 10-print records over a minimum time span of 5 y. In regard to the persistence of fingerprints, the longitudinal analysis on a single (right index) finger demonstrates that (i) genuine match scores tend to significantly decrease when time interval between two fingerprints in comparison increases, whereas the change in impostor match scores is negligible; and (ii) fingerprint recognition accuracy at operational settings, nevertheless, tends to be stable as the time interval increases up to 12 y, the maximum time span in the dataset. However, the uncertainty of temporal stability of fingerprint recognition accuracy becomes substantially large if either of the two fingerprints being compared is of poor quality. The conclusions drawn from 10-finger fusion analysis coincide with the conclusions from single-finger analysis.

  3. Sonority contours in word recognition

    NASA Astrophysics Data System (ADS)

    McLennan, Sean

    2003-04-01

    Contrary to the Generativist distinction between competence and performance which asserts that speech or perception errors are due to random, nonlinguistic factors, it seems likely that errors are principled and possibly governed by some of the same constraints as language. A preliminary investigation of errors modeled after the child's ``Chain Whisper'' game (a degraded stimulus task) suggests that a significant number of recognition errors can be characterized as an improvement in syllable sonority contour towards the linguistically least-marked, voiceless-stop-plus-vowel syllable. An independent study of sonority contours showed that approximately half of the English lexicon can be uniquely identified by their contour alone. Additionally, ``sororities'' (groups of words that share a single sonority contour), surprisingly, show no correlation to familiarity or frequency in either size or membership. Together these results imply that sonority contours may be an important factor in word recognition and in defining word ``neighborhoods.'' Moreover, they suggest that linguistic markedness constraints may be more prevalent in performance-related phenomena than previously accepted.

  4. Longitudinal study of fingerprint recognition

    PubMed Central

    Yoon, Soweon; Jain, Anil K.

    2015-01-01

    Human identification by fingerprints is based on the fundamental premise that ridge patterns from distinct fingers are different (uniqueness) and a fingerprint pattern does not change over time (persistence). Although the uniqueness of fingerprints has been investigated by developing statistical models to estimate the probability of error in comparing two random samples of fingerprints, the persistence of fingerprints has remained a general belief based on only a few case studies. In this study, fingerprint match (similarity) scores are analyzed by multilevel statistical models with covariates such as time interval between two fingerprints in comparison, subject’s age, and fingerprint image quality. Longitudinal fingerprint records of 15,597 subjects are sampled from an operational fingerprint database such that each individual has at least five 10-print records over a minimum time span of 5 y. In regard to the persistence of fingerprints, the longitudinal analysis on a single (right index) finger demonstrates that (i) genuine match scores tend to significantly decrease when time interval between two fingerprints in comparison increases, whereas the change in impostor match scores is negligible; and (ii) fingerprint recognition accuracy at operational settings, nevertheless, tends to be stable as the time interval increases up to 12 y, the maximum time span in the dataset. However, the uncertainty of temporal stability of fingerprint recognition accuracy becomes substantially large if either of the two fingerprints being compared is of poor quality. The conclusions drawn from 10-finger fusion analysis coincide with the conclusions from single-finger analysis. PMID:26124106

  5. Dynamic chemistry of anion recognition

    SciTech Connect

    Custelcean, Radu

    2012-01-01

    In the past 40 years, anion recognition by synthetic receptors has grown into a rich and vibrant research topic, developing into a distinct branch of Supramolecular Chemistry. Traditional anion receptors comprise organic scaffolds functionalized with complementary binding groups that are assembled by multistep organic synthesis. Recently, a new approach to anion receptors has emerged, in which the host is dynamically self-assembled in the presence of the anionic guest, via reversible bond formation between functional building units. While coordination bonds were initially employed for the self-assembly of the anion hosts, more recent studies demonstrated that reversible covalent bonds can serve the same purpose. In both cases, due to their labile connections, the molecular constituents have the ability to assemble, dissociate, and recombine continuously, thereby creating a dynamic combinatorial library (DCL) of receptors. The anionic guests, through specific molecular recognition, may then amplify (express) the formation of a particular structure among all possible combinations (real or virtual) by shifting the equilibria involved towards the most optimal receptor. This approach is not limited to solution self-assembly, but is equally applicable to crystallization, where the fittest anion-binding crystal may be selected. Finally, the pros and cons of employing dynamic combinatorial chemistry (DCC) vs molecular design for developing anion receptors, and the implications of both approaches to selective anion separations, will be discussed.

  6. Innate immune recognition of cancer.

    PubMed

    Woo, Seng-Ryong; Corrales, Leticia; Gajewski, Thomas F

    2015-01-01

    The observation that a subset of cancer patients show evidence for spontaneous CD8+ T cell priming against tumor-associated antigens has generated renewed interest in the innate immune pathways that might serve as a bridge to an adaptive immune response to tumors. Manipulation of this endogenous T cell response with therapeutic intent-for example, using blocking antibodies inhibiting PD-1/PD-L1 (programmed death-1/programmed death ligand 1) interactions-is showing impressive clinical results. As such, understanding the innate immune mechanisms that enable this T cell response has important clinical relevance. Defined innate immune interactions in the cancer context include recognition by innate cell populations (NK cells, NKT cells, and γδ T cells) and also by dendritic cells and macrophages in response to damage-associated molecular patterns (DAMPs). Recent evidence has indicated that the major DAMP driving host antitumor immune responses is tumor-derived DNA, sensed by the stimulator of interferon gene (STING) pathway and driving type I IFN production. A deeper knowledge of the clinically relevant innate immune pathways involved in the recognition of tumors is leading toward new therapeutic strategies for cancer treatment.

  7. Mobility in the European Chemicals Industry Sector: The Role of Transparency and Recognition of Vocational Qualifications. CEDEFOP Panorama Series.

    ERIC Educational Resources Information Center

    Rolfe, Heather

    Research was conducted in Europe to determine the following: (1) the current situation in the chemicals industry in regard to transparency, recognition, and transfer of qualifications; (2) the obstacles to transparency and recognition of qualifications in the industry; and (3) the key areas for future action and possible measures to promote…

  8. Appearance and Reality: Does a Recognition Test Really Improve Subsequent Recall and Recognition?

    ERIC Educational Resources Information Center

    Mandler, George; Rabinowitz, Jan C.

    1981-01-01

    That additional exposure to memorial material improves subsequent retrieval probabilities was explored. The effect of a recognition test on subsequent recall and recognition of categorized lists was studied. Prior recognition tests increased recall of original items, but also increased intrusions. Similarly, prior exposure increased hit rates and…

  9. Intelligent Facial Recognition Systems: Technology advancements for security applications

    SciTech Connect

    Beer, C.L.

    1993-07-01

    Insider problems such as theft and sabotage can occur within the security and surveillance realm of operations when unauthorized people obtain access to sensitive areas. A possible solution to these problems is a means to identify individuals (not just credentials or badges) in a given sensitive area and provide full time personnel accountability. One approach desirable at Department of Energy facilities for access control and/or personnel identification is an Intelligent Facial Recognition System (IFRS) that is non-invasive to personnel. Automatic facial recognition does not require the active participation of the enrolled subjects, unlike most other biological measurement (biometric) systems (e.g., fingerprint, hand geometry, or eye retinal scan systems). It is this feature that makes an IFRS attractive for applications other than access control such as emergency evacuation verification, screening, and personnel tracking. This paper discusses current technology that shows promising results for DOE and other security applications. A survey of research and development in facial recognition identified several companies and universities that were interested and/or involved in the area. A few advanced prototype systems were also identified. Sandia National Laboratories is currently evaluating facial recognition systems that are in the advanced prototype stage. The initial application for the evaluation is access control in a controlled environment with a constant background and with cooperative subjects. Further evaluations will be conducted in a less controlled environment, which may include a cluttered background and subjects that are not looking towards the camera. The outcome of the evaluations will help identify areas of facial recognition systems that need further development and will help to determine the effectiveness of the current systems for security applications.

  10. Rule-Based Orientation Recognition Of A Moving Object

    NASA Astrophysics Data System (ADS)

    Gove, Robert J.

    1989-03-01

    This paper presents a detailed description and a comparative analysis of the algorithms used to determine the position and orientation of an object in real-time. The exemplary object, a freely moving gold-fish in an aquarium, provides "real-world" motion, with definable characteristics of motion (the fish never swims upside-down) and the complexities of a non-rigid body. For simplicity of implementation, and since a restricted and stationary viewing domain exists (fish-tank), we reduced the problem of obtaining 3D correspondence information to trivial alignment calculations by using two cameras orthogonally viewing the object. We applied symbolic processing techniques to recognize the 3-D orientation of a moving object of known identity in real-time. Assuming motion, each new frame (sensed by the two cameras) provides images of the object's profile which has most likely undergone translation, rotation, scaling and/or bending of the non-rigid object since the previous frame. We developed an expert system which uses heuristics of the object's motion behavior in the form of rules and information obtained via low-level image processing (like numerical inertial axis calculations) to dynamically estimate the object's orientation. An inference engine provides these estimates at frame rates of up to 10 per second (which is essentially real-time). The advantages of the rule-based approach to orientation recognition will be compared other pattern recognition techniques. Our results of an investigation of statistical pattern recognition, neural networks, and procedural techniques for orientation recognition will be included. We implemented the algorithms in a rapid-prototyping environment, the TI-Ezplorer, equipped with an Odyssey and custom imaging hardware. A brief overview of the workstation is included to clarify one motivation for our choice of algorithms. These algorithms exploit two facets of the prototype image processing and understanding workstation - both low

  11. Recognition of handwritten similar Chinese characters by self-growing probabilistic decision-based neural network.

    PubMed

    Fu, H C; Xu, Y Y; Chang, H Y

    1999-12-01

    Recognition of similar (confusion) characters is a difficult problem in optical character recognition (OCR). In this paper, we introduce a neural network solution that is capable of modeling minor differences among similar characters, and is robust to various personal handwriting styles. The Self-growing Probabilistic Decision-based Neural Network (SPDNN) is a probabilistic type neural network, which adopts a hierarchical network structure with nonlinear basis functions and a competitive credit-assignment scheme. Based on the SPDNN model, we have constructed a three-stage recognition system. First, a coarse classifier determines a character to be input to one of the pre-defined subclasses partitioned from a large character set, such as Chinese mixed with alphanumerics. Then a character recognizer determines the input image which best matches the reference character in the subclass. Lastly, the third module is a similar character recognizer, which can further enhance the recognition accuracy among similar or confusing characters. The prototype system has demonstrated a successful application of SPDNN to similar handwritten Chinese recognition for the public database CCL/HCCR1 (5401 characters x200 samples). Regarding performance, experiments on the CCL/HCCR1 database produced 90.12% recognition accuracy with no rejection, and 94.11% accuracy with 6.7% rejection, respectively. This recognition accuracy represents about 4% improvement on the previously announced performance. As to processing speed, processing before recognition (including image preprocessing, segmentation, and feature extraction) requires about one second for an A4 size character image, and recognition consumes approximately 0.27 second per character on a Pentium-100 based personal computer, without use of any hardware accelerator or co-processor.

  12. Object Recognition using Feature- and Color-Based Methods

    NASA Technical Reports Server (NTRS)

    Duong, Tuan; Duong, Vu; Stubberud, Allen

    2008-01-01

    An improved adaptive method of processing image data in an artificial neural network has been developed to enable automated, real-time recognition of possibly moving objects under changing (including suddenly changing) conditions of illumination and perspective. The method involves a combination of two prior object-recognition methods one based on adaptive detection of shape features and one based on adaptive color segmentation to enable recognition in situations in which either prior method by itself may be inadequate. The chosen prior feature-based method is known as adaptive principal-component analysis (APCA); the chosen prior color-based method is known as adaptive color segmentation (ACOSE). These methods are made to interact with each other in a closed-loop system to obtain an optimal solution of the object-recognition problem in a dynamic environment. One of the results of the interaction is to increase, beyond what would otherwise be possible, the accuracy of the determination of a region of interest (containing an object that one seeks to recognize) within an image. Another result is to provide a minimized adaptive step that can be used to update the results obtained by the two component methods when changes of color and apparent shape occur. The net effect is to enable the neural network to update its recognition output and improve its recognition capability via an adaptive learning sequence. In principle, the improved method could readily be implemented in integrated circuitry to make a compact, low-power, real-time object-recognition system. It has been proposed to demonstrate the feasibility of such a system by integrating a 256-by-256 active-pixel sensor with APCA, ACOSE, and neural processing circuitry on a single chip. It has been estimated that such a system on a chip would have a volume no larger than a few cubic centimeters, could operate at a rate as high as 1,000 frames per second, and would consume in the order of milliwatts of power.

  13. Determination of secondary structure in the initiation region of ovalbumin mRNA.

    PubMed Central

    Liarakos, C D; Maddox, R P; Hilscher, K A; Bishop, J R; McGuire, D K; Kopper, R A

    1988-01-01

    We have analyzed the secondary structure in the region surrounding the initiation codons of both cellular and synthetic versions of ovalbumin mRNA. RNase V1 cleavage sites and structure-dependent, chemically modified bases in cellular ovalbumin mRNA were determined by reverse transcription of hen poly A(+) RNA using ovalbumin-specific, synthetic DNA primers. These results indicate an extensive region of unpaired nucleotides preceding the initiation codon and a region of base-paired nucleotides including and following the initiation codon. A synthetic ovalbumin mRNA (SP65.OV) was prepared by run-off transcription of a cloned ovalbumin cDNA (pSP65.OV). Identical regions of hen ovalbumin and SP65.OV mRNAs gave identical patterns of structure-dependent base modifications. A computer program for determining RNA secondary structure was used to find a 5'-region structure for ovalbumin mRNA that is consistent with our data. Images PMID:3205742

  14. Effects of saturation contrast on color recognition in night vision goggles

    NASA Astrophysics Data System (ADS)

    Havig, Paul R.; Marasco, Peter L.; Post, David L.; Ellwanger, Harold L.; Reis, George A.

    2004-09-01

    In the past we have examined the luminance contrast ratios required to maintain color recognition in helmet-mounted displays (HMDs). Using typical daytime viewing conditions as simulated backgrounds we were able to determine 95% correct color recognition thresholds resulting in luminance contrast ratios averaging 1.17:1. Last year we adapted this research to determine the best colors to maintain color recognition of symbology that is on a night vision goggle (NVG) image. We simulated NVG P43 green phosphor and determined 95% correct color recognition thresholds. Results indicated that, on average, a luminance contrast ratio of nearly 1.5:1 was required to maintain color recognition. Review of the studies indicated that our simulated P43 phosphor was a much more saturated background, so saturation contrast may play as important a role as luminance contrast. A P45 white phosphor NVG may therefore be less problematic. Here we investigate the effects of both luminance and saturation contrast by manipulating color mixtures of green, yellow, and red symbology against two different backgrounds, P43 green and P45 white. We discuss our results in terms of both luminance and saturation contrast required for the maintenance of color recognition in NVGs.

  15. Aircraft recognition and tracking device

    NASA Astrophysics Data System (ADS)

    Filis, Dimitrios P.; Renios, Christos I.

    2011-11-01

    The technology of aircraft recognition and tracking has various applications in all areas of air navigation, be they civil or military, spanning from air traffic control and regulation at civilian airports to anti-aircraft weapon handling and guidance for military purposes.1, 18 The system presented in this thesis is an alternative implementation of identifying and tracking flying objects, which benefits from the optical spectrum by using an optical camera built into a servo motor (pan-tilt unit). More specifically, through the purpose-developed software, when a target (aircraft) enters the field of view of the camera18, it is both detected and identified.5, 22 Then the servo motor, being provided with data on target position and velocity, tracks the aircraft while it is in constant communication with the camera (Fig. 1). All the features are so designed as to operate under real time conditions.

  16. Place recognition using batlike sonar.

    PubMed

    Vanderelst, Dieter; Steckel, Jan; Boen, Andre; Peremans, Herbert; Holderied, Marc W

    2016-08-02

    Echolocating bats have excellent spatial memory and are able to navigate to salient locations using bio-sonar. Navigating and route-following require animals to recognize places. Currently, it is mostly unknown how bats recognize places using echolocation. In this paper, we propose template based place recognition might underlie sonar-based navigation in bats. Under this hypothesis, bats recognize places by remembering their echo signature - rather than their 3D layout. Using a large body of ensonification data collected in three different habitats, we test the viability of this hypothesis assessing two critical properties of the proposed echo signatures: (1) they can be uniquely classified and (2) they vary continuously across space. Based on the results presented, we conclude that the proposed echo signatures satisfy both criteria. We discuss how these two properties of the echo signatures can support navigation and building a cognitive map.

  17. New methods in iris recognition.

    PubMed

    Daugman, John

    2007-10-01

    This paper presents the following four advances in iris recognition: 1) more disciplined methods for detecting and faithfully modeling the iris inner and outer boundaries with active contours, leading to more flexible embedded coordinate systems; 2) Fourier-based methods for solving problems in iris trigonometry and projective geometry, allowing off-axis gaze to be handled by detecting it and "rotating" the eye into orthographic perspective; 3) statistical inference methods for detecting and excluding eyelashes; and 4) exploration of score normalizations, depending on the amount of iris data that is available in images and the required scale of database search. Statistical results are presented based on 200 billion iris cross-comparisons that were generated from 632500 irises in the United Arab Emirates database to analyze the normalization issues raised in different regions of receiver operating characteristic curves.

  18. Automatic recognition of auroral forms

    NASA Astrophysics Data System (ADS)

    Pudovkin, Mikhail I.; Steen, Ake; Nikolaev, N. V.; Kornilov, O. I.; Brandstrom, Urban; Gustavsson, Bjorn; Rydesater, Peter

    1999-03-01

    A method for recognition of geometrical shapes in auroral forms is presented. The method is based on the analysis of isolines of auroral luminosity shapes. The basic variables used are the angle, (phi) (s), between the tangent of the contour and the x-axis of an arbitrary coordinate system, and the differential, d(phi) (s), as a function of the distance, s, along the contour. The analysis also includes Fourier transformation of the experimental function d(phi) (s) obtained for the observed auroral forms, and the comparison of the power spectrum, F(k), with those for a series of model contours. Some dynamical characteristics of the aurora are also discussed.

  19. Brain wave recognition of words.

    PubMed

    Suppes, P; Lu, Z L; Han, B

    1997-12-23

    Electrical and magnetic brain waves of seven subjects under three experimental conditions were recorded for the purpose of recognizing which one of seven words was processed. The analysis consisted of averaging over trials to create prototypes and test samples, to both of which Fourier transforms were applied, followed by filtering and an inverse transformation to the time domain. The filters used were optimal predictive filters, selected for each subject and condition. Recognition rates, based on a least-squares criterion, varied widely, but all but one of 24 were significantly different from chance. The two best were above 90%. These results show that brain waves carry substantial information about the word being processed under experimental conditions of conscious awareness.

  20. Task-oriented situation recognition

    NASA Astrophysics Data System (ADS)

    Bauer, Alexander; Fischer, Yvonne

    2010-04-01

    From the advances in computer vision methods for the detection, tracking and recognition of objects in video streams, new opportunities for video surveillance arise: In the future, automated video surveillance systems will be able to detect critical situations early enough to enable an operator to take preventive actions, instead of using video material merely for forensic investigations. However, problems such as limited computational resources, privacy regulations and a constant change in potential threads have to be addressed by a practical automated video surveillance system. In this paper, we show how these problems can be addressed using a task-oriented approach. The system architecture of the task-oriented video surveillance system NEST and an algorithm for the detection of abnormal behavior as part of the system are presented and illustrated for the surveillance of guests inside a video-monitored building.

  1. Robotic CCD microscope for enhanced crystal recognition

    DOEpatents

    Segelke, Brent W.; Toppani, Dominique

    2007-11-06

    A robotic CCD microscope and procedures to automate crystal recognition. The robotic CCD microscope and procedures enables more accurate crystal recognition, leading to fewer false negative and fewer false positives, and enable detection of smaller crystals compared to other methods available today.

  2. Sleep Enhances Explicit Recollection in Recognition Memory

    ERIC Educational Resources Information Center

    Drosopoulos, Spyridon; Wagner, Ullrich; Born, Jan

    2005-01-01

    Recognition memory is considered to be supported by two different memory processes, i.e., the explicit recollection of information about a previous event and an implicit process of recognition based on a contextual sense of familiarity. Both types of memory supposedly rely on distinct memory systems. Sleep is known to enhance the consolidation of…

  3. Object Recognition Memory and the Rodent Hippocampus

    ERIC Educational Resources Information Center

    Broadbent, Nicola J.; Gaskin, Stephane; Squire, Larry R.; Clark, Robert E.

    2010-01-01

    In rodents, the novel object recognition task (NOR) has become a benchmark task for assessing recognition memory. Yet, despite its widespread use, a consensus has not developed about which brain structures are important for task performance. We assessed both the anterograde and retrograde effects of hippocampal lesions on performance in the NOR…

  4. Isolated Speech Recognition Using Artificial Neural Networks

    DTIC Science & Technology

    2007-11-02

    In this project Artificial Neural Networks are used as research tool to accomplish Automated Speech Recognition of normal speech. A small size...the first stage of this work are satisfactory and thus the application of artificial neural networks in conjunction with cepstral analysis in isolated word recognition holds promise.

  5. Recognition hypermnesia: how to get it.

    PubMed

    Bergstein, Jacquelyn; Erdelyi, Matthew

    2008-10-01

    Although recall hypermnesia (enhanced recall) over time with repeated testing has by now become an established empirical fact, its recognition counterpart, recognition hypermnesia, has defied clear-cut laboratory confirmation. In four studies, which relied on the retrieval component of recognition memory, it was shown that recognition memory, indexed by d', reliably improved over three successive recognition tests. The stimuli consisted of 140 cartoons, each comprising a picture and a verbal caption. Recognition memory was tested on transforms or part-forms (parts) of the original stimulus material (pictures only, verbal paraphrases of the pictures, the latent content of the cartoons, or the combination of paraphrases and latent contents). The strongest effects were obtained when the originally presented cartoons were tested on their latent (deep semantic) contents. Recognition hypermnesia for part-forms or transforms of earlier presented stimuli has potentially wide-ranging implications since real-world recognition--of faces, texts, visual scenes--usually involves recognising stimuli that are variants, not exact copies, of the originally encountered materials.

  6. Automatic Intention Recognition in Conversation Processing

    ERIC Educational Resources Information Center

    Holtgraves, Thomas

    2008-01-01

    A fundamental assumption of many theories of conversation is that comprehension of a speaker's utterance involves recognition of the speaker's intention in producing that remark. However, the nature of intention recognition is not clear. One approach is to conceptualize a speaker's intention in terms of speech acts [Searle, J. (1969). "Speech…

  7. Adult Word Recognition and Visual Sequential Memory

    ERIC Educational Resources Information Center

    Holmes, V. M.

    2012-01-01

    Two experiments were conducted investigating the role of visual sequential memory skill in the word recognition efficiency of undergraduate university students. Word recognition was assessed in a lexical decision task using regularly and strangely spelt words, and nonwords that were either standard orthographically legal strings or items made from…

  8. Gesture recognition for interactive exercise programs.

    PubMed

    Perkins, Jedediah; Pavel, Misha; Jimison, Holly B; Scott, Susan

    2008-01-01

    This paper describes a gesture recognition system which can recognize seated exercises that will be incorporated into an in-home automated interactive exercise program. Hidden Markov Models (HMMs) are used as a motion classifier, with motion features extracted from the grayscale images and the location of the subject's head estimated at initialization. An overall recognition rate of 94.1% is achieved.

  9. Recognition without Awareness: Encoding and Retrieval Factors

    ERIC Educational Resources Information Center

    Craik, Fergus I. M.; Rose, Nathan S.; Gopie, Nigel

    2015-01-01

    The article reports 4 experiments that explore the notion of recognition without awareness using words as the material. Previous work by Voss and associates has shown that complex visual patterns were correctly selected as targets in a 2-alternative forced-choice (2-AFC) recognition test although participants reported that they were guessing. The…

  10. Implicit Relational Effects in Associative Recognition

    ERIC Educational Resources Information Center

    Algarabel, S.; Pitarque, A.; Combita, L. M.; Rodriguez, L. A.

    2013-01-01

    We study the contribution of implicit relatedness to associative recognition in two experiments. In the first experiment, we showed an implicit improvement in recognition when the stimulus elements of each word pair shared common letters and they were unpaired at test. Moreover, when asked to study the stimuli under divided attention, recollection…

  11. Recognition without Awareness: An Elusive Phenomenon

    ERIC Educational Resources Information Center

    Jeneson, Annette; Kirwan, C. Brock; Squire, Larry R.

    2010-01-01

    Two recent studies described conditions under which recognition memory performance appeared to be driven by nondeclarative memory. Specifically, participants successfully discriminated old images from highly similar new images even when no conscious memory for the images could be retrieved. Paradoxically, recognition performance was better when…

  12. Performing speech recognition research with hypercard

    NASA Technical Reports Server (NTRS)

    Shepherd, Chip

    1993-01-01

    The purpose of this paper is to describe a HyperCard-based system for performing speech recognition research and to instruct Human Factors professionals on how to use the system to obtain detailed data about the user interface of a prototype speech recognition application.

  13. Speech recognition: how good is good enough?

    PubMed

    Krohn, Richard

    2002-03-01

    Since its infancy in the early 1990s, the technology of speech recognition has undergone a rapid evolution. Not only has the reliability of the programming improved dramatically, the return on investment has become increasingly compelling. The author describes some of the latest health care applications of speech-recognition technology, and how the next advances will be made in this area.

  14. Syllable Transposition Effects in Korean Word Recognition

    ERIC Educational Resources Information Center

    Lee, Chang H.; Kwon, Youan; Kim, Kyungil; Rastle, Kathleen

    2015-01-01

    Research on the impact of letter transpositions in visual word recognition has yielded important clues about the nature of orthographic representations. This study investigated the impact of syllable transpositions on the recognition of Korean multisyllabic words. Results showed that rejection latencies in visual lexical decision for…

  15. Online Handwriting Recognition for Indic Scripts

    NASA Astrophysics Data System (ADS)

    Bharath, A.; Madhvanath, Sriganesh

    Online handwriting recognition refers to the problem of machine recognition of handwriting captured in the form of pen trajectories. The recognition technology holds significant promise for Indic scripts, given that the Indic languages are used by a sixth of the world’s population, and the greater ease of use of handwriting-based text input for these scripts compared to keyboard-based methods. Even though the recognition of handwritten Devanagari, Bangla, and Tamil has received significant attention in recent times, one may say that research efforts directed at Indic script recognition in general are in their early stages. The structure of the scripts and the variety of shapes and writing styles pose challenges that are different from other scripts and hence require customized techniques for feature representation and recognition. In this chapter, we describe the challenges in recognizing online handwriting in Indic scripts and provide an overview of the state of the art for isolated character and word recognition. We then present in brief some of the promising applications, starting with handwriting-based text input systems (IMEs) that have been built for entering Indic scripts. In the last section, we provide a few pointers to resources such as tools and data sets that are currently available for online Indic script recognition research. endabstract

  16. Sources of Interference in Recognition Testing

    ERIC Educational Resources Information Center

    Annis, Jeffrey; Malmberg, Kenneth J.; Criss, Amy H.; Shiffrin, Richard M.

    2013-01-01

    Recognition memory accuracy is harmed by prior testing (a.k.a., output interference [OI]; Tulving & Arbuckle, 1966). In several experiments, we interpolated various tasks between recognition test trials. The stimuli and the tasks were more similar (lexical decision [LD] of words and nonwords) or less similar (gender identification of male and…

  17. BDNF controls object recognition memory reconsolidation.

    PubMed

    Radiske, Andressa; Rossato, Janine I; Gonzalez, Maria Carolina; Köhler, Cristiano A; Bevilaqua, Lia R; Cammarota, Martín

    2017-03-06

    Reconsolidation restabilizes memory after reactivation. Previously, we reported that the hippocampus is engaged in object recognition memory reconsolidation to allow incorporation of new information into the original engram. Here we show that BDNF is sufficient for this process, and that blockade of BDNF function in dorsal CA1 impairs updating of the reactivated recognition memory trace.

  18. Proline-rich Sequence Recognition

    PubMed Central

    Schlundt, Andreas; Sticht, Jana; Piotukh, Kirill; Kosslick, Daniela; Jahnke, Nadin; Keller, Sandro; Schuemann, Michael; Krause, Eberhard; Freund, Christian

    2009-01-01

    The tumor maintenance protein Tsg101 has recently gained much attention because of its involvement in endosomal sorting, virus release, cytokinesis, and cancerogenesis. The ubiquitin-E2-like variant (UEV) domain of the protein interacts with proline-rich sequences of target proteins that contain P(S/T)AP amino acid motifs and weakly binds to the ubiquitin moiety of proteins committed to sorting or degradation. Here we performed peptide spot analysis and phage display to refine the peptide binding specificity of the Tsg101 UEV domain. A mass spectrometric proteomics approach that combines domain-based pulldown experiments, binding site inactivation, and stable isotope labeling by amino acids in cell culture (SILAC) was then used to delineate the relative importance of the peptide and ubiquitin binding sites. Clearly “PTAP” interactions dominate target recognition, and we identified several novel binders as for example the poly(A)-binding protein 1 (PABP1), Sec24b, NFκB2, and eIF4b. For PABP1 and eIF4b the interactions were confirmed in the context of the corresponding full-length proteins in cellular lysates. Therefore, our results strongly suggest additional roles of Tsg101 in cellular regulation of mRNA translation. Regulation of Tsg101 itself by the ubiquitin ligase TAL (Tsg101-associated ligase) is most likely conferred by a single PSAP binding motif that enables the interaction with Tsg101 UEV. Together with the results from the accompanying article (Kofler, M., Schuemann, M., Merz, C., Kosslick, D., Schlundt, A., Tannert, A., Schaefer, M., Lührmann, R., Krause, E., and Freund, C. (2009) Proline-rich sequence recognition: I. Marking GYF and WW domain assembly sites in early spliceosomal complexes. Mol. Cell. Proteomics 8, 2461–2473) on GYF and WW domain pathways our work defines major proline-rich sequence-mediated interaction networks that contribute to the modular assembly of physiologically relevant protein complexes. PMID:19542561

  19. Optoelectronic-based face recognition versus electronic PCA-based face recognition

    NASA Astrophysics Data System (ADS)

    Alsamman, A.

    2003-11-01

    Face recognition based on principal component analysis (PCA) using eigenfaces is popular in face recognition markets. In this paper we present a comparison between various optoelectronic face recognition techniques and principal component analysis (PCA) based technique for face recognition. Computer simulations are used to study the effectiveness of PCA based technique especially for facial images with a high level of distortion. Results are then compared to various distortion-invariant optoelectronic face recognition algorithms such as synthetic discriminant functions (SDF), projection-slice SDF, optical correlator based neural networks, and pose estimation based correlation.

  20. Intact recognition of facial expression, gender, and age in patients with impaired recognition of face identity.

    PubMed

    Tranel, D; Damasio, A R; Damasio, H

    1988-05-01

    We conducted a series of experiments to assess the ability to recognize the meaning of facial expressions, gender, and age in four patients with severe impairments of the recognition of facial identity. In three patients the recognition of face identity could be dissociated from that of facial expression, age, and gender. In one, all forms of face recognition were impaired. Thus, a given lesion may preclude one type of recognition but not another. We conclude that (1) the cognitive demands posed by different forms of recognition are met at different processing levels, and (2) different levels depend on different neural substrates.

  1. Review of chart recognition in document images

    NASA Astrophysics Data System (ADS)

    Liu, Yan; Lu, Xiaoqing; Qin, Yeyang; Tang, Zhi; Xu, Jianbo

    2013-01-01

    As an effective information transmitting way, chart is widely used to represent scientific statistics datum in books, research papers, newspapers etc. Though textual information is still the major source of data, there has been an increasing trend of introducing graphs, pictures, and figures into the information pool. Text recognition techniques for documents have been accomplished using optical character recognition (OCR) software. Chart recognition techniques as a necessary supplement of OCR for document images are still an unsolved problem due to the great subjectiveness and variety of charts styles. This paper reviews the development process of chart recognition techniques in the past decades and presents the focuses of current researches. The whole process of chart recognition is presented systematically, which mainly includes three parts: chart segmentation, chart classification, and chart Interpretation. In each part, the latest research work is introduced. In the last, the paper concludes with a summary and promising future research direction.

  2. Small feature recognition of moving targets

    NASA Astrophysics Data System (ADS)

    Sokolnikov, Andre

    2013-03-01

    This paper presents an approach related to automated recognition of small features of movable targets including fast moving objects such as airplanes, etc. Small features recognition is a challenging problem in both fields: pattern recognition of particular configurations and of complexes comprising a number of configurations. Specific target details, although well characterized by their features are often arranged in an elaborated way which makes the recognition task very difficult and welcomes new ideas (approaches). On the other hand, the variety of small characters (features) is intrinsically linked to the technology development of the identified targets and is unavoidable. Due to the complexity of possible technological designs, the feature representation is one of the key issues in optical pattern recognition. A flexible hierarchical prediction modeling is proposed with application examples.

  3. Enantioselective Recognition by Chiral Supramolecular Gels.

    PubMed

    Zhang, Li; Jin, Qingxian; Liu, Minghua

    2016-10-06

    Chiral supramolecular gels, in which small organic molecules self-assemble into chiral nanostructures and entangle each other to immobilize solvents through various noncovalent interactions, can work as a matrix for enantioselective recognition on chiral analytes. Through gelation and the formation of well-defined nanostructures, the chiral sense of the component molecules can be accumulated or amplified, and thus, the enantioselective recognition ability can be enhanced. Furthermore, a chiral microenvironment formed in the gel networks could provide additional stereochemical recognition geometry and attribute to efficient recognition. In this focus review, enantioselective recognition on chiral analytes through chiral supramolecular gels, with either amplified signals or the gel-sol phase transition, is discussed. This review is expected to provide useful insights into the design and fabrication of supramolecular gel systems with chiral features and high enantioselectivity.

  4. Macromolecular recognition and macroscopic interactions by cyclodextrins.

    PubMed

    Harada, Akira; Takashima, Yoshinori

    2013-10-01

    Herein macromolecular recognition by cyclodextrins (CDs) is summarized. Recognition of macromolecules by CDs is classified as main-chain recognition or side-chain recognition. We found that CDs form inclusion complexes with various polymers with high selectivity. Polyrotaxanes in which many CDs are entrapped in a polymer chain were prepared. Tubular polymers were prepared from the polyrotaxanes. CDs were found to recognize side-chains of polymers selectively. CD host polymers were found to form gels with guest polymers in water. These gels showed self-healing properties. When azobenzene was used as a guest, the gel showed sol-gel transition by photoirradiation. When ferrocene was used, redox-responsive gels were obtained. Macroscopic self-assembly through molecular recognition has been discovered. Photoswitchable gel association and dissociation have been observed.

  5. Machine parts recognition using a trinary associative memory

    NASA Technical Reports Server (NTRS)

    Awwal, Abdul Ahad S.; Karim, Mohammad A.; Liu, Hua-Kuang

    1989-01-01

    The convergence mechanism of vectors in Hopfield's neural network in relation to recognition of partially known patterns is studied in terms of both inner products and Hamming distance. It has been shown that Hamming distance should not always be used in determining the convergence of vectors. Instead, inner product weighting coefficients play a more dominant role in certain data representations for determining the convergence mechanism. A trinary neuron representation for associative memory is found to be more effective for associative recall. Applications of the trinary associative memory to reconstruct machine part images that are partially missing are demonstrated by means of computer simulation as examples of the usefulness of this approach.

  6. Practical automatic Arabic license plate recognition system

    NASA Astrophysics Data System (ADS)

    Mohammad, Khader; Agaian, Sos; Saleh, Hani

    2011-02-01

    Since 1970's, the need of an automatic license plate recognition system, sometimes referred as Automatic License Plate Recognition system, has been increasing. A license plate recognition system is an automatic system that is able to recognize a license plate number, extracted from image sensors. In specific, Automatic License Plate Recognition systems are being used in conjunction with various transportation systems in application areas such as law enforcement (e.g. speed limit enforcement) and commercial usages such as parking enforcement and automatic toll payment private and public entrances, border control, theft and vandalism control. Vehicle license plate recognition has been intensively studied in many countries. Due to the different types of license plates being used, the requirement of an automatic license plate recognition system is different for each country. [License plate detection using cluster run length smoothing algorithm ].Generally, an automatic license plate localization and recognition system is made up of three modules; license plate localization, character segmentation and optical character recognition modules. This paper presents an Arabic license plate recognition system that is insensitive to character size, font, shape and orientation with extremely high accuracy rate. The proposed system is based on a combination of enhancement, license plate localization, morphological processing, and feature vector extraction using the Haar transform. The performance of the system is fast due to classification of alphabet and numerals based on the license plate organization. Experimental results for license plates of two different Arab countries show an average of 99 % successful license plate localization and recognition in a total of more than 20 different images captured from a complex outdoor environment. The results run times takes less time compared to conventional and many states of art methods.

  7. CD1 mediated T cell recognition of glycolipids.

    PubMed

    Zajonc, Dirk M; Kronenberg, Mitchell

    2007-10-01

    Specialized subsets of T lymphocytes can distinguish the carbohydrate portions of microbial and self-glycolipids when they are presented by proteins in the CD1 family of antigen presenting molecules. Recent immunochemical and structural analyses indicate that the chemical composition of the presented carbohydrate, together with its precise orientation above the CD1 binding groove, determines if a particular T cell is activated. More recently, however, it has been shown that the lipid backbone of the glycolipid, buried inside the CD1 protein, also can have an impact on T cell activation. While glycolipid recognition is a relatively new category of T cell specificity, the powerful combination of microbial antigen discovery and structural biochemistry has provided great insight into the mechanism of carbohydrate recognition.

  8. Target Recognition Using Neural Networks for Model Deformation Measurements

    NASA Technical Reports Server (NTRS)

    Ross, Richard W.; Hibler, David L.

    1999-01-01

    Optical measurements provide a non-invasive method for measuring deformation of wind tunnel models. Model deformation systems use targets mounted or painted on the surface of the model to identify known positions, and photogrammetric methods are used to calculate 3-D positions of the targets on the model from digital 2-D images. Under ideal conditions, the reflective targets are placed against a dark background and provide high-contrast images, aiding in target recognition. However, glints of light reflecting from the model surface, or reduced contrast caused by light source or model smoothness constraints, can compromise accurate target determination using current algorithmic methods. This paper describes a technique using a neural network and image processing technologies which increases the reliability of target recognition systems. Unlike algorithmic methods, the neural network can be trained to identify the characteristic patterns that distinguish targets from other objects of similar size and appearance and can adapt to changes in lighting and environmental conditions.

  9. Process dissociation, single-process theories, and recognition memory.

    PubMed

    Ratcliff, R; Van Zandt, T; McKoon, G

    1995-12-01

    According to the assumptions of L. L. Jacoby's (1991) process dissociation method, performance in recognition memory is determined by the combination of an unconscious familiarity process and a conscious intentional recollection process. The process dissociation method is used to produce estimates of the contributions of the 2 components to recognition performance. This article investigates whether the method provides the correct estimates of components if performance actually depends on only a single process or on 2 processes different from those assumed by the method. The SAM model (G. Gillund & R. M. Shiffrin, 1984) was used to produce simulated data based on a single process. Variants of SAM with 2 processes and R. C. Atkinson and J. F. Juola's (1973) 2-process model were used to produce data based on 2 processes.

  10. Markov sequential pattern recognition : dependency and the unknown class.

    SciTech Connect

    Malone, Kevin Thomas; Haschke, Greg Benjamin; Koch, Mark William

    2004-10-01

    The sequential probability ratio test (SPRT) minimizes the expected number of observations to a decision and can solve problems in sequential pattern recognition. Some problems have dependencies between the observations, and Markov chains can model dependencies where the state occupancy probability is geometric. For a non-geometric process we show how to use the effective amount of independent information to modify the decision process, so that we can account for the remaining dependencies. Along with dependencies between observations, a successful system needs to handle the unknown class in unconstrained environments. For example, in an acoustic pattern recognition problem any sound source not belonging to the target set is in the unknown class. We show how to incorporate goodness of fit (GOF) classifiers into the Markov SPRT, and determine the worse case nontarget model. We also develop a multiclass Markov SPRT using the GOF concept.

  11. Remembering or knowing others? Person recognition and recollective experience.

    PubMed

    Brandt, Karen R; Macrae, C Neil; Schloerscheidt, Astrid M; Milne, Alan B

    2003-01-01

    Using Tulving's (1985) remember/know procedure, the present research investigated the experiential concomitants of person recognition. Noting basic differences in the manner in which the mind processes expectancy-related material, it was anticipated that facial typicality would be a critical determinant of people's recollective experiences (i.e., remembering vs knowing). In particular, it was expected that whereas remember responses would be more prevalent for distinctive than typical faces, know responses would reflect the opposite pattern. The results of two experiments provided general support for these predictions. In addition, the recollective advantage for distinctive faces was traced to the availability of attentional resources at encoding. These results are considered in the context of contemporary issues in person recognition and social cognition.

  12. A new paradigm for pattern recognition of drugs.

    PubMed

    Potemkin, Vladimir A; Grishina, Maria A

    2008-01-01

    A new paradigm is suggested for pattern recognition of drugs. The approach is based on the combined application of the 4D/3D quantitative structure-activity relationship (QSAR) algorithms BiS and ConGO. The first algorithm, BiS/MC (multiconformational), is used for the search for the conformers interacting with a receptor. The second algorithm, ConGO, has been suggested for the detailed study of the selected conformers' electron density and for the search for the electron structure fragments that determine the pharmacophore and antipharmacophore parts of the compounds. In this work we suggest using a new AlteQ method for the evaluation of the molecular electron density. AlteQ describes the experimental electron density (determined by low-temperature highly accurate X-ray analysis) much better than a number of quantum approaches. Herein this is shown using a comparison of the computed electron density with the results of highly accurate X-ray analysis. In the present study the desirability function is used for the first time for the analysis of the effects of the electron structure in the process of pattern recognition of active and inactive compounds. The suggested method for pattern recognition has been used for the investigation of various sets of compounds such as DNA-antimetabolites, fXa inhibitors, 5-HT(1A), and alpha(1)-AR receptors inhibitors. The pharmacophore and antipharmacophore fragments have been found in the electron structures of the compounds. It has been shown that the pattern recognition cross-validation quality for the datasets is unity.

  13. A new paradigm for pattern recognition of drugs

    NASA Astrophysics Data System (ADS)

    Potemkin, Vladimir A.; Grishina, Maria A.

    2008-06-01

    A new paradigm is suggested for pattern recognition of drugs. The approach is based on the combined application of the 4D/3D quantitative structure-activity relationship (QSAR) algorithms BiS and ConGO. The first algorithm, BiS/MC (multiconformational), is used for the search for the conformers interacting with a receptor. The second algorithm, ConGO, has been suggested for the detailed study of the selected conformers' electron density and for the search for the electron structure fragments that determine the pharmacophore and antipharmacophore parts of the compounds. In this work we suggest using a new AlteQ method for the evaluation of the molecular electron density. AlteQ describes the experimental electron density (determined by low-temperature highly accurate X-ray analysis) much better than a number of quantum approaches. Herein this is shown using a comparison of the computed electron density with the results of highly accurate X-ray analysis. In the present study the desirability function is used for the first time for the analysis of the effects of the electron structure in the process of pattern recognition of active and inactive compounds. The suggested method for pattern recognition has been used for the investigation of various sets of compounds such as DNA-antimetabolites, fXa inhibitors, 5-HT1A, and α1-AR receptors inhibitors. The pharmacophore and antipharmacophore fragments have been found in the electron structures of the compounds. It has been shown that the pattern recognition cross-validation quality for the datasets is unity.

  14. Apply lightweight recognition algorithms in optical music recognition

    NASA Astrophysics Data System (ADS)

    Pham, Viet-Khoi; Nguyen, Hai-Dang; Nguyen-Khac, Tung-Anh; Tran, Minh-Triet

    2015-02-01

    The problems of digitalization and transformation of musical scores into machine-readable format are necessary to be solved since they help people to enjoy music, to learn music, to conserve music sheets, and even to assist music composers. However, the results of existing methods still require improvements for higher accuracy. Therefore, the authors propose lightweight algorithms for Optical Music Recognition to help people to recognize and automatically play musical scores. In our proposal, after removing staff lines and extracting symbols, each music symbol is represented as a grid of identical M ∗ N cells, and the features are extracted and classified with multiple lightweight SVM classifiers. Through experiments, the authors find that the size of 10 ∗ 12 cells yields the highest precision value. Experimental results on the dataset consisting of 4929 music symbols taken from 18 modern music sheets in the Synthetic Score Database show that our proposed method is able to classify printed musical scores with accuracy up to 99.56%.

  15. Recognition of a signal peptide by the signal recognition particle

    PubMed Central

    Janda, Claudia Y.; Li, Jade; Oubridge, Chris; Hernández, Helena; Robinson, Carol V.; Nagai, Kiyoshi

    2010-01-01

    Targeting of proteins to appropriate sub-cellular compartments is a crucial process in all living cells. Secretory and membrane proteins usually contain an N-terminal signal peptide, which is recognised by the signal recognition particle (SRP) when nascent polypeptide chains emerge from the ribosome. The SRP-ribosome nascent chain complex is then targeted through its GTP-dependent interaction with SRP-receptor to the protein-conducting channel on endoplasmic reticulum membrane in eukaryotes or plasma membrane in bacteria. A universally conserved component of SRP1, 2, SRP54 or its bacterial homolog, fifty-four homolog (Ffh), binds the signal peptides which have a highly divergent sequence divisible into a positively charged n-region, an h-region commonly containing 8-20 hydrophobic residues and a polar c-region 3-5. No structure has been reported that exemplified SRP54 binding of any signal sequence. We have produced a fusion protein between Sulfolobus solfataricus SRP54 and a signal peptide connected via a flexible linker. This fusion protein oligomerises in solution, through interaction between the SRP54 and signal peptide moieties belonging to different chains, and it is functional, able to bind SRP RNA and SRP-receptor FtsY. Here we present the crystal structure at 3.5 Å resolution of an SRP54-signal peptide complex in the dimer, which reveals how a signal sequence is recognised by SRP54. PMID:20364120

  16. Top-down facilitation of visual recognition

    PubMed Central

    Bar, M.; Kassam, K. S.; Ghuman, A. S.; Boshyan, J.; Schmid, A. M.; Dale, A. M.; Hämäläinen, M. S.; Marinkovic, K.; Schacter, D. L.; Rosen, B. R.; Halgren, E.

    2006-01-01

    Cortical analysis related to visual object recognition is traditionally thought to propagate serially along a bottom-up hierarchy of ventral areas. Recent proposals gradually promote the role of top-down processing in recognition, but how such facilitation is triggered remains a puzzle. We tested a specific model, proposing that low spatial frequencies facilitate visual object recognition by initiating top-down processes projected from orbitofrontal to visual cortex. The present study combined magnetoencephalography, which has superior temporal resolution, functional magnetic resonance imaging, and a behavioral task that yields successful recognition with stimulus repetitions. Object recognition elicited differential activity that developed in the left orbitofrontal cortex 50 ms earlier than it did in recognition-related areas in the temporal cortex. This early orbitofrontal activity was directly modulated by the presence of low spatial frequencies in the image. Taken together, the dynamics we revealed provide strong support for the proposal of how top-down facilitation of object recognition is initiated, and our observations are used to derive predictions for future research. PMID:16407167

  17. The neural substrate of gesture recognition.

    PubMed

    Villarreal, Mirta; Fridman, Esteban A; Amengual, Alejandra; Falasco, German; Gerschcovich, Eliana Roldan; Gerscovich, Eliana Roldan; Ulloa, Erlinda R; Leiguarda, Ramon C

    2008-01-01

    Previous studies have linked action recognition with a particular pool of neurons located in the ventral premotor cortex, the posterior parietal cortex and the superior temporal sulcus (the mirror neuron system). However, it is still unclear if transitive and intransitive gestures share the same neural substrates during action-recognition processes. In the present study, we used event-related functional magnetic resonance imaging (fMRI) to assess the cortical areas active during recognition of pantomimed transitive actions, intransitive gestures, and meaningless control actions. Perception of all types of gestures engaged the right pre-supplementary motor area (pre-SMA), and bilaterally in the posterior superior temporal cortex, the posterior parietal cortex, occipitotemporal regions and visual cortices. Activation of the posterior superior temporal sulcus/superior temporal gyrus region was found in both hemispheres during recognition of transitive and intransitive gestures, and in the right hemisphere during the control condition; the middle temporal gyrus showed activation in the left hemisphere when subjects recognized transitive and intransitive gestures; activation of the left inferior parietal lobe and intraparietal sulcus (IPS) was mainly observed in the left hemisphere during recognition of the three conditions. The most striking finding was the greater activation of the left inferior frontal gyrus (IFG) during recognition of intransitive actions. Results show that a similar neural substrate, albeit, with a distinct engagement underlies the cognitive processing of transitive and intransitive gestures recognition. These findings suggest that selective disruptions in these circuits may lead to distinct clinical deficits.

  18. Heuristics for test recognition using contextual information

    NASA Astrophysics Data System (ADS)

    Baraghimian, Tony

    1995-01-01

    Competitive electronic imaging systems are emerging due to rapidly declining processing power and storage costs. Imaging converts information on paper to electronic pictures. For applications involving large quantities of paper documents, the resulting pictures are further processed by automated character recognition systems, resulting in a text representation of the original document. Current character recognition accuracy varies from one implementation to the next, and greatly depends on each particular application. We define a set of information fusion rules for combining character recognition system output. The combined result has a higher character recognition accuracy and lower error rate than either of the individual recognizer outputs taken separately. This new set of fusion heuristics takes advantage of the following information from multiple text string recognition systems simultaneously: (1) multiple hypotheses and associated confidences for each character in a text string; (2) multiple text string segmentation hypotheses; (3) separate or combined hypotheses for both uppercase and lowercase alphabetic characters; and (4) overall text string hypotheses and associated confidences. Traditionally, only the last of these four information groups is used for fusion of multiple classifications within character recognition systems. We report on a nationally sponsored character recognition benchmark, with results indicating increased accuracy using the heuristic rules described.

  19. Disintegration, recognition, and violence: a theoretical perspective.

    PubMed

    Heitmeyer, Wilhelm; Anhut, Reimund

    2008-01-01

    The literature explaining deviance, criminality, or violence offers a broad spectrum of approaches in criminology and sociology. Mostly the theories focus on specific levels of explanation like the macrolevel (for example, strain theories) or the microlevel (for example, self-control theory).This article presents a relatively new theoretical approach combining different levels and focusing on three dimensions associated with specific kinds of recognition: social-structural, institutional, and socioemotional. The social-structural dimension refers to access to the functional systems of society and the accompanying recognition of position, status, and so on. The institutional dimension concentrates on the opportunity to participate in public affairs with the aim of getting moral recognition. The socioemotional dimension emphasizes the quantity and quality of integration in and social support from families, friends, partners, and so on, which provide emotional recognition.The underlying idea is that lack of access, participation, and belonging causes a lack of recognition. When this happens, social and individual problems increase. Thus, deviant and violent behavior can be seen as one potential reaction to a lack of recognition and as a way to gain status and recognition in a different manner (for example, with a delinquent peer group or other gang).

  20. [Face recognition in patients with schizophrenia].

    PubMed

    Doi, Hirokazu; Shinohara, Kazuyuki

    2012-07-01

    It is well known that patients with schizophrenia show severe deficiencies in social communication skills. These deficiencies are believed to be partly derived from abnormalities in face recognition. However, the exact nature of these abnormalities exhibited by schizophrenic patients with respect to face recognition has yet to be clarified. In the present paper, we review the main findings on face recognition deficiencies in patients with schizophrenia, particularly focusing on abnormalities in the recognition of facial expression and gaze direction, which are the primary sources of information of others' mental states. The existing studies reveal that the abnormal recognition of facial expression and gaze direction in schizophrenic patients is attributable to impairments in both perceptual processing of visual stimuli, and cognitive-emotional responses to social information. Furthermore, schizophrenic patients show malfunctions in distributed neural regions, ranging from the fusiform gyrus recruited in the structural encoding of facial stimuli, to the amygdala which plays a primary role in the detection of the emotional significance of stimuli. These findings were obtained from research in patient groups with heterogeneous characteristics. Because previous studies have indicated that impairments in face recognition in schizophrenic patients might vary according to the types of symptoms, it is of primary importance to compare the nature of face recognition deficiencies and the impairments of underlying neural functions across sub-groups of patients.

  1. Textual emotion recognition for enhancing enterprise computing

    NASA Astrophysics Data System (ADS)

    Quan, Changqin; Ren, Fuji

    2016-05-01

    The growing interest in affective computing (AC) brings a lot of valuable research topics that can meet different application demands in enterprise systems. The present study explores a sub area of AC techniques - textual emotion recognition for enhancing enterprise computing. Multi-label emotion recognition in text is able to provide a more comprehensive understanding of emotions than single label emotion recognition. A representation of 'emotion state in text' is proposed to encompass the multidimensional emotions in text. It ensures the description in a formal way of the configurations of basic emotions as well as of the relations between them. Our method allows recognition of the emotions for the words bear indirect emotions, emotion ambiguity and multiple emotions. We further investigate the effect of word order for emotional expression by comparing the performances of bag-of-words model and sequence model for multi-label sentence emotion recognition. The experiments show that the classification results under sequence model are better than under bag-of-words model. And homogeneous Markov model showed promising results of multi-label sentence emotion recognition. This emotion recognition system is able to provide a convenient way to acquire valuable emotion information and to improve enterprise competitive ability in many aspects.

  2. Selective networks and recognition automata.

    PubMed

    Reeke, G N; Edelman, G M

    1984-01-01

    The results we have presented demonstrate that a network based on a selective principle can function in the absence of forced learning or an a priori program to give recognition, classification, generalization, and association. While Darwin II is not a model of any actual nervous system, it does set out to solve one of the same problems that evolution had to solve--the need to form categories in a bottom-up manner from information in the environment, without incorporating the assumptions of any particular observer. The key features of the model that make this possible are (1) Darwin II incorporates selective networks whose initial specificities enable them to respond without instruction to unfamiliar stimuli; (2) degeneracy provides multiple possibilities of response to any one stimulus, at the same time providing functional redundancy against component failure; (3) the output of Darwin II is a pattern of response, making use of the simultaneous responses of multiple degenerate groups to avoid the need for very high specificity and the combinatorial disaster that would imply; (4) reentry within individual networks vitiates the limitations described by Minsky and Papert for a class of perceptual automata lacking such connections; and (5) reentry between intercommunicating networks with different functions gives rise to new functions, such as association, that either one alone could not display. The two kinds of network are roughly analogous to the two kinds of category formation that people use: Darwin, corresponding to the exemplar description of categories, and Wallace, corresponding to the probabilistic matching description of categories. These principles lead to a new class of pattern-recognizing machine of which Darwin II is just an example. There are a number of obvious extensions to this work that we are pursuing. These include giving Darwin II the capability to deal with stimuli that are in motion, an ability that probably precedes the ability of biological

  3. Investigating gait recognition in the short-wave infrared (SWIR) spectrum: dataset and challenges

    NASA Astrophysics Data System (ADS)

    DeCann, Brian; Ross, Arun; Dawson, Jeremy

    2013-05-01

    In the biometrics community, challenge datasets are often released to determine the robustness of state-of-the- art algorithms to conditions that can confound recognition accuracy. In the context of automated human gait recognition, evaluation has predominantly been conducted on video data acquired in the active visible spectral band, although recent literature has explored recognition in the passive thermal band. The advent of sophisticated sensors has piqued interest in performing gait recognition in other spectral bands such as short-wave infrared (SWIR), due to their use in military-based tactical applications and the possibility of operating in nighttime environments. Further, in many operational scenarios, the environmental variables are not controlled, thereby posing several challenges to traditional recognition schemes. In this work, we discuss the possibility of performing gait recognition in the SWIR spectrum by first assembling a dataset, referred to as the WVU Outdoor SWIR Gait (WOSG) Dataset, and then evaluate the performance of three gait recognition algorithms on the dataset. The dataset consists of 155 subjects and represents gait information acquired under multiple walking paths in an uncontrolled, outdoor environment. Detailed experimental analysis suggests the benefits of distributing this new challenging dataset to the broader research community. In particular, the following observations were made: (a) the importance of SWIR imagery in acquiring data covertly for surveillance applications; (b) the difficulty in extracting human silhouettes in low-contrast SWIR imagery; (c) the impact of silhouette quality on overall recognition accuracy; (d) the possibility of matching gait sequences pertaining to different walking trajectories; and (e) the need for developing sophisticated gait recognition algorithms to handle data acquired in unconstrained environments.

  4. Training and search methods for speech recognition.

    PubMed Central

    Jelinek, F

    1995-01-01

    Speech recognition involves three processes: extraction of acoustic indices from the speech signal, estimation of the probability that the observed index string was caused by a hypothesized utterance segment, and determination of the recognized utterance via a search among hypothesized alternatives. This paper is not concerned with the first process. Estimation of the probability of an index string involves a model of index production by any given utterance segment (e.g., a word). Hidden Markov models (HMMs) are used for this purpose [Makhoul, J. & Schwartz, R. (1995) Proc. Natl. Acad. Sci. USA 92, 9956-9963]. Their parameters are state transition probabilities and output probability distributions associated with the transitions. The Baum algorithm that obtains the values of these parameters from speech data via their successive reestimation will be described in this paper. The recognizer wishes to find the most probable utterance that could have caused the observed acoustic index string. That probability is the product of two factors: the probability that the utterance will produce the string and the probability that the speaker will wish to produce the utterance (the language model probability). Even if the vocabulary size is moderate, it is impossible to search for the utterance exhaustively. One practical algorithm is described [Viterbi, A. J. (1967) IEEE Trans. Inf. Theory IT-13, 260-267] that, given the index string, has a high likelihood of finding the most probable utterance. PMID:7479810

  5. Social justice and the politics of recognition.

    PubMed

    Arfken, Michael

    2013-09-01

    Comments on the original article, "Psychology and social justice: Why we do what we do" by M. J. T. Vasquez (see record 2012-18676-002). Vasquez pointed to numerous initiatives and task forces that the American Psychological Association (APA) has established to address the marginalization and subordination of various groups. There is little doubt that the concerns addressed by these initiatives and task forces are important and play a central role in the development of a just society. Although Vasquez noted that "social realities are important determinants of distress" she failed to appreciate the extent to which our social relations emerge against the background of specific political and economic structures. The cost of this oversight is the perpetuation of a politics of recognition that does little to address the economic inequalities that are a defining feature of unjust societies. Were APA to restrict its attention to psychological distress or access to resources, it would place APA in the service of maintaining rather than transforming the existing structure of society. APA should consider developing initiatives and task forces to investigate the role that capitalism plays in the perpetuation of inequality and exploitation. It may also be time to reflect on why an institution that claims to be dedicated to social justice has had so little to say about one of the dominant features of modern society.

  6. Automatic target recognition apparatus and method

    SciTech Connect

    Baumgart, Chris W.; Ciarcia, Christopher A.

    2000-01-01

    An automatic target recognition apparatus (10) is provided, having a video camera/digitizer (12) for producing a digitized image signal (20) representing an image containing therein objects which objects are to be recognized if they meet predefined criteria. The digitized image signal (20) is processed within a video analysis subroutine (22) residing in a computer (14) in a plurality of parallel analysis chains such that the objects are presumed to be lighter in shading than the background in the image in three of the chains and further such that the objects are presumed to be darker than the background in the other three chains. In two of the chains the objects are defined by surface texture analysis using texture filter operations. In another two of the chains the objects are defined by background subtraction operations. In yet another two of the chains the objects are defined by edge enhancement processes. In each of the analysis chains a calculation operation independently determines an error factor relating to the probability that the objects are of the type which should be recognized, and a probability calculation operation combines the results of the analysis chains.

  7. Isolated digit recognition without time alignment

    NASA Astrophysics Data System (ADS)

    Gay, Jeffrey Mark

    1994-12-01

    This thesis examines methods for isolated digit recognition without using time alignment. Resource requirements for isolated word recognizers that use time alignment can become prohibitively large as the vocabulary to be classified grows. Thus, methods capable of achieving recognition rates comparable to those obtained with current methods using these techniques are needed. The goals of this research are to find feature sets for speech recognition that perform well without using time alignment, and to identify classifiers that provide good performance with these features. Using the digits from the TI46 database, baseline speaker-independent recognition rates of 95.2% for the complete speaker set and 98.1% for the male speaker set are established using dynamic time warping (DTW). This work begins with features derived from spectrograms of each digit. Based on a critical band frequency scale covering the telephone bandwidth (300-3000 Hz), these critical band energy features are classified alone and in combination with several other feature sets, with several different classifiers. With this method, there is one 'short' feature vector per word. For speaker-independent recognition using the complete speaker set and a multi-layer perceptron (MLP) classifier, a recognition rate of 92.4% is achieved. For the same classifier with the male speaker set, a recognition rate of 97.1% is achieved. For the male speaker set, there is no statistical difference between results using DTW, and those using the MLP and no time alignment. This shows that there are feature sets that may provide high recognition rates for isolated word recognition without the need for time alignment.

  8. Recognition in a social symbiosis: chemical phenotypes and nestmate recognition behaviors of neotropical parabiotic ants.

    PubMed

    Emery, Virginia J; Tsutsui, Neil D

    2013-01-01

    Social organisms rank among the most abundant and ecologically dominant species on Earth, in part due to exclusive recognition systems that allow cooperators to be distinguished from exploiters. Exploiters, such as social parasites, manipulate their hosts' recognition systems, whereas cooperators are expected to minimize interference with their partner's recognition abilities. Despite our wealth of knowledge about recognition in single-species social nests, less is known of the recognition systems in multi-species nests, particularly involving cooperators. One uncommon type of nesting symbiosis, called parabiosis, involves two species of ants sharing a nest and foraging trails in ostensible cooperation. Here, we investigated recognition cues (cuticular hydrocarbons) and recognition behaviors in the parabiotic mixed-species ant nests of Camponotus femoratus and Crematogaster levior in North-Eastern Amazonia. We found two sympatric, cryptic Cr. levior chemotypes in the population, with one type in each parabiotic colony. Although they share a nest, very few hydrocarbons were shared between Ca. femoratus and either Cr. levior chemotype. The Ca. femoratus hydrocarbons were also unusually long-chained branched alkenes and dienes, compounds not commonly found amongst ants. Despite minimal overlap in hydrocarbon profile, there was evidence of potential interspecific nestmate recognition -Cr. levior ants were more aggressive toward Ca. femoratus non-nestmates than Ca. femoratus nestmates. In contrast to the prediction that sharing a nest could weaken conspecific recognition, each parabiotic species also maintains its own aggressive recognition behaviors to exclude conspecific non-nestmates. This suggests that, despite cohabitation, parabiotic ants maintain their own species-specific colony odors and recognition mechanisms. It is possible that such social symbioses are enabled by the two species each using their own separate recognition cues, and that interspecific nestmate

  9. Evolutionarily diverse determinants of meiotic DNA break and recombination landscapes across the genome

    PubMed Central

    Fowler, Kyle R.; Sasaki, Mariko; Milman, Neta

    2014-01-01

    Fission yeast Rec12 (Spo11 homolog) initiates meiotic recombination by forming developmentally programmed DNA double-strand breaks (DSBs). DSB distributions influence patterns of heredity and genome evolution, but the basis of the highly nonrandom choice of Rec12 cleavage sites is poorly understood, largely because available maps are of relatively low resolution and sensitivity. Here, we determined DSBs genome-wide at near-nucleotide resolution by sequencing the oligonucleotides attached to Rec12 following DNA cleavage. The single oligonucleotide size class allowed us to deeply sample all break events. We find strong evidence across the genome for differential DSB repair accounting for crossover invariance (constant cM/kb in spite of DSB hotspots). Surprisingly, about half of all crossovers occur in regions where DSBs occur at low frequency and are widely dispersed in location from cell to cell. These previously undetected, low-level DSBs thus play an outsized and crucial role in meiosis. We further find that the influence of underlying nucleotide sequence and chromosomal architecture differs in multiple ways from that in budding yeast. DSBs are not strongly restricted to nucleosome-depleted regions, as they are in budding yeast, but are nevertheless spatially influenced by chromatin structure. Our analyses demonstrate that evolutionarily fluid factors contribute to crossover initiation and regulation. PMID:25024163

  10. Asymmetric bulges and mismatches determine 20-nt microRNA formation in plants

    PubMed Central

    Lee, Wen-Chi; Lu, Shin-Hua; Lu, Ming-Hsuan; Yang, Chen-Jui; Wu, Shu-Hsing; Chen, Ho-Ming

    2015-01-01

    Plant microRNAs (miRNAs) are predominantly 21 nucleotides (nt) long but non-canonical lengths of 22 and 20 nt are commonly observed in diverse plant species. While miRNAs longer than 21 nt can be attributed to the neglect of unpaired bases within asymmetric bulges by the ruler function of DICER-LIKE 1 (DCL1), how 20-nt miRNA is generated remains obscure. Analysis of small RNA data revealed that 20-nt miRNA can be divided into 3 main groups featured by atypical 3′ overhangs or shorter duplex regions. Asymmetric bulges or mismatches at specific positions are commonly observed within each group and were shown to be crucial for 20-nt miRNA formation. Analysis of DCL1 cleavage sites on 20-nt miRNA precursors suggests that these determinants might alter precursor structure or trigger 3′-end decay of mature miRNA. The results herein advance our understanding of miRNA biogenesis and demonstrate that the effect of asymmetric bulges on miRNA length could be position-dependent. PMID:26383777

  11. Purposive recognition: an active and qualitative approach

    NASA Astrophysics Data System (ADS)

    Rivlin, Ehud; Aloimonos, Yiannis; Rosenfeld, Azriel

    1992-04-01

    We propose an alternative way to study the problem of visual recognition which is closer to the spirit emerging from Brooks' work on building robots than to Marr's reconstructive approach. Our theory is purposive in the sense that recognition is considered in the context of an agent performing it in an environment, along with the agent's intentions that translate into a set of behaviors; it is qualitative in the sense that only partial recovery is needed; it is active in the sense that various partial recovery tasks need for recognition are achieved through active vision; and it is opportunistic in the sense that every available cue is used.

  12. Automatic recognition of targets from hyperspectra images

    NASA Astrophysics Data System (ADS)

    Lampropoulos, George A.; Li, Yifeng; Boulter, James F.

    1998-12-01

    In this paper, we present the formulation of the problem for recognition of targets from hyperspectra images. It is shown that conventional recognition techniques may be extended to hyperspectra images for the distribution process. It is also shown that the recognition process is directly proportional to the number of multispectra frames that represent each target. For the discrimination process we propose a parametric and a nonparametric process in which both are extensions to Fisher and Fukunaga-Mantock methods respectively. Examples that show the composition of hyperspectra features are presented.

  13. Segmentation-free ocular detection and recognition

    NASA Astrophysics Data System (ADS)

    Rodriguez, Andres; Panza, Jeffrey; Vijaya Kumar, B. V. K.

    2011-06-01

    Iris recognition is a well-known technique to identify persons. However this technique requires high resolution images in order to automatically segment the iris. In some scenarios obtaining the required resolution may be difficult. In this paper, we investigate the recognition of ocular regions using correlation filters without segmenting the iris region. This method uses the whole eye region and surrounding areas, i.e., the ocular region, for identification. In our experiments we use the recently developed Quadratic Correlation Filter and show that at low resolutions segmentation-free ocular recognition can succeed while iris segmentation fails.

  14. Gait recognition based on integral outline

    NASA Astrophysics Data System (ADS)

    Ming, Guan; Fang, Lv

    2017-02-01

    Biometric identification technology replaces traditional security technology, which has become a trend, and gait recognition also has become a hot spot of research because its feature is difficult to imitate and theft. This paper presents a gait recognition system based on integral outline of human body. The system has three important aspects: the preprocessing of gait image, feature extraction and classification. Finally, using a method of polling to evaluate the performance of the system, and summarizing the problems existing in the gait recognition and the direction of development in the future.

  15. Modelling of DNA-protein recognition

    NASA Technical Reports Server (NTRS)

    Rein, R.; Garduno, R.; Colombano, S.; Nir, S.; Haydock, K.; Macelroy, R. D.

    1980-01-01

    Computer model-building procedures using stereochemical principles together with theoretical energy calculations appear to be, at this stage, the most promising route toward the elucidation of DNA-protein binding schemes and recognition principles. A review of models and bonding principles is conducted and approaches to modeling are considered, taking into account possible di-hydrogen-bonding schemes between a peptide and a base (or a base pair) of a double-stranded nucleic acid in the major groove, aspects of computer graphic modeling, and a search for isogeometric helices. The energetics of recognition complexes is discussed and several models for peptide DNA recognition are presented.

  16. Hippocampus and neocortex: recognition and spatial memory.

    PubMed

    Vann, Seralynne D; Albasser, Mathieu M

    2011-06-01

    Recognition and spatial memory are typically associated with the perirhinal cortex and hippocampal formation, respectively. Solely focusing on these structures for these specific mnemonic functions may, however, be limiting progress in the field. The distinction between these subdivisions of memory is becoming less defined as, for example, hippocampal cells traditionally considered to encode locations also encode place-object associations. There is increasing evidence for the involvement of overlapping networks of brain structures for aspects of both spatial and recognition memory. Future models of spatial and recognition memory will have to extend beyond the hippocampus and perirhinal cortex to incorporate a wider network of cortical and subcortical structures.

  17. Traditional facial tattoos disrupt face recognition processes.

    PubMed

    Buttle, Heather; East, Julie

    2010-01-01

    Factors that are important to successful face recognition, such as features, configuration, and pigmentation/reflectance, are all subject to change when a face has been engraved with ink markings. Here we show that the application of facial tattoos, in the form of spiral patterns (typically associated with the Maori tradition of a Moko), disrupts face recognition to a similar extent as face inversion, with recognition accuracy little better than chance performance (2AFC). These results indicate that facial tattoos can severely disrupt our ability to recognise a face that previously did not have the pattern.

  18. Cortical Networks for Visual Self-Recognition

    NASA Astrophysics Data System (ADS)

    Sugiura, Motoaki

    This paper briefly reviews recent developments regarding the brain mechanisms of visual self-recognition. A special cognitive mechanism for visual self-recognition has been postulated based on behavioral and neuropsychological evidence, but its neural substrate remains controversial. Recent functional imaging studies suggest that multiple cortical mechanisms play self-specific roles during visual self-recognition, reconciling the existing controversy. Respective roles for the left occipitotemporal, right parietal, and frontal cortices in symbolic, visuospatial, and conceptual aspects of self-representation have been proposed.

  19. Combinatorial methods for gene recognition

    SciTech Connect

    Pevzner, P.A.

    1997-10-29

    The major result of the project is the development of a new approach to gene recognition called spliced alignment algorithm. They have developed an algorithm and implemented a software tool (for both IBM PC and UNIX platforms) which explores all possible exon assemblies in polynomial time and finds the multi-exon structure with the best fit to a related protein. Unlike other existing methods, the algorithm successfully performs exons assemblies even in the case of short exons or exons with unusual codon usage; they also report correct assemblies for the genes with more than 10 exons provided a homologous protein is already known. On a test sample of human genes with known mammalian relatives the average overlap between the predicted and the actual genes was 99%, which is remarkably well as compared to other existing methods. At that, the algorithm absolute correctly reconstructed 87% of genes. The rare discrepancies between the predicted and real axon-intron structures were restricted either to extremely short initial or terminal exons or proved to be results of alternative splicing. Moreover, the algorithm performs reasonably well with non-vertebrate and even prokaryote targets. The spliced alignment software PROCRUSTES has been in extensive use by the academic community since its announcement in August, 1996 via the WWW server (www-hto.usc.edu/software/procrustes) and by biotech companies via the in-house UNIX version.

  20. DCT-based iris recognition.

    PubMed

    Monro, Donald M; Rakshit, Soumyadip; Zhang, Dexin

    2007-04-01

    This paper presents a novel iris coding method based on differences of discrete cosine transform (DCT) coefficients of overlapped angular patches from normalized iris images. The feature extraction capabilities of the DCT are optimized on the two largest publicly available iris image data sets, 2,156 images of 308 eyes from the CASIA database and 2,955 images of 150 eyes from the Bath database. On this data, we achieve 100 percent Correct Recognition Rate (CRR) and perfect Receiver-Operating Characteristic (ROC) Curves with no registered false accepts or rejects. Individual feature bit and patch position parameters are optimized for matching through a product-of-sum approach to Hamming distance calculation. For verification, a variable threshold is applied to the distance metric and the False Acceptance Rate (FAR) and False Rejection Rate (FRR) are recorded. A new worst-case metric is proposed for predicting practical system performance in the absence of matching failures, and the worst case theoretical Equal Error Rate (EER) is predicted to be as low as 2.59 x 10(-4) on the available data sets.

  1. Viral cell recognition and entry.

    PubMed Central

    Rossmann, M. G.

    1994-01-01

    Rhinovirus infection is initiated by the recognition of a specific cell-surface receptor. The major group of rhinovirus serotypes attach to intercellular adhesion molecule-1 (ICAM-1). The attachment process initiates a series of conformational changes resulting in the loss of genomic RNA from the virion. X-ray crystallography and sequence comparisons suggested that a deep crevice or canyon is the site on the virus recognized by the cellular receptor molecule. This has now been verified by electron microscopy of human rhinovirus 14 (HRV14) and HRV16 complexed with a soluble component of ICAM-1. A hydrophobic pocket underneath the canyon is the site of binding of various hydrophobic drug compounds that can inhibit attachment and uncoating. This pocket is also associated with an unidentified, possibly cellular in origin, "pocket factor." The pocket factor binding site overlaps the binding site of the receptor. It is suggested that competition between the pocket factor and receptor regulates the conformational changes required for the initiation of the entry of the genomic RNA into the cell. PMID:7849588

  2. Learning curve of speech recognition.

    PubMed

    Kauppinen, Tomi A; Kaipio, Johanna; Koivikko, Mika P

    2013-12-01

    Speech recognition (SR) speeds patient care processes by reducing report turnaround times. However, concerns have emerged about prolonged training and an added secretarial burden for radiologists. We assessed how much proofing radiologists who have years of experience with SR and radiologists new to SR must perform, and estimated how quickly the new users become as skilled as the experienced users. We studied SR log entries for 0.25 million reports from 154 radiologists and after careful exclusions, defined a group of 11 experienced radiologists and 71 radiologists new to SR (24,833 and 122,093 reports, respectively). Data were analyzed for sound file and report lengths, character-based error rates, and words unknown to the SR's dictionary. Experienced radiologists corrected 6 characters for each report and for new users, 11. Some users presented a very unfavorable learning curve, with error rates not declining as expected. New users' reports were longer, and data for the experienced users indicates that their reports, initially equally lengthy, shortened over a period of several years. For most radiologists, only minor corrections of dictated reports were necessary. While new users adopted SR quickly, with a subset outperforming experienced users from the start, identification of users struggling with SR will help facilitate troubleshooting and support.

  3. Place recognition using batlike sonar

    PubMed Central

    Vanderelst, Dieter; Steckel, Jan; Boen, Andre; Peremans, Herbert; Holderied, Marc W

    2016-01-01

    Echolocating bats have excellent spatial memory and are able to navigate to salient locations using bio-sonar. Navigating and route-following require animals to recognize places. Currently, it is mostly unknown how bats recognize places using echolocation. In this paper, we propose template based place recognition might underlie sonar-based navigation in bats. Under this hypothesis, bats recognize places by remembering their echo signature - rather than their 3D layout. Using a large body of ensonification data collected in three different habitats, we test the viability of this hypothesis assessing two critical properties of the proposed echo signatures: (1) they can be uniquely classified and (2) they vary continuously across space. Based on the results presented, we conclude that the proposed echo signatures satisfy both criteria. We discuss how these two properties of the echo signatures can support navigation and building a cognitive map. DOI: http://dx.doi.org/10.7554/eLife.14188.001 PMID:27481189

  4. Distributed nestmate recognition in ants

    PubMed Central

    Esponda, Fernando; Gordon, Deborah M.

    2015-01-01

    We propose a distributed model of nestmate recognition, analogous to the one used by the vertebrate immune system, in which colony response results from the diverse reactions of many ants. The model describes how individual behaviour produces colony response to non-nestmates. No single ant knows the odour identity of the colony. Instead, colony identity is defined collectively by all the ants in the colony. Each ant responds to the odour of other ants by reference to its own unique decision boundary, which is a result of its experience of encounters with other ants. Each ant thus recognizes a particular set of chemical profiles as being those of non-nestmates. This model predicts, as experimental results have shown, that the outcome of behavioural assays is likely to be variable, that it depends on the number of ants tested, that response to non-nestmates changes over time and that it changes in response to the experience of individual ants. A distributed system allows a colony to identify non-nestmates without requiring that all individuals have the same complete information and helps to facilitate the tracking of changes in cuticular hydrocarbon profiles, because only a subset of ants must respond to provide an adequate response. PMID:25833853

  5. Distributed nestmate recognition in ants.

    PubMed

    Esponda, Fernando; Gordon, Deborah M

    2015-05-07

    We propose a distributed model of nestmate recognition, analogous to the one used by the vertebrate immune system, in which colony response results from the diverse reactions of many ants. The model describes how individual behaviour produces colony response to non-nestmates. No single ant knows the odour identity of the colony. Instead, colony identity is defined collectively by all the ants in the colony. Each ant responds to the odour of other ants by reference to its own unique decision boundary, which is a result of its experience of encounters with other ants. Each ant thus recognizes a particular set of chemical profiles as being those of non-nestmates. This model predicts, as experimental results have shown, that the outcome of behavioural assays is likely to be variable, that it depends on the number of ants tested, that response to non-nestmates changes over time and that it changes in response to the experience of individual ants. A distributed system allows a colony to identify non-nestmates without requiring that all individuals have the same complete information and helps to facilitate the tracking of changes in cuticular hydrocarbon profiles, because only a subset of ants must respond to provide an adequate response.

  6. Recurrent Processing during Object Recognition

    PubMed Central

    O’Reilly, Randall C.; Wyatte, Dean; Herd, Seth; Mingus, Brian; Jilk, David J.

    2013-01-01

    How does the brain learn to recognize objects visually, and perform this difficult feat robustly in the face of many sources of ambiguity and variability? We present a computational model based on the biology of the relevant visual pathways that learns to reliably recognize 100 different object categories in the face of naturally occurring variability in location, rotation, size, and lighting. The model exhibits robustness to highly ambiguous, partially occluded inputs. Both the unified, biologically plausible learning mechanism and the robustness to occlusion derive from the role that recurrent connectivity and recurrent processing mechanisms play in the model. Furthermore, this interaction of recurrent connectivity and learning predicts that high-level visual representations should be shaped by error signals from nearby, associated brain areas over the course of visual learning. Consistent with this prediction, we show how semantic knowledge about object categories changes the nature of their learned visual representations, as well as how this representational shift supports the mapping between perceptual and conceptual knowledge. Altogether, these findings support the potential importance of ongoing recurrent processing throughout the brain’s visual system and suggest ways in which object recognition can be understood in terms of interactions within and between processes over time. PMID:23554596

  7. A Fast Goal Recognition Technique Based on Interaction Estimates

    NASA Technical Reports Server (NTRS)

    E-Martin, Yolanda; R-Moreno, Maria D.; Smith, David E.

    2015-01-01

    Goal Recognition is the task of inferring an actor's goals given some or all of the actor's observed actions. There is considerable interest in Goal Recognition for use in intelligent personal assistants, smart environments, intelligent tutoring systems, and monitoring user's needs. In much of this work, the actor's observed actions are compared against a generated library of plans. Recent work by Ramirez and Geffner makes use of AI planning to determine how closely a sequence of observed actions matches plans for each possible goal. For each goal, this is done by comparing the cost of a plan for that goal with the cost of a plan for that goal that includes the observed actions. This approach yields useful rankings, but is impractical for real-time goal recognition in large domains because of the computational expense of constructing plans for each possible goal. In this paper, we introduce an approach that propagates cost and interaction information in a plan graph, and uses this information to estimate goal probabilities. We show that this approach is much faster, but still yields high quality results.

  8. Auditory orientation in crickets: Pattern recognition controls reactive steering

    NASA Astrophysics Data System (ADS)

    Poulet, James F. A.; Hedwig, Berthold

    2005-10-01

    Many groups of insects are specialists in exploiting sensory cues to locate food resources or conspecifics. To achieve orientation, bees and ants analyze the polarization pattern of the sky, male moths orient along the females' odor plume, and cicadas, grasshoppers, and crickets use acoustic signals to locate singing conspecifics. In comparison with olfactory and visual orientation, where learning is involved, auditory processing underlying orientation in insects appears to be more hardwired and genetically determined. In each of these examples, however, orientation requires a recognition process identifying the crucial sensory pattern to interact with a localization process directing the animal's locomotor activity. Here, we characterize this interaction. Using a sensitive trackball system, we show that, during cricket auditory behavior, the recognition process that is tuned toward the species-specific song pattern controls the amplitude of auditory evoked steering responses. Females perform small reactive steering movements toward any sound patterns. Hearing the male's calling song increases the gain of auditory steering within 2-5 s, and the animals even steer toward nonattractive sound patterns inserted into the speciesspecific pattern. This gain control mechanism in the auditory-to-motor pathway allows crickets to pursue species-specific sound patterns temporarily corrupted by environmental factors and may reflect the organization of recognition and localization networks in insects. localization | phonotaxis

  9. Shape recognition of acoustic scatterers using the singularity expansion method

    NASA Astrophysics Data System (ADS)

    Cao, Pei; Wu, Jiu Hui

    2017-03-01

    Acoustic target recognition for two-dimensional (2D) acoustic scatterers is investigated using the singularity expansion method (SEM). Based on the Watson transformation series of the scattering field, the SEM poles can be calculated and their physical interpretation given, along with the exact normal mode for any acoustic scattering problem. Typical oscillatory phenomena appear as a series of damped sinusoidal signals in the time domain and as a standing-wave distribution in the space. These external oscillation modes are associated with the SEM poles. We note that the positions of these poles in the complex frequency plane are uniquely determined by the shape and flexible characteristics of the target regardless of the waveforms and positions of the incident signals. We then infer that SEM poles can be used as the characteristic parameters for target shape recognition. The relationship between the positions of SEM poles and the geometrical characters of 2D scatterers has been established not only for cylinders but also for other general 2D scatterers. The new method and the related calculation results provide an effective way to perform shape recognition using an acoustic scattering field, with potential applications in non-destructive testing and acoustic imaging.

  10. Perspective projection for variance pose face recognition from camera calibration

    NASA Astrophysics Data System (ADS)

    Fakhir, M. M.; Woo, W. L.; Chambers, J. A.; Dlay, S. S.

    2016-04-01

    Variance pose is an important research topic in face recognition. The alteration of distance parameters across variance pose face features is a challenging. We provide a solution for this problem using perspective projection for variance pose face recognition. Our method infers intrinsic camera parameters of the image which enable the projection of the image plane into 3D. After this, face box tracking and centre of eyes detection can be identified using our novel technique to verify the virtual face feature measurements. The coordinate system of the perspective projection for face tracking allows the holistic dimensions for the face to be fixed in different orientations. The training of frontal images and the rest of the poses on FERET database determine the distance from the centre of eyes to the corner of box face. The recognition system compares the gallery of images against different poses. The system initially utilises information on position of both eyes then focuses principally on closest eye in order to gather data with greater reliability. Differentiation between the distances and position of the right and left eyes is a unique feature of our work with our algorithm outperforming other state of the art algorithms thus enabling stable measurement in variance pose for each individual.

  11. Hand posture recognition using jointly optical flow and dimensionality reduction

    NASA Astrophysics Data System (ADS)

    Boughnim, Nabil; Marot, Julien; Fossati, Caroline; Bourennane, Salah

    2013-12-01

    Hand posture recognition is generally addressed by using either YC b C r (luminance and chrominance components) or HSV (hue, saturation, value) mappings which assume that a hand can be distinguished from the background from some colorfulness and luminance properties. This can hardly be used when a dark hand, or a hand of any color, is under study. In addition, existing recognition processes rely on descriptors or geometric shapes which can be reliable; this comes at the expense of an increased computational complexity. To cope with these drawbacks, this paper proposes a four-step method recognition technique consisting of (i) a pyramidal optical flow for the detection of large movements and hence determine the region of interest containing the expected hand, (ii) a preprocessing step to compute the hand contour while ensuring geometric and illumination invariance, (iii) an image scanning method providing a signature which characterizes non-star-shaped contours with a one-pixel precision, and (iv) a posture classification method where a sphericity criterion preselects a set of candidate postures, principal component analysis reduces the dimensionality of the data, and Mahalanobis distance is used as a criterion to identify the hand posture in any test image. The proposed technique has been assessed in terms of its performances including the computational complexity using both visual and statistical results.

  12. Apramycin Recognition by the Human Ribosomal Decoding Site

    SciTech Connect

    Hermann,T.; Tereshko, V.; Skripkin, E.; Patel, D.

    2007-01-01

    Aminoglycoside antibiotics bind specifically to the bacterial ribosomal decoding-site RNA and thereby interfere with fidelity but not efficiency of translation. Apramycin stands out among aminoglycosides for its mechanism of action which is based on blocking translocation and its ability to bind also to the eukaryotic decoding site despite differences in key residues required for apramycin recognition by the bacterial target. To elucidate molecular recognition of the eukaryotic decoding site by apramycin we have determined the crystal structure of an oligoribonucleotide containing the human sequence free and in complex with the antibiotic at 1.5 {angstrom} resolution. The drug binds in the deep groove of the RNA which forms a continuously stacked helix comprising non-canonical C{center_dot}A and G{center_dot}A base pairs and a bulged-out adenine. The binding mode of apramycin at the human decoding-site RNA is distinct from aminoglycoside recognition of the bacterial target, suggesting a molecular basis for the actions of apramycin in eukaryotes and bacteria.

  13. Kin recognition: Competition and cooperation in Impatiens (Balsaminaceae).

    PubMed

    Murphy, Guillermo P; Dudley, Susan A

    2009-11-01

    The ability to recognize kin is an important element in social behavior and can lead to the evolution of altruism. Recently, it has been shown that plants are capable of kin recognition through root interactions. Here we tested for kin recognition in a North American species of Impatiens that has a high opportunity of growing with kin and responds strongly to aboveground competition. We measured how the plants responded to the aboveground light quality cues of competition and to the presence of root neighbors and determined whether the responses depended on whether the neighbors were siblings or strangers. The study families were identified by DNA sequencing as members of the same species, provisionally identified as Impatiens pallida (hereafter I. cf. pallida). We found that I. cf. pallida plants were capable of kin recognition, but only in the presence of another plant's roots. Several traits responded to relatedness in shared pots, including increased leaf to root allocation with strangers and increased stem elongation and branchiness in response to kin, potentially indicating both increased competition toward strangers and reduced interference (cooperation) toward kin. Impatiens cf. pallida responded to both competition cues simultaneously, with the responses to the aboveground competition cue dependent on the presence of the belowground competition cue.

  14. Temporal regulation of kin recognition maintains recognition-cue diversity and suppresses cheating.

    PubMed

    Ho, Hsing-I; Shaulsky, Gad

    2015-05-28

    Kin recognition, the ability to distinguish kin from non-kin, can facilitate cooperation between relatives. Evolutionary theory predicts that polymorphism in recognition cues, which is essential for effective recognition, would be unstable. Individuals carrying rare recognition cues would benefit less from social interactions than individuals with common cues, leading to loss of the genetic-cue diversity. We test this evolutionary hypothesis in Dictyostelium discoideum, which forms multicellular fruiting bodies by aggregation and utilizes two polymorphic membrane proteins to facilitate preferential cooperation. Surprisingly, we find that rare recognition variants are tolerated and maintain their frequencies among incompatible majority during development. Although the rare variants are initially excluded from the aggregates, they subsequently rejoin the aggregate and produce spores. Social cheating is also refrained in late development, thus limiting the cost of chimerism. Our results suggest a potential mechanism to sustain the evolutionary stability of kin-recognition genes and to suppress cheating.

  15. When false recognition is unopposed by true recognition: gist-based memory distortion in Alzheimer's disease.

    PubMed

    Budson, A E; Daffner, K R; Desikan, R; Schacter, D L

    2000-04-01

    The authors examined false recognition of semantic associates in patients with probable Alzheimer's disease (AD), older adults, and young adults using a paradigm that provided rates of false recognition after single and multiple exposures to word lists. Using corrected false recognition scores to control for unrelated false alarms, the authors found that (a) the level of false recognition after a single list exposure was lower in AD patients than in controls; (b) across 5 trials, false recognition increased in AD patients, decreased in young adults, and showed a fluctuating pattern in older adults; and (c) all groups showed an increase in true recognition over the 5 trials. Analyses suggested that AD patients built up semantic gist across trials, whereas both control groups were able to use increased item-specific recollection and more conservative response criteria to suppress gist-based false alarms.

  16. Sequence-Specific Recognition and Cleavage of Telomeric Repeat (TTAGG)n by Endonuclease of Non-Long Terminal Repeat Retrotransposon TRAS1

    PubMed Central

    Anzai, Tomohiro; Takahashi, Hidekazu; Fujiwara, Haruhiko

    2001-01-01

    The telomere of the silkworm Bombyx mori consists of (TTAGG/CCTAA)n repeats and harbors a large number of telomeric repeat-specific non-long terminal repeat retrotransposons, such as TRAS1 and SART1. To understand how these retrotransposons recognize and integrate into the telomeric repeat in a sequence-specific manner, we expressed the apurinic-apryrimidinic endonuclease-like endonuclease domain of TRAS1 (TRAS1 EN), which is supposed to digest the target DNA, and characterized its enzymatic properties. Purified TRAS1 EN could generate specific nicks on both strands of the telomeric repeat sequence between T and A of the (TTAGG)n strand (bottom strand) and between C and T of the (CCTAA)n strand (top strand). These sites are consistent with insertion sites expected from the genomic structure of boundary regions of TRAS1. Time course studies of nicking activities on both strands revealed that the cleavages on the bottom strand preceded those on the top strand, supporting the target-primed reverse transcription model. TRAS1 EN could cleave the telomeric repeats specifically even if it was flanked by longer tracts of nontelomeric sequence, indicating that the target site specificity of the TRAS1 element was mainly determined by its EN domain. Based on mutation analyses, TRAS1 EN recognizes less than 10 bp around the initial cleavage site (upstream 7 bp and downstream 3 bp), and the GTTAG sequence especially is essential for the cleavage reaction on the bottom strand (5′. . . TTAGGTT ↓ AGG . . . 3′). TRAS1 EN, the first identified endonuclease digesting telomeric repeats, may be used as a genetic tool to shorten the telomere in insects and some other organisms. PMID:11113185

  17. Shape recognition for capacitive touch display

    NASA Astrophysics Data System (ADS)

    Guarneri, I.; Capra, A.; Farinella, G. M.; Battiato, S.

    2013-03-01

    In this paper we present a technique to classify five common classes of shapes acquired with a capacitive touch display: finger, ear, cheek, hand hold, half ear-half cheek. The need of algorithms able to discriminate among the aforementioned shapes comes from the growing diffusion of touch screen based consumer devices (e.g. smartphones, tablet, etc.). In this context, detection and the recognition of fingers are fundamental tasks in many touch based user applications (e.g., mobile games). Shape recognition algorithms are also extremely useful to identify accidental touches in order to avoid involuntary activation of the device functionalities (e.g., accidental calls). Our solution makes use of simple descriptors designed to capture discriminative information of the considered classes of shapes. The recognition is performed through a decision tree based approach whose parameters are learned on a set of labeled samples. Experimental results demonstrate that the proposed solution achieves good recognition accuracy.

  18. History of Maternal Recognition of Pregnancy.

    PubMed

    Bazer, Fuller W

    2015-01-01

    The mechanism for signaling pregnancy recognition is highly variable among species, and the signaling molecule itself varies between estrogens in pigs to chorionic gonadotrophin in primates. This chapter provides insight into the menstrual cycle of women and estrous cycles of rodents, dog, cat, pigs, sheep, rabbits, and marsupials, as well as the hormones required for pregnancy recognition. Pregnancy recognition involves specific hormones such as prolactin in rodents or interferons in ruminants and estrogens in pigs that in their own way ensure the maintenance of the corpus luteum and its secretion of progesterone which is the hormone of pregnancy. However, these pregnancy recognition signals may also modify gene expression in a cell-specific and temporal manner to ensure the growth and development of the conceptus. This chapter provides some historical aspects of the development of understanding of mechanisms for the establishment and maintenance of pregnancy in several species of mammals.

  19. Relevance feedback-based building recognition

    NASA Astrophysics Data System (ADS)

    Li, Jing; Allinson, Nigel M.

    2010-07-01

    Building recognition is a nontrivial task in computer vision research which can be utilized in robot localization, mobile navigation, etc. However, existing building recognition systems usually encounter the following two problems: 1) extracted low level features cannot reveal the true semantic concepts; and 2) they usually involve high dimensional data which require heavy computational costs and memory. Relevance feedback (RF), widely applied in multimedia information retrieval, is able to bridge the gap between the low level visual features and high level concepts; while dimensionality reduction methods can mitigate the high-dimensional problem. In this paper, we propose a building recognition scheme which integrates the RF and subspace learning algorithms. Experimental results undertaken on our own building database show that the newly proposed scheme appreciably enhances the recognition accuracy.

  20. A Neural Network Based Speech Recognition System

    DTIC Science & Technology

    1990-02-01

    encoder and identifies individual words. This use of neural networks offers two advantages over conventional algorithmic detectors: the detection...environment. Keywords: Artificial intelligence; Neural networks : Back propagation; Speech recognition.