Sample records for accurate trna recognition

  1. The tRNA Elbow in Structure, Recognition and Evolution

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    Jinwei Zhang


    Full Text Available Prominent in the L-shaped three-dimensional structure of tRNAs is the “elbow” where their two orthogonal helical stacks meet. It has a conserved structure arising from the interaction of the terminal loops of the D- and T-stem-loops, and presents to solution a flat face of a tertiary base pair between the D- and T-loops. In addition to the ribosome, which interacts with the elbow in all three of its tRNA binding sites, several cellular RNAs and many proteins are known to recognize the elbow. At least three classes of non-coding RNAs, namely 23S rRNA, ribonuclease P, and the T-box riboswitches, recognize the tRNA elbow employing an identical structural motif consisting of two interdigitated T-loops. In contrast, structural solutions to tRNA-elbow recognition by proteins are varied. Some enzymes responsible for post-transcriptional tRNA modification even disrupt the elbow structure in order to access their substrate nucleotides. The evolutionary origin of the elbow is mysterious, but, because it does not explicitly participate in the flow of genetic information, it has been proposed to be a late innovation. Regardless, it is biologically essential. Even some viruses that hijack the cellular machinery using tRNA decoys have convergently evolved near-perfect mimics of the tRNA elbow.

  2. Saturation of recognition elements blocks evolution of new tRNA identities. (United States)

    Saint-Léger, Adélaïde; Bello, Carla; Dans, Pablo D; Torres, Adrian Gabriel; Novoa, Eva Maria; Camacho, Noelia; Orozco, Modesto; Kondrashov, Fyodor A; Ribas de Pouplana, Lluís


    Understanding the principles that led to the current complexity of the genetic code is a central question in evolution. Expansion of the genetic code required the selection of new transfer RNAs (tRNAs) with specific recognition signals that allowed them to be matured, modified, aminoacylated, and processed by the ribosome without compromising the fidelity or efficiency of protein synthesis. We show that saturation of recognition signals blocks the emergence of new tRNA identities and that the rate of nucleotide substitutions in tRNAs is higher in species with fewer tRNA genes. We propose that the growth of the genetic code stalled because a limit was reached in the number of identity elements that can be effectively used in the tRNA structure.

  3. The Enzymatic Paradox of Yeast Arginyl-tRNA Synthetase: Exclusive Arginine Transfer Controlled by a Flexible Mechanism of tRNA Recognition. (United States)

    McShane, Ariel; Hok, Eveline; Tomberlin, Jensen; Eriani, Gilbert; Geslain, Renaud


    Identity determinants are essential for the accurate recognition of transfer RNAs by aminoacyl-tRNA synthetases. To date, arginine determinants in the yeast Saccharomyces cerevisiae have been identified exclusively in vitro and only on a limited number of tRNA Arginine isoacceptors. In the current study, we favor a full cellular approach and expand the investigation of arginine determinants to all four tRNA Arg isoacceptors. More precisely, this work scrutinizes the relevance of the tRNA nucleotides at position 20, 35 and 36 in the yeast arginylation reaction. We built 21 mutants by site-directed mutagenesis and tested their functionality in YAL5, a previously engineered yeast knockout deficient for the expression of tRNA Arg CCG. Arginylation levels were also monitored using Northern blot. Our data collected in vivo correlate with previous observations. C35 is the prominent arginine determinant followed by G36 or U36 (G/U36). In addition, although there is no major arginine determinant in the D loop, the recognition of tRNA Arg ICG relies to some extent on the nucleotide at position 20. This work refines the existing model for tRNA Arg recognition. Our observations indicate that yeast Arginyl-tRNA synthetase (yArgRS) relies on distinct mechanisms to aminoacylate the four isoacceptors. Finally, according to our refined model, yArgRS is able to accommodate tRNA Arg scaffolds presenting N34, C/G35 and G/A/U36 anticodons while maintaining specificity. We discuss the mechanistic and potential physiological implications of these findings.

  4. Species-specific identity elements of tRNA Trp

    Institute of Scientific and Technical Information of China (English)


    Through the comparisons among 91 tRNA Trp sequences from prokaryotes, archea and eukaryotes, the potential species-specific identity elements of tRNA Trp are found to be located within acceptor stem, dihydrouridine (D) stem, anticodon(AC) stem and discriminator base. Mutagenesis of B. subtilis tRNA Trp to the eukaryotic consensus se quence, in vitro transcription and enzymatic assay of tRNA Trp toward different tryptophanyl-tRNA synthetases (TrpRS) were employed to shed light on these species-specific identity elements and demonstrate the accurate recognition and the coevolution between tRNA and TrpRS. B. subtilis tRNA Trp with its acceptor stem and discriminator base transplanted by eukaryotic counterparts exhibited diminished reactivity toward B. subtilis enzyme but could be efficiently aminoacylated by rat liver crude enzyme. In contrast, B. subtilis tRNA Trp analog with the eukaryotic anticodon stem and D stem retains its recognition by B. subtilis enzyme. The results provide a strong evidence that the species-specific identity elements of tRNA Trp are orientated within the acceptor stem and discriminator base of tRNA Trp, and the anticodon stem and D stem are of little importance to the interaction between tRNA Trp and its cognate synthetase (TrpRS).

  5. Structural basis for recognition of cognate tRNA by tyrosyl-tRNA synthetase from three kingdoms. (United States)

    Tsunoda, Masaru; Kusakabe, Yoshio; Tanaka, Nobutada; Ohno, Satoshi; Nakamura, Masashi; Senda, Toshiya; Moriguchi, Tomohisa; Asai, Norio; Sekine, Mitsuo; Yokogawa, Takashi; Nishikawa, Kazuya; Nakamura, Kazuo T


    The specific aminoacylation of tRNA by tyrosyl-tRNA synthetases (TyrRSs) relies on the identity determinants in the cognate tRNA(Tyr)s. We have determined the crystal structure of Saccharomyces cerevisiae TyrRS (SceTyrRS) complexed with a Tyr-AMP analog and the native tRNA(Tyr)(GPsiA). Structural information for TyrRS-tRNA(Tyr) complexes is now full-line for three kingdoms. Because the archaeal/eukaryotic TyrRSs-tRNA(Tyr)s pairs do not cross-react with their bacterial counterparts, the recognition modes of the identity determinants by the archaeal/eukaryotic TyrRSs were expected to be similar to each other but different from that by the bacterial TyrRSs. Interestingly, however, the tRNA(Tyr) recognition modes of SceTyrRS have both similarities and differences compared with those in the archaeal TyrRS: the recognition of the C1-G72 base pair by SceTyrRS is similar to that by the archaeal TyrRS, whereas the recognition of the A73 by SceTyrRS is different from that by the archaeal TyrRS but similar to that by the bacterial TyrRS. Thus, the lack of cross-reactivity between archaeal/eukaryotic and bacterial TyrRS-tRNA(Tyr) pairs most probably lies in the different sequence of the last base pair of the acceptor stem (C1-G72 vs G1-C72) of tRNA(Tyr). On the other hand, the recognition mode of Tyr-AMP is conserved among the TyrRSs from the three kingdoms.

  6. Unexpected expansion of tRNA substrate recognition by the yeast m1G9 methyltransferase Trm10 (United States)

    Swinehart, William E.; Henderson, Jeremy C.; Jackman, Jane E.


    N-1 Methylation of the nearly invariant purine residue found at position 9 of tRNA is a nucleotide modification found in multiple tRNA species throughout Eukarya and Archaea. First discovered in Saccharomyces cerevisiae, the tRNA methyltransferase Trm10 is a highly conserved protein both necessary and sufficient to catalyze all known instances of m1G9 modification in yeast. Although there are 19 unique tRNA species that contain a G at position 9 in yeast, and whose fully modified sequence is known, only 9 of these tRNA species are modified with m1G9 in wild-type cells. The elements that allow Trm10 to distinguish between structurally similar tRNA species are not known, and sequences that are shared between all substrate or all nonsubstrate tRNAs have not been identified. Here, we demonstrate that the in vitro methylation activity of yeast Trm10 is not sufficient to explain the observed pattern of modification in vivo, as additional tRNA species are substrates for Trm10 m1G9 methyltransferase activity. Similarly, overexpression of Trm10 in yeast yields m1G9 containing tRNA species that are ordinarily unmodified in vivo. Thus, yeast Trm10 has a significantly broader tRNA substrate specificity than is suggested by the observed pattern of modification in wild-type yeast. These results may shed light onto the suggested involvement of Trm10 in other pathways in other organisms, particularly in higher eukaryotes that contain up to three different genes with sequence similarity to the single TRM10 gene in yeast, and where these other enzymes have been implicated in pathways beyond tRNA processing. PMID:23793893

  7. Hetero subunit interaction and RNA recognition of yeast tRNA (m7G46) methyltransferase synthesized in a wheat germ cell-free translation system. (United States)

    Muneyoshi, Yuki; Matsumoto, Keisuke; Tomikawa, Chie; Toyooka, Takashi; Ochi, Anna; Masaoka, Takashi; Endo, Yaeta; Hori, Hiroyuki


    Yeast tRNA (m(7)G46) methyltransferase contains two protein subunits (Trm8 and Trm82). The enzyme catalyzes a methyl-transfer from S-adenosyl-L-methionine to the N(7) atom of guanine at position 46 in tRNA. We deviced synthesis of active Trm8-Trm82 heterodimer in a wheat germ cell-free translation system. When Trm8 or Trm82 mRNA were used for a synthesis, Trm8 or Trm82 protein could be synthesized. Upon mixing the synthesized Trm8 and Trm82 proteins, no active Trm8-Trm82 heterodimer was produced. Active Trm8-Trm82 heterodimer was only synthesized under conditions, in which both Trm8 and Trm82 mRNAs were co-translated. To address the RNA recognition mechanism of the Trm8-Trm82 complex, we investigated methyl acceptance activities of eight truncated yeast tRNA(Phe) transcripts. In this meeting, we demonstrate that yeast Trm8-Trm82 has stricter recognition requirements for the tRNA molecule as compared to the bacterial enzyme, TrmB.

  8. Accurate invariant pattern recognition for perspective camera model (United States)

    Serikova, Mariya G.; Pantyushina, Ekaterina N.; Zyuzin, Vadim V.; Korotaev, Valery V.; Rodrigues, Joel J. P. C.


    In this work we present a pattern recognition method based on geometry analysis of a flat pattern. The method provides reliable detection of the pattern in the case when significant perspective deformation is present in the image. The method is based on the fact that collinearity of the lines remains unchanged under perspective transformation. So the recognition feature is the presence of two lines, containing four points each. Eight points form two squares for convenience of applying corner detection algorithms. The method is suitable for automatic pattern detection in a dense environment of false objects. In this work we test the proposed method for statistics of detection and algorithm's performance. For estimation of pattern detection quality we performed image simulation process with random size and spatial frequency of background clutter while both translational (range varied from 200 mm to 1500 mm) and rotational (up to 60°) deformations in given pattern position were added. Simulated measuring system included a camera (4000x4000 sensor with 25 mm lens) and a flat pattern. Tests showed that the proposed method demonstrates no more than 1% recognition error when number of false targets is up to 40.

  9. Biosynthesis and functions of sulfur modifications in tRNA

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    Naoki eShigi


    Full Text Available Sulfur is an essential element for a variety of cellular constituents in all living organisms. In tRNA molecules, there are many sulfur-containing nucleosides, such as the derivatives of 2‑thiouridine (s2U, 4-thiouridine (s4U, 2-thiocytidine (s2C, and 2-methylthioadenosine (ms2A. Earlier studies established the functions of these modifications for accurate and efficient translation, including proper recognition of the codons in mRNA or stabilization of tRNA structure. In many cases, the biosynthesis of these sulfur modifications starts with cysteine desulfurases, which catalyze the generation of persulfide (an activated form of sulfur from cysteine. Many sulfur-carrier proteins are responsible for delivering this activated sulfur to each biosynthesis pathway. Finally, specific modification enzymes activate target tRNAs and then incorporate sulfur atoms. Intriguingly, the biosynthesis of 2-thiouridine in all domains of life is functionally and evolutionarily related to the ubiquitin-like post-translational modification system of cellular proteins in eukaryotes. This review summarizes the recent characterization of the biosynthesis of sulfur modifications in tRNA and the novel roles of this modification in cellular functions in various model organisms, with a special emphasis on 2-thiouridine derivatives. Each biosynthesis pathway of sulfur-containing molecules is mutually modulated via sulfur trafficking, and 2-thiouridine and codon usage bias have been proposed to control the translation of specific genes.

  10. Escherichia coli methionyl-tRNA formyltransferase: role of amino acids conserved in the linker region and in the C-terminal domain on the specific recognition of the initiator tRNA. (United States)

    Gite, S; Li, Y; Ramesh, V; RajBhandary, U L


    The formylation of initiator methionyl-tRNA by methionyl-tRNA formyltransferase (MTF) is important for the initiation of protein synthesis in eubacteria. We are studying the molecular mechanisms of recognition of the initiator tRNA by Escherichia coli MTF. MTF from eubacteria contains an approximately 100-amino acid C-terminal extension that is not found in the E. coli glycinamide ribonucleotide formyltransferase, which, like MTF, use N(10)-formyltetrahydrofolate as a formyl group donor. This C-terminal extension, which forms a distinct structural domain, is attached to the N-terminal domain through a linker region. Here, we describe the effect of (i) substitution mutations on some nineteen basic, aromatic and other conserved amino acids in the linker region and in the C-terminal domain of MTF and (ii) deletion mutations from the C-terminus on enzyme activity. We show that the positive charge on two of the lysine residues in the linker region leading to the C-terminal domain are important for enzyme activity. Mutation of some of the basic amino acids in the C-terminal domain to alanine has mostly small effects on the kinetic parameters, whereas mutation to glutamic acid has large effects. However, the deletion of 18, 20, or 80 amino acids from the C-terminus has very large effects on enzyme activity. Overall, our results support the notion that the basic amino acid residues in the C-terminal domain provide a positively charged channel that is used for the nonspecific binding of tRNA, whereas some of the amino acids in the linker region play an important role in activity of MTF.

  11. Shaping tRNA (United States)

    Priano, Christine


    This model-building activity provides a quick, visual, hands-on tool that allows students to examine more carefully the cloverleaf structure of a typical tRNA molecule. When used as a supplement to lessons that involve gene expression, this exercise reinforces several concepts in molecular genetics, including nucleotide base-pairing rules, the…

  12. Why has (reasonably accurate) Automatic Speech Recognition been so hard to achieve?

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    Wegmann, Steven


    Hidden Markov models (HMMs) have been successfully applied to automatic speech recognition for more than 35 years in spite of the fact that a key HMM assumption -- the statistical independence of frames -- is obviously violated by speech data. In fact, this data/model mismatch has inspired many attempts to modify or replace HMMs with alternative models that are better able to take into account the statistical dependence of frames. However it is fair to say that in 2010 the HMM is the consensus model of choice for speech recognition and that HMMs are at the heart of both commercially available products and contemporary research systems. In this paper we present a preliminary exploration aimed at understanding how speech data depart from HMMs and what effect this departure has on the accuracy of HMM-based speech recognition. Our analysis uses standard diagnostic tools from the field of statistics -- hypothesis testing, simulation and resampling -- which are rarely used in the field of speech recognition. Our ma...

  13. Simple Learned Weighted Sums of Inferior Temporal Neuronal Firing Rates Accurately Predict Human Core Object Recognition Performance. (United States)

    Majaj, Najib J; Hong, Ha; Solomon, Ethan A; DiCarlo, James J


    database of images for evaluating object recognition performance. We used multielectrode arrays to characterize hundreds of neurons in the visual ventral stream of nonhuman primates and measured the object recognition performance of >100 human observers. Remarkably, we found that simple learned weighted sums of firing rates of neurons in monkey inferior temporal (IT) cortex accurately predicted human performance. Although previous work led us to expect that IT would outperform V4, we were surprised by the quantitative precision with which simple IT-based linking hypotheses accounted for human behavior.

  14. A cross-race effect in metamemory: Predictions of face recognition are more accurate for members of our own race. (United States)

    Hourihan, Kathleen L; Benjamin, Aaron S; Liu, Xiping


    The Cross-Race Effect (CRE) in face recognition is the well-replicated finding that people are better at recognizing faces from their own race, relative to other races. The CRE reveals systematic limitations on eyewitness identification accuracy and suggests that some caution is warranted in evaluating cross-race identification. The CRE is a problem because jurors value eyewitness identification highly in verdict decisions. In the present paper, we explore how accurate people are in predicting their ability to recognize own-race and other-race faces. Caucasian and Asian participants viewed photographs of Caucasian and Asian faces, and made immediate judgments of learning during study. An old/new recognition test replicated the CRE: both groups displayed superior discriminability of own-race faces, relative to other-race faces. Importantly, relative metamnemonic accuracy was also greater for own-race faces, indicating that the accuracy of predictions about face recognition is influenced by race. This result indicates another source of concern when eliciting or evaluating eyewitness identification: people are less accurate in judging whether they will or will not recognize a face when that face is of a different race than they are. This new result suggests that a witness's claim of being likely to recognize a suspect from a lineup should be interpreted with caution when the suspect is of a different race than the witness.

  15. The Dynamics of Unfolded versus Folder tRNA: The Role of Electrostatic Interactions

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    Roh, J H [University of Maryland; Tyagi, M. [NCNR and University of Maryland; Briber, R M [University of Maryland; Woodson, S.A. [Johns Hopkins University; Sokolov, Alexei P [ORNL


    The dynamics of RNA contributes to its biological functions such as ligand recognition and catalysis. Using quasielastic neutron scattering spectroscopy, we show that Mg2+ greatly increases the picosecond to nanosecond dynamics of hydrated tRNA while stabilizing its folded structure. Analyses of the atomic mean-squared displacement, relaxation time, persistence length, and fraction of mobile atoms showed that unfolded tRNA is more rigid than folded tRNA. This same result was found for a sulfonated polystyrene, indicating that the increased dynamics in Mg2+ arises from improved charge screening of the polyelectrolyte rather than specific interactions with the folded tRNA. These results are opposite to the relationship between structural compactness and internal dynamics for proteins in which the folded state is more rigid than the denatured state. We conclude that RNA dynamics are strongly influenced by the electrostatic environment, in addition to the motions of local waters.

  16. Network of tRNA Gene Sequences

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    WEI Fang-ping; LI Sheng; MA Hong-ru


    A network of 3719 tRNA gene sequences was constructed using simplest alignment. Its topology, degree distribution and clustering coefficient were studied. The behaviors of the network shift from fluctuated distribution to scale-free distribution when the similarity degree of the tRNA gene sequences increases. The tRNA gene sequences with the same anticodon identity are more self-organized than those with different anticodon identities and form local clusters in the network. Some vertices of the local cluster have a high connection with other local clusters, and the probable reason was given. Moreover, a network constructed by the same number of random tRNA sequences was used to make comparisons. The relationships between the properties of the tRNA similarity network and the characters of tRNA evolutionary history were discussed.

  17. Sequence, structure, and stacking: specifics of tRNA anchoring to the T box riboswitch. (United States)

    Grigg, Jason C; Ke, Ailong


    The term riboswitch usually refers to small molecule sensing regulatory modules in the 5' untranslated regions of a mRNA. They are typically comprised of separate ligand binding and regulatory domains. The T box riboswitch is unique from other identified riboswitches because its effector is an essential macromolecule, tRNA. It senses the aminoacylation state of tRNA to regulate genes involved in a variety of functions relating to amino acid metabolism and tRNA aminoacylation. T box riboswitches performs an intuitively simple process using a complex structured RNA element and, until recently, the underlying mechanisms were poorly understood. Only two sequence-specific contacts had been previously identified: (1) between the specifier sequence (codon) and the tRNA anticodon and (2) between an anti-terminator stem loop and the tRNA acceptor arm CCA tail. tRNA aminoacylation blocks the latter interaction and therefore serves as the switch between termination and anti-termination. Outside of these two contacts, the structure and functions of T box riboswitches have come to light in some recent studies. We recently described the X-ray crystal structure of the highly conserved T box riboswitch distal Stem I region and demonstrated that this region interacts with the tRNA elbow to anchor it to the riboswitch. Independently, Lehmann et al. used sequence homology search to arrive at a similar model for Stem I-tRNA interactions. The model was further supported by two recent structures of the Stem I-tRNA complex, determined independently by our group and by Zhang and Ferré-D'Amaré. This article highlights some of these contributions to synthesize an updated model for tRNA recognition by the T box riboswitch.

  18. Methylated nucleosides in tRNA and tRNA methyltransferases

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    Hiroyuki eHori


    Full Text Available To date, more than 90 modified nucleosides have been found in tRNA and the biosynthetic pathways of the majority of tRNA modifications include a methylation step(s. Recent studies of the biosynthetic pathways have demonstrated that the availability of methyl group donors for the methylation in tRNA is important for correct and efficient protein synthesis. In this review, I focus on the methylated nucleosides and tRNA methyltransferases. The primary functions of tRNA methylations are linked to the different steps of protein synthesis, such as the stabilization of tRNA structure, reinforcement of the codon–anticodon interaction, regulation of wobble base pairing, and prevention of frameshift errors. However, beyond these basic functions, recent studies have demonstrated that tRNA methylations are also involved in the RNA quality control system and regulation of tRNA localization in the cell. In a thermophilic eubacterium, tRNA modifications and the modification enzymes form a network that responses to temperature changes. Furthermore, several modifications are involved in genetic diseases, infections, and the immune response. Moreover, structural, biochemical, and bioinformatics studies of tRNA methyltransferases have been clarifying the details of tRNA methyltransferases and have enabled these enzymes to be classified. In the final section, the evolution of modification enzymes is discussed.

  19. Circularly permuted tRNA genes: their expression and implications for their physiological relevance and development.

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    Akiko eSoma


    Full Text Available A number of genome analyses and searches using programs that focus on the RNA-specific bulge-helix-bulge (BHB motif have uncovered a wide variety of disrupted tRNA genes. The results of these analyses have shown that genetic information encoding functional RNAs is described in the genome cryptically and is retrieved using various strategies. One such strategy is represented by circularly permuted tRNA genes, in which the sequences encoding the 5′-half and 3′-half of the specific tRNA are separated and inverted on the genome. Biochemical analyses have defined a processing pathway in which the termini of tRNA precursors (pre-tRNAs are ligated to form a characteristic circular RNA intermediate, which is then cleaved at the acceptor-stem to generate the typical cloverleaf structure with functional termini. The sequences adjacent to the processing site located between the 3′-half and the 5′-half of pre-tRNAs potentially form a BHB motif, which is the dominant recognition site for the tRNA-intron splicing endonuclease, suggesting that circularization of pre-tRNAs depends on the splicing machinery. Some permuted tRNAs contain a BHB-mediated intron in their 5′- or 3′-half, meaning that removal of an intron, as well as swapping of the 5′- and 3′-halves, are required during maturation of their pre-tRNAs. To date, 34 permuted tRNA genes have been identified from six species of unicellular algae and one archaeon. Although their physiological significance and mechanism of development remain unclear, the splicing system of BHB motifs seems to have played a key role in the formation of permuted tRNA genes. In this review, current knowledge of circularly permuted tRNA genes is presented and some unanswered questions regarding these species are discussed.

  20. The Cambridge Face Tracker: Accurate, Low Cost Measurement of Head Posture Using Computer Vision and Face Recognition Software (United States)

    Thomas, Peter B. M.; Baltrušaitis, Tadas; Robinson, Peter; Vivian, Anthony J.


    Purpose We validate a video-based method of head posture measurement. Methods The Cambridge Face Tracker uses neural networks (constrained local neural fields) to recognize facial features in video. The relative position of these facial features is used to calculate head posture. First, we assess the accuracy of this approach against videos in three research databases where each frame is tagged with a precisely measured head posture. Second, we compare our method to a commercially available mechanical device, the Cervical Range of Motion device: four subjects each adopted 43 distinct head postures that were measured using both methods. Results The Cambridge Face Tracker achieved confident facial recognition in 92% of the approximately 38,000 frames of video from the three databases. The respective mean error in absolute head posture was 3.34°, 3.86°, and 2.81°, with a median error of 1.97°, 2.16°, and 1.96°. The accuracy decreased with more extreme head posture. Comparing The Cambridge Face Tracker to the Cervical Range of Motion Device gave correlation coefficients of 0.99 (P < 0.0001), 0.96 (P < 0.0001), and 0.99 (P < 0.0001) for yaw, pitch, and roll, respectively. Conclusions The Cambridge Face Tracker performs well under real-world conditions and within the range of normally-encountered head posture. It allows useful quantification of head posture in real time or from precaptured video. Its performance is similar to that of a clinically validated mechanical device. It has significant advantages over other approaches in that subjects do not need to wear any apparatus, and it requires only low cost, easy-to-setup consumer electronics. Translational Relevance Noncontact assessment of head posture allows more complete clinical assessment of patients, and could benefit surgical planning in future. PMID:27730008

  1. Amino acid modifications on tRNA

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    Jing Yuan; Kelly Sheppard; Dieter S(o)ll


    The accurate formation of cognate aminoacyl-transfer RNAs (aa-tRNAs) is essential for the fidelity of translation.Most amino acids are esterified onto their cognate tRNA isoacceptors directly by aa.tRNA synthetases.However,in the case of four amino acids (Gin,Asn,Cys and Sec),aminoacyl-tRNAs are made through indirect pathways in many organisms across all three domains of life.The process begins with the charging ofnoncognate amino acids to tRNAs by a specialized synthetase in the case of Cys-tRNAcys formation or by synthetases with relaxed specificity,such as the non-discriminating glutamyl-tRNA,non-discriminating aspartyl-tRNA and seryl-tRNA synthetases.The resulting misacylated tRNAs are then converted to cognate pairs through transformation of the amino acids on the tRNA,which is catalyzed by a group of tRNA-dependent modifying enzymes,such as tRNA-dependent amidotransferases,Sep-tRNA:Cys-tRNA synthase,O-phosphoseryi-tRNA kinase and Sep-tRNA:Sec-tRNA synthase.The majority of these indirect pathways are widely spread in all domains of life and thought to be part of the evolutionary process.

  2. Is tRNA binding or tRNA mimicry mandatory for translation factors? (United States)

    Kristensen, Ole; Laurberg, Martin; Liljas, Anders; Selmer, Maria


    tRNA is the adaptor in the translation process. The ribosome has three sites for tRNA, the A-, P-, and E-sites. The tRNAs bridge between the ribosomal subunits with the decoding site and the mRNA on the small or 30S subunit and the peptidyl transfer site on the large or 50S subunit. The possibility that translation release factors could mimic tRNA has been discussed for a long time, since their function is very similar to that of tRNA. They identify stop codons of the mRNA presented in the decoding site and hydrolyse the nascent peptide from the peptidyl tRNA in the peptidyl transfer site. The structures of eubacterial release factors are not yet known, and the first example of tRNA mimicry was discovered when elongation factor G (EF-G) was found to have a closely similar shape to a complex of elongation factor Tu (EF-Tu) with aminoacyl-tRNA. An even closer imitation of the tRNA shape is seen in ribosome recycling factor (RRF). The number of proteins mimicking tRNA is rapidly increasing. This primarily concerns translation factors. It is now evident that in some sense they are either tRNA mimics, GTPases or possibly both.

  3. Exploratory Data Analysis of Acceleration Signals to Select Light-Weight and Accurate Features for Real-Time Activity Recognition on Smartphones

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    Seok-Won Lee


    Full Text Available Smartphone-based activity recognition (SP-AR recognizes users’ activities using the embedded accelerometer sensor. Only a small number of previous works can be classified as online systems, i.e., the whole process (pre-processing, feature extraction, and classification is performed on the device. Most of these online systems use either a high sampling rate (SR or long data-window (DW to achieve high accuracy, resulting in short battery life or delayed system response, respectively. This paper introduces a real-time/online SP-AR system that solves this problem. Exploratory data analysis was performed on acceleration signals of 6 activities, collected from 30 subjects, to show that these signals are generated by an autoregressive (AR process, and an accurate AR-model in this case can be built using a low SR (20 Hz and a small DW (3 s. The high within class variance resulting from placing the phone at different positions was reduced using kernel discriminant analysis to achieve position-independent recognition. Neural networks were used as classifiers. Unlike previous works, true subject-independent evaluation was performed, where 10 new subjects evaluated the system at their homes for 1 week. The results show that our features outperformed three commonly used features by 40% in terms of accuracy for the given SR and DW.

  4. tRNA acceptor-stem and anticodon bases embed separate features of amino acid chemistry. (United States)

    Carter, Charles W; Wolfenden, Richard


    The universal genetic code is a translation table by which nucleic acid sequences can be interpreted as polypeptides with a wide range of biological functions. That information is used by aminoacyl-tRNA synthetases to translate the code. Moreover, amino acid properties dictate protein folding. We recently reported that digital correlation techniques could identify patterns in tRNA identity elements that govern recognition by synthetases. Our analysis, and the functionality of truncated synthetases that cannot recognize the tRNA anticodon, support the conclusion that the tRNA acceptor stem houses an independent code for the same 20 amino acids that likely functioned earlier in the emergence of genetics. The acceptor-stem code, related to amino acid size, is distinct from a code in the anticodon that is related to amino acid polarity. Details of the acceptor-stem code suggest that it was useful in preserving key properties of stereochemically-encoded peptides that had developed the capacity to interact catalytically with RNA. The quantitative embedding of the chemical properties of amino acids into tRNA bases has implications for the origins of molecular biology.

  5. tRNA Biology in Mitochondria

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    Thalia Salinas-Giegé


    Full Text Available Mitochondria are the powerhouses of eukaryotic cells. They are considered as semi-autonomous because they have retained genomes inherited from their prokaryotic ancestor and host fully functional gene expression machineries. These organelles have attracted considerable attention because they combine bacterial-like traits with novel features that evolved in the host cell. Among them, mitochondria use many specific pathways to obtain complete and functional sets of tRNAs as required for translation. In some instances, tRNA genes have been partially or entirely transferred to the nucleus and mitochondria require precise import systems to attain their pool of tRNAs. Still, tRNA genes have also often been maintained in mitochondria. Their genetic arrangement is more diverse than previously envisaged. The expression and maturation of mitochondrial tRNAs often use specific enzymes that evolved during eukaryote history. For instance many mitochondria use a eukaryote-specific RNase P enzyme devoid of RNA. The structure itself of mitochondrial encoded tRNAs is also very diverse, as e.g., in Metazoan, where tRNAs often show non canonical or truncated structures. As a result, the translational machinery in mitochondria evolved adapted strategies to accommodate the peculiarities of these tRNAs, in particular simplified identity rules for their aminoacylation. Here, we review the specific features of tRNA biology in mitochondria from model species representing the major eukaryotic groups, with an emphasis on recent research on tRNA import, maturation and aminoacylation.

  6. Ion concentration dependent tRNA folding energy landscapes (United States)

    Li, Rongzhong; Cho, Samuel


    The RNA folding is highly dependent on the ionic conditions of its environment in the cell because the surrounding ions electrostatically screen the charged phosphates that line the RNA backbone. Recent studies (Cho, Pincus, and Thirumalai, PNAS, 2007; Biyun, Cho, and Thirumalai, JACS, 2011) demonstrated that the coarse-grained model we use accurately captures the RNA folding mechanisms by incorporating a Debye-Huckel potential to screen the electrostatics. We compare the ion-concentration dependent tRNA folding mechanism to the classical thermodynamic melting profiles of Crothers and co-workers, and we observe excellent agreement. We also supported our findings by performing empirical force field MD simulations with CHARMM and AMBER, and we observe remarkably comparable qualitative similarities between the average base-base distances from simulations and the empirically measured base-stacking potentials from the well-known Turner's Rules.

  7. Compilation of tRNA sequences. (United States)

    Sprinzl, M; Grueter, F; Spelzhaus, A; Gauss, D H


    This compilation presents in a small space the tRNA sequences so far published. The numbering of tRNAPhe from yeast is used following the rules proposed by the participants of the Cold Spring Harbor Meeting on tRNA 1978 (1,2;Fig. 1). This numbering allows comparisons with the three dimensional structure of tRNAPhe. The secondary structure of tRNAs is indicated by specific underlining. In the primary structure a nucleoside followed by a nucleoside in brackets or a modification in brackets denotes that both types of nucleosides can occupy this position. Part of a sequence in brackets designates a piece of sequence not unambiguosly analyzed. Rare nucleosides are named according to the IUPACIUB rules (for complicated rare nucleosides and their identification see Table 1); those with lengthy names are given with the prefix x and specified in the footnotes. Footnotes are numbered according to the coordinates of the corresponding nucleoside and are indicated in the sequence by an asterisk. The references are restricted to the citation of the latest publication in those cases where several papers deal with one sequence. For additional information the reader is referred either to the original literature or to other tRNA sequence compilations (3-7). Mutant tRNAs are dealt with in a compilation by J. Celis (8). The compilers would welcome any information by the readers regarding missing material or erroneous presentation. On the basis of this numbering system computer printed compilations of tRNA sequences in a linear form and in cloverleaf form are in preparation.

  8. Kinetic Analysis of tRNA Methylfransferases (United States)

    Hou, Ya-Ming; Masuda, Isao


    Transfer RNA (tRNA) molecules contain many chemical modifications that are introduced after transcription. A major form of these modifications is methyl transfer to bases and backbone groups, using S-adenosyl methionine (AdoMet) as the methyl donor. Each methylation confers a specific advantage to tRNA in structure or in function. A remarkable methylation is to the G37 base on the 3' side of the anticodon to generate m1G37-tRNA, which suppresses frameshift errors during protein synthesis and is therefore essential for cell growth in all three domains of life. This methylation is catalyzed by TrmD in bacteria and by Trm5 in eukaryotes and archaea. Although TrmD and Trm5 catalyze the same methylation reaction, kinetic analysis reveal that these two enzymes are unrelated to each other and are distinct in their reaction mechanism. This chapter summarizes the kinetic assays that are used to reveal the distinction between TrmD and Trm5. Three types of assays are described, the steady-state, the pre-steady-state, and the single turnover assays, which collectively provide the basis for mechanistic investigation of AdoMet-dependent methyl transfer reactions. PMID:26253967

  9. RNA versatility governs tRNA function: Why tRNA flexibility is essential beyond the translation cycle. (United States)

    Kuhn, Claus-D


    tRNAs undergo multiple conformational changes during the translation cycle that are required for tRNA translocation and proper communication between the ribosome and translation factors. Recent structural data on how destabilized tRNAs utilize the CCA-adding enzyme to proofread themselves put a spotlight on tRNA flexibility beyond the translation cycle. In analogy to tRNA surveillance, this review finds that other processes also exploit versatile tRNA folding to achieve, amongst others, specific aminoacylation, translational regulation by riboswitches or a block of bacterial translation. tRNA flexibility is thereby not restricted to the hinges utilized during translation. In contrast, the flexibility of tRNA is distributed all over its L-shape and is actively exploited by the tRNA-interacting partners to discriminate one tRNA from another. Since the majority of tRNA modifications also modulate tRNA flexibility it seems that cells devote enormous resources to tightly sense and regulate tRNA structure. This is likely required for error-free protein synthesis.

  10. Exon structure requirements for yeast tRNA ligase

    Institute of Scientific and Technical Information of China (English)

    刘建华; 金由辛; 王德宝


    Different nucleotides were introduced into nucleotides 32, 37 and 38 of yeast tRNAphe precursors via oligonucleotide directed mutations. Pre-tRNAs were prepared using T7-transcription in vitro and spliced with the purified yeast tRNA endonuclease and tRNA ligase. It is demonstrated that tRNA ligase activities will be inhibited by the 5’-double-stranded end of 3’-halves.

  11. Structure of a bacterial ribonuclease P holoenzyme in complex with tRNA. (United States)

    Reiter, Nicholas J; Osterman, Amy; Torres-Larios, Alfredo; Swinger, Kerren K; Pan, Tao; Mondragón, Alfonso


    Ribonuclease (RNase) P is the universal ribozyme responsible for 5'-end tRNA processing. We report the crystal structure of the Thermotoga maritima RNase P holoenzyme in complex with tRNA(Phe). The 154 kDa complex consists of a large catalytic RNA (P RNA), a small protein cofactor and a mature tRNA. The structure shows that RNA-RNA recognition occurs through shape complementarity, specific intermolecular contacts and base-pairing interactions. Soaks with a pre-tRNA 5' leader sequence with and without metal help to identify the 5' substrate path and potential catalytic metal ions. The protein binds on top of a universally conserved structural module in P RNA and interacts with the leader, but not with the mature tRNA. The active site is composed of phosphate backbone moieties, a universally conserved uridine nucleobase, and at least two catalytically important metal ions. The active site structure and conserved RNase P-tRNA contacts suggest a universal mechanism of catalysis by RNase P.

  12. Formation of the conserved pseudouridine at position 55 in archaeal tRNA. (United States)

    Roovers, Martine; Hale, Caryn; Tricot, Catherine; Terns, Michael P; Terns, Rebecca M; Grosjean, Henri; Droogmans, Louis


    Pseudouridine (Psi) located at position 55 in tRNA is a nearly universally conserved RNA modification found in all three domains of life. This modification is catalyzed by TruB in bacteria and by Pus4 in eukaryotes, but so far the Psi55 synthase has not been identified in archaea. In this work, we report the ability of two distinct pseudouridine synthases from the hyperthermophilic archaeon Pyrococcus furiosus to specifically modify U55 in tRNA in vitro. These enzymes are (pfu)Cbf5, a protein known to play a role in RNA-guided modification of rRNA, and (pfu)PsuX, a previously uncharacterized enzyme that is not a member of the TruB/Pus4/Cbf5 family of pseudouridine synthases. (pfu)PsuX is hereafter renamed (pfu)Pus10. Both enzymes specifically modify tRNA U55 in vitro but exhibit differences in substrate recognition. In addition, we find that in a heterologous in vivo system, (pfu)Pus10 efficiently complements an Escherichia coli strain deficient in the bacterial Psi55 synthase TruB. These results indicate that it is probable that (pfu)Cbf5 or (pfu)Pus10 (or both) is responsible for the introduction of pseudouridine at U55 in tRNAs in archaea. While we cannot unequivocally assign the function from our results, both possibilities represent unexpected functions of these proteins as discussed herein.


    Institute of Scientific and Technical Information of China (English)

    ZHENG Jing; GONG Sha-sha; TANG Xiao-wen; ZHU Yi; GUAN Min-xin


    Mutations in mitochondrial tRNA genes have been shown to be associated with maternally inherited syn-dromic and non-syndromic deafness. Among those, mutations such as tRNALeu(UUR) 3243A>G associated with syndromic deafness are often present in heteroplasmy, and the non-syndromic deafness-associated tRNA mu-tations including tRNASer(UCN) 7445A>G are often in homoplasmy or in high levels of heteroplasmy. These tRNA mutations are the primary factors underlying the development of hearing loss. However, other tRNA mutations such as tRNAThr 15927G>A and tRNASer(UCN) 7444G>A are insufficient to produce a deafness phe-notype, but always act in synergy with the primary mitochondrial DNA mutations, and can modulate their phenotypic manifestation. These tRNA mutations may alter the structure and function of the corresponding mitochondrial tRNAs and cause failures in tRNAs metabolism. Thereby, the impairment of mitochondrial protein synthesis and subsequent defects in respiration caused by these tRNA mutations, results in mitochon-drial dysfunctions and eventually leads to the development of hearing loss. Here, we summarized the deaf-ness-associated mitochondrial tRNA mutations and discussed the pathophysiology of these mitochondrial tRNA mutations, and we hope these data will provide a foundation for the early diagnosis, management, and treatment of maternally inherited deafness.

  14. Fingerprint recognition


    Diefenderfer, Graig T.


    The use of biometrics is an evolving component in today's society. Fingerprint recognition continues to be one of the most widely used biometric systems. This thesis explores the various steps present in a fingerprint recognition system. The study develops a working algorithm to extract fingerprint minutiae from an input fingerprint image. This stage incorporates a variety of image pre-processing steps necessary for accurate minutiae extraction and includes two different methods of ridge thin...

  15. MMB-GUI: a fast morphing method demonstrates a possible ribosomal tRNA translocation trajectory. (United States)

    Tek, Alex; Korostelev, Andrei A; Flores, Samuel Coulbourn


    Easy-to-use macromolecular viewers, such as UCSF Chimera, are a standard tool in structural biology. They allow rendering and performing geometric operations on large complexes, such as viruses and ribosomes. Dynamical simulation codes enable modeling of conformational changes, but may require considerable time and many CPUs. There is an unmet demand from structural and molecular biologists for software in the middle ground, which would allow visualization combined with quick and interactive modeling of conformational changes, even of large complexes. This motivates MMB-GUI. MMB uses an internal-coordinate, multiscale approach, yielding as much as a 2000-fold speedup over conventional simulation methods. We use Chimera as an interactive graphical interface to control MMB. We show how this can be used for morphing of macromolecules that can be heterogeneous in biopolymer type, sequence, and chain count, accurately recapitulating structural intermediates. We use MMB-GUI to create a possible trajectory of EF-G mediated gate-passing translocation in the ribosome, with all-atom structures. This shows that the GUI makes modeling of large macromolecules accessible to a wide audience. The morph highlights similarities in tRNA conformational changes as tRNA translocates from A to P and from P to E sites and suggests that tRNA flexibility is critical for translocation completion.

  16. Diversity in mechanism and function of tRNA methyltransferases (United States)

    Swinehart, William E; Jackman, Jane E


    tRNA molecules undergo extensive post-transcriptional processing to generate the mature functional tRNA species that are essential for translation in all organisms. These processing steps include the introduction of numerous specific chemical modifications to nucleotide bases and sugars; among these modifications, methylation reactions are by far the most abundant. The tRNA methyltransferases comprise a diverse enzyme superfamily, including members of multiple structural classes that appear to have arisen independently during evolution. Even among closely related family members, examples of unusual substrate specificity and chemistry have been observed. Here we review recent advances in tRNA methyltransferase mechanism and function with a particular emphasis on discoveries of alternative substrate specificities and chemistry associated with some methyltransferases. Although the molecular function for a specific tRNA methylation may not always be clear, mutations in tRNA methyltransferases have been increasingly associated with human disease. The impact of tRNA methylation on human biology is also discussed. PMID:25626150

  17. The La protein functions redundantly with tRNA modification enzymes to ensure tRNA structural stability. (United States)

    Copela, Laura A; Chakshusmathi, Ghadiyaram; Sherrer, R Lynn; Wolin, Sandra L


    Although the La protein stabilizes nascent pre-tRNAs from nucleases, influences the pathway of pre-tRNA maturation, and assists correct folding of certain pre-tRNAs, it is dispensable for growth in both budding and fission yeast. Here we show that the Saccharomyces cerevisiae La shares functional redundancy with both tRNA modification enzymes and other proteins that contact tRNAs during their biogenesis. La is important for growth in the presence of mutations in either the arginyl tRNA synthetase or the tRNA modification enzyme Trm1p. In addition, two pseudouridine synthases, PUS3 and PUS4, are important for growth in strains carrying a mutation in tRNA(Arg)(CCG) and are essential when La is deleted in these strains. Depletion of Pus3p results in accumulation of the aminoacylated mutant tRNA(Arg)(CCG) in nuclei, while depletion of Pus4p results in decreased stability of the mutant tRNA. Interestingly, the degradation of mutant unstable forms of tRNA(Arg)(CCG) does not require the Trf4p poly(A) polymerase, suggesting that yeast cells possess multiple pathways for tRNA decay. These data demonstrate that La functions redundantly with both tRNA modifications and proteins that associate with tRNAs to achieve tRNA structural stability and efficient biogenesis.

  18. Iris Recognition Technique

    Institute of Scientific and Technical Information of China (English)

    XIE Mei


    The demand on security is increasing greatly in these years and biometric recognition gradually becomes a hot field of research. Iris recognition is a new branch of biometric recognition, which is regarded as the most stable, safe and accurate biometric recognition method. In these years, much progress in this field has been made by scholars and experts of different countries. In this paper, some successful iris recognition methods are listed and their performance are compared. Furthermore, the existing problems and challenges are discussed.

  19. Reverse Translocation of tRNA in the Ribosome



    A widely held view is that directional movement of tRNA in the ribosome is determined by an intrinsic mechanism and driven thermodynamically by transpeptidation. Here, we show that, in certain ribosomal complexes, the pretranslocation (PRE) state is thermodynamically favored over the posttranslocation (POST) state. Spontaneous and efficient conversion from the POST to PRE state is observed when EF-G is depleted from ribosomes in the POST state or when tRNA is added to the E site of ribosomes ...

  20. tRNA nucleotide 47: an evolutionary enigma. (United States)

    Cermakian, N; McClain, W H; Cedergren, R


    A previous analysis of tRNA sequences suggested a correlation between the absence of a nucleotide at position 47 (nt 47) in the extra loop and the presence of a U13:G22 base pair in the D-stem. We have evaluated the significance of this correlation by determining the in vivo activity of tRNAs containing either a C13:G22 or a U13:G22 pair in tRNA molecules with or without nt 47. Although this correlation might reflect some malfunction of tRNAs lacking nt 47, but containing the C13:G22, assays of the in vivo suppressor activity showed that this tRNA is actually more active than the tRNA with the features found in the database, i.e., a U13:G22 base pair and no nt 47. Moreover, analogous constructs with a GGC anticodon permitted the growth of an Escherichia coli strain deleted for tRNA(Ala)GGC genes equally well. On the other hand, long-term growth experiments with competing E. coli strains harboring the tRNA lacking nt 47, either with the C13:G22 or the U13:G22 base pair demonstrated that the U13:G22 tRNA overtook the C13:G22 strain even when the starting proportion of strains favored the C13:G22 strain. Thus, the preference for the U13:G22 tRNA lacking nt 47 in the sequence database is most likely due to factors that come into play during extended growth or latency rather than to the ability of the tRNA to engage in protein synthesis.

  1. Recognition of tRNAs with a long variable arm by aminoacyl-tRNA synthetases

    Directory of Open Access Journals (Sweden)

    Tukalo M. A.


    Full Text Available In prokaryotic cells three tRNA species, tRNASer, tRNALeu and tRNATyr, possess a long variable arm of 11–20 nucleotides (type 2 tRNA rather than usual 4 or 5 nucleotides (type 1 tRNA. In this review we have summarized the results of our research on the structural basis for recognition and discrimination of type 2 tRNAs by Thermus thermophilus seryl-, tyrosyl- and leucyl-tRNA synthetases (SerRS, TyrRS and LeuRS obtained by X-ray crystallography and chemical probing tRNA in solution. Crystal structures are now known of all three aminoacyl-tRNA synthetases complexed with type 2 tRNAs and the different modes of tRNA recognition represented by these structures will be discussed. In particular, emphasis will be given to the results on recognition of characteristic shape of type 2 tRNAs by cognate synthetases. In tRNASer, tRNATyr and tRNALeu the orientation of the long variable arm with respect to the body of the tRNA is different and is controlled by different packing of the core. In the case of SerRS the N-terminal domain and in the case of TyrRS, the C-terminal domain, bind to the characteristic long variable arm of the cognate RNA, thus recognizing the unique shape of the tRNA. The core of T. thermophilus tRNALeu has several layers of unusual base-pairs, which are revealed by the crystal structure of tRNALeu complexed with T. thermophilus LeuRS and by probing a ligand-free tRNA by specific chemical reagents in solution. In the crystal structure of the LeuRS-tRNALeu complex the unique D-stem structure is recognized by the C-terminal domain of LeuRS and these data are in good agreement with those obtained in solution. LeuRS has canonical class I mode of tRNA recognition, approaching the tRNA acceptor stem from the D-stem and minor groove of the acceptor stem side. SerRS also has canonical class II mode of tRNA recognition and approaches tRNASer from opposite, variable stem and major groove of acceptor stem site. And finally, TyrRS in strong

  2. Origins and Early Evolution of the tRNA Molecule

    Directory of Open Access Journals (Sweden)

    Koji Tamura


    Full Text Available Modern transfer RNAs (tRNAs are composed of ~76 nucleotides and play an important role as “adaptor” molecules that mediate the translation of information from messenger RNAs (mRNAs. Many studies suggest that the contemporary full-length tRNA was formed by the ligation of half-sized hairpin-like RNAs. A minihelix (a coaxial stack of the acceptor stem on the T-stem of tRNA can function both in aminoacylation by aminoacyl tRNA synthetases and in peptide bond formation on the ribosome, indicating that it may be a vestige of the ancestral tRNA. The universal CCA-3′ terminus of tRNA is also a typical characteristic of the molecule. “Why CCA?” is the fundamental unanswered question, but several findings give a comprehensive picture of its origin. Here, the origins and early evolution of tRNA are discussed in terms of various perspectives, including nucleotide ligation, chiral selectivity of amino acids, genetic code evolution, and the organization of the ribosomal peptidyl transferase center (PTC. The proto-tRNA molecules may have evolved not only as adaptors but also as contributors to the composition of the ribosome.

  3. Roles of Trm9- and ALKBH8-like proteins in the formation of modified wobble uridines in Arabidopsis tRNA

    DEFF Research Database (Denmark)

    Leihne, Vibeke; Kirpekar, Finn; Vågbø, Cathrine B


    Uridine at the wobble position of tRNA is usually modified, and modification is required for accurate and efficient protein translation. In eukaryotes, wobble uridines are modified into 5-methoxycarbonylmethyluridine (mcm(5)U), 5-carbamoylmethyluridine (ncm(5)U) or derivatives thereof. Here, we d...

  4. A Fast, Accurate and Easy to Implement Method for Pose Recognition of an Intramedullary Nail using a Tracked C-arm (United States)

    Esfandiari, H.; Amiri, S.; Lichti, D. D.; Anglin, C.


    A C-arm is a mobile X-ray device that is frequently used during orthopaedic surgeries. It consists of a semi-circular, arc-shaped arm that holds an X-ray transmitter at one end and an X-ray detector at the other. Intramedullary nail (IM nail) fixation is a popular orthopaedic surgery in which a metallic rod is placed into the patient's fractured bone (femur or tibia) and fixed using metal screws. The main challenge of IM-nail fixation surgery is to achieve the X-ray shot in which the distal holes of the IM nail appear as circles (desired view) so that the surgeon can easily insert the screws. Although C-arm X-ray devices are routinely used in IM-nail fixation surgeries, the surgeons or radiation technologists (rad-techs) usually use it in a trial-and-error manner. This method raises both radiation exposure and surgery time. In this study, we have designed and developed an IM-nail distal locking navigation technique that leads to more accurate and faster screw placement with a lower radiation dose and a minimum number of added steps to the operation to make it more accepted within the orthopaedic community. The specific purpose of this study was to develop and validate an automated technique for identifying the current pose of the IM nail relative to the C-arm. An accuracy assessment was performed to test the reliability of the navigation results. Translational accuracy was demonstrated to be better than 1 mm, roll and pitch rotations better than 2° and yaw rotational accuracy better than 2-5° depending on the separate angle. Computation time was less than 3.5 seconds.

  5. Structural Dynamics of a Mitochondrial tRNA Possessing Weak Thermodynamic Stability (United States)


    Folding dynamics are ubiquitously involved in controlling the multivariate functions of RNAs. While the high thermodynamic stabilities of some RNAs favor purely native states at equilibrium, it is unclear whether weakly stable RNAs exist in random, partially folded states or sample well-defined, globally folded conformations. Using a folding assay that precisely tracks the formation of native aminoacylable tRNA, we show that the folding of a weakly stable human mitochondrial (hmt) leucine tRNA is hierarchical with a distinct kinetic folding intermediate. The stabilities of the native and intermediate conformers are separated by only about 1.2 kcal/mol, and the species are readily interconvertible. Comparison of folding dynamics between unmodified and fully modified tRNAs reveals that post-transcriptional modifications produce a more constrained native structure that does not sample intermediate conformations. These structural dynamics may thus be crucial for recognition by some modifying enzymes in vivo, especially those targeting the globular core region, by allowing access to pretransition state conformers. Reduced conformational sampling of the native, modified tRNAs could then permit improved performance in downstream processes of translation. More generally, weak stabilities of small RNAs that fold in the absence of chaperone proteins may facilitate conformational switching that is central to biological function. PMID:24520994

  6. Reverse translocation of tRNA in the ribosome. (United States)

    Shoji, Shinichiro; Walker, Sarah E; Fredrick, Kurt


    A widely held view is that directional movement of tRNA in the ribosome is determined by an intrinsic mechanism and driven thermodynamically by transpeptidation. Here, we show that, in certain ribosomal complexes, the pretranslocation (PRE) state is thermodynamically favored over the posttranslocation (POST) state. Spontaneous and efficient conversion from the POST to PRE state is observed when EF-G is depleted from ribosomes in the POST state or when tRNA is added to the E site of ribosomes containing P-site tRNA. In the latter assay, the rate of tRNA movement is increased by streptomycin and neomycin, decreased by tetracycline, and not affected by the acylation state of the tRNA. In one case, we provide evidence that complex conversion occurs by reverse translocation (i.e., direct movement of the tRNAs from the E and P sites to the P and A sites, respectively). These findings have important implications for the energetics of translocation.

  7. Shared Sulfur Mobilization Routes for tRNA Thiolation and Molybdenum Cofactor Biosynthesis in Prokaryotes and Eukaryotes

    Directory of Open Access Journals (Sweden)

    Silke Leimkühler


    Full Text Available Modifications of transfer RNA (tRNA have been shown to play critical roles in the biogenesis, metabolism, structural stability and function of RNA molecules, and the specific modifications of nucleobases with sulfur atoms in tRNA are present in pro- and eukaryotes. Here, especially the thiomodifications xm5s2U at the wobble position 34 in tRNAs for Lys, Gln and Glu, were suggested to have an important role during the translation process by ensuring accurate deciphering of the genetic code and by stabilization of the tRNA structure. The trafficking and delivery of sulfur nucleosides is a complex process carried out by sulfur relay systems involving numerous proteins, which not only deliver sulfur to the specific tRNAs but also to other sulfur-containing molecules including iron–sulfur clusters, thiamin, biotin, lipoic acid and molybdopterin (MPT. Among the biosynthesis of these sulfur-containing molecules, the biosynthesis of the molybdenum cofactor (Moco and the synthesis of thio-modified tRNAs in particular show a surprising link by sharing protein components for sulfur mobilization in pro- and eukaryotes.

  8. Probing tRNA interaction with biogenic polyamines. (United States)

    Ouameur, Amin Ahmed; Bourassa, Philippe; Tajmir-Riahi, Heidar-Ali


    Biogenic polyamines are found to modulate protein synthesis at different levels. This effect may be explained by the ability of polyamines to bind and influence the secondary structure of tRNA, mRNA, and rRNA. We report the interaction between tRNA and the three biogenic polyamines putrescine, spermidine, spermine, and cobalt(III)hexamine at physiological conditions, using FTIR spectroscopy, capillary electrophoresis, and molecular modeling. The results indicated that tRNA was stabilized at low biogenic polyamine concentration, as a consequence of polyamine interaction with the backbone phosphate group. The main tRNA reactive sites for biogenic polyamine at low concentration were guanine-N7/O6, uracil-O2/O4, adenine-N3, and 2'OH of the ribose. At high polyamine concentration, the interaction involves guanine-N7/O6, adenine-N7, uracil-O2 reactive sites, and the backbone phosphate group. The participation of the polycation primary amino group, in the interaction and the presence of the hydrophobic contact, are also shown. The binding affinity of biogenic polyamine to tRNA molecule was in the order of spermine > spermidine > putrescine with K(Spm) = 8.7 × 10(5) M(-1), K(Spd) = 6.1 × 10(5) M(-1), and K(Put) = 1.0 × 10(5) M(-1), which correlates with their positively charged amino group content. Hill analysis showed positive cooperativity for the biogenic polyamines and negative cooperativity for cobalt-hexamine. Cobalt(III)hexamine contains high- and low-affinity sites in tRNA with K(1) = 3.2 × 10(5) M(-1) and K(2) = 1.7 × 10(5) M(-1), that have been attributed to the interactions with guanine-N7 sites and the backbone PO(2) group, respectively. This mechanism of tRNA binding could explain the condensation phenomenon observed at high Co(III) content, as previously shown in the Co(III)-DNA complexes.

  9. Research and Application of Neural Network in Targets Recognition of Accurate Strike%神经网络在精确打击目标识别中的应用研究

    Institute of Scientific and Technical Information of China (English)

    李丽荣; 王从庆


    目标识别正确与否直接影响到防空火力的部署、分配及有效打击.利用BP神经网络识别精确打击目标并进行了仿真实验.建立了样本库,提取图像的不变矩作为神经网络的输入量,分别采用基本梯度下降算法、有动量和自适应学习速率梯度下降算法和Levenberg-Marguardt优化算法训练BP网络.仿真结果表明,不变矩理论很好地解决了3维物体的2维图像在旋转、平移、缩放时能否成功提取图像特征的问题,而采用LM优化算法的BP神经网络训练速度快,识别准确率高.%Targets recognition directly affects the arrangement,distribution and effective attack of antiaircraft fire.BP neural network is used to recognize targets for accurate strike and a simulation experiment is made.Sample storage is set up; moment invariant of the pictures is taken as the input of the neural network.Basic gradient descent algorithm,gradient descent with momentum and adaptive learning rate algorithm and Levenberg-Marguardt (LM) optimization algorithm are employed to train BP network.The simulation results show that the moment invariant theory can resolve the problem of two-dimensional image character collection after revolution,translation and scaling.The BP neural network using LM optimization algorithm achieves a good classification precision and speed.

  10. Gold nanoparticles combined with highly expressed amber suppressor tRNA: a future antibacterial agent

    Directory of Open Access Journals (Sweden)

    Xiaoda Song


    Full Text Available "nAmber suppressor tRNA is a mutant allele coding for a tRNA, whose anticodon is altered in such a way that the suppressor tRNA inserts an amino acid at an amber codon in translation which leads to suppressing (preventing termination. And some Amber suppressor tRNA strains were found. We propose that gold nanoparticles combined with highly expressed amber suppressor tRNA which can be uptake by cells and recognized by AARS (aminoacyl tRNA synthetase will lead to the formation of C-terminally extended proteins. These proteins probably will not work properly, leading bacteria's death. Because of the difference of tRNA between prokaryotic and eukaryotic cells, even between different bacteria species, this amber suppressor tRNA is orthogonal for other species and cannot be recognized by AARS, therefore has no toxicity to other species. May it be an excellent antibacterial agent in the future? In this article we provide a screening method for the highly expressed amber suppressor tRNA using randomly bases mutation, radioactive selection, activity test in vivo, and finally linkage of the amber suppressor tRNA to gold nanoparticles.

  11. Capture, unfolding, and detection of individual tRNA molecules using a nanopore device

    Directory of Open Access Journals (Sweden)

    Andrew M Smith


    Full Text Available Transfer RNAs (tRNA are the most common RNA molecules in cells and have critical roles as both translators of the genetic code and regulators of protein synthesis. As such, numerous methods have focused on studying tRNA abundance and regulation, with the most widely used methods being RNA-seq and microarrays. Though revolutionary to transcriptomics, these assays are limited by an inability to encode tRNA modifications in the requisite cDNA. These modifications are abundant in tRNA and critical to their function. Here we describe proof-of-concept experiments where individual tRNA molecules are examined as linear strands using a biological nanopore. This method utilizes an enzymatically ligated synthetic DNA adapter to concentrate tRNA at the lipid bilayer of the nanopore device and efficiently denature individual tRNA molecules as they are pulled through the α-hemolysin (α-HL nanopore. Additionally, the DNA adapter provides a loading site for ϕ29 DNA polymerase (ϕ29 DNAP, which acts as a brake on the translocating tRNA. This increases the dwell time of adapted tRNA in the nanopore, allowing us to identify the region of the nanopore signal that is produced by the translocating tRNA itself. Using adapter-modified E. coli tRNAfMet and tRNALys, we show that the nanopore signal during controlled translocation is dependent on the identity of the tRNA. This confirms that adapter-modified tRNA can translocate end-to-end through nanopores and provides the foundation for future work in direct sequencing of individual transfer RNA with a nanopore-based device.

  12. Charging Levels of Four tRNA Species in Escherichia coli Rel+ and REL- Strains during Amino Acid Starvation: A Simple Model for the Effect of ppGpp on Translational Accuracy

    DEFF Research Database (Denmark)

    Sørensen, M.A.


    tenfold to 40-fold. This reduction corresponds much better with the decreased rate of protein synthesis during starvation than that reported earlier. The determination of the charging levels of tRNA2Arg and tRNA1Thr during starvation were accurate enough to demonstrate that charging levels were at least......Escherichia coli strains mutated in the relA gene lack the ability to produce ppGpp during amino acid starvation. One consequence of this deficiency is a tenfold increase in misincorporation at starved codons compared to the wild-type. Previous work had shown that the charging levels of tRNAs were...... the same in Rel+ and Rel- strains and reduced, at most, two- to fivefold in both strains during starvation. The present reinvestigation of the charging levels of tRNA2Arg, tRNA1Thr, tRNA1Leu and tRNAHis during starvation of isogenic Rel+ and Rel- strains showed that starvation reduced charging levels...

  13. Analysis of the complement and molecular evolution of tRNA genes in cow

    Directory of Open Access Journals (Sweden)

    Barris Wesley C


    Full Text Available Abstract Background Detailed information regarding the number and organization of transfer RNA (tRNA genes at the genome level is becoming readily available with the increase of DNA sequencing of whole genomes. However the identification of functional tRNA genes is challenging for species that have large numbers of repetitive elements containing tRNA derived sequences, such as Bos taurus. Reliable identification and annotation of entire sets of tRNA genes allows the evolution of tRNA genes to be understood on a genomic scale. Results In this study, we explored the B. taurus genome using bioinformatics and comparative genomics approaches to catalogue and analyze cow tRNA genes. The initial analysis of the cow genome using tRNAscan-SE identified 31,868 putative tRNA genes and 189,183 pseudogenes, where 28,830 of the 31,868 predicted tRNA genes were classified as repetitive elements by the RepeatMasker program. We then used comparative genomics to further discriminate between functional tRNA genes and tRNA-derived sequences for the remaining set of 3,038 putative tRNA genes. For our analysis, we used the human, chimpanzee, mouse, rat, horse, dog, chicken and fugu genomes to predict that the number of active tRNA genes in cow lies in the vicinity of 439. Of this set, 150 tRNA genes were 100% identical in their sequences across all nine vertebrate genomes studied. Using clustering analyses, we identified a new tRNA-GlyCCC subfamily present in all analyzed mammalian genomes. We suggest that this subfamily originated from an ancestral tRNA-GlyGCC gene via a point mutation prior to the radiation of the mammalian lineages. Lastly, in a separate analysis we created phylogenetic profiles for each putative cow tRNA gene using a representative set of genomes to gain an overview of common evolutionary histories of tRNA genes. Conclusion The use of a combination of bioinformatics and comparative genomics approaches has allowed the confident identification of a

  14. CLP1 as a novel player in linking tRNA splicing to neurodegenerative disorders. (United States)

    Weitzer, Stefan; Hanada, Toshikatsu; Penninger, Josef M; Martinez, Javier


    Defects in RNA metabolic pathways are well-established causes for neurodegenerative disorders. Several mutations in genes involved in pre-messenger RNA (pre-mRNA) and tRNA metabolism, RNA stability and protein translation have been linked to motor neuron diseases. Our study on a mouse carrying a catalytically inactive version of the RNA kinase CLP1, a component of the tRNA splicing endonuclease complex, revealed a neurological disorder characterized by progressive loss of lower spinal motor neurons. Surprisingly, mutant mice accumulate a novel class of tRNA-derived fragments. In addition, patients with homozygous missense mutations in CLP1 (R140H) were recently identified who suffer from severe motor-sensory defects, cortical dysgenesis and microcephaly, and exhibit alterations in transfer RNA (tRNA) splicing. Here, we review functions of CLP1 in different RNA pathways and provide hypotheses on the role of the tRNA splicing machinery in the generation of tRNA fragments and the molecular links to neurodegenerative disorders. We further immerse the biology of tRNA splicing into topics of (t)RNA metabolism and oxidative stress, putting forward the idea that defects in tRNA processing leading to tRNA fragment accumulation might trigger the development of neurodegenerative diseases.

  15. Functional specificity of amino acid at position 246 in the tRNA mimicry domain of bacterial release factor 2. (United States)

    Uno, M; Ito, K; Nakamura, Y


    The termination of protein synthesis in bacteria requires codon-specific polypeptide release factors RF-1 (UAG/UAA specific) and RF-2 (UGA/UAA specific). We have proposed that release factors mimic tRNA and recognize the stop codon for polypeptide release (Nakamura et al (1996) Cell 87, 147-150). In contrast to the textbook view, genetic experiments have indicated that Escherichia coli RF-2 terminates translation very weakly at UAA while Salmonella RF-2 decodes this signal efficiently. Moreover, an excess of E coli RF-2 was toxic to cells while an excess of Salmonella RF-2 was not. These two RF-2 proteins are identical except for 16 out of 365 amino acids. Fragment swap experiments and site-directed mutagenesis revealed that a residue at position 246 is solely responsible for these two phenotypes. Upon substituting Ala (equivalent to Salmonella RF-2) for Thr-246 of E coli RF-2, the protein acquired increased release activity for UAA as well as for UGA. These results led us to conclude that E coli RF-2 activity is potentially weak and that the amino acid at position 246 plays a crucial role, not for codon discrimination, but for stop codon recognition or polypeptide release, presumably constituting an essential moiety of tRNA mimicry or interacting with peptidyltransferase centers of the ribosome.

  16. Perspectives and Insights into the Competition for Aminoacyl-tRNAs between the Translational Machinery and for tRNA Dependent Non-Ribosomal Peptide Bond Formation

    Directory of Open Access Journals (Sweden)

    Angela W. S. Fung


    Full Text Available Aminoacyl-tRNA protein transferases catalyze the transfer of amino acids from aminoacyl-tRNAs to polypeptide substrates. Different forms of these enzymes are found in the different kingdoms of life and have been identified to be central to a wide variety of cellular processes. L/F-transferase is the sole member of this class of enzyme found in Escherichia coli and catalyzes the transfer of leucine to the N-termini of proteins which result in the targeted degradation of the modified protein. Recent investigations on the tRNA specificity of L/F-transferase have revealed the unique recognition nucleotides for a preferred Leu-tRNALeu isoacceptor substrate. In addition to discussing this tRNA selectivity by L/F-transferase, we present and discuss a hypothesis and its implications regarding the apparent competition for this aminoacyl-tRNA between L/F-transferase and the translational machinery. Our discussion reveals a hypothetical involvement of the bacterial stringent response that occurs upon amino acid limitation as a potential cellular event that may reduce this competition and provide the opportunity for L/F-transferase to readily increase its access to the pool of aminoacylated tRNA substrates.

  17. The local dynamics of unfolded versus folded tRNA in comparison to synthetic polyelectrolytes and the role of electrostatic interactions (United States)

    Roh, Joon Ho; Tyagi, Madhu; Briber, Robert M.; Woodson, Sarah A.; Sokolov, Alexei


    The local dynamics of RNA is strongly coupled to biological functions such as ligand recognition and catalysis. We have used quasielastic neutron scattering spectroscopy to follow the local motion of RNA and a synthetic polyelectrolyte as a function of Mg2+ concentration. We have observed that increasing Mg+2 concentration increases the picosecond to nanosecond dynamics of hydrated tRNA while stabilizing the tRNA folded structure. Analyses of the atomic mean-squared displacement, relaxation time, persistence length, and fraction of mobile atoms showed that unfolded tRNA is more rigid than in the folded state. This same behavior was observed for sulfonated polystyrene indicating that the increased dynamics in arises from charge screening of the polyelectrolyte rather than specific interactions. These results are opposite to what is observed for proteins for the relationship between the unfolded/folded states and the internal dynamics where the folded state is observed to be more rigid than the unfolded state. We conclude that the local dynamics for both bio- and synthetic polymers are strongly influenced by the electrostatic environment.

  18. An alanine tRNA gene cluster from Nephila clavipes. (United States)

    Luciano, E; Candelas, G C


    We report the sequence of a 2.3-kb genomic DNA fragment from the orb-web spider, Nephila clavipes (Nc). The fragment contains four regions of high homology to tRNA(Ala). The members of this irregularly spaced cluster of genes are oriented in the same direction and have the same anticodon (GCA), but their sequence differs at several positions. Initiation and termination signals, as well as consensus intragenic promoter sequences characteristic of tRNA genes, have been identified in all genes. tRNA(Ala) are involved in the regulation of the fibroin synthesis in the large ampullate Nc glands.

  19. tRNA concentration fine tunes protein solubility. (United States)

    Fedyunin, Ivan; Lehnhardt, Lothar; Böhmer, Nadine; Kaufmann, Paul; Zhang, Gong; Ignatova, Zoya


    Clusters of codons pairing to low-abundance tRNAs synchronize the translation with co-translational folding of single domains in multidomain proteins. Although proven with some examples, the impact of the ribosomal speed on the folding and solubility on a global, cell-wide level remains elusive. Here we show that upregulation of three low-abundance tRNAs in Escherichia coli increased the aggregation propensity of several cellular proteins as a result of an accelerated elongation rate. Intriguingly, alterations in the concentration of the natural tRNA pool compromised the solubility of various chaperones consequently rendering the solubility of some chaperone-dependent proteins.

  20. Antibiotic inhibition of the movement of tRNA substrates through a peptidyl transferase cavity

    DEFF Research Database (Denmark)

    Porse, B T; Rodriguez-Fonseca, C; Leviev, I;


    The present review attempts to deal with movement of tRNA substrates through the peptidyl transferase centre on the large ribosomal subunit and to explain how this movement is interrupted by antibiotics. It builds on the concept of hybrid tRNA states forming on ribosomes and on the observed movem...

  1. tRNA - RMG | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...genomes of other plants. Data file File name: File URL: Download License Update History of This Database Site Policy | Contact Us tRNA - RMG | LSDB Archive ...

  2. tRNA evolution from the proto-tRNA minihelix world (United States)

    Root-Bernstein, Robert; Kim, Yunsoo; Sanjay, Adithya; Burton, Zachary F.


    ABSTRACT Multiple models have been advanced for the evolution of cloverleaf tRNA. Here, the conserved archaeal tRNA core (75-nt) is posited to have evolved from ligation of three proto-tRNA minihelices (31-nt) and two-symmetrical 9-nt deletions within joined acceptor stems (93 – 18 = 75-nt). The primary evidence for this conclusion is that the 5-nt stem 7-nt anticodon loop and the 5-nt stem 7-nt T loop are structurally homologous and related by coding sequence. We posit that the D loop was generated from a third minihelix (31-nt) in which the stem and loop became rearranged after 9-nt acceptor stem deletions and cloverleaf folding. The most 3´-5-nt segment of the D loop and the 5-nt V loop are apparent remnants of the joined acceptor stems (14 – 9 = 5-nt). Before refolding in the tRNA cloverleaf, we posit that the 3′-5-nt segment of the D loop and the 5-nt V loop were paired, and, in the tRNA cloverleaf, frequent pairing of positions 29 (D loop) and 47 (V loop) remains (numbered on a 75-nt tRNA cloverleaf core). Amazingly, after >3.5 billion years of evolutionary pressure on the tRNA cloverleaf structure, a model can be constructed that convincingly describes the genesis of 75/75-nt conserved archaeal tRNA core positions. Judging from the tRNA structure, cloverleaf tRNA appears to represent at least a second-generation scheme (and possibly a third-generation scheme) that replaced a robust 31-nt minihelix protein-coding system, evidence for which is preserved in the cloverleaf structure. Understanding tRNA evolution provides insights into ribosome and rRNA evolution. PMID:27636862

  3. Unusual domain architecture of aminoacyl tRNA synthetases and their paralogs from Leishmania major

    Directory of Open Access Journals (Sweden)

    Gowri V S


    Full Text Available Abstract Background Leishmania major, a protozoan parasite, is the causative agent of cutaneous leishmaniasis. Due to the development of resistance against the currently available anti-leishmanial drugs, there is a growing need for specific inhibitors and novel drug targets. In this regards, aminoacyl tRNA synthetases, the linchpins of protein synthesis, have received recent attention among the kinetoplastid research community. This is the first comprehensive survey of the aminoacyl tRNA synthetases, their paralogs and other associated proteins from L. major. Results A total of 26 aminoacyl tRNA synthetases were identified using various computational and bioinformatics tools. Phylogenetic analysis and domain architectures of the L. major aminoacyl tRNA synthetases suggest a probable archaeal/eukaryotic origin. Presence of additional domains or N- or C-terminal extensions in 11 aminoacyl tRNA synthetases from L. major suggests possibilities such as additional tRNA binding or oligomerization or editing activity. Five freestanding editing domains were identified in L. major. Domain assignment revealed a novel asparagine tRNA synthetase paralog, asparagine synthetase A which has been so far reported from prokaryotes and archaea. Conclusions A comprehensive bioinformatic analysis revealed 26 aminoacyl tRNA synthetases and five freestanding editing domains in L. major. Identification of two EMAP (endothelial monocyte-activating polypeptide II-like proteins similar to human EMAP II-like proteins suggests their participation in multisynthetase complex formation. While the phylogeny of tRNA synthetases suggests a probable archaeal/eukaryotic origin, phylogeny of asparagine synthetase A strongly suggests a bacterial origin. The unique features identified in this work provide rationale for designing inhibitors against parasite aminoacyl tRNA synthetases and their paralogs.

  4. Enzymology of tRNA modification in the bacterial MnmEG pathway. (United States)

    Armengod, M-Eugenia; Moukadiri, Ismaïl; Prado, Silvia; Ruiz-Partida, Rafael; Benítez-Páez, Alfonso; Villarroya, Magda; Lomas, Rodrigo; Garzón, María J; Martínez-Zamora, Ana; Meseguer, Salvador; Navarro-González, Carmen


    Among all RNAs, tRNA exhibits the largest number and the widest variety of post-transcriptional modifications. Modifications within the anticodon stem loop, mainly at the wobble position and purine-37, collectively contribute to stabilize the codon-anticodon pairing, maintain the translational reading frame, facilitate the engagement of the ribosomal decoding site and enable translocation of tRNA from the A-site to the P-site of the ribosome. Modifications at the wobble uridine (U34) of tRNAs reading two degenerate codons ending in purine are complex and result from the activity of two multi-enzyme pathways, the IscS-MnmA and MnmEG pathways, which independently work on positions 2 and 5 of the U34 pyrimidine ring, respectively, and from a third pathway, controlled by TrmL (YibK), that modifies the 2'-hydroxyl group of the ribose. MnmEG is the only common pathway to all the mentioned tRNAs, and involves the GTP- and FAD-dependent activity of the MnmEG complex and, in some cases, the activity of the bifunctional enzyme MnmC. The Escherichia coli MnmEG complex catalyzes the incorporation of an aminomethyl group into the C5 atom of U34 using methylene-tetrahydrofolate and glycine or ammonium as donors. The reaction requires GTP hydrolysis, probably to assemble the active site of the enzyme or to carry out substrate recognition. Inactivation of the evolutionarily conserved MnmEG pathway produces a pleiotropic phenotype in bacteria and mitochondrial dysfunction in human cell lines. While the IscS-MnmA pathway and the MnmA-mediated thiouridylation reaction are relatively well understood, we have limited information on the reactions mediated by the MnmEG, MnmC and TrmL enzymes and on the precise role of proteins MnmE and MnmG in the MnmEG complex activity. This review summarizes the present state of knowledge on these pathways and what we still need to know, with special emphasis on the MnmEG pathway.

  5. Genetic code translation displays a linear trade-off between efficiency and accuracy of tRNA selection (United States)

    Johansson, Magnus; Zhang, Jingji; Ehrenberg, Måns


    Rapid and accurate translation of the genetic code into protein is fundamental to life. Yet due to lack of a suitable assay, little is known about the accuracy-determining parameters and their correlation with translational speed. Here, we develop such an assay, based on Mg2+ concentration changes, to determine maximal accuracy limits for a complete set of single-mismatch codon–anticodon interactions. We found a simple, linear trade-off between efficiency of cognate codon reading and accuracy of tRNA selection. The maximal accuracy was highest for the second codon position and lowest for the third. The results rationalize the existence of proofreading in code reading and have implications for the understanding of tRNA modifications, as well as of translation error-modulating ribosomal mutations and antibiotics. Finally, the results bridge the gap between in vivo and in vitro translation and allow us to calibrate our test tube conditions to represent the environment inside the living cell. PMID:22190491

  6. Effect of correlated tRNA abundances on translation errors and evolution of codon usage bias.

    Directory of Open Access Journals (Sweden)

    Premal Shah


    Full Text Available Despite the fact that tRNA abundances are thought to play a major role in determining translation error rates, their distribution across the genetic code and the resulting implications have received little attention. In general, studies of codon usage bias (CUB assume that codons with higher tRNA abundance have lower missense error rates. Using a model of protein translation based on tRNA competition and intra-ribosomal kinetics, we show that this assumption can be violated when tRNA abundances are positively correlated across the genetic code. Examining the distribution of tRNA abundances across 73 bacterial genomes from 20 different genera, we find a consistent positive correlation between tRNA abundances across the genetic code. This work challenges one of the fundamental assumptions made in over 30 years of research on CUB that codons with higher tRNA abundances have lower missense error rates and that missense errors are the primary selective force responsible for CUB.

  7. Effect of correlated tRNA abundances on translation errors and evolution of codon usage bias. (United States)

    Shah, Premal; Gilchrist, Michael A


    Despite the fact that tRNA abundances are thought to play a major role in determining translation error rates, their distribution across the genetic code and the resulting implications have received little attention. In general, studies of codon usage bias (CUB) assume that codons with higher tRNA abundance have lower missense error rates. Using a model of protein translation based on tRNA competition and intra-ribosomal kinetics, we show that this assumption can be violated when tRNA abundances are positively correlated across the genetic code. Examining the distribution of tRNA abundances across 73 bacterial genomes from 20 different genera, we find a consistent positive correlation between tRNA abundances across the genetic code. This work challenges one of the fundamental assumptions made in over 30 years of research on CUB that codons with higher tRNA abundances have lower missense error rates and that missense errors are the primary selective force responsible for CUB.

  8. Interaction of tRNA with Eukaryotic Ribosome

    Directory of Open Access Journals (Sweden)

    Dmitri Graifer


    Full Text Available This paper is a review of currently available data concerning interactions of tRNAs with the eukaryotic ribosome at various stages of translation. These data include the results obtained by means of cryo-electron microscopy and X-ray crystallography applied to various model ribosomal complexes, site-directed cross-linking with the use of tRNA derivatives bearing chemically or photochemically reactive groups in the CCA-terminal fragment and chemical probing of 28S rRNA in the region of the peptidyl transferase center. Similarities and differences in the interactions of tRNAs with prokaryotic and eukaryotic ribosomes are discussed with concomitant consideration of the extent of resemblance between molecular mechanisms of translation in eukaryotes and bacteria.

  9. tRNA and Its Activation Targets as Biomarkers and Regulators of Breast Cancer (United States)


    therapies . We are working on identifying protein or RNA targets that are mis-regulated due to the high levels of tRNA found in breast cancer cells...shown. The upper and lower bars indicate the range of individual tRNA abun- dances . (D) Heat map of tRNA abundances upon tRNAi Met overexpression...2010. Chimeric tRNAs as tools to induce pro- teome damage and identify components of stress responses. Nucleic Acids Res 38: e30. Kadaba S, Krueger A

  10. Biosynthesis of threonylcarbamoyl adenosine (t6A), a universal tRNA nucleoside. (United States)

    Deutsch, Christopher; El Yacoubi, Basma; de Crécy-Lagard, Valérie; Iwata-Reuyl, Dirk


    The anticodon stem-loop (ASL) of transfer RNAs (tRNAs) drives decoding by interacting directly with the mRNA through codon/anticodon pairing. Chemically complex nucleoside modifications found in the ASL at positions 34 or 37 are known to be required for accurate decoding. Although over 100 distinct modifications have been structurally characterized in tRNAs, only a few are universally conserved, among them threonylcarbamoyl adenosine (t(6)A), found at position 37 in the anticodon loop of a subset of tRNA. Structural studies predict an important role for t(6)A in translational fidelity, and in vivo work supports this prediction. Although pioneering work in the 1970s identified the fundamental substrates for t(6)A biosynthesis, the enzymes responsible for its biosynthesis have remained an enigma. We report here the discovery that in bacteria four proteins (YgjD, YrdC, YjeE, and YeaZ) are both necessary and sufficient for t(6)A biosynthesis in vitro. Notably, YrdC and YgjD are members of universally conserved families that were ranked among the top 10 proteins of unknown function in need of functional characterization, while YeaZ and YjeE are specific to bacteria. This latter observation, coupled with the essentiality of all four proteins in bacteria, establishes this pathway as a compelling new target for antimicrobial development.

  11. Pattern recognition

    CERN Document Server

    Theodoridis, Sergios


    Pattern recognition is a scientific discipline that is becoming increasingly important in the age of automation and information handling and retrieval. Patter Recognition, 2e covers the entire spectrum of pattern recognition applications, from image analysis to speech recognition and communications. This book presents cutting-edge material on neural networks, - a set of linked microprocessors that can form associations and uses pattern recognition to ""learn"" -and enhances student motivation by approaching pattern recognition from the designer's point of view. A direct result of more than 10

  12. Structures of the Bacterial Ribosome in Classical and Hybrid States of tRNA Binding

    Energy Technology Data Exchange (ETDEWEB)

    Dunkle, Jack A.; Wang, Leyi; Feldman, Michael B.; Pulk, Arto; Chen, Vincent B.; Kapral, Gary J.; Noeske, Jonas; Richardson, Jane S.; Blanchard, Scott C.; Cate, Jamie H. Doudna (Cornell); (UCB); (Duke)


    During protein synthesis, the ribosome controls the movement of tRNA and mRNA by means of large-scale structural rearrangements. We describe structures of the intact bacterial ribosome from Escherichia coli that reveal how the ribosome binds tRNA in two functionally distinct states, determined to a resolution of {approx}3.2 angstroms by means of x-ray crystallography. One state positions tRNA in the peptidyl-tRNA binding site. The second, a fully rotated state, is stabilized by ribosome recycling factor and binds tRNA in a highly bent conformation in a hybrid peptidyl/exit site. The structures help to explain how the ratchet-like motion of the two ribosomal subunits contributes to the mechanisms of translocation, termination, and ribosome recycling.

  13. Extensive and evolutionarily persistent mitochondrial tRNA editing in Velvet Worms (phylum Onychophora). (United States)

    Segovia, Romulo; Pett, Walker; Trewick, Steve; Lavrov, Dennis V


    Mitochondrial genomes of onychophorans (velvet worms) present an interesting problem: Some previous studies reported them lacking several transfer RNA (tRNA) genes, whereas others found that all their tRNA genes were present but severely reduced. To resolve this discrepancy, we determined complete mitochondrial DNA (mtDNA) sequences of the onychophorans Oroperipatus sp. and Peripatoides sympatrica as well as cDNA sequences from 14 and 10 of their tRNAs, respectively. We show that tRNA genes in these genomes are indeed highly reduced and encode truncated molecules, which are restored to more conventional structures by extensive tRNA editing. During this editing process, up to 34 nucleotides are added to the tRNA sequences encoded in Oroperipatus sp. mtDNA, rebuilding the aminoacyl acceptor stem, the TΨC arm, and in some extreme cases, the variable arm and even a part of the anticodon stem. The editing is less extreme in P. sympatrica in which at least a part of the TΨC arm is always encoded in mtDNA. When the entire TΨC arm is added de novo in Oroperipatus sp., the sequence of this arm is either identical or similar among different tRNA species, yet the sequences show substantial variation for each tRNA. These observations suggest that the arm is rebuilt, at least in part, by a template-independent mechanism and argue against the alternative possibility that tRNA genes or their parts are imported from the nucleus. By contrast, the 3' end of the aminoacyl acceptor stem is likely restored by a template-dependent mechanism. The extreme tRNA editing reported here has been preserved for >140 My as it was found in both extant families of onychophorans. Furthermore, a similar type of tRNA editing may be present in several other groups of arthropods, which show a high degree of tRNA gene reduction in their mtDNA.

  14. Human Emotion Recognition System

    Directory of Open Access Journals (Sweden)

    Dilbag Singh


    Full Text Available This paper discusses the application of feature extraction of facial expressions with combination of neural network for the recognition of different facial emotions (happy, sad, angry, fear, surprised, neutral etc... Humans are capable of producing thousands of facial actions during communication that vary in complexity, intensity, and meaning. This paper analyses the limitations with existing system Emotion recognition using brain activity. In this paper by using an existing simulator I have achieved 97 percent accurate results and it is easy and simplest way than Emotion recognition using brain activity system. Purposed system depends upon human face as we know face also reflects the human brain activities or emotions. In this paper neural network has been used for better results. In the end of paper comparisons of existing Human Emotion Recognition System has been made with new one.

  15. Effect of PEG and mPEG-anthracene on tRNA aggregation and particle formation. (United States)

    Froehlich, E; Mandeville, J S; Arnold, D; Kreplak, L; Tajmir-Riahi, H A


    Poly(ethylene glycol) (PEG) and its derivatives are synthetic polymers with major applications in gene and drug delivery systems. Synthetic polymers are also used to transport miRNA and siRNA in vitro. We studied the interaction of tRNA with several PEGs of different compositions, such as PEG 3350, PEG 6000, and mPEG-anthracene under physiological conditions. FTIR, UV-visible, CD, and fluorescence spectroscopic methods as well as atomic force microscopy (AFM) were used to analyze the PEG binding mode, the binding constant, and the effects of polymer complexation on tRNA stability, aggregation, and particle formation. Structural analysis showed that PEG-tRNA interaction occurs via RNA bases and the backbone phosphate group with both hydrophilic and hydrophobic contacts. The overall binding constants of K(PEG 3350-tRNA)= 1.9 (±0.5) × 10(4) M(-1), K(PEG 6000-tRNA) = 8.9 (±1) × 10(4) M(-1), and K(mPEG-anthracene)= 1.2 (±0.40) × 10(3) M(-1) show stronger polymer-RNA complexation by PEG 6000 and by PEG 3350 than the mPEG-anthracene. AFM imaging showed that PEG complexes contain on average one tRNA with PEG 3350, five tRNA with PEG 6000, and ten tRNA molecules with mPEG-anthracene. tRNA aggregation and particle formation occurred at high polymer concentrations, whereas it remains in A-family structure.

  16. Flipping of the ribosomal A-site adenines provides a basis for tRNA selection (United States)

    Zeng, Xiancheng; Chugh, Jeetender; Casiano-Negroni, Anette; Al-Hashimi, Hashim M.; Brooks, Charles L.


    Ribosomes control the missense error rate of ~10−4 during translation though quantitative contributions of individual mechanistic steps of the conformational changes yet to be fully determined. Biochemical and biophysical studies led to a qualitative tRNA selection model in which ribosomal A-site residues A1492 and A1493 (A1492/3) flip out in response to cognate tRNA binding, promoting the subsequent reactions, but not in the case of near cognate or non-cognate tRNA. However, this model was recently questioned by X-ray structures revealing conformations of extrahelical A1492/3 and domain closure of the decoding center in both cognate and near-cognate tRNA bound ribosome complexes, suggesting that the non-specific flipping of A1492/3 has no active role in tRNA selection. We explore this question by carrying out molecular dynamics (MD) simulations, aided with fluorescence and NMR experiments, to probe the free energy cost of extrahelical flipping of 1492/3 and the strain energy associated with domain conformational change. Our rigorous calculations demonstrate that the A1492/3 flipping is indeed a specific response to the binding of cognate tRNA, contributing 3 kcal/mol to the specificity of tRNA selection. Furthermore, the different A-minor interactions in cognate and near-cognate complexes propagate into the conformational strain and contribute another 4 kcal/mol in domain closure. The recent structure of ribosome with features of extrahelical A1492/3 and closed domain in near-cognate complex is reconciled by possible tautomerization of the wobble base pair in mRNA-tRNA. These results quantitatively rationalize other independent experimental observations and explain the ribosomal discrimination mechanism of selecting cognate versus near-cognate tRNA. PMID:24813122

  17. Base-pairing versatility determines wobble sites in tRNA anticodons of vertebrate mitogenomes.

    Directory of Open Access Journals (Sweden)

    Miguel M Fonseca

    Full Text Available BACKGROUND: Vertebrate mitochondrial genomes typically have one transfer RNA (tRNA for each synonymous codon family. This limited anticodon repertoire implies that each tRNA anticodon needs to wobble (establish a non-Watson-Crick base pairing between two nucleotides in RNA molecules to recognize one or more synonymous codons. Different hypotheses have been proposed to explain the factors that determine the nucleotide composition of wobble sites in vertebrate mitochondrial tRNA anticodons. Until now, the two major postulates--the "codon-anticodon adaptation hypothesis" and the "wobble versatility hypothesis"--have not been formally tested in vertebrate mitochondria because both make the same predictions regarding the composition of anticodon wobble sites. The same is true for the more recent "wobble cost hypothesis". PRINCIPAL FINDINGS: In this study we have analyzed the occurrence of synonymous codons and tRNA anticodon wobble sites in 1553 complete vertebrate mitochondrial genomes, focusing on three fish species with mtDNA codon usage bias reversal (L-strand is GT-rich. These mitogenomes constitute an excellent opportunity to study the evolution of the wobble nucleotide composition of tRNA anticodons because due to the reversal the predictions for the anticodon wobble sites differ between the existing hypotheses. We observed that none of the wobble sites of tRNA anticodons in these unusual mitochondrial genomes coevolved to match the new overall codon usage bias, suggesting that nucleotides at the wobble sites of tRNA anticodons in vertebrate mitochondrial genomes are determined by wobble versatility. CONCLUSIONS/SIGNIFICANCE: Our results suggest that, at wobble sites of tRNA anticodons in vertebrate mitogenomes, selection favors the most versatile nucleotide in terms of wobble base-pairing stability and that wobble site composition is not influenced by codon usage. These results are in agreement with the "wobble versatility hypothesis".

  18. Structural arrangement of tRNA binding sites on Escherichia coli ribosomes, as revealed from data on affinity labelling with photoactivatable tRNA derivatives. (United States)

    Graifer, D M; Babkina, G T; Matasova, N B; Vladimirov, S N; Karpova, G G; Vlassov, V V


    A systematic study of protein environment of tRNA in ribosomes in model complexes representing different translation steps was carried out using the affinity labelling of the ribosomes with tRNA derivatives bearing aryl azide groups scattered statistically over tRNA guanine residues. Analysis of the proteins crosslinked to tRNA derivatives showed that the location of the derivatives in the aminoacyl (A) site led to the labelling of the proteins S5 and S7 in all complexes studied, whereas the labelling of the proteins S2, S8, S9, S11, S14, S16, S17, S18, S19, S21 as well as L9, L11, L14, L15, L21, L23, L24, L29 depended on the state of tRNA in A site. Similarly, the location of tRNA derivatives in the peptidyl (P) site resulted in the labelling of the proteins L27, S11, S13 and S19 in all states, whereas the labelling of the proteins S5, S7, S9, S12, S14, S20, S21 as well as L2, L13, L14, L17, L24, L27, L31, L32, L33 depended on the type of complex. The derivatives of tRNA(fMet) were found to crosslink to S1, S3, S5, S7, S9, S14 and L1, L2, L7/L12, L27. Based on the data obtained, a general principle of the dynamic functioning of ribosomes has been proposed: (i) the formation of each type of ribosomal complex is accompanied by changes in mutual arrangement of proteins - 'conformational adjustment' of the ribosome - and (ii) a ribosome can dynamically change its internal structure at each step of initiation and elongation; on the 70 S ribosome there are no rigidly fixed structures forming tRNA-binding sites (primarily A and P sites).

  19. Enzymatic tRNA acylation by acid and alpha-hydroxy acid analogues of amino acids. (United States)

    Owczarek, Alina; Safro, Mark; Wolfson, Alexey D


    Incorporation of unnatural amino acids with unique chemical functionalities has proven to be a valuable tool for expansion of the functional repertoire and properties of proteins as well as for structure-function analysis. Incorporation of alpha-hydroxy acids (primary amino group is substituted with hydroxyl) leads to the synthesis of proteins with peptide bonds being substituted by ester bonds. Practical application of this modification is limited by the necessity to prepare corresponding acylated tRNA by chemical synthesis. We investigated the possibility of enzymatic incorporation of alpha-hydroxy acid and acid analogues (lacking amino group) of amino acids into tRNA using aminoacyl-tRNA synthetases (aaRSs). We studied direct acylation of tRNAs by alpha-hydroxy acid and acid analogues of amino acids and corresponding chemically synthesized analogues of aminoacyl-adenylates. Using adenylate analogues we were able to enzymatically acylate tRNA with amino acid analogues which were otherwise completely inactive in direct aminoacylation reaction, thus bypassing the natural mechanisms ensuring the selectivity of tRNA aminoacylation. Our results are the first demonstration that the use of synthetic aminoacyl-adenylates as substrates in tRNA aminoacylation reaction may provide a way for incorporation of unnatural amino acids into tRNA, and consequently into proteins.

  20. Codon-Anticodon Recognition in the Bacillus subtilis glyQS T Box Riboswitch: RNA-DEPENDENT CODON SELECTION OUTSIDE THE RIBOSOME. (United States)

    Caserta, Enrico; Liu, Liang-Chun; Grundy, Frank J; Henkin, Tina M


    Many amino acid-related genes in Gram-positive bacteria are regulated by the T box riboswitch. The leader RNA of genes in the T box family controls the expression of downstream genes by monitoring the aminoacylation status of the cognate tRNA. Previous studies identified a three-nucleotide codon, termed the "Specifier Sequence," in the riboswitch that corresponds to the amino acid identity of the downstream genes. Pairing of the Specifier Sequence with the anticodon of the cognate tRNA is the primary determinant of specific tRNA recognition. This interaction mimics codon-anticodon pairing in translation but occurs in the absence of the ribosome. The goal of the current study was to determine the effect of a full range of mismatches for comparison with codon recognition in translation. Mutations were individually introduced into the Specifier Sequence of the glyQS leader RNA and tRNA(Gly) anticodon to test the effect of all possible pairing combinations on tRNA binding affinity and antitermination efficiency. The functional role of the conserved purine 3' of the Specifier Sequence was also verifiedin this study. We found that substitutions at the Specifier Sequence resulted in reduced binding, the magnitude of which correlates well with the predicted stability of the RNA-RNA pairing. However, the tolerance for specific mismatches in antitermination was generally different from that during decoding, which reveals a unique tRNA recognition pattern in the T box antitermination system.

  1. Accurate recognition of hairs in canned mushroom under different kinds of lighting conditions%不同照明条件下菌菇罐头中发丝的准确识别

    Institute of Scientific and Technical Information of China (English)

    王秀萍; 何忠蛟


    为了实现菌菇罐头工业化生产过程中发丝异物的自动识别,该文提出了一种基于发丝中轴特征的图像识别方法。由于菌菇罐头中含水且表面不平整,不同照明条件对发丝识别效果有较大影响。因为普通照明条件下反光与阴影干扰远多于理想照明条件下反光与阴影干扰,所以普通照明条件下菌菇罐头中发丝的识别难度更大。该文用带Gaussian滤波的Hessian矩阵法提取发丝中轴特征,通过取阈值、非局部极大值抑制、8邻域连接得到中轴线,结合平行边缘特征,剔除残留的菌菇阴影中轴线,识别出发丝中轴线。试验结果表明:普通照明条件下,该方法的识别性能远好于平行边缘法、正交旋转滤波器法、四阶优化旋转滤波器法和Gaussian核平移线性组合法;对2种照明条件下采集的常见发丝(含黑色、直径70μm)的原始图片和特种发丝(含黄色、直径50μm)的原始图片,该方法都能够准确识别出发丝;尤其对较难识别的普通照明条件下复杂形状的常见发丝和特种发丝,该方法识别结果的准确率分别是0.98637和0.97007。该方法可用于菌菇罐头生产企业的发丝图像识别。%In order to achieve automatic recognition of hair impurities in the canned mushroom production process, an image recognition method based on the hair centerline feature is proposed in this paper. The proposed approach recognizes the hair centerline based on the Hessian matrices with Gaussian filtering. Under ideal lighting conditions and general lighting conditions, Hessian matrices are obtained after the original image is filtered 6 times using one-dimensional Gaussian derivative filters. The centerline pixels of the hairs and the shadows are obtained by calculating the eigenvalues of every pixel’s Hessian matrix. After employing non-maximum suppression, 8-neighbour linkage, and parallel edge analysis, the hairs

  2. A newly discovered tRNA(1Asp) gene (aspV) of Escherichia coli K12. (United States)

    Horiuchi, T; Nagasawa, T; Takano, K; Sekiguchi, M


    We report a new tRNA(1Asp) gene near the dnaQ gene, which is located at 5 min on the Escherichia coli linkage map. We named it aspV. The sequence corresponding to the mature tRNA is identical with that of the two previously identified tRNA(1Asp) genes (aspT and aspU), but there is no homology in the sequences of their 3'- and 5'-flanking regions.

  3. Yeast mitochondrial threonyl-tRNA synthetase recognizes tRNA isoacceptors by distinct mechanisms and promotes CUN codon reassignment

    Energy Technology Data Exchange (ETDEWEB)

    Ling, Jiqiang; Peterson, Kaitlyn M.; Simonovic, Ivana; Cho, Chris; Soll, Dieter; Simonovic, Miljan (Yale); (UIC)


    Aminoacyl-tRNA synthetases (aaRSs) ensure faithful translation of mRNA into protein by coupling an amino acid to a set of tRNAs with conserved anticodon sequences. Here, we show that in mitochondria of Saccharomyces cerevisiae, a single aaRS (MST1) recognizes and aminoacylates two natural tRNAs that contain anticodon loops of different size and sequence. Besides a regular ?? with a threonine (Thr) anticodon, MST1 also recognizes an unusual ??, which contains an enlarged anticodon loop and an anticodon triplet that reassigns the CUN codons from leucine to threonine. Our data show that MST1 recognizes the anticodon loop in both tRNAs, but employs distinct recognition mechanisms. The size but not the sequence of the anticodon loop is critical for ?? recognition, whereas the anticodon sequence is essential for aminoacylation of ??. The crystal structure of MST1 reveals that, while lacking the N-terminal editing domain, the enzyme closely resembles the bacterial threonyl-tRNA synthetase (ThrRS). A detailed structural comparison with Escherichia coli ThrRS, which is unable to aminoacylate ??, reveals differences in the anticodon-binding domain that probably allow recognition of the distinct anticodon loops. Finally, our mutational and modeling analyses identify the structural elements in MST1 (e.g., helix {alpha}11) that define tRNA selectivity. Thus, MTS1 exemplifies that a single aaRS can recognize completely divergent anticodon loops of natural isoacceptor tRNAs and that in doing so it facilitates the reassignment of the genetic code in yeast mitochondria.

  4. Sequence-structure-function relationships of a tRNA (m7G46) methyltransferase studied by homology modeling and site-directed mutagenesis. (United States)

    Purta, Elzbieta; van Vliet, Françoise; Tricot, Catherine; De Bie, Lara G; Feder, Marcin; Skowronek, Krzysztof; Droogmans, Louis; Bujnicki, Janusz M


    The Escherichia coli TrmB protein and its Saccharomyces cerevisiae ortholog Trm8p catalyze the S-adenosyl-L-methionine-dependent formation of 7-methylguanosine at position 46 (m7G46) in tRNA. To learn more about the sequence-structure-function relationships of these enzymes we carried out a thorough bioinformatics analysis of the tRNA:m7G methyltransferase (MTase) family to predict sequence regions and individual amino acid residues that may be important for the interactions between the MTase and the tRNA substrate, in particular the target guanosine 46. We used site-directed mutagenesis to construct a series of alanine substitutions and tested the activity of the mutants to elucidate the catalytic and tRNA-recognition mechanism of TrmB. The functional analysis of the mutants, together with the homology model of the TrmB structure and the results of the phylogenetic analysis, revealed the crucial residues for the formation of the substrate-binding site and the catalytic center in tRNA:m7G MTases.

  5. Calcium regulates the expression of a Dictyostelium discoideum asparaginyl tRNA synthetase gene

    Indian Academy of Sciences (India)

    Jyoti K Jaiswal; Vidyanand Nanjundiah


    In a screen for calcium-regulated gene expression during growth and development of Dictyostelium discoideum we have identified an asparaginyl tRNA synthetase (ddAsnRS) gene, the second tRNA synthetase gene identified in this organism. The ddAsnRS gene shows many unique features. One, it is repressed by lowering cellular calcium, making it the first known calcium-regulated tRNA synthetase. Two, despite the calcium-dependence, its expression is unaltered during the cell cycle, making this the first D. discoideum gene to show a calcium-dependent but cell cycle phase-independent expression. Finally, the N-terminal domain of the predicted ddAsnRS protein shows higher sequence similarity to Glutaminyl tRNA synthetases than to other Asn tRNA synthetases. These unique features of the AsnRS from this primitive eukaryote not only point to a novel mechanism regulating the components of translation machinery and gene expression by calcium, but also hint at a link between the evolution of GlnRS and AsnRS in eukaryotes.

  6. Molecular mechanisms of template-independent RNA polymerization by tRNA nucleotidyltransferases

    Directory of Open Access Journals (Sweden)

    Kozo eTomita


    Full Text Available The universal 3'-terminal CCA sequence of tRNA is built and/or synthesized by the CCA-adding enzyme, CTP:(ATP tRNA nucleotidyltransferase. This RNA polymerase has no nucleic acid template, but faithfully synthesizes the defined CCA sequence on the 3'-terminus of tRNA at one time, using CTP and ATP as substrates. The mystery of CCA-addition without a nucleic acid template by unique RNA polymerases has long fascinated researchers in the field of RNA enzymology. In this review, the mechanisms of RNA polymerization by the remarkable CCA-adding enzyme and its related enzymes are presented, based on their structural features.

  7. Dynamical analysis of tRNA Gln-GlnRS complex using normal mode calculation (United States)

    Nakamura, Shugo; Ikeguchi, Mitsunori; Shimizu, Kentaro


    We applied normal mode calculation in internal coordinates to a complex of glutamine transfer RNA (tRNA Gln) and glutaminyl-tRNA synthetase (GlnRS). Calculated deviations of atoms agreed well with those obtained from X-ray data. The differences of motions corresponding to low mode frequencies between the free state and the complex state were analyzed. For GlnRS, many motions in the free state were conserved in the complex state, while the dynamics of tRNA Gln was largely affected by the complex formation. Superimposed images of the conserved and non-conserved motions of tRNA Gln clearly indicated the restricted direction of motions in the complex.

  8. Emerging roles of tRNA in adaptive translation, signalling dynamics and disease. (United States)

    Kirchner, Sebastian; Ignatova, Zoya


    tRNAs, nexus molecules between mRNAs and proteins, have a central role in translation. Recent discoveries have revealed unprecedented complexity of tRNA biosynthesis, modification patterns, regulation and function. In this Review, we present emerging concepts regarding how tRNA abundance is dynamically regulated and how tRNAs (and their nucleolytic fragments) are centrally involved in stress signalling and adaptive translation, operating across a wide range of timescales. Mutations in tRNAs or in genes affecting tRNA biogenesis are also linked to complex human diseases with surprising heterogeneity in tissue vulnerability, and we highlight cell-specific aspects that modulate the disease penetrance of tRNA-based pathologies.

  9. A voltage-gated pore for translocation of tRNA

    Energy Technology Data Exchange (ETDEWEB)

    Koley, Sandip; Adhya, Samit, E-mail:


    Highlights: •A tRNA translocating complex was assembled from purified proteins. •The complex translocates tRNA at a membrane potential of ∼60 mV. •Translocation requires Cys and His residues in the Fe–S center of RIC6 subunit. -- Abstract: Very little is known about how nucleic acids are translocated across membranes. The multi-subunit RNA Import Complex (RIC) from mitochondria of the kinetoplastid protozoon Leishmania tropica induces translocation of tRNAs across artificial or natural membranes, but the nature of the translocation pore remains unknown. We show that subunits RIC6 and RIC9 assemble on the membrane in presence of subunit RIC4A to form complex R3. Atomic Force Microscopy of R3 revealed particles with an asymmetric surface groove of ∼20 nm rim diameter and ∼1 nm depth. R3 induced translocation of tRNA into liposomes when the pH of the medium was lowered to ∼6 in the absence of ATP. R3-mediated tRNA translocation could also be induced at neutral pH by a K{sup +} diffusion potential with an optimum of 60–70 mV. Point mutations in the Cys{sub 2}–His{sub 2} Fe-binding motif of RIC6, which is homologous to the respiratory Complex III Fe–S protein, abrogated import induced by low pH but not by K{sup +} diffusion potential. These results indicate that the R3 complex forms a pore that is gated by a proton-generated membrane potential and that the Fe–S binding region of RIC6 has a role in proton translocation. The tRNA import complex of L. tropica thus contains a novel macromolecular channel distinct from the mitochondrial protein import pore that is apparently involved in tRNA import in some species.

  10. Attribute measure recognition approach and its applications to emitter recognition

    Institute of Scientific and Technical Information of China (English)

    GUAN Xin; HE You; YI Xiao


    This paper studies the emitter recognition problem. A new recognition method based on attribute measure for emitter recognition is put forward. The steps of the method are presented. The approach to determining the weight coefficient is also discussed. Moreover, considering the temporal redundancy of emitter information detected by multi-sensor system, this new recognition method is generalized to multi-sensor system. A method based on the combination of attribute measure and D-S evidence theory is proposed. The implementation of D-S reasoning is always restricted by basic probability assignment function. Constructing basic probability assignment function based on attribute measure is presented in multi-sensor recognition system. Examples of recognizing the emitter purpose and system are selected to demonstrate the method proposed. Experimental results show that the performance of this new method is accurate and effective.

  11. Hydration of protein–RNA recognition sites (United States)

    Barik, Amita; Bahadur, Ranjit Prasad


    We investigate the role of water molecules in 89 protein–RNA complexes taken from the Protein Data Bank. Those with tRNA and single-stranded RNA are less hydrated than with duplex or ribosomal proteins. Protein–RNA interfaces are hydrated less than protein–DNA interfaces, but more than protein–protein interfaces. Majority of the waters at protein–RNA interfaces makes multiple H-bonds; however, a fraction do not make any. Those making H-bonds have preferences for the polar groups of RNA than its partner protein. The spatial distribution of waters makes interfaces with ribosomal proteins and single-stranded RNA relatively ‘dry’ than interfaces with tRNA and duplex RNA. In contrast to protein–DNA interfaces, mainly due to the presence of the 2′OH, the ribose in protein–RNA interfaces is hydrated more than the phosphate or the bases. The minor groove in protein–RNA interfaces is hydrated more than the major groove, while in protein–DNA interfaces it is reverse. The strands make the highest number of water-mediated H-bonds per unit interface area followed by the helices and the non-regular structures. The preserved waters at protein–RNA interfaces make higher number of H-bonds than the other waters. Preserved waters contribute toward the affinity in protein–RNA recognition and should be carefully treated while engineering protein–RNA interfaces. PMID:25114050

  12. Research on Radar Emitter Attribute Recognition Method

    Institute of Scientific and Technical Information of China (English)


    In order to solve emitter recognition problems in a practical reconnaissance environment, attribute mathematics is introduced. The basic concepts and theory of attribute set and attribute measure are described in detail. A new attribute recognition method based on attribute measure is presented in this paper. Application example is given, which demonstrates this new method is accurate and effective. Moreover, computer simulation for recognizing the emitter purpose is selected, and compared with classical statistical pattern recognition through simulation. The excellent experimental results demonstrate that this is a brand-new attribute recognition method as compared to existing statistical pattern recognition techniques.

  13. An evaluation of mitochondrial tRNA gene evolution and its relation to the genetic code. (United States)

    Cedergren, R J


    Extensive sequence data on mitochondrial (mt) tRNAs give for the first time an opportunity to evaluate tRNA gene evolution in this organelle. Deductions from these gene structures relate to the evolution of tRNA genes in other cellular systems and to the origin of the genetic code. Mt tRNAs, in contrast to the prokaryotic nature of chloroplastic tRNA structure, can not at the present time be definitely related to either prokaryotic or eukaryotic tRNAs, probably because of a higher mutation rate in mitochondria. Fungal mt tRNAs having the same anticodon and function are generally similar enough to be considered homologous. Comparisons af all mt tRNA sequences contained in the same mitochondrion indicate that some tRNAs originated by duplication of a prototypic gene which, after divergence, led to tRNAs having different amino acid specificities. The deviant mt genetic code, although admittedly permitting a simpler decoding mechanism, is not useful in determining whether the origin of mitochondria had preceded or was derived from prokaryotes or eukaryotes, since the genetic code is variable even among mitochondria. Variants of the mt genetic code lead to speculation on the nature of the primordial code and its relation to the present "universal" code.

  14. A correlation between N2-dimethylguanosine presence and alternate tRNA conformers. (United States)

    Steinberg, S; Cedergren, R


    Even though the evolutionary conservation of the cloverleaf model is strongly suggestive of powerful constraints on the secondary structure of functional tRNAs, some mitochondrial tRNAs cannot be folded into this form. From the optimal base pairing pattern of these recalcitrant tRNAs, structural correlations between the length of the anticodon stem and the lengths of connector regions between the two helical domains, formed by the coaxial stacking of the anticodon and D-stems and the acceptor and T-stems, have been derived and used to scan the tRNA and tRNA gene database. We show here that some cytosolic tRNA gene sequences that are compatible with the cloverleaf model can also be folded into patterns proposed for the unusual mitochondrial tRNAs. Furthermore, the ability to be folded into these atypical structures correlates in the mature RNA sequences with the presence of dimethylguanosine, whose role may be to prevent the unusual mitochondrial tRNA pattern folding.

  15. Machine News and Volatility: The Dow Jones Industrial Average and the TRNA Sentiment Series

    NARCIS (Netherlands)

    D.E. Allen (David); A.K. Singh (Abhay)


    markdownabstract__Abstract__ This paper features an analysis of the relationship between the volatility of the Dow Jones Industrial Average (DJIA) Index and a sentiment news series using daily data obtained from the Thomson Reuters News Analytics (TRNA) provided by SIRCA (The Securities Industry Re

  16. Pentamidine binds to tRNA through non-specific hydrophobic interactions and inhibits aminoacylation and translation. (United States)

    Sun, Tao; Zhang, Yi


    The selective and potent inhibition of mitochondrial translation in Saccharomyces cerevisiae by pentamidine suggests a novel antimicrobial action for this drug. Electrophoresis mobility shift assay, T1 ribonuclease footprinting, hydroxyl radical footprinting and isothermal titration calorimetry collectively demonstrated that pentamidine non-specifically binds to two distinct classes of sites on tRNA. The binding was driven by favorable entropy changes indicative of a large hydrophobic interaction, suggesting that the aromatic rings of pentamidine are inserted into the stacked base pairs of tRNA helices. Pentamidine binding disrupts the tRNA secondary structure and masks the anticodon loop in the tertiary structure. Consistently, we showed that pentamidine specifically inhibits tRNA aminoacylation but not the cognate amino acid adenylation. Pentamidine inhibited protein translation in vitro with an EC(50) equivalent to that binds to tRNA and inhibits tRNA aminoacylation in vitro, but drastically higher than that inhibits translation in vivo, supporting the established notion that the antimicrobial activity of pentamidine is largely due to its selective accumulation by the pathogen rather than by the host cell. Therefore, interrupting tRNA aminoacylation by the entropy-driven non-specific binding is an important mechanism of pentamidine in inhibiting protein translation, providing new insights into the development of antimicrobial drugs.

  17. Mitochondrial tRNA cleavage by tRNA-targeting ribonuclease causes mitochondrial dysfunction observed in mitochondrial disease

    Energy Technology Data Exchange (ETDEWEB)

    Ogawa, Tetsuhiro, E-mail:; Shimizu, Ayano; Takahashi, Kazutoshi; Hidaka, Makoto; Masaki, Haruhiko, E-mail:


    Highlights: • MTS-tagged ribonuclease was translocated successfully to the mitochondrial matrix. • MTS-tagged ribonuclease cleaved mt tRNA and reduced COX activity. • Easy and reproducible method of inducing mt tRNA dysfunction. - Abstract: Mitochondrial DNA (mtDNA) is a genome possessed by mitochondria. Since reactive oxygen species (ROS) are generated during aerobic respiration in mitochondria, mtDNA is commonly exposed to the risk of DNA damage. Mitochondrial disease is caused by mitochondrial dysfunction, and mutations or deletions on mitochondrial tRNA (mt tRNA) genes are often observed in mtDNA of patients with the disease. Hence, the correlation between mt tRNA activity and mitochondrial dysfunction has been assessed. Then, cybrid cells, which are constructed by the fusion of an enucleated cell harboring altered mtDNA with a ρ{sup 0} cell, have long been used for the analysis due to difficulty in mtDNA manipulation. Here, we propose a new method that involves mt tRNA cleavage by a bacterial tRNA-specific ribonuclease. The ribonuclease tagged with a mitochondrial-targeting sequence (MTS) was successfully translocated to the mitochondrial matrix. Additionally, mt tRNA cleavage, which resulted in the decrease of cytochrome c oxidase (COX) activity, was observed.

  18. Different sequence signatures in the upstream regions of plant and animal tRNA genes shape distinct modes of regulation. (United States)

    Zhang, Gong; Lukoszek, Radoslaw; Mueller-Roeber, Bernd; Ignatova, Zoya


    In eukaryotes, the transcription of tRNA genes is initiated by the concerted action of transcription factors IIIC (TFIIIC) and IIIB (TFIIIB) which direct the recruitment of polymerase III. While TFIIIC recognizes highly conserved, intragenic promoter elements, TFIIIB binds to the non-coding 5'-upstream regions of the tRNA genes. Using a systematic bioinformatic analysis of 11 multicellular eukaryotic genomes we identified a highly conserved TATA motif followed by a CAA-motif in the tRNA upstream regions of all plant genomes. Strikingly, the 5'-flanking tRNA regions of the animal genomes are highly heterogeneous and lack a common conserved sequence signature. Interestingly, in the animal genomes the tRNA species that read the same codon share conserved motifs in their upstream regions. Deep-sequencing analysis of 16 human tissues revealed multiple splicing variants of two of the TFIIIB subunits, Bdp1 and Brf1, with tissue-specific expression patterns. These multiple forms most likely modulate the TFIIIB-DNA interactions and explain the lack of a uniform signature motif in the tRNA upstream regions of animal genomes. The anticodon-dependent 5'-flanking motifs provide a possible mechanism for independent regulation of the tRNA transcription in various human tissues.

  19. Insights into the Structural Dynamics of Nucleocytoplasmic Transport of tRNA by Exportin-t. (United States)

    Gupta, Asmita; Kailasam, Senthilkumar; Bansal, Manju


    Exportin-t (Xpot) transports mature 5'- and 3'-end processed tRNA from the nucleus to the cytoplasm by associating with a small G-protein Ran (RAs-related nuclear protein), in the nucleus. The release of tRNA in cytoplasm involves RanGTP hydrolysis. Despite the availability of crystal structures of nuclear and cytosolic forms of Xpot, the molecular details regarding the sequential events leading to tRNA release and subsequent conformational changes occurring in Xpot remain unknown. We have performed a combination of classical all-atom and accelerated molecular dynamics simulations on a set of complexes involving Xpot to study a range of features including conformational flexibility of free and cargo-bound Xpot and functionally critical contacts between Xpot and its cargo. The systems investigated include free Xpot and its different complexes, bound either to Ran (GTP/GDP) or tRNA or both. This approach provided a statistically reliable estimate of structural dynamics of Xpot after cargo release. The mechanistic basis for Xpot opening after cargo release has been explained in terms of dynamic structural hinges, about which neighboring region could be displaced to facilitate the nuclear to cytosolic state transition. Post-RanGTP hydrolysis, a cascade of events including local conformational change in RanGTP and loss of critical contacts at Xpot/tRNA interface suggest factors responsible for eventual release of tRNA. The level of flexibility in different Xpot complexes varied depending on the arrangement of individual HEAT repeats. Current study provides one of the most comprehensive and robust analysis carried out on this protein using molecular dynamics schemes.

  20. Structural rules and conformational compensations in the tRNA L-form. (United States)

    Steinberg, S; Leclerc, F; Cedergren, R


    The mitochondrial tRNAs (mtRNA) of five distinct, secondary structure types have been identified in the tRNA sequence compilation, and the three-dimensional modeling for representative sequences of these types has been carried out using a new criterion for the lengths of the helical domains and connector regions in a full-sized tRNA conformation. This criterion has been derived from the analysis of the known structures of cytosolic tRNAs and states that in the tRNA structure nucleotide 59 of the T-loop should stack onto Domain 1. To ensure this, Domain 1 must have 12 layers of stacked nucleotides, and in the case of a deletion of a base-pair in the T-stem, an additional 13th layer is required. Although a number of mitochondrial tRNAs harbored deficiencies in this criterion and, therefore, could not be modeled directly, this disability could be corrected and modeling accomplished by invoking structural compensations derived from one of two unusual aspects of these tRNAs. One class of these tRNAs contained an unpaired nucleotide in their anticodon stem, and their three-dimensional structure was successfully modeled when the unpaired nucleotide was intercalated into the helical domain of the stem. The second class contained more than the required number of nucleotides connecting the tRNA helical domains; the conformational flexibility of these nucleotides allowed them to take the place of the absent layers. The conformational compensation that we report rationalizes disparate features of these tRNAs and suggests that the stacking of nucleotide 59 on Domain 1 is an essential feature of the three-dimensional L-form of tRNA.

  1. Evolution meets disease: penetrance and functional epistasis of mitochondrial tRNA mutations. (United States)

    Moreno-Loshuertos, Raquel; Ferrín, Gustavo; Acín-Pérez, Rebeca; Gallardo, M Esther; Viscomi, Carlo; Pérez-Martos, Acisclo; Zeviani, Massimo; Fernández-Silva, Patricio; Enríquez, José Antonio


    About half of the mitochondrial DNA (mtDNA) mutations causing diseases in humans occur in tRNA genes. Particularly intriguing are those pathogenic tRNA mutations than can reach homoplasmy and yet show very different penetrance among patients. These mutations are scarce and, in addition to their obvious interest for understanding human pathology, they can be excellent experimental examples to model evolution and fixation of mitochondrial tRNA mutations. To date, the only source of this type of mutations is human patients. We report here the generation and characterization of the first mitochondrial tRNA pathological mutation in mouse cells, an m.3739G>A transition in the mitochondrial mt-Ti gene. This mutation recapitulates the molecular hallmarks of a disease-causing mutation described in humans, an m.4290T>C transition affecting also the human mt-Ti gene. We could determine that the pathogenic molecular mechanism, induced by both the mouse and the human mutations, is a high frequency of abnormal folding of the tRNA(Ile) that cannot be charged with isoleucine. We demonstrate that the cells harboring the mouse or human mutant tRNA have exacerbated mitochondrial biogenesis triggered by an increase in mitochondrial ROS production as a compensatory response. We propose that both the nature of the pathogenic mechanism combined with the existence of a compensatory mechanism can explain the penetrance pattern of this mutation. This particular behavior can allow a scenario for the evolution of mitochondrial tRNAs in which the fixation of two alleles that are individually deleterious can proceed in two steps and not require the simultaneous mutation of both.

  2. Substrate recognition by ribonucleoprotein ribonuclease MRP. (United States)

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


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

  3. Binding of tRNA nucleotidyltransferase to Affi-Gel Blue: rapid purification of the enzyme and binding studies. (United States)

    Deutscher, M P; Masiakowski, P


    Rabbit liver tRNA nucleotidyldransferase bound to columns of Affi-Gel Blue and could be specifically eluted with tRNA. This observation led to development of a rapid purification procedure for the enzyme. The adsorbent was also used to assess interaction of tRNA nucleotidyltransferase with various polynucleotides and substrates. The enzyme could be efficiently desorbed from Affi-Gel Blue by low concentrations of tRNA-C-C, less well by tRNA-C-C-A, and not at all by poly(A), poly(C), ATP or CTP.

  4. Robotic CCD microscope for enhanced crystal recognition (United States)

    Segelke, Brent W.; Toppani, Dominique


    A robotic CCD microscope and procedures to automate crystal recognition. The robotic CCD microscope and procedures enables more accurate crystal recognition, leading to fewer false negative and fewer false positives, and enable detection of smaller crystals compared to other methods available today.

  5. Selection of functional tRNA primers and primer binding site sequences from a retroviral combinatorial library: identification of new functional tRNA primers in murine leukemia virus replication

    DEFF Research Database (Denmark)

    Lund, Anders Henrik; Duch, M; Pedersen, F S


    . While most of the selected primer binding sites are complementary to the 3'-end of tRNA((Pro)), we also retrieved PBS sequences matching four other tRNA molecules and demonstrate that Akv murine leukemia virus vectors may efficiently replicate using tRNA(Arg(CCU)), tRNA(Phe(GAA))and a hitherto unknown......Retroviral reverse transcription is initiated from a cellular tRNA molecule and all known exogenous isolates of murine leukemia virus utilise a tRNA(Pro)molecule. While several studies suggest flexibility in murine leukemia virus primer utilisation, studies on human immunodeficiency virus and avian...... retro-viruses have revealed evidence of molecular adapt-ation towards the specific tRNA isoacceptor used as replication primer. In this study, murine leukemia virus tRNA utilisation is investigated by in vivo screening of a retroviral vector combinatorial library with randomised primer binding sites...

  6. Identification and analysis of candidate fungal tRNA 3'-end processing endonucleases tRNase Zs, homologs of the putative prostate cancer susceptibility protein ELAC2

    Directory of Open Access Journals (Sweden)

    Zhao Wei


    Full Text Available Abstract Background tRNase Z is the endonuclease that is responsible for the 3'-end processing of tRNA precursors, a process essential for tRNA 3'-CCA addition and subsequent tRNA aminoacylation. Based on their sizes, tRNase Zs can be divided into the long (tRNase ZL and short (tRNase ZS forms. tRNase ZL is thought to have arisen from a tandem gene duplication of tRNase ZS with further sequence divergence. The species distribution of tRNase Z is complex. Fungi represent an evolutionarily diverse group of eukaryotes. The recent proliferation of fungal genome sequences provides an opportunity to explore the structural and functional diversity of eukaryotic tRNase Zs. Results We report a survey and analysis of candidate tRNase Zs in 84 completed fungal genomes, spanning a broad diversity of fungi. We find that tRNase ZL is present in all fungi we have examined, whereas tRNase ZS exists only in the fungal phyla Basidiomycota, Chytridiomycota and Zygomycota. Furthermore, we find that unlike the Pezizomycotina and Saccharomycotina, which contain a single tRNase ZL, Schizosaccharomyces fission yeasts (Taphrinomycotina contain two tRNase ZLs encoded by two different tRNase ZL genes. These two tRNase ZLs are most likely localized to the nucleus and mitochondria, respectively, suggesting partitioning of tRNase Z function between two different tRNase ZLs in fission yeasts. The fungal tRNase Z phylogeny suggests that tRNase ZSs are ancestral to tRNase ZLs. Additionally, the evolutionary relationship of fungal tRNase ZLs is generally consistent with known phylogenetic relationships among the fungal species and supports tRNase ZL gene duplication in certain fungal taxa, including Schizosaccharomyces fission yeasts. Analysis of tRNase Z protein sequences reveals putative atypical substrate binding domains in most fungal tRNase ZSs and in a subset of fungal tRNase ZLs. Finally, we demonstrate the presence of pseudo-substrate recognition and catalytic motifs at

  7. An RNA-binding complex involved in ribosome biogenesis contains a protein with homology to tRNA CCA-adding enzyme.

    Directory of Open Access Journals (Sweden)

    Jinzhong Lin


    Full Text Available A multitude of proteins and small nucleolar RNAs transiently associate with eukaryotic ribosomal RNAs to direct their modification and processing and the assembly of ribosomal proteins. Utp22 and Rrp7, two interacting proteins with no recognizable domain, are components of the 90S preribosome or the small subunit processome that conducts early processing of 18S rRNA. Here, we determine the cocrystal structure of Utp22 and Rrp7 complex at 1.97 Å resolution and the NMR structure of a C-terminal fragment of Rrp7, which is not visible in the crystal structure. The structure reveals that Utp22 surprisingly resembles a dimeric class I tRNA CCA-adding enzyme yet with degenerate active sites, raising an interesting evolutionary connection between tRNA and rRNA processing machineries. Rrp7 binds extensively to Utp22 using a deviant RNA recognition motif and an extended linker. Functional sites on the two proteins were identified by structure-based mutagenesis in yeast. We show that Rrp7 contains a flexible RNA-binding C-terminal tail that is essential for association with preribosomes. RNA-protein crosslinking shows that Rrp7 binds at the central domain of 18S rRNA and shares a neighborhood with two processing H/ACA snoRNAs snR30 and snR10. Depletion of snR30 prevents the stable assembly of Rrp7 into preribosomes. Our results provide insight into the evolutionary origin and functional context of Utp22 and Rrp7.

  8. Speaking Fluently And Accurately

    Institute of Scientific and Technical Information of China (English)



    Even after many years of study,students make frequent mistakes in English. In addition, many students still need a long time to think of what they want to say. For some reason, in spite of all the studying, students are still not quite fluent.When I teach, I use one technique that helps students not only speak more accurately, but also more fluently. That technique is dictations.

  9. Protozoan ALKBH8 Oxygenases Display both DNA Repair and tRNA Modification Activities

    DEFF Research Database (Denmark)

    Zdżalik, Daria; Vågbø, Cathrine B; Kirpekar, Finn;


    1-8 and FTO. Mammalian and plant ALKBH8 are tRNA hydroxylases targeting 5-methoxycarbonylmethyl-modified uridine (mcm5U) at the wobble position of tRNAGly(UCC). In contrast, the genomes of some bacteria encode a protein with strong sequence homology to ALKBH8, and robust DNA repair activity......, interestingly, two protozoan ALKBH8s also catalyzed wobble uridine modification of tRNA, thus displaying a dual in vitro activity. Also, we found the modification status of tRNAGly(UCC) to be unaltered in an ALKBH8 deficient mutant of Agrobacterium tumefaciens, indicating that bacterial ALKBH8s have a function......The ALKBH family of Fe(II) and 2-oxoglutarate dependent oxygenases comprises enzymes that display sequence homology to AlkB from E. coli, a DNA repair enzyme that uses an oxidative mechanism to dealkylate methyl and etheno adducts on the nucleobases. Humans have nine different ALKBH proteins, ALKBH...

  10. let-65 is cytoplasmic methionyl tRNA synthetase in C. elegans

    Directory of Open Access Journals (Sweden)

    Maha Z. Alriyami


    Full Text Available Cytoplasmic methionyl tRNA synthetase (MetRS is one of more than 20 cytoplasmic aminoacyl tRNA synthetase enzymes (ARS. This family of enzymes catalyzes a process fundamental for protein translation. Using a combination of genetic mapping, oligonucleotide array comparative genomic hybridization, and phenotypic correlation, we show that mutations in the essential gene, let-65, reside within the predicted Caenorhabditis elegans homologue of MetRS, which we have named mars-1. We demonstrate that the lethality associated with alleles of let-65 is fully rescued by a transgenic array that spans the mars-1 genomic region. Furthermore, sequence analysis reveals that six let-65 alleles lead to the alteration of highly conserved amino acids.

  11. RNA fragments mimicking tRNA analogs interact with cytochrome c. (United States)

    Pawlowska, Roza; Janicka, Magdalena; Jedrzejczyk, Dominika; Chworos, Arkadiusz


    In times, when drug seeking assays focus on the natural molecular triggers and their analogs, a deeper insight into molecular mechanisms governing the initial step of intrinsic apoptosis (cytochrome c release) is essential to suppress the immortality of pathologically changed cells. In this study, we examined RNA molecules mimicking mitochondrial tRNAs interacting with cytochrome c and possibly affecting its cellular function. tRNA analogs were designed and synthesized prior to the conformational analysis and gel assays clearly stating the nucleic acid-protein complex formation. The circular dichroism spectroscopic (CD) and microscale thermophoresis examination revealed the structural and conformational differences between four tRNA analogs in their interactions with cytochrome c. Obtained CD spectra and gel studies resulted in the complex ratio estimation and conclusion that not only the complex formation may be preferential towards specific tRNAs present in the cell, but nucleobase modifications are not essential for such interaction.

  12. tRNA modifying enzymes, NSUN2 and METTL1, determine sensitivity to 5-fluorouracil in HeLa cells.

    Directory of Open Access Journals (Sweden)

    Mayumi Okamoto


    Full Text Available Nonessential tRNA modifications by methyltransferases are evolutionarily conserved and have been reported to stabilize mature tRNA molecules and prevent rapid tRNA decay (RTD. The tRNA modifying enzymes, NSUN2 and METTL1, are mammalian orthologs of yeast Trm4 and Trm8, which are required for protecting tRNA against RTD. A simultaneous overexpression of NSUN2 and METTL1 is widely observed among human cancers suggesting that targeting of both proteins provides a novel powerful strategy for cancer chemotherapy. Here, we show that combined knockdown of NSUN2 and METTL1 in HeLa cells drastically potentiate sensitivity of cells to 5-fluorouracil (5-FU whereas heat stress of cells revealed no effects. Since NSUN2 and METTL1 are phosphorylated by Aurora-B and Akt, respectively, and their tRNA modifying activities are suppressed by phosphorylation, overexpression of constitutively dephosphorylated forms of both methyltransferases is able to suppress 5-FU sensitivity. Thus, NSUN2 and METTL1 are implicated in 5-FU sensitivity in HeLa cells. Interfering with methylation of tRNAs might provide a promising rationale to improve 5-FU chemotherapy of cancer.

  13. tRNADB-CE: tRNA gene database well-timed in the era of big sequence data. (United States)

    Abe, Takashi; Inokuchi, Hachiro; Yamada, Yuko; Muto, Akira; Iwasaki, Yuki; Ikemura, Toshimichi


    The tRNA gene data base curated by experts "tRNADB-CE" ( was constructed by analyzing 1,966 complete and 5,272 draft genomes of prokaryotes, 171 viruses', 121 chloroplasts', and 12 eukaryotes' genomes plus fragment sequences obtained by metagenome studies of environmental samples. 595,115 tRNA genes in total, and thus two times of genes compiled previously, have been registered, for which sequence, clover-leaf structure, and results of sequence-similarity and oligonucleotide-pattern searches can be browsed. To provide collective knowledge with help from experts in tRNA researches, we added a column for enregistering comments to each tRNA. By grouping bacterial tRNAs with an identical sequence, we have found high phylogenetic preservation of tRNA sequences, especially at the phylum level. Since many species-unknown tRNAs from metagenomic sequences have sequences identical to those found in species-known prokaryotes, the identical sequence group (ISG) can provide phylogenetic markers to investigate the microbial community in an environmental ecosystem. This strategy can be applied to a huge amount of short sequences obtained from next-generation sequencers, as showing that tRNADB-CE is a well-timed database in the era of big sequence data. It is also discussed that batch-learning self-organizing-map with oligonucleotide composition is useful for efficient knowledge discovery from big sequence data.

  14. tRNADB-CE: tRNA gene database well-timed in the era of big sequence data

    Directory of Open Access Journals (Sweden)

    Takashi eAbe


    Full Text Available The tRNA Gene Data Base Curated by Experts tRNADB-CE ( was constructed by analyzing 1,966 complete and 5,272 draft genomes of prokaryotes, 171 viruses’, 121 chloroplasts’, and 12 eukaryotes’ genomes plus fragment sequences obtained by metagenome studies of environmental samples. 595,115 tRNA genes in total, and thus two times of genes compiled previously, have been registered, for which sequence, clover-leaf structure, and results of sequence-similarity and oligonucleotide-pattern searches can be browsed. To provide collective knowledge with help from experts in tRNA researches, we added a column for enregistering comments to each tRNA. By grouping bacterial tRNAs with an identical sequence, we have found high phylogenetic preservation of tRNA sequences, especially at the phylum level. Since many species-unknown tRNAs from metagenomic sequences have sequences identical to those found in species-known prokaryotes, the identical sequence group can provide phylogenetic markers to investigate the microbial community in an environmental ecosystem. This strategy can be applied to a huge amount of short sequences obtained from next-generation sequencers, as showing that tRNADB-CE is a well-timed database in the era of big sequence data. It is also discussed that BLSOM with oligonucleotide composition is useful for efficient knowledge discovery from big sequence data.

  15. RNA Polymerase III Output Is Functionally Linked to tRNA Dimethyl-G26 Modification.

    Directory of Open Access Journals (Sweden)

    Aneeshkumar G Arimbasseri


    Full Text Available Control of the differential abundance or activity of tRNAs can be important determinants of gene regulation. RNA polymerase (RNAP III synthesizes all tRNAs in eukaryotes and it derepression is associated with cancer. Maf1 is a conserved general repressor of RNAP III under the control of the target of rapamycin (TOR that acts to integrate transcriptional output and protein synthetic demand toward metabolic economy. Studies in budding yeast have indicated that the global tRNA gene activation that occurs with derepression of RNAP III via maf1-deletion is accompanied by a paradoxical loss of tRNA-mediated nonsense suppressor activity, manifested as an antisuppression phenotype, by an unknown mechanism. We show that maf1-antisuppression also occurs in the fission yeast S. pombe amidst general activation of RNAP III. We used tRNA-HydroSeq to document that little changes occurred in the relative levels of different tRNAs in maf1Δ cells. By contrast, the efficiency of N2,N2-dimethyl G26 (m(22G26 modification on certain tRNAs was decreased in response to maf1-deletion and associated with antisuppression, and was validated by other methods. Over-expression of Trm1, which produces m(22G26, reversed maf1-antisuppression. A model that emerges is that competition by increased tRNA levels in maf1Δ cells leads to m(22G26 hypomodification due to limiting Trm1, reducing the activity of suppressor-tRNASerUCA and accounting for antisuppression. Consistent with this, we show that RNAP III mutations associated with hypomyelinating leukodystrophy decrease tRNA transcription, increase m(22G26 efficiency and reverse antisuppression. Extending this more broadly, we show that a decrease in tRNA synthesis by treatment with rapamycin leads to increased m(22G26 modification and that this response is conserved among highly divergent yeasts and human cells.

  16. The core domain of Aquifex aeolicus tRNA (m7G46) methyltransferase has the methyl-transfer activity to tRNA. (United States)

    Tomikawa, Chie; Hori, Hiroyuki


    Transfer RNA (m(7)G46) methyltransferase [TrmB] catalyses the transfer of methyl groups from S-adenosyl-L-methionine to the N(7)-atom of guanine at position 46 in tRNA. TrmB proteins from thermophilic bacteria such as Aquifex aeolicus have a long C-terminal region as compared to those from mesophilic bacteria. Further, N-terminal region observed in TrmB proteins from mesophiles is missing in A. aeolicus TrmB. Therefore, we considered that this distinct C-terminal region in A. aeolicus TrmB might compensate the N-terminal region in mesophile TrmB and function as a part of tRNA binding site. To confirm this idea, we deleted the C-terminal region by introduction of the stop codon at position 202. To our surprise, methyl-transfer assay using yeast tRNA(Phe) transcript clearly showed that the resultant mutant protein (Glu202Stop) had an enzymatic activity. Thus, the core domain of the A. aeolicus TrmB has a methyl-transfer activity.

  17. RNase MRP cleaves pre-tRNASer-Met in the tRNA maturation pathway. (United States)

    Saito, Yuichiro; Takeda, Jun; Adachi, Kousuke; Nobe, Yuko; Kobayashi, Junya; Hirota, Kouji; Oliveira, Douglas V; Taoka, Masato; Isobe, Toshiaki


    Ribonuclease mitochondrial RNA processing (RNase MRP) is a multifunctional ribonucleoprotein (RNP) complex that is involved in the maturation of various types of RNA including ribosomal RNA. RNase MRP consists of a potential catalytic RNA and several protein components, all of which are required for cell viability. We show here that the temperature-sensitive mutant of rmp1, the gene for a unique protein component of RNase MRP, accumulates the dimeric tRNA precursor, pre-tRNA(Ser-Met). To examine whether RNase MRP mediates tRNA maturation, we purified the RNase MRP holoenzyme from the fission yeast Schizosaccharomyces pombe and found that the enzyme directly and selectively cleaves pre-tRNA(Ser-Met), suggesting that RNase MRP participates in the maturation of specific tRNA in vivo. In addition, mass spectrometry-based ribonucleoproteomic analysis demonstrated that this RNase MRP consists of one RNA molecule and 11 protein components, including a previously unknown component Rpl701. Notably, limited nucleolysis of RNase MRP generated an active catalytic core consisting of partial mrp1 RNA fragments, which constitute "Domain 1" in the secondary structure of RNase MRP, and 8 proteins. Thus, the present study provides new insight into the structure and function of RNase MRP.

  18. Silent Polymorphisms: Can the tRNA Population Explain Changes in Protein Properties?

    Directory of Open Access Journals (Sweden)

    Tamara Fernández-Calero


    Full Text Available Silent mutations are being intensively studied. We previously showed that the estrogen receptor alpha Ala87’s synonymous polymorphism affects its functional properties. Whereas a link has been clearly established between the effect of silent mutations, tRNA abundance and protein folding in prokaryotes, this connection remains controversial in eukaryotic systems. Although a synonymous polymorphism can affect mRNA structure or the interaction with specific ligands, it seems that the relative frequencies of isoacceptor tRNAs could play a key role in the protein-folding process, possibly through modulation of translation kinetics. Conformational changes could be subtle but enough to cause alterations in solubility, proteolysis profiles, functional parameters or intracellular targeting. Interestingly, recent advances describe dramatic changes in the tRNA population associated with proliferation, differentiation or response to chemical, physical or biological stress. In addition, several reports reveal changes in tRNAs’ posttranscriptional modifications in different physiological or pathological conditions. In consequence, since changes in the cell state imply quantitative and/or qualitative changes in the tRNA pool, they could increase the likelihood of protein conformational variants, related to a particular codon usage during translation, with consequences of diverse significance. These observations emphasize the importance of genetic code flexibility in the co-translational protein-folding process.

  19. Silent Polymorphisms: Can the tRNA Population Explain Changes in Protein Properties? (United States)

    Fernández-Calero, Tamara; Cabrera-Cabrera, Florencia; Ehrlich, Ricardo; Marín, Mónica


    Silent mutations are being intensively studied. We previously showed that the estrogen receptor alpha Ala87’s synonymous polymorphism affects its functional properties. Whereas a link has been clearly established between the effect of silent mutations, tRNA abundance and protein folding in prokaryotes, this connection remains controversial in eukaryotic systems. Although a synonymous polymorphism can affect mRNA structure or the interaction with specific ligands, it seems that the relative frequencies of isoacceptor tRNAs could play a key role in the protein-folding process, possibly through modulation of translation kinetics. Conformational changes could be subtle but enough to cause alterations in solubility, proteolysis profiles, functional parameters or intracellular targeting. Interestingly, recent advances describe dramatic changes in the tRNA population associated with proliferation, differentiation or response to chemical, physical or biological stress. In addition, several reports reveal changes in tRNAs’ posttranscriptional modifications in different physiological or pathological conditions. In consequence, since changes in the cell state imply quantitative and/or qualitative changes in the tRNA pool, they could increase the likelihood of protein conformational variants, related to a particular codon usage during translation, with consequences of diverse significance. These observations emphasize the importance of genetic code flexibility in the co-translational protein-folding process. PMID:26901226

  20. Facial Recognition

    Directory of Open Access Journals (Sweden)

    Mihalache Sergiu


    Full Text Available During their lifetime, people learn to recognize thousands of faces that they interact with. Face perception refers to an individual's understanding and interpretation of the face, particularly the human face, especially in relation to the associated information processing in the brain. The proportions and expressions of the human face are important to identify origin, emotional tendencies, health qualities, and some social information. From birth, faces are important in the individual's social interaction. Face perceptions are very complex as the recognition of facial expressions involves extensive and diverse areas in the brain. Our main goal is to put emphasis on presenting human faces specialized studies, and also to highlight the importance of attractiviness in their retention. We will see that there are many factors that influence face recognition.

  1. Semantic information can facilitate covert face recognition in congenital prosopagnosia. (United States)

    Rivolta, Davide; Schmalzl, Laura; Coltheart, Max; Palermo, Romina


    People with congenital prosopagnosia have never developed the ability to accurately recognize faces. This single case investigation systematically investigates covert and overt face recognition in "C.," a 69 year-old woman with congenital prosopagnosia. Specifically, we: (a) describe the first assessment of covert face recognition in congenital prosopagnosia using multiple tasks; (b) show that semantic information can contribute to covert recognition; and (c) provide a theoretical explanation for the mechanisms underlying covert face recognition.

  2. Document recognition serving people with disabilities (United States)

    Fruchterman, James R.


    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, 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. Optimization protein productivity of human interleukin-2 through codon usage, gene copy number and intracellular tRNA concentration in CHO cells. (United States)

    Ou, Kua-Chun; Wang, Chih-Yang; Liu, Kuan-Ting; Chen, Yi-Ling; Chen, Yi-Chen; Lai, Ming-Derg; Yen, Meng-Chi


    Transfer RNA (tRNA) abundance is one of the critical factors for the enhancement of protein productivity in prokaryotic and eukaryotic hosts. Gene copy number of tRNA and tRNA codon usage bias are generally used to match tRNA abundance of protein-expressing hosts and to optimize the codons of recombinant proteins. Because sufficient concentration of intracellular tRNA and optimized codons of recombinant proteins enhanced translation efficiency, we hypothesized that sufficient supplement of host's tRNA improved protein productivity in mammalian cells. First, the small tRNA sequencing results of CHO-K1 cells showed moderate positive correlation with gene copy number and codon usage bias. Modification of human interleukin-2 (IL-2) through codons with high gene copy number and high codon usage bias (IL-2 HH, modified on Leu, Thr, Glu) significantly increased protein productivity in CHO-K1 cells. In contrast, modification through codons with relatively high gene copy number and low codon usage bias (IL-2 HL, modified on Ala, Thr, Val), or relatively low gene copy number and low codon usage bias (IL-2 LH, modified on Ala, Thr, Val) did not increase IL-2 productivity significantly. Furthermore, supplement of the alanine tRNA or threonine tRNA increased IL-2 productivity of IL-2 HL. In summary, we revealed a potential strategy to enhance productivity of recombinant proteins, which may be applied in production of protein drug or design of DNA vaccine.

  4. Speaker Recognition

    DEFF Research Database (Denmark)

    Mølgaard, Lasse Lohilahti; Jørgensen, Kasper Winther


    Speaker recognition is basically divided into speaker identification and speaker verification. Verification is the task of automatically determining if a person really is the person he or she claims to be. This technology can be used as a biometric feature for verifying the identity of a person...... in applications like banking by telephone and voice mail. The focus of this project is speaker identification, which consists of mapping a speech signal from an unknown speaker to a database of known speakers, i.e. the system has been trained with a number of speakers which the system can recognize....

  5. The recognition of work


    Nierling, Linda


    The following article argues that recognition structures in work relations differ significantly in the sphere of paid work in contrast to unpaid work in private spheres. According to the systematic approach on recognition of Axel Honneth three different levels of recognition are identified: the interpersonal recognition, organisational recognition and societal recognition. Based on this framework it can be stated that recognition structures in the sphere of paid work and in private spheres di...

  6. Acquired prosopagnosia without word recognition deficits. (United States)

    Susilo, Tirta; Wright, Victoria; Tree, Jeremy J; Duchaine, Bradley


    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. Accurate pose estimation for forensic identification (United States)

    Merckx, Gert; Hermans, Jeroen; Vandermeulen, Dirk


    In forensic authentication, one aims to identify the perpetrator among a series of suspects or distractors. A fundamental problem in any recognition system that aims for identification of subjects in a natural scene is the lack of constrains on viewing and imaging conditions. In forensic applications, identification proves even more challenging, since most surveillance footage is of abysmal quality. In this context, robust methods for pose estimation are paramount. In this paper we will therefore present a new pose estimation strategy for very low quality footage. Our approach uses 3D-2D registration of a textured 3D face model with the surveillance image to obtain accurate far field pose alignment. Starting from an inaccurate initial estimate, the technique uses novel similarity measures based on the monogenic signal to guide a pose optimization process. We will illustrate the descriptive strength of the introduced similarity measures by using them directly as a recognition metric. Through validation, using both real and synthetic surveillance footage, our pose estimation method is shown to be accurate, and robust to lighting changes and image degradation.

  8. A human tRNA methyltransferase 9-like protein prevents tumour growth by regulating LIN9 and HIF1-α (United States)

    Begley, Ulrike; Sosa, Maria Soledad; Avivar-Valderas, Alvaro; Patil, Ashish; Endres, Lauren; Estrada, Yeriel; Chan, Clement TY; Su, Dan; Dedon, Peter C; Aguirre-Ghiso, Julio A; Begley, Thomas


    Emerging evidence points to aberrant regulation of translation as a driver of cell transformation in cancer. Given the direct control of translation by tRNA modifications, tRNA modifying enzymes may function as regulators of cancer progression. Here, we show that a tRNA methyltransferase 9-like (hTRM9L/KIAA1456) mRNA is down-regulated in breast, bladder, colorectal, cervix and testicular carcinomas. In the aggressive SW620 and HCT116 colon carcinoma cell lines, hTRM9L is silenced and its re-expression and methyltransferase activity dramatically suppressed tumour growth in vivo. This growth inhibition was linked to decreased proliferation, senescence-like G0/G1-arrest and up-regulation of the RB interacting protein LIN9. Additionally, SW620 cells re-expressing hTRM9L did not respond to hypoxia via HIF1-α-dependent induction of GLUT1. Importantly, hTRM9L-negative tumours were highly sensitive to aminoglycoside antibiotics and this was associated with altered tRNA modification levels compared to antibiotic resistant hTRM9L-expressing SW620 cells. Our study links hTRM9L and tRNA modifications to inhibition of tumour growth via LIN9 and HIF1-α-dependent mechanisms. It also suggests that aminoglycoside antibiotics may be useful to treat hTRM9L-deficient tumours. PMID:23381944

  9. N7-Methylguanine at position 46 (m7G46) in tRNA from Thermus thermophilus is required for cell viability at high temperatures through a tRNA modification network. (United States)

    Tomikawa, Chie; Yokogawa, Takashi; Kanai, Tamotsu; Hori, Hiroyuki


    N(7)-methylguanine at position 46 (m(7)G46) in tRNA is produced by tRNA (m(7)G46) methyltransferase (TrmB). To clarify the role of this modification, we made a trmB gene disruptant (DeltatrmB) of Thermus thermophilus, an extreme thermophilic eubacterium. The absence of TrmB activity in cell extract from the DeltatrmB strain and the lack of the m(7)G46 modification in tRNA(Phe) were confirmed by enzyme assay, nucleoside analysis and RNA sequencing. When the DeltatrmB strain was cultured at high temperatures, several modified nucleotides in tRNA were hypo-modified in addition to the lack of the m(7)G46 modification. Assays with tRNA modification enzymes revealed hypo-modifications of Gm18 and m(1)G37, suggesting that the m(7)G46 positively affects their formations. Although the lack of the m(7)G46 modification and the hypo-modifications do not affect the Phe charging activity of tRNA(Phe), they cause a decrease in melting temperature of class I tRNA and degradation of tRNA(Phe) and tRNA(Ile). (35)S-Met incorporation into proteins revealed that protein synthesis in DeltatrmB cells is depressed above 70 degrees C. At 80 degrees C, the DeltatrmB strain exhibits a severe growth defect. Thus, the m(7)G46 modification is required for cell viability at high temperatures via a tRNA modification network, in which the m(7)G46 modification supports introduction of other modifications.

  10. Optical Kerr effect of tRNA solution induced by femtosecond laser pulses (United States)

    Kucia, Weronika E.; Sharma, Gargi; Joseph, Cecil S.; Sarbak, Szymon; Oliver, Cameron; Dobek, Andrzej; Giles, Robert H.


    The optical Kerr effect (OKE) in a transfer ribonucleic acid (tRNA) solution induced by femtosecond pulses of linearly polarized pump light (λi = 800 nm) and sounded by probe light (λp = 800 nm) was studied. The measurements were performed to find nonlinear optical parameters describing a single molecule (molecular Kerr constant K, mean nonlinear third order optical polarizability cpi) and to compare them with our previous OKE results obtained in ns and ps time range. The OKE experiment has proven to be an efficient method to obtain the nonlinear parameters of single molecules in solution, which reflects dynamic structure changes.

  11. Movement of the 3'-end of tRNA through the peptidyl transferase centre and its inhibition by antibiotics

    DEFF Research Database (Denmark)

    Kirillov, Stanislav; Porse, Bo Torben; Vester, Birthe;


    Determining how antibiotics inhibit ribosomal activity requires a detailed understanding of the interactions and relative movement of tRNA, mRNA and the ribosome. Recent models for the formation of hybrid tRNA binding sites during the elongation cycle have provided a basis for re-evaluating earlier......RNA-ribosome binding. Nevertheless, these relatively weak interactions determine the unidirectional movement of tRNAs through the ribosome and, moreover, they appear to be particularly susceptible to perturbation by antibiotics. Here we summarise current ideas relating particularly to the movement of the 3'-ends of t......RNA through the ribosome and consider possible inhibitory mechanisms of the peptidyl transferase antibiotics....

  12. La adaptación a la deficiencia de zinc en cianobacterias. Papel de treonil-trna sintetasas duplicadas



    Falta palabras claves Las aminoacil tRNA sintetasas (aaRSs) son las enzimas que catalizan la carga del aminoácido en el tRNA y son las responsables de mantener la fidelidad en la traducción del código genético. Las aaRSs son componentes esenciales de la síntesis proteica y son ubicuas en todos los dominios de la vida (Ibba y Sol, 2000; Perona y Hadd, 2012). La cianobacteria filamentosa Anabaena sp.PCC 7120 contiene dos genes de treonil tRNA sintetasa, alr0335(thrS1) y all4723 (thrS2), ...

  13. Anticodon Modifications in the tRNA Set of LUCA and the Fundamental Regularity in the Standard Genetic Code (United States)

    van der Gulik, Peter T. S.; Hoff, Wouter D.


    Based on (i) an analysis of the regularities in the standard genetic code and (ii) comparative genomics of the anticodon modification machinery in the three branches of life, we derive the tRNA set and its anticodon modifications as it was present in LUCA. Previously we proposed that an early ancestor of LUCA contained a set of 23 tRNAs with unmodified anticodons that was capable of translating all 20 amino acids while reading 55 of the 61 sense codons of the standard genetic code (SGC). Here we use biochemical and genomic evidence to derive that LUCA contained a set of 44 or 45 tRNAs containing 2 or 3 modifications while reading 59 or 60 of the 61 sense codons. Subsequent tRNA modifications occurred independently in the Bacteria and Eucarya, while the Archaea have remained quite close to the tRNA set as it was present in LUCA. PMID:27454314

  14. RNA polymerase II induced transcription of tRNA genes and processing of the mRNAs in yeast

    Institute of Scientific and Technical Information of China (English)


    Only 5'-halves were produced when the terminator sequence for RNA polymerase (pol) 1II transcrip-tion was inserted into the intron of yeast tRNATyr gene. If a promoter and a terminator for pol II transcription flanked it,the tRNA gene could be transcribed by pol II, but the transcripts could not be processed into mature tRNAs. In con-trast, tRNA gene could also be transcribed by pol III and the transcripts could be processed into mature tRNAs even if a promoter and a terminator for pol II transcription flanked it. Pol II transcripts, modified with a self-cleaved hannner-head structure at 3'-end, were processed into mature tRNAs in the medium containing 100 mmol/L Mg2+ , indicating that the 3'-long trailer sequence blocks the maturation of tRNA gene transcripts by pol II.

  15. Mouse Models Targeting Selenocysteine tRNA Expression for Elucidating the Role of Selenoproteins in Health and Development

    Directory of Open Access Journals (Sweden)

    Dolph L. Hatfield


    Full Text Available Selenium (Se deficiency has been known for many years to be associated with disease, impaired growth and a variety of other metabolic disorders in mammals. Only recently has the major role that Se-containing proteins, designated selenoproteins, play in many aspects of health and development begun to emerge. Se is incorporated into protein by way of the Se-containing amino acid, selenocysteine (Sec. The synthesis of selenoproteins is dependent on Sec tRNA for insertion of Sec, the 21st amino acid in the genetic code, into protein. We have taken advantage of this dependency to modulate the expression of Sec tRNA that in turn modulates the expression of selenoproteins by generating transgenic, conditional knockout, transgenic/standard knockout and transgenic/conditional knockout mouse models, all of which involve the Sec tRNA gene, to elucidate the intracellular roles of this protein class.

  16. Chemical recognition software

    Energy Technology Data Exchange (ETDEWEB)

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


    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.

  17. Chemical recognition software

    Energy Technology Data Exchange (ETDEWEB)

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


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

  18. Emotion Recognition (United States)

    Neiberg, Daniel; Elenius, Kjell; Burger, Susanne

    Studies of expressive speech have shown that discrete emotions such as anger, fear, joy, and sadness can be accurately communicated, also cross-culturally, and that each emotion is associated with reasonably specific acoustic characteristics [8]. However, most previous research has been conducted on acted emotions. These certainly have something in common with naturally occurring emotions but may also be more intense and prototypical than authentic, everyday expressions [6, 13]. Authentic emotions are, on the other hand, often a combination of different affective states and occur rather infrequently in everyday life.

  19. Structure and Activity of an Aminoacyl-tRNA Synthetase that Charges tRNA with Nitro-Tryptophan

    Energy Technology Data Exchange (ETDEWEB)

    Buddha,M.; Crane, B.


    The most divergent of two tryptophanyl tRNA synthetases (TrpRS II) found in Deinococcus radiodurans interacts with a nitric oxide synthase protein that produces 4-nitro-tryptophan (4-NRP). TrpRS II efficiently charges transfer RNATrp with 4-NRP and 5-hydroxy-tryptophan (5-HRP). The crystal structures of TrpRS II bound to tryptophan and 5-HRP reveal residue substitutions that accommodate modified indoles. A class of auxiliary bacterial TrpRSs conserve this capacity to charge tRNA with nonstandard amino acids.

  20. One ancestor for two codes viewed from the perspective of two complementary modes of tRNA aminoacylation

    Directory of Open Access Journals (Sweden)

    Szathmáry Eörs


    Full Text Available Abstract Background The genetic code is brought into action by 20 aminoacyl-tRNA synthetases. These enzymes are evenly divided into two classes (I and II that recognize tRNAs from the minor and major groove sides of the acceptor stem, respectively. We have reported recently that: (1 ribozymic precursors of the synthetases seem to have used the same two sterically mirror modes of tRNA recognition, (2 having these two modes might have helped in preventing erroneous aminoacylation of ancestral tRNAs with complementary anticodons, yet (3 the risk of confusion for the presumably earliest pairs of complementarily encoded amino acids had little to do with anticodons. Accordingly, in this communication we focus on the acceptor stem. Results Our main result is the emergence of a palindrome structure for the acceptor stem's common ancestor, reconstructed from the phylogenetic trees of Bacteria, Archaea and Eukarya. In parallel, for pairs of ancestral tRNAs with complementary anticodons, we present updated evidence of concerted complementarity of the second bases in the acceptor stems. These two results suggest that the first pairs of "complementary" amino acids that were engaged in primordial coding, such as Gly and Ala, could have avoided erroneous aminoacylation if and only if the acceptor stems of their adaptors were recognized from the same, major groove, side. The class II protein synthetases then inherited this "primary preference" from isofunctional ribozymes. Conclusion Taken together, our results support the hypothesis that the genetic code per se (the one associated with the anticodons and the operational code of aminoacylation (associated with the acceptor diverged from a common ancestor that probably began developing before translation. The primordial advantage of linking some amino acids (most likely glycine and alanine to the ancestral acceptor stem may have been selective retention in a protocell surrounded by a leaky membrane for use in

  1. From End to End: tRNA Editing at 5'- and 3'-Terminal Positions (United States)

    Betat, Heike; Long, Yicheng; Jackman, Jane E.; Mörl, Mario


    During maturation, tRNA molecules undergo a series of individual processing steps, ranging from exo- and endonucleolytic trimming reactions at their 5'- and 3'-ends, specific base modifications and intron removal to the addition of the conserved 3'-terminal CCA sequence. Especially in mitochondria, this plethora of processing steps is completed by various editing events, where base identities at internal positions are changed and/or nucleotides at 5'- and 3'-ends are replaced or incorporated. In this review, we will focus predominantly on the latter reactions, where a growing number of cases indicate that these editing events represent a rather frequent and widespread phenomenon. While the mechanistic basis for 5'- and 3'-end editing differs dramatically, both reactions represent an absolute requirement for generating a functional tRNA. Current in vivo and in vitro model systems support a scenario in which these highly specific maturation reactions might have evolved out of ancient promiscuous RNA polymerization or quality control systems. PMID:25535083

  2. From End to End: tRNA Editing at 5'- and 3'-Terminal Positions

    Directory of Open Access Journals (Sweden)

    Heike Betat


    Full Text Available During maturation, tRNA molecules undergo a series of individual processing steps, ranging from exo- and endonucleolytic trimming reactions at their 5'- and 3'-ends, specific base modifications and intron removal to the addition of the conserved 3'-terminal CCA sequence. Especially in mitochondria, this plethora of processing steps is completed by various editing events, where base identities at internal positions are changed and/or nucleotides at 5'- and 3'-ends are replaced or incorporated. In this review, we will focus predominantly on the latter reactions, where a growing number of cases indicate that these editing events represent a rather frequent and widespread phenomenon. While the mechanistic basis for 5'- and 3'-end editing differs dramatically, both reactions represent an absolute requirement for generating a functional tRNA. Current in vivo and in vitro model systems support a scenario in which these highly specific maturation reactions might have evolved out of ancient promiscuous RNA polymerization or quality control systems.

  3. Mutations induced by monofunctional and bifunctional phosphoramide mustards in supF tRNA gene. (United States)

    Mudipalli, A; Maccubbin, A E; Nadadur, S S; Struck, R F; Gurtoo, H L


    The relative mutagenicity, nature of the mutations and the sequence specificity of mutations induced by the bifunctional alkylating agent, phosphoramide mustard (PM) and a monofunctional derivative, dechloroethyl phosphoramide mustard (dePM), were analyzed by the Ames test and by an in vitro shuttle vector mutagenesis assay. Both PM and dePM increased the mutation frequency above background in either assay. However, on an equimolar basis, dePM was less mutagenic than PM. In the in vitro shuttle vector mutagenesis assay, sequencing demonstrated that about 40% of the mutant plasmids contained more than one mutation in the supF tRNA gene segment of the plasmid. About 70% of the mutations observed in dePM-treated plasmids were single base substitutions with A:T and G:C base pairs being mutated at equivalent rates. In contrast, only about 50% of the mutations observed in PM-treated plasmids were single base substitutions, 80% of which involved G:C base pairs. Single base deletions and insertions were found in approximately equal proportions with both compounds; however, these lesions were in greater abundance in PM-treated plasmids. Putative hot-spots for mutation in the supF tRNA gene included base pairs at position 102 and 110 for PM and positions 170 and 171 for dePM.

  4. Structural Basis for Specific Inhibition of tRNA Synthetase by an ATP Competitive Inhibitor. (United States)

    Fang, Pengfei; Han, Hongyan; Wang, Jing; Chen, Kaige; Chen, Xin; Guo, Min


    Pharmaceutical inhibitors of aminoacyl-tRNA synthetases demand high species and family specificity. The antimalarial ATP-mimetic cladosporin selectively inhibits Plasmodium falciparum LysRS (PfLysRS). How the binding to a universal ATP site achieves the specificity is unknown. Here we report three crystal structures of cladosporin with human LysRS, PfLysRS, and a Pf-like human LysRS mutant. In all three structures, cladosporin occupies the class defining ATP-binding pocket, replacing the adenosine portion of ATP. Three residues holding the methyltetrahydropyran moiety of cladosporin are critical for the specificity of cladosporin against LysRS over other class II tRNA synthetase families. The species-exclusive inhibition of PfLysRS is linked to a structural divergence beyond the active site that mounts a lysine-specific stabilizing response to binding cladosporin. These analyses reveal that inherent divergence of tRNA synthetase structural assembly may allow for highly specific inhibition even through the otherwise universal substrate binding pocket and highlight the potential for structure-driven drug development.

  5. Chemical and Conformational Diversity of Modified Nucleosides Affects tRNA Structure and Function

    Directory of Open Access Journals (Sweden)

    Ville Y. P. Väre


    Full Text Available RNAs are central to all gene expression through the control of protein synthesis. Four major nucleosides, adenosine, guanosine, cytidine and uridine, compose RNAs and provide sequence variation, but are limited in contributions to structural variation as well as distinct chemical properties. The ability of RNAs to play multiple roles in cellular metabolism is made possible by extensive variation in length, conformational dynamics, and the over 100 post-transcriptional modifications. There are several reviews of the biochemical pathways leading to RNA modification, but the physicochemical nature of modified nucleosides and how they facilitate RNA function is of keen interest, particularly with regard to the contributions of modified nucleosides. Transfer RNAs (tRNAs are the most extensively modified RNAs. The diversity of modifications provide versatility to the chemical and structural environments. The added chemistry, conformation and dynamics of modified nucleosides occurring at the termini of stems in tRNA’s cloverleaf secondary structure affect the global three-dimensional conformation, produce unique recognition determinants for macromolecules to recognize tRNAs, and affect the accurate and efficient decoding ability of tRNAs. This review will discuss the impact of specific chemical moieties on the structure, stability, electrochemical properties, and function of tRNAs.

  6. An entropy based analysis of the relationship between the DOW JONES Index and the TRNA Sentiment series

    NARCIS (Netherlands)

    D.E. Allen (David); M.J. McAleer (Michael); A.K. Singh (Abhay)


    textabstractThis paper features an analysis of the relationship between the DOW JONES Industrial Average Index (DJIA) and a sentiment news series using daily data obtained from the Thomson Reuters News Analytics (TRNA)1 provided by SIRCA (The Securities Industry Research Centre of the Asia Pacic). T

  7. Direct Regulation of tRNA and 5S rRNA Gene Transcription by Polo-like Kinase 1

    NARCIS (Netherlands)

    Fairley, Jennifer A.; Mitchell, Louise E.; Berg, Tracy; Kenneth, Niall S.; von Schubert, Conrad; Sillje, Herman H. W.; Medema, Rene H.; Nigg, Erich A.; White, Robert J.


    Polo-like kinase Plk1 controls numerous aspects of cell-cycle progression. We show that it associates with tRNA and 5S rRNA genes and regulates their transcription by RNA polymerase Ill (pol Ill) through direct binding and phosphorylation of transcription factor Brit During interphase, Plk1 promotes

  8. Evidence that the mitochondrial leucyl tRNA synthetase (LARS2) gene represents a novel type 2 diabetes susceptibility gene

    NARCIS (Netherlands)

    L.M. 't Hart (Leen); H.A.P. Pols (Huib); T. Hansen (Torben); I. Rietveld (Ingrid); J.M. Dekker (Jacqueline); J.A. Maassen (Johannes); M.G.A.A.M. Nijpels (Giel); G.M.C. Janssen (George); P.P. Arp (Pascal); R.J. Heine (Robert); A.G. Uitterlinden (André); T. Jorgensen (Torben); C.M. van Duijn (Cock); K. Borch-Johnsen; O. Pedersen (Oluf)


    textabstractPreviously, we have shown that a mutation in the mitochondrial DNA-encoded tRNA(Leu(UUR)) gene is associated with type 2 diabetes. One of the consequences of this mutation is a reduced aminoacylation of tRNA(Leu(UUR)). In this study, we have examined whether variants in the leucyl tRNA s

  9. Face Recognition Using Local Quantized Patterns and Gabor Filters (United States)

    Khryashchev, V.; Priorov, A.; Stepanova, O.; Nikitin, A.


    The problem of face recognition in a natural or artificial environment has received a great deal of researchers' attention over the last few years. A lot of methods for accurate face recognition have been proposed. Nevertheless, these methods often fail to accurately recognize the person in difficult scenarios, e.g. low resolution, low contrast, pose variations, etc. We therefore propose an approach for accurate and robust face recognition by using local quantized patterns and Gabor filters. The estimation of the eye centers is used as a preprocessing stage. The evaluation of our algorithm on different samples from a standardized FERET database shows that our method is invariant to the general variations of lighting, expression, occlusion and aging. The proposed approach allows about 20% correct recognition accuracy increase compared with the known face recognition algorithms from the OpenCV library. The additional use of Gabor filters can significantly improve the robustness to changes in lighting conditions.

  10. Gesture Recognition Summarization

    Institute of Scientific and Technical Information of China (English)

    ZHANG Ting-fang; FENG Zhi-quan; SU Yuan-yuan; JIANG Yan


    Gesture recognition is an important research in the field of human-computer interaction. Hand Gestures are strong variable and flexible, so the gesture recognition has always been an important challenge for the researchers. In this paper, we first outlined the development of gestures recognition, and different classification of gestures based on different purposes. Then we respectively introduced common methods used in the process of gesture segmentation, feature extraction and recognition. Finally, the gesture recognition was summarized and the studying prospects were given.

  11. Keep it Accurate and Diverse

    DEFF Research Database (Denmark)

    Ali Bagheri, Mohammad; Gao, Qigang; Guerrero, Sergio Escalera


    The performance of different action recognition tech- niques has recently been studied by several computer vision researchers. However, the potential improvement in classi- fication through classifier fusion by ensemble-based meth- ods has remained unattended. In this work, we evaluate the perfor......The performance of different action recognition tech- niques has recently been studied by several computer vision researchers. However, the potential improvement in classi- fication through classifier fusion by ensemble-based meth- ods has remained unattended. In this work, we evaluate...... the performance of an ensemble of action learning techniques, each performing the recognition task from a different per- spective. The underlying idea is that instead of aiming a very sophisticated and powerful representation/learning technique, we can learn action categories using a set of relatively simple...... and diverse classifiers, each trained with different feature set. In addition, combining the outputs of several learners can reduce the risk of an unfortunate selec- tion of a learner on an unseen action recognition scenario. This leads to having a more robust and general-applicable framework. In order...

  12. Limited diagnostic value of enzyme analysis in patients with mitochondrial tRNA mutations

    DEFF Research Database (Denmark)

    Wibrand, Flemming; Jeppesen, Tina Dysgaard; Frederiksen, Anja L


    We evaluated the diagnostic value of respiratory chain (RC) enzyme analysis of muscle in adult patients with mitochondrial myopathy (MM). RC enzyme activity was measured in muscle biopsies from 39 patients who carry either the 3243A>G mutation, other tRNA point mutations, or single, large....... Only 10% of patients with the 3243A>G point mutation had decreased enzyme activity of one or more RC complexes, whereas this was the case for 83% of patients with other point mutations and 62% of patients with deletions. Abnormal muscle histochemistry was found in 65%, 100%, and 85% of patients......-scale deletions of mtDNA. Findings were compared with those obtained from asymptomatic relatives with the 3243A>G mutation, myotonic dystrophy patients, and healthy subjects. Plasma lactate concentration, maximal oxygen uptake, and ragged-red fibers/cytochrome c-negative fibers in muscle were also determined...

  13. On origin of genetic code and tRNA before translation

    Directory of Open Access Journals (Sweden)

    Szathmáry Eörs


    Full Text Available Abstract Background Synthesis of proteins is based on the genetic code - a nearly universal assignment of codons to amino acids (aas. A major challenge to the understanding of the origins of this assignment is the archetypal "key-lock vs. frozen accident" dilemma. Here we re-examine this dilemma in light of 1 the fundamental veto on "foresight evolution", 2 modular structures of tRNAs and aminoacyl-tRNA synthetases, and 3 the updated library of aa-binding sites in RNA aptamers successfully selected in vitro for eight amino acids. Results The aa-binding sites of arginine, isoleucine and tyrosine contain both their cognate triplets, anticodons and codons. We have noticed that these cases might be associated with palindrome-dinucleotides. For example, one-base shift to the left brings arginine codons CGN, with CG at 1-2 positions, to the respective anticodons NCG, with CG at 2-3 positions. Formally, the concomitant presence of codons and anticodons is also expected in the reverse situation, with codons containing palindrome-dinucleotides at their 2-3 positions, and anticodons exhibiting them at 1-2 positions. A closer analysis reveals that, surprisingly, RNA binding sites for Arg, Ile and Tyr "prefer" (exactly as in the actual genetic code the anticodon(2-3/codon(1-2 tetramers to their anticodon(1-2/codon(2-3 counterparts, despite the seemingly perfect symmetry of the latter. However, since in vitro selection of aa-specific RNA aptamers apparently had nothing to do with translation, this striking preference provides a new strong support to the notion of the genetic code emerging before translation, in response to catalytic (and possibly other needs of ancient RNA life. Consistently with the pre-translation origin of the code, we propose here a new model of tRNA origin by the gradual, Fibonacci process-like, elongation of a tRNA molecule from a primordial coding triplet and 5'DCCA3' quadruplet (D is a base-determinator to the eventual 76 base

  14. tRNA Core Hypothesis for the Transition from the RNA World to the Ribonucleoprotein World

    Directory of Open Access Journals (Sweden)

    Savio T. de Farias


    Full Text Available Herein we present the tRNA core hypothesis, which emphasizes the central role of tRNAs molecules in the origin and evolution of fundamental biological processes. tRNAs gave origin to the first genes (mRNA and the peptidyl transferase center (rRNA, proto-tRNAs were at the core of a proto-translation system, and the anticodon and operational codes then arose in tRNAs molecules. Metabolic pathways emerged from evolutionary pressures of the decoding systems. The transitions from the RNA world to the ribonucleoprotein world to modern biological systems were driven by three kinds of tRNAs transitions, to wit, tRNAs leading to both mRNA and rRNA.

  15. Structural basis for full-spectrum inhibition of translational functions on a tRNA synthetase (United States)

    Fang, Pengfei; Yu, Xue; Jeong, Seung Jae; Mirando, Adam; Chen, Kaige; Chen, Xin; Kim, Sunghoon; Francklyn, Christopher S.; Guo, Min


    The polyketide natural product borrelidin displays antibacterial, antifungal, antimalarial, anticancer, insecticidal and herbicidal activities through the selective inhibition of threonyl-tRNA synthetase (ThrRS). How borrelidin simultaneously attenuates bacterial growth and suppresses a variety of infections in plants and animals is not known. Here we show, using X-ray crystal structures and functional analyses, that a single molecule of borrelidin simultaneously occupies four distinct subsites within the catalytic domain of bacterial and human ThrRSs. These include the three substrate-binding sites for amino acid, ATP and tRNA associated with aminoacylation, and a fourth ‘orthogonal’ subsite created as a consequence of binding. Thus, borrelidin competes with all three aminoacylation substrates, providing a potent and redundant mechanism to inhibit ThrRS during protein synthesis. These results highlight a surprising natural design to achieve the quadrivalent inhibition of translation through a highly conserved family of enzymes. PMID:25824639

  16. Insertion near the mitochondrial tyrosine tRNA gene in patients with mitochondrial diseases

    Energy Technology Data Exchange (ETDEWEB)

    Goto, Y.; Nonaka, I. [National Institute of Neuroscience, Tokyo (Japan); Horai, S. [National Institute of Genetics, Mishima (Japan)


    The 3243 mutation commonly found in patients with mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes (MELAS) has been occasionally detected in patients with chronic progressive external opthalmoplegia (CPEO). To elucidate the molecular mechanism underlying this phenomenon, an extensive mitochondrial (mt) DNA study was performed on such a patient (3243-CPEO). The newly discovered insertion was located in the noncoding region between cytrochrome c oxidase subunit 1 and tyrosine tRNA. The insertion was not found in 58 or 22 CPEO patients with or without mtDNA large-scale deletion but in another 3243-CPEO patient. In addition, the insertion was present in 1 of 116 normal Japanese, who had no 3243 mutation, and in 3 of 68 3243-MELAS patients. These results raise the possibility that the phenotypic expression of the 3243 mutation could be modulated or arranged by additional mtDNA mutations.

  17. Natural aminoacyl tRNA synthetase fragment enhances cardiac function after myocardial infarction.

    Directory of Open Access Journals (Sweden)

    Margaret E McCormick

    Full Text Available A naturally-occurring fragment of tyrosyl-tRNA synthetase (TyrRS has been shown in higher eukaryotes to 'moonlight' as a pro-angiogenic cytokine in addition to its primary role in protein translation. Pro-angiogenic cytokines have previously been proposed to be promising therapeutic mechanisms for the treatment of myocardial infarction. Here, we show that systemic delivery of the natural fragment of TyRS, mini-TyrRS, improves heart function in mice after myocardial infarction. This improvement is associated with reduced formation of scar tissue, increased angiogenesis of cardiac capillaries, recruitment of c-kitpos cells and proliferation of myocardial fibroblasts. This work demonstrates that mini-TyrRS has beneficial effects on cardiac repair and regeneration and offers support for the notion that elucidation of the ever expanding repertoire of noncanonical functions of aminoacyl tRNA synthetases offers unique opportunities for development of novel therapeutics.

  18. The nucleotide sequence of histidine tRNA gamma of Drosophila melanogaster.


    Altwegg, M; Kubli, E


    The nucleotide sequence of D. melanogaster histidine tRNA gamma was determined to be: pG-G-C-C-G-U-G-A-U-C-G-U-C-psi-A-G-D-G-G-D-D-A-G-G-A-C-C-C-C-A-C-G-psi-U-G-U-G- m1G-C-C-G-U-G-G-U-A-A-C-C-m5C-A-G-G-U-psi-C-G-m1A-A-U-C-C-U-G-G-U-C-A-C-G-G-m5C -A-C-C-AOH. An additional unpaired G is found at the 5' end, and the T in the TpsiC loop is replaced by a U.


    NARCIS (Netherlands)

    Hamanaka, M.; Yamada, K.


    On­line character recognition which can adapt to handwriting quality is proposed. In character recognition, it is difficult to recognize both clearly and roughly written characters accurately. For Japanese characters, the number of strokes is often slightly varied when characters are written roughly

  20. Formation of tRNA granules in the nucleus of heat-induced human cells

    Energy Technology Data Exchange (ETDEWEB)

    Miyagawa, Ryu [Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032 (Japan); Department of Biological Science, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654 (Japan); Mizuno, Rie [Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032 (Japan); Watanabe, Kazunori, E-mail: [Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032 (Japan); Ijiri, Kenichi [Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032 (Japan); Department of Biological Science, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654 (Japan)


    Highlights: Black-Right-Pointing-Pointer tRNAs are tranlocated into the nucleus in heat-induced HeLa cells. Black-Right-Pointing-Pointer tRNAs form the unique granules in the nucleus. Black-Right-Pointing-Pointer tRNA ganules overlap with nuclear stress granules. -- Abstract: The stress response, which can trigger various physiological phenomena, is important for living organisms. For instance, a number of stress-induced granules such as P-body and stress granule have been identified. These granules are formed in the cytoplasm under stress conditions and are associated with translational inhibition and mRNA decay. In the nucleus, there is a focus named nuclear stress body (nSB) that distinguishes these structures from cytoplasmic stress granules. Many splicing factors and long non-coding RNA species localize in nSBs as a result of stress. Indeed, tRNAs respond to several kinds of stress such as heat, oxidation or starvation. Although nuclear accumulation of tRNAs occurs in starved Saccharomyces cerevisiae, this phenomenon is not found in mammalian cells. We observed that initiator tRNA{sup Met} (Meti) is actively translocated into the nucleus of human cells under heat stress. During this study, we identified unique granules of Meti that overlapped with nSBs. Similarly, elongator tRNA{sup Met} was translocated into the nucleus and formed granules during heat stress. Formation of tRNA granules is closely related to the translocation ratio. Then, all tRNAs may form the specific granules.

  1. Chromatographic evidence that the AAA-coding isoacceptor of lysine tRNA primes DNA synthesis in murine mammary tumor virus

    Energy Technology Data Exchange (ETDEWEB)

    Waters, L.C.


    Most of the tRNA encapsulated within the murine mammary tumor virus is tRNA/sup LYS/. The reversed-phase chromatographic pattern of tRNA/sup LYS/ isoacceptors in the viral free tRNA and in the 70 S-associated tRNA that is released at 65/sup 0/ is similar to the pattern in virus-producing cells. However, the more tightly bound 70 S-associated tRNA/sup LYS/ is significantly enriched in the AAA-coding isoacceptor. This isoacceptor, but not the AAG-coding one, primes MuMTV 35 S RNA-directed DNA synthesis in vitro.

  2. ORNL Biometric Eye Model for Iris Recognition

    Energy Technology Data Exchange (ETDEWEB)

    Santos-Villalobos, Hector J [ORNL; Barstow, Del R [ORNL; Karakaya, Mahmut [ORNL; Chaum, Edward [University of Tennessee, Knoxville (UTK); Boehnen, Chris Bensing [ORNL


    Iris recognition has been proven to be an accurate and reliable biometric. However, the recognition of non-ideal iris images such as off angle images is still an unsolved problem. We propose a new biometric targeted eye model and a method to reconstruct the off-axis eye to its frontal view allowing for recognition using existing methods and algorithms. This allows for existing enterprise level algorithms and approaches to be largely unmodified by using our work as a pre-processor to improve performance. In addition, we describe the `Limbus effect' and its importance for an accurate segmentation of off-axis irides. Our method uses an anatomically accurate human eye model and ray-tracing techniques to compute a transformation function, which reconstructs the iris to its frontal, non-refracted state. Then, the same eye model is used to render a frontal view of the reconstructed iris. The proposed method is fully described and results from synthetic data are shown to establish an upper limit on performance improvement and establish the importance of the proposed approach over traditional linear elliptical unwrapping methods. Our results with synthetic data demonstrate the ability to perform an accurate iris recognition with an image taken as much as 70 degrees off-axis.

  3. Using local alignments for relation recognition

    NARCIS (Netherlands)

    S. Katrenko; P. Adriaans; M. van Someren


    This paper discusses the problem of marrying structural similarity with semantic relatedness for Information Extraction from text. Aiming at accurate recognition of relations, we introduce local alignment kernels and explore various possibilities of using them for this task. We give a definition of

  4. Conditional Random Fields for Activity Recognition (United States)


    are important for accurate recognition. Huynh and Schiele used features such as fast Fourier transform coefficients computed over windows of...Friedman. The Elements of Statistical Learning. Springer, August 2001. [40] P.J. Hubert. Robust Statistics. Wiley, 1981. [41] Tâm Huynh and Bernt Schiele

  5. Characterization of 67 mitochondrial tRNA gene rearrangements in the Hymenoptera suggests that mitochondrial tRNA gene position is selectively neutral. (United States)

    Dowton, Mark; Cameron, Stephen L; Dowavic, Jessica I; Austin, Andy D; Whiting, Michael F


    We present entire sequences of two hymenopteran mitochondrial genomes and the major portion of three others. We combined these data with nine previously sequenced hymenopteran mitochondrial genomes. This allowed us to infer and analyze the evolution of the 67 mitochondrial gene rearrangements so far found in this order. All of these involve tRNA genes, whereas four also involve larger (protein-coding or ribosomal RNA) genes. We find that the vast majority of mitochondrial gene rearrangements are independently derived. A maximum of four of these rearrangements represent shared, derived organizations, whereas three are convergently derived. The remaining mitochondrial gene rearrangements represent new mitochondrial genome organizations. These data are consistent with the proposal that there are an enormous number of alternative mitochondrial genome organizations possible and that mitochondrial genome organization is, for the most part, selectively neutral. Nevertheless, some mitochondrial genes appear less mobile than others. Genes close to the noncoding region are generally more mobile but only marginally so. Some mitochondrial genes rearrange in a pattern consistent with the duplication/random loss model, but more mitochondrial genes move in a pattern inconsistent with this model. An increased rate of mitochondrial gene rearrangement is not tightly associated with the evolution of parasitism. Although parasitic lineages tend to have more mitochondrial gene rearrangements than nonparasitic lineages, there are exceptions (e.g., Orussus and Schlettererius). It is likely that only a small proportion of the total number of mitochondrial gene rearrangements that have occurred during the evolution of the Hymenoptera have been sampled in the present study.

  6. Automatic modulation recognition of communication signals

    CERN Document Server

    Azzouz, Elsayed Elsayed


    Automatic modulation recognition is a rapidly evolving area of signal analysis. In recent years, interest from the academic and military research institutes has focused around the research and development of modulation recognition algorithms. Any communication intelligence (COMINT) system comprises three main blocks: receiver front-end, modulation recogniser and output stage. Considerable work has been done in the area of receiver front-ends. The work at the output stage is concerned with information extraction, recording and exploitation and begins with signal demodulation, that requires accurate knowledge about the signal modulation type. There are, however, two main reasons for knowing the current modulation type of a signal; to preserve the signal information content and to decide upon the suitable counter action, such as jamming. Automatic Modulation Recognition of Communications Signals describes in depth this modulation recognition process. Drawing on several years of research, the authors provide a cr...

  7. Novel Techniques for Dialectal Arabic Speech Recognition

    CERN Document Server

    Elmahdy, Mohamed; Minker, Wolfgang


    Novel Techniques for Dialectal Arabic Speech describes approaches to improve automatic speech recognition for dialectal Arabic. Since speech resources for dialectal Arabic speech recognition are very sparse, the authors describe how existing Modern Standard Arabic (MSA) speech data can be applied to dialectal Arabic speech recognition, while assuming that MSA is always a second language for all Arabic speakers. In this book, Egyptian Colloquial Arabic (ECA) has been chosen as a typical Arabic dialect. ECA is the first ranked Arabic dialect in terms of number of speakers, and a high quality ECA speech corpus with accurate phonetic transcription has been collected. MSA acoustic models were trained using news broadcast speech. In order to cross-lingually use MSA in dialectal Arabic speech recognition, the authors have normalized the phoneme sets for MSA and ECA. After this normalization, they have applied state-of-the-art acoustic model adaptation techniques like Maximum Likelihood Linear Regression (MLLR) and M...

  8. Object reading: text recognition for object recognition

    NARCIS (Netherlands)

    Karaoglu, S.; van Gemert, J.C.; Gevers, T.


    We propose to use text recognition to aid in visual object class recognition. To this end we first propose a new algorithm for text detection in natural images. The proposed text detection is based on saliency cues and a context fusion step. The algorithm does not need any parameter tuning and can d

  9. Efficient Interaction Recognition through Positive Action Representation

    Directory of Open Access Journals (Sweden)

    Tao Hu


    Full Text Available This paper proposes a novel approach to decompose two-person interaction into a Positive Action and a Negative Action for more efficient behavior recognition. A Positive Action plays the decisive role in a two-person exchange. Thus, interaction recognition can be simplified to Positive Action-based recognition, focusing on an action representation of just one person. Recently, a new depth sensor has become widely available, the Microsoft Kinect camera, which provides RGB-D data with 3D spatial information for quantitative analysis. However, there are few publicly accessible test datasets using this camera, to assess two-person interaction recognition approaches. Therefore, we created a new dataset with six types of complex human interactions (i.e., named K3HI, including kicking, pointing, punching, pushing, exchanging an object, and shaking hands. Three types of features were extracted for each Positive Action: joint, plane, and velocity features. We used continuous Hidden Markov Models (HMMs to evaluate the Positive Action-based interaction recognition method and the traditional two-person interaction recognition approach with our test dataset. Experimental results showed that the proposed recognition technique is more accurate than the traditional method, shortens the sample training time, and therefore achieves comprehensive superiority.

  10. Biophysical insights into the intercalative interaction of surfactant cobalt(III) complexes of certain diimine ligands bound to yeast tRNA: Effects of hydrophobicity. (United States)

    Nagaraj, Karuppiah; Sakthinathan, Subramanian; Arunachalam, Sankaralingam


    The interaction of two surfactant cobalt(III) complexes, cis-[Co(ip)₂(DA)₂](ClO₄)₃ 1 and cis-[Co(dpq)₂(DA)₂](ClO₄)₃ 2 where ip=imidazo[4,5-f][1,10]phenanthroline and dpq=dipyrido[3,2-d:2'-3'-f]quinoxaline with yeast tRNA have been explored by using electronic absorption, competitive binding, electrochemical studies and viscosity measurements. The results suggest that these complexes can bind to tRNA by intercalation. The presence of hydrophobic diimine ligand and the long aliphatic double chains of these complexes facilitate its intercalative interaction with the hydrophobic interior of the tRNA. The extent of tRNA binding of complex 2 has greater affinity than that of complex containing imidazo[4,5-f][1,10]phenanthroline ligands.

  11. Electrophysiological distinctions between recognition memory with and without awareness. (United States)

    Ko, Philip C; Duda, Bryant; Hussey, Erin P; Ally, Brandon A


    The influence of implicit memory representations on explicit recognition may help to explain cases of accurate recognition decisions made with high uncertainty. During a recognition task, implicit memory may enhance the fluency of a test item, biasing decision processes to endorse it as "old". This model may help explain recognition-without-identification, a remarkable phenomenon in which participants make highly accurate recognition decisions despite the inability to identify the test item. The current study investigated whether recognition-without-identification for pictures elicits a similar pattern of neural activity as other types of accurate recognition decisions made with uncertainty. Further, this study also examined whether recognition-without-identification for pictures could be attained by the use of perceptual and conceptual information from memory. To accomplish this, participants studied pictures and then performed a recognition task under difficult viewing conditions while event-related potentials (ERPs) were recorded. Behavioral results showed that recognition was highly accurate even when test items could not be identified, demonstrating recognition-without-identification. The behavioral performance also indicated that recognition-without-identification was mediated by both perceptual and conceptual information, independently of one another. The ERP results showed dramatically different memory related activity during the early 300 to 500ms epoch for identified items that were studied compared to unidentified items that were studied. Similar to previous work highlighting accurate recognition without retrieval awareness, test items that were not identified, but correctly endorsed as "old," elicited a negative posterior old/new effect (i.e., N300). In contrast, test items that were identified and correctly endorsed as "old," elicited the classic positive frontal old/new effect (i.e., FN400). Importantly, both of these effects were elicited under

  12. Hierarchical Recognition Scheme for Human Facial Expression Recognition Systems

    Directory of Open Access Journals (Sweden)

    Muhammad Hameed Siddiqi


    Full Text Available 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.

  13. Recognition of human face based on improved multi-sample

    Institute of Scientific and Technical Information of China (English)

    LIU Xia; LI Lei-lei; LI Ting-jun; LIU Lu; ZHANG Ying


    In order to solve the problem caused by variation illumination in human face recognition, we bring forward a face recognition algorithm based on the improved muhi-sample. In this algorithm, the face image is processed with Retinex theory, meanwhile, the Gabor filter is adopted to perform the feature extraction. The experimental results show that the application of Retinex theory improves the recognition accuracy, and makes the algorithm more robust to the variation illumination. The Gabor filter is more effective and accurate for extracting more useable facial local features. It is proved that the proposed algorithm has good recognition accuracy and it is stable under variation illumination.

  14. Voice Recognition Technology: Has It Come of Age?

    Directory of Open Access Journals (Sweden)

    Joseph R. Zumalt


    Full Text Available Voice recognition software allows computer users to bypass their keyboards and use their voices to enter text. While the library literature is somewhat silent about voice recognition technology, the medical and legal communities have reported some success using it. Voice recognition software was tested for dictation accuracy and usability within an agriculture library at the University of Illinois. Dragon NaturallySpeaking 8.0 was found to be more accurate than speech recognition within Microsoft Office 2003. Helpful Web sites and a short history regarding this breakthrough technology are included.

  15. Meta-Recognition: The Theory and Practice of Recognition Score Analysis. (United States)

    Scheirer, Walter J; Rocha, A; Micheals, Ross J; Boult, Terrance E


    In this paper, we define meta-recognition, a performance prediction method for recognition algorithms, and examine the theoretical basis for its postrecognition score analysis form through the use of the statistical extreme value theory (EVT). The ability to predict the performance of a recognition system based on its outputs for each match instance is desirable for a number of important reasons, including automatic threshold selection for determining matches and nonmatches, and automatic algorithm selection or weighting for multi-algorithm fusion. The emerging body of literature on postrecognition score analysis has been largely constrained to biometrics, where the analysis has been shown to successfully complement or replace image quality metrics as a predictor. We develop a new statistical predictor based upon the Weibull distribution, which produces accurate results on a per instance recognition basis across different recognition problems. Experimental results are provided for two different face recognition algorithms, a fingerprint recognition algorithm, a SIFT-based object recognition system, and a content-based image retrieval system.

  16. Determination of the Specificity Landscape for Ribonuclease P Processing of Precursor tRNA 5' Leader Sequences. (United States)

    Niland, Courtney N; Zhao, Jing; Lin, Hsuan-Chun; Anderson, David R; Jankowsky, Eckhard; Harris, Michael E


    Maturation of tRNA depends on a single endonuclease, ribonuclease P (RNase P), to remove highly variable 5' leader sequences from precursor tRNA transcripts. Here, we use high-throughput enzymology to report multiple-turnover and single-turnover kinetics for Escherichia coli RNase P processing of all possible 5' leader sequences, including nucleotides contacting both the RNA and protein subunits of RNase P. The results reveal that the identity of N(-2) and N(-3) relative to the cleavage site at N(1) primarily control alternative substrate selection and act at the level of association not the cleavage step. As a consequence, the specificity for N(-1), which contacts the active site and contributes to catalysis, is suppressed. This study demonstrates high-throughput RNA enzymology as a means to globally determine RNA specificity landscapes and reveals the mechanism of substrate discrimination by a widespread and essential RNA-processing enzyme.

  17. Recognition and Toleration

    DEFF Research Database (Denmark)

    Lægaard, Sune


    Recognition and toleration are ways of relating to the diversity characteristic of multicultural societies. The article concerns the possible meanings of toleration and recognition, and the conflict that is often claimed to exist between these two approaches to diversity. Different forms...... or interpretations of recognition and toleration are considered, confusing and problematic uses of the terms are noted, and the compatibility of toleration and recognition is discussed. The article argues that there is a range of legitimate and importantly different conceptions of both toleration and recognition...

  18. Recognition accuracy by experienced men and women players of basketball. (United States)

    Millslagle, Duane G


    This study examined 30 experienced basketball players' recognition accuracy by sex, playing position (guard, forward, and center), and situations in the game of basketball. The study used a perceptual cognitive paradigm in which subjects viewed slides of structured and unstructured game situations and accurately recognized the presence or absence of the basketball. A significant difference in recognition accuracy by sex, players' position, and structure of the game situation was found. Male players' recognition accuracy was better than the female players'. The recognition accuracy of subjects who played guard was better than that of subjects who played forward or center. The players' recognition accuracy was more accurate when observing structured plays versus unstructured plays. The conclusion of this study suggested that experienced basketball players differ in their cognitive and visual searching processes by sex and player position within the sport of basketball.

  19. Characterization of the tRNA and ribosome-dependent pppGpp-synthesis by recombinant stringent factor from Escherichia coli. (United States)

    Knutsson Jenvert, Rose-Marie; Holmberg Schiavone, Lovisa


    Stringent factor is a ribosome-dependent ATP:GTP pyrophosphoryl transferase that synthesizes (p)ppGpp upon nutrient deprivation. It is activated by unacylated tRNA in the ribosomal amino-acyl site (A-site) but it is unclear how activation occurs. A His-tagged stringent factor was isolated by affinity-chromatography and precipitation. This procedure yielded a protein of high purity that displayed (a) a low endogenous pyrophosphoryl transferase activity that was inhibited by the antibiotic tetracycline; (b) a low ribosome-dependent activity that was inhibited by the A-site specific antibiotics thiostrepton, micrococcin, tetracycline and viomycin; (c) a tRNA- and ribosome-dependent activity amounting to 4500 pmol pppGpp per pmol stringent factor per minute. Footprinting analysis showed that stringent factor interacted with ribosomes that contained tRNAs bound in classical states. Maximal activity was seen when the ribosomal A-site was presaturated with unacylated tRNA. Less tRNA was required to reach maximal activity when stringent factor and unacylated tRNA were added simultaneously to ribosomes, suggesting that stringent factor formed a complex with tRNA in solution that had higher affinity for the ribosomal A-site. However, tRNA-saturation curves, performed at two different ribosome/stringent factor ratios and filter-binding assays, did not support this hypothesis.

  20. The initiator methionine tRNA drives cell migration and invasion leading to increased metastatic potential in melanoma

    Directory of Open Access Journals (Sweden)

    Joanna Birch


    Full Text Available The cell's repertoire of transfer RNAs (tRNAs has been linked to cancer. Recently, the level of the initiator methionine tRNA (tRNAiMet in stromal fibroblasts has been shown to influence extracellular matrix (ECM secretion to drive tumour growth and angiogenesis. Here we show that increased tRNAiMet within cancer cells does not influence tumour growth, but drives cell migration and invasion via a mechanism that is independent from ECM synthesis and dependent on α5β1 integrin and levels of the translation initiation ternary complex. In vivo and ex vivo migration (but not proliferation of melanoblasts is significantly enhanced in transgenic mice which express additional copies of the tRNAiMet gene. We show that increased tRNAiMet in melanoma drives migratory, invasive behaviour and metastatic potential without affecting cell proliferation and primary tumour growth, and that expression of RNA polymerase III-associated genes (which drive tRNA expression are elevated in metastases by comparison with primary tumours. Thus, specific alterations to the cancer cell tRNA repertoire drive a migration/invasion programme that may lead to metastasis.

  1. The tRNA 30-end Processing Enzyme tRNase Z2 Contributes to Chloroplast Biogenesis in Rice

    Institute of Scientific and Technical Information of China (English)

    Tuan Long; Dong Guo; Dong He; Wenjie Shen; Xianghua Li


    tRNase Z (TRZ) is a ubiquitous endonuclease that removes the 30-trailer from precursor tRNAs during maturation. In yeast and animals, TRZ regulates the cell cycle via its (t)RNA processing activity;however, its physiological function in higher plants has not been well characterized. This study describes the identification of a rice (Oryza sativa) TRZ2 mutant; plants homozygous for the osatrz2 mutation were albinos with deficient chlorophyll content. A microscopic analysis of the mutant plants revealed that the transition of proplastids to chloroplasts was arrested at an early stage, and the number and size of the plastids in callus cells was substantially decreased. A genetic complementation test and an RNA interference analysis confirmed that disruption of OsaTRZ2 was responsible for the mutant phenotype. OsaTRZ2 is expressed in all rice tissues, but is preferentially expressed in leaves, sheathes, and calli. OsaTRZ2 was subcellularly localized in chloroplasts, and displayed tRNA 30-end processing activity in both in vitro and in vivo assays. In the osatrz2 mutants, transcription of plastid-encoded and nucleus-encoded RNA polymerases was severely reduced and moderately increased, respectively. These results suggest that the tRNA 30 processing activity of OsaTRZ2 contributes to chloroplast biogenesis.

  2. Trying on tRNA for Size: RNase P and the T-box Riboswitch as Molecular Rulers. (United States)

    Zhang, Jinwei; Ferré-DAmaré, Adrian R


    Length determination is a fundamental problem in biology and chemistry. Numerous proteins measure distances on linear biopolymers to exert effects with remarkable spatial precision. Recently, ruler-like devices made of noncoding RNAs have been structurally and biochemically characterized. Two prominent examples are the RNase P ribozyme and the T-box riboswitch. Both act as molecular calipers. The two RNAs clamp onto the elbow of tRNA (or pre-tRNA) and make distance measurements orthogonal to each other. Here, we compare and contrast the molecular ruler characteristics of these RNAs. RNase P appears pre-configured to measure a fixed distance on pre-tRNA to ensure the fidelity of its maturation. RNase P is a multiple-turnover ribozyme, and its rigid structure efficiently selects pre-tRNAs, cleaves, and releases them. In contrast, the T-box is flexible and segmented, an architecture that adapts to the intrinsically flexible tRNA. The tripartite T-box inspects the overall shape, anticodon sequence, and aminoacylation status of an incoming tRNA while it folds co-transcriptionally, leading to a singular, conditional genetic switching event. The elucidation of the structures and mechanisms of action of these two RNA molecular rulers may augur the discovery of new RNA measuring devices in noncoding and viral transcriptomes, and inform the design of artificial RNA rulers.

  3. Trying on tRNA for Size: RNase P and the T-box Riboswitch as Molecular Rulers

    Directory of Open Access Journals (Sweden)

    Jinwei Zhang


    Full Text Available Length determination is a fundamental problem in biology and chemistry. Numerous proteins measure distances on linear biopolymers to exert effects with remarkable spatial precision. Recently, ruler-like devices made of noncoding RNAs have been structurally and biochemically characterized. Two prominent examples are the RNase P ribozyme and the T-box riboswitch. Both act as molecular calipers. The two RNAs clamp onto the elbow of tRNA (or pre-tRNA and make distance measurements orthogonal to each other. Here, we compare and contrast the molecular ruler characteristics of these RNAs. RNase P appears pre-configured to measure a fixed distance on pre-tRNA to ensure the fidelity of its maturation. RNase P is a multiple-turnover ribozyme, and its rigid structure efficiently selects pre-tRNAs, cleaves, and releases them. In contrast, the T-box is flexible and segmented, an architecture that adapts to the intrinsically flexible tRNA. The tripartite T-box inspects the overall shape, anticodon sequence, and aminoacylation status of an incoming tRNA while it folds co-transcriptionally, leading to a singular, conditional genetic switching event. The elucidation of the structures and mechanisms of action of these two RNA molecular rulers may augur the discovery of new RNA measuring devices in noncoding and viral transcriptomes, and inform the design of artificial RNA rulers.

  4. The initiator methionine tRNA drives cell migration and invasion leading to increased metastatic potential in melanoma (United States)

    Birch, Joanna; Clarke, Cassie J.; Campbell, Andrew D.; Campbell, Kirsteen; Mitchell, Louise; Liko, Dritan; Kalna, Gabriela; Strathdee, Douglas; Sansom, Owen J.; Neilson, Matthew; Blyth, Karen


    ABSTRACT The cell's repertoire of transfer RNAs (tRNAs) has been linked to cancer. Recently, the level of the initiator methionine tRNA (tRNAiMet) in stromal fibroblasts has been shown to influence extracellular matrix (ECM) secretion to drive tumour growth and angiogenesis. Here we show that increased tRNAiMet within cancer cells does not influence tumour growth, but drives cell migration and invasion via a mechanism that is independent from ECM synthesis and dependent on α5β1 integrin and levels of the translation initiation ternary complex. In vivo and ex vivo migration (but not proliferation) of melanoblasts is significantly enhanced in transgenic mice which express additional copies of the tRNAiMet gene. We show that increased tRNAiMet in melanoma drives migratory, invasive behaviour and metastatic potential without affecting cell proliferation and primary tumour growth, and that expression of RNA polymerase III-associated genes (which drive tRNA expression) are elevated in metastases by comparison with primary tumours. Thus, specific alterations to the cancer cell tRNA repertoire drive a migration/invasion programme that may lead to metastasis. PMID:27543055

  5. MD Simulations of tRNA and Aminoacyl-tRNA Synthetases: Dynamics, Folding, Binding, and Allostery

    Directory of Open Access Journals (Sweden)

    Rongzhong Li


    Full Text Available While tRNA and aminoacyl-tRNA synthetases are classes of biomolecules that have been extensively studied for decades, the finer details of how they carry out their fundamental biological functions in protein synthesis remain a challenge. Recent molecular dynamics (MD simulations are verifying experimental observations and providing new insight that cannot be addressed from experiments alone. Throughout the review, we briefly discuss important historical events to provide a context for how far the field has progressed over the past few decades. We then review the background of tRNA molecules, aminoacyl-tRNA synthetases, and current state of the art MD simulation techniques for those who may be unfamiliar with any of those fields. Recent MD simulations of tRNA dynamics and folding and of aminoacyl-tRNA synthetase dynamics and mechanistic characterizations are discussed. We highlight the recent successes and discuss how important questions can be addressed using current MD simulations techniques. We also outline several natural next steps for computational studies of AARS:tRNA complexes.

  6. Several RNase T2 enzymes function in induced tRNA and rRNA turnover in the ciliate Tetrahymena

    DEFF Research Database (Denmark)

    Andersen, Kasper Langebjerg; Collins, Kathleen


    RNase T2 enzymes are produced by a wide range of organisms and have been implicated to function in diverse cellular processes, including stress-induced anticodon loop cleavage of mature tRNAs to generate tRNA halves. Here we describe a family of eight RNase T2 genes (RNT2A-RNT2H) in the ciliate...... Tetrahymena thermophila. We constructed strains lacking individual or combinations of these RNT2 genes that were viable but had distinct cellular and molecular phenotypes. In strains lacking only one Rnt2 protein or lacking a subfamily of three catalytically inactive Rnt2 proteins, starvation-induced tRNA...... fragments continued to accumulate, with only a minor change in fragment profile in one strain. We therefore generated strains lacking pairwise combinations of the top three candidates for Rnt2 tRNases. Each of these strains showed a distinct starvation-specific profile of tRNA and rRNA fragment accumulation...

  7. Relationships among the cyclostome braconid (Hymenoptera: Braconidae) subfamilies inferred from a mitochondrial tRNA gene rearrangement. (United States)

    Dowton, M


    The arrangement of mitochondrial tRNA genes for lysine (K) and aspartate (D) from the junction of the cytochrome oxidase II and ATPase 8 genes was determined in a range of hymenopteran taxa. This indicated that the ancestral arrangement for the order is 'KD', as found in the Diptera (represented by Drosophila and Anopheles) and basal Orthoptera. Most Hymenoptera that evolved after the appearance of parasitism also have the 'KD' arrangement, including noncyclostome braconids. However, most cyclostome braconids have either a 'DK' or a 'DHK' arrangement (where 'H' refers to the tRNA gene for Histidine). In both cases, the aspartate tRNA gene is encoded on the mitochondrial N-strand, rather than the J-strand as is usually the case. This rearrangement identified a monophyletic group not previously recognized, consisting of Rogadinae + Braconinae + Gnamptodontinae + Histeromerinae + Rhyssalinae + Betylobraconinae + Opiinae + Alysiinae. Only one cyclostome subfamily (Doryctinae) retained the 'KD' arrangement, suggesting this to be the most basal of the cyclostome subfamilies, consistent with ectoparasitism being plesiomorphic for the cyclostomes. However, the Aphidiinae also retained the 'KD' arrangement, leaving unresolved the issue of whether they should be included within the cyclostomes.

  8. Structure of a class II preQ1 riboswitch reveals ligand recognition by a new fold. (United States)

    Liberman, Joseph A; Salim, Mohammad; Krucinska, Jolanta; Wedekind, Joseph E


    PreQ1 riboswitches regulate genes by binding the pyrrolopyrimidine intermediate preQ1 during the biosynthesis of the essential tRNA base queuosine. We report what is to our knowledge the first preQ1-II riboswitch structure at 2.3-Å resolution, which uses a previously uncharacterized fold to achieve effector recognition at the confluence of a three-way helical junction flanking a pseudoknotted ribosome-binding site. The results account for translational control mediated by the preQ1-II riboswitch class and expand the known repertoire of ligand-binding modes used by regulatory RNAs.

  9. Convolution neural networks for ship type recognition (United States)

    Rainey, Katie; Reeder, John D.; Corelli, Alexander G.


    Algorithms to automatically recognize ship type from satellite imagery are desired for numerous maritime applications. This task is difficult, and example imagery accurately labeled with ship type is hard to obtain. Convolutional neural networks (CNNs) have shown promise in image recognition settings, but many of these applications rely on the availability of thousands of example images for training. This work attempts to under- stand for which types of ship recognition tasks CNNs might be well suited. We report the results of baseline experiments applying a CNN to several ship type classification tasks, and discuss many of the considerations that must be made in approaching this problem.


    Institute of Scientific and Technical Information of China (English)

    Zhang Wencong; Li Xin; Yao Peng; Li Bin; Zhuang Zhenquan


    The accuracy of face alignment affects greatly the performance of a face recognition system.Since the face alignment is usually conducted using eye positions, the algorithm for accurate eye localization is essential for the accurate face recognition. In this paper, an algorithm is proposed for eye localization. First, the proper AdaBoost detection is adaptively trained to segment the region based on the special gray distribution in the region. After that, a fast radial symmetry operator is used to precisely locate the center of eyes. Experimental results show that the method can accurately locate the eyes, and it is robust to the variations of face poses, illuminations, expressions, and accessories.

  11. A Survey of Protein Fold Recognition Algorithms

    Directory of Open Access Journals (Sweden)

    M. S. Abual-Rub


    Full Text Available Problem statement: Predicting the tertiary structure of proteins from their linear sequence is really a big challenge in biology. This challenge is related to the fact that the traditional computational methods are not powerful enough to search for the correct structure in the huge conformational space. This inadequate capability of the computational methods, however, is a major obstacle in facing this problem. Trying to solve the problem of the protein fold recognition, most of the researchers have examined the use of the protein threading technique. This problem is known as NP-hard; researchers have used various methods such as neural networks, Monte Carlo, support vector machine and genetic algorithms to solve it. Some researchers tried the use of the parallel evolutionary methods for protein fold recognition but it is less well known. Approach: We reviewed various algorithms that have been developed for protein structure prediction by threading and fold recognition. Moreover, we provided a survey of parallel evolutionary methods for protein fold recognition. Results: The findings of this survey showed that evolutionary methods can be used to resolve the protein fold recognition problem. Conclusion: There are two aspects of protein fold recognition problem: First is the computational difficulty and second is that current energy functions are still not accurate enough to calculate the free energy of a given conformation.

  12. Implicit Recognition Based on Lateralized Perceptual Fluency

    Directory of Open Access Journals (Sweden)

    Iliana M. Vargas


    Full Text Available In some circumstances, accurate recognition of repeated images in an explicit memory test is driven by implicit memory. We propose that this “implicit recognition” results from perceptual fluency that influences responding without awareness of memory retrieval. Here we examined whether recognition would vary if images appeared in the same or different visual hemifield during learning and testing. Kaleidoscope images were briefly presented left or right of fixation during divided-attention encoding. Presentation in the same visual hemifield at test produced higher recognition accuracy than presentation in the opposite visual hemifield, but only for guess responses. These correct guesses likely reflect a contribution from implicit recognition, given that when the stimulated visual hemifield was the same at study and test, recognition accuracy was higher for guess responses than for responses with any level of confidence. The dramatic difference in guessing accuracy as a function of lateralized perceptual overlap between study and test suggests that implicit recognition arises from memory storage in visual cortical networks that mediate repetition-induced fluency increments.

  13. The selective tRNA aminoacylation mechanism based on a single G•U pair. (United States)

    Naganuma, Masahiro; Sekine, Shun-ichi; Chong, Yeeting Esther; Guo, Min; Yang, Xiang-Lei; Gamper, Howard; Hou, Ya-Ming; Schimmel, Paul; Yokoyama, Shigeyuki


    Ligation of tRNAs with their cognate amino acids, by aminoacyl-tRNA synthetases, establishes the genetic code. Throughout evolution, tRNA(Ala) selection by alanyl-tRNA synthetase (AlaRS) has depended predominantly on a single wobble base pair in the acceptor stem, G3•U70, mainly on the kcat level. Here we report the crystal structures of an archaeal AlaRS in complex with tRNA(Ala) with G3•U70 and its A3•U70 variant. AlaRS interacts with both the minor- and the major-groove sides of G3•U70, widening the major groove. The geometry difference between G3•U70 and A3•U70 is transmitted along the acceptor stem to the 3'-CCA region. Thus, the 3'-CCA region of tRNA(Ala) with G3•U70 is oriented to the reactive route that reaches the active site, whereas that of the A3•U70 variant is folded back into the non-reactive route. This novel mechanism enables the single wobble pair to dominantly determine the specificity of tRNA selection, by an approximate 100-fold difference in kcat.

  14. Single-Turnover Kinetics of Methyl Transfer to tRNA by Methyltransferases (United States)

    Hou, Ya-Ming


    Summary Methyl transfer from S-adenosyl methionine (abbreviated as AdoMet) to biologically active molecules such as mRNAs and tRNAs is one of the most fundamental and widespread reactions in nature, occurring in all three domains of life. The measurement of kinetic constants of AdoMet-dependent methyl transfer is therefore important for understanding the reaction mechanism in the context of biology. When kinetic constants of methyl transfer are measured in steady state over multiple rounds of turnover, the meaning of these constants is difficult to define and is often limited by non-chemical steps of the reaction, such as product release after each turnover. Here the measurement of kinetic constants of methyl transfer by tRNA methyltransferases in rapid equilibrium binding condition for one methyl transfer is described. The advantage of such a measurement is that the meaning of kinetic constants can be directly assigned to the steps associated with the chemistry of methyl transfer, including the substrate binding affinity to the methyl transferase, the pre-chemistry re-arrangement of the active site, and the chemical step of methyl transfer. An additional advantage is that kinetic constants measured for one methyl transfer can be correlated with structural information of the methyl transferase to gain direct insight into its reaction mechanism. PMID:26965259

  15. Essentiality of threonylcarbamoyladenosine (t(6)A), a universal tRNA modification, in bacteria. (United States)

    Thiaville, Patrick C; El Yacoubi, Basma; Köhrer, Caroline; Thiaville, Jennifer J; Deutsch, Chris; Iwata-Reuyl, Dirk; Bacusmo, Jo Marie; Armengaud, Jean; Bessho, Yoshitaka; Wetzel, Collin; Cao, Xiaoyu; Limbach, Patrick A; RajBhandary, Uttam L; de Crécy-Lagard, Valérie


    Threonylcarbamoyladenosine (t(6)A) is a modified nucleoside universally conserved in tRNAs in all three kingdoms of life. The recently discovered genes for t(6)A synthesis, including tsaC and tsaD, are essential in model prokaryotes but not essential in yeast. These genes had been identified as antibacterial targets even before their functions were known. However, the molecular basis for this prokaryotic-specific essentiality has remained a mystery. Here, we show that t(6)A is a strong positive determinant for aminoacylation of tRNA by bacterial-type but not by eukaryotic-type isoleucyl-tRNA synthetases and might also be a determinant for the essential enzyme tRNA(Ile)-lysidine synthetase. We confirm that t(6)A is essential in Escherichia coli and a survey of genome-wide essentiality studies shows that genes for t(6)A synthesis are essential in most prokaryotes. This essentiality phenotype is not universal in Bacteria as t(6)A is dispensable in Deinococcus radiodurans, Thermus thermophilus, Synechocystis PCC6803 and Streptococcus mutans. Proteomic analysis of t(6)A(-) D. radiodurans strains revealed an induction of the proteotoxic stress response and identified genes whose translation is most affected by the absence of t(6)A in tRNAs. Thus, although t(6)A is universally conserved in tRNAs, its role in translation might vary greatly between organisms.

  16. Selective charging of tRNA isoacceptors induced by amino-acid starvation (United States)

    Dittmar, Kimberly A; Sørensen, Michael A; Elf, Johan; Ehrenberg, Måns; Pan, Tao


    Aminoacylated (charged) transfer RNA isoacceptors read different messenger RNA codons for the same amino acid. The concentration of an isoacceptor and its charged fraction are principal determinants of the translation rate of its codons. A recent theoretical model predicts that amino-acid starvation results in ‘selective charging' where the charging levels of some tRNA isoacceptors will be low and those of others will remain high. Here, we developed a microarray for the analysis of charged fractions of tRNAs and measured charging for all Escherichia coli tRNAs before and during leucine, threonine or arginine starvation. Before starvation, most tRNAs were fully charged. During starvation, the isoacceptors in the leucine, threonine or arginine families showed selective charging when cells were starved for their cognate amino acid, directly confirming the theoretical prediction. Codons read by isoacceptors that retain high charging can be used for efficient translation of genes that are essential during amino-acid starvation. Selective charging can explain anomalous patterns of codon usage in the genes for different families of proteins. PMID:15678157

  17. Multimodal eye recognition (United States)

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


    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).

  18. Pattern recognition & machine learning

    CERN Document Server

    Anzai, Y


    This is the first text to provide a unified and self-contained introduction to visual pattern recognition and machine learning. It is useful as a general introduction to artifical intelligence and knowledge engineering, and no previous knowledge of pattern recognition or machine learning is necessary. Basic for various pattern recognition and machine learning methods. Translated from Japanese, the book also features chapter exercises, keywords, and summaries.

  19. Aging and solid shape recognition: Vision and haptics. (United States)

    Norman, J Farley; Cheeseman, Jacob R; Adkins, Olivia C; Cox, Andrea G; Rogers, Connor E; Dowell, Catherine J; Baxter, Michael W; Norman, Hideko F; Reyes, Cecia M


    The ability of 114 younger and older adults to recognize naturally-shaped objects was evaluated in three experiments. The participants viewed or haptically explored six randomly-chosen bell peppers (Capsicum annuum) in a study session and were later required to judge whether each of twelve bell peppers was "old" (previously presented during the study session) or "new" (not presented during the study session). When recognition memory was tested immediately after study, the younger adults' (Experiment 1) performance for vision and haptics was identical when the individual study objects were presented once. Vision became superior to haptics, however, when the individual study objects were presented multiple times. When 10- and 20-min delays (Experiment 2) were inserted in between study and test sessions, no significant differences occurred between vision and haptics: recognition performance in both modalities was comparable. When the recognition performance of older adults was evaluated (Experiment 3), a negative effect of age was found for visual shape recognition (younger adults' overall recognition performance was 60% higher). There was no age effect, however, for haptic shape recognition. The results of the present experiments indicate that the visual recognition of natural object shape is different from haptic recognition in multiple ways: visual shape recognition can be superior to that of haptics and is affected by aging, while haptic shape recognition is less accurate and unaffected by aging.

  20. A Modified Back propagation Algorithm for Optical Character Recognition

    Directory of Open Access Journals (Sweden)

    Jitendra Shrivastav


    Full Text Available Character Recognition (CR has been an active area of research and due to its diverse applicable environment; it continues to be a challenging research topic. There is a clear need for optical character recognition in order to provide a fast and accurate method to search both existing images as well as large archives of existing paper documents. However, existing optical character recognition programs suffer from a flawed tradeoff between speed and accuracy, making it less attractive for large quantities of documents. In this thesis, we present a new neural network based method for optical character recognition as well as handwritten character recognition. Experimental results show that our proposed method achieves highest percent accuracy in optical character recognition. We present an overview of existing handwritten character recognition techniques. All these algorithms are described more or less on their own. Handwritten character recognition is a very popular and computationally expensive task. We also explain the fundamentals of handwritten character recognition. We describe today’s approaches for handwritten character recognition. From the broad variety of efficient techniques that have been developed we will compare the most important ones. We will systematize the techniques and analyze their performance based on both their run time performance and theoretical considerations. Their strengths and weaknesses are also investigated. It turns out that the behavior of the algorithms is much more similar as to be expected.

  1. Experiences in Pattern Recognition for Machine Olfaction (United States)

    Bessant, C.


    Pattern recognition is essential for translating complex olfactory sensor responses into simple outputs that are relevant to users. Many approaches to pattern recognition have been applied in this field, including multivariate statistics (e.g. discriminant analysis), artificial neural networks (ANNs) and support vector machines (SVMs). Reviewing our experience of using these techniques with many different sensor systems reveals some useful insights. Most importantly, it is clear beyond any doubt that the quantity and selection of samples used to train and test a pattern recognition system are by far the most important factors in ensuring it performs as accurately and reliably as possible. Here we present evidence for this assertion and make suggestions for best practice based on these findings.

  2. Comparison of associative recognition versus source recognition. (United States)

    Park, Heekyeong; Abellanoza, Cheryl; Schaeffer, James D


    The importance of the medial temporal lobe (MTL) for memory of arbitrary associations has been well established. However, the contribution of the MTL in concurrent retrieval of different classes of associations remains unclear. The present fMRI study investigated neural correlates of concurrent retrieval of associative and source memories. Participants studied a list of object pairs with two study tasks and judged the status and context of the pair during test. Associative retrieval was supported by neural activity in bilateral prefrontal cortex and left ventral occipito-temporal cortex, while source recognition was linked to activity in the right caudate. Both the hippocampus and MTL cortex showed retrieval activity for associative and source memory. Importantly, greater brain activity for successful associative recognition accompanied with successful source recognition was evident in left perirhinal and anterior hippocampal regions. These results indicate that the MTL is critical in the retrieval of different classes of associations.

  3. Distinguishing highly confident accurate and inaccurate memory: insights about relevant and irrelevant influences on memory confidence. (United States)

    Chua, Elizabeth F; Hannula, Deborah E; Ranganath, Charan


    It is generally believed that accuracy and confidence in one's memory are related, but there are many instances when they diverge. Accordingly it is important to disentangle the factors that contribute to memory accuracy and confidence, especially those factors that contribute to confidence, but not accuracy. We used eye movements to separately measure fluent cue processing, the target recognition experience, and relative evidence assessment on recognition confidence and accuracy. Eye movements were monitored during a face-scene associative recognition task, in which participants first saw a scene cue, followed by a forced-choice recognition test for the associated face, with confidence ratings. Eye movement indices of the target recognition experience were largely indicative of accuracy, and showed a relationship to confidence for accurate decisions. In contrast, eye movements during the scene cue raised the possibility that more fluent cue processing was related to higher confidence for both accurate and inaccurate recognition decisions. In a second experiment we manipulated cue familiarity, and therefore cue fluency. Participants showed higher confidence for cue-target associations for when the cue was more familiar, especially for incorrect responses. These results suggest that over-reliance on cue familiarity and under-reliance on the target recognition experience may lead to erroneous confidence.

  4. Efficient and accurate fragmentation methods. (United States)

    Pruitt, Spencer R; Bertoni, Colleen; Brorsen, Kurt R; Gordon, Mark S


    Conspectus Three novel fragmentation methods that are available in the electronic structure program GAMESS (general atomic and molecular electronic structure system) are discussed in this Account. The fragment molecular orbital (FMO) method can be combined with any electronic structure method to perform accurate calculations on large molecular species with no reliance on capping atoms or empirical parameters. The FMO method is highly scalable and can take advantage of massively parallel computer systems. For example, the method has been shown to scale nearly linearly on up to 131 000 processor cores for calculations on large water clusters. There have been many applications of the FMO method to large molecular clusters, to biomolecules (e.g., proteins), and to materials that are used as heterogeneous catalysts. The effective fragment potential (EFP) method is a model potential approach that is fully derived from first principles and has no empirically fitted parameters. Consequently, an EFP can be generated for any molecule by a simple preparatory GAMESS calculation. The EFP method provides accurate descriptions of all types of intermolecular interactions, including Coulombic interactions, polarization/induction, exchange repulsion, dispersion, and charge transfer. The EFP method has been applied successfully to the study of liquid water, π-stacking in substituted benzenes and in DNA base pairs, solvent effects on positive and negative ions, electronic spectra and dynamics, non-adiabatic phenomena in electronic excited states, and nonlinear excited state properties. The effective fragment molecular orbital (EFMO) method is a merger of the FMO and EFP methods, in which interfragment interactions are described by the EFP potential, rather than the less accurate electrostatic potential. The use of EFP in this manner facilitates the use of a smaller value for the distance cut-off (Rcut). Rcut determines the distance at which EFP interactions replace fully quantum

  5. Accurate determination of antenna directivity

    DEFF Research Database (Denmark)

    Dich, Mikael


    The derivation of a formula for accurate estimation of the total radiated power from a transmitting antenna for which the radiated power density is known in a finite number of points on the far-field sphere is presented. The main application of the formula is determination of directivity from power......-pattern measurements. The derivation is based on the theory of spherical wave expansion of electromagnetic fields, which also establishes a simple criterion for the required number of samples of the power density. An array antenna consisting of Hertzian dipoles is used to test the accuracy and rate of convergence...

  6. Iris Recognition: The Consequences of Image Compression

    Directory of Open Access Journals (Sweden)

    Bishop DanielA


    Full Text Available Iris recognition for human identification is one of the most accurate biometrics, and its employment is expanding globally. The use of portable iris systems, particularly in law enforcement applications, is growing. In many of these applications, the portable device may be required to transmit an iris image or template over a narrow-bandwidth communication channel. Typically, a full resolution image (e.g., VGA is desired to ensure sufficient pixels across the iris to be confident of accurate recognition results. To minimize the time to transmit a large amount of data over a narrow-bandwidth communication channel, image compression can be used to reduce the file size of the iris image. In other applications, such as the Registered Traveler program, an entire iris image is stored on a smart card, but only 4 kB is allowed for the iris image. For this type of application, image compression is also the solution. This paper investigates the effects of image compression on recognition system performance using a commercial version of the Daugman iris2pi algorithm along with JPEG-2000 compression, and links these to image quality. Using the ICE 2005 iris database, we find that even in the face of significant compression, recognition performance is minimally affected.

  7. Peptide markers of aminoacyl tRNA synthetases facilitate taxa counting in metagenomic data

    Directory of Open Access Journals (Sweden)

    Persi Erez


    Full Text Available Abstract Background Taxa counting is a major problem faced by analysis of metagenomic data. The most popular method relies on analysis of 16S rRNA sequences, but some studies employ also protein based analyses. It would be advantageous to have a method that is applicable directly to short sequences, of the kind extracted from samples in modern metagenomic research. This is achieved by the technique proposed here. Results We employ specific peptides, deduced from aminoacyl tRNA synthetases, as markers for the occurrence of single genes in data. Sequences carrying these markers are aligned and compared with each other to provide a lower limit for taxa counts in metagenomic data. The method is compared with 16S rRNA searches on a set of known genomes. The taxa counting problem is analyzed mathematically and a heuristic algorithm is proposed. When applied to genomic contigs of a recent human gut microbiome study, the taxa counting method provides information on numbers of different species and strains. We then apply our method to short read data and demonstrate how it can be calibrated to cope with errors. Comparison to known databases leads to estimates of the percentage of novelties, and the type of phyla involved. Conclusions A major advantage of our method is its simplicity: it relies on searching sequences for the occurrence of just 4000 specific peptides belonging to the S61 subgroup of aaRS enzymes. When compared to other methods, it provides additional insight into the taxonomic contents of metagenomic data. Furthermore, it can be directly applied to short read data, avoiding the need for genomic contig reconstruction, and taking into account short reads that are otherwise discarded as singletons. Hence it is very suitable for a fast analysis of next generation sequencing data.

  8. Engineering and Validation of a Vector for Concomitant Expression of Rare Transfer RNA (tRNA) and HIV-1 nef Genes in Escherichia coli. (United States)

    Mualif, Siti Aisyah; Teow, Sin-Yeang; Omar, Tasyriq Che; Chew, Yik Wei; Yusoff, Narazah Mohd; Ali, Syed A


    Relative ease in handling and manipulation of Escherichia coli strains make them primary candidate to express proteins heterologously. Overexpression of heterologous genes that contain codons infrequently used by E. coli is related with difficulties such as mRNA instability, early termination of transcription and/or translation, deletions and/or misincorporation, and cell growth inhibition. These codon bias -associated problems are addressed by co-expressing ColE1-compatible, rare tRNA expressing helper plasmids. However, this approach has inadequacies, which we have addressed by engineering an expression vector that concomitantly expresses the heterologous protein of interest, and rare tRNA genes in E. coli. The expression vector contains three (argU, ileY, leuW) rare tRNA genes and a useful multiple cloning site for easy in-frame cloning. To maintain the overall size of the parental plasmid vector, the rare tRNA genes replaced the non-essential DNA segments in the vector. The cloned gene is expressed under the control of T7 promoter and resulting recombinant protein has a C-terminal 6His tag for IMAC-mediated purification. We have evaluated the usefulness of this expression vector by expressing three HIV-1 genes namely HIV-1 p27 (nef), HIV-1 p24 (ca), and HIV-1 vif in NiCo21(DE3) E.coli and demonstrated the advantages of using expression vector that concomitantly expresses rare tRNA and heterologous genes.

  9. Silent mutations in sight: co-variations in tRNA abundance as a key to unravel consequences of silent mutations. (United States)

    Czech, Andreas; Fedyunin, Ivan; Zhang, Gong; Ignatova, Zoya


    Mutations that alter the amino acid sequence are known to potentially exert deleterious effects on protein function, whereas substitutions of nucleotides without amino acid change are assumed to be neutral for the protein's functionality. However, cumulative evidence suggests that synonymous substitutions might also induce phenotypic variability by affecting splicing accuracy, translation fidelity, and conformation and function of proteins. tRNA isoacceptors mediate the translation of codons to amino acids, and asymmetric tRNA abundance causes variations in the rate of translation of each single triplet. Consequently, the effect of a silent point mutation in the coding region could be significant due to differential abundances of the cognate tRNA(s), emphasizing the importance of precise assessment of tRNA composition. Here, we provide an overview of the methods used to quantitatively determine the concentrations of tRNA species and discuss synonymous mutations in the context of tRNA composition of the cell, thus providing a new twist on the detrimental impact of the silent mutations.

  10. Multimodal recognition of emotions

    NARCIS (Netherlands)

    Datcu, D.


    This thesis proposes algorithms and techniques to be used for automatic recognition of six prototypic emotion categories by computer programs, based on the recognition of facial expressions and emotion patterns in voice. Considering the applicability in real-life conditions, the research is carried

  11. Recognition measured values


    LEITKEP, Zdeněk


    This work deals recognition measured values. The main task is to find suitable method for preprocessing images and create interface to software performing recognition. Created application will be used primarily to analyze the photos on site acquisition. Application is developed in Java and properly documented on javadoc level.

  12. Handwritten Digits Recognition


    Grand, Eric


    My work of diploma consisted in developing a Windows application for the recognition of the handwritten digits. The source images come from a pen-scanner. The user can also draw the digits directly with the mouse and do the recognition of it. In this software, I integrated the SVM Light reconizer.

  13. Accurate Modeling of Advanced Reflectarrays

    DEFF Research Database (Denmark)

    Zhou, Min

    Analysis and optimization methods for the design of advanced printed re ectarrays have been investigated, and the study is focused on developing an accurate and efficient simulation tool. For the analysis, a good compromise between accuracy and efficiency can be obtained using the spectral domain...... to the POT. The GDOT can optimize for the size as well as the orientation and position of arbitrarily shaped array elements. Both co- and cross-polar radiation can be optimized for multiple frequencies, dual polarization, and several feed illuminations. Several contoured beam reflectarrays have been designed...... using the GDOT to demonstrate its capabilities. To verify the accuracy of the GDOT, two offset contoured beam reflectarrays that radiate a high-gain beam on a European coverage have been designed and manufactured, and subsequently measured at the DTU-ESA Spherical Near-Field Antenna Test Facility...

  14. The Accurate Particle Tracer Code

    CERN Document Server

    Wang, Yulei; Qin, Hong; Yu, Zhi


    The Accurate Particle Tracer (APT) code is designed for large-scale particle simulations on dynamical systems. Based on a large variety of advanced geometric algorithms, APT possesses long-term numerical accuracy and stability, which are critical for solving multi-scale and non-linear problems. Under the well-designed integrated and modularized framework, APT serves as a universal platform for researchers from different fields, such as plasma physics, accelerator physics, space science, fusion energy research, computational mathematics, software engineering, and high-performance computation. The APT code consists of seven main modules, including the I/O module, the initialization module, the particle pusher module, the parallelization module, the field configuration module, the external force-field module, and the extendible module. The I/O module, supported by Lua and Hdf5 projects, provides a user-friendly interface for both numerical simulation and data analysis. A series of new geometric numerical methods...

  15. Accurate ab initio spin densities

    CERN Document Server

    Boguslawski, Katharina; Legeza, Örs; Reiher, Markus


    We present an approach for the calculation of spin density distributions for molecules that require very large active spaces for a qualitatively correct description of their electronic structure. Our approach is based on the density-matrix renormalization group (DMRG) algorithm to calculate the spin density matrix elements as basic quantity for the spatially resolved spin density distribution. The spin density matrix elements are directly determined from the second-quantized elementary operators optimized by the DMRG algorithm. As an analytic convergence criterion for the spin density distribution, we employ our recently developed sampling-reconstruction scheme [J. Chem. Phys. 2011, 134, 224101] to build an accurate complete-active-space configuration-interaction (CASCI) wave function from the optimized matrix product states. The spin density matrix elements can then also be determined as an expectation value employing the reconstructed wave function expansion. Furthermore, the explicit reconstruction of a CA...

  16. Accurate thickness measurement of graphene. (United States)

    Shearer, Cameron J; Slattery, Ashley D; Stapleton, Andrew J; Shapter, Joseph G; Gibson, Christopher T


    Graphene has emerged as a material with a vast variety of applications. The electronic, optical and mechanical properties of graphene are strongly influenced by the number of layers present in a sample. As a result, the dimensional characterization of graphene films is crucial, especially with the continued development of new synthesis methods and applications. A number of techniques exist to determine the thickness of graphene films including optical contrast, Raman scattering and scanning probe microscopy techniques. Atomic force microscopy (AFM), in particular, is used extensively since it provides three-dimensional images that enable the measurement of the lateral dimensions of graphene films as well as the thickness, and by extension the number of layers present. However, in the literature AFM has proven to be inaccurate with a wide range of measured values for single layer graphene thickness reported (between 0.4 and 1.7 nm). This discrepancy has been attributed to tip-surface interactions, image feedback settings and surface chemistry. In this work, we use standard and carbon nanotube modified AFM probes and a relatively new AFM imaging mode known as PeakForce tapping mode to establish a protocol that will allow users to accurately determine the thickness of graphene films. In particular, the error in measuring the first layer is reduced from 0.1-1.3 nm to 0.1-0.3 nm. Furthermore, in the process we establish that the graphene-substrate adsorbate layer and imaging force, in particular the pressure the tip exerts on the surface, are crucial components in the accurate measurement of graphene using AFM. These findings can be applied to other 2D materials.

  17. Accurate thickness measurement of graphene (United States)

    Shearer, Cameron J.; Slattery, Ashley D.; Stapleton, Andrew J.; Shapter, Joseph G.; Gibson, Christopher T.


    Graphene has emerged as a material with a vast variety of applications. The electronic, optical and mechanical properties of graphene are strongly influenced by the number of layers present in a sample. As a result, the dimensional characterization of graphene films is crucial, especially with the continued development of new synthesis methods and applications. A number of techniques exist to determine the thickness of graphene films including optical contrast, Raman scattering and scanning probe microscopy techniques. Atomic force microscopy (AFM), in particular, is used extensively since it provides three-dimensional images that enable the measurement of the lateral dimensions of graphene films as well as the thickness, and by extension the number of layers present. However, in the literature AFM has proven to be inaccurate with a wide range of measured values for single layer graphene thickness reported (between 0.4 and 1.7 nm). This discrepancy has been attributed to tip-surface interactions, image feedback settings and surface chemistry. In this work, we use standard and carbon nanotube modified AFM probes and a relatively new AFM imaging mode known as PeakForce tapping mode to establish a protocol that will allow users to accurately determine the thickness of graphene films. In particular, the error in measuring the first layer is reduced from 0.1-1.3 nm to 0.1-0.3 nm. Furthermore, in the process we establish that the graphene-substrate adsorbate layer and imaging force, in particular the pressure the tip exerts on the surface, are crucial components in the accurate measurement of graphene using AFM. These findings can be applied to other 2D materials.

  18. 5′ Processing of tRNA Precursors Can Be Modulated by the Human La Antigen Phosphoprotein†


    Fan, Hao; Goodier, John L.; Chamberlain, Joel R.; Engelke, David R.; Richard J. Maraia


    Eukaryotic precursor (pre)-tRNAs are processed at both ends prior to maturation. Pre-tRNAs and other nascent transcripts synthesized by RNA polymerase III are bound at their 3′ ends at the sequence motif UUUOH [3′ oligo(U)] by the La antigen, a conserved phosphoprotein whose role in RNA processing has been associated previously with 3′-end maturation only. We show that in addition to its role in tRNA 3′-end maturation, human La protein can also modulate 5′ processing of pre-tRNAs. Both the La...

  19. Recognition of Arabic Sign Language Alphabet Using Polynomial Classifiers



    Building an accurate automatic sign language recognition system is of great importance in facilitating efficient communication with deaf people. In this paper, we propose the use of polynomial classifiers as a classification engine for the recognition of Arabic sign language (ArSL) alphabet. Polynomial classifiers have several advantages over other classifiers in that they do not require iterative training, and that they are highly computationally scalable with the number of classes. Based on...

  20. Data Mining and Pattern Recognition Models for Identifying Inherited Diseases

    DEFF Research Database (Denmark)

    Iddamalgoda, Lahiru; Das, Partha S; Aponso, Achala;


    Data mining and pattern recognition methods reveal interesting findings in genetic studies, especially on how the genetic makeup is associated with inherited diseases. Although researchers have proposed various data mining models for biomedical approaches, there remains a challenge in accurately...... prioritizing the single nucleotide polymorphisms (SNP) associated with the disease. In this commentary, we review the state-of-art data mining and pattern recognition models for identifying inherited diseases and deliberate the need of binary classification- and scoring-based prioritization methods...

  1. Active Finger Recognition from Surface EMG Signal Using Bayesian Filter (United States)

    Araki, Nozomu; Hoashi, Yuki; Konishi, Yasuo; Mabuchi, Kunihiko; Ishigaki, Hiroyuki

    This paper proposed an active finger recognition method using Bayesian filter in order to control a myoelectric hand. We have previously proposed a finger joint angle estimation method based on measured surface electromyography (EMG) signals and a linear model. However, when we estimate 2 or more finger angles by this estimation method, the estimation angle of the inactive finger is not accurate. This is caused by interference of surface EMG signal. To solve this interference problem, we proposed active finger recognition method from the amplitude spectrum of surface EMG signal using Bayesian filter. To confirm the effectiveness of this recognition method, we developed a myoelectric hand simulator that implements proposed recognition algorithm and carried out real-time recognition experiment.

  2. Handbook of Face Recognition

    CERN Document Server

    Li, Stan Z


    This highly anticipated new edition provides a comprehensive account of face recognition research and technology, spanning the full range of topics needed for designing operational face recognition systems. After a thorough introductory chapter, each of the following chapters focus on a specific topic, reviewing background information, up-to-date techniques, and recent results, as well as offering challenges and future directions. Features: fully updated, revised and expanded, covering the entire spectrum of concepts, methods, and algorithms for automated face detection and recognition systems

  3. Mobile intention recognition

    CERN Document Server

    Kiefer, Peter


    Mobile Intention Recognition addresses problems of practical relevance for mobile system engineers: how can we make mobile assistance systems more intelligent? How can we model and recognize patterns of human behavior which span more than a limited spatial context? This text provides an overview on plan and intention recognition, ranging from the late 1970s to very recent approaches. This overview is unique as it discusses approaches with respect to the specificities of mobile intention recognition. This book covers problems from research on mobile assistance systems using methods from artific

  4. PCA facial expression recognition (United States)

    El-Hori, Inas H.; El-Momen, Zahraa K.; Ganoun, Ali


    This paper explores and compares techniques for automatically recognizing facial actions in sequences of images. The comparative study of Facial Expression Recognition (FER) techniques namely Principal Component's analysis (PCA) and PCA with Gabor filters (GF) is done. The objective of this research is to show that PCA with Gabor filters is superior to the first technique in terms of recognition rate. To test and evaluates their performance, experiments are performed using real database by both techniques. The universally accepted five principal emotions to be recognized are: Happy, Sad, Disgust and Angry along with Neutral. The recognition rates are obtained on all the facial expressions.

  5. A More Accurate Fourier Transform

    CERN Document Server

    Courtney, Elya


    Fourier transform methods are used to analyze functions and data sets to provide frequencies, amplitudes, and phases of underlying oscillatory components. Fast Fourier transform (FFT) methods offer speed advantages over evaluation of explicit integrals (EI) that define Fourier transforms. This paper compares frequency, amplitude, and phase accuracy of the two methods for well resolved peaks over a wide array of data sets including cosine series with and without random noise and a variety of physical data sets, including atmospheric $\\mathrm{CO_2}$ concentrations, tides, temperatures, sound waveforms, and atomic spectra. The FFT uses MIT's FFTW3 library. The EI method uses the rectangle method to compute the areas under the curve via complex math. Results support the hypothesis that EI methods are more accurate than FFT methods. Errors range from 5 to 10 times higher when determining peak frequency by FFT, 1.4 to 60 times higher for peak amplitude, and 6 to 10 times higher for phase under a peak. The ability t...

  6. Forensic speaker recognition

    NARCIS (Netherlands)

    Meuwly, Didier


    The aim of forensic speaker recognition is to establish links between individuals and criminal activities, through audio speech recordings. This field is multidisciplinary, combining predominantly phonetics, linguistics, speech signal processing, and forensic statistics. On these bases, expert-based

  7. Work and Recognition

    DEFF Research Database (Denmark)

    Willig, Rasmus


    individual and collective identity formation and has led to an increase in social pathological illnesses such as stress and depression. By juxtaposing these analyses with Honneth’s theory on recognition, we conclude that the contemporary logic of work is unable to provide adequate forms of recognition......The article deals with the relationship between work and recognition, taking Axel Honneth’s social-philosophical theory of the struggle for recognition as its point of departure. In order to give sociological substance to Honneth’s theory, we turn to three contemporary social theorists - Jean......-Pierre Le Goff, Christophe Dejours and Emmanuel Renault. In spite of many differences, their work is united by a critical description of the logic of work and its consequences for individual individuation. These theorists agree that the growth of autonomy, flexibility and mobility has destabilised...

  8. Global shape mimicry of tRNA within a viral internal ribosome entry site mediates translational reading frame selection. (United States)

    Au, Hilda H; Cornilescu, Gabriel; Mouzakis, Kathryn D; Ren, Qian; Burke, Jordan E; Lee, Seonghoon; Butcher, Samuel E; Jan, Eric


    The dicistrovirus intergenic region internal ribosome entry site (IRES) adopts a triple-pseudoknotted RNA structure and occupies the core ribosomal E, P, and A sites to directly recruit the ribosome and initiate translation at a non-AUG codon. A subset of dicistrovirus IRESs directs translation in the 0 and +1 frames to produce the viral structural proteins and a +1 overlapping open reading frame called ORFx, respectively. Here we show that specific mutations of two unpaired adenosines located at the core of the three-helical junction of the honey bee dicistrovirus Israeli acute paralysis virus (IAPV) IRES PKI domain can uncouple 0 and +1 frame translation, suggesting that the structure adopts distinct conformations that contribute to 0 or +1 frame translation. Using a reconstituted translation system, we show that ribosomes assembled on mutant IRESs that direct exclusive 0 or +1 frame translation lack reading frame fidelity. Finally, a nuclear magnetic resonance/small-angle X-ray scattering hybrid approach reveals that the PKI domain of the IAPV IRES adopts an RNA structure that resembles a complete tRNA. The tRNA shape-mimicry enables the viral IRES to gain access to the ribosome tRNA-binding sites and form intermolecular contacts with the ribosome that are necessary for initiating IRES translation in a specific reading frame.

  9. Functional consequences of T-stem mutations in E. coli tRNA Thr UGU in vitro and in vivo

    DEFF Research Database (Denmark)

    Saks, Margaret E; Sanderson, Lee E; Choi, Daniel S;


    unable to support growth of E. coli or are less effective than the wild-type sequence. Since the inviable T-stem sequences are often present in other E. coli tRNAs, it appears that T-stem sequences in each tRNA body have evolved to optimize function in a different way. Although mutations of tRNAThr can...... to mutations in three T-stem base pairs in a quantitatively identical manner. However, tRNAThr differs from other tRNAs by also using its rare A52–C62 pair as a negative specificity determinant. Using a plasmid-based tRNA gene replacement strategy, we show that many of the tRNAThrUGU T-stem changes are either......The binding affinities between Escherichia coli EF-Tu and 34 single and double base-pair changes in the T stem of E. coli tRNAThrUGU were compared with similar data obtained previously for several aa-tRNAs binding to Thermus thermophilus EF-Tu. With a single exception, the two proteins bound...

  10. Fluctuations between multiple EF-G-induced chimeric tRNA states during translocation on the ribosome (United States)

    Adio, Sarah; Senyushkina, Tamara; Peske, Frank; Fischer, Niels; Wintermeyer, Wolfgang; Rodnina, Marina V.


    The coupled translocation of transfer RNA and messenger RNA through the ribosome entails large-scale structural rearrangements, including step-wise movements of the tRNAs. Recent structural work has visualized intermediates of translocation induced by elongation factor G (EF-G) with tRNAs trapped in chimeric states with respect to 30S and 50S ribosomal subunits. The functional role of the chimeric states is not known. Here we follow the formation of translocation intermediates by single-molecule fluorescence resonance energy transfer. Using EF-G mutants, a non-hydrolysable GTP analogue, and fusidic acid, we interfere with either translocation or EF-G release from the ribosome and identify several rapidly interconverting chimeric tRNA states on the reaction pathway. EF-G engagement prevents backward transitions early in translocation and increases the fraction of ribosomes that rapidly fluctuate between hybrid, chimeric and posttranslocation states. Thus, the engagement of EF-G alters the energetics of translocation towards a flat energy landscape, thereby promoting forward tRNA movement.

  11. GidA, a tRNA modification enzyme, contributes to the growth and virulence of Streptococcus suis serotype 2

    Directory of Open Access Journals (Sweden)

    Ting eGao


    Full Text Available Glucose-inhibited division protein (GidA, is a tRNA modification enzyme functioning together with MnmE in the addition of a carboxymethylaminomethyl group to position 5 of the anticodon wobble uridine of tRNA. Here, we report a GidA homologue from a Chinese isolate SC-19 of the zoonotic Streptococcus suis serotype 2 (SS2. gidA disruption led to a defective growth, increased capsule thickness, and reduced hemolytic activity. Moreover, the gidA deletion mutant (ΔgidA displayed reduced mortality and bacterial loads in mice, reduced ability of adhesion to and invasion in epithelial cells, and increased sensitivity to phagocytosis. The iTRAQ analysis identified 372 differentially expressed (182 up- and 190 down-regulated proteins in ΔgidA and SC-19. Numerous DNA replication, cell division and virulence associated proteins were downregulated, whereas many capsule synthesis enzymes were upregulated by gidA disruption. This is consistent with the phenotypes of the mutant. Thus, GidA is a translational regulator that plays an important role in the growth, cell division, capsule biosynthesis, and virulence of SS2. Our findings provide new insight into the regulatory function of GidA in bacterial pathogens.

  12. Structure, Mechanism, and Specificity of a Eukaryal tRNA Restriction Enzyme Involved in Self-Nonself Discrimination

    Directory of Open Access Journals (Sweden)

    Anupam K. Chakravarty


    Full Text Available tRNA restriction by anticodon nucleases underlies cellular stress responses and self-nonself discrimination in a wide range of taxa. Anticodon breakage inhibits protein synthesis, which, in turn, results in growth arrest or cell death. The eukaryal ribotoxin PaT secreted by Pichia acaciae inhibits growth of Saccharomyces cerevisiae via cleavage of tRNAGln(UUG. We find that recombinant PaT incises a synthetic tRNAGln(UUG stem-loop RNA by transesterification at a single site 3′ of the wobble uridine, yielding 2′,3′-cyclic phosphate and 5′-OH ends. Incision is suppressed by replacement of the wobble nucleobase with adenine or guanine. The crystal structure of PaT reveals a distinctive fold and active site, essential components of which are demonstrated by mutagenesis. Pichia acaciae evades self-toxicity via a distinctive intracellular immunity protein, ImmPaT, which binds PaT and blocks nuclease activity. Our results highlight the evolutionary diversity of tRNA restriction and immunity systems.

  13. Crystal structure of Bacillus subtilis TrmB, the tRNA (m7G46) methyltransferase. (United States)

    Zegers, Ingrid; Gigot, Daniel; van Vliet, Françoise; Tricot, Catherine; Aymerich, Stéphane; Bujnicki, Janusz M; Kosinski, Jan; Droogmans, Louis


    The structure of Bacillus subtilis TrmB (BsTrmB), the tRNA (m7G46) methyltransferase, was determined at a resolution of 2.1 A. This is the first structure of a member of the TrmB family to be determined by X-ray crystallography. It reveals a unique variant of the Rossmann-fold methyltransferase (RFM) structure, with the N-terminal helix folded on the opposite site of the catalytic domain. The architecture of the active site and a computational docking model of BsTrmB in complex with the methyl group donor S-adenosyl-L-methionine and the tRNA substrate provide an explanation for results from mutagenesis studies of an orthologous enzyme from Escherichia coli (EcTrmB). However, unlike EcTrmB, BsTrmB is shown here to be dimeric both in the crystal and in solution. The dimer interface has a hydrophobic core and buries a potassium ion and five water molecules. The evolutionary analysis of the putative interface residues in the TrmB family suggests that homodimerization may be a specific feature of TrmBs from Bacilli, which may represent an early stage of evolution to an obligatory dimer.

  14. Crystallization and preliminary crystallographic analysis of tRNA (m{sup 7}G46) methyltransferase from Escherichia coli

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Qi; Gao, Yang; Yang, Weili; Zhou, Huihao; Gao, Yongxiang; Zhang, Xiao; Teng, Maikun, E-mail:; Niu, Liwen, E-mail: [Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230027 (China); Key Laboratory of Structural Biology, Chinese Academy of Sciences, 96 Jinzhai Road, Hefei, Anhui 230027 (China)


    tRNA (m{sup 7}G46) methyltransferase from E. coli was overexpressed, purified and crystallized. Diffraction data were collected to 2.04 Å resolution. Transfer RNA (tRNA) (m{sup 7}G46) methyltransferase (TrmB) belongs to the Rossmann-fold methyltransferase (RFM) family and uses S-adenosyl-l-methionine (SAM) as the methyl-group donor to catalyze the formation of N{sup 7}-methylguanosine (m{sup 7}G) at position 46 in the variable loop of tRNAs. After attempts to crystallize full-length Escherichia coli TrmB (EcTrmB) failed, a truncated protein lacking the first 32 residues of the N-terminus but with an additional His{sub 6} tag at the C-terminus was crystallized by the hanging-drop vapour-diffusion method using polyethylene glycol 3350 (PEG 3350) as precipitant at 283 K. An X-ray diffraction data set was collected using a single flash-cooled crystal that belonged to space group P2{sub 1}.

  15. The Recognition Of Fatigue

    DEFF Research Database (Denmark)

    Elsass, Peter; Jensen, Bodil; Mørup, Rikke;


    Elsass P., Jensen B., Morup R., Thogersen M.H. (2007). The Recognition Of Fatigue: A qualitative study of life-stories from rehabilitation clients. International Journal of Psychosocial Rehabilitation. 11 (2), 75-87......Elsass P., Jensen B., Morup R., Thogersen M.H. (2007). The Recognition Of Fatigue: A qualitative study of life-stories from rehabilitation clients. International Journal of Psychosocial Rehabilitation. 11 (2), 75-87...

  16. Evaluating music emotion recognition

    DEFF Research Database (Denmark)

    Sturm, Bob L.


    A fundamental problem with nearly all work in music genre recognition (MGR)is that evaluation lacks validity with respect to the principal goals of MGR. This problem also occurs in the evaluation of music emotion recognition (MER). Standard approaches to evaluation, though easy to implement, do...... not reliably differentiate between recognizing genre or emotion from music, or by virtue of confounding factors in signals (e.g., equalization). We demonstrate such problems for evaluating an MER system, and conclude with recommendations....

  17. Why recognition is rational

    Directory of Open Access Journals (Sweden)

    Clintin P. Davis-Stober


    Full Text Available The Recognition Heuristic (Gigerenzer and Goldstein, 1996; Goldstein and Gigerenzer, 2002 makes the counter-intuitive prediction that a decision maker utilizing less information may do as well as, or outperform, an idealized decision maker utilizing more information. We lay a theoretical foundation for the use of single-variable heuristics such as the Recognition Heuristic as an optimal decision strategy within a linear modeling framework. We identify conditions under which over-weighting a single predictor is a mini-max strategy among a class of a priori chosen weights based on decision heuristics with respect to a measure of statistical lack of fit we call ``risk''. These strategies, in turn, outperform standard multiple regression as long as the amount of data available is limited. We also show that, under related conditions, weighting only one variable and ignoring all others produces the same risk as ignoring the single variable and weighting all others. This approach has the advantage of generalizing beyond the original environment of the Recognition Heuristic to situations with more than two choice options, binary or continuous representations of recognition, and to other single variable heuristics. We analyze the structure of data used in some prior recognition tasks and find that it matches the sufficient conditions for optimality in our results. Rather than being a poor or adequate substitute for a compensatory model, the Recognition Heuristic closely approximates an optimal strategy when a decision maker has finite data about the world.

  18. Single and Multiple Hand Gesture Recognition Systems: A Comparative Analysis

    Directory of Open Access Journals (Sweden)

    Siddharth Rautaray


    Full Text Available With the evolution of higher computing speed, efficient communication technologies, and advanced display techniques the legacy HCI techniques become obsolete and are no more helpful in accurate and fast flow of information in present day computing devices. Hence the need of user friendly human machine interfaces for real time interfaces for human computer interaction have to be designed and developed to make the man machine interaction more intuitive and user friendly. The vision based hand gesture recognition affords users with the ability to interact with computers in more natural and intuitive ways. These gesture recognition systems generally consist of three main modules like hand segmentation, hand tracking and gesture recognition from hand features, designed using different image processing techniques which are further integrated with different applications. An increase use of new interfaces based on hand gesture recognition designed to cope up with the computing devices for interaction. This paper is an effort to provide a comparative analysis between such real time vision based hand gesture recognition systems which are based on interaction using single and multiple hand gestures. Single hand gesture based recognition systems (SHGRS have fewer complexes to implement, with a constraint to the count of different gestures which is large enough with various permutations and combinations of gesture, which is possible with multiple hands in multiple hand gesture recognition systems (MHGRS. The thorough comparative analysis has been done on various other vital parameters for the recognition systems.

  19. Structural basis for duplex RNA recognition and cleavage by Archaeoglobus fulgidus C3PO (United States)

    Parizotto, Eneida A; Lowe, Edward D; Parker, James S


    Oligomeric complexes of Trax and Translin proteins, known as C3POs, participate in a variety of eukaryotic nucleic acid metabolism pathways including RNAi and tRNA processing. In RNAi in humans and Drosophila, C3PO activates pre-RISC by removing the passenger strand of the siRNA precursor duplex using nuclease activity present in Trax. It is not known how C3POs engage with nucleic acid substrates. Here we identify a single protein from Archaeoglobus fulgidus that assembles into an octamer with striking similarity to human C3PO. The structure in complex with duplex RNA reveals that the octamer entirely encapsulates a single thirteen base-pair RNA duplex inside a large inner cavity. Trax-like subunit catalytic sites target opposite strands of the duplex for cleavage, separated by seven base pairs. The structure provides insight into the mechanism of RNA recognition and cleavage by an archaeal C3PO-like complex. PMID:23353787

  20. Optical correlation recognition based on LCOS (United States)

    Tang, Mingchuan; Wu, Jianhong


    Vander-Lugt correlator[1] plays an important role in optical pattern recognition due to the characteristics of accurate positioning and high signal-to-noise ratio. The ideal Vander-Lugt correlator should have the ability of outputting strong and sharp correlation peak in allusion to the true target, in the existing Spatial Light Modulators[2], Liquid Crystal On Silicon(LCOS) has been the most competitive candidate for the matched filter owing to the continuous phase modulation peculiarity. Allowing for the distortions of the target to be identified including rotations, scaling changes, perspective changes, which can severely impact the correlation recognition results, herein, we present a modified Vander-Lugt correlator based on the LCOS by means of applying an iterative algorithm to the design of the filter so that the correlator can invariant to the distortions while maintaining good performance. The results of numerical simulation demonstrate that the filter could get the similar recognition results for all the training images. And the experiment shows that the modified correlator achieves the 180° rotating tolerance significantly improving the recognition efficiency of the correlator.

  1. A new approach for sclera vein recognition (United States)

    Thomas, N. L.; Du, Yingzi; Zhou, Zhi


    The vein structure in the sclera is stable over time, unique to each person, and well suited for human identification. A few researchers have performed sclera vein pattern recognition and reported promising initial results. Sclera recognition poses several challenges: the vein structure moves and deforms with the movement of the eye; images of sclera patterns are often defocused and/or saturated; and, most importantly, the vein structure in the sclera is multi-layered and has complex non-linear deformation. In this paper, we proposed a new method for sclera recognition: First, we developed a color-based sclera region estimation scheme for sclera segmentation. Second, we designed a Gabor wavelet-based sclera pattern enhancement method, and an adaptive thresholding method to emphasize and binarize the sclera vein patterns. Third, we proposed a line descriptor-based feature extraction, registration, and matching method that is illumination-, scale-, orientation-, and deformation-invariant, and can mitigate the multi-layered deformation effects exhibited in the sclera and tolerate segmentation error. It is empirically verified using the UBIRIS database that the proposed method can perform accurate sclera recognition.

  2. 38 CFR 4.46 - Accurate measurement. (United States)


    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2010-07-01 2010-07-01 false Accurate measurement. 4... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate measurement of the length of stumps, excursion of joints, dimensions and location of scars with respect...

  3. Metacognitive Processes in Emotion Recognition: Are They Different in Adults with Asperger's Disorder? (United States)

    Sawyer, Alyssa C. P.; Williamson, Paul; Young, Robyn


    Deficits in emotion recognition and social interaction characterize individuals with Asperger's Disorder (AS). Moreover they also appear to be less able to accurately use confidence to gauge their emotion recognition accuracy (i.e., metacognitive monitoring). The aim of this study was to extend this finding by considering both monitoring and…

  4. Locally Linear Discriminate Embedding for Face Recognition

    Directory of Open Access Journals (Sweden)

    Eimad E. Abusham


    Full Text Available A novel method based on the local nonlinear mapping is presented in this research. The method is called Locally Linear Discriminate Embedding (LLDE. LLDE preserves a local linear structure of a high-dimensional space and obtains a compact data representation as accurately as possible in embedding space (low dimensional before recognition. For computational simplicity and fast processing, Radial Basis Function (RBF classifier is integrated with the LLDE. RBF classifier is carried out onto low-dimensional embedding with reference to the variance of the data. To validate the proposed method, CMU-PIE database has been used and experiments conducted in this research revealed the efficiency of the proposed methods in face recognition, as compared to the linear and non-linear approaches.

  5. Sulfur transfer and activation by ubiquitin-like modifier system Uba4•Urm1 link protein urmylation and tRNA thiolation in yeast

    Directory of Open Access Journals (Sweden)

    André Jüdes


    Full Text Available Urm1 is a unique dual-function member of the ubiquitin protein family and conserved from yeast to man. It acts both as a protein modifier in ubiquitin-like urmylation and as a sulfur donor for tRNA thiolation, which in concert with the Elongator pathway forms 5-methoxy-carbonyl-methyl-2-thio (mcm5s2 modified wobble uridines (U34 in anticodons. Using Saccharomyces cerevisiae as a model to study a relationship between these two functions, we examined whether cultivation temperature and sulfur supply previously implicated in the tRNA thiolation branch of the URM1 pathway also contribute to proper urmylation. Monitoring Urm1 conjugation, we found urmylation of the peroxiredoxin Ahp1 is suppressed either at elevated cultivation temperatures or under sulfur starvation. In line with this, mutants with sulfur transfer defects that are linked to enzymes (Tum1, Uba4 required for Urm1 activation by thiocarboxylation (Urm1-COSH were found to maintain drastically reduced levels of Ahp1 urmylation and mcm5s2U34 modification. Moreover, as revealed by site specific mutagenesis, the S-transfer rhodanese domain (RHD in the E1-like activator (Uba4 crucial for Urm1-COSH formation is critical but not essential for protein urmylation and tRNA thiolation. In sum, sulfur supply, transfer and activation chemically link protein urmylation and tRNA thiolation. These are features that distinguish the ubiquitin-like modifier system Uba4•Urm1 from canonical ubiquitin family members and will help elucidate whether, in addition to their mechanistic links, the protein and tRNA modification branches of the URM1 pathway may also relate in function to one another.

  6. Engineering and Validation of a Vector for Concomitant Expression of Rare Transfer RNA (tRNA and HIV-1 nef Genes in Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Siti Aisyah Mualif

    Full Text Available Relative ease in handling and manipulation of Escherichia coli strains make them primary candidate to express proteins heterologously. Overexpression of heterologous genes that contain codons infrequently used by E. coli is related with difficulties such as mRNA instability, early termination of transcription and/or translation, deletions and/or misincorporation, and cell growth inhibition. These codon bias -associated problems are addressed by co-expressing ColE1-compatible, rare tRNA expressing helper plasmids. However, this approach has inadequacies, which we have addressed by engineering an expression vector that concomitantly expresses the heterologous protein of interest, and rare tRNA genes in E. coli. The expression vector contains three (argU, ileY, leuW rare tRNA genes and a useful multiple cloning site for easy in-frame cloning. To maintain the overall size of the parental plasmid vector, the rare tRNA genes replaced the non-essential DNA segments in the vector. The cloned gene is expressed under the control of T7 promoter and resulting recombinant protein has a C-terminal 6His tag for IMAC-mediated purification. We have evaluated the usefulness of this expression vector by expressing three HIV-1 genes namely HIV-1 p27 (nef, HIV-1 p24 (ca, and HIV-1 vif in NiCo21(DE3 E.coli and demonstrated the advantages of using expression vector that concomitantly expresses rare tRNA and heterologous genes.

  7. Human gait recognition via deterministic learning. (United States)

    Zeng, Wei; Wang, Cong


    Recognition of temporal/dynamical patterns is among the most difficult pattern recognition tasks. Human gait recognition is a typical difficulty in the area of dynamical pattern recognition. It classifies and identifies individuals by their time-varying gait signature data. Recently, a new dynamical pattern recognition method based on deterministic learning theory was presented, in which a time-varying dynamical pattern can be effectively represented in a time-invariant manner and can be rapidly recognized. In this paper, we present a new model-based approach for human gait recognition via the aforementioned method, specifically for recognizing people by gait. The approach consists of two phases: a training (learning) phase and a test (recognition) phase. In the training phase, side silhouette lower limb joint angles and angular velocities are selected as gait features. A five-link biped model for human gait locomotion is employed to demonstrate that functions containing joint angle and angular velocity state vectors characterize the gait system dynamics. Due to the quasi-periodic and symmetrical characteristics of human gait, the gait system dynamics can be simplified to be described by functions of joint angles and angular velocities of one side of the human body, thus the feature dimension is effectively reduced. Locally-accurate identification of the gait system dynamics is achieved by using radial basis function (RBF) neural networks (NNs) through deterministic learning. The obtained knowledge of the approximated gait system dynamics is stored in constant RBF networks. A gait signature is then derived from the extracted gait system dynamics along the phase portrait of joint angles versus angular velocities. A bank of estimators is constructed using constant RBF networks to represent the training gait patterns. In the test phase, by comparing the set of estimators with the test gait pattern, a set of recognition errors are generated, and the average L(1) norms

  8. Touchless palmprint recognition systems

    CERN Document Server

    Genovese, Angelo; Scotti, Fabio


    This book examines the context, motivation and current status of biometric systems based on the palmprint, with a specific focus on touchless and less-constrained systems. It covers new technologies in this rapidly evolving field and is one of the first comprehensive books on palmprint recognition systems.It discusses the research literature and the most relevant industrial applications of palmprint biometrics, including the low-cost solutions based on webcams. The steps of biometric recognition are described in detail, including acquisition setups, algorithms, and evaluation procedures. Const

  9. Recognition as care

    DEFF Research Database (Denmark)

    Ahlmark, Nanna; Whyte, Susan Reynolds; Harting, Janneke


    This longitudinal study provides critical insight into the social processes of municipal diabetes training for Arabic-speaking immigrants in Denmark focusing on participants’ experiences. Our study builds on observations of three diabetes courses and 36 interviews with participants at the start of......-based and solidarity-based recognition to analyse what was at stake in these experiences, and we engage Annemarie Mol’s concept of a logic of care to show how recognition unfolded practically during the training. We propose that participants’ wider social context and experiences of misrecognition situated the training...

  10. [Prosopagnosia and facial expression recognition]. (United States)

    Koyama, Shinichi


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

  11. Evidence that the mitochondrial leucyl tRNA synthetase (LARS2) gene represents a novel type 2 diabetes susceptibility gene

    DEFF Research Database (Denmark)

    hart, Leen M; Hansen, Torben; Rietveld, Ingrid;


    Previously, we have shown that a mutation in the mitochondrial DNA-encoded tRNA(Leu(UUR)) gene is associated with type 2 diabetes. One of the consequences of this mutation is a reduced aminoacylation of tRNA(Leu(UUR)). In this study, we have examined whether variants in the leucyl tRNA synthetase...... gene (LARS2), involved in aminoacylation of tRNA(Leu(UUR)), associate with type 2 diabetes. Direct sequencing of LARS2 cDNA from 25 type 2 diabetic subjects revealed eight single nucleotide polymorphisms. Two of the variants were examined in 7,836 subjects from four independent populations...... no significant differences in clinical variables between carriers and noncarriers. In this study, we provide evidence that the LARS2 gene may represent a novel type 2 diabetes susceptibility gene. The mechanism by which the H324Q variant enhances type 2 diabetes risk needs to be further established...

  12. Interaction of Ru(Ⅱ) Complex with Yeast tRNA Studied by Isothermal Titration Calorimetry

    Institute of Scientific and Technical Information of China (English)

    徐宏; 刘敛洪; 刘志刚; 梁毅; 张鹏; 杜芬; 周兵瑞; 计亮年


    The interaction of metal complex with RNA has been studied by isothermal titration calorimetry (ITC) for the first time. ITC experiments show that complex [Ru(phen)2MPIP]2+ {phen= 1,10-phenanthroline, MP[P-2-(4-methylphenyl)imidazo[4,5-f]-1, 10-phenanthroline} interacts with yeast tRNA in terms of a model for a singleset of identical sites through intercalation, which is consistent with our previous observation obtained from spectroscopic methods, and this binding process was driven by a moderately favorable enthalpy decrease in combination with a moderately favorable entropy increase, suggesting that ITC is an effective method for deep studying the interactions of metal complexes with RNA.

  13. In vitro substrate specificities of 3'-5' polymerases correlate with biological outcomes of tRNA 5'-editing reactions. (United States)

    Long, Yicheng; Jackman, Jane E


    Protozoan mitochondrial tRNAs (mt-tRNAs) are repaired by a process known as 5'-editing. Mt-tRNA sequencing revealed organism-specific patterns of editing G-U base pairs, wherein some species remove G-U base pairs during 5'-editing, while others retain G-U pairs in the edited tRNA. We tested whether 3'-5' polymerases that catalyze the repair step of 5'-editing exhibit organism-specific preferences that explain the treatment of G-U base pairs. Biochemical and kinetic approaches revealed that a 3'-5' polymerase from Acanthamoeba castellanii tolerates G-U wobble pairs in editing substrates much more readily than several other enzymes, consistent with its biological pattern of editing.

  14. Crystallization and preliminary crystallographic analysis of tRNA (m7G46) methyltransferase from Escherichia coli (United States)

    Liu, Qi; Gao, Yang; Yang, Weili; Zhou, Huihao; Gao, Yongxiang; Zhang, Xiao; Teng, Maikun; Niu, Liwen


    Transfer RNA (tRNA) (m7G46) methyltransferase (TrmB) belongs to the Rossmann-fold methyltransferase (RFM) family and uses S-adenosyl-l-methionine (SAM) as the methyl-group donor to catalyze the formation of N 7-­methylguanosine (m7G) at position 46 in the variable loop of tRNAs. After attempts to crystallize full-length Escherichia coli TrmB (EcTrmB) failed, a truncated protein lacking the first 32 residues of the N-terminus but with an additional His6 tag at the C-terminus was crystallized by the hanging-drop vapour-diffusion method using polyethylene glycol 3350 (PEG 3350) as precipitant at 283 K. An X-ray diffraction data set was collected using a single flash-cooled crystal that belonged to space group P21. PMID:18678947

  15. Crystallization and preliminary crystallographic analysis of tRNA (m(7)G46) methyltransferase from Escherichia coli. (United States)

    Liu, Qi; Gao, Yang; Yang, Weili; Zhou, Huihao; Gao, Yongxiang; Zhang, Xiao; Teng, Maikun; Niu, Liwen


    Transfer RNA (tRNA) (m(7)G46) methyltransferase (TrmB) belongs to the Rossmann-fold methyltransferase (RFM) family and uses S-adenosyl-L-methionine (SAM) as the methyl-group donor to catalyze the formation of N(7)-methylguanosine (m(7)G) at position 46 in the variable loop of tRNAs. After attempts to crystallize full-length Escherichia coli TrmB (EcTrmB) failed, a truncated protein lacking the first 32 residues of the N-terminus but with an additional His(6) tag at the C-terminus was crystallized by the hanging-drop vapour-diffusion method using polyethylene glycol 3350 (PEG 3350) as precipitant at 283 K. An X-ray diffraction data set was collected using a single flash-cooled crystal that belonged to space group P2(1).

  16. Real-time affine invariant gesture recognition for LED smart lighting control (United States)

    Chen, Xu; Liao, Miao; Feng, Xiao-Fan


    Gesture recognition has attracted extensive research interest in the field of human computer interaction. Realtime affine invariant gesture recognition is an important and challenging problem. This paper presents a robust affine view invariant gesture recognition system for realtime LED smart light control. As far as we know, this is the first time that gesture recognition has been applied for control LED smart light in realtime. Employing skin detection, hand blobs captured from a top view camera are first localized and aligned. Subsequently, SVM classifiers trained on HOG features and robust shape features are then utilized for gesture recognition. By accurately recognizing two types of gestures ("gesture 8" and a "5 finger gesture"), a user is enabled to toggle lighting on/off efficiently and control light intensity on a continuous scale. In each case, gesture recognition is rotation- and translation-invariant. Extensive evaluations in an office setting demonstrate the effectiveness and robustness of the proposed gesture recognition algorithm.

  17. Global translational impacts of the loss of the tRNA modification t6A in yeast

    Directory of Open Access Journals (Sweden)

    Patrick C. Thiaville


    Full Text Available The universal tRNA modification t6A is found at position 37 of nearly all tRNAs decoding ANN codons. The absence of t6A37 leads to severe growth defects in baker’s yeast, phenotypes similar to those caused by defects in mcm5s2U34 synthesis. Mutants in mcm5s2U34 can be suppressed by overexpression of tRNALysUUU, but we show t6A phenotypes could not be suppressed by expressing any individual ANN decoding tRNA, and t6A and mcm5s2U are not determinants for each other’s formation. Our results suggest that t6A deficiency, like mcm5s2U deficiency, leads to protein folding defects, and show that the absence of t6A led to stress sensitivities (heat, ethanol, salt and sensitivity to TOR pathway inhibitors. Additionally, L-homoserine suppressed the slow growth phenotype seen in t6A-deficient strains, and proteins aggregates and Advanced Glycation End-products (AGEs were increased in the mutants. The global consequences on translation caused by t6A absence were examined by ribosome profiling. Interestingly, the absence of t6A did not lead to global translation defects, but did increase translation initiation at upstream non-AUG codons and increased frame-shifting in specific genes. Analysis of codon occupancy rates suggests that one of the major roles of t6A is to homogenize the process of elongation by slowing the elongation rate at codons decoded by high abundance tRNAs and I34:C3 pairs while increasing the elongation rate of rare tRNAs and G34:U3 pairs. This work reveals that the consequences of t6A absence are complex and multilayered and has set the stage to elucidate the molecular basis of the observed phenotypes.

  18. Nonlinear fusion for face recognition using fuzzy integral (United States)

    Chen, Xuerong; Jing, Zhongliang; Xiao, Gang


    Face recognition based only on the visual spectrum is not accurate or robust enough to be used in uncontrolled environments. Recently, infrared (IR) imagery of human face is considered as a promising alternative to visible imagery due to its relative insensitive to illumination changes. However, IR has its own limitations. In order to fuse information from the two modalities to achieve better result, we propose a new fusion recognition scheme based on nonlinear decision fusion, using fuzzy integral to fuse the objective evidence supplied by each modality. The scheme also employs independent component analysis (ICA) for feature extraction and support vector machines (SVMs) for classification evidence. Recognition rate is used to evaluate the proposed scheme. Experimental results show the scheme improves recognition performance substantially.

  19. Sunspot drawings handwritten character recognition method based on deep learning (United States)

    Zheng, Sheng; Zeng, Xiangyun; Lin, Ganghua; Zhao, Cui; Feng, Yongli; Tao, Jinping; Zhu, Daoyuan; Xiong, Li


    High accuracy scanned sunspot drawings handwritten characters recognition is an issue of critical importance to analyze sunspots movement and store them in the database. This paper presents a robust deep learning method for scanned sunspot drawings handwritten characters recognition. The convolution neural network (CNN) is one algorithm of deep learning which is truly successful in training of multi-layer network structure. CNN is used to train recognition model of handwritten character images which are extracted from the original sunspot drawings. We demonstrate the advantages of the proposed method on sunspot drawings provided by Chinese Academy Yunnan Observatory and obtain the daily full-disc sunspot numbers and sunspot areas from the sunspot drawings. The experimental results show that the proposed method achieves a high recognition accurate rate.

  20. Persian Sign Language Recognition Using Radial Distance and Fourier Transform

    Directory of Open Access Journals (Sweden)

    Bahare Jalilian


    Full Text Available This paper provides a novel hand gesture recognition method to recognize 32 static signs of the Persian Sign Language (PSL alphabets. Accurate hand segmentation is the first and important step in sign language recognition systems. Here, we propose a method for hand segmentation that helps to build a better vision based sign language recognition system. The proposed method is based on YCbCr color space, single Gaussian model and Bayes rule. It detects region of hand in complex background and non-uniform illumination. Hand gesture features are extracted by radial distance and Fourier transform. Finally, the Euclidean distanceis used to compute the similarity between the input signs and all training feature vectors in the database. The system is tested on 480 posture images of the PSL, 15 images for each 32 signs. Experimental results show that our approach is capable to recognize all 32 PSL alphabets with 95.62% recognition rate.

  1. Facial Emotion Recognition Using Context Based Multimodal Approach

    Directory of Open Access Journals (Sweden)

    Priya Metri


    Full Text Available Emotions play a crucial role in person to person interaction. In recent years, there has been a growing interest in improving all aspects of interaction between humans and computers. The ability to understand human emotions is desirable for the computer in several applications especially by observing facial expressions. This paper explores a ways of human-computer interaction that enable the computer to be more aware of the user’s emotional expressions we present a approach for the emotion recognition from a facial expression, hand and body posture. Our model uses multimodal emotion recognition system in which we use two different models for facial expression recognition and for hand and body posture recognition and then combining the result of both classifiers using a third classifier which give the resulting emotion . Multimodal system gives more accurate result than a signal or bimodal system

  2. Fusion of visible and infrared imagery for face recognition

    Institute of Scientific and Technical Information of China (English)

    Xuerong Chen(陈雪荣); Zhongliang Jing(敬忠良); Shaoyuan Sun(孙韶媛); Gang Xiao(肖刚)


    In recent years face recognition has received substantial attention, but still remained very challenging in real applications. Despite the variety of approaches and tools studied, face recognition is not accurate or robust enough to be used in uncontrolled environments. Infrared (IR) imagery of human faces offers a promising alternative to visible imagery, however, IR has its own limitations. In this paper, a scheme to fuse information from the two modalities is proposed. The scheme is based on eigenfaces and probabilistic neural network (PNN), using fuzzy integral to fuse the objective evidence supplied by each modality. Recognition rate is used to evaluate the fusion scheme. Experimental results show that the scheme improves recognition performance substantially.

  3. Strong memories obscure weak memories in associative recognition. (United States)

    Verde, Michael F; Rotello, Caren M


    The list strength effect, in which strengthening some memories has a detrimental effect on the retrieval of other memories, has generally not been found in item recognition. The present study shows that the list strength effect does occur in associative recognition. Study materials were sets of overlapping word pairs (A-B, A-C, D-B, etc.). Within critical sets of words, strong pairs were presented three times at study, as compared with one presentation for weak pairs. In Experiment 1, associative recognition for weak pairs was less accurate than that for baseline pairs, and response times for hits were slower. In Experiment 2, receiver-operating characteristic curve data provided further evidence of poor accuracy for weak pairs. These findings support a qualitative distinction between item and associative recognition.


    Directory of Open Access Journals (Sweden)



    Full Text Available In radio communication systems, signal modulation format recognition is a significant characteristic used in radio signal monitoring and identification. Over the past few decades, modulation formats have become increasingly complex, which has led to the problem of how to accurately and promptly recognize a modulation format. In addressing these challenges, the development of automatic modulation recognition systems that can classify a radio signal’s modulation format has received worldwide attention. Decision-theoretic methods and pattern recognition solutions are the two typical automatic modulation recognition approaches. While decision-theoretic approaches use probabilistic or likelihood functions, pattern recognition uses feature-based methods. This study applies the pattern recognition approach based on statistical parameters, using an artificial neural network to classify five different digital modulation formats. The paper deals with automatic recognition of both inter-and intra-classes of digitally modulated signals in contrast to most of the existing algorithms in literature that deal with either inter-class or intra-class modulation format recognition. The results of this study show that accurate and prompt modulation recognition is possible beyond the lower bound of 5 dB commonly acclaimed in literature. The other significant contribution of this paper is the usage of the Python programming language which reduces computational complexity that characterizes other automatic modulation recognition classifiers developed using the conventional MATLAB neural network toolbox.

  5. Automatic aircraft recognition (United States)

    Hmam, Hatem; Kim, Jijoong


    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.

  6. Recognition of fractal graphs

    NARCIS (Netherlands)

    Perepelitsa, VA; Sergienko, [No Value; Kochkarov, AM


    Definitions of prefractal and fractal graphs are introduced, and they are used to formulate mathematical models in different fields of knowledge. The topicality of fractal-graph recognition from the point of view, of fundamental improvement in the efficiency of the solution of algorithmic problems i

  7. Tolerance and recognition

    Directory of Open Access Journals (Sweden)

    Hans Marius Hansteen


    Full Text Available Even though “toleration” and “recognition” designate opposing attitudes (to tolerate something, implies a negative stance towards it, whereas recognition seems to imply a positive one, the concepts do not constitute mutually exclusive alternatives. However, “toleration” is often associated with liberal universalism, focusing on individual rights, whereas “recognition” often connotes communitarian perspectives, focusing on relations and identity. This paper argues that toleration may be founded on recognition, and that recognition may imply toleration. In outlining a differentiated understanding of the relationship between toleration and recognition, it seems apt to avoid an all-to-general dichotomy between universalism and particularism or, in other words, to reach beyond the debate between liberalism and communitarianism in political philosophy.The paper takes as its starting point the view that the discussion on toleration and diversity in intercultural communication is one of the contexts where it seems important to get beyond the liberal/communitarian dichotomy. Some basic features of Rainer Forst’s theory of toleration and Axel Honneth’s theory of the struggle for recognition are presented, in order to develop a more substantial understanding of the relationship between the concepts of toleration and recognition. One lesson from Forst is that toleration is a normatively dependent concept, i.e., that it is impossible to deduce principles for toleration and its limits from a theory of toleration as such. A central lesson from Honneth is that recognition – understood as a basic human need – is always conflictual and therefore dynamic.Accordingly, a main point in the paper is that the theory of struggles for and about recognition (where struggles for designates struggles within an established order of recognition, and struggles about designates struggles that challenge established orders of recognition may clarify what

  8. Automatic object recognition (United States)

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


    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.

  9. Pattern recognition in bioinformatics. (United States)

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


    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.

  10. Integration trumps selection in object recognition. (United States)

    Saarela, Toni P; Landy, Michael S


    Finding and recognizing objects is a fundamental task of vision. Objects can be defined by several "cues" (color, luminance, texture, etc.), and humans can integrate sensory cues to improve detection and recognition [1-3]. Cortical mechanisms fuse information from multiple cues [4], and shape-selective neural mechanisms can display cue invariance by responding to a given shape independent of the visual cue defining it [5-8]. Selective attention, in contrast, improves recognition by isolating a subset of the visual information [9]. Humans can select single features (red or vertical) within a perceptual dimension (color or orientation), giving faster and more accurate responses to items having the attended feature [10, 11]. Attention elevates neural responses and sharpens neural tuning to the attended feature, as shown by studies in psychophysics and modeling [11, 12], imaging [13-16], and single-cell and neural population recordings [17, 18]. Besides single features, attention can select whole objects [19-21]. Objects are among the suggested "units" of attention because attention to a single feature of an object causes the selection of all of its features [19-21]. Here, we pit integration against attentional selection in object recognition. We find, first, that humans can integrate information near optimally from several perceptual dimensions (color, texture, luminance) to improve recognition. They cannot, however, isolate a single dimension even when the other dimensions provide task-irrelevant, potentially conflicting information. For object recognition, it appears that there is mandatory integration of information from multiple dimensions of visual experience. The advantage afforded by this integration, however, comes at the expense of attentional selection.

  11. A neuromorphic system for video object recognition. (United States)

    Khosla, Deepak; Chen, Yang; Kim, Kyungnam


    Automated video object recognition is a topic of emerging importance in both defense and civilian applications. This work describes an accurate and low-power neuromorphic architecture and system for real-time automated video object recognition. Our system, Neuormorphic Visual Understanding of Scenes (NEOVUS), is inspired by computational neuroscience models of feed-forward object detection and classification pipelines for processing visual data. The NEOVUS architecture is inspired by the ventral (what) and dorsal (where) streams of the mammalian visual pathway and integrates retinal processing, object detection based on form and motion modeling, and object classification based on convolutional neural networks. The object recognition performance and energy use of the NEOVUS was evaluated by the Defense Advanced Research Projects Agency (DARPA) under the Neovision2 program using three urban area video datasets collected from a mix of stationary and moving platforms. These datasets are challenging and include a large number of objects of different types in cluttered scenes, with varying illumination and occlusion conditions. In a systematic evaluation of five different teams by DARPA on these datasets, the NEOVUS demonstrated the best performance with high object recognition accuracy and the lowest energy consumption. Its energy use was three orders of magnitude lower than two independent state of the art baseline computer vision systems. The dynamic power requirement for the complete system mapped to commercial off-the-shelf (COTS) hardware that includes a 5.6 Megapixel color camera processed by object detection and classification algorithms at 30 frames per second was measured at 21.7 Watts (W), for an effective energy consumption of 5.45 nanoJoules (nJ) per bit of incoming video. These unprecedented results show that the NEOVUS has the potential to revolutionize automated video object recognition toward enabling practical low-power and mobile video processing

  12. A Massively Parallel Face Recognition System

    Directory of Open Access Journals (Sweden)

    Lahdenoja Olli


    Full Text Available We present methods for processing the LBPs (local binary patterns with a massively parallel hardware, especially with CNN-UM (cellular nonlinear network-universal machine. In particular, we present a framework for implementing a massively parallel face recognition system, including a dedicated highly accurate algorithm suitable for various types of platforms (e.g., CNN-UM and digital FPGA. We study in detail a dedicated mixed-mode implementation of the algorithm and estimate its implementation cost in the view of its performance and accuracy restrictions.

  13. A Massively Parallel Face Recognition System

    Directory of Open Access Journals (Sweden)

    Ari Paasio


    Full Text Available We present methods for processing the LBPs (local binary patterns with a massively parallel hardware, especially with CNN-UM (cellular nonlinear network-universal machine. In particular, we present a framework for implementing a massively parallel face recognition system, including a dedicated highly accurate algorithm suitable for various types of platforms (e.g., CNN-UM and digital FPGA. We study in detail a dedicated mixed-mode implementation of the algorithm and estimate its implementation cost in the view of its performance and accuracy restrictions.

  14. Accurate platelet counting in an insidious case of pseudothrombocytopenia. (United States)

    Lombarts, A J; Zijlstra, J J; Peters, R H; Thomasson, C G; Franck, P F


    Anticoagulant-induced aggregation of platelets leads to pseudothrombocytopenia. Blood cell counters generally trigger alarms to alert the user. We describe an insidious case of pseudothrombocytopenia, where the complete absence of Coulter counter alarms both in ethylenediaminetetraacetic acid blood and in citrate or acid citrate dextrose blood samples was compounded by the fact that the massive aggregates were exclusively found at the edges of the blood smear. Non-recognition of pseudothrombocytopenia can have serious diagnostic and therapeutic consequences. While the anti-aggregant mixture citrate-theophylline-adenosine-dipyridamole completely failed in preventing pseudothrombocytopenia, addition of iloprost to anticoagulants only partially prevented the aggregation. Only the prior addition of gentamicin to any anticoagulant used resulted in a complete prevention of pseudothrombocytopenia and enabled to count accurately the platelets.

  15. Autonomy and Recognition

    Directory of Open Access Journals (Sweden)

    Miguel Giusti


    Full Text Available Resumen:El presente ensayo contiene dos partes. En la primera se hace una breve descripción de las carencias de la reflexión moral a las que parece venir al encuentro el concepto de reconocimiento. Charles Taylor y Axel Honneth, protagonistas en estos debates, dan buenas razones para dirigir la discusión hacia el tema del reconocimiento, pero no coinciden ni en su definición, ni en el modo de recuperar la tesis de Hegel, ni tampoco en la forma de tratar la relación entre autonomía y reconocimiento. En la segunda parte se analiza la concepción propiamente hegeliana, con la intención de destacar el nexo esencial, no la ruptura, que existe entre la noción de reconocimiento y el modelo conceptual de la voluntad libre o del espíritu. Abstract:This essay is divided into two parts. The first one is a short description of the deficiencies of moral reflection, which seem to lead the discussion towards the concept of recognition. Charles Taylor and Axel Honneth, two of the protagonists of these debates, give very good reasons for turning the argument towards the issue of recognition, but they do not agree on its definition, on the way to recover the Hegelian thesis, or on how to approach the relationship between autonomy and recognition. The second part constitutes an analysis of the Hegelian conception of recognition, in order to highlight the essential link –rather than the rupture– between the notion of recognition and the conceptual model of free will or spirit.

  16. Galeotti on recognition as inclusion

    DEFF Research Database (Denmark)

    Lægaard, Sune


    Anna Elisabetta Galeotti's theory of 'toleration as recognition' has been criticised by Peter Jones for being conceptually incoherent, since liberal toleration presupposes a negative attitude to differences, whereas multicultural recognition requires positive affirmation hereof. The paper spells ...

  17. Are School Placement Recommendations Accurate? The Effect of Students' Ethnicity on Teachers' Judgments and Recognition Memory (United States)

    Glock, Sabine; Krolak-Schwerdt, Sabine; Pit-ten Cate, Ineke M.


    Educational research has provided evidence that racial and ethnic minority students are disadvantaged in today's educational systems. Teachers' stereotypical expectations are believed to contribute to these disadvantages because teachers make decisions about grades, special education, tracking, and school placement. Research so far has shown that…

  18. Fast and accurate image recognition algorithms for fresh produce food safety sensing (United States)

    Yang, Chun-Chieh; Kim, Moon S.; Chao, Kuanglin; Kang, Sukwon; Lefcourt, Alan M.


    This research developed and evaluated the multispectral algorithms derived from hyperspectral line-scan fluorescence imaging under violet LED excitation for detection of fecal contamination on Golden Delicious apples. The algorithms utilized the fluorescence intensities at four wavebands, 680 nm, 684 nm, 720 nm, and 780 nm, for computation of simple functions for effective detection of contamination spots created on the apple surfaces using four concentrations of aqueous fecal dilutions. The algorithms detected more than 99% of the fecal spots. The effective detection of feces showed that a simple multispectral fluorescence imaging algorithm based on violet LED excitation may be appropriate to detect fecal contamination on fast-speed apple processing lines.


    Directory of Open Access Journals (Sweden)



    Full Text Available The recognition and assessment of the component elements of the annual financial statements’ structures is crucial in order that the information released by them fulfils the qualitative characteristics and the reflected image is a “true and fair view”. Therefore, our approach takes into consideration the recognition and assessment methods for the component elements of the financial statements’ structures, as well as certain possible risks arising from the erroneous recognition or non-recognition of some of these elements.

  20. Supporting Quality Teachers with Recognition (United States)

    Andrews, Hans A.


    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.…

  1. Superficial Priming in Episodic Recognition (United States)

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


    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…

  2. Word Recognition in Auditory Cortex (United States)

    DeWitt, Iain D. J.


    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…

  3. Six Regularities of Source Recognition (United States)

    Glanzer, Murray; Hilford, Andy; Kim, Kisok


    In recent work, researchers have shown that source-recognition memory can be incorporated in an extended signal detection model that covers both it and item-recognition memory (A. Hilford, M. Glanzer, K. Kim, & L. T. DeCarlo, 2002). In 5 experiments, using learning variables that have an established effect on item recognition, the authors tested…

  4. Forensic Face Recognition: A Survey

    NARCIS (Netherlands)

    Ali, Tauseef; Spreeuwers, Luuk; Veldhuis, Raymond; Quaglia, Adamo; Epifano, Calogera M.


    The improvements of automatic face recognition during the last 2 decades have disclosed new applications like border control and camera surveillance. A new application field is forensic face recognition. Traditionally, face recognition by human experts has been used in forensics, but now there is a

  5. The C-terminal region of thermophilic tRNA (m7G46) methyltransferase (TrmB) stabilizes the dimer structure and enhances fidelity of methylation. (United States)

    Tomikawa, Chie; Ochi, Anna; Hori, Hiroyuki


    Transfer RNA (m(7)G46) methyltransferase catalyzes methyl-transfer from S-adenosyl-L-methionine to N(7) atom of the semi-conserved G46 base in tRNA. Aquifex aeolicus is a hyper thermophilic eubacterium that grows at close to 95 degrees C. A. aeolicus tRNA (m(7)G46) methyltransferase [TrmB] has an elongated C-terminal region as compared with mesophilic counterparts. In this study, the authors focused on the functions of this C-terminal region. Analytic gel filtration chromatography and amino acid sequencing reveled that the start point (Glu202) of the C-terminal region is often cleaved by proteases during purification steps and the C-terminal region tightly binds to another subunit even in the presence of 6M urea. Because the C-terminal region contains abundant basic amino acid residues, the authors assumed that some of these residues might be involved in tRNA binding. To address this idea, the authors prepared eight alanine substitution mutant proteins. However, measurements of initial velocities of these mutant proteins suggested that the basic amino acid residues in the C-terminal region are not involved in tRNA binding. The authors investigated effects of the deletion of the C-terminal region. Deletion mutant protein of the C-terminal region (the core protein) was precipitated by incubation at 85 degrees C, while the wild type protein was soluble at that temperature, demonstrating that the C-terminal region contributes to the protein stability at high temperatures. The core protein had a methyl-transfer activity to yeast tRNA(Phe) transcript. Furthermore, the core protein slowly methylated tRNA transcripts, which did not contain G46 base. Moreover, the modified base was identified as m(7)G by two-dimensional thin layer chromatography. Thus, the deletion of the C-terminal region causes nonspecific methylation of N(7) atom of guanine base(s) in tRNA transcripts.

  6. Human Lips-Contour Recognition and Tracing

    Directory of Open Access Journals (Sweden)

    Md. Hasan Tareque


    Full Text Available Human-lip detection is an important criterion for many automated modern system in present day. Like computerized speech reading, face recognition etc. system can work more precisely if human-lip can detect accurately. There are many processes for detecting human-lip. In this paper an approach is developed so that the region of a human-lip can be detected, we called it lip contour. For this a region-based Active Contour Model (ACM is introduced with watershed segmentation. In this model we used global energy terms instead of local energy terms because, global energy gives better convergence rate for malicious environment. At the time of ACM initialization by using H8 based on Lyapunov stability theory, the system gives more accurate and stable result.

  7. Peptidyl transferase antibiotics perturb the relative positioning of the 3'-terminal adenosine of P/P'-site-bound tRNA and 23S rRNA in the ribosome

    DEFF Research Database (Denmark)

    Kirillov, S V; Porse, B T; Garrett, R A


    A range of antibiotic inhibitors that act within the peptidyl transferase center of the ribosome were examined for their capacity to perturb the relative positioning of the 3' end of P/P'-site-bound tRNA and the Escherichia coli ribosome. The 3'-terminal adenosines of deacylated tRNA and N...... decreases, at one or more rRNA sites but, with the exception of chloramphenicol, did not affect cross-linking to the ribosomal proteins. Moreover, the effects were closely similar for both deacylated and N-Ac-Phe-tRNAs, indicating that the drugs selectively perturb the 3' terminus of the tRNA. The strongest......-ribosome complexes. It is concluded that the antibiotics perturb the relative positioning of the 3' end of the P/P'-site-bound tRNA and the peptidyl transferase loop region of 23S rRNA....

  8. Vehicle License Plate Recognition Syst

    Directory of Open Access Journals (Sweden)

    Meenakshi,R. B. Dubey


    Full Text Available The vehicle license plate recognition system has greater efficiency for vehicle monitoring in automatic zone access control. This Plate recognition system will avoid special tags, since all vehicles possess a unique registration number plate. A number of techniques have been used for car plate characters recognition. This system uses neural network character recognition and pattern matching of characters as two character recognition techniques. In this approach multilayer feed-forward back-propagation algorithm is used. The performance of the proposed algorithm has been tested on several car plates and provides very satisfactory results.

  9. PCA Based Rapid and Real Time Face Recognition Technique

    Directory of Open Access Journals (Sweden)

    T R Chandrashekar


    Full Text Available Economical and efficient that is used in various applications is face Biometric which has been a popular form biometric system. Face recognition system is being a topic of research for last few decades. Several techniques are proposed to improve the performance of face recognition system. Accuracy is tested against intensity, distance from camera, and pose variance. Multiple face recognition is another subtopic which is under research now a day. Speed at which the technique works is a parameter under consideration to evaluate a technique. As an example a support vector machine performs really well for face recognition but the computational efficiency degrades significantly with increase in number of classes. Eigen Face technique produces quality features for face recognition but the accuracy is proved to be comparatively less to many other techniques. With increase in use of core processors in personal computers and application demanding speed in processing and multiple face detection and recognition system (for example an entry detection system in shopping mall or an industry, demand for such systems are cumulative as there is a need for automated systems worldwide. In this paper we propose a novel system of face recognition developed with C# .Net that can detect multiple faces and can recognize the faces parallel by utilizing the system resources and the core processors. The system is built around Haar Cascade based face detection and PCA based face recognition system with C#.Net. Parallel library designed for .Net is used to aide to high speed detection and recognition of the real time faces. Analysis of the performance of the proposed technique with some of the conventional techniques reveals that the proposed technique is not only accurate, but also is fast in comparison to other techniques.

  10. Electrocardiogram (ECG) pattern modeling and recognition via deterministic learning

    Institute of Scientific and Technical Information of China (English)

    Xunde DONG; Cong WANG; Junmin HU; Shanxing OU


    A method for electrocardiogram (ECG) pattern modeling and recognition via deterministic learning theory is presented in this paper. Instead of recognizing ECG signals beat-to-beat, each ECG signal which contains a number of heartbeats is recognized. The method is based entirely on the temporal features (i.e., the dynamics) of ECG patterns, which contains complete information of ECG patterns. A dynamical model is employed to demonstrate the method, which is capable of generating synthetic ECG signals. Based on the dynamical model, the method is shown in the following two phases:the identification (training) phase and the recognition (test) phase. In the identification phase, the dynamics of ECG patterns is accurately modeled and expressed as constant RBF neural weights through the deterministic learning. In the recognition phase, the modeling results are used for ECG pattern recognition. The main feature of the proposed method is that the dynamics of ECG patterns is accurately modeled and is used for ECG pattern recognition. Experimental studies using the Physikalisch-Technische Bundesanstalt (PTB) database are included to demonstrate the effectiveness of the approach.

  11. Statistical feature extraction based iris recognition system

    Indian Academy of Sciences (India)



    Iris recognition systems have been proposed by numerous researchers using different feature extraction techniques for accurate and reliable biometric authentication. In this paper, a statistical feature extraction technique based on correlation between adjacent pixels has been proposed and implemented. Hamming distance based metric has been used for matching. Performance of the proposed iris recognition system (IRS) has been measured by recording false acceptance rate (FAR) and false rejection rate (FRR) at differentthresholds in the distance metric. System performance has been evaluated by computing statistical features along two directions, namely, radial direction of circular iris region and angular direction extending from pupil tosclera. Experiments have also been conducted to study the effect of number of statistical parameters on FAR and FRR. Results obtained from the experiments based on different set of statistical features of iris images show thatthere is a significant improvement in equal error rate (EER) when number of statistical parameters for feature extraction is increased from three to six. Further, it has also been found that increasing radial/angular resolution,with normalization in place, improves EER for proposed iris recognition system

  12. Macromolecular recognition in the Protein Data Bank

    Energy Technology Data Exchange (ETDEWEB)

    Janin, Joël, E-mail: [Laboratoire d’Enzymologie et de Biochimie Structurales, UPR9063, CNRS, 91198 Gif-sur-Yvette (France); Institut de Biochimie et Biologie Moléculaire et Cellulaire, UMR8619, Bâtiment 430, Université Paris-Sud, 91405 Orsay (France); Rodier, Francis [Laboratoire d’Enzymologie et de Biochimie Structurales, UPR9063, CNRS, 91198 Gif-sur-Yvette (France); Chakrabarti, Pinak [Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Calcutta 700 054 (India); Bahadur, Ranjit P. [Institut de Biochimie et Biologie Moléculaire et Cellulaire, UMR8619, Bâtiment 430, Université Paris-Sud, 91405 Orsay (France); Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Calcutta 700 054 (India); Laboratoire d’Enzymologie et de Biochimie Structurales, UPR9063, CNRS, 91198 Gif-sur-Yvette (France)


    X-ray structures in the PDB illustrate both the specific recognition of two polypeptide chains in protein–protein complexes and dimeric proteins and their nonspecific interaction at crystal contacts. Crystal structures deposited in the Protein Data Bank illustrate the diversity of biological macromolecular recognition: transient interactions in protein–protein and protein–DNA complexes and permanent assemblies in homodimeric proteins. The geometric and physical chemical properties of the macromolecular interfaces that may govern the stability and specificity of recognition are explored in complexes and homodimers compared with crystal-packing interactions. It is found that crystal-packing interfaces are usually much smaller; they bury fewer atoms and are less tightly packed than in specific assemblies. Standard-size interfaces burying 1200–2000 Å{sup 2} of protein surface occur in protease–inhibitor and antigen–antibody complexes that assemble with little or no conformation changes. Short-lived electron-transfer complexes have small interfaces; the larger size of the interfaces observed in complexes involved in signal transduction and homodimers correlates with the presence of conformation changes, often implicated in biological function. Results of the CAPRI (critical assessment of predicted interactions) blind prediction experiment show that docking algorithms efficiently and accurately predict the mode of assembly of proteins that do not change conformation when they associate. They perform less well in the presence of large conformation changes and the experiment stimulates the development of novel procedures that can handle such changes.

  13. Dance recognition system using lower body movement. (United States)

    Simpson, Travis T; Wiesner, Susan L; Bennett, Bradford C


    The current means of locating specific movements in film necessitate hours of viewing, making the task of conducting research into movement characteristics and patterns tedious and difficult. This is particularly problematic for the research and analysis of complex movement systems such as sports and dance. While some systems have been developed to manually annotate film, to date no automated way of identifying complex, full body movement exists. With pattern recognition technology and knowledge of joint locations, automatically describing filmed movement using computer software is possible. This study used various forms of lower body kinematic analysis to identify codified dance movements. We created an algorithm that compares an unknown move with a specified start and stop against known dance moves. Our recognition method consists of classification and template correlation using a database of model moves. This system was optimized to include nearly 90 dance and Tai Chi Chuan movements, producing accurate name identification in over 97% of trials. In addition, the program had the capability to provide a kinematic description of either matched or unmatched moves obtained from classification recognition.

  14. Face Behavior Recognition Through Support Vector Machines

    Directory of Open Access Journals (Sweden)

    Haval A. Ahmed


    Full Text Available Communication between computers and humans has grown to be a major field of research. Facial Behavior Recognition through computer algorithms is a motivating and difficult field of research for establishing emotional interactions between humans and computers. Although researchers have suggested numerous methods of emotion recognition within the literature of this field, as yet, these research works have mainly focused on one method for their system output i.e. used one facial database for assessing their works. This may diminish the generalization method and additionally it might shrink the comparability range. A proposed technique for recognizing emotional expressions that are expressed through facial aspects of still images is presented. This technique uses the Support Vector Machines (SVM as a classifier of emotions. Substantive problems are considered such as diversity in facial databases, the samples included in each database, the number of facial expressions experienced an accurate method of extracting facial features, and the variety of structural models. After many experiments and the results of different models being compared, it is determined that this approach produces high recognition rates.

  15. Gait Recognition Using Image Self-Similarity

    Directory of Open Access Journals (Sweden)

    Cutler Ross G


    Full Text Available Gait is one of the few biometrics that can be measured at a distance, and is hence useful for passive surveillance as well as biometric applications. Gait recognition research is still at its infancy, however, and we have yet to solve the fundamental issue of finding gait features which at once have sufficient discrimination power and can be extracted robustly and accurately from low-resolution video. This paper describes a novel gait recognition technique based on the image self-similarity of a walking person. We contend that the similarity plot encodes a projection of gait dynamics. It is also correspondence-free, robust to segmentation noise, and works well with low-resolution video. The method is tested on multiple data sets of varying sizes and degrees of difficulty. Performance is best for fronto-parallel viewpoints, whereby a recognition rate of 98% is achieved for a data set of 6 people, and 70% for a data set of 54 people.

  16. A platform for discovery and quantification of modified ribonucleosides in RNA: Application to stress-induced reprogramming of tRNA modifications (United States)

    Cai, Weiling Maggie; Chionh, Yok Hian; Hia, Fabian; Gu, Chen; Kellner, Stefanie; McBee, Megan E.; Ng, Chee Sheng; Pang, Yan Ling Joy; Prestwich, Erin G.; Lim, Kok Seong; Babu, I. Ramesh; Begley, Thomas J.; Dedon, Peter C.


    Here we describe an analytical platform for systems-level quantitative analysis of modified ribonucleosides in any RNA species, with a focus on stress-induced reprogramming of tRNA as part of a system of translational control of cell stress response. The chapter emphasizes strategies and caveats for each of the seven steps of the platform workflow: 1) RNA isolation, 2) RNA purification, 3) RNA hydrolysis to individual ribonucleosides, 4) chromatographic resolution of ribonucleosides, 5) identification of the full set of modified ribonucleosides, 6) mass spectrometric quantification of ribonucleosides, 6) interrogation of ribonucleoside datasets, and 7) mapping the location of stress-sensitive modifications in individual tRNA molecules. We have focused on the critical determinants of analytical sensitivity, specificity, precision and accuracy in an effort to ensure the most biologically meaningful data on mechanisms of translational control of cell stress response. The methods described here should find wide use in virtually any analysis involving RNA modifications. PMID:26253965

  17. Tuning Iris Recognition for Noisy Images (United States)

    Ferreira, Artur; Lourenço, André; Pinto, Bárbara; Tendeiro, Jorge

    The use of iris recognition for human authentication has been spreading in the past years. Daugman has proposed a method for iris recognition, composed by four stages: segmentation, normalization, feature extraction, and matching. In this paper we propose some modifications and extensions to Daugman's method to cope with noisy images. These modifications are proposed after a study of images of CASIA and UBIRIS databases. The major modification is on the computationally demanding segmentation stage, for which we propose a faster and equally accurate template matching approach. The extensions on the algorithm address the important issue of pre-processing, that depends on the image database, being mandatory when we have a non infra-red camera, like a typical WebCam. For this scenario, we propose methods for reflection removal and pupil enhancement and isolation. The tests, carried out by our C# application on grayscale CASIA and UBIRIS images, show that the template matching segmentation method is more accurate and faster than the previous one, for noisy images. The proposed algorithms are found to be efficient and necessary when we deal with non infra-red images and non uniform illumination.

  18. A Facile Three-Component One-Pot Synthesis of Structurally Constrained Tetrahydrofurans, Which Are t-RNA Synthetase Inhibitor Analogues

    Institute of Scientific and Technical Information of China (English)

    LU,Chong-Dao; CHEN,Zhi-Yong; HU,Wen-Hao; MI,Ai-Qiao


    @@ A one-pot procedure for the efficient synthesis of a small library of t-RNA inhibitor analogues was developed. Thus,Rh2(OAc)4 catalyzed three-component 1,3-dipolar cycloaddition reactions of carbonyl ylides derived from diazoindan-1,3-dione and aldehydes with other dipolarophiles in 1,1,2,2-tetrachloroethane at 80 ℃ gave ring fused tetrahydrofurans having three stereocenters in good yield.

  19. Secondary structure and feature of mitochondrial tRNA genes of the Ussurian tube-nosed bat Murina ussuriensis (Chiroptera: Vespertilionidae

    Directory of Open Access Journals (Sweden)

    Kwang Bae Yoon


    Full Text Available The complete mitogenome (NC_021119 of the Ussurian tube-nosed bat Murina ussuriensis (Chiroptera: Vespertilionidae was annotated and characterized in our recent publication ( Here we provide additional information on methods in detail for obtaining the complete sequence of M. ussuriensis mitogenome. In addition, we describe characteristics of 22 tRNA genes and secondary structure and feature of 22 tRNAs of M. ussuriensis mitogenome.

  20. Defective i6A37 modification of mitochondrial and cytosolic tRNAs results from pathogenic mutations in TRIT1 and its substrate tRNA. (United States)

    Yarham, John W; Lamichhane, Tek N; Pyle, Angela; Mattijssen, Sandy; Baruffini, Enrico; Bruni, Francesco; Donnini, Claudia; Vassilev, Alex; He, Langping; Blakely, Emma L; Griffin, Helen; Santibanez-Koref, Mauro; Bindoff, Laurence A; Ferrero, Ileana; Chinnery, Patrick F; McFarland, Robert; Maraia, Richard J; Taylor, Robert W


    Identifying the genetic basis for mitochondrial diseases is technically challenging given the size of the mitochondrial proteome and the heterogeneity of disease presentations. Using next-generation exome sequencing, we identified in a patient with severe combined mitochondrial respiratory chain defects and corresponding perturbation in mitochondrial protein synthesis, a homozygous p.Arg323Gln mutation in TRIT1. This gene encodes human tRNA isopentenyltransferase, which is responsible for i6A37 modification of the anticodon loops of a small subset of cytosolic and mitochondrial tRNAs. Deficiency of i6A37 was previously shown in yeast to decrease translational efficiency and fidelity in a codon-specific manner. Modelling of the p.Arg323Gln mutation on the co-crystal structure of the homologous yeast isopentenyltransferase bound to a substrate tRNA, indicates that it is one of a series of adjacent basic side chains that interact with the tRNA backbone of the anticodon stem, somewhat removed from the catalytic center. We show that patient cells bearing the p.Arg323Gln TRIT1 mutation are severely deficient in i6A37 in both cytosolic and mitochondrial tRNAs. Complete complementation of the i6A37 deficiency of both cytosolic and mitochondrial tRNAs was achieved by transduction of patient fibroblasts with wild-type TRIT1. Moreover, we show that a previously-reported pathogenic m.7480A>G mt-tRNASer(UCN) mutation in the anticodon loop sequence A36A37A38 recognised by TRIT1 causes a loss of i6A37 modification. These data demonstrate that deficiencies of i6A37 tRNA modification should be considered a potential mechanism of human disease caused by both nuclear gene and mitochondrial DNA mutations while providing insight into the structure and function of TRIT1 in the modification of cytosolic and mitochondrial tRNAs.

  1. Defective i6A37 modification of mitochondrial and cytosolic tRNAs results from pathogenic mutations in TRIT1 and its substrate tRNA.

    Directory of Open Access Journals (Sweden)

    John W Yarham


    Full Text Available Identifying the genetic basis for mitochondrial diseases is technically challenging given the size of the mitochondrial proteome and the heterogeneity of disease presentations. Using next-generation exome sequencing, we identified in a patient with severe combined mitochondrial respiratory chain defects and corresponding perturbation in mitochondrial protein synthesis, a homozygous p.Arg323Gln mutation in TRIT1. This gene encodes human tRNA isopentenyltransferase, which is responsible for i6A37 modification of the anticodon loops of a small subset of cytosolic and mitochondrial tRNAs. Deficiency of i6A37 was previously shown in yeast to decrease translational efficiency and fidelity in a codon-specific manner. Modelling of the p.Arg323Gln mutation on the co-crystal structure of the homologous yeast isopentenyltransferase bound to a substrate tRNA, indicates that it is one of a series of adjacent basic side chains that interact with the tRNA backbone of the anticodon stem, somewhat removed from the catalytic center. We show that patient cells bearing the p.Arg323Gln TRIT1 mutation are severely deficient in i6A37 in both cytosolic and mitochondrial tRNAs. Complete complementation of the i6A37 deficiency of both cytosolic and mitochondrial tRNAs was achieved by transduction of patient fibroblasts with wild-type TRIT1. Moreover, we show that a previously-reported pathogenic m.7480A>G mt-tRNASer(UCN mutation in the anticodon loop sequence A36A37A38 recognised by TRIT1 causes a loss of i6A37 modification. These data demonstrate that deficiencies of i6A37 tRNA modification should be considered a potential mechanism of human disease caused by both nuclear gene and mitochondrial DNA mutations while providing insight into the structure and function of TRIT1 in the modification of cytosolic and mitochondrial tRNAs.

  2. A new method of edge detection for object recognition (United States)

    Maddox, Brian G.; Rhew, Benjamin


    Traditional edge detection systems function by returning every edge in an input image. This can result in a large amount of clutter and make certain vectorization algorithms less accurate. Accuracy problems can then have a large impact on automated object recognition systems that depend on edge information. A new method of directed edge detection can be used to limit the number of edges returned based on a particular feature. This results in a cleaner image that is easier for vectorization. Vectorized edges from this process could then feed an object recognition system where the edge data would also contain information as to what type of feature it bordered.

  3. Identification and sequence analysis of metazoan tRNA 3'-end processing enzymes tRNase Zs.

    Directory of Open Access Journals (Sweden)

    Zhikang Wang

    Full Text Available tRNase Z is the endonuclease responsible for removing the 3'-trailer sequences from precursor tRNAs, a prerequisite for the addition of the CCA sequence. It occurs in the short (tRNase Z(S and long (tRNase Z(L forms. Here we report the identification and sequence analysis of candidate tRNase Zs from 81 metazoan species. We found that the vast majority of deuterostomes, lophotrochozoans and lower metazoans have one tRNase Z(S and one tRNase Z(L genes, whereas ecdysozoans possess only a single tRNase Z(L gene. Sequence analysis revealed that in metazoans, a single nuclear tRNase Z(L gene is likely to encode both the nuclear and mitochondrial forms of tRNA 3'-end processing enzyme through mechanisms that include alternative translation initiation from two in-frame start codons and alternative splicing. Sequence conservation analysis revealed a variant PxKxRN motif, PxPxRG, which is located in the N-terminal region of tRNase Z(Ss. We also identified a previously unappreciated motif, AxDx, present in the C-terminal region of both tRNase Z(Ss and tRNase Z(Ls. The AxDx motif consisting mainly of a very short loop is potentially close enough to form hydrogen bonds with the loop containing the PxKxRN or PxPxRG motif. Through complementation analysis, we demonstrated the likely functional importance of the AxDx motif. In conclusion, our analysis supports the notion that in metazoans a single tRNase Z(L has evolved to participate in both nuclear and mitochondrial tRNA 3'-end processing, whereas tRNase Z(S may have evolved new functions. Our analysis also unveils new evolutionarily conserved motifs in tRNase Zs, including the C-terminal AxDx motif, which may have functional significance.

  4. A tRNA body with high affinity for EF-Tu hastens ribosomal incorporation of unnatural amino acids. (United States)

    Ieong, Ka-Weng; Pavlov, Michael Y; Kwiatkowski, Marek; Ehrenberg, Måns; Forster, Anthony C


    There is evidence that tRNA bodies have evolved to reduce differences between aminoacyl-tRNAs in their affinity to EF-Tu. Here, we study the kinetics of incorporation of L-amino acids (AAs) Phe, Ala allyl-glycine (aG), methyl-serine (mS), and biotinyl-lysine (bK) using a tRNA(Ala)-based body (tRNA(AlaB)) with a high affinity for EF-Tu. Results are compared with previous data on the kinetics of incorporation of the same AAs using a tRNA(PheB) body with a comparatively low affinity for EF-Tu. All incorporations exhibited fast and slow phases, reflecting the equilibrium fraction of AA-tRNA in active ternary complex with EF-Tu:GTP before the incorporation reaction. Increasing the concentration of EF-Tu increased the amplitude of the fast phase and left its rate unaltered. This allowed estimation of the affinity of each AA-tRNA to EF-Tu:GTP during translation, showing about a 10-fold higher EF-Tu affinity for AA-tRNAs formed from the tRNA(AlaB) body than from the tRNA(PheB) body. At ∼1 µM EF-Tu, tRNA(AlaB) conferred considerably faster incorporation kinetics than tRNA(PheB), especially in the case of the bulky bK. In contrast, the swap to the tRNA(AlaB) body did not increase the fast phase fraction of N-methyl-Phe incorporation, suggesting that the slow incorporation of N-methyl-Phe had a different cause than low EF-Tu:GTP affinity. The total time for AA-tRNA release from EF-Tu:GDP, accommodation, and peptidyl transfer on the ribosome was similar for the tRNA(AlaB) and tRNA(PheB) bodies. We conclude that a tRNA body with high EF-Tu affinity can greatly improve incorporation of unnatural AAs in a potentially generalizable manner.

  5. Non-Conserved Residues in Clostridium acetobutylicum tRNAAla Contribute to tRNA Tuning for Efficient Antitermination of the alaS T Box Riboswitch

    Directory of Open Access Journals (Sweden)

    Liang-Chun Liu


    Full Text Available The T box riboswitch regulates expression of amino acid-related genes in Gram-positive bacteria by monitoring the aminoacylation status of a specific tRNA, the binding of which affects the folding of the riboswitch into mutually exclusive terminator or antiterminator structures. Two main pairing interactions between the tRNA and the leader RNA have been demonstrated to be necessary, but not sufficient, for efficient antitermination. In this study, we used the Clostridium acetobutylicum alaS gene, which encodes alanyl-tRNA synthetase, to investigate the specificity of the tRNA response. We show that the homologous C. acetobutylicum tRNAAla directs antitermination of the C. acetobutylicum alaS gene in vitro, but the heterologous Bacillus subtilis tRNAAla (with the same anticodon and acceptor end does not. Base substitutions at positions that vary between these two tRNAs revealed synergistic and antagonistic effects. Variation occurs primarily at positions that are not conserved in tRNAAla species, which indicates that these non-conserved residues contribute to optimal antitermination of the homologous alaS gene. This study suggests that elements in tRNAAla may have coevolved with the homologous alaS T box leader RNA for efficient antitermination.

  6. A model for mis-sense error in protein synthesis: mis-charged cognate tRNA versus mis-reading of codon

    CERN Document Server

    Dutta, Annwesha


    The sequence of amino acid monomers in the primary structure of protein is decided by the corresponding sequence of codons (triplets of nucleic acid monomers) on the template messenger RNA (mRNA). The polymerization of a protein, by incorporation of the successive amino acid monomers, is carried out by a molecular machine called ribosome. Transfer RNA (tRNA) molecules, each species of which is "charged" with a specific amino acid, enters the ribosome and participates in the reading of the codon by the ribosome. Both mis-reading of mRNA codon and prior mis-charging of a tRNA can lead to "mis-sense" error, i.e,. erroneous substitution of a correct amino acid monomer by an incorrect one during the synthesis of a protein. We develop a theoretical model of protein synthesis that allows for both types of contributions to the "mis-sense" error. We report exact analytical formulae for several quantities that characterize the interplay of mis-charging of tRNA and mis-reading of mRNA. The average rate of elongation of ...

  7. A Neuromorphic System for Video Object Recognition

    Directory of Open Access Journals (Sweden)

    Deepak eKhosla


    Full Text Available Automated video object recognition is a topic of emerging importance in both defense and civilian applications. This work describes an accurate and low-power neuromorphic architecture and system for real-time automated video object recognition. Our system, Neuormorphic Visual Understanding of Scenes (NEOVUS, is inspired by recent findings in computational neuroscience on feed-forward object detection and classification pipelines for processing and extracting relevant information from visual data. The NEOVUS architecture is inspired by the ventral (what and dorsal (where streams of the mammalian visual pathway and combines retinal processing, form-based and motion-based object detection, and convolutional neural nets based object classification. Our system was evaluated by the Defense Advanced Research Projects Agency (DARPA under the NEOVISION2 program on a variety of urban area video datasets collected from both stationary and moving platforms. The datasets are challenging as they include a large number of targets in cluttered scenes with varying illumination and occlusion conditions. The NEOVUS system was also mapped to commercially available off-the-shelf hardware. The dynamic power requirement for the system that includes a 5.6Mpixel retinal camera processed by object detection and classification algorithms at 30 frames per second was measured at 21.7 Watts (W, for an effective energy consumption of 5.4 nanoJoules (nJ per bit of incoming video. In a systematic evaluation of five different teams by DARPA on three aerial datasets, the NEOVUS demonstrated the best performance with the highest recognition accuracy and at least three orders of magnitude lower energy consumption than two independent state of the art computer vision systems. These unprecedented results show that the NEOVUS has the potential to revolutionize automated video object recognition towards enabling practical low-power and mobile video processing applications.

  8. Hypnotizability and haptics: visual recognition of unimanually explored 'nonmeaningful' objects. (United States)

    Castellani, E; Carli, G; Santarcangelo, E L


    The cognitive trait of hypnotizability modulates sensorimotor integration and mental imagery. In particular, earlier results show that visual recognition of 'nonmeaningful', unfamiliar objects bimanually explored is faster and more accurate in subjects with high (Highs) than with low hypnotizability (Lows). The present study was aimed at investigating whether Highs exhibit a similar advantage after unimanual exploration. Recognition frequency (RF) and Recognition time (RT) of correct recognitions of the explored objects were recorded. The results showed the absence of any hypnotizability-related difference in recognition frequencies. In addition, RF of the right and left hand was comparable in Highs as in Lows, while slight differences were found in RT. We suggest that hemispheric co-operation played a key role in the better performance of Highs in the bimanual task previously studied. In the unimanual exploration, the task's characteristics (favoring the left hand), hypnotizability-related cerebral asymmetry (favoring the right hand in Highs) and the possible preferential verbal style of recognition in Lows (favoring the right hand in this group) antagonize each other and prevent the occurrence of major differences between the performance of Highs and Lows.

  9. A Survey on Banknote Recognition Methods by Various Sensors. (United States)

    Lee, Ji Woo; Hong, Hyung Gil; Kim, Ki Wan; Park, Kang Ryoung


    Despite a decrease in the use of currency due to the recent growth in the use of electronic financial transactions, real money transactions remain very important in the global market. While performing transactions with real money, touching and counting notes by hand, is still a common practice in daily life, various types of automated machines, such as ATMs and banknote counters, are essential for large-scale and safe transactions. This paper presents studies that have been conducted in four major areas of research (banknote recognition, counterfeit banknote detection, serial number recognition, and fitness classification) in the accurate banknote recognition field by various sensors in such automated machines, and describes the advantages and drawbacks of the methods presented in those studies. While to a limited extent some surveys have been presented in previous studies in the areas of banknote recognition or counterfeit banknote recognition, this paper is the first of its kind to review all four areas. Techniques used in each of the four areas recognize banknote information (denomination, serial number, authenticity, and physical condition) based on image or sensor data, and are actually applied to banknote processing machines across the world. This study also describes the technological challenges faced by such banknote recognition techniques and presents future directions of research to overcome them.

  10. Facial Expression Recognition Using Stationary Wavelet Transform Features

    Directory of Open Access Journals (Sweden)

    Huma Qayyum


    Full Text Available Humans use facial expressions to convey personal feelings. Facial expressions need to be automatically recognized to design control and interactive applications. Feature extraction in an accurate manner is one of the key steps in automatic facial expression recognition system. Current frequency domain facial expression recognition systems have not fully utilized the facial elements and muscle movements for recognition. In this paper, stationary wavelet transform is used to extract features for facial expression recognition due to its good localization characteristics, in both spectral and spatial domains. More specifically a combination of horizontal and vertical subbands of stationary wavelet transform is used as these subbands contain muscle movement information for majority of the facial expressions. Feature dimensionality is further reduced by applying discrete cosine transform on these subbands. The selected features are then passed into feed forward neural network that is trained through back propagation algorithm. An average recognition rate of 98.83% and 96.61% is achieved for JAFFE and CK+ dataset, respectively. An accuracy of 94.28% is achieved for MS-Kinect dataset that is locally recorded. It has been observed that the proposed technique is very promising for facial expression recognition when compared to other state-of-the-art techniques.

  11. Cross-person activity recognition using reduced kernel extreme learning machine. (United States)

    Deng, Wan-Yu; Zheng, Qing-Hua; Wang, Zhong-Min


    Activity recognition based on mobile embedded accelerometer is very important for developing human-centric pervasive applications such as healthcare, personalized recommendation and so on. However, the distribution of accelerometer data is heavily affected by varying users. The performance will degrade when the model trained on one person is used to others. To solve this problem, we propose a fast and accurate cross-person activity recognition model, known as TransRKELM (Transfer learning Reduced Kernel Extreme Learning Machine) which uses RKELM (Reduced Kernel Extreme Learning Machine) to realize initial activity recognition model. In the online phase OS-RKELM (Online Sequential Reduced Kernel Extreme Learning Machine) is applied to update the initial model and adapt the recognition model to new device users based on recognition results with high confidence level efficiently. Experimental results show that, the proposed model can adapt the classifier to new device users quickly and obtain good recognition performance.

  12. Vision-based posture recognition using an ensemble classifier and a vote filter (United States)

    Ji, Peng; Wu, Changcheng; Xu, Xiaonong; Song, Aiguo; Li, Huijun


    Posture recognition is a very important Human-Robot Interaction (HRI) way. To segment effective posture from an image, we propose an improved region grow algorithm which combining with the Single Gauss Color Model. The experiment shows that the improved region grow algorithm can get the complete and accurate posture than traditional Single Gauss Model and region grow algorithm, and it can eliminate the similar region from the background at the same time. In the posture recognition part, and in order to improve the recognition rate, we propose a CNN ensemble classifier, and in order to reduce the misjudgments during a continuous gesture control, a vote filter is proposed and applied to the sequence of recognition results. Comparing with CNN classifier, the CNN ensemble classifier we proposed can yield a 96.27% recognition rate, which is better than that of CNN classifier, and the proposed vote filter can improve the recognition result and reduce the misjudgments during the consecutive gesture switch.

  13. Laboratory Building for Accurate Determination of Plutonium

    Institute of Scientific and Technical Information of China (English)


    <正>The accurate determination of plutonium is one of the most important assay techniques of nuclear fuel, also the key of the chemical measurement transfer and the base of the nuclear material balance. An

  14. Understanding the Code: keeping accurate records. (United States)

    Griffith, Richard


    In his continuing series looking at the legal and professional implications of the Nursing and Midwifery Council's revised Code of Conduct, Richard Griffith discusses the elements of accurate record keeping under Standard 10 of the Code. This article considers the importance of accurate record keeping for the safety of patients and protection of district nurses. The legal implications of records are explained along with how district nurses should write records to ensure these legal requirements are met.

  15. Visual affect recognition

    CERN Document Server

    Stathopoulou, I-O


    It is generally known that human faces, as well as body motions and gestures, provide a wealth of information about a person, such as age, race, sex and emotional state. This monograph primarily studies the perception of facial expression of emotion, and secondarily of motion and gestures, with the purpose of developing a fully automated visual affect recognition system for use in modes of human/computer interaction. The book begins with a survey of the literature on emotion perception, followed by a description of empirical studies conducted with human participants and the construction of a '

  16. Advances in Speech Recognition

    CERN Document Server

    Neustein, Amy


    This volume is comprised of contributions from eminent leaders in the speech industry, and presents a comprehensive and in depth analysis of the progress of speech technology in the topical areas of mobile settings, healthcare and call centers. The material addresses the technical aspects of voice technology within the framework of societal needs, such as the use of speech recognition software to produce up-to-date electronic health records, not withstanding patients making changes to health plans and physicians. Included will be discussion of speech engineering, linguistics, human factors ana

  17. Recent progress in fingerprint recognition

    Institute of Scientific and Technical Information of China (English)


    Fingerprint recognition has been increasingly used to realize personal identification in civilian's daily life, such as ID card, fingerprints hard disk and so on. Great improvement has been achieved in the on-line fingerprint sensing technology and automatic fingerprint recognition algorithms. Various fingerprint recognition techniques, including fingerprint acquisition, classification, enhancement and matching, are highly improved. This paper overviews recent advances in fingerprint recognition and summarizes the algorithm proposed for every step with special focuses on the enhancement of low-quality fingerprints and the matching of the distorted fingerprint images. Both issues are believed to be significant and challenging tasks. In addition, we also discuss the common evaluation for the fingerprint recognition algorithm of the Fingerprint Verification Competition 2004 (FVC2004) and the Fingerprint Vendor Technology Evaluation 2003 (FpVTE2003), based on which we could measure the performance of the recognition algorithm objectively and uniformly.

  18. Human activity recognition and prediction

    CERN Document Server


    This book provides a unique view of human activity recognition, especially fine-grained human activity structure learning, human-interaction recognition, RGB-D data based action recognition, temporal decomposition, and causality learning in unconstrained human activity videos. The techniques discussed give readers tools that provide a significant improvement over existing methodologies of video content understanding by taking advantage of activity recognition. It links multiple popular research fields in computer vision, machine learning, human-centered computing, human-computer interaction, image classification, and pattern recognition. In addition, the book includes several key chapters covering multiple emerging topics in the field. Contributed by top experts and practitioners, the chapters present key topics from different angles and blend both methodology and application, composing a solid overview of the human activity recognition techniques. .

  19. [Comparative studies of face recognition]. (United States)

    Kawai, Nobuyuki


    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. (United States)

    Shakeshaft, Nicholas G; Plomin, Robert


    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. Structure-function relations in the NTPase domain of the antiviral tRNA ribotoxin Escherichia coli PrrC

    Energy Technology Data Exchange (ETDEWEB)

    Meineke, Birthe; Shuman, Stewart, E-mail:


    Breakage of tRNA by Escherichia coli anticodon nuclease PrrC (EcoPrrC) underlies a host antiviral response to phage T4 infection. Expression of EcoPrrC is cytocidal in yeast, signifying that PrrC ribotoxicity crosses phylogenetic domain boundaries. EcoPrrC consists of an N-terminal NTPase module that resembles ABC transporters and a C-terminal nuclease module that is sui generis. PrrC homologs are prevalent in many other bacteria. Here we report that Haemophilus influenzae PrrC is toxic in E. coli and yeast. To illuminate structure-activity relations, we conducted a new round of mutational analysis of EcoPrrC guided by primary structure conservation among toxic PrrC homologs. We indentify 17 candidate active site residues in the NTPase module that are essential for toxicity in yeast when EcoPrrC is expressed at high gene dosage. Their functions could be educed by integrating mutational data with the atomic structure of the transition-state complex of a homologous ABC protein.

  2. Evolutionary Limitation and Opportunities for Developing tRNA Synthetase Inhibitors with 5-Binding-Mode Classification

    Directory of Open Access Journals (Sweden)

    Pengfei Fang


    Full Text Available Aminoacyl-tRNA synthetases (aaRSs are enzymes that catalyze the transfer of amino acids to their cognate tRNAs as building blocks for translation. Each of the aaRS families plays a pivotal role in protein biosynthesis and is indispensable for cell growth and survival. In addition, aaRSs in higher species have evolved important non-translational functions. These translational and non-translational functions of aaRS are attractive for developing antibacterial, antifungal, and antiparasitic agents and for treating other human diseases. The interplay between amino acids, tRNA, ATP, EF-Tu and non-canonical binding partners, had shaped each family with distinct pattern of key sites for regulation, with characters varying among species across the path of evolution. These sporadic variations in the aaRSs offer great opportunity to target these essential enzymes for therapy. Up to this day, growing numbers of aaRS inhibitors have been discovered and developed. Here, we summarize the latest developments and structural studies of aaRS inhibitors, and classify them with distinct binding modes into five categories.

  3. Mitochondrial 16S rRNA Is Methylated by tRNA Methyltransferase TRMT61B in All Vertebrates (United States)

    Bar-Yaacov, Dan; Frumkin, Idan; Yashiro, Yuka; Schlesinger, Orr; Bieri, Philipp; Greber, Basil; Ban, Nenad; Zarivach, Raz; Alfonta, Lital; Pilpel, Yitzhak; Suzuki, Tsutomu; Mishmar, Dan


    The mitochondrial ribosome, which translates all mitochondrial DNA (mtDNA)-encoded proteins, should be tightly regulated pre- and post-transcriptionally. Recently, we found RNA-DNA differences (RDDs) at human mitochondrial 16S (large) rRNA position 947 that were indicative of post-transcriptional modification. Here, we show that these 16S rRNA RDDs result from a 1-methyladenosine (m1A) modification introduced by TRMT61B, thus being the first vertebrate methyltransferase that modifies both tRNA and rRNAs. m1A947 is conserved in humans and all vertebrates having adenine at the corresponding mtDNA position (90% of vertebrates). However, this mtDNA base is a thymine in 10% of the vertebrates and a guanine in the 23S rRNA of 95% of bacteria, suggesting alternative evolutionary solutions. m1A, uridine, or guanine may stabilize the local structure of mitochondrial and bacterial ribosomes. Experimental assessment of genome-edited Escherichia coli showed that unmodified adenine caused impaired protein synthesis and growth. Our findings revealed a conserved mechanism of rRNA modification that has been selected instead of DNA mutations to enable proper mitochondrial ribosome function. PMID:27631568

  4. Trade-offs between tRNA abundance and mRNA secondary structure support smoothing of translation elongation rate (United States)

    Gorochowski, Thomas E.; Ignatova, Zoya; Bovenberg, Roel A.L.; Roubos, Johannes A.


    Translation of protein from mRNA is a complex multi-step process that occurs at a non-uniform rate. Variability in ribosome speed along an mRNA enables refinement of the proteome and plays a critical role in protein biogenesis. Detailed single protein studies have found both tRNA abundance and mRNA secondary structure as key modulators of translation elongation rate, but recent genome-wide ribosome profiling experiments have not observed significant influence of either on translation efficiency. Here we provide evidence that this results from an inherent trade-off between these factors. We find codons pairing to high-abundance tRNAs are preferentially used in regions of high secondary structure content, while codons read by significantly less abundant tRNAs are located in lowly structured regions. By considering long stretches of high and low mRNA secondary structure in Saccharomyces cerevisiae and Escherichia coli and comparing them to randomized-gene models and experimental expression data, we were able to distinguish clear selective pressures and increased protein expression for specific codon choices. The trade-off between secondary structure and tRNA-concentration based codon choice allows for compensation of their independent effects on translation, helping to smooth overall translational speed and reducing the chance of potentially detrimental points of excessively slow or fast ribosome movement. PMID:25765653

  5. Speech recognition in university classrooms


    Wald, Mike; Bain, Keith; Basson, Sara H


    The LIBERATED LEARNING PROJECT (LLP) is an applied research project studying two core questions: 1) Can speech recognition (SR) technology successfully digitize lectures to display spoken words as text in university classrooms? 2) Can speech recognition technology be used successfully as an alternative to traditional classroom notetaking for persons with disabilities? This paper addresses these intriguing questions and explores the underlying complex relationship between speech recognition te...

  6. Pilgrims Face Recognition Dataset -- HUFRD


    Aly, Salah A.


    In this work, we define a new pilgrims face recognition dataset, called HUFRD dataset. The new developed dataset presents various pilgrims' images taken from outside the Holy Masjid El-Harram in Makkah during the 2011-2012 Hajj and Umrah seasons. Such dataset will be used to test our developed facial recognition and detection algorithms, as well as assess in the missing and found recognition system \\cite{crowdsensing}.

  7. Speech Recognition on Mobile Devices

    DEFF Research Database (Denmark)

    Tan, Zheng-Hua; Lindberg, Børge


    The enthusiasm of deploying automatic speech recognition (ASR) on mobile devices is driven both by remarkable advances in ASR technology and by the demand for efficient user interfaces on such devices as mobile phones and personal digital assistants (PDAs). This chapter presents an overview of ASR...... in the mobile context covering motivations, challenges, fundamental techniques and applications. Three ASR architectures are introduced: embedded speech recognition, distributed speech recognition and network speech recognition. Their pros and cons and implementation issues are discussed. Applications within...... command and control, text entry and search are presented with an emphasis on mobile text entry....

  8. Frequency-Based Fingerprint Recognition (United States)

    Aguilar, Gualberto; Sánchez, Gabriel; Toscano, Karina; Pérez, Héctor

    abstract Fingerprint recognition is one of the most popular methods used for identification with greater success degree. Fingerprint has unique characteristics called minutiae, which are points where a curve track ends, intersects, or branches off. In this chapter a fingerprint recognition method is proposed in which a combination of Fast Fourier Transform (FFT) and Gabor filters is used for image enhancement. A novel recognition stage using local features for recognition is also proposed. Also a verification stage is introduced to be used when the system output has more than one person.

  9. Markov Models for Handwriting Recognition

    CERN Document Server

    Plotz, Thomas


    Since their first inception, automatic reading systems have evolved substantially, yet the recognition of handwriting remains an open research problem due to its substantial variation in appearance. With the introduction of Markovian models to the field, a promising modeling and recognition paradigm was established for automatic handwriting recognition. However, no standard procedures for building Markov model-based recognizers have yet been established. This text provides a comprehensive overview of the application of Markov models in the field of handwriting recognition, covering both hidden

  10. Study of Face Recognition Techniques

    Directory of Open Access Journals (Sweden)

    Sangeeta Kaushik


    Full Text Available A study of both face recognition and detection techniques is carried out using the algorithms like Principal Component Analysis (PCA, Kernel Principal Component Analysis (KPCA, Linear Discriminant Analysis (LDA and Line Edge Map (LEM. These algorithms show different rates of accuracy under different conditions. The automatic recognition of human faces presents a challenge to the pattern recognition community. Typically, human faces are different in shapes with minor similarity from person to person. Furthermore, lighting condition changes, facial expressions and pose variations further complicate the face recognition task as one of the difficult problems in pattern analysis.

  11. Radically enhanced molecular recognition

    KAUST Repository

    Trabolsi, Ali


    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. © 2010 Macmillan Publishers Limited. All rights reserved.

  12. Can changes in eye movement scanning alter the age-related deficit in recognition memory?

    Directory of Open Access Journals (Sweden)

    Jessica P.K. Chan


    Full Text Available Older adults typically exhibit poorer face recognition compared to younger adults. These recognition differences may be due to underlying age-related changes in eye movement scanning. We examined whether older adults’ recognition could be improved by yoking their eye movements to those of younger adults. Participants studied younger and older faces, under free viewing conditions (bases, through a gaze-contingent moving window (own, or a moving window which replayed the eye movements of a base participant (yoked. During the recognition test, participants freely viewed the faces with no viewing restrictions. Own-age recognition biases were observed for older adults in all viewing conditions, suggesting that this effect occurs independently of scanning. Participants in the bases condition had the highest recognition accuracy, and participants in the yoked condition were more accurate than participants in the own condition. Among yoked participants, recognition did not depend on age of the base participant. These results suggest that successful encoding for all participants requires the bottom-up contribution of peripheral information, regardless of the locus of control of the viewer. Although altering the pattern of eye movements did not increase recognition, the amount of sampling of the face during encoding predicted subsequent recognition accuracy for all participants. Increased sampling may confer some advantages for subsequent recognition, particularly for people who have declining memory abilities.

  13. Reactive sulfur species regulate tRNA methylthiolation and contribute to insulin secretion. (United States)

    Takahashi, Nozomu; Wei, Fan-Yan; Watanabe, Sayaka; Hirayama, Mayumi; Ohuchi, Yuya; Fujimura, Atsushi; Kaitsuka, Taku; Ishii, Isao; Sawa, Tomohiro; Nakayama, Hideki; Akaike, Takaaki; Tomizawa, Kazuhito


    The 2-methylthio (ms(2)) modification at A37 of tRNAs is critical for accurate decoding, and contributes to metabolic homeostasis in mammals. However, the regulatory mechanism of ms(2) modification remains largely unknown. Here, we report that cysteine hydropersulfide (CysSSH), a newly identified reactive sulfur species, is involved in ms(2) modification in cells. The suppression of intracellular CysSSH production rapidly reduced ms(2) modification, which was rescued by the application of an exogenous CysSSH donor. Using a unique and stable isotope-labeled CysSSH donor, we show that CysSSH was capable of specifically transferring its reactive sulfur atom to the cysteine residues of ms(2)-modifying enzymes as well as ms(2) modification. Furthermore, the suppression of CysSSH production impaired insulin secretion and caused glucose intolerance in both a pancreatic β-cell line and mouse model. These results demonstrate that intracellular CysSSH is a novel sulfur source for ms(2) modification, and that it contributes to insulin secretion.

  14. A Spatial Frequency Account of the Detriment that Local Processing of Navon Letters Has on Face Recognition (United States)

    Hills, Peter J.; Lewis, Michael B.


    Five minutes of processing the local features of a Navon letter causes a detriment in subsequent face-recognition performance (Macrae & Lewis, 2002). We hypothesize a perceptual after effect explanation of this effect in which face recognition is less accurate after adapting to high-spatial frequencies at high contrasts. Five experiments were…

  15. Mandarin Digits Speech Recognition Using Support Vector Machines

    Institute of Scientific and Technical Information of China (English)

    XIE Xiang; KUANG Jing-ming


    A method of applying support vector machine (SVM) in speech recognition was proposed, and a speech recognition system for mandarin digits was built up by SVMs. In the system, vectors were linearly extracted from speech feature sequence to make up time-aligned input patterns for SVM, and the decisions of several 2-class SVM classifiers were employed for constructing an N-class classifier. Four kinds of SVM kernel functions were compared in the experiments of speaker-independent speech recognition of mandarin digits. And the kernel of radial basis function has the highest accurate rate of 99.33%, which is better than that of the baseline system based on hidden Markov models (HMM) (97.08%). And the experiments also show that SVM can outperform HMM especially when the samples for learning were very limited.

  16. Unaware person recognition from the body when face identification fails. (United States)

    Rice, Allyson; Phillips, P Jonathon; Natu, Vaidehi; An, Xiaobo; O'Toole, Alice J


    How does one recognize a person when face identification fails? Here, we show that people rely on the body but are unaware of doing so. State-of-the-art face-recognition algorithms were used to select images of people with almost no useful identity information in the face. Recognition of the face alone in these cases was near chance level, but recognition of the person was accurate. Accuracy in identifying the person without the face was identical to that in identifying the whole person. Paradoxically, people reported relying heavily on facial features over noninternal face and body features in making their identity decisions. Eye movements indicated otherwise, with gaze duration and fixations shifting adaptively toward the body and away from the face when the body was a better indicator of identity than the face. This shift occurred with no cost to accuracy or response time. Human identity processing may be partially inaccessible to conscious awareness.

  17. Weakly Supervised Recognition of Daily Life Activities with Wearable Sensors. (United States)

    Stikic, Maja; Larlus, Diane; Ebert, Sandra; Schiele, Bernt


    This paper considers scalable and unobtrusive activity recognition using on-body sensing for context awareness in wearable computing. Common methods for activity recognition rely on supervised learning requiring substantial amounts of labeled training data. Obtaining accurate and detailed annotations of activities is challenging, preventing the applicability of these approaches in real-world settings. This paper proposes new annotation strategies that substantially reduce the required amount of annotation. We explore two learning schemes for activity recognition that effectively leverage such sparsely labeled data together with more easily obtainable unlabeled data. Experimental results on two public data sets indicate that both approaches obtain results close to fully supervised techniques. The proposed methods are robust to the presence of erroneous labels occurring in real-world annotation data.

  18. A Random Forest-based ensemble method for activity recognition. (United States)

    Feng, Zengtao; Mo, Lingfei; Li, Meng


    This paper presents a multi-sensor ensemble approach to human physical activity (PA) recognition, using random forest. We designed an ensemble learning algorithm, which integrates several independent Random Forest classifiers based on different sensor feature sets to build a more stable, more accurate and faster classifier for human activity recognition. To evaluate the algorithm, PA data collected from the PAMAP (Physical Activity Monitoring for Aging People), which is a standard, publicly available database, was utilized to train and test. The experimental results show that the algorithm is able to correctly recognize 19 PA types with an accuracy of 93.44%, while the training is faster than others. The ensemble classifier system based on the RF (Random Forest) algorithm can achieve high recognition accuracy and fast calculation.

  19. Bus Passenger Recognition and Track of Video Sequence

    Directory of Open Access Journals (Sweden)

    Donghua Zhou


    Full Text Available Study on bus passenger recognition and track of video sequence is a research aiming at realizing making a statistics on passenger flow volume of bus, which not only helps traffic services center rationally schedule vehicles, but also can avoid overload. The system makes machine vision technology and digital image processing technique applied in customer counting of bus. The key questions in the study include effective collection of video image, effective extraction of moving object in sequence images, recognition of moving targets, trace and count of moving objects. The paper makes deep analysis on relevant technology from the perspective of the theory and practical application of the algorithm, and the study makes achievements. The theoretical algorithm for the study on bus passenger recognition and track of video sequence is distinctive. The practical experiments indicate that the system can satisfy the real-time requirements, and can accurately make statistics on the number of passengers, which has great application value.

  20. Utp22p acts in concert with Utp8p to channel aminoacyl-tRNA from the nucleolus to the nuclear tRNA export receptor Los1p but not Msn5p. (United States)

    Eswara, Manoja B K; Clayton, Ashley; Mangroo, Dev


    Utp8p is an essential nucleolar protein that channels aminoacyl-tRNAs from aminoacyl-tRNA synthetases in the nucleolus to the nuclear tRNA export receptors located in the nucleoplasm and nuclear pore complex in Saccharomyces cerevisiae. Utp8p is also part of the U3 snoRNA-associated protein complex involved in 18S rRNA biogenesis in the nucleolus. We report that Utp22p, which is another member of the U3 snoRNA-associated protein complex, is also an intranuclear component of the nuclear tRNA export machinery. Depletion of Utp22p results in nuclear retention of mature tRNAs derived from intron-containing and intronless precursors. Moreover, Utp22p copurifies with the nuclear tRNA export receptor Los1p, the aminoacyl-tRNA synthetase Tys1p and Utp8p, but not with the RanGTPase Gsp1p and the nuclear tRNA export receptor Msn5p. Utp22p interacts directly with Utp8p and Los1p in a tRNA-independent manner in vitro. Utp22p also interacts directly with Tys1p, but this binding is stimulated when Tys1p is bound to tRNA. However, Utp22p, unlike Utp8p, does not bind tRNA saturably. These data suggest that Utp22p recruits Utp8p to aminoacyl-tRNA synthetases in the nucleolus to collect aminoacyl-tRNA and then accompanies the Utp8p-tRNA complex to deliver the aminoacyl-tRNAs to Los1p but not Msn5p. It is possible that Nrap/Nol6, the mammalian orthologue of Utp22p, plays a role in channelling aminoacyl-tRNA to the nuclear tRNA export receptor exportin-t.

  1. The Legal Recognition of Sign Languages (United States)

    De Meulder, Maartje


    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…

  2. Accurate tracking control in LOM application

    Institute of Scientific and Technical Information of China (English)


    The fabrication of accurate prototype from CAD model directly in short time depends on the accurate tracking control and reference trajectory planning in (Laminated Object Manufacture) LOM application. An improvement on contour accuracy is acquired by the introduction of a tracking controller and a trajectory generation policy. A model of the X-Y positioning system of LOM machine is developed as the design basis of tracking controller. The ZPETC (Zero Phase Error Tracking Controller) is used to eliminate single axis following error, thus reduce the contour error. The simulation is developed on a Maltab model based on a retrofitted LOM machine and the satisfied result is acquired.

  3. Iris Recognition Using Wavelet

    Directory of Open Access Journals (Sweden)

    Khaliq Masood


    Full Text Available Biometric systems are getting more attention in the present era. Iris recognition is one of the most secure and authentic among the other biometrics and this field demands more authentic, reliable and fast algorithms to implement these biometric systems in real time. In this paper, an efficient localization technique is presented to identify pupil and iris boundaries using histogram of the iris image. Two small portions of iris have been used for polar transformation to reduce computational time and to increase the efficiency of the system. Wavelet transform is used for feature vector generation. Rotation of iris is compensated without shifts in the iris code. System is tested on Multimedia University Iris Database and results show that proposed system has encouraging performance.

  4. SAR: Stroke Authorship Recognition

    KAUST Repository

    Shaheen, Sara


    Are simple strokes unique to the artist or designer who renders them? If so, can this idea be used to identify authorship or to classify artistic drawings? Also, could training methods be devised to develop particular styles? To answer these questions, we propose the Stroke Authorship Recognition (SAR) approach, a novel method that distinguishes the authorship of 2D digitized drawings. SAR converts a drawing into a histogram of stroke attributes that is discriminative of authorship. We provide extensive classification experiments on a large variety of data sets, which validate SAR\\'s ability to distinguish unique authorship of artists and designers. We also demonstrate the usefulness of SAR in several applications including the detection of fraudulent sketches, the training and monitoring of artists in learning a particular new style and the first quantitative way to measure the quality of automatic sketch synthesis tools. © 2015 The Eurographics Association and John Wiley & Sons Ltd.

  5. Forensic Face Recognition: A Survey

    NARCIS (Netherlands)

    Ali, Tauseef; Veldhuis, Raymond; Spreeuwers, Luuk


    Beside a few papers which focus on the forensic aspects of automatic face recognition, there is not much published about it in contrast to the literature on developing new techniques and methodologies for biometric face recognition. In this report, we review forensic facial identification which is t

  6. Side-View Face Recognition

    NARCIS (Netherlands)

    Santemiz, Pinar; Spreeuwers, Luuk J.; Veldhuis, Raymond N.J.; Biggelaar , van den Olivier


    As a widely used biometrics, face recognition has many advantages such as being non-intrusive, natural and passive. On the other hand, in real-life scenarios with uncontrolled environment, pose variation up to side-view positions makes face recognition a challenging work. In this paper we discuss th

  7. Quantum-Limited Image Recognition (United States)


    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

  8. FILTWAM and Voice Emotion Recognition

    NARCIS (Netherlands)

    Bahreini, Kiavash; Nadolski, Rob; Westera, Wim


    This paper introduces the voice emotion recognition part of our framework for improving learning through webcams and microphones (FILTWAM). This framework enables multimodal emotion recognition of learners during game-based learning. The main goal of this study is to validate the use of microphone d

  9. Coordinate Transformations in Object Recognition (United States)

    Graf, Markus


    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…

  10. Study on Unequal Error Protection for Distributed Speech Recognition System

    Institute of Scientific and Technical Information of China (English)

    XIE Xiang; WANG Si-yao; LIU Jia-kang


    The unequal error protection (UEP) is applied in distributed speech recognition (DSR) system and three schemes are proposed. All of these three schemes are evaluated on the GSM simulating platform for recognizing mandarin digit strings and compared with the equal error protection (EEP) scheme. Experiments show that UEP can protect the data transmitted in DSR system more effectively, which results in a higher word accurate rate of DSR system.

  11. Geometric features for voxel-based surface recognition


    Yarotsky, Dmitry


    We introduce a library of geometric voxel features for CAD surface recognition/retrieval tasks. Our features include local versions of the intrinsic volumes (the usual 3D volume, surface area, integrated mean and Gaussian curvature) and a few closely related quantities. We also compute Haar wavelet and statistical distribution features by aggregating raw voxel features. We apply our features to object classification on the ESB data set and demonstrate accurate results with a small number of s...

  12. Pattern Recognition by Combined Invariants

    Institute of Scientific and Technical Information of China (English)

    WANG Xiaohong; ZHAO Rongchun


    A feature-based recognition of objectsor patterns independent of their position, size, orien-tation and other variations has been the goal of muchrecent research. The existing approaches to invarianttwo-dimensional pattern recognition are useless whenpattern is blurred. In this paper, we present a novelpattern recognition system which can solve the prob-lem by using combined invariants as image features.The classification technique we choose for our systemis weighted normalized cross correlation. The mean ofthe intraclass standard deviations of the kth featureover the total number of prototypes for each class isused as a weighting factor during the classification pro-cess to improve recognition accuracy. The feasibilityof our pattern recognition system and the invarianceof the combined features with respect to translation,scaling, rotation and blurring are approved by numer-ical experiments on head images.

  13. Online handwritten mathematical expression recognition (United States)

    Büyükbayrak, Hakan; Yanikoglu, Berrin; Erçil, Aytül


    We describe a system for recognizing online, handwritten mathematical expressions. The system is designed with a user-interface for writing scientific articles, supporting the recognition of basic mathematical expressions as well as integrals, summations, matrices etc. A feed-forward neural network recognizes symbols which are assumed to be single-stroke and a recursive algorithm parses the expression by combining neural network output and the structure of the expression. Preliminary results show that writer-dependent recognition rates are very high (99.8%) while writer-independent symbol recognition rates are lower (75%). The interface associated with the proposed system integrates the built-in recognition capabilities of the Microsoft's Tablet PC API for recognizing textual input and supports conversion of hand-drawn figures into PNG format. This enables the user to enter text, mathematics and draw figures in a single interface. After recognition, all output is combined into one LATEX code and compiled into a PDF file.

  14. Viewpoint Manifolds for Action Recognition

    Directory of Open Access Journals (Sweden)

    Souvenir Richard


    Full Text Available Abstract Action recognition from video is a problem that has many important applications to human motion analysis. In real-world settings, the viewpoint of the camera cannot always be fixed relative to the subject, so view-invariant action recognition methods are needed. Previous view-invariant methods use multiple cameras in both the training and testing phases of action recognition or require storing many examples of a single action from multiple viewpoints. In this paper, we present a framework for learning a compact representation of primitive actions (e.g., walk, punch, kick, sit that can be used for video obtained from a single camera for simultaneous action recognition and viewpoint estimation. Using our method, which models the low-dimensional structure of these actions relative to viewpoint, we show recognition rates on a publicly available dataset previously only achieved using multiple simultaneous views.

  15. Viewpoint Manifolds for Action Recognition

    Directory of Open Access Journals (Sweden)

    Richard Souvenir


    Full Text Available Action recognition from video is a problem that has many important applications to human motion analysis. In real-world settings, the viewpoint of the camera cannot always be fixed relative to the subject, so view-invariant action recognition methods are needed. Previous view-invariant methods use multiple cameras in both the training and testing phases of action recognition or require storing many examples of a single action from multiple viewpoints. In this paper, we present a framework for learning a compact representation of primitive actions (e.g., walk, punch, kick, sit that can be used for video obtained from a single camera for simultaneous action recognition and viewpoint estimation. Using our method, which models the low-dimensional structure of these actions relative to viewpoint, we show recognition rates on a publicly available dataset previously only achieved using multiple simultaneous views.

  16. Optimizing Face Recognition Using PCA

    Directory of Open Access Journals (Sweden)

    Manal Abdullah


    Full Text Available Principle Component Analysis PCA is a classical feature extraction and data representation technique widely used in pattern recognition. It is one of the most successful techniques in face recognition. But it has drawback of high computational especially for big size database. This paper conducts a study to optimize the time complexity of PCA (eigenfaces that does not affects the recognition performance. The authors minimize the participated eigenvectors which consequently decreases the computational time. A comparison is done to compare the differences between the recognition time in the original algorithm and in the enhanced algorithm. The performance of the original and the enhanced proposed algorithm is tested on face94 face database. Experimental results show that the recognition time is reduced by 35% by applying our proposed enhanced algorithm. DET Curves are used to illustrate the experimental results.

  17. Optimizing Face Recognition Using PCA

    Directory of Open Access Journals (Sweden)

    Manal Abdullah


    Full Text Available Principle Component Analysis PCA is a classical feature extraction and data representation technique widely used in pattern recognition. It is one of the most successful techniques in face recognition. But it has drawback of high computational especially for big size database. This paper conducts a study to optimize the time complexity of PCA (eigenfaces that does not affects the recognition performance. The authorsminimize the participated eigenvectors which consequently decreases the computational time. A comparison is done to compare the differences between the recognition time in the original algorithm and in the enhanced algorithm. The performance of the original and the enhanced proposed algorithm is tested on face94 face database. Experimental results show that the recognition time is reduced by 35% by applying our proposed enhanced algorithm. DET Curves are used to illustrate the experimental results.

  18. Accurate Switched-Voltage voltage averaging circuit


    金光, 一幸; 松本, 寛樹


    Abstract ###This paper proposes an accurate Switched-Voltage (SV) voltage averaging circuit. It is presented ###to compensated for NMOS missmatch error at MOS differential type voltage averaging circuit. ###The proposed circuit consists of a voltage averaging and a SV sample/hold (S/H) circuit. It can ###operate using nonoverlapping three phase clocks. Performance of this circuit is verified by PSpice ###simulations.

  19. Accurate overlaying for mobile augmented reality

    NARCIS (Netherlands)

    Pasman, W; van der Schaaf, A; Lagendijk, RL; Jansen, F.W.


    Mobile augmented reality requires accurate alignment of virtual information with objects visible in the real world. We describe a system for mobile communications to be developed to meet these strict alignment criteria using a combination of computer vision. inertial tracking and low-latency renderi

  20. Recognition memory impairments caused by false recognition of novel objects. (United States)

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


    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.

  1. Reconstitution and characterization of eukaryotic N6-threonylcarbamoylation of tRNA using a minimal enzyme system. (United States)

    Wan, Leo C K; Mao, Daniel Y L; Neculai, Dante; Strecker, Jonathan; Chiovitti, David; Kurinov, Igor; Poda, Gennadiy; Thevakumaran, Neroshan; Yuan, Fang; Szilard, Rachel K; Lissina, Elena; Nislow, Corey; Caudy, Amy A; Durocher, Daniel; Sicheri, Frank


    The universally conserved Kae1/Qri7/YgjD and Sua5/YrdC protein families have been implicated in growth, telomere homeostasis, transcription and the N6-threonylcarbamoylation (t(6)A) of tRNA, an essential modification required for translational fidelity by the ribosome. In bacteria, YgjD orthologues operate in concert with the bacterial-specific proteins YeaZ and YjeE, whereas in archaeal and eukaryotic systems, Kae1 operates as part of a larger macromolecular assembly called KEOPS with Bud32, Cgi121, Gon7 and Pcc1 subunits. Qri7 orthologues function in the mitochondria and may represent the most primitive member of the Kae1/Qri7/YgjD protein family. In accordance with previous findings, we confirm that Qri7 complements Kae1 function and uncover that Qri7 complements the function of all KEOPS subunits in growth, t(6)A biosynthesis and, to a partial degree, telomere maintenance. These observations suggest that Kae1 provides a core essential function that other subunits within KEOPS have evolved to support. Consistent with this inference, Qri7 alone is sufficient for t(6)A biosynthesis with Sua5 in vitro. In addition, the 2.9 Å crystal structure of Qri7 reveals a simple homodimer arrangement that is supplanted by the heterodimerization of YgjD with YeaZ in bacteria and heterodimerization of Kae1 with Pcc1 in KEOPS. The partial complementation of telomere maintenance by Qri7 hints that KEOPS has evolved novel functions in higher organisms.

  2. Cardiac abnormalities in diabetic patients with mutation in the mitochondrial tRNA {sup Leu(UUR)}Gene

    Energy Technology Data Exchange (ETDEWEB)

    Ueno, Hiroshi [Hyogo Medical Center for Adults, Akashi (Japan); Shiotani, Hideyuki


    An A-to-G transition at position 3243 of the mitochondrial DNA is known to be a pathogenic factor for mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes (MELAS), diabetes and cardiomyopathy. This mutation causes dysfunction of the central nervous system in MELAS. Because the heart, as well as the brain and nervous system, is highly dependent on the energy produced by mitochondrial oxidation, these tissues are more vulnerable to mitochondrial defects. Cardiac abnormalities were assessed in 10 diabetic patients associated with this mutation using echocardiography and {sup 123}I-metaiodobenzylguanidine (MIBG) scintigraphy, and compared with 19 diabetic patients without the mutation. Duration of diabetes, therapy, control of blood glucose and diabetic complications, such as diabetic retinopathy and nephropathy, were not different between the 2 groups. Diabetic patients with the mutation had a significantly thicker interventricular septum (16.8{+-}3.7 vs 11.0{+-}1.6 mm, p<0.001) than those without the mutation. Fractional shortening was lower in diabetic patients with the mutation than those without it (30.7{+-}7.0 vs 42.5{+-}6.6, p<0.001). MIBG uptake on the delayed MIBG image was significantly lower in diabetic patients with the mutation than in those without the mutation (mean value of the heart to mediastinum ratio: 1.6{+-}0.2 vs 2.0{+-}0.4, p>0.05). In conclusion, left ventricular hypertrophy with or without abnormal wall motion and severely reduced MIBG uptake may be characteristic in diabetic patients with a mutation in the mitochondrial tRNA {sup Leu(UUR)} gene. (author)

  3. Mutations in the mitochondrial tRNA Ser(AGY) gene are associated with deafness, retinal degeneration, myopathy and epilepsy. (United States)

    Tuppen, Helen A L; Naess, Karin; Kennaway, Nancy G; Al-Dosary, Mazhor; Lesko, Nicole; Yarham, John W; Bruhn, Helene; Wibom, Rolf; Nennesmo, Inger; Weleber, Richard G; Blakely, Emma L; Taylor, Robert W; McFarland, Robert


    Although over 200 pathogenic mitochondrial DNA (mtDNA) mutations have been reported to date, determining the genetic aetiology of many cases of mitochondrial disease is still not straightforward. Here, we describe the investigations undertaken to uncover the underlying molecular defect(s) in two unrelated Caucasian patients with suspected mtDNA disease, who presented with similar symptoms of myopathy, deafness, neurodevelopmental delay, epilepsy, marked fatigue and, in one case, retinal degeneration. Histochemical and biochemical evidence of mitochondrial respiratory chain deficiency was observed in the patient muscle biopsies and both patients were discovered to harbour a novel heteroplasmic mitochondrial tRNA (mt-tRNA)(Ser(AGY)) (MTTS2) mutation (m.12264C>T and m.12261T>C, respectively). Clear segregation of the m.12261T>C mutation with the biochemical defect, as demonstrated by single-fibre radioactive RFLP, confirmed the pathogenicity of this novel variant in patient 2. However, unusually high levels of m.12264C>T mutation within both COX-positive (98.4 ± 1.5%) and COX-deficient (98.2 ± 2.1%) fibres in patient 1 necessitated further functional investigations to prove its pathogenicity. Northern blot analysis demonstrated the detrimental effect of the m.12264C>T mutation on mt-tRNA(Ser(AGY)) stability, ultimately resulting in decreased steady-state levels of fully assembled complexes I and IV, as shown by blue-native polyacrylamide gel electrophoresis. Our findings expand the spectrum of pathogenic mutations associated with the MTTS2 gene and highlight MTTS2 mutations as an important cause of retinal and syndromic auditory impairment.

  4. A catalytic intermediate and several flavin redox states stabilized by folate-dependent tRNA methyltransferase from Bacillus subtilis. (United States)

    Hamdane, Djemel; Guerineau, Vincent; Un, Sun; Golinelli-Pimpaneau, Beatrice


    The flavoprotein TrmFO catalyzes the C5 methylation of uridine 54 in the TΨC loop of tRNAs using 5,10-methylenetetrahydrofolate (CH(2)THF) as a methylene donor and FAD as a reducing agent. Here, we report biochemical and spectroscopic studies that unravel the remarkable capability of Bacillus subtilis TrmFO to stabilize, in the presence of oxygen, several flavin-reduced forms, including an FADH(•) radical, and a catalytic intermediate endowed with methylating activity. The FADH(•) radical was characterized by high-field electron paramagnetic resonance and electron nuclear double-resonance spectroscopies. Interestingly, the enzyme exhibited tRNA methylation activity in the absence of both an added carbon donor and an external reducing agent, indicating that a reaction intermediate, containing presumably CH(2)THF and FAD hydroquinone, is present in the freshly purified enzyme. Isolation by acid treatment, under anaerobic conditions, of noncovalently bound molecules, followed by mass spectrometry analysis, confirmed the presence in TrmFO of nonmodified FAD. Addition of formaldehyde to the purified enzyme protects the reduced flavins from decay by probably preventing degradation of CH(2)THF. The absence of air-stable reduced FAD species during anaerobic titration of oxidized TrmFO, performed in the absence or presence of added CH(2)THF, argues against their thermodynamic stabilization but rather implicates their kinetic trapping by the enzyme. Altogether, the unexpected isolation of a stable catalytic intermediate suggests that the flavin-binding pocket of TrmFO is a highly insulated environment, diverting the reduced FAD present in this intermediate from uncoupled reactions.

  5. The yfiC gene of E. coli encodes an adenine-N6 methyltransferase that specifically modifies A37 of tRNA1Val(cmo5UAC). (United States)

    Golovina, Anna Y; Sergiev, Petr V; Golovin, Andrey V; Serebryakova, Marina V; Demina, Irina; Govorun, Vadim M; Dontsova, Olga A


    Transfer RNA is highly modified. Nucleotide 37 of the anticodon loop is represented by various modified nucleotides. In Escherichia coli, the valine-specific tRNA (cmo(5)UAC) contains a unique modification, N(6)-methyladenosine, at position 37; however, the enzyme responsible for this modification is unknown. Here we demonstrate that the yfiC gene of E. coli encodes an enzyme responsible for the methylation of A37 in tRNA(1)(Val). Inactivation of yfiC gene abolishes m(6)A formation in tRNA(1)(Val), while expression of the yfiC gene from a plasmid restores the modification. Additionally, unmodified tRNA(1)(Val) can be methylated by recombinant YfiC protein in vitro. Although the methylation of m(6)A in tRNA(1)(Val) by YfiC has little influence on the cell growth under standard conditions, the yfiC gene confers a growth advantage under conditions of osmotic and oxidative stress.

  6. Determination of the number of copies of genes coding for 5s-rRNA and tRNA in the genomes of 43 species of wheat and Aegilops

    Energy Technology Data Exchange (ETDEWEB)

    Vakhitov, V.A.; Gimalov, F.R.; Nikonorov, Yu.M.


    The number of 5s-rRNA and tRNA genes has been studied in 43 species of wheat and Aegilops differing in ploidy level, genomic composition and origin. It has been demonstrated that the repeatability of the 5s-rRNA and tRNA genes increases in wheat with increasing ploidy level, but not in proportion to the genome size. In Aegilops, in distinction from wheat, the relative as well as absolute number of 5s-RNA genes increases with increasing ploidy level. The proportion of the sequences coding for tRNA in the dipoloid and polyploid Aegilops species is practically similar, while the number of tRNA genes increases almost 2-3 times with increasing ploidy level. Large variability has been recorded between the species with similar genomic composition and ploidy level in respect of the number of the 5s-rRNA and tRNA genes. It has been demonstrated that integration of the initial genomes of the amphidiploids is accompanied by elimination of a particular part of these genomes. It has been concluded that the mechanisms of establishment and evolution of genomes in the intra- and intergeneric allopolyploids are not identical.

  7. Vision-based Recognition of Activities by a Humanoid Robot

    Directory of Open Access Journals (Sweden)

    Mounîm A. El-Yacoubi


    Full Text Available We present an autonomous assistive robotic system for human activity recognition from video sequences. Due to the large variability inherent to video capture from a non-fixed robot (as opposed to a fixed camera, as well as the robot’s limited computing resources, implementation has been guided by robustness to this variability and by memory and computing speed efficiency. To accommodate motion speed variability across users, we encode motion using dense interest point trajectories. Our recognition model harnesses the dense interest point bag-of-words representation through an intersection kernel-based SVM that better accommodates the large intra-class variability stemming from a robot operating in different locations and conditions. To contextually assess the engine as implemented in the robot, we compare it with the most recent approaches of human action recognition performed on public datasets (non-robot-based, including a novel approach of our own that is based on a two-layer SVM-hidden conditional random field sequential recognition model. The latter’s performance is among the best within the recent state of the art. We show that our robot-based recognition engine, while less accurate than the sequential model, nonetheless shows good performances, especially given the adverse test conditions of the robot, relative to those of a fixed camera.

  8. Early effects of duloxetine on emotion recognition in healthy volunteers. (United States)

    Bamford, Susan; Penton-Voak, Ian; Pinkney, Verity; Baldwin, David S; Munafò, Marcus R; Garner, Matthew


    The serotonin-noradrenaline reuptake inhibitor (SNRI) duloxetine is an effective treatment for major depression and generalised anxiety disorder. Neuropsychological models of antidepressant drug action suggest therapeutic effects might be mediated by the early correction of maladaptive biases in emotion processing, including the recognition of emotional expressions. Sub-chronic administration of duloxetine (for two weeks) produces adaptive changes in neural circuitry implicated in emotion processing; however, its effects on emotional expression recognition are unknown. Forty healthy participants were randomised to receive either 14 days of duloxetine (60 mg/day, titrated from 30 mg after three days) or matched placebo (with sham titration) in a double-blind, between-groups, repeated-measures design. On day 0 and day 14 participants completed a computerised emotional expression recognition task that measured sensitivity to the six primary emotions. Thirty-eight participants (19 per group) completed their course of tablets and were included in the analysis. Results provide evidence that duloxetine, compared to placebo, may reduce the accurate recognition of sadness. Drug effects were driven by changes in participants' ability to correctly detect subtle expressions of sadness, with greater change observed in the placebo relative to the duloxetine group. These effects occurred in the absence of changes in mood. Our preliminary findings require replication, but complement recent evidence that sadness recognition is a therapeutic target in major depression, and a mechanism through which SNRIs could resolve negative biases in emotion processing to achieve therapeutic effects.

  9. Wood recognition using image texture features.

    Directory of Open Access Journals (Sweden)

    Hang-jun Wang

    Full Text Available Inspired by theories of higher local order autocorrelation (HLAC, this paper presents a simple, novel, yet very powerful approach for wood recognition. The method is suitable for wood database applications, which are of great importance in wood related industries and administrations. At the feature extraction stage, a set of features is extracted from Mask Matching Image (MMI. The MMI features preserve the mask matching information gathered from the HLAC methods. The texture information in the image can then be accurately extracted from the statistical and geometrical features. In particular, richer information and enhanced discriminative power is achieved through the length histogram, a new histogram that embodies the width and height histograms. The performance of the proposed approach is compared to the state-of-the-art HLAC approaches using the wood stereogram dataset ZAFU WS 24. By conducting extensive experiments on ZAFU WS 24, we show that our approach significantly improves the classification accuracy.

  10. Comparison of fusion methods based on DST and DBN in human activity recognition

    Institute of Scientific and Technical Information of China (English)


    Ambient assistive living environments require sophisticated information fusion and reasoning techniques to accurately identify activities of a person under care. In this paper, we explain, compare and discuss the application of two powerful fusion methods, namely dynamic Bayesian networks (DBN) and Dempster-Shafer theory (DST), for human activity recognition. Both methods are described, the implementation of activity recognition based on these methods is explained, and model acquisition and composition are ...

  11. Chaotic Neural Network for Biometric Pattern Recognition

    Directory of Open Access Journals (Sweden)

    Kushan Ahmadian


    Full Text Available Biometric pattern recognition emerged as one of the predominant research directions in modern security systems. It plays a crucial role in authentication of both real-world and virtual reality entities to allow system to make an informed decision on granting access privileges or providing specialized services. The major issues tackled by the researchers are arising from the ever-growing demands on precision and performance of security systems and at the same time increasing complexity of data and/or behavioral patterns to be recognized. In this paper, we propose to deal with both issues by introducing the new approach to biometric pattern recognition, based on chaotic neural network (CNN. The proposed method allows learning the complex data patterns easily while concentrating on the most important for correct authentication features and employs a unique method to train different classifiers based on each feature set. The aggregation result depicts the final decision over the recognized identity. In order to train accurate set of classifiers, the subspace clustering method has been used to overcome the problem of high dimensionality of the feature space. The experimental results show the superior performance of the proposed method.

  12. Kernel learning algorithms for face recognition

    CERN Document Server

    Li, Jun-Bao; Pan, Jeng-Shyang


    Kernel Learning Algorithms for Face Recognition covers the framework of kernel based face recognition. This book discusses the advanced kernel learning algorithms and its application on face recognition. This book also focuses on the theoretical deviation, the system framework and experiments involving kernel based face recognition. Included within are algorithms of kernel based face recognition, and also the feasibility of the kernel based face recognition method. This book provides researchers in pattern recognition and machine learning area with advanced face recognition methods and its new

  13. Prevalence of the A1555G (12S rRNA and tRNA Ser(UCN mitochondrial mutations in hearing-impaired Brazilian patients

    Directory of Open Access Journals (Sweden)

    R.S. Abreu-Silva


    Full Text Available Mitochondrial mutations are responsible for at least 1% of the cases of hereditary deafness, but the contribution of each mutation has not yet been defined in African-derived or native American genetic backgrounds. A total of 203 unselected hearing-impaired patients were screened for the presence of the mitochondrial mutation A1555G in the 12S rRNA gene and mutations in the tRNA Ser(UCN gene in order to assess their frequency in the ethnically admixed Brazilian population. We found four individuals with A1555G mutation (2%, which is a frequency similar to those reported for European-derived populations in unselected samples. On the other hand, complete sequencing of the tRNA Ser(UCN did not reveal reported pathogenic substitutions, namely A7445G, 7472insC, T7510C, or T7511C. Instead, other rare substitutions were found such as T1291C, A7569G, and G7444A. To evaluate the significance of these findings, 110 "European-Brazilians" and 190 "African-Brazilians" unrelated hearing controls were screened. The T1291C, A7569G and G7444A substitutions were each found in about 1% (2/190 of individuals of African ancestry, suggesting that they are probably polymorphic. Our results indicate that screening for the A1555G mutation is recommended among all Brazilian deaf patients, while testing for mutations in the tRNA Ser(UCN gene should be considered only when other frequent deafness-causing mutations have been excluded or in the presence of a maternal transmission pattern.

  14. Prevalence of the A1555G (12S rRNA and tRNA Ser(UCN mitochondrial mutations in hearing-impaired Brazilian patients

    Directory of Open Access Journals (Sweden)

    Abreu-Silva R.S.


    Full Text Available Mitochondrial mutations are responsible for at least 1% of the cases of hereditary deafness, but the contribution of each mutation has not yet been defined in African-derived or native American genetic backgrounds. A total of 203 unselected hearing-impaired patients were screened for the presence of the mitochondrial mutation A1555G in the 12S rRNA gene and mutations in the tRNA Ser(UCN gene in order to assess their frequency in the ethnically admixed Brazilian population. We found four individuals with A1555G mutation (2%, which is a frequency similar to those reported for European-derived populations in unselected samples. On the other hand, complete sequencing of the tRNA Ser(UCN did not reveal reported pathogenic substitutions, namely A7445G, 7472insC, T7510C, or T7511C. Instead, other rare substitutions were found such as T1291C, A7569G, and G7444A. To evaluate the significance of these findings, 110 "European-Brazilians" and 190 "African-Brazilians" unrelated hearing controls were screened. The T1291C, A7569G and G7444A substitutions were each found in about 1% (2/190 of individuals of African ancestry, suggesting that they are probably polymorphic. Our results indicate that screening for the A1555G mutation is recommended among all Brazilian deaf patients, while testing for mutations in the tRNA Ser(UCN gene should be considered only when other frequent deafness-causing mutations have been excluded or in the presence of a maternal transmission pattern.


    Directory of Open Access Journals (Sweden)

    Rohit S Bavi


    Full Text Available Modified nucleic acid bases are most commonly found in tRNA. These may contain modifications from simple methylation to addition of bulky groups. Methylation of the four canonical nucleotide bases at a wide variety of positions is particularly prominent among the known modification. Methylation of N2 group of guanine is a relatively common modification in tRNA and rRNA. N2-methylguanosine (m2G is the second most often encountered nucleoside in E. coli tRNAs. N2, N2-dimethylguanosine (m22G is found in the majority of eukaryotic tRNAs and involved in forming base pair interactions with adjacent bases. Hence, in order to understand the structural significance of these methylated nucleic acid bases we have carried out molecular dynamics simulation to see the salvation effect. The results obtained shows iso-energetic conformational behaviors for m2G and m22G. The simulation trajectory of m2G shows regular periodical fluctuations suggesting that m2G is equally stable as either s-cis or s-trans rotamers. The two rotamers of m2G may interact canonically or non-canonically with opposite base as s-trans m2G26:C/A/U44 and s-cis m2G26:A/U44. The free rotations around the C-N bond could be the possible reason for these iso-energetic conformations. Dimethylation of G has almost no influence on base pairing with either A or U. Thus, these results reveal that modified nucleosides m2G and m22G may play an important role to prevent tRNA from adopting the unusual mitochondrial like conformation.

  16. The mitochondrial genome of the stingless bee Melipona bicolor (Hymenoptera, Apidae, Meliponini: sequence, gene organization and a unique tRNA translocation event conserved across the tribe Meliponini

    Directory of Open Access Journals (Sweden)

    Daniela Silvestre


    Full Text Available At present a complete mtDNA sequence has been reported for only two hymenopterans, the Old World honey bee, Apis mellifera and the sawfly Perga condei. Among the bee group, the tribe Meliponini (stingless bees has some distinction due to its Pantropical distribution, great number of species and large importance as main pollinators in several ecosystems, including the Brazilian rain forest. However few molecular studies have been conducted on this group of bees and few sequence data from mitochondrial genomes have been described. In this project, we PCR amplified and sequenced 78% of the mitochondrial genome of the stingless bee Melipona bicolor (Apidae, Meliponini. The sequenced region contains all of the 13 mitochondrial protein-coding genes, 18 of 22 tRNA genes, and both rRNA genes (one of them was partially sequenced. We also report the genome organization (gene content and order, gene translation, genetic code, and other molecular features, such as base frequencies, codon usage, gene initiation and termination. We compare these characteristics of M. bicolor to those of the mitochondrial genome of A. mellifera and other insects. A highly biased A+T content is a typical characteristic of the A. mellifera mitochondrial genome and it was even more extreme in that of M. bicolor. Length and compositional differences between M. bicolor and A. mellifera genes were detected and the gene order was compared. Eleven tRNA gene translocations were observed between these two species. This latter finding was surprising, considering the taxonomic proximity of these two bee tribes. The tRNA Lys gene translocation was investigated within Meliponini and showed high conservation across the Pantropical range of the tribe.

  17. Spectral recognition of graphs

    Directory of Open Access Journals (Sweden)

    Cvetković Dragoš


    Full Text Available At some time, in the childhood of spectral graph theory, it was conjectured that non-isomorphic graphs have different spectra, i.e. that graphs are characterized by their spectra. Very quickly this conjecture was refuted and numerous examples and families of non-isomorphic graphs with the same spectrum (cospectral graphs were found. Still some graphs are characterized by their spectra and several mathematical papers are devoted to this topic. In applications to computer sciences, spectral graph theory is considered as very strong. The benefit of using graph spectra in treating graphs is that eigenvalues and eigenvectors of several graph matrices can be quickly computed. Spectral graph parameters contain a lot of information on the graph structure (both global and local including some information on graph parameters that, in general, are computed by exponential algorithms. Moreover, in some applications in data mining, graph spectra are used to encode graphs themselves. The Euclidean distance between the eigenvalue sequences of two graphs on the same number of vertices is called the spectral distance of graphs. Some other spectral distances (also based on various graph matrices have been considered as well. Two graphs are considered as similar if their spectral distance is small. If two graphs are at zero distance, they are cospectral. In this sense, cospectral graphs are similar. Other spectrally based measures of similarity between networks (not necessarily having the same number of vertices have been used in Internet topology analysis, and in other areas. The notion of spectral distance enables the design of various meta-heuristic (e.g., tabu search, variable neighbourhood search algorithms for constructing graphs with a given spectrum (spectral graph reconstruction. Several spectrally based pattern recognition problems appear in many areas (e.g., image segmentation in computer vision, alignment of protein-protein interaction networks in bio

  18. A study on target recognition fusion algorithm based on fuzzy theory (United States)

    Han, Feng; Yang, WanHai


    In the process of the multi-sensors target recognition fusion, focused on the problem that it is difficult to determine the reliability of each sensor and how the data measured by different sensors are fused, a multi-sensor target recognition fusion method based on fuzzy theory is proposed. The mutual supportability of multiple sensors is obtained from the correlation function. Then by the membership function, the reliability of information provide by each sensor is gained. Finally, the supposed fusion result of multi-sensors target recognition can be produced on the basis of fuzzy integration function. The method is simple computationally and can objectively reflect the reliability of each sensor and interrelationship between these sensors. By applying the method to the target recognition, the simulation experiment shows that it can identify the target accurately and is an effective and feasible multi-sensors target recognition fusion method.

  19. Multiscale Recognition Algorithm for Eye Ground Texture Based on Fusion Threshold Equalization

    Directory of Open Access Journals (Sweden)

    Zhongsheng Qiu


    Full Text Available The eye ground texture is disturbed by non ideal imaging factor such as noise, it will affect the clinical diagnosis in practice, an improved multi scale retina eye ground texture recognition algorithm is proposed based on fusion area threshold. The nonlinear sampling multi-scale transform is used to analyze the geometric space coefficient of retinal vessels with multi direction and shift invariant features, the regional threshold filtering is integrated, it is used to suppress the effect of non-uniform blocks for texture recognition. The maximum likelihood local mean standard deviation analysis is used for texture parameters estimation and recognition. The noise reduced greatly, accurate identification of texture feature is obtained. Simulation results show that the algorithm can well characterize the retinal vascular texture, it has good performance in different texture feature recognition, the recognition accuracy is improved, and it has good robustness.

  20. X-ray structure of tRNA pseudouridine synthase TruD reveals an inserted domain with a novel fold. (United States)

    Ericsson, Ulrika B; Nordlund, Pär; Hallberg, B Martin


    Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine in structural RNA. The pseudouridine synthase TruD, that modifies U13 in tRNA, belongs to a recently identified and large family of pseudouridine synthases present in all kingdoms of life. We report here the crystal structure of Escherichia coli TruD at 2.0 A resolution. The structure reveals an overall V-shaped molecule with an RNA-binding cleft formed between two domains: a catalytic domain and an insertion domain. The catalytic domain has a fold similar to that of the catalytic domains of previously characterised pseudouridine synthases, whereas the insertion domain displays a novel fold.

  1. Impact of P-Site tRNA and antibiotics on ribosome mediated protein folding: studies using the Escherichia coli ribosome.

    Directory of Open Access Journals (Sweden)

    Surojit Mondal

    Full Text Available BACKGROUND: The ribosome, which acts as a platform for mRNA encoded polypeptide synthesis, is also capable of assisting in folding of polypeptide chains. The peptidyl transferase center (PTC that catalyzes peptide bond formation resides in the domain V of the 23S rRNA of the bacterial ribosome. Proper positioning of the 3' -CCA ends of the A- and P-site tRNAs via specific interactions with the nucleotides of the PTC are crucial for peptidyl transferase activity. This RNA domain is also the center for ribosomal chaperoning activity. The unfolded polypeptide chains interact with the specific nucleotides of the PTC and are released in a folding competent form. In vitro transcribed RNA corresponding to this domain (bDV RNA also displays chaperoning activity. RESULTS: The present study explores the effects of tRNAs, antibiotics that are A- and P-site PTC substrate analogs (puromycin and blasticidin and macrolide antibiotics (erythromycin and josamycin on the chaperoning ability of the E. coli ribosome and bDV RNA. Our studies using mRNA programmed ribosomes show that a tRNA positioned at the P-site effectively inhibits the ribosome's chaperoning function. We also show that the antibiotic blasticidin (that mimics the interaction between 3'-CCA end of P/P-site tRNA with the PTC is more effective in inhibiting ribosome and bDV RNA chaperoning ability than either puromycin or the macrolide antibiotics. Mutational studies of the bDV RNA could identify the nucleotides U2585 and G2252 (both of which interact with P-site tRNA to be important for its chaperoning ability. CONCLUSION: Both protein synthesis and their proper folding are crucial for maintenance of a functional cellular proteome. The PTC of the ribosome is attributed with both these abilities. The silencing of the chaperoning ability of the ribosome in the presence of P-site bound tRNA might be a way to segregate these two important functions.

  2. Effect of chemical carcinogens and partial hepatectomy on in vivo ( sup 35 S)methionine interaction with rat liver tRNA

    Energy Technology Data Exchange (ETDEWEB)

    Kanduc, D.; Aresta, A.; Rossiello, M.R.; Ranieri, T.; Quagliariello, E. (Universita di Bari (Italy))


    The effect of carcinogens given by a single or multiple injections on the extent of ({sup 35}S)methionine interaction with hepatic tRNA was studied in normal and partially hepatectomized rats. Either partial hepatectomy or administration of ethionine (100 or 330 mg/kg body weight) and dimethylnitrosamine (120 mg/kg body weight) by multiple i.p. injections inhibited the ({sup 35}S)methionine-tRNA interaction, while administration of hepatocarcinogenic chemicals plus PH resulted rather in a stimulation. Methylnitrosourea enhanced the extent of interaction when administered in a single dose (100 mg per kg body weight) 18 h after partial hepatectomy.

  3. Logo Recognition Theory and Practice

    CERN Document Server

    Chen, Jingying


    Used by companies, organizations, and even individuals to promote recognition of their brand, logos can also act as a valuable means of identifying the source of a document. E-business applications can retrieve and catalog products according to their logos. Governmental agencies can easily inspect goods using smart mobile devices that use logo recognition techniques. However, because logos are two-dimensional shapes of varying complexity, the recognition process can be challenging. Although promising results have been found for clean logos, they have not been as robust for noisy logos. Logo Re

  4. Accurate colorimetric feedback for RGB LED clusters (United States)

    Man, Kwong; Ashdown, Ian


    We present an empirical model of LED emission spectra that is applicable to both InGaN and AlInGaP high-flux LEDs, and which accurately predicts their relative spectral power distributions over a wide range of LED junction temperatures. We further demonstrate with laboratory measurements that changes in LED spectral power distribution with temperature can be accurately predicted with first- or second-order equations. This provides the basis for a real-time colorimetric feedback system for RGB LED clusters that can maintain the chromaticity of white light at constant intensity to within +/-0.003 Δuv over a range of 45 degrees Celsius, and to within 0.01 Δuv when dimmed over an intensity range of 10:1.

  5. Accurate guitar tuning by cochlear implant musicians.

    Directory of Open Access Journals (Sweden)

    Thomas Lu

    Full Text Available Modern cochlear implant (CI users understand speech but find difficulty in music appreciation due to poor pitch perception. Still, some deaf musicians continue to perform with their CI. Here we show unexpected results that CI musicians can reliably tune a guitar by CI alone and, under controlled conditions, match simultaneously presented tones to <0.5 Hz. One subject had normal contralateral hearing and produced more accurate tuning with CI than his normal ear. To understand these counterintuitive findings, we presented tones sequentially and found that tuning error was larger at ∼ 30 Hz for both subjects. A third subject, a non-musician CI user with normal contralateral hearing, showed similar trends in performance between CI and normal hearing ears but with less precision. This difference, along with electric analysis, showed that accurate tuning was achieved by listening to beats rather than discriminating pitch, effectively turning a spectral task into a temporal discrimination task.

  6. Macromolecular recognition: Recognition of polymer side chains by cyclodextrin (United States)

    Hashidzume, Akihito; Harada, Akira


    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.

  7. Efficient Accurate Context-Sensitive Anomaly Detection

    Institute of Scientific and Technical Information of China (English)


    For program behavior-based anomaly detection, the only way to ensure accurate monitoring is to construct an efficient and precise program behavior model. A new program behavior-based anomaly detection model,called combined pushdown automaton (CPDA) model was proposed, which is based on static binary executable analysis. The CPDA model incorporates the optimized call stack walk and code instrumentation technique to gain complete context information. Thereby the proposed method can detect more attacks, while retaining good performance.

  8. On accurate determination of contact angle (United States)

    Concus, P.; Finn, R.


    Methods are proposed that exploit a microgravity environment to obtain highly accurate measurement of contact angle. These methods, which are based on our earlier mathematical results, do not require detailed measurement of a liquid free-surface, as they incorporate discontinuous or nearly-discontinuous behavior of the liquid bulk in certain container geometries. Physical testing is planned in the forthcoming IML-2 space flight and in related preparatory ground-based experiments.

  9. Accurate Control of Josephson Phase Qubits (United States)


    61 ~1986!. 23 K. Kraus, States, Effects, and Operations: Fundamental Notions of Quantum Theory, Lecture Notes in Physics , Vol. 190 ~Springer-Verlag... PHYSICAL REVIEW B 68, 224518 ~2003!Accurate control of Josephson phase qubits Matthias Steffen,1,2,* John M. Martinis,3 and Isaac L. Chuang1 1Center...for Bits and Atoms and Department of Physics , MIT, Cambridge, Massachusetts 02139, USA 2Solid State and Photonics Laboratory, Stanford University

  10. Accurate guitar tuning by cochlear implant musicians. (United States)

    Lu, Thomas; Huang, Juan; Zeng, Fan-Gang


    Modern cochlear implant (CI) users understand speech but find difficulty in music appreciation due to poor pitch perception. Still, some deaf musicians continue to perform with their CI. Here we show unexpected results that CI musicians can reliably tune a guitar by CI alone and, under controlled conditions, match simultaneously presented tones to electric analysis, showed that accurate tuning was achieved by listening to beats rather than discriminating pitch, effectively turning a spectral task into a temporal discrimination task.

  11. Synthesizing Accurate Floating-Point Formulas


    Ioualalen, Arnault; Martel, Matthieu


    International audience; Many critical embedded systems perform floating-point computations yet their accuracy is difficult to assert and strongly depends on how formulas are written in programs. In this article, we focus on the synthesis of accurate formulas mathematically equal to the original formulas occurring in source codes. In general, an expression may be rewritten in many ways. To avoid any combinatorial explosion, we use an intermediate representation, called APEG, enabling us to rep...

  12. A character recognition scheme based on object oriented design for Tibetan buddhist texts

    Directory of Open Access Journals (Sweden)

    Chen-Yuan Liu


    Full Text Available The purpose of this study is to develop a plausible method to code and compile Buddhist texts from original Tibetan scripts into Romanized form. Using GUI (Graphical User Interface based on Object Oriented Design, a dictionary of Tibetan characters can be easily made for Buddhist literature researchers. It is hoped that a computer system capable of highly accurate character recognition will be actively used by all scholars engaged in Buddhist literature research. In the present study, an efficient automatic recognition method for Tibetan characters is established. The result of the experiments performed is that the recognition rate achieved is 99.4% for 28,954 characters.

  13. Accurate structural correlations from maximum likelihood superpositions.

    Directory of Open Access Journals (Sweden)

    Douglas L Theobald


    Full Text Available The cores of globular proteins are densely packed, resulting in complicated networks of structural interactions. These interactions in turn give rise to dynamic structural correlations over a wide range of time scales. Accurate analysis of these complex correlations is crucial for understanding biomolecular mechanisms and for relating structure to function. Here we report a highly accurate technique for inferring the major modes of structural correlation in macromolecules using likelihood-based statistical analysis of sets of structures. This method is generally applicable to any ensemble of related molecules, including families of nuclear magnetic resonance (NMR models, different crystal forms of a protein, and structural alignments of homologous proteins, as well as molecular dynamics trajectories. Dominant modes of structural correlation are determined using principal components analysis (PCA of the maximum likelihood estimate of the correlation matrix. The correlations we identify are inherently independent of the statistical uncertainty and dynamic heterogeneity associated with the structural coordinates. We additionally present an easily interpretable method ("PCA plots" for displaying these positional correlations by color-coding them onto a macromolecular structure. Maximum likelihood PCA of structural superpositions, and the structural PCA plots that illustrate the results, will facilitate the accurate determination of dynamic structural correlations analyzed in diverse fields of structural biology.

  14. Effective indexing for face recognition (United States)

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


    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.

  15. Iris Recognition using Orthogonal Transforms

    Directory of Open Access Journals (Sweden)

    M.Mani Roja


    Full Text Available Iris Recognition is a biometric recognition technique in which features of the iris are used to uniquely identify individuals. Iris recognition has over the years emerged as one of the most accuratebiometric techniques as opposed to other biometric techniques like face, signature and fingerprint. First, the iris image is pre processed using canny edge detector using a Gaussian filter. The iris edge and the pupil edge are extracted using image morphological operation, image opening. After normalization of red, green and blue components of the colour iris using Euclidean distance method, they are combined to form the localized colour iris. For feature vectors extraction, orthogonal transforms like discrete cosine transform, discrete sine transform and discrete Fourier transform have been considered. The proposed iris recognition system is very time efficient and it takes less than 1 second to grant authentication.

  16. Similarity measures for face recognition

    CERN Document Server

    Vezzetti, Enrico


    Face recognition has several applications, including security, such as (authentication and identification of device users and criminal suspects), and in medicine (corrective surgery and diagnosis). Facial recognition programs rely on algorithms that can compare and compute the similarity between two sets of images. This eBook explains some of the similarity measures used in facial recognition systems in a single volume. Readers will learn about various measures including Minkowski distances, Mahalanobis distances, Hansdorff distances, cosine-based distances, among other methods. The book also summarizes errors that may occur in face recognition methods. Computer scientists "facing face" and looking to select and test different methods of computing similarities will benefit from this book. The book is also useful tool for students undertaking computer vision courses.

  17. Gesture recognition on smart cameras (United States)

    Dziri, Aziz; Chevobbe, Stephane; Darouich, Mehdi


    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.

  18. Pattern recognition and string matching

    CERN Document Server

    Cheng, Xiuzhen


    The research and development of pattern recognition have proven to be of importance in science, technology, and human activity. Many useful concepts and tools from different disciplines have been employed in pattern recognition. Among them is string matching, which receives much theoretical and practical attention. String matching is also an important topic in combinatorial optimization. This book is devoted to recent advances in pattern recognition and string matching. It consists of twenty eight chapters written by different authors, addressing a broad range of topics such as those from classifica­ tion, matching, mining, feature selection, and applications. Each chapter is self-contained, and presents either novel methodological approaches or applications of existing theories and techniques. The aim, intent, and motivation for publishing this book is to pro­ vide a reference tool for the increasing number of readers who depend upon pattern recognition or string matching in some way. This includes student...

  19. Defect Recognition in Thermosonic Imaging

    Institute of Scientific and Technical Information of China (English)

    CHEN Dapeng; WU Naiming; ZHANG Zheng


    This work is aimed at developing an effective method for defect recognition in thermosonic imaging.The heat mechanism of thermosonic imaging is introduced,and the problem for defect recognition is discussed.For this purpose,defect existing in the inner wall of a metal pipeline specimen and defects embedded in a carbon fiber reinforced plastic (CFRP) laminate are tested.The experimental data are processed by pulse phase thermography (PPT) method to show the phase images at different frequencies,and the characteristic of phase angle vs frequency curve of thermal anomalies and sound area is analyzed.A binary image,which is based on the characteristic value of defects,is obtained by a new recognition algorithm to show the defects.Results demonstrate good defect recognition performance for thermosonic imaging,and the reliability of this technique can be improved by the method.

  20. Pattern Recognition Theory of Mind



    I propose that pattern recognition, memorization and processing are key concepts that can be a principle set for the theoretical modeling of the mind function. Most of the questions about the mind functioning can be answered by a descriptive modeling and definitions from these principles. An understandable consciousness definition can be drawn based on the assumption that a pattern recognition system can recognize its own patterns of activity. The principles, descriptive modeling and definiti...

  1. [Neurological disease and facial recognition]. (United States)

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


    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.

  2. On Tangut Historical Documents Recognition* (United States)

    Liu, Changqing

    As the Tangut studies have made progress, a considerable number of Tangut historical documents' copies have been published. It is of great importance to carry out digitalization and domestication of these copies. The paper firstly makes an initial processing of images by global threshold, then dissect the photocopies by scanning. Finally adopts the recognition approach of principal component analysis. The experiment shows that a better recognition can be achieved by calculation without extra time.

  3. Voice congruency facilitates word recognition.

    Directory of Open Access Journals (Sweden)

    Sandra Campeanu

    Full Text Available 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.

  4. Pattern Recognition Using Neural Networks

    Directory of Open Access Journals (Sweden)

    Santaji Ghorpade


    Full Text Available Face Recognition has been identified as one of the attracting research areas and it has drawn the attention of many researchers due to its varying applications such as security systems, medical systems,entertainment, etc. Face recognition is the preferred mode of identification by humans: it is natural,robust and non-intrusive. A wide variety of systems requires reliable personal recognition schemes to either confirm or determine the identity of an individual requesting their services. The purpose of such schemes is to ensure that the rendered services are accessed only by a legitimate user and no one else.Examples of such applications include secure access to buildings, computer systems, laptops, cellular phones, and ATMs. In the absence of robust personal recognition schemes, these systems are vulnerable to the wiles of an impostor.In this paper we have developed and illustrated a recognition system for human faces using a novel Kohonen self-organizing map (SOM or Self-Organizing Feature Map (SOFM based retrieval system.SOM has good feature extracting property due to its topological ordering. The Facial Analytics results for the 400 images of AT&T database reflects that the face recognition rate using one of the neural network algorithm SOM is 85.5% for 40 persons.

  5. Holistic processing predicts face recognition. (United States)

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


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

  6. Comparing Face Detection and Recognition Techniques


    Korra, Jyothi


    This paper implements and compares different techniques for face detection and recognition. One is find where the face is located in the images that is face detection and second is face recognition that is identifying the person. We study three techniques in this paper: Face detection using self organizing map (SOM), Face recognition by projection and nearest neighbor and Face recognition using SVM.

  7. Accurate measurement of unsteady state fluid temperature (United States)

    Jaremkiewicz, Magdalena


    In this paper, two accurate methods for determining the transient fluid temperature were presented. Measurements were conducted for boiling water since its temperature is known. At the beginning the thermometers are at the ambient temperature and next they are immediately immersed into saturated water. The measurements were carried out with two thermometers of different construction but with the same housing outer diameter equal to 15 mm. One of them is a K-type industrial thermometer widely available commercially. The temperature indicated by the thermometer was corrected considering the thermometers as the first or second order inertia devices. The new design of a thermometer was proposed and also used to measure the temperature of boiling water. Its characteristic feature is a cylinder-shaped housing with the sheath thermocouple located in its center. The temperature of the fluid was determined based on measurements taken in the axis of the solid cylindrical element (housing) using the inverse space marching method. Measurements of the transient temperature of the air flowing through the wind tunnel using the same thermometers were also carried out. The proposed measurement technique provides more accurate results compared with measurements using industrial thermometers in conjunction with simple temperature correction using the inertial thermometer model of the first or second order. By comparing the results, it was demonstrated that the new thermometer allows obtaining the fluid temperature much faster and with higher accuracy in comparison to the industrial thermometer. Accurate measurements of the fast changing fluid temperature are possible due to the low inertia thermometer and fast space marching method applied for solving the inverse heat conduction problem.

  8. Niche Genetic Algorithm with Accurate Optimization Performance

    Institute of Scientific and Technical Information of China (English)

    LIU Jian-hua; YAN De-kun


    Based on crowding mechanism, a novel niche genetic algorithm was proposed which can record evolutionary direction dynamically during evolution. After evolution, the solutions's precision can be greatly improved by means of the local searching along the recorded direction. Simulation shows that this algorithm can not only keep population diversity but also find accurate solutions. Although using this method has to take more time compared with the standard GA, it is really worth applying to some cases that have to meet a demand for high solution precision.

  9. Accurate estimation of indoor travel times

    DEFF Research Database (Denmark)

    Prentow, Thor Siiger; Blunck, Henrik; Stisen, Allan


    the InTraTime method for accurately estimating indoor travel times via mining of historical and real-time indoor position traces. The method learns during operation both travel routes, travel times and their respective likelihood---both for routes traveled as well as for sub-routes thereof. In...... are collected within the building complex. Results indicate that InTraTime is superior with respect to metrics such as deployment cost, maintenance cost and estimation accuracy, yielding an average deviation from actual travel times of 11.7 %. This accuracy was achieved despite using a minimal-effort setup...

  10. Accurate diagnosis is essential for amebiasis

    Institute of Scientific and Technical Information of China (English)


    @@ Amebiasis is one of the three most common causes of death from parasitic disease, and Entamoeba histolytica is the most widely distributed parasites in the world. Particularly, Entamoeba histolytica infection in the developing countries is a significant health problem in amebiasis-endemic areas with a significant impact on infant mortality[1]. In recent years a world wide increase in the number of patients with amebiasis has refocused attention on this important infection. On the other hand, improving the quality of parasitological methods and widespread use of accurate tecniques have improved our knowledge about the disease.

  11. The first accurate description of an aurora (United States)

    Schröder, Wilfried


    As technology has advanced, the scientific study of auroral phenomena has increased by leaps and bounds. A look back at the earliest descriptions of aurorae offers an interesting look into how medieval scholars viewed the subjects that we study.Although there are earlier fragmentary references in the literature, the first accurate description of the aurora borealis appears to be that published by the German Catholic scholar Konrad von Megenberg (1309-1374) in his book Das Buch der Natur (The Book of Nature). The book was written between 1349 and 1350.

  12. New law requires 'medically accurate' lesson plans. (United States)


    The California Legislature has passed a bill requiring all textbooks and materials used to teach about AIDS be medically accurate and objective. Statements made within the curriculum must be supported by research conducted in compliance with scientific methods, and published in peer-reviewed journals. Some of the current lesson plans were found to contain scientifically unsupported and biased information. In addition, the bill requires material to be "free of racial, ethnic, or gender biases." The legislation is supported by a wide range of interests, but opposed by the California Right to Life Education Fund, because they believe it discredits abstinence-only material.

  13. Universality: Accurate Checks in Dyson's Hierarchical Model (United States)

    Godina, J. J.; Meurice, Y.; Oktay, M. B.


    In this talk we present high-accuracy calculations of the susceptibility near βc for Dyson's hierarchical model in D = 3. Using linear fitting, we estimate the leading (γ) and subleading (Δ) exponents. Independent estimates are obtained by calculating the first two eigenvalues of the linearized renormalization group transformation. We found γ = 1.29914073 ± 10 -8 and, Δ = 0.4259469 ± 10-7 independently of the choice of local integration measure (Ising or Landau-Ginzburg). After a suitable rescaling, the approximate fixed points for a large class of local measure coincide accurately with a fixed point constructed by Koch and Wittwer.

  14. A kinetic framework for tRNA ligase and enforcement of a 2'-phosphate requirement for ligation highlights the design logic of an RNA repair machine. (United States)

    Remus, Barbara S; Shuman, Stewart


    tRNA ligases are essential components of informational and stress-response pathways entailing repair of RNA breaks with 2',3'-cyclic phosphate and 5'-OH ends. Plant and fungal tRNA ligases comprise three catalytic domains. Phosphodiesterase and kinase modules heal the broken ends to generate the 3'-OH, 2'-PO₄, and 5'-PO₄ required for sealing by the ligase. We exploit RNA substrates with different termini to define rates of individual steps or subsets of steps along the repair pathway of plant ligase AtRNL. The results highlight rate-limiting transactions, how repair is affected by active-site mutations, and how mutations are bypassed by RNA alterations. We gain insights to 2'-PO₄ specificity by showing that AtRNL is deficient in transferring AMP to pRNAOH to form AppRNAOH but proficient at sealing pre-adenylylated AppRNAOH. This strategy for discriminating 2'-PO₄ versus 2'-OH ends provides a quality-control checkpoint to ensure that only purposeful RNA breaks are sealed and to avoid nonspecific "capping" of 5'-PO₄ ends.

  15. Association between allelic variation due to short tandem repeats in tRNA gene of Entamoeba histolytica and clinical phenotypes of amoebiasis. (United States)

    Jaiswal, Virendra; Ghoshal, Ujjala; Mittal, Balraj; Dhole, Tapan N; Ghoshal, Uday C


    Genotypes of Entamoeba histolytica (E. histolytica) may contribute clinical phenotypes of amoebiasis such as amoebic liver abscess (ALA), dysentery and asymptomatic cyst passers state. Hence, we evaluated allelic variation due to short tandem repeats (STRs) in tRNA gene of E. histolytica and clinical phenotypes of amoebiasis. Asymptomatic cyst passers (n=24), patients with dysentery (n=56) and ALA (n=107) were included. Extracted DNA from stool (dysentery, asymptomatic cyst passers) and liver aspirate was amplified using 6 E. histolytica specific tRNA-linked STRs (D-A, A-L, N-K2, R-R, S-Q, and S(TGA)-D) primers. PCR products were subjected to sequencing. Association between allelic variation and clinical phenotypes was analyzed. A total of 9 allelic variations were found in D-A, 8 in A-L, 4 in N-K2, 5 in R-R, 10 in S(TAG)-D and 7 in S-Q loci. A significant association was found between allelic variants and clinical phenotypes of amoebiasis. This study reveals that allelic variation due to short tandem repeats (STRs) in tRNA gene of E. histolytica is associated different clinical outcome of amoebiasis.

  16. Yeast H2A.Z, FACT complex and RSC regulate transcription of tRNA gene through differential dynamics of flanking nucleosomes. (United States)

    Mahapatra, Sahasransu; Dewari, Pooran S; Bhardwaj, Anubhav; Bhargava, Purnima


    FACT complex is involved in elongation and ensures fidelity in the initiation step of transcription by RNA polymerase (pol) II. Histone variant H2A.Z is found in nucleosomes at the 5'-end of many genes. We report here H2A.Z-chaperone activity of the yeast FACT complex on the short, nucleosome-free, non-coding, pol III-transcribed yeast tRNA genes. On a prototype gene, yeast SUP4, chromatin remodeler RSC and FACT regulate its transcription through novel mechanisms, wherein the two gene-flanking nucleosomes containing H2A.Z, play different roles. Nhp6, which ensures transcription fidelity and helps load yFACT onto the gene flanking nucleosomes, has inhibitory role. RSC maintains a nucleosome abutting the gene terminator downstream, which results in reduced transcription rate in active state while H2A.Z probably helps RSC in keeping the gene nucleosome-free and serves as stress-sensor. All these factors maintain an epigenetic state which allows the gene to return quickly from repressed to active state and tones down the expression from the active SUP4 gene, required probably to maintain the balance in cellular tRNA pool.

  17. Congenital encephalomyopathy and adult-onset myopathy and diabetes mellitus: Different phenotypic associations of a new heteroplasmic mtDNA tRNA glutamic acid mutation

    Energy Technology Data Exchange (ETDEWEB)

    Hanna, M.G.; Nelson, I.; Sweeney, M.G.; Cooper, J.M.; Watkins, P.J.; Morgan-Hughes, J.A.; Harding, A.E. [Kings College Hospital, London (United Kingdom)


    We report the clinical, biochemical, and molecular genetic findings in a family with an unusual mitochondrial disease phenotype harboring a novel mtDNA tRNA glutamic acid mutation at position 14709. The proband and his sister presented with congenital myopathy and mental retardation and subsequently developed cerebellar ataxia. Other family members had either adult-onset diabetes mellitus with muscle weakness or adult-onset diabetes mellitus alone. Ragged-red and cytochrome c oxidase (COX)-negative fibers were present in muscle biopsies. Biochemical studies of muscle mitochondria showed reduced complex I and IV activities. The mtDNA mutation was heteroplasmic in blood and muscle in all matrilineal relatives analyzed. Primary myoblast, but not fibroblast, cultures containing high proportions of mutant mtDNA exhibited impaired mitochondrial translation. These observations indicate that mtDNA tRNA point mutations should be considered in the differential diagnosis of congenital myopathy. In addition they illustrate the diversity of phenotypes associated with this mutation in the same family and further highlight the association between mtDNA mutations and diabetes mellitus. 43 refs., 4 figs., 1 tab.

  18. How Accurately can we Calculate Thermal Systems?

    Energy Technology Data Exchange (ETDEWEB)

    Cullen, D; Blomquist, R N; Dean, C; Heinrichs, D; Kalugin, M A; Lee, M; Lee, Y; MacFarlan, R; Nagaya, Y; Trkov, A


    I would like to determine how accurately a variety of neutron transport code packages (code and cross section libraries) can calculate simple integral parameters, such as K{sub eff}, for systems that are sensitive to thermal neutron scattering. Since we will only consider theoretical systems, we cannot really determine absolute accuracy compared to any real system. Therefore rather than accuracy, it would be more precise to say that I would like to determine the spread in answers that we obtain from a variety of code packages. This spread should serve as an excellent indicator of how accurately we can really model and calculate such systems today. Hopefully, eventually this will lead to improvements in both our codes and the thermal scattering models that they use in the future. In order to accomplish this I propose a number of extremely simple systems that involve thermal neutron scattering that can be easily modeled and calculated by a variety of neutron transport codes. These are theoretical systems designed to emphasize the effects of thermal scattering, since that is what we are interested in studying. I have attempted to keep these systems very simple, and yet at the same time they include most, if not all, of the important thermal scattering effects encountered in a large, water-moderated, uranium fueled thermal system, i.e., our typical thermal reactors.

  19. Accurate pattern registration for integrated circuit tomography

    Energy Technology Data Exchange (ETDEWEB)

    Levine, Zachary H.; Grantham, Steven; Neogi, Suneeta; Frigo, Sean P.; McNulty, Ian; Retsch, Cornelia C.; Wang, Yuxin; Lucatorto, Thomas B.


    As part of an effort to develop high resolution microtomography for engineered structures, a two-level copper integrated circuit interconnect was imaged using 1.83 keV x rays at 14 angles employing a full-field Fresnel zone plate microscope. A major requirement for high resolution microtomography is the accurate registration of the reference axes in each of the many views needed for a reconstruction. A reconstruction with 100 nm resolution would require registration accuracy of 30 nm or better. This work demonstrates that even images that have strong interference fringes can be used to obtain accurate fiducials through the use of Radon transforms. We show that we are able to locate the coordinates of the rectilinear circuit patterns to 28 nm. The procedure is validated by agreement between an x-ray parallax measurement of 1.41{+-}0.17 {mu}m and a measurement of 1.58{+-}0.08 {mu}m from a scanning electron microscope image of a cross section.

  20. Accurate determination of characteristic relative permeability curves (United States)

    Krause, Michael H.; Benson, Sally M.


    A recently developed technique to accurately characterize sub-core scale heterogeneity is applied to investigate the factors responsible for flowrate-dependent effective relative permeability curves measured on core samples in the laboratory. The dependency of laboratory measured relative permeability on flowrate has long been both supported and challenged by a number of investigators. Studies have shown that this apparent flowrate dependency is a result of both sub-core scale heterogeneity and outlet boundary effects. However this has only been demonstrated numerically for highly simplified models of porous media. In this paper, flowrate dependency of effective relative permeability is demonstrated using two rock cores, a Berea Sandstone and a heterogeneous sandstone from the Otway Basin Pilot Project in Australia. Numerical simulations of steady-state coreflooding experiments are conducted at a number of injection rates using a single set of input characteristic relative permeability curves. Effective relative permeability is then calculated from the simulation data using standard interpretation methods for calculating relative permeability from steady-state tests. Results show that simplified approaches may be used to determine flowrate-independent characteristic relative permeability provided flow rate is sufficiently high, and the core heterogeneity is relatively low. It is also shown that characteristic relative permeability can be determined at any typical flowrate, and even for geologically complex models, when using accurate three-dimensional models.

  1. Accurate taxonomic assignment of short pyrosequencing reads. (United States)

    Clemente, José C; Jansson, Jesper; Valiente, Gabriel


    Ambiguities in the taxonomy dependent assignment of pyrosequencing reads are usually resolved by mapping each read to the lowest common ancestor in a reference taxonomy of all those sequences that match the read. This conservative approach has the drawback of mapping a read to a possibly large clade that may also contain many sequences not matching the read. A more accurate taxonomic assignment of short reads can be made by mapping each read to the node in the reference taxonomy that provides the best precision and recall. We show that given a suffix array for the sequences in the reference taxonomy, a short read can be mapped to the node of the reference taxonomy with the best combined value of precision and recall in time linear in the size of the taxonomy subtree rooted at the lowest common ancestor of the matching sequences. An accurate taxonomic assignment of short reads can thus be made with about the same efficiency as when mapping each read to the lowest common ancestor of all matching sequences in a reference taxonomy. We demonstrate the effectiveness of our approach on several metagenomic datasets of marine and gut microbiota.

  2. Holistic face processing can inhibit recognition of forensic facial composites. (United States)

    McIntyre, Alex H; Hancock, Peter J B; Frowd, Charlie D; Langton, Stephen R H


    Facial composite systems help eyewitnesses to show the appearance of criminals. However, likenesses created by unfamiliar witnesses will not be completely accurate, and people familiar with the target can find them difficult to identify. Faces are processed holistically; we explore whether this impairs identification of inaccurate composite images and whether recognition can be improved. In Experiment 1 (n = 64) an imaging technique was used to make composites of celebrity faces more accurate and identification was contrasted with the original composite images. Corrected composites were better recognized, confirming that errors in production of the likenesses impair identification. The influence of holistic face processing was explored by misaligning the top and bottom parts of the composites (cf. Young, Hellawell, & Hay, 1987). Misalignment impaired recognition of corrected composites but identification of the original, inaccurate composites significantly improved. This effect was replicated with facial composites of noncelebrities in Experiment 2 (n = 57). We conclude that, like real faces, facial composites are processed holistically: recognition is impaired because unlike real faces, composites contain inaccuracies and holistic face processing makes it difficult to perceive identifiable features. This effect was consistent across composites of celebrities and composites of people who are personally familiar. Our findings suggest that identification of forensic facial composites can be enhanced by presenting composites in a misaligned format.

  3. Postencoding cognitive processes in the cross-race effect: Categorization and individuation during face recognition. (United States)

    Ho, Michael R; Pezdek, Kathy


    The cross-race effect (CRE) describes the finding that same-race faces are recognized more accurately than cross-race faces. According to social-cognitive theories of the CRE, processes of categorization and individuation at encoding account for differential recognition of same- and cross-race faces. Recent face memory research has suggested that similar but distinct categorization and individuation processes also occur postencoding, at recognition. Using a divided-attention paradigm, in Experiments 1A and 1B we tested and confirmed the hypothesis that distinct postencoding categorization and individuation processes occur during the recognition of same- and cross-race faces. Specifically, postencoding configural divided-attention tasks impaired recognition accuracy more for same-race than for cross-race faces; on the other hand, for White (but not Black) participants, postencoding featural divided-attention tasks impaired recognition accuracy more for cross-race than for same-race faces. A social categorization paradigm used in Experiments 2A and 2B tested the hypothesis that the postencoding in-group or out-group social orientation to faces affects categorization and individuation processes during the recognition of same-race and cross-race faces. Postencoding out-group orientation to faces resulted in categorization for White but not for Black participants. This was evidenced by White participants' impaired recognition accuracy for same-race but not for cross-race out-group faces. Postencoding in-group orientation to faces had no effect on recognition accuracy for either same-race or cross-race faces. The results of Experiments 2A and 2B suggest that this social orientation facilitates White but not Black participants' individuation and categorization processes at recognition. Models of recognition memory for same-race and cross-race faces need to account for processing differences that occur at both encoding and recognition.

  4. Iris Recognition for Partially Occluded Images: Methodology and Sensitivity Analysis

    Directory of Open Access Journals (Sweden)

    A. Poursaberi


    Full Text Available Accurate iris detection is a crucial part of an iris recognition system. One of the main issues in iris segmentation is coping with occlusion that happens due to eyelids and eyelashes. In the literature, some various methods have been suggested to solve the occlusion problem. In this paper, two different segmentations of iris are presented. In the first algorithm, a circle is located around the pupil with an appropriate diameter. The iris area encircled by the circular boundary is used for recognition purposes then. In the second method, again a circle is located around the pupil with a larger diameter. This time, however, only the lower part of the encircled iris area is utilized for individual recognition. Wavelet-based texture features are used in the process. Hamming and harmonic mean distance classifiers are exploited as a mixed classifier in suggested algorithm. It is observed that relying on a smaller but more reliable part of the iris, though reducing the net amount of information, improves the overall performance. Experimental results on CASIA database show that our method has a promising performance with an accuracy of 99.31%. The sensitivity of the proposed method is analyzed versus contrast, illumination, and noise as well, where lower sensitivity to all factors is observed when the lower half of the iris is used for recognition.

  5. An Efficiency Analysis of Augmented Reality Marker Recognition Algorithm

    Directory of Open Access Journals (Sweden)

    Kurpytė Dovilė


    Full Text Available The article reports on the investigation of augmented reality system which is designed for identification and augmentation of 100 different square markers. Marker recognition efficiency was investigated by rotating markers along x and y axis directions in range from −90° to 90°. Virtual simulations of four environments were developed: a an intense source of light, b an intense source of light falling from the left side, c the non-intensive light source falling from the left side, d equally falling shadows. The graphics were created using the OpenGL graphics computer hardware interface; image processing was programmed in C++ language using OpenCV, while augmented reality was developed in Java programming language using NyARToolKit. The obtained results demonstrate that augmented reality marker recognition algorithm is accurate and reliable in the case of changing lighting conditions and rotational angles - only 4 % markers were unidentified. Assessment of marker recognition efficiency let to propose marker classification strategy in order to use it for grouping various markers into distinct markers’ groups possessing similar recognition properties.

  6. Emotion recognition in music changes across the adult life span. (United States)

    Lima, Cesar F; Castro, Sao Luis


    In comparison with other modalities, the recognition of emotion in music has received little attention. An unexplored question is whether and how emotion recognition in music changes as a function of ageing. In the present study, healthy adults aged between 17 and 84 years (N=114) judged the magnitude to which a set of musical excerpts (Vieillard et al., 2008) expressed happiness, peacefulness, sadness and fear/threat. The results revealed emotion-specific age-related changes: advancing age was associated with a gradual decrease in responsiveness to sad and scary music from middle age onwards, whereas the recognition of happiness and peacefulness, both positive emotional qualities, remained stable from young adulthood to older age. Additionally, the number of years of music training was associated with more accurate categorisation of the musical emotions examined here. We argue that these findings are consistent with two accounts on how ageing might influence the recognition of emotions: motivational changes towards positivity and, to a lesser extent, selective neuropsychological decline.

  7. A unified framework for gesture recognition and spatiotemporal gesture segmentation. (United States)

    Alon, Jonathan; Athitsos, Vassilis; Yuan, Quan; Sclaroff, Stan


    Within the context of hand gesture recognition, spatiotemporal gesture segmentation is the task of determining, in a video sequence, where the gesturing hand is located and when the gesture starts and ends. Existing gesture recognition methods typically assume either known spatial segmentation or known temporal segmentation, or both. This paper introduces a unified framework for simultaneously performing spatial segmentation, temporal segmentation, and recognition. In the proposed framework, information flows both bottom-up and top-down. A gesture can be recognized even when the hand location is highly ambiguous and when information about when the gesture begins and ends is unavailable. Thus, the method can be applied to continuous image streams where gestures are performed in front of moving, cluttered backgrounds. The proposed method consists of three novel contributions: a spatiotemporal matching algorithm that can accommodate multiple candidate hand detections in every frame, a classifier-based pruning framework that enables accurate and early rejection of poor matches to gesture models, and a subgesture reasoning algorithm that learns which gesture models can falsely match parts of other longer gestures. The performance of the approach is evaluated on two challenging applications: recognition of hand-signed digits gestured by users wearing short-sleeved shirts, in front of a cluttered background, and retrieval of occurrences of signs of interest in a video database containing continuous, unsegmented signing in American Sign Language (ASL).

  8. Improving Protein Fold Recognition by Deep Learning Networks (United States)

    Jo, Taeho; Hou, Jie; Eickholt, Jesse; Cheng, Jianlin


    For accurate recognition of protein folds, a deep learning network method (DN-Fold) was developed to predict if a given query-template protein pair belongs to the same structural fold. The input used stemmed from the protein sequence and structural features extracted from the protein pair. We evaluated the performance of DN-Fold along with 18 different methods on Lindahl’s benchmark dataset and on a large benchmark set extracted from SCOP 1.75 consisting of about one million protein pairs, at three different levels of fold recognition (i.e., protein family, superfamily, and fold) depending on the evolutionary distance between protein sequences. The correct recognition rate of ensembled DN-Fold for Top 1 predictions is 84.5%, 61.5%, and 33.6% and for Top 5 is 91.2%, 76.5%, and 60.7% at family, superfamily, and fold levels, respectively. We also evaluated the performance of single DN-Fold (DN-FoldS), which showed the comparable results at the level of family and superfamily, compared to ensemble DN-Fold. Finally, we extended the binary classification problem of fold recognition to real-value regression task, which also show a promising performance. DN-Fold is freely available through a web server at

  9. Web Video Event Recognition by Semantic Analysis From Ubiquitous Documents. (United States)

    Yu, Litao; Yang, Yang; Huang, Zi; Wang, Peng; Song, Jingkuan; Shen, Heng Tao


    In recent years, the task of event recognition from videos has attracted increasing interest in multimedia area. While most of the existing research was mainly focused on exploring visual cues to handle relatively small-granular events, it is difficult to directly analyze video content without any prior knowledge. Therefore, synthesizing both the visual and semantic analysis is a natural way for video event understanding. In this paper, we study the problem of Web video event recognition, where Web videos often describe large-granular events and carry limited textual information. Key challenges include how to accurately represent event semantics from incomplete textual information and how to effectively explore the correlation between visual and textual cues for video event understanding. We propose a novel framework to perform complex event recognition from Web videos. In order to compensate the insufficient expressive power of visual cues, we construct an event knowledge base by deeply mining semantic information from ubiquitous Web documents. This event knowledge base is capable of describing each event with comprehensive semantics. By utilizing this base, the textual cues for a video can be significantly enriched. Furthermore, we introduce a two-view adaptive regression model, which explores the intrinsic correlation between the visual and textual cues of the videos to learn reliable classifiers. Extensive experiments on two real-world video data sets show the effectiveness of our proposed framework and prove that the event knowledge base indeed helps improve the performance of Web video event recognition.

  10. Face recognition with multi-resolution spectral feature images.

    Directory of Open Access Journals (Sweden)

    Zhan-Li Sun

    Full Text Available The one-sample-per-person problem has become an active research topic for face recognition in recent years because of its challenges and significance for real-world applications. However, achieving relatively higher recognition accuracy is still a difficult problem due to, usually, too few training samples being available and variations of illumination and expression. To alleviate the negative effects caused by these unfavorable factors, in this paper we propose a more accurate spectral feature image-based 2DLDA (two-dimensional linear discriminant analysis ensemble algorithm for face recognition, with one sample image per person. In our algorithm, multi-resolution spectral feature images are constructed to represent the face images; this can greatly enlarge the training set. The proposed method is inspired by our finding that, among these spectral feature images, features extracted from some orientations and scales using 2DLDA are not sensitive to variations of illumination and expression. In order to maintain the positive characteristics of these filters and to make correct category assignments, the strategy of classifier committee learning (CCL is designed to combine the results obtained from different spectral feature images. Using the above strategies, the negative effects caused by those unfavorable factors can be alleviated efficiently in face recognition. Experimental results on the standard databases demonstrate the feasibility and efficiency of the proposed method.

  11. Probing binding hot spots at protein-RNA recognition sites. (United States)

    Barik, Amita; Nithin, Chandran; Karampudi, Naga Bhushana Rao; Mukherjee, Sunandan; Bahadur, Ranjit Prasad


    We use evolutionary conservation derived from structure alignment of polypeptide sequences along with structural and physicochemical attributes of protein-RNA interfaces to probe the binding hot spots at protein-RNA recognition sites. We find that the degree of conservation varies across the RNA binding proteins; some evolve rapidly compared to others. Additionally, irrespective of the structural class of the complexes, residues at the RNA binding sites are evolutionary better conserved than those at the solvent exposed surfaces. For recognitions involving duplex RNA, residues interacting with the major groove are better conserved than those interacting with the minor groove. We identify multi-interface residues participating simultaneously in protein-protein and protein-RNA interfaces in complexes where more than one polypeptide is involved in RNA recognition, and show that they are better conserved compared to any other RNA binding residues. We find that the residues at water preservation site are better conserved than those at hydrated or at dehydrated sites. Finally, we develop a Random Forests model using structural and physicochemical attributes for predicting binding hot spots. The model accurately predicts 80% of the instances of experimental ΔΔG values in a particular class, and provides a stepping-stone towards the engineering of protein-RNA recognition sites with desired affinity.

  12. Probing binding hot spots at protein–RNA recognition sites (United States)

    Barik, Amita; Nithin, Chandran; Karampudi, Naga Bhushana Rao; Mukherjee, Sunandan; Bahadur, Ranjit Prasad


    We use evolutionary conservation derived from structure alignment of polypeptide sequences along with structural and physicochemical attributes of protein–RNA interfaces to probe the binding hot spots at protein–RNA recognition sites. We find that the degree of conservation varies across the RNA binding proteins; some evolve rapidly compared to others. Additionally, irrespective of the structural class of the complexes, residues at the RNA binding sites are evolutionary better conserved than those at the solvent exposed surfaces. For recognitions involving duplex RNA, residues interacting with the major groove are better conserved than those interacting with the minor groove. We identify multi-interface residues participating simultaneously in protein–protein and protein–RNA interfaces in complexes where more than one polypeptide is involved in RNA recognition, and show that they are better conserved compared to any other RNA binding residues. We find that the residues at water preservation site are better conserved than those at hydrated or at dehydrated sites. Finally, we develop a Random Forests model using structural and physicochemical attributes for predicting binding hot spots. The model accurately predicts 80% of the instances of experimental ΔΔG values in a particular class, and provides a stepping-stone towards the engineering of protein–RNA recognition sites with desired affinity. PMID:26365245

  13. Iris Recognition for Partially Occluded Images: Methodology and Sensitivity Analysis (United States)

    Poursaberi, A.; Araabi, B. N.


    Accurate iris detection is a crucial part of an iris recognition system. One of the main issues in iris segmentation is coping with occlusion that happens due to eyelids and eyelashes. In the literature, some various methods have been suggested to solve the occlusion problem. In this paper, two different segmentations of iris are presented. In the first algorithm, a circle is located around the pupil with an appropriate diameter. The iris area encircled by the circular boundary is used for recognition purposes then. In the second method, again a circle is located around the pupil with a larger diameter. This time, however, only the lower part of the encircled iris area is utilized for individual recognition. Wavelet-based texture features are used in the process. Hamming and harmonic mean distance classifiers are exploited as a mixed classifier in suggested algorithm. It is observed that relying on a smaller but more reliable part of the iris, though reducing the net amount of information, improves the overall performance. Experimental results on CASIA database show that our method has a promising performance with an accuracy of 99.31%. The sensitivity of the proposed method is analyzed versus contrast, illumination, and noise as well, where lower sensitivity to all factors is observed when the lower half of the iris is used for recognition.

  14. Kazakh Traditional Dance Gesture Recognition (United States)

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


    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.

  15. An audiovisual emotion recognition system (United States)

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


    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.

  16. Toward Accurate and Quantitative Comparative Metagenomics (United States)

    Nayfach, Stephen; Pollard, Katherine S.


    Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized. PMID:27565341

  17. Apparatus for accurately measuring high temperatures (United States)

    Smith, D.D.

    The present invention is a thermometer used for measuring furnace temperatures in the range of about 1800/sup 0/ to 2700/sup 0/C. The thermometer comprises a broadband multicolor thermal radiation sensor positioned to be in optical alignment with the end of a blackbody sight tube extending into the furnace. A valve-shutter arrangement is positioned between the radiation sensor and the sight tube and a chamber for containing a charge of high pressure gas is positioned between the valve-shutter arrangement and the radiation sensor. A momentary opening of the valve shutter arrangement allows a pulse of the high gas to purge the sight tube of air-borne thermal radiation contaminants which permits the radiation sensor to accurately measure the thermal radiation emanating from the end of the sight tube.

  18. Accurate renormalization group analyses in neutrino sector

    Energy Technology Data Exchange (ETDEWEB)

    Haba, Naoyuki [Graduate School of Science and Engineering, Shimane University, Matsue 690-8504 (Japan); Kaneta, Kunio [Kavli IPMU (WPI), The University of Tokyo, Kashiwa, Chiba 277-8568 (Japan); Takahashi, Ryo [Graduate School of Science and Engineering, Shimane University, Matsue 690-8504 (Japan); Yamaguchi, Yuya [Department of Physics, Faculty of Science, Hokkaido University, Sapporo 060-0810 (Japan)


    We investigate accurate renormalization group analyses in neutrino sector between ν-oscillation and seesaw energy scales. We consider decoupling effects of top quark and Higgs boson on the renormalization group equations of light neutrino mass matrix. Since the decoupling effects are given in the standard model scale and independent of high energy physics, our method can basically apply to any models beyond the standard model. We find that the decoupling effects of Higgs boson are negligible, while those of top quark are not. Particularly, the decoupling effects of top quark affect neutrino mass eigenvalues, which are important for analyzing predictions such as mass squared differences and neutrinoless double beta decay in an underlying theory existing at high energy scale.

  19. Accurate Weather Forecasting for Radio Astronomy (United States)

    Maddalena, Ronald J.


    The NRAO Green Bank Telescope routinely observes at wavelengths from 3 mm to 1 m. As with all mm-wave telescopes, observing conditions depend upon the variable atmospheric water content. The site provides over 100 days/yr when opacities are low enough for good observing at 3 mm, but winds on the open-air structure reduce the time suitable for 3-mm observing where pointing is critical. Thus, to maximum productivity the observing wavelength needs to match weather conditions. For 6 years the telescope has used a dynamic scheduling system (recently upgraded; that requires accurate multi-day forecasts for winds and opacities. Since opacity forecasts are not provided by the National Weather Services (NWS), I have developed an automated system that takes available forecasts, derives forecasted opacities, and deploys the results on the web in user-friendly graphical overviews ( rmaddale/Weather). The system relies on the "North American Mesoscale" models, which are updated by the NWS every 6 hrs, have a 12 km horizontal resolution, 1 hr temporal resolution, run to 84 hrs, and have 60 vertical layers that extend to 20 km. Each forecast consists of a time series of ground conditions, cloud coverage, etc, and, most importantly, temperature, pressure, humidity as a function of height. I use the Liebe's MWP model (Radio Science, 20, 1069, 1985) to determine the absorption in each layer for each hour for 30 observing wavelengths. Radiative transfer provides, for each hour and wavelength, the total opacity and the radio brightness of the atmosphere, which contributes substantially at some wavelengths to Tsys and the observational noise. Comparisons of measured and forecasted Tsys at 22.2 and 44 GHz imply that the forecasted opacities are good to about 0.01 Nepers, which is sufficient for forecasting and accurate calibration. Reliability is high out to 2 days and degrades slowly for longer-range forecasts.

  20. A developmental study of the own-age face recognition bias in children. (United States)

    Hills, Peter J


    The own-age bias is one in which people recognize faces of people their own age more accurately than faces of other ages (e.g., Anastasi & Rhodes, 2005, 2006) and appears to be, at least, partially based on experience (Harrison & Hole, 2009). Indeed, Hills and Lewis (2011a) have shown that 8-year-old faces are more accurately recognized by 8-year-old children than by 6- or 11-year-old children, suggesting the own-age bias develops rapidly. The present study explores the own-age bias in a developmental study in participants aged 6-10 years. Ninety participants (divided into 3 groups of 30 on the basis of their age at the first time of testing) undertook a standard old/new recognition paradigm in which their recognition accuracy was measured for 8- and 20-year-old faces. Results showed that when the participants were 8 years old, they recognized 8-year-old faces more accurately than when they were 7 or 9 years old. This effect was found to be based on mechanisms that differ from simple developmental improvement. This is the first study to show the development of the own-age bias in face recognition using a longitudinal design. These results show that the face recognition system is updated on the basis of recent experience and/or motivation to process faces, creating recognition biases.

  1. An articulatorily constrained, maximum entropy approach to speech recognition and speech coding

    Energy Technology Data Exchange (ETDEWEB)

    Hogden, J.


    Hidden Markov models (HMM`s) are among the most popular tools for performing computer speech recognition. One of the primary reasons that HMM`s typically outperform other speech recognition techniques is that the parameters used for recognition are determined by the data, not by preconceived notions of what the parameters should be. This makes HMM`s better able to deal with intra- and inter-speaker variability despite the limited knowledge of how speech signals vary and despite the often limited ability to correctly formulate rules describing variability and invariance in speech. In fact, it is often the case that when HMM parameter values are constrained using the limited knowledge of speech, recognition performance decreases. However, the structure of an HMM has little in common with the mechanisms underlying speech production. Here, the author argues that by using probabilistic models that more accurately embody the process of speech production, he can create models that have all the advantages of HMM`s, but that should more accurately capture the statistical properties of real speech samples--presumably leading to more accurate speech recognition. The model he will discuss uses the fact that speech articulators move smoothly and continuously. Before discussing how to use articulatory constraints, he will give a brief description of HMM`s. This will allow him to highlight the similarities and differences between HMM`s and the proposed technique.

  2. Recognition of anxiety disorders by family physicians after rigorous medical record case extraction: results of the Netherlands Study of Depression and Anxiety.

    NARCIS (Netherlands)

    Janssen, E.H.C.; Ven, P.M. van de; Terluin, B.; Verhaak, P.F.M.; Marwijk, H.W.J. van; Smolders, M.; Meer, K. van der; Penninx, B.W.J.H.; Hout, H.P.J. van


    Objective: Previous studies reported low and inconsistent rates of recognition of anxiety disorders by family physicians (FPs). Our objectives were to examine (a) which combination of indications within medical records most accurately reflects recognition of anxiety disorders and (b) whether patient

  3. Recognition of anxiety disorders by family physicians after rigorous medical record case extraction Results of the Netherlands Study of Depression and Anxiety

    NARCIS (Netherlands)

    Janssen, Evelien H. C.; van de Ven, Peter M.; Terluin, Berend; Verhaak, Peter F. M.; van Marwijk, Harm W. J.; Smolders, Mirrian; van der Meer, Klaas; Penninx, Brenda W. J. H.; van Hout, Hein P. J.


    Objective: Previous studies reported low and inconsistent rates of recognition of anxiety disorders by family physicians (FPs). Our objectives were to examine (a) which combination of indications within medical records most accurately reflects recognition of anxiety disorders and (b) whether patient

  4. Approaching system equilibrium with accurate or not accurate feedback information in a two-route system (United States)

    Zhao, Xiao-mei; Xie, Dong-fan; Li, Qi


    With the development of intelligent transport system, advanced information feedback strategies have been developed to reduce traffic congestion and enhance the capacity. However, previous strategies provide accurate information to travelers and our simulation results show that accurate information brings negative effects, especially in delay case. Because travelers prefer to the best condition route with accurate information, and delayed information cannot reflect current traffic condition but past. Then travelers make wrong routing decisions, causing the decrease of the capacity and the increase of oscillations and the system deviating from the equilibrium. To avoid the negative effect, bounded rationality is taken into account by introducing a boundedly rational threshold BR. When difference between two routes is less than the BR, routes have equal probability to be chosen. The bounded rationality is helpful to improve the efficiency in terms of capacity, oscillation and the gap deviating from the system equilibrium.

  5. Early development of visual recognition. (United States)

    Plebe, Alessio; Domenella, Rosaria Grazia


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

  6. Mandarin recognition over the telephone (United States)

    Kao, Yuhung


    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.

  7. Mobile-Customer Identity Recognition

    Institute of Scientific and Technical Information of China (English)

    LI Zhan; XU Ji-sheng; XU Min; SUN Hong


    By utilizing artificial intelligence and pattern recognition techniques, we propose an integrated mobile-customer identity recognition approach in this paper, based on customer's behavior characteristics extracted from the customer information database. To verify the effectiveness of this approach, a test has been run on the dataset consisting of 1 000 customers in 3 consecutive months. The result is compared with the real dataset in the fourth month consisting of 162 customers, which has been set as the customers for recognition. The high correct rate of the test (96.30%), together with 1.87% of the judge-by-mistake rate and 7.82% of the leaving-out rate, demonstrates the effectiveness of this approach.

  8. Emotion-independent face recognition (United States)

    De Silva, Liyanage C.; Esther, Kho G. P.


    Current face recognition techniques tend to work well when recognizing faces under small variations in lighting, facial expression and pose, but deteriorate under more extreme conditions. In this paper, a face recognition system to recognize faces of known individuals, despite variations in facial expression due to different emotions, is developed. The eigenface approach is used for feature extraction. Classification methods include Euclidean distance, back propagation neural network and generalized regression neural network. These methods yield 100% recognition accuracy when the training database is representative, containing one image representing the peak expression for each emotion of each person apart from the neutral expression. The feature vectors used for comparison in the Euclidean distance method and for training the neural network must be all the feature vectors of the training set. These results are obtained for a face database consisting of only four persons.

  9. DNA recognition by synthetic constructs. (United States)

    Pazos, Elena; Mosquera, Jesús; Vázquez, M Eugenio; Mascareñas, José L


    The interaction of transcription factors with specific DNA sites is key for the regulation of gene expression. Despite the availability of a large body of structural data on protein-DNA complexes, we are still far from fully understanding the molecular and biophysical bases underlying such interactions. Therefore, the development of non-natural agents that can reproduce the DNA-recognition properties of natural transcription factors remains a major and challenging goal in chemical biology. In this review we summarize the basics of double-stranded DNA recognition by transcription factors, and describe recent developments in the design and preparation of synthetic DNA binders. We mainly focus on synthetic peptides that have been designed by following the DNA interaction of natural proteins, and we discuss how the tools of organic synthesis can be used to make artificial constructs equipped with functionalities that introduce additional properties to the recognition process, such as sensing and controllability.

  10. Does aging impair first impression accuracy? Differentiating emotion recognition from complex social inferences. (United States)

    Krendl, Anne C; Rule, Nicholas O; Ambady, Nalini


    Young adults can be surprisingly accurate at making inferences about people from their faces. Although these first impressions have important consequences for both the perceiver and the target, it remains an open question whether first impression accuracy is preserved with age. Specifically, could age differences in impressions toward others stem from age-related deficits in accurately detecting complex social cues? Research on aging and impression formation suggests that young and older adults show relative consensus in their first impressions, but it is unknown whether they differ in accuracy. It has been widely shown that aging disrupts emotion recognition accuracy, and that these impairments may predict deficits in other social judgments, such as detecting deceit. However, it is unclear whether general impression formation accuracy (e.g., emotion recognition accuracy, detecting complex social cues) relies on similar or distinct mechanisms. It is important to examine this question to evaluate how, if at all, aging might affect overall accuracy. Here, we examined whether aging impaired first impression accuracy in predicting real-world outcomes and categorizing social group membership. Specifically, we studied whether emotion recognition accuracy and age-related cognitive decline (which has been implicated in exacerbating deficits in emotion recognition) predict first impression accuracy. Our results revealed that emotion recognition accuracy did not predict first impression accuracy, nor did age-related cognitive decline impair it. These findings suggest that domains of social perception outside of emotion recognition may rely on mechanisms that are relatively unimpaired by aging.

  11. Gesture Recognition Using Character Recognition Techniques on Two-dimensional Eigenspace


    大野, 宏; 山本, 正信; Ohno, Hiroshi; Yamamoto, Masanobu


    This paper describes a novel method for gesture recognition using character recognition techniques on two-dimensional eigenspace. An image-based approach can capture human body poses in 3D motion from multiple image sequences. The sequence of poses can be reduced into a trajectory on the two-dimensional eigenspace with preserving the main features in gesture, so that the gesture recognition equals the character recognition. Experiments for the gesture recognition using some character recognit...

  12. CCD camera automatic calibration technology and ellipse recognition algorithm

    Institute of Scientific and Technical Information of China (English)

    Changku Sun; Xiaodong Zhang; Yunxia Qu


    A novel two-dimensional (2D) pattern used in camera calibration is presented. With one feature circle located at the center, an array of circles is photo-etched on this pattern. An ellipse recognition algorithm is proposed to implement the acquisition of interest calibration points without human intervention. According to the circle arrangement of the pattern, the relation between three-dimensional (3D) and 2D coordinates of these points can be established automatically and accurately. These calibration points are computed for intrinsic parameters calibration of charge-coupled device (CCD) camera with Tsai method. A series of experiments have shown that the algorithm is robust and reliable with the calibration error less than 0.4 pixel. This new calibration pattern and ellipse recognition algorithm can be widely used in computer vision.

  13. The own-age face recognition bias is task dependent. (United States)

    Proietti, Valentina; Macchi Cassia, Viola; Mondloch, Catherine J


    The own-age bias (OAB) in face recognition (more accurate recognition of own-age than other-age faces) is robust among young adults but not older adults. We investigated the OAB under two different task conditions. In Experiment 1 young and older adults (who reported more recent experience with own than other-age faces) completed a match-to-sample task with young and older adult faces; only young adults showed an OAB. In Experiment 2 young and older adults completed an identity detection task in which we manipulated the identity strength of target and distracter identities by morphing each face with an average face in 20% steps. Accuracy increased with identity strength and facial age influenced older adults' (but not younger adults') strategy, but there was no evidence of an OAB. Collectively, these results suggest that the OAB depends on task demands and may be absent when searching for one identity.

  14. Fashioning the Face: Sensorimotor Simulation Contributes to Facial Expression Recognition. (United States)

    Wood, Adrienne; Rychlowska, Magdalena; Korb, Sebastian; Niedenthal, Paula


    When we observe a facial expression of emotion, we often mimic it. This automatic mimicry reflects underlying sensorimotor simulation that supports accurate emotion recognition. Why this is so is becoming more obvious: emotions are patterns of expressive, behavioral, physiological, and subjective feeling responses. Activation of one component can therefore automatically activate other components. When people simulate a perceived facial expression, they partially activate the corresponding emotional state in themselves, which provides a basis for inferring the underlying emotion of the expresser. We integrate recent evidence in favor of a role for sensorimotor simulation in emotion recognition. We then connect this account to a domain-general understanding of how sensory information from multiple modalities is integrated to generate perceptual predictions in the brain.

  15. Automatic Vehicle License Recognition Based on Video Vehicular Detection System

    Institute of Scientific and Technical Information of China (English)

    YANG Zhaoxuan; CHEN Yang; HE Yinghua; WU Jun


    Traditional methods of license character extraction cannot meet the requirements of recognition accuracy and speed rendered by the video vehicular detection system.Therefore, a license plate localization method based on multi-scale edge detection and a character segmentation algorithm based on Markov random field model is presented.Results of experiments demonstrate that the method yields more accurate license character extraction in contrast to traditional localization method based on edge detection by difference operator and character segmentation based on threshold.The accuracy increases from 90% to 94% under preferable illumination, while under poor condition, it increases more than 5%.When the two improved algorithms are used, the accuracy and speed of automatic license recognition meet the system's requirement even under the noisy circumstance or uneven illumination.

  16. Pattern Recognition of EEG Signals and Applications in Robotics

    Institute of Scientific and Technical Information of China (English)

    ZHANG Xiao-dong; CHENG Zhi-qiang; LI De-jun


    With the rapid development of brain computer interface (simply called BCI),electroencephalography (EEG) will be another interesting bio-electrical signal applied in robotics after EMG.In order to realize it finally,the accurate measurement and pattern recognition of EEG signal must be a very important and elementary research objective.Based on our current researches and some reports from the other international colleagues in the field,we deeply discuss the basic characteristics of EEG signal,the development and selection of EEG measurement system,feature extraction and recognition methods of EEG signal,and then review EEG's applications in robotics as well as the future research trends in this paper.

  17. Identification of Alfalfa Leaf Diseases Using Image Recognition Technology (United States)

    Qin, Feng; Liu, Dongxia; Sun, Bingda; Ruan, Liu; Ma, Zhanhong; Wang, Haiguang


    Common leaf spot (caused by Pseudopeziza medicaginis), rust (caused by Uromyces striatus), Leptosphaerulina leaf spot (caused by Leptosphaerulina briosiana) and Cercospora leaf spot (caused by Cercospora medicaginis) are the four common types of alfalfa leaf diseases. Timely and accurate diagnoses of these diseases are critical for disease management, alfalfa quality control and the healthy development of the alfalfa industry. In this study, the identification and diagnosis of the four types of alfalfa leaf diseases were investigated using pattern recognition algorithms based on image-processing technology. A sub-image with one or multiple typical lesions was obtained by artificial cutting from each acquired digital disease image. Then the sub-images were segmented using twelve lesion segmentation methods integrated with clustering algorithms (including K_means clustering, fuzzy C-means clustering and K_median clustering) and supervised classification algorithms (including logistic regression analysis, Naive Bayes algorithm, classification and regression tree, and linear discriminant analysis). After a comprehensive comparison, the segmentation method integrating the K_median clustering algorithm and linear discriminant analysis was chosen to obtain lesion images. After the lesion segmentation using this method, a total of 129 texture, color and shape features were extracted from the lesion images. Based on the features selected using three methods (ReliefF, 1R and correlation-based feature selection), disease recognition models were built using three supervised learning methods, including the random forest, support vector machine (SVM) and K-nearest neighbor methods. A comparison of the recognition results of the models was conducted. The results showed that when the ReliefF method was used for feature selection, the SVM model built with the most important 45 features (selected from a total of 129 features) was the optimal model. For this SVM model, the

  18. Do people have insight into their face recognition abilities? (United States)

    Palermo, Romina; Rossion, Bruno; Rhodes, Gillian; Laguesse, Renaud; Tez, Tolga; Hall, Bronwyn; Albonico, Andrea; Malaspina, Manuela; Daini, Roberta; Irons, Jessica; Al-Janabi, Shahd; Taylor, Libby C; Rivolta, Davide; McKone, Elinor


    Diagnosis of developmental or congenital prosopagnosia (CP) involves self-report of everyday face recognition difficulties, which are corroborated with poor performance on behavioural tests. This approach requires accurate self-evaluation. We examine the extent to which typical adults have insight into their face recognition abilities across four experiments involving nearly 300 participants. The experiments used five tests of face recognition ability: two that tap into the ability to learn and recognize previously unfamiliar faces [the Cambridge Face Memory Test, CFMT; Duchaine, B., & Nakayama, K. (2006). The Cambridge Face Memory Test: Results for neurologically intact individuals and an investigation of its validity using inverted face stimuli and prosopagnosic participants. Neuropsychologia, 44(4), 576-585. doi:10.1016/j.neuropsychologia.2005.07.001; and a newly devised test based on the CFMT but where the study phases involve watching short movies rather than viewing static faces-the CFMT-Films] and three that tap face matching [Benton Facial Recognition Test, BFRT; Benton, A., Sivan, A., Hamsher, K., Varney, N., & Spreen, O. (1983). Contribution to neuropsychological assessment. New York: Oxford University Press; and two recently devised sequential face matching tests]. Self-reported ability was measured with the 15-item Kennerknecht et al. questionnaire [Kennerknecht, I., Ho, N. Y., & Wong, V. C. (2008). Prevalence of hereditary prosopagnosia (HPA) in Hong Kong Chinese population. American Journal of Medical Genetics Part A, 146A(22), 2863-2870. doi:10.1002/ajmg.a.32552]; two single-item questions assessing face recognition ability; and a new 77-item meta-cognition questionnaire. Overall, we find that adults with typical face recognition abilities have only modest insight into their ability to recognize faces on behavioural tests. In a fifth experiment, we assess self-reported face recognition ability in people with CP and find that some people who expect to

  19. A Survey: Face Recognition Techniques

    Directory of Open Access Journals (Sweden)

    Muhammad Sharif


    Full Text Available In this study, the existing techniques of face recognition are to be encountered along with their pros and cons to conduct a brief survey. The most general methods include Eigenface (Eigenfeatures, Hidden Markov Model (HMM, geometric based and template matching approaches. This survey actually performs analysis on these approaches in order to constitute face representations which will be discussed as under. In the second phase of the survey, factors affecting the recognition rates and processes are also discussed along with the solutions provided by different authors.

  20. Simultaneous tracking and activity recognition

    DEFF Research Database (Denmark)

    Manfredotti, Cristina Elena; Fleet, David J.; Hamilton, Howard J.


    Many tracking problems involve several distinct objects interacting with each other. We develop a framework that takes into account interactions between objects allowing the recognition of complex activities. In contrast to classic approaches that consider distinct phases of tracking and activity...... be used to improve the prediction step of the tracking, while, at the same time, tracking information can be used for online activity recognition. Experimental results in two different settings show that our approach 1) decreases the error rate and improves the identity maintenance of the positional...

  1. Individual Recognition in Ant Queens

    DEFF Research Database (Denmark)

    D'Ettorre, Patrizia; Heinze, Jürgen


    Personal relationships are the cornerstone of vertebrate societies, but insect societies are either too large for individual recognition, or their members were assumed to lack the necessary cognitive abilities 1 and 2 . This paradigm has been challenged by the recent discovery that paper wasps...... recognize each other's unique facial color patterns [3] . Individual recognition is advantageous when dominance hierarchies control the partitioning of work and reproduction 2 and 4 . Here, we show that unrelated founding queens of the ant Pachycondyla villosa use chemical cues to recognize each other...

  2. Traffic-Sign Recognition Systems

    CERN Document Server

    Escalera, Sergio


    This work presents a full generic approach to the detection and recognition of traffic signs. The approach is based on the latest computer vision methods for object detection, and on powerful methods for multiclass classification. The challenge was to robustly detect a set of different sign classes in real time, and to classify each detected sign into a large, extensible set of classes. To address this challenge, several state-of-the-art methods were developed that can be used for different recognition problems. Following an introduction to the problems of traffic sign detection and categoriza

  3. Pattern Recognition Theory of Mind

    CERN Document Server

    de Paiva, Gilberto


    I propose that pattern recognition, memorization and processing are key concepts that can be a principle set for the theoretical modeling of the mind function. Most of the questions about the mind functioning can be answered by a descriptive modeling and definitions from these principles. An understandable consciousness definition can be drawn based on the assumption that a pattern recognition system can recognize its own patterns of activity. The principles, descriptive modeling and definitions can be a basis for theoretical and applied research on cognitive sciences, particularly at artificial intelligence studies.

  4. Human ear recognition by computer

    CERN Document Server

    Bhanu, Bir; Chen, Hui


    Biometrics deals with recognition of individuals based on their physiological or behavioral characteristics. The human ear is a new feature in biometrics that has several merits over the more common face, fingerprint and iris biometrics. Unlike the fingerprint and iris, it can be easily captured from a distance without a fully cooperative subject, although sometimes it may be hidden with hair, scarf and jewellery. Also, unlike a face, the ear is a relatively stable structure that does not change much with the age and facial expressions. ""Human Ear Recognition by Computer"" is the first book o

  5. Discriminative learning for speech recognition

    CERN Document Server

    He, Xiadong


    In this book, we introduce the background and mainstream methods of probabilistic modeling and discriminative parameter optimization for speech recognition. The specific models treated in depth include the widely used exponential-family distributions and the hidden Markov model. A detailed study is presented on unifying the common objective functions for discriminative learning in speech recognition, namely maximum mutual information (MMI), minimum classification error, and minimum phone/word error. The unification is presented, with rigorous mathematical analysis, in a common rational-functio

  6. Unequal recognition, misrecognition and injustice

    DEFF Research Database (Denmark)

    Lægaard, Sune


    Euro-multiculturalism is (1) concerned with religiously defined immigrant minorities; (2) sees policies of recognition as a means to secure multicultural equality between groups; (3) endorses the moderate secularism of European states; and (4) adopts a contextualist approach to answering the norm......Euro-multiculturalism is (1) concerned with religiously defined immigrant minorities; (2) sees policies of recognition as a means to secure multicultural equality between groups; (3) endorses the moderate secularism of European states; and (4) adopts a contextualist approach to answering...... endorses moderate secularism and contextualism....

  7. Acoustic modeling for emotion recognition

    CERN Document Server

    Anne, Koteswara Rao; Vankayalapati, Hima Deepthi


     This book presents state of art research in speech emotion recognition. Readers are first presented with basic research and applications – gradually more advance information is provided, giving readers comprehensive guidance for classify emotions through speech. Simulated databases are used and results extensively compared, with the features and the algorithms implemented using MATLAB. Various emotion recognition models like Linear Discriminant Analysis (LDA), Regularized Discriminant Analysis (RDA), Support Vector Machines (SVM) and K-Nearest neighbor (KNN) and are explored in detail using prosody and spectral features, and feature fusion techniques.

  8. The enigmatic mitochondrial genome of Rhabdopleura compacta (Pterobranchia reveals insights into selection of an efficient tRNA system and supports monophyly of Ambulacraria

    Directory of Open Access Journals (Sweden)

    Stadler Peter F


    Full Text Available Abstract Background The Hemichordata comprises solitary-living Enteropneusta and colonial-living Pterobranchia, sharing morphological features with both Chordata and Echinodermata. Despite their key role for understanding deuterostome evolution, hemichordate phylogeny is controversial and only few molecular data are available for phylogenetic analysis. Furthermore, mitochondrial sequences are completely lacking for pterobranchs. Therefore, we determined and analyzed the complete mitochondrial genome of the pterobranch Rhabdopleura compacta to elucidate deuterostome evolution. Thereby, we also gained important insights in mitochondrial tRNA evolution. Results The mitochondrial DNA of Rhabdopleura compacta corresponds in size and gene content to typical mitochondrial genomes of metazoans, but shows the strongest known strand-specific mutational bias in the nucleotide composition among deuterostomes with a very GT-rich main-coding strand. The order of the protein-coding genes in R. compacta is similar to that of the deuterostome ground pattern. However, the protein-coding genes have been highly affected by a strand-specific mutational pressure showing unusual codon frequency and amino acid composition. This composition caused extremely long branches in phylogenetic analyses. The unusual codon frequency points to a selection pressure on the tRNA translation system to codon-anticodon sequences of highest versatility instead of showing adaptations in anticodon sequences to the most frequent codons. Furthermore, an assignment of the codon AGG to Lysine has been detected in the mitochondrial genome of R. compacta, which is otherwise observed only in the mitogenomes of some arthropods. The genomes of these arthropods do not have such a strong strand-specific bias as found in R. compacta but possess an identical mutation in the anticodon sequence of the tRNALys. Conclusion A strong reversed asymmetrical mutational constraint in the mitochondrial genome of

  9. Virulence characteristics of Salmonella following deletion of genes encoding the tRNA modification enzymes GidA and MnmE. (United States)

    Shippy, Daniel C; Eakley, Nicholas M; Lauhon, Charles T; Bochsler, Philip N; Fadl, Amin A


    Salmonella is an important foodborne pathogen causing major public health problems throughout the world due to the consumption of contaminated food. Our previous studies have shown that deletion of glucose-inhibited division (gidA) gene significantly altered Salmonella virulence in both in vitro and in vivo models of infection. In Escherichia coli, GidA and MnmE have been shown to modify several bacterial factors by a post-transcriptional mechanism to modify tRNA. Therefore, we hypothesize that GidA and MnmE complex together to modulate virulence genes in Salmonella using a similar mechanism. To test our hypothesis, and to examine the relative contribution of GidA and MnmE in modulation of Salmonella virulence, we constructed gidA and mnmE single mutants as well as a gidA mnmE double mutant strain of Salmonella. Results from the in vitro data displayed a reduction in growth, motility, intracellular replication, and invasion of T84 intestinal epithelial cells in the mutant strains compared to the wild-type Salmonella strain. The in vivo data showed a significant attenuation of the mutant strains as indicated by the induction of inflammatory cytokines and chemokines, as well as in the severity of histopathological lesions in the liver and spleen, compared to mice infected with the wild-type strain. Also, a significant increase in the LD50 was observed in mice infected with the mutant strains, and mice immunized with the mutants were protected against a lethal dose of wild-type Salmonella. A pull-down assay indicated that Salmonella GidA and MnmE bind together, and HPLC analysis revealed that deletion of gidA and/or mnmE altered Salmonella tRNA modification. Overall, the data suggest MnmE and GidA bind together and use a post-transcriptional mechanism to modify tRNA to regulate Salmonella pathogenesis.

  10. The transition from noncoded to coded protein synthesis: did coding mRNAs arise from stability-enhancing binding partners to tRNA?

    Directory of Open Access Journals (Sweden)

    Tate Warren


    Full Text Available Abstract Background Understanding the origin of protein synthesis has been notoriously difficult. We have taken as a starting premise Wolf and Koonin's view that "evolution of the translation system is envisaged to occur in a compartmentalized ensemble of replicating, co-selected RNA segments, i.e., in an RNA world containing ribozymes with versatile activities". Presentation of the hypothesis We propose that coded protein synthesis arose from a noncoded process in an RNA world as a natural consequence of the accumulation of a range of early tRNAs and their serendipitous RNA binding partners. We propose that, initially, RNA molecules with 3' CCA termini that could be aminoacylated by ribozymes, together with an ancestral peptidyl transferase ribozyme, produced small peptides with random or repetitive sequences. Our concept is that the first tRNA arose in this context from the ligation of two RNA hairpins and could be similarly aminoacylated at its 3' end to become a substrate for peptidyl transfer catalyzed by the ancestral ribozyme. Within this RNA world we hypothesize that proto-mRNAs appeared first simply as serendipitous binding partners, forming complementary base pair interactions with the anticodon loops of tRNA pairs. Initially this may have enhanced stability of the paired tRNA molecules so they were held together in close proximity, better positioning the 3' CCA termini for peptidyl transfer and enhancing the rate of peptide synthesis. If there were a selective advantage for the ensemble through the peptide products synthesized, it would provide a natural pathway for the evolution of a coding system with the expansion of a cohort of different tRNAs and their binding partners. The whole process could have occurred quite unremarkably for such a profound acquisition. Testing the hypothesis It should be possible to test the different parts of our model using the isolated contemporary 50S ribosomal subunit initially, and then with RNAs

  11. Pattern Recognition Based Detection Recognition of Traffic Sign Using SVM

    Directory of Open Access Journals (Sweden)

    S. Sathiya


    Full Text Available The objective of this work describes a method for Traffic sign detection and recognition from the traffic panel board(signage. It detect the traffic signs especially for Indian conditions. Images are acquired through the camera and it is invariant to size then it is scaled. It consist of the following steps, first, it detect the traffic sign, if it has sufficient contrast from the background then we use sobel edge detection technique and morphological dilation. Second, extract the detected traffic sign from the board using row count and column count. Third, to extract the feature using DCT, DWT and Hybrid DWT-DCT. In training phase, DCT 20 highest energy coefficients are extracted, In DWT 300 features extracted from each traffic sign and in Hybrid DWT-DCT 20 features are extracted. Finally recognition are performed through SVM. The application is to improve the efficiency of transportation networks through applications of communication visually impaired person wear the camera to identify the traffic destination board. Experimental results show that state-of-the-art algorithms obtains highly competitive performance and is especially efficient to different levels of corruptions. The performance of Traffic Sign recognition is evaluated for Traffic Sign board image and the system achieves a recognition rate of 86% using DCT, 90% using DWT and 96% using Hybrid DWT-DCT and SVM.

  12. Improving recognition of pain by calling attention to its various faces

    NARCIS (Netherlands)

    Kunz, M; Lautenbacher, S


    BACKGROUND: The ability to accurately recognize facial expressions of pain is known to affect clinical decision making and delivery of care. Although recognition accuracy for facial expressions of pain is well above chance level, substantial shortcomings have also been reported which stress the need

  13. Predicting the Accuracy of Facial Affect Recognition: The Interaction of Child Maltreatment and Intellectual Functioning (United States)

    Shenk, Chad E.; Putnam, Frank W.; Noll, Jennie G.


    Previous research demonstrates that both child maltreatment and intellectual performance contribute uniquely to the accurate identification of facial affect by children and adolescents. The purpose of this study was to extend this research by examining whether child maltreatment affects the accuracy of facial recognition differently at varying…

  14. Robust Sign Language Recognition System Using ToF Depth Cameras

    CERN Document Server

    Zahedi, Morteza


    Sign language recognition is a difficult task, yet required for many applications in real-time speed. Using RGB cameras for recognition of sign languages is not very successful in practical situations and accurate 3D imaging requires expensive and complex instruments. With introduction of Time-of-Flight (ToF) depth cameras in recent years, it has become easier to scan the environment for accurate, yet fast depth images of the objects without the need of any extra calibrating object. In this paper, a robust system for sign language recognition using ToF depth cameras is presented for converting the recorded signs to a standard and portable XML sign language named SiGML for easy transferring and converting to real-time 3D virtual characters animations. Feature extraction using moments and classification using nearest neighbor classifier are used to track hand gestures and significant result of 100% is achieved for the proposed approach.

  15. A new paradigm for pattern recognition of drugs. (United States)

    Potemkin, Vladimir A; Grishina, Maria A


    A new paradigm is suggested for pattern recognition of drugs. The approach is based on the combined application of the 4D/3D quantitative structure-activity relationship (QSAR) algorithms BiS and ConGO. The first algorithm, BiS/MC (multiconformational), is used for the search for the conformers interacting with a receptor. The second algorithm, ConGO, has been suggested for the detailed study of the selected conformers' electron density and for the search for the electron structure fragments that determine the pharmacophore and antipharmacophore parts of the compounds. In this work we suggest using a new AlteQ method for the evaluation of the molecular electron density. AlteQ describes the experimental electron density (determined by low-temperature highly accurate X-ray analysis) much better than a number of quantum approaches. Herein this is shown using a comparison of the computed electron density with the results of highly accurate X-ray analysis. In the present study the desirability function is used for the first time for the analysis of the effects of the electron structure in the process of pattern recognition of active and inactive compounds. The suggested method for pattern recognition has been used for the investigation of various sets of compounds such as DNA-antimetabolites, fXa inhibitors, 5-HT(1A), and alpha(1)-AR receptors inhibitors. The pharmacophore and antipharmacophore fragments have been found in the electron structures of the compounds. It has been shown that the pattern recognition cross-validation quality for the datasets is unity.

  16. Pattern recognition in speech and language processing

    CERN Document Server

    Chou, Wu


    Minimum Classification Error (MSE) Approach in Pattern Recognition, Wu ChouMinimum Bayes-Risk Methods in Automatic Speech Recognition, Vaibhava Goel and William ByrneA Decision Theoretic Formulation for Adaptive and Robust Automatic Speech Recognition, Qiang HuoSpeech Pattern Recognition Using Neural Networks, Shigeru KatagiriLarge Vocabulary Speech Recognition Based on Statistical Methods, Jean-Luc GauvainToward Spontaneous Speech Recognition and Understanding, Sadaoki FuruiSpeaker Authentication, Qi Li and Biing-Hwang JuangHMMs for Language Processing Problems, Ri

  17. Fast and accurate exhaled breath ammonia measurement. (United States)

    Solga, Steven F; Mudalel, Matthew L; Spacek, Lisa A; Risby, Terence H


    This exhaled breath ammonia method uses a fast and highly sensitive spectroscopic method known as quartz enhanced photoacoustic spectroscopy (QEPAS) that uses a quantum cascade based laser. The monitor is coupled to a sampler that measures mouth pressure and carbon dioxide. The system is temperature controlled and specifically designed to address the reactivity of this compound. The sampler provides immediate feedback to the subject and the technician on the quality of the breath effort. Together with the quick response time of the monitor, this system is capable of accurately measuring exhaled breath ammonia representative of deep lung systemic levels. Because the system is easy to use and produces real time results, it has enabled experiments to identify factors that influence measurements. For example, mouth rinse and oral pH reproducibly and significantly affect results and therefore must be controlled. Temperature and mode of breathing are other examples. As our understanding of these factors evolves, error is reduced, and clinical studies become more meaningful. This system is very reliable and individual measurements are inexpensive. The sampler is relatively inexpensive and quite portable, but the monitor is neither. This limits options for some clinical studies and provides rational for future innovations.

  18. Noninvasive hemoglobin monitoring: how accurate is enough? (United States)

    Rice, Mark J; Gravenstein, Nikolaus; Morey, Timothy E


    Evaluating the accuracy of medical devices has traditionally been a blend of statistical analyses, at times without contextualizing the clinical application. There have been a number of recent publications on the accuracy of a continuous noninvasive hemoglobin measurement device, the Masimo Radical-7 Pulse Co-oximeter, focusing on the traditional statistical metrics of bias and precision. In this review, which contains material presented at the Innovations and Applications of Monitoring Perfusion, Oxygenation, and Ventilation (IAMPOV) Symposium at Yale University in 2012, we critically investigated these metrics as applied to the new technology, exploring what is required of a noninvasive hemoglobin monitor and whether the conventional statistics adequately answer our questions about clinical accuracy. We discuss the glucose error grid, well known in the glucose monitoring literature, and describe an analogous version for hemoglobin monitoring. This hemoglobin error grid can be used to evaluate the required clinical accuracy (±g/dL) of a hemoglobin measurement device to provide more conclusive evidence on whether to transfuse an individual patient. The important decision to transfuse a patient usually requires both an accurate hemoglobin measurement and a physiologic reason to elect transfusion. It is our opinion that the published accuracy data of the Masimo Radical-7 is not good enough to make the transfusion decision.

  19. Accurate free energy calculation along optimized paths. (United States)

    Chen, Changjun; Xiao, Yi


    The path-based methods of free energy calculation, such as thermodynamic integration and free energy perturbation, are simple in theory, but difficult in practice because in most cases smooth paths do not exist, especially for large molecules. In this article, we present a novel method to build the transition path of a peptide. We use harmonic potentials to restrain its nonhydrogen atom dihedrals in the initial state and set the equilibrium angles of the potentials as those in the final state. Through a series of steps of geometrical optimization, we can construct a smooth and short path from the initial state to the final state. This path can be used to calculate free energy difference. To validate this method, we apply it to a small 10-ALA peptide and find that the calculated free energy changes in helix-helix and helix-hairpin transitions are both self-convergent and cross-convergent. We also calculate the free energy differences between different stable states of beta-hairpin trpzip2, and the results show that this method is more efficient than the conventional molecular dynamics method in accurate free energy calculation.

  20. Accurate fission data for nuclear safety

    CERN Document Server

    Solders, A; Jokinen, A; Kolhinen, V S; Lantz, M; Mattera, A; Penttila, H; Pomp, S; Rakopoulos, V; Rinta-Antila, S


    The Accurate fission data for nuclear safety (AlFONS) project aims at high precision measurements of fission yields, using the renewed IGISOL mass separator facility in combination with a new high current light ion cyclotron at the University of Jyvaskyla. The 30 MeV proton beam will be used to create fast and thermal neutron spectra for the study of neutron induced fission yields. Thanks to a series of mass separating elements, culminating with the JYFLTRAP Penning trap, it is possible to achieve a mass resolving power in the order of a few hundred thousands. In this paper we present the experimental setup and the design of a neutron converter target for IGISOL. The goal is to have a flexible design. For studies of exotic nuclei far from stability a high neutron flux (10^12 neutrons/s) at energies 1 - 30 MeV is desired while for reactor applications neutron spectra that resembles those of thermal and fast nuclear reactors are preferred. It is also desirable to be able to produce (semi-)monoenergetic neutrons...

  1. Towards Accurate Modeling of Moving Contact Lines

    CERN Document Server

    Holmgren, Hanna


    A main challenge in numerical simulations of moving contact line problems is that the adherence, or no-slip boundary condition leads to a non-integrable stress singularity at the contact line. In this report we perform the first steps in developing the macroscopic part of an accurate multiscale model for a moving contact line problem in two space dimensions. We assume that a micro model has been used to determine a relation between the contact angle and the contact line velocity. An intermediate region is introduced where an analytical expression for the velocity exists. This expression is used to implement boundary conditions for the moving contact line at a macroscopic scale, along a fictitious boundary located a small distance away from the physical boundary. Model problems where the shape of the interface is constant thought the simulation are introduced. For these problems, experiments show that the errors in the resulting contact line velocities converge with the grid size $h$ at a rate of convergence $...

  2. Does a pneumotach accurately characterize voice function? (United States)

    Walters, Gage; Krane, Michael


    A study is presented which addresses how a pneumotach might adversely affect clinical measurements of voice function. A pneumotach is a device, typically a mask, worn over the mouth, in order to measure time-varying glottal volume flow. By measuring the time-varying difference in pressure across a known aerodynamic resistance element in the mask, the glottal volume flow waveform is estimated. Because it adds aerodynamic resistance to the vocal system, there is some concern that using a pneumotach may not accurately portray the behavior of the voice. To test this hypothesis, experiments were performed in a simplified airway model with the principal dimensions of an adult human upper airway. A compliant constriction, fabricated from silicone rubber, modeled the vocal folds. Variations of transglottal pressure, time-averaged volume flow, model vocal fold vibration amplitude, and radiated sound with subglottal pressure were performed, with and without the pneumotach in place, and differences noted. Acknowledge support of NIH Grant 2R01DC005642-10A1.

  3. Accurate lineshape spectroscopy and the Boltzmann constant. (United States)

    Truong, G-W; Anstie, J D; May, E F; Stace, T M; Luiten, A N


    Spectroscopy has an illustrious history delivering serendipitous discoveries and providing a stringent testbed for new physical predictions, including applications from trace materials detection, to understanding the atmospheres of stars and planets, and even constraining cosmological models. Reaching fundamental-noise limits permits optimal extraction of spectroscopic information from an absorption measurement. Here, we demonstrate a quantum-limited spectrometer that delivers high-precision measurements of the absorption lineshape. These measurements yield a very accurate measurement of the excited-state (6P1/2) hyperfine splitting in Cs, and reveals a breakdown in the well-known Voigt spectral profile. We develop a theoretical model that accounts for this breakdown, explaining the observations to within the shot-noise limit. Our model enables us to infer the thermal velocity dispersion of the Cs vapour with an uncertainty of 35 p.p.m. within an hour. This allows us to determine a value for Boltzmann's constant with a precision of 6 p.p.m., and an uncertainty of 71 p.p.m.

  4. Accurate upper body rehabilitation system using kinect. (United States)

    Sinha, Sanjana; Bhowmick, Brojeshwar; Chakravarty, Kingshuk; Sinha, Aniruddha; Das, Abhijit


    The growing importance of Kinect as a tool for clinical assessment and rehabilitation is due to its portability, low cost and markerless system for human motion capture. However, the accuracy of Kinect in measuring three-dimensional body joint center locations often fails to meet clinical standards of accuracy when compared to marker-based motion capture systems such as Vicon. The length of the body segment connecting any two joints, measured as the distance between three-dimensional Kinect skeleton joint coordinates, has been observed to vary with time. The orientation of the line connecting adjoining Kinect skeletal coordinates has also been seen to differ from the actual orientation of the physical body segment. Hence we have proposed an optimization method that utilizes Kinect Depth and RGB information to search for the joint center location that satisfies constraints on body segment length and as well as orientation. An experimental study have been carried out on ten healthy participants performing upper body range of motion exercises. The results report 72% reduction in body segment length variance and 2° improvement in Range of Motion (ROM) angle hence enabling to more accurate measurements for upper limb exercises.

  5. Accurate thermoplasmonic simulation of metallic nanoparticles (United States)

    Yu, Da-Miao; Liu, Yan-Nan; Tian, Fa-Lin; Pan, Xiao-Min; Sheng, Xin-Qing


    Thermoplasmonics leads to enhanced heat generation due to the localized surface plasmon resonances. The measurement of heat generation is fundamentally a complicated task, which necessitates the development of theoretical simulation techniques. In this paper, an efficient and accurate numerical scheme is proposed for applications with complex metallic nanostructures. Light absorption and temperature increase are, respectively, obtained by solving the volume integral equation (VIE) and the steady-state heat diffusion equation through the method of moments (MoM). Previously, methods based on surface integral equations (SIEs) were utilized to obtain light absorption. However, computing light absorption from the equivalent current is as expensive as O(NsNv), where Ns and Nv, respectively, denote the number of surface and volumetric unknowns. Our approach reduces the cost to O(Nv) by using VIE. The accuracy, efficiency and capability of the proposed scheme are validated by multiple simulations. The simulations show that our proposed method is more efficient than the approach based on SIEs under comparable accuracy, especially for the case where many incidents are of interest. The simulations also indicate that the temperature profile can be tuned by several factors, such as the geometry configuration of array, beam direction, and light wavelength.

  6. Fast and Provably Accurate Bilateral Filtering. (United States)

    Chaudhury, Kunal N; Dabhade, Swapnil D


    The bilateral filter is a non-linear filter that uses a range filter along with a spatial filter to perform edge-preserving smoothing of images. A direct computation of the bilateral filter requires O(S) operations per pixel, where S is the size of the support of the spatial filter. In this paper, we present a fast and provably accurate algorithm for approximating the bilateral filter when the range kernel is Gaussian. In particular, for box and Gaussian spatial filters, the proposed algorithm can cut down the complexity to O(1) per pixel for any arbitrary S . The algorithm has a simple implementation involving N+1 spatial filterings, where N is the approximation order. We give a detailed analysis of the filtering accuracy that can be achieved by the proposed approximation in relation to the target bilateral filter. This allows us to estimate the order N required to obtain a given accuracy. We also present comprehensive numerical results to demonstrate that the proposed algorithm is competitive with the state-of-the-art methods in terms of speed and accuracy.

  7. Education Quality, Reading Recognition, and Racial Differences in the Neuropsychological Outcome from Traumatic Brain Injury (United States)

    Silverberg, Noah D.; Hanks, Robin A.; Tompkins, Season C.


    Ethnically diverse examinees tend to perform lower on neuropsychological tests. The practice of adjusting normative comparisons for the education level and/or race to prevent overpathologizing low scores is problematic. Education quality, as measured by reading recognition, appears to be a more accurate benchmark for premorbid functioning in certain populations. The present study aimed to extend this line of research to traumatic brain injury (TBI). We hypothesized that a measure of reading recognition, the Wechsler Test of Adult Reading (WTAR), would account for racial differences in neuropsychological performance after TBI. Fifty participants (72% African American, 28% Caucasian) with moderate to severe TBI underwent neuropsychological testing at 1-year post-injury. Reading recognition accounted for all the same variance in neuropsychological performance as race and education (together), as well as considerable additional variance. Estimation of premorbid functioning in African Americans with TBI could be refined by considering reading recognition. PMID:23858087

  8. Low-Complexity Hand Gesture Recognition System for Continuous Streams of Digits and Letters. (United States)

    Poularakis, Stergios; Katsavounidis, Ioannis


    In this paper, we propose a complete gesture recognition framework based on maximum cosine similarity and fast nearest neighbor (NN) techniques, which offers high-recognition accuracy and great computational advantages for three fundamental problems of gesture recognition: 1) isolated recognition; 2) gesture verification; and 3) gesture spotting on continuous data streams. To support our arguments, we provide a thorough evaluation on three large publicly available databases, examining various scenarios, such as noisy environments, limited number of training examples, and time delay in system's response. Our experimental results suggest that this simple NN-based approach is quite accurate for trajectory classification of digits and letters and could become a promising approach for implementations on low-power embedded systems.


    Directory of Open Access Journals (Sweden)

    D. Sathish Kumar


    Full Text Available Face recognition is one of the intensive areas of research in computer vision and pattern recognition but many of which are focused on recognition of faces under varying facial expressions and pose variation. A constrained optical flow algorithm discussed in this paper, recognizes facial images involving various expressions based on motion vector computation. In this paper, an optical flow computation algorithm which computes the frames of varying facial gestures, and integrating with synthesized image in a probabilistic environment has been proposed. Also Histogram Equalization technique has been used to overcome the effect of illuminations while capturing the input data using camera devices. It also enhances the contrast of the image for better processing. The experimental results confirm that the proposed face recognition system is more robust and recognizes the facial images under varying expressions and pose variations more accurately.

  10. Education quality, reading recognition, and racial differences in the neuropsychological outcome from traumatic brain injury. (United States)

    Silverberg, Noah D; Hanks, Robin A; Tompkins, Season C


    Ethnically diverse examinees tend to perform lower on neuropsychological tests. The practice of adjusting normative comparisons for the education level and/or race to prevent overpathologizing low scores is problematic. Education quality, as measured by reading recognition, appears to be a more accurate benchmark for premorbid functioning in certain populations. The present study aimed to extend this line of research to traumatic brain injury (TBI). We hypothesized that a measure of reading recognition, the Wechsler Test of Adult Reading (WTAR), would account for racial differences in neuropsychological performance after TBI. Fifty participants (72% African American, 28% Caucasian) with moderate to severe TBI underwent neuropsychological testing at 1-year post-injury. Reading recognition accounted for all the same variance in neuropsychological performance as race and education (together), as well as considerable additional variance. Estimation of premorbid functioning in African Americans with TBI could be refined by considering reading recognition.

  11. Towards automatic forensic face recognition

    NARCIS (Netherlands)

    Ali, Tauseef; Spreeuwers, Luuk; Veldhuis, Raymond


    In this paper we present a methodology and experimental results for evidence evaluation in the context of forensic face recognition. In forensic applications, the matching score (hereafter referred to as similarity score) from a biometric system must be represented as a Likelihood Ratio (LR). In our

  12. Output Interference in Recognition Memory (United States)

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


    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…

  13. Face recognition, a landmarks tale

    NARCIS (Netherlands)

    Beumer, Gerrit Maarten


    Face recognition is a technology that appeals to the imagination of many people. This is particularly reflected in the popularity of science-fiction films and forensic detective series such as CSI, CSI New York, CSI Miami, Bones and NCIS. Although these series tend to be set in the present, their a

  14. Mobile Visual Recognition on Smartphones

    Directory of Open Access Journals (Sweden)

    Zhenwen Gui


    Full Text Available This paper addresses the recognition of large-scale outdoor scenes on smartphones by fusing outputs of inertial sensors and computer vision techniques. The main contributions can be summarized as follows. Firstly, we propose an ORD (overlap region divide method to plot image position area, which is fast enough to find the nearest visiting area and can also reduce the search range compared with the traditional approaches. Secondly, the vocabulary tree-based approach is improved by introducing GAGCC (gravity-aligned geometric consistency constraint. Our method involves no operation in the high-dimensional feature space and does not assume a global transform between a pair of images. Thus, it substantially reduces the computational complexity and memory usage, which makes the city scale image recognition feasible on the smartphone. Experiments on a collected database including 0.16 million images show that the proposed method demonstrates excellent recognition performance, while maintaining the average recognition time about 1 s.

  15. Action Recognition using Motion Primitives

    DEFF Research Database (Denmark)

    Moeslund, Thomas B.; Fihl, Preben; Holte, Michael Boelstoft

    The number of potential applications has made automatic recognition of human actions a very active research area. Different approaches have been followed based on trajectories through some state space. In this paper we also model an action as a trajectory through a state space, but we represent t...

  16. Motion Primitives for Action Recognition

    DEFF Research Database (Denmark)

    Fihl, Preben; Holte, Michael Boelstoft; Moeslund, Thomas B.


    The number of potential applications has made automatic recognition of human actions a very active research area. Different approaches have been followed based on trajectories through some state space. In this paper we also model an action as a trajectory through a state space, but we represent t...

  17. Emotion recognition during cocaine intoxication. (United States)

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


    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.

  18. Phosphate Recognition in Structural Biology

    NARCIS (Netherlands)

    Hirsch, Anna K.H.; Fischer, Felix R.; Diederich, François


    Drug-discovery research in the past decade has seen an increased selection of targets with phosphate recognition sites, such as protein kinases and phosphatases, in the past decade. This review attempts, with the help of database-mining tools, to give an overview of the most important principles in

  19. Age-invariant face recognition. (United States)

    Park, Unsang; Tong, Yiying; Jain, Anil K


    One of the challenges in automatic face recognition is to achieve temporal invariance. In other words, the goal is to come up with a representation and matching scheme that is robust to changes due to facial aging. Facial aging is a complex process that affects both the 3D shape of the face and its texture (e.g., wrinkles). These shape and texture changes degrade the performance of automatic face recognition systems. However, facial aging has not received substantial attention compared to other facial variations due to pose, lighting, and expression. We propose a 3D aging modeling technique and show how it can be used to compensate for the age variations to improve the face recognition performance. The aging modeling technique adapts view-invariant 3D face models to the given 2D face aging database. The proposed approach is evaluated on three different databases (i.g., FG-NET, MORPH, and BROWNS) using FaceVACS, a state-of-the-art commercial face recognition engine.

  20. License plate recognition using DTCNNs

    NARCIS (Netherlands)

    ter Brugge, M.H; Stevens, J.H; Nijhuis, J.A G; Spaanenburg, L; Tavsanonoglu, V


    Automatic license plate recognition requires a series of complex image processing steps. For practical use, the amount of data to he processed must be minimized early on. This paper shows that the computationally most intensive steps can be realized by DTCNNs. Moreover; high-level operations like fi