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Endogenous peptides bound to HLA-A3 possess a specific combination of anchor residues that permit identification of potential antigenic peptides.

DiBrino, M; Parker, K C; Shiloach, J; Knierman, M; Lukszo, J; Turner, R V; Biddison, W E; Coligan, J E
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em 15/02/1993 Português
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A motif specific to peptides that bind to the human class I major histocompatibility complex molecule HLA-A3 was identified by sequence analysis of HPLC fractions containing endogenous peptides. Twenty-six different sequences were obtained, 19 of which were nonamers. The majority of these endogenous peptide sequences contained Leu at position (P)2, while most sequences contained Tyr or Lys at P9. In addition, Phe was shared by 16 sequences at P3. Synthetic peptides corresponding to endogenous peptide sequences were shown to bind to HLA-A3. The importance of Leu at P2 and Tyr or Lys at P9 ("anchor" residues) for peptide binding to HLA-A3 was demonstrated by the following results: (i) peptides GLFGGGGGY, GLFGGGGGK, and GLGGGGFGY, but not GLFGGGGGV, specifically bound to HLA-A3 and (ii) six nonapeptides from within the influenza A nucleoprotein, matrix, and polymerase proteins, selected for synthesis based upon their possession of P2 and P9 anchor residues, were shown to bind HLA-A3. In contrast, none of a set of eight peptides that bound to HLA-A2, or six that bound to HLA-B27, bound detectably to HLA-A3. These findings provide a rationale for the design and selection of peptides that can be recognized by HLA-A3-restricted T cells.

Allele-specific B pocket transplant in class I major histocompatibility complex protein changes requirement for anchor residue at P2 of peptide.

Colbert, R A; Rowland-Jones, S L; McMichael, A J; Frelinger, J A
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em 15/07/1993 Português
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To investigate the role of an anchoring pocket in allele-specific peptide presentation by a major histocompatibility complex class I molecule, we "transplanted" a B pocket from HLA-A*0201 into HLA-B*2705 by site-directed mutagenesis. The resulting protein, designated B27.A2B, binds a different set of endogenous peptides than B*2705 as evidenced by complete loss of allorecognition as well as restored expression in the antigen processing-defective mutant cell line T2. B27.A2B also fails to present an HLA-B27-restricted influenza virus peptide [nucleoprotein (383-391)] to cytotoxic T lymphocytes (CTLs). However, substitution of leucine, the predominant P2 anchor residue in A*0201-restricted peptides, for arginine, the P2 anchor in nucleoprotein-(383-391) and other B*2705-restricted peptides, restores recognition of B27.A2B by the same B*2705-restricted peptide-specific CTLs. These results demonstrate that a dominant polymorphic pocket in a class I molecule, through interaction with the anchor residue of an antigenic peptide, can distinguish among peptides differing by only a single amino acid and thus determine the allelic specificity of peptide presentation.

Comparative analysis of bacterial genomes: identification of divergent regions in mycobacterial strains using an anchor-based approach

Vishnoi, Anchal; Roy, Rahul; Bhattacharya, Alok
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
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Comparative genomic approaches are useful in identifying molecular differences between organisms. Currently available methods fail to identify small changes in genomes, such as expansion of short repetitive motifs and to analyse divergent sequences. In this report, we describe an anchor-based whole genome comparison (ABWGC) method. ABWGC is based on random sampling of anchor sequences from one genome, followed by analysis of sampled and homologous regions from the target genome. The method was applied to compare two strains of Mycobacterium tuberculosis CDC1551 and H37Rv. ABWGC was able to identify a total of 104 indels including 20 expansion of short repetitive sequences and five recombination events. It included 18 new unidentified genomic differences. ABWGC also identified 188 SNPs including eight new ones. The method was also used to compare M. tuberculosis H37Rv and M. avium genomes. ABWGC was able to correctly pick 1002 additional indels (size >100 nt) between the two organisms in contrast to MUMmer, a popular tool for comparative genomics. ABWGC was able to identify correctly repeat expansion and indels in a set of simulated sequences. The study also revealed important role of small repeat expansion in the evolution of M. tuberculosis strains.

Identification of an altered peptide ligand based on the endogenously presented, rheumatoid arthritis-associated, human cartilage glycoprotein-39(263–275) epitope: an MHC anchor variant peptide for immune modulation

Boots, Annemieke MH; Hubers, Henk; Kouwijzer, Milou; den Hoed-van Zandbrink, Leontien; Westrek-Esselink, Bernice M; van Doorn, Cindy; Stenger, Rachel; Bos, Ebo S; van Lierop, Marie-jose C; Verheijden, Gijs F; Timmers, Cornelis M; van Staveren, Catharina J
Fonte: BioMed Central Publicador: BioMed Central
Tipo: Artigo de Revista Científica
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We sought to identify an altered peptide ligand (APL) based on the endogenously expressed synovial auto-epitope of human cartilage glycoprotein-39 (HC gp-39) for modulation of cognate, HLA-DR4-restricted T cells. For this purpose we employed a panel of well-characterized T cell hybridomas generated from HC gp-39-immunized HLA-DR4 transgenic mice. The hybridomas all respond to the HC gp-39(263–275) epitope when bound to HLA-DR4(B1*0401) but differ in their fine specificities. First, the major histocompatibility complex (MHC) and T-cell receptor (TCR) contact residues were identified by analysis of single site substituted analogue peptides for HLA-DR4 binding and cognate T cell recognition using both T hybridomas and polyclonal T cells from peptide-immunized HLA-DR4 transgenic mice. Analysis of single site substituted APL by cognate T cells led to identification of Phe265 as the dominant MHC anchor. The amino acids Ala268, Ser269, Glu271 and Thr272 constituted the major TCR contact residues, as substitution at these positions did not affect HLA-DR4(B1*0401) binding but abrogated T cell responses. A structural model for visualisation of TCR recognition was derived. Second, a set of non-classical APLs, modified at the MHC key anchor position but with unaltered TCR contacts...

Integration of novel SSR and gene-based SNP marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome

Nayak, Spurthi N.; Zhu, Hongyan; Varghese, Nicy; Datta, Subhojit; Choi, Hong-Kyu; Horres, Ralf; Jüngling, Ruth; Singh, Jagbir; Kavi Kishor, P. B.; Sivaramakrishnan, S.; Hoisington, Dave A.; Kahl, Günter; Winter, Peter; Cook, Douglas R.; Varshney, Rajeev
Fonte: Springer-Verlag Publicador: Springer-Verlag
Tipo: Artigo de Revista Científica
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This study presents the development and mapping of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers in chickpea. The mapping population is based on an inter-specific cross between domesticated and non-domesticated genotypes of chickpea (Cicer arietinum ICC 4958 × C. reticulatum PI 489777). This same population has been the focus of previous studies, permitting integration of new and legacy genetic markers into a single genetic map. We report a set of 311 novel SSR markers (designated ICCM—ICRISAT chickpea microsatellite), obtained from an SSR-enriched genomic library of ICC 4958. Screening of these SSR markers on a diverse panel of 48 chickpea accessions provided 147 polymorphic markers with 2–21 alleles and polymorphic information content value 0.04–0.92. Fifty-two of these markers were polymorphic between parental genotypes of the inter-specific population. We also analyzed 233 previously published (H-series) SSR markers that provided another set of 52 polymorphic markers. An additional 71 gene-based SNP markers were developed from transcript sequences that are highly conserved between chickpea and its near relative Medicago truncatula. By using these three approaches, 175 new marker loci along with 407 previously reported marker loci were integrated to yield an improved genetic map of chickpea. The integrated map contains 521 loci organized into eight linkage groups that span 2...

Anchor-Based Whole Genome Phylogeny (ABWGP): A Tool for Inferring Evolutionary Relationship among Closely Related Microorganims

Vishnoi, Anchal; Roy, Rahul; Prasad, Hanumanthappa K.; Bhattacharya, Alok
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Publicado em 30/11/2010 Português
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Phenotypic behavior of a group of organisms can be studied using a range of molecular evolutionary tools that help to determine evolutionary relationships. Traditionally a gene or a set of gene sequences was used for generating phylogenetic trees. Incomplete evolutionary information in few selected genes causes problems in phylogenetic tree construction. Whole genomes are used as remedy. Now, the task is to identify the suitable parameters to extract the hidden information from whole genome sequences that truly represent evolutionary information. In this study we explored a random anchor (a stretch of 100 nucleotides) based approach (ABWGP) for finding distance between any two genomes, and used the distance estimates to compute evolutionary trees. A number of strains and species of Mycobacteria were used for this study. Anchor-derived parameters, such as cumulative normalized score, anchor order and indels were computed in a pair-wise manner, and the scores were used to compute distance/phylogenetic trees. The strength of branching was determined by bootstrap analysis. The terminal branches are clearly discernable using the distance estimates described here. In general, different measures gave similar trees except the trees based on indels. Overall the tree topology reflected the known biology of the organisms. This was also true for different strains of Escherichia coli. A new whole genome-based approach has been described here for studying evolutionary relationships among bacterial strains and species.

Identification of Anchor Genes during Kidney Development Defines Ontological Relationships, Molecular Subcompartments and Regulatory Pathways

Thiagarajan, Rathi D.; Georgas, Kylie M.; Rumballe, Bree A.; Lesieur, Emmanuelle; Chiu, Han Sheng; Taylor, Darrin; Tang, Dave T. P.; Grimmond, Sean M.; Little, Melissa H.
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Publicado em 28/02/2011 Português
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The development of the mammalian kidney is well conserved from mouse to man. Despite considerable temporal and spatial data on gene expression in mammalian kidney development, primarily in rodent species, there is a paucity of genes whose expression is absolutely specific to a given anatomical compartment and/or developmental stage, defined here as ‘anchor’ genes. We previously generated an atlas of gene expression in the developing mouse kidney using microarray analysis of anatomical compartments collected via laser capture microdissection. Here, this data is further analysed to identify anchor genes via stringent bioinformatic filtering followed by high resolution section in situ hybridisation performed on 200 transcripts selected as specific to one of 11 anatomical compartments within the midgestation mouse kidney. A total of 37 anchor genes were identified across 6 compartments with the early proximal tubule being the compartment richest in anchor genes. Analysis of minimal and evolutionarily conserved promoter regions of this set of 25 anchor genes identified enrichment of transcription factor binding sites for Hnf4a and Hnf1b, RbpJ (Notch signalling), PPARγ:RxRA and COUP-TF family transcription factors. This was reinforced by GO analyses which also identified these anchor genes as targets in processes including epithelial proliferation and proximal tubular function. As well as defining anchor genes...

Identification of an Anchor Residue for CheA-CheY Interactions in the Chemotaxis System of Escherichia coli ▿

Thakor, Hemang; Nicholas, Sarah; Porter, Ian M.; Hand, Nicole; Stewart, Richard C.
Fonte: American Society for Microbiology Publicador: American Society for Microbiology
Tipo: Artigo de Revista Científica
Publicado em /08/2011 Português
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Transfer of a phosphoryl group from autophosphorylated CheA (P-CheA) to CheY is an important step in the bacterial chemotaxis signal transduction pathway. This reaction involves CheY (i) binding to the P2 domain of P-CheA and then (ii) acquiring the phosphoryl group from the P1 domain. Crystal structures indicated numerous side chain interactions at the CheY-P2 binding interface. To investigate the individual contributions of the P2 side chains involved in these contacts, we analyzed the effects of eight alanine substitution mutations on CheA-CheY binding interactions. An F214A substitution in P2 caused ∼1,000-fold reduction in CheA-CheY binding affinity, while Ala substitutions at other P2 positions had small effects (E171A, E178A, and I216A) or no detectable effects (H181A, D202A, D207A, and C213A) on binding affinity. These results are discussed in relation to previous in silico predictions of hot-spot and anchor positions at the CheA-CheY interface. We also investigated the consequences of these mutations for chemotaxis signal transduction in living cells. CheA(F214A) was defective in mediating localization of CheY-YFP to the large clusters of signaling proteins that form at the poles of Escherichia coli cells, while the other CheA variants did not differ from wild-type (wt) CheA (CheAwt) in this regard. In our set of mutants...

HyBloc: Localization in Sensor Networks with Adverse Anchor Placement

Cheng, King-Yip; Lui, King-Shan; Tam, Vincent
Fonte: Molecular Diversity Preservation International (MDPI) Publicador: Molecular Diversity Preservation International (MDPI)
Tipo: Artigo de Revista Científica
Publicado em 08/01/2009 Português
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To determine the geographical positions of sensors, numerous localization algorithms have been proposed in recent years. The positions of sensors are inferred from the connectivity between sensors and a set of nodes called anchors which know their precise locations. We investigate the effect of adverse placement and density of anchors on the accuracies of different algorithms. We develop an algorithm called HyBrid Localization (HyBloc) to provide reliable localization service with a limited number of clustered anchors. HyBloc is distributed in nature with reasonable message overhead. Through simulations, we demonstrate that HyBloc provides more accurate location estimates than some existing distributed algorithms when there are only a few anchors. HyBloc also performs well when anchors are clustered together.

An SSR-based genetic map of pepper (Capsicum annuum L.) serves as an anchor for the alignment of major pepper maps

Mimura, Yutaka; Inoue, Takahiro; Minamiyama, Yasuhiro; Kubo, Nakao
Fonte: Japanese Society of Breeding Publicador: Japanese Society of Breeding
Tipo: Artigo de Revista Científica
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Of the Capsicum peppers (Capsicum spp.), cultivated C. annuum is the most commercially important, but has lacked an intraspecific linkage map based on sequence-specific PCR markers in accord with haploid chromosome numbers. We constructed a linkage map of pepper using a doubled haploid (DH) population derived from a cross between two C. annuum genotypes, a bell-type cultivar ‘California Wonder’ and a Malaysian small-fruited cultivar ‘LS2341 (JP187992)’, which is used as a source of resistance to bacterial wilt (Ralstonia solanacearum). A set of 253 markers (151 SSRs, 90 AFLPs, 10 CAPSs and 2 sequence-tagged sites) was on the map which we constructed, spanning 1,336 cM. This is the first SSR-based map to consist of 12 linkage groups, corresponding to the haploid chromosome number in an intraspecific cross of C. annuum. As this map has a lot of PCR-based anchor markers, it is easy to compare it to other pepper genetic maps. Therefore, this map and the newly developed markers will be useful for cultivated C. annuum breeding.

Structure and Topology of the Huntingtin 1–17 Membrane Anchor by a Combined Solution and Solid-State NMR Approach

Michalek, Matthias; Salnikov, Evgeniy S.; Bechinger, Burkhard
Fonte: The Biophysical Society Publicador: The Biophysical Society
Tipo: Artigo de Revista Científica
Publicado em 06/08/2013 Português
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The very amino-terminal domain of the huntingtin protein is directly located upstream of the protein’s polyglutamine tract, plays a decisive role in several important properties of this large protein and in the development of Huntington’s disease. This huntingtin 1–17 domain is on the one hand known to markedly increase polyglutamine aggregation rates and on the other hand has been shown to be involved in cellular membrane interactions. Here, we determined the high-resolution structure of huntingtin 1–17 in dodecyl phosphocholine micelles and the topology of its helical domain in oriented phosphatidylcholine bilayers. Using two-dimensional solution NMR spectroscopy the low-energy conformations of the polypeptide were identified in the presence of dodecyl phosphocholine detergent micelles. In a next step a set of four solid-state NMR angular restraints was obtained from huntingtin 1–17 labeled with 15N and 2H at selected sites. Of the micellar ensemble of helical conformations only a limited set agrees in quantitative detail with the solid-state angular restraints of huntingtin 1–17 obtained in supported planar lipid bilayers. Thereby, the solid-state NMR data were used to further refine the domain structure in phospholipid bilayers. At the same time its membrane topology was determined and different motional regimes of this membrane-associated domain were explored. The pronounced structural transitions of huntingtin 1–17 upon membrane-association result in a α-helical conformation from K6 to F17...

A Deformable Generic 3D Model of Haptoral Anchor of Monogenean

Teo, Bee Guan; Dhillon, Sarinder Kaur; Lim, Lee Hong Susan
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Publicado em 28/10/2013 Português
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In this paper, a digital 3D model which allows for visualisation in three dimensions and interactive manipulation is explored as a tool to help us understand the structural morphology and elucidate the functions of morphological structures of fragile microorganisms which defy live studies. We developed a deformable generic 3D model of haptoral anchor of dactylogyridean monogeneans that can subsequently be deformed into different desired anchor shapes by using direct manipulation deformation technique. We used point primitives to construct the rectangular building blocks to develop our deformable 3D model. Point primitives are manually marked on a 2D illustration of an anchor on a Cartesian graph paper and a set of Cartesian coordinates for each point primitive is manually extracted from the graph paper. A Python script is then written in Blender to construct 3D rectangular building blocks based on the Cartesian coordinates. The rectangular building blocks are stacked on top or by the side of each other following their respective Cartesian coordinates of point primitive. More point primitives are added at the sites in the 3D model where more structural variations are likely to occur, in order to generate complex anchor structures. We used Catmull-Clark subdivision surface modifier to smoothen the surface and edge of the generic 3D model to obtain a smoother and more natural 3D shape and antialiasing option to reduce the jagged edges of the 3D model. This deformable generic 3D model can be deformed into different desired 3D anchor shapes through direct manipulation deformation technique by aligning the vertices (pilot points) of the newly developed deformable generic 3D model onto the 2D illustrations of the desired shapes and moving the vertices until the desire 3D shapes are formed. In this generic 3D model all the vertices present are deployed for displacement during deformation.

MT4-(MMP17) and MT6-MMP (MMP25), A unique set of membrane-anchored matrix metalloproteinases: properties and expression in cancer

Sohail, Anjum; Sun, Qing; Zhao, Huiren; Bernardo, M. Margarida; Cho, Jin-Ah; Fridman, Rafael
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em /06/2008 Português
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The process of cancer progression involves the action of multiple proteolytic systems, among which the family of matrix metalloproteinases (MMPs) play a pivotal role. The MMPs evolved to accomplish their proteolytic tasks in multiple cellular and tissue microenvironments including lipid rafts by incorporation and deletions of specific structural domains. The membrane type-MMPs (MT-MMPs) incorporated membrane anchoring domains that display these proteases at the cell surface, and thus they are optimal pericellular proteolytic machines. Two members of the MT-MMP subfamily, MMP-17 (MT4-MMP) and MMP-25 (MT6-MMP), are anchored to the plasma membrane via a glycosyl-phosphatidyl inositol (GPI) anchor, which confers these enzymes a unique set of regulatory and functional mechanisms that separates them from the rest of the MMP family. Discovered almost a decade ago, the body of work on GPI-MT-MMPs today is still surprisingly limited when compared to other MT-MMPs. However, new evidence shows that the GPI-MT-MMPs are highly expressed in human cancer, where they are associated with progression. Accumulating biochemical and functional evidence also highlights their distinct properties. In this review, we summarize the structural, biochemical, and biological properties of GPI-MT-MMPs and present an overview of their expression and role in cancer. We further discuss the potential implications of GPI-anchoring for enzyme function. Finally...

Relaxing Routing Table to Alleviate Dynamism in P2P Systems

Fang, Hui; Hsu, Wen Jing; Rudolph, Larry
Fonte: MIT - Massachusetts Institute of Technology Publicador: MIT - Massachusetts Institute of Technology
Tipo: Artigo de Revista Científica Formato: 85408 bytes; application/pdf
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In dynamic P2P networks, nodes join and depart from the system frequently, which partially damages the predefined P2P structure, and impairs the system performance such as basic lookup functionality. Therefore stabilization process has to be done to restore the logical topology. This paper presents an approach to relax the requirement on routing tables to provide provably better stability than fixed structured P2P systems. We propose a relaxed Chord that keeps the O(logN) number of hops for greedy lookup, but it requires less stabilization overhead. It allows a tradeoff between lookup efficiency and structure flexibility without adding any overhead to the system. In the relaxed routing structure, each routing entry ("finger") of the node is allowed to vary within a set of values. Each node only needs to keep a certain number of fingers that point to nodes in its anchor set. This relaxation reduces the burden of state management of the node. The relaxed routing scheme provides an alternative structure other than randomized P2P and deterministic P2P, by relaxing on finger selection. It provides good flexibility and therefore extends the system functioning time.; Singapore-MIT Alliance (SMA)

The epididymal soluble prion protein forms a high-molecular-mass complex in association with hydrophobic proteins

Ecroyd, H.; Belghazi, M.; Dacheux, J.L.; Gatti, J.L.
Fonte: Portland Press Publicador: Portland Press
Tipo: Artigo de Revista Científica
Publicado em //2005 Português
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We have shown previously that a ‘soluble’ form of PrP (prion protein), not associated with membranous vesicles, exists in the male reproductive fluid [Ecroyd, Sarradin, Dacheux and Gatti (2004) Biol. Reprod. 71, 993–1001]. Attempts to purify this ‘soluble’ PrP indicated that it behaves like a high-molecular-mass complex of more than 350 kDa and always co-purified with the same set of proteins. The main associated proteins were sequenced by MS and were found to match to clusterin (apolipoprotein J), BPI (bacterial permeability-increasing protein), carboxylesterase-like urinary excreted protein (cauxin), b-mannosidase and b-galactosidase. Immunoblotting and enzymatic assay confirmed the presence of clusterin and a cauxin-like protein and showed that a 17 kDa hydrophobic epididymal protein was also associated with this complex. These associated proteins were not separated by a high ionic strength treatment but were by 2-mercaptoethanol, probably due to its action on reducing disulphide bonds that maintain the interaction of components of the complex. Our results suggest that the associated PrP retains its GPI (glycosylphosphatidylinositol) anchor, in contrast with brain-derived PrP, and that it is resistant to cleavage by phosphatidylinositol-specific phospholipase C. Based on these results...

Anchor model fusion for emotion recognition in speech

Ortego Resa, Carlos; López Moreno, Ignacio; Ramos, Daniel; González-Rodríguez, Joaquín
Fonte: Springer Berlin Heidelberg Publicador: Springer Berlin Heidelberg
Tipo: conferenceObject; bookPart
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Proceedings of Joint COST 2101 and 2102 International Conference, BioID_MultiComm 2009, Madrid (Spain); The final publication is available at Springer via http://dx.doi.org/10.1007/978-3-642-04391-8_7; In this work, a novel method for system fusion in emotion recognition for speech is presented. The proposed approach, namely Anchor Model Fusion (AMF), exploits the characteristic behaviour of the scores of a speech utterance among different emotion models, by a mapping to a back-end anchor-model feature space followed by a SVM classifier. Experiments are presented in three different databases: Ahumada III, with speech obtained from real forensic cases; and SUSAS Actual and SUSAS Simulated. Results comparing AMF with a simple sum-fusion scheme after normalization show a significant performance improvement of the proposed technique for two of the three experimental set-ups, without degrading performance in the third one.

Anchor Node Localization for Wireless Sensor Networks Using Video and Compass Information Fusion

Pescaru, Dan; Curiac, Daniel-Ioan
Fonte: MDPI Publicador: MDPI
Tipo: Artigo de Revista Científica
Publicado em 03/03/2014 Português
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Distributed sensing, computing and communication capabilities of wireless sensor networks require, in most situations, an efficient node localization procedure. In the case of random deployments in harsh or hostile environments, a general localization process within global coordinates is based on a set of anchor nodes able to determine their own position using GPS receivers. In this paper we propose another anchor node localization technique that can be used when GPS devices cannot accomplish their mission or are considered to be too expensive. This novel technique is based on the fusion of video and compass data acquired by the anchor nodes and is especially suitable for video- or multimedia-based wireless sensor networks. For these types of wireless networks the presence of video cameras is intrinsic, while the presence of digital compasses is also required for identifying the cameras' orientations.

A new class of Paramecium surface proteins anchored in the plasma membrane by a glycosylinositol phospholipid. Membrane anchor of Paramecium cross-reacting glycoproteins.

Deregnaucourt, C; Keller, A M; Capdeville, Y
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em 15/07/1988 Português
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Treatment of paramecia with ethanol or Triton X-100 solubilizes a major membrane protein, namely the surface antigen (SAg), and a set of glycopeptides in the range 40-60 kDa, which cross-react with the SAg. We demonstrate that these glycopeptides, called 'cross-reacting glycoproteins' (CRGs), are distinct molecules from the SAg. First, after purification of CRGs from ethanolic extracts of Paramecium primaurelia expressing the 156G SAg, the amino acid composition of a given CRG was found to be different from, and incompatible with, that of the 156G SAg. Secondly, we showed that the CRGs, although not immunologically detectable, are present in fractions containing the myristoylated form of the 156G SAg. The treatment of these fractions by phosphatidylinositol-specific phospholipases C enables us to reveal the CRGs through the unmasking of two distinct epitopes. One is the 'cross-reacting determinant' (CRD), initially described for the variant surface glycoproteins (VSGs) of Trypanosoma; the other determinant, called 'det-2355', is specific to the SAg and to the CRGs. Our results suggest that (1) phosphatidylinositol is covalently linked to the CRGs and (2) the CRD and the det-2355 are localized in the same region of the CRGs. We propose that the CRGs are a new set of surface proteins anchored in the cell membrane of Paramecium via a glycosylinositol phospholipid...

Partial Network Alignment with Anchor Meta Path and Truncated Generic Stable Matching

Zhang, Jiawei; Shao, Weixiang; Wang, Senzhang; Kong, Xiangnan; Yu, Philip S.
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 16/06/2015 Português
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To enjoy more social network services, users nowadays are usually involved in multiple online social networks simultaneously. The shared users between different networks are called anchor users, while the remaining unshared users are named as non-anchor users. Connections between accounts of anchor users in different networks are defined as anchor links and networks partially aligned by anchor links can be represented as partially aligned networks. In this paper, we want to predict anchor links between partially aligned social networks, which is formally defined as the partial network alignment problem. The partial network alignment problem is very difficult to solve because of the following two challenges: (1) the lack of general features for anchor links, and (2) the "one-to-one$_\le$" (one to at most one) constraint on anchor links. To address these two challenges, a new method PNA (Partial Network Aligner) is proposed in this paper. PNA (1) extracts a set of explicit anchor adjacency features and latent topological features for anchor links based on the anchor meta path concept and tensor decomposition techniques, and (2) utilizes the generic stable matching to identify the non-anchor users to prune the redundant anchor links attached to them. Extensive experiments conducted on two real-world partially aligned social networks demonstrate that PNA can solve the partial network alignment problem very well and outperform all the other comparison methods with significant advantages.; Comment: 12 pages...

Mobile Anchor Assisted Node Localization for Wireless Sensor Networks

Chen, Hongyang; Shi, Qingjiang; Huang, Pei; Poor, H. Vincent; Sezaki, Kaoru
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 04/08/2009 Português
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In this paper, a cooperative localization algorithm is proposed that considers the existence of obstacles in mobilityassisted wireless sensor networks (WSNs). In this scheme, a mobile anchor (MA) node cooperates with static sensor nodes and moves actively to refine location performance. The localization accuracy of the proposed algorithm can be improved further by changing the transmission range of mobile anchor node. The algorithm takes advantage of cooperation betweenMAs and static sensors while, at the same time, taking into account the relay node availability to make the best use of beacon signals. For achieving high localization accuracy and coverage, a novel convex position estimation algorithm is proposed, which can effectively solve the localization problem when infeasible points occur because of the effects of radio irregularity and obstacles. This method is the only range-free based convex method to solve the localization problem when the feasible set of localization inequalities is empty. Simulation results demonstrate the effectiveness of this algorithm.; Comment: 5 pages, 6 figures, IEEE PIMRC 2009