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Sample records for gene mention recognition

  1. Overview of BioCreative II gene mention recognition.

    PubMed

    Smith, Larry; Tanabe, Lorraine K; Ando, Rie Johnson nee; Kuo, Cheng-Ju; Chung, I-Fang; Hsu, Chun-Nan; Lin, Yu-Shi; Klinger, Roman; Friedrich, Christoph M; Ganchev, Kuzman; Torii, Manabu; Liu, Hongfang; Haddow, Barry; Struble, Craig A; Povinelli, Richard J; Vlachos, Andreas; Baumgartner, William A; Hunter, Lawrence; Carpenter, Bob; Tsai, Richard Tzong-Han; Dai, Hong-Jie; Liu, Feng; Chen, Yifei; Sun, Chengjie; Katrenko, Sophia; Adriaans, Pieter; Blaschke, Christian; Torres, Rafael; Neves, Mariana; Nakov, Preslav; Divoli, Anna; Maña-López, Manuel; Mata, Jacinto; Wilbur, W John

    2008-01-01

    Nineteen teams presented results for the Gene Mention Task at the BioCreative II Workshop. In this task participants designed systems to identify substrings in sentences corresponding to gene name mentions. A variety of different methods were used and the results varied with a highest achieved F1 score of 0.8721. Here we present brief descriptions of all the methods used and a statistical analysis of the results. We also demonstrate that, by combining the results from all submissions, an F score of 0.9066 is feasible, and furthermore that the best result makes use of the lowest scoring submissions.

  2. Overview of BioCreative II gene mention recognition

    PubMed Central

    Smith, Larry; Tanabe, Lorraine K; Ando, Rie Johnson nee; Kuo, Cheng-Ju; Chung, I-Fang; Hsu, Chun-Nan; Lin, Yu-Shi; Klinger, Roman; Friedrich, Christoph M; Ganchev, Kuzman; Torii, Manabu; Liu, Hongfang; Haddow, Barry; Struble, Craig A; Povinelli, Richard J; Vlachos, Andreas; Baumgartner, William A; Hunter, Lawrence; Carpenter, Bob; Tsai, Richard Tzong-Han; Dai, Hong-Jie; Liu, Feng; Chen, Yifei; Sun, Chengjie; Katrenko, Sophia; Adriaans, Pieter; Blaschke, Christian; Torres, Rafael; Neves, Mariana; Nakov, Preslav; Divoli, Anna; Maña-López, Manuel; Mata, Jacinto; Wilbur, W John

    2008-01-01

    Nineteen teams presented results for the Gene Mention Task at the BioCreative II Workshop. In this task participants designed systems to identify substrings in sentences corresponding to gene name mentions. A variety of different methods were used and the results varied with a highest achieved F1 score of 0.8721. Here we present brief descriptions of all the methods used and a statistical analysis of the results. We also demonstrate that, by combining the results from all submissions, an F score of 0.9066 is feasible, and furthermore that the best result makes use of the lowest scoring submissions. PMID:18834493

  3. Anatomical entity mention recognition at literature scale

    PubMed Central

    Pyysalo, Sampo; Ananiadou, Sophia

    2014-01-01

    Motivation: Anatomical entities ranging from subcellular structures to organ systems are central to biomedical science, and mentions of these entities are essential to understanding the scientific literature. Despite extensive efforts to automatically analyze various aspects of biomedical text, there have been only few studies focusing on anatomical entities, and no dedicated methods for learning to automatically recognize anatomical entity mentions in free-form text have been introduced. Results: We present AnatomyTagger, a machine learning-based system for anatomical entity mention recognition. The system incorporates a broad array of approaches proposed to benefit tagging, including the use of Unified Medical Language System (UMLS)- and Open Biomedical Ontologies (OBO)-based lexical resources, word representations induced from unlabeled text, statistical truecasing and non-local features. We train and evaluate the system on a newly introduced corpus that substantially extends on previously available resources, and apply the resulting tagger to automatically annotate the entire open access scientific domain literature. The resulting analyses have been applied to extend services provided by the Europe PubMed Central literature database. Availability and implementation: All tools and resources introduced in this work are available from http://nactem.ac.uk/anatomytagger. Contact: sophia.ananiadou@manchester.ac.uk Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:24162468

  4. Automated Recognition of Brain Region Mentions in Neuroscience Literature

    PubMed Central

    French, Leon; Lane, Suzanne; Xu, Lydia; Pavlidis, Paul

    2009-01-01

    The ability to computationally extract mentions of neuroanatomical regions from the literature would assist linking to other entities within and outside of an article. Examples include extracting reports of connectivity or region-specific gene expression. To facilitate text mining of neuroscience literature we have created a corpus of manually annotated brain region mentions. The corpus contains 1,377 abstracts with 18,242 brain region annotations. Interannotator agreement was evaluated for a subset of the documents, and was 90.7% and 96.7% for strict and lenient matching respectively. We observed a large vocabulary of over 6,000 unique brain region terms and 17,000 words. For automatic extraction of brain region mentions we evaluated simple dictionary methods and complex natural language processing techniques. The dictionary methods based on neuroanatomical lexicons recalled 36% of the mentions with 57% precision. The best performance was achieved using a conditional random field (CRF) with a rich feature set. Features were based on morphological, lexical, syntactic and contextual information. The CRF recalled 76% of mentions at 81% precision, by counting partial matches recall and precision increase to 86% and 92% respectively. We suspect a large amount of error is due to coordinating conjunctions, previously unseen words and brain regions of less commonly studied organisms. We found context windows, lemmatization and abbreviation expansion to be the most informative techniques. The corpus is freely available at http://www.chibi.ubc.ca/WhiteText/. PMID:19750194

  5. NTTMUNSW BioC modules for recognizing and normalizing species and gene/protein mentions.

    PubMed

    Dai, Hong-Jie; Singh, Onkar; Jonnagaddala, Jitendra; Su, Emily Chia-Yu

    2016-01-01

    In recent years, the number of published biomedical articles has increased as researchers have focused on biological domains to investigate the functions of biological objects, such as genes and proteins. However, the ambiguous nature of genes and their products have rendered the literature more complex for readers and curators of molecular interaction databases. To address this challenge, a normalization technique that can link variants of biological objects to a single, standardized form was applied. In this work, we developed a species normalization module, which recognizes species names and normalizes them to NCBI Taxonomy IDs. Unlike most previous work, which ignored the prefix of a gene name that represents an abbreviation of the species name to which the gene belongs, the recognition results of our module include the prefixed species. The developed species normalization module achieved an overall F-score of 0.954 on an instance-level species normalization corpus. For gene normalization, two separate modules were respectively employed to recognize gene mentions and normalize those mentions to their Entrez Gene IDs by utilizing a multistage normalization algorithm developed for processing full-text articles. All of the developed modules are BioC-compatible .NET framework libraries and are publicly available from the NuGet gallery.Database URL: https://sites.google.com/site/hjdairesearch/Projects/isn-corpus.

  6. Evaluating the automatic mapping of human gene and protein mentions to unique identifiers.

    PubMed

    Morgan, Alexander A; Wellner, Benjamin; Colombe, Jeffrey B; Arens, Robert; Colosimo, Marc E; Hirschman, Lynette

    2007-01-01

    We have developed a challenge task for the second BioCreAtIvE (Critical Assessment of Information Extraction in Biology) that requires participating systems to provide lists of the EntrezGene (formerly LocusLink) identifiers for all human genes and proteins mentioned in a MEDLINE abstract. We are distributing 281 annotated abstracts and another 5,000 noisily annotated abstracts along with a gene name lexicon to participants. We have performed a series of baseline experiments to better characterize this dataset and form a foundation for participant exploration.

  7. tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles.

    PubMed

    Cejuela, Juan Miguel; McQuilton, Peter; Ponting, Laura; Marygold, Steven J; Stefancsik, Raymund; Millburn, Gillian H; Rost, Burkhard

    2014-01-01

    The breadth and depth of biomedical literature are increasing year upon year. To keep abreast of these increases, FlyBase, a database for Drosophila genomic and genetic information, is constantly exploring new ways to mine the published literature to increase the efficiency and accuracy of manual curation and to automate some aspects, such as triaging and entity extraction. Toward this end, we present the 'tagtog' system, a web-based annotation framework that can be used to mark up biological entities (such as genes) and concepts (such as Gene Ontology terms) in full-text articles. tagtog leverages manual user annotation in combination with automatic machine-learned annotation to provide accurate identification of gene symbols and gene names. As part of the BioCreative IV Interactive Annotation Task, FlyBase has used tagtog to identify and extract mentions of Drosophila melanogaster gene symbols and names in full-text biomedical articles from the PLOS stable of journals. We show here the results of three experiments with different sized corpora and assess gene recognition performance and curation speed. We conclude that tagtog-named entity recognition improves with a larger corpus and that tagtog-assisted curation is quicker than manual curation. DATABASE URL: www.tagtog.net, www.flybase.org.

  8. 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.

  9. nala: text mining natural language mutation mentions.

    PubMed

    Cejuela, Juan Miguel; Bojchevski, Aleksandar; Uhlig, Carsten; Bekmukhametov, Rustem; Kumar Karn, Sanjeev; Mahmuti, Shpend; Baghudana, Ashish; Dubey, Ankit; Satagopam, Venkata P; Rost, Burkhard

    2017-06-15

    The extraction of sequence variants from the literature remains an important task. Existing methods primarily target standard (ST) mutation mentions (e.g. 'E6V'), leaving relevant mentions natural language (NL) largely untapped (e.g. 'glutamic acid was substituted by valine at residue 6'). We introduced three new corpora suggesting named-entity recognition (NER) to be more challenging than anticipated: 28-77% of all articles contained mentions only available in NL. Our new method nala captured NL and ST by combining conditional random fields with word embedding features learned unsupervised from the entire PubMed. In our hands, nala substantially outperformed the state-of-the-art. For instance, we compared all unique mentions in new discoveries correctly detected by any of three methods (SETH, tmVar, or nala ). Neither SETH nor tmVar discovered anything missed by nala , while nala uniquely tagged 33% mentions. For NL mentions the corresponding value shot up to 100% nala -only. Source code, API and corpora freely available at: http://tagtog.net/-corpora/IDP4+ . nala@rostlab.org. Supplementary data are available at Bioinformatics online.

  10. Assigning roles to protein mentions: the case of transcription factors.

    PubMed

    Yang, Hui; Keane, John; Bergman, Casey M; Nenadic, Goran

    2009-10-01

    Transcription factors (TFs) play a crucial role in gene regulation, and providing structured and curated information about them is important for genome biology. Manual curation of TF related data is time-consuming and always lags behind the actual knowledge available in the biomedical literature. Here we present a machine-learning text mining approach for identification and tagging of protein mentions that play a TF role in a given context to support the curation process. More precisely, the method explicitly identifies those protein mentions in text that refer to their potential TF functions. The prediction features are engineered from the results of shallow parsing and domain-specific processing (recognition of relevant appearing in phrases) and a phrase-based Conditional Random Fields (CRF) model is used to capture the content and context information of candidate entities. The proposed approach for the identification of TF mentions has been tested on a set of evidence sentences from the TRANSFAC and FlyTF databases. It achieved an F-measure of around 51.5% with a precision of 62.5% using 5-fold cross-validation evaluation. The experimental results suggest that the phrase-based CRF model benefits from the flexibility to use correlated domain-specific features that describe the dependencies between TFs and other entities. To the best of our knowledge, this work is one of the first attempts to apply text-mining techniques to the task of assigning semantic roles to protein mentions.

  11. Systematic feature evaluation for gene name recognition.

    PubMed

    Hakenberg, Jörg; Bickel, Steffen; Plake, Conrad; Brefeld, Ulf; Zahn, Hagen; Faulstich, Lukas; Leser, Ulf; Scheffer, Tobias

    2005-01-01

    In task 1A of the BioCreAtIvE evaluation, systems had to be devised that recognize words and phrases forming gene or protein names in natural language sentences. We approach this problem by building a word classification system based on a sliding window approach with a Support Vector Machine, combined with a pattern-based post-processing for the recognition of phrases. The performance of such a system crucially depends on the type of features chosen for consideration by the classification method, such as pre- or postfixes, character n-grams, patterns of capitalization, or classification of preceding or following words. We present a systematic approach to evaluate the performance of different feature sets based on recursive feature elimination, RFE. Based on a systematic reduction of the number of features used by the system, we can quantify the impact of different feature sets on the results of the word classification problem. This helps us to identify descriptive features, to learn about the structure of the problem, and to design systems that are faster and easier to understand. We observe that the SVM is robust to redundant features. RFE improves the performance by 0.7%, compared to using the complete set of attributes. Moreover, a performance that is only 2.3% below this maximum can be obtained using fewer than 5% of the features.

  12. Gene prediction by pattern recognition and homology search

    SciTech Connect

    Xu, Y.; Uberbacher, E.C.

    1996-05-01

    This paper presents an algorithm for combining pattern recognition-based exon prediction and database homology search in gene model construction. The goal is to use homologous genes or partial genes existing in the database as reference models while constructing (multiple) gene models from exon candidates predicted by pattern recognition methods. A unified framework for gene modeling is used for genes ranging from situations with strong homology to no homology in the database. To maximally use the homology information available, the algorithm applies homology on three levels: (1) exon candidate evaluation, (2) gene-segment construction with a reference model, and (3) (complete) gene modeling. Preliminary testing has been done on the algorithm. Test results show that (a) perfect gene modeling can be expected when the initial exon predictions are reasonably good and a strong homology exists in the database; (b) homology (not necessarily strong) in general helps improve the accuracy of gene modeling; (c) multiple gene modeling becomes feasible when homology exists in the database for the involved genes.

  13. Development of the first-mention bias*

    PubMed Central

    HARTSHORNE, JOSHUA K.; NAPPA, REBECCA; SNEDEKER, JESSE

    2015-01-01

    In many contexts, pronouns are interpreted as referring to the character mentioned first in the previous sentence, an effect called the ‘first-mention bias’. While adults can rapidly use the first-mention bias to guide pronoun interpretation, it is unclear when this bias emerges during development. Curiously, experiments with children between two and three years old show successful use of order of mention, while experiments with older children (four to five years old) do not. While this could suggest U-shaped development, it could also reflect differences in the methodologies employed. We show that children can indeed use first-mention information, but do so too slowly to have been detected in previous work reporting null results. Comparison across the present and previously published studies suggests that the speed at which children deploy first-mention information increases greatly during the preschool years. PMID:24735525

  14. Development of the first-mention bias.

    PubMed

    Hartshorne, Joshua K; Nappa, Rebecca; Snedeker, Jesse

    2015-03-01

    In many contexts, pronouns are interpreted as referring to the character mentioned first in the previous sentence, an effect called the 'first-mention bias'. While adults can rapidly use the first-mention bias to guide pronoun interpretation, it is unclear when this bias emerges during development. Curiously, experiments with children between two and three years old show successful use of order of mention, while experiments with older children (four to five years old) do not. While this could suggest U-shaped development, it could also reflect differences in the methodologies employed. We show that children can indeed use first-mention information, but do so too slowly to have been detected in previous work reporting null results. Comparison across the present and previously published studies suggests that the speed at which children deploy first-mention information increases greatly during the preschool years.

  15. The advantage of first mention in Spanish

    PubMed Central

    CARREIRAS, MANUEL; GERNSBACHER, MORTON ANN; VILLA, VICTOR

    2015-01-01

    An advantage of first mention—that is, faster access to participants mentioned first in a sentence—has previously been demonstrated only in English. We report three experiments demonstrating that the advantage of first mention occurs also in Spanish sentences, regardless of whether the first-mentioned participants are syntactic subjects, and regardless, too, of whether they are proper names or inanimate objects. Because greater word-order flexibility is allowed in Spanish than in English (e.g., nonpassive object-verb-subject constructions exist in Spanish), these findings provide additional evidence that the advantage of first mention is a general cognitive phenomenon. PMID:24203596

  16. Spliced alignment: A new approach to gene recognition

    SciTech Connect

    Gelfand, M.S.; Mironov, A.A.; Pevzner, P.A.

    1996-12-31

    Gene structure prediction is one of the most important problems in computational molecular biology. Previous attempts to solve this problem were based on statistics and artificial intelligence and, surprisingly enough, applications of theoretical computer science methods for gene recognition were almost unexplored. Recent advances in large-scale cDNA sequencing open a way towards a new combinatorial approach to gene recognition. This paper describes a spliced alignment algorithm and a software tool 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 recognizes genes even in the case of short exons or exons with unusual codon usage; the authors also report correct assemblies for genes with more than 10 exons. On a test sample of human genes with known mammalian relatives the average correlation between the predicted and the actual genes was 99%, which is a very high accuracy as compared with other existing methods. The algorithm correctly reconstructed 87% of genes and the rare discrepancies between the predicted and real exon-intron structures were caused by either (i) extremely short (less than 5 amino acids) initial or terminal exons, or (ii) alternative splicing, or (iii) errors in database feature tables. 38 refs., 3 tabs.

  17. Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification

    SciTech Connect

    Hyatt, Philip Douglas; Chen, Gwo-Liang; Larimer, Frank W; LoCascio, Philip F; Hauser, Loren John; Land, Miriam L

    2010-01-01

    Background The quality of automated gene prediction in microbial organisms has improved steadily over the past decade, but there is still room for improvement. Increasing the number of correct identifications, both of genes and of the translation initiation sites for each gene, and reducing the overall number of false positives, are all desirable goals. Results With our years of experience in manually curating genomes for the Joint Genome Institute, we developed a new gene prediction algorithm called Prodigal (PROkaryotic DYnamic programming Gene-finding ALgorithm). With Prodigal, we focused specifically on the three goals of improved gene structure prediction, improved translation initiation site recognition, and reduced false positives. We compared the results of Prodigal to existing gene-finding methods to demonstrate that it met each of these objectives. Conclusion We built a fast, lightweight, open source gene prediction program called Prodigal (http://compbio.ornl.gov/prodigal/). Prodigal achieved good results compared to existing methods, and we believe it will be a valuable asset to automated microbial annotation pipelines.

  18. Resolving Partial Name Mentions Using String Metrics

    DTIC Science & Technology

    2007-12-01

    handling: 1. The partial name mention Jason W did not resolve to its canonical name Jason Wolfe. 2. As a consequence of this, a following partial name...Waterman, M.S., Identification of Common Molecular Subsequences, Journal of Molecular Biology, 147, 195-197, 1981. [7] Irving, R.W., Plagiarism and

  19. Candidate genes for individual recognition in Polistes fuscatus paper wasps.

    PubMed

    Berens, A J; Tibbetts, E A; Toth, A L

    2016-02-01

    Few animals are known to individually recognize conspecifics, i.e. learn and recall unique individuals during subsequent encounters, and nearly all are social vertebrates. Remarkably, the social paper wasp Polistes fuscatus has recently been discovered to possess this ability, which is useful for remembering identities during competitive social interactions. We analyzed brain gene expression in staged encounters between pairs of individuals to explore potential mechanisms underlying wasps' ability to recall familiar individuals using real-time qRT-PCR. We identified four candidate genes (IP3K, IP3R, Nckx30C and Su(var)2-10) that were down-regulated in the presence of familiar individuals compared to single wasps and pairs of wasps meeting for the first time. These candidate genes are related to calcium signaling, therefore, we treated wasps with lithium chloride, a pharmacological agent that inhibits calcium signaling in neurons. This treatment decreased aggression in paper wasps, but did not affect expression of genes related to calcium signaling. The results suggest calcium signaling differences may be related to individual memory recall in wasps, and we present four promising candidate genes for future study. These data suggest genes associated with dominance behavior may be co-opted for individual recognition, but further work is needed to establish a causal association with the behavior.

  20. Prodigal: prokaryotic gene recognition and translation initiation site identification

    SciTech Connect

    Chen, Gwo-Liang; LoCascio, Philip F; Land, Miriam L; Larimer, Frank W; Hauser, Loren John

    2010-01-01

    The quality of automated gene prediction in microbial organisms has improved steadily over the past decade, but there is still room for improvement. Increasing the number of correct identifications, both of genes and of the translation initiation sites for each gene, and reducing the overall number of false positives, are all desirable goals. With our years of experience in manually curating genomes for the Joint Genome Institute, we developed a new gene prediction algorithm called Prodigal (PROkaryotic DYnamic programming Gene-finding ALgorithm). With Prodigal, we focused specifically on the three goals of improved gene structure prediction, improved translation initiation site recognition, and reduced false positives. We compared the results of Prodigal to existing gene-finding methods to demonstrate that it met each of these objectives. We built a fast, lightweight, open source gene prediction program called Prodigal http://compbio.ornl.gov/prodigal/. Prodigal achieved good results compared to existing methods, and we believe it will be a valuable asset to automated microbial annotation pipelines. The goals of Prodigal were to attain greater sensitivity in identifying existing genes, to predict translation initiation sites more accurately, and to minimize the number of false positive predictions. The results of Prodigal were compared to existing methods for both purely experimentally verified genes as well as curated Genbank files for a number of genomes. Prodigal's performance was found to be comparable or better to existing methods in the prediction of genes while also predicting fewer overall genes. In the prediction of translation initiation sites, Prodigal performed competitively with existing methods. Prodigal is currently already in use at many institutions, and it has been used to annotate all finished microbial genomes submitted to Genbank by DOE-JGI in 2008 and onward (a substantial percentage of the overall finished microbial genomes at NCBI). It is

  1. [Key effect genes responding to nerve injury identified by gene ontology and computer pattern recognition].

    PubMed

    Pan, Qian; Peng, Jin; Zhou, Xue; Yang, Hao; Zhang, Wei

    2012-07-01

    In order to screen out important genes from large gene data of gene microarray after nerve injury, we combine gene ontology (GO) method and computer pattern recognition technology to find key genes responding to nerve injury, and then verify one of these screened-out genes. Data mining and gene ontology analysis of gene chip data GSE26350 was carried out through MATLAB software. Cd44 was selected from screened-out key gene molecular spectrum by comparing genes' different GO terms and positions on score map of principal component. Function interferences were employed to influence the normal binding of Cd44 and one of its ligands, chondroitin sulfate C (CSC), to observe neurite extension. Gene ontology analysis showed that the first genes on score map (marked by red *) mainly distributed in molecular transducer activity, receptor activity, protein binding et al molecular function GO terms. Cd44 is one of six effector protein genes, and attracted us with its function diversity. After adding different reagents into the medium to interfere the normal binding of CSC and Cd44, varying-degree remissions of CSC's inhibition on neurite extension were observed. CSC can inhibit neurite extension through binding Cd44 on the neuron membrane. This verifies that important genes in given physiological processes can be identified by gene ontology analysis of gene chip data.

  2. Coenzyme Recognition and Gene Regulation by a Flavin Mononucleotide Riboswitch

    SciTech Connect

    Serganov, A.; Huang, L; Patel, D

    2009-01-01

    The biosynthesis of several protein cofactors is subject to feedback regulation by riboswitches. Flavin mononucleotide (FMN)-specific riboswitches also known as RFN elements, direct expression of bacterial genes involved in the biosynthesis and transport of riboflavin (vitamin B2) and related compounds. Here we present the crystal structures of the Fusobacterium nucleatum riboswitch bound to FMN, riboflavin and antibiotic roseoflavin. The FMN riboswitch structure, centred on an FMN-bound six-stem junction, does not fold by collinear stacking of adjacent helices, typical for folding of large RNAs. Rather, it adopts a butterfly-like scaffold, stapled together by opposingly directed but nearly identically folded peripheral domains. FMN is positioned asymmetrically within the junctional site and is specifically bound to RNA through interactions with the isoalloxazine ring chromophore and direct and Mg{sup 2+}-mediated contacts with the phosphate moiety. Our structural data, complemented by binding and footprinting experiments, imply a largely pre-folded tertiary RNA architecture and FMN recognition mediated by conformational transitions within the junctional binding pocket. The inherent plasticity of the FMN-binding pocket and the availability of large openings make the riboswitch an attractive target for structure-based design of FMN-like antimicrobial compounds. Our studies also explain the effects of spontaneous and antibiotic-induced deregulatory mutations and provided molecular insights into FMN-based control of gene expression in normal and riboflavin-overproducing bacterial strains.

  3. ORF Organization and Gene Recognition in the Yeast Genome

    PubMed Central

    Li, Hong; Zhang, Lirong

    2003-01-01

    Some rules on gene recognition and ORF organization in the Saccharomyces cerevisiae genome are demonstrated by statistical analyses of sequence data. This study includes: (a) The random frame rule—that the six reading frames W1, W2, W3, C1, C2 and C3 in the double-stranded genome are randomly occupied by ORFs (related phenomena on ORF overlapping are also discussed). (b) The inhomogeneity rule—coding and non-coding ORFs differ in inhomogeneity of base composition in the three codon positions. By use of the inhomogeneity index (IHI), one can make a distinction between coding (IHI > 14) and non-coding (IHI ≤ 14) ORFs at 95% accuracy. We find that ‘spurious’ ORFs (with IHI ≤ 14) are distributed mainly in three classes of ORFs, namely, those with ‘similarity to unknown proteins’, those with ‘no similarity’, or ‘questionable ORFs’. The total number of spurious ORFs (which are unlikely to be regarded as coding ORFs) is estimated to be 470. (c) The evaluation of ORF length distribution shows that below 200 amino acids the occurrence of ATG initiator ORFs is close to random. PMID:18629282

  4. Overview of tomato (Solanum lycopersicum) candidate pathogen recognition genes reveals important Solanum R locus dynamics.

    PubMed

    Andolfo, G; Sanseverino, W; Rombauts, S; Van de Peer, Y; Bradeen, J M; Carputo, D; Frusciante, L; Ercolano, M R

    2013-01-01

    To investigate the genome-wide spatial arrangement of R loci, a complete catalogue of tomato (Solanum lycopersicum) and potato (Solanum tuberosum) nucleotide-binding site (NBS) NBS, receptor-like protein (RLP) and receptor-like kinase (RLK) gene repertories was generated. Candidate pathogen recognition genes were characterized with respect to structural diversity, phylogenetic relationships and chromosomal distribution. NBS genes frequently occur in clusters of related gene copies that also include RLP or RLK genes. This scenario is compatible with the existence of selective pressures optimizing coordinated transcription. A number of duplication events associated with lineage-specific evolution were discovered. These findings suggest that different evolutionary mechanisms shaped pathogen recognition gene cluster architecture to expand and to modulate the defence repertoire. Analysis of pathogen recognition gene clusters associated with documented resistance function allowed the identification of adaptive divergence events and the reconstruction of the evolution history of these loci. Differences in candidate pathogen recognition gene number and organization were found between tomato and potato. Most candidate pathogen recognition gene orthologues were distributed at less than perfectly matching positions, suggesting an ongoing lineage-specific rearrangement. Indeed, a local expansion of Toll/Interleukin-1 receptor (TIR)-NBS-leucine-rich repeat (LRR) (TNL) genes in the potato genome was evident. Taken together, these findings have implications for improved understanding of the mechanisms of molecular adaptive selection at Solanum R loci. © 2012 The Authors. New Phytologist © 2012 New Phytologist Trust.

  5. Computerized system for recognition of autism on the basis of gene expression microarray data.

    PubMed

    Latkowski, Tomasz; Osowski, Stanislaw

    2015-01-01

    The aim of this paper is to provide a means to recognize a case of autism using gene expression microarrays. The crucial task is to discover the most important genes which are strictly associated with autism. The paper presents an application of different methods of gene selection, to select the most representative input attributes for an ensemble of classifiers. The set of classifiers is responsible for distinguishing autism data from the reference class. Simultaneous application of a few gene selection methods enables analysis of the ill-conditioned gene expression matrix from different points of view. The results of selection combined with a genetic algorithm and SVM classifier have shown increased accuracy of autism recognition. Early recognition of autism is extremely important for treatment of children and increases the probability of their recovery and return to normal social communication. The results of this research can find practical application in early recognition of autism on the basis of gene expression microarray analysis.

  6. Women in Music Education in the United States: Names Mentioned in History Books.

    ERIC Educational Resources Information Center

    Livingston, Carolyn

    1997-01-01

    Identifies those women mentioned most frequently in general U.S. music education history books and examines the contexts in which the books discussed their work. Surveys individuals interested in music education history to determine name recognition of these women and opinions regarding the importance of their contributions. (MJP)

  7. Twelve- and 16-Month-Old Infants Recognize Properties of Mentioned Absent Things

    ERIC Educational Resources Information Center

    Saylor, Megan M.

    2004-01-01

    Absent reference comprehension is a critical achievement of early development, yet little is known about its emergence. In the current study, 12- and 16-month-old infants' recognition of properties of mentioned absent things was used as an index of absent reference comprehension. Infants were presented with displays matching the color and prior…

  8. Twelve- and 16-Month-Old Infants Recognize Properties of Mentioned Absent Things

    ERIC Educational Resources Information Center

    Saylor, Megan M.

    2004-01-01

    Absent reference comprehension is a critical achievement of early development, yet little is known about its emergence. In the current study, 12- and 16-month-old infants' recognition of properties of mentioned absent things was used as an index of absent reference comprehension. Infants were presented with displays matching the color and prior…

  9. The Advantage of First Mention in Korean The Temporal Contributions of Syntactic, Semantic, and Pragmatic Factors

    PubMed Central

    Kim, Sung-il; Lee, Jae-ho; Gernsbacher, Morton Ann

    2015-01-01

    Using Korean, we investigated how syntactic, semantic, and pragmatic factors influence the representation of a sentence, in particular, the relative accessibility of different components of a sentence representation. In six experiments, participants performed a probe recognition task after reading each of a series of sentences. We manipulated the rate at which each word of the sentence was presented (250 and 500 ms) and the interval between the sentence-final word and the probe-recognition test word (immediate, 500 ms delay, and 1000 ms delay). We also manipulated the syntactic position (subject versus object), semantic role (agent versus patient), and order of mention (first- versus second-mentioned participant) of the probed item. Pragmatic factors (the order of mention) strongly influenced accessibility immediately and through the longest delay, whereas syntactic and semantic factors had little effect. PMID:15614990

  10. Recognition- and defense-related gene expression at 3 resynthesis stages in lichen symbionts.

    PubMed

    Athukorala, Sarangi N P; Piercey-Normore, Michele D

    2015-01-01

    Recognition and defense responses are early events in plant-pathogen interactions and between lichen symbionts. The effect of elicitors on responses between lichen symbionts is not well understood. The objective of this study was to compare the difference in recognition- and defense-related gene expression as a result of culture extracts (containing secreted water-soluble elicitors) from compatible and incompatible interactions at each of 3 resynthesis stages in the symbionts of Cladonia rangiferina. This study investigated gene expression by quantitative PCR in cultures of C. rangiferina and its algal partner, Asterochloris glomerata/irregularis, after incubation with liquid extracts from cultures of compatible and incompatible interactions at 3 early resynthesis stages. Recognition-related genes were significantly upregulated only after physical contact, demonstrating symbiont recognition in later resynthesis stages than expected. One of 3 defense-related genes, chit, showed significant downregulation in early resynthesis stages and upregulation in the third resynthesis stage, demonstrating a need for the absence of chitinase early in thallus formation and a need for its presence in later stages as an algal defense reaction. This study revealed that recognition- and defense-related genes are triggered by components in culture extracts at 3 stages of resynthesis, and some defense-related genes may be induced throughout thallus growth. The parasitic nature of the interaction shows parallels between lichen symbionts and plant pathogenic systems.

  11. Automatic recognition of topic-classified relations between prostate cancer and genes using MEDLINE abstracts.

    PubMed

    Chun, Hong-Woo; Tsuruoka, Yoshimasa; Kim, Jin-Dong; Shiba, Rie; Nagata, Naoki; Hishiki, Teruyoshi; Tsujii, Jun'ichi

    2006-11-24

    Automatic recognition of relations between a specific disease term and its relevant genes or protein terms is an important practice of bioinformatics. Considering the utility of the results of this approach, we identified prostate cancer and gene terms with the ID tags of public biomedical databases. Moreover, considering that genetics experts will use our results, we classified them based on six topics that can be used to analyze the type of prostate cancers, genes, and their relations. We developed a maximum entropy-based named entity recognizer and a relation recognizer and applied them to a corpus-based approach. We collected prostate cancer-related abstracts from MEDLINE, and constructed an annotated corpus of gene and prostate cancer relations based on six topics by biologists. We used it to train the maximum entropy-based named entity recognizer and relation recognizer. Topic-classified relation recognition achieved 92.1% precision for the relation (an increase of 11.0% from that obtained in a baseline experiment). For all topics, the precision was between 67.6 and 88.1%. A series of experimental results revealed two important findings: a carefully designed relation recognition system using named entity recognition can improve the performance of relation recognition, and topic-classified relation recognition can be effectively addressed through a corpus-based approach using manual annotation and machine learning techniques.

  12. Oxytocin, vasopressin and estrogen receptor gene expression in relation to social recognition in female mice

    PubMed Central

    Clipperton-Allen, Amy E.; Lee, Anna W.; Reyes, Anny; Devidze, Nino; Phan, Anna; Pfaff, Donald W.; Choleris, Elena

    2012-01-01

    Inter- and intra-species differences in social behavior and recognition-related hormones and receptors suggest that different distribution and/or expression patterns may relate to social recognition. We used qRT-PCR to investigate naturally occurring differences in expression of estrogen receptor-alpha (ERα), ER-beta (ERβ), progesterone receptor (PR), oxytocin (OT) and receptor, and vasopressin (AVP) and receptors in proestrous female mice. Following four 5 min exposures to the same two conspecifics, one was replaced with a novel mouse in the final trial (T5). Gene expression was examined in mice showing high (85–100%) and low (40–60%) social recognition scores (i.e., preferential novel mouse investigation in T5) in eight socially-relevant brain regions. Results supported OT and AVP involvement in social recognition, and suggest that in the medial preoptic area, increased OT and AVP mRNA, together with ERα and ERβ gene activation, relate to improved social recognition. Initial social investigation correlated with ERs, PR and OTR in the dorsolateral septum, suggesting that these receptors may modulate social interest without affecting social recognition. Finally, increased lateral amygdala gene activation in the LR mice may be associated with general learning impairments, while decreased lateral amygdala activity may indicate more efficient cognitive mechanisms in the HR mice. PMID:22079582

  13. Drosophila GRAIL: An intelligent system for gene recognition in Drosophila DNA sequences

    SciTech Connect

    Xu, Ying; Einstein, J.R.; Uberbacher, E.C.; Helt, G.; Rubin, G.

    1995-06-01

    An AI-based system for gene recognition in Drosophila DNA sequences was designed and implemented. The system consists of two main modules, one for coding exon recognition and one for single gene model construction. The exon recognition module finds a coding exon by recognition of its splice junctions (or translation start) and coding potential. The core of this module is a set of neural networks which evaluate an exon candidate for the possibility of being a true coding exon using the ``recognized`` splice junction (or translation start) and coding signals. The recognition process consists of four steps: generation of an exon candidate pool, elimination of improbable candidates using heuristic rules, candidate evaluation by trained neural networks, and candidate cluster resolution and final exon prediction. The gene model construction module takes as input the clustered exon candidates and builds a ``best`` possible single gene model using an efficient dynamic programming algorithm. 129 Drosophila sequences consisting of 441 coding exons including 216358 coding bases were extructed from GenBank and used to build statistical matrices and to train the neural networks. On this training set the system recognized 97% of the coding messages and predicted only 5% false messages. Among the ``correctly`` predicted exons, 68% match the actual exon exactly and 96% have at least one edge predicted correctly. On an independent test set consisting of 30 Drosophila sequences, the system recognized 96% of the coding messages and predicted 7% false messages.

  14. Unexpected Roles for Core Promoter Recognition Factors in Cell-type Specific Transcription and Gene Regulation

    PubMed Central

    Goodrich, James A.

    2010-01-01

    Until recently, the eukaryotic core promoter recognition complex was generally thought to play an essential but passive role in the regulation of gene expression. However, recent evidence indicates that core-promoter recognition complexes in conjunction with “non-prototypic” subunits may play a critical regulatory role in driving cell specific programs of transcription during development. Furthermore, new roles for components of these complexes have been identified beyond development, for example in mediating interactions with chromatin and in maintaining active gene expression across cell divisions. PMID:20628347

  15. Las Vegas algorithms for gene recognition: Suboptimal and error-tolerant spliced alignment

    SciTech Connect

    Sze, Sing-Hoi; Pevzner, P.A.

    1997-12-01

    Recently, Gelfand, Mironov and Pevzner proposed a spliced alignment approach to gene recognition that provides 99% accurate recognition of human gene if a related mammalian protein is available. However, even 99% accurate gene predictions are insufficient for automated sequence annotation in large-scale sequencing projects and therefore have to be complemented by experimental gene verification. 100% accurate gene predictions would lead to a substantial reduction of experimental work on gene identification. Our goal is to develop an algorithm that either predicts an exon assembly with accuracy sufficient for sequence annotation or warns a biologist that the accuracy of a prediction is insufficient and further experimental work is required. We study suboptimal and error-tolerant spliced alignment problems as the first steps towards such an algorithm, and report an algorithm which provides 100% accurate recognition of human genes in 37% of cases (if a related mammalian protein is available). For 52% of genes, the algorithm predicts at least one exon with 100% accuracy. 30 refs., 1 fig., 3 tabs.

  16. A Genetic Approach to Promoter Recognition during Trans Induction of Viral Gene Expression

    NASA Astrophysics Data System (ADS)

    Coen, Donald M.; Weinheimer, Steven P.; McKnight, Steven L.

    1986-10-01

    Viral infection of mammalian cells entails the regulated induction of viral gene expression. The induction of many viral genes, including the herpes simplex virus gene encoding thymidine kinase (tk), depends on viral regulatory proteins that act in trans. Because recognition of the tk promoter by cellular transcription factors is well understood, its trans induction by viral regulatory proteins may serve as a useful model for the regulation of eukaryotic gene expression. A comprehensive set of mutations was therefore introduced into the chromosome of herpes simplex virus at the tk promoter to directly analyze the effects of promoter mutations on tk transcription. The promoter domains required for efficient tk expression under conditions of trans induction corresponded to those important for recognition by cellular transcription factors. Thus, trans induction of tk expression may be catalyzed initially by the interaction of viral regulatory proteins with cellular transcription factors.

  17. Network Security via Biometric Recognition of Patterns of Gene Expression

    NASA Technical Reports Server (NTRS)

    Shaw, Harry C.

    2016-01-01

    Molecular biology provides the ability to implement forms of information and network security completely outside the bounds of legacy security protocols and algorithms. This paper addresses an approach which instantiates the power of gene expression for security. Molecular biology provides a rich source of gene expression and regulation mechanisms, which can be adopted to use in the information and electronic communication domains. Conventional security protocols are becoming increasingly vulnerable due to more intensive, highly capable attacks on the underlying mathematics of cryptography. Security protocols are being undermined by social engineering and substandard implementations by IT organizations. Molecular biology can provide countermeasures to these weak points with the current security approaches. Future advances in instruments for analyzing assays will also enable this protocol to advance from one of cryptographic algorithms to an integrated system of cryptographic algorithms and real-time expression and assay of gene expression products.

  18. Network Security via Biometric Recognition of Patterns of Gene Expression

    NASA Technical Reports Server (NTRS)

    Shaw, Harry C.

    2016-01-01

    Molecular biology provides the ability to implement forms of information and network security completely outside the bounds of legacy security protocols and algorithms. This paper addresses an approach which instantiates the power of gene expression for security. Molecular biology provides a rich source of gene expression and regulation mechanisms, which can be adopted to use in the information and electronic communication domains. Conventional security protocols are becoming increasingly vulnerable due to more intensive, highly capable attacks on the underlying mathematics of cryptography. Security protocols are being undermined by social engineering and substandard implementations by IT (Information Technology) organizations. Molecular biology can provide countermeasures to these weak points with the current security approaches. Future advances in instruments for analyzing assays will also enable this protocol to advance from one of cryptographic algorithms to an integrated system of cryptographic algorithms and real-time assays of gene expression products.

  19. Medical Treatment and Medicinal Charms Mentioned in the Atharvanic Literature

    PubMed Central

    Bhide, V.V.

    1981-01-01

    The ancient Vedic texts Provides us with valuable information and guide lines on various multi-faced aspects of human life. The present discussion is limited to the medical treatment and medicinal charms mentioned in the Atharvanic literature with specific consideration to Kausikasutra for better understanding of the rites and actions mentioned in Atharvanaveda. PMID:22556455

  20. 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

  1. Giving Good Directions: Order of Mention Reflects Visual Salience.

    PubMed

    Clarke, Alasdair D F; Elsner, Micha; Rohde, Hannah

    2015-01-01

    In complex stimuli, there are many different possible ways to refer to a specified target. Previous studies have shown that when people are faced with such a task, the content of their referring expression reflects visual properties such as size, salience, and clutter. Here, we extend these findings and present evidence that (i) the influence of visual perception on sentence construction goes beyond content selection and in part determines the order in which different objects are mentioned and (ii) order of mention influences comprehension. Study 1 (a corpus study of reference productions) shows that when a speaker uses a relational description to mention a salient object, that object is treated as being in the common ground and is more likely to be mentioned first. Study 2 (a visual search study) asks participants to listen to referring expressions and find the specified target; in keeping with the above result, we find that search for easy-to-find targets is faster when the target is mentioned first, while search for harder-to-find targets is facilitated by mentioning the target later, after a landmark in a relational description. Our findings show that seemingly low-level and disparate mental "modules" like perception and sentence planning interact at a high level and in task-dependent ways.

  2. Giving Good Directions: Order of Mention Reflects Visual Salience

    PubMed Central

    Clarke, Alasdair D. F.; Elsner, Micha; Rohde, Hannah

    2015-01-01

    In complex stimuli, there are many different possible ways to refer to a specified target. Previous studies have shown that when people are faced with such a task, the content of their referring expression reflects visual properties such as size, salience, and clutter. Here, we extend these findings and present evidence that (i) the influence of visual perception on sentence construction goes beyond content selection and in part determines the order in which different objects are mentioned and (ii) order of mention influences comprehension. Study 1 (a corpus study of reference productions) shows that when a speaker uses a relational description to mention a salient object, that object is treated as being in the common ground and is more likely to be mentioned first. Study 2 (a visual search study) asks participants to listen to referring expressions and find the specified target; in keeping with the above result, we find that search for easy-to-find targets is faster when the target is mentioned first, while search for harder-to-find targets is facilitated by mentioning the target later, after a landmark in a relational description. Our findings show that seemingly low-level and disparate mental “modules” like perception and sentence planning interact at a high level and in task-dependent ways. PMID:26696914

  3. MHC-restricted antigen presentation and recognition: constraints on gene, recombinant and peptide vaccines in humans.

    PubMed

    Cunha-Neto, E

    1999-02-01

    The target of any immunization is to activate and expand lymphocyte clones with the desired recognition specificity and the necessary effector functions. In gene, recombinant and peptide vaccines, the immunogen is a single protein or a small assembly of epitopes from antigenic proteins. Since most immune responses against protein and peptide antigens are T-cell dependent, the molecular target of such vaccines is to generate at least 50-100 complexes between MHC molecule and the antigenic peptide per antigen-presenting cell, sensitizing a T cell population of appropriate clonal size and effector characteristics. Thus, the immunobiology of antigen recognition by T cells must be taken into account when designing new generation peptide- or gene-based vaccines. Since T cell recognition is MHC-restricted, and given the wide polymorphism of the different MHC molecules, distinct epitopes may be recognized by different individuals in the population. Therefore, the issue of whether immunization will be effective in inducing a protective immune response, covering the entire target population, becomes an important question. Many pathogens have evolved molecular mechanisms to escape recognition by the immune system by variation of antigenic protein sequences. In this short review, we will discuss the several concepts related to selection of amino acid sequences to be included in DNA and peptide vaccines.

  4. Gene expression pattern recognition algorithm inferences to classify samples exposed to chemical agents

    NASA Astrophysics Data System (ADS)

    Bushel, Pierre R.; Bennett, Lee; Hamadeh, Hisham; Green, James; Ableson, Alan; Misener, Steve; Paules, Richard; Afshari, Cynthia

    2002-06-01

    We present an analysis of pattern recognition procedures used to predict the classes of samples exposed to pharmacologic agents by comparing gene expression patterns from samples treated with two classes of compounds. Rat liver mRNA samples following exposure for 24 hours with phenobarbital or peroxisome proliferators were analyzed using a 1700 rat cDNA microarray platform. Sets of genes that were consistently differentially expressed in the rat liver samples following treatment were stored in the MicroArray Project System (MAPS) database. MAPS identified 238 genes in common that possessed a low probability (P < 0.01) of being randomly detected as differentially expressed at the 95% confidence level. Hierarchical cluster analysis on the 238 genes clustered specific gene expression profiles that separated samples based on exposure to a particular class of compound.

  5. Self-recognition in social amoebae is mediated by allelic pairs of tiger genes.

    PubMed

    Hirose, Shigenori; Benabentos, Rocio; Ho, Hsing-I; Kuspa, Adam; Shaulsky, Gad

    2011-07-22

    Free-living cells of the social amoebae Dictyostelium discoideum can aggregate and develop into multicellular fruiting bodies in which many die altruistically as they become stalk cells that support the surviving spores. Dictyostelium cells exhibit kin discrimination--a potential defense against cheaters, which sporulate without contributing to the stalk. Kin discrimination depends on strain relatedness, and the polymorphic genes tgrB1 and tgrC1 are potential components of that mechanism. Here, we demonstrate a direct role for these genes in kin discrimination. We show that a matching pair of tgrB1 and tgrC1 alleles is necessary and sufficient for attractive self-recognition, which is mediated by differential cell-cell adhesion. We propose that TgrB1 and TgrC1 proteins mediate this adhesion through direct binding. This system is a genetically tractable ancient model of eukaryotic self-recognition.

  6. Genetic variation in the serotonin transporter gene influences ERP old/new effects during recognition memory

    PubMed Central

    Ross, Robert S.; Medrano, Paolo; Boyle, Kaitlin; Smolen, Andrew; Curran, Tim; Nyhus, Erika

    2015-01-01

    Recognition memory is defined as the ability to recognize a previously encountered stimulus and has been associated with spatially and temporally distinct event related potentials (ERPs). Allelic variations of the serotonin transporter gene (SLC6A4) have recently been shown to impact memory performance. Common variants of the serotonin transporter-linked polymorphic region (5HTTLPR) of the SLC6A4 gene result in long (l) and short (s) allelic variants with carriers of the s allele having lowered transcriptional efficiency. Thus, the current study examines the effects polymorphisms of the SLC6A4 gene have on performance and ERP amplitudes commonly associated with recognition memory. Electroencephalogram (EEG), genetic, and behavioral data were collected from sixty participants as they performed an item and source memory recognition task. In both tasks, participants studied and encoded 200 words, which were then mixed with 200 new words during retrieval. Participants were monitored with EEG during the retrieval portion of each memory task. EEG electrodes were grouped into four ROIs, left anterior superior, right anterior superior, left posterior superior, and right posterior superior. ERP mean amplitudes during hits in the item and source memory task were compared to correctly recognizing new items (correct rejections). Results show that s-carriers have decreased mean hit amplitudes in both the right anterior superior ROI 1000–1500 ms post stimulus during the source memory task and the left anterior superior ROI 300–500 ms post stimulus during the item memory task. These results suggest that individual differences due to genetic variation of the serotonin transporter gene influences recognition memory. PMID:26423665

  7. Dopamine receptor D4 (DRD4) gene modulates the influence of informational masking on speech recognition.

    PubMed

    Xie, Zilong; Maddox, W Todd; Knopik, Valerie S; McGeary, John E; Chandrasekaran, Bharath

    2015-01-01

    Listeners vary substantially in their ability to recognize speech in noisy environments. Here we examined the role of genetic variation on individual differences in speech recognition in various noise backgrounds. Background noise typically varies in the levels of energetic masking (EM) and informational masking (IM) imposed on target speech. Relative to EM, release from IM is hypothesized to place greater demand on executive function to selectively attend to target speech while ignoring competing noises. Recent evidence suggests that the long allele variant in exon III of the DRD4 gene, primarily expressed in the prefrontal cortex, may be associated with enhanced selective attention to goal-relevant high-priority information even in the face of interference. We investigated the extent to which this polymorphism is associated with speech recognition in IM and EM conditions. In an unscreened adult sample (Experiment 1) and a larger screened replication sample (Experiment 2), we demonstrate that individuals with the DRD4 long variant show better recognition performance in noise conditions involving significant IM, but not in EM conditions. In Experiment 2, we also obtained neuropsychological measures to assess the underlying mechanisms. Mediation analysis revealed that this listening condition-specific advantage was mediated by enhanced executive attention/working memory capacity in individuals with the long allele variant. These findings suggest that DRD4 may contribute specifically to individual differences in speech recognition ability in noise conditions that place demands on executive function. Copyright © 2014 Elsevier Ltd. All rights reserved.

  8. Dopamine receptor D4 (DRD4) gene modulates the influence of informational masking on speech recognition

    PubMed Central

    Xie, Zilong; Maddox, W. Todd; Knopik, Valerie S.; McGeary, John E.; Chandrasekaran, Bharath

    2014-01-01

    Listeners vary substantially in their ability to recognize speech in noisy environments. Here we examined the role of genetic variation on individual differences in speech recognition in various noise backgrounds. Background noise typically varies in the levels of energetic masking (EM) and informational masking (IM) imposed on target speech. Relative to EM, release from IM is hypothesized to place greater demand on executive function to selectively attend to target speech while ignoring competing noises. Recent evidence suggests that the long allele variant in exon III of the DRD4 gene, primarily expressed in the prefrontal cortex, may be associated with enhanced selective attention to goal-relevant high-priority information even in the face of interference. We investigated the extent to which this polymorphism is associated with speech recognition in IM and EM conditions. In an unscreened adult sample (Experiment 1) and a larger screened replication sample (Experiment 2), we demonstrate that individuals with the DRD4 long variant show better recognition performance in noise conditions involving significant IM, but not in EM conditions. In Experiment 2, we also obtained neuropsychological measures to assess the underlying mechanisms. Mediation analyses revealed that this listening condition-specific advantage was mediated by enhanced executive attention/working memory capacity in individuals with the long allele variant. These findings suggest that DRD4 may contribute specifically to individual differences in speech recognition ability in noise conditions that place demands on executive function. PMID:25497692

  9. Common polymorphism in the oxytocin receptor gene (OXTR) is associated with human social recognition skills

    PubMed Central

    Skuse, David H.; Lori, Adriana; Cubells, Joseph F.; Lee, Irene; Conneely, Karen N.; Puura, Kaija; Lehtimäki, Terho; Binder, Elisabeth B.; Young, Larry J.

    2014-01-01

    The neuropeptides oxytocin and vasopressin are evolutionarily conserved regulators of social perception and behavior. Evidence is building that they are critically involved in the development of social recognition skills within rodent species, primates, and humans. We investigated whether common polymorphisms in the genes encoding the oxytocin and vasopressin 1a receptors influence social memory for faces. Our sample comprised 198 families, from the United Kingdom and Finland, in whom a single child had been diagnosed with high-functioning autism. Previous research has shown that impaired social perception, characteristic of autism, extends to the first-degree relatives of autistic individuals, implying heritable risk. Assessments of face recognition memory, discrimination of facial emotions, and direction of gaze detection were standardized for age (7–60 y) and sex. A common SNP in the oxytocin receptor (rs237887) was strongly associated with recognition memory in combined probands, parents, and siblings after correction for multiple comparisons. Homozygotes for the ancestral A allele had impairments in the range −0.6 to −1.15 SD scores, irrespective of their diagnostic status. Our findings imply that a critical role for the oxytocin system in social recognition has been conserved across perceptual boundaries through evolution, from olfaction in rodents to visual memory in humans. PMID:24367110

  10. Recognition of cloned vesicular stomatitis virus internal and external gene products by cytotoxic T lymphocytes

    PubMed Central

    1986-01-01

    It has generally been assumed that most if not all CTL specific for vesicular stomatitis virus (VSV)-infected cells recognize the viral glycoprotein (G), an integral membrane protein abundantly expressed on infected cell surfaces. Using recombinant vaccinia viruses containing copies of cloned VSV genes to examine CTL recognition of VSV, we have confirmed that G is recognized by VSV-specific CTL. More interestingly, however, we have also found that nucleocapsid protein (N), an internal virion protein, can be detected on infected cell surfaces using mAb, and serves as a major target antigen for VSV-specific CTL. In contrast to the highly serotype-specific recognition of G, N is recognized by a major population of CTL able to lyse cells infected with either the Indiana or New Jersey VSV serotypes. Using target cells expressing a cloned MHC class I gene, we could directly show that CTL recognition of N occurs in the context of the MHC Ld molecule. PMID:3011949

  11. Exploring brand-name drug mentions on Twitter for pharmacovigilance.

    PubMed

    Carbonell, Pablo; Mayer, Miguel A; Bravo, Àlex

    2015-01-01

    Twitter has been proposed by several studies as a means to track public health trends such as influenza and Ebola outbreaks by analyzing user messages in order to measure different population features and interests. In this work we analyze the number and features of mentions on Twitter of drug brand names in order to explore the potential usefulness of the automated detection of drug side effects and drug-drug interactions on social media platforms such as Twitter. This information can be used for the development of predictive models for drug toxicity, drug-drug interactions or drug resistance. Taking into account the large number of drug brand mentions that we found on Twitter, it is promising as a tool for the detection, understanding and monitoring the way people manage prescribed drugs.

  12. Neural Androgen Receptors Modulate Gene Expression and Social Recognition But Not Social Investigation

    PubMed Central

    Karlsson, Sara A.; Studer, Erik; Kettunen, Petronella; Westberg, Lars

    2016-01-01

    The role of sex and androgen receptors (ARs) for social preference and social memory is rather unknown. In this study of mice we compared males, females and males lacking ARs specifically in the nervous system, ARNesDel, with respect to social preference, assessed with the three-chambered apparatus test, and social recognition, assessed with the social discrimination procedure. In the social discrimination test we also evaluated the tentative importance of the sex of the stimulus animal. Novel object recognition and olfaction were investigated to complement the results from the social tests. Gene expression analysis was performed to reveal molecules involved in the effects of sex and androgens on social behaviors. All three test groups showed social preference in the three-chambered apparatus test. In both social tests an AR-independent sexual dimorphism was seen in the persistence of social investigation of female conspecifics, whereas the social interest toward male stimuli mice was similar in all groups. Male and female controls recognized conspecifics independent of their sex, whereas ARNesDel males recognized female but not male stimuli mice. Moreover, the non-social behaviors were not affected by AR deficiency. The gene expression analyses of hypothalamus and amygdala indicated that Oxtr, Cd38, Esr1, Cyp19a1, Ucn3, Crh, and Gtf2i were differentially expressed between the three groups. In conclusion, our results suggest that ARs are required for recognition of male but not female conspecifics, while being dispensable for social investigation toward both sexes. In addition, the AR seems to regulate genes related to oxytocin, estrogen and William’s syndrome. PMID:27014003

  13. Sequence search and analysis of gene products containing RNA recognition motifs in the human genome.

    PubMed

    Malhotra, Sony; Sowdhamini, Ramanathan

    2014-12-22

    Gene expression is tightly regulated at both transcriptional and post-transcriptional levels. RNA-binding proteins are involved in post-transcriptional gene regulation events. They are involved in a variety of functions such as splicing, alternative splicing, nuclear import and export of mRNA, RNA stability and translation. There are several well-characterized RNA-binding motifs present in a whole genome, such as RNA recognition motif (RRM), KH domain, zinc-fingers etc. In the present study, we have investigated human genome for the presence of RRM-containing gene products starting from RRM domains in the Pfam (Protein family database) repository. In Pfam, seven families are recorded to contain RRM-containing proteins. We studied these families for their taxonomic representation, sequence features (identity, length, phylogeny) and structural properties (mapping conservation on the structures). We then examined the presence of RRM-containing gene products in Homo sapiens genome and identified 928 RRM-containing gene products. These were studied for their predicted domain architectures, biological processes, involvement in pathways, disease relevance and disorder content. RRM domains were observed to occur multiple times in a single polypeptide. However, there are 56 other co-existing domains involved in different regulatory functions. Further, functional enrichment analysis revealed that RRM-containing gene products are mainly involved in biological functions such as mRNA splicing and its regulation. Our sequence analysis identified RRM-containing gene products in the human genome and provides insights into their domain architectures and biological functions. Since mRNA splicing and gene regulation are important in the cellular machinery, this analysis provides an early overview of genes that carry out these functions.

  14. Molecular Recognition Enables Nanosubstrate-Mediated Delivery of Gene-Encapsulated Nanoparticles with High Efficiency

    PubMed Central

    2015-01-01

    Substrate-mediated gene delivery is a promising method due to its unique ability to preconcentrate exogenous genes onto designated substrates. However, many challenges remain to enable continuous and multiround delivery of the gene using the same substrates without depositing payloads and immobilizing cells in each round of delivery. Herein we introduce a gene delivery system, nanosubstrate-mediated delivery (NSMD) platform, based on two functional components with nanoscale features, including (1) DNA⊂SNPs, supramolecular nanoparticle (SNP) vectors for gene encapsulation, and (2) Ad-SiNWS, adamantane (Ad)-grafted silicon nanowire substrates. The multivalent molecular recognition between the Ad motifs on Ad-SiNWS and the β-cyclodextrin (CD) motifs on DNA⊂SNPs leads to dynamic assembly and local enrichment of DNA⊂SNPs from the surrounding medium onto Ad-SiNWS. Subsequently, once cells settled on the substrate, DNA⊂SNPs enriched on Ad-SiNWS were introduced through the cell membranes by intimate contact with individual nanowires on Ad-SiNWS, resulting in a highly efficient delivery of exogenous genes. Most importantly, sequential delivery of multiple batches of exogenous genes on the same batch cells settled on Ad-SiNWS was realized by sequential additions of the corresponding DNA⊂SNPs with equivalent efficiency. Moreover, using the NSMD platform in vivo, cells recruited on subcutaneously transplanted Ad-SiNWS were also efficiently transfected with exogenous genes loaded into SNPs, validating the in vivo feasibility of this system. We believe that this nanosubstrate-mediated delivery platform will provide a superior system for in vitro and in vivo gene delivery and can be further used for the encapsulation and delivery of other biomolecules. PMID:24708312

  15. Differential Expression of Genes Involved in Host Recognition, Attachment, and Degradation in the Mycoparasite Tolypocladium ophioglossoides

    PubMed Central

    Quandt, C. Alisha; Di, Yanming; Elser, Justin; Jaiswal, Pankaj; Spatafora, Joseph W.

    2016-01-01

    The ability of a fungus to infect novel hosts is dependent on changes in gene content, expression, or regulation. Examining gene expression under simulated host conditions can explore which genes may contribute to host jumping. Insect pathogenesis is the inferred ancestral character state for species of Tolypocladium, however several species are parasites of truffles, including Tolypocladium ophioglossoides. To identify potentially crucial genes in this interkingdom host switch, T. ophioglossoides was grown on four media conditions: media containing the inner and outer portions of its natural host (truffles of Elaphomyces), cuticles from an ancestral host (beetle), and a rich medium (Yeast Malt). Through high-throughput RNASeq of mRNA from these conditions, many differentially expressed genes were identified in the experiment. These included PTH11-related G-protein-coupled receptors (GPCRs) hypothesized to be involved in host recognition, and also found to be upregulated in insect pathogens. A divergent chitinase with a signal peptide was also found to be highly upregulated on media containing truffle tissue, suggesting an exogenous degradative activity in the presence of the truffle host. The adhesin gene, Mad1, was highly expressed on truffle media as well. A BiNGO analysis of overrepresented GO terms from genes expressed during each growth condition found that genes involved in redox reactions and transmembrane transport were the most overrepresented during T. ophioglossoides growth on truffle media, suggesting their importance in growth on fungal tissue as compared to other hosts and environments. Genes involved in secondary metabolism were most highly expressed during growth on insect tissue, suggesting that their products may not be necessary during parasitism of Elaphomyces. This study provides clues into understanding genetic mechanisms underlying the transition from insect to truffle parasitism. PMID:26801645

  16. A Scalable Framework to Detect Personal Health Mentions on Twitter

    PubMed Central

    Fabbri, Daniel; Rosenbloom, S Trent

    2015-01-01

    Background Biomedical research has traditionally been conducted via surveys and the analysis of medical records. However, these resources are limited in their content, such that non-traditional domains (eg, online forums and social media) have an opportunity to supplement the view of an individual’s health. Objective The objective of this study was to develop a scalable framework to detect personal health status mentions on Twitter and assess the extent to which such information is disclosed. Methods We collected more than 250 million tweets via the Twitter streaming API over a 2-month period in 2014. The corpus was filtered down to approximately 250,000 tweets, stratified across 34 high-impact health issues, based on guidance from the Medical Expenditure Panel Survey. We created a labeled corpus of several thousand tweets via a survey, administered over Amazon Mechanical Turk, that documents when terms correspond to mentions of personal health issues or an alternative (eg, a metaphor). We engineered a scalable classifier for personal health mentions via feature selection and assessed its potential over the health issues. We further investigated the utility of the tweets by determining the extent to which Twitter users disclose personal health status. Results Our investigation yielded several notable findings. First, we find that tweets from a small subset of the health issues can train a scalable classifier to detect health mentions. Specifically, training on 2000 tweets from four health issues (cancer, depression, hypertension, and leukemia) yielded a classifier with precision of 0.77 on all 34 health issues. Second, Twitter users disclosed personal health status for all health issues. Notably, personal health status was disclosed over 50% of the time for 11 out of 34 (33%) investigated health issues. Third, the disclosure rate was dependent on the health issue in a statistically significant manner (P<.001). For instance, more than 80% of the tweets about

  17. Health-Promoting Verses as mentioned in the Holy Quran.

    PubMed

    Aboul-Enein, Basil H

    2016-06-01

    The Quran is regarded as both the spiritual and behavioral guidance for all Muslims. This narrative study was designed at examining relevant health-promoting verses in the Quran and to identify the chapters and verses where keywords and phrases are mentioned relevant to health promotion and behavior. Twenty-eight verses were identified, with a focus on diet and nutrition, personal hygiene, alcohol abstention, and the importance of a healthy lifestyle. These results suggest that the Quran could serve as an influential medium for culturally competent public health practitioners in diverse populations, particularly in Muslim communities, for improving and maintaining healthy behaviors.

  18. Combining classifiers generated by multi-gene genetic programming for protein fold recognition using genetic algorithm.

    PubMed

    Bardsiri, Mahshid Khatibi; Eftekhari, Mahdi; Mousavi, Reza

    2015-01-01

    In this study the problem of protein fold recognition, that is a classification task, is solved via a hybrid of evolutionary algorithms namely multi-gene Genetic Programming (GP) and Genetic Algorithm (GA). Our proposed method consists of two main stages and is performed on three datasets taken from the literature. Each dataset contains different feature groups and classes. In the first step, multi-gene GP is used for producing binary classifiers based on various feature groups for each class. Then, different classifiers obtained for each class are combined via weighted voting so that the weights are determined through GA. At the end of the first step, there is a separate binary classifier for each class. In the second stage, the obtained binary classifiers are combined via GA weighting in order to generate the overall classifier. The final obtained classifier is superior to the previous works found in the literature in terms of classification accuracy.

  19. Quorum sensing in Chromobacterium violaceum: DNA recognition and gene regulation by the CviR receptor.

    PubMed

    Stauff, Devin L; Bassler, Bonnie L

    2011-08-01

    The bacterial pathogen Chromobacterium violaceum uses a LuxIR-type quorum-sensing system to detect and respond to changes in cell population density. CviI synthesizes the autoinducer C(10)-homoserine lactone (C(10)-HSL), and CviR is a cytoplasmic DNA binding transcription factor that activates gene expression following binding to C(10)-HSL. A number of behaviors are controlled by quorum sensing in C. violaceum. However, few genes have been shown to be directly controlled by CviR, in part because the DNA motif bound by CviR is not well characterized. Here, we define the DNA sequence required for promoter recognition by CviR. Using in vivo data generated from a library of point mutations in a CviR-regulated promoter, we find that CviR binds to a palindrome with the ideal sequence CTGNCCNNNNGGNCAG. We constructed a position weight matrix using these in vivo data and scanned the C. violaceum genome to predict CviR binding sites. We measured direct activation of the identified promoters by CviR and found that CviR controls the expression of the promoter for a chitinase, a type VI secretion-related gene, a transcriptional regulator gene, a guanine deaminase gene, and cviI. Indeed, regulation of cviI expression by CviR generates a canonical quorum-sensing positive-feedback loop.

  20. Antibodies Raised Against Chlamydial Lipopolysaccharide Antigens Reveal Convergence in Germline Gene Usage and Differential Epitope Recognition

    PubMed Central

    Brooks, Cory L; Müller-Loennies, Sven; Borisova, Svetlana N.; Brade, Lore; Kosma, Paul; Hirama, Tomoko; MacKenzie, C. Roger; Brade, Helmut; Evans, Stephen V

    2011-01-01

    In order to explore monoclonal antibody recognition carbohydrate antigens, several structures from two monoclonal antibodies directed against carbohydrate epitopes derived from chlamydial LPS have been solved to high resolution. With the exception of CDR H3, antibodies S54-10 and S73-2 are both derived from the same set of germline gene segments as the previously reported structures S25-2 and S45-18. Despite this similarity, the antibodies differ in specificity and the mechanism by which they recognize their cognate antigen. S54-10 uses an unrelated CDR H3 to recognize its antigen in a fashion analogous to S45-18; however, S73-2 recognizes the same antigen as S45-18 and S54-10 in a wholly unrelated manner. Together, these antibody-antigen structures provide snapshots into how the immune system uses the same set of inherited germline gene segments to generate multiple possible specificities that allow for differential recognition of epitopes, and how unrelated CDR H3 sequences can result in convergent binding of clinically-relevant bacterial antigens. PMID:20000757

  1. Cloning and characterization of the peptidoglycan recognition protein genes in the mosquito, Armigeres subalbatus (Diptera: Culicidae).

    PubMed

    Wang, Songjie; Conant, Gavin C; Ou, Ruguang; Beerntsen, Brenda T

    2012-05-01

    Peptidoglycan recognition proteins (PGRPs) are a group of proteins that are responsible for the recognition and, in some cases, binding of peptidoglycan (PGN), a unique cell wall component of bacteria, and initiation of immune responses to various types of pathogens. In the current study, full-length cDNA sequences of multiple PGRPs, identified via a database search, were cloned in the mosquito Armigeres subalbatus (Coquillett). During cloning, a novel transcript variant (isoform) of AsPGRP-LC (As: Ar. subalbatus) was also identified that shares a large 5' end fragment with AsPGRP-LC. All four AsPGRP genes (six transcripts) contain a conserved PGRP domain, an ortholog of the amidase-2 domain. Based on predicted functional domain, the six Ar. subalbatus PGRPs resemble both short (AsPGRP-S1) and long (AsPGRP-LBa, AsPGRP-LBb, AsPGRP-LCa, AsPGRP-LCb, and AsPGRP-LE) forms of PGRPs as in other insects. Sequence alignments showed that PGRPs are conserved across Dipterans. Phylogenetic analysis indicated that PGRPs represent an ancient gene family that has primarily diverged through speciation events among these Dipterans, with only a limited number of lineage specific gene duplications. Developmental profiling of the six AsPGRP transcripts using real-time polymerase chain reaction revealed that AsPGRP-LCa and AsPGRP-LCb are constitutively expressed at high levels in all developmental stages, while AsPGRP-S1, AsPGRP-LBa, AsPGRP-LBb, and AsPGRP-LE transcripts have low expression in most of the life stages and are increased only at certain times. Tissue profiling of the six AsPGRP transcripts showed that they are expressed in various patterns, even between the different isoforms of the same PGRP gene, indicating that these AsPGRPs may play different functions.

  2. GENETAG: a tagged corpus for gene/protein named entity recognition.

    PubMed

    Tanabe, Lorraine; Xie, Natalie; Thom, Lynne H; Matten, Wayne; Wilbur, W John

    2005-01-01

    Named entity recognition (NER) is an important first step for text mining the biomedical literature. Evaluating the performance of biomedical NER systems is impossible without a standardized test corpus. The annotation of such a corpus for gene/protein name NER is a difficult process due to the complexity of gene/protein names. We describe the construction and annotation of GENETAG, a corpus of 20K MEDLINE sentences for gene/protein NER. 15K GENETAG sentences were used for the BioCreAtIvE Task 1A Competition. To ensure heterogeneity of the corpus, MEDLINE sentences were first scored for term similarity to documents with known gene names, and 10K high- and 10K low-scoring sentences were chosen at random. The original 20K sentences were run through a gene/protein name tagger, and the results were modified manually to reflect a wide definition of gene/protein names subject to a specificity constraint, a rule that required the tagged entities to refer to specific entities. Each sentence in GENETAG was annotated with acceptable alternatives to the gene/protein names it contained, allowing for partial matching with semantic constraints. Semantic constraints are rules requiring the tagged entity to contain its true meaning in the sentence context. Application of these constraints results in a more meaningful measure of the performance of an NER system than unrestricted partial matching. The annotation of GENETAG required intricate manual judgments by annotators which hindered tagging consistency. The data were pre-segmented into words, to provide indices supporting comparison of system responses to the "gold standard". However, character-based indices would have been more robust than word-based indices. GENETAG Train, Test and Round1 data and ancillary programs are freely available at ftp://ftp.ncbi.nlm.nih.gov/pub/tanabe/GENETAG.tar.gz. A newer version of GENETAG-05, will be released later this year.

  3. Expression of pattern recognition receptor genes and mortality in patients with colorectal adenocarcinoma.

    PubMed

    Royse, Kathryn E; Chen, Liang; Berger, David H; Ittmann, Michael M; El-Serag, Hashem B; Balentine, Courtney J; Graham, David Y; Richardson, Peter A; Rumbaut, Rolando E; Shen, Xiaoyun; White, Donna L; Jiao, Li

    2017-01-01

    Toll-like receptors (TLRs) and the receptor for advanced glycation end products (AGER) are pattern recognition receptors that regulate intestinal inflammatory homeostasis. However, their relevance in colorectal cancer (CRC) prognosis is unclear. We investigated expression of TLRs, AGER, and interacting proteins in association with CRC mortality in a retrospective cohort study of 65 males diagnosed with primary resectable CRC between 2002 and 2009. Multiplex quantitative nuclease protection assay was used to quantify the expression of 19 genes in archived tissues of tumor and paired adjacent normal mucosa. We evaluated the association between log2 (tumor/normal) expression ratios for single and combined genes and all-cause mortality using multivariable Cox regression analysis. The false discovery rate adjusted q-value less than 0.10 indicated statistical significance for single gene. Five-year survival time was calculated from diagnosis of CRC to death, lost to follow-up, or December 31, 2014. Compared to paired normal mucosa, expression levels of AGER, IL1A, MYD88, and TLR5 were lower (q = 0.0002); while CXCL8 and S100P were higher (q = 0.0002) in tumor epithelia. Higher tumor expression of IL1A (HRadj = 0.68, 95% CI: 0.49-0.94), IL6 (HRadj = 0.70, 95% CI: 0.52-0.94), MyD88 (HRadj = 0.53, 95% CI: 0.30-0.93), and TLR5 (HRadj = 0.71, 95% CI: 0.52-0.98) was associated with higher mortality risk. There was a synergistic effect on lower five-year survival in lower co-expressers of IL-6 and MyD88 (P < 0.0001). Our findings suggest that a TLRs/MyD88-mediated inflammatory response may play a role in CRC prognosis. The role of pattern recognition receptor-mediated immunity in CRC mortality warrants further research.

  4. Surface EMG-based Sketching Recognition Using Two Analysis Windows and Gene Expression Programming

    PubMed Central

    Yang, Zhongliang; Chen, Yumiao

    2016-01-01

    Sketching is one of the most important processes in the conceptual stage of design. Previous studies have relied largely on the analyses of sketching process and outcomes; whereas surface electromyographic (sEMG) signals associated with sketching have received little attention. In this study, we propose a method in which 11 basic one-stroke sketching shapes are identified from the sEMG signals generated by the forearm and upper arm muscles from 4 subjects. Time domain features such as integrated electromyography, root mean square and mean absolute value were extracted with analysis windows of two length conditions for pattern recognition. After reducing data dimensionality using principal component analysis, the shapes were classified using Gene Expression Programming (GEP). The performance of the GEP classifier was compared to the Back Propagation neural network (BPNN) and the Elman neural network (ENN). Feature extraction with the short analysis window (250 ms with a 250 ms increment) improved the recognition rate by around 6.4% averagely compared with the long analysis window (2500 ms with a 2500 ms increment). The average recognition rate for the eleven basic one-stroke sketching patterns achieved by the GEP classifier was 96.26% in the training set and 95.62% in the test set, which was superior to the performance of the BPNN and ENN classifiers. The results show that the GEP classifier is able to perform well with either length of the analysis window. Thus, the proposed GEP model show promise for recognizing sketching based on sEMG signals. PMID:27790083

  5. Surface EMG-based Sketching Recognition Using Two Analysis Windows and Gene Expression Programming.

    PubMed

    Yang, Zhongliang; Chen, Yumiao

    2016-01-01

    Sketching is one of the most important processes in the conceptual stage of design. Previous studies have relied largely on the analyses of sketching process and outcomes; whereas surface electromyographic (sEMG) signals associated with sketching have received little attention. In this study, we propose a method in which 11 basic one-stroke sketching shapes are identified from the sEMG signals generated by the forearm and upper arm muscles from 4 subjects. Time domain features such as integrated electromyography, root mean square and mean absolute value were extracted with analysis windows of two length conditions for pattern recognition. After reducing data dimensionality using principal component analysis, the shapes were classified using Gene Expression Programming (GEP). The performance of the GEP classifier was compared to the Back Propagation neural network (BPNN) and the Elman neural network (ENN). Feature extraction with the short analysis window (250 ms with a 250 ms increment) improved the recognition rate by around 6.4% averagely compared with the long analysis window (2500 ms with a 2500 ms increment). The average recognition rate for the eleven basic one-stroke sketching patterns achieved by the GEP classifier was 96.26% in the training set and 95.62% in the test set, which was superior to the performance of the BPNN and ENN classifiers. The results show that the GEP classifier is able to perform well with either length of the analysis window. Thus, the proposed GEP model show promise for recognizing sketching based on sEMG signals.

  6. Possible dosage effect of maternally expressed genes on visual recognition memory in Prader-Willi syndrome.

    PubMed

    Joseph, B; Egli, M; Sutcliffe, J S; Thompson, T

    2001-01-08

    Seventeen patients with Prader-Willi syndrome (7 with paternal deletion of chromosome 15q11-q13 and 10 with maternal uniparental disomy [UPD]), and 9 controls performed a computerized visual recognition task. A series of color digital photographs were presented; most were presented twice, but the remainder appeared only once. Photographs presented twice were separated in their presentation by either 0, 10, 30, 50 or 100 intervening photographs. Subjects indicated whether each photograph had been presented previously. This procedure was implemented twice, once using photographs of foods, and once using photographs of nonfood objects. As the number of intervening photographs between the first and second presentation increased, subjects were less likely to remember having seen the photograph before. Performance by UPD subjects was less affected by increasing the number of intervening photographs relative to the other two groups, suggesting they had superior visual recognition memory. This raises the possibility of a beneficial effect of having two copies maternally expressed genes on chromosome 15. UBE3A is suggested as a possible candidate for this effect.

  7. Differential Recognition of Highly Divergent Downy Mildew Avirulence Gene Alleles by RPP1 Resistance Genes from Two Arabidopsis Lines

    PubMed Central

    Rehmany, Anne P.; Gordon, Anna; Rose, Laura E.; Allen, Rebecca L.; Armstrong, Miles R.; Whisson, Stephen C.; Kamoun, Sophien; Tyler, Brett M.; Birch, Paul R.J.; Beynon, Jim L.

    2005-01-01

    The perception of downy mildew avirulence (Arabidopsis thaliana Recognized [ATR]) gene products by matching Arabidopsis thaliana resistance (Recognition of Peronospora parasitica [RPP]) gene products triggers localized cell death (a hypersensitive response) in the host plant, and this inhibits pathogen development. The oomycete pathogen, therefore, is under selection pressure to alter the form of these gene products to prevent detection. That the pathogen maintains these genes indicates that they play a positive role in pathogen survival. Despite significant progress in cloning plant RPP genes and characterizing essential plant components of resistance signaling pathways, little progress has been made in identifying the oomycete molecules that trigger them. Concluding a map-based cloning effort, we have identified an avirulence gene, ATR1NdWsB, that is detected by RPP1 from the Arabidopsis accession Niederzenz in the cytoplasm of host plant cells. We report the cloning of six highly divergent alleles of ATR1NdWsB from eight downy mildew isolates and demonstrate that the ATR1NdWsB alleles are differentially recognized by RPP1 genes from two Arabidopsis accessions (Niederzenz and Wassilewskija). RPP1-Nd recognizes a single allele of ATR1NdWsB; RPP1-WsB also detects this allele plus three additional alleles with divergent sequences. The Emco5 isolate expresses an allele of ATR1NdWsB that is recognized by RPP1-WsB, but the isolate evades detection in planta. Although the Cala2 isolate is recognized by RPP1-WsA, the ATR1NdWsB allele from Cala2 is not, demonstrating that RPP1-WsA detects a novel ATR gene product. Cloning of ATR1NdWsB has highlighted the presence of a highly conserved novel amino acid motif in avirulence proteins from three different oomycetes. The presence of the motif in additional secreted proteins from plant pathogenic oomycetes and its similarity to a host-targeting signal from malaria parasites suggest a conserved role in pathogenicity. PMID

  8. Differential recognition of highly divergent downy mildew avirulence gene alleles by RPP1 resistance genes from two Arabidopsis lines.

    PubMed

    Rehmany, Anne P; Gordon, Anna; Rose, Laura E; Allen, Rebecca L; Armstrong, Miles R; Whisson, Stephen C; Kamoun, Sophien; Tyler, Brett M; Birch, Paul R J; Beynon, Jim L

    2005-06-01

    The perception of downy mildew avirulence (Arabidopsis thaliana Recognized [ATR]) gene products by matching Arabidopsis thaliana resistance (Recognition of Peronospora parasitica [RPP]) gene products triggers localized cell death (a hypersensitive response) in the host plant, and this inhibits pathogen development. The oomycete pathogen, therefore, is under selection pressure to alter the form of these gene products to prevent detection. That the pathogen maintains these genes indicates that they play a positive role in pathogen survival. Despite significant progress in cloning plant RPP genes and characterizing essential plant components of resistance signaling pathways, little progress has been made in identifying the oomycete molecules that trigger them. Concluding a map-based cloning effort, we have identified an avirulence gene, ATR1NdWsB, that is detected by RPP1 from the Arabidopsis accession Niederzenz in the cytoplasm of host plant cells. We report the cloning of six highly divergent alleles of ATR1NdWsB from eight downy mildew isolates and demonstrate that the ATR1NdWsB alleles are differentially recognized by RPP1 genes from two Arabidopsis accessions (Niederzenz and Wassilewskija). RPP1-Nd recognizes a single allele of ATR1NdWsB; RPP1-WsB also detects this allele plus three additional alleles with divergent sequences. The Emco5 isolate expresses an allele of ATR1NdWsB that is recognized by RPP1-WsB, but the isolate evades detection in planta. Although the Cala2 isolate is recognized by RPP1-WsA, the ATR1NdWsB allele from Cala2 is not, demonstrating that RPP1-WsA detects a novel ATR gene product. Cloning of ATR1NdWsB has highlighted the presence of a highly conserved novel amino acid motif in avirulence proteins from three different oomycetes. The presence of the motif in additional secreted proteins from plant pathogenic oomycetes and its similarity to a host-targeting signal from malaria parasites suggest a conserved role in pathogenicity.

  9. Practical applicability of Nyayas - (Maxims) mentioned in Chakrapani Tika.

    PubMed

    Vyas, Mahesh Kumar; Dwivedi, Rambabu

    2014-01-01

    The Nyayas - (Maxims) are of two types: (1) Loukika Nyaya and (2) Shastriya Nyaya. Loukika Nyayas are the one which are used by the common public in day today life whereas Shastriya Nyayas are the one which are used by the authors of the treatise to explore their concepts. Most commonly by using the meaning and gist of Loukika Nyaya, the Shastriya Nyayas were put forth by the Granthakaras. Moreover, notion of Nyaya depends upon the situation, place, and topic of explanation mainly. To explain the meaning of the topic, these Nyayas helped since Vaidika Kala. They teach hidden meaning correctly. As like Vedas, these Nyayas are also a part of other Shastras and so as in Ayurveda Shastra too. While explaining the Nidana, Chikitsa, etc., these Nyayas were utilized by the Acharyas of Ayurveda. To discern these Nyayas in their entirety at one place with examples is necessary for easy understanding of the Shastra. Here is an attempt to explore such Nyayas mentioned in Ayurveda for the benefit of easy understanding of the subject.

  10. Practical applicability of Nyayas – (Maxims) mentioned in Chakrapani Tika

    PubMed Central

    Vyas, Mahesh Kumar; Dwivedi, Rambabu

    2014-01-01

    The Nyayas – (Maxims) are of two types: (1) Loukika Nyaya and (2) Shastriya Nyaya. Loukika Nyayas are the one which are used by the common public in day today life whereas Shastriya Nyayas are the one which are used by the authors of the treatise to explore their concepts. Most commonly by using the meaning and gist of Loukika Nyaya, the Shastriya Nyayas were put forth by the Granthakaras. Moreover, notion of Nyaya depends upon the situation, place, and topic of explanation mainly. To explain the meaning of the topic, these Nyayas helped since Vaidika Kala. They teach hidden meaning correctly. As like Vedas, these Nyayas are also a part of other Shastras and so as in Ayurveda Shastra too. While explaining the Nidana, Chikitsa, etc., these Nyayas were utilized by the Acharyas of Ayurveda. To discern these Nyayas in their entirety at one place with examples is necessary for easy understanding of the Shastra. Here is an attempt to explore such Nyayas mentioned in Ayurveda for the benefit of easy understanding of the subject. PMID:26664230

  11. Gene Ontology synonym generation rules lead to increased performance in biomedical concept recognition.

    PubMed

    Funk, Christopher S; Cohen, K Bretonnel; Hunter, Lawrence E; Verspoor, Karin M

    2016-09-09

    Gene Ontology (GO) terms represent the standard for annotation and representation of molecular functions, biological processes and cellular compartments, but a large gap exists between the way concepts are represented in the ontology and how they are expressed in natural language text. The construction of highly specific GO terms is formulaic, consisting of parts and pieces from more simple terms. We present two different types of manually generated rules to help capture the variation of how GO terms can appear in natural language text. The first set of rules takes into account the compositional nature of GO and recursively decomposes the terms into their smallest constituent parts. The second set of rules generates derivational variations of these smaller terms and compositionally combines all generated variants to form the original term. By applying both types of rules, new synonyms are generated for two-thirds of all GO terms and an increase in F-measure performance for recognition of GO on the CRAFT corpus from 0.498 to 0.636 is observed. Additionally, we evaluated the combination of both types of rules over one million full text documents from Elsevier; manual validation and error analysis show we are able to recognize GO concepts with reasonable accuracy (88 %) based on random sampling of annotations. In this work we present a set of simple synonym generation rules that utilize the highly compositional and formulaic nature of the Gene Ontology concepts. We illustrate how the generated synonyms aid in improving recognition of GO concepts on two different biomedical corpora. We discuss other applications of our rules for GO ontology quality assurance, explore the issue of overgeneration, and provide examples of how similar methodologies could be applied to other biomedical terminologies. Additionally, we provide all generated synonyms for use by the text-mining community.

  12. Preliminary evidence of association between EFHC2, a gene implicated in fear recognition, and harm avoidance.

    PubMed

    Blaya, Carolina; Moorjani, Priya; Salum, Giovanni Abrahão; Gonçalves, Leonardo; Weiss, Lauren A; Leistner-Segal, Sandra; Manfro, Gisele G; Smoller, Jordan W

    2009-03-06

    Genetic variation at the EF-hand domain containing 2 gene (EFHC2) locus has been associated with fear recognition in Turner syndrome. The aim of this study was to examine whether EFHC2 variants are associated with non-syndromic anxiety-related traits [harm avoidance (HA) and behavioral inhibition (BI)] and with panic disorder (PD). Our sample comprised 127 PD patients and 132 controls without psychiatric disorder. We genotyped nine SNPs within the EFHC2 locus and used PLINK to perform association analyses. An intronic SNP (rs1562875) was associated with HA (permuted p=0.031) accounting alone for over 3% of variance in this trait. This same SNP was nominally, but not empirically, associated with BI (r(2)=0.022; nominal p=0.022) and PD (OR=2.64; nominal p=0.009). The same association was found in a subsample of only females. In sum, we observed evidence of association between a variant in EFHC2, a gene previously associated with the processing of fear and social threat, and HA. Larger studies are warranted to confirm this association.

  13. The mouse and human genes encoding the recognition component of the N-end rule pathway

    PubMed Central

    Kwon, Yong Tae; Reiss, Yuval; Fried, Victor A.; Hershko, Avram; Yoon, Jeong Kyo; Gonda, David K.; Sangan, Pitchai; Copeland, Neal G.; Jenkins, Nancy A.; Varshavsky, Alexander

    1998-01-01

    The N-end rule relates the in vivo half-life of a protein to the identity of its N-terminal residue. The N-end rule pathway is one proteolytic pathway of the ubiquitin system. The recognition component of this pathway, called N-recognin or E3, binds to a destabilizing N-terminal residue of a substrate protein and participates in the formation of a substrate-linked multiubiquitin chain. We report the cloning of the mouse and human Ubr1 cDNAs and genes that encode a mammalian N-recognin called E3α. Mouse UBR1p (E3α) is a 1,757-residue (200-kDa) protein that contains regions of sequence similarity to the 225-kDa Ubr1p of the yeast Saccharomyces cerevisiae. Mouse and human UBR1p have apparent homologs in other eukaryotes as well, thus defining a distinct family of proteins, the UBR family. The residues essential for substrate recognition by the yeast Ubr1p are conserved in the mouse UBR1p. The regions of similarity among the UBR family members include a putative zinc finger and RING-H2 finger, another zinc-binding domain. Ubr1 is located in the middle of mouse chromosome 2 and in the syntenic 15q15-q21.1 region of human chromosome 15. Mouse Ubr1 spans ≈120 kilobases of genomic DNA and contains ≈50 exons. Ubr1 is ubiquitously expressed in adults, with skeletal muscle and heart being the sites of highest expression. In mouse embryos, the Ubr1 expression is highest in the branchial arches and in the tail and limb buds. The cloning of Ubr1 makes possible the construction of Ubr1-lacking mouse strains, a prerequisite for the functional understanding of the mammalian N-end rule pathway. PMID:9653112

  14. Gene polymorphisms in pattern recognition receptors and susceptibility to idiopathic recurrent vulvovaginal candidiasis

    PubMed Central

    Rosentul, Diana C.; Delsing, Corine E.; Jaeger, Martin; Plantinga, Theo S.; Oosting, Marije; Costantini, Irene; Venselaar, Hanka; Joosten, Leo A. B.; van der Meer, Jos W. M.; Dupont, Bertrand; Kullberg, Bart-Jan; Sobel, Jack D.; Netea, Mihai G.

    2014-01-01

    Objective: Approximately 5% of women suffer from recurrent vulvovaginal candidiasis (RVVC). It has been hypothesized that genetic factors play an important role in the susceptibility to RVVC. The aim of this study was to assess the effect of genetic variants of genes encoding for pattern recognition receptors (PRRs) on susceptibility to RVVC. Study design: For the study, 119 RVVC patients and 263 healthy controls were recruited. Prevalence of polymorphisms in five PRRs involved in recognition of Candida were investigated in patients and controls. In silico and functional studies were performed to assess their functional effects. Results: Single nucleotide polymorphisms (SNPs) in TLR1, TLR4, CLEC7A, and CARD9 did not affect the susceptibility to RVVC. In contrast, a non-synonymous polymorphism in TLR2 (rs5743704, Pro631His) increased the susceptibility to RVVC almost 3-fold. Furthermore, the TLR2 rs5743704 SNP had deleterious effects on protein function as assessed by in silico analysis, and in vitro functional assays suggested that it reduces production of IL-17 and IFNγ upon stimulation of peripheral blood mononuclear cells with Candida albicans. No effects were observed on serum mannose-binding lectin concentrations. Condensation: This study demonstrates the association of susceptibility to RVVC with genetic variation in TLR2, most likely caused by decreased induction of mucosal antifungal host defense. Conclusion: Genetic variation in TLR2 may significantly enhance susceptibility to RVVC by modulating host defense mechanisms against Candida. Additional studies are warranted to assess systematically the role of host genetic variation for susceptibility to RVVC. PMID:25295030

  15. Peptidoglycan Recognition Protein Genes and Risk of Parkinson’s Disease

    PubMed Central

    Goldman, Samuel M.; Kamel, Freya; Ross, G. Webster; Jewell, Sarah A.; Marras, Connie; Hoppin, Jane A.; Umbach, David M.; Bhudhikanok, Grace S.; Meng, Cheryl; Korell, Monica; Comyns, Kathleen; Hauser, Robert A.; Jankovic, Joseph; Factor, Stewart A.; Bressman, Susan; Lyons, Kelly E.; Sandler, Dale P.; Langston, J. William; Tanner, Caroline M.

    2014-01-01

    Increased gut permeability, inflammation, and colonic α-synuclein pathology are present in early Parkinson’s disease (PD) and have been proposed to contribute to PD pathogenesis. Peptidoglycan is a structural component of the bacterial cell wall. Peptidoglycan recognition proteins (PGRPs) maintain healthy gut microbial flora by regulating the immune response to both commensal and harmful bacteria. We tested the hypothesis that variants in genes that encode PGRPs are associated with PD risk. Participants in two independent case-control studies were genotyped for 30 single-nucleotide polymorphisms (SNPs) in the four PGLYRP genes. Using logistic regression to estimate odds ratios (OR) and 95% confidence intervals (CI) adjusted for potential confounding variables, we conducted analyses in each study, separately and pooled. One SNP failed the assay, and three had little to no variation. The ORs were similar in both study populations. In pooled analyses, three of seven PGLYRP2 SNPs (rs3813135, rs733731, rs892145), one of five PGLYRP3 SNPs (rs2987763), and six of nine PGLYRP4 SNPs (rs10888557, rs12063091, rs3006440, rs3006448, rs3006458, and rs3014864) were significantly associated with PD risk. Association was strongest for PGLYRP4 5’untranslated region (UTR) SNP rs10888557 (GG reference, CG OR 0.6 [95%CI 0.4–0.9], CC OR 0.15 [95%CI 0.04–0.6]; log-additive P-trend, 0.0004). Common variants in PGLYRP genes are associated with PD risk in two independent studies. These results require replication, but they are consistent with hypotheses of a causative role for the gut microbiota and gastrointestinal immune response in PD. PMID:24838182

  16. Molecular recognition of genomic DNA in a condensate with a model surfactant for potential gene-delivery applications.

    PubMed

    Singh, Priya; Choudhury, Susobhan; Chandra, Goutam Kumar; Lemmens, Peter; Pal, Samir Kumar

    2016-04-01

    The functionality of a gene carrying nucleic acid in an artificial gene-delivery system is important for the overall efficiency of the vehicle in vivo. Here, we have studied a well-known artificial gene-delivery system, which is a condensate of calf thymus DNA (CT-DNA) with a model cationic surfactant cetyltrimethylammonium bromide (CTAB) to investigate the molecular recognition of the genomic DNA in the condensate. While dynamic light scattering (DLS) and circular dichroism (CD) reveal structural aspects of the condensate and the constituting DNA respectively, picosecond resolved polarization gated spectroscopy and Förster resonance energy transfer (FRET) reveal molecular recognition of the genomic DNA in the condensate. We have considered ethidium bromide (EB) and crystal violet (CV), which are well known DNA-binding agents through intercalative (specific) and electrostatic (non-specific) interactions, respectively, as model ligands for the molecular recognition studies. A fluorescent cationic surfactant, Nonyl Acridine Orange (NAO) is considered to be a mimic of CTAB in the condensate. The polarization gated fluorescence of NAO at various temperatures has been used to investigate the local microviscosity of the condensate. The excellent spectral overlap of NAO emission and the absorption spectra of both EB and CV allow us to investigate FRET-distances of the ligands with respect to NAO in the condensate at various temperatures and thermal stability of ligand-binding of the genomic DNA. The thermodynamic properties of the molecular recognition have also been explored using Van't Hoff equation. We have also extended our studies to molecular recognition of the genomic DNA in the condensate as dried thin films. This has important implications for its application in bioelectronics.

  17. 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.

  18. A CRF-based system for recognizing chemical entity mentions (CEMs) in biomedical literature.

    PubMed

    Xu, Shuo; An, Xin; Zhu, Lijun; Zhang, Yunliang; Zhang, Haodong

    2015-01-01

    In order to improve information access on chemical compounds and drugs (chemical entities) described in text repositories, it is very crucial to be able to identify chemical entity mentions (CEMs) automatically within text. The CHEMDNER challenge in BioCreative IV was specially designed to promote the implementation of corresponding systems that are able to detect mentions of chemical compounds and drugs, which has two subtasks: CDI (Chemical Document Indexing) and CEM. Our system processing pipeline consists of three major components: pre-processing (sentence detection, tokenization), recognition (CRF-based approach), and post-processing (rule-based approach and format conversion). In our post-challenge system, the cost parameter in CRF model was optimized by 10-fold cross validation with grid search, and word representations feature induced by Brown clustering method was introduced. For the CEM subtask, our official runs were ranked in top position by obtaining maximum 88.79% precision, 69.08% recall and 77.70% balanced F-measure, which were improved further to 88.43% precision, 76.48% recall and 82.02% balanced F-measure in our post-challenge system. In our system, instead of extracting a CEM as a whole, we regarded it as a sequence labeling problem. Though our current system has much room for improvement, our system is valuable in showing that the performance in term of balanced F-measure can be improved largely by utilizing large amounts of relatively inexpensive un-annotated PubMed abstracts and optimizing the cost parameter in CRF model. From our practice and lessons, if one directly utilizes some open-source natural language processing (NLP) toolkits, such as OpenNLP, Standford CoreNLP, false positive (FP) rate may be very high. It is better to develop some additional rules to minimize the FP rate if one does not want to re-train the related models. Our CEM recognition system is available at: http://www.SciTeMiner.org/XuShuo/Demo/CEM.

  19. A CRF-based system for recognizing chemical entity mentions (CEMs) in biomedical literature

    PubMed Central

    2015-01-01

    Background In order to improve information access on chemical compounds and drugs (chemical entities) described in text repositories, it is very crucial to be able to identify chemical entity mentions (CEMs) automatically within text. The CHEMDNER challenge in BioCreative IV was specially designed to promote the implementation of corresponding systems that are able to detect mentions of chemical compounds and drugs, which has two subtasks: CDI (Chemical Document Indexing) and CEM. Results Our system processing pipeline consists of three major components: pre-processing (sentence detection, tokenization), recognition (CRF-based approach), and post-processing (rule-based approach and format conversion). In our post-challenge system, the cost parameter in CRF model was optimized by 10-fold cross validation with grid search, and word representations feature induced by Brown clustering method was introduced. For the CEM subtask, our official runs were ranked in top position by obtaining maximum 88.79% precision, 69.08% recall and 77.70% balanced F-measure, which were improved further to 88.43% precision, 76.48% recall and 82.02% balanced F-measure in our post-challenge system. Conclusions In our system, instead of extracting a CEM as a whole, we regarded it as a sequence labeling problem. Though our current system has much room for improvement, our system is valuable in showing that the performance in term of balanced F-measure can be improved largely by utilizing large amounts of relatively inexpensive un-annotated PubMed abstracts and optimizing the cost parameter in CRF model. From our practice and lessons, if one directly utilizes some open-source natural language processing (NLP) toolkits, such as OpenNLP, Standford CoreNLP, false positive (FP) rate may be very high. It is better to develop some additional rules to minimize the FP rate if one does not want to re-train the related models. Our CEM recognition system is available at: http

  20. The mate recognition protein gene mediates reproductive isolation and speciation in the Brachionus plicatilis cryptic species complex.

    PubMed

    Gribble, Kristin E; Mark Welch, David B

    2012-08-01

    Chemically mediated prezygotic barriers to reproduction likely play an important role in speciation. In facultatively sexual monogonont rotifers from the Brachionus plicatilis cryptic species complex, mate recognition of females by males is mediated by the Mate Recognition Protein (MRP), a globular glycoprotein on the surface of females, encoded by the mmr-b gene family. In this study, we sequenced mmr-b copies from 27 isolates representing 11 phylotypes of the B. plicatilis species complex, examined the mode of evolution and selection of mmr-b, and determined the relationship between mmr-b genetic distance and mate recognition among isolates. Isolates of the B. plicatilis species complex have 1-4 copies of mmr-b, each composed of 2-9 nearly identical tandem repeats. The repeats within a gene copy are generally more similar than are gene copies among phylotypes, suggesting concerted evolution. Compared to housekeeping genes from the same isolates, mmr-b has accumulated only half as many synonymous differences but twice as many non-synonymous differences. Most of the amino acid differences between repeats appear to occur on the outer face of the protein, and these often result in changes in predicted patterns of phosphorylation. However, we found no evidence of positive selection driving these differences. Isolates with the most divergent copies were unable to mate with other isolates and rarely self-crossed. Overall the degree of mate recognition was significantly correlated with the genetic distance of mmr-b. Discrimination of compatible mates in the B. plicatilis species complex is determined by proteins encoded by closely related copies of a single gene, mmr-b. While concerted evolution of the tandem repeats in mmr-b may function to maintain identity, it can also lead to the rapid spread of a mutation through all copies in the genome and thus to reproductive isolation. The mmr-b gene is evolving rapidly, and novel alleles may be maintained and increase in

  1. Tet1 Oxidase Regulates Neuronal Gene Transcription, Active DNA Hydroxy-methylation, Object Location Memory, and Threat Recognition Memory

    PubMed Central

    Kumar, Dinesh; Aggarwal, Milan; Kaas, Garrett A.; Lewis, John; Wang, Jing; Ross, Daniel L.; Zhong, Chun; Kennedy, Andrew; Song, Hongjun; Sweatt, J. David

    2015-01-01

    A dynamic equilibrium between DNA methylation and demethylation of neuronal activity-regulated genes is crucial for memory processes. However, the mechanisms underlying this equilibrium remain elusive. Tet1 oxidase has been shown to play a key role in the active DNA demethylation in the CNS. In this study, we used Tet1 gene knockout (Tet1KO) mice to examine the involvement of Tet1 in memory consolidation and storage in the adult brain. We found that Tet1 ablation leads to: altered expression of numerous neuronal activity-regulated genes, compensatory upregulation of active demethylation pathway genes, and upregulation of various epigenetic modifiers. Moreover, Tet1KO mice showed an enhancement in the consolidation and storage of threat recognition (cued and contextual fear conditioning) and object location memories. We conclude that Tet1 plays a critical role in regulating neuronal transcription and in maintaining the epigenetic state of the brain associated with memory consolidation and storage. PMID:26644996

  2. A cytochrome P450 gene plays a role in the recognition of sex pheromones in the tobacco cutworm, Spodoptera litura.

    PubMed

    Feng, B; Zheng, K; Li, C; Guo, Q; Du, Y

    2017-08-01

    Cytochrome P450 (P450 or CYP) genes are involved in fundamental physiological functions, and might be also associated with the olfactory recognition of sex pheromones in beetles and moths. A P450 gene, Spodoptera litura CYP4L4 (SlituCYP4L4), was cloned for the first time from the antennae of S. litura. SlituCYP4L4 was almost exclusively expressed in the adult stage and predominantly expressed in the adult antennae. In situ hybridization showed that SlituCYP4L4 localized mainly at the base of the long sensilla trichoidea, which responds to sex pheromone components. Pretreatment with an S. litura sex pheromone significantly reduced the expression levels of SlituCYP4L4, consistent with other genes involved in sex pheromone recognition. The expression level of SlituCYP4L4 was different in moths collected with different ratios of sex pheromone lures and collected in different geographical locations. After gene knockdown of SlituCYP4L4 in the antennae, the electroantennogram (EAG) responses of male and female moths to (9Z,11E)-tetradecadienyl acetate or (9Z,12E)-tetradecadienyl acetate were significantly decreased. In contrast, EAG responses to plant volatiles and sex pheromones of other moth species were not significantly influenced in these moths. SlituCYP4L4 was also expressed in the gustatory tissues and sensilla, which suggests that SlituCYP4L4 may have other functions in the chemosensory system. Our results have shown for the first time the function of a CYP gene with appendage-specific expression in insect sex pheromone recognition, especially in adult moths. © 2017 The Royal Entomological Society.

  3. MutationFinder: a high-performance system for extracting point mutation mentions from text.

    PubMed

    Caporaso, J Gregory; Baumgartner, William A; Randolph, David A; Cohen, K Bretonnel; Hunter, Lawrence

    2007-07-15

    Discussion of point mutations is ubiquitous in biomedical literature, and manually compiling databases or literature on mutations in specific genes or proteins is tedious. We present an open-source, rule-based system, MutationFinder, for extracting point mutation mentions from text. On blind test data, it achieves nearly perfect precision and a markedly improved recall over a baseline. MutationFinder, along with a high-quality gold standard data set, and a scoring script for mutation extraction systems have been made publicly available. Implementations, source code and unit tests are available in Python, Perl and Java. MutationFinder can be used as a stand-alone script, or imported by other applications. http://bionlp.sourceforge.net.

  4. Spatial patterns of diversity at the putative recognition domain of resistance gene candidates in wild bean populations.

    PubMed

    de Meaux, J; Neema, C

    2003-01-01

    Leucine Rich Repeats (LRR) domains have been identified on most known plant resistance genes and appear to be involved in the specific recognition of pathogen strains. Here we explore the processes which may drive the evolution of this putative recognition domain. We developed AFLP markers specifically situated in the LRR domain of members of the PRLJ1 complex Resistance Gene Candidate (RGC) family identified in common bean (Phaseolus vulgaris). Diversity for these markers was assessed in ten wild populations of P. vulgaris and compared to locally co-occurring pathogen populations of Colletotrichum lindemuthianum. Nine PRLJ1 LRR specific markers were obtained. Marker sequences revealed that RGC diversity at PRLJ1 is similar to that at other complex R-loci. Wild bean populations showed contrasting levels of PRLJ1 LRR diversity and were all significantly differentiated. We could not detect an effect of local C. lindemuthianum population diversity on the spatial distribution of P. vulgaris PRLJ1 diversity. However, host populations have been previously assessed for neutral (RAPD) markers and for resistance phenotypes to six strains of C. lindemuthianum isolated from cultivated bean fields. A comparative analysis of PRLJ1 LRR diversity and host diversity for resistance phenotypes indicated that evolutionary processes related to the antagonistic C. lindemuthianum/P. vulgaris interaction are likely to have shaped molecular diversity of the putative recognition domains of the PRLJ1 RGC family members.

  5. Peptidoglycan recognition protein genes and their roles in the innate immune pathways of the red flour beetle, Tribolium castaneum.

    PubMed

    Koyama, Hiroaki; Kato, Daiki; Minakuchi, Chieka; Tanaka, Toshiharu; Yokoi, Kakeru; Miura, Ken

    2015-11-01

    We have previously demonstrated that the functional Toll and IMD innate immune pathways indeed exist in the model beetle, Tribolium castaneum while the beetle's pathways have broader specificity in terms of microbial activation than that of Drosophila. To elucidate the molecular basis of this broad microbial activation, we here focused on potential upstream sensors of the T. castaneum innate immune pathways, peptidoglycan recognition proteins (PGRPs). Our phenotype analyses utilizing RNA interference-based comprehensive gene knockdown followed by bacterial challenge suggested: PGRP-LA functions as a pivotal sensor of the IMD pathway for both Gram-negative and Gram-positive bacteria; PGRP-LC acts as an IMD pathway-associated sensor mainly for Gram-negative bacteria; PGRP-LE also has some roles in Gram-negative bacterial recognition of the IMD pathway. On the other hand, we did not obtain clear phenotype changes by gene knockdown of short-type PGRP genes, probably because of highly inducible nature of these genes. Our results may collectively account for the promiscuous bacterial activation of the T. castaneum innate immune pathways at least in part.

  6. Curatable Named-Entity Recognition Using Semantic Relations.

    PubMed

    Hsu, Yi-Yu; Kao, Hung-Yu

    2015-01-01

    Named-entity recognition (NER) plays an important role in the development of biomedical databases. However, the existing NER tools produce multifarious named-entities which may result in both curatable and non-curatable markers. To facilitate biocuration with a straightforward approach, classifying curatable named-entities is helpful with regard to accelerating the biocuration workflow. Co-occurrence Interaction Nexus with Named-entity Recognition (CoINNER) is a web-based tool that allows users to identify genes, chemicals, diseases, and action term mentions in the Comparative Toxicogenomic Database (CTD). To further discover interactions, CoINNER uses multiple advanced algorithms to recognize the mentions in the BioCreative IV CTD Track. CoINNER is developed based on a prototype system that annotated gene, chemical, and disease mentions in PubMed abstracts at BioCreative 2012 Track I (literature triage). We extended our previous system in developing CoINNER. The pre-tagging results of CoINNER were developed based on the state-of-the-art named entity recognition tools in BioCreative III. Next, a method based on conditional random fields (CRFs) is proposed to predict chemical and disease mentions in the articles. Finally, action term mentions were collected by latent Dirichlet allocation (LDA). At the BioCreative IV CTD Track, the best F-measures reached for gene/protein, chemical/drug and disease NER were 54 percent while CoINNER achieved a 61.5 percent F-measure. System URL: http://ikmbio.csie.ncku.edu.tw/coinner/ introduction.htm.

  7. Patterns of evolution at the gametophytic self-incompatibility Sorbus aucuparia (Pyrinae) S pollen genes support the non-self recognition by multiple factors model

    PubMed Central

    Aguiar, Bruno; Vieira, Jorge; Cunha, Ana E.; Fonseca, Nuno A.; Reboiro-Jato, David; Reboiro-Jato, Miguel; Fdez-Riverola, Florentino; Raspé, Olivier; Vieira, Cristina P.

    2013-01-01

    S-RNase-based gametophytic self-incompatibility evolved once before the split of the Asteridae and Rosidae. In Prunus (tribe Amygdaloideae of Rosaceae), the self-incompatibility S-pollen is a single F-box gene that presents the expected evolutionary signatures. In Malus and Pyrus (subtribe Pyrinae of Rosaceae), however, clusters of F-box genes (called SFBBs) have been described that are expressed in pollen only and are linked to the S-RNase gene. Although polymorphic, SFBB genes present levels of diversity lower than those of the S-RNase gene. They have been suggested as putative S-pollen genes, in a system of non-self recognition by multiple factors. Subsets of allelic products of the different SFBB genes interact with non-self S-RNases, marking them for degradation, and allowing compatible pollinations. This study performed a detailed characterization of SFBB genes in Sorbus aucuparia (Pyrinae) to address three predictions of the non-self recognition by multiple factors model. As predicted, the number of SFBB genes was large to account for the many S-RNase specificities. Secondly, like the S-RNase gene, the SFBB genes were old. Thirdly, amino acids under positive selection—those that could be involved in specificity determination—were identified when intra-haplotype SFBB genes were analysed using codon models. Overall, the findings reported here support the non-self recognition by multiple factors model. PMID:23606363

  8. LysM domains mediate lipochitin–oligosaccharide recognition and Nfr genes extend the symbiotic host range

    PubMed Central

    Radutoiu, Simona; Madsen, Lene H; Madsen, Esben B; Jurkiewicz, Anna; Fukai, Eigo; Quistgaard, Esben M H; Albrektsen, Anita S; James, Euan K; Thirup, Søren; Stougaard, Jens

    2007-01-01

    Legume–Rhizobium symbiosis is an example of selective cell recognition controlled by host/non-host determinants. Individual bacterial strains have a distinct host range enabling nodulation of a limited set of legume species and vice versa. We show here that expression of Lotus japonicus Nfr1 and Nfr5 Nod-factor receptor genes in Medicago truncatula and L. filicaulis, extends their host range to include bacterial strains, Mesorhizobium loti or DZL, normally infecting L. japonicus. As a result, the symbiotic program is induced, nodules develop and infection threads are formed. Using L. japonicus mutants and domain swaps between L. japonicus and L. filicaulis NFR1 and NFR5, we further demonstrate that LysM domains of the NFR1 and NFR5 receptors mediate perception of the bacterial Nod-factor signal and that recognition depends on the structure of the lipochitin–oligosaccharide Nod-factor. We show that a single amino-acid variation in the LysM2 domain of NFR5 changes recognition of the Nod-factor synthesized by the DZL strain and suggests a possible binding site for bacterial lipochitin–oligosaccharide signal molecules. PMID:17690687

  9. LysM domains mediate lipochitin-oligosaccharide recognition and Nfr genes extend the symbiotic host range.

    PubMed

    Radutoiu, Simona; Madsen, Lene H; Madsen, Esben B; Jurkiewicz, Anna; Fukai, Eigo; Quistgaard, Esben M H; Albrektsen, Anita S; James, Euan K; Thirup, Søren; Stougaard, Jens

    2007-09-05

    Legume-Rhizobium symbiosis is an example of selective cell recognition controlled by host/non-host determinants. Individual bacterial strains have a distinct host range enabling nodulation of a limited set of legume species and vice versa. We show here that expression of Lotus japonicus Nfr1 and Nfr5 Nod-factor receptor genes in Medicago truncatula and L. filicaulis, extends their host range to include bacterial strains, Mesorhizobium loti or DZL, normally infecting L. japonicus. As a result, the symbiotic program is induced, nodules develop and infection threads are formed. Using L. japonicus mutants and domain swaps between L. japonicus and L. filicaulis NFR1 and NFR5, we further demonstrate that LysM domains of the NFR1 and NFR5 receptors mediate perception of the bacterial Nod-factor signal and that recognition depends on the structure of the lipochitin-oligosaccharide Nod-factor. We show that a single amino-acid variation in the LysM2 domain of NFR5 changes recognition of the Nod-factor synthesized by the DZL strain and suggests a possible binding site for bacterial lipochitin-oligosaccharide signal molecules.

  10. Structural Mechanisms of Peptide Recognition and Allosteric Modulation of Gene Regulation by the RRNPP Family of Quorum-Sensing Regulators.

    PubMed

    Do, Hackwon; Kumaraswami, Muthiah

    2016-07-17

    The members of RRNPP family of bacterial regulators sense population density-specific secreted oligopeptides and modulate the expression of genes involved in cellular processes, such as sporulation, competence, virulence, biofilm formation, conjugative plasmid transfer and antibiotic resistance. Signaling by RRNPP regulators include several steps: generation and secretion of the signaling oligopeptides, re-internalization of the signaling molecules into the cytoplasm, signal sensing by the cytosolic RRNPP regulators, signal-specific allosteric structural changes in the regulators, and interaction of the regulators with their respective regulatory target and gene regulation. The recently determined structures of the RRNPP regulators provide insight into the mechanistic aspects for several steps in this signaling circuit. In this review, we discuss the structural principles underlying peptide specificity, regulatory target recognition, and ligand-induced allostery in RRNPP regulators and its impact on gene regulation. Despite the conserved tertiary structure of these regulators, structural analyses revealed unexpected diversity in the mechanism of activation and molecular strategies that couple the peptide-induced allostery to gene regulation. Although these structural studies provide a sophisticated understanding of gene regulation by RRNPP regulators, much needs to be learned regarding the target DNA binding by yet-to-be characterized RNPP regulators and the several aspects of signaling by Rgg regulators. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. PHD Finger Recognition of Unmodified Histone H3R2 Links UHRF1 to Regulation of Euchromatic Gene Expression

    SciTech Connect

    Rajakumara, Eerappa; Wang, Zhentian; Ma, Honghui; Hu, Lulu; Chen, Hao; Lin, Yan; Guo, Rui; Wu, Feizhen; Li, Haitao; Lan, Fei; Shi, Yujiang Geno; Xu, Yanhui; Patel, Dinshaw J.; Shi, Yang

    2011-08-29

    Histone methylation occurs on both lysine and arginine residues, and its dynamic regulation plays a critical role in chromatin biology. Here we identify the UHRF1 PHD finger (PHD{sub UHRF1}), an important regulator of DNA CpG methylation, as a histone H3 unmodified arginine 2 (H3R2) recognition modality. This conclusion is based on binding studies and cocrystal structures of PHD{sub UHRF1} bound to histone H3 peptides, where the guanidinium group of unmodified R2 forms an extensive intermolecular hydrogen bond network, with methylation of H3R2, but not H3K4 or H3K9, disrupting complex formation. We have identified direct target genes of UHRF1 from microarray and ChIP studies. Importantly, we show that UHRF1's ability to repress its direct target gene expression is dependent on PHD{sub UHRF1} binding to unmodified H3R2, thereby demonstrating the functional importance of this recognition event and supporting the potential for crosstalk between histone arginine methylation and UHRF1 function.

  12. Perceived Parenting Mediates Serotonin Transporter Gene (5-HTTLPR) and Neural System Function during Facial Recognition: A Pilot Study

    PubMed Central

    Nishikawa, Saori

    2015-01-01

    This study examined changes in prefrontal oxy-Hb levels measured by NIRS (Near-Infrared Spectroscopy) during a facial-emotion recognition task in healthy adults, testing a mediational/moderational model of these variables. Fifty-three healthy adults (male = 35, female = 18) aged between 22 to 37 years old (mean age = 24.05 years old) provided saliva samples, completed a EMBU questionnaire (Swedish acronym for Egna Minnen Beträffande Uppfostran [My memories of upbringing]), and participated in a facial-emotion recognition task during NIRS recording. There was a main effect of maternal rejection on RoxH (right frontal activation during an ambiguous task), and a gene × environment (G×E) interaction on RoxH, suggesting that individuals who carry the SL or LL genotype and who endorse greater perceived maternal rejection show less right frontal activation than SL/LL carriers with lower perceived maternal rejection. Finally, perceived parenting style played a mediating role in right frontal activation via the 5-HTTLPR genotype. Early-perceived parenting might influence neural activity in an uncertain situation i.e. rating ambiguous faces among individuals with certain genotypes. This preliminary study makes a small contribution to the mapping of an influence of gene and behaviour on the neural system. More such attempts should be made in order to clarify the links. PMID:26418317

  13. PHD Finger Recognition of Unmodified Histone H3R2 Links UHRF1 to Regulation of Euchromatic Gene Expression

    SciTech Connect

    E Rajakumara; Z Wang; H Ma; L Hu; H Chen; Y Lin; R Guo; F Wu; H Li; et al.

    2011-12-31

    Histone methylation occurs on both lysine and arginine residues, and its dynamic regulation plays a critical role in chromatin biology. Here we identify the UHRF1 PHD finger (PHD{sub UHRF1}), an important regulator of DNA CpG methylation, as a histone H3 unmodified arginine 2 (H3R2) recognition modality. This conclusion is based on binding studies and cocrystal structures of PHD{sub UHRF1} bound to histone H3 peptides, where the guanidinium group of unmodified R2 forms an extensive intermolecular hydrogen bond network, with methylation of H3R2, but not H3K4 or H3K9, disrupting complex formation. We have identified direct target genes of UHRF1 from microarray and ChIP studies. Importantly, we show that UHRF1's ability to repress its direct target gene expression is dependent on PHD{sub UHRF1} binding to unmodified H3R2, thereby demonstrating the functional importance of this recognition event and supporting the potential for crosstalk between histone arginine methylation and UHRF1 function.

  14. PHD Finger Recognition of Unmodified Histone H3R2 Links UHRF1 to Regulation of Euchromatic Gene Expression

    PubMed Central

    Ma, Honghui; Hu, Lulu; Chen, Hao; Lin, Yan; Guo, Rui; Wu, Feizhen; Li, Haitao; Lan, Fei; Shi, Yujiang Geno; Xu, Yanhui; Patel, Dinshaw J.; Shi, Yang

    2015-01-01

    SUMMARY Histone methylation occurs on both lysine and arginine residues, and its dynamic regulation plays a critical role in chromatin biology. Here we identify the UHRF1 PHD finger (PHDUHRF1), an important regulator of DNA CpG methylation, as a histone H3 unmodified arginine 2 (H3R2) recognition modality. This conclusion is based on binding studies and cocrystal structures of PHDUHRF1 bound to histone H3 peptides, where the guanidinium group of unmodified R2 forms an extensive intermolecular hydrogen bond network, with methylation of H3R2, but not H3K4 or H3K9, disrupting complex formation. We have identified direct target genes of UHRF1 from microarray and ChIP studies. Importantly, we show that UHRF1's ability to repress its direct target gene expression is dependent on PHDUHRF1 binding to unmodified H3R2, thereby demonstrating the functional importance of this recognition event and supporting the potential for crosstalk between histone arginine methylation and UHRF1 function. PMID:21777816

  15. Perceived Parenting Mediates Serotonin Transporter Gene (5-HTTLPR) and Neural System Function during Facial Recognition: A Pilot Study.

    PubMed

    Nishikawa, Saori; Toshima, Tamotsu; Kobayashi, Masao

    2015-01-01

    This study examined changes in prefrontal oxy-Hb levels measured by NIRS (Near-Infrared Spectroscopy) during a facial-emotion recognition task in healthy adults, testing a mediational/moderational model of these variables. Fifty-three healthy adults (male = 35, female = 18) aged between 22 to 37 years old (mean age = 24.05 years old) provided saliva samples, completed a EMBU questionnaire (Swedish acronym for Egna Minnen Beträffande Uppfostran [My memories of upbringing]), and participated in a facial-emotion recognition task during NIRS recording. There was a main effect of maternal rejection on RoxH (right frontal activation during an ambiguous task), and a gene × environment (G × E) interaction on RoxH, suggesting that individuals who carry the SL or LL genotype and who endorse greater perceived maternal rejection show less right frontal activation than SL/LL carriers with lower perceived maternal rejection. Finally, perceived parenting style played a mediating role in right frontal activation via the 5-HTTLPR genotype. Early-perceived parenting might influence neural activity in an uncertain situation i.e. rating ambiguous faces among individuals with certain genotypes. This preliminary study makes a small contribution to the mapping of an influence of gene and behaviour on the neural system. More such attempts should be made in order to clarify the links.

  16. Inferring gene structures in genomic sequences using pattern recognition and expressed sequence tags

    SciTech Connect

    Xu, Y.; Mural, R.; Uberbacher, E.

    1997-02-01

    Computational methods for gene identification in genomic sequences typically have two phases: coding region prediction and gene parsing. While there are many effective methods for predicting coding regions (exons), parsing the predicted exons into proper gene structures, to a large extent, remains an unsolved problem. This paper presents an algorithm for inferring gene structures from predicted exon candidates, based on Expressed Sequence Tags (ESTs) and biological intuition/rules. The algorithm first finds all the related ESTs in the EST database (dbEST) for each predicted exon, and infers the boundaries of one or a series of genes based on the available EST information and biological rules. Then it constructs gene models within each pair of gene boundaries, that are most consistent with the EST information. By exploiting EST information and biological rules, the algorithm can (1) model complicated multiple gene structures, including embedded genes, (2) identify falsely-predicted exons and locate missed exons, and (3) make more accurate exon boundary predictions. The algorithm has been implemented and tested on long genomic sequences with a number of genes. Test results show that very accurate (predicted) gene models can be expected when related ESTs exist for the predicted exons.

  17. Inferring gene structures in genomic sequences using pattern recognition and expressed sequence tags.

    PubMed

    Xu, Y; Mural, R J; Uberbacher, E C

    1997-01-01

    Computational methods for gene identification in genomic sequences typically have two phases: coding region prediction and gene parsing. While there are many effective methods for predicting coding regions (exons), parsing the predicted exons into proper gene structures, to a large extent, remains an unsolved problem. This paper presents an algorithm for inferring gene structures from predicted exon candidates, based on Expressed Sequence Tags (ESTs) and biological intuition/rules. The algorithm first finds all the related ESTs in the EST database (dbEST) for each predicted exon, and infers the boundaries of one or a series of genes based on the available EST information and biological rules. Then it constructs gene models within each pair of gene boundaries, that are most consistent with the EST information. By exploiting EST information and biological rules, the algorithm can (1) model complicated multiple gene structures, including embedded genes, (2) identify falsely-predicted exons and locate missed exons, and (3) make more accurate exon boundary predictions. The algorithm has been implemented and tested on long genomic sequences with a number of genes. Test results show that very accurate (predicted) gene models can be expected when related ESTs exist for the predicted exons.

  18. Genomic clusters, putative pathogen recognition molecules, and antimicrobial genes are induced by infection of C. elegans with M. nematophilum

    PubMed Central

    O’Rourke, Delia; Baban, Dilair; Demidova, Maria; Mott, Richard; Hodgkin, Jonathan

    2006-01-01

    The interaction between the nematode Caenorhabditis elegans and a Gram-positive bacterial pathogen, Microbacterium nematophilum, provides a model for an innate immune response in nematodes. This pathogen adheres to the rectal and post-anal cuticle of the worm, causing slowed growth, constipation, and a defensive swelling response of rectal hypodermal cells. To explore the genomic responses that the worm activates after pathogenic attack we used microarray analysis of transcriptional changes induced after 6-h infection, comparing virulent with avirulent infection. We defined 89 genes with statistically significant expression changes of at least twofold, of which 68 were up-regulated and 21 were down-regulated. Among the former, those encoding C-type lectin domains were the most abundant class. Many of the 89 genes exhibit genomic clustering, and we identified one large cluster of 62 genes, of which most were induced in response to infection. We tested 41 of the induced genes for involvement in immunity using mutants or RNAi, finding that six of these are required for the swelling response and five are required more generally for defense. Our results indicate that C-type lectins and other putative pathogen-recognition molecules are important for innate immune defense in C. elegans. We also found significant induction of genes encoding lysozymes, proteases, and defense-related proteins, as well as various domains of unknown function. The genes induced during infection by M. nematophilum appear largely distinct from genes induced by other pathogens, suggesting that C. elegans mounts pathogen-specific responses to infection. PMID:16809667

  19. Challenges in the association of human single nucleotide polymorphism mentions with unique database identifiers

    PubMed Central

    2011-01-01

    Background Most information on genomic variations and their associations with phenotypes are covered exclusively in scientific publications rather than in structured databases. These texts commonly describe variations using natural language; database identifiers are seldom mentioned. This complicates the retrieval of variations, associated articles, as well as information extraction, e. g. the search for biological implications. To overcome these challenges, procedures to map textual mentions of variations to database identifiers need to be developed. Results This article describes a workflow for normalization of variation mentions, i.e. the association of them to unique database identifiers. Common pitfalls in the interpretation of single nucleotide polymorphism (SNP) mentions are highlighted and discussed. The developed normalization procedure achieves a precision of 98.1 % and a recall of 67.5% for unambiguous association of variation mentions with dbSNP identifiers on a text corpus based on 296 MEDLINE abstracts containing 527 mentions of SNPs. The annotated corpus is freely available at http://www.scai.fraunhofer.de/snp-normalization-corpus.html. Conclusions Comparable approaches usually focus on variations mentioned on the protein sequence and neglect problems for other SNP mentions. The results presented here indicate that normalizing SNPs described on DNA level is more difficult than the normalization of SNPs described on protein level. The challenges associated with normalization are exemplified with ambiguities and errors, which occur in this corpus. PMID:21992066

  20. The expression pattern of the murine Hoxa-10 gene and the sequence recognition of its homeodomain reveal specific properties of Abdominal B-like genes.

    PubMed Central

    Benson, G V; Nguyen, T H; Maas, R L

    1995-01-01

    Homeobox genes of the Abdominal B (AbdB) family constitute a distinct subset of vertebrate Hox genes. Analysis of the murine Hoxa-10 gene, one member of this family, revealed several properties specific to this class. Two transcripts of Hoxa-10, a10-1 and a10-2, encode homeodomain proteins of 55 kDa (399 amino acids) and 16 kDa (96 amino acids), respectively. These proteins have identical homeodomains and C-terminal regions encoded by a common 3' exon but differ significantly in the sizes of their N-terminal regions because of the usage of alternative 5' exons. The 5' exon of the a10-2 form is also present in transcripts of Hoxa-9, the next 3' gene, indicating that splicing can occur between adjacent AbdB Hox genes within a cluster. Both Hoxa-10 transcripts demonstrated identical patterns of expression in the posterior body and proximal limb bud, differentiating them from AbdB morphogenetic and regulatory transcripts and suggesting a role with other AbdB Hox genes in the patterning of these structures. Finally, a binding site selection identified the sequence AA(A/T)TTTTATTAC as the Hoxa-10 homeodomain consensus binding site, with a TTAT core sequence. Preferential recognition of a TTAT core therefore differentiates the AbdB class from Antennapedia (Antp) class gene products which bind a TAAT core. Thus, in vertebrates, structural similarities, coordinate transcriptional regulation, sites of expression, and binding site preferences all serve to distinguish AbdB from Antp Hox genes. PMID:7862151

  1. Recognition of chimeric small-subunit ribosomal DNAs composed of genes from uncultivated microorganisms

    NASA Technical Reports Server (NTRS)

    Kopczynski, E. D.; Bateson, M. M.; Ward, D. M.

    1994-01-01

    When PCR was used to recover small-subunit (SSU) rRNA genes from a hot spring cyanobacterial mat community, chimeric SSU rRNA sequences which exhibited little or no secondary structural abnormality were recovered. They were revealed as chimeras of SSU rRNA genes of uncultivated species through separate phylogenetic analysis of short sequence domains.

  2. Recognition of chimeric small-subunit ribosomal DNAs composed of genes from uncultivated microorganisms

    NASA Technical Reports Server (NTRS)

    Kopczynski, E. D.; Bateson, M. M.; Ward, D. M.

    1994-01-01

    When PCR was used to recover small-subunit (SSU) rRNA genes from a hot spring cyanobacterial mat community, chimeric SSU rRNA sequences which exhibited little or no secondary structural abnormality were recovered. They were revealed as chimeras of SSU rRNA genes of uncultivated species through separate phylogenetic analysis of short sequence domains.

  3. How the Scientific Community Reacts to Newly Submitted Preprints: Article Downloads, Twitter Mentions, and Citations

    PubMed Central

    Shuai, Xin; Pepe, Alberto; Bollen, Johan

    2012-01-01

    We analyze the online response to the preprint publication of a cohort of 4,606 scientific articles submitted to the preprint database arXiv.org between October 2010 and May 2011. We study three forms of responses to these preprints: downloads on the arXiv.org site, mentions on the social media site Twitter, and early citations in the scholarly record. We perform two analyses. First, we analyze the delay and time span of article downloads and Twitter mentions following submission, to understand the temporal configuration of these reactions and whether one precedes or follows the other. Second, we run regression and correlation tests to investigate the relationship between Twitter mentions, arXiv downloads, and article citations. We find that Twitter mentions and arXiv downloads of scholarly articles follow two distinct temporal patterns of activity, with Twitter mentions having shorter delays and narrower time spans than arXiv downloads. We also find that the volume of Twitter mentions is statistically correlated with arXiv downloads and early citations just months after the publication of a preprint, with a possible bias that favors highly mentioned articles. PMID:23133597

  4. How the scientific community reacts to newly submitted preprints: article downloads, Twitter mentions, and citations.

    PubMed

    Shuai, Xin; Pepe, Alberto; Bollen, Johan

    2012-01-01

    We analyze the online response to the preprint publication of a cohort of 4,606 scientific articles submitted to the preprint database arXiv.org between October 2010 and May 2011. We study three forms of responses to these preprints: downloads on the arXiv.org site, mentions on the social media site Twitter, and early citations in the scholarly record. We perform two analyses. First, we analyze the delay and time span of article downloads and Twitter mentions following submission, to understand the temporal configuration of these reactions and whether one precedes or follows the other. Second, we run regression and correlation tests to investigate the relationship between Twitter mentions, arXiv downloads, and article citations. We find that Twitter mentions and arXiv downloads of scholarly articles follow two distinct temporal patterns of activity, with Twitter mentions having shorter delays and narrower time spans than arXiv downloads. We also find that the volume of Twitter mentions is statistically correlated with arXiv downloads and early citations just months after the publication of a preprint, with a possible bias that favors highly mentioned articles.

  5. Hemagglutinin gene shuffling among Clostridium botulinum serotypes C and D yields distinct sugar recognition of the botulinum toxin complex.

    PubMed

    Miyata, Keita; Suzuki, Tomonori; Hayashi, Shintaro; Miyashita, Shin-Ichiro; Ohyama, Tohru; Niwa, Koichi; Watanabe, Toshihiro; Sagane, Yoshimasa

    2015-10-01

    Clostridium botulinum strains produce a large-sized toxin complex (TC) that is composed of botulinum neurotoxin (BoNT), non-toxic non-hemagglutinin and three different hemagglutinins (HA-70, HA-33 and HA-17). HA components enhance toxin delivery across the intestinal cell wall in a sugar chain-dependent manner. Here we characterized the sugar recognition of serotype D strain 1873 (D-1873) botulinum L-TC. Most L-TCs produced by serotype C and D strains bind to cells via interactions between HA-33 and cell surface sialo-oligosaccharides. However, like the previously reported L-TC produced by serotype C strain Yoichi (C-Yoichi), D-1873 L-TC binds only to cells that have been treated with neuraminidase, indicating that they recognize asialo-oligosaccharides. The D-1873 HA-33 amino acid sequence is similar to that of C-Yoichi, but had lower similarity to the majority of serotype C and D HA-33s. A comparison of TC component primary structures for 12 serotype C and D strains suggested that at least three types of HA-33 genes exist, and these are shuffled among the serotype C and D strains independently of BoNT serotype. This shuffling produces the distinct sugar recognition of serotype C and D botulinum TCs. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  6. [HNF1B-related disease: paradigm of a developmental gene and unexpected recognition of a new renal disease].

    PubMed

    Chauveau, Dominique; Faguer, Stanislas; Bandin, Flavio; Guigonis, Vincent; Chassaing, Nicolas; Decramer, Stéphane

    2013-11-01

    HNF1B encodes for a transcription factor involved in the early development of the kidney, pancreas, liver and genital tract. Mutations in HNF1B are dominantly inherited and consist of whole-gene deletion, or small mutation. De novo mutation occurs in half of tested kindreds. HNF1B-related disease combines renal and non-renal manifestations. Renal involvement is heterogeneous and may escape early recognition. During fetal life and childhood, it mostly consists of hyperechogenic kidneys or bilateral renal cystic hypodysplasia. The adult phenotype encompasses tubulointerstitial profile at presentation and slowly progressive renal decline (-2 ml/min/year). Renal involvement includes renal cysts (mostly few cortical cysts), a solitary kidney, pelvi-caliceal abnormalities, hypokalemia and hypomagnesemia related to tubular leak, and more rarely, Fanconi syndrome and chromophobe renal carcinoma. The latter warrants ultrasound screening. Extrarenal phenotype consists of diabetes mellitus (MODY-5), exocrine pancreas failure and pancreas atrophy; fluctuation liver tests abnormalities; diverse genital tract abnormalities in females or infertility in males; and mild mental retardation in rare individuals. Phenotype heterogeneity within families is striking. Individuals progressing to end-stage renal disease are eligible for kidney transplantation (or combined pancreas and kidney transplantation for diabetic individuals). While HNF1B disease was still unknown one decade ago, it has emerged as the second most prevalent dominantly inherited kidney disease. Data available pave the way for early recognition and improved specific management, including genetic counselling.

  7. OSIRISv1.2: A named entity recognition system for sequence variants of genes in biomedical literature

    PubMed Central

    Furlong, Laura I; Dach, Holger; Hofmann-Apitius, Martin; Sanz, Ferran

    2008-01-01

    Background Single Nucleotide Polymorphisms, among other type of sequence variants, constitute key elements in genetic epidemiology and pharmacogenomics. While sequence data about genetic variation is found at databases such as dbSNP, clues about the functional and phenotypic consequences of the variations are generally found in biomedical literature. The identification of the relevant documents and the extraction of the information from them are hampered by the large size of literature databases and the lack of widely accepted standard notation for biomedical entities. Thus, automatic systems for the identification of citations of allelic variants of genes in biomedical texts are required. Results Our group has previously reported the development of OSIRIS, a system aimed at the retrieval of literature about allelic variants of genes . Here we describe the development of a new version of OSIRIS (OSIRISv1.2, ) which incorporates a new entity recognition module and is built on top of a local mirror of the MEDLINE collection and HgenetInfoDB: a database that collects data on human gene sequence variations. The new entity recognition module is based on a pattern-based search algorithm for the identification of variation terms in the texts and their mapping to dbSNP identifiers. The performance of OSIRISv1.2 was evaluated on a manually annotated corpus, resulting in 99% precision, 82% recall, and an F-score of 0.89. As an example, the application of the system for collecting literature citations for the allelic variants of genes related to the diseases intracranial aneurysm and breast cancer is presented. Conclusion OSIRISv1.2 can be used to link literature references to dbSNP database entries with high accuracy, and therefore is suitable for collecting current knowledge on gene sequence variations and supporting the functional annotation of variation databases. The application of OSIRISv1.2 in combination with controlled vocabularies like MeSH provides a way to

  8. Bioenergetics and gene silencing approaches for unraveling nucleotide recognition by the human EIF2C2/Ago2 PAZ domain.

    PubMed

    Kandeel, Mahmoud; Al-Taher, Abdullah; Nakashima, Remi; Sakaguchi, Tomoya; Kandeel, Ali; Nagaya, Yuki; Kitamura, Yoshiaki; Kitade, Yukio

    2014-01-01

    Gene silencing and RNA interference are major cellular processes that control gene expression via the cleavage of target mRNA. Eukaryotic translation initiation factor 2C2 (EIF2C2, Argonaute protein 2, Ago2) is considered to be the major player of RNAi as it is the core component of RISC complexes. While a considerable amount of research has focused on RNA interference and its associated mechanisms, the nature and mechanisms of nucleotide recognition by the PAZ domain of EIF2C2/Ago2 have not yet been characterized. Here, we demonstrate that the EIF2C2/Ago2 PAZ domain has an inherent lack of binding to adenine nucleotides, a feature that highlights the poor binding of 3'-adenylated RNAs with the PAZ domain as well as the selective high trimming of the 3'-ends of miRNA containing adenine nucleotides. We further show that the PAZ domain selectively binds all ribonucleotides (except adenosine), whereas it poorly recognizes deoxyribonucleotides. In this context, the modification of dTMP to its ribonucleotide analogue gave a drastic improvement of binding enthalpy and, hence, binding affinity. Additionally, higher in vivo gene silencing efficacy was correlated with the stronger PAZ domain binders. These findings provide new insights into the nature of the interactions of the EIF2C2/Ago2 PAZ domain.

  9. Genetic interaction of an origin recognition complex subunit and the Polycomb group gene MEDEA during seed development.

    PubMed

    Collinge, Margaret A; Spillane, Charles; Köhler, Claudia; Gheyselinck, Jacqueline; Grossniklaus, Ueli

    2004-04-01

    The eukaryotic origin recognition complex (ORC) is made up of six subunits and functions in nuclear DNA replication, chromatin structure, and gene silencing in both fungi and metazoans. We demonstrate that disruption of a plant ORC subunit homolog, AtORC2 of Arabidopsis (Arabidopsis thaliana), causes a zygotic lethal mutant phenotype (orc2). Seeds of orc2 abort early, typically producing embryos with up to eight cells. Nuclear division in the endosperm is arrested at an earlier developmental stage: only approximately four nuclei are detected in orc2 endosperm. The endosperm nuclei in orc2 are dramatically enlarged, a phenotype that is most similar to class B titan mutants, which include mutants in structural maintenance of chromosomes (SMC) cohesins. The highest levels of ORC2 gene expression were found in preglobular embryos, coinciding with the stage at which homozygous orc2 mutant seeds arrest. The homologs of the other five Arabidopsis ORC subunits are also expressed at this developmental stage. The orc2 mutant phenotype is partly suppressed by a mutation in the Polycomb group gene MEDEA. In double mutants between orc2 and medea (mea), orc2 homozygotes arrest later with a phenotype intermediate between those of mea and orc2 single mutants. Either alterations in chromatin structure or the release of cell cycle checkpoints by the mea mutation may allow more cell and nuclear divisions to occur in orc2 homozygous seeds.

  10. Bioenergetics and Gene Silencing Approaches for Unraveling Nucleotide Recognition by the Human EIF2C2/Ago2 PAZ Domain

    PubMed Central

    Kandeel, Mahmoud; Al-Taher, Abdullah; Nakashima, Remi; Sakaguchi, Tomoya; Kandeel, Ali; Nagaya, Yuki; Kitamura, Yoshiaki; Kitade, Yukio

    2014-01-01

    Gene silencing and RNA interference are major cellular processes that control gene expression via the cleavage of target mRNA. Eukaryotic translation initiation factor 2C2 (EIF2C2, Argonaute protein 2, Ago2) is considered to be the major player of RNAi as it is the core component of RISC complexes. While a considerable amount of research has focused on RNA interference and its associated mechanisms, the nature and mechanisms of nucleotide recognition by the PAZ domain of EIF2C2/Ago2 have not yet been characterized. Here, we demonstrate that the EIF2C2/Ago2 PAZ domain has an inherent lack of binding to adenine nucleotides, a feature that highlights the poor binding of 3′-adenylated RNAs with the PAZ domain as well as the selective high trimming of the 3′-ends of miRNA containing adenine nucleotides. We further show that the PAZ domain selectively binds all ribonucleotides (except adenosine), whereas it poorly recognizes deoxyribonucleotides. In this context, the modification of dTMP to its ribonucleotide analogue gave a drastic improvement of binding enthalpy and, hence, binding affinity. Additionally, higher in vivo gene silencing efficacy was correlated with the stronger PAZ domain binders. These findings provide new insights into the nature of the interactions of the EIF2C2/Ago2 PAZ domain. PMID:24788663

  11. Regions in the Z5 mating gene of Schizophyllum commune involved in Y-Z binding and recognition.

    PubMed

    Wu, J; Ullrich, R C; Novotny, C P

    1996-10-28

    The A alpha mating locus of the woodrotting fungus Schizophyllum commune encodes two multiallelic genes, Y and Z, which regulate the A-pathway of development. The Y alleles contain a homeobox, suggesting that the Y proteins may be DNA-binding regulatory proteins. During mating, development is induced when Y from one mating partner interacts with Z from the other mating partner; self combinations of Y and Z are inactive. Two-hybrid analyses indicate that nonself combinations of Y and Z form heteromultimers and self combinations do not. To understand Y-Z binding and self-nonself recognition further we used mutagenesis and chimeras to identify regions in one allele of Z(Z5) that are involved in these processes. Here we report the results, which broadly define regions in Z5 that are essential for activity, Y-Z binding and Z5 allelic specificity.

  12. Arabidopsis MBP1 gene encodes a conserved ubiquitin recognition component of the 26S proteasome

    SciTech Connect

    Nocker, S. Van; Deveraux, Q.; Rechsteiner, M.

    1996-01-23

    Multiubiquitin chain attachment is a key step leading to the selective degradation of abnormal polypeptides and many important regulatory proteins by the eukaryotic 26S proteasome. However, the mechanism by which the 26S complex recognizes this posttranslational modification is unknown. Using synthetic multiubiquitin chains to probe an expression library for interacting proteins, we have isolated an Arabidopsis cDNA, designated MBP1, that encodes a 41-kDa acidic protein exhibiting high affinity for chains, especially those containing four or more ubiquitins. Based on similar physical and immunological properties, multiubiquitin binding affinities, and peptide sequence, MBP1 is homologous to subunit 5a of the human 26S proteasome. Structurally related proteins also exist in yeast, Caenorhabditis, and other plant species. Given their binding properties, association with the 26S proteasome, and widespread distribution, MBP1, S5a, and related proteins likely function as essential ubiquitin recognition components of the 26S proteasome. 35 refs., 3 figs.

  13. NAAG peptidase inhibitors and deletion of NAAG peptidase gene enhance memory in novel object recognition test

    PubMed Central

    Janczura, Karolina J.; Olszewski, Rafal T.; Bzdega, Tomasz; Bacich, Dean J.; Heston, Warren D.; Neale, Joseph H.

    2012-01-01

    The peptide neurotransmitter N-acetylaspartylglutamate (NAAG) is inactivated by the extracellular enzyme glutamate carboxypeptidase II. Inhibitors of this enzyme reverse dizocilpine (MK-801)-induced impairment of short-term memory in the novel object recognition test. The objective of this study was to test the hypothesis that NAAG peptidase inhibition enhances the long-term (24 hr delay) memory of C57BL mice in this test. These mice and mice in which glutamate carboxypeptidase II had been knocked out were presented with two identical objects to explore for 10 minutes on day 1 and tested with one of these familiar objects and one novel object on day 2. Memory was assessed as the degree to which the mice recalled the familiar object and explored the novel object to a greater extent on day 2. Uninjected mice or mice injected with saline prior to the acquisition session on day 1 demonstrated a lack of memory of the acquisition experience by exploring the familiar and novel objects to the same extent on day 2. Mice treated with glutamate carboxypeptidase II inhibitors ZJ43 or 2-PMPA prior to the acquisition trial explored the novel object significantly more time than the familiar object on day 2. Consistent with these results, mice in which glutamate carboxypeptidase II had been knocked out distinguished the novel from the familiar object on day 2 while their heterozygous colony mates did not. Inhibition of glutamate carboxypeptidase II enhances recognition memory, a therapeutic action that might be useful in treatment of memory deficits related to age and neurological disorders. PMID:23200894

  14. CLK-dependent exon recognition and conjoined gene formation revealed with a novel small molecule inhibitor.

    PubMed

    Funnell, Tyler; Tasaki, Shinya; Oloumi, Arusha; Araki, Shinsuke; Kong, Esther; Yap, Damian; Nakayama, Yusuke; Hughes, Christopher S; Cheng, S-W Grace; Tozaki, Hirokazu; Iwatani, Misa; Sasaki, Satoshi; Ohashi, Tomohiro; Miyazaki, Tohru; Morishita, Nao; Morishita, Daisuke; Ogasawara-Shimizu, Mari; Ohori, Momoko; Nakao, Shoichi; Karashima, Masatoshi; Sano, Masaya; Murai, Aiko; Nomura, Toshiyuki; Uchiyama, Noriko; Kawamoto, Tomohiro; Hara, Ryujiro; Nakanishi, Osamu; Shumansky, Karey; Rosner, Jamie; Wan, Adrian; McKinney, Steven; Morin, Gregg B; Nakanishi, Atsushi; Shah, Sohrab; Toyoshiba, Hiroyoshi; Aparicio, Samuel

    2017-12-01

    CDC-like kinase phosphorylation of serine/arginine-rich proteins is central to RNA splicing reactions. Yet, the genomic network of CDC-like kinase-dependent RNA processing events remains poorly defined. Here, we explore the connectivity of genomic CDC-like kinase splicing functions by applying graduated, short-exposure, pharmacological CDC-like kinase inhibition using a novel small molecule (T3) with very high potency, selectivity, and cell-based stability. Using RNA-Seq, we define CDC-like kinase-responsive alternative splicing events, the large majority of which monotonically increase or decrease with increasing CDC-like kinase inhibition. We show that distinct RNA-binding motifs are associated with T3 response in skipped exons. Unexpectedly, we observe dose-dependent conjoined gene transcription, which is associated with motif enrichment in the last and second exons of upstream and downstream partners, respectively. siRNA knockdown of CLK2-associated genes significantly increases conjoined gene formation. Collectively, our results reveal an unexpected role for CDC-like kinase in conjoined gene formation, via regulation of 3'-end processing and associated splicing factors.The phosphorylation of serine/arginine-rich proteins by CDC-like kinase is a central regulatory mechanism for RNA splicing reactions. Here, the authors synthesize a novel small molecule CLK inhibitor and map CLK-responsive alternative splicing events and discover an effect on conjoined gene transcription.

  15. Cloning and antibody recognition analysis of the canine 5-lipoxygenase gene.

    PubMed

    Loftus, John P; Morgan, Stewart K; Wakshlag, Joseph J

    2011-08-15

    5-Lipoxygenase cDNA was prepared from canine white blood cells revealing the full-length message using an oligonucleotide capping method. The sequenced 5-Lipoxygenase open reading frame revealed a 2031 base pair message encoding a 676 amino acid protein. The amino acid sequence showed mild variation with the presumed canine sequence, as well as differences in important residues of known phosphorylation observed in other species. The sequence had between 86 and 92% homology with other species, revealing a highly conserved sequence. Confirmation of gene product identity was achieved through transient transfection of the gene in a V5-Histidine tagged pcDNA 3.1 vector into a known canine cell line. Both V5 antibody and 5-lipoxygenase antibody confirmed the gene product using Western blotting and immunoflourescence. Copyright © 2011 Elsevier B.V. All rights reserved.

  16. The Markyt visualisation, prediction and benchmark platform for chemical and gene entity recognition at BioCreative/CHEMDNER challenge

    PubMed Central

    Pérez-Pérez, Martin; Pérez-Rodríguez, Gael; Rabal, Obdulia; Vazquez, Miguel; Oyarzabal, Julen; Fdez-Riverola, Florentino; Valencia, Alfonso; Krallinger, Martin; Lourenço, Anália

    2016-01-01

    Biomedical text mining methods and technologies have improved significantly in the last decade. Considerable efforts have been invested in understanding the main challenges of biomedical literature retrieval and extraction and proposing solutions to problems of practical interest. Most notably, community-oriented initiatives such as the BioCreative challenge have enabled controlled environments for the comparison of automatic systems while pursuing practical biomedical tasks. Under this scenario, the present work describes the Markyt Web-based document curation platform, which has been implemented to support the visualisation, prediction and benchmark of chemical and gene mention annotations at BioCreative/CHEMDNER challenge. Creating this platform is an important step for the systematic and public evaluation of automatic prediction systems and the reusability of the knowledge compiled for the challenge. Markyt was not only critical to support the manual annotation and annotation revision process but also facilitated the comparative visualisation of automated results against the manually generated Gold Standard annotations and comparative assessment of generated results. We expect that future biomedical text mining challenges and the text mining community may benefit from the Markyt platform to better explore and interpret annotations and improve automatic system predictions. Database URL: http://www.markyt.org, https://github.com/sing-group/Markyt PMID:27542845

  17. Analysis of gene expression profiles of Lactobacillus paracasei induced by direct contact with Saccharomyces cerevisiae through recognition of yeast mannan

    PubMed Central

    YAMASAKI-YASHIKI, Shino; SAWADA, Hiroshi; KINO-OKA, Masahiro; KATAKURA, Yoshio

    2016-01-01

    Co-culture of lactic acid bacteria (LAB) and yeast induces specific responses that are not observed in pure culture. Gene expression profiles of Lactobacillus paracasei ATCC 334 co-cultured with Saccharomyces cerevisiae IFO 0216 were analyzed by DNA microarray, and the responses induced by direct contact with the yeast cells were investigated. Coating the LAB cells with recombinant DnaK, which acts as an adhesive protein between LAB and yeast cells, enhanced the ratio of adhesion of the LAB cells to the yeast cells. The signals induced by direct contact were clarified by removal of the LAB cells unbound to the yeast cells. The genes induced by direct contact with heat-inactivated yeast cells were very similar to both those induced by the intact yeast cells and those induced by a soluble mannan. The top 20 genes upregulated by direct contact with the heat-inactivated yeast cells mainly encoded proteins related to exopolysaccharide synthesis, modification of surface proteins, and transport systems. In the case of the most upregulated gene, LSEI_0669, encoding a protein that has a region homologous to polyprenyl glycosylphosphotransferase, the expression level was upregulated 7.6-, 11.0-, and 8.8-fold by the heat-inactivated yeast cells, the intact yeast cells, and the soluble mannan, respectively, whereas it was only upregulated 1.8-fold when the non-adherent LAB cells were not removed before RNA extraction. Our results indicated that the LAB responded to direct contact with the yeast cells through recognition of mannan on the surface of the yeast. PMID:28243547

  18. Recognition of Scared Faces and the Serotonin Transporter Gene in Young Children: The Generation R Study

    ERIC Educational Resources Information Center

    Szekely, Eszter; Herba, Catherine M.; Arp, Pascal P.; Uitterlinden, Andre G.; Jaddoe, Vincent W. V.; Hofman, Albert; Verhulst, Frank C.; Hudziak, James J.; Tiemeier, Henning

    2011-01-01

    Background: Previous research highlights the significance of a functional polymorphism located in the promoter region (5-HTTLPR) of the serotonin transporter gene in emotional behaviour. This study examined the effect of the 5-HTTLPR polymorphism on emotion processing in a large number of healthy preschoolers. Methods: The 5-HTTLPR genotype was…

  19. Recognition of Scared Faces and the Serotonin Transporter Gene in Young Children: The Generation R Study

    ERIC Educational Resources Information Center

    Szekely, Eszter; Herba, Catherine M.; Arp, Pascal P.; Uitterlinden, Andre G.; Jaddoe, Vincent W. V.; Hofman, Albert; Verhulst, Frank C.; Hudziak, James J.; Tiemeier, Henning

    2011-01-01

    Background: Previous research highlights the significance of a functional polymorphism located in the promoter region (5-HTTLPR) of the serotonin transporter gene in emotional behaviour. This study examined the effect of the 5-HTTLPR polymorphism on emotion processing in a large number of healthy preschoolers. Methods: The 5-HTTLPR genotype was…

  20. Molecular Evolution of the CYP2D Subfamily in Primates: Purifying Selection on Substrate Recognition Sites without the Frequent or Long-Tract Gene Conversion

    PubMed Central

    Yasukochi, Yoshiki; Satta, Yoko

    2015-01-01

    The human cytochrome P450 (CYP) 2D6 gene is a member of the CYP2D gene subfamily, along with the CYP2D7P and CYP2D8P pseudogenes. Although the CYP2D6 enzyme has been studied extensively because of its clinical importance, the evolution of the CYP2D subfamily has not yet been fully understood. Therefore, the goal of this study was to reveal the evolutionary process of the human drug metabolic system. Here, we investigate molecular evolution of the CYP2D subfamily in primates by comparing 14 CYP2D sequences from humans to New World monkey genomes. Window analysis and statistical tests revealed that entire genomic sequences of paralogous genes were extensively homogenized by gene conversion during molecular evolution of CYP2D genes in primates. A neighbor-joining tree based on genomic sequences at the nonsubstrate recognition sites showed that CYP2D6 and CYP2D8 genes were clustered together due to gene conversion. In contrast, a phylogenetic tree using amino acid sequences at substrate recognition sites did not cluster the CYP2D6 and CYP2D8 genes, suggesting that the functional constraint on substrate specificity is one of the causes for purifying selection at the substrate recognition sites. Our results suggest that the CYP2D gene subfamily in primates has evolved to maintain the regioselectivity for a substrate hydroxylation activity between individual enzymes, even though extensive gene conversion has occurred across CYP2D coding sequences. PMID:25808902

  1. Contrasting Networks for Recognition Memory and Recency Memory Revealed by Immediate-Early Gene Imaging in the Rat

    PubMed Central

    2014-01-01

    The expression of the immediate-early gene c-fos was used to compare networks of activity associated with recency memory (temporal order memory) and recognition memory. In Experiment 1, rats were first familiarized with sets of objects and then given pairs of different, familiar objects to explore. For the recency test group, each object in a pair was separated by 110 min in the time between their previous presentations. For the recency control test, each object in a pair was separated by less than a 1 min between their prior presentations. Temporal discrimination of the objects correlated with c-fos activity in the recency test group in several sites, including area Te2, the perirhinal cortex, lateral entorhinal cortex, as well as the dentate gyrus, hippocampal fields CA3 and CA1. For both the test and control conditions, network models were derived using structural equation modeling. The recency test model emphasized serial connections from the perirhinal cortex to lateral entorhinal cortex and then to the CA1 subfield. The recency control condition involved more parallel pathways, but again highlighted CA1 within the hippocampus. Both models contrasted with those derived from tests of object recognition (Experiment 2), because stimulus novelty was associated with pathways from the perirhinal cortex to lateral entorhinal cortex that then involved both the dentate gyrus (and CA3) and CA1 in parallel. The present findings implicate CA1 for the processing of familiar stimuli, including recency discriminations, while the dentate gyrus and CA3 pathways are recruited when the perirhinal cortex signals novel stimuli. PMID:24933661

  2. A bimetallic nanocomposite modified genosensor for recognition and determination of thalassemia gene.

    PubMed

    Hamidi-Asl, Ezat; Raoof, Jahan Bakhsh; Naghizadeh, Nahid; Akhavan-Niaki, Haleh; Ojani, Reza; Banihashemi, Ali

    2016-10-01

    The main roles of DNA in the cells are to maintain and properly express genetic information. It is important to have analytical methods capable of fast and sensitive detection of DNA damage. DNA hybridization sensors are well suited for diagnostics and other purposes, including determination of bacteria and viruses. Beta thalassemias (βth) are due to mutations in the β-globin gene. In this study, an electrochemical biosensor which detects the sequences related to the β-globin gene issued from real samples amplified by polymerase chain reaction (PCR) is described for the first time. The biosensor relies on the immobilization of 20-mer single stranded oligonucleotide (probe) related to βth sequence on the carbon paste electrode (CPE) modified by 15% silver (Ag) and platinum (Pt) nanoparticles to prepare the bimetallic nanocomposite electrode and hybridization of this oligonucleotide with its complementary sequence (target). The extent of hybridization between the probe and target sequences was shown by using linear sweep voltammetry (LSV) with methylene blue (MB) as hybridization indicator. The selectivity of sensor was investigated using PCR samples containing non-complementary oligonucleotides. The detection limit of biosensor was calculated about 470.0pg/μL. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Human genes and pseudogenes for the 7SL RNA component of signal recognition particle.

    PubMed Central

    Ullu, E; Weiner, A M

    1984-01-01

    Of the several hundred 7SL RNA-like sequences that are dispersed in human DNA, no more than four are likely to represent genes for 7SL RNA; the majority are 7SL pseudogenes which appear to result from the reverse flow of genetic information from 7SL RNA back into genomic DNA. We present the sequence of five 7SL pseudogenes displaying an unprecedented diversity of structures. All are truncated copies of 7SL RNA, but the site of truncation can occur at either the 5' end, the 3' end or at both ends of the RNA sequence. We suggest that such diverse 7SL pseudogenes are generated by different but related pathways. In particular, we argue that two of the loci are secondary 7SL pseudogenes which derive from RNA polymerase III transcripts of primary (preexisting) 7SL pseudogenes. We also report the isolation and characterisation of a human genomic clone carrying two linked 7SL RNA coding regions, 7L30.1 and 7L30.2. The 7L30.2 locus differs by several single base changes from the known human 7SL RNA sequences and does not appear to be expressed at a detectable level in HeLa cells. The 7L30.1 locus is an authentic 7SL RNA gene encoding one of the three sequence variants of human 7SL RNA. Images Fig. 1. Fig. 5. Fig. 6. Fig. 7. PMID:6084597

  4. Occupational Portrayal of Men and Women on the Most Frequently Mentioned Television Shows of Preschool Children.

    ERIC Educational Resources Information Center

    Shechtman, Stephen A.

    The purpose of this study was to assess the distribution of male vs. female occupational portrayals in terms of occupational prestige on the six television shows most frequently mentioned by preschool children. The following shows were viewed and analyzed six times: Sesame Street, Bugs Bunny, Roadrunner, Batman, Flintstones, and Happy Days.…

  5. TRITIUM LABORATORY, TRA666, INTERIOR. CAMERA IS IN DOORWAY MENTIONED IN ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    TRITIUM LABORATORY, TRA-666, INTERIOR. CAMERA IS IN DOORWAY MENTIONED IN ID-33-G-175 AND LOOKS EAST INTO ANNEX, BUILT AS A SPECIAL TRITIUM LAB. INL NEGATIVE NO. HD46-25-2. Mike Crane, Photographer, 2/2005 - Idaho National Engineering Laboratory, Test Reactor Area, Materials & Engineering Test Reactors, Scoville, Butte County, ID

  6. Variation in genes of β-glucan recognition pathway and susceptibility to opportunistic infections in HIV-positive patients.

    PubMed

    Rosentul, Diana C; Plantinga, Theo S; Papadopoulos, Antonios; Joosten, Leo A B; Antoniadou, Anastasia; Venselaar, Hanka; Kullberg, Bart-Jan; van der Meer, Jos W M; Giamarellos-Bourboulis, Evangelos J; Netea, Mihai G

    2011-01-01

    Opportunistic infections are the main cause of morbidity and death among HIV-positive patients. Most of these infections are linked to the immunodeficiency due to low CD4+ counts. However, not all patients with low CD4+ counts are equally susceptible to infections, and we hypothesize that variability in genes of innate immunity may also play an important role. The dectin-1/CARD9 pathway is crucial for recognition of both fungal and bacterial pathogens. The aim of this study was to assess the possible association between the occurrence of opportunistic infections and single nucleotide polymorphisms in DECTIN-1 and CARD9 in a cohort of 187 HIV-infected patients. The incidence of oropharyngeal candidiasis and other opportunistic infections was not influenced by either the Y238X DECTIN-1 or the S12N CARD9 polymorphism. Surprisingly however, the prevalence of pneumonia was significantly higher in patients bearing the defective variant DECTIN-1 allele. These results suggest a role of dectin-1 in the host defense against respiratory bacterial infections, and future studies are warranted to confirm this association.

  7. Characterization of Choristoneura fumiferana genes of the sixth subunit of the origin recognition complex: CfORC6.

    PubMed

    Wang, Xaiochun; Carstens, Eric B; Feng, Qili

    2006-11-30

    A new protein was cloned and identified as the sixth subunit of Choristoneura fumiferana origin recognition complex (CfORC6). The newly identified 43 kDa protein CfORC6 is much bigger than DmORC6 (25.7 kDa) and HsORC6 (28.1 kDa), though itos 23.85% identical to DmORC6 and 23.81% identical to HsORC6. Although the molecular weight of CfORC6 is close to ScORc6 (50 kDa), CfORC6 is only 14.03% identical to ScORC6. By alignment, it was found that the N-terminal of CfORC6 has about 30% identities with other ORC6s, but about 100aa of C-terminal of CfORC6 has no identity with other ORC6s. Like ScORC6, CfORC6 has many potential phosphorylation sites, (S/T)PXK. Like DmORC6, CfORC6 has leucine-rich region in the relevant site. Northern Blot showed that CfORC6 mRNA is about 2,000nt. Southern Blot confirmed that there is one copy of CfORC6 gene in spruce budworm genome. Western blot showed that infection of Cf124T cells with CfMNPV didnot affect the expression levels of CfORC6, at least up to 26 hr post infection.

  8. Text and Structural Data Mining of Influenza Mentions in Web and Social Media

    SciTech Connect

    Corley, Courtney D.; Cook, Diane; Mikler, Armin R.; Singh, Karan P.

    2010-02-22

    Text and structural data mining of Web and social media (WSM) provides a novel disease surveillance resource and can identify online communities for targeted public health communications (PHC) to assure wide dissemination of pertinent information. WSM that mention influenza are harvested over a 24-week period, 5-October-2008 to 21-March-2009. Link analysis reveals communities for targeted PHC. Text mining is shown to identify trends in flu posts that correlate to real-world influenza-like-illness patient report data. We also bring to bear a graph-based data mining technique to detect anomalies among flu blogs connected by publisher type, links, and user-tags.

  9. Green Team Recognized with HHS Green Champion Award Honorable Mention | Poster

    Cancer.gov

    Courtesy of the NCI at Frederick Green Team The NCI at Frederick Green Team received a Department of Health and Human Services (HHS) Green Champion Award honorable mention in June for the team’s plant swap initiative, begun in October 2012.  “The Green Team has been doing a great job this past year, and it is wonderful that their efforts have been recognized by the HHS through the Green Champion Awards,” said Craig Reynolds, Ph.D., director of the NCI Office of Scientific Operations (OSO). 

  10. Time and Causation in Discourse: Temporal Proximity, Implicit Causality, and Re-mention Biases.

    PubMed

    Dery, Jeruen E; Bittner, Dagmar

    2016-08-01

    Using referential processing in discourse featuring implicit causality verbs as a test case, we demonstrate how a discourse's causal and temporal dimensions interact. We show that referential processing is affected by multiple discourse biases, and that these biases do not have uniform effects. In three discourse continuation experiments, we show that the bias to re-mention a particular referent in discourse involving implicit causality verbs is not only affected by the verb's implicit causality bias, but also by the discourse's temporal structure, which at times, can even override the implicit causality bias. Our results add to the growing number of studies that show how various discourse dimensions interact in discourse processing.

  11. Text and structural data mining of influenza mentions in Web and social media.

    PubMed

    Corley, Courtney D; Cook, Diane J; Mikler, Armin R; Singh, Karan P

    2010-02-01

    Text and structural data mining of web and social media (WSM) provides a novel disease surveillance resource and can identify online communities for targeted public health communications (PHC) to assure wide dissemination of pertinent information. WSM that mention influenza are harvested over a 24-week period, 5 October 2008 to 21 March 2009. Link analysis reveals communities for targeted PHC. Text mining is shown to identify trends in flu posts that correlate to real-world influenza-like illness patient report data. We also bring to bear a graph-based data mining technique to detect anomalies among flu blogs connected by publisher type, links, and user-tags.

  12. Using Nonexperts for Annotating Pharmacokinetic Drug-Drug Interaction Mentions in Product Labeling: A Feasibility Study

    PubMed Central

    Ning, Yifan; Hernandez, Andres; Horn, John R; Jacobson, Rebecca; Boyce, Richard D

    2016-01-01

    Background Because vital details of potential pharmacokinetic drug-drug interactions are often described in free-text structured product labels, manual curation is a necessary but expensive step in the development of electronic drug-drug interaction information resources. The use of nonexperts to annotate potential drug-drug interaction (PDDI) mentions in drug product label annotation may be a means of lessening the burden of manual curation. Objective Our goal was to explore the practicality of using nonexpert participants to annotate drug-drug interaction descriptions from structured product labels. By presenting annotation tasks to both pharmacy experts and relatively naïve participants, we hoped to demonstrate the feasibility of using nonexpert annotators for drug-drug information annotation. We were also interested in exploring whether and to what extent natural language processing (NLP) preannotation helped improve task completion time, accuracy, and subjective satisfaction. Methods Two experts and 4 nonexperts were asked to annotate 208 structured product label sections under 4 conditions completed sequentially: (1) no NLP assistance, (2) preannotation of drug mentions, (3) preannotation of drug mentions and PDDIs, and (4) a repeat of the no-annotation condition. Results were evaluated within the 2 groups and relative to an existing gold standard. Participants were asked to provide reports on the time required to complete tasks and their perceptions of task difficulty. Results One of the experts and 3 of the nonexperts completed all tasks. Annotation results from the nonexpert group were relatively strong in every scenario and better than the performance of the NLP pipeline. The expert and 2 of the nonexperts were able to complete most tasks in less than 3 hours. Usability perceptions were generally positive (3.67 for expert, mean of 3.33 for nonexperts). Conclusions The results suggest that nonexpert annotation might be a feasible option for comprehensive

  13. Green Team Recognized with HHS Green Champion Award Honorable Mention | Poster

    Cancer.gov

    Courtesy of the NCI at Frederick Green Team The NCI at Frederick Green Team received a Department of Health and Human Services (HHS) Green Champion Award honorable mention in June for the team’s plant swap initiative, begun in October 2012.  “The Green Team has been doing a great job this past year, and it is wonderful that their efforts have been recognized by the HHS through the Green Champion Awards,” said Craig Reynolds, Ph.D., director of the NCI Office of Scientific Operations (OSO). 

  14. Text and Structural Data Mining of Influenza Mentions in Web and Social Media

    PubMed Central

    Corley, Courtney D.; Cook, Diane J.; Mikler, Armin R.; Singh, Karan P.

    2010-01-01

    Text and structural data mining of web and social media (WSM) provides a novel disease surveillance resource and can identify online communities for targeted public health communications (PHC) to assure wide dissemination of pertinent information. WSM that mention influenza are harvested over a 24-week period, 5 October 2008 to 21 March 2009. Link analysis reveals communities for targeted PHC. Text mining is shown to identify trends in flu posts that correlate to real-world influenza-like illness patient report data. We also bring to bear a graph-based data mining technique to detect anomalies among flu blogs connected by publisher type, links, and user-tags. PMID:20616993

  15. Identification of an amino acid residue required for differential recognition of a viral movement protein by the Tomato mosaic virus resistance gene Tm-2(2).

    PubMed

    Kobayashi, Michie; Yamamoto-Katou, Ayako; Katou, Shinpei; Hirai, Katsuyuki; Meshi, Tetsuo; Ohashi, Yuko; Mitsuhara, Ichiro

    2011-07-01

    The Tm-2 gene of tomato and its allelic gene, Tm-2(2), confer resistance to Tomato mosaic virus (ToMV) and encode a member of the coiled-coil/nucleotide binding-ARC/leucine-rich repeat (LRR) protein class of plant resistance (R) genes. Despite exhibiting only four amino acid differences between the products of Tm-2 and Tm-2(2), Tm-2(2) confers resistance to ToMV mutant B7, whereas Tm-2 is broken by ToMV-B7. An Agrobacterium-mediated transient expression system was used to study the mechanism of differential recognition of the movement proteins (MPs), an avirulence factor for ToMV resistance, of ToMV-B7 by Tm-2 and Tm-2(2). Although resistance induced by Tm-2 and Tm-2(2) is not usually accompanied by hypersensitive response (HR), Tm-2 and Tm-2(2) induced HR-like cell death by co-expression with MP of a wild-type ToMV, a strain that causes resistance for these R genes, and Tm-2(2) but not Tm-2 induced cell death with B7-MP in this system. Site-directed amino acid mutagenesis revealed that Tyr-767 in the LRR of Tm-2(2) is required for the specific recognition of the B7-MP. These results suggest that the Tyr residue in LRR contributes to the recognition of B7-MP, and that Tm-2 and Tm-2(2) are involved in HR cell death.

  16. Relevance of the Mention of Antioxidant Properties in Yogurt Labels: In Vitro Evaluation and Chromatographic Analysis

    PubMed Central

    Pereira, Eliana; Barros, Lillian; Ferreira, Isabel C. F. R.

    2013-01-01

    The purpose of the inclusion of fruit (natural additives) in yogurt aims to increase its antioxidant activity and functionality. Herein, a comparative study of the antioxidant potential of yogurts with pieces of various fruits was performed, including yogurts with mention of antioxidant properties in the label. Free radicals scavenging activity, reducing power and inhibition of lipid peroxidation were evaluated by in vitro assays, as were the contents in antioxidants such as phenolics, flavonoids, sugars and tocopherols. After analyzing thirteen yogurts containing fruit pieces and a natural one (control), the most interesting were yogurts with pieces of berries (for phenolics, flavonoids and 2,2-dipheny-1-picrylhydrazyl (DPPH) scavenging activity), pineapple (for reducing power), blackberry (for β-carotene bleaching inhibition), blackberry “antioxidant” (for tocopherols) and cherry (for sugars). The mention of “antioxidant” in the label was relevant for tocopherols, sugars, DPPH scavenging activity and reducing power. No synergisms were observed in yogurts prepared with pieces of different fruits. Nevertheless, the addition of fruit pieces to yogurt was favorable for antioxidant content, increasing the protection of the consumer against diseases related to oxidative stress. PMID:26787624

  17. Rice MEL2, the RNA recognition motif (RRM) protein, binds in vitro to meiosis-expressed genes containing U-rich RNA consensus sequences in the 3'-UTR.

    PubMed

    Miyazaki, Saori; Sato, Yutaka; Asano, Tomoya; Nagamura, Yoshiaki; Nonomura, Ken-Ichi

    2015-10-01

    Post-transcriptional gene regulation by RNA recognition motif (RRM) proteins through binding to cis-elements in the 3'-untranslated region (3'-UTR) is widely used in eukaryotes to complete various biological processes. Rice MEIOSIS ARRESTED AT LEPTOTENE2 (MEL2) is the RRM protein that functions in the transition to meiosis in proper timing. The MEL2 RRM preferentially associated with the U-rich RNA consensus, UUAGUU[U/A][U/G][A/U/G]U, dependently on sequences and proportionally to MEL2 protein amounts in vitro. The consensus sequences were located in the putative looped structures of the RNA ligand. A genome-wide survey revealed a tendency of MEL2-binding consensus appearing in 3'-UTR of rice genes. Of 249 genes that conserved the consensus in their 3'-UTR, 13 genes spatiotemporally co-expressed with MEL2 in meiotic flowers, and included several genes whose function was supposed in meiosis; such as Replication protein A and OsMADS3. The proteome analysis revealed that the amounts of small ubiquitin-related modifier-like protein and eukaryotic translation initiation factor3-like protein were dramatically altered in mel2 mutant anthers. Taken together with transcriptome and gene ontology results, we propose that the rice MEL2 is involved in the translational regulation of key meiotic genes on 3'-UTRs to achieve the faithful transition of germ cells to meiosis.

  18. Gene polymorphisms of Toll-like and related recognition receptors in relation to the vaginal carriage of Gardnerella vaginalis and Atopobium vaginae.

    PubMed

    Verstraelen, Hans; Verhelst, Rita; Nuytinck, Lieve; Roelens, Kristien; De Meester, Els; De Vos, Daniel; Van Thielen, Martine; Rossau, Rudi; Delva, Wim; De Backer, Ellen; Vaneechoutte, Mario; Temmerman, Marleen

    2009-01-01

    Host genetic factors have previously been found to act as determinants of differential susceptibility to major infectious diseases. It is less clear whether such polymorphisms may also impose on pathogen recognition in mucosal overgrowth conditions such as bacterial vaginosis, an anaerobic overgrowth condition characterised by the presence of a vaginal biofilm consisting of the Gram-positive anaerobes Gardnerella vaginalis and Atopobium vaginae. We selected 34 single nucleotide polymorphisms pertaining to 9 genes involved with Toll-like receptor-mediated pathogen recognition and/or regulation (LBP, CD14, TLR1, TLR2, TLR4, TLR6, MD2, CARD15 and SIGIRR) and assessed in a nested case-control study their putative association with bacterial vaginosis, as diagnosed by Gram staining, and with the vaginal carriage of A. vaginae and G. vaginalis, as determined by species-specific PCR, among 144 pregnant women. Carriage of G. vaginalis during early pregnancy was associated with the -1155A>G substitution in the promoter region of the MD2 gene (p=0.041). The presence of A. vaginae during the first half of the pregnancy was significantly associated with the CD14 intron 2 1342G>T (p=0.039), the TLR1 exon 4 743A>G (p=0.038), and the CARD15 exon 4 14772A>T (p=0.012) polymorphisms, and marginally significantly associated with the LBP exon13 26842C>T (p=0.056), the CD14 promoter -260C>T (p=0.052), and the TLR1 promoter -7202A>G (p=0.062) polymorphisms. However, no association between gene polymorphisms and bacterial vaginosis as such could be documented. Our data suggest that some degree of genetic susceptibility involving pathogen recognition may occur with the key bacterial vaginosis organism, A. vaginae.

  19. Phonetic spelling filter for keyword selection in drug mention mining from social media.

    PubMed

    Pimpalkhute, Pranoti; Patki, Apurv; Nikfarjam, Azadeh; Gonzalez, Graciela

    2014-01-01

    Social media postings are rich in information that often remain hidden and inaccessible for automatic extraction due to inherent limitations of the site's APIs, which mostly limit access via specific keyword-based searches (and limit both the number of keywords and the number of postings that are returned). When mining social media for drug mentions, one of the first problems to solve is how to derive a list of variants of the drug name (common misspellings) that can capture a sufficient number of postings. We present here an approach that filters the potential variants based on the intuition that, faced with the task of writing an unfamiliar, complex word (the drug name), users will tend to revert to phonetic spelling, and we thus give preference to variants that reflect the phonemes of the correct spelling. The algorithm allowed us to capture 50.4 - 56.0 % of the user comments using only about 18% of the variants.

  20. SkipCor: Skip-Mention Coreference Resolution Using Linear-Chain Conditional Random Fields

    PubMed Central

    Žitnik, Slavko; Šubelj, Lovro; Bajec, Marko

    2014-01-01

    Coreference resolution tries to identify all expressions (called mentions) in observed text that refer to the same entity. Beside entity extraction and relation extraction, it represents one of the three complementary tasks in Information Extraction. In this paper we describe a novel coreference resolution system SkipCor that reformulates the problem as a sequence labeling task. None of the existing supervised, unsupervised, pairwise or sequence-based models are similar to our approach, which only uses linear-chain conditional random fields and supports high scalability with fast model training and inference, and a straightforward parallelization. We evaluate the proposed system against the ACE 2004, CoNLL 2012 and SemEval 2010 benchmark datasets. SkipCor clearly outperforms two baseline systems that detect coreferentiality using the same features as SkipCor. The obtained results are at least comparable to the current state-of-the-art in coreference resolution. PMID:24956272

  1. Pattern mining for extraction of mentions of Adverse Drug Reactions from user comments.

    PubMed

    Nikfarjam, Azadeh; Gonzalez, Graciela H

    2011-01-01

    Rapid growth of online health social networks has enabled patients to communicate more easily with each other. This way of exchange of opinions and experiences has provided a rich source of information about drugs and their effectiveness and more importantly, their possible adverse reactions. We developed a system to automatically extract mentions of Adverse Drug Reactions (ADRs) from user reviews about drugs in social network websites by mining a set of language patterns. The system applied association rule mining on a set of annotated comments to extract the underlying patterns of colloquial expressions about adverse effects. The patterns were tested on a set of unseen comments to evaluate their performance. We reached to precision of 70.01% and recall of 66.32% and F-measure of 67.96%.

  2. Pattern Mining for Extraction of mentions of Adverse Drug Reactions from User Comments

    PubMed Central

    Nikfarjam, Azadeh; Gonzalez, Graciela H.

    2011-01-01

    Rapid growth of online health social networks has enabled patients to communicate more easily with each other. This way of exchange of opinions and experiences has provided a rich source of information about drugs and their effectiveness and more importantly, their possible adverse reactions. We developed a system to automatically extract mentions of Adverse Drug Reactions (ADRs) from user reviews about drugs in social network websites by mining a set of language patterns. The system applied association rule mining on a set of annotated comments to extract the underlying patterns of colloquial expressions about adverse effects. The patterns were tested on a set of unseen comments to evaluate their performance. We reached to precision of 70.01% and recall of 66.32% and F-measure of 67.96%. PMID:22195162

  3. Microtask crowdsourcing for disease mention annotation in PubMed abstracts.

    PubMed

    Good, Benjamin M; Nanis, Max; Wu, Chunlei; Su, Andrew I

    2015-01-01

    Identifying concepts and relationships in biomedical text enables knowledge to be applied in computational analyses. Many biological natural language processing (BioNLP) projects attempt to address this challenge, but the state of the art still leaves much room for improvement. Progress in BioNLP research depends on large, annotated corpora for evaluating information extraction systems and training machine learning models. Traditionally, such corpora are created by small numbers of expert annotators often working over extended periods of time. Recent studies have shown that workers on microtask crowdsourcing platforms such as Amazon's Mechanical Turk (AMT) can, in aggregate, generate high-quality annotations of biomedical text. Here, we investigated the use of the AMT in capturing disease mentions in PubMed abstracts. We used the NCBI Disease corpus as a gold standard for refining and benchmarking our crowdsourcing protocol. After several iterations, we arrived at a protocol that reproduced the annotations of the 593 documents in the 'training set' of this gold standard with an overall F measure of 0.872 (precision 0.862, recall 0.883). The output can also be tuned to optimize for precision (max = 0.984 when recall = 0.269) or recall (max = 0.980 when precision = 0.436). Each document was completed by 15 workers, and their annotations were merged based on a simple voting method. In total 145 workers combined to complete all 593 documents in the span of 9 days at a cost of $.066 per abstract per worker. The quality of the annotations, as judged with the F measure, increases with the number of workers assigned to each task; however minimal performance gains were observed beyond 8 workers per task. These results add further evidence that microtask crowdsourcing can be a valuable tool for generating well-annotated corpora in BioNLP. Data produced for this analysis are available at http://figshare.com/articles/Disease_Mention_Annotation_with_Mechanical_Turk/1126402.

  4. The explicit mentioning of reporting guidelines in urogynecology journals in 2013: A bibliometric study.

    PubMed

    Koch, Marianne; Riss, Paul; Umek, Wolfgang; Hanzal, Engelbert

    2016-03-01

    Poor reporting of research may limit critical appraisal and reproducibility, whereas adherence to reporting guidelines (RG) can guarantee completeness and transparency. We aimed to determine the explicit citing of RGs (CONSORT, PRISMA, STROBE) in urogynecology articles in 2013, the requirements of relevant journals and a potential difference between urogynecology and general gynecology journals. All urogynecologic articles published between January and December 2013 in the journals NAU, IUJ, FPMRS, GREEN, AJOG, and BJOG were included. Issues were searched for systematic reviews, RCTs, cohort studies, case-control studies and cross-sectional studies. Each electronic article was searched for the term PRISMA, CONSORT, or STROBE according to the study design. Instructions to Authors of the six journals were screened for requirement of using RGs. We included 296 articles (243 observational studies, 40 RCTs, and 13 systematic reviews). The use of PRISMA guidelines was explicitly declared in 54% of systematic reviews, CONSORT guidelines were referenced in 25% of RCTs and STROBE in 1.2% of observational studies. The use of CONSORT is required by all journals except FPMRS. PRISMA and STROBE are only compulsory in the journals GREEN, AJOG, and BJOG. The overall rate of explicit mentioning of RGs comparing urogynecology and general gynecology journals was 6.7% versus 7.1%, respectively. The explicit mentioning of RGs was on a relatively low level. A slightly higher adherence was recognized among general gynecology journals compared to urogynecology journals. Stronger efforts should be taken to further promote the use of RGs in urogynecology. © 2015 Wiley Periodicals, Inc.

  5. Sequence and structural diversity of the S locus genes from different lines with the same self-recognition specificities in Brassica oleracea.

    PubMed Central

    Kusaba, M; Matsushita, M; Okazaki, K; Satta, Y; Nishio, T

    2000-01-01

    Self-incompatibility (SI) is a mechanism for preventing self-fertilization in flowering plants. In Brassica, it is controlled by a single multi-allelic locus, S, and it is believed that two highly polymorphic genes in the S locus, SLG and SRK, play central roles in self-recognition in stigmas. SRK is a putative receptor protein kinase, whose extracellular domain exhibits high similarity to SLG. We analyzed two pairs of lines showing cross-incompatibility (S(2) and S(2-b); S(13) and S(13-b)). In S(2) and S(2-b), SRKs were more highly conserved than SLGs. This was also the case with S(13) and S(13-b). This suggests that the SRKs of different lines must be conserved for the lines to have the same self-recognition specificity. In particular, SLG(2-b) showed only 88. 5% identity to SLG(2), which is comparable to that between the SLGs of different S haplotypes, while SRK(2-b) showed 97.3% identity to SRK(2) in the S domain. These findings suggest that the SLGs in these S haplotypes are not important for self-recognition in SI. PMID:10628999

  6. Sequence-Based Appraisal of the Genes Encoding Neck and Carbohydrate Recognition Domain of Conglutinin in Blackbuck (Antilope cervicapra) and Goat (Capra hircus)

    PubMed Central

    Barik, Sasmita; Sidappa, Chandra Mohan; Saini, Mohini; Doreswamy, Ramesh; Das, Asit; Sharma, Anil K.; Gupta, Praveen K.

    2014-01-01

    Conglutinin, a collagenous C-type lectin, acts as soluble pattern recognition receptor (PRR) in recognition of pathogens. In the present study, genes encoding neck and carbohydrate recognition domain (NCRD) of conglutinin in goat and blackbuck were amplified, cloned, and sequenced. The obtained 488 bp ORFs encoding NCRD were submitted to NCBI with accession numbers KC505182 and KC505183. Both nucleotide and predicted amino acid sequences were analysed with sequences of other ruminants retrieved from NCBI GenBank using DNAstar and Megalign5.2 software. Sequence analysis revealed maximum similarity of blackbuck sequence with wild ruminants like nilgai and buffalo, whereas goat sequence displayed maximum similarity with sheep sequence at both nucleotide and amino acid level. Phylogenetic analysis further indicated clear divergence of wild ruminants from the domestic ruminants in separate clusters. The predicted secondary structures of NCRD protein in goat and blackbuck using SWISSMODEL ProtParam online software were found to possess 6 beta-sheets and 3 alpha-helices which are identical to the result obtained in case of sheep, cattle, buffalo, and nilgai. However, quaternary structure in goat, sheep, and cattle was found to differ from that of buffalo, nilgai, and blackbuck, suggesting a probable variation in the efficiency of antimicrobial activity among wild and domestic ruminants. PMID:25028649

  7. RPS2, an Arabidopsis disease resistance locus specifying recognition of Pseudomonas syringae strains expressing the avirulence gene avrRpt2.

    PubMed Central

    Kunkel, B N; Bent, A F; Dahlbeck, D; Innes, R W; Staskawicz, B J

    1993-01-01

    A molecular genetic approach was used to identify and characterize plant genes that control bacterial disease resistance in Arabidopsis. A screen for mutants with altered resistance to the bacterial pathogen Pseudomonas syringae pv. tomato (Pst) expressing the avirulence gene avrRpt2 resulted in the isolation of four susceptible rps (resistance to P. syringae) mutants. The rps mutants lost resistance specifically to bacterial strains expressing avrRpt2 as they retained resistance to Pst strains expressing the avirulence genes avrB or avrRpm1. Genetic analysis indicated that in each of the four rps mutants, susceptibility was due to a single mutation mapping to the same locus on chromosome 4. Identification of a resistance locus with specificity for a single bacterial avirulence gene suggests that this locus, designated RPS2, controls specific recognition of bacteria expressing the avirulence gene avrRpt2. Ecotype Wü-0, a naturally occurring line that is susceptible to Pst strains expressing avrRpt2, appears to lack a functional allele at RPS2, demonstrating that there is natural variation at the RPS2 locus among wild populations of Arabidopsis. PMID:8400869

  8. Concept of Sukha (comfort) mentioned in Dhatusarata (tissue excellence) w.s.r. to vocational guidance.

    PubMed

    Waghulade, Hemangini; Harit, Mahesh Kumar

    2014-01-01

    Agni (digestive fire), Prakruti (constitution), Dhatusarata (tissue excellence), Dosha (bio-energies) are the specialties of Ayurveda on which diagnosis, treatment and research are based. The description of Dhatusarata (tissue excellence) has been given under Dashavidha Pariksha (tenfold examination) in Charak Samhita, Viman Sthana, 8(th) chapter. Some qualities, which are mentioned in Dhatusarata are difficult to assess, e.g. Sukha, Aishwarya, Upabhoga, Bala, etc., There is a need to develop some quantitative parameters to measure these qualities according to tissue excellence i.e. Dhatusarata. By assessing Dhatu Sarata, one can judge the true strength of a particular Dhatu but only the ability or strength is not enough to get success; the liking or interest is also essential to achieve success. The purpose of this study is to elaborate the concept of Dhatusarata and reveal different aspects of Sukha according to the quality of that particular Dhatu in context of vocational guidance. It will help to establish interrelationship between Dhatusarata and vocational guidance. It will be assessed whether this Sukha quality is merely happiness or having different shades according to the excellence of Dhatus and whether this study is useful in guiding the person to choose appropriate profession, which will be according to his liking and ability. It has been concluded that shades of Sukha quality varies with particular Dhatusaras, which may be helpful in guiding a suitable profession to an individual which will be according to his ability and liking i.e. Sukha for intimate success.

  9. Concept of Sukha (comfort) mentioned in Dhatusarata (tissue excellence) w.s.r. to vocational guidance

    PubMed Central

    Waghulade, Hemangini; Harit, Mahesh Kumar

    2014-01-01

    Agni (digestive fire), Prakruti (constitution), Dhatusarata (tissue excellence), Dosha (bio–energies) are the specialties of Ayurveda on which diagnosis, treatment and research are based. The description of Dhatusarata (tissue excellence) has been given under Dashavidha Pariksha (tenfold examination) in Charak Samhita, Viman Sthana, 8th chapter. Some qualities, which are mentioned in Dhatusarata are difficult to assess, e.g. Sukha, Aishwarya, Upabhoga, Bala, etc., There is a need to develop some quantitative parameters to measure these qualities according to tissue excellence i.e. Dhatusarata. By assessing Dhatu Sarata, one can judge the true strength of a particular Dhatu but only the ability or strength is not enough to get success; the liking or interest is also essential to achieve success. The purpose of this study is to elaborate the concept of Dhatusarata and reveal different aspects of Sukha according to the quality of that particular Dhatu in context of vocational guidance. It will help to establish interrelationship between Dhatusarata and vocational guidance. It will be assessed whether this Sukha quality is merely happiness or having different shades according to the excellence of Dhatus and whether this study is useful in guiding the person to choose appropriate profession, which will be according to his liking and ability. It has been concluded that shades of Sukha quality varies with particular Dhatusaras, which may be helpful in guiding a suitable profession to an individual which will be according to his ability and liking i.e. Sukha for intimate success. PMID:26195895

  10. Genetic Affinity of the Bhil, Kol and Gond Mentioned in Epic Ramayana.

    PubMed

    Chaubey, Gyaneshwer; Kadian, Anurag; Bala, Saroj; Rao, Vadlamudi Raghavendra

    2015-01-01

    Kol, Bhil and Gond are some of the ancient tribal populations known from the Ramayana, one of the Great epics of India. Though there have been studies about their affinity based on classical and haploid genetic markers, the molecular insights of their relationship with other tribal and caste populations of extant India is expected to give more clarity about the the question of continuity vs. discontinuity. In this study, we scanned >97,000 of single nucleotide polymorphisms among three major ancient tribes mentioned in Ramayana, namely Bhil, Kol and Gond. The results obtained were then compared at inter and intra population levels with neighboring and other world populations. Using various statistical methods, our analysis suggested that the genetic architecture of these tribes (Kol and Gond) was largely similar to their surrounding tribal and caste populations, while Bhil showed closer affinity with Dravidian and Austroasiatic (Munda) speaking tribes. The haplotype based analysis revealed a massive amount of genome sharing among Bhil, Kol, Gond and with other ethnic groups of South Asian descent. On the basis of genetic component sharing among different populations, we anticipate their primary founding over the indigenous Ancestral South Indian (ASI) component has prevailed in the genepool over the last several thousand years.

  11. Genetic Affinity of the Bhil, Kol and Gond Mentioned in Epic Ramayana

    PubMed Central

    Chaubey, Gyaneshwer; Kadian, Anurag; Bala, Saroj; Rao, Vadlamudi Raghavendra

    2015-01-01

    Kol, Bhil and Gond are some of the ancient tribal populations known from the Ramayana, one of the Great epics of India. Though there have been studies about their affinity based on classical and haploid genetic markers, the molecular insights of their relationship with other tribal and caste populations of extant India is expected to give more clarity about the the question of continuity vs. discontinuity. In this study, we scanned >97,000 of single nucleotide polymorphisms among three major ancient tribes mentioned in Ramayana, namely Bhil, Kol and Gond. The results obtained were then compared at inter and intra population levels with neighboring and other world populations. Using various statistical methods, our analysis suggested that the genetic architecture of these tribes (Kol and Gond) was largely similar to their surrounding tribal and caste populations, while Bhil showed closer affinity with Dravidian and Austroasiatic (Munda) speaking tribes. The haplotype based analysis revealed a massive amount of genome sharing among Bhil, Kol, Gond and with other ethnic groups of South Asian descent. On the basis of genetic component sharing among different populations, we anticipate their primary founding over the indigenous Ancestral South Indian (ASI) component has prevailed in the genepool over the last several thousand years. PMID:26061398

  12. Therapeutic significance and pharmacological activities of antidiarrheal medicinal plants mention in Ayurveda: A review

    PubMed Central

    Mishra, Ashish; Seth, Ankit; Maurya, Santosh Kumar

    2016-01-01

    Diarrhea is a serious problem affecting 3-5 billion people per year around the world, especially children of below 5 years. 70% of the world population uses traditional and indigenous medicine for their primary health care. The facts of these indigenous remedies are passed verbally and sometimes as documents. Since ancient time, Ayurveda is the main system of healing in South East Asian countries. Indian literature from ayurvedic texts and other books claim the potency of several plants in the treatment of diarrhea. As the global prospective of ayurvedic medicine is increasing, interest regarding the scientific basis of their action is parallely increasing. Researchers are doing experiments to establish the relation between the claimed action and observed pharmacological activities. In the present article, an attempt was made to compile the scientific basis of medicinal plants used to cure diarrhea in Ayurveda. Literature was collected via electronic search (PubMed, ScienceDirect, Medline, and Google Scholar) from published articles that reports antidiarrheal activity of plants that were mentioned in Ayurveda classics. A total of 109 plant species belonging to 58 families were reported for their antidiarrheal activity. Several Indian medicinal plants have demonstrated promising antidiarrheal effects, but the studies on the antidiarrheal potentials of these plants are not taken beyond proof of concept stage. It is hoped that the article would stimulate future clinical studies because of the paucity of knowledge in this area. PMID:27366356

  13. Therapeutic significance and pharmacological activities of antidiarrheal medicinal plants mention in Ayurveda: A review.

    PubMed

    Mishra, Ashish; Seth, Ankit; Maurya, Santosh Kumar

    2016-01-01

    Diarrhea is a serious problem affecting 3-5 billion people per year around the world, especially children of below 5 years. 70% of the world population uses traditional and indigenous medicine for their primary health care. The facts of these indigenous remedies are passed verbally and sometimes as documents. Since ancient time, Ayurveda is the main system of healing in South East Asian countries. Indian literature from ayurvedic texts and other books claim the potency of several plants in the treatment of diarrhea. As the global prospective of ayurvedic medicine is increasing, interest regarding the scientific basis of their action is parallely increasing. Researchers are doing experiments to establish the relation between the claimed action and observed pharmacological activities. In the present article, an attempt was made to compile the scientific basis of medicinal plants used to cure diarrhea in Ayurveda. Literature was collected via electronic search (PubMed, ScienceDirect, Medline, and Google Scholar) from published articles that reports antidiarrheal activity of plants that were mentioned in Ayurveda classics. A total of 109 plant species belonging to 58 families were reported for their antidiarrheal activity. Several Indian medicinal plants have demonstrated promising antidiarrheal effects, but the studies on the antidiarrheal potentials of these plants are not taken beyond proof of concept stage. It is hoped that the article would stimulate future clinical studies because of the paucity of knowledge in this area.

  14. Categorization of Cathartic (Purgative) Medicines Mentioned in TPM Resources According to Their Specific Function.

    PubMed

    Abolghasemi, Jafar

    2016-05-01

    According to traditional Persian medicine (TPM) resources, the human digestive system includes four steps. In the first step, gastric digestion, the ingested food pours into the stomach and changes into the leachate called chylous due to the heat produced in the stomach. In the second step, hepatic digestion, the chylous enters in the liver through mesenteric vessels and transforms into the quadruple humors, sanguine, phlegm, bile and black bile due to the liver heat. In the case of humor predominance, using moshel or cathartic medicines is considered as a strategic medical plan. In this study, we introduce cathartic (purgative) medicines mentioned in TPM resources according to their specific function. Literature review of TPM resources, including Canon of Medicine and Aghili's Makhzan-ul-Adwiah was performed in order to find cathartics cited in the aforementioned books, prescribed specifically for different humor's predominance in the body. The survey found that the cathartics are categorized into eight groups: Cathartic of "balgham" such as "Citrullus colocynthis and Colchicum autumnale"Cathartic of bile such as "Prunus domestica and Alhagi Camelorum A. maurorum"Cathartic of "sovda" such as "lajward stone and Armenian stone"Cathartic of "Ma'a-e-asfar" such as "Marrubium vulgarre and Rivand extract"Cathartic of melancholy and phlegm such as "Cuscuta epithymum and Adiantum capillus venerisCathartic of bile and phlegm such as "Nepeta menthoides and Fumaria parviflora"Cathartic of "Ma'a-e-asfar and phlegm such as Urtica dioica and Qsa'alhmarCathartic of all mucus such as "Cassia acutifolia" and "kharbaghe Aswad". Medical students of traditional Persian medicine should be familiar with cathartics and purgatives specific for each humor. In this study, cathartics has classified into main cathartics of phlegm, bile, black bile, Ma'a-e-asfar, black bile and phlegm, Ma'a-e-asfar and phlegm, as well as cathartic of all triple humors for a better memorization and feasibility

  15. Origin of the diversity in DNA recognition domains in phasevarion associated modA genes of pathogenic Neisseria and Haemophilus influenzae.

    PubMed

    Gawthorne, Jayde A; Beatson, Scott A; Srikhanta, Yogitha N; Fox, Kate L; Jennings, Michael P

    2012-01-01

    Phase variable restriction-modification (R-M) systems have been identified in a range of pathogenic bacteria. In some it has been demonstrated that the random switching of the mod (DNA methyltransferase) gene mediates the coordinated expression of multiple genes and constitutes a phasevarion (phase variable regulon). ModA of Neisseria and Haemophilus influenzae contain a highly variable, DNA recognition domain (DRD) that defines the target sequence that is modified by methylation and is used to define modA alleles. 18 distinct modA alleles have been identified in H. influenzae and the pathogenic Neisseria. To determine the origin of DRD variability, the 18 modA DRDs were used to search the available databases for similar sequences. Significant matches were identified between several modA alleles and mod gene from distinct bacterial species, indicating one source of the DRD variability was via horizontal gene transfer. Comparison of DRD sequences revealed significant mosaicism, indicating exchange between the Neisseria and H. influenzae modA alleles. Regions of high inter- and intra-allele similarity indicate that some modA alleles had undergone recombination more frequently than others, generating further diversity. Furthermore, the DRD from some modA alleles, such as modA12, have been transferred en bloc to replace the DRD from different modA alleles.

  16. Origin of the Diversity in DNA Recognition Domains in Phasevarion Associated modA Genes of Pathogenic Neisseria and Haemophilus influenzae

    PubMed Central

    Gawthorne, Jayde A.; Beatson, Scott A.; Srikhanta, Yogitha N.; Fox, Kate L.; Jennings, Michael P.

    2012-01-01

    Phase variable restriction-modification (R-M) systems have been identified in a range of pathogenic bacteria. In some it has been demonstrated that the random switching of the mod (DNA methyltransferase) gene mediates the coordinated expression of multiple genes and constitutes a phasevarion (phase variable regulon). ModA of Neisseria and Haemophilus influenzae contain a highly variable, DNA recognition domain (DRD) that defines the target sequence that is modified by methylation and is used to define modA alleles. 18 distinct modA alleles have been identified in H. influenzae and the pathogenic Neisseria. To determine the origin of DRD variability, the 18 modA DRDs were used to search the available databases for similar sequences. Significant matches were identified between several modA alleles and mod gene from distinct bacterial species, indicating one source of the DRD variability was via horizontal gene transfer. Comparison of DRD sequences revealed significant mosaicism, indicating exchange between the Neisseria and H. influenzae modA alleles. Regions of high inter- and intra-allele similarity indicate that some modA alleles had undergone recombination more frequently than others, generating further diversity. Furthermore, the DRD from some modA alleles, such as modA12, have been transferred en bloc to replace the DRD from different modA alleles. PMID:22457715

  17. RBM24 promotes U1 snRNP recognition of the mutated 5' splice site in the IKBKAP gene of familial dysautonomia.

    PubMed

    Ohe, Kenji; Yoshida, Mayumi; Nakano-Kobayashi, Akiko; Hosokawa, Motoyasu; Sako, Yukiya; Sakuma, Maki; Okuno, Yukiko; Usui, Tomomi; Ninomiya, Kensuke; Nojima, Takayuki; Kataoka, Naoyuki; Hagiwara, Masatoshi

    2017-09-01

    The 5' splice site mutation (IVS20+6T>C) of the inhibitor of κ light polypeptide gene enhancer in B cells, kinase complex-associated protein (IKBKAP) gene in familial dysautonomia (FD) is at the sixth intronic nucleotide of the 5' splice site. It is known to weaken U1 snRNP recognition and result in an aberrantly spliced mRNA product in neuronal tissue, but normally spliced mRNA in other tissues. Aberrantly spliced IKBKAP mRNA abrogates IKK complex-associated protein (IKAP)/elongator protein 1 (ELP1) expression and results in a defect of neuronal cell development in FD. To elucidate the tissue-dependent regulatory mechanism, we screened an expression library of major RNA-binding proteins (RBPs) with our mammalian dual-color splicing reporter system and identified RBM24 as a regulator. RBM24 functioned as a cryptic intronic splicing enhancer binding to an element (IVS20+13-29) downstream from the intronic 5' splice site mutation in the IKBKAP gene and promoted U1 snRNP recognition only to the mutated 5' splice site (and not the wild-type 5' splice site). Our results show that tissue-specific expression of RBM24 can explain the neuron-specific aberrant splicing of IKBKAP exon 20 in familial dysautonomia, and that ectopic expression of RBM24 in neuronal tissue could be a novel therapeutic target of the disease. © 2017 Ohe et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  18. Sequence variation and recognition specificity of the avirulence gene AvrPiz-t in Magnaporthe oryzae field populations

    USDA-ARS?s Scientific Manuscript database

    Magnaporthe oryzae, the rice blast pathogen, causes significant annual yield loss of rice worldwide. Currently, the most effective disease control approach is deployment of host resistance through introduction of resistance (R) genes into elite cultivars. The function of each R gene relies on the sp...

  19. Categorization of Cathartic (Purgative) Medicines Mentioned in TPM Resources According to Their Specific Function

    PubMed Central

    Abolghasemi, Jafar

    2016-01-01

    Background: According to traditional Persian medicine (TPM) resources, the human digestive system includes four steps. In the first step, gastric digestion, the ingested food pours into the stomach and changes into the leachate called chylous due to the heat produced in the stomach. In the second step, hepatic digestion, the chylous enters in the liver through mesenteric vessels and transforms into the quadruple humors, sanguine, phlegm, bile and black bile due to the liver heat. In the case of humor predominance, using moshel or cathartic medicines is considered as a strategic medical plan. In this study, we introduce cathartic (purgative) medicines mentioned in TPM resources according to their specific function. Methods: Literature review of TPM resources, including Canon of Medicine and Aghili’s Makhzan-ul-Adwiah was performed in order to find cathartics cited in the aforementioned books, prescribed specifically for different humor’s predominance in the body. Results: The survey found that the cathartics are categorized into eight groups: Cathartic of “balgham” such as “Citrullus colocynthis and Colchicum autumnale”Cathartic of bile such as “Prunus domestica and Alhagi Camelorum A. maurorum”Cathartic of “sovda” such as “lajward stone and Armenian stone”Cathartic of “Ma’a-e-asfar” such as “Marrubium vulgarre and Rivand extract”Cathartic of melancholy and phlegm such as “Cuscuta epithymum and Adiantum capillus venerisCathartic of bile and phlegm such as “Nepeta menthoides and Fumaria parviflora”Cathartic of “Ma’a-e-asfar and phlegm such as Urtica dioica and Qsa’alhmarCathartic of all mucus such as “Cassia acutifolia” and “kharbaghe Aswad” Conclusion: Medical students of traditional Persian medicine should be familiar with cathartics and purgatives specific for each humor. In this study, cathartics has classified into main cathartics of phlegm, bile, black bile, Ma’a-e-asfar, black bile and phlegm, Ma

  20. Categorization of Cathartic (Purgative) Medicines Mentioned in TPM Resources According to Their Specific Function

    PubMed Central

    Abolghasemi, Jafar

    2016-01-01

    Background: According to traditional Persian medicine (TPM) resources, the human digestive system includes four steps. In the first step, gastric digestion, the ingested food pours into the stomach and changes into the leachate called chylous due to the heat produced in the stomach. In the second step, hepatic digestion, the chylous enters in the liver through mesenteric vessels and transforms into the quadruple humors, sanguine, phlegm, bile and black bile due to the liver heat. In the case of humor predominance, using moshel or cathartic medicines is considered as a strategic medical plan. In this study, we introduce cathartic (purgative) medicines mentioned in TPM resources according to their specific function. Methods: Literature review of TPM resources, including Canon of Medicine and Aghili’s Makhzan-ul-Adwiah was performed in order to find cathartics cited in the aforementioned books, prescribed specifically for different humor’s predominance in the body. Results: The survey found that the cathartics are categorized into eight groups: Cathartic of “balgham” such as “Citrullus colocynthis and Colchicum autumnale”Cathartic of bile such as “Prunus domestica and Alhagi Camelorum A. maurorum”Cathartic of “sovda” such as “lajward stone and Armenian stone”Cathartic of “Ma’a-e-asfar” such as “Marrubium vulgarre and Rivand extract”Cathartic of melancholy and phlegm such as “Cuscuta epithymum and Adiantum capillus venerisCathartic of bile and phlegm such as “Nepeta menthoides and Fumaria parviflora”Cathartic of “Ma’a-e-asfar and phlegm such as Urtica dioica and Qsa’alhmarCathartic of all mucus such as “Cassia acutifolia” and “kharbaghe Aswad” Conclusion: Medical students of traditional Persian medicine should be familiar with cathartics and purgatives specific for each humor. In this study, cathartics has classified into main cathartics of phlegm, bile, black bile, Ma’a-e-asfar, black bile and phlegm, Ma

  1. Fingerprint Recognition

    DTIC Science & Technology

    2006-06-01

    their central lines. The rule- based algorithm developed for character recognition by Ahmed and Ward (2002) can be applied to a fingerprint image...REFERENCES Ahmed, M., & Ward, R. (2002). A rotation invariant rule- based thinning algorithm for character recognition . IEEE Transactions on Pattern...various steps present in a fingerprint recognition system. The study develops a working algorithm to extract fingerprint minutiae from an input

  2. Core-sigma interaction: probing the interaction of the bacteriophage T4 gene 55 promoter recognition protein with E.coli RNA polymerase core.

    PubMed Central

    Léonetti, J P; Wong, K; Geiduschek, E P

    1998-01-01

    The bacterial RNA polymerase sigma subunits are key participants in the early steps of RNA synthesis, conferring specificity of promoter recognition, facilitating promoter opening and promoter clearance, and responding to diverse transcriptional regulators. The T4 gene 55 protein (gp55), the sigma protein of the bacteriophage T4 late genes, is one of the smallest and most divergent members of this family. Protein footprinting was used to identify segments of gp55 that become buried upon binding to RNA polymerase core, and are therefore likely to constitute its interface with the core enzyme. Site-directed mutagenesis in two parts of this contact surface generated gene 55 proteins that are defective in polymerase-binding to different degrees. Alignment with the sequences of the sigma proteins and with a recently determined structure of a large segment of sigma70 suggests that the gp55 counterpart of sigma70 regions 2.1 and 2.2 is involved in RNA polymerase core binding, and that sigma70 and gp55 may be structurally similar in this region. The diverse phenotypes of the mutants implicate this region of gp55 in multiple aspects of sigma function. PMID:9482743

  3. Co-expression of the mating-type genes involved in internuclear recognition is lethal in Podospora anserina.

    PubMed Central

    Coppin, E; Debuchy, R

    2000-01-01

    In the heterothallic filamentous fungus Podospora anserina, four mating-type genes encoding transcriptional factors have been characterized: FPR1 in the mat+ sequence and FMR1, SMR1, and SMR2 in the alternative mat- sequence. Fertilization is controlled by FPR1 and FMR1. After fertilization, male and female nuclei, which have divided in the same cell, form mat+/mat- pairs during migration into the ascogenous hyphae. Previous data indicate that the formation of mat+/mat- pairs is controlled by FPR1, FMR1, and SMR2. SMR1 was postulated to be necessary for initial development of ascogenous hyphae. In this study, we investigated the transcriptional control of the mat genes by seeking mat transcripts during the vegetative and sexual phase and fusing their promoter to a reporter gene. The data indicate that FMR1 and FPR1 are expressed in both mycelia and perithecia, whereas SMR1 and SMR2 are transcribed in perithecia. Increased or induced vegetative expression of the four mat genes has no effect when the recombined gene is solely in the wild-type strain. However, the combination of resident FPR1 with deregulated SMR2 and overexpressed FMR1 in the same nucleus is lethal. This lethality is suppressed by the expression of SMR1, confirming that SMR1 operates downstream of the other mat genes. PMID:10835389

  4. Sitagliptin, a dipeptidyl peptidase-4 inhibitor, improves recognition memory, oxidative stress and hippocampal neurogenesis and upregulates key genes involved in cognitive decline.

    PubMed

    Gault, V A; Lennox, R; Flatt, P R

    2015-04-01

    To examine whether prolonged dipeptidyl peptidase-4 (DPP-4) inhibition can reverse learning and memory impairment in high-fat-fed mice. High-fat-fed mice received oral sitagliptin (50 mg/kg body weight) once daily or saline vehicle over 21 days. An additional group of mice on standard chow received saline vehicle. Energy intake, body weight, glucose and insulin concentrations were measured at regular intervals. Glucose tolerance, insulin sensitivity, novel object recognition, DPP-4 activity, hormone analysis, hippocampal gene expression and histology were performed. Sitagliptin decreased circulating DPP-4 activity and improved glucose tolerance, glucose-stimulated insulin secretion and insulin sensitivity, and reduced plasma triglycerides and cholesterol levels. DPP-4 inhibition improved recognition memory (1.2-fold increase) without affecting hypermoteric activity or anxiety levels. Improvement in memory and learning was linked to reduced immunostaining for 8-oxoguanine and increased doublecortin staining in the hippocampus, which were indicative of reduced brain oxidative stress and increased hippocampal neurogenesis, respectively. These effects were associated with significant upregulation of hippocampal gene expression of glucagon-like peptide-1 (GLP-1) receptor, glucose-dependent insulinotropic polypeptide receptor, synaptophysin, sirtuin 1, glycogen synthase kinase 3β, superdioxide mutase 2, nuclear factor (erythroid-derived 2)-like 2 and vascular endothelial growth factor. Total plasma and brain GLP-1 concentrations were significantly increased after sitagliptin therapy, whereas DPP-4 activity in brain tissue was not altered. These studies show that sitagliptin can reverse memory impairment in high-fat-fed mice and is also associated with improved insulin sensitivity, enhanced hippocampal neurogenesis and reduced oxidative stress. DPP-4 inhibitors may therefore exhibit dual benefits by improving metabolic control and reducing the decline in cognitive

  5. miRNAs may regulate GABAergic transmission associated genes in aged rats with anesthetics-induced recognition and working memory dysfunction.

    PubMed

    Shan, Ligang; Ma, Duo; Zhang, Chengshen; Xiong, Wei; Zhang, Yi

    2017-09-01

    Isoflurane and sevoflurane are widely used anesthetics in surgery and administration of these anesthetics could lead to postoperative cognitive dysfunction (POCD). However, the mechanisms remain unclear. Aged Wistar rats were exposed to isoflurane and sevoflurane for 2 or 4h. Recognition memory and spatial working memory were measured using Novel object recognition (NOR) and Y-maze test, respectively. Apoptotic cells were detected by TUNEL staining. miRNA expression was measured by Real-time PCR while protein expression was measured by Western blot. Dual-Luciferase reporter assay was used to establish the direct relationship between miRNAs and Gabra5 and gephyrin gene expression. Exposure to isoflurane and sevoflurane for 2 or 4h significantly decreased the NOR index in the NOR test and spontaneous alternations in arm entries in the Y-maze test in aged rats. TUNEL staining showed that isoflurane and sevoflurane administration significantly induced apoptosis in the mPFC and hippocampus. The protein level of α5 GABAA receptor (α5GABAAR), gephyrin, and dystrophin were significantly increased, whereas the expression of miR-30a, miR-31, miR-190a, and miR-190b was significantly decreased in the hippocampus and mPFC in aged rats exposed to isoflurane and sevoflurane compared to control rats. The protein levels of α5GABAAR, gephyrin, and dystrophin protein in the hippocampus and the mPFC significantly correlated with NOR index and spontaneous alternations. Dual-Luciferase reporter assay showed that miR-30a and miR-190a/b mimics significantly inhibited Gabra5 and gephyrin gene expression, respectively. There might be a miRNAs-GABAergic transmission pathway which may be involved in the pathophysiological alteration in anesthetics-induced POCD. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Annotated Gene and Proteome Data Support Recognition of Interconnections Between the Results of Different Experiments in Space Research

    NASA Astrophysics Data System (ADS)

    Bauer, Johann; Wehland, Markus; Pietsch, Jessica; Sickmann, Albert; Weber, Gerhard; Grimm, Daniela

    2016-06-01

    In a series of studies, human thyroid and endothelial cells exposed to real or simulated microgravity were analyzed in terms of changes in gene expression patterns or protein content. Due to the limitation of available cells in many space research experiments, comparative and control experiments had to be done in a serial manner. Therefore, detected genes or proteins were annotated with gene names and SwissProt numbers, in order to allow searches for interconnections between results obtained in different experiments by different methods. A crosscheck of several studies on the behavior of cytoskeletal genes and proteins suggested that clusters of cytoskeletal components change differently under the influence of microgravity and/or vibration in different cell types. The result that LOX and ISG15 gene expression were clearly altered during the Shenzhou-8 spaceflight mission could be estimated by comparison with the results of other experiments. The more than 100-fold down-regulation of LOX supports our hypothesis that the amount and stability of extracellular matrix have a great influence on the formation of three-dimensional aggregates under microgravity. The approximately 40-fold up-regulation of ISG15 cannot yet be explained in detail, but strongly suggests that ISGylation, an alternative form of posttranslational modification, plays a role in longterm cultures.

  7. Bringing sketch recognition into your hands.

    PubMed

    Nataneli, G; Faloutsos, P

    2011-01-01

    The paper mentions that a flexible method of sketch recognition works consistently across a variety of software and hardware platforms, including mobile devices such as the Nintendo DS and iPhone. An example application employs this method to drive facial expressions.

  8. A sex recognition glycoprotein is encoded by the plus mating-type gene fus1 of Chlamydomonas reinhardtii.

    PubMed Central

    Ferris, P J; Woessner, J P; Goodenough, U W

    1996-01-01

    Sexual fusion between plus and minus gametes of the unicellular green alga Chlamydomonas reinhardtii entails adhesion between plus-specific and minus-specific "fringe" proteins displayed on the plasma membrane of gametic mating structures. We report the identification of the gene (fus1) encoding the plus fringe glycoprotein, which resides in a unique domain of the mating-type plus (mt+) locus, and which was identified by transposon insertions in three fusion-defective mutant strains. Transformation with fus1+ restores fringe and fusion competence to these mutants and to the pseudo-plus mutant imp11 mt-, defective in minus differentiation. The fus1 gene is remarkable in lacking the codon bias found in all other nuclear genes of C. reinhardtii. Images PMID:8856667

  9. 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.

  10. The wheat Snn7 gene confers susceptibility upon recognition of the Parastagonospora nodorum necrotrophic effector SnTox7

    USDA-ARS?s Scientific Manuscript database

    Parastagonospora nodorum is a necrotrophic fungal pathogen that causes the disease Septoria nodorum blotch (SNB) on wheat. The fungus produces necrotrophic effectors (NEs), that when recognized by corresponding host genes, cause cell death, which ultimately leads to disease. To date, eight host ge...

  11. Expression of two H-2K genes, syngeneic and allogeneic, as a strategy for potentiating immune recognition of tumor cells.

    PubMed

    Mandelboim, O; Vadai, E; Feldman, M; Eisenbach, L

    1995-12-01

    Metastatic clones of some tumors manifest an impaired expression of class I major histocompatibility complex (MHC) antigens. High metastatic, low immunogenic Lewis lung carcinoma clones (C57BL-H-2b origin) express low levels of the H-2Kb MHC antigen. These cells metastasize spontaneously in C57BL/6J mice. Transfection of syngeneic or allogeneic H-2K genes converted such cells to the nonmetastatic state, but did not prevent the growth of the local tumors. Transfection of two H-2K genes, syngeneic and allogeneic, into the highly metastatic clone D122, resulted in reduction of the growth rates of the transfectants and protected the mice from D122 metastases. In contrast, cells transfected with a single class I gene (syngeneic or allogeneic) gave partial protection, or did not protect the mice at all from D122 metastases. The combination of syngeneic and allogeneic genes in the same tumor cell elevated the immunogenic properties of the expressing cells and potentiated the immune response as was demonstrated by in vitro cytotoxicity analysis and by limiting dilution cytotoxicity analysis. Increased immunogenicity by double transfection may constitute an effective therapeutic modality.

  12. Gene expression values of pattern-recognition receptors in porcine leukocytes and their response to Salmonella enterica serovar Typhimurium infection.

    PubMed

    Osvaldova, Alena; Stepanova, Hana; Faldyna, Martin; Matiasovic, Jan

    2017-03-01

    Pattern-recognition receptors (PRRs) recognize pathogen-associated molecular patterns and play an important role in triggering innate immune responses. PRRs distribution and function is well documented in mice and humans, but studies in pigs are scarce. Salmonella enterica serovar Typhimurium is common pathogen found in pigs and was used as a model for interaction with PRRs. This study investigated expression of PRRs in porcine leukocyte subpopulations at the mRNA level. Eight subpopulations of leukocytes comprising NK cells, Th, Tc, double positive T cells and γδ T cells, B cells, monocytes and neutrophils were sorted, and the expression of 12 PRRs was measured, including selected Toll-like receptors and their co-receptors, NOD-like receptor NOD2, RP-105, CD14, and dectin. The highest expression rates of most PRRs were observed in monocytes and neutrophils. The B cells expressed high levels of TLR1, TLR6, TLR9, TLR10, and RP-105. Only monocytes and γδ T cells were found to respond to Salmonella enterica serovar Typhimurium infection by intensification of PRRs expression. In Th and B cells, PRRs mRNA down-regulation was detected after infection.

  13. β-Glucan-supplemented diets increase poly(I:C)-induced gene expression of Mx, possibly via Tlr3-mediated recognition mechanism in common carp (Cyprinus carpio).

    PubMed

    Falco, Alberto; Miest, Joanna J; Pionnier, Nicolas; Pietretti, Danilo; Forlenza, Maria; Wiegertjes, Geert F; Hoole, David

    2014-02-01

    We have previously observed that in common carp (Cyprinus carpio), administration of β-glucan (MacroGard®) as feed additive leads to a lower expression of pro-inflammatory cytokines suggesting that this immunostimulant may be preventing an acute and potentially dangerous response to infection, particularly in the gut. However, in general, mechanisms to detect and eliminate pathogens must also be induced in order to achieve an efficient clearance of the infection. Protection against viral diseases acquired through β-glucan-supplemented feed has been extensively reported for several experimental models in fish but the underlining mechanisms are still unknown. Thus, in order to better characterize the antiviral action induced by β-glucans in fish, MacroGard® was administered daily to common carp in the form of supplemented commercial food pellets. Carp were fed for a period of 25 days prior to intra-peritoneal injection with polyinosinic:polycytidylic acid (poly(I:C)), a well-known double-stranded RNA mimic that triggers a type-I interferon (IFN) response. Subsequently, a set of immune related genes, including mx, were analysed by real-time PCR on liver, spleen, head kidney and mid gut tissues. Results obtained confirmed that treatment with β-glucan alone generally down-regulated the mRNA expression of selected cytokines when compared to untreated fish, while mx gene expression remained stable or was slightly up-regulated. Injection with poly(I:C) induced a similar down-regulated gene expression pattern for cytokines in samples from β-glucan fed fish. In contrast, poly(I:C) injection markedly increased mx gene expression in samples from β-glucan fed fish but hardly in samples from fish fed control feed. In an attempt to explain the high induction of mx, we studied Toll-like receptor 3 (TLR3) gene expression in these carp. TLR3 is a prototypical pattern recognition receptor considered important for the binding of viral double-stranded RNA and triggering of a

  14. Recognition of H3K9 methylation by GLP is required for efficient establishment of H3K9 methylation, rapid target gene repression, and mouse viability

    PubMed Central

    Liu, Nan; Zhang, Zhuqiang; Jiang, Yonghua; Meng, Lingjun; Xiong, Jun; Zhao, Zuodong; Zhou, Xiaohua; Li, Jia; Li, Hong; Zheng, Yong; Chen, She; Cai, Tao; Gao, Shaorong

    2015-01-01

    GLP and G9a are major H3K9 dimethylases and are essential for mouse early embryonic development. GLP and G9a both harbor ankyrin repeat domains that are capable of binding H3K9 methylation. However, the functional significance of their recognition of H3K9 methylation is unknown. Here, we report that the histone methyltransferase activities of GLP and G9a are stimulated by neighboring nucleosomes that are premethylated at H3K9. These stimulation events function in cis and are dependent on the H3K9 methylation binding activities of ankyrin repeat domains of GLP and G9a. Disruption of the H3K9 methylation-binding activity of GLP in mice causes growth retardation of embryos, ossification defects of calvaria, and postnatal lethality due to starvation of the pups. In mouse embryonic stem cells (ESCs) harboring a mutant GLP that lacks H3K9me1-binding activity, critical pluripotent genes, including Oct4 and Nanog, display inefficient establishment of H3K9me2 and delayed gene silencing during differentiation. Collectively, our study reveals a new activation mechanism for GLP and G9a that plays an important role in ESC differentiation and mouse viability. PMID:25637356

  15. Third-Person Effect and Pandemic Flu: The Role of Severity, Self-Efficacy Method Mentions, and Message Source.

    PubMed

    Lee, Hyunmin; Park, Sun-A

    2016-12-01

    Within the context of a pandemic flu, this experiment investigated whether source (government officials or physicians), severity condition (high or low), and mention of self-efficacy method (mention present or absent) in H1N1 health news affected participants' (a) perception of media influence on self and others and (b) intentions to get vaccinated. Results found support for third-person effects, and the magnitude of the effects grew with social distance. Main effect of source, as well as interaction effects among the independent variables on third-person effect and vaccination intentions, were also found.

  16. NodV and NodW, a second flavonoid recognition system regulating nod gene expression in Bradyrhizobium japonicum.

    PubMed Central

    Loh, J; Garcia, M; Stacey, G

    1997-01-01

    In Bradyrhizobium japonicum, members of two global regulatory families, a LysR-type regulator, NodD1, and a two-component regulatory system, NodVW, positively regulate nod gene expression in response to plant-produced isoflavone signals. By analogy to other two-component systems, NodV and NodW are thought to activate transcription via a series of phosphorylation steps. These include the phosphorylation of NodV in response to the plant signal and the subsequent activation of NodW via the transfer of the phosphoryl group to an aspartate residue in the receiver domain of NodW. In this study, we demonstrated that NodW can be phosphorylated in vitro by both acetyl phosphate and its cognate kinase, NodV. In addition, in vivo experiments indicate that phosphorylation is induced by genistein, a known isoflavone nod gene inducer in B. japonicum. By using site-directed mutagenesis, a NodWD70N mutant in which the aspartate residue at the proposed phosphorylation site was converted to an asparagine residue was generated. This mutant was not phosphorylated in either in vitro or in vivo assays. Comparisons of the biological activity of both the wild-type and mutant proteins indicate that phosphorylation of NodW is essential for the ability of NodW to activate nod gene expression. PMID:9139921

  17. 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.

  18. Is R. S. Peters' Way of Mentioning Women in His Texts Detrimental to Philosophy of Education? Some Considerations and Questions

    ERIC Educational Resources Information Center

    Lees, Helen E.

    2012-01-01

    Discussion in this article considers the unfortunate way R.S. Peters made mention of women when it was pertinent to his argumentation: portraying them, directly or indirectly, as abuse-able (murderable), deficient, aberrant, clueless and inconstant. It is argued that the high profile and esteem within which Peter's texts are held within philosophy…

  19. Is R. S. Peters' Way of Mentioning Women in His Texts Detrimental to Philosophy of Education? Some Considerations and Questions

    ERIC Educational Resources Information Center

    Lees, Helen E.

    2012-01-01

    Discussion in this article considers the unfortunate way R.S. Peters made mention of women when it was pertinent to his argumentation: portraying them, directly or indirectly, as abuse-able (murderable), deficient, aberrant, clueless and inconstant. It is argued that the high profile and esteem within which Peter's texts are held within philosophy…

  20. Pattern recognition in bioinformatics.

    PubMed

    de Ridder, Dick; de Ridder, Jeroen; Reinders, Marcel J T

    2013-09-01

    Pattern recognition is concerned with the development of systems that learn to solve a given problem using a set of example instances, each represented by a number of features. These problems include clustering, the grouping of similar instances; classification, the task of assigning a discrete label to a given instance; and dimensionality reduction, combining or selecting features to arrive at a more useful representation. The use of statistical pattern recognition algorithms in bioinformatics is pervasive. Classification and clustering are often applied to high-throughput measurement data arising from microarray, mass spectrometry and next-generation sequencing experiments for selecting markers, predicting phenotype and grouping objects or genes. Less explicitly, classification is at the core of a wide range of tools such as predictors of genes, protein function, functional or genetic interactions, etc., and used extensively in systems biology. A course on pattern recognition (or machine learning) should therefore be at the core of any bioinformatics education program. In this review, we discuss the main elements of a pattern recognition course, based on material developed for courses taught at the BSc, MSc and PhD levels to an audience of bioinformaticians, computer scientists and life scientists. We pay attention to common problems and pitfalls encountered in applications and in interpretation of the results obtained.

  1. Hepatitis C Virus Frameshift/Alternate Reading Frame Protein Suppresses Interferon Responses Mediated by Pattern Recognition Receptor Retinoic-Acid-Inducible Gene-I

    PubMed Central

    Park, Seung Bum; Seronello, Scott; Mayer, Wasima; Ojcius, David M.

    2016-01-01

    Hepatitis C virus (HCV) actively evades host interferon (IFN) responses but the mechanisms of how it does so are not completely understood. In this study, we present evidence for an HCV factor that contributes to the suppression of retinoic-acid-inducible gene-I (RIG-I)-mediated IFN induction. Expression of frameshift/alternate reading frame protein (F/ARFP) from HCV -2/+1 frame in Huh7 hepatoma cells suppressed type I IFN responses stimulated by HCV RNA pathogen-associated molecular pattern (PAMP) and poly(IC). The suppression occurred independently of other HCV factors; and activation of interferon stimulated genes, TNFα, IFN-λ1, and IFN-λ2/3 was likewise suppressed by HCV F/ARFP. Point mutations in the full-length HCV sequence (JFH1 genotype 2a strain) were made to introduce premature termination codons in the -2/+1 reading frame coding for F/ARFP while preserving the original reading frame, which enhanced IFNα and IFNβ induction by HCV. The potentiation of IFN response by the F/ARFP mutations was diminished in Huh7.5 cells, which already have a defective RIG-I, and by decreasing RIG-I expression in Huh7 cells. Furthermore, adding F/ARFP back via trans-complementation suppressed IFN induction in the F/ARFP mutant. The F/ARFP mutants, on the other hand, were not resistant to exogenous IFNα. Finally, HCV-infected human liver samples showed significant F/ARFP antibody reactivity, compared to HCV-uninfected control livers. Therefore, HCV F/ARFP likely cooperates with other viral factors to suppress type I and III IFN induction occurring through the RIG-I signaling pathway. This study identifies a novel mechanism of pattern recognition receptor modulation by HCV and suggests a biological function of the HCV alternate reading frame in the modulation of host innate immunity. PMID:27404108

  2. Public hospital quality report awareness: evidence from National and Californian Internet searches and social media mentions, 2012

    PubMed Central

    Huesch, Marco D; Currid-Halkett, Elizabeth; Doctor, Jason N

    2014-01-01

    Objectives Publicly available hospital quality reports seek to inform consumers of important healthcare quality and affordability attributes, and may inform consumer decision-making. To understand how much consumers search for such information online on one Internet search engine, whether they mention such information in social media and how positively they view this information. Setting and design A leading Internet search engine (Google) was the main focus of the study. Google Trends and Google Adwords keyword analyses were performed for national and Californian searches between 1 August 2012 and 31 July 2013 for keywords related to ‘top hospital’, best hospital’, and ‘hospital quality’, as well as for six specific hospital quality reports. Separately, a proprietary social media monitoring tool was used to investigate blog, forum, social media and traditional media mentions of, and sentiment towards, major public reports of hospital quality in California in 2012. Primary outcome measures (1) Counts of searches for keywords performed on Google; (2) counts of and (3) sentiment of mentions of public reports on social media. Results National Google search volume for 75 hospital quality-related terms averaged 610 700 searches per month with strong variation by keyword and by state. A commercial report (Healthgrades) was more commonly searched for nationally on Google than the federal government's Hospital Compare, which otherwise dominated quality-related search terms. Social media references in California to quality reports were generally few, and commercially produced hospital quality reports were more widely mentioned than state (Office of Statewide Healthcare Planning and Development (OSHPD)), or non-profit (CalHospitalCompare) reports. Conclusions Consumers are somewhat aware of hospital quality based on Internet search activity and social media disclosures. Public stakeholders may be able to broaden their quality dissemination initiatives by

  3. Public hospital quality report awareness: evidence from National and Californian Internet searches and social media mentions, 2012.

    PubMed

    Huesch, Marco D; Currid-Halkett, Elizabeth; Doctor, Jason N

    2014-03-11

    Publicly available hospital quality reports seek to inform consumers of important healthcare quality and affordability attributes, and may inform consumer decision-making. To understand how much consumers search for such information online on one Internet search engine, whether they mention such information in social media and how positively they view this information. A leading Internet search engine (Google) was the main focus of the study. Google Trends and Google Adwords keyword analyses were performed for national and Californian searches between 1 August 2012 and 31 July 2013 for keywords related to 'top hospital', best hospital', and 'hospital quality', as well as for six specific hospital quality reports. Separately, a proprietary social media monitoring tool was used to investigate blog, forum, social media and traditional media mentions of, and sentiment towards, major public reports of hospital quality in California in 2012. (1) Counts of searches for keywords performed on Google; (2) counts of and (3) sentiment of mentions of public reports on social media. National Google search volume for 75 hospital quality-related terms averaged 610 700 searches per month with strong variation by keyword and by state. A commercial report (Healthgrades) was more commonly searched for nationally on Google than the federal government's Hospital Compare, which otherwise dominated quality-related search terms. Social media references in California to quality reports were generally few, and commercially produced hospital quality reports were more widely mentioned than state (Office of Statewide Healthcare Planning and Development (OSHPD)), or non-profit (CalHospitalCompare) reports. Consumers are somewhat aware of hospital quality based on Internet search activity and social media disclosures. Public stakeholders may be able to broaden their quality dissemination initiatives by advertising on Google or Twitter and using social media interactively with consumers looking

  4. Commercial Online Social Network Data and Statin Side-Effect Surveillance: A Pilot Observational Study of Aggregate Mentions on Facebook.

    PubMed

    Huesch, Marco D

    2017-07-26

    Surveillance of the safety of prescribed drugs after marketing approval has been secured remains fraught with complications. Formal ascertainment by providers and reporting to adverse-event registries, formal surveys by manufacturers, and mining of electronic medical records are all well-known approaches with varying degrees of difficulty, cost, and success. Novel approaches may be a useful adjunct, especially approaches that mine or sample internet-based methods such as online social networks. A novel commercial software-as-a-service data-mining product supplied by Sysomos from Datasift/Facebook was used to mine all mentions on Facebook of statins and stain-related side effects in the US in the 1-month period 9 January 2017 through 8 February 2017. A total of 4.3% of all 25,700 mentions of statins also mentioned typical stain-related side effects. Multiple methodological weaknesses stymie interpretation of this percentage, which is however not inconsistent with estimates that 5-20% of patients taking statins will experience typical side effects at some time. Future work on pharmacovigilance may be informed by this novel commercial tool, but the inability to mine the full text of a posting poses serious challenges to content categorization.

  5. Policy documents as sources for measuring societal impact: how often is climate change research mentioned in policy-related documents?

    PubMed

    Bornmann, Lutz; Haunschild, Robin; Marx, Werner

    2016-01-01

    In the current UK Research Excellence Framework (REF) and the Excellence in Research for Australia (ERA), societal impact measurements are inherent parts of the national evaluation systems. In this study, we deal with a relatively new form of societal impact measurements. Recently, Altmetric-a start-up providing publication level metrics-started to make data for publications available which have been mentioned in policy documents. We regard this data source as an interesting possibility to specifically measure the (societal) impact of research. Using a comprehensive dataset with publications on climate change as an example, we study the usefulness of the new data source for impact measurement. Only 1.2 % (n = 2341) out of 191,276 publications on climate change in the dataset have at least one policy mention. We further reveal that papers published in Nature and Science as well as from the areas "Earth and related environmental sciences" and "Social and economic geography" are especially relevant in the policy context. Given the low coverage of the climate change literature in policy documents, this study can be only a first attempt to study this new source of altmetrics data. Further empirical studies are necessary, because mentions in policy documents are of special interest in the use of altmetrics data for measuring target-oriented the broader impact of research.

  6. 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)

  7. Trend in rates for deaths with mention of schizophrenia on death certificates of US residents, 1999-2010.

    PubMed

    Polednak, Anthony P

    2014-07-01

    Trends in mortality rates for schizophrenia using multiple causes of death (including contributory causes) coded on death certificates in the US resident population apparently have not been reported. Age-standardized rates for deaths per 100,000 in 1999-2010 at age 15+ years (and for 15-64 and 65+ years) with mention of schizophrenia were examined for the US resident population, including variation by age, gender, race (blacks/African Americans and whites) and region. Deaths at age 15+ years coded with schizophrenia as underlying cause were only 12 % of all deaths with mention of schizophrenia, for which the rate declined from 1.58 in 1999 (3,407 deaths) to 1.32 in 2010 (3,422 deaths) (percentage change or PC = -16 %). Declines were larger in females than males, in whites than blacks, and occurred in the Northeast, Midwest and South but not the West. The rate increased for age 15-64 years (PC = +28 %) (mainly in males), however, while declining for age 65+ years (PC = -35 %). For deaths at age 15-64 years with schizophrenia coded as other than the underlying cause, the largest continuous increase was for endocrine-metabolic diseases (predominantly diabetes mellitus) as underlying cause, with smaller increases in males for cardiovascular diseases, external causes and neoplasms. Trends in the US rate for deaths with mention of schizophrenia varied among the sociodemographic groups examined. The lack of decline for age 15-64 years requires further study especially with regard to mediators (e.g., obesity) of excess mortality in schizophrenia identified from cohort studies.

  8. 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.

  9. What Can We Learn about Mental Health Needs from Tweets Mentioning Dementia on World Alzheimer’s Day?

    PubMed Central

    Yoon, Sunmoo

    2017-01-01

    Background Twitter can address the mental health challenges of dementia care. The aims of this study is to explore the contents and user interactions of tweets mentioning dementia to gain insights for dementia care. Methods We collected 35,260 tweets mentioning Alzheimer’s or dementia on World Alzheimer’s Day, September 21st in 2015. Topic modeling and social network analysis were applied to uncover content and structure of user communication. Results Global users generated keywords related to mental health and care including #psychology and #mental health. There were similarities and differences between the UK and the US in tweet content. The macro-level analysis uncovered substantial public interest on dementia. The meso-level network analysis revealed that top leaders of communities were spiritual organizations and traditional media. Conclusions The application of topic modeling and multi-level network analysis while incorporating visualization techniques can promote a global level understanding regarding public attention, interests, and insights regarding dementia care and mental health. PMID:27803262

  10. Word Order and World Order: Titles of Intergroup Conflicts May Increase Ethnocentrism by Mentioning the In-Group First.

    PubMed

    Oeberst, Aileen; Matschke, Christina

    2017-04-03

    The title of a historical event is usually the first thing we learn about that event. This article investigates whether group order in supposedly neutral conflict titles (e.g., Polish-Russian War) is systematically biased toward naming the in-group first (e.g., Polish-Russian War in Polish; Russian-Polish War in Russian) and whether group order affects perceptions of the groups involved. Based on linguistic evidence that individuals have the tendency to name themselves first, we expected and found a systematic tendency to name the in-group first in N = 172 real-world titles of historical conflicts from more than 40 languages (Study 1), under controlled conditions with participants from different cultures (Studies 2a and 2b), and in a minimal group experiment (Study 3), which identifies group membership as a crucial factor and rules out alternative explanations. Furthermore, based on findings on perception, it is predicted and found in 3 studies (Study 4, 5a, and 5b) that a group is perceived as more important when mentioned first rather than second. This effect depended, however, on group order in the questions asked. Additionally, the first group was consistently associated with more power. Combined, seemingly neutral conflict titles may therefore increase ethnocentrism as it is the in-group that is mostly mentioned first and because of that perceived as more important. (PsycINFO Database Record

  11. A rule-based named-entity recognition method for knowledge extraction of evidence-based dietary recommendations

    PubMed Central

    2017-01-01

    Evidence-based dietary information represented as unstructured text is a crucial information that needs to be accessed in order to help dietitians follow the new knowledge arrives daily with newly published scientific reports. Different named-entity recognition (NER) methods have been introduced previously to extract useful information from the biomedical literature. They are focused on, for example extracting gene mentions, proteins mentions, relationships between genes and proteins, chemical concepts and relationships between drugs and diseases. In this paper, we present a novel NER method, called drNER, for knowledge extraction of evidence-based dietary information. To the best of our knowledge this is the first attempt at extracting dietary concepts. DrNER is a rule-based NER that consists of two phases. The first one involves the detection and determination of the entities mention, and the second one involves the selection and extraction of the entities. We evaluate the method by using text corpora from heterogeneous sources, including text from several scientifically validated web sites and text from scientific publications. Evaluation of the method showed that drNER gives good results and can be used for knowledge extraction of evidence-based dietary recommendations. PMID:28644863

  12. [Productivity of doctoral programs in Psychology with Quality Mention in journal articles included in Journal Citation Reports].

    PubMed

    Musi-Lechuga, Bertha; Olivas-Ávila, José; Castro, Angel

    2011-08-01

    The main objective of the present study was to classify doctoral programs with Quality Mention in Psychology based on their scientific productivity. For this purpose, articles in the Web of Science published by professors teaching in these doctoral programs were analyzed. In addition, we analyzed scientific journals in which these professors tend to publish more papers and the evolution in the number of papers published until 2009. Results showed that the most productive doctoral program was the Neurosciences program at the University of Oviedo. This program showed a ratio of 40 articles--published in journals included in Journal Citation Reports--by each professor. In contrast, other programs did not reach a ratio of 10 articles per professor. Regarding journals, results showed that 9 out of the 20 most popular journals are Hispanic and a gradual increase in the number of published papers was also observed. Lastly, results and implications for quality assessment are discussed.

  13. Disorder recognition in clinical texts using multi-label structured SVM.

    PubMed

    Lin, Wutao; Ji, Donghong; Lu, Yanan

    2017-01-31

    Information extraction in clinical texts enables medical workers to find out problems of patients faster as well as makes intelligent diagnosis possible in the future. There has been a lot of work about disorder mention recognition in clinical narratives. But recognition of some more complicated disorder mentions like overlapping ones is still an open issue. This paper proposes a multi-label structured Support Vector Machine (SVM) based method for disorder mention recognition. We present a multi-label scheme which could be used in complicated entity recognition tasks. We performed three sets of experiments to evaluate our model. Our best F1-Score on the 2013 Conference and Labs of the Evaluation Forum data set is 0.7343. There are six types of labels in our multi-label scheme, all of which are represented by 24-bit binary numbers. The binary digits of each label contain information about different disorder mentions. Our multi-label method can recognize not only disorder mentions in the form of contiguous or discontiguous words but also mentions whose spans overlap with each other. The experiments indicate that our multi-label structured SVM model outperforms the condition random field (CRF) model for this disorder mention recognition task. The experiments show that our multi-label scheme surpasses the baseline. Especially for overlapping disorder mentions, the F1-Score of our multi-label scheme is 0.1428 higher than the baseline BIOHD1234 scheme. This multi-label structured SVM based approach is demonstrated to work well with this disorder recognition task. The novel multi-label scheme we presented is superior to the baseline and it can be used in other models to solve various types of complicated entity recognition tasks as well.

  14. Recognition intent and visual word recognition.

    PubMed

    Wang, Man-Ying; Ching, Chi-Le

    2009-03-01

    This study adopted a change detection task to investigate whether and how recognition intent affects the construction of orthographic representation in visual word recognition. Chinese readers (Experiment 1-1) and nonreaders (Experiment 1-2) detected color changes in radical components of Chinese characters. Explicit recognition demand was imposed in Experiment 2 by an additional recognition task. When the recognition was implicit, a bias favoring the radical location informative of character identity was found in Chinese readers (Experiment 1-1), but not nonreaders (Experiment 1-2). With explicit recognition demands, the effect of radical location interacted with radical function and word frequency (Experiment 2). An estimate of identification performance under implicit recognition was derived in Experiment 3. These findings reflect the joint influence of recognition intent and orthographic regularity in shaping readers' orthographic representation. The implication for the role of visual attention in word recognition was also discussed.

  15. 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

  16. Automatically quantifying the scientific quality and sensationalism of news records mentioning pandemics: validating a maximum entropy machine-learning model.

    PubMed

    Hoffman, Steven J; Justicz, Victoria

    2016-07-01

    To develop and validate a method for automatically quantifying the scientific quality and sensationalism of individual news records. After retrieving 163,433 news records mentioning the Severe Acute Respiratory Syndrome (SARS) and H1N1 pandemics, a maximum entropy model for inductive machine learning was used to identify relationships among 500 randomly sampled news records that correlated with systematic human assessments of their scientific quality and sensationalism. These relationships were then computationally applied to automatically classify 10,000 additional randomly sampled news records. The model was validated by randomly sampling 200 records and comparing human assessments of them to the computer assessments. The computer model correctly assessed the relevance of 86% of news records, the quality of 65% of records, and the sensationalism of 73% of records, as compared to human assessments. Overall, the scientific quality of SARS and H1N1 news media coverage had potentially important shortcomings, but coverage was not too sensationalizing. Coverage slightly improved between the two pandemics. Automated methods can evaluate news records faster, cheaper, and possibly better than humans. The specific procedure implemented in this study can at the very least identify subsets of news records that are far more likely to have particular scientific and discursive qualities. Copyright © 2016 Elsevier Inc. All rights reserved.

  17. Pharmacovigilance from social media: mining adverse drug reaction mentions using sequence labeling with word embedding cluster features

    PubMed Central

    Sarker, Abeed; O’Connor, Karen; Ginn, Rachel

    2015-01-01

    Objective Social media is becoming increasingly popular as a platform for sharing personal health-related information. This information can be utilized for public health monitoring tasks, particularly for pharmacovigilance, via the use of natural language processing (NLP) techniques. However, the language in social media is highly informal, and user-expressed medical concepts are often nontechnical, descriptive, and challenging to extract. There has been limited progress in addressing these challenges, and thus far, advanced machine learning-based NLP techniques have been underutilized. Our objective is to design a machine learning-based approach to extract mentions of adverse drug reactions (ADRs) from highly informal text in social media. Methods We introduce ADRMine, a machine learning-based concept extraction system that uses conditional random fields (CRFs). ADRMine utilizes a variety of features, including a novel feature for modeling words’ semantic similarities. The similarities are modeled by clustering words based on unsupervised, pretrained word representation vectors (embeddings) generated from unlabeled user posts in social media using a deep learning technique. Results ADRMine outperforms several strong baseline systems in the ADR extraction task by achieving an F-measure of 0.82. Feature analysis demonstrates that the proposed word cluster features significantly improve extraction performance. Conclusion It is possible to extract complex medical concepts, with relatively high performance, from informal, user-generated content. Our approach is particularly scalable, suitable for social media mining, as it relies on large volumes of unlabeled data, thus diminishing the need for large, annotated training data sets. PMID:25755127

  18. tmChem: a high performance approach for chemical named entity recognition and normalization

    PubMed Central

    2015-01-01

    Chemical compounds and drugs are an important class of entities in biomedical research with great potential in a wide range of applications, including clinical medicine. Locating chemical named entities in the literature is a useful step in chemical text mining pipelines for identifying the chemical mentions, their properties, and their relationships as discussed in the literature. We introduce the tmChem system, a chemical named entity recognizer created by combining two independent machine learning models in an ensemble. We use the corpus released as part of the recent CHEMDNER task to develop and evaluate tmChem, achieving a micro-averaged f-measure of 0.8739 on the CEM subtask (mention-level evaluation) and 0.8745 f-measure on the CDI subtask (abstract-level evaluation). We also report a high-recall combination (0.9212 for CEM and 0.9224 for CDI). tmChem achieved the highest f-measure reported in the CHEMDNER task for the CEM subtask, and the high recall variant achieved the highest recall on both the CEM and CDI tasks. We report that tmChem is a state-of-the-art tool for chemical named entity recognition and that performance for chemical named entity recognition has now tied (or exceeded) the performance previously reported for genes and diseases. Future research should focus on tighter integration between the named entity recognition and normalization steps for improved performance. The source code and a trained model for both models of tmChem is available at: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/tmChem. The results of running tmChem (Model 2) on PubMed are available in PubTator: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator PMID:25810774

  19. Character-level neural network for biomedical named entity recognition.

    PubMed

    Gridach, Mourad

    2017-06-01

    Biomedical named entity recognition (BNER), which extracts important named entities such as genes and proteins, is a challenging task in automated systems that mine knowledge in biomedical texts. The previous state-of-the-art systems required large amounts of task-specific knowledge in the form of feature engineering, lexicons and data pre-processing to achieve high performance. In this paper, we introduce a novel neural network architecture that benefits from both word- and character-level representations automatically, by using a combination of bidirectional long short-term memory (LSTM) and conditional random field (CRF) eliminating the need for most feature engineering tasks. We evaluate our system on two datasets: JNLPBA corpus and the BioCreAtIvE II Gene Mention (GM) corpus. We obtained state-of-the-art performance by outperforming the previous systems. To the best of our knowledge, we are the first to investigate the combination of deep neural networks, CRF, word embeddings and character-level representation in recognizing biomedical named entities. Copyright © 2017 Elsevier Inc. All rights reserved.

  20. The neuroecology of competitor recognition.

    PubMed

    Grether, Gregory F

    2011-11-01

    Territorial animals can be expected to distinguish among the types of competitors and noncompetitors that they encounter on a regular basis, including prospective mates and rivals of their own species, but they may not correctly classify individuals of other species. Closely related species often have similar phenotypes and this can cause confusion when formerly allopatric populations first come into contact. Errors in recognizing competitors can have important ecological and evolutionary effects. I review what is known about the mechanisms of competitor recognition in animals generally, focusing on cases in which the targets of recognition include other species. Case studies include damselflies, ants, skinks, salamanders, reef fishes, and birds. In general, recognition systems consist of a phenotypic cue (e.g., chemical, color, song), a neural template against which cues are compared, a motor response (e.g., aggression), and sensory integration circuits for context dependency of the response (if any). Little is known about how competitor recognition systems work at the neural level, but inferences about specificity of cues and about sensory integration can be drawn from the responses of territory residents to simulated intruders. Competitor recognition often involves multiple cues in the same, or different, sensory modalities. The same cues and templates are often, but not always, used for intraspecific and interspecific recognition. Experiments have shown that imprinting on local cues is common, which may enable templates to track evolved changes in cues automatically. The dependence of aggression and tolerance on context is important even in the simplest systems. Species in which mechanisms of competitor recognition are best known offer untapped opportunities to examine how competitor-recognition systems evolve (e.g., by comparing allopatric and sympatric populations). Cues that are gene products (peptides, proteins) may provide insights into rates of evolution

  1. Phrasal recognition.

    PubMed

    Farhadi, Ali; Sadeghi, Mohammad Amin

    2013-12-01

    In this paper, we introduce visual phrases, complex visual composites like "a person riding a horse." Visual phrases often display significantly reduced visual complexity compared to their component objects because the appearance of those objects can change profoundly when they participate in relations. We introduce a dataset suitable for phrasal recognition that uses familiar PASCAL object categories, and demonstrate significant experimental gains resulting from exploiting visual phrases. We show that a visual phrase detector significantly outperforms a baseline which detects component objects and reasons about relations, even though visual phrase training sets tend to be smaller than those for objects. We argue that any multiclass detection system must decode detector outputs to produce final results; this is usually done with nonmaximum suppression. We describe a novel decoding procedure that can account accurately for local context without solving difficult inference problems. We show this decoding procedure outperforms the state of the art. Finally, we show that decoding a combination of phrasal and object detectors produces real improvements in detector results.

  2. Cell line name recognition in support of the identification of synthetic lethality in cancer from text

    PubMed Central

    Kaewphan, Suwisa; Van Landeghem, Sofie; Ohta, Tomoko; Van de Peer, Yves; Ginter, Filip; Pyysalo, Sampo

    2016-01-01

    Motivation: The recognition and normalization of cell line names in text is an important task in biomedical text mining research, facilitating for instance the identification of synthetically lethal genes from the literature. While several tools have previously been developed to address cell line recognition, it is unclear whether available systems can perform sufficiently well in realistic and broad-coverage applications such as extracting synthetically lethal genes from the cancer literature. In this study, we revisit the cell line name recognition task, evaluating both available systems and newly introduced methods on various resources to obtain a reliable tagger not tied to any specific subdomain. In support of this task, we introduce two text collections manually annotated for cell line names: the broad-coverage corpus Gellus and CLL, a focused target domain corpus. Results: We find that the best performance is achieved using NERsuite, a machine learning system based on Conditional Random Fields, trained on the Gellus corpus and supported with a dictionary of cell line names. The system achieves an F-score of 88.46% on the test set of Gellus and 85.98% on the independently annotated CLL corpus. It was further applied at large scale to 24 302 102 unannotated articles, resulting in the identification of 5 181 342 cell line mentions, normalized to 11 755 unique cell line database identifiers. Availability and implementation: The manually annotated datasets, the cell line dictionary, derived corpora, NERsuite models and the results of the large-scale run on unannotated texts are available under open licenses at http://turkunlp.github.io/Cell-line-recognition/. Contact: sukaew@utu.fi PMID:26428294

  3. Cell line name recognition in support of the identification of synthetic lethality in cancer from text.

    PubMed

    Kaewphan, Suwisa; Van Landeghem, Sofie; Ohta, Tomoko; Van de Peer, Yves; Ginter, Filip; Pyysalo, Sampo

    2016-01-15

    The recognition and normalization of cell line names in text is an important task in biomedical text mining research, facilitating for instance the identification of synthetically lethal genes from the literature. While several tools have previously been developed to address cell line recognition, it is unclear whether available systems can perform sufficiently well in realistic and broad-coverage applications such as extracting synthetically lethal genes from the cancer literature. In this study, we revisit the cell line name recognition task, evaluating both available systems and newly introduced methods on various resources to obtain a reliable tagger not tied to any specific subdomain. In support of this task, we introduce two text collections manually annotated for cell line names: the broad-coverage corpus Gellus and CLL, a focused target domain corpus. We find that the best performance is achieved using NERsuite, a machine learning system based on Conditional Random Fields, trained on the Gellus corpus and supported with a dictionary of cell line names. The system achieves an F-score of 88.46% on the test set of Gellus and 85.98% on the independently annotated CLL corpus. It was further applied at large scale to 24 302 102 unannotated articles, resulting in the identification of 5 181 342 cell line mentions, normalized to 11 755 unique cell line database identifiers. The manually annotated datasets, the cell line dictionary, derived corpora, NERsuite models and the results of the large-scale run on unannotated texts are available under open licenses at http://turkunlp.github.io/Cell-line-recognition/. sukaew@utu.fi. © The Author 2015. Published by Oxford University Press.

  4. Named entity recognition and classification in biomedical text using classifier ensemble.

    PubMed

    Saha, Sriparna; Ekbal, Asif; Sikdar, Utpal Kumar

    2015-01-01

    Named Entity Recognition and Classification (NERC) is an important task in information extraction for biomedicine domain. Biomedical Named Entities include mentions of proteins, genes, DNA, RNA, etc. which, in general, have complex structures and are difficult to recognise. In this paper, we propose a Single Objective Optimisation based classifier ensemble technique using the search capability of Genetic Algorithm (GA) for NERC in biomedical texts. Here, GA is used to quantify the amount of voting for each class in each classifier. We use diverse classification methods like Conditional Random Field and Support Vector Machine to build a number of models depending upon the various representations of the set of features and/or feature templates. The proposed technique is evaluated with two benchmark datasets, namely JNLPBA 2004 and GENETAG. Experiments yield the overall F- measure values of 75.97% and 95.90%, respectively. Comparisons with the existing systems show that our proposed system achieves state-of-the-art performance.

  5. 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.

  6. Complexity reduction with recognition rate maintained for online handwritten Japanese text recognition

    NASA Astrophysics Data System (ADS)

    Gao, Jinfeng; Zhu, Bilan; Nakagawa, Masaki

    2012-01-01

    The paper presents complexity reduction of an on-line handwritten Japanese text recognition system by selecting an optimal off-line recognizer in combination with an on-line recognizer, geometric context evaluation and linguistic context evaluation. The result is that a surprisingly small off-line recognizer, which alone is weak, produces nearly the best recognition rate in combination with other evaluation factors in remarkably small space and time complexity. Generally speaking, lower dimensions with less principle components produce a smaller set of prototypes, which reduce memory-cost and time-cost. It degrades the recognition rate, however, so that we need to compromise them. In an evaluation function with the above-mentioned multiple factors combined, the configuration of only 50 dimensions with as little as 5 principle components for the off-line recognizer keeps almost the best accuracy 97.87% (the best accuracy 97.92%) for text recognition while it suppresses the total memory-cost from 99.4 MB down to 32 MB and the average time-cost of character recognition for text recognition from 0.1621 ms to 0.1191 ms compared with the traditional offline recognizer with 160 dimensions and 50 principle components.

  7. 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.

  8. How many scientific papers are mentioned in policy-related documents? An empirical investigation using Web of Science and Altmetric data.

    PubMed

    Haunschild, Robin; Bornmann, Lutz

    2017-01-01

    In this short communication, we provide an overview of a relatively newly provided source of altmetrics data which could possibly be used for societal impact measurements in scientometrics. Recently, Altmetric-a start-up providing publication level metrics-started to make data for publications available which have been mentioned in policy-related documents. Using data from Altmetric, we study how many papers indexed in the Web of Science (WoS) are mentioned in policy-related documents. We find that less than 0.5% of the papers published in different subject categories are mentioned at least once in policy-related documents. Based on our results, we recommend that the analysis of (WoS) publications with at least one policy-related mention is repeated regularly (annually) in order to check the usefulness of the data. Mentions in policy-related documents should not be used for impact measurement until new policy-related sites are tracked.

  9. Machine Recognition vs Human Recognition of Voices

    DTIC Science & Technology

    2012-05-01

    good as seen in NIST Speaker Recognition Evaluations, performance can still suffer when the environmental conditions, emotions , or recording quality...recognized. The accuracy of speaker recognition for disyllables was 87%. For monosyllables, it was 81%, consonant- vowel excerpts were 63%, and... vowel excerpts were 56%. Thus, they demonstrated that the identification performance decreased as the number of phonemes decreased. In [2], the

  10. Exploring a recognition-induced recognition decrement

    PubMed Central

    Dopkins, Stephen; Ngo, Catherine Trinh; Sargent, Jesse

    2007-01-01

    Four experiments explored a recognition decrement that is associated with the recognition of a word from a short list. The stimulus material for demonstrating the phenomenon was a list of words of different syntactic types. A word from the list was recognized less well following a decision that a word of the same type had occurred in the list than following a decision that such a word had not occurred in the list. A recognition decrement did not occur for a word of a given type following a positive recognition decision to a word of a different type. A recognition decrement did not occur when the list consisted exclusively of nouns. It was concluded that the phenomenon may reflect a criterion shift but probably does not reflect a list strength effect, suppression, or familiarity attribution consequent to a perceived discrepancy between actual and expected fluency. PMID:17063915

  11. Building Group Recognition.

    ERIC Educational Resources Information Center

    Chartier, George

    1994-01-01

    Discusses the value of name recognition for theater companies. Describes steps toward identity and recognition, analyzing the group, the mission statement, symbolic logic, designing and identity, developing a communications plan, and meaningful activities. (SR)

  12. Speech Recognition by Computer.

    ERIC Educational Resources Information Center

    Levinson, Stephen E.; Liberman, Mark Y.

    1981-01-01

    Speech recognition by computers is discussed, including methods of recognizing isolated words and procedures for analyzing connected speech. Describes Bell Laboratories' speech recognition system which attempts to combine major elements of human communication into a single operating unit. (DS)

  13. Speech recognition and understanding

    SciTech Connect

    Vintsyuk, T.K.

    1983-05-01

    This article discusses the automatic processing of speech signals with the aim of finding a sequence of works (speech recognition) or a concept (speech understanding) being transmitted by the speech signal. The goal of the research is to develop an automatic typewriter that will automatically edit and type text under voice control. A dynamic programming method is proposed in which all possible class signals are stored, after which the presented signal is compared to all the stored signals during the recognition phase. Topics considered include element-by-element recognition of words of speech, learning speech recognition, phoneme-by-phoneme speech recognition, the recognition of connected speech, understanding connected speech, and prospects for designing speech recognition and understanding systems. An application of the composition dynamic programming method for the solution of basic problems in the recognition and understanding of speech is presented.

  14. Incorporating domain knowledge in chemical and biomedical named entity recognition with word representations.

    PubMed

    Munkhdalai, Tsendsuren; Li, Meijing; Batsuren, Khuyagbaatar; Park, Hyeon Ah; Choi, Nak Hyeon; Ryu, Keun Ho

    2015-01-01

    Chemical and biomedical Named Entity Recognition (NER) is an essential prerequisite task before effective text mining can begin for biochemical-text data. Exploiting unlabeled text data to leverage system performance has been an active and challenging research topic in text mining due to the recent growth in the amount of biomedical literature. We present a semi-supervised learning method that efficiently exploits unlabeled data in order to incorporate domain knowledge into a named entity recognition model and to leverage system performance. The proposed method includes Natural Language Processing (NLP) tasks for text preprocessing, learning word representation features from a large amount of text data for feature extraction, and conditional random fields for token classification. Other than the free text in the domain, the proposed method does not rely on any lexicon nor any dictionary in order to keep the system applicable to other NER tasks in bio-text data. We extended BANNER, a biomedical NER system, with the proposed method. This yields an integrated system that can be applied to chemical and drug NER or biomedical NER. We call our branch of the BANNER system BANNER-CHEMDNER, which is scalable over millions of documents, processing about 530 documents per minute, is configurable via XML, and can be plugged into other systems by using the BANNER Unstructured Information Management Architecture (UIMA) interface. BANNER-CHEMDNER achieved an 85.68% and an 86.47% F-measure on the testing sets of CHEMDNER Chemical Entity Mention (CEM) and Chemical Document Indexing (CDI) subtasks, respectively, and achieved an 87.04% F-measure on the official testing set of the BioCreative II gene mention task, showing remarkable performance in both chemical and biomedical NER. BANNER-CHEMDNER system is available at: https://bitbucket.org/tsendeemts/banner-chemdner.

  15. Does the Child's Actual Participation Make a Difference? Positive and Negative Emotion States Mentioned by Mothers of Young Children during Narrative Construction

    ERIC Educational Resources Information Center

    Landau, Rivka; Yanay, Niza; Eshel, Yohanan; Ben-Aaron, Miriam

    2006-01-01

    The study examined the rate that mothers mentioned positive and negative emotion states and emotion calls during narrative construction from a text-free children's picture book illustrating happy and emotionally charged situations. Ninety-three mothers of 3- to 4-year-old kibbutz children were divided into three groups: (1) the child was not…

  16. Identification and gene expression of multiple peptidoglycan recognition proteins (PGRPs) in the deep-sea mussel Bathymodiolus azoricus, involvement in symbiosis?

    PubMed

    Détrée, Camille; Lallier, François H; Tanguy, Arnaud; Mary, Jean

    2017-05-01

    The relationship between the deep-sea mussel Bathymodiolus azoricus and its thiotrophic (SOX) and methanotrophic (MOX) symbionts has been ecologically and functionally well studied. Endosymbiosis is common in deep-sea hydrothermal vent fauna, yet little is known about the molecular mechanisms underlying the regulation of interactions between host and symbionts. In this study we focused on a group of pattern recognition receptors (PRR), called PGRPs that are able to recognize the peptidoglycan of bacterial cell wall. We first characterised the different PGRPs isoforms in B. azoricus gills and identified five paralogs. Among them two displayed a signal peptide. Then, specific probes designed for each paralog were used to perform real-time PCR quantification in gills of individuals showing various bacterial content as a result of in situ experimental procedures. Overall we found a decrease of PGRPs expression when symbionts amount decreases, suggesting an implication of PGRPs in the regulation of symbionts in B. azoricus gills. We therefore hypothesize that secreted proteins could act as cooperation signals to induce colonisation of symbiotic tissue while non-secreted proteins may regulate the density of endosymbionts within the gill tissue. Copyright © 2017 Elsevier Inc. All rights reserved.

  17. An Abd-B class HOX.PBX recognition sequence is required for expression from the mouse Ren-1c gene.

    PubMed

    Pan, L; Xie, Y; Black, T A; Jones, C A; Pruitt, S C; Gross, K W

    2001-08-31

    Expression from the mouse Ren-1(c) gene in As4.1 cells is dependent on a proximal promoter element (PPE) located at approximately -60 and a 241-base pair enhancer region located at -2625 relative to the transcription start site. The PPE (TAATAAATCAA) is identical to a consensus HOX.PBX binding sequence. Further, PBX1b has been shown to be a component of a PPE-specific binding complex present in nuclear extracts from As4.1 cells. The binding affinities of different paralog HOX members to the PPE were examined in the absence or presence of PBX1b. HOXB6, -B7, and -C8 failed to bind the PPE alone but showed weak affinity in the presence of PBX1b. In contrast, HOXD10 and to a lesser degree HOXB9 bound the PPE with high affinities regardless of whether PBX1b was present. Abd-B HOX members, including HOXD10, -A10, -A9, -B9, and -C9, are expressed in As4.1 cells. The ability of HOX and PBX1b to form a ternary complex with PREP1 on the PPE is also demonstrated both in vivo and in vitro. Point mutations in either the HOX or PBX half-site of the PPE disrupted the formation of the HOX.PBX complex and dramatically decreased transcriptional activity of the Ren-1(c) gene demonstrating that both the HOX and PBX half-sites are critical for mouse renin gene expression. These results strongly implicate Abd-B class Hox genes and their cofactors as major determinants of the sites of renin expression.

  18. Recognition of a core fragment of Beauveria bassiana hydrophobin gene promoter (P hyd1) and its special use in improving fungal biocontrol potential

    PubMed Central

    Wang, Zheng-Liang; Ying, Sheng-Hua; Feng, Ming-Guang

    2013-01-01

    To identify a suitable promoter for use in engineering fungal entomopathogens to improve heterologous gene expression and fungal biocontrol potential, a 1798 bp promoter (Phyd1) upstream of Beauveria bassiana class I hydrophobin gene (hyd1) was optimized by upstream truncation and site-directed mutation. A truncated 1290 bp fragment (Phyd1-t1) drove eGFP expression in B. bassiana much more efficiently than full-length Phyd1. Further truncating Phyd1-t1 to 1179, 991 and 791 bp or mutating one of the binding domains of three transcription factors in Phyd1-t1 reduced significantly the expression of eGFP (enhanced green fluorescence protein). Under Phyd1-t1 control, eGFP was expressed more abundantly in conidiogenic cells and conidia than in mycelia. Therefore, Phyd1-t1 was used to integrate a bacterium-derived, insect midgut-specific toxin (vip3Aa1) gene into B. bassiana, yielding a transgenic strain (BbHV8) expressing 9.8-fold more toxin molecules in conidia than a counterpart strain (BbV28) expressing the toxin under the control of PgpdA, a promoter widely used for gene expression in fungi. Consequently, BbHV8 showed much higher per os virulence to Spodoptera litura larvae than BbV28 in standardized bioassays with normal conidia for both cuticle penetration and ingestion or heat-killed conidia for ingestion only. Conclusively, Phyd1-t1 is a useful tool for enhancing beneficial protein expression, such as vip3Aa1, in fungal conidia, which are the active ingredients of mycoinsecticides. PMID:22639846

  19. Recognition of a core fragment ofBeauveria bassiana hydrophobin gene promoter (P hyd1) and its special use in improving fungal biocontrol potential.

    PubMed

    Wang, Zheng-Liang; Ying, Sheng-Hua; Feng, Ming-Guang

    2013-01-01

    To identify a suitable promoter for use in engineering fungal entomopathogens to improve heterologous gene expression and fungal biocontrol potential, a 1798 bp promoter (P hyd1) upstream of Beauveria bassiana class I hydrophobin gene (hyd1) was optimized by upstream truncation and site-directed mutation. A truncated 1290 bp fragment (P hyd1-t1) drove eGFP expression in B. bassiana much more efficiently than full-length P hyd1. Further truncating P hyd1-t1 to 1179, 991 and 791 bp or mutating one of the binding domains of three transcription factors in P hyd1-t1 reduced significantly the expression of eGFP (enhanced green fluorescence protein). Under P hyd1-t1 control, eGFP was expressed more abundantly in conidiogenic cells and conidia than in mycelia. Therefore, P hyd1-t1 was used to integrate a bacterium-derived, insect midgut-specific toxin (vip3Aa1) gene into B. bassiana, yielding a transgenic strain (BbHV8) expressing 9.8-fold more toxin molecules in conidia than a counterpart strain (BbV28) expressing the toxin under the control of P gpdA, a promoter widely used for gene expression in fungi. Consequently, BbHV8 showed much higher per os virulence to Spodoptera litura larvae than BbV28 in standardized bioassays with normal conidia for both cuticle penetration and ingestion or heat-killed conidia for ingestion only. Conclusively, P hyd1-t1 is a useful tool for enhancing beneficial protein expression, such as vip3Aa1, in fungal conidia, which are the active ingredients of mycoinsecticides.

  20. Recognition of Potentially Novel Human Disease-Associated Pathogens by Implementation of Systematic 16S rRNA Gene Sequencing in the Diagnostic Laboratory▿ †

    PubMed Central

    Keller, Peter M.; Rampini, Silvana K.; Büchler, Andrea C.; Eich, Gerhard; Wanner, Roger M.; Speck, Roberto F.; Böttger, Erik C.; Bloemberg, Guido V.

    2010-01-01

    Clinical isolates that are difficult to identify by conventional means form a valuable source of novel human pathogens. We report on a 5-year study based on systematic 16S rRNA gene sequence analysis. We found 60 previously unknown 16S rRNA sequences corresponding to potentially novel bacterial taxa. For 30 of 60 isolates, clinical relevance was evaluated; 18 of the 30 isolates analyzed were considered to be associated with human disease. PMID:20631113

  1. 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.

  2. 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.

  3. Antigen Recognition By Variable Lymphocyte Receptors

    SciTech Connect

    Han, B.W.; Herrin, B.R.; Cooper, M.D.; Wilson, I.A.

    2009-05-18

    Variable lymphocyte receptors (VLRs) rather than antibodies play the primary role in recognition of antigens in the adaptive immune system of jawless vertebrates. Combinatorial assembly of leucine-rich repeat (LRR) gene segments achieves the required repertoire for antigen recognition. We have determined a crystal structure for a VLR-antigen complex, VLR RBC36 in complex with the H-antigen trisaccharide from human blood type O erythrocytes, at 1.67 angstrom resolution. RBC36 binds the H-trisaccharide on the concave surface of the LRR modules of the solenoid structure where three key hydrophilic residues, multiple van der Waals interactions, and the highly variable insert of the carboxyl-terminal LRR module determine antigen recognition and specificity. The concave surface assembled from the most highly variable regions of the LRRs, along with diversity in the sequence and length of the highly variable insert, can account for the recognition of diverse antigens by VLRs.

  4. Recognition and rejection of self in plant reproduction.

    PubMed

    Nasrallah, June B

    2002-04-12

    Plant self-incompatibility (SI) systems are unique among self/nonself recognition systems in being based on the recognition of self rather than nonself. SI in crucifer species is controlled by highly polymorphic and co-evolving genes linked in a complex. Self recognition is based on allele-specific interactions between stigma receptors and pollen ligands that result in the arrest of pollen tube development. Commonalities and differences between SI and other self/nonself discrimination systems are discussed.

  5. 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.

  6. 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).

  7. Genes

    MedlinePlus

    ... Search Search MedlinePlus GO GO About MedlinePlus Site Map FAQs Customer Support Health Topics Drugs & Supplements Videos & Tools Español You Are Here: Home → Medical Encyclopedia → Genes URL of this page: //medlineplus.gov/ency/article/ ...

  8. 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…

  9. 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…

  10. Selective Amplification of SPR Biosensor Signal for Recognition of rpoB Gene Fragments by Use of Gold Nanoparticles Modified by Thiolated DNA

    NASA Astrophysics Data System (ADS)

    Matsishin, M.; Rachkov, A.; Lopatynskyi, A.; Chegel, V.; Soldatkin, A.; El'skaya, A.

    2017-04-01

    An experimental approach for improving the sensitivity of the surface plasmon resonance (SPR) DNA hybridization sensor using gold nanoparticles (GNPs), modified by specific oligonucleotides, was elaborated. An influence of the ionic strength on the aggregation stability of unmodified GNPs and GNPs modified by the thiolated oligonucleotides was investigated by monitoring a value of light extinction at 520 nm that can be considered as a measure of a quantity of the non-aggregated GNPs. While the unmodified GNPs started to aggregate in 0.2 × saline-sodium citrate (SSC), GNPs modified by the negatively charged oligonucleotides were more stable at increasing ionic strength up to 0.5 × SSC. A bioselective element of the SPR DNA hybridization sensor was formed by immobilization on the gold sensor surface of the thiolated oligonucleotides P2, the sequence of which is a fragment of the rpoB gene of Mycobacterium tuberculosis. The injections into the measuring flow cell of the SPR spectrometer of various concentrations of GNPs modified by the complementary oligonucleotides T2-18m caused the pronounced concentration-dependent sequence-specific sensor responses. The magnitude of the sensor responses was much higher than in the case of the free standing complementary oligonucleotides. According to the obtained experimental data, the usage of GNPs modified by specific oligonucleotides can amplify the sensor response of the SPR DNA hybridization sensor in 1200 times.

  11. Phospholipid-nucleic acid recognition: energetics of DNA-Mg2+-phosphatidylcholine ternary complex formation and its further compaction as a gene delivery formulation.

    PubMed

    Süleymanoglu, Erhan

    2006-01-01

    Thermodynamic features related to the preparation and use of self-assemblies formed between multilamellar and unilamellar zwitterionic liposomes and polynucleotides with various conformation and sizes are presented. The divalent metal cation-induced adsorption, aggregation, and adhesion between single- and double-stranded polyribonucleotides and phosphatidylcholine vesicles was followed by differential adiabatic scanning microcalorimetry. Nucleic acid condensation and compaction mediated by Mg2+ was followed, with regard to interfacial interaction with unilamellar vesicles. Microcalorimetric measurements of synthetic phospholipid vesicles and poly(ribo)nucleotides and their ternary complexes with inorganic cations were used to build the thermodynamic model of their structural transitions. The increased thermal stability of the phospholipid bilayers is achieved by affecting their melting transition temperature by nucleic acid-induced electrostatic charge screening. Measurements give evidence for the stabilization of polynucleotide helices upon their association with liposomes in the presence of divalent metal cations. Such an induced aggregation of vesicles leads either to heterogeneous multilamellar DNA-lipid arrangements or to DNA-induced bilayer destabilization and lipid fusion. The further employment of these polyelectrolyte nanostructures as improved formulations in therapeutic gene delivery trials, as well as in DNA chromatography, is discussed.

  12. Visual object recognition.

    PubMed

    Logothetis, N K; Sheinberg, D L

    1996-01-01

    Visual object recognition is of fundamental importance to most animals. The diversity of tasks that any biological recognition system must solve suggests that object recognition is not a single, general purpose process. In this review, we consider evidence from the fields of psychology, neuropsychology, and neurophysiology, all of which supports the idea that there are multiple systems for recognition. Data from normal adults, infants, animals, and brain damaged patients reveal a major distinction between the classification of objects at a basic category level and the identification of individual objects from a homogeneous object class. An additional distinction between object representations used for visual perception and those used for visually guided movements provides further support for a multiplicity of visual recognition systems. Recent evidence from psychophysical and neurophysiological studies indicates that one system may represent objects by combinations of multiple views, or aspects, and another may represent objects by structural primitives and their spatial interrelationships.

  13. 8 CFR 292.2 - Organizations qualified for recognition; requests for recognition; withdrawal of recognition...

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 8 Aliens and Nationality 1 2010-01-01 2010-01-01 false Organizations qualified for recognition; requests for recognition; withdrawal of recognition; accreditation of representatives; roster. 292.2... REPRESENTATION AND APPEARANCES § 292.2 Organizations qualified for recognition; requests for recognition...

  14. Recognition as a challenging label-free optical sensing system

    NASA Astrophysics Data System (ADS)

    Gauglitz, Günter

    2013-05-01

    Optical biosensors are increasingly used in application areas of environmental analysis, healthcare and food safety. The quality of the biosensor's results depends on the interaction layer, the detection principles, and evaluation strategies, not only on the biopolymer layer but also especially on recognition elements. Using label-free optical sensing, non-specific interaction between sample and transducer has to be reduced, and the selectivity of recognition elements has to be improved. For this reason, strategies to avoid non-specific interaction even in blood and milk are discussed, a variety of upcoming recognition is given. Based on the classification of direct optical detection methods, some examples for the above mentioned applications are reviewed. Trends as well as advantages of parallel multisport detection for kinetic evaluation are also part of the lecture.

  15. The Recognition of Web Pages' Hyperlinks by People with Intellectual Disabilities: An Evaluation Study

    ERIC Educational Resources Information Center

    Rocha, Tania; Bessa, Maximino; Goncalves, Martinho; Cabral, Luciana; Godinho, Francisco; Peres, Emanuel; Reis, Manuel C.; Magalhaes, Luis; Chalmers, Alan

    2012-01-01

    Background: One of the most mentioned problems of web accessibility, as recognized in several different studies, is related to the difficulty regarding the perception of what is or is not clickable in a web page. In particular, a key problem is the recognition of hyperlinks by a specific group of people, namely those with intellectual…

  16. The Recognition of Web Pages' Hyperlinks by People with Intellectual Disabilities: An Evaluation Study

    ERIC Educational Resources Information Center

    Rocha, Tania; Bessa, Maximino; Goncalves, Martinho; Cabral, Luciana; Godinho, Francisco; Peres, Emanuel; Reis, Manuel C.; Magalhaes, Luis; Chalmers, Alan

    2012-01-01

    Background: One of the most mentioned problems of web accessibility, as recognized in several different studies, is related to the difficulty regarding the perception of what is or is not clickable in a web page. In particular, a key problem is the recognition of hyperlinks by a specific group of people, namely those with intellectual…

  17. CLASSIFICATION OF THE GENUS ISHIGE (ISHIGEALES, PHAEOPHYCEAE) IN THE NORTH PACIFIC OCEAN WITH RECOGNITION OF ISHIGE FOLIACEA BASED ON PLASTID rbcl AND MITOCHONDRIAL cox3 GENE SEQUENCES(1).

    PubMed

    Lee, Kyung Min; Boo, Ga Hun; Riosmena-Rodriguez, Rafael; Shin, Jong-Ahm; Boo, Sung Min

    2009-08-01

    The taxonomy and biogeography of a genus with species that occur in geographically isolated regions is interesting. The brown algal genus Ishige Yendo is a good example, with species that apparently inhabit warm regions of both the northwestern and northeastern Pacific Ocean. We determined the sequences of mitochondrial cox3 and plastid rbcL genes from specimens of the genus collected over its distributional range. Analyses of the 86 cox3 and 97 rbcL sequences resulted in congruent trees in which Ishige sinicola (Setch. et N. L. Gardner) Chihara consisted of two distinct clades: one comprising samples from Korea and Japan, and the other comprising samples from the Gulf of California. Additional observations of the morphology and anatomy of the specimens agree with the molecular data. On the basis of results, we reinstated Ishige foliacea S. Okamura (considered a synonym of I. sinicola from the Gulf of California) for plants from the northwest Pacific region and designated a specimen in the Yendo Herbarium (SAP) as the lectotype. I. foliacea is distinguished by large (up to 20 cm) and wide (up to 20 mm) thalli, with a cortex of 4-7 cells, and a medulla composed of long, tangled hyphal cells. Both cox3 and rbcL sequence data strongly support the sister-area relationship between the northwest Pacific region and the Gulf of California. A likely explanation for this pattern would be the presence of a species ancestral to contemporary species of Ishige in both regions during the paleogeological period, with descendants later isolated by distance.

  18. Thermodynamics of b-HLH-LZ protein binding to DNA: the energetic importance of protein-DNA contacts in site-specific E-box recognition by the complete gene product of the Max p21 transcription factor.

    PubMed

    Meier-Andrejszki, Laura; Bjelić, Sasa; Naud, Jean-François; Lavigne, Pierre; Jelesarov, Ilian

    2007-10-30

    The Myc/Mad/Max network of dimeric basic region-helix-loop-helix-leucine zipper (b-HLH-LZ) transcription factors bind to enhancer box sequences (E-box) in the promotors of a large set of genes that control cell metabolism, proliferation, and differentiation. Max (Myc-associated factor X) is the obligate heterodimerization partner of Myc and Mad proteins. On the other hand, Max is the only member of the family capable of forming a stable homodimer. As part of the transcriptional regulation mechanism, Myc/Max and Mad/Max heterodimers and Max homodimers are thought to compete for binding to the E-box target sequences. E-box recognition is structurally supported by the b-HLH-LZ structural motif, which also promotes dimerization. However, the actual dimerization and heterodimerization constants of the complete gene products and their affinities for E-box sequences are not known. Also, the detailed thermodynamic characterization of DNA binding by these transcription factors has not been done yet. Such knowledge is necessary for complete understanding of the transcriptional regulation carried out by the Myc/Mad/Max network. Here, we report the first in-depth thermodynamic characterization of the stability and specific DNA binding of a full length gene product of the Myc/Mad/Max family, namely, Max protein isoform p21 (Max p21). Using calorimetric methods (DSC and ITC) we have determined the dimerization constant of Max p21 in the low micromolar range, and the Max p21/E-box complex dissociation constant in the low nanomolar range at 37 degrees C. The association is driven by a large exothermic effect, which is partly compensated by entropic factors. The energetic contribution to binding affinity of seven highly conserved residues that contact the DNA was probed by X-to-Ala mutagenesis. The results demonstrate that high binding affinity critically relies on the side chain of Arg 26. Furthermore, the mutational analysis points to the important role of the persistent helical

  19. The multicoloured world of promoter recognition complexes

    PubMed Central

    Müller, Ferenc; Tora, Làszlò

    2004-01-01

    The expression pattern of regulated genes changes dynamically depending on the developmental stage and the differentiation state of the cell. Transcription factors regulate cellular events at the gene expression level by communicating signals to the general transcription machinery that forms a preinitiation complex (PIC) at class II core promoters. Recent data strongly suggest that PICs are composed of different sets of factors at distinct promoters, reflecting the spatiotemporal profile of gene expression in multicellular organisms. Thus, today it is important to ask the question: how universal are the promoter recognition factors? This review will focus on findings that support the new idea that core promoter recognition by distinct factors is an additional level of transcriptional regulation and that this step is developmentally regulated. PMID:14685269

  20. 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.

  1. 8 CFR 1292.2 - Organizations qualified for recognition; requests for recognition; withdrawal of recognition...

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 8 Aliens and Nationality 1 2010-01-01 2010-01-01 false Organizations qualified for recognition; requests for recognition; withdrawal of recognition; accreditation of representatives; roster. 1292.2... IMMIGRATION REGULATIONS REPRESENTATION AND APPEARANCES § 1292.2 Organizations qualified for recognition...

  2. 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.

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

    PubMed

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

    2009-09-09

    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. 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, suggests that the

  4. Probabilistic Open Set Recognition

    NASA Astrophysics Data System (ADS)

    Jain, Lalit Prithviraj

    Real-world tasks in computer vision, pattern recognition and machine learning often touch upon the open set recognition problem: multi-class recognition with incomplete knowledge of the world and many unknown inputs. An obvious way to approach such problems is to develop a recognition system that thresholds probabilities to reject unknown classes. Traditional rejection techniques are not about the unknown; they are about the uncertain boundary and rejection around that boundary. Thus traditional techniques only represent the "known unknowns". However, a proper open set recognition algorithm is needed to reduce the risk from the "unknown unknowns". This dissertation examines this concept and finds existing probabilistic multi-class recognition approaches are ineffective for true open set recognition. We hypothesize the cause is due to weak adhoc assumptions combined with closed-world assumptions made by existing calibration techniques. Intuitively, if we could accurately model just the positive data for any known class without overfitting, we could reject the large set of unknown classes even under this assumption of incomplete class knowledge. For this, we formulate the problem as one of modeling positive training data by invoking statistical extreme value theory (EVT) near the decision boundary of positive data with respect to negative data. We provide a new algorithm called the PI-SVM for estimating the unnormalized posterior probability of class inclusion. This dissertation also introduces a new open set recognition model called Compact Abating Probability (CAP), where the probability of class membership decreases in value (abates) as points move from known data toward open space. We show that CAP models improve open set recognition for multiple algorithms. Leveraging the CAP formulation, we go on to describe the novel Weibull-calibrated SVM (W-SVM) algorithm, which combines the useful properties of statistical EVT for score calibration with one-class and binary

  5. Toward hyperspectral face recognition

    NASA Astrophysics Data System (ADS)

    Robila, Stefan A.

    2008-02-01

    Face recognition continues to meet significant challenges in reaching accurate results and still remains one of the activities where humans outperform technology. An attractive approach in improving face identification is provided by the fusion of multiple imaging sources such as visible and infrared images. Hyperspectral data, i.e. images collected over hundreds of narrow contiguous light spectrum intervals constitute a natural choice for expanding face recognition image fusion, especially since it may provide information beyond the normal visible range, thus exceeding the normal human sensing. In this paper we investigate the efficiency of hyperspectral face recognition through an in house experiment that collected data in over 120 bands within the visible and near infrared range. The imagery was produced using an off the shelf sensor in both indoors and outdoors with the subjects being photographed from various angles. Further processing included spectra collection and feature extraction. Human matching performance based on spectral properties is discussed.

  6. Multiclass Cancer Classification by Using Fuzzy Support Vector Machine and Binary Decision Tree With Gene Selection

    PubMed Central

    2005-01-01

    We investigate the problems of multiclass cancer classification with gene selection from gene expression data. Two different constructed multiclass classifiers with gene selection are proposed, which are fuzzy support vector machine (FSVM) with gene selection and binary classification tree based on SVM with gene selection. Using F test and recursive feature elimination based on SVM as gene selection methods, binary classification tree based on SVM with F test, binary classification tree based on SVM with recursive feature elimination based on SVM, and FSVM with recursive feature elimination based on SVM are tested in our experiments. To accelerate computation, preselecting the strongest genes is also used. The proposed techniques are applied to analyze breast cancer data, small round blue-cell tumors, and acute leukemia data. Compared to existing multiclass cancer classifiers and binary classification tree based on SVM with F test or binary classification tree based on SVM with recursive feature elimination based on SVM mentioned in this paper, FSVM based on recursive feature elimination based on SVM can find most important genes that affect certain types of cancer with high recognition accuracy. PMID:16046822

  7. [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.

  8. 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.

  9. 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

  10. 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…

  11. Geophysical Signal Recognition,

    DTIC Science & Technology

    1981-01-01

    quite helpful in the magnetosphere. Detecting a particular in earthquake prediction . However pattern recog- micropulsation event can provide a diagnosis...bio- In su..a.iry, application of pattern recognition to medical signals, progress in geophysical signal earthquake prediction is in its infancy

  12. 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)

  13. 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…

  14. Intralist Cueing of Recognition

    ERIC Educational Resources Information Center

    Slamecka, Norman J.

    1975-01-01

    Two experiments tested for effects of intralist cues upon recognition probability. Categorized and random lists were each tested, with targets appearing with zero, one or three intralist cues. Experiments showed substantial effects of trials and list type, but not of intralist context. (CHK)

  15. 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)

  16. Recognition for Employed Inventors.

    ERIC Educational Resources Information Center

    Sanders, Howard J.

    1980-01-01

    Presents arguments for monetary rewards and other forms of recognition by employers for inventions of employed inventors, particularly as the concept applies to stimulating innovativeness in America. Discusses the controversy of federally mandated compensation for employed inventors. The efforts of the American Chemical Society along these lines…

  17. 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.

  18. Recognition Memory for Pseudowords

    ERIC Educational Resources Information Center

    Greene, Robert L.

    2004-01-01

    Participants are more likely to give positive responses on a recognition test to pseudowords (pronounceable nonwords) than words. A series of experiments suggests that this difference reflects the greater overall familiarity of pseudowords than of words. Pseudowords receive higher ratings of similarity to a studied list than do words. Pseudowords…

  19. 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.

  20. Perceived Task-Difficulty Recognition from Log-File Information for the Use in Adaptive Intelligent Tutoring Systems

    ERIC Educational Resources Information Center

    Janning, Ruth; Schatten, Carlotta; Schmidt-Thieme, Lars

    2016-01-01

    Recognising students' emotion, affect or cognition is a relatively young field and still a challenging task in the area of intelligent tutoring systems. There are several ways to use the output of these recognition tasks within the system. The approach most often mentioned in the literature is using it for giving feedback to the students. The…

  1. Perceived Task-Difficulty Recognition from Log-File Information for the Use in Adaptive Intelligent Tutoring Systems

    ERIC Educational Resources Information Center

    Janning, Ruth; Schatten, Carlotta; Schmidt-Thieme, Lars

    2016-01-01

    Recognising students' emotion, affect or cognition is a relatively young field and still a challenging task in the area of intelligent tutoring systems. There are several ways to use the output of these recognition tasks within the system. The approach most often mentioned in the literature is using it for giving feedback to the students. The…

  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. PA01.24. A literature study on the medicinal preparations mentioned in Sri Lankan indigenous medicine for chronic wound healing

    PubMed Central

    Karandugoda, K.K.I.E.; Perera, B.S.R.; Pushpakumara, A.A.J.

    2012-01-01

    Purpose: Chronic wounds are a challenge to the modern medical science since there is no proper medication to correct this imbalance as to stimulate and enhance the growth of healthy granulation tissue making the wound fill up. When Sri Lankan traditional medicine is concerned it has been strewn with a large number of medicinal formulas for wound healing especially for granulation tissue formation. The primary intention of this study was to collect these formulas and analyse them to come up with the most frequently used herbal, mineral and animal material. It was also wished to analyse their pharmacodynamics properties to see how they agree with Ayurvedic theories in healing a wound. Method: For this purpose, a literature study was carried out by referring 30 major Sri Lankan Traditional texts and manuscripts. Formulas which particularly prescribed for tissue formation (Vrana ropana) were retrieved. They were studied, analysed and were calculated to come up with the mostly used ingredients. Result: At the end of the study 152 formulas were analysed gathering 157 herbal material, 10 minerals and 8 materials of animal origin i.e. 176 materials in total. The analysis revealed that Ficus religiosa, Ridi thuththam (Calamine) and Bee's wax as the most frequently mentioned material in wound healing formulae in Sri Lankan traditional medical texts. Pharmacodynamic analysis showed essential properties in nutrition and growth. Conclusion: It was seen that the Sri Lankan Traditional Medicine possesses a rich pool of medicinal formulas for chronic wound healing. Ficus religiosa, Ridi thuththam (Calamine) and Bee's wax as the most frequently used materials with herbal, mineral and animal origin respectively in wound healing formulae in Sri Lankan traditional medical texts.

  4. PTX3, a humoral pattern recognition molecule at the interface between microbe and matrix recognition.

    PubMed

    Garlanda, Cecilia; Jaillon, Sebastien; Doni, Andrea; Bottazzi, Barbara; Mantovani, Alberto

    2016-02-01

    Innate immunity consists of a cellular and a humoral arm. PTX3 is a fluid patter recognition molecule (PRM) with antibody-like properties. Gene targeted mice and genetic associations in humans suggest that PTX3 plays a non-redundant role in resistance against selected pathogens (e.g. Aspergillus fumigatus, Pseudomonas aeruginosa, uropathogenic Escherichia coli) and in the regulation of inflammation. PTX3 acts as an extrinsic oncosuppressor by taming complement elicited tumor-promoting inflammation. Recent results indicate that, by interacting with provisional matrix components, PTX3 contributes to the orchestration of tissue repair. An acidic pH sets PTX3 in a tissue repair mode, while retaining anti-microbial recognition. Based on these data and scattered information on humoral PRM and matrix components, we surmise that matrix and microbial recognition are related functions in evolution. Copyright © 2015 Elsevier Ltd. All rights reserved.

  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. 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…

  7. 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…

  8. Supporting Quality Teachers with Recognition

    ERIC Educational Resources Information Center

    Andrews, Hans A.

    2011-01-01

    Value has been found in providing recognition and awards programs for excellent teachers. Research has also found a major lack of these programs in both the USA and in Australia. Teachers receiving recognition and awards for their teaching have praised recognition programs as providing motivation for them to continue high-level instruction.…

  9. 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…

  10. 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…

  11. Superficial Priming in Episodic Recognition

    ERIC Educational Resources Information Center

    Dopkins, Stephen; Sargent, Jesse; Ngo, Catherine T.

    2010-01-01

    We explored the effect of superficial priming in episodic recognition and found it to be different from the effect of semantic priming in episodic recognition. Participants made recognition judgments to pairs of items, with each pair consisting of a prime item and a test item. Correct positive responses to the test item were impeded if the prime…

  12. 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…

  13. When true recognition suppresses false recognition: evidence from amnesic patients.

    PubMed

    Schacter, D L; Verfaellie, M; Anes, M D; Racine, C

    1998-11-01

    False recognition occurs when people mistakenly claim that a novel item is familiar. After studying lists of semantically related words, healthy controls show extraordinarily high levels of false recognition to nonstudied lures that are semantic associates of study list words. In previous experiments, we found that both Korsakoff and non-Korsakoff amnesic patients show reduced levels of false recognition to semantic associates, implying that the medial temporal/diencephalic structures that are damaged in amnesic patients are involved in the encoding and/or retrieval of information that underlies false recognition. These data contrast with earlier results indicating greater false recognition in Korsakoff amnesics than in control subjects. The present experiment tests the hypothesis that greater or lesser false recognition of semantic associates in amnesic patients, relative to normal controls, can be demonstrated by creating conditions that are more or less conducive to allowing true recognition to suppress false recognition. With repeated presentation and testing of lists of semantic associates, control subjects and both Korsakoff and non-Korsakoff amnesics showed increasing levels of true recognition across trials. However, control subjects exhibited decreasing levels of false recognition across trials, whereas Korsakoff amnesic patients showed increases across trials and non-Korsakoff amnesics showed a fluctuating pattern. Consideration of signal detection analyses and differences between the two types of amnesic patients provides insight into how mechanisms of veridical episodic memory can be used to suppress false recognition.

  14. Is Early Word-form Processing Stress-full? How Natural Variability Supports Recognition

    PubMed Central

    Bortfeld, Heather; Morgan, James L.

    2010-01-01

    In a series of studies, we examined how mothers naturally stress words across multiple mentions in speech to their infants and how this marking influences infants’ recognition of words in fluent speech. We first collected samples of mothers’ infant-directed speech using a technique that induced multiple repetitions of target words. Acoustic analyses revealed that mothers systematically alternated between emphatic and nonemphatic stress when talking to their infants. Using the headturn preference procedure, we then tested 7.5-month-old infants on their ability to detect familiarized bisyllabic words in fluent speech. Stress of target words (emphatic and nonemphatic) was systematically varied across familiarization and recognition phases of four experiments. Results indicated that, although infants generally prefer listening to words produced with emphatic stress, recognition was enhanced when the degree of emphatic stress at familiarization matched the degree of emphatic stress at recognition. PMID:20159653

  15. Improving the recognition of fingerprint biometric system using enhanced image fusion

    NASA Astrophysics Data System (ADS)

    Alsharif, Salim; El-Saba, Aed; Stripathi, Reshma

    2010-04-01

    Fingerprints recognition systems have been widely used by financial institutions, law enforcement, border control, visa issuing, just to mention few. Biometric identifiers can be counterfeited, but considered more reliable and secure compared to traditional ID cards or personal passwords methods. Fingerprint pattern fusion improves the performance of a fingerprint recognition system in terms of accuracy and security. This paper presents digital enhancement and fusion approaches that improve the biometric of the fingerprint recognition system. It is a two-step approach. In the first step raw fingerprint images are enhanced using high-frequency-emphasis filtering (HFEF). The second step is a simple linear fusion process between the raw images and the HFEF ones. It is shown that the proposed approach increases the verification and identification of the fingerprint biometric recognition system, where any improvement is justified using the correlation performance metrics of the matching algorithm.

  16. Use of morphological analysis in protein name recognition.

    PubMed

    Yamamoto, Kaoru; Kudo, Taku; Konagaya, Akihiko; Matsumoto, Yuji

    2004-12-01

    Protein name recognition aims to detect each and every protein names appearing in a PubMed abstract. The task is not simple, as the graphic word boundary (space separator) assumed in conventional preprocessing does not necessarily coincide with the protein name boundary. Such boundary disagreement caused by tokenization ambiguity has usually been ignored in conventional preprocessing of general English. In this paper, we argue that boundary disagreement poses serious limitations in biomedical English text processing, not to mention protein name recognition. Our key idea for dealing with the boundary disagreement is to apply techniques used in Japanese morphological analysis where there are no word boundaries. Having evaluated the proposed method with GENIA corpus 3.02, we obtain F-measure of 69.01 on a strict criterion and 79.32 on a relaxed criterion. The result is comparable to other published work in protein name recognition, without resorting to manually prepared ad hoc feature engineering. Further, compared to the conventional preprocessing, the use of morphological analysis as preprocessing improves the performance of protein name recognition and reduces the execution time.

  17. Image recognition: Visual grouping, recognition, and learning

    PubMed Central

    Buhmann, Joachim M.; Malik, Jitendra; Perona, Pietro

    1999-01-01

    Vision extracts useful information from images. Reconstructing the three-dimensional structure of our environment and recognizing the objects that populate it are among the most important functions of our visual system. Computer vision researchers study the computational principles of vision and aim at designing algorithms that reproduce these functions. Vision is difficult: the same scene may give rise to very different images depending on illumination and viewpoint. Typically, an astronomical number of hypotheses exist that in principle have to be analyzed to infer a correct scene description. Moreover, image information might be extracted at different levels of spatial and logical resolution dependent on the image processing task. Knowledge of the world allows the visual system to limit the amount of ambiguity and to greatly simplify visual computations. We discuss how simple properties of the world are captured by the Gestalt rules of grouping, how the visual system may learn and organize models of objects for recognition, and how one may control the complexity of the description that the visual system computes. PMID:10588681

  18. Image recognition: visual grouping, recognition, and learning.

    PubMed

    Buhmann, J M; Malik, J; Perona, P

    1999-12-07

    Vision extracts useful information from images. Reconstructing the three-dimensional structure of our environment and recognizing the objects that populate it are among the most important functions of our visual system. Computer vision researchers study the computational principles of vision and aim at designing algorithms that reproduce these functions. Vision is difficult: the same scene may give rise to very different images depending on illumination and viewpoint. Typically, an astronomical number of hypotheses exist that in principle have to be analyzed to infer a correct scene description. Moreover, image information might be extracted at different levels of spatial and logical resolution dependent on the image processing task. Knowledge of the world allows the visual system to limit the amount of ambiguity and to greatly simplify visual computations. We discuss how simple properties of the world are captured by the Gestalt rules of grouping, how the visual system may learn and organize models of objects for recognition, and how one may control the complexity of the description that the visual system computes.

  19. Recognition of Teaching Excellence*

    PubMed Central

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

    2010-01-01

    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. PMID:21301598

  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. Optical Pattern Recognition

    NASA Astrophysics Data System (ADS)

    Yu, Francis T. S.; Jutamulia, Suganda

    1998-06-01

    This book provides a comprehensive review of optical pattern recognition, covering theoretical aspects as well as details of practical implementations and signal processing techniques. The first chapter is devoted to pattern recognition performed with optical correlators. Later chapters discuss new approaches based on neural networks, wavelet transforms, and the fractional Fourier transform. The book also covers nonlinear filter methods and optical-electronic hybrid systems. The final part deals with the devices and materials employed in modern systems, such as photorefractive crystals, microlasers, and liquid crystal spatial light modulators. The volume gives many examples of working systems that integrate optics, electronics, and computers, and it covers a range of new developments from mathematical theories to novel optical materials. It will be of great interest to graduate students and researchers in optical engineering and machine vision.

  2. 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.

  3. Advanced Pattern Recognition.

    DTIC Science & Technology

    1983-05-01

    classification via statistical pattern recognition; image preprocessing, enhancement, and filtering; image warping , resampling, and point positioning; and...obj_region training files *•* Edit Programs »*» mode_filter ( mdf ) - mode filtering of a classified image (noise cleaning) edge_thin - thin... mdf 5 5 comments: experimental Method to segregate Water, Urban, Vegetation urban edges method_type: edge measurements: avg 3/ep_smooth 2

  4. Recognition by Prototypes

    DTIC Science & Technology

    1992-12-01

    as many other cues, such as color , texture, motion. views ii cf each model Mi, is composed of the k eigen- and context, and objects are categorized in...such as color and texture. [15] Grirnson W.E.L. and Lozano-P~rez T., 1984. Model-based recognition and localization from Acknowledgement sparse data...but not to see. A case study of visual agnosia . gie. Lawrence Erlbaum Associates, Pub., London. [2] Bajcsy R. and Solina F., 1987. Three dimensional

  5. 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.

  6. Taxa and names in Cynoglossum sensu lato (Boraginaceae, Cynoglosseae): an annotated, synonymic inventory, with links to the protologues and mention of original material

    PubMed Central

    Stier, Victoria

    2015-01-01

    , types and original specimens, especially when their digital images are available online, are mentioned with their locations and accession numbers. Comments are added whenever appropriate, especially to explain nomenclatural assessments that are not self-evident. PMID:25941451

  7. Pattern Recognition Control Design

    NASA Technical Reports Server (NTRS)

    Gambone, Elisabeth A.

    2018-01-01

    Spacecraft control algorithms must know the expected vehicle response to any command to the available control effectors, such as reaction thrusters or torque devices. Spacecraft control system design approaches have traditionally relied on the estimated vehicle mass properties to determine the desired force and moment, as well as knowledge of the effector performance to efficiently control the spacecraft. A pattern recognition approach was used to investigate the relationship between the control effector commands and spacecraft responses. Instead of supplying the approximated vehicle properties and the thruster performance characteristics, a database of information relating the thruster ring commands and the desired vehicle response was used for closed-loop control. A Monte Carlo simulation data set of the spacecraft dynamic response to effector commands was analyzed to establish the influence a command has on the behavior of the spacecraft. A tool developed at NASA Johnson Space Center to analyze flight dynamics Monte Carlo data sets through pattern recognition methods was used to perform this analysis. Once a comprehensive data set relating spacecraft responses with commands was established, it was used in place of traditional control methods and gains set. This pattern recognition approach was compared with traditional control algorithms to determine the potential benefits and uses.

  8. 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

  9. Pattern Recognition Control Design

    NASA Technical Reports Server (NTRS)

    Gambone, Elisabeth

    2016-01-01

    Spacecraft control algorithms must know the expected spacecraft response to any command to the available control effectors, such as reaction thrusters or torque devices. Spacecraft control system design approaches have traditionally relied on the estimated vehicle mass properties to determine the desired force and moment, as well as knowledge of the effector performance to efficiently control the spacecraft. A pattern recognition approach can be used to investigate the relationship between the control effector commands and the spacecraft responses. Instead of supplying the approximated vehicle properties and the effector performance characteristics, a database of information relating the effector commands and the desired vehicle response can be used for closed-loop control. A Monte Carlo simulation data set of the spacecraft dynamic response to effector commands can be analyzed to establish the influence a command has on the behavior of the spacecraft. A tool developed at NASA Johnson Space Center (Ref. 1) to analyze flight dynamics Monte Carlo data sets through pattern recognition methods can be used to perform this analysis. Once a comprehensive data set relating spacecraft responses with commands is established, it can be used in place of traditional control laws and gains set. This pattern recognition approach can be compared with traditional control algorithms to determine the potential benefits and uses.

  10. 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.

  11. Infrared target recognition

    NASA Astrophysics Data System (ADS)

    Singstock, Brian D.

    1991-12-01

    In this thesis, three approaches were used for Automatic Target Recognition (ATR). These approaches were shape, moment and Fourier generated features, Karhunen-Loeve Transform (KLT) generated features and Discrete Cosine Transform (DCT) generated features. The KLT approach was modelled after the face recognition research by Suarez, AFIT, and Turk and Pentland, MIT. A KLT is taken of a reduced covariance matrix, composed all three classes of targets, and the resulting eigenimages are used to reconstruct the original images. The reconstruction coefficients for each original image are found by taking the dot product of the original image with each eigenimage. These reconstruction coefficients were implemented as features into a three layer backprop with momentum network. Using the hold one-cut-out technique of testing data, the net could correctly differentiate the targets 100 percent of the time. Using standard features, the correct classification rate was 99.33 percent. The DCT was also taken of each image, and 16 low frequency Fourier components were kept as features. These recognition rates were compared to FFT results where each set contained the top five feature, as determined by a saliency test. The results proved that the DCT and the FFT were equivalent concerning classification of targets.

  12. Recognition memory for faces: when familiarity supports associative recognition judgments.

    PubMed

    Yonelinas, A P; Kroll, N E; Dobbins, I G; Soltani, M

    1999-12-01

    Recognition memory for single items can be dissociated from recognition memory for the associations between items. For example, recognition tests for single words produce curvilinear receiver operating characteristics (ROCs), but associative recognition tests for word pairs produce linear ROCs. These dissociations are consistent with dual-process theories of recognition and suggest that associative recognition relies on recollection but that item recognition relies on a combination of recollection and assessments of familiarity. In the present study, we examined associative recognition ROCs for facial stimuli by manipulating the central and external features, in order to determine whether linear ROCs would be observed for stimuli other than arbitrary word pairs. When the faces were presented upright, familiarity estimates were significantly above zero, and the associative ROCs were curvilinear, suggesting that familiarity contributed to associative judgments. However, presenting the faces upside down effectively eliminated the contribution of familiarity to associative recognition, and the ROCs were linear. The results suggest that familiarity can support associative recognition judgments, if the associated components are encoded as a coherent gestalt, as in upright faces.

  13. Common themes and differences in SAM recognition among SAM riboswitches

    PubMed Central

    Price, Ian R.; Grigg, Jason C.; Ke, Ailong

    2014-01-01

    The recent discovery of short cis-acting RNA elements termed riboswitches has caused a paradigm shift in our understanding of genetic regulatory mechanisms. The three distinct superfamilies of S-adenosyl-L-methionine (SAM) riboswitches are the most commonly found riboswitch classes in nature. These RNAs represent three independent evolutionary solutions to achieve specific SAM recognition. This review summarizes research on 1) modes of gene regulatory mechanisms, 2) common themes and differences in ligand recognition, and 3) ligand-induced conformational dynamics among SAM riboswitch families. The body of work on the SAM riboswitch families constitutes a useful primer to the topic of gene regulatory RNAs as a whole. PMID:24863160

  14. Graph optimized Laplacian eigenmaps for face recognition

    NASA Astrophysics Data System (ADS)

    Dornaika, F.; Assoum, A.; Ruichek, Y.

    2015-01-01

    In recent years, a variety of nonlinear dimensionality reduction techniques (NLDR) have been proposed in the literature. They aim to address the limitations of traditional techniques such as PCA and classical scaling. Most of these techniques assume that the data of interest lie on an embedded non-linear manifold within the higher-dimensional space. They provide a mapping from the high-dimensional space to the low-dimensional embedding and may be viewed, in the context of machine learning, as a preliminary feature extraction step, after which pattern recognition algorithms are applied. Laplacian Eigenmaps (LE) is a nonlinear graph-based dimensionality reduction method. It has been successfully applied in many practical problems such as face recognition. However the construction of LE graph suffers, similarly to other graph-based DR techniques from the following issues: (1) the neighborhood graph is artificially defined in advance, and thus does not necessary benefit the desired DR task; (2) the graph is built using the nearest neighbor criterion which tends to work poorly due to the high-dimensionality of original space; and (3) its computation depends on two parameters whose values are generally uneasy to assign, the neighborhood size and the heat kernel parameter. To address the above-mentioned problems, for the particular case of the LPP method (a linear version of LE), L. Zhang et al.1 have developed a novel DR algorithm whose idea is to integrate graph construction with specific DR process into a unified framework. This algorithm results in an optimized graph rather than a predefined one.

  15. Recognition Imaging of Acetylated Chromatin Using a DNA Aptamer

    PubMed Central

    Lin, Liyun; Fu, Qiang; Williams, Berea A.R.; Azzaz, Abdelhamid M.; Shogren-Knaak, Michael A.; Chaput, John C.; Lindsay, Stuart

    2009-01-01

    Histone acetylation plays an important role in the regulation of gene expression. A DNA aptamer generated by in vitro selection to be highly specific for histone H4 protein acetylated at lysine 16 was used as a recognition element for atomic force microscopy-based recognition imaging of synthetic nucleosomal arrays with precisely controlled acetylation. The aptamer proved to be reasonably specific at recognizing acetylated histones, with recognition efficiencies of 60% on-target and 12% off-target. Though this selectivity is much poorer than the >2000:1 equilibrium specificity of the aptamer, it is a large improvement on the performance of a ChIP-quality antibody, which is not selective at all in this application, and it should permit high-fidelity recognition with repeated imaging. The ability to image the precise location of posttranslational modifications may permit nanometer-scale investigation of their effect on chromatin structure. PMID:19751687

  16. Smart pattern recognition

    NASA Astrophysics Data System (ADS)

    Alfalou, A.; Brosseau, C.; Alam, M. S.

    2013-03-01

    The purpose of this paper is to test correlation methods for pattern recognition applications. A broad overview of the main correlation architectures is first given. Many correlation data are compared with those obtained from standard pattern recognition methods. We used our simulations to predict improved decisional performance from correlation methods. More specifically, we are focused on the POF filter and composite filter family. We present an optimized composite correlation filter, called asymmetric segmented phase-only filter (ASPOF) for mobile target recognition applications. The main objective is to find a compromise between the number of references to be merged in the correlation filter and the time needed for making a decision. We suggest an all-numerical implementation of a VanderLugt (VLC) type composite filter. The aim of this all-numerical implementation is to take advantage of the benefits of the correlation methods and make the correlator easily reconfigurable for various scenarios. The use of numerical implementation of the optical Fourier transform improves the decisional performance of the correlator. Further, it renders the correlator less sensitive to the saturation phenomenon caused by the increased number of references used for fabricating the composite filter. Different tests are presented making use of the peak-to-correlation energy criterion and ROC curves. These tests confirm the validity ofour technique. Elderly fall detection and underwater mine detection are two applications which are considered for illustrating the benefits of our approach. The present work is motivated by the need for detailed discussions of the choice of the correlation architecture for these specific applications, pre-processing in the input plane and post processing in the output plane techniques for such analysis.

  17. Disorders of visual recognition.

    PubMed

    De Renzi, E

    2000-01-01

    Agnosias are disorders of recognition, specific to one sensory channel, that affect either the perceptual analysis of the stimulus or the recognition of its meaning. In the visual modality, objects, faces, and colors can be separately disrupted. Apperceptive object agnosia refers to failure to achieve a structured description of the shape of the object. Associative agnosia refers to inability to attribute a meaning to a correctly perceived stimulus. It must be differentiated from optic aphasia, in which the object is recognized but cannot be named in the visual modality. Associative agnosia and optic aphasia are associated with left occipitotemporal damage, and they differ more quantitatively than qualitatively. The inability to recognize familiar faces (prosopagnosia) can appear in isolation and be, in some cases, associated with a lesion confined to the occipitotemporal region of the right hemisphere. These findings are supportive of the idea that faces have a separate representation in the brain. Disorders of color cognition can affect color categorization, color-name association, and color-object association. They are linked to left hemisphere damage. The ability to recognize objects presented in the visual modality is a hierarchical process in which several cortical areas, corresponding to about 30% of the cortical mantle, participate. Their selective lesion results in a gamut of disorders whose identification provides the experienced neurologist with clues to the locus of damage and contributes to the understanding of the cognitive architecture underpinning recognition. They can result either in the inability to detect any change occurring in the visual field or in the impairment of further stages of the recognition process, from the analysis of the perceptual properties of the stimulus (form, color, motion, depth, etc.) to the achievement of its structural description and, eventually, the attribution of a meaning. In this paper, I focus on the diagnostic and

  18. 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.

  19. [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.

  20. 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.

  1. Genetic specificity of face recognition

    PubMed Central

    Shakeshaft, Nicholas G.; Plomin, Robert

    2015-01-01

    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. PMID:26417086

  2. 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

  3. Retina vascular network recognition

    NASA Astrophysics Data System (ADS)

    Tascini, Guido; Passerini, Giorgio; Puliti, Paolo; Zingaretti, Primo

    1993-09-01

    The analysis of morphological and structural modifications of the retina vascular network is an interesting investigation method in the study of diabetes and hypertension. Normally this analysis is carried out by qualitative evaluations, according to standardized criteria, though medical research attaches great importance to quantitative analysis of vessel color, shape and dimensions. The paper describes a system which automatically segments and recognizes the ocular fundus circulation and micro circulation network, and extracts a set of features related to morphometric aspects of vessels. For this class of images the classical segmentation methods seem weak. We propose a computer vision system in which segmentation and recognition phases are strictly connected. The system is hierarchically organized in four modules. Firstly the Image Enhancement Module (IEM) operates a set of custom image enhancements to remove blur and to prepare data for subsequent segmentation and recognition processes. Secondly the Papilla Border Analysis Module (PBAM) automatically recognizes number, position and local diameter of blood vessels departing from optical papilla. Then the Vessel Tracking Module (VTM) analyses vessels comparing the results of body and edge tracking and detects branches and crossings. Finally the Feature Extraction Module evaluates PBAM and VTM output data and extracts some numerical indexes. Used algorithms appear to be robust and have been successfully tested on various ocular fundus images.

  4. 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.

  5. 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.

  6. 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

  7. Multisensory encoding improves auditory recognition.

    PubMed

    Moran, Zachary D; Bachman, Peter; Pham, Phillip; Cho, Seong Hah; Cannon, Tyrone D; Shams, Ladan

    2013-01-01

    Recent studies have challenged the long-held belief that recognition is unfailingly degraded by contextual differences between study and test items. In these studies, recognition of pictures presented in silence was better when during study or initial exposure the images were accompanied by a semantically congruent sound rather than silence. In the present study, we sought to examine the generalization of this phenomenon to auditory recognition and found a significant improvement in the recognition of auditory items when coupled with a congruent picture. We discuss these findings within the framework of the redintegration hypothesis of memory retrieval as well as Bayesian inference and learning.

  8. Sudden event recognition: a survey.

    PubMed

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

    2013-08-05

    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.

  9. 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…

  10. Teaching and the Dialectic of Recognition

    ERIC Educational Resources Information Center

    Huttunen, Rauno; Heikkinen, Hannu L. T.

    2004-01-01

    In this article, the processes of recognition within education are discussed. Frequently, recognition is reduced to polite behaviour or etiquette. Another narrow view of recognition is, behaviouristically speaking, to regard it as mere feedback. We claim that authentic recognition is a different matter. Receiving recognition, as Charles Taylor has…

  11. 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…

  12. A modular framework for biomedical concept recognition.

    PubMed

    Campos, David; Matos, Sérgio; Oliveira, José Luís

    2013-09-24

    Concept recognition is an essential task in biomedical information extraction, presenting several complex and unsolved challenges. The development of such solutions is typically performed in an ad-hoc manner or using general information extraction frameworks, which are not optimized for the biomedical domain and normally require the integration of complex external libraries and/or the development of custom tools. This article presents Neji, an open source framework optimized for biomedical concept recognition built around four key characteristics: modularity, scalability, speed, and usability. It integrates modules for biomedical natural language processing, such as sentence splitting, tokenization, lemmatization, part-of-speech tagging, chunking and dependency parsing. Concept recognition is provided through dictionary matching and machine learning with normalization methods. Neji also integrates an innovative concept tree implementation, supporting overlapped concept names and respective disambiguation techniques. The most popular input and output formats, namely Pubmed XML, IeXML, CoNLL and A1, are also supported. On top of the built-in functionalities, developers and researchers can implement new processing modules or pipelines, or use the provided command-line interface tool to build their own solutions, applying the most appropriate techniques to identify heterogeneous biomedical concepts. Neji was evaluated against three gold standard corpora with heterogeneous biomedical concepts (CRAFT, AnEM and NCBI disease corpus), achieving high performance results on named entity recognition (F1-measure for overlap matching: species 95%, cell 92%, cellular components 83%, gene and proteins 76%, chemicals 65%, biological processes and molecular functions 63%, disorders 85%, and anatomical entities 82%) and on entity normalization (F1-measure for overlap name matching and correct identifier included in the returned list of identifiers: species 88%, cell 71%, cellular

  13. A modular framework for biomedical concept recognition

    PubMed Central

    2013-01-01

    Background Concept recognition is an essential task in biomedical information extraction, presenting several complex and unsolved challenges. The development of such solutions is typically performed in an ad-hoc manner or using general information extraction frameworks, which are not optimized for the biomedical domain and normally require the integration of complex external libraries and/or the development of custom tools. Results This article presents Neji, an open source framework optimized for biomedical concept recognition built around four key characteristics: modularity, scalability, speed, and usability. It integrates modules for biomedical natural language processing, such as sentence splitting, tokenization, lemmatization, part-of-speech tagging, chunking and dependency parsing. Concept recognition is provided through dictionary matching and machine learning with normalization methods. Neji also integrates an innovative concept tree implementation, supporting overlapped concept names and respective disambiguation techniques. The most popular input and output formats, namely Pubmed XML, IeXML, CoNLL and A1, are also supported. On top of the built-in functionalities, developers and researchers can implement new processing modules or pipelines, or use the provided command-line interface tool to build their own solutions, applying the most appropriate techniques to identify heterogeneous biomedical concepts. Neji was evaluated against three gold standard corpora with heterogeneous biomedical concepts (CRAFT, AnEM and NCBI disease corpus), achieving high performance results on named entity recognition (F1-measure for overlap matching: species 95%, cell 92%, cellular components 83%, gene and proteins 76%, chemicals 65%, biological processes and molecular functions 63%, disorders 85%, and anatomical entities 82%) and on entity normalization (F1-measure for overlap name matching and correct identifier included in the returned list of identifiers: species 88

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. Relative contributions of spectral and temporal cues for phoneme recognition

    NASA Astrophysics Data System (ADS)

    Xu, Li; Thompson, Catherine S.; Pfingst, Bryan E.

    2005-05-01

    Cochlear implants provide users with limited spectral and temporal information. In this study, the amount of spectral and temporal information was systematically varied through simulations of cochlear implant processors using a noise-excited vocoder. Spectral information was controlled by varying the number of channels between 1 and 16, and temporal information was controlled by varying the lowpass cutoff frequencies of the envelope extractors from 1 to 512 Hz. Consonants and vowels processed using those conditions were presented to seven normal-hearing native-English-speaking listeners for identification. The results demonstrated that both spectral and temporal cues were important for consonant and vowel recognition with the spectral cues having a greater effect than the temporal cues for the ranges of numbers of channels and lowpass cutoff frequencies tested. The lowpass cutoff for asymptotic performance in consonant and vowel recognition was 16 and 4 Hz, respectively. The number of channels at which performance plateaued for consonants and vowels was 8 and 12, respectively. Within the above-mentioned ranges of lowpass cutoff frequency and number of channels, the temporal and spectral cues showed a tradeoff for phoneme recognition. Information transfer analyses showed different relative contributions of spectral and temporal cues in the perception of various phonetic/acoustic features. .

  20. 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.

  1. Methods of Teaching Speech Recognition

    ERIC Educational Resources Information Center

    Rader, Martha H.; Bailey, Glenn A.

    2010-01-01

    Objective: This article introduces the history and development of speech recognition, addresses its role in the business curriculum, outlines related national and state standards, describes instructional strategies, and discusses the assessment of student achievement in speech recognition classes. Methods: Research methods included a synthesis of…

  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. 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…

  4. Children's Recognition of Cartoon Voices.

    ERIC Educational Resources Information Center

    Spence, Melanie J.; Rollins, Pamela R.; Jerger, Susan

    2002-01-01

    A study examined developmental changes in talker recognition skills by assessing 72 children's (ages 3-5) recognition of 20 cartoon characters' voices. Four- and 5-year-old children recognized more of the voices than did 3-year-olds. All children were more accurate at recognizing more familiar characters than less familiar characters. (Contains…

  5. 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.

  6. Quantum-Limited Image Recognition

    DTIC Science & Technology

    1989-12-01

    J. S. Bomba ,’Alpha-numeric character recognition using local operations,’ Fall Joint Comput. Conf., 218-224 (1959). 53. D. Barnea and H. Silverman...for Chapter 6 1. J. S. Bomba ,’Alpha-numeric character recognition using local operations,’ Fall Joint Comput. Conf., 218-224 (1959). 2. D. Bamea and H

  7. 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.

  8. 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.

  9. Speech Recognition: How Do We Teach It?

    ERIC Educational Resources Information Center

    Barksdale, Karl

    2002-01-01

    States that growing use of speech recognition software has made voice writing an essential computer skill. Describes how to present the topic, develop basic speech recognition skills, and teach speech recognition outlining, writing, proofreading, and editing. (Contains 14 references.) (SK)

  10. 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

  11. Pattern recognition in spectra

    NASA Astrophysics Data System (ADS)

    Gebran, M.; Paletou, F.

    2017-06-01

    We present a new automated procedure that simultaneously derives the effective temperature Teff, surface gravity log g, metallicity [Fe/H], and equatorial projected rotational velocity ve sin i for stars. The procedure is inspired by the well-known PCA-based inversion of spectropolarimetric full-Stokes solar data, which was used both for Zeeman and Hanle effects. The efficiency and accuracy of this procedure have been proven for FGK, A, and late type dwarf stars of K and M spectral types. Learning databases are generated from the Elodie stellar spectra library using observed spectra for which fundamental parameters were already evaluated or with synthetic data. The synthetic spectra are calculated using ATLAS9 model atmospheres. This technique helped us to detect many peculiar stars such as Am, Ap, HgMn, SiEuCr and binaries. This fast and efficient technique could be used every time a pattern recognition is needed. One important application is the understanding of the physical properties of planetary surfaces by comparing aboard instrument data to synthetic ones.

  12. 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.

  13. 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

  14. 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.

  15. Expression of intron-containing C. elegans heat shock genes in mouse cells demonstrates divergence of 3' splice site recognition sequences between nematodes and vertebrates, and an inhibitory effect of heat shock on the mammalian splicing apparatus.

    PubMed Central

    Kay, R J; Russnak, R H; Jones, D; Mathias, C; Candido, E P

    1987-01-01

    Splicing of a pair of intron-containing heat shock genes from Caenorhabditis elegans has been studied in transfected mouse cells. The hsp16-1 and hsp16-48 genes of C. elegans encode 16,000 Da heat shock polypeptides. Each gene contains a short intron of 52 (hsp16-1) or 55 (hsp16-48) base pairs. When these genes were introduced into mouse cells, they were efficiently induced following heat shock, but splicing of the introns was abnormal. In mouse cells, cleavage of the hsp16 transcripts occurred at the correct 5' splice sites, but the 3' splice sites were located at AG dinucleotides downstream of the correct sites. This aberrant splicing was not solely due to the small size of the C. elegans introns, since a hsp16-1 gene containing an intron enlarged by tandem duplication showed exactly the same splicing pattern. The mouse cells thus seem to be unable to recognize the natural 3' splice sites of the C. elegans transcripts. The efficiency of splicing was greatly reduced under heat shock conditions, and unspliced transcripts accumulated in the nucleus. During a subsequent recovery period at 37 degrees C, these transcripts were spliced and transported to the cytoplasm. Images PMID:3588308

  16. 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.

  17. 3D object recognition in TOF data sets

    NASA Astrophysics Data System (ADS)

    Hess, Holger; Albrecht, Martin; Grothof, Markus; Hussmann, Stephan; Oikonomidis, Nikolaos; Schwarte, Rudolf

    2003-08-01

    In the last years 3D-Vision systems based on the Time-Of-Flight (TOF) principle have gained more importance than Stereo Vision (SV). TOF offers a direct depth-data acquisition, whereas SV involves a great amount of computational power for a comparable 3D data set. Due to the enormous progress in TOF-techniques, nowadays 3D cameras can be manufactured and be used for many practical applications. Hence there is a great demand for new accurate algorithms for 3D object recognition and classification. This paper presents a new strategy and algorithm designed for a fast and solid object classification. A challenging example - accurate classification of a (half-) sphere - demonstrates the performance of the developed algorithm. Finally, the transition from a general model of the system to specific applications such as Intelligent Airbag Control and Robot Assistance in Surgery are introduced. The paper concludes with the current research results in the above mentioned fields.

  18. The Molecular Recognition Paradigm of Environmental Chemicals with Biomacromolecules.

    PubMed

    Zhang, Wenjing; Pan, Liumeng; Wang, Haifei; Lv, Xuan; Ding, Keke

    2017-01-01

    The interactions of ligands with biomacromolecules play a fundamental role in almost all bioprocesses occuring in living organisms. The binding of ligands can cause the conformational changes of biomacromolecules, possibly affecting their physiological functions. The interactions of ligands with biomacromolecules are thus becoming a research hotspot. However, till now, there still lacks a systematic compilation of review with the focus on the interactions between environmental chemicals and biomacromolecules. In this review, we focus on the molecular recognition paradigm of environmental chemicals with biomacromolecules and chemical basis for driving the complex formation. The state-of-the-art review on in vitro and in silico studies on interaction of organic chemicals with transport proteins, nuclear receptors and CYP450 enzymes was provided, and the enantioselective interactions of chiral environmental chemicals was also mentioned.

  19. Stimulus Recognition and Associative Coding

    ERIC Educational Resources Information Center

    Runquist, Willard N.; Evans, Annabel

    1972-01-01

    Purpose of this experiment was to investigate the relationship between stimulus recognition and various learning conditions which were designed to affect both stimulus encoding and associative learning in a paired-associate task. (Authors)

  20. 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.

  1. Molecular recognition of bilayer vesicles.

    PubMed

    Voskuhl, Jens; Ravoo, Bart Jan

    2009-02-01

    Vesicles have been a versatile topic of research in chemistry ever since the discovery that, besides phospholipids, synthetic amphiphiles can also form molecular bilayers enclosing a small aqueous compartment. Non-covalent interactions of receptors and ligands or hosts and guests at vesicle surfaces resemble recognition processes at biological membranes, including cell recognition, adhesion and fusion. Molecular recognition at membranes is often mediated by a multivalent instead of a monovalent interaction. This tutorial review describes the basics as well as the latest developments in biomimetic supramolecular chemistry of bilayer vesicles. We describe how molecular recognition can mediate the interaction between vesicles, and how the biomimetic supramolecular chemistry of vesicles furthers our understanding of biological membranes.

  2. 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.

  3. 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.

  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. 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

  6. [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.

  7. [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

  8. Chemical named entity recognition in patents by domain knowledge and unsupervised feature learning.

    PubMed

    Zhang, Yaoyun; Xu, Jun; Chen, Hui; Wang, Jingqi; Wu, Yonghui; Prakasam, Manu; Xu, Hua

    2016-01-01

    Medicinal chemistry patents contain rich information about chemical compounds. Although much effort has been devoted to extracting chemical entities from scientific literature, limited numbers of patent mining systems are publically available, probably due to the lack of large manually annotated corpora. To accelerate the development of information extraction systems for medicinal chemistry patents, the 2015 BioCreative V challenge organized a track on Chemical and Drug Named Entity Recognition from patent text (CHEMDNER patents). This track included three individual subtasks: (i) Chemical Entity Mention Recognition in Patents (CEMP), (ii) Chemical Passage Detection (CPD) and (iii) Gene and Protein Related Object task (GPRO). We participated in the two subtasks of CEMP and CPD using machine learning-based systems. Our machine learning-based systems employed the algorithms of conditional random fields (CRF) and structured support vector machines (SSVMs), respectively. To improve the performance of the NER systems, two strategies were proposed for feature engineering: (i) domain knowledge features of dictionaries, chemical structural patterns and semantic type information present in the context of the candidate chemical and (ii) unsupervised feature learning algorithms to generate word representation features by Brown clustering and a novel binarized Word embedding to enhance the generalizability of the system. Further, the system output for the CPD task was yielded based on the patent titles and abstracts with chemicals recognized in the CEMP task.The effects of the proposed feature strategies on both the machine learning-based systems were investigated. Our best system achieved the second best performance among 21 participating teams in CEMP with a precision of 87.18%, a recall of 90.78% and aF-measure of 88.94% and was the top performing system among nine participating teams in CPD with a sensitivity of 98.60%, a specificity of 87.21%, an accuracy of 94.75%, a

  9. Chemical named entity recognition in patents by domain knowledge and unsupervised feature learning

    PubMed Central

    Zhang, Yaoyun; Xu, Jun; Chen, Hui; Wang, Jingqi; Wu, Yonghui; Prakasam, Manu; Xu, Hua

    2016-01-01

    Medicinal chemistry patents contain rich information about chemical compounds. Although much effort has been devoted to extracting chemical entities from scientific literature, limited numbers of patent mining systems are publically available, probably due to the lack of large manually annotated corpora. To accelerate the development of information extraction systems for medicinal chemistry patents, the 2015 BioCreative V challenge organized a track on Chemical and Drug Named Entity Recognition from patent text (CHEMDNER patents). This track included three individual subtasks: (i) Chemical Entity Mention Recognition in Patents (CEMP), (ii) Chemical Passage Detection (CPD) and (iii) Gene and Protein Related Object task (GPRO). We participated in the two subtasks of CEMP and CPD using machine learning-based systems. Our machine learning-based systems employed the algorithms of conditional random fields (CRF) and structured support vector machines (SSVMs), respectively. To improve the performance of the NER systems, two strategies were proposed for feature engineering: (i) domain knowledge features of dictionaries, chemical structural patterns and semantic type information present in the context of the candidate chemical and (ii) unsupervised feature learning algorithms to generate word representation features by Brown clustering and a novel binarized Word embedding to enhance the generalizability of the system. Further, the system output for the CPD task was yielded based on the patent titles and abstracts with chemicals recognized in the CEMP task. The effects of the proposed feature strategies on both the machine learning-based systems were investigated. Our best system achieved the second best performance among 21 participating teams in CEMP with a precision of 87.18%, a recall of 90.78% and a F-measure of 88.94% and was the top performing system among nine participating teams in CPD with a sensitivity of 98.60%, a specificity of 87.21%, an accuracy of 94.75%, a

  10. Visual recognition memory across contexts.

    PubMed

    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 familiarization and test occurred in different rooms. In contrast, 12- and 18-month-old infants exhibited recognition irrespective of testing room. Thus, flexibility across a change of room was observed at a younger age than flexibility across a change of background that has previously been seen with the VPC procedure (Robinson & Pascalis, 2004). To determine if limitations in representational flexibility across a change of background could be overcome by experiences during encoding, in Experiment 2, 6-, 9-, 12- and 18-month-old infants were familiarized with a picture on multiple backgrounds. At all ages, infants showed recognition across a change in background at test. These findings indicate that dissociating an item from its context during encoding may be an important factor in understanding the representational flexibility of visual recognition memory in infancy. Developmental changes in representational flexibility are likely driven by changes in the functional maturity of the hippocampal formation, and experience. © 2010 Blackwell Publishing Ltd.

  11. 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.

  12. Sampling design for face recognition

    NASA Astrophysics Data System (ADS)

    Yan, Yanjun; Osadciw, Lisa A.

    2006-04-01

    A face recognition system consists of two integrated parts: One is the face recognition algorithm, the other is the selected classifier and derived features by the algorithm from a data set. The face recognition algorithm definitely plays a central role, but this paper does not aim at evaluating the algorithm, but deriving the best features for this algorithm from a specific database through sampling design of the training set, which directs how the sample should be collected and dictates the sample space. Sampling design can help exert the full potential of the face recognition algorithm without overhaul. Conventional statistical analysis usually assume some distribution to draw the inference, but the design-based inference does not assume any distribution of the data and it does not assume the independency between the sample observations. The simulations illustrates that the systematic sampling scheme performs better than the simple random sampling scheme, and the systematic sampling is comparable to using all available training images in recognition performance. Meanwhile the sampling schemes can save the system resources and alleviate the overfitting problem. However, the post stratification by sex is not shown to be significant in improving the recognition performance.

  13. Voice Congruency Facilitates Word Recognition

    PubMed Central

    Campeanu, Sandra; Craik, Fergus I. M.; Alain, Claude

    2013-01-01

    Behavioral studies of spoken word memory have shown that context congruency facilitates both word and source recognition, though the level at which context exerts its influence remains equivocal. We measured event-related potentials (ERPs) while participants performed both types of recognition task with words spoken in four voices. Two voice parameters (i.e., gender and accent) varied between speakers, with the possibility that none, one or two of these parameters was congruent between study and test. Results indicated that reinstating the study voice at test facilitated both word and source recognition, compared to similar or no context congruency at test. Behavioral effects were paralleled by two ERP modulations. First, in the word recognition test, the left parietal old/new effect showed a positive deflection reflective of context congruency between study and test words. Namely, the same speaker condition provided the most positive deflection of all correctly identified old words. In the source recognition test, a right frontal positivity was found for the same speaker condition compared to the different speaker conditions, regardless of response success. Taken together, the results of this study suggest that the benefit of context congruency is reflected behaviorally and in ERP modulations traditionally associated with recognition memory. PMID:23527021

  14. Voice congruency facilitates word recognition.

    PubMed

    Campeanu, Sandra; Craik, Fergus I M; Alain, Claude

    2013-01-01

    Behavioral studies of spoken word memory have shown that context congruency facilitates both word and source recognition, though the level at which context exerts its influence remains equivocal. We measured event-related potentials (ERPs) while participants performed both types of recognition task with words spoken in four voices. Two voice parameters (i.e., gender and accent) varied between speakers, with the possibility that none, one or two of these parameters was congruent between study and test. Results indicated that reinstating the study voice at test facilitated both word and source recognition, compared to similar or no context congruency at test. Behavioral effects were paralleled by two ERP modulations. First, in the word recognition test, the left parietal old/new effect showed a positive deflection reflective of context congruency between study and test words. Namely, the same speaker condition provided the most positive deflection of all correctly identified old words. In the source recognition test, a right frontal positivity was found for the same speaker condition compared to the different speaker conditions, regardless of response success. Taken together, the results of this study suggest that the benefit of context congruency is reflected behaviorally and in ERP modulations traditionally associated with recognition memory.

  15. The role of dynamic conformational ensembles in biomolecular recognition.

    PubMed

    Boehr, David D; Nussinov, Ruth; Wright, Peter E

    2009-11-01

    Molecular recognition is central to all biological processes. For the past 50 years, Koshland's 'induced fit' hypothesis has been the textbook explanation for molecular recognition events. However, recent experimental evidence supports an alternative mechanism. 'Conformational selection' postulates that all protein conformations pre-exist, and the ligand selects the most favored conformation. Following binding the ensemble undergoes a population shift, redistributing the conformational states. Both conformational selection and induced fit appear to play roles. Following binding by a primary conformational selection event, optimization of side chain and backbone interactions is likely to proceed by an induced fit mechanism. Conformational selection has been observed for protein-ligand, protein-protein, protein-DNA, protein-RNA and RNA-ligand interactions. These data support a new molecular recognition paradigm for processes as diverse as signaling, catalysis, gene regulation and protein aggregation in disease, which has the potential to significantly impact our views and strategies in drug design, biomolecular engineering and molecular evolution.

  16. Selective Recognition of H3.1K36 Dimethylation/H4K16 Acetylation Facilitates the Regulation of All-trans-retinoic Acid (ATRA)-responsive Genes by Putative Chromatin Reader ZMYND8*

    PubMed Central

    Adhikary, Santanu; Sanyal, Sulagna; Basu, Moitri; Sengupta, Isha; Sen, Sabyasachi; Srivastava, Dushyant Kumar; Roy, Siddhartha; Das, Chandrima

    2016-01-01

    ZMYND8 (zinc finger MYND (Myeloid, Nervy and DEAF-1)-type containing 8), a newly identified component of the transcriptional coregulator network, was found to interact with the Nucleosome Remodeling and Deacetylase (NuRD) complex. Previous reports have shown that ZMYND8 is instrumental in recruiting the NuRD complex to damaged chromatin for repressing transcription and promoting double strand break repair by homologous recombination. However, the mode of transcription regulation by ZMYND8 has remained elusive. Here, we report that through its specific key residues present in its conserved chromatin-binding modules, ZMYND8 interacts with the selective epigenetic marks H3.1K36Me2/H4K16Ac. Furthermore, ZMYND8 shows a clear preference for canonical histone H3.1 over variant H3.3. Interestingly, ZMYND8 was found to be recruited to several developmental genes, including the all-trans-retinoic acid (ATRA)-responsive ones, through its modified histone-binding ability. Being itself inducible by ATRA, this zinc finger transcription factor is involved in modulating other ATRA-inducible genes. We found that ZMYND8 interacts with transcription initiation-competent RNA polymerase II phosphorylated at Ser-5 in a DNA template-dependent manner and can alter the global gene transcription. Overall, our study identifies that ZMYND8 has CHD4-independent functions in regulating gene expression through its modified histone-binding ability. PMID:26655721

  17. A genetic screen for novel components of the Ras/Mitogen-activated protein kinase signaling pathway that interact with the yan gene of Drosophila identifies split ends, a new RNA recognition motif-containing protein.

    PubMed Central

    Rebay, I; Chen, F; Hsiao, F; Kolodziej, P A; Kuang, B H; Laverty, T; Suh, C; Voas, M; Williams, A; Rubin, G M

    2000-01-01

    The receptor tyrosine kinase (RTK) signaling pathway is used reiteratively during the development of all multicellular organisms. While the core RTK/Ras/MAPK signaling cassette has been studied extensively, little is known about the nature of the downstream targets of the pathway or how these effectors regulate the specificity of cellular responses. Drosophila yan is one of a few downstream components identified to date, functioning as an antagonist of the RTK/Ras/MAPK pathway. Previously, we have shown that ectopic expression of a constitutively active protein (yan(ACT)) inhibits the differentiation of multiple cell types. In an effort to identify new genes functioning downstream in the Ras/MAPK/yan pathway, we have performed a genetic screen to isolate dominant modifiers of the rough eye phenotype associated with eye-specific expression of yan(ACT). Approximately 190,000 mutagenized flies were screened, and 260 enhancers and 90 suppressors were obtained. Among the previously known genes we recovered are four RTK pathway components, rolled (MAPK), son-of-sevenless, Star, and pointed, and two genes, eyes absent and string, that have not been implicated previously in RTK signaling events. We also isolated mutations in five previously uncharacterized genes, one of which, split ends, we have characterized molecularly and have shown to encode a member of the RRM family of RNA-binding proteins. PMID:10655223

  18. 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…

  19. The earliest mention of a black bag

    PubMed Central

    Tsoucalas, Gregory; Kousoulis, Antonis A.; Tsoucalas, Ioannis; Androutsos, George

    2011-01-01

    A black bag, needed especially for home visits, has been used since the time of Hippocrates who, in his treatise “On good manners”, gave the first detailed description of a medical bag with guidelines for the required equipment and structure. Ancient Egyptian and Palestinian references also date back at least two millenniums. PMID:22126217

  20. Beyond econophysics (not to mention mainstream economics)

    NASA Astrophysics Data System (ADS)

    Gallegati, Mauro

    2016-12-01

    Econophysics has produced innovative and empirically relevant results in at least four areas of research: financial markets, growth and distribution of firms and countries, the distribution of income and wealth, and contagion, robustness and resilience of networks. All these results are inexplicable by the actual mainstream economic model. Yet econophysics requires not only a new economy, but also a "new" physics, which is based on non-ergodicity, on social dynamics whose elementary constituents are heterogeneous interacting social agents linked by networks.

  1. 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.

  2. ClusType: Effective Entity Recognition and Typing by Relation Phrase-Based Clustering

    PubMed Central

    Ren, Xiang; El-Kishky, Ahmed; Wang, Chi; Tao, Fangbo; Voss, Clare R.; Ji, Heng; Han, Jiawei

    2015-01-01

    Entity recognition is an important but challenging research problem. In reality, many text collections are from specific, dynamic, or emerging domains, which poses significant new challenges for entity recognition with increase in name ambiguity and context sparsity, requiring entity detection without domain restriction. In this paper, we investigate entity recognition (ER) with distant-supervision and propose a novel relation phrase-based ER framework, called ClusType, that runs data-driven phrase mining to generate entity mention candidates and relation phrases, and enforces the principle that relation phrases should be softly clustered when propagating type information between their argument entities. Then we predict the type of each entity mention based on the type signatures of its co-occurring relation phrases and the type indicators of its surface name, as computed over the corpus. Specifically, we formulate a joint optimization problem for two tasks, type propagation with relation phrases and multi-view relation phrase clustering. Our experiments on multiple genres—news, Yelp reviews and tweets—demonstrate the effectiveness and robustness of ClusType, with an average of 37% improvement in F1 score over the best compared method. PMID:26705503

  3. ClusType: Effective Entity Recognition and Typing by Relation Phrase-Based Clustering.

    PubMed

    Ren, Xiang; El-Kishky, Ahmed; Wang, Chi; Tao, Fangbo; Voss, Clare R; Ji, Heng; Han, Jiawei

    2015-08-01

    Entity recognition is an important but challenging research problem. In reality, many text collections are from specific, dynamic, or emerging domains, which poses significant new challenges for entity recognition with increase in name ambiguity and context sparsity, requiring entity detection without domain restriction. In this paper, we investigate entity recognition (ER) with distant-supervision and propose a novel relation phrase-based ER framework, called ClusType, that runs data-driven phrase mining to generate entity mention candidates and relation phrases, and enforces the principle that relation phrases should be softly clustered when propagating type information between their argument entities. Then we predict the type of each entity mention based on the type signatures of its co-occurring relation phrases and the type indicators of its surface name, as computed over the corpus. Specifically, we formulate a joint optimization problem for two tasks, type propagation with relation phrases and multi-view relation phrase clustering. Our experiments on multiple genres-news, Yelp reviews and tweets-demonstrate the effectiveness and robustness of ClusType, with an average of 37% improvement in F1 score over the best compared method.

  4. Disease named entity recognition by combining conditional random fields and bidirectional recurrent neural networks.

    PubMed

    Wei, Qikang; Chen, Tao; Xu, Ruifeng; He, Yulan; Gui, Lin

    2016-01-01

    The recognition of disease and chemical named entities in scientific articles is a very important subtask in information extraction in the biomedical domain. Due to the diversity and complexity of disease names, the recognition of named entities of diseases is rather tougher than those of chemical names. Although there are some remarkable chemical named entity recognition systems available online such as ChemSpot and tmChem, the publicly available recognition systems of disease named entities are rare. This article presents a system for disease named entity recognition (DNER) and normalization. First, two separate DNER models are developed. One is based on conditional random fields model with a rule-based post-processing module. The other one is based on the bidirectional recurrent neural networks. Then the named entities recognized by each of the DNER model are fed into a support vector machine classifier for combining results. Finally, each recognized disease named entity is normalized to a medical subject heading disease name by using a vector space model based method. Experimental results show that using 1000 PubMed abstracts for training, our proposed system achieves an F1-measure of 0.8428 at the mention level and 0.7804 at the concept level, respectively, on the testing data of the chemical-disease relation task in BioCreative V.Database URL: http://219.223.252.210:8080/SS/cdr.html. © The Author(s) 2016. Published by Oxford University Press.

  5. Recognition of composition and of microphysical characteristics of aerosol clouds in multifrequency sounding

    NASA Astrophysics Data System (ADS)

    Bravy, Boris G.; Vasiliev, German K.; Agroskin, Vladimir Y.

    2002-02-01

    The recognition of composition and of microphysical characteristics of aerosol impurities is one of the most urgent tasks in monitoring of atmosphere. Some approaches to its solution are considered in the work. At first stage we were limited to five substances: fine-dispersion water and dust as background aerosol components of atmosphere; coarse- dispersion tributilamin, turbine oil and petroleum as possible impurities. Tributilamin was chosen as spectral analog of V gases. The modeling of input spectra and the recognition were carried out on 12 discrete lines in 2.9 - 4 micrometers spectral rage. As is well known, in this range the considered impurities have the pronounced spectral dependences of aerosol backscattering, the so-called spectral resonances. Spectra of aerosol backscattering for these substances were calculated with Mie theory. We applied evolutionary algorithm (genetic algorithm) and also more traditional optimization methods, namely gradient descent method, for recognition procedure. The comparative analysis of the mentioned methods was done; the concrete results of recognition and the dependence of recognition efficiency on the number of wavelength channels and on the accuracy of spectrum recording are given.

  6. Disease named entity recognition by combining conditional random fields and bidirectional recurrent neural networks

    PubMed Central

    Wei, Qikang; Chen, Tao; Xu, Ruifeng; He, Yulan; Gui, Lin

    2016-01-01

    The recognition of disease and chemical named entities in scientific articles is a very important subtask in information extraction in the biomedical domain. Due to the diversity and complexity of disease names, the recognition of named entities of diseases is rather tougher than those of chemical names. Although there are some remarkable chemical named entity recognition systems available online such as ChemSpot and tmChem, the publicly available recognition systems of disease named entities are rare. This article presents a system for disease named entity recognition (DNER) and normalization. First, two separate DNER models are developed. One is based on conditional random fields model with a rule-based post-processing module. The other one is based on the bidirectional recurrent neural networks. Then the named entities recognized by each of the DNER model are fed into a support vector machine classifier for combining results. Finally, each recognized disease named entity is normalized to a medical subject heading disease name by using a vector space model based method. Experimental results show that using 1000 PubMed abstracts for training, our proposed system achieves an F1-measure of 0.8428 at the mention level and 0.7804 at the concept level, respectively, on the testing data of the chemical-disease relation task in BioCreative V. Database URL: http://219.223.252.210:8080/SS/cdr.html PMID:27777244

  7. 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

  8. Bidirectional Modulation of Recognition Memory

    PubMed Central

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

    2015-01-01

    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

  9. 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.

  10. An introduction to object recognition.

    PubMed

    Liter, J C; Bülthoff, H H

    1998-01-01

    In this report we present a general introduction to object recognition. We begin with brief discussions of the terminology used in the object recognition literature and the psychophysical tasks that are used to investigate object recognition. We then discuss models of shape representation. We dispense with the idea that shape representations are like the 3-D models used in computer aided design and explore instead models of shape representation that are based on future descriptions. As these descriptions encode only the features that are visible from a particular viewpoint, they are generally viewpoint-specific. We discuss various means of achieving viewpoint-invariant recognition using such descriptions, including reliance on diagnostic features visible from a wide range of viewpoints, storage of multiple descriptions for each object, and the use of transformation mechanisms. Finally, we discuss how differences in viewpoint dependence that are often observed for within-category and between-category recognition tasks could be due to differences in the types of features that are naturally available to distinguish among different objects in these tasks.

  11. 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.

  12. 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.

  13. Cystic fibrosis modifier genes.

    PubMed Central

    Davies, Jane; Alton, Eric; Griesenbach, Uta

    2005-01-01

    Since the recognition that CFTR genotype was not a good predictor of pulmonary disease severity in CF, several candidate modifier genes have been identified. It is unlikely that a single modifier gene will be found, but more probable that several haplotypes in combination may contribute, which in itself presents a major methodological challenge. The aims of such studies are to increase our understanding of disease pathogenesis, to aid prognosis and ultimately to lead to the development of novel treatments. PMID:16025767

  14. Chemical named entities recognition: a review on approaches and applications

    PubMed Central

    2014-01-01

    The rapid increase in the flow rate of published digital information in all disciplines has resulted in a pressing need for techniques that can simplify the use of this information. The chemistry literature is very rich with information about chemical entities. Extracting molecules and their related properties and activities from the scientific literature to “text mine” these extracted data and determine contextual relationships helps research scientists, particularly those in drug development. One of the most important challenges in chemical text mining is the recognition of chemical entities mentioned in the texts. In this review, the authors briefly introduce the fundamental concepts of chemical literature mining, the textual contents of chemical documents, and the methods of naming chemicals in documents. We sketch out dictionary-based, rule-based and machine learning, as well as hybrid chemical named entity recognition approaches with their applied solutions. We end with an outlook on the pros and cons of these approaches and the types of chemical entities extracted. PMID:24834132

  15. Chemical named entities recognition: a review on approaches and applications.

    PubMed

    Eltyeb, Safaa; Salim, Naomie

    2014-01-01

    The rapid increase in the flow rate of published digital information in all disciplines has resulted in a pressing need for techniques that can simplify the use of this information. The chemistry literature is very rich with information about chemical entities. Extracting molecules and their related properties and activities from the scientific literature to "text mine" these extracted data and determine contextual relationships helps research scientists, particularly those in drug development. One of the most important challenges in chemical text mining is the recognition of chemical entities mentioned in the texts. In this review, the authors briefly introduce the fundamental concepts of chemical literature mining, the textual contents of chemical documents, and the methods of naming chemicals in documents. We sketch out dictionary-based, rule-based and machine learning, as well as hybrid chemical named entity recognition approaches with their applied solutions. We end with an outlook on the pros and cons of these approaches and the types of chemical entities extracted.

  16. Common themes and differences in SAM recognition among SAM riboswitches.

    PubMed

    Price, Ian R; Grigg, Jason C; Ke, Ailong

    2014-10-01

    The recent discovery of short cis-acting RNA elements termed riboswitches has caused a paradigm shift in our understanding of genetic regulatory mechanisms. The three distinct superfamilies of S-adenosyl-l-methionine (SAM) riboswitches are the most commonly found riboswitch classes in nature. These RNAs represent three independent evolutionary solutions to achieve specific SAM recognition. This review summarizes research on 1) modes of gene regulatory mechanisms, 2) common themes and differences in ligand recognition, and 3) ligand-induced conformational dynamics among SAM riboswitch families. The body of work on the SAM riboswitch families constitutes a useful primer to the topic of gene regulatory RNAs as a whole. This article is part of a Special Issue entitled: Riboswitches. Copyright © 2014 Elsevier B.V. All rights reserved.

  17. Functional Connectivity of Multiple Brain Regions Required for the Consolidation of Social Recognition Memory.

    PubMed

    Tanimizu, Toshiyuki; Kenney, Justin W; Okano, Emiko; Kadoma, Kazune; Frankland, Paul W; Kida, Satoshi

    2017-04-12

    Social recognition memory is an essential and basic component of social behavior that is used to discriminate familiar and novel animals/humans. Previous studies have shown the importance of several brain regions for social recognition memories; however, the mechanisms underlying the consolidation of social recognition memory at the molecular and anatomic levels remain unknown. Here, we show a brain network necessary for the generation of social recognition memory in mice. A mouse genetic study showed that cAMP-responsive element-binding protein (CREB)-mediated transcription is required for the formation of social recognition memory. Importantly, significant inductions of the CREB target immediate-early genes c-fos and Arc were observed in the hippocampus (CA1 and CA3 regions), medial prefrontal cortex (mPFC), anterior cingulate cortex (ACC), and amygdala (basolateral region) when social recognition memory was generated. Pharmacological experiments using a microinfusion of the protein synthesis inhibitor anisomycin showed that protein synthesis in these brain regions is required for the consolidation of social recognition memory. These findings suggested that social recognition memory is consolidated through the activation of CREB-mediated gene expression in the hippocampus/mPFC/ACC/amygdala. Network analyses suggested that these four brain regions show functional connectivity with other brain regions and, more importantly, that the hippocampus functions as a hub to integrate brain networks and generate social recognition memory, whereas the ACC and amygdala are important for coordinating brain activity when social interaction is initiated by connecting with other brain regions. We have found that a brain network composed of the hippocampus/mPFC/ACC/amygdala is required for the consolidation of social recognition memory.SIGNIFICANCE STATEMENT Here, we identify brain networks composed of multiple brain regions for the consolidation of social recognition memory. We

  18. Genome filtering using methylation-sensitive restriction enzymes with six-base pair recognition sites

    USDA-ARS?s Scientific Manuscript database

    The large fraction of repetitive DNA in many plant genomes has complicated all aspects of DNA sequencing and assembly, and thus techniques that enrich for genes and low-copy sequences have been employed to isolate gene space. Methyl sensitive restriction enzymes with six base pair recognition sites...

  19. Stereotype associations and emotion recognition.

    PubMed

    Bijlstra, Gijsbert; Holland, Rob W; Dotsch, Ron; Hugenberg, Kurt; Wigboldus, Daniel H J

    2014-05-01

    We investigated whether stereotype associations between specific emotional expressions and social categories underlie stereotypic emotion recognition biases. Across two studies, we replicated previously documented stereotype biases in emotion recognition using both dynamic (Study 1) and static (Study 2) expression displays. Stereotype consistent expressions were more quickly decoded than stereotype inconsistent expression on Moroccan and White male faces. Importantly, we found consistent and novel evidence that participants' associations between ethnicities and emotions, as measured with a newly developed emotion Implicit Association Test (eIAT), predicted the strength of their ethnicity-based stereotype biases in expression recognition. In both studies, as perceivers' level of Moroccan-anger and Dutch-sadness associations (compared with the opposite) increased, so did perceivers' tendency to decode anger more readily on Moroccan faces and sadness on White faces. The observed stereotype effect seemed to be independent of implicit prejudice (Study 2), suggesting dissociable effects of prejudices and stereotypes in expression perception.

  20. 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.

  1. 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.

  2. Children's recognition of cartoon voices.

    PubMed

    Spence, Melanie J; Rollins, Pamela R; Jerger, Susan

    2002-02-01

    We examined developmental changes in talker recognition skills by assessing 3-, 4-, and 5-year-old children's recognition of 20 cartoon characters' voices. For each participant, the character set was subdivided into more and less familiar talkers based on the participant's ability to name each character. Four- and 5- year-old children recognized more of the voices (81% and 86%, respectively) than did 3-year-olds (61%), although performance of all age groups was well above chance. All groups of children were more accurate at recognizing more familiar than less familiar characters. These results suggest that indexical information about a talker becomes an integral part of the perceptual record in memory and can be used by children at a very young age. These results are important because children's ability to learn vocal sources may be an important aid to the development of spoken word recognition.

  3. Furin gene (fur) regulation in differentiating human megakaryoblastic Dami cells: involvement of the proximal GATA recognition motif in the P1 promoter and impact on the maturation of furin substrates.

    PubMed

    Laprise, Marie-Hélène; Grondin, Francine; Cayer, Pauline; McDonald, Patrick P; Dubois, Claire M

    2002-11-15

    The convertase furin is involved in the maturation of key growth/aggregation mediators synthesized by the platelet producers, megakaryocytes, but the regulation of furin in these cells remains unknown. Computer-assisted search of the furin promoter sequence revealed multiple potential binding motifs for GATA-1, suggesting that furin is expressed and regulated in these cells. Using megakaryoblastic Dami cells, we observed that fur mRNA expression increased gradually on phorbol 12-myristate 13-acetate-induced differentiation, reaching maximum levels (8.3-fold increase) at 10 days. Transient transfections with P1, P1A, or P1B fur-LUC-promoter constructs revealed that in Dami cells, the P1 promoter is the strongest and the most sensitive to forced expression of GATA-1. Coexpression of GATA-1 and its comodulator, Friend of GATA-1 (FOG-1), resulted in a cooperative increase in P1 activity. Deletion analysis indicated that important GATA-1-regulated sequences are located in the most proximal region of the P1 promoter. Further analysis revealed 2 potential GATA-binding motifs at positions -66 and +62. Point mutation of each of the 2 motifs indicated that the intactness of the first GATA site is required for full basal and GATA-1-stimulated promoter activity. Finally, the inhibition of furin activity through gene transfer of the inhibitor alpha1-AT-PDX led to a block in maturation of the furin substrates transforming growth factor-beta1 and platelet-derived growth factor. Taken together, these results indicate that the most proximal GATA element in the P1 promoter is needed for fur gene expression in megakaryoblastic cells. They also suggest that proper regulation of the fur gene in megakaryocytes has an impact on the activation of furin substrates involved in megakaryocyte maturation and platelet functions.

  4. Diverse functions of WD40 repeat proteins in histone recognition

    PubMed Central

    Suganuma, Tamaki; Pattenden, Samantha G.; Workman, Jerry L.

    2008-01-01

    WD40 repeat proteins have been shown to bind the histone H3 tail at the center of their β-propeller structure. In contrast, in this issue of Genes & Development, Song and colleagues (pp. 1313–1318) demonstrate that the WD40 repeat protein p55 binds a structured region of H4 through a novel binding pocket on the side of β-propeller, illustrating a diversity of histone recognition by WD40 repeat proteins. PMID:18483215

  5. 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.

  6. Recognition memory, and head injury.

    PubMed

    Brooks, D N

    1974-07-01

    Severely head injured adults were tested on a recognition memory procedure involving the identification of eight recurring shapes among a series of 160. Compared with a control group, the tested patients showed many fewer correct responses. Their type of error was commonly a failure to recognize rather than a false recognition. The severity of the memory deficit was related to the length of post-traumatic amnesia (PTA), but to neither the presence of neurological signs at the time of memory testing, nor to the time after injury at which the patients were tested. The older patients showed a more significant relationship between PTA and memory score than the younger patients.

  7. 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.

  8. Emotion recognition during cocaine intoxication.

    PubMed

    Kuypers, K P C; Steenbergen, L; Theunissen, E L; Toennes, S W; Ramaekers, J G

    2015-11-01

    Chronic or repeated cocaine use has been linked to impairments in social skills. It is not clear whether cocaine is responsible for this impairment or whether other factors, like polydrug use, distort the observed relation. We aimed to investigate this relation by means of a placebo-controlled experimental study. Additionally, associations between stressor-related activity (cortisol, cardiovascular parameters) induced by the biological stressor cocaine, and potential cocaine effects on emotion recognition were studied. Twenty-four healthy recreational cocaine users participated in this placebo-controlled within-subject study. Participants were tested between 1 and 2 h after treatment with oral cocaine (300 mg) or placebo. Emotion recognition of low and high intensity expressions of basic emotions (fear, anger, disgust, sadness, and happiness) was tested. Findings show that cocaine impaired recognition of negative emotions; this was mediated by the intensity of the presented emotions. When high intensity expressions of Anger and Disgust were shown, performance under influence of cocaine 'normalized' to placebo-like levels while it made identification of Sadness more difficult. The normalization of performance was most notable for participants with the largest cortisol responses in the cocaine condition compared to placebo. It was demonstrated that cocaine impairs recognition of negative emotions, depending on the intensity of emotion expression and cortisol response. Copyright © 2015 Elsevier B.V. and ECNP. All rights reserved.

  9. 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…

  10. Face recognition for uncontrolled environments

    NASA Astrophysics Data System (ADS)

    Podilchuk, Christine; Hulbert, William; Flachsbart, Ralph; Barinov, Lev

    2010-04-01

    A new face recognition algorithm has been proposed which is robust to variations in pose, expression, illumination and occlusions such as sunglasses. The algorithm is motivated by the Edit Distance used to determine the similarity between strings of one dimensional data such as DNA and text. The key to this approach is how to extend the concept of an Edit Distance on one-dimensional data to two-dimensional image data. The algorithm is based on mapping one image into another and using the characteristics of the mapping to determine a two-dimensional Pictorial-Edit Distance or P-Edit Distance. We show how the properties of the mapping are similar to insertion, deletion and substitution errors defined in an Edit Distance. This algorithm is particularly well suited for face recognition in uncontrolled environments such as stand-off and other surveillance applications. We will describe an entire system designed for face recognition at a distance including face detection, pose estimation, multi-sample fusion of video frames and identification. Here we describe how the algorithm is used for face recognition at a distance, present some initial results and describe future research directions.(

  11. 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)

  12. Object recognition using metric shape.

    PubMed

    Lee, Young-Lim; Lind, Mats; Bingham, Ned; Bingham, Geoffrey P

    2012-09-15

    Most previous studies of 3D shape perception have shown a general inability to visually perceive metric shape. In line with this, studies of object recognition have shown that only qualitative differences, not quantitative or metric ones can be used effectively for object recognition. Recently, Bingham and Lind (2008) found that large perspective changes (≥ 45°) allow perception of metric shape and Lee and Bingham (2010) found that this, in turn, allowed accurate feedforward reaches-to-grasp objects varying in metric shape. We now investigated whether this information would allow accurate and effective recognition of objects that vary in respect to metric shape. Both judgment accuracies (d') and reaction times confirmed that, with the availability of visual information in large perspective changes, recognition of objects using quantitative as compared to qualitative properties was equivalent in accuracy and speed of judgments. The ability to recognize objects based on their metric shape is, therefore, a function of the availability or unavailability of requisite visual information. These issues and results are discussed in the context of the Two Visual System hypothesis of Milner and Goodale (1995, 2006). 2012 Elsevier Ltd. All rights reserved

  13. 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

  14. The Army word recognition system

    NASA Technical Reports Server (NTRS)

    Hadden, David R.; Haratz, David

    1977-01-01

    The application of speech recognition technology in the Army command and control area is presented. The problems associated with this program are described as well as as its relevance in terms of the man/machine interactions, voice inflexions, and the amount of training needed to interact with and utilize the automated system.

  15. 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…

  16. 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…

  17. Pattern recognition system and procedures

    NASA Technical Reports Server (NTRS)

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

    1972-01-01

    The ratio transformation technique is used to determine effective features as function of time in remote multiple sensing of crops and soils. The selection of quantizer parameters for a two-class recognition problem under the criteria of minimizing the probability of errors is also discussed.

  18. 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.

  19. 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…

  20. Clustering Techniques in Speaker Recognition

    DTIC Science & Technology

    1994-03-01

    Quantization ................................ 9 2.5 Fuzzy Clustering ................................... 13 2.5.1 The Fuzzy k- Means Algorithm...techniques, vector quantization, Fuzzy k- Means and Artificial Neural Networks applied to speech for speaker identification. 2 II. Literature Review...recognition. Ruspini provided one of the first applications of fuzzy logic in clustering, he extended the conventional k- means algorithm into the Fuzzy k

  1. Sequence selective recognition of double-stranded RNA using triple helix-forming peptide nucleic acids.

    PubMed

    Zengeya, Thomas; Gupta, Pankaj; Rozners, Eriks

    2014-01-01

    Noncoding RNAs are attractive targets for molecular recognition because of the central role they play in gene expression. Since most noncoding RNAs are in a double-helical conformation, recognition of such structures is a formidable problem. Herein, we describe a method for sequence-selective recognition of biologically relevant double-helical RNA (illustrated on ribosomal A-site RNA) using peptide nucleic acids (PNA) that form a triple helix in the major grove of RNA under physiologically relevant conditions. Protocols for PNA preparation and binding studies using isothermal titration calorimetry are described in detail.

  2. 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. Copyright © 2015 Elsevier B.V. All rights reserved.

  3. Public domain optical character recognition

    NASA Astrophysics Data System (ADS)

    Garris, Michael D.; Blue, James L.; Candela, Gerald T.; Dimmick, Darrin L.; Geist, Jon C.; Grother, Patrick J.; Janet, Stanley A.; Wilson, Charles L.

    1995-03-01

    A public domain document processing system has been developed by the National Institute of Standards and Technology (NIST). The system is a standard reference form-based handprint recognition system for evaluating optical character recognition (OCR), and it is intended to provide a baseline of performance on an open application. The system's source code, training data, performance assessment tools, and type of forms processed are all publicly available. The system recognizes the handprint entered on handwriting sample forms like the ones distributed with NIST Special Database 1. From these forms, the system reads hand-printed numeric fields, upper and lowercase alphabetic fields, and unconstrained text paragraphs comprised of words from a limited-size dictionary. The modular design of the system makes it useful for component evaluation and comparison, training and testing set validation, and multiple system voting schemes. The system contains a number of significant contributions to OCR technology, including an optimized probabilistic neural network (PNN) classifier that operates a factor of 20 times faster than traditional software implementations of the algorithm. The source code for the recognition system is written in C and is organized into 11 libraries. In all, there are approximately 19,000 lines of code supporting more than 550 subroutines. Source code is provided for form registration, form removal, field isolation, field segmentation, character normalization, feature extraction, character classification, and dictionary-based postprocessing. The recognition system has been successfully compiled and tested on a host of UNIX workstations. This paper gives an overview of the recognition system's software architecture, including descriptions of the various system components along with timing and accuracy statistics.

  4. Environmental Recognition and Guidance Control for Autonomous Vehicles using Dual Vision Sensor and Applications

    NASA Astrophysics Data System (ADS)

    Moriwaki, Katsumi; Koike, Issei; Sano, Tsuyoshi; Fukunaga, Tetsuya; Tanaka, Katsuyuki

    We propose a new method of environmental recognition around an autonomous vehicle using dual vision sensor and navigation control based on binocular images. We consider to develop a guide robot that can play the role of a guide dog as the aid to people such as the visually impaired or the aged, as an application of above-mentioned techniques. This paper presents a recognition algorithm, which finds out the line of a series of Braille blocks and the boundary line between a sidewalk and a roadway where a difference in level exists by binocular images obtained from a pair of parallelarrayed CCD cameras. This paper also presents a tracking algorithm, with which the guide robot traces along a series of Braille blocks and avoids obstacles and unsafe areas which exist in the way of a person with the guide robot.

  5. Speech Recognition: Its Place in Business Education.

    ERIC Educational Resources Information Center

    Szul, Linda F.; Bouder, Michele

    2003-01-01

    Suggests uses of speech recognition devices in the classroom for students with disabilities. Compares speech recognition software packages and provides guidelines for selection and teaching. (Contains 14 references.) (SK)

  6. 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.

  7. 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.

  8. Hypertrophic cardiomyopathy: Clinical recognition and management

    SciTech Connect

    Ten Cate, F.J.

    1985-01-01

    This book contains 14 chapters. Some of the titles are: Hemodynamics and angiography; Familial and genetic aspects; Recognition and management in children; Morphologic and microscopic aspects of hypertrophic cardiomyopathy; Clinical recognition; and Management with beta-adrenergic blocking drugs.

  9. 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.

  10. Effect of yeast-derived products and distillers dried grains with solubles (DDGS) on antibody-mediated immune response and gene expression of pattern recognition receptors and cytokines in broiler chickens immunized with T-cell dependent antigens.

    PubMed

    Alizadeh, M; Rodriguez-Lecompte, J C; Echeverry, H; Crow, G H; Slominski, B A

    2016-04-01

    This study evaluated the effect of yeast-derived products on innate and antibody mediated immune response in broiler chickens following immunization with sheep red blood cells (SRBC) and bovine serum albumin (BSA). One-day-old male broiler chickens (Ross-308) were randomly assigned to 6 dietary treatments of 9 replicate cages of 5 birds each per treatment. Dietary treatments consisted of a Control diet without antibiotic, and diets containing 11 mg/kg of virginiamycin, 0.25% of yeast cell wall (YCW), 0.2% of a commercial product Maxi-Gen Plus containing processed yeast and nucleotides, 0.05% of nucleotides, or a diet containing 10% of DDGS. On days 21 and 28 post-hatching, 5 birds per treatment were immunized intramuscularly with both SRBC and BSA. One week after each immunization, blood samples were collected. Serum samples were analyzed by hemagglutination test for antibody response to SRBC, and by ELISA for serum IgM and IgG response to BSA. On d 35, 5 birds per treatment were euthanized and the tissue samples from the cecal tonsils were collected to assess the gene expression of toll-like receptors TLR2b, TLR4, and TLR21, monocyte mannose receptor (MMR), and cytokines IL-10, IL-13, IL-4, IL-12p35, and IFN-γ. The results for gene expression analysis demonstrated that the diet supplemented with YCW increased the expression of TLR2b and T-helper type 2 cytokines IL-10, IL-4, and IL-13 relative to the Control; and the expression of TLR4 and IL-13 was upregulated in the nucleotide-containing diet. However, the diets containing antibiotics or Maxi-Gen Plus downregulated the expression of IFN-γ compared to the control. The primary antibody response to SRBC was not affected by diets. However, the diet containing YCW increased the secondary antibody response to SRBC compared to the antibiotic treatment. Neither primary nor secondary IgG and IgM response against BSA were affected by diets. In conclusion, supplementation of the diet with YCW stimulated Th2 cell

  11. Quest Hierarchy for Hyperspectral Face Recognition

    DTIC Science & Technology

    2011-03-01

    Recognition Rate for Eigenfaces, Eigenfeatures and Combined [24] 41 Neural Networks A promising approach for complex pattern... recognition is the application of neural networks (NN). Given the dimensionality of the face recognition problem and the desire to recreate the human... recognition with only a small sample of stored images for an individual. By using a 2D log polar Gabor transform within an artificial neural network

  12. 8 CFR 292.2 - Organizations qualified for recognition; requests for recognition; withdrawal of recognition...

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... non-profit religious, charitable, social service, or similar organization established in the United... recognition on a Form G-27 directly with the Board, along with proof of service of a copy of the application.... The district director shall include proof of service of a copy of such recommendation or request on...

  13. 8 CFR 1292.2 - Organizations qualified for recognition; requests for recognition; withdrawal of recognition...

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ...) Qualifications of organizations. A non-profit religious, charitable, social service, or similar organization... recognition on a Form G-27 directly with the Board, along with proof of service of a copy of the application.... The district director shall include proof of service of a copy of such recommendation or request on...

  14. Pattern-Recognition Receptors and Gastric Cancer

    PubMed Central

    Castaño-Rodríguez, Natalia; Kaakoush, Nadeem O.; Mitchell, Hazel M.

    2014-01-01

    Chronic inflammation has been associated with an increased risk of several human malignancies, a classic example being gastric adenocarcinoma (GC). Development of GC is known to result from infection of the gastric mucosa by Helicobacter pylori, which initially induces acute inflammation and, in a subset of patients, progresses over time to chronic inflammation, gastric atrophy, intestinal metaplasia, dysplasia, and finally intestinal-type GC. Germ-line encoded receptors known as pattern-recognition receptors (PRRs) are critical for generating mature pro-inflammatory cytokines that are crucial for both Th1 and Th2 responses. Given that H. pylori is initially targeted by PRRs, it is conceivable that dysfunction within genes of this arm of the immune system could modulate the host response against H. pylori infection, and subsequently influence the emergence of GC. Current evidence suggests that Toll-like receptors (TLRs) (TLR2, TLR3, TLR4, TLR5, and TLR9), nucleotide-binding oligomerization domain (NOD)-like receptors (NLRs) (NOD1, NOD2, and NLRP3), a C-type lectin receptor (DC-SIGN), and retinoic acid-inducible gene (RIG)-I-like receptors (RIG-I and MDA-5), are involved in both the recognition of H. pylori and gastric carcinogenesis. In addition, polymorphisms in genes involved in the TLR (TLR1, TLR2, TLR4, TLR5, TLR9, and CD14) and NLR (NOD1, NOD2, NLRP3, NLRP12, NLRX1, CASP1, ASC, and CARD8) signaling pathways have been shown to modulate the risk of H. pylori infection, gastric precancerous lesions, and/or GC. Further, the modulation of PRRs has been suggested to suppress H. pylori-induced inflammation and enhance GC cell apoptosis, highlighting their potential relevance in GC therapeutics. In this review, we present current advances in our understanding of the role of the TLR and NLR signaling pathways in the pathogenesis of GC, address the involvement of other recently identified PRRs in GC, and discuss the potential implications of PRRs in GC immunotherapy

  15. Photoreceptor-mediated kin recognition in plants.

    PubMed

    Crepy, María A; Casal, Jorge J

    2015-01-01

    Although cooperative interactions among kin have been established in a variety of biological systems, their occurrence in plants remains controversial. Plants of Arabidopsis thaliana were grown in rows of either a single or multiple accessions. Plants recognized kin neighbours and horizontally reoriented leaf growth, a response not observed when plants were grown with nonkin. Plant kin recognition involved the perception of the vertical red/far-red light and blue light profiles. Disruption of the light profiles, mutations at the PHYTOCHROME B, CRYPTOCHROME 1 or 2, or PHOTOTROPIN 1 or 2 photoreceptor genes or mutations at the TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS1 gene required for auxin (growth hormone) synthesis impaired the response. The leaf-position response increases plant self-shading, decreases mutual shading between neighbours and increases fitness. Light signals from neighbours are known to shape a more competitive plant body. Here we show that photosensory receptors mediate cooperative rather than competitive interactions among kin neighbours by reducing the competition for local pools of resources.

  16. Hierarchical Recognition Scheme for Human Facial Expression Recognition Systems

    PubMed Central

    Siddiqi, Muhammad Hameed; Lee, Sungyoung; Lee, Young-Koo; Khan, Adil Mehmood; Truc, Phan Tran Ho

    2013-01-01

    Over the last decade, human facial expressions recognition (FER) has emerged as an important research area. Several factors make FER a challenging research problem. These include varying light conditions in training and test images; need for automatic and accurate face detection before feature extraction; and high similarity among different expressions that makes it difficult to distinguish these expressions with a high accuracy. This work implements a hierarchical linear discriminant analysis-based facial expressions recognition (HL-FER) system to tackle these problems. Unlike the previous systems, the HL-FER uses a pre-processing step to eliminate light effects, incorporates a new automatic face detection scheme, employs methods to extract both global and local features, and utilizes a HL-FER to overcome the problem of high similarity among different expressions. Unlike most of the previous works that were evaluated using a single dataset, the performance of the HL-FER is assessed using three publicly available datasets under three different experimental settings: n-fold cross validation based on subjects for each dataset separately; n-fold cross validation rule based on datasets; and, finally, a last set of experiments to assess the effectiveness of each module of the HL-FER separately. Weighted average recognition accuracy of 98.7% across three different datasets, using three classifiers, indicates the success of employing the HL-FER for human FER. PMID:24316568

  17. 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

  18. 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

  19. Environmental enrichment improves novel object recognition and enhances agonistic behavior in male mice.

    PubMed

    Mesa-Gresa, Patricia; Pérez-Martinez, Asunción; Redolat, Rosa

    2013-01-01

    Environmental enrichment (EE) is an experimental paradigm in which rodents are housed in complex environments containing objects that provide stimulation, the effects of which are expected to improve the welfare of these subjects. EE has been shown to considerably improve learning and memory in rodents. However, knowledge about the effects of EE on social interaction is generally limited and rather controversial. Thus, our aim was to evaluate both novel object recognition and agonistic behavior in NMRI mice receiving EE, hypothesizing enhanced cognition and slightly enhanced agonistic interaction upon EE rearing. During a 4-week period half the mice (n = 16) were exposed to EE and the other half (n = 16) remained in a standard environment (SE). On PND 56-57, animals performed the object recognition test, in which recognition memory was measured using a discrimination index. The social interaction test consisted of an encounter between an experimental animal and a standard opponent. Results indicated that EE mice explored the new object for longer periods than SE animals (P < .05). During social encounters, EE mice devoted more time to sociability and agonistic behavior (P < .05) than their non-EE counterparts. In conclusion, EE has been shown to improve object recognition and increase agonistic behavior in adolescent/early adulthood mice. In the future we intend to extend this study on a longitudinal basis in order to assess in more depth the effect of EE and the consistency of the above-mentioned observations in NMRI mice. Copyright © 2013 Wiley Periodicals, Inc.

  20. Robust Optical Recognition of Cursive Pashto Script Using Scale, Rotation and Location Invariant Approach.

    PubMed

    Ahmad, Riaz; Naz, Saeeda; Afzal, Muhammad Zeshan; Amin, Sayed Hassan; Breuel, Thomas

    2015-01-01

    The presence of a large number of unique shapes called ligatures in cursive languages, along with variations due to scaling, orientation and location provides one of the most challenging pattern recognition problems. Recognition of the large number of ligatures is often a complicated task in oriental languages such as Pashto, Urdu, Persian and Arabic. Research on cursive script recognition often ignores the fact that scaling, orientation, location and font variations are common in printed cursive text. Therefore, these variations are not included in image databases and in experimental evaluations. This research uncovers challenges faced by Arabic cursive script recognition in a holistic framework by considering Pashto as a test case, because Pashto language has larger alphabet set than Arabic, Persian and Urdu. A database containing 8000 images of 1000 unique ligatures having scaling, orientation and location variations is introduced. In this article, a feature space based on scale invariant feature transform (SIFT) along with a segmentation framework has been proposed for overcoming the above mentioned challenges. The experimental results show a significantly improved performance of proposed scheme over traditional feature extraction techniques such as principal component analysis (PCA).

  1. Robust Optical Recognition of Cursive Pashto Script Using Scale, Rotation and Location Invariant Approach

    PubMed Central

    Ahmad, Riaz; Naz, Saeeda; Afzal, Muhammad Zeshan; Amin, Sayed Hassan; Breuel, Thomas

    2015-01-01

    The presence of a large number of unique shapes called ligatures in cursive languages, along with variations due to scaling, orientation and location provides one of the most challenging pattern recognition problems. Recognition of the large number of ligatures is often a complicated task in oriental languages such as Pashto, Urdu, Persian and Arabic. Research on cursive script recognition often ignores the fact that scaling, orientation, location and font variations are common in printed cursive text. Therefore, these variations are not included in image databases and in experimental evaluations. This research uncovers challenges faced by Arabic cursive script recognition in a holistic framework by considering Pashto as a test case, because Pashto language has larger alphabet set than Arabic, Persian and Urdu. A database containing 8000 images of 1000 unique ligatures having scaling, orientation and location variations is introduced. In this article, a feature space based on scale invariant feature transform (SIFT) along with a segmentation framework has been proposed for overcoming the above mentioned challenges. The experimental results show a significantly improved performance of proposed scheme over traditional feature extraction techniques such as principal component analysis (PCA). PMID:26368566

  2. Genes and Gene Therapy

    MedlinePlus

    ... correctly, a child can have a genetic disorder. Gene therapy is an experimental technique that uses genes to ... or prevent disease. The most common form of gene therapy involves inserting a normal gene to replace an ...

  3. GAYE: a face recognition system

    NASA Astrophysics Data System (ADS)

    Kepenekci, Burcu; Tek, F. Boray; Cilingir, Onur; Sakarya, Ufuk; Akar, Gozde B.

    2004-05-01

    In this paper, a new face recognition system, GAYE, is presented. GAYE is a fully automatic system that detects and recognizes faces in cluttered scenes. The input of the system is any digitized image/image sequence that includes face/faces. The basic building blocks of the system are face detection, feature extraction and feature comparison. Face detection is based on skin color segmentation. For feature extraction, a novel approach is proposed that depends on the Gabor wavelet transform of the face image. By comparing facial feature vectors system finally makes a decision if the incoming person is recognized or not. Real time system tests show that GAYE achieves a recognition ratio over %90.

  4. Slow Molecular Recognition by RNA.

    PubMed

    Gleitsman, Kristin R; Sengupta, Raghuvir N; Herschlag, Daniel

    2017-09-28

    Molecular recognition is central to biological processes, function, and specificity. Proteins associate with ligands with maximal rates that match the theoretical limit set by the rate of diffusional collision and with a wide range of observed values. As less is known about RNA association, we compiled association rate constants for all RNA/ligand complexes that we could find in the literature. Like proteins, RNAs exhibit a wide range of association rate constants. However, the fastest RNA association rates are considerably slower than those of the fastest protein associations and fall well below the diffusional limit. The apparently general observation of slow association with RNAs has implications for evolution and for modern-day biology. Our compilation highlights a quantitative molecular property that can contribute to biological understanding and underscores our limited physical understanding of molecular recognition events. Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  5. 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.

  6. Effect of yeast-derived products and distillers dried grains with solubles (DDGS) on growth performance, gut morphology, and gene expression of pattern recognition receptors and cytokines in broiler chickens.

    PubMed

    Alizadeh, M; Rodriguez-Lecompte, J C; Rogiewicz, A; Patterson, R; Slominski, B A

    2016-03-01

    An experiment was carried out to investigate the effect of yeast-derived products and distillers' dried grains with solubles (DDGS) on growth performance, small intestinal morphology, and innate immune response in broiler chickens from 1 to 21 d of age. Nine replicates of 5 birds each were assigned to dietary treatments consisting of a control diet without antibiotic (C), and diets containing 11 mg/kg of virginiamycin, 0.25% of yeast cell wall (YCW), 0.2% of a commercial product Maxi-Gen Plus, 0.025% of nucleotides, 0.05% of nucleotides, or a diet containing 10% of DDGS. On d 21, 5 birds per treatment were euthanized and approximately 5-cm long duodenum, jejunum, and ileum segments were collected for intestinal morphology measurements. Cecal tonsils and spleen were collected to measure the gene expression of toll-like receptors TLR2b, TLR4, and TLR21, macrophage mannose receptor (MMR), and cytokines IFN-γ, IL-12, IL-10, and IL-4. No significant difference was observed for growth performance parameters. However, diets containing 0.05% of nucleotides and YCW significantly increased (P < 0.05) villus height in the jejunum. Furthermore, the number of the goblet cells per unit area in the ileum was increased (P < 0.05) in diets supplemented with yeast-derived products. The expression of TLR2b in the spleen was down-regulated for diets supplemented with nucleotides and antibiotic. In addition, lower expression of TLR21 and MMR was observed in the spleen of birds receiving yeast-derived products and antibiotic. However, expression of TLR4 in the spleen was up-regulated in diets supplemented with YCW and nucleotides. The expression of IFN-γ and IL-12 was down-regulated in the spleen of birds fed diets supplemented with yeast-derived products. In addition, inclusion of YCW, Maxi-Gen Plus, or 0.05% of nucleotides down-regulated the expression of IL-10 and IL-4 in the cecal tonsils. In conclusion, down-regulation of receptors and cytokines in spleen and cecal tonsils of

  7. Analysis, recognition, and interpretation of speech signals

    NASA Astrophysics Data System (ADS)

    Vintziuk, Taras Klimovich

    The problems of the machine analysis, recognition, semantic interpretation, synthesis, and compressed speech transmission are examined with reference to oral man-machine dialogue in formalized and natural languages for applications in data collection, processing, and control systems. Methods for the recognition of individual words and continuous speech, signal segmentation and self-segmentation, speech recognition learning, recognition of the voice of a particular operator, recognition of multiple speakers, and selection of signal matching and signal analysis techniques are discussed from a unified standpoint based on the use of dynamic programming.

  8. 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.

  9. Which way up? Recognition of homologous DNA segments in parallel and antiparallel alignments

    NASA Astrophysics Data System (ADS)

    O'Lee, Dominic J.; Wynveen, Aaron; Albrecht, Tim; Kornyshev, Alexei A.

    2015-01-01

    Homologous gene shuffling between DNA molecules promotes genetic diversity and is an important pathway for DNA repair. For this to occur, homologous genes need to find and recognize each other. However, despite its central role in homologous recombination, the mechanism of homology recognition has remained an unsolved puzzle of molecular biology. While specific proteins are known to play a role at later stages of recombination, an initial coarse grained recognition step has, however, been proposed. This relies on the sequence dependence of the DNA structural parameters, such as twist and rise, mediated by intermolecular interactions, in particular, electrostatic ones. In this proposed mechanism, sequences that have the same base pair text, or are homologous, have lower interaction energy than those sequences with uncorrelated base pair texts. The difference between the two energies is termed the "recognition energy." Here, we probe how the recognition energy changes when one DNA fragment slides past another, and consider, for the first time, homologous sequences in antiparallel alignment. This dependence on sliding is termed the "recognition well." We find there is a recognition well for anti-parallel, homologous DNA tracts, but only a very shallow one, so that their interaction will differ little from the interaction between two nonhomologous tracts. This fact may be utilized in single molecule experiments specially targeted to test the theory. As well as this, we test previous theoretical approximations in calculating the recognition well for parallel molecules against MC simulations and consider more rigorously the optimization of the orientations of the fragments about their long axes upon calculating these recognition energies. The more rigorous treatment affects the recognition energy a little, when the molecules are considered rigid. When torsional flexibility of the DNA molecules is introduced, we find excellent agreement between the analytical

  10. Which way up? Recognition of homologous DNA segments in parallel and antiparallel alignments.

    PubMed

    O' Lee, Dominic J; Wynveen, Aaron; Albrecht, Tim; Kornyshev, Alexei A

    2015-01-28

    Homologous gene shuffling between DNA molecules promotes genetic diversity and is an important pathway for DNA repair. For this to occur, homologous genes need to find and recognize each other. However, despite its central role in homologous recombination, the mechanism of homology recognition has remained an unsolved puzzle of molecular biology. While specific proteins are known to play a role at later stages of recombination, an initial coarse grained recognition step has, however, been proposed. This relies on the sequence dependence of the DNA structural parameters, such as twist and rise, mediated by intermolecular interactions, in particular, electrostatic ones. In this proposed mechanism, sequences that have the same base pair text, or are homologous, have lower interaction energy than those sequences with uncorrelated base pair texts. The difference between the two energies is termed the "recognition energy." Here, we probe how the recognition energy changes when one DNA fragment slides past another, and consider, for the first time, homologous sequences in antiparallel alignment. This dependence on sliding is termed the "recognition well." We find there is a recognition well for anti-parallel, homologous DNA tracts, but only a very shallow one, so that their interaction will differ little from the interaction between two nonhomologous tracts. This fact may be utilized in single molecule experiments specially targeted to test the theory. As well as this, we test previous theoretical approximations in calculating the recognition well for parallel molecules against MC simulations and consider more rigorously the optimization of the orientations of the fragments about their long axes upon calculating these recognition energies. The more rigorous treatment affects the recognition energy a little, when the molecules are considered rigid. When torsional flexibility of the DNA molecules is introduced, we find excellent agreement between the analytical

  11. 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

  12. Associative Interference and Recognition Memory.

    ERIC Educational Resources Information Center

    Underwood, Benton J.; And Others

    Three experiments tested the generality of the conclusion that associative unlearning is minimal in the A-B, A-D paradigm. In Experiment 1, single-trial study of A-D, following single-trial study of A-B, did not produce retroactive inhibition in the recognition of A-B. In Experiment 2, A-B was acquired by associative matching. The interpolated…

  13. [Towards real recognition of osteoarthritis].

    PubMed

    Grange, Laurent

    2016-01-01

    Osteoarthritis suffers from a low profile among society and public authorities. However, the impact of this disease on the daily lives of those affected is considerable. Work remains to be done to ensure greater recognition of the disease and improve patient management. The osteoarthritis forum, which ran from September 2014 to June 2015, put forward proposals brought together in a white paper on osteoarthritis. Mobilisation is underway. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  14. 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

  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. Visual recognition of permuted words

    NASA Astrophysics Data System (ADS)

    Rashid, Sheikh Faisal; Shafait, Faisal; Breuel, Thomas M.

    2010-02-01

    In current study we examine how letter permutation affects in visual recognition of words for two orthographically dissimilar languages, Urdu and German. We present the hypothesis that recognition or reading of permuted and non-permuted words are two distinct mental level processes, and that people use different strategies in handling permuted words as compared to normal words. A comparison between reading behavior of people in these languages is also presented. We present our study in context of dual route theories of reading and it is observed that the dual-route theory is consistent with explanation of our hypothesis of distinction in underlying cognitive behavior for reading permuted and non-permuted words. We conducted three experiments in lexical decision tasks to analyze how reading is degraded or affected by letter permutation. We performed analysis of variance (ANOVA), distribution free rank test, and t-test to determine the significance differences in response time latencies for two classes of data. Results showed that the recognition accuracy for permuted words is decreased 31% in case of Urdu and 11% in case of German language. We also found a considerable difference in reading behavior for cursive and alphabetic languages and it is observed that reading of Urdu is comparatively slower than reading of German due to characteristics of cursive script.

  17. Modeling protein recognition of carbohydrates.

    PubMed

    Laederach, Alain; Reilly, Peter J

    2005-09-01

    We have a limited understanding of the details of molecular recognition of carbohydrates by proteins, which is critical to a multitude of biological processes. Furthermore, carbohydrate-modifying proteins such as glycosyl hydrolases and phosphorylases are of growing importance as potential drug targets. Interactions between proteins and carbohydrates have complex thermodynamics, and in general the specific positioning of only a few hydroxyl groups determines their binding affinities. A thorough understanding of both carbohydrate and protein structures is thus essential to predict these interactions. An atomic-level view of carbohydrate recognition through structures of carbohydrate-active enzymes complexed with transition-state inhibitors reveals some of the distinctive molecular features unique to protein-carbohydrate complexes. However, the inherent flexibility of carbohydrates and their often water-mediated hydrogen bonding to proteins makes simulation of their complexes difficult. Nonetheless, recent developments such as the parameterization of specific force fields and docking scoring functions have greatly improved our ability to predict protein-carbohydrate interactions. We review protein-carbohydrate complexes having defined molecular requirements for specific carbohydrate recognition by proteins, providing an overview of the different computational techniques available to model them. Copyright 2005 Wiley-Liss, Inc.

  18. Additive attacks on speaker recognition

    NASA Astrophysics Data System (ADS)

    Farrokh Baroughi, Alireza; Craver, Scott

    2014-02-01

    Speaker recognition is used to identify a speaker's voice from among a group of known speakers. A common method of speaker recognition is a classification based on cepstral coefficients of the speaker's voice, using a Gaussian mixture model (GMM) to model each speaker. In this paper we try to fool a speaker recognition system using additive noise such that an intruder is recognized as a target user. Our attack uses a mixture selected from a target user's GMM model, inverting the cepstral transformation to produce noise samples. In our 5 speaker data base, we achieve an attack success rate of 50% with a noise signal at 10dB SNR, and 95% by increasing noise power to 0dB SNR. The importance of this attack is its simplicity and flexibility: it can be employed in real time with no processing of an attacker's voice, and little computation is needed at the moment of detection, allowing the attack to be performed by a small portable device. For any target user, knowing that user's model or voice sample is sufficient to compute the attack signal, and it is enough that the intruder plays it while he/she is uttering to be classiffed as the victim.

  19. 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%.

  20. 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.

  1. Infant Visual Attention and Object Recognition

    PubMed Central

    Reynolds, Greg D.

    2015-01-01

    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. PMID:25596333

  2. Using discrete Tchebichef transform on speech recognition

    NASA Astrophysics Data System (ADS)

    Ernawan, Ferda; Noersasongko, Edi; Abu, Nur Azman

    2011-12-01

    Speech recognition is becoming popular in current development on mobile devices. Presumably, mobile devices have limited computational power, memory size and battery life. In general, speech recognition is a heavy process that required large sample data within each window. Fast Fourier Transform (FFT) is the most popular transform in speech recognition. In addition, FFT operates in complex field with imaginary numbers. This paper proposes an approach based on discrete orthonormal Tchebichef polynomials as a possible alternative to FFT. Discrete Tchebichef Transform (DTT) shall be utilized here instead of FFT. The preliminary experimental result shows that speech recognition using DTT produces a simpler and efficient transformation for speech recognition. The frequency formants using FFT and DTT have been compared. The result showed that, they have produced relatively identical output in term of basic vowel and consonant recognition. DTT has the potential to provide simpler computing with DTT coefficient real numbers only than FFT on speech recognition.

  3. Optical pattern recognition for printed music notation

    NASA Astrophysics Data System (ADS)

    Homenda, Wladyslaw

    1995-03-01

    The paper presents problems related to automated recognition of printed music notation. Music notation recognition is a challenging problem in both fields: pattern recognition and knowledge representation. Music notation symbols, though well characterized by their features, are arranged in elaborated way in real music notation, which makes recognition task very difficult and still open for new ideas. On the other hand, the aim of the system, i.e. application of acquired printed music into further processing requires special representation of music data. Due to complexity of music nature and music notation, music representation is one of the key issue in music notation recognition and music processing. The problems of pattern recognition and knowledge representation in context or music processing are discussed in this paper. MIDISCAN, the computer system for music notation recognition and music processing, is presented.

  4. 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.

  5. 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.

  6. 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

  7. Thermodynamic Modeling of Donor Splice Site Recognition in pre-mRNA

    NASA Astrophysics Data System (ADS)

    Aalberts, Daniel P.; Garland, Jeffrey A.

    2004-03-01

    When eukaryotic genes are edited by the spliceosome, the first step in intron recognition is the binding of a U1 snRNA with the donor (5') splice site. We model this interaction thermodynamically to identify splice sites. Applied to a set of 65 annotated genes, our Finding with Binding method achieves a significant separation between real and false sites. Analyzing binding patterns allows us to discard a large number of decoy sites. Our results improve statistics-based methods for donor site recognition, demonstrating the promise of physical modeling to find functional elements in the genome.

  8. Thermodynamic modeling of donor splice site recognition in pre-mRNA

    NASA Astrophysics Data System (ADS)

    Garland, Jeffrey A.; Aalberts, Daniel P.

    2004-04-01

    When eukaryotic genes are edited by the spliceosome, the first step in intron recognition is the binding of a U1 small nuclear RNA with the donor ( 5' ) splice site. We model this interaction thermodynamically to identify splice sites. Applied to a set of 65 annotated genes, our “finding with binding” method achieves a significant separation between real and false sites. Analyzing binding patterns allows us to discard a large number of decoy sites. Our results improve statistics-based methods for donor site recognition, demonstrating the promise of physical modeling to find functional elements in the genome.

  9. Recognition of a polymorphic monocyte antigen in HLA.

    PubMed

    van Leeuwen, A; Termijtelen, A; Shaw, S; van Rood, J J

    1982-08-05

    The serological recognition of 'new' gene products of the HLA system can be accomplished by selecting sera with strong leucocyte antibodies and testing these against a panel of cells obtained from donors which are compatible for the known HLA antigens with the antibody producer. This approach, which we termed the HLA-CAP approach (compatible with antibody producer), was essential in the recognition of what is now called the HLA-DR locus and of non HLA-linked T-cell subgroups. Using the same technique, we have defined here several sera recognizing a structure on monocytes similar to one of the alleles of the HLA-linked PL3 or secondary B-cell (SB) system, so far only recognized by cellular techniques.

  10. Importance of Nucleic Acid Recognition in Inflammation and Autoimmunity.

    PubMed

    Barrat, Franck J; Elkon, Keith B; Fitzgerald, Katherine A

    2016-01-01

    An important concept in immunology is the classification of immune responses as either innate or adaptive, based on whether the antigen receptors are encoded in the germline or generated somatically by gene rearrangement. The innate immune system is an ancient mode of immunity, and by being a first layer in our defense against infectious agents, it is essential for our ability to develop rapid and sustained responses to pathogens. We discuss the importance of nucleic acid recognition by the innate immune system to mounting an appropriate immune response to pathogens and also how inflammation driven by uncontrolled recognition of self-nucleic acids can lead to autoimmune diseases. We also summarize current efforts to either harness the immune system using agonists of nucleic acid-specific innate sensors or, on the contrary, by using inhibitors in autoimmune situations.

  11. 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…

  12. A new selective developmental deficit: Impaired object recognition with normal face recognition.

    PubMed

    Germine, Laura; Cashdollar, Nathan; Düzel, Emrah; Duchaine, Bradley

    2011-05-01

    Studies of developmental deficits in face recognition, or developmental prosopagnosia, have shown that individuals who have not suffered brain damage can show face recognition impairments coupled with normal object recognition (Duchaine and Nakayama, 2005; Duchaine et al., 2006; Nunn et al., 2001). However, no developmental cases with the opposite dissociation - normal face recognition with impaired object recognition - have been reported. The existence of a case of non-face developmental visual agnosia would indicate that the development of normal face recognition mechanisms does not rely on the development of normal object recognition mechanisms. To see whether a developmental variant of non-face visual object agnosia exists, we conducted a series of web-based object and face recognition tests to screen for individuals showing object recognition memory impairments but not face recognition impairments. Through this screening process, we identified AW, an otherwise normal 19-year-old female, who was then tested in the lab on face and object recognition tests. AW's performance was impaired in within-class visual recognition memory across six different visual categories (guns, horses, scenes, tools, doors, and cars). In contrast, she scored normally on seven tests of face recognition, tests of memory for two other object categories (houses and glasses), and tests of recall memory for visual shapes. Testing confirmed that her impairment was not related to a general deficit in lower-level perception, object perception, basic-level recognition, or memory. AW's results provide the first neuropsychological evidence that recognition memory for non-face visual object categories can be selectively impaired in individuals without brain damage or other memory impairment. These results indicate that the development of recognition memory for faces does not depend on intact object recognition memory and provide further evidence for category-specific dissociations in visual

  13. Germline and somatic diversification of immune recognition elements in Metazoa.

    PubMed

    Pasquier, Louis Du

    2006-04-15

    The histories of the immune systems of Metazoa during evolution are envisaged like as many adaptations to the continuous diversification of immune receptors and effectors genes under the pressure of changing environments. A basic diversity of potential immune receptor genes existed in primitive Metazoa. Their subsequent recruitment into immunity, their diversification revolving around the conservation of signaling cascades was paralleled by cell specialization and the introduction of regulatory networks. Polymorphism, duplication and somatic mechanisms of diversification affected independently and still affect different gene families in many phyla, creating a greater variety of immune system exhibiting sometimes little homology but much analogy to one another. Diversity and multiplicity of receptors was generated by duplication and creation of multigene families. Independently in several phyla further diversity is created somatically by alternate splicing, somatic mutation, gene conversion and gene rearrangement. In several instances combinatorial usage of polypeptide chains or genes segments increases the repertoire of the recognition structures. Metazoa had to adapt to the conditions generated by this diversity: the control of expression of multiple genes and the risk of autoimmunity.

  14. Infrared face recognition using texture descriptors

    NASA Astrophysics Data System (ADS)

    Akhloufi, Moulay A.; Bendada, Abdelhakim

    2010-05-01

    Face recognition is an area of computer vision that has attracted a lot of interest from the research community. A growing demand for robust face recognition software in security applications has driven the development of interesting approaches in this field. A large quantity of research in face recognition deals with visible face images. In the visible spectrum the illumination and face expressions changes represent a significant challenge for the recognition system. To avoid these problems, researchers proposed recently the use of 3D and infrared imaging for face recognition. In this work, we introduce a new framework for infrared face recognition using texture descriptors. This framework exploits linear and non linear dimensionality reduction techniques for face learning and recognition in the texture space. Active and passive infrared imaging modalities are used and comparison with visible face recognition is performed. Two multispectral face recognition databases were used in our experiments: Equinox Database (Visible, SWIR, MWIR, LWIR) and Laval University Multispectral Database (Visible, NIR, MWIR, LWIR). The obtained results show high increase in recognition performance when texture descriptors like LBP (Local Binary Pattern) and LTP (Local Ternary Pattern) are used. The best result was obtained in the short wave infrared spectrum (SWIR) using non linear dimensionality reduction techniques.

  15. Face Processing: Models For Recognition

    NASA Astrophysics Data System (ADS)

    Turk, Matthew A.; Pentland, Alexander P.

    1990-03-01

    The human ability to process faces is remarkable. We can identify perhaps thousands of faces learned throughout our lifetime and read facial expression to understand such subtle qualities as emotion. These skills are quite robust, despite sometimes large changes in the visual stimulus due to expression, aging, and distractions such as glasses or changes in hairstyle or facial hair. Computers which model and recognize faces will be useful in a variety of applications, including criminal identification, human-computer interface, and animation. We discuss models for representing faces and their applicability to the task of recognition, and present techniques for identifying faces and detecting eye blinks.

  16. 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

  17. 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.

  18. Neurophysiological correlates of word recognition in dyslexia.

    PubMed

    Schulte-Körne, G; Deimel, W; Bartling, J; Remschmidt, H

    2004-07-01

    The neurobiological basis of learning word spellings and recognition of recently learned words was assessed in a learning experiment in 9 dyslexics and 9 controls male adolescents. In a recognition paradigm previously learned pseudowords and graphic symbols were presented 50 times each interspersed pseudo-randomly between 3 unlearned items which were repeated 50 times and 150 filler pseudowords. The electrophysiological correlate of recognition of learned pseudowords and graphic symbols was a positivity around 600 ms. For pseudowords the amplitude of this ERP component was significantly attenuated in the dyslexic group, no differences between the groups were found for recognition of graphic material. These data suggest that dyslexic children are able to learn the spelling of simple words, however, the neurophysiological correlate of recognition of these learned words is significantly attenuated. This result strengthens the view that dyslexic children are not generally impaired in recognition memory but specific for linguistic material like words.

  19. Familiar people recognition disorders: an introductory review.

    PubMed

    Gainotti, Guido

    2014-01-01

    The aim of this introduction is to provide a general background for the individual contributions dealing with different aspects of familiar people recognition disorders. Following are the main points considered in this survey: 1) the cognitive models proposed to explain the functional architecture of processes subsuming familiar people recognition; 2) the different roles of the right and left hemisphere in identifying people by face voice and name; 3) the anatomical structures and the cognitive processes involved in face and voice recognition; 4) the interactions that exist among the perceptual processes subsuming face and voice recognition, but not people's faces, voices and proper names; 5) the patterns of multimodal defects of familiar people recognition and their implications for current cognitive models. Finally, there is a short discussion of two models advanced to explain the role of the anterior temporal lobes in people recognition.

  20. 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

  1. Kannada character recognition system using neural network

    NASA Astrophysics Data System (ADS)

    Kumar, Suresh D. S.; Kamalapuram, Srinivasa K.; Kumar, Ajay B. R.

    2013-03-01

    Handwriting recognition has been one of the active and challenging research areas in the field of pattern recognition. It has numerous applications which include, reading aid for blind, bank cheques and conversion of any hand written document into structural text form. As there is no sufficient number of works on Indian language character recognition especially Kannada script among 15 major scripts in India. In this paper an attempt is made to recognize handwritten Kannada characters using Feed Forward neural networks. A handwritten Kannada character is resized into 20x30 Pixel. The resized character is used for training the neural network. Once the training process is completed the same character is given as input to the neural network with different set of neurons in hidden layer and their recognition accuracy rate for different Kannada characters has been calculated and compared. The results show that the proposed system yields good recognition accuracy rates comparable to that of other handwritten character recognition systems.

  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. 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.

  4. 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

  5. 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

  6. Speech Recognition: Acoustic, Phonetic and Lexical

    DTIC Science & Technology

    1985-10-01

    sffl^ss^t-iftsasisiiBiSiBa :.%^v 00 o o o CO < I Q < "END-OF-FISCAL YEAR" REPORT Speech Recognition; Acoustic, Phonetic and Lexical...Virginia 22217 10. SOURCg OP PUNOINO NQS. PROGRAM I Li MINT NO. 1. TITUS Inciua* itcnniy dauifltaiuuii Speech Recognition; Acoustic, Phonetic and...34 Letter 1. Contract Information (a) Title: Speech Recognition: Acoustic, Phonetic , and Lexical Knowledge Representation (b) ONR Contract No.: N00014

  7. Auditory Modeling for Noisy Speech Recognition.

    DTIC Science & Technology

    2000-01-01

    recognition, audio signal processing, and multilingual language translation to design and demonstrate an advanced audio interface for speech recognition...and provides applications to multilingual spoken language translation. As a future Phase III commercial product, this system will perform real time... multilingual speech recognition in noisy vehicles, offices and factories. The potential market for this technology includes any commercial speech and translation application in noisy environments.

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. Disruptive camouflage impairs object recognition

    PubMed Central

    Webster, Richard J.; Hassall, Christopher; Herdman, Chris M.; Godin, Jean-Guy J.; Sherratt, Thomas N.

    2013-01-01

    Whether hiding from predators, or avoiding battlefield casualties, camouflage is widely employed to prevent detection. Disruptive coloration is a seemingly well-known camouflage mechanism proposed to function by breaking up an object's salient features (for example their characteristic outline), rendering objects more difficult to recognize. However, while a wide range of animals are thought to evade detection using disruptive patterns, there is no direct experimental evidence that disruptive coloration impairs recognition. Using humans searching for computer-generated moth targets, we demonstrate that the number of edge-intersecting patches on a target reduces the likelihood of it being detected, even at the expense of reduced background matching. Crucially, eye-tracking data show that targets with more edge-intersecting patches were looked at for longer periods prior to attack, and passed-over more frequently during search tasks. We therefore show directly that edge patches enhance survivorship by impairing recognition, confirming that disruptive coloration is a distinct camouflage strategy, not simply an artefact of background matching. PMID:24152693

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  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. Facial affect recognition and schizotypal personality characteristics.

    PubMed

    Abbott, Gavin R; Green, Melissa J

    2013-02-01

    Deficits in facial affect recognition are well established in schizophrenia, yet relatively little research has examined facial affect recognition in hypothetically psychosis-prone or 'schizotypal' individuals. Those studies that have examined social cognition in psychosis-prone individuals have paid little attention to the association between facial emotion recognition and particular schizotypal personality features. The present study therefore sought to investigate relationships between facial emotion recognition and the different aspects of schizotypy. Facial affect recognition accuracy was examined in 50 psychiatrically healthy individuals assessed for level of schizotypy using the Schizotypal Personality Questionnaire. This instrument provides a multidimensional measure of schizophrenia proneness, encompassing 'cognitive-perceptual', 'interpersonal' and 'disorganized' features of schizotypy. It was hypothesized that the cognitive-perceptual and interpersonal aspects of schizotypy would be associated with difficulties identifying facial expressions of emotion during a forced-choice recognition task using a standardized series of colour photographs. As predicted, interpersonal aspects of schizotypy (particularly social anxiety) were associated with reduced accuracy on the facial affect recognition task, but there was no association between affect recognition accuracy and cognitive-perceptual features of schizotypy. These results suggest that subtle deficits in facial affect recognition in otherwise psychiatrically healthy individuals may be related to the vulnerability for interpersonal communication difficulties, as seen in schizophrenia. © 2012 Wiley Publishing Asia Pty Ltd.

  20. RESEARCH ON SPEECH COMMUNICATION. AUTOMATIC SPEECH RECOGNITION.

    DTIC Science & Technology

    SPEECH RECOGNITION, AUTOMATIC), EXPERIMENTAL DATA, THEORY, ENGLISH LANGUAGE, PHONETICS, LINGUISTICS, AIR FORCE RESEARCH, FEASIBILITY STUDIES, ACOUSTICS, VOCABULARY, SPEECH REPRESENTATION, WORD ASSOCIATION

  1. Deciphering the protein-RNA recognition code: combining large-scale quantitative methods with structural biology.

    PubMed

    Hennig, Janosch; Sattler, Michael

    2015-08-01

    RNA binding proteins (RBPs) are key factors for the regulation of gene expression by binding to cis elements, i.e. short sequence motifs in RNAs. Recent studies demonstrate that cooperative binding of multiple RBPs is important for the sequence-specific recognition of RNA and thereby enables the regulation of diverse biological activities by a limited set of RBPs. Cross-linking immuno-precipitation (CLIP) and other recently developed high-throughput methods provide comprehensive, genome-wide maps of protein-RNA interactions in the cell. Structural biology gives detailed insights into molecular mechanisms and principles of RNA recognition by RBPs, but has so far focused on single RNA binding proteins and often on single RNA binding domains. The combination of high-throughput methods and detailed structural biology studies is expected to greatly advance our understanding of the code for protein-RNA recognition in gene regulation, as we review in this article. © 2015 WILEY Periodicals, Inc.

  2. Sequence Recognition in the Pairing of DNA Duplexes

    NASA Astrophysics Data System (ADS)

    Kornyshev, A. A.; Leikin, S.

    2001-04-01

    Pairing of DNA fragments with homologous sequences occurs in gene shuffling, DNA repair, and other vital processes. While chemical individuality of base pairs is hidden inside the double helix, x ray and NMR revealed sequence-dependent modulation of the structure of DNA backbone. Here we show that the resulting modulation of the DNA surface charge pattern enables duplexes longer than ~50 base pairs to recognize sequence homology electrostatically at a distance of up to several water layers. This may explain the local recognition observed in pairing of homologous chromosomes and the observed length dependence of homologous recombination.

  3. Geometry Of Discrete Sets With Applications To Pattern Recognition

    NASA Astrophysics Data System (ADS)

    Sinha, Divyendu

    1990-03-01

    In this paper we present a new framework for discrete black and white images that employs only integer arithmetic. This framework is shown to retain the essential characteristics of the framework for Euclidean images. We propose two norms and based on them, the permissible geometric operations on images are defined. The basic invariants of our geometry are line images, structure of image and the corresponding local property of strong attachment of pixels. The permissible operations also preserve the 3x3 neighborhoods, area, and perpendicularity. The structure, patterns, and the inter-pattern gaps in a discrete image are shown to be conserved by the magnification and contraction process. Our notions of approximate congruence, similarity and symmetry are similar, in character, to the corresponding notions, for Euclidean images [1]. We mention two discrete pattern recognition algorithms that work purely with integers, and which fit into our framework. Their performance has been shown to be at par with the performance of traditional geometric schemes. Also, all the undesired effects of finite length registers in fixed point arithmetic that plague traditional algorithms, are non-existent in this family of algorithms.

  4. Data compressor designed to improve recognition of magnetic phases

    NASA Astrophysics Data System (ADS)

    Vogel, E. E.; Saravia, G.; Cortez, L. V.

    2012-02-01

    Data compressors available in the web have been used to determine magnetic phases for two-dimensional (2D) systems [E. Vogel, G. Saravia, F. Bachmann, B. Fierro, J. Fischer, Phase transitions in Edwards-Anderson model by means of information theory, Physica A 388 2009 4075-4082]. In the present work, we push this line forward along four different directions. First, the compressor itself: we design a new data compressor, named wlzip, optimized for the recognition of information having physical (or scientific) information instead of the random digital information usually compressed. Second, for the first time we extend the data compression analysis to the 3D Ising ferromagnetic model using wlzip. Third, we discuss the tuning possibilities of wlzip in terms of the number of digits considered in the compression to yield maximum definition; in this way, the transition temperature of both 2D and 3D Ising ferromagnets can be reported with very good resolution. Fourth, the extension of the time window through which the data file is actually compressed is also considered to get optimum accuracy. The paper is focused on the new compressor, its algorithm in general and the way to apply it. Advantages and disadvantages of wlzip are discussed. Toward the end, we mention other possible applications of this technique to recognize stable and unstable regimes in the evolution of variables in meteorology (such as pollution content or atmospheric pressure), biology (blood pressure) and econophysics (prices of the stock market).

  5. Dreaming and waking consciousness: a character recognition study.

    PubMed

    Kahn, D; Stickgold, R; Pace-Schott, E F; Hobson, J A

    2000-12-01

    The formal features of dream characters were studied in a sample of 320 dream reports submitted by 33 adult subjects (13 male, 20 female) of varying ages in a university extension course. Subjects were queried by questionnaire about dream characters immediately after recording their dreams upon awakening in their normal home setting. It was found that 48% of characters represented a named personage known to the dreamer, 35% were generically identified by their social role (e.g., policeman) or abstract relation to the dreamer (e.g., a friend) while only 16% were wholly novel. Seventy-seven percent of characters were pseudosensorily present in the dream whereas 23% were present only by mention or thought. Subjects were allowed to endorse one or more of four bases of recognition and, among named characters, 32% were identified by 'appearance', 21% by 'behavior', 45% by 'face', and 44% by 'just knowing' (with the respective percentages for generic characters being 39%, 38%, 9% and 40%). Fourteen percent of named and generic characters had associated some element of bizarreness most frequently consisting of an incongruous feature. Comparing the 25 longest and 25 shortest reports, named subjects were significantly more common in the shortest reports whereas generic and unknown characters were more common in the longest reports. Results are interpreted in neurocognitive terms as possibly reflecting a decrease during dreaming relative to waking in the exchange of information between inferotemporal face identification areas and prefrontal areas subserving logic and working memory.

  6. A Neural Basis of Facial Action Recognition in Humans

    PubMed Central

    Srinivasan, Ramprakash; Golomb, Julie D.

    2016-01-01

    By combining different facial muscle actions, called action units, humans can produce an extraordinarily large number of facial expressions. Computational models and studies in cognitive science and social psychology have long hypothesized that the brain needs to visually interpret these action units to understand other people's actions and intentions. Surprisingly, no studies have identified the neural basis of the visual recognition of these action units. Here, using functional magnetic resonance imaging and an innovative machine learning analysis approach, we identify a consistent and differential coding of action units in the brain. Crucially, in a brain region thought to be responsible for the processing of changeable aspects of the face, multivoxel pattern analysis could decode the presence of specific action units in an image. This coding was found to be consistent across people, facilitating the estimation of the perceived action units on participants not used to train the multivoxel decoder. Furthermore, this coding of action units was identified when participants attended to the emotion category of the facial expression, suggesting an interaction between the visual analysis of action units and emotion categorization as predicted by the computational models mentioned above. These results provide the first evidence for a representation of action units in the brain and suggest a mechanism for the analysis of large numbers of facial actions and a loss of this capacity in psychopathologies. SIGNIFICANCE STATEMENT Computational models and studies in cognitive and social psychology propound that visual recognition of facial expressions requires an intermediate step to identify visible facial changes caused by the movement of specific facial muscles. Because facial expressions are indeed created by moving one's facial muscles, it is logical to assume that our visual system solves this inverse problem. Here, using an innovative machine learning method and

  7. A Neural Basis of Facial Action Recognition in Humans.

    PubMed

    Srinivasan, Ramprakash; Golomb, Julie D; Martinez, Aleix M

    2016-04-20

    By combining different facial muscle actions, called action units, humans can produce an extraordinarily large number of facial expressions. Computational models and studies in cognitive science and social psychology have long hypothesized that the brain needs to visually interpret these action units to understand other people's actions and intentions. Surprisingly, no studies have identified the neural basis of the visual recognition of these action units. Here, using functional magnetic resonance imaging and an innovative machine learning analysis approach, we identify a consistent and differential coding of action units in the brain. Crucially, in a brain region thought to be responsible for the processing of changeable aspects of the face, multivoxel pattern analysis could decode the presence of specific action units in an image. This coding was found to be consistent across people, facilitating the estimation of the perceived action units on participants not used to train the multivoxel decoder. Furthermore, this coding of action units was identified when participants attended to the emotion category of the facial expression, suggesting an interaction between the visual analysis of action units and emotion categorization as predicted by the computational models mentioned above. These results provide the first evidence for a representation of action units in the brain and suggest a mechanism for the analysis of large numbers of facial actions and a loss of this capacity in psychopathologies. Computational models and studies in cognitive and social psychology propound that visual recognition of facial expressions requires an intermediate step to identify visible facial changes caused by the movement of specific facial muscles. Because facial expressions are indeed created by moving one's facial muscles, it is logical to assume that our visual system solves this inverse problem. Here, using an innovative machine learning method and neuroimaging data, we identify

  8. A Distractor-Free Test of Recognition and a Target-Free Test of False Recognition.

    ERIC Educational Resources Information Center

    Ley, Ronald

    A method for measuring recognition memory (free of distractors) and false recognition was based on the assumption that the subject was "honest." A distractor-free test of word recognition (a single-item test trial in which the 36 targets were presented prior to the 36 distractors) was compared with a traditional target-distractor…

  9. 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…

  10. Mammalian social odours: attraction and individual recognition

    PubMed Central

    Brennan, Peter A; Kendrick, Keith M

    2006-01-01

    Mammalian social systems rely on signals passed between individuals conveying information including sex, reproductive status, individual identity, ownership, competitive ability and health status. Many of these signals take the form of complex mixtures of molecules sensed by chemosensory systems and have important influences on a variety of behaviours that are vital for reproductive success, such as parent–offspring attachment, mate choice and territorial marking. This article aims to review the nature of these chemosensory cues and the neural pathways mediating their physiological and behavioural effects. Despite the complexities of mammalian societies, there are instances where single molecules can act as classical pheromones attracting interest and approach behaviour. Chemosignals with relatively high volatility can be used to signal at a distance and are sensed by the main olfactory system. Most mammals also possess a vomeronasal system, which is specialized to detect relatively non-volatile chemosensory cues following direct contact. Single attractant molecules are sensed by highly specific receptors using a labelled line pathway. These act alongside more complex mixtures of signals that are required to signal individual identity. There are multiple sources of such individuality chemosignals, based on the highly polymorphic genes of the major histocompatibility complex (MHC) or lipocalins such as the mouse major urinary proteins. The individual profile of volatile components that make up an individual odour signature can be sensed by the main olfactory system, as the pattern of activity across an array of broadly tuned receptor types. In addition, the vomeronasal system can respond highly selectively to non-volatile peptide ligands associated with the MHC, acting at the V2r class of vomeronasal receptor. The ability to recognize individuals or their genetic relatedness plays an important role in mammalian social behaviour. Thus robust systems for olfactory

  11. Gene name identification and normalization using a model organism database.

    PubMed

    Morgan, Alexander A; Hirschman, Lynette; Colosimo, Marc; Yeh, Alexander S; Colombe, Jeff B

    2004-12-01

    Biology has now become an information science, and researchers are increasingly dependent on expert-curated biological databases to organize the findings from the published literature. We report here on a series of experiments related to the application of natural language processing to aid in the curation process for FlyBase. We focused on listing the normalized form of genes and gene products discussed in an article. We broke this into two steps: gene mention tagging in text, followed by normalization of gene names. For gene mention tagging, we adopted a statistical approach. To provide training data, we were able to reverse engineer the gene lists from the associated articles and abstracts, to generate text labeled (imperfectly) with gene mentions. We then evaluated the quality of the noisy training data (precision of 78%, recall 88%) and the quality of the HMM tagger output trained on this noisy data (precision 78%, recall 71%). In order to generate normalized gene lists, we explored two approaches. First, we explored simple pattern matching based on synonym lists to obtain a high recall/low precision system (recall 95%, precision 2%). Using a series of filters, we were able to improve precision to 50% with a recall of 72% (balanced F-measure of 0.59). Our second approach combined the HMM gene mention tagger with various filters to remove ambiguous mentions; this approach achieved an F-measure of 0.72 (precision 88%, recall 61%). These experiments indicate that the lexical resources provided by FlyBase are complete enough to achieve high recall on the gene list task, and that normalization requires accurate disambiguation; different strategies for tagging and normalization trade off recall for precision.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. Recognition of movement object collision

    NASA Astrophysics Data System (ADS)

    Chang, Hsiao Tsu; Sun, Geng-tian; Zhang, Yan

    1991-03-01

    The paper explores the collision recognition of two objects in both crisscross and revolution motions A mathematical model has been established based on the continuation theory. The objects of any shape may be regarded as being built of many 3siniplexes or their convex hulls. Therefore the collision problem of two object in motion can be reduced to the collision of two corresponding 3siinplexes on two respective objects accordingly. Thus an optimized algorithm is developed for collision avoidance which is suitable for computer control and eliminating the need for vision aid. With this algorithm computation time has been reduced significantly. This algorithm is applicable to the path planning of mobile robots And also is applicable to collision avoidance of the anthropomorphic arms grasping two complicated shaped objects. The algorithm is realized using LISP language on a VAX8350 minicomputer.

  17. 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.

  18. Recognition of factitial hand injuries.

    PubMed

    Carlson, M J; Linscheid, R L; Lucas, A R

    1977-01-01

    Facitial injuries with various presentations occur with some frequency to the hand because it is a body part that is easily accessible. Methods used to produce wounds included insertion of porcupine quills, application of constrictive rubber bands, mascara injections and excoriation of healing wounds. It is important to recognize the factitial origin in order to avoid needless repetitive surgery and permanent hand disability. No specific pattern of psychopathology was found in our cases. The patients' attitude toward their lesions was one of bland unconcern and stoicism. The patients were resistant to psychiatric referral and persisted in seeking medical responsibility for cure. Successful management requires early suspicion and prompt recognition as well as establishment of non-accusatory relationship with the primary physician. Confrontation should be avoided if possible. Even if reinforced with collaborative evidence, such confrontation will have limited effect on the patient's subsequent behavior.

  19. 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.

  20. 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