Array based Discovery of Aptamer Pairs (Open Access Publisher’s Version)

DTIC Science & Technology

2014-12-11

Array-based Discovery of Aptamer Pairs Minseon Cho,†,‡ Seung Soo Oh,‡ Jeff Nie,§ Ron Stewart,§ Monte J. Radeke,⊥ Michael Eisenstein,†,‡ Peter J...bidentate” target recognition, with affinities greatly exceeding either monovalent component. DNA aptamers are especially well-suited for such...constructs, because they can be linked via standard synthesis techniques without requiring chemical conjugation. Unfortunately, aptamer pairs are difficult

Structural basis of DNA folding and recognition in an AMP-DNA aptamer complex: distinct architectures but common recognition motifs for DNA and RNA aptamers complexed to AMP.

PubMed

Lin, C H; Patel, D J

1997-11-01

Structural studies by nuclear magnetic resonance (NMR) of RNA and DNA aptamer complexes identified through in vitro selection and amplification have provided a wealth of information on RNA and DNA tertiary structure and molecular recognition in solution. The RNA and DNA aptamers that target ATP (and AMP) with micromolar affinity exhibit distinct binding site sequences and secondary structures. We report below on the tertiary structure of the AMP-DNA aptamer complex in solution and compare it with the previously reported tertiary structure of the AMP-RNA aptamer complex in solution. The solution structure of the AMP-DNA aptamer complex shows, surprisingly, that two AMP molecules are intercalated at adjacent sites within a rectangular widened minor groove. Complex formation involves adaptive binding where the asymmetric internal bubble of the free DNA aptamer zippers up through formation of a continuous six-base mismatch segment which includes a pair of adjacent three-base platforms. The AMP molecules pair through their Watson-Crick edges with the minor groove edges of guanine residues. These recognition G.A mismatches are flanked by sheared G.A and reversed Hoogsteen G.G mismatch pairs. The AMP-DNA aptamer and AMP-RNA aptamer complexes have distinct tertiary structures and binding stoichiometries. Nevertheless, both complexes have similar structural features and recognition alignments in their binding pockets. Specifically, AMP targets both DNA and RNA aptamers by intercalating between purine bases and through identical G.A mismatch formation. The recognition G.A mismatch stacks with a reversed Hoogsteen G.G mismatch in one direction and with an adenine base in the other direction in both complexes. It is striking that DNA and RNA aptamers selected independently from libraries of 10(14) molecules in each case utilize identical mismatch alignments for molecular recognition with micromolar affinity within binding-site pockets containing common structural elements.

Video-based face recognition via convolutional neural networks

NASA Astrophysics Data System (ADS)

Bao, Tianlong; Ding, Chunhui; Karmoshi, Saleem; Zhu, Ming

2017-06-01

Face recognition has been widely studied recently while video-based face recognition still remains a challenging task because of the low quality and large intra-class variation of video captured face images. In this paper, we focus on two scenarios of video-based face recognition: 1)Still-to-Video(S2V) face recognition, i.e., querying a still face image against a gallery of video sequences; 2)Video-to-Still(V2S) face recognition, in contrast to S2V scenario. A novel method was proposed in this paper to transfer still and video face images to an Euclidean space by a carefully designed convolutional neural network, then Euclidean metrics are used to measure the distance between still and video images. Identities of still and video images that group as pairs are used as supervision. In the training stage, a joint loss function that measures the Euclidean distance between the predicted features of training pairs and expanding vectors of still images is optimized to minimize the intra-class variation while the inter-class variation is guaranteed due to the large margin of still images. Transferred features are finally learned via the designed convolutional neural network. Experiments are performed on COX face dataset. Experimental results show that our method achieves reliable performance compared with other state-of-the-art methods.

Associative recognition: a case of recall-to-reject processing.

PubMed

Rotello, C M; Heit, E

2000-09-01

Two-process accounts of recognition memory assume that memory judgments are based on both a rapidly available familiarity-based process and a slower, more accurate, recall-based mechanism. Past experiments on the time course of item recognition have not supported the recall-to-reject account of the second process, in which the retrieval of an old item is used to reject a similar foil (Rotello & Heit, 1999). In three new experiments, using analyses similar to those of Rotello and Heit, we found robust evidence for recall-to-reject processing in associative recognition, for word pairs, and for list-discrimination judgments. Put together, these results have implications for two-process accounts of recognition.

Distinguishing familiarity from fluency for the compound word pair effect in associative recognition.

PubMed

Ahmad, Fahad N; Hockley, William E

2017-09-01

We examined whether processing fluency contributes to associative recognition of unitized pre-experimental associations. In Experiments 1A and 1B, we minimized perceptual fluency by presenting each word of pairs on separate screens at both study and test, yet the compound word (CW) effect (i.e., hit and false-alarm rates greater for CW pairs with no difference in discrimination) did not reduce. In Experiments 2A and 2B, conceptual fluency was examined by comparing transparent (e.g., hand bag) and opaque (e.g., rag time) CW pairs in lexical decision and associative recognition tasks. Lexical decision was faster for transparent CWs (Experiment 2A) but in associative recognition, the CW effect did not differ by CW pair type (Experiment 2B). In Experiments 3A and 3B, we examined whether priming that increases processing fluency would influence the CW effect. In Experiment 3A, CW and non-compound word pairs were preceded with matched and mismatched primes at test in an associative recognition task. In Experiment 3B, only transparent and opaque CW pairs were presented. Results showed that presenting matched versus mismatched primes at test did not influence the CW effect. The CW effect in yes-no associative recognition is due to reliance on enhanced familiarity of unitized CW pairs.

Stringent Nucleotide Recognition by the Ribosome at the Middle Codon Position

PubMed Central

Liu, Wei; Shin, Dongwon; Ng, Martin; Sanbonmatsu, Karissa Y.; Tor, Yitzhak; Cooperman, Barry S.

2017-01-01

Accurate translation of the genetic code depends on mRNA:tRNA codon:anticodon base pairing. Here we exploit an emissive, isosteric adenosine surrogate that allows direct measurement of the kinetics of codon:anticodon base formation during protein synthesis. Our results suggest that codon:anticodon base pairing is subject to tighter constraints at the middle position than at the 5′- and 3′-positions, and further suggest a sequential mechanism of formation of the three base pairs in the codon:anticodon helix. PMID:28850078

Modelling of DNA-protein recognition

NASA Technical Reports Server (NTRS)

Rein, R.; Garduno, R.; Colombano, S.; Nir, S.; Haydock, K.; Macelroy, R. D.

1980-01-01

Computer model-building procedures using stereochemical principles together with theoretical energy calculations appear to be, at this stage, the most promising route toward the elucidation of DNA-protein binding schemes and recognition principles. A review of models and bonding principles is conducted and approaches to modeling are considered, taking into account possible di-hydrogen-bonding schemes between a peptide and a base (or a base pair) of a double-stranded nucleic acid in the major groove, aspects of computer graphic modeling, and a search for isogeometric helices. The energetics of recognition complexes is discussed and several models for peptide DNA recognition are presented.

A benefit of context reinstatement to recognition memory in aging: the role of familiarity processes.

PubMed

Ward, Emma V; Maylor, Elizabeth A; Poirier, Marie; Korko, Malgorzata; Ruud, Jens C M

2017-11-01

Reinstatement of encoding context facilitates memory for targets in young and older individuals (e.g., a word studied on a particular background scene is more likely to be remembered later if it is presented on the same rather than a different scene or no scene), yet older adults are typically inferior at recalling and recognizing target-context pairings. This study examined the mechanisms of the context effect in normal aging. Age differences in word recognition by context condition (original, switched, none, new), and the ability to explicitly remember target-context pairings were investigated using word-scene pairs (Experiment 1) and word-word pairs (Experiment 2). Both age groups benefited from context reinstatement in item recognition, although older adults were significantly worse than young adults at identifying original pairings and at discriminating between original and switched pairings. In Experiment 3, participants were given a three-alternative forced-choice recognition task that allowed older individuals to draw upon intact familiarity processes in selecting original pairings. Performance was age equivalent. Findings suggest that heightened familiarity associated with context reinstatement is useful for boosting recognition memory in aging.

Improving associative memory in older adults with unitization.

PubMed

Ahmad, Fahad N; Fernandes, Myra; Hockley, William E

2015-01-01

We examined if unitization inherent preexperimentally could reduce the associative deficit in older adults. In Experiment 1, younger and older adults studied compound word (CW; e.g., store keeper) and noncompound word (NCW; e.g., needle birth) pairs. We found a reduction in the age-related associative deficit such that older but not younger adults showed a discrimination advantage for CW relative to NCW pairs on a yes-no associative recognition test. These results suggest that CW compared to NCW word pairs provide schematic support that older adults can use to improve their memory. In Experiment 2, reducing study time in younger adults decreased associative recognition performance, but did not produce a discrimination advantage for CW pairs. In Experiment 3, both older and younger adults showed a discrimination advantage for CW pairs on a two-alternative forced-choice recognition test, which encourages greater use of familiarity. These results suggest that test format influenced young adults' use of familiarity during associative recognition of unitized pairs, and that older adults rely more on familiarity than recollection for associative recognition. Unitization of preexperimental associations, as in CW pairs, can alleviate age-related associative deficits.

Recognition tunneling measurement of the conductance of DNA bases embedded in self-assembled monolayers.

PubMed

Huang, Shuo; Chang, Shuai; He, Jin; Zhang, Peiming; Liang, Feng; Tuchband, Michael; Li, Shengqing; Lindsay, Stuart

2010-12-09

The DNA bases interact strongly with gold electrodes, complicating efforts to measure the tunneling conductance through hydrogen-bonded Watson Crick base pairs. When bases are embedded in a self-assembled alkane-thiol monolayer to minimize these interactions, new features appear in the tunneling data. These new features track the predictions of density-functional calculations quite well, suggesting that they reflect tunnel conductance through hydrogen-bonded base pairs.

Recognition tunneling measurement of the conductance of DNA bases embedded in self-assembled monolayers

PubMed Central

Huang, Shuo; Chang, Shuai; He, Jin; Zhang, Peiming; Liang, Feng; Tuchband, Michael; Li, Shengqing; Lindsay, Stuart

2010-01-01

The DNA bases interact strongly with gold electrodes, complicating efforts to measure the tunneling conductance through hydrogen-bonded Watson Crick base pairs. When bases are embedded in a self-assembled alkane-thiol monolayer to minimize these interactions, new features appear in the tunneling data. These new features track the predictions of density-functional calculations quite well, suggesting that they reflect tunnel conductance through hydrogen-bonded base pairs. PMID:21197382

Support Vector Machine-based classification of protein folds using the structural properties of amino acid residues and amino acid residue pairs.

PubMed

Shamim, Mohammad Tabrez Anwar; Anwaruddin, Mohammad; Nagarajaram, H A

2007-12-15

Fold recognition is a key step in the protein structure discovery process, especially when traditional sequence comparison methods fail to yield convincing structural homologies. Although many methods have been developed for protein fold recognition, their accuracies remain low. This can be attributed to insufficient exploitation of fold discriminatory features. We have developed a new method for protein fold recognition using structural information of amino acid residues and amino acid residue pairs. Since protein fold recognition can be treated as a protein fold classification problem, we have developed a Support Vector Machine (SVM) based classifier approach that uses secondary structural state and solvent accessibility state frequencies of amino acids and amino acid pairs as feature vectors. Among the individual properties examined secondary structural state frequencies of amino acids gave an overall accuracy of 65.2% for fold discrimination, which is better than the accuracy by any method reported so far in the literature. Combination of secondary structural state frequencies with solvent accessibility state frequencies of amino acids and amino acid pairs further improved the fold discrimination accuracy to more than 70%, which is approximately 8% higher than the best available method. In this study we have also tested, for the first time, an all-together multi-class method known as Crammer and Singer method for protein fold classification. Our studies reveal that the three multi-class classification methods, namely one versus all, one versus one and Crammer and Singer method, yield similar predictions. Dataset and stand-alone program are available upon request.

Superficial Priming in Episodic Recognition

ERIC Educational Resources Information Center

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

2010-01-01

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

The picture superiority effect in associative recognition.

PubMed

Hockley, William E

2008-10-01

The picture superiority effect has been well documented in tests of item recognition and recall. The present study shows that the picture superiority effect extends to associative recognition. In three experiments, students studied lists consisting of random pairs of concrete words and pairs of line drawings; then they discriminated between intact (old) and rearranged (new) pairs of words and pictures at test. The discrimination advantage for pictures over words was seen in a greater hit rate for intact picture pairs, but there was no difference in the false alarm rates for the two types of stimuli. That is, there was no mirror effect. The same pattern of results was found when the test pairs consisted of the verbal labels of the pictures shown at study (Experiment 4), indicating that the hit rate advantage for picture pairs represents an encoding benefit. The results have implications for theories of the picture superiority effect and models of associative recognition.

Early Decomposition in Visual Word Recognition: Dissociating Morphology, Form, and Meaning

ERIC Educational Resources Information Center

Marslen-Wilson, William D.; Bozic, Mirjana; Randall, Billi

2008-01-01

The role of morphological, semantic, and form-based factors in the early stages of visual word recognition was investigated across different SOAs in a masked priming paradigm, focusing on English derivational morphology. In a first set of experiments, stimulus pairs co-varying in morphological decomposability and in semantic and orthographic…

Differences in binding and monitoring mechanisms contribute to lifespan age differences in false memory.

PubMed

Fandakova, Yana; Shing, Yee Lee; Lindenberger, Ulman

2013-10-01

Based on a 2-component framework of episodic memory development across the lifespan (Shing & Lindenberger, 2011), we examined the contribution of memory-related binding and monitoring processes to false memory susceptibility in childhood and old age. We administered a repeated continuous recognition task to children (N = 20, 10-12 years), younger adults (N = 20, 20-27 years), and older adults (N = 21, 68-76 years). Participants saw the same set of unrelated word pairs in 3 consecutive runs and their task was to identify pair reoccurrences within runs. Across runs, correct detection of repeated pairs decreased in children only, whereas false recognition of lure pairs showed a greater increase in older adults than in children or younger adults. False recognition of rearranged pairs decreased across runs for all participants. This decrease was most pronounced in children, in particular for high-confidence memory errors. We conclude that memory binding mechanisms are sufficiently developed in children to facilitate memory monitoring and reduce false memory for associative information. In contrast, older adults show senescent impairments in both binding and monitoring mechanisms that both contribute to elevated illusory recollections in old age. We conclude that binding and monitoring processes during memory performance follow different developmental trajectories from childhood to old age.

Simplified biased random walk model for RecA-protein-mediated homology recognition offers rapid and accurate self-assembly of long linear arrays of binding sites

NASA Astrophysics Data System (ADS)

Kates-Harbeck, Julian; Tilloy, Antoine; Prentiss, Mara

2013-07-01

Inspired by RecA-protein-based homology recognition, we consider the pairing of two long linear arrays of binding sites. We propose a fully reversible, physically realizable biased random walk model for rapid and accurate self-assembly due to the spontaneous pairing of matching binding sites, where the statistics of the searched sample are included. In the model, there are two bound conformations, and the free energy for each conformation is a weakly nonlinear function of the number of contiguous matched bound sites.

Performance of Language-Coordinated Collective Systems: A Study of Wine Recognition and Description

PubMed Central

Zubek, Julian; Denkiewicz, Michał; Dębska, Agnieszka; Radkowska, Alicja; Komorowska-Mach, Joanna; Litwin, Piotr; Stępień, Magdalena; Kucińska, Adrianna; Sitarska, Ewa; Komorowska, Krystyna; Fusaroli, Riccardo; Tylén, Kristian; Rączaszek-Leonardi, Joanna

2016-01-01

Most of our perceptions of and engagements with the world are shaped by our immersion in social interactions, cultural traditions, tools and linguistic categories. In this study we experimentally investigate the impact of two types of language-based coordination on the recognition and description of complex sensory stimuli: that of red wine. Participants were asked to taste, remember and successively recognize samples of wines within a larger set in a two-by-two experimental design: (1) either individually or in pairs, and (2) with or without the support of a sommelier card—a cultural linguistic tool designed for wine description. Both effectiveness of recognition and the kinds of errors in the four conditions were analyzed. While our experimental manipulations did not impact recognition accuracy, bias-variance decomposition of error revealed non-trivial differences in how participants solved the task. Pairs generally displayed reduced bias and increased variance compared to individuals, however the variance dropped significantly when they used the sommelier card. The effect of sommelier card reducing the variance was observed only in pairs, individuals did not seem to benefit from the cultural linguistic tool. Analysis of descriptions generated with the aid of sommelier cards shows that pairs were more coherent and discriminative than individuals. The findings are discussed in terms of global properties and dynamics of collective systems when constrained by different types of cultural practices. PMID:27729875

Evidence for conformational capture mechanism for damage recognition by NER protein XPC/Rad4.

NASA Astrophysics Data System (ADS)

Chakraborty, Sagnik; Steinbach, Peter J.; Paul, Debamita; Min, Jung-Hyun; Ansari, Anjum

Altered flexibility of damaged DNA sites is considered to play an important role in damage recognition by DNA repair proteins. Characterizing lesion-induced DNA dynamics has remained a challenge. We have combined ps-resolved fluorescence lifetime measurements with cytosine analog FRET pair uniquely sensitive to local unwinding/twisting to analyze DNA conformational distributions. This innovative approach maps out with unprecedented sensitivity the alternative conformations accessible to a series of DNA constructs containing 3-base-pair mismatch, suitable model lesions for the DNA repair protein xeroderma pigmentosum C (XPC) complex. XPC initiates eukaryotic nucleotide excision repair by recognizing various DNA lesions primarily through DNA deformability. Structural studies show that Rad4 (yeast ortholog of XPC) unwinds DNA at the lesion site and flips out two nucleotide pairs. Our results elucidate a broad range of conformations accessible to mismatched DNA even in the absence of the protein. Notably, the most severely distorted conformations share remarkable resemblance to the deformed conformation seen in the crystal structure of the Rad4-bound ``recognition'' complex supporting for the first time a possible ``conformational capture'' mechanism for damage recognition by XPC/Rad4. NSF Univ of Illinois-Chicago.

Extending the language of DNA molecular recognition by polyamides: unexpected influence of imidazole and pyrrole arrangement on binding affinity and specificity.

PubMed

Buchmueller, Karen L; Staples, Andrew M; Howard, Cameron M; Horick, Sarah M; Uthe, Peter B; Le, N Minh; Cox, Kari K; Nguyen, Binh; Pacheco, Kimberly A O; Wilson, W David; Lee, Moses

2005-01-19

Pyrrole (Py) and imidazole (Im) polyamides can be designed to target specific DNA sequences. The effect that the pyrrole and imidazole arrangement, plus DNA sequence, have on sequence specificity and binding affinity has been investigated using DNA melting (DeltaT(M)), circular dichroism (CD), and surface plasmon resonance (SPR) studies. SPR results obtained from a complete set of triheterocyclic polyamides show a dramatic difference in the affinity of f-ImPyIm for its cognate DNA (K(eq) = 1.9 x 10(8) M(-1)) and f-PyPyIm for its cognate DNA (K(eq) = 5.9 x 10(5) M(-1)), which could not have been anticipated prior to characterization of these compounds. Moreover, f-ImPyIm has a 10-fold greater affinity for CGCG than distamycin A has for its cognate, AATT. To understand this difference, the triamide dimers are divided into two structural groupings: central and terminal pairings. The four possible central pairings show decreasing selectivity and affinity for their respective cognate sequences: -ImPy > -PyPy- > -PyIm- approximately -ImIm-. These results extend the language of current design motifs for polyamide sequence recognition to include the use of "words" for recognizing two adjacent base pairs, rather than "letters" for binding to single base pairs. Thus, polyamides designed to target Watson-Crick base pairs should utilize the strength of -ImPy- and -PyPy- central pairings. The f/Im and f/Py terminal groups yielded no advantage for their respective C/G or T/A base pairs. The exception is with the -ImPy- central pairing, for which f/Im has a 10-fold greater affinity for C/G than f/Py has for T/A.

Polymerase recognition of 2-thio-iso-guanine·5-methyl-4-pyrimidinone (iGs·P)--A new DD/AA base pair.

PubMed

Lee, Dong-Kye; Switzer, Christopher

2016-02-15

Polymerase specificity is reported for a previously unknown base pair with a non-standard DD/AA hydrogen bonding pattern: 2-thio-iso-guanine·5-methyl-4-pyrimidinone. Our findings suggest that atomic substitution may provide a solution for low fidelity previously associated with enzymatic copying of iso-guanine. Copyright © 2016 Elsevier Ltd. All rights reserved.

Individual recognition based on communication behaviour of male fowl.

PubMed

Smith, Carolynn L; Taubert, Jessica; Weldon, Kimberly; Evans, Christopher S

2016-04-01

Correctly directing social behaviour towards a specific individual requires an ability to discriminate between conspecifics. The mechanisms of individual recognition include phenotype matching and familiarity-based recognition. Communication-based recognition is a subset of familiarity-based recognition wherein the classification is based on behavioural or distinctive signalling properties. Male fowl (Gallus gallus) produce a visual display (tidbitting) upon finding food in the presence of a female. Females typically approach displaying males. However, males may tidbit without food. We used the distinctiveness of the visual display and the unreliability of some males to test for communication-based recognition in female fowl. We manipulated the prior experience of the hens with the males to create two classes of males: S(+) wherein the tidbitting signal was paired with a food reward to the female, and S (-) wherein the tidbitting signal occurred without food reward. We then conducted a sequential discrimination test with hens using a live video feed of a familiar male. The results of the discrimination tests revealed that hens discriminated between categories of males based on their signalling behaviour. These results suggest that fowl possess a communication-based recognition system. This is the first demonstration of live-to-video transfer of recognition in any species of bird. Copyright © 2016 Elsevier B.V. All rights reserved.

The relational luring effect: Retrieval of relational information during associative recognition.

PubMed

Popov, Vencislav; Hristova, Penka; Anders, Royce

2017-05-01

Here we argue that semantic relations (e.g., works in: nurse-hospital) have abstract independent representations in long-term memory (LTM) and that the same representation is accessed by all exemplars of a specific relation. We present evidence from 2 associative recognition experiments that uncovered a novel relational luring effect (RLE) in recognition memory. Participants studied word pairs, and then discriminated between intact (old) pairs and recombined lures. In the first experiment participants responded more slowly to lures that were relationally similar (table-cloth) to studied pairs (floor-carpet), in contrast to relationally dissimilar lures (pipe-water). Experiment 2 extended the RLE by showing a continuous effect of relational lure strength on recognition times (RTs), false alarms, and hits. It used a continuous pair recognition task, where each recombined lure or target could be preceded by 0, 1, 2, 3 or 4 different exemplars of the same relation. RTs and false alarms increased linearly with the number of different previously seen relationally similar pairs. Moreover, more typical exemplars of a given relation lead to a stronger RLE. Finally, hits for intact pairs also rose with the number of previously studied different relational instances. These results suggest that semantic relations exist as independent representations in LTM and that during associative recognition these representations can be a spurious source of familiarity. We discuss the implications of the RLE for current models of semantic and episodic memory, unitization in associative recognition, analogical reasoning and retrieval, as well as constructive memory research. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Recognition is Used as One Cue Among Others in Judgment and Decision Making

ERIC Educational Resources Information Center

Richter, Tobias; Spath, Pamela

2006-01-01

Three experiments with paired comparisons were conducted to test the noncompensatory character of the recognition heuristic (D. G. Goldstein & G. Gigerenzer, 2002) in judgment and decision making. Recognition and knowledge about the recognized alternative were manipulated. In Experiment 1, participants were presented pairs of animal names where…

Recognition of T·G mismatched base pairs in DNA by stacked imidazole-containing polyamides: surface plasmon resonance and circular dichroism studies

PubMed Central

Lacy, Eilyn R.; Cox, Kari K.; Wilson, W. David; Lee, Moses

2002-01-01

An imidazole-containing polyamide trimer, f-ImImIm, where f is a formamido group, was recently found using NMR methods to recognize T·G mismatched base pairs. In order to characterize in detail the T·G recognition affinity and specificity of imidazole-containing polyamides, f-ImIm, f-ImImIm and f-PyImIm were synthesized. The kinetics and thermodynamics for the polyamides binding to Watson–Crick and mismatched (containing one or two T·G, A·G or G·G mismatched base pairs) hairpin oligonucleotides were determined by surface plasmon resonance and circular dichroism (CD) methods. f-ImImIm binds significantly more strongly to the T·G mismatch-containing oligonucleotides than to the sequences with other mismatched or with Watson–Crick base pairs. Compared with the Watson–Crick CCGG sequence, f-ImImIm associates more slowly with DNAs containing T·G mismatches in place of one or two C·G base pairs and, more importantly, the dissociation rate from the T·G oligonucleotides is very slow (small kd). These results clearly demonstrate the binding selectivity and enhanced affinity of side-by-side imidazole/imidazole pairings for T·G mismatches and show that the affinity and specificity increase arise from much lower kd values with the T·G mismatched duplexes. CD titration studies of f-ImImIm complexes with T·G mismatched sequences produce strong induced bands at ∼330 nm with clear isodichroic points, in support of a single minor groove complex. CD DNA bands suggest that the complexes remain in the B conformation. PMID:11937638

Heteroditopic receptors for ion-pair recognition.

PubMed

McConnell, Anna J; Beer, Paul D

2012-05-21

Ion-pair recognition is a new field of research emerging from cation and anion coordination chemistry. Specific types of heteroditopic receptor designs for ion pairs and the complexity of ion-pair binding are discussed to illustrate key concepts such as cooperativity. The importance of this area of research is reflected by the wide variety of potential applications of ion-pair receptors, including applications as membrane transport and salt solubilization agents and sensors. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Extensions of the picture superiority effect in associative recognition.

PubMed

Hockley, William E; Bancroft, Tyler

2011-12-01

Previous research has shown that the picture superiority effect (PSE) is seen in tests of associative recognition for random pairs of line drawings compared to pairs of concrete words (Hockley, 2008). In the present study we demonstrated that the PSE for associative recognition is still observed when subjects have correctly identified the individual items of each pair as old (Experiment 1), and that this effect is not due to rehearsal borrowing (Experiment 2). The PSE for associative recognition also is shown to be present but attenuated for mixed picture-word pairs (Experiment 3), and similar in magnitude for pairs of simple black and white line drawings and coloured photographs of detailed objects (Experiment 4). The results are consistent with the view that the semantic meaning of nameable pictures is activated faster than that of words thereby affording subjects more time to generate and elaborate meaningful associations between items depicted in picture form. PsycINFO Database Record (c) 2011 APA, all rights reserved.

Recall deficits in stroke patients with thalamic lesions covary with damage to the parvocellular mediodorsal nucleus of the thalamus.

PubMed

Pergola, Giulio; Güntürkün, Onur; Koch, Benno; Schwarz, Michael; Daum, Irene; Suchan, Boris

2012-08-01

The functional role of the mediodorsal thalamic nucleus (MD) and its cortical network in memory processes is discussed controversially. While Aggleton and Brown (1999) suggested a role for recognition and not recall, Van der Werf et al. (2003) suggested that this nucleus is functionally related to executive function and strategic retrieval, based on its connections to the prefrontal cortices (PFC). The present study used a lesion approach including patients with focal thalamic lesions to examine the functions of the MD, the intralaminar nuclei and the midline nuclei in memory processing. A newly designed pair association task was used, which allowed the assessment of recognition and cued recall performance. Volume loss in thalamic nuclei was estimated as a predictor for alterations in memory performance. Patients performed poorer than healthy controls on recognition accuracy and cued recall. Furthermore, patients responded slower than controls specifically on recognition trials followed by successful cued recall of the paired associate. Reduced recall of picture pairs and increased response times during recognition followed by cued recall covaried with the volume loss in the parvocellular MD. This pattern suggests a role of this thalamic region in recall and thus recollection, which does not fit the framework proposed by Aggleton and Brown (1999). The functional specialization of the parvocellular MD accords with its connectivity to the dorsolateral PFC, highlighting the role of this thalamocortical network in explicit memory (Van der Werf et al., 2003). Copyright © 2012 Elsevier Ltd. All rights reserved.

Nucleic acid constructs containing orthogonal site selective recombinases (OSSRs)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gilmore, Joshua M.; Anderson, J. Christopher; Dueber, John E.

The present invention provides for a recombinant nucleic acid comprising a nucleotide sequence comprising a plurality of constructs, wherein each construct independently comprises a nucleotide sequence of interest flanked by a pair of recombinase recognition sequences. Each pair of recombinase recognition sequences is recognized by a distinct recombinase. Optionally, each construct can, independently, further comprise one or more genes encoding a recombinase capable of recognizing the pair of recombinase recognition sequences of the construct. The recombinase can be an orthogonal (non-cross reacting), site-selective recombinase (OSSR).

Memory effects of sleep, emotional valence, arousal and novelty in children.

PubMed

Vermeulen, Marije C M; van der Heijden, Kristiaan B; Benjamins, Jeroen S; Swaab, Hanna; van Someren, Eus J W

2017-06-01

Effectiveness of memory consolidation is determined by multiple factors, including sleep after learning, emotional valence, arousal and novelty. Few studies investigated how the effect of sleep compares with (and interacts with) these other factors, of which virtually none are in children. The present study did so by repeated assessment of declarative memory in 386 children (45% boys) aged 9-11 years through an online word-pair task. Children were randomly assigned to either a morning or evening learning session of 30 unrelated word-pairs with positive, neutral or negative valenced cues and neutral targets. After immediately assessing baseline recognition, delayed recognition was recorded either 12 or 24 h later, resulting in four different assessment schedules. One week later, the procedure was repeated with exactly the same word-pairs to evaluate whether effects differed for relearning versus original novel learning. Mixed-effect logistic regression models were used to evaluate how the probability of correct recognition was affected by sleep, valence, arousal, novelty and their interactions. Both immediate and delayed recognition were worse for pairs with negatively valenced or less arousing cue words. Relearning improved immediate and delayed word-pair recognition. In contrast to these effects, sleep did not affect recognition, nor did sleep moderate the effects of arousal, valence and novelty. The findings suggest a robust inclination of children to specifically forget the pairing of words to negatively valenced cue words. In agreement with a recent meta-analysis, children seem to depend less on sleep for the consolidation of information than has been reported for adults, irrespective of the emotional valence, arousal and novelty of word-pairs. © 2017 European Sleep Research Society.

Unusual target site disruption by the rare-cutting HNH restriction endonuclease PacI

PubMed Central

Shen, Betty; Heiter, Daniel F.; Chan, Siu-Hong; Wang, Hua; Xu, Shuang-Yong; Morgan, Richard D.; Wilson, Geoffrey G.; Stoddard, Barry L.

2010-01-01

The crystal structure of the rare-cutting HNH restriction endonuclease PacI in complex with its eight base pair target recognition sequence 5'-TTAATTAA-3' has been determined to 1.9 Å resolution. The enzyme forms an extended homodimer, with each subunit containing two zinc-bound motifs surrounding a ββα-metal catalytic site. The latter is unusual in that a tyrosine residue likely initiates strand-cleavage. PacI dramatically distorts its target sequence from Watson-Crick duplex DNA basepairing, with every base separated from its original partner. Two bases on each strand are unpaired, four are engaged in non-canonical A:A and T:T base pairs, and the remaining two bases are matched with new Watson-Crick partners. This represents a highly unusual DNA binding mechanism for a restriction endonuclease, and implies that initial recognition of the target site might involve significantly different contacts from those visualized in the DNA-bound cocrystal structures. PMID:20541511

Comparing Facial 3D Analysis With DNA Testing to Determine Zygosities of Twins.

PubMed

Vuollo, Ville; Sidlauskas, Mantas; Sidlauskas, Antanas; Harila, Virpi; Salomskiene, Loreta; Zhurov, Alexei; Holmström, Lasse; Pirttiniemi, Pertti; Heikkinen, Tuomo

2015-06-01

The aim of this study was to compare facial 3D analysis to DNA testing in twin zygosity determinations. Facial 3D images of 106 pairs of young adult Lithuanian twins were taken with a stereophotogrammetric device (3dMD, Atlanta, Georgia) and zygosity was determined according to similarity of facial form. Statistical pattern recognition methodology was used for classification. The results showed that in 75% to 90% of the cases, zygosity determinations were similar to DNA-based results. There were 81 different classification scenarios, including 3 groups, 3 features, 3 different scaling methods, and 3 threshold levels. It appeared that coincidence with 0.5 mm tolerance is the most suitable feature for classification. Also, leaving out scaling improves results in most cases. Scaling was expected to equalize the magnitude of differences and therefore lead to better recognition performance. Still, better classification features and a more effective scaling method or classification in different facial areas could further improve the results. In most of the cases, male pair zygosity recognition was at a higher level compared with females. Erroneously classified twin pairs appear to be obvious outliers in the sample. In particular, faces of young dizygotic (DZ) twins may be so similar that it is very hard to define a feature that would help classify the pair as DZ. Correspondingly, monozygotic (MZ) twins may have faces with quite different shapes. Such anomalous twin pairs are interesting exceptions, but they form a considerable portion in both zygosity groups.

An unusual mode of DNA duplex association: Watson-Crick interaction of all-purine deoxyribonucleic acids.

PubMed

Battersby, Thomas R; Albalos, Maria; Friesenhahn, Michel J

2007-05-01

Nucleic acid duplexes associating through purine-purine base pairing have been constructed and characterized in a remarkable demonstration of nucleic acids with mixed sequence and a natural backbone in an alternative duplex structure. The antiparallel deoxyribose all-purine duplexes associate specifically through Watson-Crick pairing, violating the nucleobase size-complementarity pairing convention found in Nature. Sequence-specific recognition displayed by these structures makes the duplexes suitable, in principle, for information storage and replication fundamental to molecular evolution in all living organisms. All-purine duplexes can be formed through association of purines found in natural ribonucleosides. Key to the formation of these duplexes is the N(3)-H tautomer of isoguanine, preferred in the duplex, but not in aqueous solution. The duplexes have relevance to evolution of the modern genetic code and can be used for molecular recognition of natural nucleic acids.

Sequence-dependent DNA deformability studied using molecular dynamics simulations.

PubMed

Fujii, Satoshi; Kono, Hidetoshi; Takenaka, Shigeori; Go, Nobuhiro; Sarai, Akinori

2007-01-01

Proteins recognize specific DNA sequences not only through direct contact between amino acids and bases, but also indirectly based on the sequence-dependent conformation and deformability of the DNA (indirect readout). We used molecular dynamics simulations to analyze the sequence-dependent DNA conformations of all 136 possible tetrameric sequences sandwiched between CGCG sequences. The deformability of dimeric steps obtained by the simulations is consistent with that by the crystal structures. The simulation results further showed that the conformation and deformability of the tetramers can highly depend on the flanking base pairs. The conformations of xATx tetramers show the most rigidity and are not affected by the flanking base pairs and the xYRx show by contrast the greatest flexibility and change their conformations depending on the base pairs at both ends, suggesting tetramers with the same central dimer can show different deformabilities. These results suggest that analysis of dimeric steps alone may overlook some conformational features of DNA and provide insight into the mechanism of indirect readout during protein-DNA recognition. Moreover, the sequence dependence of DNA conformation and deformability may be used to estimate the contribution of indirect readout to the specificity of protein-DNA recognition as well as nucleosome positioning and large-scale behavior of nucleic acids.

Continued effects of context reinstatement in recognition.

PubMed

Hanczakowski, Maciej; Zawadzka, Katarzyna; Macken, Bill

2015-07-01

The context reinstatement effect refers to the enhanced memory performance found when the context information paired with a target item at study is re-presented at test. Here we investigated the consequences of the way that context information is processed in such a setting that gives rise to its beneficial effect on item recognition memory. Specifically, we assessed whether reinstating context in a recognition test facilitates subsequent memory for this context, beyond the facilitation conferred by presentation of the same context with a different study item. Reinstating the study context at test led to better accuracy in two-alternative forced choice recognition for target faces than did re-pairing those faces with another context encountered during the study phase. The advantage for reinstated over re-paired conditions occurred for both within-subjects (Exp. 1) and between-subjects (Exp. 2) manipulations. Critically, in a subsequent recognition test for the contexts themselves, contexts that had previously served in the reinstated condition were recognized better than contexts that had previously served in the re-paired context condition. This constitutes the first demonstration of continuous effects of context reinstatement on memory for context.

Euro Banknote Recognition System for Blind People.

PubMed

Dunai Dunai, Larisa; Chillarón Pérez, Mónica; Peris-Fajarnés, Guillermo; Lengua Lengua, Ismael

2017-01-20

This paper presents the development of a portable system with the aim of allowing blind people to detect and recognize Euro banknotes. The developed device is based on a Raspberry Pi electronic instrument and a Raspberry Pi camera, Pi NoIR (No Infrared filter) dotted with additional infrared light, which is embedded into a pair of sunglasses that permit blind and visually impaired people to independently handle Euro banknotes, especially when receiving their cash back when shopping. The banknote detection is based on the modified Viola and Jones algorithms, while the banknote value recognition relies on the Speed Up Robust Features (SURF) technique. The accuracies of banknote detection and banknote value recognition are 84% and 97.5%, respectively.

Euro Banknote Recognition System for Blind People

PubMed Central

Dunai Dunai, Larisa; Chillarón Pérez, Mónica; Peris-Fajarnés, Guillermo; Lengua Lengua, Ismael

2017-01-01

This paper presents the development of a portable system with the aim of allowing blind people to detect and recognize Euro banknotes. The developed device is based on a Raspberry Pi electronic instrument and a Raspberry Pi camera, Pi NoIR (No Infrared filter) dotted with additional infrared light, which is embedded into a pair of sunglasses that permit blind and visually impaired people to independently handle Euro banknotes, especially when receiving their cash back when shopping. The banknote detection is based on the modified Viola and Jones algorithms, while the banknote value recognition relies on the Speed Up Robust Features (SURF) technique. The accuracies of banknote detection and banknote value recognition are 84% and 97.5%, respectively. PMID:28117703

Classification of pseudo pairs between nucleotide bases and amino acids by analysis of nucleotide-protein complexes.

PubMed

Kondo, Jiro; Westhof, Eric

2011-10-01

Nucleotide bases are recognized by amino acid residues in a variety of DNA/RNA binding and nucleotide binding proteins. In this study, a total of 446 crystal structures of nucleotide-protein complexes are analyzed manually and pseudo pairs together with single and bifurcated hydrogen bonds observed between bases and amino acids are classified and annotated. Only 5 of the 20 usual amino acid residues, Asn, Gln, Asp, Glu and Arg, are able to orient in a coplanar fashion in order to form pseudo pairs with nucleotide bases through two hydrogen bonds. The peptide backbone can also form pseudo pairs with nucleotide bases and presents a strong bias for binding to the adenine base. The Watson-Crick side of the nucleotide bases is the major interaction edge participating in such pseudo pairs. Pseudo pairs between the Watson-Crick edge of guanine and Asp are frequently observed. The Hoogsteen edge of the purine bases is a good discriminatory element in recognition of nucleotide bases by protein side chains through the pseudo pairing: the Hoogsteen edge of adenine is recognized by various amino acids while the Hoogsteen edge of guanine is only recognized by Arg. The sugar edge is rarely recognized by either the side-chain or peptide backbone of amino acid residues.

Classification of pseudo pairs between nucleotide bases and amino acids by analysis of nucleotide–protein complexes

PubMed Central

Kondo, Jiro; Westhof, Eric

2011-01-01

Nucleotide bases are recognized by amino acid residues in a variety of DNA/RNA binding and nucleotide binding proteins. In this study, a total of 446 crystal structures of nucleotide–protein complexes are analyzed manually and pseudo pairs together with single and bifurcated hydrogen bonds observed between bases and amino acids are classified and annotated. Only 5 of the 20 usual amino acid residues, Asn, Gln, Asp, Glu and Arg, are able to orient in a coplanar fashion in order to form pseudo pairs with nucleotide bases through two hydrogen bonds. The peptide backbone can also form pseudo pairs with nucleotide bases and presents a strong bias for binding to the adenine base. The Watson–Crick side of the nucleotide bases is the major interaction edge participating in such pseudo pairs. Pseudo pairs between the Watson–Crick edge of guanine and Asp are frequently observed. The Hoogsteen edge of the purine bases is a good discriminatory element in recognition of nucleotide bases by protein side chains through the pseudo pairing: the Hoogsteen edge of adenine is recognized by various amino acids while the Hoogsteen edge of guanine is only recognized by Arg. The sugar edge is rarely recognized by either the side-chain or peptide backbone of amino acid residues. PMID:21737431

Structure, recognition and adaptive binding in RNA aptamer complexes.

PubMed

Patel, D J; Suri, A K; Jiang, F; Jiang, L; Fan, P; Kumar, R A; Nonin, S

1997-10-10

Novel features of RNA structure, recognition and discrimination have been recently elucidated through the solution structural characterization of RNA aptamers that bind cofactors, aminoglycoside antibiotics, amino acids and peptides with high affinity and specificity. This review presents the solution structures of RNA aptamer complexes with adenosine monophosphate, flavin mononucleotide, arginine/citrulline and tobramycin together with an example of hydrogen exchange measurements of the base-pair kinetics for the AMP-RNA aptamer complex. A comparative analysis of the structures of these RNA aptamer complexes yields the principles, patterns and diversity associated with RNA architecture, molecular recognition and adaptive binding associated with complex formation.

Enantiospecific recognition of DNA sequences by a proflavine Tröger base.

PubMed

Bailly, C; Laine, W; Demeunynck, M; Lhomme, J

2000-07-05

The DNA interaction of a chiral Tröger base derived from proflavine was investigated by DNA melting temperature measurements and complementary biochemical assays. DNase I footprinting experiments demonstrate that the binding of the proflavine-based Tröger base is both enantio- and sequence-specific. The (+)-isomer poorly interacts with DNA in a non-sequence-selective fashion. In sharp contrast, the corresponding (-)-isomer recognizes preferentially certain DNA sequences containing both A. T and G. C base pairs, such as the motifs 5'-GTT. AAC and 5'-ATGA. TCAT. This is the first experimental demonstration that acridine-type Tröger bases can be used for enantiospecific recognition of DNA sequences. Copyright 2000 Academic Press.

Assessing a Metacognitive Account of Associative Memory Impairments in Temporal Lobe Epilepsy

PubMed Central

Kemp, Steven; Souchay, Céline; Moulin, Chris J. A.

2016-01-01

Previous research has pointed to a deficit in associative recognition in temporal lobe epilepsy (TLE). Associative recognition tasks require discrimination between various combinations of words which have and have not been seen previously (such as old-old or old-new pairs). People with TLE tend to respond to rearranged old-old pairs as if they are “intact” old-old pairs, which has been interpreted as a failure to use a recollection strategy to overcome the familiarity of two recombined words into a new pairing. We examined this specific deficit in the context of metacognition, using postdecision confidence judgements at test. We expected that TLE patients would show inappropriate levels of confidence for associative recognition. Although TLE patients reported lower confidence levels in their responses overall, they were sensitive to the difficulty of varying pair types in their judgements and gave significantly higher confidence ratings for their correct answers. We conclude that a strategic deficit is not at play in the associative recognition of people with TLE, insofar as they are able to monitor the status of their memory system. This adds to a growing body of research suggesting that recollection is impaired in TLE, but not metacognition. PMID:27721992

Recall and recognition of verbal paired associates in early Alzheimer's disease.

PubMed

Lowndes, G J; Saling, M M; Ames, D; Chiu, E; Gonzalez, L M; Savage, G R

2008-07-01

The primary impairment in early Alzheimer's disease (AD) is encoding/consolidation, resulting from medial temporal lobe (MTL) pathology. AD patients perform poorly on cued-recall paired associate learning (PAL) tasks, which assess the ability of the MTLs to encode relational memory. Since encoding and retrieval processes are confounded within performance indexes on cued-recall PAL, its specificity for AD is limited. Recognition paradigms tend to show good specificity for AD, and are well tolerated, but are typically less sensitive than recall tasks. Associate-recognition is a novel PAL task requiring a combination of recall and recognition processes. We administered a verbal associate-recognition test and cued-recall analogue to 22 early AD patients and 55 elderly controls to compare their ability to discriminate these groups. Both paradigms used eight arbitrarily related word pairs (e.g., pool-teeth) with varying degrees of imageability. Associate-recognition was equally effective as the cued-recall analogue in discriminating the groups, and logistic regression demonstrated classification rates by both tasks were equivalent. These preliminary findings provide support for the clinical value of this recognition tool. Conceptually it has potential for greater specificity in informing neuropsychological diagnosis of AD in clinical samples but this requires further empirical support.

Multiple ways to the prior occurrence of an event: an electrophysiological dissociation of experimental and conceptually driven familiarity in recognition memory.

PubMed

Wiegand, Iris; Bader, Regine; Mecklinger, Axel

2010-11-11

Recent research has shown that familiarity contributes to associative memory when the to-be-associated stimuli are unitized during encoding. However, the specific processes underlying familiarity-based recognition of unitized representations are still indefinite. In this study, we present electrophysiologically dissociable early old/new effects, presumably related to two different kinds of familiarity inherent in associative recognition tasks. In a study-test associative recognition memory paradigm, we employed encoding conditions that established unitized representations of two pre-experimentally unrelated words, e.g. vegetable-bible. We compared event-related potentials (ERP) during the retrieval of these unitized word pairs using different retrieval cues. Word pairs presented in the same order as during unitization at encoding elicited a parietally distributed early old/new effect which we interpret as reflecting conceptually driven familiarity for newly formed concepts. Conversely, word pairs presented in reversed order only elicited a topographically dissociable early effect, i.e. the mid-frontal old/new effect, the putative correlate of experimental familiarity. The late parietal old/new effect, the putative ERP correlate of recollection, was obtained irrespective of word order, though it was larger for words presented in same order. These results indicate that familiarity may not be a unitary process and that different task demands can promote the assessment of conceptually driven familiarity for novel unitized concepts or experimentally-induced increments of experimental familiarity, respectively. Copyright © 2010 Elsevier B.V. All rights reserved.

Visual Recognition Memory, Paired-Associate Learning, and Reading Achievement.

ERIC Educational Resources Information Center

Anderson, Roger H.; Samuels, S. Jay

The relationship between visual recognition memory and performance on a paired-associate task for good and poor readers was investigated. Subjects were three groups of 21, 21, and 22 children each, with mean IQ's of 98.2, 108.1, and 118.0, respectively. Three experimental tasks, individually administered to each subject, measured visual…

Robust Indoor Human Activity Recognition Using Wireless Signals.

PubMed

Wang, Yi; Jiang, Xinli; Cao, Rongyu; Wang, Xiyang

2015-07-15

Wireless signals-based activity detection and recognition technology may be complementary to the existing vision-based methods, especially under the circumstance of occlusions, viewpoint change, complex background, lighting condition change, and so on. This paper explores the properties of the channel state information (CSI) of Wi-Fi signals, and presents a robust indoor daily human activity recognition framework with only one pair of transmission points (TP) and access points (AP). First of all, some indoor human actions are selected as primitive actions forming a training set. Then, an online filtering method is designed to make actions' CSI curves smooth and allow them to contain enough pattern information. Each primitive action pattern can be segmented from the outliers of its multi-input multi-output (MIMO) signals by a proposed segmentation method. Lastly, in online activities recognition, by selecting proper features and Support Vector Machine (SVM) based multi-classification, activities constituted by primitive actions can be recognized insensitive to the locations, orientations, and speeds.

Semantic memory influences episodic retrieval by increased familiarity.

PubMed

Wang, Yujuan; Mao, Xinrui; Li, Bingcan; Lu, Baoqing; Guo, Chunyan

2016-07-06

The role of familiarity in associative recognition has been investigated in a number of studies, which have indicated that familiarity can facilitate recognition under certain circumstances. The ability of a pre-experimentally existing common representation to boost the contribution of familiarity has rarely been investigated. In addition, although many studies have investigated the interactions between semantic memory and episodic retrieval, the conditions that influence the presence of specific patterns were unclear. This study aimed to address these two questions. We manipulated the degree of overlap between the two representations using synonym and nonsynonym pairs in an associative recognition task. Results indicated that an increased degree of overlap enhanced recognition performance. The analysis of event-related potentials effects in the test phase showed that synonym pairs elicited both types of old/rearranged effects, whereas nonsynonym pairs elicited a late old/rearranged effect. These results confirmed that a common representation, irrespective of source, was necessary for assuring the presence of familiarity, but a common representation could not distinguish associative recognition depending on familiarity alone. Moreover, our expected double dissociation between familiarity and recollection was absent, which indicated that mode selection may be influenced by the degree of distinctness between old and rearranged pairs rather than the degree of overlap between representations.

Using crypts as iris minutiae

NASA Astrophysics Data System (ADS)

Shen, Feng; Flynn, Patrick J.

2013-05-01

Iris recognition is one of the most reliable biometric technologies for identity recognition and verification, but it has not been used in a forensic context because the representation and matching of iris features are not straightforward for traditional iris recognition techniques. In this paper we concentrate on the iris crypt as a visible feature used to represent the characteristics of irises in a similar way to fingerprint minutiae. The matching of crypts is based on their appearances and locations. The number of matching crypt pairs found between two irises can be used for identity verification and the convenience of manual inspection makes iris crypts a potential candidate for forensic applications.

Use of the recognition heuristic depends on the domain's recognition validity, not on the recognition validity of selected sets of objects.

PubMed

Pohl, Rüdiger F; Michalkiewicz, Martha; Erdfelder, Edgar; Hilbig, Benjamin E

2017-07-01

According to the recognition-heuristic theory, decision makers solve paired comparisons in which one object is recognized and the other not by recognition alone, inferring that recognized objects have higher criterion values than unrecognized ones. However, success-and thus usefulness-of this heuristic depends on the validity of recognition as a cue, and adaptive decision making, in turn, requires that decision makers are sensitive to it. To this end, decision makers could base their evaluation of the recognition validity either on the selected set of objects (the set's recognition validity), or on the underlying domain from which the objects were drawn (the domain's recognition validity). In two experiments, we manipulated the recognition validity both in the selected set of objects and between domains from which the sets were drawn. The results clearly show that use of the recognition heuristic depends on the domain's recognition validity, not on the set's recognition validity. In other words, participants treat all sets as roughly representative of the underlying domain and adjust their decision strategy adaptively (only) with respect to the more general environment rather than the specific items they are faced with.

A rule of seven in Watson-Crick base-pairing of mismatched sequences.

PubMed

Cisse, Ibrahim I; Kim, Hajin; Ha, Taekjip

2012-05-13

Sequence recognition through base-pairing is essential for DNA repair and gene regulation, but the basic rules governing this process remain elusive. In particular, the kinetics of annealing between two imperfectly matched strands is not well characterized, despite its potential importance in nucleic acid-based biotechnologies and gene silencing. Here we use single-molecule fluorescence to visualize the multiple annealing and melting reactions of two untethered strands inside a porous vesicle, allowing us to precisely quantify the annealing and melting rates. The data as a function of mismatch position suggest that seven contiguous base pairs are needed for rapid annealing of DNA and RNA. This phenomenological rule of seven may underlie the requirement for seven nucleotides of complementarity to seed gene silencing by small noncoding RNA and may help guide performance improvement in DNA- and RNA-based bio- and nanotechnologies, in which off-target effects can be detrimental.

Incorporating a guanidine-modified cytosine base into triplex-forming PNAs for the recognition of a C-G pyrimidine–purine inversion site of an RNA duplex

PubMed Central

Toh, Desiree-Faye Kaixin; Devi, Gitali; Patil, Kiran M.; Qu, Qiuyu; Maraswami, Manikantha; Xiao, Yunyun; Loh, Teck Peng; Zhao, Yanli; Chen, Gang

2016-01-01

RNA duplex regions are often involved in tertiary interactions and protein binding and thus there is great potential in developing ligands that sequence-specifically bind to RNA duplexes. We have developed a convenient synthesis method for a modified peptide nucleic acid (PNA) monomer with a guanidine-modified 5-methyl cytosine base. We demonstrated by gel electrophoresis, fluorescence and thermal melting experiments that short PNAs incorporating the modified residue show high binding affinity and sequence specificity in the recognition of an RNA duplex containing an internal inverted Watson-Crick C-G base pair. Remarkably, the relatively short PNAs show no appreciable binding to DNA duplexes or single-stranded RNAs. The attached guanidine group stabilizes the base triple through hydrogen bonding with the G base in a C-G pair. Selective binding towards an RNA duplex over a single-stranded RNA can be rationalized by the fact that alkylation of the amine of a 5-methyl C base blocks the Watson–Crick edge. PNAs incorporating multiple guanidine-modified cytosine residues are able to enter HeLa cells without any transfection agent. PMID:27596599

2-Methoxypyridine as a Thymidine Mimic in Watson-Crick Base Pairs of DNA and PNA: Synthesis, Thermal Stability, and NMR Structural Studies.

PubMed

Novosjolova, Irina; Kennedy, Scott D; Rozners, Eriks

2017-11-02

The development of nucleic acid base-pair analogues that use new modes of molecular recognition is important both for fundamental research and practical applications. The goal of this study was to evaluate 2-methoxypyridine as a cationic thymidine mimic in the A-T base pair. The hypothesis was that including protonation in the Watson-Crick base pairing scheme would enhance the thermal stability of the DNA double helix without compromising the sequence selectivity. DNA and peptide nucleic acid (PNA) sequences containing the new 2-methoxypyridine nucleobase (P) were synthesized and studied by using UV thermal melting and NMR spectroscopy. Introduction of P nucleobase caused a loss of thermal stability of ≈10 °C in DNA-DNA duplexes and ≈20 °C in PNA-DNA duplexes over a range of mildly acidic to neutral pH. Despite the decrease in thermal stability, the NMR structural studies showed that P-A formed the expected protonated base pair at pH 4.3. Our study demonstrates the feasibility of cationic unnatural base pairs; however, future optimization of such analogues will be required. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Electrophysiological Correlates of Familiarity and Recollection in Associative Recognition: Contributions of Perceptual and Conceptual Processing to Unitization

PubMed Central

Li, Bingcan; Mao, Xinrui; Wang, Yujuan; Guo, Chunyan

2017-01-01

It is generally accepted that associative recognition memory is supported by recollection. In addition, recent research indicates that familiarity can support associative memory, especially when two items are unitized into a single item. Both perceptual and conceptual manipulations can be used to unitize items, but few studies have compared these two methods of unitization directly. In the present study, we investigated the effects of familiarity and recollection on successful retrieval of items that were unitized perceptually or conceptually. Participants were instructed to remember either a Chinese two-character compound or unrelated word-pairs, which were presented simultaneously or sequentially. Participants were then asked to recognize whether word-pairs were intact or rearranged. Event-related potential (ERP) recordings were performed during the recognition phase of the study. Two-character compounds were better discriminated than unrelated word-pairs and simultaneous presentation was found to elicit better discrimination than sequential presentation for unrelated word-pairs only. ERP recordings indicated that the early intact/rearranged effects (FN400), typically associated with familiarity, were elicited in compound word-pairs with both simultaneous and sequential presentation, and in simultaneously presented unrelated word-pairs, but not in sequentially presented unrelated word-pairs. In contrast, the late positive complex (LPC) effects associated with recollection were elicited in all four conditions. Together, these results indicate that while the engagement of familiarity in associative recognition is affected by both perceptual and conceptual unitization, conceptual unitization promotes a higher level of unitization (LOU). In addition, the engagement of recollection was not affected by unitized manipulations. It should be noted, however, that due to experimental design, the effects presented here may be due to semantic rather than episodic memory and future studies should take this into consideration when manipulating rearranged pairs. PMID:28400723

Auditory Temporal Order Discrimination and Backward Recognition Masking in Adults with Dyslexia

ERIC Educational Resources Information Center

Griffiths, Yvonne M.; Hill, Nicholas I.; Bailey, Peter J.; Snowling, Margaret J.

2003-01-01

The ability of 20 adult dyslexic readers to extract frequency information from successive tone pairs was compared with that of IQ-matched controls using temporal order discrimination and auditory backward recognition masking (ABRM) tasks. In both paradigms, the interstimulus interval (ISI) between tones in a pair was either short (20 ms) or long…

Metal-mediated DNA base pairing: alternatives to hydrogen-bonded Watson-Crick base pairs.

PubMed

Takezawa, Yusuke; Shionoya, Mitsuhiko

2012-12-18

With its capacity to store and transfer the genetic information within a sequence of monomers, DNA forms its central role in chemical evolution through replication and amplification. This elegant behavior is largely based on highly specific molecular recognition between nucleobases through the specific hydrogen bonds in the Watson-Crick base pairing system. While the native base pairs have been amazingly sophisticated through the long history of evolution, synthetic chemists have devoted considerable efforts to create alternative base pairing systems in recent decades. Most of these new systems were designed based on the shape complementarity of the pairs or the rearrangement of hydrogen-bonding patterns. We wondered whether metal coordination could serve as an alternative driving force for DNA base pairing and why hydrogen bonding was selected on Earth in the course of molecular evolution. Therefore, we envisioned an alternative design strategy: we replaced hydrogen bonding with another important scheme in biological systems, metal-coordination bonding. In this Account, we provide an overview of the chemistry of metal-mediated base pairing including basic concepts, molecular design, characteristic structures and properties, and possible applications of DNA-based molecular systems. We describe several examples of artificial metal-mediated base pairs, such as Cu(2+)-mediated hydroxypyridone base pair, H-Cu(2+)-H (where H denotes a hydroxypyridone-bearing nucleoside), developed by us and other researchers. To design the metallo-base pairs we carefully chose appropriate combinations of ligand-bearing nucleosides and metal ions. As expected from their stronger bonding through metal coordination, DNA duplexes possessing metallo-base pairs exhibited higher thermal stability than natural hydrogen-bonded DNAs. Furthermore, we could also use metal-mediated base pairs to construct or induce other high-order structures. These features could lead to metal-responsive functional DNA molecules such as artificial DNAzymes and DNA machines. In addition, the metallo-base pairing system is a powerful tool for the construction of homogeneous and heterogeneous metal arrays, which can lead to DNA-based nanomaterials such as electronic wires and magnetic devices. Recently researchers have investigated these systems as enzyme replacements, which may offer an additional contribution to chemical biology and synthetic biology through the expansion of the genetic alphabet.

A Thiazole Coumarin (TC) Turn-On Fluorescence Probe for AT-Base Pair Detection and Multipurpose Applications in Different Biological Systems

NASA Astrophysics Data System (ADS)

Narayanaswamy, Nagarjun; Kumar, Manoj; Das, Sadhan; Sharma, Rahul; Samanta, Pralok K.; Pati, Swapan K.; Dhar, Suman K.; Kundu, Tapas K.; Govindaraju, T.

2014-09-01

Sequence-specific recognition of DNA by small turn-on fluorescence probes is a promising tool for bioimaging, bioanalytical and biomedical applications. Here, the authors report a novel cell-permeable and red fluorescent hemicyanine-based thiazole coumarin (TC) probe for DNA recognition, nuclear staining and cell cycle analysis. TC exhibited strong fluorescence enhancement in the presence of DNA containing AT-base pairs, but did not fluoresce with GC sequences, single-stranded DNA, RNA and proteins. The fluorescence staining of HeLa S3 and HEK 293 cells by TC followed by DNase and RNase digestion studies depicted the selective staining of DNA in the nucleus over the cytoplasmic region. Fluorescence-activated cell sorting (FACS) analysis by flow cytometry demonstrated the potential application of TC in cell cycle analysis in HEK 293 cells. Metaphase chromosome and malaria parasite DNA imaging studies further confirmed the in vivo diagnostic and therapeutic applications of probe TC. Probe TC may find multiple applications in fluorescence spectroscopy, diagnostics, bioimaging and molecular and cell biology.

A Thiazole Coumarin (TC) Turn-On Fluorescence Probe for AT-Base Pair Detection and Multipurpose Applications in Different Biological Systems

PubMed Central

Narayanaswamy, Nagarjun; Kumar, Manoj; Das, Sadhan; Sharma, Rahul; Samanta, Pralok K.; Pati, Swapan K.; Dhar, Suman K.; Kundu, Tapas K.; Govindaraju, T.

2014-01-01

Sequence-specific recognition of DNA by small turn-on fluorescence probes is a promising tool for bioimaging, bioanalytical and biomedical applications. Here, the authors report a novel cell-permeable and red fluorescent hemicyanine-based thiazole coumarin (TC) probe for DNA recognition, nuclear staining and cell cycle analysis. TC exhibited strong fluorescence enhancement in the presence of DNA containing AT-base pairs, but did not fluoresce with GC sequences, single-stranded DNA, RNA and proteins. The fluorescence staining of HeLa S3 and HEK 293 cells by TC followed by DNase and RNase digestion studies depicted the selective staining of DNA in the nucleus over the cytoplasmic region. Fluorescence-activated cell sorting (FACS) analysis by flow cytometry demonstrated the potential application of TC in cell cycle analysis in HEK 293 cells. Metaphase chromosome and malaria parasite DNA imaging studies further confirmed the in vivo diagnostic and therapeutic applications of probe TC. Probe TC may find multiple applications in fluorescence spectroscopy, diagnostics, bioimaging and molecular and cell biology. PMID:25252596

Strength-based criterion shifts in recognition memory.

PubMed

Singer, Murray

2009-10-01

In manipulations of stimulus strength between lists, a more lenient signal detection criterion is more frequently applied to a weak than to a strong stimulus class. However, with randomly intermixed weak and strong test probes, such a criterion shift often does not result. A procedure that has yielded delay-based within-list criterion shifts was applied to strength manipulations in recognition memory for categorized word lists. When participants made semantic ratings about each stimulus word, strength-based criterion shifts emerged regardless of whether words from pairs of categories were studied in separate blocks (Experiment 1) or in intermixed blocks (Experiment 2). In Experiment 3, the criterion shift persisted under the semantic-rating study task, but not under rote memorization. These findings suggest that continually adjusting the recognition decision criterion is cognitively feasible. They provide a technique for manipulating the criterion shift, and they identify competing theoretical accounts of these effects.

Mechanism Underlying the Nucleobase-Distinguishing Ability of Benzopyridopyrimidine (BPP).

PubMed

Kochman, Michał A; Bil, Andrzej; Miller, R J Dwayne

2017-11-02

Benzopyridopyrimidine (BPP) is a fluorescent nucleobase analogue capable of forming base pairs with adenine (A) and guanine (G) at different sites. When incorporated into oligodeoxynucleotides, it is capable of differentiating between the two purine nucleobases by virtue of the fact that its fluorescence is largely quenched when it is base-paired to guanine, whereas base-pairing to adenine causes only a slight reduction of the fluorescence quantum yield. In the present article, the photophysics of BPP is investigated through computer simulations. BPP is found to be a good charge acceptor, as demonstrated by its positive and appreciably large electron affinity. The selective quenching process is attributed to charge transfer (CT) from the purine nucleobase, which is predicted to be efficient in the BPP-G base pair, but essentially inoperative in the BPP-A base pair. The CT process owes its high selectivity to a combination of two factors: the ionization potential of guanine is lower than that of adenine, and less obviously, the site occupied by guanine enables a greater stabilization of the CT state through electrostatic interactions than the one occupied by adenine. The case of BPP illustrates that molecular recognition via hydrogen bonding can enhance the selectivity of photoinduced CT processes.

Visual paired-associate learning: in search of material-specific effects in adult patients who have undergone temporal lobectomy.

PubMed

Smith, Mary Lou; Bigel, Marla; Miller, Laurie A

2011-02-01

The mesial temporal lobes are important for learning arbitrary associations. It has previously been demonstrated that left mesial temporal structures are involved in learning word pairs, but it is not yet known whether comparable lesions in the right temporal lobe impair visually mediated associative learning. Patients who had undergone left (n=16) or right (n=18) temporal lobectomy for relief of intractable epilepsy and healthy controls (n=13) were administered two paired-associate learning tasks assessing their learning and memory of pairs of abstract designs or pairs of symbols in unique locations. Both patient groups had deficits in learning the designs, but only the right temporal group was impaired in recognition. For the symbol location task, differences were not found in learning, but again a recognition deficit was found for the right temporal group. The findings implicate the mesial temporal structures in relational learning. They support a material-specific effect for recognition but not for learning and recall of arbitrary visual and visual-spatial associative information. Copyright © 2010 Elsevier Inc. All rights reserved.

The Impact of a Modified Repeated-Reading Strategy Paired with Optical Character Recognition on the Reading Rates of Students with Visual Impairments

ERIC Educational Resources Information Center

Pattillo, Suzan Trefry; Heller, Kathryn Wolf; Smith, Maureen

2004-01-01

The repeated-reading strategy and optical character recognition were paired to demonstrate a functional relationship between the combined strategies and two factors: the reading rates of students with visual impairments and the students' self-perceptions, or attitudes, toward reading. The results indicated that all five students increased their…

THE EFFECT OF WORD ASSOCIATIONS ON THE RECOGNITION OF FLASHED WORDS.

ERIC Educational Resources Information Center

SAMUELS, S. JAY

THE HYPOTHESIS THAT WHEN ASSOCIATED PAIRS OF WORDS ARE PRESENTED, SPEED OF RECOGNITION WILL BE FASTER THAN WHEN NONASSOCIATED WORD PAIRS ARE PRESENTED OR WHEN A TARGET WORD IS PRESENTED BY ITSELF WAS TESTED. TWENTY UNIVERSITY STUDENTS, INITIALLY SCREENED FOR VISION, WERE ASSIGNED RANDOMLY TO ROWS OF A 5 X 5 REPEATED-MEASURES LATIN SQUARE DESIGN.…

Scene recognition based on integrating active learning with dictionary learning

NASA Astrophysics Data System (ADS)

Wang, Chengxi; Yin, Xueyan; Yang, Lin; Gong, Chengrong; Zheng, Caixia; Yi, Yugen

2018-04-01

Scene recognition is a significant topic in the field of computer vision. Most of the existing scene recognition models require a large amount of labeled training samples to achieve a good performance. However, labeling image manually is a time consuming task and often unrealistic in practice. In order to gain satisfying recognition results when labeled samples are insufficient, this paper proposed a scene recognition algorithm named Integrating Active Learning and Dictionary Leaning (IALDL). IALDL adopts projective dictionary pair learning (DPL) as classifier and introduces active learning mechanism into DPL for improving its performance. When constructing sampling criterion in active learning, IALDL considers both the uncertainty and representativeness as the sampling criteria to effectively select the useful unlabeled samples from a given sample set for expanding the training dataset. Experiment results on three standard databases demonstrate the feasibility and validity of the proposed IALDL.

Random Forest-Based Recognition of Isolated Sign Language Subwords Using Data from Accelerometers and Surface Electromyographic Sensors.

PubMed

Su, Ruiliang; Chen, Xiang; Cao, Shuai; Zhang, Xu

2016-01-14

Sign language recognition (SLR) has been widely used for communication amongst the hearing-impaired and non-verbal community. This paper proposes an accurate and robust SLR framework using an improved decision tree as the base classifier of random forests. This framework was used to recognize Chinese sign language subwords using recordings from a pair of portable devices worn on both arms consisting of accelerometers (ACC) and surface electromyography (sEMG) sensors. The experimental results demonstrated the validity of the proposed random forest-based method for recognition of Chinese sign language (CSL) subwords. With the proposed method, 98.25% average accuracy was obtained for the classification of a list of 121 frequently used CSL subwords. Moreover, the random forests method demonstrated a superior performance in resisting the impact of bad training samples. When the proportion of bad samples in the training set reached 50%, the recognition error rate of the random forest-based method was only 10.67%, while that of a single decision tree adopted in our previous work was almost 27.5%. Our study offers a practical way of realizing a robust and wearable EMG-ACC-based SLR systems.

Twin hydroxymethyluracil-A base pair steps define the binding site for the DNA-binding protein TF1.

PubMed

Grove, A; Figueiredo, M L; Galeone, A; Mayol, L; Geiduschek, E P

1997-05-16

The DNA-bending protein TF1 is the Bacillus subtilis bacteriophage SPO1-encoded homolog of the bacterial HU proteins and the Escherichia coli integration host factor. We recently proposed that TF1, which binds with high affinity (Kd was approximately 3 nM) to preferred sites within the hydroxymethyluracil (hmU)-containing phage genome, identifies its binding sites based on sequence-dependent DNA flexibility. Here, we show that two hmU-A base pair steps coinciding with two previously proposed sites of DNA distortion are critical for complex formation. The affinity of TF1 is reduced 10-fold when both of these hmU-A base pair steps are replaced with A-hmU, G-C, or C-G steps; only modest changes in affinity result when substitutions are made at other base pairs of the TF1 binding site. Replacement of all hmU residues with thymine decreases the affinity of TF1 greatly; remarkably, the high affinity is restored when the two hmU-A base pair steps corresponding to previously suggested sites of distortion are reintroduced into otherwise T-containing DNA. T-DNA constructs with 3-base bulges spaced apart by 9 base pairs of duplex also generate nM affinity of TF1. We suggest that twin hmU-A base pair steps located at the proposed sites of distortion are key to target site selection by TF1 and that recognition is based largely, if not entirely, on sequence-dependent DNA flexibility.

Structural basis for the recognition of guide RNA and target DNA heteroduplex by Argonaute

PubMed Central

Miyoshi, Tomohiro; Ito, Kosuke; Murakami, Ryo; Uchiumi, Toshio

2016-01-01

Argonaute proteins are key players in the gene silencing mechanisms mediated by small nucleic acids in all domains of life from bacteria to eukaryotes. However, little is known about the Argonaute protein that recognizes guide RNA/target DNA. Here, we determine the 2 Å crystal structure of Rhodobacter sphaeroides Argonaute (RsAgo) in a complex with 18-nucleotide guide RNA and its complementary target DNA. The heteroduplex maintains Watson–Crick base-pairing even in the 3′-region of the guide RNA between the N-terminal and PIWI domains, suggesting a recognition mode by RsAgo for stable interaction with the target strand. In addition, the MID/PIWI interface of RsAgo has a system that specifically recognizes the 5′ base-U of the guide RNA, and the duplex-recognition loop of the PAZ domain is important for the DNA silencing activity. Furthermore, we show that Argonaute discriminates the nucleic acid type (RNA/DNA) by recognition of the duplex structure of the seed region. PMID:27325485

Structural basis for the recognition of guide RNA and target DNA heteroduplex by Argonaute.

PubMed

Miyoshi, Tomohiro; Ito, Kosuke; Murakami, Ryo; Uchiumi, Toshio

2016-06-21

Argonaute proteins are key players in the gene silencing mechanisms mediated by small nucleic acids in all domains of life from bacteria to eukaryotes. However, little is known about the Argonaute protein that recognizes guide RNA/target DNA. Here, we determine the 2 Å crystal structure of Rhodobacter sphaeroides Argonaute (RsAgo) in a complex with 18-nucleotide guide RNA and its complementary target DNA. The heteroduplex maintains Watson-Crick base-pairing even in the 3'-region of the guide RNA between the N-terminal and PIWI domains, suggesting a recognition mode by RsAgo for stable interaction with the target strand. In addition, the MID/PIWI interface of RsAgo has a system that specifically recognizes the 5' base-U of the guide RNA, and the duplex-recognition loop of the PAZ domain is important for the DNA silencing activity. Furthermore, we show that Argonaute discriminates the nucleic acid type (RNA/DNA) by recognition of the duplex structure of the seed region.

A practical approach for writer-dependent symbol recognition using a writer-independent symbol recognizer.

PubMed

LaViola, Joseph J; Zeleznik, Robert C

2007-11-01

We present a practical technique for using a writer-independent recognition engine to improve the accuracy and speed while reducing the training requirements of a writer-dependent symbol recognizer. Our writer-dependent recognizer uses a set of binary classifiers based on the AdaBoost learning algorithm, one for each possible pairwise symbol comparison. Each classifier consists of a set of weak learners, one of which is based on a writer-independent handwriting recognizer. During online recognition, we also use the n-best list of the writer-independent recognizer to prune the set of possible symbols and thus reduce the number of required binary classifications. In this paper, we describe the geometric and statistical features used in our recognizer and our all-pairs classification algorithm. We also present the results of experiments that quantify the effect incorporating a writer-independent recognition engine into a writer-dependent recognizer has on accuracy, speed, and user training time.

PNA containing isocytidine nucleobase: synthesis and recognition of double helical RNA

PubMed Central

Zengeya, Thomas; Li, Ming; Rozners, Eriks

2011-01-01

Peptide nucleic acid (PNA1) containing a 5-methylisocytidine (iC) nucleobase has been synthesized. Triple helix formation between PNA1 and RNA hairpins having variable base pairs interacting with iC was studied using isothermal titration calorimetry. The iC nucleobase recognized the proposed target, C-G inversion in polypurine tract of RNA, with slightly higher affinity than the natural nucleobases, though the sequence selectivity of recognition was low. Compared to non-modified PNA, PNA1 had lower affinity for its RNA target. PMID:21333533

Global RNA Fold and Molecular Recognition for a pfl Riboswitch Bound to ZMP, a Master Regulator of One-Carbon Metabolism

DOE PAGES

Ren, Aiming; Rajashankar, Kanagalaghatta R.; Patel, Dinshaw J.

2015-06-25

ZTP, the pyrophosphorylated analog of ZMP (5- amino-4-imidazole carboxamide ribose-5'-monophosphate), was identified as an alarmone that senses 10-formyl-tetrahydroflate deficiency in bacteria. Recently, a pfl riboswitch was identified that selectively binds ZMP and regulates genes associated with purine biosynthesis and one-carbon metabolism. Here we report on the structure of the ZMP-bound Thermosinus carboxydivorans pfl riboswitch sensing domain, thereby defining the pseudoknot-based tertiary RNA fold, the binding-pocket architecture, and principles underlying ligand recognition specificity. Molecular recognition involves shape complementarity, with the ZMP 5-amino and carboxamide groups paired with the Watson-Crick edge of an invariant uracil, and the imidazole ring sandwiched between guanines,more » while the sugar hydroxyls form intermolecular hydrogen bond contacts. The burial of the ZMP base and ribose moieties, together with unanticipated coordination of the carboxamide by Mg 2+, contrasts with exposure of the 5'-phosphate to solvent. Lastly, our studies highlight the principles underlying RNA-based recognition of ZMP, a master regulator of one-carbon metabolism.« less

Global RNA Fold and Molecular Recognition for a pfl Riboswitch Bound to ZMP, a Master Regulator of One-Carbon Metabolism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ren, Aiming; Rajashankar, Kanagalaghatta R.; Patel, Dinshaw J.

ZTP, the pyrophosphorylated analog of ZMP (5- amino-4-imidazole carboxamide ribose-5'-monophosphate), was identified as an alarmone that senses 10-formyl-tetrahydroflate deficiency in bacteria. Recently, a pfl riboswitch was identified that selectively binds ZMP and regulates genes associated with purine biosynthesis and one-carbon metabolism. Here we report on the structure of the ZMP-bound Thermosinus carboxydivorans pfl riboswitch sensing domain, thereby defining the pseudoknot-based tertiary RNA fold, the binding-pocket architecture, and principles underlying ligand recognition specificity. Molecular recognition involves shape complementarity, with the ZMP 5-amino and carboxamide groups paired with the Watson-Crick edge of an invariant uracil, and the imidazole ring sandwiched between guanines,more » while the sugar hydroxyls form intermolecular hydrogen bond contacts. The burial of the ZMP base and ribose moieties, together with unanticipated coordination of the carboxamide by Mg 2+, contrasts with exposure of the 5'-phosphate to solvent. Lastly, our studies highlight the principles underlying RNA-based recognition of ZMP, a master regulator of one-carbon metabolism.« less

Evolution of I-SceI Homing Endonucleases with Increased DNA Recognition Site Specificity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Joshi, Rakesh; Ho, Kwok Ki; Tenney, Kristen

2013-09-18

Elucidating how homing endonucleases undergo changes in recognition site specificity will facilitate efforts to engineer proteins for gene therapy applications. I-SceI is a monomeric homing endonuclease that recognizes and cleaves within an 18-bp target. It tolerates limited degeneracy in its target sequence, including substitution of a C:G{sub +4} base pair for the wild-type A:T{sub +4} base pair. Libraries encoding randomized amino acids at I-SceI residue positions that contact or are proximal to A:T{sub +4} were used in conjunction with a bacterial one-hybrid system to select I-SceI derivatives that bind to recognition sites containing either the A:T{sub +4} or the C:G{submore » +4} base pairs. As expected, isolates encoding wild-type residues at the randomized positions were selected using either target sequence. All I-SceI proteins isolated using the C:G{sub +4} recognition site included small side-chain substitutions at G100 and either contained (K86R/G100T, K86R/G100S and K86R/G100C) or lacked (G100A, G100T) a K86R substitution. Interestingly, the binding affinities of the selected variants for the wild-type A:T{sub +4} target are 4- to 11-fold lower than that of wild-type I-SceI, whereas those for the C:G{sub +4} target are similar. The increased specificity of the mutant proteins is also evident in binding experiments in vivo. These differences in binding affinities account for the observed -36-fold difference in target preference between the K86R/G100T and wild-type proteins in DNA cleavage assays. An X-ray crystal structure of the K86R/G100T mutant protein bound to a DNA duplex containing the C:G{sub +4} substitution suggests how sequence specificity of a homing enzyme can increase. This biochemical and structural analysis defines one pathway by which site specificity is augmented for a homing endonuclease.« less

Improving Protein Fold Recognition by Deep Learning Networks.

PubMed

Jo, Taeho; Hou, Jie; Eickholt, Jesse; Cheng, Jianlin

2015-12-04

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 http://iris.rnet.missouri.edu/dnfold.

Image processing strategies based on saliency segmentation for object recognition under simulated prosthetic vision.

PubMed

Li, Heng; Su, Xiaofan; Wang, Jing; Kan, Han; Han, Tingting; Zeng, Yajie; Chai, Xinyu

2018-01-01

Current retinal prostheses can only generate low-resolution visual percepts constituted of limited phosphenes which are elicited by an electrode array and with uncontrollable color and restricted grayscale. Under this visual perception, prosthetic recipients can just complete some simple visual tasks, but more complex tasks like face identification/object recognition are extremely difficult. Therefore, it is necessary to investigate and apply image processing strategies for optimizing the visual perception of the recipients. This study focuses on recognition of the object of interest employing simulated prosthetic vision. We used a saliency segmentation method based on a biologically plausible graph-based visual saliency model and a grabCut-based self-adaptive-iterative optimization framework to automatically extract foreground objects. Based on this, two image processing strategies, Addition of Separate Pixelization and Background Pixel Shrink, were further utilized to enhance the extracted foreground objects. i) The results showed by verification of psychophysical experiments that under simulated prosthetic vision, both strategies had marked advantages over Direct Pixelization in terms of recognition accuracy and efficiency. ii) We also found that recognition performance under two strategies was tied to the segmentation results and was affected positively by the paired-interrelated objects in the scene. The use of the saliency segmentation method and image processing strategies can automatically extract and enhance foreground objects, and significantly improve object recognition performance towards recipients implanted a high-density implant. Copyright © 2017 Elsevier B.V. All rights reserved.

Effects of Emotion on Associative Recognition: Valence and Retention Interval Matter

PubMed Central

Pierce, Benton H.; Kensinger, Elizabeth A.

2011-01-01

In two experiments, we examined the effects of emotional valence and arousal on associative binding. Participants studied negative, positive, and neutral word pairs, followed by an associative recognition test. In Experiment 1, with a short-delayed test, accuracy for intact pairs was equivalent across valences, whereas accuracy for rearranged pairs was lower for negative than for positive and neutral pairs. In Experiment 2, we tested participants after a one-week delay and found that accuracy was greater for intact negative than for intact neutral pairs, whereas rearranged pair accuracy was equivalent across valences. These results suggest that, although negative emotional valence impairs associative binding after a short delay, it may improve binding after a longer delay. The results also suggest that valence, as well as arousal, needs to be considered when examining the effects of emotion on associative memory. PMID:21401233

Control of box C/D snoRNP assembly by N6-methylation of adenine.

PubMed

Huang, Lin; Ashraf, Saira; Wang, Jia; Lilley, David Mj

2017-09-01

N 6 -methyladenine is the most widespread mRNA modification. A subset of human box C/D snoRNA species have target GAC sequences that lead to formation of N 6 -methyladenine at a key trans Hoogsteen-sugar A·G base pair, of which half are methylated in vivo The GAC target is conserved only in those that are methylated. Methylation prevents binding of the 15.5-kDa protein and the induced folding of the RNA Thus, the assembly of the box C/D snoRNP could in principle be regulated by RNA methylation at its critical first stage. Crystallography reveals that N 6 -methylation of adenine prevents the formation of trans Hoogsteen-sugar A·G base pairs, explaining why the box C/D RNA cannot adopt its kinked conformation. More generally, our data indicate that sheared A·G base pairs (but not Watson-Crick base pairs) are more susceptible to disruption by N 6 mA methylation and are therefore possible regulatory sites. The human signal recognition particle RNA and many related Alu retrotransposon RNA species are also methylated at N6 of an adenine that forms a sheared base pair with guanine and mediates a key tertiary interaction. © 2017 The Authors. Published under the terms of the CC BY 4.0 license.

Functions of graphemic and phonemic codes in visual word-recognition.

PubMed

Meyer, D E; Schvaneveldt, R W; Ruddy, M G

1974-03-01

Previous investigators have argued that printed words are recognized directly from visual representations and/or phonological representations obtained through phonemic recoding. The present research tested these hypotheses by manipulating graphemic and phonemic relations within various pairs of letter strings. Ss in two experiments classified the pairs as words or nonwords. Reaction times and error rates were relatively small for word pairs (e.g., BRIBE-TRIBE) that were both graphemically, and phonemically similar. Graphemic similarity alone inhibited performance on other word pairs (e.g., COUCH-TOUCH). These and other results suggest that phonological representations play a significant role in visual word recognition and that there is a dependence between successive phonemic-encoding operations. An encoding-bias model is proposed to explain the data.

Molecular recognition of 7-(2-octadecyloxycarbonylethyl)guanine to cytidine at the air/water interface and LB film studied by Fourier transform infrared spectroscopy

NASA Astrophysics Data System (ADS)

Miao, Wangen; Luo, Xuzhong; Liang, Yingqiu

2003-03-01

Monolayer behavior of a nucleolipid amphiphile, 7-(2-octadecyloxycarbonylethyl)guanine (ODCG), on aqueous cytidine solution was investigated by means of surface-molecular area ( π- A) isotherms. It indicates that molecular recognition by hydrogen bonding is present between ODCG monolayer and the cytidine in subphase. The Fourier transform infrared (FTIR) transmission spectroscopic result indicates that the cytidine molecules in the subphase can be transferred onto solid substrates by Langmuir-Blodgett (LB) technique as a result of the formation of Watson-Crick base-pairing at the air/water interface. Investigation by rotating polarized FTIR transmission also suggests that the headgroup recognition of this amphiphile to the dissolved cytidine influence the orientation of the tailchains.

Intrinsic flexibility of B-DNA: the experimental TRX scale.

PubMed

Heddi, Brahim; Oguey, Christophe; Lavelle, Christophe; Foloppe, Nicolas; Hartmann, Brigitte

2010-01-01

B-DNA flexibility, crucial for DNA-protein recognition, is sequence dependent. Free DNA in solution would in principle be the best reference state to uncover the relation between base sequences and their intrinsic flexibility; however, this has long been hampered by a lack of suitable experimental data. We investigated this relationship by compiling and analyzing a large dataset of NMR (31)P chemical shifts in solution. These measurements reflect the BI <--> BII equilibrium in DNA, intimately correlated to helicoidal descriptors of the curvature, winding and groove dimensions. Comparing the ten complementary DNA dinucleotide steps indicates that some steps are much more flexible than others. This malleability is primarily controlled at the dinucleotide level, modulated by the tetranucleotide environment. Our analyses provide an experimental scale called TRX that quantifies the intrinsic flexibility of the ten dinucleotide steps in terms of Twist, Roll, and X-disp (base pair displacement). Applying the TRX scale to DNA sequences optimized for nucleosome formation reveals a 10 base-pair periodic alternation of stiff and flexible regions. Thus, DNA flexibility captured by the TRX scale is relevant to nucleosome formation, suggesting that this scale may be of general interest to better understand protein-DNA recognition.

Base pairing between the 3' exon and an internal guide sequence increases 3' splice site specificity in the Tetrahymena self-splicing rRNA intron.

PubMed Central

Suh, E R; Waring, R B

1990-01-01

It has been proposed that recognition of the 3' splice site in many group I introns involves base pairing between the start of the 3' exon and a region of the intron known as the internal guide sequence (R. W. Davies, R. B. Waring, J. Ray, T. A. Brown, and C. Scazzocchio, Nature [London] 300:719-724, 1982). We have examined this hypothesis, using the self-splicing rRNA intron from Tetrahymena thermophila. Mutations in the 3' exon that weaken this proposed pairing increased use of a downstream cryptic 3' splice site. Compensatory mutations in the guide sequence that restore this pairing resulted in even stronger selection of the normal 3' splice site. These changes in 3' splice site usage were more pronounced in the background of a mutation (414A) which resulted in an adenine instead of a guanine being the last base of the intron. These results show that the proposed pairing (P10) plays an important role in ensuring that cryptic 3' splice sites are selected against. Surprisingly, the 414A mutation alone did not result in activation of the cryptic 3' splice site. Images PMID:2342465

Dual-Process Models of Associative Recognition in Young and Older Adults: Evidence from Receiver Operating Characteristics

ERIC Educational Resources Information Center

Healy, Michael R.; Light, Leah L.; Chung, Christie

2005-01-01

In 3 experiments, young and older adults studied lists of unrelated word pairs and were given confidence-rated item and associative recognition tests. Several different models of recognition were fit to the confidence-rating data using techniques described by S. Macho (2002, 2004). Concordant with previous findings, item recognition data were best…

Maintenance rehearsal: the key to the role attention plays in storage and forgetting.

PubMed

McFarlane, Kimberley A; Humphreys, Michael S

2012-07-01

Research with the maintenance-rehearsal paradigm, in which word pairs are rehearsed as distractor material during a series of digit recall trials, has previously indicated that low frequency and new word pairs capture attention to a greater degree than high frequency and old word pairs. This impacts delayed recognition of the pairs and interferes with immediate digit recall. The effect on immediate digit recall may provide the missing converging evidence for the role of attention in memory. In the current study, 3 experiments were conducted to further investigate the role of attention capture and novelty in storage and forgetting. In addition to the previously established effects, the novelty of switching rehearsal between 2 pairs was found to impair both digit recall and memory for the first pair. The attentional effects we obtained were dependent upon participant expectation, and forgetting appears to be due to interference with consolidation rather than decay or traditional associative interference. Finally, the attentional effects we observed in associative recognition were primarily reflected in a lowering of the false alarm rate with increases in the strength of the parent pairs. Although dual-process models can accommodate this finding on the assumption that recollection is invoked at test alongside familiarity, we showed that the level of recall in this paradigm is so small that recollection can be ruled out. Accordingly, our results are challenging for the existing models of associative recognition to accommodate. 2012 APA, all rights reserved

Improving Protein Fold Recognition by Deep Learning Networks

NASA Astrophysics Data System (ADS)

Jo, Taeho; Hou, Jie; Eickholt, Jesse; Cheng, Jianlin

2015-12-01

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 http://iris.rnet.missouri.edu/dnfold.

The Role of the Association in Recognition Memory.

ERIC Educational Resources Information Center

Underwood, Benton J.

The purpose of the eight experiments was to assess the role which associations between two words played in recognition decisions. The evidence on weak associations established in the laboratory indicated that association was playing a small role, but that the recognition performance on pairs of words was highly predictable from frequency…

Implicit Relational Effects in Associative Recognition

ERIC Educational Resources Information Center

Algarabel, S.; Pitarque, A.; Combita, L. M.; Rodriguez, L. A.

2013-01-01

We study the contribution of implicit relatedness to associative recognition in two experiments. In the first experiment, we showed an implicit improvement in recognition when the stimulus elements of each word pair shared common letters and they were unpaired at test. Moreover, when asked to study the stimuli under divided attention, recollection…

Orthographic effects in spoken word recognition: Evidence from Chinese.

PubMed

Qu, Qingqing; Damian, Markus F

2017-06-01

Extensive evidence from alphabetic languages demonstrates a role of orthography in the processing of spoken words. Because alphabetic systems explicitly code speech sounds, such effects are perhaps not surprising. However, it is less clear whether orthographic codes are involuntarily accessed from spoken words in languages with non-alphabetic systems, in which the sound-spelling correspondence is largely arbitrary. We investigated the role of orthography via a semantic relatedness judgment task: native Mandarin speakers judged whether or not spoken word pairs were related in meaning. Word pairs were either semantically related, orthographically related, or unrelated. Results showed that relatedness judgments were made faster for word pairs that were semantically related than for unrelated word pairs. Critically, orthographic overlap on semantically unrelated word pairs induced a significant increase in response latencies. These findings indicate that orthographic information is involuntarily accessed in spoken-word recognition, even in a non-alphabetic language such as Chinese.

Memory Asymmetry of Forward and Backward Associations in Recognition Tasks

PubMed Central

Yang, Jiongjiong; Zhu, Zijian; Mecklinger, Axel; Fang, Zhiyong; Li, Han

2013-01-01

There is an intensive debate on whether memory for serial order is symmetric. The objective of this study was to explore whether associative asymmetry is modulated by memory task (recognition vs. cued recall). Participants were asked to memorize word triples (Experiment 1–2) or pairs (Experiment 3–6) during the study phase. They then recalled the word by a cue during a cued recall task (Experiment 1–4), and judged whether the presented two words were in the same or in a different order compared to the study phase during a recognition task (Experiment 1–6). To control for perceptual matching between the study and test phase, participants were presented with vertical test pairs when they made directional judgment in Experiment 5. In Experiment 6, participants also made associative recognition judgments for word pairs presented at the same or the reversed position. The results showed that forward associations were recalled at similar levels as backward associations, and that the correlations between forward and backward associations were high in the cued recall tasks. On the other hand, the direction of forward associations was recognized more accurately (and more quickly) than backward associations, and their correlations were comparable to the control condition in the recognition tasks. This forward advantage was also obtained for the associative recognition task. Diminishing positional information did not change the pattern of associative asymmetry. These results suggest that associative asymmetry is modulated by cued recall and recognition manipulations, and that direction as a constituent part of a memory trace can facilitate associative memory. PMID:22924326

Minimizing Skin Color Differences Does Not Eliminate the Own-Race Recognition Advantage in Infants

PubMed Central

Anzures, Gizelle; Pascalis, Olivier; Quinn, Paul C.; Slater, Alan M.; Lee, Kang

2011-01-01

An abundance of experience with own-race faces and limited to no experience with other-race faces has been associated with better recognition memory for own-race faces in infants, children, and adults. This study investigated the developmental origins of this other-race effect (ORE) by examining the role of a salient perceptual property of faces—that of skin color. Six- and 9-month-olds’ recognition memory for own- and other-race faces was examined using infant-controlled habituation and visual-paired comparison at test. Infants were shown own- or other-race faces in color or with skin color cues minimized in grayscale images. Results for the color stimuli replicated previous findings that infants show an ORE in face recognition memory. Results for the grayscale stimuli showed that even when a salient perceptual cue to race, such as skin color information, is minimized, 6- to 9-month-olds, nonetheless, show an ORE in their face recognition memory. Infants’ use of shape-based and configural cues for face recognition is discussed. PMID:22039335

Impaired recognition of faces and objects in dyslexia: Evidence for ventral stream dysfunction?

PubMed

Sigurdardottir, Heida Maria; Ívarsson, Eysteinn; Kristinsdóttir, Kristjana; Kristjánsson, Árni

2015-09-01

The objective of this study was to establish whether or not dyslexics are impaired at the recognition of faces and other complex nonword visual objects. This would be expected based on a meta-analysis revealing that children and adult dyslexics show functional abnormalities within the left fusiform gyrus, a brain region high up in the ventral visual stream, which is thought to support the recognition of words, faces, and other objects. 20 adult dyslexics (M = 29 years) and 20 matched typical readers (M = 29 years) participated in the study. One dyslexic-typical reader pair was excluded based on Adult Reading History Questionnaire scores and IS-FORM reading scores. Performance was measured on 3 high-level visual processing tasks: the Cambridge Face Memory Test, the Vanderbilt Holistic Face Processing Test, and the Vanderbilt Expertise Test. People with dyslexia are impaired in their recognition of faces and other visually complex objects. Their holistic processing of faces appears to be intact, suggesting that dyslexics may instead be specifically impaired at part-based processing of visual objects. The difficulty that people with dyslexia experience with reading might be the most salient manifestation of a more general high-level visual deficit. (c) 2015 APA, all rights reserved).

In infancy the timing of emergence of the other-race effect is dependent on face gender.

PubMed

Tham, Diana Su Yun; Bremner, J Gavin; Hay, Dennis

2015-08-01

Poorer recognition of other-race faces relative to own-race faces is well documented from late infancy to adulthood. Research has revealed an increase in the other-race effect (ORE) during the first year of life, but there is some disagreement regarding the age at which it emerges. Using cropped faces to eliminate discrimination based on external features, visual paired comparison and spontaneous visual preference measures were used to investigate the relationship between ORE and face gender at 3-4 and 8-9 months. Caucasian-White 3- to 4-month-olds' discrimination of Chinese, Malay, and Caucasian-White faces showed an own-race advantage for female faces alone whereas at 8-9 months the own-race advantage was general across gender. This developmental effect is accompanied by a preference for female over male faces at 4 months and no gender preference at 9 months. The pattern of recognition advantage and preference suggests that there is a shift from a female-based own-race recognition advantage to a general own-race recognition advantage, in keeping with a visual and social experience-based account of ORE. Copyright © 2015 Elsevier Inc. All rights reserved.

Maintenance Rehearsal: The Key to the Role Attention Plays in Storage and Forgetting

ERIC Educational Resources Information Center

McFarlane, Kimberley A.; Humphreys, Michael S.

2012-01-01

Research with the maintenance-rehearsal paradigm, in which word pairs are rehearsed as distractor material during a series of digit recall trials, has previously indicated that low frequency and new word pairs capture attention to a greater degree than high frequency and old word pairs. This impacts delayed recognition of the pairs and interferes…

Hyper-Binding across Time: Age Differences in the Effect of Temporal Proximity on Paired-Associate Learning

ERIC Educational Resources Information Center

Campbell, Karen L.; Trelle, Alexandra; Hasher, Lynn

2014-01-01

Older adults show hyper- (or excessive) binding effects for simultaneously and sequentially presented distraction. Here, we addressed the potential role of hyper-binding in paired-associate learning. Older and younger adults learned a list of word pairs and then received an associative recognition task in which rearranged pairs were formed from…

Tell Me Everything You Discussed: Children's Memory for Dyadic Conversations after a 1-Week or a 3-Week Delay.

PubMed

Lawson, Monica; London, Kamala

2015-08-01

In child abuse investigations, children are often asked to recount previous conversations related to the allegations (i.e., "conversational testimony"). To explore children's ability to provide conversational testimony, we staged a semi-structured novel dyadic conversation between an adult researcher and 8-year-old children (n = 90). Children's gist recall and recognition memory for their own statements, their conversational partner's statements, and question-answer pairs were tested after either a 1-week or a 3-week delay. The results revealed that children recounted a minority of the conversation, although children recalled more after a short delay (7%) than after a long delay (4%). A majority of children's free recall statements were accurate (68%); however, approximately one-third of their free recall statements were incorrect. Children almost exclusively recounted their own statements, and rarely recalled any of the adult's statements or the question-answer pairs during free recall. Reports of the adult's statements and question-answer pairs increased with cued recall questioning, but remained minimal. During recognition testing, children were able to distinguish between true and false recognition items for their own statements and the adult's statements, but performed at chance level on recognition items concerning question-answer pairs. Forensic implications of the results are discussed. Copyright © 2015 John Wiley & Sons, Ltd.

A star recognition method based on the Adaptive Ant Colony algorithm for star sensors.

PubMed

Quan, Wei; Fang, Jiancheng

2010-01-01

A new star recognition method based on the Adaptive Ant Colony (AAC) algorithm has been developed to increase the star recognition speed and success rate for star sensors. This method draws circles, with the center of each one being a bright star point and the radius being a special angular distance, and uses the parallel processing ability of the AAC algorithm to calculate the angular distance of any pair of star points in the circle. The angular distance of two star points in the circle is solved as the path of the AAC algorithm, and the path optimization feature of the AAC is employed to search for the optimal (shortest) path in the circle. This optimal path is used to recognize the stellar map and enhance the recognition success rate and speed. The experimental results show that when the position error is about 50″, the identification success rate of this method is 98% while the Delaunay identification method is only 94%. The identification time of this method is up to 50 ms.

Crystal structure correlations with the intrinsic thermodynamics of human carbonic anhydrase inhibitor binding

PubMed Central

Smirnov, Alexey; Zubrienė, Asta; Manakova, Elena; Gražulis, Saulius

2018-01-01

The structure-thermodynamics correlation analysis was performed for a series of fluorine- and chlorine-substituted benzenesulfonamide inhibitors binding to several human carbonic anhydrase (CA) isoforms. The total of 24 crystal structures of 16 inhibitors bound to isoforms CA I, CA II, CA XII, and CA XIII provided the structural information of selective recognition between a compound and CA isoform. The binding thermodynamics of all structures was determined by the analysis of binding-linked protonation events, yielding the intrinsic parameters, i.e., the enthalpy, entropy, and Gibbs energy of binding. Inhibitor binding was compared within structurally similar pairs that differ by para- or meta-substituents enabling to obtain the contributing energies of ligand fragments. The pairs were divided into two groups. First, similar binders—the pairs that keep the same orientation of the benzene ring exhibited classical hydrophobic effect, a less exothermic enthalpy and a more favorable entropy upon addition of the hydrophobic fragments. Second, dissimilar binders—the pairs of binders that demonstrated altered positions of the benzene rings exhibited the non-classical hydrophobic effect, a more favorable enthalpy and variable entropy contribution. A deeper understanding of the energies contributing to the protein-ligand recognition should lead toward the eventual goal of rational drug design where chemical structures of ligands could be designed based on the target protein structure. PMID:29503769

Molecular recognition of 7-(2-octadecyloxycarbonylethyl)guanine to cytidine at the air/water interface and LB film studied by Fourier transform infrared spectroscopy.

PubMed

Miao, Wangen; Luo, Xuzhong; Liang, Yingqiu

2003-03-15

Monolayer behavior of a nucleolipid amphiphile, 7-(2-octadecyloxycarbonylethyl)guanine (ODCG), on aqueous cytidine solution was investigated by means of surface-molecular area (pi-A) isotherms. It indicates that molecular recognition by hydrogen bonding is present between ODCG monolayer and the cytidine in subphase. The Fourier transform infrared (FTIR) transmission spectroscopic result indicates that the cytidine molecules in the subphase can be transferred onto solid substrates by Langmuir-Blodgett (LB) technique as a result of the formation of Watson-Crick base-pairing at the air/water interface. Investigation by rotating polarized FTIR transmission also suggests that the headgroup recognition of this amphiphile to the dissolved cytidine influence the orientation of the tailchains. Copyright 2002 Elsevier Science B.V.

Generalizations of the subject-independent feature set for music-induced emotion recognition.

PubMed

Lin, Yuan-Pin; Chen, Jyh-Horng; Duann, Jeng-Ren; Lin, Chin-Teng; Jung, Tzyy-Ping

2011-01-01

Electroencephalogram (EEG)-based emotion recognition has been an intensely growing field. Yet, how to achieve acceptable accuracy on a practical system with as fewer electrodes as possible is less concerned. This study evaluates a set of subject-independent features, based on differential power asymmetry of symmetric electrode pairs [1], with emphasis on its applicability to subject variability in music-induced emotion classification problem. Results of this study have evidently validated the feasibility of using subject-independent EEG features to classify four emotional states with acceptable accuracy in second-scale temporal resolution. These features could be generalized across subjects to detect emotion induced by music excerpts not limited to the music database that was used to derive the emotion-specific features.

Tensor manifold-based extreme learning machine for 2.5-D face recognition

NASA Astrophysics Data System (ADS)

Chong, Lee Ying; Ong, Thian Song; Teoh, Andrew Beng Jin

2018-01-01

We explore the use of the Gabor regional covariance matrix (GRCM), a flexible matrix-based descriptor that embeds the Gabor features in the covariance matrix, as a 2.5-D facial descriptor and an effective means of feature fusion for 2.5-D face recognition problems. Despite its promise, matching is not a trivial problem for GRCM since it is a special instance of a symmetric positive definite (SPD) matrix that resides in non-Euclidean space as a tensor manifold. This implies that GRCM is incompatible with the existing vector-based classifiers and distance matchers. Therefore, we bridge the gap of the GRCM and extreme learning machine (ELM), a vector-based classifier for the 2.5-D face recognition problem. We put forward a tensor manifold-compliant ELM and its two variants by embedding the SPD matrix randomly into reproducing kernel Hilbert space (RKHS) via tensor kernel functions. To preserve the pair-wise distance of the embedded data, we orthogonalize the random-embedded SPD matrix. Hence, classification can be done using a simple ridge regressor, an integrated component of ELM, on the random orthogonal RKHS. Experimental results show that our proposed method is able to improve the recognition performance and further enhance the computational efficiency.

Interspecific aggression and character displacement of competitor recognition in Hetaerina damselflies.

PubMed

Anderson, Christopher N; Grether, Gregory F

2010-02-22

In zones of sympatry between closely related species, species recognition errors in a competitive context can cause character displacement in agonistic signals and competitor recognition functions, just as species recognition errors in a mating context can cause character displacement in mating signals and mate recognition. These two processes are difficult to distinguish because the same traits can serve as both agonistic and mating signals. One solution is to test for sympatric shifts in recognition functions. We studied competitor recognition in Hetaerina damselflies by challenging territory holders with live tethered conspecific and heterospecific intruders. Heterospecific intruders elicited less aggression than conspecific intruders in species pairs with dissimilar wing coloration (H. occisa/H. titia, H. americana/H. titia) but not in species pairs with similar wing coloration (H. occisa/H. cruentata, H. americana/H. cruentata). Natural variation in the area of black wing pigmentation on H. titia intruders correlated negatively with heterospecific aggression. To directly examine the role of wing coloration, we blackened the wings of H. occisa or H. americana intruders and measured responses of conspecific territory holders. This treatment reduced territorial aggression at multiple sites where H. titia is present, but not at allopatric sites. These results provide strong evidence for agonistic character displacement.

Energy Landscape and Pathways for Transitions between Watson-Crick and Hoogsteen Base Pairing in DNA.

PubMed

Chakraborty, Debayan; Wales, David J

2018-01-04

The recent discovery that Hoogsteen (HG) base pairs are widespread in DNA across diverse sequences and positional contexts could have important implications for understanding DNA replication and DNA-protein recognition. While evidence is emerging that the Hoogsteen conformation could be a thermodynamically accessible conformation of the DNA duplex and provide a means to expand its functionality, relatively little is known about the molecular mechanism underlying the Watson-Crick (WC) to HG transition. In this Perspective, we describe pathways and kinetics for this transition at an atomic level of detail, using the energy landscape perspective. We show that competition between the duplex conformations results in a double funnel landscape, which explains some recent experimental observations. The interconversion pathways feature a number of intermediates, with a variable number of WC and HG base pairs. The relatively slow kinetics, with possible deviations from two-state behavior, suggest that this conformational switch is likely to be a challenging target for both simulation and experiment.

AzaHx, a novel fluorescent, DNA minor groove and G·C recognition element: Synthesis and DNA binding properties of a p-anisyl-4-aza-benzimidazole-pyrrole-imidazole (azaHx-PI) polyamide.

PubMed

Satam, Vijay; Babu, Balaji; Patil, Pravin; Brien, Kimberly A; Olson, Kevin; Savagian, Mia; Lee, Megan; Mepham, Andrew; Jobe, Laura Beth; Bingham, John P; Pett, Luke; Wang, Shuo; Ferrara, Maddi; Bruce, Chrystal D; Wilson, W David; Lee, Moses; Hartley, John A; Kiakos, Konstantinos

2015-09-01

The design, synthesis, and DNA binding properties of azaHx-PI or p-anisyl-4-aza-benzimidazole-pyrrole-imidazole (5) are described. AzaHx, 2-(p-anisyl)-4-aza-benzimidazole-5-carboxamide, is a novel, fluorescent DNA recognition element, derived from Hoechst 33258 to recognize G·C base pairs. Supported by theoretical data, the results from DNase I footprinting, CD, ΔT(M), and SPR studies provided evidence that an azaHx/IP pairing, formed from antiparallel stacking of two azaHx-PI molecules in a side-by-side manner in the minor groove, selectively recognized a C-G doublet. AzaHx-PI was found to target 5'-ACGCGT-3', the Mlu1 Cell Cycle Box (MCB) promoter sequence with specificity and significant affinity (K(eq) 4.0±0.2×10(7) M(-1)). Copyright © 2015 Elsevier Ltd. All rights reserved.

Investigation of the effectiveness of traffic sign training in terms of training methods and sign characteristics.

PubMed

Ng, Annie W Y; Chan, Alan H S

2011-06-01

This research investigated whether different training methods had any effect on the effectiveness of traffic sign training and whether there were any relationships between traffic sign characteristics and effectiveness of the training. Thirty-six participants were randomly assigned into 4 equal-sized groups (control, paired-associate learning, recall training, and recognition training) to study the learnability of Mainland China traffic signs. In paired-associate learning, participants studied each traffic sign along with a referent describing its meaning. In addition to being informed of the meaning of traffic signs, both recall training and recognition training provided participants with questions and feedback. For recall training, the questioning process was a recall task in which participants had to produce a meaning for a given traffic sign from memory. For recognition training, the questioning process was a recognition task that required participants to identify the most appropriate referent corresponding to a given sign. No traffic sign training was given to the control group. Each training method significantly improved comprehension of the meaning of traffic signs. Participants from recall training performed better in a posttraining test than those from paired-associate learning and recognition training, indicating that the recall training elicited a deeper level of learning. In addition, questioning and feedback had a positive influence on training effectiveness. Performance in the posttest was found to be better when the questioning process matched the test process. Regarding the traffic sign characteristics, semantic closeness had a long-lasting effect, in terms of the timescale of this experiment on traffic sign comprehension, and traffic signs were perceived as more meaningful after their intended meanings were studied. Recall training is more effective in enhancing comprehension of traffic signs than paired-associate learning and recognition training. The findings of this study provide a basis for useful recommendations for designing symbol-training programs to improve road safety for road users.

The role of multimodal signals in species recognition between tree-killing bark beetles in a narrow sympatric zone.

Treesearch

Deepa S. Pureswaran; Richard W. Hofstetter; Brian Sullivan; Kristen A. Potter

2016-01-01

When related species coexist, selection pressure should favor evolution of species recognition mechanisms to prevent interspecific pairing and wasteful reproductive encounters. We investigated the potential role of pheromone and acoustic signals in species recognition between two species of tree-killing bark beetles, the southern pine beetle, Dendroctonus frontalis...

A Novel Anti-Spoofing Solution for Iris Recognition Toward Cosmetic Contact Lens Attack Using Spectral ICA Analysis.

PubMed

Hsieh, Sheng-Hsun; Li, Yung-Hui; Wang, Wei; Tien, Chung-Hao

2018-03-06

In this study, we maneuvered a dual-band spectral imaging system to capture an iridal image from a cosmetic-contact-lens-wearing subject. By using the independent component analysis to separate individual spectral primitives, we successfully distinguished the natural iris texture from the cosmetic contact lens (CCL) pattern, and restored the genuine iris patterns from the CCL-polluted image. Based on a database containing 200 test image pairs from 20 CCL-wearing subjects as the proof of concept, the recognition accuracy (False Rejection Rate: FRR) was improved from FRR = 10.52% to FRR = 0.57% with the proposed ICA anti-spoofing scheme.

Codon-Anticodon Recognition in the Bacillus subtilis glyQS T Box Riboswitch

PubMed Central

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

2015-01-01

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 tRNAGly 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. PMID:26229106

Data-centric method for object observation through scattering media

NASA Astrophysics Data System (ADS)

Tanida, Jun; Horisaki, Ryoichi

2018-03-01

A data-centric method is introduced for object observation through scattering media. A large number of training pairs are used to characterize the relation between the object and the observation signals based on machine learning. Using the method object information can be retrieved even from strongly-disturbed signals. As potential applications, object recognition, imaging, and focusing through scattering media were demonstrated.

Effects of Phonological and Orthographic Shifts on Children's Processing of Written Morphology: A Time-Course Study

ERIC Educational Resources Information Center

Quémart, Pauline; Casalis, Séverine

2014-01-01

We report two experiments that investigated whether phonological and/or orthographic shifts in a base word interfere with morphological processing by French 3rd, 4th, and 5th graders and adults (as a control group) along the time course of visual word recognition. In both experiments, prime-target pairs shared four possible relationships:…

Uracil recognition by replicative DNA polymerases is limited to the archaea, not occurring with bacteria and eukarya.

PubMed

Wardle, Josephine; Burgers, Peter M J; Cann, Isaac K O; Darley, Kate; Heslop, Pauline; Johansson, Erik; Lin, Li-Jung; McGlynn, Peter; Sanvoisin, Jonathan; Stith, Carrie M; Connolly, Bernard A

2008-02-01

Family B DNA polymerases from archaea such as Pyrococcus furiosus, which live at temperatures approximately 100 degrees C, specifically recognize uracil in DNA templates and stall replication in response to this base. Here it is demonstrated that interaction with uracil is not restricted to hyperthermophilic archaea and that the polymerase from mesophilic Methanosarcina acetivorans shows identical behaviour. The family B DNA polymerases replicate the genomes of archaea, one of the three fundamental domains of life. This publication further shows that the DNA replicating polymerases from the other two domains, bacteria (polymerase III) and eukaryotes (polymerases delta and epsilon for nuclear DNA and polymerase gamma for mitochondrial) are also unable to recognize uracil. Uracil occurs in DNA as a result of deamination of cytosine, either in G:C base-pairs or, more rapidly, in single stranded regions produced, for example, during replication. The resulting G:U mis-pairs/single stranded uracils are promutagenic and, unless repaired, give rise to G:C to A:T transitions in 50% of the progeny. The confinement of uracil recognition to polymerases of the archaeal domain is discussed in terms of the DNA repair pathways necessary for the elimination of uracil.

Flying in tune: sexual recognition in mosquitoes.

PubMed

Gibson, Gabriella; Russell, Ian

2006-07-11

Mosquitoes hear with their antennae, which in most species are sexually dimorphic. Johnston, who discovered the mosquito auditory organ at the base of the antenna 150 years ago, speculated that audition was involved with mating behaviour. Indeed, male mosquitoes are attracted to female flight tones. The male auditory organ has been proposed to act as an acoustic filter for female flight tones, but female auditory behavior is unknown. We show, for the first time, interactive auditory behavior between males and females that leads to sexual recognition. Individual males and females both respond to pure tones by altering wing-beat frequency. Behavioral auditory tuning curves, based on minimum threshold sound levels that elicit a change in wing-beat frequency to pure tones, are sharper than the mechanical tuning of the antennae, with males being more sensitive than females. We flew opposite-sex pairs of tethered Toxorhynchites brevipalpis and found that each mosquito alters its wing-beat frequency in response to the flight tone of the other, so that within seconds their flight-tone frequencies are closely matched, if not completely synchronized. The flight tones of same-sex pairs may converge in frequency but eventually diverge dramatically.

Roles of the amino group of purine bases in the thermodynamic stability of DNA base pairing.

PubMed

Nakano, Shu-ichi; Sugimoto, Naoki

2014-08-05

The energetic aspects of hydrogen-bonded base-pair interactions are important for the design of functional nucleotide analogs and for practical applications of oligonucleotides. The present study investigated the contribution of the 2-amino group of DNA purine bases to the thermodynamic stability of oligonucleotide duplexes under different salt and solvent conditions, using 2'-deoxyriboinosine (I) and 2'-deoxyribo-2,6-diaminopurine (D) as non-canonical nucleotides. The stability of DNA duplexes was changed by substitution of a single base pair in the following order: G • C > D • T ≈ I • C > A • T > G • T > I • T. The apparent stabilization energy due to the presence of the 2-amino group of G and D varied depending on the salt concentration, and decreased in the water-ethanol mixed solvent. The effects of salt concentration on the thermodynamics of DNA duplexes were found to be partially sequence-dependent, and the 2-amino group of the purine bases might have an influence on the binding of ions to DNA through the formation of a stable base-paired structure. Our results also showed that physiological salt conditions were energetically favorable for complementary base recognition, and conversely, low salt concentration media and ethanol-containing solvents were effective for low stringency oligonucleotide hybridization, in the context of conditions employed in this study.

Holistic word processing in dyslexia

PubMed Central

Conway, Aisling; Misra, Karuna

2017-01-01

People with dyslexia have difficulty learning to read and many lack fluent word recognition as adults. In a novel task that borrows elements of the ‘word superiority’ and ‘word inversion’ paradigms, we investigate whether holistic word recognition is impaired in dyslexia. In Experiment 1 students with dyslexia and controls judged the similarity of pairs of 6- and 7-letter words or pairs of words whose letters had been partially jumbled. The stimuli were presented in both upright and inverted form with orthographic regularity and orientation randomized from trial to trial. While both groups showed sensitivity to orthographic regularity, both word inversion and letter jumbling were more detrimental to skilled than dyslexic readers supporting the idea that the latter may read in a more analytic fashion. Experiment 2 employed the same task but using shorter, 4- and 5-letter words and a design where orthographic regularity and stimuli orientation was held constant within experimental blocks to encourage the use of either holistic or analytic processing. While there was no difference in reaction time between the dyslexic and control groups for inverted stimuli, the students with dyslexia were significantly slower than controls for upright stimuli. These findings suggest that holistic word recognition, which is largely based on the detection of orthographic regularity, is impaired in dyslexia. PMID:29121046

Tunneling readout of hydrogen-bonding based recognition

PubMed Central

Chang, Shuai; He, Jin; Kibel, Ashley; Lee, Myeong; Sankey, Otto; Zhang, Peiming; Lindsay, Stuart

2009-01-01

Hydrogen bonding has a ubiquitous role in electron transport1,2 and in molecular recognition, with DNA base-pairing being the best known example.3 Scanning tunneling microscope (STM) images4 and measurements of the decay of tunnel-current as a molecular junction is pulled apart by the STM tip, 5 are sensitive to hydrogen-bonded interactions. Here we show that these tunnel-decay signals can be used to measure the strength of hydrogen bonding in DNA basepairs. Junctions that are held together by three hydrogen bonds per basepair (e.g., guanine-cytosine interactions) are stiffer than junctions held together by two hydrogen bonds per basepair (e.g., adenine-thymine interactions). Similar, but less-pronounced, effects are observed on the approach of the tunneling probe, implying that hydrogen-bond dependent attractive forces also have a role in determining the rise of current. These effects provide new mechanisms for making sensors that transduce a molecular recognition event into an electronic signal. PMID:19421214

Differential stabilities and sequence-dependent base pair opening dynamics of Watson-Crick base pairs with 5-hydroxymethylcytosine, 5-formylcytosine, or 5-carboxylcytosine.

PubMed

Szulik, Marta W; Pallan, Pradeep S; Nocek, Boguslaw; Voehler, Markus; Banerjee, Surajit; Brooks, Sonja; Joachimiak, Andrzej; Egli, Martin; Eichman, Brandt F; Stone, Michael P

2015-02-10

5-Hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) form during active demethylation of 5-methylcytosine (5mC) and are implicated in epigenetic regulation of the genome. They are differentially processed by thymine DNA glycosylase (TDG), an enzyme involved in active demethylation of 5mC. Three modified Dickerson-Drew dodecamer (DDD) sequences, amenable to crystallographic and spectroscopic analyses and containing the 5'-CG-3' sequence associated with genomic cytosine methylation, containing 5hmC, 5fC, or 5caC placed site-specifically into the 5'-T(8)X(9)G(10)-3' sequence of the DDD, were compared. The presence of 5caC at the X(9) base increased the stability of the DDD, whereas 5hmC or 5fC did not. Both 5hmC and 5fC increased imino proton exchange rates and calculated rate constants for base pair opening at the neighboring base pair A(5):T(8), whereas 5caC did not. At the oxidized base pair G(4):X(9), 5fC exhibited an increase in the imino proton exchange rate and the calculated kop. In all cases, minimal effects to imino proton exchange rates occurred at the neighboring base pair C(3):G(10). No evidence was observed for imino tautomerization, accompanied by wobble base pairing, for 5hmC, 5fC, or 5caC when positioned at base pair G(4):X(9); each favored Watson-Crick base pairing. However, both 5fC and 5caC exhibited intranucleobase hydrogen bonding between their formyl or carboxyl oxygens, respectively, and the adjacent cytosine N(4) exocyclic amines. The lesion-specific differences observed in the DDD may be implicated in recognition of 5hmC, 5fC, or 5caC in DNA by TDG. However, they do not correlate with differential excision of 5hmC, 5fC, or 5caC by TDG, which may be mediated by differences in transition states of the enzyme-bound complexes.

Differential stabilities and sequence-dependent base pair opening dynamics of Watson–Crick base pairs with 5-hydroxymethylcytosine, 5-formylcytosine, or 5-carboxylcytosine

DOE PAGES

Szulik, Marta W.; Pallan, Pradeep S.; Nocek, Boguslaw; ...

2015-01-29

5-Hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) form during active demethylation of 5-methylcytosine (5mC) and are implicated in epigenetic regulation of the genome. They are differentially processed by thymine DNA glycosylase (TDG), an enzyme involved in active demethylation of 5mC. Three modified Dickerson–Drew dodecamer (DDD) sequences, amenable to crystallographic and spectroscopic analyses and containing the 5'-CG-3' sequence associated with genomic cytosine methylation, containing 5hmC, 5fC, or 5caC placed site-specifically into the 5'-T 8X 9G 10-3' sequence of the DDD, were compared. The presence of 5caC at the X9 base increased the stability of the DDD, whereas 5hmC or 5fC didmore » not. Both 5hmC and 5fC increased imino proton exchange rates and calculated rate constants for base pair opening at the neighboring base pair A 5:T 8, whereas 5caC did not. At the oxidized base pair G 4:X 9, 5fC exhibited an increase in the imino proton exchange rate and the calculated k op. In all cases, minimal effects to imino proton exchange rates occurred at the neighboring base pair C 3:G 10. No evidence was observed for imino tautomerization, accompanied by wobble base pairing, for 5hmC, 5fC, or 5caC when positioned at base pair G 4:X 9; each favored Watson–Crick base pairing. However, both 5fC and 5caC exhibited intranucleobase hydrogen bonding between their formyl or carboxyl oxygens, respectively, and the adjacent cytosine N 4 exocyclic amines. The lesion-specific differences observed in the DDD may be implicated in recognition of 5hmC, 5fC, or 5caC in DNA by TDG. Furthermore, they do not correlate with differential excision of 5hmC, 5fC, or 5caC by TDG, which may be mediated by differences in transition states of the enzyme-bound complexes.« less

Differential Stabilities and Sequence-Dependent Base Pair Opening Dynamics of Watson–Crick Base Pairs with 5-Hydroxymethylcytosine, 5-Formylcytosine, or 5-Carboxylcytosine

PubMed Central

2016-01-01

5-Hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) form during active demethylation of 5-methylcytosine (5mC) and are implicated in epigenetic regulation of the genome. They are differentially processed by thymine DNA glycosylase (TDG), an enzyme involved in active demethylation of 5mC. Three modified Dickerson–Drew dodecamer (DDD) sequences, amenable to crystallographic and spectroscopic analyses and containing the 5′-CG-3′ sequence associated with genomic cytosine methylation, containing 5hmC, 5fC, or 5caC placed site-specifically into the 5′-T8X9G10-3′ sequence of the DDD, were compared. The presence of 5caC at the X9 base increased the stability of the DDD, whereas 5hmC or 5fC did not. Both 5hmC and 5fC increased imino proton exchange rates and calculated rate constants for base pair opening at the neighboring base pair A5:T8, whereas 5caC did not. At the oxidized base pair G4:X9, 5fC exhibited an increase in the imino proton exchange rate and the calculated kop. In all cases, minimal effects to imino proton exchange rates occurred at the neighboring base pair C3:G10. No evidence was observed for imino tautomerization, accompanied by wobble base pairing, for 5hmC, 5fC, or 5caC when positioned at base pair G4:X9; each favored Watson–Crick base pairing. However, both 5fC and 5caC exhibited intranucleobase hydrogen bonding between their formyl or carboxyl oxygens, respectively, and the adjacent cytosine N4 exocyclic amines. The lesion-specific differences observed in the DDD may be implicated in recognition of 5hmC, 5fC, or 5caC in DNA by TDG. However, they do not correlate with differential excision of 5hmC, 5fC, or 5caC by TDG, which may be mediated by differences in transition states of the enzyme-bound complexes. PMID:25632825

I Know My Neighbour: Individual Recognition in Octopus vulgaris

PubMed Central

Tricarico, Elena; Borrelli, Luciana; Gherardi, Francesca; Fiorito, Graziano

2011-01-01

Background Little is known about individual recognition (IR) in octopuses, although they have been abundantly studied for their sophisticated behaviour and learning capacities. Indeed, the ability of octopuses to recognise conspecifics is suggested by a number of clues emerging from both laboratory studies (where they appear to form and maintain dominance hierarchies) and field observations (octopuses of neighbouring dens display little agonism between each other). To fill this gap in knowledge, we investigated the behaviour of 24 size-matched pairs of Octopus vulgaris in laboratory conditions. Methodology/Principal Findings The experimental design was composed of 3 phases: Phase 1 (acclimatization): 12 “sight-allowed” (and 12 “isolated”) pairs were maintained for 3 days in contiguous tanks separated by a transparent (and opaque) partition to allow (and block) the vision of the conspecific; Phase 2 (cohabitation): members of each pair (both sight-allowed and isolated) were transferred into an experimental tank and were allowed to interact for 15 min every day for 3 consecutive days; Phase 3 (test): each pair (both sight-allowed and isolated) was subject to a switch of an octopus to form pairs composed of either familiar (“sham switches”) or unfamiliar conspecifics (“real switches”). Longer latencies (i.e. the time elapsed from the first interaction) and fewer physical contacts in the familiar pairs as opposed to the unfamiliar pairs were used as proxies for recognition. Conclusions Octopuses appear able to recognise conspecifics and to remember the individual previously met for at least one day. To the best of our knowledge, this is the first experimental study showing the occurrence of a form of IR in cephalopods. Future studies should clarify whether this is a “true” IR. PMID:21533257

The first does the work, but the third time's the charm: the effects of massed repetition on episodic encoding of multimodal face-name associations.

PubMed

Mangels, Jennifer A; Manzi, Alberto; Summerfield, Christopher

2010-03-01

In social interactions, it is often necessary to rapidly encode the association between visually presented faces and auditorily presented names. The present study used event-related potentials to examine the neural correlates of associative encoding for multimodal face-name pairs. We assessed study-phase processes leading to high-confidence recognition of correct pairs (and consistent rejection of recombined foils) as compared to lower-confidence recognition of correct pairs (with inconsistent rejection of recombined foils) and recognition failures (misses). Both high- and low-confidence retrieval of face-name pairs were associated with study-phase activity suggestive of item-specific processing of the face (posterior inferior temporal negativity) and name (fronto-central negativity). However, only those pairs later retrieved with high confidence recruited a sustained centro-parietal positivity that an ancillary localizer task suggested may index an association-unique process. Additionally, we examined how these processes were influenced by massed repetition, a mnemonic strategy commonly employed in everyday situations to improve face-name memory. Differences in subsequent memory effects across repetitions suggested that associative encoding was strongest at the initial presentation, and thus, that the initial presentation has the greatest impact on memory formation. Yet, exploratory analyses suggested that the third presentation may have benefited later memory by providing an opportunity for extended processing of the name. Thus, although encoding of the initial presentation was critical for establishing a strong association, the extent to which processing was sustained across subsequent immediate (massed) presentations may provide additional encoding support that serves to differentiate face-name pairs from similar (recombined) pairs by providing additional encoding opportunities for the less dominant stimulus dimension (i.e., name).

Social Recognition Memory: The Effect of Other People's Responses for Previously Seen and Unseen Items

ERIC Educational Resources Information Center

Wright, Daniel B.; Mathews, Sorcha A.; Skagerberg, Elin M.

2005-01-01

When people discuss their memories, what one person says can influence what another personal reports. In 3 studies, participants were shown sets of stimuli and then given recognition memory tests to measure the effect of one person's response on another's. The 1st study (n=24) used word recognition with participant-confederate pairs and found that…

Evaluating structural pattern recognition for handwritten math via primitive label graphs

NASA Astrophysics Data System (ADS)

Zanibbi, Richard; Mouchère, Harold; Viard-Gaudin, Christian

2013-01-01

Currently, structural pattern recognizer evaluations compare graphs of detected structure to target structures (i.e. ground truth) using recognition rates, recall and precision for object segmentation, classification and relationships. In document recognition, these target objects (e.g. symbols) are frequently comprised of multiple primitives (e.g. connected components, or strokes for online handwritten data), but current metrics do not characterize errors at the primitive level, from which object-level structure is obtained. Primitive label graphs are directed graphs defined over primitives and primitive pairs. We define new metrics obtained by Hamming distances over label graphs, which allow classification, segmentation and parsing errors to be characterized separately, or using a single measure. Recall and precision for detected objects may also be computed directly from label graphs. We illustrate the new metrics by comparing a new primitive-level evaluation to the symbol-level evaluation performed for the CROHME 2012 handwritten math recognition competition. A Python-based set of utilities for evaluating, visualizing and translating label graphs is publicly available.

2-Thiouracil deprived of thiocarbonyl function preferentially base pairs with guanine rather than adenine in RNA and DNA duplexes

PubMed Central

Sochacka, Elzbieta; Szczepanowski, Roman H.; Cypryk, Marek; Sobczak, Milena; Janicka, Magdalena; Kraszewska, Karina; Bartos, Paulina; Chwialkowska, Anna; Nawrot, Barbara

2015-01-01

2-Thiouracil-containing nucleosides are essential modified units of natural and synthetic nucleic acids. In particular, the 5-substituted-2-thiouridines (S2Us) present in tRNA play an important role in tuning the translation process through codon–anticodon interactions. The enhanced thermodynamic stability of S2U-containing RNA duplexes and the preferred S2U-A versus S2U-G base pairing are appreciated characteristics of S2U-modified molecular probes. Recently, we have demonstrated that 2-thiouridine (alone or within an RNA chain) is predominantly transformed under oxidative stress conditions to 4-pyrimidinone riboside (H2U) and not to uridine. Due to the important biological functions and various biotechnological applications for sulfur-containing nucleic acids, we compared the thermodynamic stabilities of duplexes containing desulfured products with those of 2-thiouracil-modified RNA and DNA duplexes. Differential scanning calorimetry experiments and theoretical calculations demonstrate that upon 2-thiouracil desulfuration to 4-pyrimidinone, the preferred base pairing of S2U with adenosine is lost, with preferred base pairing with guanosine observed instead. Therefore, biological processes and in vitro assays in which oxidative desulfuration of 2-thiouracil-containing components occurs may be altered. Moreover, we propose that the H2U-G base pair is a suitable model for investigation of the preferred recognition of 3′-G-ending versus A-ending codons by tRNA wobble nucleosides, which may adopt a 4-pyrimidinone-type structural motif. PMID:25690900

A calix[4]arene strapped calix[4]pyrrole: an ion-pair receptor displaying three different cesium cation recognition modes.

PubMed

Kim, Sung Kuk; Sessler, Jonathan L; Gross, Dustin E; Lee, Chang-Hee; Kim, Jong Seung; Lynch, Vincent M; Delmau, Laetitia H; Hay, Benjamin P

2010-04-28

An ion-pair receptor, the calix[4]pyrrole-calix[4]arene pseudodimer 2, bearing a strong anion-recognition site but not a weak cation-recognition site, has been synthesized and characterized by standard spectroscopic means and via single-crystal X-ray diffraction analysis. In 10% CD(3)OD in CDCl(3) (v/v), this new receptor binds neither the Cs(+) cation nor the F(-) anion when exposed to these species in the presence of other counterions; however, it forms a stable 1:1 solvent-separated CsF complex when exposed to these two ions in concert with one another in this same solvent mixture. In contrast to what is seen in the case of a previously reported crown ether "strapped" calixarene-calixpyrrole ion-pair receptor 1 (J. Am. Chem. Soc. 2008, 130, 13162-13166), where Cs(+) cation recognition takes place within the crown, in 2.CsF cation recognition takes place within the receptor cavity itself, as inferred from both single-crystal X-ray diffraction analyses and (1)H NMR spectroscopic studies. This binding mode is supported by calculations carried out using the MMFF94 force field model. In 10% CD(3)OD in CDCl(3) (v/v), receptor 2 shows selectivity for CsF over the Cs(+) salts of Cl(-), Br(-), and NO(3)(-) but will bind these other cesium salts in the absence of fluoride, both in solution and in the solid state. In the case of CsCl, an unprecedented 2:2 complex is observed in the solid state that is characterized by two different ion-pair binding modes. One of these consists of a contact ion pair with the cesium cation and chloride anion both being bound within the central binding pocket and in direct contact with one another. The other mode involves a chloride anion bound to the pyrrole NH protons of a calixpyrrole subunit and a cesium cation sandwiched between two cone shaped calix[4]pyrroles originating from separate receptor units. In contrast to what is seen for CsF and CsCl, single-crystal X-ray structural analyses and (1)H NMR spectroscopic studies reveal that receptor 2 forms a 1:1 complex with CsNO(3), with the ions bound in the form of a contact ion pair. Thus, depending on the counteranion, receptor 2 is able to stabilize three different ion-pair binding modes with Cs(+), namely solvent-bridged, contact, and host-separated.

Error Tolerant Plan Recognition: An Empirical Investigation

DTIC Science & Technology

2015-05-01

structure can differ drastically in semantics. For instance, a plan to travel to a grocery store to buy milk might coincidentally be structurally...algorithm for its ability to tolerate input errors, and that storing and leveraging state information in its plan representation substantially...proposed a novel representation for storing and organizing plans in a plan library, based on action-state pairs and abstract states. It counts the

Proflavine sensitivity of RNA processing in isolated nuclei.

PubMed Central

Yannarell, A; Niemann, M; Schumm, D E; Webb, T E

1977-01-01

The intercalating agent proflavine inhibits the processing and subsequent release of preformed messenger RNA and ribosomal RNA from isolated liver nuclei to surrogate cytoplasm. The direct effect of proflavine on these processes, as monitored in a reconstituted cell-free system, supports the theory that base-paired segments (i.e. hairpin loops) in the precursor RNA's are involved as recognition sites in nuclear RNA processing. PMID:866181

DNA sequence alignment by microhomology sampling during homologous recombination

PubMed Central

Qi, Zhi; Redding, Sy; Lee, Ja Yil; Gibb, Bryan; Kwon, YoungHo; Niu, Hengyao; Gaines, William A.; Sung, Patrick

2015-01-01

Summary Homologous recombination (HR) mediates the exchange of genetic information between sister or homologous chromatids. During HR, members of the RecA/Rad51 family of recombinases must somehow search through vast quantities of DNA sequence to align and pair ssDNA with a homologous dsDNA template. Here we use single-molecule imaging to visualize Rad51 as it aligns and pairs homologous DNA sequences in real-time. We show that Rad51 uses a length-based recognition mechanism while interrogating dsDNA, enabling robust kinetic selection of 8-nucleotide (nt) tracts of microhomology, which kinetically confines the search to sites with a high probability of being a homologous target. Successful pairing with a 9th nucleotide coincides with an additional reduction in binding free energy and subsequent strand exchange occurs in precise 3-nt steps, reflecting the base triplet organization of the presynaptic complex. These findings provide crucial new insights into the physical and evolutionary underpinnings of DNA recombination. PMID:25684365

Humming in Tune: Sex and Species Recognition by Mosquitoes on the Wing

PubMed Central

Gibson, Gabriella; Warren, Ben

2010-01-01

Mosquitoes are more sensitive to sound than any other insect due to the remarkable properties of their antennae and Johnston’s organ at the base of each antenna. Male mosquitoes detect and locate female mosquitoes by hearing the female’s flight tone, but until recently we had no idea that females also respond to male flight tones. Our investigation of a novel mechanism of sex recognition in Toxorhynchites brevipalpis revealed that male and female mosquitoes actively respond to the flight tones of other flying mosquitoes by altering their own wing-beat frequencies. Male–female pairs converge on a shared harmonic of their respective fundamental flight tones, whereas same sex pairs diverge. Most frequency matching occurs at frequencies beyond the detection range of the Johnston’s organ but within the range of mechanical responsiveness of the antennae. We have shown that this is possible because the Johnston’s organ is tuned to, and able to detect difference tones in, the harmonics of antennal vibrations which are generated by the combined input of flight tones from both mosquitoes. Acoustic distortion in hearing organs exists usually as an interesting epiphenomenon. Mosquitoes, however, appear to use it as a sensory cue that enables male–female pairs to communicate through a signal that depends on auditory interactions between them. Frequency matching may also provide a means of species recognition. Morphologically identical but reproductively isolated molecular forms of Anopheles gambiae fly in the same mating swarms, but rarely hybridize. Extended frequency matching occurs almost exclusively between males and females of the same molecular form, suggesting that this behavior is associated with observed assortative mating. PMID:20976515

Structural basis for microRNA targeting

DOE PAGES

Schirle, Nicole T.; Sheu-Gruttadauria, Jessica; MacRae, Ian J.

2014-10-31

MicroRNAs (miRNAs) control expression of thousands of genes in plants and animals. miRNAs function by guiding Argonaute proteins to complementary sites in messenger RNAs (mRNAs) targeted for repression. In this paper, we determined crystal structures of human Argonaute-2 (Ago2) bound to a defined guide RNA with and without target RNAs representing miRNA recognition sites. These structures suggest a stepwise mechanism, in which Ago2 primarily exposes guide nucleotides (nt) 2 to 5 for initial target pairing. Pairing to nt 2 to 5 promotes conformational changes that expose nt 2 to 8 and 13 to 16 for further target recognition. Interactions withmore » the guide-target minor groove allow Ago2 to interrogate target RNAs in a sequence-independent manner, whereas an adenosine binding-pocket opposite guide nt 1 further facilitates target recognition. Spurious slicing of miRNA targets is avoided through an inhibitory coordination of one catalytic magnesium ion. Finally, these results explain the conserved nucleotide-pairing patterns in animal miRNA target sites first observed over two decades ago.« less

A picture is worth a thousand words? Not when it comes to associative memory of older adults.

PubMed

Guez, Jonathan; Lev, Dror

2016-02-01

Properties of the binding mechanism in associative recognition were studied by examining the influence of the pictorial superiority effect on the age-related associative deficit. The informative aspect of associative recognition is the recollection of the pairing. Previous findings indicate that recollection is susceptible to aging and that pictorial presentation can enhance recollection and facilitate associative recognition. Pictorial presentation was found to facilitate item recognition by both young and older adults, associative recognition by young adults, but not associative recognition by older adults. Our findings support the hypothesis that the binding mechanism in associative recognition is content independent. Theoretical implications are discussed. (c) 2016 APA, all rights reserved).

The role of familiarity in binary choice inferences.

PubMed

Honda, Hidehito; Abe, Keiga; Matsuka, Toshihiko; Yamagishi, Kimihiko

2011-07-01

In research on the recognition heuristic (Goldstein & Gigerenzer, Psychological Review, 109, 75-90, 2002), knowledge of recognized objects has been categorized as "recognized" or "unrecognized" without regard to the degree of familiarity of the recognized object. In the present article, we propose a new inference model--familiarity-based inference. We hypothesize that when subjective knowledge levels (familiarity) of recognized objects differ, the degree of familiarity of recognized objects will influence inferences. Specifically, people are predicted to infer that the more familiar object in a pair of two objects has a higher criterion value on the to-be-judged dimension. In two experiments, using a binary choice task, we examined inferences about populations in a pair of two cities. Results support predictions of familiarity-based inference. Participants inferred that the more familiar city in a pair was more populous. Statistical modeling showed that individual differences in familiarity-based inference lie in the sensitivity to differences in familiarity. In addition, we found that familiarity-based inference can be generally regarded as an ecologically rational inference. Furthermore, when cue knowledge about the inference criterion was available, participants made inferences based on the cue knowledge about population instead of familiarity. Implications of the role of familiarity in psychological processes are discussed.

A Novel Anti-Spoofing Solution for Iris Recognition Toward Cosmetic Contact Lens Attack Using Spectral ICA Analysis

PubMed Central

Hsieh, Sheng-Hsun; Wang, Wei; Tien, Chung-Hao

2018-01-01

In this study, we maneuvered a dual-band spectral imaging system to capture an iridal image from a cosmetic-contact-lens-wearing subject. By using the independent component analysis to separate individual spectral primitives, we successfully distinguished the natural iris texture from the cosmetic contact lens (CCL) pattern, and restored the genuine iris patterns from the CCL-polluted image. Based on a database containing 200 test image pairs from 20 CCL-wearing subjects as the proof of concept, the recognition accuracy (False Rejection Rate: FRR) was improved from FRR = 10.52% to FRR = 0.57% with the proposed ICA anti-spoofing scheme. PMID:29509692

Recognition and Matching of Clustered Mature Litchi Fruits Using Binocular Charge-Coupled Device (CCD) Color Cameras

PubMed Central

Wang, Chenglin; Tang, Yunchao; Zou, Xiangjun; Luo, Lufeng; Chen, Xiong

2017-01-01

Recognition and matching of litchi fruits are critical steps for litchi harvesting robots to successfully grasp litchi. However, due to the randomness of litchi growth, such as clustered growth with uncertain number of fruits and random occlusion by leaves, branches and other fruits, the recognition and matching of the fruit become a challenge. Therefore, this study firstly defined mature litchi fruit as three clustered categories. Then an approach for recognition and matching of clustered mature litchi fruit was developed based on litchi color images acquired by binocular charge-coupled device (CCD) color cameras. The approach mainly included three steps: (1) calibration of binocular color cameras and litchi image acquisition; (2) segmentation of litchi fruits using four kinds of supervised classifiers, and recognition of the pre-defined categories of clustered litchi fruit using a pixel threshold method; and (3) matching the recognized clustered fruit using a geometric center-based matching method. The experimental results showed that the proposed recognition method could be robust against the influences of varying illumination and occlusion conditions, and precisely recognize clustered litchi fruit. In the tested 432 clustered litchi fruits, the highest and lowest average recognition rates were 94.17% and 92.00% under sunny back-lighting and partial occlusion, and sunny front-lighting and non-occlusion conditions, respectively. From 50 pairs of tested images, the highest and lowest matching success rates were 97.37% and 91.96% under sunny back-lighting and non-occlusion, and sunny front-lighting and partial occlusion conditions, respectively. PMID:29112177

The Functional Architecture of Visual Object Recognition

DTIC Science & Technology

1991-07-01

different forms of agnosia can provide clues to the representations underlying normal object recognition (Farah, 1990). For example, the pair-wise...patterns of deficit and sparing occur. In a review of 99 published cases of agnosia , the observed patterns of co- occurrence implicated two underlying

Light-emitting self-assembled peptide nucleic acids exhibit both stacking interactions and Watson-Crick base pairing.

PubMed

Berger, Or; Adler-Abramovich, Lihi; Levy-Sakin, Michal; Grunwald, Assaf; Liebes-Peer, Yael; Bachar, Mor; Buzhansky, Ludmila; Mossou, Estelle; Forsyth, V Trevor; Schwartz, Tal; Ebenstein, Yuval; Frolow, Felix; Shimon, Linda J W; Patolsky, Fernando; Gazit, Ehud

2015-04-01

The two main branches of bionanotechnology involve the self-assembly of either peptides or DNA. Peptide scaffolds offer chemical versatility, architectural flexibility and structural complexity, but they lack the precise base pairing and molecular recognition available with nucleic acid assemblies. Here, inspired by the ability of aromatic dipeptides to form ordered nanostructures with unique physical properties, we explore the assembly of peptide nucleic acids (PNAs), which are short DNA mimics that have an amide backbone. All 16 combinations of the very short di-PNA building blocks were synthesized and assayed for their ability to self-associate. Only three guanine-containing di-PNAs-CG, GC and GG-could form ordered assemblies, as observed by electron microscopy, and these di-PNAs efficiently assembled into discrete architectures within a few minutes. The X-ray crystal structure of the GC di-PNA showed the occurrence of both stacking interactions and Watson-Crick base pairing. The assemblies were also found to exhibit optical properties including voltage-dependent electroluminescence and wide-range excitation-dependent fluorescence in the visible region.

Using Dictionary Pair Learning for Seizure Detection.

PubMed

Ma, Xin; Yu, Nana; Zhou, Weidong

2018-02-13

Automatic seizure detection is extremely important in the monitoring and diagnosis of epilepsy. The paper presents a novel method based on dictionary pair learning (DPL) for seizure detection in the long-term intracranial electroencephalogram (EEG) recordings. First, for the EEG data, wavelet filtering and differential filtering are applied, and the kernel function is performed to make the signal linearly separable. In DPL, the synthesis dictionary and analysis dictionary are learned jointly from original training samples with alternating minimization method, and sparse coefficients are obtained by using of linear projection instead of costly [Formula: see text]-norm or [Formula: see text]-norm optimization. At last, the reconstructed residuals associated with seizure and nonseizure sub-dictionary pairs are calculated as the decision values, and the postprocessing is performed for improving the recognition rate and reducing the false detection rate of the system. A total of 530[Formula: see text]h from 20 patients with 81 seizures were used to evaluate the system. Our proposed method has achieved an average segment-based sensitivity of 93.39%, specificity of 98.51%, and event-based sensitivity of 96.36% with false detection rate of 0.236/h.

Representational Account of Memory: Insights from Aging and Synesthesia.

PubMed

Pfeifer, Gaby; Ward, Jamie; Chan, Dennis; Sigala, Natasha

2016-12-01

The representational account of memory envisages perception and memory to be on a continuum rather than in discretely divided brain systems [Bussey, T. J., & Saksida, L. M. Memory, perception, and the ventral visual-perirhinal-hippocampal stream: Thinking outside of the boxes. Hippocampus, 17, 898-908, 2007]. We tested this account using a novel between-group design with young grapheme-color synesthetes, older adults, and young controls. We investigated how the disparate sensory-perceptual abilities between these groups translated into associative memory performance for visual stimuli that do not induce synesthesia. ROI analyses of the entire ventral visual stream showed that associative retrieval (a pair-associate retrieved in the absence of a visual stimulus) yielded enhanced activity in young and older adults' visual regions relative to synesthetes, whereas associative recognition (deciding whether a visual stimulus was the correct pair-associate) was characterized by enhanced activity in synesthetes' visual regions relative to older adults. Whole-brain analyses at associative retrieval revealed an effect of age in early visual cortex, with older adults showing enhanced activity relative to synesthetes and young adults. At associative recognition, the group effect was reversed: Synesthetes showed significantly enhanced activity relative to young and older adults in early visual regions. The inverted group effects observed between retrieval and recognition indicate that reduced sensitivity in visual cortex (as in aging) comes with increased activity during top-down retrieval and decreased activity during bottom-up recognition, whereas enhanced sensitivity (as in synesthesia) shows the opposite pattern. Our results provide novel evidence for the direct contribution of perceptual mechanisms to visual associative memory based on the examples of synesthesia and aging.

Effects of bilateral eye movements on the retrieval of item, associative, and contextual information.

PubMed

Parker, Andrew; Relph, Sarah; Dagnall, Neil

2008-01-01

Two experiments are reported that investigate the effects of saccadic bilateral eye movements on the retrieval of item, associative, and contextual information. Experiment 1 compared the effects of bilateral versus vertical versus no eye movements on tests of item recognition, followed by remember-know responses and associative recognition. Supporting previous research, bilateral eye movements enhanced item recognition by increasing the hit rate and decreasing the false alarm rate. Analysis of remember-know responses indicated that eye movement effects were accompanied by increases in remember responses. The test of associative recognition found that bilateral eye movements increased correct responses to intact pairs and decreased false alarms to rearranged pairs. Experiment 2 assessed the effects of eye movements on the recall of intrinsic (color) and extrinsic (spatial location) context. Bilateral eye movements increased correct recall for both types of context. The results are discussed within the framework of dual-process models of memory and the possible neural underpinnings of these effects are considered.

Phoneme Awareness, Visual-Verbal Paired-Associate Learning, and Rapid Automatized Naming as Predictors of Individual Differences in Reading Ability

ERIC Educational Resources Information Center

Warmington, Meesha; Hulme, Charles

2012-01-01

This study examines the concurrent relationships between phoneme awareness, visual-verbal paired-associate learning, rapid automatized naming (RAN), and reading skills in 7- to 11-year-old children. Path analyses showed that visual-verbal paired-associate learning and RAN, but not phoneme awareness, were unique predictors of word recognition,…

Modeling meiotic chromosome pairing: nuclear envelope attachment, telomere-led active random motion, and anomalous diffusion

PubMed Central

Marshall, Wallace F.; Fung, Jennifer C.

2016-01-01

The recognition and pairing of homologous chromosomes during meiosis is a complex physical and molecular process involving a combination of polymer dynamics and molecular recognition events. Two highly conserved features of meiotic chromosome behavior are the attachment of telomeres to the nuclear envelope and the active random motion of telomeres driven by their interaction with cytoskeletal motor proteins. Both of these features have been proposed to facilitate the process of homolog pairing, but exactly what role these features play in meiosis remains poorly understood. Here we investigate the roles of active motion and nuclear envelope tethering using a Brownian dynamics simulation in which meiotic chromosomes are represented by a Rouse polymer model subjected to tethering and active forces at the telomeres. We find that tethering telomeres to the nuclear envelope slows down pairing relative to the rates achieved by un-attached chromosomes, but that randomly-directed active forces applied to the telomeres speeds up pairing dramatically in a manner that depends on the statistical properties of the telomere force fluctuations. The increased rate of initial pairing cannot be explained by stretching out of the chromosome conformation but instead seems to correlate with anomalous diffusion of sub-telomeric regions. PMID:27046097

Modeling meiotic chromosome pairing: nuclear envelope attachment, telomere-led active random motion, and anomalous diffusion

NASA Astrophysics Data System (ADS)

Marshall, Wallace F.; Fung, Jennifer C.

2016-04-01

The recognition and pairing of homologous chromosomes during meiosis is a complex physical and molecular process involving a combination of polymer dynamics and molecular recognition events. Two highly conserved features of meiotic chromosome behavior are the attachment of telomeres to the nuclear envelope and the active random motion of telomeres driven by their interaction with cytoskeletal motor proteins. Both of these features have been proposed to facilitate the process of homolog pairing, but exactly what role these features play in meiosis remains poorly understood. Here we investigate the roles of active motion and nuclear envelope tethering using a Brownian dynamics simulation in which meiotic chromosomes are represented by a Rouse polymer model subjected to tethering and active forces at the telomeres. We find that tethering telomeres to the nuclear envelope slows down pairing relative to the rates achieved by unattached chromosomes, but that randomly directed active forces applied to the telomeres speed up pairing dramatically in a manner that depends on the statistical properties of the telomere force fluctuations. The increased rate of initial pairing cannot be explained by stretching out of the chromosome conformation but instead seems to correlate with anomalous diffusion of sub-telomeric regions.

Engineering Translational Activators with CRISPR-Cas System.

PubMed

Du, Pei; Miao, Chensi; Lou, Qiuli; Wang, Zefeng; Lou, Chunbo

2016-01-15

RNA parts often serve as critical components in genetic engineering. Here we report a design of translational activators which is composed of an RNA endoribonuclease (Csy4) and two exchangeable RNA modules. Csy4, a member of Cas endoribonuclease, cleaves at a specific recognition site; this cleavage releases a cis-repressive RNA module (crRNA) from the masked ribosome binding site (RBS), which subsequently allows the downstream translation initiation. Unlike small RNA as a translational activator, the endoribonuclease-based activator is able to efficiently unfold the perfect RBS-crRNA pairing. As an exchangeable module, the crRNA-RBS duplex was forwardly and reversely engineered to modulate the dynamic range of translational activity. We further showed that Csy4 and its recognition site, together as a module, can also be replaced by orthogonal endoribonuclease-recognition site homologues. These modularly structured, high-performance translational activators would endow the programming of gene expression in the translation level with higher feasibility.

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

NASA Astrophysics Data System (ADS)

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

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

Synthesis, base pairing and structure studies of geranylated RNA

PubMed Central

Wang, Rui; Vangaveti, Sweta; Ranganathan, Srivathsan V.; Basanta-Sanchez, Maria; Haruehanroengra, Phensinee; Chen, Alan; Sheng, Jia

2016-01-01

Natural RNAs utilize extensive chemical modifications to diversify their structures and functions. 2-Thiouridine geranylation is a special hydrophobic tRNA modification that has been discovered very recently in several bacteria, such as Escherichia coli, Enterobacter aerogenes, Pseudomonas aeruginosa and Salmonella Typhimurium. The geranylated residues are located in the first anticodon position of tRNAs specific for lysine, glutamine and glutamic acid. This big hydrophobic terpene functional group affects the codon recognition patterns and reduces frameshifting errors during translation. We aimed to systematically study the structure, function and biosynthesis mechanism of this geranylation pathway, as well as answer the question of why nature uses such a hydrophobic modification in hydrophilic RNA systems. Recently, we have synthesized the deoxy-analog of S-geranyluridine and showed the geranylated T-G pair is much stronger than the geranylated T-A pair and other mismatched pairs in the B-form DNA duplex context, which is consistent with the observation that the geranylated tRNAGluUUC recognizes GAG more efficiently than GAA. In this manuscript we report the synthesis and base pairing specificity studies of geranylated RNA oligos. We also report extensive molecular simulation studies to explore the structural features of the geranyl group in the context of A-form RNA and its effect on codon–anticodon interaction during ribosome binding. PMID:27307604

Application of biomolecular recognition via magnetic nanoparticle in nanobiotechnology

NASA Astrophysics Data System (ADS)

Shen, Wei-Zheng; Cetinel, Sibel; Montemagno, Carlo

2018-05-01

The marriage of biomolecular recognition and magnetic nanoparticle creates tremendous opportunities in the development of advanced technology both in academic research and in industrial sectors. In this paper, we review current progress on the magnetic nanoparticle-biomolecule hybrid systems, particularly employing the recognition pairs of DNA-DNA, DNA-protein, protein-protein, and protein-inorganics in several nanobiotechnology application areas, including molecular biology, diagnostics, medical treatment, industrial biocatalysts, and environmental separations.

The telltale face: possible mechanisms behind defector and cooperator recognition revealed by emotional facial expression metrics.

PubMed

Kovács-Bálint, Zsófia; Bereczkei, Tamás; Hernádi, István

2013-11-01

In this study, we investigated the role of facial cues in cooperator and defector recognition. First, a face image database was constructed from pairs of full face portraits of target subjects taken at the moment of decision-making in a prisoner's dilemma game (PDG) and in a preceding neutral task. Image pairs with no deficiencies (n = 67) were standardized for orientation and luminance. Then, confidence in defector and cooperator recognition was tested with image rating in a different group of lay judges (n = 62). Results indicate that (1) defectors were better recognized (58% vs. 47%), (2) they looked different from cooperators (p < .01), (3) males but not females evaluated the images with a relative bias towards the cooperator category (p < .01), and (4) females were more confident in detecting defectors (p < .05). According to facial microexpression analysis, defection was strongly linked with depressed lower lips and less opened eyes. Significant correlation was found between the intensity of micromimics and the rating of images in the cooperator-defector dimension. In summary, facial expressions can be considered as reliable indicators of momentary social dispositions in the PDG. Females may exhibit an evolutionary-based overestimation bias to detecting social visual cues of the defector face. © 2012 The British Psychological Society.

Solid-phase proximity ligation assays for individual or parallel protein analyses with readout via real-time PCR or sequencing.

PubMed

Nong, Rachel Yuan; Wu, Di; Yan, Junhong; Hammond, Maria; Gu, Gucci Jijuan; Kamali-Moghaddam, Masood; Landegren, Ulf; Darmanis, Spyros

2013-06-01

Solid-phase proximity ligation assays share properties with the classical sandwich immunoassays for protein detection. The proteins captured via antibodies on solid supports are, however, detected not by single antibodies with detectable functions, but by pairs of antibodies with attached DNA strands. Upon recognition by these sets of three antibodies, pairs of DNA strands brought in proximity are joined by ligation. The ligated reporter DNA strands are then detected via methods such as real-time PCR or next-generation sequencing (NGS). We describe how to construct assays that can offer improved detection specificity by virtue of recognition by three antibodies, as well as enhanced sensitivity owing to reduced background and amplified detection. Finally, we also illustrate how the assays can be applied for parallel detection of proteins, taking advantage of the oligonucleotide ligation step to avoid background problems that might arise with multiplexing. The protocol for the singleplex solid-phase proximity ligation assay takes ~5 h. The multiplex version of the assay takes 7-8 h depending on whether quantitative PCR (qPCR) or sequencing is used as the readout. The time for the sequencing-based protocol includes the library preparation but not the actual sequencing, as times may vary based on the choice of sequencing platform.

Word segmentation in phonemically identical and prosodically different sequences using cochlear implants: A case study.

PubMed

Basirat, Anahita

2017-01-01

Cochlear implant (CI) users frequently achieve good speech understanding based on phoneme and word recognition. However, there is a significant variability between CI users in processing prosody. The aim of this study was to examine the abilities of an excellent CI user to segment continuous speech using intonational cues. A post-lingually deafened adult CI user and 22 normal hearing (NH) subjects segmented phonemically identical and prosodically different sequences in French such as 'l'affiche' (the poster) versus 'la fiche' (the sheet), both [lafiʃ]. All participants also completed a minimal pair discrimination task. Stimuli were presented in auditory-only and audiovisual presentation modalities. The performance of the CI user in the minimal pair discrimination task was 97% in the auditory-only and 100% in the audiovisual condition. In the segmentation task, contrary to the NH participants, the performance of the CI user did not differ from the chance level. Visual speech did not improve word segmentation. This result suggests that word segmentation based on intonational cues is challenging when using CIs even when phoneme/word recognition is very well rehabilitated. This finding points to the importance of the assessment of CI users' skills in prosody processing and the need for specific interventions focusing on this aspect of speech communication.

A Universal Vacant Parking Slot Recognition System Using Sensors Mounted on Off-the-Shelf Vehicles.

PubMed

Suhr, Jae Kyu; Jung, Ho Gi

2018-04-16

An automatic parking system is an essential part of autonomous driving, and it starts by recognizing vacant parking spaces. This paper proposes a method that can recognize various types of parking slot markings in a variety of lighting conditions including daytime, nighttime, and underground. The proposed method can readily be commercialized since it uses only those sensors already mounted on off-the-shelf vehicles: an around-view monitor (AVM) system, ultrasonic sensors, and in-vehicle motion sensors. This method first detects separating lines by extracting parallel line pairs from AVM images. Parking slot candidates are generated by pairing separating lines based on the geometric constraints of the parking slot. These candidates are confirmed by recognizing their entrance positions using line and corner features and classifying their occupancies using ultrasonic sensors. For more reliable recognition, this method uses the separating lines and parking slots not only found in the current image but also found in previous images by tracking their positions using the in-vehicle motion-sensor-based vehicle odometry. The proposed method was quantitatively evaluated using a dataset obtained during the day, night, and underground, and it outperformed previous methods by showing a 95.24% recall and a 97.64% precision.

Gender in facial representations: a contrast-based study of adaptation within and between the sexes.

PubMed

Oruç, Ipek; Guo, Xiaoyue M; Barton, Jason J S

2011-01-18

Face aftereffects are proving to be an effective means of examining the properties of face-specific processes in the human visual system. We examined the role of gender in the neural representation of faces using a contrast-based adaptation method. If faces of different genders share the same representational face space, then adaptation to a face of one gender should affect both same- and different-gender faces. Further, if these aftereffects differ in magnitude, this may indicate distinct gender-related factors in the organization of this face space. To control for a potential confound between physical similarity and gender, we used a Bayesian ideal observer and human discrimination data to construct a stimulus set in which pairs of different-gender faces were equally dissimilar as same-gender pairs. We found that the recognition of both same-gender and different-gender faces was suppressed following a brief exposure of 100 ms. Moreover, recognition was more suppressed for test faces of a different-gender than those of the same-gender as the adaptor, despite the equivalence in physical and psychophysical similarity. Our results suggest that male and female faces likely occupy the same face space, allowing transfer of aftereffects between the genders, but that there are special properties that emerge along gender-defining dimensions of this space.

A Universal Vacant Parking Slot Recognition System Using Sensors Mounted on Off-the-Shelf Vehicles

PubMed Central

2018-01-01

An automatic parking system is an essential part of autonomous driving, and it starts by recognizing vacant parking spaces. This paper proposes a method that can recognize various types of parking slot markings in a variety of lighting conditions including daytime, nighttime, and underground. The proposed method can readily be commercialized since it uses only those sensors already mounted on off-the-shelf vehicles: an around-view monitor (AVM) system, ultrasonic sensors, and in-vehicle motion sensors. This method first detects separating lines by extracting parallel line pairs from AVM images. Parking slot candidates are generated by pairing separating lines based on the geometric constraints of the parking slot. These candidates are confirmed by recognizing their entrance positions using line and corner features and classifying their occupancies using ultrasonic sensors. For more reliable recognition, this method uses the separating lines and parking slots not only found in the current image but also found in previous images by tracking their positions using the in-vehicle motion-sensor-based vehicle odometry. The proposed method was quantitatively evaluated using a dataset obtained during the day, night, and underground, and it outperformed previous methods by showing a 95.24% recall and a 97.64% precision. PMID:29659512

Energetic basis for selective recognition of T*G mismatched base pairs in DNA by imidazole-rich polyamides.

PubMed

Lacy, Eilyn R; Nguyen, Binh; Le, Minh; Cox, Kari K; OHare, Caroline; Hartley, John A; Lee, Moses; Wilson, W David

2004-01-01

To complement available structure and binding results and to develop a detailed understanding of the basis for selective molecular recognition of T.G mismatches in DNA by imidazole containing polyamides, a full thermodynamic profile for formation of the T.G-polyamide complex has been determined. The amide-linked heterocycles f-ImImIm and f-PyImIm (where f is formamido group, Im is imidazole and Py is pyrrole) were studied by using biosensor-surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) with a T.G mismatch containing DNA hairpin duplex and a similar DNA with only Watson-Crick base pairs. Large negative binding enthalpies for all of the polyamide-DNA complexes indicate that the interactions are enthalpically driven. SPR results show slower complex formation and stronger binding of f-ImImIm to the T.G than to the match site. The thermodynamic analysis indicates that the enhanced binding to the T.G site is the result of better entropic contributions. Negative heat capacity changes for the complex are correlated with calculated solvent accessible surface area changes and indicate hydrophobic contributions to complex formation. DNase I footprinting analysis in a long DNA sequence provided supporting evidence that f-ImImIm binds selectively to T.G mismatch sites.

Energetic basis for selective recognition of T·G mismatched base pairs in DNA by imidazole-rich polyamides

PubMed Central

Lacy, Eilyn R.; Nguyen, Binh; Le, Minh; Cox, Kari K.; O'Hare, Caroline; Hartley, John A.; Lee, Moses; Wilson, W. David

2004-01-01

To complement available structure and binding results and to develop a detailed understanding of the basis for selective molecular recognition of T·G mismatches in DNA by imidazole containing polyamides, a full thermodynamic profile for formation of the T·G–polyamide complex has been determined. The amide-linked heterocycles f-ImImIm and f-PyImIm (where f is formamido group, Im is imidazole and Py is pyrrole) were studied by using biosensor-surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) with a T·G mismatch containing DNA hairpin duplex and a similar DNA with only Watson–Crick base pairs. Large negative binding enthalpies for all of the polyamide–DNA complexes indicate that the interactions are enthalpically driven. SPR results show slower complex formation and stronger binding of f-ImImIm to the T·G than to the match site. The thermodynamic analysis indicates that the enhanced binding to the T·G site is the result of better entropic contributions. Negative heat capacity changes for the complex are correlated with calculated solvent accessible surface area changes and indicate hydrophobic contributions to complex formation. DNase I footprinting analysis in a long DNA sequence provided supporting evidence that f-ImImIm binds selectively to T·G mismatch sites. PMID:15064359

Evaluation of tooth-click triggering and speech recognition in assistive technology for computer access.

PubMed

Simpson, Tyler; Gauthier, Michel; Prochazka, Arthur

2010-02-01

Computer access can play an important role in employment and leisure activities following spinal cord injury. The authors' prior work has shown that a tooth-click detecting device, when paired with an optical head mouse, may be used by people with tetraplegia for controlling cursor movement and mouse button clicks. To compare the efficacy of tooth clicks to speech recognition and that of an optical head mouse to a gyrometer head mouse for cursor and mouse button control of a computer. Six able-bodied and 3 tetraplegic subjects used the devices listed above to produce cursor movements and mouse clicks in response to a series of prompts displayed on a computer. The time taken to move to and click on each target was recorded. The use of tooth clicks in combination with either an optical head mouse or a gyrometer head mouse can provide hands-free cursor movement and mouse button control at a speed of up to 22% of that of a standard mouse. Tooth clicks were significantly faster at generating mouse button clicks than speech recognition when paired with either type of head mouse device. Tooth-click detection performed better than speech recognition when paired with both the optical head mouse and the gyrometer head mouse. Such a system may improve computer access for people with tetraplegia.

Self-Assembled Core-Satellite Gold Nanoparticle Networks for Ultrasensitive Detection of Chiral Molecules by Recognition Tunneling Current.

PubMed

Zhang, Yuanchao; Liu, Jingquan; Li, Da; Dai, Xing; Yan, Fuhua; Conlan, Xavier A; Zhou, Ruhong; Barrow, Colin J; He, Jin; Wang, Xin; Yang, Wenrong

2016-05-24

Chirality sensing is a very challenging task. Here, we report a method for ultrasensitive detection of chiral molecule l/d-carnitine based on changes in the recognition tunneling current across self-assembled core-satellite gold nanoparticle (GNP) networks. The recognition tunneling technique has been demonstrated to work at the single molecule level where the binding between the reader molecules and the analytes in a nanojunction. This process was observed to generate a unique and sensitive change in tunneling current, which can be used to identify the analytes of interest. The molecular recognition mechanism between amino acid l-cysteine and l/d-carnitine has been studied with the aid of SERS. The different binding strength between homo- or heterochiral pairs can be effectively probed by the copper ion replacement fracture. The device resistance was measured before and after the sequential exposures to l/d-carnitine and copper ions. The normalized resistance change was found to be extremely sensitive to the chirality of carnitine molecule. The results suggested that a GNP networks device optimized for recognition tunneling was successfully built and that such a device can be used for ultrasensitive detection of chiral molecules.

An uracil-linked hydroxyflavone probe for the recognition of ATP

PubMed Central

Bojtár, Márton; Janzsó-Berend, Péter Zoltán; Mester, Dávid; Hessz, Dóra; Kállay, Mihály; Kubinyi, Miklós

2018-01-01

Background: Nucleotides are essential molecules in living systems due to their paramount importance in various physiological processes. In the past years, numerous attempts were made to selectively recognize and detect these analytes, especially ATP using small-molecule fluorescent chemosensors. Despite the various solutions, the selective detection of ATP is still challenging due to the structural similarity of various nucleotides. In this paper, we report the conjugation of a uracil nucleobase to the known 4’-dimethylamino-hydroxyflavone fluorophore. Results: The complexation of this scaffold with ATP is already known. The complex is held together by stacking and electrostatic interactions. To achieve multi-point recognition, we designed the uracil-appended version of this probe to include complementary base-pairing interactions. The theoretical calculations revealed the availability of multiple complex structures. The synthesis was performed using click chemistry and the nucleotide recognition properties of the probe were evaluated using fluorescence spectroscopy. Conclusions: The first, uracil-containing fluorescent ATP probe based on a hydroxyflavone fluorophore was synthesized and evaluated. A selective complexation with ATP was observed and a ratiometric response in the excitation spectrum. PMID:29719572

Strength Is in Numbers: Can Concordant Artificial Listeners Improve Prediction of Emotion from Speech?

PubMed

Martinelli, Eugenio; Mencattini, Arianna; Daprati, Elena; Di Natale, Corrado

2016-01-01

Humans can communicate their emotions by modulating facial expressions or the tone of their voice. Albeit numerous applications exist that enable machines to read facial emotions and recognize the content of verbal messages, methods for speech emotion recognition are still in their infancy. Yet, fast and reliable applications for emotion recognition are the obvious advancement of present 'intelligent personal assistants', and may have countless applications in diagnostics, rehabilitation and research. Taking inspiration from the dynamics of human group decision-making, we devised a novel speech emotion recognition system that applies, for the first time, a semi-supervised prediction model based on consensus. Three tests were carried out to compare this algorithm with traditional approaches. Labeling performances relative to a public database of spontaneous speeches are reported. The novel system appears to be fast, robust and less computationally demanding than traditional methods, allowing for easier implementation in portable voice-analyzers (as used in rehabilitation, research, industry, etc.) and for applications in the research domain (such as real-time pairing of stimuli to participants' emotional state, selective/differential data collection based on emotional content, etc.).

Motion-based signaling in sympatric species of Australian agamid lizards.

PubMed

Ramos, Jose A; Peters, Richard A

2017-08-01

Signaling species occurring in sympatry are often exposed to similar environmental constraints, so similar adaptations to enhance signal efficacy are expected. However, potentially opposing selective pressures might be present to ensure species recognition. Here, we analyzed the movement-based signals of two pairs of sympatric lizard species to consider how reliable communication is maintained while avoiding misidentification. Our novel approach allows us to quantify signal contrast with plant motion noise at any site we measure, including those utilized by other species. Ctenophorus caudicinctus and Gowidon longirostris differed in display complexity and motor pattern use. They also differed in overall morphology, but their signal contrast scores are strikingly similar. These results demonstrate similar adaptations to their shared environment while maintaining species recognition cues. In contrast, Ctenophorus fordi and Ctenophorus pictus are much closer in appearance, but C. pictus produces considerably higher signal contrast scores, which we suggest is attributable to the absence of territoriality in C. fordi. Taken together, our data provide evidence for adaptation to the local environment in movement-based signals, while also meeting species recognition requirements, but the selective pressure to deal with local conditions is mediated by signal function.

Branding Your Post-School Outcomes Data Collection Process

ERIC Educational Resources Information Center

National Post-School Outcomes Center, 2013

2013-01-01

The purpose of "Branding your Post-School Outcomes Data Collection Process" is to help state education agencies create brand recognition with youths, families, and school personnel for the post-school outcomes survey. Recognition--paired with information about the survey purpose, who is conducting the interview, and how the information…

Congruent and Incongruent Semantic Context Influence Vowel Recognition

ERIC Educational Resources Information Center

Wotton, J. M.; Elvebak, R. L.; Moua, L. C.; Heggem, N. M.; Nelson, C. A.; Kirk, K. M.

2011-01-01

The influence of sentence context on the recognition of naturally spoken vowels degraded by reverberation and Gaussian noise was investigated. Target words were paired to have similar consonant sounds but different vowels (e.g., map/mop) and were embedded early in sentences which provided three types of semantic context. Fifty-eight…

The formation of catalytically competent enzyme-substrate complex is not a bottleneck in lesion excision by human alkyladenine DNA glycosylase.

PubMed

Kuznetsov, N A; Kiryutin, A S; Kuznetsova, A A; Panov, M S; Barsukova, M O; Yurkovskaya, A V; Fedorova, O S

2017-04-01

Human alkyladenine DNA glycosylase (AAG) protects DNA from alkylated and deaminated purine lesions. AAG flips out the damaged nucleotide from the double helix of DNA and catalyzes the hydrolysis of the N-glycosidic bond to release the damaged base. To understand better, how the step of nucleotide eversion influences the overall catalytic process, we performed a pre-steady-state kinetic analysis of AAG interaction with specific DNA-substrates, 13-base pair duplexes containing in the 7th position 1-N6-ethenoadenine (εA), hypoxanthine (Hx), and the stable product analogue tetrahydrofuran (F). The combination of the fluorescence of tryptophan, 2-aminopurine, and 1-N6-ethenoadenine was used to record conformational changes of the enzyme and DNA during the processes of DNA lesion recognition, damaged base eversion, excision of the N-glycosidic bond, and product release. The thermal stability of the duplexes characterized by the temperature of melting, T m , and the rates of spontaneous opening of individual nucleotide base pairs were determined by NMR spectroscopy. The data show that the relative thermal stability of duplexes containing a particular base pair in position 7, (T m (F/T) < T m (εA/T) < T m (Hx/T) < T m (A/T)) correlates with the rate of reversible spontaneous opening of the base pair. However, in contrast to that, the catalytic lesion excision rate is two orders of magnitude higher for Hx-containing substrates than for substrates containing εA, proving that catalytic activity is not correlated with the stability of the damaged base pair. Our study reveals that the formation of the catalytically competent enzyme-substrate complex is not the bottleneck controlling the catalytic activity of AAG.

Face recognition by applying wavelet subband representation and kernel associative memory.

PubMed

Zhang, Bai-Ling; Zhang, Haihong; Ge, Shuzhi Sam

2004-01-01

In this paper, we propose an efficient face recognition scheme which has two features: 1) representation of face images by two-dimensional (2-D) wavelet subband coefficients and 2) recognition by a modular, personalised classification method based on kernel associative memory models. Compared to PCA projections and low resolution "thumb-nail" image representations, wavelet subband coefficients can efficiently capture substantial facial features while keeping computational complexity low. As there are usually very limited samples, we constructed an associative memory (AM) model for each person and proposed to improve the performance of AM models by kernel methods. Specifically, we first applied kernel transforms to each possible training pair of faces sample and then mapped the high-dimensional feature space back to input space. Our scheme using modular autoassociative memory for face recognition is inspired by the same motivation as using autoencoders for optical character recognition (OCR), for which the advantages has been proven. By associative memory, all the prototypical faces of one particular person are used to reconstruct themselves and the reconstruction error for a probe face image is used to decide if the probe face is from the corresponding person. We carried out extensive experiments on three standard face recognition datasets, the FERET data, the XM2VTS data, and the ORL data. Detailed comparisons with earlier published results are provided and our proposed scheme offers better recognition accuracy on all of the face datasets.

Binding neutral information to emotional contexts: Brain dynamics of long-term recognition memory.

PubMed

Ventura-Bort, Carlos; Löw, Andreas; Wendt, Julia; Moltó, Javier; Poy, Rosario; Dolcos, Florin; Hamm, Alfons O; Weymar, Mathias

2016-04-01

There is abundant evidence in memory research that emotional stimuli are better remembered than neutral stimuli. However, effects of an emotionally charged context on memory for associated neutral elements is also important, particularly in trauma and stress-related disorders, where strong memories are often activated by neutral cues due to their emotional associations. In the present study, we used event-related potentials (ERPs) to investigate long-term recognition memory (1-week delay) for neutral objects that had been paired with emotionally arousing or neutral scenes during encoding. Context effects were clearly evident in the ERPs: An early frontal ERP old/new difference (300-500 ms) was enhanced for objects encoded in unpleasant compared to pleasant and neutral contexts; and a late central-parietal old/new difference (400-700 ms) was observed for objects paired with both pleasant and unpleasant contexts but not for items paired with neutral backgrounds. Interestingly, objects encoded in emotional contexts (and novel objects) also prompted an enhanced frontal early (180-220 ms) positivity compared to objects paired with neutral scenes indicating early perceptual significance. The present data suggest that emotional--particularly unpleasant--backgrounds strengthen memory for items encountered within these contexts and engage automatic and explicit recognition processes. These results could help in understanding binding mechanisms involved in the activation of trauma-related memories by neutral cues.

Saccharomyces cerevisiae Msh2-Msh3 acts in repair of base-base mispairs.

PubMed

Harrington, Jill M; Kolodner, Richard D

2007-09-01

DNA mismatch repair is thought to act through two subpathways involving the recognition of base-base and insertion/deletion mispairs by the Msh2-Msh6 heterodimer and the recognition of insertion/deletion mispairs by the Msh2-Msh3 heterodimer. Here, through genetic and biochemical approaches, we describe a previously unidentified role of the Msh2-Msh3 heterodimer in the recognition of base-base mispairs and the suppression of homology-mediated duplication and deletion mutations. Saccharomyces cerevisiae msh3 mutants did not show an increase in the rate of base substitution mutations by the CAN1 forward mutation assay compared to the rate for the wild type but did show an altered spectrum of base substitution mutations, including an increased accumulation of base pair changes from GC to CG and from AT to TA; msh3 mutants also accumulated homology-mediated duplication and deletion mutations. The mutation spectrum of mlh3 mutants paralleled that of msh3 mutants, suggesting that the Mlh1-Mlh3 heterodimer may also play a role in the repair of base-base mispairs and in the suppression of homology-mediated duplication and deletion mutations. Mispair binding analysis with purified Msh2-Msh3 and DNA substrates derived from CAN1 sequences found to be mutated in vivo demonstrated that Msh2-Msh3 exhibited robust binding to specific base-base mispairs that was consistent with functional mispair binding.

Saccharomyces cerevisiae Msh2-Msh3 Acts in Repair of Base-Base Mispairs▿ †

PubMed Central

Harrington, Jill M.; Kolodner, Richard D.

2007-01-01

DNA mismatch repair is thought to act through two subpathways involving the recognition of base-base and insertion/deletion mispairs by the Msh2-Msh6 heterodimer and the recognition of insertion/deletion mispairs by the Msh2-Msh3 heterodimer. Here, through genetic and biochemical approaches, we describe a previously unidentified role of the Msh2-Msh3 heterodimer in the recognition of base-base mispairs and the suppression of homology-mediated duplication and deletion mutations. Saccharomyces cerevisiae msh3 mutants did not show an increase in the rate of base substitution mutations by the CAN1 forward mutation assay compared to the rate for the wild type but did show an altered spectrum of base substitution mutations, including an increased accumulation of base pair changes from GC to CG and from AT to TA; msh3 mutants also accumulated homology-mediated duplication and deletion mutations. The mutation spectrum of mlh3 mutants paralleled that of msh3 mutants, suggesting that the Mlh1-Mlh3 heterodimer may also play a role in the repair of base-base mispairs and in the suppression of homology-mediated duplication and deletion mutations. Mispair binding analysis with purified Msh2-Msh3 and DNA substrates derived from CAN1 sequences found to be mutated in vivo demonstrated that Msh2-Msh3 exhibited robust binding to specific base-base mispairs that was consistent with functional mispair binding. PMID:17636021

Test of the Practicality and Feasibility of EDoF-Empowered Image Sensors for Long-Range Biometrics.

PubMed

Hsieh, Sheng-Hsun; Li, Yung-Hui; Tien, Chung-Hao

2016-11-25

For many practical applications of image sensors, how to extend the depth-of-field (DoF) is an important research topic; if successfully implemented, it could be beneficial in various applications, from photography to biometrics. In this work, we want to examine the feasibility and practicability of a well-known "extended DoF" (EDoF) technique, or "wavefront coding," by building real-time long-range iris recognition and performing large-scale iris recognition. The key to the success of long-range iris recognition includes long DoF and image quality invariance toward various object distance, which is strict and harsh enough to test the practicality and feasibility of EDoF-empowered image sensors. Besides image sensor modification, we also explored the possibility of varying enrollment/testing pairs. With 512 iris images from 32 Asian people as the database, 400-mm focal length and F/6.3 optics over 3 m working distance, our results prove that a sophisticated coding design scheme plus homogeneous enrollment/testing setups can effectively overcome the blurring caused by phase modulation and omit Wiener-based restoration. In our experiments, which are based on 3328 iris images in total, the EDoF factor can achieve a result 3.71 times better than the original system without a loss of recognition accuracy.

TAL effector-DNA specificity.

PubMed

Scholze, Heidi; Boch, Jens

2010-01-01

TAL effectors are important virulence factors of bacterial plant pathogenic Xanthomonas, which infect a wide variety of plants including valuable crops like pepper, rice, and citrus. TAL proteins are translocated via the bacterial type III secretion system into host cells and induce transcription of plant genes by binding to target gene promoters. Members of the TAL effector family differ mainly in their central domain of tandemly arranged repeats of typically 34 amino acids each with hypervariable di-amino acids at positions 12 and 13. We recently showed that target DNA-recognition specificity of TAL effectors is encoded in a modular and clearly predictable mode. The repeats of TAL effectors feature a surprising one repeat-to-one-bp correlation with different repeat types exhibiting a different DNA base pair specificity. Accordingly, we predicted DNA specificities of TAL effectors and generated artificial TAL proteins with novel DNA recognition specificities. We describe here novel artificial TALs and discuss implications for the DNA recognition specificity. The unique TAL-DNA binding domain allows design of proteins with potentially any given DNA recognition specificity enabling many uses for biotechnology.

Chiral Recognition in Molecular and Macromolecular Pairs of(S)- and (R)- 1-Cyano-2-Methylpropyl 4’((4-(8-Vinyloxyoctyloxy)Benzoyl) Biphenyl-4-Carboxylate Enantiomers

DTIC Science & Technology

1994-06-30

above please provide a graphical abstract of the paper ar, return it to the Editorial Office as soon as possible. 4oeg0 o F-99S or TS A& I DTI•’ I J. u1...TCLSICAON 2.LIMITATION OF ABSTRAC •F oFPORT OF THIS PAGE OF ABSTRACT . unclass ified Graphical Abstracts for Perkin Txans. 1 Example TITLE GRAPHICAL ... ABSTRACT AUTHORS’ N AMES Template (S)-II Chiral recognition in molecular and . -- macromolecular pairs of (S)- and -- (R)-i-cyano-2-methyipropyl 4’-{[4

Individually adapted imagery improves brain-computer interface performance in end-users with disability.

PubMed

Scherer, Reinhold; Faller, Josef; Friedrich, Elisabeth V C; Opisso, Eloy; Costa, Ursula; Kübler, Andrea; Müller-Putz, Gernot R

2015-01-01

Brain-computer interfaces (BCIs) translate oscillatory electroencephalogram (EEG) patterns into action. Different mental activities modulate spontaneous EEG rhythms in various ways. Non-stationarity and inherent variability of EEG signals, however, make reliable recognition of modulated EEG patterns challenging. Able-bodied individuals who use a BCI for the first time achieve - on average - binary classification performance of about 75%. Performance in users with central nervous system (CNS) tissue damage is typically lower. User training generally enhances reliability of EEG pattern generation and thus also robustness of pattern recognition. In this study, we investigated the impact of mental tasks on binary classification performance in BCI users with central nervous system (CNS) tissue damage such as persons with stroke or spinal cord injury (SCI). Motor imagery (MI), that is the kinesthetic imagination of movement (e.g. squeezing a rubber ball with the right hand), is the "gold standard" and mainly used to modulate EEG patterns. Based on our recent results in able-bodied users, we hypothesized that pair-wise combination of "brain-teaser" (e.g. mental subtraction and mental word association) and "dynamic imagery" (e.g. hand and feet MI) tasks significantly increases classification performance of induced EEG patterns in the selected end-user group. Within-day (How stable is the classification within a day?) and between-day (How well does a model trained on day one perform on unseen data of day two?) analysis of variability of mental task pair classification in nine individuals confirmed the hypothesis. We found that the use of the classical MI task pair hand vs. feed leads to significantly lower classification accuracy - in average up to 15% less - in most users with stroke or SCI. User-specific selection of task pairs was again essential to enhance performance. We expect that the gained evidence will significantly contribute to make imagery-based BCI technology become accessible to a larger population of users including individuals with special needs due to CNS damage.

Individually Adapted Imagery Improves Brain-Computer Interface Performance in End-Users with Disability

PubMed Central

Scherer, Reinhold; Faller, Josef; Friedrich, Elisabeth V. C.; Opisso, Eloy; Costa, Ursula; Kübler, Andrea; Müller-Putz, Gernot R.

2015-01-01

Brain-computer interfaces (BCIs) translate oscillatory electroencephalogram (EEG) patterns into action. Different mental activities modulate spontaneous EEG rhythms in various ways. Non-stationarity and inherent variability of EEG signals, however, make reliable recognition of modulated EEG patterns challenging. Able-bodied individuals who use a BCI for the first time achieve - on average - binary classification performance of about 75%. Performance in users with central nervous system (CNS) tissue damage is typically lower. User training generally enhances reliability of EEG pattern generation and thus also robustness of pattern recognition. In this study, we investigated the impact of mental tasks on binary classification performance in BCI users with central nervous system (CNS) tissue damage such as persons with stroke or spinal cord injury (SCI). Motor imagery (MI), that is the kinesthetic imagination of movement (e.g. squeezing a rubber ball with the right hand), is the "gold standard" and mainly used to modulate EEG patterns. Based on our recent results in able-bodied users, we hypothesized that pair-wise combination of "brain-teaser" (e.g. mental subtraction and mental word association) and "dynamic imagery" (e.g. hand and feet MI) tasks significantly increases classification performance of induced EEG patterns in the selected end-user group. Within-day (How stable is the classification within a day?) and between-day (How well does a model trained on day one perform on unseen data of day two?) analysis of variability of mental task pair classification in nine individuals confirmed the hypothesis. We found that the use of the classical MI task pair hand vs. feed leads to significantly lower classification accuracy - in average up to 15% less - in most users with stroke or SCI. User-specific selection of task pairs was again essential to enhance performance. We expect that the gained evidence will significantly contribute to make imagery-based BCI technology become accessible to a larger population of users including individuals with special needs due to CNS damage. PMID:25992718

Multilingual Data Selection for Low Resource Speech Recognition

DTIC Science & Technology

2016-09-12

Figure 1: Identification of language clusters using scores from an LID system training languages used in the Base and OP1 evaluation periods of the Babel...the posterior scores over frames. For a set of languages that are used to train the lan- guage identification (LID) network, pairs of languages that...which are combined during test time to produce 10 dimensional language 3854 Figure 3: Identification of language clusters using scores from individually

Novelty preference in patients with developmental amnesia.

PubMed

Munoz, M; Chadwick, M; Perez-Hernandez, E; Vargha-Khadem, F; Mishkin, M

2011-12-01

To re-examine whether or not selective hippocampal damage reduces novelty preference in visual paired comparison (VPC), we presented two different versions of the task to a group of patients with developmental amnesia (DA), each of whom sustained this form of pathology early in life. Compared with normal control participants, the DA group showed a delay-dependent reduction in novelty preference on one version of the task and an overall reduction on both versions combined. Because VPC is widely considered to be a measure of incidental recognition, the results appear to support the view that the hippocampus contributes to recognition memory. A difficulty for this conclusion, however, is that according to one current view the hippocampal contribution to recognition is limited to task conditions that encourage recollection of an item in some associated context, and according to another current view, to recognition of an item with the high confidence judgment that reflects a strong memory. By contrast, VPC, throughout which the participant remains entirely uninstructed other than to view the stimuli, would seem to lack such task conditions and so would likely lead to recognition based on familiarity rather than recollection or, alternatively, weak memories rather than strong. However, before concluding that the VPC impairment therefore contradicts both current views regarding the role of the hippocampus in recognition memory, two possibilities that would resolve this issue need to be investigated. One is that some variable in VPC, such as the extended period of stimulus encoding during familiarization, overrides its incidental nature, and, because this condition promotes either recollection- or strength-based recognition, renders the task hippocampal-dependent. The other possibility is that VPC, rather than providing a measure of incidental recognition, actually assesses an implicit, information-gathering process modulated by habituation, for which the hippocampus is also partly responsible, independent of its role in recognition. Copyright © 2010 Wiley Periodicals, Inc.

Automatic Speech Recognition Technology as an Effective Means for Teaching Pronunciation

ERIC Educational Resources Information Center

Elimat, Amal Khalil; AbuSeileek, Ali Farhan

2014-01-01

This study aimed to explore the effect of using automatic speech recognition technology (ASR) on the third grade EFL students' performance in pronunciation, whether teaching pronunciation through ASR is better than regular instruction, and the most effective teaching technique (individual work, pair work, or group work) in teaching pronunciation…

Development of Flexible Visual Recognition Memory in Human Infants

ERIC Educational Resources Information Center

Robinson, Astri J.; Pascalis, Olivier

2004-01-01

Research using the visual paired comparison task has shown that visual recognition memory across changing contexts is dependent on the integrity of the hippocampal formation in human adults and in monkeys. The acquisition of contextual flexibility may contribute to the change in memory performance that occurs late in the first year of life. To…

Brief Report: Face-Specific Recognition Deficits in Young Children with Autism Spectrum Disorders

ERIC Educational Resources Information Center

Bradshaw, Jessica; Shic, Frederick; Chawarska, Katarzyna

2011-01-01

This study used eyetracking to investigate the ability of young children with autism spectrum disorders (ASD) to recognize social (faces) and nonsocial (simple objects and complex block patterns) stimuli using the visual paired comparison (VPC) paradigm. Typically developing (TD) children showed evidence for recognition of faces and simple…

Noradrenergic induction of odor-specific neural habituation and olfactory memories

PubMed Central

Shea, Stephen D.; Katz, Lawrence C.; Mooney, Richard

2008-01-01

For many mammals, individual recognition of conspecifics relies on olfactory cues. Certain individual recognition memories are thought to be stored when conspecific odor cues coincide with surges of noradrenaline (NA) triggered by intensely arousing social events. Such familiar stimuli elicit reduced behavioral responses, a change likely related to NA-dependent plasticity in the olfactory bulb (OB). In addition to its role in these ethological memories, NA signaling in the OB appears to be relevant for the discrimination of more arbitrary odorants as well. Nonetheless, no NA-gated mechanism of long-term plasticity in the OB has ever been directly observed in vivo. Here we report that NA release from locus coeruleus (LC), when coupled to odor presentation, acts locally in the main olfactory bulb (MOB) to cause a specific long-lasting suppression of respones to paired odors. These effects were observed for both food odors and urine, an important social recognition cue. Moreover, in subsequent behavioral tests, mice exhibited habituation to paired urine stimuli, suggesting that this LC-mediated olfactory neural plasticity, induced under anesthesia, can store an individual recognition memory that is observable upon recovery. PMID:18923046

Semantic congruence affects hippocampal response to repetition of visual associations.

PubMed

McAndrews, Mary Pat; Girard, Todd A; Wilkins, Leanne K; McCormick, Cornelia

2016-09-01

Recent research has shown complementary engagement of the hippocampus and medial prefrontal cortex (mPFC) in encoding and retrieving associations based on pre-existing or experimentally-induced schemas, such that the latter supports schema-congruent information whereas the former is more engaged for incongruent or novel associations. Here, we attempted to explore some of the boundary conditions in the relative involvement of those structures in short-term memory for visual associations. The current literature is based primarily on intentional evaluation of schema-target congruence and on study-test paradigms with relatively long delays between learning and retrieval. We used a continuous recognition paradigm to investigate hippocampal and mPFC activation to first and second presentations of scene-object pairs as a function of semantic congruence between the elements (e.g., beach-seashell versus schoolyard-lamp). All items were identical at first and second presentation and the context scene, which was presented 500ms prior to the appearance of the target object, was incidental to the task which required a recognition response to the central target only. Very short lags 2-8 intervening stimuli occurred between presentations. Encoding the targets with congruent contexts was associated with increased activation in visual cortical regions at initial presentation and faster response time at repetition, but we did not find enhanced activation in mPFC relative to incongruent stimuli at either presentation. We did observe enhanced activation in the right anterior hippocampus, as well as regions in visual and lateral temporal and frontal cortical regions, for the repetition of incongruent scene-object pairs. This pattern demonstrates rapid and incidental effects of schema processing in hippocampal, but not mPFC, engagement during continuous recognition. Copyright © 2016 Elsevier Ltd. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rechkoblit, Olga; Delaney, James C.; Essigmann, John M.

DNA is susceptible to alkylation damage by a number of environmental agents that modify the Watson-Crick edge of the bases. Such lesions, if not repaired, may be bypassed by Y-family DNA polymerases. The bypass polymerase Dpo4 is strongly inhibited by 1-methylguanine (m1G) and 3-methylcytosine (m3C), with nucleotide incorporation opposite these lesions being predominantly mutagenic. Further, extension after insertion of both correct and incorrect bases, introduces additional base substitution and deletion errors. Crystal structures of the Dpo4 ternary extension complexes with correct and mismatched 3'-terminal primer bases opposite the lesions reveal that both m1G and m3C remain positioned within the DNAmore » template/primer helix. However, both correct and incorrect pairing partners exhibit pronounced primer terminal nucleotide distortion, being primarily evicted from the DNA helix when opposite m1G or misaligned when pairing with m3C. Our studies provide insights into mechanisms related to hindered and mutagenic bypass of methylated lesions and models associated with damage recognition by repair demethylases.« less

Heterospecific pairing and hybridization between Nasutitermes corniger and N. ephratae

NASA Astrophysics Data System (ADS)

Hartke, Tamara R.; Rosengaus, Rebeca B.

2011-09-01

The sympatric neotropical termites Nasutitermes corniger and Nasutitermes ephratae are clearly distinguishable based on morphology, nest architecture, defensive secretion composition, and molecular markers. However, given the extensive ecological, geographical, and behavioral overlap of these closely related species, the potential for interbreeding may exist. To explore this possibility, heterospecific pairs were formed experimentally to examine courtship and colony-establishment behaviors, and reproductive potential. Courtship and nest construction behavior occurred in heterospecific pairs in a similar manner to that of conspecific pairs. Survival of pairs depended upon the species of the female partner. N. ephratae females paired with N. corniger males produced as many offspring as conspecific pairs. N. corniger females mated to N. ephratae males, however, produced significantly fewer offspring at 60 days post-establishment than the reciprocal cross or conspecific N. ephratae or N. corniger pairs. This was also the only pairing in which any aggression was observed. Heterospecific pairs and groups formed in mate choice mesocosms, suggesting that species recognition between these two termites is not an important aspect of mate choice. Overall, species mismatch tolerance and hybrid offspring viability are high. The present data, together with previous evidence from defensive secretions and isozyme analysis, suggest that hybridization may periodically occur in nature, and that reproductive barriers between these two species may be incomplete. Hybridization could provide a rare but important source of genetic diversity and may ensure mating opportunities for the more abundant sex of alates in each species.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Szulik, Marta W.; Pallan, Pradeep S.; Nocek, Boguslaw

5-Hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) form during active demethylation of 5-methylcytosine (5mC) and are implicated in epigenetic regulation of the genome. They are differentially processed by thymine DNA glycosylase (TDG), an enzyme involved in active demethylation of 5mC. Three modified Dickerson–Drew dodecamer (DDD) sequences, amenable to crystallographic and spectroscopic analyses and containing the 5'-CG-3' sequence associated with genomic cytosine methylation, containing 5hmC, 5fC, or 5caC placed site-specifically into the 5'-T 8X 9G 10-3' sequence of the DDD, were compared. The presence of 5caC at the X9 base increased the stability of the DDD, whereas 5hmC or 5fC didmore » not. Both 5hmC and 5fC increased imino proton exchange rates and calculated rate constants for base pair opening at the neighboring base pair A 5:T 8, whereas 5caC did not. At the oxidized base pair G 4:X 9, 5fC exhibited an increase in the imino proton exchange rate and the calculated k op. In all cases, minimal effects to imino proton exchange rates occurred at the neighboring base pair C 3:G 10. No evidence was observed for imino tautomerization, accompanied by wobble base pairing, for 5hmC, 5fC, or 5caC when positioned at base pair G 4:X 9; each favored Watson–Crick base pairing. However, both 5fC and 5caC exhibited intranucleobase hydrogen bonding between their formyl or carboxyl oxygens, respectively, and the adjacent cytosine N 4 exocyclic amines. The lesion-specific differences observed in the DDD may be implicated in recognition of 5hmC, 5fC, or 5caC in DNA by TDG. Furthermore, they do not correlate with differential excision of 5hmC, 5fC, or 5caC by TDG, which may be mediated by differences in transition states of the enzyme-bound complexes.« less

Parietal lesion effects on cued recall following pair associate learning.

PubMed

Ben-Zvi, Shir; Soroker, Nachum; Levy, Daniel A

2015-07-01

We investigated the involvement of the posterior parietal cortex in episodic memory in a lesion-effects study of cued recall following pair-associate learning. Groups of patients who had experienced first-incident stroke, generally in middle cerebral artery territory, and exhibited damage that included lateral posterior parietal regions, were tested within an early post-stroke time window. In three experiments, patients and matched healthy comparison groups executed repeated study and cued recall test blocks of pairs of words (Experiment 1), pairs of object pictures (Experiment 2), or pairs of object pictures and environmental sounds (Experiment 3). Patients' brain CT scans were subjected to quantitative analysis of lesion volumes. Behavioral and lesion data were used to compute correlations between area lesion extent and memory deficits, and to conduct voxel-based lesion-symptom mapping. These analyses implicated lateral ventral parietal cortex, especially the angular gyrus, in cued recall deficits, most pronouncedly in the cross-modal picture-sound pairs task, though significant parietal lesion effects were also found in the unimodal word pairs and picture pairs tasks. In contrast to an earlier study in which comparable parietal lesions did not cause deficits in item recognition, these results indicate that lateral posterior parietal areas make a substantive contribution to demanding forms of recollective retrieval as represented by cued recall, especially for complex associative representations. Copyright © 2015 Elsevier Ltd. All rights reserved.

Automatic anatomy recognition using neural network learning of object relationships via virtual landmarks

NASA Astrophysics Data System (ADS)

Yan, Fengxia; Udupa, Jayaram K.; Tong, Yubing; Xu, Guoping; Odhner, Dewey; Torigian, Drew A.

2018-03-01

The recently developed body-wide Automatic Anatomy Recognition (AAR) methodology depends on fuzzy modeling of individual objects, hierarchically arranging objects, constructing an anatomy ensemble of these models, and a dichotomous object recognition-delineation process. The parent-to-offspring spatial relationship in the object hierarchy is crucial in the AAR method. We have found this relationship to be quite complex, and as such any improvement in capturing this relationship information in the anatomy model will improve the process of recognition itself. Currently, the method encodes this relationship based on the layout of the geometric centers of the objects. Motivated by the concept of virtual landmarks (VLs), this paper presents a new one-shot AAR recognition method that utilizes the VLs to learn object relationships by training a neural network to predict the pose and the VLs of an offspring object given the VLs of the parent object in the hierarchy. We set up two neural networks for each parent-offspring object pair in a body region, one for predicting the VLs and another for predicting the pose parameters. The VL-based learning/prediction method is evaluated on two object hierarchies involving 14 objects. We utilize 54 computed tomography (CT) image data sets of head and neck cancer patients and the associated object contours drawn by dosimetrists for routine radiation therapy treatment planning. The VL neural network method is found to yield more accurate object localization than the currently used simple AAR method.

Synthesis, base pairing and structure studies of geranylated RNA.

PubMed

Wang, Rui; Vangaveti, Sweta; Ranganathan, Srivathsan V; Basanta-Sanchez, Maria; Haruehanroengra, Phensinee; Chen, Alan; Sheng, Jia

2016-07-27

Natural RNAs utilize extensive chemical modifications to diversify their structures and functions. 2-Thiouridine geranylation is a special hydrophobic tRNA modification that has been discovered very recently in several bacteria, such as Escherichia coli, Enterobacter aerogenes, Pseudomonas aeruginosa and Salmonella Typhimurium The geranylated residues are located in the first anticodon position of tRNAs specific for lysine, glutamine and glutamic acid. This big hydrophobic terpene functional group affects the codon recognition patterns and reduces frameshifting errors during translation. We aimed to systematically study the structure, function and biosynthesis mechanism of this geranylation pathway, as well as answer the question of why nature uses such a hydrophobic modification in hydrophilic RNA systems. Recently, we have synthesized the deoxy-analog of S-geranyluridine and showed the geranylated T-G pair is much stronger than the geranylated T-A pair and other mismatched pairs in the B-form DNA duplex context, which is consistent with the observation that the geranylated tRNA(Glu) UUC recognizes GAG more efficiently than GAA. In this manuscript we report the synthesis and base pairing specificity studies of geranylated RNA oligos. We also report extensive molecular simulation studies to explore the structural features of the geranyl group in the context of A-form RNA and its effect on codon-anticodon interaction during ribosome binding. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Functional cross‐hemispheric shift between object‐place paired associate memory and spatial memory in the human hippocampus

PubMed Central

Lee, Choong‐Hee; Ryu, Jungwon; Lee, Sang‐Hun; Kim, Hakjin

2016-01-01

ABSTRACT The hippocampus plays critical roles in both object‐based event memory and spatial navigation, but it is largely unknown whether the left and right hippocampi play functionally equivalent roles in these cognitive domains. To examine the hemispheric symmetry of human hippocampal functions, we used an fMRI scanner to measure BOLD activity while subjects performed tasks requiring both object‐based event memory and spatial navigation in a virtual environment. Specifically, the subjects were required to form object‐place paired associate memory after visiting four buildings containing discrete objects in a virtual plus maze. The four buildings were visually identical, and the subjects used distal visual cues (i.e., scenes) to differentiate the buildings. During testing, the subjects were required to identify one of the buildings when cued with a previously associated object, and when shifted to a random place, the subject was expected to navigate to the previously chosen building. We observed that the BOLD activity foci changed from the left hippocampus to the right hippocampus as task demand changed from identifying a previously seen object (object‐cueing period) to searching for its paired‐associate place (object‐cued place recognition period). Furthermore, the efficient retrieval of object‐place paired associate memory (object‐cued place recognition period) was correlated with the BOLD response of the left hippocampus, whereas the efficient retrieval of relatively pure spatial memory (spatial memory period) was correlated with the right hippocampal BOLD response. These findings suggest that the left and right hippocampi in humans might process qualitatively different information for remembering episodic events in space. © 2016 The Authors Hippocampus Published by Wiley Periodicals, Inc. PMID:27009679

Interaction of influenza virus polymerase with viral RNA in the 'corkscrew' conformation.

PubMed

Flick, R; Hobom, G

1999-10-01

The influenza virus RNA (vRNA) promoter structure is known to consist of the 5'- and 3'-terminal sequences of the RNA, within very narrow boundaries of 16 and 15 nucleotides, respectively. A complete set of single nucleotide substitutions led to the previously proposed model of a binary hooked or 'corkscrew' conformation for the vRNA promoter when it interacts with the viral polymerase. This functional structure is confirmed here with a complete set of complementary double substitutions, of both the regular A:U and G:C type and also the G:U type of base-pair exchanges. The proposed structure consists of a six base-pair RNA rod in the distal element in conjunction with two stem-loop structures of two short-range base-pairs (positions 2-9; 3-8). These support an exposed tetranucleotide loop within each branch of the proximal element, in an overall oblique organization due to a central unpaired A residue at position 10 in the 5' sequence. Long-range base-pairing between the entire 5' and 3' branches, as required for an unmodified 'panhandle' model, has been excluded for the proximal element, while it is known to represent the mode of interaction within the distal element. A large number of short-range base-pair exchanges in the proximal element constitute promoter-up mutations, which show activities several times above that of the wild-type in reporter gene assays. The unique overall conformation and rather few invariant nucleotides appear to be the core elements in vRNA recognition by polymerase and also in viral ribonucleoprotein packaging, to allow discrimination against the background of other RNA molecules in the cell.

Recognition of building group patterns in topographic maps based on graph partitioning and random forest

NASA Astrophysics Data System (ADS)

He, Xianjin; Zhang, Xinchang; Xin, Qinchuan

2018-02-01

Recognition of building group patterns (i.e., the arrangement and form exhibited by a collection of buildings at a given mapping scale) is important to the understanding and modeling of geographic space and is hence essential to a wide range of downstream applications such as map generalization. Most of the existing methods develop rigid rules based on the topographic relationships between building pairs to identify building group patterns and thus their applications are often limited. This study proposes a method to identify a variety of building group patterns that allow for map generalization. The method first identifies building group patterns from potential building clusters based on a machine-learning algorithm and further partitions the building clusters with no recognized patterns based on the graph partitioning method. The proposed method is applied to the datasets of three cities that are representative of the complex urban environment in Southern China. Assessment of the results based on the reference data suggests that the proposed method is able to recognize both regular (e.g., the collinear, curvilinear, and rectangular patterns) and irregular (e.g., the L-shaped, H-shaped, and high-density patterns) building group patterns well, given that the correctness values are consistently nearly 90% and the completeness values are all above 91% for three study areas. The proposed method shows promises in automated recognition of building group patterns that allows for map generalization.

Implicit multisensory associations influence voice recognition.

PubMed

von Kriegstein, Katharina; Giraud, Anne-Lise

2006-10-01

Natural objects provide partially redundant information to the brain through different sensory modalities. For example, voices and faces both give information about the speech content, age, and gender of a person. Thanks to this redundancy, multimodal recognition is fast, robust, and automatic. In unimodal perception, however, only part of the information about an object is available. Here, we addressed whether, even under conditions of unimodal sensory input, crossmodal neural circuits that have been shaped by previous associative learning become activated and underpin a performance benefit. We measured brain activity with functional magnetic resonance imaging before, while, and after participants learned to associate either sensory redundant stimuli, i.e. voices and faces, or arbitrary multimodal combinations, i.e. voices and written names, ring tones, and cell phones or brand names of these cell phones. After learning, participants were better at recognizing unimodal auditory voices that had been paired with faces than those paired with written names, and association of voices with faces resulted in an increased functional coupling between voice and face areas. No such effects were observed for ring tones that had been paired with cell phones or names. These findings demonstrate that brief exposure to ecologically valid and sensory redundant stimulus pairs, such as voices and faces, induces specific multisensory associations. Consistent with predictive coding theories, associative representations become thereafter available for unimodal perception and facilitate object recognition. These data suggest that for natural objects effective predictive signals can be generated across sensory systems and proceed by optimization of functional connectivity between specialized cortical sensory modules.

Associative Information in Memory: Evidence from Cued Recall

ERIC Educational Resources Information Center

Aue, William R.; Criss, Amy H.; Fischetti, Nicholas W.

2012-01-01

The representation of item and associative information in episodic memory was investigated using cued recall and single item recognition. In the first four experiments, participants studied two lists constructed such that some items presented in a pair during List 1 were rearranged to create new pairs in List 2 and were accompanied by pairs…

Does Kaniso activate CASINO?: input coding schemes and phonology in visual-word recognition.

PubMed

Acha, Joana; Perea, Manuel

2010-01-01

Most recent input coding schemes in visual-word recognition assume that letter position coding is orthographic rather than phonological in nature (e.g., SOLAR, open-bigram, SERIOL, and overlap). This assumption has been drawn - in part - by the fact that the transposed-letter effect (e.g., caniso activates CASINO) seems to be (mostly) insensitive to phonological manipulations (e.g., Perea & Carreiras, 2006, 2008; Perea & Pérez, 2009). However, one could argue that the lack of a phonological effect in prior research was due to the fact that the manipulation always occurred in internal letter positions - note that phonological effects tend to be stronger for the initial syllable (Carreiras, Ferrand, Grainger, & Perea, 2005). To reexamine this issue, we conducted a masked priming lexical decision experiment in which we compared the priming effect for transposed-letter pairs (e.g., caniso-CASINO vs. caviro-CASINO) and for pseudohomophone transposed-letter pairs (kaniso-CASINO vs. kaviro-CASINO). Results showed a transposed-letter priming effect for the correctly spelled pairs, but not for the pseudohomophone pairs. This is consistent with the view that letter position coding is (primarily) orthographic in nature.

Derivatization of DNAs with Selenium at 6-Position of Guanine for Function and Crystal Structure Studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Salon, J.; Jiang, J; Sheng, J

2008-01-01

To investigate nucleic acid base pairing and stacking via atom-specific mutagenesis and crystallography, we have synthesized for the first time the 6-Se-deoxyguanosine phosphoramidite and incorporated it into DNAs via solid-phase synthesis with a coupling yield over 97%. We found that the UV absorption of the Se-DNAs red-shifts over 100 nm to 360 nm ({Epsilon} = 2.3 x 10{sup 4} M{sup -1} cm{sup -1}), the Se-DNAs are yellow colored, and this Se modification is relatively stable in water and at elevated temperature. Moreover, we successfully crystallized a ternary complex of the Se-G-DNA, RNA and RNase H. The crystal structure determination andmore » analysis reveal that the overall structures of the native and Se-modified nucleic acid duplexes are very similar, the selenium atom participates in a Se-mediated hydrogen bond (Se H-N), and the {sup Se}G and C form a base pair similar to the natural G-C pair though the Se-modification causes the base-pair to shift (approximately 0.3 {angstrom}). Our biophysical and structural studies provide new insights into the nucleic acid flexibility, duplex recognition and stability. Furthermore, this novel selenium modification of nucleic acids can be used to investigate chemogenetics and structure of nucleic acids and their protein complexes.« less

Using maintenance rehearsal to explore recognition memory.

PubMed

Humphreys, Michael S; Maguire, Angela M; McFarlane, Kimberley A; Burt, Jennifer S; Bolland, Scott W; Murray, Krista L; Dunn, Ryan

2010-01-01

We examined associative and item recognition using the maintenance rehearsal paradigm. Our intent was to control for mnemonic strategies; to produce a low, graded level of learning; and to provide evidence of the role of attention in long-term memory. An advantage for low-frequency words emerged in both associative and item recognition at very low levels of learning. This early emergence casts doubt on explanations based on the traditional concept of recollection. A comparison of false alarms supports a role for item information or the joint use of cues but not familiarity in producing associative false alarms. We may also have found a way to measure the amount of attention being paid to a to-be-learned item or pair, independently of memory performance on the attended item. This result may be an important step in determining whether coherent theories about the role of attention in long- and short-term memory can be created. (PsycINFO Database Record (c) 2009 APA, all rights reserved).

Verbal recall and recognition in twins discordant for schizophrenia

PubMed Central

van Erp, Theo G.M.; Therman, Sebastian; Pirkola, Tiia; Tuulio-Henriksson, Annamari; Glahn, David C.; Bachman, Peter; Huttunen, Matti O.; Lönnqvist, Jouko; Hietanen, Marja; Kaprio, Jaakko; Koskenvuo, Markku; Cannon, Tyrone D.

2008-01-01

The nature, neural underpinnings, and etiology of deficits in verbal declarative memory in patients with schizophrenia remain unclear. To examine the contributions of genes and environment to verbal recall and recognition performance in this disorder, the California Verbal Learning Test was administered to a large population-based Finnish twin sample, which included schizophrenic and schizoaffective patients, their non-ill monozygotic (MZ) and dizygotic (DZ) co-twins, and healthy control twins. Compared with controls, patients and their co-twins showed relatively greater performance deficits on free recall compared with recognition. Intra-pair differences between patients and their non-ill co-twins in hippocampal volume and memory performance were highly positively correlated. These findings are consistent with the view that genetic influences are associated with reduced verbal recall in schizophrenia, but that non-genetic influences further compromise these abnormalities in patients who manifest the full-blown schizophrenia phenotype, with this additional degree of disease-related declarative memory deficit mediated in part by hippocampal pathology. PMID:18442861

When the face fits: recognition of celebrities from matching and mismatching faces and voices.

PubMed

Stevenage, Sarah V; Neil, Greg J; Hamlin, Iain

2014-01-01

The results of two experiments are presented in which participants engaged in a face-recognition or a voice-recognition task. The stimuli were face-voice pairs in which the face and voice were co-presented and were either "matched" (same person), "related" (two highly associated people), or "mismatched" (two unrelated people). Analysis in both experiments confirmed that accuracy and confidence in face recognition was consistently high regardless of the identity of the accompanying voice. However accuracy of voice recognition was increasingly affected as the relationship between voice and accompanying face declined. Moreover, when considering self-reported confidence in voice recognition, confidence remained high for correct responses despite the proportion of these responses declining across conditions. These results converged with existing evidence indicating the vulnerability of voice recognition as a relatively weak signaller of identity, and results are discussed in the context of a person-recognition framework.

Memory Asymmetry of Forward and Backward Associations in Recognition Tasks

ERIC Educational Resources Information Center

Yang, Jiongjiong; Zhao, Peng; Zhu, Zijian; Mecklinger, Axel; Fang, Zhiyong; Li, Han

2013-01-01

There is an intensive debate on whether memory for serial order is symmetric. The objective of this study was to explore whether associative asymmetry is modulated by memory task (recognition vs. cued recall). Participants were asked to memorize word triples (Experiments 1-2) or pairs (Experiments 3-6) during the study phase. They then recalled…

Western pine beetle populations in Arizona and California differ in the composition of their aggregation pheromones

Treesearch

Deepa S. Pureswaran; Richard W. Hofstetter; Brian T. Sullivan; Amanda M. Grady; Cavell Brownie

2016-01-01

When related species coexist, selection pressure should favor evolution of species recognition mechanisms to prevent interspecific pairing and wasteful reproductive encounters. We investigated the potential role of pheromone and acoustic signals in species recognition between two species of tree-killing bark beetles, the southern pine beetle, Dendroctonus frontalis...

Effects of Visual and Auditory Perceptual Aptitudes and Letter Discrimination Pretraining on Word Recognition.

ERIC Educational Resources Information Center

Janssen, David Rainsford

This study investigated alternate methods of letter discrimination pretraining and word recognition training in young children. Seventy kindergarten children were trained to recognize eight printed words in a vocabulary list by a mixed-list paired-associate method. Four of the stimulus words had visual response choices (pictures) and four had…

Stimulus Similarity and Encoding Time Influence Incidental Recognition Memory in Adult Monkeys with Selective Hippocampal Lesions

ERIC Educational Resources Information Center

Zeamer, Alyson; Meunier, Martine; Bachevalier, Jocelyne

2011-01-01

Recognition memory impairment after selective hippocampal lesions in monkeys is more profound when measured with visual paired-comparison (VPC) than with delayed nonmatching-to-sample (DNMS). To clarify this issue, we assessed the impact of stimuli similarity and encoding duration on the VPC performance in monkeys with hippocampal lesions and…

Translation Recognition in Highly Proficient Hindi-English Bilinguals: The Influence of Different Scripts but Connectable Phonologies

ERIC Educational Resources Information Center

Sunderman, Gretchen L.; Priya, Kanu

2012-01-01

This study investigates the phonological nature of the lexical links in the bilingual lexicon using different-script bilinguals. Highly proficient Hindi-English bilinguals performed a translation recognition task (i.e., decide whether two words presented sequentially are a correct translation pair). For the critical trials, the second word was a…

Stability of miRNA 5′terminal and seed regions is correlated with experimentally observed miRNA-mediated silencing efficacy

PubMed Central

Hibio, Naoki; Hino, Kimihiro; Shimizu, Eigo; Nagata, Yoshiro; Ui-Tei, Kumiko

2012-01-01

MicroRNAs (miRNAs) are key regulators of sequence-specific gene silencing. However, crucial factors that determine the efficacy of miRNA-mediated target gene silencing are poorly understood. Here we mathematized base-pairing stability and showed that miRNAs with an unstable 5′ terminal duplex and stable seed-target duplex exhibit strong silencing activity. The results are consistent with the previous findings that an RNA strand with unstable 5′ terminal in miRNA duplex easily loads onto the RNA-induced silencing complex (RISC), and miRNA recognizes target mRNAs with seed-complementary sequences to direct posttranscriptional repression. Our results suggested that both the unwinding and target recognition processes of miRNAs could be proficiently controlled by the thermodynamics of base-pairing in protein-free condition. Interestingly, such thermodynamic parameters might be evolutionarily well adapted to the body temperatures of various species. PMID:23251782

Gender in Facial Representations: A Contrast-Based Study of Adaptation within and between the Sexes

PubMed Central

Oruç, Ipek; Guo, Xiaoyue M.; Barton, Jason J. S.

2011-01-01

Face aftereffects are proving to be an effective means of examining the properties of face-specific processes in the human visual system. We examined the role of gender in the neural representation of faces using a contrast-based adaptation method. If faces of different genders share the same representational face space, then adaptation to a face of one gender should affect both same- and different-gender faces. Further, if these aftereffects differ in magnitude, this may indicate distinct gender-related factors in the organization of this face space. To control for a potential confound between physical similarity and gender, we used a Bayesian ideal observer and human discrimination data to construct a stimulus set in which pairs of different-gender faces were equally dissimilar as same-gender pairs. We found that the recognition of both same-gender and different-gender faces was suppressed following a brief exposure of 100ms. Moreover, recognition was more suppressed for test faces of a different-gender than those of the same-gender as the adaptor, despite the equivalence in physical and psychophysical similarity. Our results suggest that male and female faces likely occupy the same face space, allowing transfer of aftereffects between the genders, but that there are special properties that emerge along gender-defining dimensions of this space. PMID:21267414

High-fidelity in vivo replication of DNA base shape mimics without Watson–Crick hydrogen bonds

PubMed Central

Delaney, James C.; Henderson, Paul T.; Helquist, Sandra A.; Morales, Juan C.; Essigmann, John M.; Kool, Eric T.

2003-01-01

We report studies testing the importance of Watson–Crick hydrogen bonding, base-pair geometry, and steric effects during DNA replication in living bacterial cells. Nonpolar DNA base shape mimics of thymine and adenine (abbreviated F and Q, respectively) were introduced into Escherichia coli by insertion into a phage genome followed by transfection of the vector into bacteria. Genetic assays showed that these two base mimics were bypassed with moderate to high efficiency in the cells and with very high efficiency under damage-response (SOS induction) conditions. Under both sets of conditions, the T-shape mimic (F) encoded genetic information in the bacteria as if it were thymine, directing incorporation of adenine opposite it with high fidelity. Similarly, the A mimic (Q) directed incorporation of thymine opposite itself with high fidelity. The data establish that Watson–Crick hydrogen bonding is not necessary for high-fidelity replication of a base pair in vivo. The results suggest that recognition of DNA base shape alone serves as the most powerful determinant of fidelity during transfer of genetic information in a living organism. PMID:12676985

Recognition by nonaromatic and stereochemical subunit-containing polyamides of the four Watson-Crick base pairs in the DNA minor groove.

PubMed

Zhang, Hong-Fei; Wu, Yan-Ling; Jiang, Shi-Kun; Wang, Pu; Sugiyama, Hiroshi; Chen, Xing-Lai; Zhang, Wen; Ji, Yan-Juan; Guo, Chuan-Xin

2012-06-18

In order to develop an optimal subunit as a T-recognition element in hairpin polyamides, 15 novel chirality-modified polyamides containing (R)-α,β-diaminopropionic acid ((R) β α-NH 2), (S)-α,β-diaminopropionic acid ((S) β α-NH 2), (1R,3S)-3-aminocyclopentanecarboxylic acid ((RS) Cp), (1S,3R)-3-amino-cyclopentanecarboxylic acid ((RS) Cp), (1R,3R)-3-aminocyclopentanecarboxylic acid ((RR) Cp) and (1S,3S)-3-amino-cyclopentanecarboxylic acid ((SS) Cp) residues were synthesized. Their binding characteristics to DNA sequences 5'-TGCNCAT-3'/3'-ACGN'GTA-5' (N⋅N'=A⋅T, T⋅A, G⋅C and C⋅G) were systemically studied by surface plasmon resonance (SPR) and molecular simulation (MSim) techniques. SPR showed that polyamide 4, AcIm-(S) β α-NH 2-ImPy-γ-ImPy-β-Py-βDp (β/(S) β α-NH 2 pair), bound to a DNA sequence containing a core binding site of 5'-TGCACAT-3' with a dissociation equilibrium constant (K(D) ) of 4.5×10(-8)  m. This was a tenfold improvement in specificity over 5'-TGCTCAT-3' (K(D) =4.5×10(-7)  M). MSim studies supported the SPR results. More importantly, for the first time, we found that chiral 3-aminocyclopentanecarboxylic acids in polyamides can be employed as base readers with only a small decrease in binding affinity to DNA. In particular, SPR showed that polyamide 9 ((RR) Cp/β pair) had a 15-fold binding preference for 5'-TGCTCAT-3' over 5'-TGCACAT-3'. A large difference in standard free energy change for A⋅T over T⋅A was determined (ΔΔG(o) =5.9 kJ mol(-1) ), as was a twofold decrease in interaction energy by MSim. Moreover, a 1:1 stoichiometry (9 to 5'-TGCTCAT-3'/3'-ACGAGTA-5') was shown by MSim to be optimal for the chiral five-membered cycle to fit the minor groove. Collectively, the study suggests that the (S)-α-amino-β-aminopropionic acid and (1R,3R)-3-aminocyclopentanecarboxylic acid can serve as a T-recognition element, and the stereochemistry and the nature of these subunits significantly influence binding properties in these recognition events. Subunit (1R,3R)-3-aminocyclopentanecarboxylic acid broadens our scope to design novel polyamides. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Using GOMS and Bayesian plan recognition to develop recognition models of operator behavior

NASA Astrophysics Data System (ADS)

Zaientz, Jack D.; DeKoven, Elyon; Piegdon, Nicholas; Wood, Scott D.; Huber, Marcus J.

2006-05-01

Trends in combat technology research point to an increasing role for uninhabited vehicles in modern warfare tactics. To support increased span of control over these vehicles human responsibilities need to be transformed from tedious, error-prone and cognition intensive operations into tasks that are more supervisory and manageable, even under intensely stressful conditions. The goal is to move away from only supporting human command of low-level system functions to intention-level human-system dialogue about the operator's tasks and situation. A critical element of this process is developing the means to identify when human operators need automated assistance and to identify what assistance they need. Toward this goal, we are developing an unmanned vehicle operator task recognition system that combines work in human behavior modeling and Bayesian plan recognition. Traditionally, human behavior models have been considered generative, meaning they describe all possible valid behaviors. Basing behavior recognition on models designed for behavior generation can offers advantages in improved model fidelity and reuse. It is not clear, however, how to reconcile the structural differences between behavior recognition and behavior modeling approaches. Our current work demonstrates that by pairing a cognitive psychology derived human behavior modeling approach, GOMS, with a Bayesian plan recognition engine, ASPRN, we can translate a behavior generation model into a recognition model. We will discuss the implications for using human performance models in this manner as well as suggest how this kind of modeling may be used to support the real-time control of multiple, uninhabited battlefield vehicles and other semi-autonomous systems.

Myotonic Dystrophy Type 1 RNA Crystal Structures Reveal Heterogeneous 1×1 Nucleotide UU Internal Loop Conformations⊥

PubMed Central

Kumar, Amit; Park, HaJeung; Fang, Pengfei; Parkesh, Raman; Guo, Min; Nettles, Kendall W.; Disney, Matthew D.

2011-01-01

RNA internal loops often display a variety of conformations in solution. Herein, we visualize conformational heterogeneity in the context of the 5′CUG/3′GUC repeat motif present in the RNA that causes myotonic dystrophy type 1 (DM1). Specifically, two crystal structures are disclosed of a model DM1 triplet repeating construct, 5′r(UUGGGC(CUG)3GUCC)2, refined to 2.20 Å and 1.52 Å resolution. Here, differences in orientation of the 5′ dangling UU end between the two structures induce changes in the backbone groove width, which reveals that non-canonical 1×1 nucleotide UU internal loops can display an ensemble of pairing conformations. In the 2.20 Å structure, CUGa, the 5′UU forms one hydrogen-bonded pairs with a 5′UU of a neighboring helix in the unit cell to form a pseudo-infinite helix. The central 1×1 nucleotide UU internal loop has no hydrogen bonds, while the terminal 1×1 nucleotide UU internal loops each form a one hydrogen-bonded pair. In the 1.52 Å structure, CUGb, the 5′ UU dangling end is tucked into the major groove of the duplex. While the canonical paired bases show no change in base pairing, in CUGb the terminal 1×1 nucleotide UU internal loops form now two hydrogen-bonded pairs. Thus, the shift in major groove induced by the 5′UU dangling end alters non-canonical base patterns. Collectively, these structures indicate that 1×1 nucleotide UU internal loops in DM1 may sample multiple conformations in vivo. This observation has implications for the recognition of this RNA, and other repeating transcripts, by protein and small molecule ligands. PMID:21988728

Myotonic dystrophy type 1 RNA crystal structures reveal heterogeneous 1 × 1 nucleotide UU internal loop conformations.

PubMed

Kumar, Amit; Park, HaJeung; Fang, Pengfei; Parkesh, Raman; Guo, Min; Nettles, Kendall W; Disney, Matthew D

2011-11-15

RNA internal loops often display a variety of conformations in solution. Herein, we visualize conformational heterogeneity in the context of the 5'CUG/3'GUC repeat motif present in the RNA that causes myotonic dystrophy type 1 (DM1). Specifically, two crystal structures of a model DM1 triplet repeating construct, 5'r[UUGGGC(CUG)(3)GUCC](2), refined to 2.20 and 1.52 Å resolution are disclosed. Here, differences in the orientation of the 5' dangling UU end between the two structures induce changes in the backbone groove width, which reveals that noncanonical 1 × 1 nucleotide UU internal loops can display an ensemble of pairing conformations. In the 2.20 Å structure, CUGa, the 5' UU forms a one hydrogen-bonded pair with a 5' UU of a neighboring helix in the unit cell to form a pseudoinfinite helix. The central 1 × 1 nucleotide UU internal loop has no hydrogen bonds, while the terminal 1 × 1 nucleotide UU internal loops each form a one-hydrogen bond pair. In the 1.52 Å structure, CUGb, the 5' UU dangling end is tucked into the major groove of the duplex. While the canonically paired bases show no change in base pairing, in CUGb the terminal 1 × 1 nucleotide UU internal loops now form two hydrogen-bonded pairs. Thus, the shift in the major groove induced by the 5' UU dangling end alters noncanonical base patterns. Collectively, these structures indicate that 1 × 1 nucleotide UU internal loops in DM1 may sample multiple conformations in vivo. This observation has implications for the recognition of this RNA, and other repeating transcripts, by protein and small molecule ligands.

Myotonic Dystrophy Type 1 RNA Crystal Structures Reveal Heterogeneous 1 × 1 Nucleotide UU Internal Loop Conformations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kumar, Amit; Park, HaJeung; Fang, Pengfei

2012-03-27

RNA internal loops often display a variety of conformations in solution. Herein, we visualize conformational heterogeneity in the context of the 5'CUG/3'GUC repeat motif present in the RNA that causes myotonic dystrophy type 1 (DM1). Specifically, two crystal structures of a model DM1 triplet repeating construct, 5'r[{und UU}GGGC(C{und U}G){sub 3}GUCC]{sub 2}, refined to 2.20 and 1.52 {angstrom} resolution are disclosed. Here, differences in the orientation of the 5' dangling UU end between the two structures induce changes in the backbone groove width, which reveals that noncanonical 1 x 1 nucleotide UU internal loops can display an ensemble of pairing conformations.more » In the 2.20 {angstrom} structure, CUGa, the 5' UU forms a one hydrogen-bonded pair with a 5' UU of a neighboring helix in the unit cell to form a pseudoinfinite helix. The central 1 x 1 nucleotide UU internal loop has no hydrogen bonds, while the terminal 1 x 1 nucleotide UU internal loops each form a one-hydrogen bond pair. In the 1.52 {angstrom} structure, CUGb, the 5' UU dangling end is tucked into the major groove of the duplex. While the canonically paired bases show no change in base pairing, in CUGb the terminal 1 x 1 nucleotide UU internal loops now form two hydrogen-bonded pairs. Thus, the shift in the major groove induced by the 5' UU dangling end alters noncanonical base patterns. Collectively, these structures indicate that 1 x 1 nucleotide UU internal loops in DM1 may sample multiple conformations in vivo. This observation has implications for the recognition of this RNA, and other repeating transcripts, by protein and small molecule ligands.« less

Hippocampal activations in mesial temporal lobe epilepsy due to hippocampal sclerosis- an observational study on intramural encoding-delayed recall paradigms using task-based memory fMRI.

PubMed

Rajesh, P G; Thomas, Bejoy; Pammi, V S Chandrasekhar; Kesavadas, C; Alexander, Aley; Radhakrishnan, Ashalatha; Thomas, S V; Menon, R N

2018-05-26

To validate concurrent utility of within-scanner encoding and delayed recognition-memory paradigms to ascertain hippocampal activations during task-based memory fMRI. Memory paradigms were designed for faces, word-pairs and abstract designs. A deep-encoding task was designed comprising of a total of 9 cycles run within a 1.5T MRI scanner. A recall session was performed after 1 h within the scanner using an event-related design. Group analysis was done with 'correct-incorrect' responses applied as parametric modulators in Statistical Parametric Mapping version 8 using boot-strap method to enable estimation of laterality indices (LI) using custom anatomical masks involving the medio-basal temporal structures. Twenty seven subjects with drug-resistant mesial temporal lobe epilepsy due to hippocampal sclerosis (MTLE-HS) [17 patients of left-MTLE and 10 patients of right-MTLE] and 21 right handed age-matched healthy controls (HC) were recruited. For the encoding paradigm blood oxygen level dependent (BOLD) responses in HC demonstrated right laterality for faces, left laterality for word pairs, and bilaterality for design encoding over the regions of interest. Both right and left MTLE-HS groups revealed left lateralisation for word-pair encoding, bilateral activation for face encoding, with design encoding in right MTLE-HS demonstrating a left shift. As opposed to lateralization shown in controls, group analysis of cued-recall BOLD signals acquired within scanner in left MTLE-HS demonstrated right lateralization for word-pairs with bilaterality for faces and designs. The right MTLE-HS group demonstrated bilateral activations for faces, word-pairs and designs. Recall-based fMRI paradigms indicate hippocampal plasticity in MTLE-HS, maximal for word-pair associate recall tasks. Copyright © 2018 Elsevier B.V. All rights reserved.

Binding to the DNA Minor Groove by Heterocyclic Dications: From AT Specific Monomers to GC Recognition with Dimers

PubMed Central

Nanjunda, Rupesh; Wilson, W. David

2012-01-01

Compounds that bind in the DNA minor groove have provided critical information on DNA molecular recognition, they have found extensive uses in biotechnology and they are providing clinically useful drugs against diseases as diverse as cancer and sleeping sickness. This review focuses on the development of clinically useful heterocyclic diamidine minor groove binders. These compounds have shown us that the classical model for minor groove binding in AT DNA sequences must be expanded in several ways: compounds with nonstandard shapes can bind strongly to the groove, water can be directly incorporated into the minor groove complex in an interfacial interaction, and the compounds can form cooperative stacked dimers to recognize GC and mixed AT/GC base pair sequences. PMID:23255206

Immediate effects of form-class constraints on spoken word recognition

PubMed Central

Magnuson, James S.; Tanenhaus, Michael K.; Aslin, Richard N.

2008-01-01

In many domains of cognitive processing there is strong support for bottom-up priority and delayed top-down (contextual) integration. We ask whether this applies to supra-lexical context that could potentially constrain lexical access. Previous findings of early context integration in word recognition have typically used constraints that can be linked to pair-wise conceptual relations between words. Using an artificial lexicon, we found immediate integration of syntactic expectations based on pragmatic constraints linked to syntactic categories rather than words: phonologically similar “nouns” and “adjectives” did not compete when a combination of syntactic and visual information strongly predicted form class. These results suggest that predictive context is integrated continuously, and that previous findings supporting delayed context integration stem from weak contexts rather than delayed integration. PMID:18675408

Recognising the forest, but not the trees: an effect of colour on scene perception and recognition.

PubMed

Nijboer, Tanja C W; Kanai, Ryota; de Haan, Edward H F; van der Smagt, Maarten J

2008-09-01

Colour has been shown to facilitate the recognition of scene images, but only when these images contain natural scenes, for which colour is 'diagnostic'. Here we investigate whether colour can also facilitate memory for scene images, and whether this would hold for natural scenes in particular. In the first experiment participants first studied a set of colour and greyscale natural and man-made scene images. Next, the same images were presented, randomly mixed with a different set. Participants were asked to indicate whether they had seen the images during the study phase. Surprisingly, performance was better for greyscale than for coloured images, and this difference is due to the higher false alarm rate for both natural and man-made coloured scenes. We hypothesized that this increase in false alarm rate was due to a shift from scrutinizing details of the image to recognition of the gist of the (coloured) image. A second experiment, utilizing images without a nameable gist, confirmed this hypothesis as participants now performed equally on greyscale and coloured images. In the final experiment we specifically targeted the more detail-based perception and recognition for greyscale images versus the more gist-based perception and recognition for coloured images with a change detection paradigm. The results show that changes to images are detected faster when image-pairs were presented in greyscale than in colour. This counterintuitive result held for both natural and man-made scenes (but not for scenes without nameable gist) and thus corroborates the shift from more detailed processing of images in greyscale to more gist-based processing of coloured images.

Strength Is in Numbers: Can Concordant Artificial Listeners Improve Prediction of Emotion from Speech?

PubMed Central

Martinelli, Eugenio; Mencattini, Arianna; Di Natale, Corrado

2016-01-01

Humans can communicate their emotions by modulating facial expressions or the tone of their voice. Albeit numerous applications exist that enable machines to read facial emotions and recognize the content of verbal messages, methods for speech emotion recognition are still in their infancy. Yet, fast and reliable applications for emotion recognition are the obvious advancement of present ‘intelligent personal assistants’, and may have countless applications in diagnostics, rehabilitation and research. Taking inspiration from the dynamics of human group decision-making, we devised a novel speech emotion recognition system that applies, for the first time, a semi-supervised prediction model based on consensus. Three tests were carried out to compare this algorithm with traditional approaches. Labeling performances relative to a public database of spontaneous speeches are reported. The novel system appears to be fast, robust and less computationally demanding than traditional methods, allowing for easier implementation in portable voice-analyzers (as used in rehabilitation, research, industry, etc.) and for applications in the research domain (such as real-time pairing of stimuli to participants’ emotional state, selective/differential data collection based on emotional content, etc.). PMID:27563724

The longer we have to forget the more we remember: The ironic effect of postcue duration in item-based directed forgetting.

PubMed

Bancroft, Tyler D; Hockley, William E; Farquhar, Riley

2013-05-01

The effects of the duration of remember and forget cues were examined to test the differential rehearsal account of item-based directed forgetting. In Experiments 1 and 2, cues were shown for 300, 600, or 900 ms, and a directed forgetting effect (better recognition of remember than forget items) was found at each duration. In addition, recognition of both remember and forget items increased with cue duration. These 2 effects did not interact. The results of Experiment 2 further showed that memory for the cue associated with the study items increased with cue duration as well. The results of Experiment 1 were replicated in Experiment 3 for cue durations of 1, 2, and 3 s. Finally, a similar pattern of results was found for cue durations of 2, 4, and 6 s for associative recognition of random word pairs. If subjects cannot immediately terminate the processing of forget items, the lingering processing of these items is as beneficial as the continued processing of remember items. Alternatively, subjects may use inefficient or counterproductive strategies that ironically improve memory for the information they wish to forget.

Test of the Practicality and Feasibility of EDoF-Empowered Image Sensors for Long-Range Biometrics

PubMed Central

Hsieh, Sheng-Hsun; Li, Yung-Hui; Tien, Chung-Hao

2016-01-01

For many practical applications of image sensors, how to extend the depth-of-field (DoF) is an important research topic; if successfully implemented, it could be beneficial in various applications, from photography to biometrics. In this work, we want to examine the feasibility and practicability of a well-known “extended DoF” (EDoF) technique, or “wavefront coding,” by building real-time long-range iris recognition and performing large-scale iris recognition. The key to the success of long-range iris recognition includes long DoF and image quality invariance toward various object distance, which is strict and harsh enough to test the practicality and feasibility of EDoF-empowered image sensors. Besides image sensor modification, we also explored the possibility of varying enrollment/testing pairs. With 512 iris images from 32 Asian people as the database, 400-mm focal length and F/6.3 optics over 3 m working distance, our results prove that a sophisticated coding design scheme plus homogeneous enrollment/testing setups can effectively overcome the blurring caused by phase modulation and omit Wiener-based restoration. In our experiments, which are based on 3328 iris images in total, the EDoF factor can achieve a result 3.71 times better than the original system without a loss of recognition accuracy. PMID:27897976

Developmental Changes in the Effects of Presentation Mode on the Storage and Retrieval of Noun Pairs in Children's Recognition Memory.

ERIC Educational Resources Information Center

Kee, Daniel W.; And Others

Four problems in children's paired-associate memory were addressed: (1) reappraisal of the presumed developmental trend in presentation mode effect during grade-school years, (2) identification of the locus of this developmental effect, (3) evaluation of the influence of combined presentation (verbal plus pictorial) relative to pictorial…

Molecular imprinting at walls of silica nanotubes for TNT recognition.

PubMed

Xie, Chenggen; Liu, Bianhua; Wang, Zhenyang; Gao, Daming; Guan, Guijian; Zhang, Zhongping

2008-01-15

This paper reports the molecular imprinting at the walls of highly uniform silica nanotubes for the recognition of 2,4,6-trinitrotoluene (TNT). It has been demonstrated that TNT templates were efficiently imprinted into the matrix of silica through the strong acid-base pairing interaction between TNT and 3-aminopropyltriethoxysilane (APTS). TNT-imprinted silica nanotubes were synthesized by the gelation reaction between APTS and tetraethylorthosilicate (TEOS), selectively occurring at the porous walls of APTS-modified alumina membranes. The removal of the original TNT templates leaves the imprinted cavities with covalently anchored amine groups at the cavity walls. A high density of recognition sites with molecular selectivity to the TNT analyte was created at the wall of silica nanotubes. Furthermore, most of these recognition sites are situated at the inside and outside surfaces of tubular walls and in the proximity of the two surfaces due to the ultrathin wall thickness of only 15 nm, providing a better site accessibility and lower mass-transfer resistance. Therefore, greater capacity and faster kinetics of uptaking target species were achieved. The silica nanotube reported herein is an ideal form of material for imprinting various organic or biological molecules toward applications in chemical/biological sensors and bioassay.

Automatic threshold selection for multi-class open set recognition

NASA Astrophysics Data System (ADS)

Scherreik, Matthew; Rigling, Brian

2017-05-01

Multi-class open set recognition is the problem of supervised classification with additional unknown classes encountered after a model has been trained. An open set classifer often has two core components. The first component is a base classifier which estimates the most likely class of a given example. The second component consists of open set logic which estimates if the example is truly a member of the candidate class. Such a system is operated in a feed-forward fashion. That is, a candidate label is first estimated by the base classifier, and the true membership of the example to the candidate class is estimated afterward. Previous works have developed an iterative threshold selection algorithm for rejecting examples from classes which were not present at training time. In those studies, a Platt-calibrated SVM was used as the base classifier, and the thresholds were applied to class posterior probabilities for rejection. In this work, we investigate the effectiveness of other base classifiers when paired with the threshold selection algorithm and compare their performance with the original SVM solution.

Recognition and Posing of Emotional Expressions by Abused Children and Their Mothers.

ERIC Educational Resources Information Center

Camras, Linda A.; And Others

1988-01-01

A total of 20 abused and 20 nonabused pairs of children of three-seven years and their mothers participated in a facial expression posing task and a facial expression recognition task. Findings suggest that abused children may not observe as often as nonabused children do the easily interpreted voluntary displays of emotion by their mothers. (RH)

Interference Effects as a Function of Semantic Similarity in the Translation Recognition Task in Bilinguals of Catalan and Spanish

ERIC Educational Resources Information Center

Moldovan, Cornelia D.; Sanchez-Casas, Rosa; Demestre, Josep; Ferre, Pilar

2012-01-01

Previous evidence has shown that word pairs that are either related in form (e.g., "ruc-berro"; donkey-watercress) or very closely semantically related (e.g., "ruc-caballo", donkey-horse) produce interference effects in a translation recognition task (Ferre et al., 2006; Guasch et al., 2008). However, these effects are not…

Genetic Influences on Early Word Recognition Abilities and Disabilities: A Study of 7-Year-Old Twins

ERIC Educational Resources Information Center

Harlaar, Nicole; Spinath, Frank M.; Dale, Philip S.; Plomin, Robert

2005-01-01

Background: A fundamental issue for child psychology concerns the origins of individual differences in early reading development. Method: A measure of word recognition, the Test of Word Reading Efficiency (TOWRE), was administered by telephone to a representative population sample of 3,909 same-sex and opposite-sex pairs of 7-year-old twins.…

Encoding instructions and stimulus presentation in local environmental context-dependent memory studies.

PubMed

Markopoulos, G; Rutherford, A; Cairns, C; Green, J

2010-08-01

Murnane and Phelps (1993) recommend word pair presentations in local environmental context (EC) studies to prevent associations being formed between successively presented items and their ECs and a consequent reduction in the EC effect. Two experiments were conducted to assess the veracity of this assumption. In Experiment 1, participants memorised single words or word pairs, or categorised them as natural or man made. Their free recall protocols were examined to assess any associations established between successively presented items. Fewest associations were observed when the item-specific encoding task (i.e., natural or man made categorisation of word referents) was applied to single words. These findings were examined further in Experiment 2, where the influence of encoding instructions and stimulus presentation on local EC dependent recognition memory was examined. Consistent with recognition dual-process signal detection model predictions and findings (e.g., Macken, 2002; Parks & Yonelinas, 2008), recollection sensitivity, but not familiarity sensitivity, was found to be local EC dependent. However, local EC dependent recognition was observed only after item-specific encoding instructions, irrespective of stimulus presentation. These findings and the existing literature suggest that the use of single word presentations and item-specific encoding enhances local EC dependent recognition.

Mate choice for major histocompatibility complex complementarity in a strictly monogamous bird, the grey partridge (Perdix perdix).

PubMed

Rymešová, Dana; Králová, Tereza; Promerová, Marta; Bryja, Josef; Tomášek, Oldřich; Svobodová, Jana; Šmilauer, Petr; Šálek, Miroslav; Albrecht, Tomáš

2017-01-01

Sexual selection has been hypothesised as favouring mate choice resulting in production of viable offspring with genotypes providing high pathogen resistance. Specific pathogen recognition is mediated by genes of the major histocompatibility complex (MHC) encoding proteins fundamental for adaptive immune response in jawed vertebrates. MHC genes may also play a role in odour-based individual recognition and mate choice, aimed at avoiding inbreeding. MHC genes are known to be involved in mate choice in a number of species, with 'good genes' (absolute criteria) and 'complementary genes' (self-referential criteria) being used to explain MHC-based mating. Here, we focus on the effect of morphological traits and variation and genetic similarity between individuals in MHC class IIB (MHCIIB) exon 2 on mating in a free-living population of a monogamous bird, the grey partridge. We found no evidence for absolute mate choice criteria as regards grey partridge MHCIIB genotypes, i.e., number and occurrence of amino acid variants, though red chroma of the spot behind eyes was positively associated with male pairing success. On the other hand, mate choice at MHCIIB was based on relative criteria as females preferentially paired with more dissimilar males having a lower number of shared amino acid variants. This observation supports the 'inbreeding avoidance' and 'complementary genes' hypotheses. Our study provides one of the first pieces of evidence for MHC-based mate choice for genetic complementarity in a strictly monogamous bird. The statistical approach employed can be recommended for testing mating preferences in cases where availability of potential mates (recorded with an appropriate method such as radio-tracking) shows considerable temporal variation. Additional genetic analyses using neutral markers may detect whether MHC-based mate choice for complementarity emerges as a by-product of general inbreeding avoidance in grey partridges.

Depth rotation and mirror-image reflection reduce affective preference as well as recognition memory for pictures of novel objects.

PubMed

Lawson, Rebecca

2004-10-01

In two experiments, the identification of novel 3-D objects was worse for depth-rotated and mirror-reflected views, compared with the study view in an implicit affective preference memory task, as well as in an explicit recognition memory task. In Experiment 1, recognition was worse and preference was lower when depth-rotated views of an object were paired with an unstudied object relative to trials when the study view of that object was shown. There was a similar trend for mirror-reflected views. In Experiment 2, the study view of an object was both recognized and preferred above chance when it was paired with either depth-rotated or mirror-reflected views of that object. These results suggest that view-sensitive representations of objects mediate performance in implicit, as well as explicit, memory tasks. The findings do not support the claim that separate episodic and structural description representations underlie performance in implicit and explicit memory tasks, respectively.

Development of a Diagnostic Tool to Detect DNA Methylation Biomarkers for Early-Stage Lung Cancer

DTIC Science & Technology

2015-02-01

include: 1) a DNA recognition domain that recognizes the specific DNA sequence of interest and 2) one half of the leucine zipper pair. The second...piece will include 1) the second half of the leucine zipper pair, 2) a flexible linker flanked by a FRET pair that determines the local (within 30 bp...each other to determine the resolution of our probes. All DNA fragments are methylated using bacterial methyltransferase. Since only a single CG

Implicit Multisensory Associations Influence Voice Recognition

PubMed Central

von Kriegstein, Katharina; Giraud, Anne-Lise

2006-01-01

Natural objects provide partially redundant information to the brain through different sensory modalities. For example, voices and faces both give information about the speech content, age, and gender of a person. Thanks to this redundancy, multimodal recognition is fast, robust, and automatic. In unimodal perception, however, only part of the information about an object is available. Here, we addressed whether, even under conditions of unimodal sensory input, crossmodal neural circuits that have been shaped by previous associative learning become activated and underpin a performance benefit. We measured brain activity with functional magnetic resonance imaging before, while, and after participants learned to associate either sensory redundant stimuli, i.e. voices and faces, or arbitrary multimodal combinations, i.e. voices and written names, ring tones, and cell phones or brand names of these cell phones. After learning, participants were better at recognizing unimodal auditory voices that had been paired with faces than those paired with written names, and association of voices with faces resulted in an increased functional coupling between voice and face areas. No such effects were observed for ring tones that had been paired with cell phones or names. These findings demonstrate that brief exposure to ecologically valid and sensory redundant stimulus pairs, such as voices and faces, induces specific multisensory associations. Consistent with predictive coding theories, associative representations become thereafter available for unimodal perception and facilitate object recognition. These data suggest that for natural objects effective predictive signals can be generated across sensory systems and proceed by optimization of functional connectivity between specialized cortical sensory modules. PMID:17002519

Study and response time for the visual recognition of 'similarity' and identity

NASA Technical Reports Server (NTRS)

Derks, P. L.; Bauer, T. M.

1974-01-01

Four subjects compared successively presented pairs of line patterns for a match between any lines in the pattern (similarity) and for a match between all lines (identity). The encoding or study times for pattern recognition from immediate memory and the latency in responses to comparison stimuli were examined. Qualitative differences within and between subjects were most evident in study times.

Hypothesis Support Mechanism for Mid-Level Visual Pattern Recognition

NASA Technical Reports Server (NTRS)

Amador, Jose J (Inventor)

2007-01-01

A method of mid-level pattern recognition provides for a pose invariant Hough Transform by parametrizing pairs of points in a pattern with respect to at least two reference points, thereby providing a parameter table that is scale- or rotation-invariant. A corresponding inverse transform may be applied to test hypothesized matches in an image and a distance transform utilized to quantify the level of match.

Dynamical Binding Modes Determine Agonistic and Antagonistic Ligand Effects in the Prostate-Specific G-Protein Coupled Receptor (PSGR).

PubMed

Wolf, Steffen; Jovancevic, Nikolina; Gelis, Lian; Pietsch, Sebastian; Hatt, Hanns; Gerwert, Klaus

2017-11-22

We analysed the ligand-based activation mechanism of the prostate-specific G-protein coupled receptor (PSGR), which is an olfactory receptor that mediates cellular growth in prostate cancer cells. Furthermore, it is an olfactory receptor with a known chemically near identic antagonist/agonist pair, α- and β-ionone. Using a combined theoretical and experimental approach, we propose that this receptor is activated by a ligand-induced rearrangement of a protein-internal hydrogen bond network. Surprisingly, this rearrangement is not induced by interaction of the ligand with the network, but by dynamic van der Waals contacts of the ligand with the involved amino acid side chains, altering their conformations and intraprotein connectivity. Ligand recognition in this GPCR is therefore highly stereo selective, but seemingly lacks any ligand recognition via polar contacts. A putative olfactory receptor-based drug design scheme will have to take this unique mode of protein/ligand action into account.

Emotionally enhanced memory for negatively arousing words: storage or retrieval advantage?

PubMed

Nadarevic, Lena

2017-12-01

People typically remember emotionally negative words better than neutral words. Two experiments are reported that investigate whether emotionally enhanced memory (EEM) for negatively arousing words is based on a storage or retrieval advantage. Participants studied non-word-word pairs that either involved negatively arousing or neutral target words. Memory for these target words was tested by means of a recognition test and a cued-recall test. Data were analysed with a multinomial model that allows the disentanglement of storage and retrieval processes in the present recognition-then-cued-recall paradigm. In both experiments the multinomial analyses revealed no storage differences between negatively arousing and neutral words but a clear retrieval advantage for negatively arousing words in the cued-recall test. These findings suggest that EEM for negatively arousing words is driven by associative processes.

Face photo-sketch synthesis and recognition.

PubMed

Wang, Xiaogang; Tang, Xiaoou

2009-11-01

In this paper, we propose a novel face photo-sketch synthesis and recognition method using a multiscale Markov Random Fields (MRF) model. Our system has three components: 1) given a face photo, synthesizing a sketch drawing; 2) given a face sketch drawing, synthesizing a photo; and 3) searching for face photos in the database based on a query sketch drawn by an artist. It has useful applications for both digital entertainment and law enforcement. We assume that faces to be studied are in a frontal pose, with normal lighting and neutral expression, and have no occlusions. To synthesize sketch/photo images, the face region is divided into overlapping patches for learning. The size of the patches decides the scale of local face structures to be learned. From a training set which contains photo-sketch pairs, the joint photo-sketch model is learned at multiple scales using a multiscale MRF model. By transforming a face photo to a sketch (or transforming a sketch to a photo), the difference between photos and sketches is significantly reduced, thus allowing effective matching between the two in face sketch recognition. After the photo-sketch transformation, in principle, most of the proposed face photo recognition approaches can be applied to face sketch recognition in a straightforward way. Extensive experiments are conducted on a face sketch database including 606 faces, which can be downloaded from our Web site (http://mmlab.ie.cuhk.edu.hk/facesketch.html).

Speech variability effects on recognition accuracy associated with concurrent task performance by pilots

NASA Technical Reports Server (NTRS)

Simpson, C. A.

1985-01-01

In the present study of the responses of pairs of pilots to aircraft warning classification tasks using an isolated word, speaker-dependent speech recognition system, the induced stress was manipulated by means of different scoring procedures for the classification task and by the inclusion of a competitive manual control task. Both speech patterns and recognition accuracy were analyzed, and recognition errors were recorded by type for an isolated word speaker-dependent system and by an offline technique for a connected word speaker-dependent system. While errors increased with task loading for the isolated word system, there was no such effect for task loading in the case of the connected word system.

Signed reward prediction errors drive declarative learning

PubMed Central

Naert, Lien; Janssens, Clio; Talsma, Durk; Van Opstal, Filip; Verguts, Tom

2018-01-01

Reward prediction errors (RPEs) are thought to drive learning. This has been established in procedural learning (e.g., classical and operant conditioning). However, empirical evidence on whether RPEs drive declarative learning–a quintessentially human form of learning–remains surprisingly absent. We therefore coupled RPEs to the acquisition of Dutch-Swahili word pairs in a declarative learning paradigm. Signed RPEs (SRPEs; “better-than-expected” signals) during declarative learning improved recognition in a follow-up test, with increasingly positive RPEs leading to better recognition. In addition, classic declarative memory mechanisms such as time-on-task failed to explain recognition performance. The beneficial effect of SRPEs on recognition was subsequently affirmed in a replication study with visual stimuli. PMID:29293493

Signed reward prediction errors drive declarative learning.

PubMed

De Loof, Esther; Ergo, Kate; Naert, Lien; Janssens, Clio; Talsma, Durk; Van Opstal, Filip; Verguts, Tom

2018-01-01

Reward prediction errors (RPEs) are thought to drive learning. This has been established in procedural learning (e.g., classical and operant conditioning). However, empirical evidence on whether RPEs drive declarative learning-a quintessentially human form of learning-remains surprisingly absent. We therefore coupled RPEs to the acquisition of Dutch-Swahili word pairs in a declarative learning paradigm. Signed RPEs (SRPEs; "better-than-expected" signals) during declarative learning improved recognition in a follow-up test, with increasingly positive RPEs leading to better recognition. In addition, classic declarative memory mechanisms such as time-on-task failed to explain recognition performance. The beneficial effect of SRPEs on recognition was subsequently affirmed in a replication study with visual stimuli.

Support for an auto-associative model of spoken cued recall: evidence from fMRI.

PubMed

de Zubicaray, Greig; McMahon, Katie; Eastburn, Mathew; Pringle, Alan J; Lorenz, Lina; Humphreys, Michael S

2007-03-02

Cued recall and item recognition are considered the standard episodic memory retrieval tasks. However, only the neural correlates of the latter have been studied in detail with fMRI. Using an event-related fMRI experimental design that permits spoken responses, we tested hypotheses from an auto-associative model of cued recall and item recognition [Chappell, M., & Humphreys, M. S. (1994). An auto-associative neural network for sparse representations: Analysis and application to models of recognition and cued recall. Psychological Review, 101, 103-128]. In brief, the model assumes that cues elicit a network of phonological short term memory (STM) and semantic long term memory (LTM) representations distributed throughout the neocortex as patterns of sparse activations. This information is transferred to the hippocampus which converges upon the item closest to a stored pattern and outputs a response. Word pairs were learned from a study list, with one member of the pair serving as the cue at test. Unstudied words were also intermingled at test in order to provide an analogue of yes/no recognition tasks. Compared to incorrectly rejected studied items (misses) and correctly rejected (CR) unstudied items, correctly recalled items (hits) elicited increased responses in the left hippocampus and neocortical regions including the left inferior prefrontal cortex (LIPC), left mid lateral temporal cortex and inferior parietal cortex, consistent with predictions from the model. This network was very similar to that observed in yes/no recognition studies, supporting proposals that cued recall and item recognition involve common rather than separate mechanisms.

Structural analysis of online handwritten mathematical symbols based on support vector machines

NASA Astrophysics Data System (ADS)

Simistira, Foteini; Papavassiliou, Vassilis; Katsouros, Vassilis; Carayannis, George

2013-01-01

Mathematical expression recognition is still a very challenging task for the research community mainly because of the two-dimensional (2d) structure of mathematical expressions (MEs). In this paper, we present a novel approach for the structural analysis between two on-line handwritten mathematical symbols of a ME, based on spatial features of the symbols. We introduce six features to represent the spatial affinity of the symbols and compare two multi-class classification methods that employ support vector machines (SVMs): one based on the "one-against-one" technique and one based on the "one-against-all", in identifying the relation between a pair of symbols (i.e. subscript, numerator, etc). A dataset containing 1906 spatial relations derived from the Competition on Recognition of Online Handwritten Mathematical Expressions (CROHME) 2012 training dataset is constructed to evaluate the classifiers and compare them with the rule-based classifier of the ILSP-1 system participated in the contest. The experimental results give an overall mean error rate of 2.61% for the "one-against-one" SVM approach, 6.57% for the "one-against-all" SVM technique and 12.31% error rate for the ILSP-1 classifier.

A language-familiarity effect for speaker discrimination without comprehension.

PubMed

Fleming, David; Giordano, Bruno L; Caldara, Roberto; Belin, Pascal

2014-09-23

The influence of language familiarity upon speaker identification is well established, to such an extent that it has been argued that "Human voice recognition depends on language ability" [Perrachione TK, Del Tufo SN, Gabrieli JDE (2011) Science 333(6042):595]. However, 7-mo-old infants discriminate speakers of their mother tongue better than they do foreign speakers [Johnson EK, Westrek E, Nazzi T, Cutler A (2011) Dev Sci 14(5):1002-1011] despite their limited speech comprehension abilities, suggesting that speaker discrimination may rely on familiarity with the sound structure of one's native language rather than the ability to comprehend speech. To test this hypothesis, we asked Chinese and English adult participants to rate speaker dissimilarity in pairs of sentences in English or Mandarin that were first time-reversed to render them unintelligible. Even in these conditions a language-familiarity effect was observed: Both Chinese and English listeners rated pairs of native-language speakers as more dissimilar than foreign-language speakers, despite their inability to understand the material. Our data indicate that the language familiarity effect is not based on comprehension but rather on familiarity with the phonology of one's native language. This effect may stem from a mechanism analogous to the "other-race" effect in face recognition.

Eyes wide open: Pupil size as a proxy for inhibition in the masked-priming paradigm.

PubMed

Geller, Jason; Still, Mary L; Morris, Alison L

2016-05-01

A core assumption underlying competitive-network models of word recognition is that in order for a word to be recognized, the representations of competing orthographically similar words must be inhibited. This inhibitory mechanism is revealed in the masked-priming lexical-decision task (LDT) when responses to orthographically similar word prime-target pairs are slower than orthographically different word prime-target pairs (i.e., inhibitory priming). In English, however, behavioral evidence for inhibitory priming has been mixed. In the present study, we utilized a physiological correlate of cognitive effort never before used in the masked-priming LDT, pupil size, to replicate and extend behavioral demonstrations of inhibitory effects (i.e., Nakayama, Sears, & Lupker, Journal of Experimental Psychology: Human Perception and Performance, 34, 1236-1260, 2008, Exp. 1). Previous research had suggested that pupil size is a reliable indicator of cognitive load, making it a promising index of lexical inhibition. Our pupillometric data replicated and extended previous behavioral findings, in that inhibition was obtained for orthographically similar word prime-target pairs. However, our response time data provided only a partial replication of Nakayama et al. Journal of Experimental Psychology: Human Perception and Performance, 34, 1236-1260, 2008. These results provide converging lines of evidence that inhibition operates in word recognition and that pupillometry is a useful addition to word recognition researchers' toolbox.

A fluorometric assay for alkaline phosphatase activity based on β-cyclodextrin-modified carbon quantum dots through host-guest recognition.

PubMed

Tang, Cong; Qian, Zhaosheng; Huang, Yuanyuan; Xu, Jiamin; Ao, Hang; Zhao, Meizhi; Zhou, Jin; Chen, Jianrong; Feng, Hui

2016-09-15

A convenient, reliable and highly sensitive assay for alkaline phosphatase (ALP) activity in the real-time manner is developed based on β-cyclodextrin-modified carbon quantum dots (β-CD-CQDs) nanoprobe through specific host-guest recognition. Carbon quantum dots were first functionalized with 3-aminophenyl boronic acid to produce boronic acid-functionalized CQDs, and then further modified with hydropropyl β-cyclodextrins (β-CD) through B-O bonds to form β-CD-CQDs nanoprobe. p-Nitrophenol phosphate disodium salt is used as the substrate of ALP, and can hydrolyze to p-nitrophenol under the catalysis of ALP. The resulting p-nitrophenol can enter the cavity of β-CD moiety in the nanoprobe due to their specific host-guest recognition, where photoinduced electron transfer process between p-nitrophenol and CQDs takes place to efficiently quench the fluorescence of the probe. The correlation between quenched fluorescence and ALP level can be used to establish quantitative evaluation of ALP activity in a broad range from 3.4 to 100.0U/L with the detection limit of 0.9U/L. This assay shows a high sensitivity to ALP even in the presence of a very high concentration of glucose. This study demonstrates a good electron donor/acceptor pair, which can be used to design general detection strategy through PET process, and also broadens the application of host-guest recognition for enzymes detection in clinical practice. Copyright © 2016 Elsevier B.V. All rights reserved.

Semantic similarity between old and new items produces false alarms in recognition memory.

PubMed

Montefinese, Maria; Zannino, Gian Daniele; Ambrosini, Ettore

2015-09-01

In everyday life, human beings can report memories of past events that did not occur or that occurred differently from the way they remember them because memory is an imperfect process of reconstruction and is prone to distortion and errors. In this recognition study using word stimuli, we investigated whether a specific operationalization of semantic similarity among concepts can modulate false memories while controlling for the possible effect of associative strength and word co-occurrence in an old-new recognition task. The semantic similarity value of each new concept was calculated as the mean cosine similarity between pairs of vectors representing that new concept and each old concept belonging to the same semantic category. Results showed that, compared with (new) low-similarity concepts, (new) high-similarity concepts had significantly higher probability of being falsely recognized as old, even after partialling out the effect of confounding variables, including associative relatedness and lexical co-occurrence. This finding supports the feature-based view of semantic memory, suggesting that meaning overlap and sharing of semantic features (which are greater when more similar semantic concepts are being processed) have an influence on recognition performance, resulting in more false alarms for new high-similarity concepts. We propose that the associative strength and word co-occurrence among concepts are not sufficient to explain illusory memories but is important to take into account also the effects of feature-based semantic relations, and, in particular, the semantic similarity among concepts.

Efficient iris recognition by characterizing key local variations.

PubMed

Ma, Li; Tan, Tieniu; Wang, Yunhong; Zhang, Dexin

2004-06-01

Unlike other biometrics such as fingerprints and face, the distinct aspect of iris comes from randomly distributed features. This leads to its high reliability for personal identification, and at the same time, the difficulty in effectively representing such details in an image. This paper describes an efficient algorithm for iris recognition by characterizing key local variations. The basic idea is that local sharp variation points, denoting the appearing or vanishing of an important image structure, are utilized to represent the characteristics of the iris. The whole procedure of feature extraction includes two steps: 1) a set of one-dimensional intensity signals is constructed to effectively characterize the most important information of the original two-dimensional image; 2) using a particular class of wavelets, a position sequence of local sharp variation points in such signals is recorded as features. We also present a fast matching scheme based on exclusive OR operation to compute the similarity between a pair of position sequences. Experimental results on 2255 iris images show that the performance of the proposed method is encouraging and comparable to the best iris recognition algorithm found in the current literature.

Solid-phase molecular recognition of cytosine based on proton-transfer reaction. Part II. supramolecular architecture in the cocrystals of cytosine and its 5-Fluoroderivative with 5-Nitrouracil

PubMed Central

2011-01-01

Background Cytosine is a biologically important compound owing to its natural occurrence as a component of nucleic acids. Cytosine plays a crucial role in DNA/RNA base pairing, through several hydrogen-bonding patterns, and controls the essential features of life as it is involved in genetic codon of 17 amino acids. The molecular recognition among cytosines, and the molecular heterosynthons of molecular salts fabricated through proton-transfer reactions, might be used to investigate the theoretical sites of cytosine-specific DNA-binding proteins and the design for molecular imprint. Results Reaction of cytosine (Cyt) and 5-fluorocytosine (5Fcyt) with 5-nitrouracil (Nit) in aqueous solution yielded two new products, which have been characterized by single-crystal X-ray diffraction. The products include a dihydrated molecular salt (CytNit) having both ionic and neutral hydrogen-bonded species, and a dihydrated cocrystal of neutral species (5FcytNit). In CytNit a protonated and an unprotonated cytosine form a triply hydrogen-bonded aggregate in a self-recognition ion-pair complex, and this dimer is then hydrogen bonded to one neutral and one anionic 5-nitrouracil molecule. In 5FcytNit the two neutral nucleobase derivatives are hydrogen bonded in pairs. In both structures conventional N-H...O, O-H...O, N-H+...N and N-H...N- intermolecular interactions are most significant in the structural assembly. Conclusion The supramolecular structure of the molecular adducts formed by cytosine and 5-fluorocytosine with 5-nitrouracil, CytNit and 5FcytNit, respectively, have been investigated in detail. CytNit and 5FcytNit exhibit widely differing hydrogen-bonding patterns, though both possess layered structures. The crystal structures of CytNit (Dpka = -0.7, molecular salt) and 5FcytNit (Dpka = -2.0, cocrystal) confirm that, at the present level of knowledge about the nature of proton-transfer process, there is not a strict correlation between the Dpka values and the proton transfer, in that the acid/base pka strength is not a definite guide to predict the location of H atoms in the solid state. Eventually, the absence in 5FcytNit of hydrogen bonds involving fluorine is in agreement with findings that covalently bound fluorine hardly ever acts as acceptor for available Brønsted acidic sites in the presence of competing heteroatom acceptors. PMID:21888640

The Effect of Rules and Discovery in the Retention and Retrieval of Braille Inkprint Letter Pairs.

ERIC Educational Resources Information Center

Nagengast, Daniel L.; And Others

The effects of rule knowledge were investigated using Braille inkprint pairs. Both recognition and recall were studied in three groups of subjects: rule knowledge, rule discovery, and no rule. Two hypotheses were tested: (1) that the group exposed to the rule would score better than would a discovery group and a control group; and (2) that all…

Biochemical behavior of N-oxidized cytosine and adenine bases in DNA polymerase-mediated primer extension reactions

PubMed Central

Tsunoda, Hirosuke; Kudo, Tomomi; Masaki, Yoshiaki; Ohkubo, Akihiro; Seio, Kohji; Sekine, Mitsuo

2011-01-01

To clarify the biochemical behavior of 2′-deoxyribonucleoside 5′-triphosphates and oligodeoxyribonucleotides (ODNs) containing cytosine N-oxide (Co) and adenine N-oxide (Ao), we examined their base recognition ability in DNA duplex formation using melting temperature (Tm) experiments and their substrate specificity in DNA polymerase-mediated replication. As the result, it was found that the Tm values of modified DNA–DNA duplexes incorporating 2′-deoxyribonucleoside N-oxide derivatives significantly decreased compared with those of the unmodified duplexes. However, single insertion reactions by DNA polymerases of Klenow fragment (KF) (exo−) and Vent (exo−) suggested that Co and Ao selectively recognized G and T, respectively. Meanwhile, the kinetic study showed that the incorporation efficiencies of the modified bases were lower than those of natural bases. Ab initio calculations suggest that these modified bases can form the stable base pairs with the original complementary bases. These results indicate that the modified bases usually recognize the original bases as partners for base pairing, except for misrecognition of dATP by the action of KF (exo−) toward Ao on the template, and the primers could be extended on the template DNA. When they misrecognized wrong bases, the chain could not be elongated so that the modified base served as the chain terminator. PMID:21300642

Biochemical behavior of N-oxidized cytosine and adenine bases in DNA polymerase-mediated primer extension reactions.

PubMed

Tsunoda, Hirosuke; Kudo, Tomomi; Masaki, Yoshiaki; Ohkubo, Akihiro; Seio, Kohji; Sekine, Mitsuo

2011-04-01

To clarify the biochemical behavior of 2'-deoxyribonucleoside 5'-triphosphates and oligodeoxyribonucleotides (ODNs) containing cytosine N-oxide (C(o)) and adenine N-oxide (A(o)), we examined their base recognition ability in DNA duplex formation using melting temperature (T(m)) experiments and their substrate specificity in DNA polymerase-mediated replication. As the result, it was found that the T(m) values of modified DNA-DNA duplexes incorporating 2'-deoxyribonucleoside N-oxide derivatives significantly decreased compared with those of the unmodified duplexes. However, single insertion reactions by DNA polymerases of Klenow fragment (KF) (exo(-)) and Vent (exo(-)) suggested that C(o) and A(o) selectively recognized G and T, respectively. Meanwhile, the kinetic study showed that the incorporation efficiencies of the modified bases were lower than those of natural bases. Ab initio calculations suggest that these modified bases can form the stable base pairs with the original complementary bases. These results indicate that the modified bases usually recognize the original bases as partners for base pairing, except for misrecognition of dATP by the action of KF (exo(-)) toward A(o) on the template, and the primers could be extended on the template DNA. When they misrecognized wrong bases, the chain could not be elongated so that the modified base served as the chain terminator.

The Effect of High Versus Low Teacher Affect and Passive Versus Active Student Activity During Music Listening on Preschool Children's Attention, Piece Preference, Time Spent Listening, and Piece Recognition.

ERIC Educational Resources Information Center

Sims, Wendy L.

1986-01-01

Small-group listening lessons and subsequent individual posttests were used to judge 94 three- through five-year-old subjects' attention, paired-comparison piece preference, time spent listening, and piece recognition. Research procedures included a modified multiple baseline design and split-screen video taping of instructional sessions.…

A conserved loop-wedge motif moderates reaction site search and recognition by FEN1.

PubMed

Thompson, Mark J; Gotham, Victoria J B; Ciani, Barbara; Grasby, Jane A

2018-06-07

DNA replication and repair frequently involve intermediate two-way junction structures with overhangs, or flaps, that must be promptly removed; a task performed by the essential enzyme flap endonuclease 1 (FEN1). We demonstrate a functional relationship between two intrinsically disordered regions of the FEN1 protein, which recognize opposing sides of the junction and order in response to the requisite substrate. Our results inform a model in which short-range translocation of FEN1 on DNA facilitates search for the annealed 3'-terminus of a primer strand, which is recognized by breaking the terminal base pair to generate a substrate with a single nucleotide 3'-flap. This recognition event allosterically signals hydrolytic removal of the 5'-flap through reaction in the opposing junction duplex, by controlling access of the scissile phosphate diester to the active site. The recognition process relies on a highly-conserved 'wedge' residue located on a mobile loop that orders to bind the newly-unpaired base. The unanticipated 'loop-wedge' mechanism exerts control over substrate selection, rate of reaction and reaction site precision, and shares features with other enzymes that recognize irregular DNA structures. These new findings reveal how FEN1 precisely couples 3'-flap verification to function.

An SRY mutation causing human sex reversal resolves a general mechanism of structure-specific DNA recognition: application to the four-way DNA junction.

PubMed

Peters, R; King, C Y; Ukiyama, E; Falsafi, S; Donahoe, P K; Weiss, M A

1995-04-11

SRY, a genetic "master switch" for male development in mammals, exhibits two biochemical activities: sequence-specific recognition of duplex DNA and sequence-independent binding to the sharp angles of four-way DNA junctions. Here, we distinguish between these activities by analysis of a mutant SRY associated with human sex reversal (46, XY female with pure gonadal dysgenesis). The substitution (168T in human SRY) alters a nonpolar side chain in the minor-groove DNA recognition alpha-helix of the HMG box [Haqq, C.M., King, C.-Y., Ukiyama, E., Haqq, T.N., Falsalfi, S., Donahoe, P.K., & Weiss, M.A. (1994) Science 266, 1494-1500]. The native (but not mutant) side chain inserts between specific base pairs in duplex DNA, interrupting base stacking at a site of induced DNA bending. Isotope-aided 1H-NMR spectroscopy demonstrates that analogous side-chain insertion occurs on binding of SRY to a four-way junction, establishing a shared mechanism of sequence- and structure-specific DNA binding. Although the mutant DNA-binding domain exhibits > 50-fold reduction in sequence-specific DNA recognition, near wild-type affinity for four-way junctions is retained. Our results (i) identify a shared SRY-DNA contact at a site of either induced or intrinsic DNA bending, (ii) demonstrate that this contact is not required to bind an intrinsically bent DNA target, and (iii) rationalize patterns of sequence conservation or diversity among HMG boxes. Clinical association of the I68T mutation with human sex reversal supports the hypothesis that specific DNA recognition by SRY is required for male sex determination.

Dual-process models of associative recognition in young and older adults: evidence from receiver operating characteristics.

PubMed

Healy, Michael R; Light, Leah L; Chung, Christie

2005-07-01

In 3 experiments, young and older adults studied lists of unrelated word pairs and were given confidence-rated item and associative recognition tests. Several different models of recognition were fit to the confidence-rating data using techniques described by S. Macho (2002, 2004). Concordant with previous findings, item recognition data were best fit by an unequal-variance signal detection theory model for both young and older adults. For both age groups, associative recognition performance was best explained by models incorporating both recollection and familiarity components. Examination of parameter estimates supported the conclusion that recollection is reduced in old age, but inferences about age differences in familiarity were highly model dependent. Implications for dual-process models of memory in old age are discussed. ((c) 2005 APA, all rights reserved).

The limited use of the fluency heuristic: Converging evidence across different procedures.

PubMed

Pohl, Rüdiger F; Erdfelder, Edgar; Michalkiewicz, Martha; Castela, Marta; Hilbig, Benjamin E

2016-10-01

In paired comparisons based on which of two objects has the larger criterion value, decision makers could use the subjectively experienced difference in retrieval fluency of the objects as a cue. According to the fluency heuristic (FH) theory, decision makers use fluency-as indexed by recognition speed-as the only cue for pairs of recognized objects, and infer that the object retrieved more speedily has the larger criterion value (ignoring all other cues and information). Model-based analyses, however, have previously revealed that only a small portion of such inferences are indeed based on fluency alone. In the majority of cases, other information enters the decision process. However, due to the specific experimental procedures, the estimates of FH use are potentially biased: Some procedures may have led to an overestimated and others to an underestimated, or even to actually reduced, FH use. In the present article, we discuss and test the impacts of such procedural variations by reanalyzing 21 data sets. The results show noteworthy consistency across the procedural variations revealing low FH use. We discuss potential explanations and implications of this finding.

High-accuracy and robust face recognition system based on optical parallel correlator using a temporal image sequence

NASA Astrophysics Data System (ADS)

Watanabe, Eriko; Ishikawa, Mami; Ohta, Maiko; Kodate, Kashiko

2005-09-01

Face recognition is used in a wide range of security systems, such as monitoring credit card use, searching for individuals with street cameras via Internet and maintaining immigration control. There are still many technical subjects under study. For instance, the number of images that can be stored is limited under the current system, and the rate of recognition must be improved to account for photo shots taken at different angles under various conditions. We implemented a fully automatic Fast Face Recognition Optical Correlator (FARCO) system by using a 1000 frame/s optical parallel correlator designed and assembled by us. Operational speed for the 1: N (i.e. matching a pair of images among N, where N refers to the number of images in the database) identification experiment (4000 face images) amounts to less than 1.5 seconds, including the pre/post processing. From trial 1: N identification experiments using FARCO, we acquired low error rates of 2.6% False Reject Rate and 1.3% False Accept Rate. By making the most of the high-speed data-processing capability of this system, much more robustness can be achieved for various recognition conditions when large-category data are registered for a single person. We propose a face recognition algorithm for the FARCO while employing a temporal image sequence of moving images. Applying this algorithm to a natural posture, a two times higher recognition rate scored compared with our conventional system. The system has high potential for future use in a variety of purposes such as search for criminal suspects by use of street and airport video cameras, registration of babies at hospitals or handling of an immeasurable number of images in a database.

Priming in Episodic and Semantic Memory.

ERIC Educational Resources Information Center

McKoon, Gail; Ratcliff, Roger

1979-01-01

Four experiments examined priming between newly learned paired associates through two procedures, lexical decision and item recognition. Results argue against a functional separation of the semantic and episodic memory systems. (Author/AM)

Recognition of platinum-DNA adducts by HMGB1a.

PubMed

Ramachandran, Srinivas; Temple, Brenda; Alexandrova, Anastassia N; Chaney, Stephen G; Dokholyan, Nikolay V

2012-09-25

Cisplatin (CP) and oxaliplatin (OX), platinum-based drugs used widely in chemotherapy, form adducts on intrastrand guanines (5'GG) in genomic DNA. DNA damage recognition proteins, transcription factors, mismatch repair proteins, and DNA polymerases discriminate between CP- and OX-GG DNA adducts, which could partly account for differences in the efficacy, toxicity, and mutagenicity of CP and OX. In addition, differential recognition of CP- and OX-GG adducts is highly dependent on the sequence context of the Pt-GG adduct. In particular, DNA binding protein domain HMGB1a binds to CP-GG DNA adducts with up to 53-fold greater affinity than to OX-GG adducts in the TGGA sequence context but shows much smaller differences in binding in the AGGC or TGGT sequence contexts. Here, simulations of the HMGB1a-Pt-DNA complex in the three sequence contexts revealed a higher number of interface contacts for the CP-DNA complex in the TGGA sequence context than in the OX-DNA complex. However, the number of interface contacts was similar in the TGGT and AGGC sequence contexts. The higher number of interface contacts in the CP-TGGA sequence context corresponded to a larger roll of the Pt-GG base pair step. Furthermore, geometric analysis of stacking of phenylalanine 37 in HMGB1a (Phe37) with the platinated guanines revealed more favorable stacking modes correlated with a larger roll of the Pt-GG base pair step in the TGGA sequence context. These data are consistent with our previous molecular dynamics simulations showing that the CP-TGGA complex was able to sample larger roll angles than the OX-TGGA complex or either CP- or OX-DNA complexes in the AGGC or TGGT sequences. We infer that the high binding affinity of HMGB1a for CP-TGGA is due to the greater flexibility of CP-TGGA compared to OX-TGGA and other Pt-DNA adducts. This increased flexibility is reflected in the ability of CP-TGGA to sample larger roll angles, which allows for a higher number of interface contacts between the Pt-DNA adduct and HMGB1a.

Making the Bend: DNA Tertiary Structure and Protein-DNA Interactions

PubMed Central

Harteis, Sabrina; Schneider, Sabine

2014-01-01

DNA structure functions as an overlapping code to the DNA sequence. Rapid progress in understanding the role of DNA structure in gene regulation, DNA damage recognition and genome stability has been made. The three dimensional structure of both proteins and DNA plays a crucial role for their specific interaction, and proteins can recognise the chemical signature of DNA sequence (“base readout”) as well as the intrinsic DNA structure (“shape recognition”). These recognition mechanisms do not exist in isolation but, depending on the individual interaction partners, are combined to various extents. Driving force for the interaction between protein and DNA remain the unique thermodynamics of each individual DNA-protein pair. In this review we focus on the structures and conformations adopted by DNA, both influenced by and influencing the specific interaction with the corresponding protein binding partner, as well as their underlying thermodynamics. PMID:25026169

Cooperativity and complexity in the binding of anions and cations to a tetratopic ion-pair host.

PubMed

Howe, Ethan N W; Bhadbhade, Mohan; Thordarson, Pall

2014-05-21

Cooperative interactions play a very important role in both natural and synthetic supramolecular systems. We report here on the cooperative binding properties of a tetratopic ion-pair host 1. This host combines two isophthalamide anion recognition sites with two unusual "half-crown/two carbonyl" cation recognition sites as revealed by the combination of single-crystal X-ray analysis of the free host and the 1:2 host:calcium cation complex, together with two-dimensional NMR and computational studies. By systematically comparing all of the binding data to several possible binding models and focusing on four different variants of the 1:2 binding model, it was in most cases possible to quantify these complex cooperative interactions. The data showed strong negative cooperativity (α = 0.01-0.05) of 1 toward chloride and acetate anions, while for cations the results were more variable. Interestingly, in the competitive (CDCl3/CD3OD (9:1, v/v)) solvent, the addition of calcium cations to the tetratopic ion-pair host 1 allosterically switched "on" chloride binding that is otherwise not present in this solvent system. The insight into the complexity of cooperative interactions revealed in this study of the tetratopic ion-pair host 1 can be used to design better cooperative supramolecular systems for information transfer and catalysis.

An overall decline both in recollection and familiarity in healthy aging.

PubMed

Pitarque, Alfonso; Sales, Alicia; Meléndez, Juan C; Mayordomo, Teresa; Satorres, Encar

2015-01-01

In the area of recognition memory, the experimental data have been inconsistent about whether or not familiarity declines in healthy aging. A recent meta-analysis concluded that familiarity is impaired when estimated with the remember-know procedure, but not with the process-dissociation procedure. We present an associative recognition experiment with remember-know judgments that allow us to estimate both recollection and familiarity using both procedures in the same task and with the same participants (a sample of healthy older people and another sample of young people). Moreover, we performed a within-subjects manipulation of the type of materials (pairs of words or pairs of pictures), and the repetition or not of the pairs during the study phase. The results show that familiarity, estimated using both estimation procedures, declines significantly with age, although the effect size obtained with the process-dissociation procedure is significantly smaller than the one obtained with the remember-know procedure. Our results show that aging is associated with significant decreases both in recollection and, to a lesser extent, familiarity.

Repetition increases false recollection in older people.

PubMed

Pitarque, Alfonso; Sales, Alicia; Meléndez, Juan Carlos; Algarabel, Salvador

2015-02-01

Aging is accompanied by an increase in false alarms on recognition tasks, and these false alarms increase with repetition in older people (but not in young people). Traditionally, this increase was thought to be due to a greater use of familiarity in older people, but it was recently pointed out that false alarms also have a clear recollection component in these people. The main objective of our study is to analyze whether the expected increase in the rate of false alarms in older people due to stimulus repetition is produced by an inadequate use of familiarity, recollection, or both processes. To do so, we carried out an associative recognition experiment using pairs of words and pairs of images (faces associated with everyday contexts), in which we analyzed whether the repetition of some of the pairs increases the rate of false alarms in older people (compared to what was found in a sample of young people), and whether this increase is due to familiarity or recollection (using a remember-know paradigm). Our results show that the increase in false alarms in older people due to repetition is produced by false recollection, calling into question both dual and single-process models of recognition. Also, older people falsely recollect details of never studied stimuli, a clear case of perceptual illusions. These results are better explained in terms of source-monitoring errors, mediated by people's retrieval expectations. © 2014 Scandinavian Psychological Associations and John Wiley & Sons Ltd.

Can we beat the biotin-avidin pair?: cucurbit[7]uril-based ultrahigh affinity host-guest complexes and their applications.

PubMed

Shetty, Dinesh; Khedkar, Jayshree K; Park, Kyeng Min; Kim, Kimoon

2015-12-07

The design of synthetic, monovalent host-guest molecular recognition pairs is still challenging and of particular interest to inquire into the limits of the affinity that can be achieved with designed systems. In this regard, cucurbit[7]uril (CB[7]), an important member of the host family cucurbit[n]uril (CB[n], n = 5-8, 10, 14), has attracted much attention because of its ability to form ultra-stable complexes with multiple guests. The strong hydrophobic effect between the host cavity and guests, ion-dipole and dipole-dipole interactions of guests with CB portals helps in cooperative and multiple noncovalent interactions that are essential for realizing such strong complexations. These highly selective, strong yet dynamic interactions can be exploited in many applications including affinity chromatography, biomolecule immobilization, protein isolation, biological catalysis, and sensor technologies. In this review, we summarize the progress in the development of high affinity guests for CB[7], factors affecting the stability of complexes, theoretical insights, and the utility of these high affinity pairs in different challenging applications.

Ribosome hijacking: a role for small protein B during trans-translation

PubMed Central

Nonin-Lecomte, Sylvie; Germain-Amiot, Noella; Gillet, Reynald; Hallier, Marc; Ponchon, Luc; Dardel, Frédéric; Felden, Brice

2009-01-01

Tight recognition of codon–anticodon pairings by the ribosome ensures the accuracy and fidelity of protein synthesis. In eubacteria, translational surveillance and ribosome rescue are performed by the ‘tmRNA–SmpB' system (transfer messenger RNA–small protein B). Remarkably, entry and accommodation of aminoacylated-tmRNA into stalled ribosomes occur without a codon–anticodon interaction but in the presence of SmpB. Here, we show that within a stalled ribosome, SmpB interacts with the three universally conserved bases G530, A1492 and A1493 that form the 30S subunit decoding centre, in which canonical codon–anticodon pairing occurs. The footprints at positions A1492 and A1493 of a small decoding centre, as well as on a set of conserved SmpB amino acids, were identified by nuclear magnetic resonance. Mutants at these residues display the same growth defects as for ΔsmpB strains. The SmpB protein has functional and structural similarities with initiation factor 1, and is proposed to be a functional mimic of the pairing between a codon and an anticodon. PMID:19132006

Ribosome hijacking: a role for small protein B during trans-translation.

PubMed

Nonin-Lecomte, Sylvie; Germain-Amiot, Noella; Gillet, Reynald; Hallier, Marc; Ponchon, Luc; Dardel, Frédéric; Felden, Brice

2009-02-01

Tight recognition of codon-anticodon pairings by the ribosome ensures the accuracy and fidelity of protein synthesis. In eubacteria, translational surveillance and ribosome rescue are performed by the 'tmRNA-SmpB' system (transfer messenger RNA-small protein B). Remarkably, entry and accommodation of aminoacylated-tmRNA into stalled ribosomes occur without a codon-anticodon interaction but in the presence of SmpB. Here, we show that within a stalled ribosome, SmpB interacts with the three universally conserved bases G530, A1492 and A1493 that form the 30S subunit decoding centre, in which canonical codon-anticodon pairing occurs. The footprints at positions A1492 and A1493 of a small decoding centre, as well as on a set of conserved SmpB amino acids, were identified by nuclear magnetic resonance. Mutants at these residues display the same growth defects as for DeltasmpB strains. The SmpB protein has functional and structural similarities with initiation factor 1, and is proposed to be a functional mimic of the pairing between a codon and an anticodon.

The neural correlates of competition during memory retrieval are modulated by attention to the cues.

PubMed

Danker, Jared F; Fincham, Jon M; Anderson, John R

2011-07-01

As people learn more facts about a concept, those facts become more difficult to remember. This is called the fan effect, where fan refers to the number of facts known about a concept. Increasing fan has been shown to decrease accuracy and increase response time and left ventrolateral prefrontal cortex (VLPFC) activity during retrieval. In this study, participants learned 36 arbitrary person-location pairings and made recognition decisions while we recorded brain activity using fMRI. We separately manipulated the fan of each person and location, as well as the training procedure with which each pair was studied. In the person focus condition, participants studied pairs with a picture of the person's face and used the person as a retrieval cue during training. In the location focus condition, participants studied pairs with a picture of the location and used the location as a retrieval cue during training. We found that the fan of the focused cue had a greater effect on response time, accuracy, and left VLPFC activity during retrieval than the fan of the unfocused cue. We also found that the parahippocampal place area (PPA) was more active during the recognition of pairs studied in the location focus condition, but not when the fan of the location was high. Overall, we found opposite effects of fan on VLPFC and PPA that were modulated by cue focus. Copyright © 2011 Elsevier Ltd. All rights reserved.

A selection of giant radio sources from NVSS

DOE PAGES

Proctor, D. D.

2016-06-01

Results of the application of pattern-recognition techniques to the problem of identifying giant radio sources (GRSs) from the data in the NVSS catalog are presented, and issues affecting the process are explored. Decision-tree pattern-recognition software was applied to training-set source pairs developed from known NVSS large-angular-size radio galaxies. The full training set consisted of 51,195 source pairs, 48 of which were known GRSs for which each lobe was primarily represented by a single catalog component. The source pairs had a maximum separation ofmore » $$20^{\\prime} $$ and a minimum component area of 1.87 square arcmin at the 1.4 mJy level. The importance of comparing the resulting probability distributions of the training and application sets for cases of unknown class ratio is demonstrated. The probability of correctly ranking a randomly selected (GRS, non-GRS) pair from the best of the tested classifiers was determined to be 97.8 ± 1.5%. The best classifiers were applied to the over 870,000 candidate pairs from the entire catalog. Images of higher-ranked sources were visually screened, and a table of over 1600 candidates, including morphological annotation, is presented. These systems include doubles and triples, wide-angle tail and narrow-angle tail, S- or Z-shaped systems, and core-jets and resolved cores. In conclusion, while some resolved-lobe systems are recovered with this technique, generally it is expected that such systems would require a different approach.« less

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

NASA Technical Reports Server (NTRS)

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

2003-01-01

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

Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs.

PubMed

Auch, Alexander F; Klenk, Hans-Peter; Göker, Markus

2010-01-28

DNA-DNA hybridization (DDH) is a widely applied wet-lab technique to obtain an estimate of the overall similarity between the genomes of two organisms. To base the species concept for prokaryotes ultimately on DDH was chosen by microbiologists as a pragmatic approach for deciding about the recognition of novel species, but also allowed a relatively high degree of standardization compared to other areas of taxonomy. However, DDH is tedious and error-prone and first and foremost cannot be used to incrementally establish a comparative database. Recent studies have shown that in-silico methods for the comparison of genome sequences can be used to replace DDH. Considering the ongoing rapid technological progress of sequencing methods, genome-based prokaryote taxonomy is coming into reach. However, calculating distances between genomes is dependent on multiple choices for software and program settings. We here provide an overview over the modifications that can be applied to distance methods based in high-scoring segment pairs (HSPs) or maximally unique matches (MUMs) and that need to be documented. General recommendations on determining HSPs using BLAST or other algorithms are also provided. As a reference implementation, we introduce the GGDC web server (http://ggdc.gbdp.org).

Nucleic acid-based nanoengineering: novel structures for biomedical applications

PubMed Central

Li, Hanying; LaBean, Thomas H.; Leong, Kam W.

2011-01-01

Nanoengineering exploits the interactions of materials at the nanometre scale to create functional nanostructures. It relies on the precise organization of nanomaterials to achieve unique functionality. There are no interactions more elegant than those governing nucleic acids via Watson–Crick base-pairing rules. The infinite combinations of DNA/RNA base pairs and their remarkable molecular recognition capability can give rise to interesting nanostructures that are only limited by our imagination. Over the past years, creative assembly of nucleic acids has fashioned a plethora of two-dimensional and three-dimensional nanostructures with precisely controlled size, shape and spatial functionalization. These nanostructures have been precisely patterned with molecules, proteins and gold nanoparticles for the observation of chemical reactions at the single molecule level, activation of enzymatic cascade and novel modality of photonic detection, respectively. Recently, they have also been engineered to encapsulate and release bioactive agents in a stimulus-responsive manner for therapeutic applications. The future of nucleic acid-based nanoengineering is bright and exciting. In this review, we will discuss the strategies to control the assembly of nucleic acids and highlight the recent efforts to build functional nucleic acid nanodevices for nanomedicine. PMID:23050076

Orchestration of Molecular Information through Higher Order Chemical Recognition

NASA Astrophysics Data System (ADS)

Frezza, Brian M.

Broadly defined, higher order chemical recognition is the process whereby discrete chemical building blocks capable of specifically binding to cognate moieties are covalently linked into oligomeric chains. These chains, or sequences, are then able to recognize and bind to their cognate sequences with a high degree of cooperativity. Principally speaking, DNA and RNA are the most readily obtained examples of this chemical phenomenon, and function via Watson-Crick cognate pairing: guanine pairs with cytosine and adenine with thymine (DNA) or uracil (RNA), in an anti-parallel manner. While the theoretical principles, techniques, and equations derived herein apply generally to any higher-order chemical recognition system, in practice we utilize DNA oligomers as a model-building material to experimentally investigate and validate our hypotheses. Historically, general purpose information processing has been a task limited to semiconductor electronics. Molecular computing on the other hand has been limited to ad hoc approaches designed to solve highly specific and unique computation problems, often involving components or techniques that cannot be applied generally in a manner suitable for precise and predictable engineering. Herein, we provide a fundamental framework for harnessing high-order recognition in a modular and programmable fashion to synthesize molecular information process networks of arbitrary construction and complexity. This document provides a solid foundation for routinely embedding computational capability into chemical and biological systems where semiconductor electronics are unsuitable for practical application.

The influence of variations in eating disorder-related symptoms on processing of emotional faces in a non-clinical female sample: An eye-tracking study.

PubMed

Sharpe, Emma; Wallis, Deborah J; Ridout, Nathan

2016-06-30

This study aimed to: (i) determine if the attention bias towards angry faces reported in eating disorders generalises to a non-clinical sample varying in eating disorder-related symptoms; (ii) examine if the bias occurs during initial orientation or later strategic processing; and (iii) confirm previous findings of impaired facial emotion recognition in non-clinical disordered eating. Fifty-two females viewed a series of face-pairs (happy or angry paired with neutral) whilst their attentional deployment was continuously monitored using an eye-tracker. They subsequently identified the emotion portrayed in a separate series of faces. The highest (n=18) and lowest scorers (n=17) on the Eating Disorders Inventory (EDI) were compared on the attention and facial emotion recognition tasks. Those with relatively high scores exhibited impaired facial emotion recognition, confirming previous findings in similar non-clinical samples. They also displayed biased attention away from emotional faces during later strategic processing, which is consistent with previously observed impairments in clinical samples. These differences were related to drive-for-thinness. Although we found no evidence of a bias towards angry faces, it is plausible that the observed impairments in emotion recognition and avoidance of emotional faces could disrupt social functioning and act as a risk factor for the development of eating disorders. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Second Language Idiom Learning in a Paired-Associate Paradigm: Effects of Direction of Learning, Direction of Testing, Idiom Imageability, and Idiom Transparency

ERIC Educational Resources Information Center

Steinel, Margarita P.; Hulstijn, Jan H.; Steinel, Wolfgang

2007-01-01

In a paired-associate learning (PAL) task, Dutch university students (n = 129) learned 20 English second language (L2) idioms either receptively or productively (i.e., L2-first language [L1] or L1-L2) and were tested in two directions (i.e., recognition or production) immediately after learning and 3 weeks later. Receptive and productive…

Subjective Learning Discounts Test Type: Evidence from an Associative Learning and Transfer Task

PubMed Central

Touron, Dayna R.; Hertzog, Christopher; Speagle, James Z.

2011-01-01

We evaluated the extent to which memory test format and test transfer influence the dynamics of metacognitive judgments. Participants completed 2 study-test phases for paired-associates, with or without transferring test type, in one of four conditions: (1) recognition then recall, (2) recall then recognition, (3) recognition throughout, or (4) recall throughout. Global judgments were made pre-study, post-study, and post-test for each phase; judgments of learning (JOLs) following item study were also collected. Results suggest that metacognitive judgment accuracy varies substantially by memory test type. Whereas underconfidence in JOLs and global predictions increases with recall practice (Koriat’s underconfidence-with-practice effect), underconfidence decreases with recognition practice. Moreover, performance changes when transferring test type were not fully anticipated by pre-test judgments. PMID:20178957

Quantitative analysis of TALE-DNA interactions suggests polarity effects.

PubMed

Meckler, Joshua F; Bhakta, Mital S; Kim, Moon-Soo; Ovadia, Robert; Habrian, Chris H; Zykovich, Artem; Yu, Abigail; Lockwood, Sarah H; Morbitzer, Robert; Elsäesser, Janett; Lahaye, Thomas; Segal, David J; Baldwin, Enoch P

2013-04-01

Transcription activator-like effectors (TALEs) have revolutionized the field of genome engineering. We present here a systematic assessment of TALE DNA recognition, using quantitative electrophoretic mobility shift assays and reporter gene activation assays. Within TALE proteins, tandem 34-amino acid repeats recognize one base pair each and direct sequence-specific DNA binding through repeat variable di-residues (RVDs). We found that RVD choice can affect affinity by four orders of magnitude, with the relative RVD contribution in the order NG > HD ≈ NN > NI > NK. The NN repeat preferred the base G over A, whereas the NK repeat bound G with 10(3)-fold lower affinity. We compared AvrBs3, a naturally occurring TALE that recognizes its target using some atypical RVD-base combinations, with a designed TALE that precisely matches 'standard' RVDs with the target bases. This comparison revealed unexpected differences in sensitivity to substitutions of the invariant 5'-T. Another surprising observation was that base mismatches at the 5' end of the target site had more disruptive effects on affinity than those at the 3' end, particularly in designed TALEs. These results provide evidence that TALE-DNA recognition exhibits a hitherto un-described polarity effect, in which the N-terminal repeats contribute more to affinity than C-terminal ones.

Research and implementation of finger-vein recognition algorithm

NASA Astrophysics Data System (ADS)

Pang, Zengyao; Yang, Jie; Chen, Yilei; Liu, Yin

2017-06-01

In finger vein image preprocessing, finger angle correction and ROI extraction are important parts of the system. In this paper, we propose an angle correction algorithm based on the centroid of the vein image, and extract the ROI region according to the bidirectional gray projection method. Inspired by the fact that features in those vein areas have similar appearance as valleys, a novel method was proposed to extract center and width of palm vein based on multi-directional gradients, which is easy-computing, quick and stable. On this basis, an encoding method was designed to determine the gray value distribution of texture image. This algorithm could effectively overcome the edge of the texture extraction error. Finally, the system was equipped with higher robustness and recognition accuracy by utilizing fuzzy threshold determination and global gray value matching algorithm. Experimental results on pairs of matched palm images show that, the proposed method has a EER with 3.21% extracts features at the speed of 27ms per image. It can be concluded that the proposed algorithm has obvious advantages in grain extraction efficiency, matching accuracy and algorithm efficiency.

Recombinase-based isothermal amplification of nucleic acids with self-avoiding molecular recognition systems (SAMRS).

PubMed

Sharma, Nidhi; Hoshika, Shuichi; Hutter, Daniel; Bradley, Kevin M; Benner, Steven A

2014-10-13

Recombinase polymerase amplification (RPA) is an isothermal method to amplify nucleic acid sequences without the temperature cycling that classical PCR uses. Instead of using heat to denature the DNA duplex, RPA uses recombination enzymes to swap single-stranded primers into the duplex DNA product; these are then extended using a strand-displacing polymerase to complete the cycle. Because RPA runs at low temperatures, it never forces the system to recreate base-pairs following Watson-Crick rules, and therefore it produces undesired products that impede the amplification of the desired product, complicating downstream analysis. Herein, we show that most of these undesired side products can be avoided if the primers contain components of a self-avoiding molecular recognition system (SAMRS). Given the precision that is necessary in the recombination systems for them to function biologically, it is surprising that they accept SAMRS. SAMRS-RPA is expected to be a powerful tool within the range of amplification techniques available to scientists. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Intelligent form removal with character stroke preservation

NASA Astrophysics Data System (ADS)

Garris, Michael D.

1996-03-01

A new technique for intelligent form removal has been developed along with a new method for evaluating its impact on optical character recognition (OCR). All the dominant lines in the image are automatically detected using the Hough line transform and intelligently erased while simultaneously preserving overlapping character strokes by computing line width statistics and keying off of certain visual cues. This new method of form removal operates on loosely defined zones with no image deskewing. Any field in which the writer is provided a horizontal line to enter a response can be processed by this method. Several examples of processed fields are provided, including a comparison of results between the new method and a commercially available forms removal package. Even if this new form removal method did not improve character recognition accuracy, it is still a significant improvement to the technology because the requirement of a priori knowledge of the form's geometric details has been greatly reduced. This relaxes the recognition system's dependence on rigid form design, printing, and reproduction by automatically detecting and removing some of the physical structures (lines) on the form. Using the National Institute of Standards and Technology (NIST) public domain form-based handprint recognition system, the technique was tested on a large number of fields containing randomly ordered handprinted lowercase alphabets, as these letters (especially those with descenders) frequently touch and extend through the line along which they are written. Preserving character strokes improves overall lowercase recognition performance by 3%, which is a net improvement, but a single performance number like this doesn't communicate how the recognition process was really influenced. There is expected to be trade- offs with the introduction of any new technique into a complex recognition system. To understand both the improvements and the trade-offs, a new analysis was designed to compare the statistical distributions of individual confusion pairs between two systems. As OCR technology continues to improve, sophisticated analyses like this are necessary to reduce the errors remaining in complex recognition problems.

Right hemisphere advantage for social recognition in the chick.

PubMed

Vallortigara, G

1992-09-01

Recognition of familiar and unfamiliar conspecifics was studied in pair-reared chicks tested binocularly or with only one eye in use. Chicks were tested on day 3 in pairs composed of either cagemates or strangers. Social discrimination, as measured by the ratio "number of pecks at the strangers/total number of pecks" was impaired in right-eyed chicks with respect to left-eyed and binocular chicks. Male chicks showed higher levels of social pecking than females, and chicks that used both eyes showed higher pecking than monocular chicks. There were no significant differences in the total number of pecks (i.e. pecks at companions plus pecks at strangers) between right- and left-eyed chicks: the impairment in social discrimination of right-eyed chicks seemed to be due partly to a reduction in pecking at strangers and partly to an increase in pecking at companions. It is suggested that neural structures fed by the left eye (mainly located at the right hemisphere) are better at processing and/or storing of visual information which allows recognition of individual conspecifics. This may be part of a wider tendency to respond to small changes in any of a variety of intrinsic stimulus properties.

Deficits in auditory processing contribute to impairments in vocal affect recognition in autism spectrum disorders: A MEG study.

PubMed

Demopoulos, Carly; Hopkins, Joyce; Kopald, Brandon E; Paulson, Kim; Doyle, Lauren; Andrews, Whitney E; Lewine, Jeffrey David

2015-11-01

The primary aim of this study was to examine whether there is an association between magnetoencephalography-based (MEG) indices of basic cortical auditory processing and vocal affect recognition (VAR) ability in individuals with autism spectrum disorder (ASD). MEG data were collected from 25 children/adolescents with ASD and 12 control participants using a paired-tone paradigm to measure quality of auditory physiology, sensory gating, and rapid auditory processing. Group differences were examined in auditory processing and vocal affect recognition ability. The relationship between differences in auditory processing and vocal affect recognition deficits was examined in the ASD group. Replicating prior studies, participants with ASD showed longer M1n latencies and impaired rapid processing compared with control participants. These variables were significantly related to VAR, with the linear combination of auditory processing variables accounting for approximately 30% of the variability after controlling for age and language skills in participants with ASD. VAR deficits in ASD are typically interpreted as part of a core, higher order dysfunction of the "social brain"; however, these results suggest they also may reflect basic deficits in auditory processing that compromise the extraction of socially relevant cues from the auditory environment. As such, they also suggest that therapeutic targeting of sensory dysfunction in ASD may have additional positive implications for other functional deficits. (c) 2015 APA, all rights reserved).

Improving Mobile Phone Speech Recognition by Personalized Amplification: Application in People with Normal Hearing and Mild-to-Moderate Hearing Loss.

PubMed

Kam, Anna Chi Shan; Sung, John Ka Keung; Lee, Tan; Wong, Terence Ka Cheong; van Hasselt, Andrew

In this study, the authors evaluated the effect of personalized amplification on mobile phone speech recognition in people with and without hearing loss. This prospective study used double-blind, within-subjects, repeated measures, controlled trials to evaluate the effectiveness of applying personalized amplification based on the hearing level captured on the mobile device. The personalized amplification settings were created using modified one-third gain targets. The participants in this study included 100 adults of age between 20 and 78 years (60 with age-adjusted normal hearing and 40 with hearing loss). The performance of the participants with personalized amplification and standard settings was compared using both subjective and speech-perception measures. Speech recognition was measured in quiet and in noise using Cantonese disyllabic words. Subjective ratings on the quality, clarity, and comfortableness of the mobile signals were measured with an 11-point visual analog scale. Subjective preferences of the settings were also obtained by a paired-comparison procedure. The personalized amplification application provided better speech recognition via the mobile phone both in quiet and in noise for people with hearing impairment (improved 8 to 10%) and people with normal hearing (improved 1 to 4%). The improvement in speech recognition was significantly better for people with hearing impairment. When the average device output level was matched, more participants preferred to have the individualized gain than not to have it. The personalized amplification application has the potential to improve speech recognition for people with mild-to-moderate hearing loss, as well as people with normal hearing, in particular when listening in noisy environments.

Recognition Tunneling

PubMed Central

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

2010-01-01

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

Minutia Tensor Matrix: A New Strategy for Fingerprint Matching

PubMed Central

Fu, Xiang; Feng, Jufu

2015-01-01

Establishing correspondences between two minutia sets is a fundamental issue in fingerprint recognition. This paper proposes a new tensor matching strategy. First, the concept of minutia tensor matrix (simplified as MTM) is proposed. It describes the first-order features and second-order features of a matching pair. In the MTM, the diagonal elements indicate similarities of minutia pairs and non-diagonal elements indicate pairwise compatibilities between minutia pairs. Correct minutia pairs are likely to establish both large similarities and large compatibilities, so they form a dense sub-block. Minutia matching is then formulated as recovering the dense sub-block in the MTM. This is a new tensor matching strategy for fingerprint recognition. Second, as fingerprint images show both local rigidity and global nonlinearity, we design two different kinds of MTMs: local MTM and global MTM. Meanwhile, a two-level matching algorithm is proposed. For local matching level, the local MTM is constructed and a novel local similarity calculation strategy is proposed. It makes full use of local rigidity in fingerprints. For global matching level, the global MTM is constructed to calculate similarities of entire minutia sets. It makes full use of global compatibility in fingerprints. Proposed method has stronger description ability and better robustness to noise and nonlinearity. Experiments conducted on Fingerprint Verification Competition databases (FVC2002 and FVC2004) demonstrate the effectiveness and the efficiency. PMID:25822489

Complementarity to an miRNA seed region is sufficient to induce moderate repression of a target transcript in the unicellular green alga Chlamydomonas reinhardtii.

PubMed

Yamasaki, Tomohito; Voshall, Adam; Kim, Eun-Jeong; Moriyama, Etsuko; Cerutti, Heriberto; Ohama, Takeshi

2013-12-01

MicroRNAs (miRNAs) are 20-24 nt non-coding RNAs that play important regulatory roles in a broad range of eukaryotes by pairing with mRNAs to direct post-transcriptional repression. The mechanistic details of miRNA-mediated post-transcriptional regulation have been well documented in multicellular model organisms. However, this process remains poorly studied in algae such as Chlamydomonas reinhardtii, and specific features of miRNA biogenesis, target mRNA recognition and subsequent silencing are not well understood. In this study, we report on the characterization of a Chlamydomonas miRNA, cre-miR1174.2, which is processed from a near-perfect hairpin RNA. Using Gaussia luciferase (gluc) reporter genes, we have demonstrated that cre-miR1174.2 is functional in Chlamydomonas and capable of triggering site-specific cleavage at the center of a perfectly complementary target sequence. A mismatch tolerance test assay, based on pools of transgenic strains, revealed that target hybridization to nucleotides of the seed region, at the 5' end of an miRNA, was sufficient to induce moderate repression of expression. In contrast, pairing to the 3' region of the miRNA was not critical for silencing. Our results suggest that the base-pairing requirements for small RNA-mediated repression in C. reinhardtii are more similar to those of metazoans compared with the extensive complementarity that is typical of land plants. Individual Chlamydomonas miRNAs may potentially modulate the expression of numerous endogenous targets as a result of these relaxed base-pairing requirements. © 2013 The Authors The Plant Journal © 2013 John Wiley & Sons Ltd.

Covalent Bonding of Pyrrolobenzodiazepines (PBDs) to Terminal Guanine Residues within Duplex and Hairpin DNA Fragments

PubMed Central

Mantaj, Julia; Jackson, Paul J. M.; Karu, Kersti; Rahman, Khondaker M.; Thurston, David E.

2016-01-01

Pyrrolobenzodiazepines (PBDs) are covalent-binding DNA-interactive agents with growing importance as payloads in Antibody Drug Conjugates (ADCs). Until now, PBDs were thought to covalently bond to C2-NH2 groups of guanines in the DNA-minor groove across a three-base-pair recognition sequence. Using HPLC/MS methodology with designed hairpin and duplex oligonucleotides, we have now demonstrated that the PBD Dimer SJG-136 and the C8-conjugated PBD Monomer GWL-78 can covalently bond to a terminal guanine of DNA, with the PBD skeleton spanning only two base pairs. Control experiments with the non-C8-conjugated anthramycin along with molecular dynamics simulations suggest that the C8-substituent of a PBD Monomer, or one-half of a PBD Dimer, may provide stability for the adduct. This observation highlights the importance of PBD C8-substituents, and also suggests that PBDs may bind to terminal guanines within stretches of DNA in cells, thus representing a potentially novel mechanism of action at the end of DNA strand breaks. PMID:27055050

Sequence-specific activation of the DNA sensor cGAS by Y-form DNA structures as found in primary HIV-1 cDNA.

PubMed

Herzner, Anna-Maria; Hagmann, Cristina Amparo; Goldeck, Marion; Wolter, Steven; Kübler, Kirsten; Wittmann, Sabine; Gramberg, Thomas; Andreeva, Liudmila; Hopfner, Karl-Peter; Mertens, Christina; Zillinger, Thomas; Jin, Tengchuan; Xiao, Tsan Sam; Bartok, Eva; Coch, Christoph; Ackermann, Damian; Hornung, Veit; Ludwig, Janos; Barchet, Winfried; Hartmann, Gunther; Schlee, Martin

2015-10-01

Cytosolic DNA that emerges during infection with a retrovirus or DNA virus triggers antiviral type I interferon responses. So far, only double-stranded DNA (dsDNA) over 40 base pairs (bp) in length has been considered immunostimulatory. Here we found that unpaired DNA nucleotides flanking short base-paired DNA stretches, as in stem-loop structures of single-stranded DNA (ssDNA) derived from human immunodeficiency virus type 1 (HIV-1), activated the type I interferon-inducing DNA sensor cGAS in a sequence-dependent manner. DNA structures containing unpaired guanosines flanking short (12- to 20-bp) dsDNA (Y-form DNA) were highly stimulatory and specifically enhanced the enzymatic activity of cGAS. Furthermore, we found that primary HIV-1 reverse transcripts represented the predominant viral cytosolic DNA species during early infection of macrophages and that these ssDNAs were highly immunostimulatory. Collectively, our study identifies unpaired guanosines in Y-form DNA as a highly active, minimal cGAS recognition motif that enables detection of HIV-1 ssDNA.

PPInterFinder--a mining tool for extracting causal relations on human proteins from literature.

PubMed

Raja, Kalpana; Subramani, Suresh; Natarajan, Jeyakumar

2013-01-01

One of the most common and challenging problem in biomedical text mining is to mine protein-protein interactions (PPIs) from MEDLINE abstracts and full-text research articles because PPIs play a major role in understanding the various biological processes and the impact of proteins in diseases. We implemented, PPInterFinder--a web-based text mining tool to extract human PPIs from biomedical literature. PPInterFinder uses relation keyword co-occurrences with protein names to extract information on PPIs from MEDLINE abstracts and consists of three phases. First, it identifies the relation keyword using a parser with Tregex and a relation keyword dictionary. Next, it automatically identifies the candidate PPI pairs with a set of rules related to PPI recognition. Finally, it extracts the relations by matching the sentence with a set of 11 specific patterns based on the syntactic nature of PPI pair. We find that PPInterFinder is capable of predicting PPIs with the accuracy of 66.05% on AIMED corpus and outperforms most of the existing systems. DATABASE URL: http://www.biomining-bu.in/ppinterfinder/

PPInterFinder—a mining tool for extracting causal relations on human proteins from literature

PubMed Central

Raja, Kalpana; Subramani, Suresh; Natarajan, Jeyakumar

2013-01-01

One of the most common and challenging problem in biomedical text mining is to mine protein–protein interactions (PPIs) from MEDLINE abstracts and full-text research articles because PPIs play a major role in understanding the various biological processes and the impact of proteins in diseases. We implemented, PPInterFinder—a web-based text mining tool to extract human PPIs from biomedical literature. PPInterFinder uses relation keyword co-occurrences with protein names to extract information on PPIs from MEDLINE abstracts and consists of three phases. First, it identifies the relation keyword using a parser with Tregex and a relation keyword dictionary. Next, it automatically identifies the candidate PPI pairs with a set of rules related to PPI recognition. Finally, it extracts the relations by matching the sentence with a set of 11 specific patterns based on the syntactic nature of PPI pair. We find that PPInterFinder is capable of predicting PPIs with the accuracy of 66.05% on AIMED corpus and outperforms most of the existing systems. Database URL: http://www.biomining-bu.in/ppinterfinder/ PMID:23325628

Pyrvinium pamoate changes alternative splicing of the serotonin receptor 2C by influencing its RNA structure

PubMed Central

Shen, Manli; Bellaousov, Stanislav; Hiller, Michael; de La Grange, Pierre; Creamer, Trevor P.; Malina, Orit; Sperling, Ruth; Mathews, David H.; Stoilov, Peter; Stamm, Stefan

2013-01-01

The serotonin receptor 2C plays a central role in mood and appetite control. It undergoes pre-mRNA editing as well as alternative splicing. The RNA editing suggests that the pre-mRNA forms a stable secondary structure in vivo. To identify substances that promote alternative exons inclusion, we set up a high-throughput screen and identified pyrvinium pamoate as a drug-promoting exon inclusion without editing. Circular dichroism spectroscopy indicates that pyrvinium pamoate binds directly to the pre-mRNA and changes its structure. SHAPE (selective 2′-hydroxyl acylation analysed by primer extension) assays show that part of the regulated 5′-splice site forms intramolecular base pairs that are removed by this structural change, which likely allows splice site recognition and exon inclusion. Genome-wide analyses show that pyrvinium pamoate regulates >300 alternative exons that form secondary structures enriched in A–U base pairs. Our data demonstrate that alternative splicing of structured pre-mRNAs can be regulated by small molecules that directly bind to the RNA, which is reminiscent to an RNA riboswitch. PMID:23393189

Evidence of protein-free homology recognition in magnetic bead force-extension experiments

NASA Astrophysics Data System (ADS)

O'Lee, D. J.; Danilowicz, C.; Rochester, C.; Kornyshev, A. A.; Prentiss, M.

2016-07-01

Earlier theoretical studies have proposed that the homology-dependent pairing of large tracts of dsDNA may be due to physical interactions between homologous regions. Such interactions could contribute to the sequence-dependent pairing of chromosome regions that may occur in the presence or the absence of double-strand breaks. Several experiments have indicated the recognition of homologous sequences in pure electrolytic solutions without proteins. Here, we report single-molecule force experiments with a designed 60 kb long dsDNA construct; one end attached to a solid surface and the other end to a magnetic bead. The 60 kb constructs contain two 10 kb long homologous tracts oriented head to head, so that their sequences match if the two tracts fold on each other. The distance between the bead and the surface is measured as a function of the force applied to the bead. At low forces, the construct molecules extend substantially less than normal, control dsDNA, indicating the existence of preferential interaction between the homologous regions. The force increase causes no abrupt but continuous unfolding of the paired homologous regions. Simple semi-phenomenological models of the unfolding mechanics are proposed, and their predictions are compared with the data.

The development of adaptive memory: Young children show enhanced retention of animacy-related information.

PubMed

Aslan, Alp; John, Thomas

2016-12-01

Previous developmental work has indicated that animacy is a foundational ontogenetic category that is given priority already early in life. Here, we investigated whether such priority is also present in children's episodic memory, examining whether young children show enhanced retention of animacy-related information. Kindergartners and younger and older elementary school children were presented with fictitious (non)words (e.g., BULA, LAFE) paired with properties characteristic of humans (e.g., "likes music"), (nonhuman) animals (e.g., "builds nests"), and inanimate things (e.g., "has four edges") and were asked to rate the animacy status of each nonword. After a retention interval, a surprise recognition test for the nonwords was administered. We found enhanced recognition of nonwords paired with human and animal properties compared with (the same) nonwords paired with inanimate properties. The size of this animacy advantage was comparable across age groups, suggesting developmental invariance of the advantage over the age range examined (i.e., 4-11years). The results support a functional-evolutionary view on memory, suggesting that already young children's memory is "tuned" to process and retain animacy. Copyright © 2016 Elsevier Inc. All rights reserved.

The Structural Basis for Recognition of the PreQ0 Metabolite by an Unusually Small Riboswitch Aptamer Domain*S⃞♦

PubMed Central

Spitale, Robert C.; Torelli, Andrew T.; Krucinska, Jolanta; Bandarian, Vahe; Wedekind, Joseph E.

2009-01-01

Riboswitches are RNA elements that control gene expression through metabolite binding. The preQ1 riboswitch exhibits the smallest known ligand-binding domain and is of interest for its economical organization and high affinity interactions with guanine-derived metabolites required to confer tRNA wobbling. Here we present the crystal structure of a preQ1 aptamer domain in complex with its precursor metabolite preQ0. The structure is highly compact with a core that features a stem capped by a well organized decaloop. The metabolite is recognized within a deep pocket via Watson-Crick pairing with C15. Additional hydrogen bonds are made to invariant bases U6 and A29. The ligand-bound state confers continuous helical stacking throughout the core fold, thus providing a platform to promote Watson-Crick base pairing between C9 of the decaloop and the first base of the ribosome-binding site, G33. The structure offers insight into the mode of ribosome-binding site sequestration by a minimal RNA fold stabilized by metabolite binding and has implications for understanding the molecular basis by which bacterial genes are regulated. PMID:19261617

Semantic and visual determinants of face recognition in a prosopagnosic patient.

PubMed

Dixon, M J; Bub, D N; Arguin, M

1998-05-01

Prosopagnosia is the neuropathological inability to recognize familiar people by their faces. It can occur in isolation or can coincide with recognition deficits for other nonface objects. Often, patients whose prosopagnosia is accompanied by object recognition difficulties have more trouble identifying certain categories of objects relative to others. In previous research, we demonstrated that objects that shared multiple visual features and were semantically close posed severe recognition difficulties for a patient with temporal lobe damage. We now demonstrate that this patient's face recognition is constrained by these same parameters. The prosopagnosic patient ELM had difficulties pairing faces to names when the faces shared visual features and the names were semantically related (e.g., Tonya Harding, Nancy Kerrigan, and Josee Chouinard -three ice skaters). He made tenfold fewer errors when the exact same faces were associated with semantically unrelated people (e.g., singer Celine Dion, actress Betty Grable, and First Lady Hillary Clinton). We conclude that prosopagnosia and co-occurring category-specific recognition problems both stem from difficulties disambiguating the stored representations of objects that share multiple visual features and refer to semantically close identities or concepts.

Normal mere exposure effect with impaired recognition in Alzheimer's disease.

PubMed

Willems, Sylvie; Adam, Stéphane; Van der Linden, Martial

2002-02-01

We investigated the mere exposure effect and the explicit memory in Alzheimer's disease (AD) patients and elderly control subjects, using unfamiliar faces. During the exposure phase, the subjects estimated the age of briefly flashed faces. The mere exposure effect was examined by presenting pairs of faces (old and new) and asking participants to select the face they liked. The participants were then presented with a forced-choice explicit recognition task. Controls subjects exhibited above-chance preference and recognition scores for old faces. The AD patients also showed the mere exposure effect but no explicit recognition. These results suggest that the processes involved in the mere exposure effect are preserved in AD patients despite their impaired explicit recognition. The results are discussed in terms of Seamon et al.'s (1995) proposal that processes involved in the mere exposure effect are equivalent to those subserving perceptual priming. These processes would depend on extrastriate areas which are relatively preserved in AD patients.

Evidence for Separate Contributions of High and Low Spatial Frequencies during Visual Word Recognition.

PubMed

Winsler, Kurt; Holcomb, Phillip J; Midgley, Katherine J; Grainger, Jonathan

2017-01-01

Previous studies have shown that different spatial frequency information processing streams interact during the recognition of visual stimuli. However, it is a matter of debate as to the contributions of high and low spatial frequency (HSF and LSF) information for visual word recognition. This study examined the role of different spatial frequencies in visual word recognition using event-related potential (ERP) masked priming. EEG was recorded from 32 scalp sites in 30 English-speaking adults in a go/no-go semantic categorization task. Stimuli were white characters on a neutral gray background. Targets were uppercase five letter words preceded by a forward-mask (#######) and a 50 ms lowercase prime. Primes were either the same word (repeated) or a different word (un-repeated) than the subsequent target and either contained only high, only low, or full spatial frequency information. Additionally within each condition, half of the prime-target pairs were high lexical frequency, and half were low. In the full spatial frequency condition, typical ERP masked priming effects were found with an attenuated N250 (sub-lexical) and N400 (lexical-semantic) for repeated compared to un-repeated primes. For HSF primes there was a weaker N250 effect which interacted with lexical frequency, a significant reversal of the effect around 300 ms, and an N400-like effect for only high lexical frequency word pairs. LSF primes did not produce any of the classic ERP repetition priming effects, however they did elicit a distinct early effect around 200 ms in the opposite direction of typical repetition effects. HSF information accounted for many of the masked repetition priming ERP effects and therefore suggests that HSFs are more crucial for word recognition. However, LSFs did produce their own pattern of priming effects indicating that larger scale information may still play a role in word recognition.

Visual Recognition of Age Class and Preference for Infantile Features: Implications for Species-Specific vs Universal Cognitive Traits in Primates

PubMed Central

Lemasson, Alban; Nagumo, Sumiharu; Masataka, Nobuo

2012-01-01

Despite not knowing the exact age of individuals, humans can estimate their rough age using age-related physical features. Nonhuman primates show some age-related physical features; however, the cognitive traits underlying their recognition of age class have not been revealed. Here, we tested the ability of two species of Old World monkey, Japanese macaques (JM) and Campbell's monkeys (CM), to spontaneously discriminate age classes using visual paired comparison (VPC) tasks based on the two distinct categories of infant and adult images. First, VPCs were conducted in JM subjects using conspecific JM stimuli. When analyzing the side of the first look, JM subjects significantly looked more often at novel images. Based on analyses of total looking durations, JM subjects looked at a novel infant image longer than they looked at a familiar adult image, suggesting the ability to spontaneously discriminate between the two age classes and a preference for infant over adult images. Next, VPCs were tested in CM subjects using heterospecific JM stimuli. CM subjects showed no difference in the side of their first look, but looked at infant JM images longer than they looked at adult images; the fact that CMs were totally naïve to JMs suggested that the attractiveness of infant images transcends species differences. This is the first report of visual age class recognition and a preference for infant over adult images in nonhuman primates. Our results suggest not only species-specific processing for age class recognition but also the evolutionary origins of the instinctive human perception of baby cuteness schema, proposed by the ethologist Konrad Lorenz. PMID:22685529

The intrinsic flexibility of the aptamer targeting the ribosomal protein S8 is a key factor for the molecular recognition.

PubMed

Autiero, Ida; Ruvo, Menotti; Improta, Roberto; Vitagliano, Luigi

2018-04-01

Aptamers are RNA/DNA biomolecules representing an emerging class of protein interactors and regulators. Despite the growing interest in these molecules, current understanding of chemical-physical basis of their target recognition is limited. Recently, the characterization of the aptamer targeting the protein-S8 has suggested that flexibility plays important functional roles. We investigated the structural versatility of the S8-aptamer by molecular dynamics simulations. Five different simulations have been conducted by varying starting structures and temperatures. The simulation of S8-aptamer complex provides a dynamic view of the contacts occurring at the complex interface. The simulation of the aptamer in ligand-free state indicates that its central region is intrinsically endowed with a remarkable flexibility. Nevertheless, none of the trajectory structures adopts the structure observed in the S8-aptamer complex. The aptamer ligand-bound is very rigid in the simulation carried out at 300 K. A structural transition of this state, providing insights into the aptamer-protein recognition process, is observed in a simulation carried out at 400 K. These data indicate that a key event in the binding is linked to the widening of the central region of the aptamer. Particularly relevant is switch of the A26 base from its ligand-free state to a location that allows the G13-C28 base-pairing. Intrinsic flexibility of the aptamer is essential for partner recognition. Present data indicate that S8 recognizes the aptamer through an induced-fit rather than a population-shift mechanism. The present study provides deeper understanding of the structural basis of the structural versatility of aptamers. Copyright © 2018 Elsevier B.V. All rights reserved.

Visual recognition of age class and preference for infantile features: implications for species-specific vs universal cognitive traits in primates.

PubMed

Sato, Anna; Koda, Hiroki; Lemasson, Alban; Nagumo, Sumiharu; Masataka, Nobuo

2012-01-01

Despite not knowing the exact age of individuals, humans can estimate their rough age using age-related physical features. Nonhuman primates show some age-related physical features; however, the cognitive traits underlying their recognition of age class have not been revealed. Here, we tested the ability of two species of Old World monkey, Japanese macaques (JM) and Campbell's monkeys (CM), to spontaneously discriminate age classes using visual paired comparison (VPC) tasks based on the two distinct categories of infant and adult images. First, VPCs were conducted in JM subjects using conspecific JM stimuli. When analyzing the side of the first look, JM subjects significantly looked more often at novel images. Based on analyses of total looking durations, JM subjects looked at a novel infant image longer than they looked at a familiar adult image, suggesting the ability to spontaneously discriminate between the two age classes and a preference for infant over adult images. Next, VPCs were tested in CM subjects using heterospecific JM stimuli. CM subjects showed no difference in the side of their first look, but looked at infant JM images longer than they looked at adult images; the fact that CMs were totally naïve to JMs suggested that the attractiveness of infant images transcends species differences. This is the first report of visual age class recognition and a preference for infant over adult images in nonhuman primates. Our results suggest not only species-specific processing for age class recognition but also the evolutionary origins of the instinctive human perception of baby cuteness schema, proposed by the ethologist Konrad Lorenz.

The prediction of human exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames

DOE Office of Scientific and Technical Information (OSTI.GOV)

Solovyev, V.V.; Salamov, A.A.; Lawrence, C.B.

1994-12-31

Discriminant analysis is applied to the problem of recognition 5`-, internal and 3`-exons in human DNA sequences. Specific recognition functions were developed for revealing exons of particular types. The method based on a splice site prediction algorithm that uses the linear Fisher discriminant to combine the information about significant triplet frequencies of various functional parts of splice site regions and preferences of oligonucleotide in protein coding and nation regions. The accuracy of our splice site recognition function is about 97%. A discriminant function for 5`-exon prediction includes hexanucleotide composition of upstream region, triplet composition around the ATG codon, ORF codingmore » potential, donor splice site potential and composition of downstream introit region. For internal exon prediction, we combine in a discriminant function the characteristics describing the 5`- intron region, donor splice site, coding region, acceptor splice site and Y-intron region for each open reading frame flanked by GT and AG base pairs. The accuracy of precise internal exon recognition on a test set of 451 exon and 246693 pseudoexon sequences is 77% with a specificity of 79% and a level of pseudoexon ORF prediction of 99.96%. The recognition quality computed at the level of individual nucleotides is 89%, for exon sequences and 98% for intron sequences. A discriminant function for 3`-exon prediction includes octanucleolide composition of upstream nation region, triplet composition around the stop codon, ORF coding potential, acceptor splice site potential and hexanucleotide composition of downstream region. We unite these three discriminant functions in exon predicting program FEX (find exons). FEX exactly predicts 70% of 1016 exons from the test of 181 complete genes with specificity 73%, and 89% exons are exactly or partially predicted. On the average, 85% of nucleotides were predicted accurately with specificity 91%.« less

Fingerprint Recognition with Identical Twin Fingerprints

PubMed Central

Yang, Xin; Tian, Jie

2012-01-01

Fingerprint recognition with identical twins is a challenging task due to the closest genetics-based relationship existing in the identical twins. Several pioneers have analyzed the similarity between twins' fingerprints. In this work we continue to investigate the topic of the similarity of identical twin fingerprints. Our study was tested based on a large identical twin fingerprint database that contains 83 twin pairs, 4 fingers per individual and six impressions per finger: 3984 (83*2*4*6) images. Compared to the previous work, our contributions are summarized as follows: (1) Two state-of-the-art fingerprint identification methods: P071 and VeriFinger 6.1 were used, rather than one fingerprint identification method in previous studies. (2) Six impressions per finger were captured, rather than just one impression, which makes the genuine distribution of matching scores more realistic. (3) A larger sample (83 pairs) was collected. (4) A novel statistical analysis, which aims at showing the probability distribution of the fingerprint types for the corresponding fingers of identical twins which have same fingerprint type, has been conducted. (5) A novel analysis, which aims at showing which finger from identical twins has higher probability of having same fingerprint type, has been conducted. Our results showed that: (a) A state-of-the-art automatic fingerprint verification system can distinguish identical twins without drastic degradation in performance. (b) The chance that the fingerprints have the same type from identical twins is 0.7440, comparing to 0.3215 from non-identical twins. (c) For the corresponding fingers of identical twins which have same fingerprint type, the probability distribution of five major fingerprint types is similar to the probability distribution for all the fingers' fingerprint type. (d) For each of four fingers of identical twins, the probability of having same fingerprint type is similar. PMID:22558204

Fingerprint recognition with identical twin fingerprints.

PubMed

Tao, Xunqiang; Chen, Xinjian; Yang, Xin; Tian, Jie

2012-01-01

Fingerprint recognition with identical twins is a challenging task due to the closest genetics-based relationship existing in the identical twins. Several pioneers have analyzed the similarity between twins' fingerprints. In this work we continue to investigate the topic of the similarity of identical twin fingerprints. Our study was tested based on a large identical twin fingerprint database that contains 83 twin pairs, 4 fingers per individual and six impressions per finger: 3984 (83*2*4*6) images. Compared to the previous work, our contributions are summarized as follows: (1) Two state-of-the-art fingerprint identification methods: P071 and VeriFinger 6.1 were used, rather than one fingerprint identification method in previous studies. (2) Six impressions per finger were captured, rather than just one impression, which makes the genuine distribution of matching scores more realistic. (3) A larger sample (83 pairs) was collected. (4) A novel statistical analysis, which aims at showing the probability distribution of the fingerprint types for the corresponding fingers of identical twins which have same fingerprint type, has been conducted. (5) A novel analysis, which aims at showing which finger from identical twins has higher probability of having same fingerprint type, has been conducted. Our results showed that: (a) A state-of-the-art automatic fingerprint verification system can distinguish identical twins without drastic degradation in performance. (b) The chance that the fingerprints have the same type from identical twins is 0.7440, comparing to 0.3215 from non-identical twins. (c) For the corresponding fingers of identical twins which have same fingerprint type, the probability distribution of five major fingerprint types is similar to the probability distribution for all the fingers' fingerprint type. (d) For each of four fingers of identical twins, the probability of having same fingerprint type is similar.

6-Oxocytidine a novel protonated C-base analogue for stable triple helix formation.

PubMed Central

Berressem, R; Engels, J W

1995-01-01

2'-O-Methyl-3'-O-phosphoramidite building blocks of 6-oxocytidine 6 and its 5-methyl derivative 7, respectively, were synthesized and incorporated via phosphoramidite chemistry in 15 mer oligodeoxynucleotides [d(T72T7), S2; d(T73T7), S3] to obtain potential Py.Pu.Py triplex forming homopyrimidine strands. UV thermal denaturation studies and CD spectroscopy of 1:1 mixtures of these oligomers and a 21 mer target duplex [d(C3A7GA7C3)-d(G3T7CT7G3), D1] with a complementary purine tract showed a nearly pH-independent (6.0-8.0) triple helix formation with melting temperatures of 21-19 degrees C and 18.5-17.5 degrees C, respectively (buffer system: 50 mM sodium cacodylate, 100 mM NaCl, 20 mM MgCl2). In contrast, with the corresponding 15mer deoxy-C-containing oligonucleotide [d(T(7)1T7), S1] triplex formation was observed only below pH 6.6. Specificity for the recognition of Watson-Crick GC-base pairs was observed by pairing the modified C-bases of the 15mers with all other possible Watson-Crick-base compositions in the target duplex [d(C3A7XA7C3)-d(G3T7YT7G3), X = A,C,T; Y = T,G,A, D2-4]. Additionally, the Watson-Crick-pairing of the modified oligomers S2 and S3 was studied. PMID:7567457

6-Oxocytidine a novel protonated C-base analogue for stable triple helix formation.

PubMed

Berressem, R; Engels, J W

1995-09-11

2'-O-Methyl-3'-O-phosphoramidite building blocks of 6-oxocytidine 6 and its 5-methyl derivative 7, respectively, were synthesized and incorporated via phosphoramidite chemistry in 15 mer oligodeoxynucleotides [d(T72T7), S2; d(T73T7), S3] to obtain potential Py.Pu.Py triplex forming homopyrimidine strands. UV thermal denaturation studies and CD spectroscopy of 1:1 mixtures of these oligomers and a 21 mer target duplex [d(C3A7GA7C3)-d(G3T7CT7G3), D1] with a complementary purine tract showed a nearly pH-independent (6.0-8.0) triple helix formation with melting temperatures of 21-19 degrees C and 18.5-17.5 degrees C, respectively (buffer system: 50 mM sodium cacodylate, 100 mM NaCl, 20 mM MgCl2). In contrast, with the corresponding 15mer deoxy-C-containing oligonucleotide [d(T(7)1T7), S1] triplex formation was observed only below pH 6.6. Specificity for the recognition of Watson-Crick GC-base pairs was observed by pairing the modified C-bases of the 15mers with all other possible Watson-Crick-base compositions in the target duplex [d(C3A7XA7C3)-d(G3T7YT7G3), X = A,C,T; Y = T,G,A, D2-4]. Additionally, the Watson-Crick-pairing of the modified oligomers S2 and S3 was studied.

A newly developed highly selective Zn2+-AcO- ion-pair sensor through partner preference: equal efficiency under solitary and colonial situation.

PubMed

Karar, Monaj; Paul, Suvendu; Biswas, Bhaskar; Majumdar, Tapas; Mallick, Arabinda

2018-05-10

Unusual self-sorting of an ion-pair under highly crowded conditions driven by a synthesized intelligent molecule 2-((E)-(3-((E)-2-hydroxy-3-methoxybenzylideneamino)-2-hydroxypropyl imino)methyl)-6-methoxyphenol, hereafter HBP, is described. When a mixture of various metal salts was allowed to react with HBP, only a specific ion-pair ZnII/AcO- in the solution simultaneously reacted, resulting in high-fidelity ion-pair recognition of HBP. This phenomenon was evidenced by significant changes in the absorption spectra and huge enhancement in emission intensity of HBP. The property that one molecule preferring one particular cation-anion pair over others is a rare but interesting phenomenon. Thus, the potential to interact selectively with the targeted ion-pair resulting in the formation of a specific complex recognized HBP as a new class of molecule that might find future applications in real time and on-site monitoring and separation of new molecules.

Role of water mediated interactions in protein-protein recognition landscapes.

PubMed

Papoian, Garegin A; Ulander, Johan; Wolynes, Peter G

2003-07-30

The energy landscape picture of protein folding and binding is employed to optimize a number of pair potentials for direct and water-mediated interactions in protein complex interfaces. We find that water-mediated interactions greatly complement direct interactions in discriminating against various types of trap interactions that model those present in the cell. We highlight the context dependent nature of knowledge-based binding potentials, as contrasted with the situation for autonomous folding. By performing a Principal Component Analysis (PCA) of the corresponding interaction matrixes, we rationalize the strength of the recognition signal for each combination of the contact type and reference trap states using the differential in the idealized "canonical" amino acid compositions of native and trap layers. The comparison of direct and water-mediated contact potential matrixes emphasizes the importance of partial solvation in stabilizing charged groups in the protein interfaces. Specific water-mediated interresidue interactions are expected to influence significantly the kinetics as well as thermodynamics of protein association.

Is a Pink Cow Still a Cow? Individual Differences in Toddlers' Vocabulary Knowledge and Lexical Representations.

PubMed

Perry, Lynn K; Saffran, Jenny R

2017-05-01

When a toddler knows a word, what does she actually know? Many categories have multiple relevant properties; for example, shape and color are relevant to membership in the category banana. How do toddlers prioritize these properties when recognizing familiar words, and are there systematic differences among children? In this study, toddlers viewed pairs of objects associated with prototypical colors. On some trials, objects were typically colored (e.g., Holstein cow and pink pig); on other trials, colors were switched (e.g., pink cow and Holstein-patterned pig). On each trial, toddlers were directed to find a target object. Overall, recognition was disrupted when colors were switched, as measured by eye movements. Moreover, individual differences in vocabularies predicted recognition differences: Toddlers who say fewer shape-based words were more disrupted by color switches. "Knowing" a word may not mean the same thing for all toddlers; different toddlers prioritize different facets of familiar objects in their lexical representations. Copyright © 2016 Cognitive Science Society, Inc.

Binding-induced Folding of Prokaryotic Ubiquitin-like Protein on the Mycobacterium Proteasomal ATPase Targets Substrates for Degradation

DOE Office of Scientific and Technical Information (OSTI.GOV)

T Wang; K Heran Darwin; H Li

2011-12-31

Mycobacterium tuberculosis uses a proteasome system that is analogous to the eukaryotic ubiquitin-proteasome pathway and is required for pathogenesis. However, the bacterial analog of ubiquitin, prokaryotic ubiquitin-like protein (Pup), is an intrinsically disordered protein that bears little sequence or structural resemblance to the highly structured ubiquitin. Thus, it was unknown how pupylated proteins were recruited to the proteasome. Here, we show that the Mycobacterium proteasomal ATPase (Mpa) has three pairs of tentacle-like coiled coils that recognize Pup. Mpa bound unstructured Pup through hydrophobic interactions and a network of hydrogen bonds, leading to the formation of an {alpha}-helix in Pup. Ourmore » work describes a binding-induced folding recognition mechanism in the Pup-proteasome system that differs mechanistically from substrate recognition in the ubiquitin-proteasome system. This key difference between the prokaryotic and eukaryotic systems could be exploited for the development of a small molecule-based treatment for tuberculosis.« less

Binding-induced folding of prokaryotic ubiquitin-like protein on the mycobacterium proteasomal ATPase targets substrates for degradation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, T.; Li, H.; Darwin, K. H.

2010-11-01

Mycobacterium tuberculosis uses a proteasome system that is analogous to the eukaryotic ubiquitin-proteasome pathway and is required for pathogenesis. However, the bacterial analog of ubiquitin, prokaryotic ubiquitin-like protein (Pup), is an intrinsically disordered protein that bears little sequence or structural resemblance to the highly structured ubiquitin. Thus, it was unknown how pupylated proteins were recruited to the proteasome. Here, we show that the Mycobacterium proteasomal ATPase (Mpa) has three pairs of tentacle-like coiled coils that recognize Pup. Mpa bound unstructured Pup through hydrophobic interactions and a network of hydrogen bonds, leading to the formation of an {alpha}-helix in Pup. Ourmore » work describes a binding-induced folding recognition mechanism in the Pup-proteasome system that differs mechanistically from substrate recognition in the ubiquitin-proteasome system. This key difference between the prokaryotic and eukaryotic systems could be exploited for the development of a small molecule-based treatment for tuberculosis.« less

A new look at emotion perception: Concepts speed and shape facial emotion recognition.

PubMed

Nook, Erik C; Lindquist, Kristen A; Zaki, Jamil

2015-10-01

Decades ago, the "New Look" movement challenged how scientists thought about vision by suggesting that conceptual processes shape visual perceptions. Currently, affective scientists are likewise debating the role of concepts in emotion perception. Here, we utilized a repetition-priming paradigm in conjunction with signal detection and individual difference analyses to examine how providing emotion labels-which correspond to discrete emotion concepts-affects emotion recognition. In Study 1, pairing emotional faces with emotion labels (e.g., "sad") increased individuals' speed and sensitivity in recognizing emotions. Additionally, individuals with alexithymia-who have difficulty labeling their own emotions-struggled to recognize emotions based on visual cues alone, but not when emotion labels were provided. Study 2 replicated these findings and further demonstrated that emotion concepts can shape perceptions of facial expressions. Together, these results suggest that emotion perception involves conceptual processing. We discuss the implications of these findings for affective, social, and clinical psychology. (c) 2015 APA, all rights reserved).

Age Differences in Memory Retrieval Shift: Governed by Feeling-of-Knowing?

PubMed Central

Hertzog, Christopher; Touron, Dayna R.

2010-01-01

The noun-pair lookup (NP) task was used to evaluate strategic shift from visual scanning to retrieval. We investigated whether age differences in feeling-of-knowing (FOK) account for older adults' delayed retrieval shift. Participants were randomly assigned to one of three conditions: (1) standard NP learning, (2) fast binary FOK judgments, or (3) Choice, where participants had to choose in advance whether to see the look-up table or respond from memory. We found small age differences in FOK magnitudes, but major age differences in memory retrieval choices that mirrored retrieval use in the standard NP task. Older adults showed lower resolution in their confidence judgments (CJs) for recognition memory tests on the NP items, and this difference appeared to influence rates of retrieval shift, given that retrieval use was correlated with CJ magnitudes in both age groups. Older adults had particular difficulty with accuracy and confidence for rearranged pairs, relative to intact pairs. Older adults' slowed retrieval shift appears to be due to (a) impaired associative learning early in practice, not just a lower FOK; but also (b) retrieval reluctance later in practice after the degree of associative learning would afford memory-based responding. PMID:21401263

Investigating the importance of Delaunay-based definition of atomic interactions in scoring of protein-protein docking results.

PubMed

Jafari, Rahim; Sadeghi, Mehdi; Mirzaie, Mehdi

2016-05-01

The approaches taken to represent and describe structural features of the macromolecules are of major importance when developing computational methods for studying and predicting their structures and interactions. This study attempts to explore the significance of Delaunay tessellation for the definition of atomic interactions by evaluating its impact on the performance of scoring protein-protein docking prediction. Two sets of knowledge-based scoring potentials are extracted from a training dataset of native protein-protein complexes. The potential of the first set is derived using atomic interactions extracted from Delaunay tessellated structures. The potential of the second set is calculated conventionally, that is, using atom pairs whose interactions were determined by their separation distances. The scoring potentials were tested against two different docking decoy sets and their performances were compared. The results show that, if properly optimized, the Delaunay-based scoring potentials can achieve higher success rate than the usual scoring potentials. These results and the results of a previous study on the use of Delaunay-based potentials in protein fold recognition, all point to the fact that Delaunay tessellation of protein structure can provide a more realistic definition of atomic interaction, and therefore, if appropriately utilized, may be able to improve the accuracy of pair potentials. Copyright © 2016 Elsevier Inc. All rights reserved.

Selective classification for improved robustness of myoelectric control under nonideal conditions.

PubMed

Scheme, Erik J; Englehart, Kevin B; Hudgins, Bernard S

2011-06-01

Recent literature in pattern recognition-based myoelectric control has highlighted a disparity between classification accuracy and the usability of upper limb prostheses. This paper suggests that the conventionally defined classification accuracy may be idealistic and may not reflect true clinical performance. Herein, a novel myoelectric control system based on a selective multiclass one-versus-one classification scheme, capable of rejecting unknown data patterns, is introduced. This scheme is shown to outperform nine other popular classifiers when compared using conventional classification accuracy as well as a form of leave-one-out analysis that may be more representative of real prosthetic use. Additionally, the classification scheme allows for real-time, independent adjustment of individual class-pair boundaries making it flexible and intuitive for clinical use.

Dactyl Alphabet Gesture Recognition in a Video Sequence Using Microsoft Kinect

NASA Astrophysics Data System (ADS)

Artyukhin, S. G.; Mestetskiy, L. M.

2015-05-01

This paper presents an efficient framework for solving the problem of static gesture recognition based on data obtained from the web cameras and depth sensor Kinect (RGB-D - data). Each gesture given by a pair of images: color image and depth map. The database store gestures by it features description, genereated by frame for each gesture of the alphabet. Recognition algorithm takes as input a video sequence (a sequence of frames) for marking, put in correspondence with each frame sequence gesture from the database, or decide that there is no suitable gesture in the database. First, classification of the frame of the video sequence is done separately without interframe information. Then, a sequence of successful marked frames in equal gesture is grouped into a single static gesture. We propose a method combined segmentation of frame by depth map and RGB-image. The primary segmentation is based on the depth map. It gives information about the position and allows to get hands rough border. Then, based on the color image border is specified and performed analysis of the shape of the hand. Method of continuous skeleton is used to generate features. We propose a method of skeleton terminal branches, which gives the opportunity to determine the position of the fingers and wrist. Classification features for gesture is description of the position of the fingers relative to the wrist. The experiments were carried out with the developed algorithm on the example of the American Sign Language. American Sign Language gesture has several components, including the shape of the hand, its orientation in space and the type of movement. The accuracy of the proposed method is evaluated on the base of collected gestures consisting of 2700 frames.

NMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG)2 Reveal a Dynamic UU Internal Loop Found in Myotonic Dystrophy Type 1†

PubMed Central

Parkesh, Raman; Fountain, Matthew; Disney, Matthew D.

2011-01-01

The NMR structure of an RNA with a copy of the 5′CUG/3′GUC motif found in the triplet repeating disorder myotonic dystrophy type 1 (DM1) is disclosed. The lowest energy conformation of the UU pair is a single hydrogen bonded structure; however, the UU protons undergo exchange indicating structural dynamics. Molecular dynamics simulations show that the single hydrogen bonded structure is the most populated one but the UU pair interconverts between 0, 1, and 2 hydrogen bonded pairs. These studies have implications for the recognition of the DM1 RNA by small molecules and proteins. PMID:21204525

The predictive power of Japanese candlestick charting in Chinese stock market

NASA Astrophysics Data System (ADS)

Chen, Shi; Bao, Si; Zhou, Yu

2016-09-01

This paper studies the predictive power of 4 popular pairs of two-day bullish and bearish Japanese candlestick patterns in Chinese stock market. Based on Morris' study, we give the quantitative details of definition of long candlestick, which is important in two-day candlestick pattern recognition but ignored by several previous researches, and we further give the quantitative definitions of these four pairs of two-day candlestick patterns. To test the predictive power of candlestick patterns on short-term price movement, we propose the definition of daily average return to alleviate the impact of correlation among stocks' overlap-time returns in statistical tests. To show the robustness of our result, two methods of trend definition are used for both the medium-market-value and large-market-value sample sets. We use Step-SPA test to correct for data snooping bias. Statistical results show that the predictive power differs from pattern to pattern, three of the eight patterns provide both short-term and relatively long-term prediction, another one pair only provide significant forecasting power within very short-term period, while the rest three patterns present contradictory results for different market value groups. For all the four pairs, the predictive power drops as predicting time increases, and forecasting power is stronger for stocks with medium market value than those with large market value.

Positive messages enhance older adults' motivation and recognition memory for physical activity programmes.

PubMed

Notthoff, Nanna; Klomp, Peter; Doerwald, Friederike; Scheibe, Susanne

2016-09-01

Although physical activity is an effective way to cope with ageing-related impairments, few older people are motivated to turn their sedentary lifestyle into an active one. Recent evidence suggests that walking can be more effectively promoted in older adults with positive messages about the benefits of walking than with negative messages about the risks of inactivity. This study examined motivation and memory as the supposed mechanisms underlying the greater effectiveness of positively framed compared to negatively framed messages for promoting activity. Older adults ( N  = 53, age 60-87 years) were introduced to six physical activity programmes that were randomly paired with either positively framed or negatively framed messages. Participants indicated how motivated they were to participate in each programme by providing ratings on attractiveness, suitability, capability and intention. They also completed surprise free recall and recognition tests. Respondents felt more motivated to participate in physical activity programmes paired with positively framed messages than in those with negatively framed ones. They also had better recognition memory for positively framed than negatively framed messages, and misremembered negatively framed messages to be positively framed. Findings support the notion that socioemotional selectivity theory-a theory of age-related changes in motivation-is a useful basis for health intervention design.

English Listeners Use Suprasegmental Cues to Lexical Stress Early During Spoken-Word Recognition

PubMed Central

Poellmann, Katja; Kong, Ying-Yee

2017-01-01

Purpose We used an eye-tracking technique to investigate whether English listeners use suprasegmental information about lexical stress to speed up the recognition of spoken words in English. Method In a visual world paradigm, 24 young English listeners followed spoken instructions to choose 1 of 4 printed referents on a computer screen (e.g., “Click on the word admiral”). Displays contained a critical pair of words (e.g., ˈadmiral–ˌadmiˈration) that were segmentally identical for their first 2 syllables but differed suprasegmentally in their 1st syllable: One word began with primary lexical stress, and the other began with secondary lexical stress. All words had phrase-level prominence. Listeners' relative proportion of eye fixations on these words indicated their ability to differentiate them over time. Results Before critical word pairs became segmentally distinguishable in their 3rd syllables, participants fixated target words more than their stress competitors, but only if targets had initial primary lexical stress. The degree to which stress competitors were fixated was independent of their stress pattern. Conclusions Suprasegmental information about lexical stress modulates the time course of spoken-word recognition. Specifically, suprasegmental information on the primary-stressed syllable of words with phrase-level prominence helps in distinguishing the word from phonological competitors with secondary lexical stress. PMID:28056135

Low-Rank Tensor Subspace Learning for RGB-D Action Recognition.

PubMed

Jia, Chengcheng; Fu, Yun

2016-07-09

Since RGB-D action data inherently equip with extra depth information compared with RGB data, recently many works employ RGB-D data in a third-order tensor representation containing spatio-temporal structure to find a subspace for action recognition. However, there are two main challenges of these methods. First, the dimension of subspace is usually fixed manually. Second, preserving local information by finding intraclass and inter-class neighbors from a manifold is highly timeconsuming. In this paper, we learn a tensor subspace, whose dimension is learned automatically by low-rank learning, for RGB-D action recognition. Particularly, the tensor samples are factorized to obtain three Projection Matrices (PMs) by Tucker Decomposition, where all the PMs are performed by nuclear norm in a close-form to obtain the tensor ranks which are used as tensor subspace dimension. Additionally, we extract the discriminant and local information from a manifold using a graph constraint. This graph preserves the local knowledge inherently, which is faster than the previous way by calculating both the intra-class and inter-class neighbors of each sample. We evaluate the proposed method on four widely used RGB-D action datasets including MSRDailyActivity3D, MSRActionPairs, MSRActionPairs skeleton and UTKinect-Action3D datasets, and the experimental results show higher accuracy and efficiency of the proposed method.

A Method of Three-Dimensional Recording of Mandibular Movement Based on Two-Dimensional Image Feature Extraction

PubMed Central

Li, Zhongke; Yang, Huifang; Lü, Peijun; Wang, Yong; Sun, Yuchun

2015-01-01

Background and Objective To develop a real-time recording system based on computer binocular vision and two-dimensional image feature extraction to accurately record mandibular movement in three dimensions. Methods A computer-based binocular vision device with two digital cameras was used in conjunction with a fixed head retention bracket to track occlusal movement. Software was developed for extracting target spatial coordinates in real time based on two-dimensional image feature recognition. A plaster model of a subject’s upper and lower dentition were made using conventional methods. A mandibular occlusal splint was made on the plaster model, and then the occlusal surface was removed. Temporal denture base resin was used to make a 3-cm handle extending outside the mouth connecting the anterior labial surface of the occlusal splint with a detection target with intersecting lines designed for spatial coordinate extraction. The subject's head was firmly fixed in place, and the occlusal splint was fully seated on the mandibular dentition. The subject was then asked to make various mouth movements while the mandibular movement target locus point set was recorded. Comparisons between the coordinate values and the actual values of the 30 intersections on the detection target were then analyzed using paired t-tests. Results The three-dimensional trajectory curve shapes of the mandibular movements were consistent with the respective subject movements. Mean XYZ coordinate values and paired t-test results were as follows: X axis: -0.0037 ± 0.02953, P = 0.502; Y axis: 0.0037 ± 0.05242, P = 0.704; and Z axis: 0.0007 ± 0.06040, P = 0.952. The t-test result showed that the coordinate values of the 30 cross points were considered statistically no significant. (P<0.05) Conclusions Use of a real-time recording system of three-dimensional mandibular movement based on computer binocular vision and two-dimensional image feature recognition technology produced a recording accuracy of approximately ± 0.1 mm, and is therefore suitable for clinical application. Certainly, further research is necessary to confirm the clinical applications of the method. PMID:26375800

Physical signals for protein-DNA recognition

NASA Astrophysics Data System (ADS)

Cao, Xiao-Qin; Zeng, Jia; Yan, Hong

2009-09-01

This paper discovers consensus physical signals around eukaryotic splice sites, transcription start sites, and replication origin start and end sites on a genome-wide scale based on their DNA flexibility profiles calculated by three different flexibility models. These salient physical signals are localized highly rigid and flexible DNAs, which may play important roles in protein-DNA recognition by the sliding search mechanism. The found physical signals lead us to a detailed hypothetical view of the search process in which a DNA-binding protein first finds a genomic region close to the target site from an arbitrary starting location by three-dimensional (3D) hopping and intersegment transfer mechanisms for long distances, and subsequently uses the one-dimensional (1D) sliding mechanism facilitated by the localized highly rigid DNAs to accurately locate the target flexible binding site within 30 bp (base pair) short distances. Guided by these physical signals, DNA-binding proteins rapidly search the entire genome to recognize a specific target site from the 3D to 1D pathway. Our findings also show that current promoter prediction programs (PPPs) based on DNA physical properties may suffer from lots of false positives because other functional sites such as splice sites and replication origins have similar physical signals as promoters do.

A protein block based fold recognition method for the annotation of twilight zone sequences.

PubMed

Suresh, V; Ganesan, K; Parthasarathy, S

2013-03-01

The description of protein backbone was recently improved with a group of structural fragments called Structural Alphabets instead of the regular three states (Helix, Sheet and Coil) secondary structure description. Protein Blocks is one of the Structural Alphabets used to describe each and every region of protein backbone including the coil. According to de Brevern (2000) the Protein Blocks has 16 structural fragments and each one has 5 residues in length. Protein Blocks fragments are highly informative among the available Structural Alphabets and it has been used for many applications. Here, we present a protein fold recognition method based on Protein Blocks for the annotation of twilight zone sequences. In our method, we align the predicted Protein Blocks of a query amino acid sequence with a library of assigned Protein Blocks of 953 known folds using the local pair-wise alignment. The alignment results with z-value ≥ 2.5 and P-value ≤ 0.08 are predicted as possible folds. Our method is able to recognize the possible folds for nearly 35.5% of the twilight zone sequences with their predicted Protein Block sequence obtained by pb_prediction, which is available at Protein Block Export server.

Better the devil you know? Nonconscious processing of identity and affect of famous faces.

PubMed

Stone, Anna; Valentine, Tim

2004-06-01

The nonconscious recognition of facial identity was investigated in two experiments featuring brief (17-msec) masked stimulus presentation to prevent conscious recognition. Faces were presented in simultaneous pairs of one famous face and one unfamiliar face, and participants attempted to select the famous face. Subsequently, participants rated the famous persons as "good" or "evil" (Experiment 1) or liked or disliked (Experiment 2). In Experiments 1 and 2, responses were less accurate to faces of persons rated evil/disliked than to faces of persons rated good/liked, and faces of persons rated evil/disliked were selected significantly below chance. Experiment 2 showed the effect in a within-items analysis: A famous face was selected less often by participants who disliked the person than by participants who liked the person, and the former were selected below chance accuracy. The within-items analysis rules out possible confounding factors based on variations in physical characteristics of the stimulus faces and confirms that the effects are due to participants' attitudes toward the famous persons. The results suggest that facial identity is recognized preconsciously, and that responses may be based on affect rather than familiarity.

Observing Holliday junction branch migration one step at a time

NASA Astrophysics Data System (ADS)

Ha, Taekjip

2004-03-01

During genetic recombination, two homologous DNA molecules undergo strand exchange to form a four-way DNA (Holliday) junction and the recognition and processing of this species by branch migration and junction resolving enzymes determine the outcome. We have used single molecule fluorescence techniques to study two intrinsic structural dynamics of the Holliday junction, stacking conformer transitions and spontaneous branch migration. Our studies show that the dynamics of branch migration, resolved with one base pair resolution, is determined by the stability of conformers which in turn depends on the local DNA sequences. Therefore, the energy landscape of Holliday junction branch migation is not uniform, but is rugged.

Training the max-margin sequence model with the relaxed slack variables.

PubMed

Niu, Lingfeng; Wu, Jianmin; Shi, Yong

2012-09-01

Sequence models are widely used in many applications such as natural language processing, information extraction and optical character recognition, etc. We propose a new approach to train the max-margin based sequence model by relaxing the slack variables in this paper. With the canonical feature mapping definition, the relaxed problem is solved by training a multiclass Support Vector Machine (SVM). Compared with the state-of-the-art solutions for the sequence learning, the new method has the following advantages: firstly, the sequence training problem is transformed into a multiclassification problem, which is more widely studied and already has quite a few off-the-shelf training packages; secondly, this new approach reduces the complexity of training significantly and achieves comparable prediction performance compared with the existing sequence models; thirdly, when the size of training data is limited, by assigning different slack variables to different microlabel pairs, the new method can use the discriminative information more frugally and produces more reliable model; last but not least, by employing kernels in the intermediate multiclass SVM, nonlinear feature space can be easily explored. Experimental results on the task of named entity recognition, information extraction and handwritten letter recognition with the public datasets illustrate the efficiency and effectiveness of our method. Copyright © 2012 Elsevier Ltd. All rights reserved.

Structure of homeodomain-leucine zipper/DNA complexes studied using hydroxyl radical cleavage of DNA and methylation interference.

PubMed

Tron, Adriana E; Comelli, Raúl N; Gonzalez, Daniel H

2005-12-27

Homeodomain-leucine zipper (HD-Zip) proteins, unlike most homeodomain proteins, bind a pseudopalindromic DNA sequence as dimers. We have investigated the structure of the DNA complexes formed by two HD-Zip proteins with different nucleotide preferences at the central position of the binding site using footprinting and interference methods. The results indicate that the respective complexes are not symmetric, with the strand bearing a central purine (top strand) showing higher protection around the central region and the bottom strand protected toward the 3' end. Binding to a sequence with a nonpreferred central base pair produces a decrease in protection in either the top or the bottom strand, depending upon the protein. Modeling studies derived from the complex formed by the monomeric Antennapedia homeodomain with DNA indicate that in the HD-Zip/DNA complex the recognition helix of one of the monomers is displaced within the major groove respective to the other one. This monomer seems to lose contacts with a part of the recognition sequence upon binding to the nonpreferred site. The results show that the structure of the complex formed by HD-Zip proteins with DNA is dependent upon both protein intrinsic characteristics and the nucleotides present at the central position of the recognition sequence.

Structural basis of UGUA recognition by the Nudix protein CFIm25 and implications for a regulatory role in mRNA 3′ processing

PubMed Central

Yang, Qin; Gilmartin, Gregory M.; Doublié, Sylvie

2010-01-01

Human Cleavage Factor Im (CFIm) is an essential component of the pre-mRNA 3′ processing complex that functions in the regulation of poly(A) site selection through the recognition of UGUA sequences upstream of the poly(A) site. Although the highly conserved 25 kDa subunit (CFIm25) of the CFIm complex possesses a characteristic α/β/α Nudix fold, CFIm25 has no detectable hydrolase activity. Here we report the crystal structures of the human CFIm25 homodimer in complex with UGUAAA and UUGUAU RNA sequences. CFIm25 is the first Nudix protein to be reported to bind RNA in a sequence-specific manner. The UGUA sequence contributes to binding specificity through an intramolecular G:A Watson–Crick/sugar-edge base interaction, an unusual pairing previously found to be involved in the binding specificity of the SAM-III riboswitch. The structures, together with mutational data, suggest a novel mechanism for the simultaneous sequence-specific recognition of two UGUA elements within the pre-mRNA. Furthermore, the mutually exclusive binding of RNA and the signaling molecule Ap4A (diadenosine tetraphosphate) by CFIm25 suggests a potential role for small molecules in the regulation of mRNA 3′ processing. PMID:20479262

Structural basis of UGUA recognition by the Nudix protein CFI(m)25 and implications for a regulatory role in mRNA 3' processing.

PubMed

Yang, Qin; Gilmartin, Gregory M; Doublié, Sylvie

2010-06-01

Human Cleavage Factor Im (CFI(m)) is an essential component of the pre-mRNA 3' processing complex that functions in the regulation of poly(A) site selection through the recognition of UGUA sequences upstream of the poly(A) site. Although the highly conserved 25 kDa subunit (CFI(m)25) of the CFI(m) complex possesses a characteristic alpha/beta/alpha Nudix fold, CFI(m)25 has no detectable hydrolase activity. Here we report the crystal structures of the human CFI(m)25 homodimer in complex with UGUAAA and UUGUAU RNA sequences. CFI(m)25 is the first Nudix protein to be reported to bind RNA in a sequence-specific manner. The UGUA sequence contributes to binding specificity through an intramolecular G:A Watson-Crick/sugar-edge base interaction, an unusual pairing previously found to be involved in the binding specificity of the SAM-III riboswitch. The structures, together with mutational data, suggest a novel mechanism for the simultaneous sequence-specific recognition of two UGUA elements within the pre-mRNA. Furthermore, the mutually exclusive binding of RNA and the signaling molecule Ap(4)A (diadenosine tetraphosphate) by CFI(m)25 suggests a potential role for small molecules in the regulation of mRNA 3' processing.

Taboo words: the effect of emotion on memory for peripheral information.

PubMed

Guillet, Rebecca; Arndt, Jason

2009-09-01

In three experiments, we examined memory for peripheral information that occurred in the same context as emotion-inducing information. In the first two experiments, participants studied either a sentence (Experiment 1) or a pair of words (Experiments 2A-2C) containing a neutral peripheral word, as well as a neutral, negative-valence, or taboo word, to induce an emotional response. At retrieval, the participants were asked to recall the neutral peripheral word from a sentence fragment or emotion-inducing word cue. In Experiment 3, we presented word pairs at encoding and tested memory with associative recognition. In all three experiments, memory for peripheral words was enhanced when it was encoded in the presence of emotionally arousing taboo words but not when it was encoded in the presence of words that were only negative in valence. These data are consistent with priority-binding theory (MacKay et al., 2004) and inconsistent with the attention-narrowing hypothesis (Easterbrook, 1959), as well as with object-based binding theory (Mather, 2007).

A challenging dissociation in masked identity priming with the lexical decision task.

PubMed

Perea, Manuel; Jiménez, María; Gómez, Pablo

2014-05-01

The masked priming technique has been used extensively to explore the early stages of visual-word recognition. One key phenomenon in masked priming lexical decision is that identity priming is robust for words, whereas it is small/unreliable for nonwords. This dissociation has usually been explained on the basis that masked priming effects are lexical in nature, and hence there should not be an identity prime facilitation for nonwords. We present two experiments whose results are at odds with the assumption made by models that postulate that identity priming is purely lexical, and also challenge the assumption that word and nonword responses are based on the same information. Our experiments revealed that for nonwords, but not for words, matched-case identity PRIME-TARGET pairs were responded to faster than mismatched-case identity prime-TARGET pairs, and this phenomenon was not modulated by the lowercase/uppercase feature similarity of the stimuli. Copyright © 2014 Elsevier B.V. All rights reserved.

Glucose-nucleobase pairs within DNA: impact of hydrophobicity, alternative linking unit and DNA polymerase nucleotide insertion studies† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc04850e

PubMed Central

Vengut-Climent, Empar; Peñalver, Pablo; Lucas, Ricardo; Gómez-Pinto, Irene; Aviñó, Anna; Muro-Pastor, Alicia M.; Galbis, Elsa; de Paz, M. Violante; Fonseca Guerra, Célia; Bickelhaupt, F. Matthias; Eritja, Ramón; González, Carlos

2018-01-01

Recently, we studied glucose-nucleobase pairs, a binding motif found in aminoglycoside–RNA recognition. DNA duplexes with glucose as a nucleobase were able to hybridize and were selective for purines. They were less stable than natural DNA but still fit well on regular B-DNA. These results opened up the possible use of glucose as a non-aromatic DNA base mimic. Here, we have studied the incorporation and thermal stability of glucose with different types of anchoring units and alternative apolar sugar-nucleobase pairs. When we explored butanetriol instead of glycerol as a wider anchoring unit, we did not gain duplex thermal stability. This result confirmed the necessity of a more conformationally restricted linker to increase the overall duplex stability. Permethylated glucose-nucleobase pairs showed similar stability to glucoside-nucleobase pairs but no selectivity for a specific nucleobase, possibly due to the absence of hydrogen bonds between them. The three-dimensional structure of the duplex solved by NMR located both, the hydrophobic permethylated glucose and the nucleobase, inside the DNA helix as in the case of glucose-nucleobase pairs. Quantum chemical calculations on glucose-nucleobase pairs indicate that the attachment of the sugar to the DNA skeleton through the OH1 or OH4 positions yields the highest binding energies. Moreover, glucose was very selective for guanine when attached through OH1 or OH4 to the DNA. Finally, we examined DNA polymerase insertion of nucleotides in front of the saccharide unit. KF– polymerase from E. coli inserted A and G opposite glc and 6dglc with low efficiency but notable selectivity. It is even capable of extending the new pair although its efficiency depended on the DNA sequence. In contrast, Bst 2.0, SIII and BIOTAQ™ DNA polymerases seem to display a loop-out mechanism possibly due to the flexible glycerol linker used instead of deoxyribose. PMID:29780486

Automatic signal extraction, prioritizing and filtering approaches in detecting post-marketing cardiovascular events associated with targeted cancer drugs from the FDA Adverse Event Reporting System (FAERS).

PubMed

Xu, Rong; Wang, Quanqiu

2014-02-01

Targeted drugs dramatically improve the treatment outcomes in cancer patients; however, these innovative drugs are often associated with unexpectedly high cardiovascular toxicity. Currently, cardiovascular safety represents both a challenging issue for drug developers, regulators, researchers, and clinicians and a concern for patients. While FDA drug labels have captured many of these events, spontaneous reporting systems are a main source for post-marketing drug safety surveillance in 'real-world' (outside of clinical trials) cancer patients. In this study, we present approaches to extracting, prioritizing, filtering, and confirming cardiovascular events associated with targeted cancer drugs from the FDA Adverse Event Reporting System (FAERS). The dataset includes records of 4,285,097 patients from FAERS. We first extracted drug-cardiovascular event (drug-CV) pairs from FAERS through named entity recognition and mapping processes. We then compared six ranking algorithms in prioritizing true positive signals among extracted pairs using known drug-CV pairs derived from FDA drug labels. We also developed three filtering algorithms to further improve precision. Finally, we manually validated extracted drug-CV pairs using 21 million published MEDLINE records. We extracted a total of 11,173 drug-CV pairs from FAERS. We showed that ranking by frequency is significantly more effective than by the five standard signal detection methods (246% improvement in precision for top-ranked pairs). The filtering algorithm we developed further improved overall precision by 91.3%. By manual curation using literature evidence, we show that about 51.9% of the 617 drug-CV pairs that appeared in both FAERS and MEDLINE sentences are true positives. In addition, 80.6% of these positive pairs have not been captured by FDA drug labeling. The unique drug-CV association dataset that we created based on FAERS could facilitate our understanding and prediction of cardiotoxic events associated with targeted cancer drugs. Copyright © 2013 Elsevier Inc. All rights reserved.

Orthographic Processing in Visual Word Identification.

ERIC Educational Resources Information Center

Humphreys, Glyn W.; And Others

1990-01-01

A series of 6 experiments involving 210 subjects from a college subject pool examined orthographic priming effects between briefly presented pairs of letter strings. A theory of othographic priming is presented, and the implications of the findings for understanding word recognition and reading are discussed. (SLD)

Alcohol and Memory: Storage and State Dependency

ERIC Educational Resources Information Center

Parker, Elizabeth S.; And Others

1976-01-01

Effects of acute alcohol intoxication on the storage phase of memory were evaluated with two tasks that minimized response retrieval: unpaced paired-associate learning with highly available responses and forced-choice picture recognition. It was concluded that storage processes are sensitive to disruption by alcohol. (CHK)

Evidence of protein-free homology recognition in magnetic bead force–extension experiments

PubMed Central

(O’) Lee, D. J.; Danilowicz, C.; Rochester, C.; Prentiss, M.

2016-01-01

Earlier theoretical studies have proposed that the homology-dependent pairing of large tracts of dsDNA may be due to physical interactions between homologous regions. Such interactions could contribute to the sequence-dependent pairing of chromosome regions that may occur in the presence or the absence of double-strand breaks. Several experiments have indicated the recognition of homologous sequences in pure electrolytic solutions without proteins. Here, we report single-molecule force experiments with a designed 60 kb long dsDNA construct; one end attached to a solid surface and the other end to a magnetic bead. The 60 kb constructs contain two 10 kb long homologous tracts oriented head to head, so that their sequences match if the two tracts fold on each other. The distance between the bead and the surface is measured as a function of the force applied to the bead. At low forces, the construct molecules extend substantially less than normal, control dsDNA, indicating the existence of preferential interaction between the homologous regions. The force increase causes no abrupt but continuous unfolding of the paired homologous regions. Simple semi-phenomenological models of the unfolding mechanics are proposed, and their predictions are compared with the data. PMID:27493568

Perceptual Simulations and Linguistic Representations Have Differential Effects on Speeded Relatedness Judgments and Recognition Memory

PubMed Central

Tse, Chi-Shing; Kurby, Christopher A.; Du, Feng

2010-01-01

We examined the effect of spatial iconicity (a perceptual simulation of canonical locations of objects) and word-order frequency on language processing and episodic memory of orientation. Participants made speeded relatedness judgments to pairs of words presented in locations typical to their real world arrangements (e.g., ceiling on top and floor on bottom). They then engaged in a surprise orientation recognition task for the word pairs. We replicated Louwerse’s finding (2008) that word-order frequency has a stronger effect on semantic relatedness judgments than spatial iconicity. This is consistent with recent suggestions that linguistic representations have a stronger impact on immediate decisions about verbal materials than perceptual simulations. In contrast, spatial iconicity enhanced episodic memory of orientation to a greater extent than word-order frequency did. This new finding indicates that perceptual simulations have an important role in episodic memory. Results are discussed with respect to theories of perceptual representation and linguistic processing. PMID:19742388

The gender congruency effect during bilingual spoken-word recognition

PubMed Central

Morales, Luis; Paolieri, Daniela; Dussias, Paola E.; Valdés kroff, Jorge R.; Gerfen, Chip; Bajo, María Teresa

2016-01-01

We investigate the ‘gender-congruency’ effect during a spoken-word recognition task using the visual world paradigm. Eye movements of Italian–Spanish bilinguals and Spanish monolinguals were monitored while they viewed a pair of objects on a computer screen. Participants listened to instructions in Spanish (encuentra la bufanda / ‘find the scarf’) and clicked on the object named in the instruction. Grammatical gender of the objects’ name was manipulated so that pairs of objects had the same (congruent) or different (incongruent) gender in Italian, but gender in Spanish was always congruent. Results showed that bilinguals, but not monolinguals, looked at target objects less when they were incongruent in gender, suggesting a between-language gender competition effect. In addition, bilinguals looked at target objects more when the definite article in the spoken instructions provided a valid cue to anticipate its selection (different-gender condition). The temporal dynamics of gender processing and cross-language activation in bilinguals are discussed. PMID:28018132

In search of memory tests equivalent for experiments on animals and humans.

PubMed

Brodziak, Andrzej; Kołat, Estera; Różyk-Myrta, Alicja

2014-12-19

Older people often exhibit memory impairments. Contemporary demographic trends cause aging of the society. In this situation, it is important to conduct clinical trials of drugs and use training methods to improve memory capacity. Development of new memory tests requires experiments on animals and then clinical trials in humans. Therefore, we decided to review the assessment methods and search for tests that evaluate analogous cognitive processes in animals and humans. This review has enabled us to propose 2 pairs of tests of the efficiency of working memory capacity in animals and humans. We propose a basic set of methods for complex clinical trials of drugs and training methods to improve memory, consisting of 2 pairs of tests: 1) the Novel Object Recognition Test - Sternberg Item Recognition Test and 2) the Object-Location Test - Visuospatial Memory Test. We postulate that further investigations of methods that are equivalent in animals experiments and observations performed on humans are necessary.

Atomic substitution reveals the structural basis for substrate adenine recognition and removal by adenine DNA glycosylase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Seongmin; Verdine, Gregory L.; Harvard)

2010-01-14

Adenine DNA glycosylase catalyzes the glycolytic removal of adenine from the promutagenic A {center_dot} oxoG base pair in DNA. The general features of DNA recognition by an adenine DNA glycosylase, Bacillus stearothermophilus MutY, have previously been revealed via the X-ray structure of a catalytically inactive mutant protein bound to an A:oxoG-containing DNA duplex. Although the structure revealed the substrate adenine to be, as expected, extruded from the DNA helix and inserted into an extrahelical active site pocket on the enzyme, the substrate adenine engaged in no direct contacts with active site residues. This feature was paradoxical, because other glycosylases havemore » been observed to engage their substrates primarily through direct contacts. The lack of direct contacts in the case of MutY suggested that either MutY uses a distinctive logic for substrate recognition or that the X-ray structure had captured a noncatalytically competent state in lesion recognition. To gain further insight into this issue, we crystallized wild-type MutY bound to DNA containing a catalytically inactive analog of 2'-deoxyadenosine in which a single 2'-H atom was replaced by fluorine. The structure of this fluorinated lesion-recognition complex (FLRC) reveals the substrate adenine buried more deeply into the active site pocket than in the prior structure and now engaged in multiple direct hydrogen bonding and hydrophobic interactions. This structure appears to capture the catalytically competent state of adenine DNA glycosylases, and it suggests a catalytic mechanism for this class of enzymes, one in which general acid-catalyzed protonation of the nucleobase promotes glycosidic bond cleavage.« less

Identification of full length bovine TLR1 and functional characterization of lipopeptide recognition by bovine TLR2/1 heterodimer

PubMed Central

Farhat, Katja; Riekenberg, Sabine; Jung, Günther; Wiesmüller, Karl-Heinz; Jungi, Thomas W.; Ulmer, Artur J.

2010-01-01

Toll-like receptors (TLR) are highly conserved pattern recognition receptors of the innate immune system. Toll-like receptor 2 (TLR2) recognizes bacterial lipopeptides in a heterodimeric complex with TLR6 or TLR1, thereby discriminating between di- or triacylated lipopeptides, respectively. Previously, we found that HEK293 cells transfected with bovine TLR2 (boTLR2) were able to respond to diacylated lipopeptides but did not recognize triacylated lipopeptides, even after cotransfection with the so far published sequence of boTLR1. In this study we now could show that primary bovine cells were in general able to detect triacylated lipopetides. A closer investigation of the boTLR1 gene locus revealed an additional ATG 195 base pairs upstream from the published start codon. Its transcription would result in an N-terminus with high identity to human and murine TLR1 (huTLR1, muTLR1). Cloning and cotransfection of this longer boTLR1 with boTLR2 now resulted in the recognition of triacylated lipopeptides by HEK293 cells, thereby resembling the ex vivo observation. Analysis of the structure-activity relationship showed that the ester-bound acid chains of these lipopeptides need to consist of at least 12 carbon atoms to activate the bovine heterodimer showing similarity to the recognition by huTLR2/huTLR1. In contrast, HEK293 cell cotransfected with muTLR2 and muTLR1 could already be activated by lipopeptides with shorter fatty acids of only 6 carbon atoms. Thus, our data indicate that the additional N-terminal nucleotides belong to the full length and functionally active boTLR1 (boTLR1-fl) which participates in a species-specific recognition of bacterial lipopeptides. PMID:20167196

A Triad of Molecular Regions Contribute to the Formation of Two Distinct MHC Class II Conformers

PubMed Central

Drake, Lisa A.; Drake, James R.

2016-01-01

MHC class II molecules present antigen-derived peptides to CD4 T cells to drive the adaptive immune response. Previous work has established that class II αβ dimers can adopt two distinct conformations, driven by the differential pairing of transmembrane domain GxxxG dimerization motifs. These class II conformers differ in their ability to be loaded with antigen-derived peptide and to effectively engage CD4 T cells. Motif 1 (M1) paired I-Ak class II molecules are efficiently loaded with peptides derived from the processing of B cell receptor-bound antigen, have unique B cell signaling properties and high T cell stimulation activity. The 11-5.2 mAb selectively binds M1 paired I-Ak class II molecules. However, the molecular determinants of 11-5.2 binding are currently unclear. Here, we report the ability of a human class II transmembrane domain to drive both M1 and M2 class II conformer formation. Protease sensitivity analysis further strengthens the idea that there are conformational differences between the extracellular domains of M1 and M2 paired class II. Finally, MHC class II chain alignments and site directed mutagenesis reveals a triad of molecular regions that contributes to 11-5.2 mAb binding. In addition to transmembrane GxxxG motif domain pairing, 11-5.2 binding is influenced directly by α chain residue Glu-71 and indirectly by the region around the inter-chain salt bridge formed by α chain Arg-52 and β chain Glu-86. These findings provide insight into the complexity of 11-5.2 mAb recognition of the M1 paired I-Ak class II conformer and further highlight the molecular heterogeneity of peptide-MHC class II complexes that drive T cell antigen recognition. PMID:27148821

Aerobic fitness and executive control of relational memory in preadolescent children.

PubMed

Chaddock, Laura; Hillman, Charles H; Buck, Sarah M; Cohen, Neal J

2011-02-01

the neurocognitive benefits of an active lifestyle in childhood have public health and educational implications, especially as children in today's technological society are becoming increasingly overweight, unhealthy, and unfit. Human and animal studies show that aerobic exercise affects both prefrontal executive control and hippocampal function. This investigation attempts to bridge these research threads by using a cognitive task to examine the relationship between aerobic fitness and executive control of relational memory in preadolescent 9- and 10-yr-old children. higher-fit and lower-fit children studied faces and houses under individual item (i.e., nonrelational) and relational encoding conditions, and the children were subsequently tested with recognition memory trials consisting of previously studied pairs and pairs of completely new items. With each subject participating in both item and relational encoding conditions, and with recognition test trials amenable to the use of both item and relational memory cues, this task afforded a challenge to the flexible use of memory, specifically in the use of appropriate encoding and retrieval strategies. Hence, the task provided a test of both executive control and memory processes. lower-fit children showed poorer recognition memory performance than higher-fit children, selectively in the relational encoding condition. No association between aerobic fitness and recognition performance was found for faces and houses studied as individual items (i.e., nonrelationally). the findings implicate childhood aerobic fitness as a factor in the ability to use effective encoding and retrieval executive control processes for relational memory material and, possibly, in the strategic engagement of prefrontal- and hippocampal-dependent systems.

Capturing specific abilities as a window into human individuality: the example of face recognition.

PubMed

Wilmer, Jeremy B; Germine, Laura; Chabris, Christopher F; Chatterjee, Garga; Gerbasi, Margaret; Nakayama, Ken

2012-01-01

Proper characterization of each individual's unique pattern of strengths and weaknesses requires good measures of diverse abilities. Here, we advocate combining our growing understanding of neural and cognitive mechanisms with modern psychometric methods in a renewed effort to capture human individuality through a consideration of specific abilities. We articulate five criteria for the isolation and measurement of specific abilities, then apply these criteria to face recognition. We cleanly dissociate face recognition from more general visual and verbal recognition. This dissociation stretches across ability as well as disability, suggesting that specific developmental face recognition deficits are a special case of a broader specificity that spans the entire spectrum of human face recognition performance. Item-by-item results from 1,471 web-tested participants, included as supplementary information, fuel item analyses, validation, norming, and item response theory (IRT) analyses of our three tests: (a) the widely used Cambridge Face Memory Test (CFMT); (b) an Abstract Art Memory Test (AAMT), and (c) a Verbal Paired-Associates Memory Test (VPMT). The availability of this data set provides a solid foundation for interpreting future scores on these tests. We argue that the allied fields of experimental psychology, cognitive neuroscience, and vision science could fuel the discovery of additional specific abilities to add to face recognition, thereby providing new perspectives on human individuality.

Nucleic acid-functionalized transition metal nanosheets for biosensing applications

PubMed Central

Mo, Liuting; Li, Juan; Liu, Qiaoling; Qiu, Liping; Tan, Weihong

2017-01-01

In clinical diagnostics, as well as food and environmental safety practices, biosensors are powerful tools for monitoring biological or biochemical processes. Two-dimensional (2D) transition metal nanomaterials, including transition metal chalcogenides (TMCs) and transition metal oxides (TMOs), are receiving growing interest for their use in biosensing applications based on such unique properties as high surface area and fluorescence quenching abilities. Meanwhile, nucleic acid probes based on Watson-Crick base-pairing rules are also being widely applied in biosensing based on their excellent recognition capability. In particular, the emergence of functional nucleic acids in the 1980s, especially aptamers, has substantially extended the recognition capability of nucleic acids to various targets, ranging from small organic molecules and metal ions to proteins and cells. Based on π-π stacking interaction between transition metal nanosheets and nucleic acids, biosensing systems can be easily assembled. Therefore, the combination of 2D transition metal nanomaterials and nucleic acids brings intriguing opportunities in bioanalysis and biomedicine. In this review, we summarize recent advances of nucleic acid-functionalized transition metal nanosheets in biosensing applications. The structure and properties of 2D transition metal nanomaterials are first discussed, emphasizing the interaction between transition metal nanosheets and nucleic acids. Then, the applications of nucleic acid-functionalized transition metal nanosheet-based biosensors are discussed in the context of different signal transducing mechanisms, including optical and electrochemical approaches. Finally, we provide our perspectives on the current challenges and opportunities in this promising field. PMID:27020066

Nucleic acid-functionalized transition metal nanosheets for biosensing applications.

PubMed

Mo, Liuting; Li, Juan; Liu, Qiaoling; Qiu, Liping; Tan, Weihong

2017-03-15

In clinical diagnostics, as well as food and environmental safety practices, biosensors are powerful tools for monitoring biological or biochemical processes. Two-dimensional (2D) transition metal nanomaterials, including transition metal chalcogenides (TMCs) and transition metal oxides (TMOs), are receiving growing interest for their use in biosensing applications based on such unique properties as high surface area and fluorescence quenching abilities. Meanwhile, nucleic acid probes based on Watson-Crick base-pairing rules are also being widely applied in biosensing based on their excellent recognition capability. In particular, the emergence of functional nucleic acids in the 1980s, especially aptamers, has substantially extended the recognition capability of nucleic acids to various targets, ranging from small organic molecules and metal ions to proteins and cells. Based on π-π stacking interaction between transition metal nanosheets and nucleic acids, biosensing systems can be easily assembled. Therefore, the combination of 2D transition metal nanomaterials and nucleic acids brings intriguing opportunities in bioanalysis and biomedicine. In this review, we summarize recent advances of nucleic acid-functionalized transition metal nanosheets in biosensing applications. The structure and properties of 2D transition metal nanomaterials are first discussed, emphasizing the interaction between transition metal nanosheets and nucleic acids. Then, the applications of nucleic acid-functionalized transition metal nanosheet-based biosensors are discussed in the context of different signal transducing mechanisms, including optical and electrochemical approaches. Finally, we provide our perspectives on the current challenges and opportunities in this promising field. Copyright © 2016 Elsevier B.V. All rights reserved.

Monotonic and Nonmonotonic Lag Effects in Paired-Associate and Recognition Memory Paradigms

ERIC Educational Resources Information Center

Glenberg, Arthur M.

1976-01-01

Three experiments are reported investigating the relationship between response recall and the spacing of repetitions as a function of the retention interval. The results of the experiments support the theory which emphasizes the nature of the cues available for retrieval. (Author/RM)

Cross-modal working memory binding and word recognition skills: how specific is the link?

PubMed

Wang, Shinmin; Allen, Richard J

2018-04-01

Recent research has suggested that the creation of temporary bound representations of information from different sources within working memory uniquely relates to word recognition abilities in school-age children. However, it is unclear to what extent this link is attributable specifically to the binding ability for cross-modal information. This study examined the performance of Grade 3 (8-9 years old) children on binding tasks requiring either temporary association formation of two visual items (i.e., within-modal binding) or pairs of visually presented abstract shapes and auditorily presented nonwords (i.e., cross-modal binding). Children's word recognition skills were related to performance on the cross-modal binding task but not on the within-modal binding task. Further regression models showed that cross-modal binding memory was a significant predictor of word recognition when memory for its constituent elements, general abilities, and crucially, within-modal binding memory were taken into account. These findings may suggest a specific link between the ability to bind information across modalities within working memory and word recognition skills.

Diagnosing criterion-level effects on memory: what aspects of memory are enhanced by repeated retrieval?

PubMed

Vaughn, Kalif E; Rawson, Katherine A

2011-09-01

Previous research has shown that increasing the criterion level (i.e., the number of times an item must be correctly retrieved during practice) improves subsequent memory, but which specific components of memory does increased criterion level enhance? In two experiments, we examined the extent to which the criterion level affects associative memory, target memory, and cue memory. Participants studied Lithuanian-English word pairs via cued recall with restudy until items were correctly recalled one to five times. In Experiment 1, participants took one of four recall tests and one of three recognition tests after a 2-day delay. In Experiment 2, participants took only recognition tests after a 1-week delay. In both experiments, increasing the criterion level enhanced associative memory, as indicated by enhanced performance on forward and backward cued-recall tests and on tests of associative recognition. An increased criterion level also improved target memory, as indicated by enhanced free recall and recognition of targets, and improved cue memory, as indicated by enhanced free recall and recognition of cues.

Synergistic binding of bHLH transcription factors to the promoter of the maize NADP-ME gene used in C4 photosynthesis is based on an ancient code found in the ancestral C3 state.

PubMed

Borba, Ana Rita; Serra, Tânia S; Górska, Alicja; Gouveia, Paulo; Cordeiro, André M; Reyna-Llorens, Ivan; Knerová, Jana; Barros, Pedro M; Abreu, Isabel A; Oliveira, M Margarida; Hibberd, Julian M; Saibo, Nelson J M

2018-04-05

C4 photosynthesis has evolved repeatedly from the ancestral C3 state to generate a carbon concentrating mechanism that increases photosynthetic efficiency. This specialised form of photosynthesis is particularly common in the PACMAD clade of grasses, and is used by many of the world's most productive crops. The C4 cycle is accomplished through cell-type specific accumulation of enzymes but cis-elements and transcription factors controlling C4 photosynthesis remain largely unknown. Using the NADP-Malic Enzyme (NADP-ME) gene as a model we tested whether mechanisms impacting on transcription in C4 plants evolved from ancestral components found in C3 species. Two basic Helix-Loop-Helix (bHLH) transcription factors, ZmbHLH128 and ZmbHLH129, were shown to bind the C4NADP-ME promoter from maize. These proteins form heterodimers and ZmbHLH129 impairs trans-activation by ZmbHLH128. Electrophoretic mobility shift assays indicate that a pair of cis-elements separated by a seven base pair spacer synergistically bind either ZmbHLH128 or ZmbHLH129. This pair of cis-elements is found in both C3 and C4 Panicoid grass species of the PACMAD clade. Our analysis is consistent with this cis-element pair originating from a single motif present in the ancestral C3 state. We conclude that C4 photosynthesis has co-opted an ancient C3 regulatory code built on G-box recognition by bHLH to regulate the NADP-ME gene. More broadly, our findings also contribute to the understanding of gene regulatory networks controlling C4 photosynthesis.

Mojo Hand, a TALEN design tool for genome editing applications.

PubMed

Neff, Kevin L; Argue, David P; Ma, Alvin C; Lee, Han B; Clark, Karl J; Ekker, Stephen C

2013-01-16

Recent studies of transcription activator-like (TAL) effector domains fused to nucleases (TALENs) demonstrate enormous potential for genome editing. Effective design of TALENs requires a combination of selecting appropriate genetic features, finding pairs of binding sites based on a consensus sequence, and, in some cases, identifying endogenous restriction sites for downstream molecular genetic applications. We present the web-based program Mojo Hand for designing TAL and TALEN constructs for genome editing applications (http://www.talendesign.org). We describe the algorithm and its implementation. The features of Mojo Hand include (1) automatic download of genomic data from the National Center for Biotechnology Information, (2) analysis of any DNA sequence to reveal pairs of binding sites based on a user-defined template, (3) selection of restriction-enzyme recognition sites in the spacer between the TAL monomer binding sites including options for the selection of restriction enzyme suppliers, and (4) output files designed for subsequent TALEN construction using the Golden Gate assembly method. Mojo Hand enables the rapid identification of TAL binding sites for use in TALEN design. The assembly of TALEN constructs, is also simplified by using the TAL-site prediction program in conjunction with a spreadsheet management aid of reagent concentrations and TALEN formulation. Mojo Hand enables scientists to more rapidly deploy TALENs for genome editing applications.

Polyelectrolyte properties of single stranded DNA measured using SAXS and single molecule FRET: beyond the wormlike chain model

PubMed Central

Meisburger, Steve P.; Sutton, Julie L.; Chen, Huimin; Pabit, Suzette A.; Kirmizialtin, Serdal; Elber, Ron; Pollack, Lois

2013-01-01

Nucleic acids are highly charged polyelectrolytes that interact strongly with salt ions. Rigid, base-paired regions are successfully described with worm like chain models, but non base-paired single stranded regions have fundamentally different polymer properties because of their greater flexibility. Recently, attention has turned to single stranded nucleic acids due to the growing recognition of their biological importance, as well as the availability of sophisticated experimental techniques sensitive to the conformation of individual molecules. We investigate polyelectrolyte properties of poly(dT), an important and widely studied model system for flexible single stranded nucleic acids, in physiologically important mixed mono- and di-valent salt. We report measurements of the form factor and interparticle interactions using SAXS, end to end distances using smFRET, and number of excess ions using ASAXS. We present a coarse-grained model that accounts for flexibility, excluded volume, and electrostatic interactions in these systems. Predictions of the model are validated against experiment. We also discuss the state of all-atom, explicit solvent Molecular Dynamics simulations of poly(dT), the next step in understanding the complexities of ion interactions with these highly charged and flexible polymers. PMID:23606337

Quantitative and qualitative evaluation of a web-based, interactive approach for teaching the management of angle-closure glaucoma.

PubMed

Blumberg, Dana M; Quigley, Harry A; Goldberg, Harry R

2009-02-01

To construct a validated Internet-based teaching system that improves diagnostic and therapeutic skills related to glaucoma diagnosis. Nonrandomized clinical trial. Thirty-four glaucoma specialists and 21 ophthalmologists-in-training. An interactive program was designed to improve the recognition of gonioscopic findings and to manage angle-closure glaucoma (ACG) patients, including technical information in performing gonioscopy, ability to recognize angle structures, and treatment choices. The behavior of participants permitted the assessment of degree of improvement related to the interaction. The program content was validated by 5 academic glaucoma subspecialists. Then, 34 fellowship-trained glaucoma specialists and 21 ophthalmology residents accessed the program. Results were evaluated using paired and nonpaired t tests and analysis of variance. Comparison of pretest and posttest scores of residents and glaucoma specialists on measures of gonioscopy recognition and questions related to ACG management. Residents improved their recognition of gonioscopic findings after viewing the program (P<0.0001), scoring significantly worse than glaucoma specialists before interacting with the program (P<0.0001), but scoring at equivalent levels to specialists after viewing the program (P=0.34). The time necessary to improve knowledge by interacting with the program was significantly related to year of residency training (P<0.0001, analysis of variance). The rate of correct answers to management questions related to ACG increased with increasing years of experience in ophthalmology, validating the education methodology (P<0.0001). A web-based teaching approach for diagnosis and management of ACG evaluated the knowledge of ophthalmologists in a manner consistent with their expected expertize. Statistically significant improvements in validated knowledge of ACG were demonstrated for this educational method.

Toward rules relating zinc finger protein sequences and DNA binding site preferences.

PubMed

Desjarlais, J R; Berg, J M

1992-08-15

Zinc finger proteins of the Cys2-His2 type consist of tandem arrays of domains, where each domain appears to contact three adjacent base pairs of DNA through three key residues. We have designed and prepared a series of variants of the central zinc finger within the DNA binding domain of Sp1 by using information from an analysis of a large data base of zinc finger protein sequences. Through systematic variations at two of the three contact positions (underlined), relatively specific recognition of sequences of the form 5'-GGGGN(G or T)GGG-3' has been achieved. These results provide the basis for rules that may develop into a code that will allow the design of zinc finger proteins with preselected DNA site specificity.

The Maximum Likelihood Estimation of Signature Transformation /MLEST/ algorithm. [for affine transformation of crop inventory data

NASA Technical Reports Server (NTRS)

Thadani, S. G.

1977-01-01

The Maximum Likelihood Estimation of Signature Transformation (MLEST) algorithm is used to obtain maximum likelihood estimates (MLE) of affine transformation. The algorithm has been evaluated for three sets of data: simulated (training and recognition segment pairs), consecutive-day (data gathered from Landsat images), and geographical-extension (large-area crop inventory experiment) data sets. For each set, MLEST signature extension runs were made to determine MLE values and the affine-transformed training segment signatures were used to classify the recognition segments. The classification results were used to estimate wheat proportions at 0 and 1% threshold values.

Improving strand pairing prediction through exploring folding cooperativity

PubMed Central

Jeong, Jieun; Berman, Piotr; Przytycka, Teresa M.

2008-01-01

The topology of β-sheets is defined by the pattern of hydrogen-bonded strand pairing. Therefore, predicting hydrogen bonded strand partners is a fundamental step towards predicting β-sheet topology. At the same time, finding the correct partners is very difficult due to long range interactions involved in strand pairing. Additionally, patterns of aminoacids observed in β-sheet formations are very general and therefore difficult to use for computational recognition of specific contacts between strands. In this work, we report a new strand pairing algorithm. To address above mentioned difficulties, our algorithm attempts to mimic elements of the folding process. Namely, in addition to ensuring that the predicted hydrogen bonded strand pairs satisfy basic global consistency constraints, it takes into account hypothetical folding pathways. Consistently with this view, introducing hydrogen bonds between a pair of strands changes the probabilities of forming hydrogen bonds between other pairs of strand. We demonstrate that this approach provides an improvement over previously proposed algorithms. We also compare the performance of this method to that of a global optimization algorithm that poses the problem as integer linear programming optimization problem and solves it using ILOG CPLEX™ package. PMID:18989036

Fast and Frugal Framing Effects?

ERIC Educational Resources Information Center

Mccloy, Rachel; Beaman, C. Philip; Frosch, Caren A.; Goddard, Kate

2010-01-01

Using 3 experiments, we examine whether simple pairwise comparison judgments, involving the "recognition heuristic" (Goldstein & Gigerenzer, 2002), are sensitive to implicit cues to the nature of the comparison required. In Experiments 1 and 2, we show that participants frequently choose the recognized option of a pair if asked to make "larger"…

The Critical Difference: Identifying the Dyslexic.

ERIC Educational Resources Information Center

Burgett, Russell; King, James

A study compared peripheral vision applied to letter-pair and Dolch word recognition. Subjects, 6 normal readers, 12 Chapter 1 students, and 34 learning disabled (and assumed dyslexic) students from grades one through three enrolled in a parochial school, a public school, and a university summer reading clinic, completed a test designed to…

Recognition Ceremony to Highlight Students' Success

Science.gov Websites

and United Tutors (CLOUT) paired volunteers with fourth graders who needed help with reading. Rockies ;This year's increase in reading scores for Denver students is something the entire city can be proud of ." NREL sponsored CLOUT to augment Denver Public Schools' reading program. Midwest Research

A novel paired domain DNA recognition motif can mediate Pax2 repression of gene transcription.

PubMed

Håvik, B; Ragnhildstveit, E; Lorens, J B; Saelemyr, K; Fauske, O; Knudsen, L K; Fjose, A

1999-12-20

The paired domain (PD) is an evolutionarily conserved DNA-binding domain encoded by the Pax gene family of developmental regulators. The Pax proteins are transcription factors and are involved in a variety of processes such as brain development, patterning of the central nervous system (CNS), and B-cell development. In this report we demonstrate that the zebrafish Pax2 PD can interact with a novel type of DNA sequences in vitro, the triple-A motif, consisting of a heptameric nucleotide sequence G/CAAACA/TC with an invariant core of three adjacent adenosines. This recognition sequence was found to be conserved in known natural Pax5 repressor elements involved in controlling the expression of the p53 and J-chain genes. By identifying similar high affinity binding sites in potential target genes of the Pax2 protein, including the pax2 gene itself, we obtained further evidence that the triple-A sites are biologically significant. The putative natural target sites also provide a basis for defining an extended consensus recognition sequence. In addition, we observed in transformation assays a direct correlation between Pax2 repressor activity and the presence of triple-A sites. The results suggest that a transcriptional regulatory function of Pax proteins can be modulated by PD binding to different categories of target sequences. Copyright 1999 Academic Press.

Molecular Recognition of 6′-N-5-Hexynoate Kanamyin A and RNA 1×1 Internal Loops Containing CA Mismatches

PubMed Central

Tran, Tuan; Disney, Matthew D.

2011-01-01

In our previous study to identify the RNA internal loops that bind an aminoglycoside derivative, we determined that 6′-N-5-hexynoate kanamycin A prefers to bind 1×1 nucleotide internal loops containing C•A mismatches. In this present study, the molecular recognition between a variety of RNAs that are mutated around the C•A loop and the ligand was investigated. Studies show that both loop nucleotides and loop closing pairs affect binding affinity. Most interestingly, it was shown that there is a correlation between the thermodynamic stability of the C•A internal loops and ligand affinity. Specifically, C•A loops that had relatively high or low stability bound the ligand most weakly whereas loops with intermediate stability bound the ligand most tightly. In contrast, there is no correlation between the likelihood that a loop forms a C-A+ pair at lower pH and ligand affinity. It was also found that a 1×1 nucleotide C•A loop that bound to the ligand with the highest affinity is identical to the consensus site in RNAs that are edited by adenosine deaminases acting on RNA type 2 (ADAR2). These studies provide a detailed investigation of factors affecting small molecule recognition of internal loops containing C•A mismatches, which are present in a variety of RNAs that cause disease. PMID:21207945

Bridging of double-stranded breaks by the nonhomologous end-joining ligation complex is modulated by DNA end chemistry.

PubMed

Reid, Dylan A; Conlin, Michael P; Yin, Yandong; Chang, Howard H; Watanabe, Go; Lieber, Michael R; Ramsden, Dale A; Rothenberg, Eli

2017-02-28

The nonhomologous end-joining (NHEJ) pathway is the primary repair pathway for DNA double strand breaks (DSBs) in humans. Repair is mediated by a core complex of NHEJ factors that includes a ligase (DNA Ligase IV; L4) that relies on juxtaposition of 3΄ hydroxyl and 5΄ phosphate termini of the strand breaks for catalysis. However, chromosome breaks arising from biological sources often have different end chemistries, and how these different end chemistries impact the way in which the core complex directs the necessary transitions from end pairing to ligation is not known. Here, using single-molecule FRET (smFRET), we show that prior to ligation, differences in end chemistry strongly modulate the bridging of broken ends by the NHEJ core complex. In particular, the 5΄ phosphate group is a recognition element for L4 and is critical for the ability of NHEJ factors to promote stable pairing of ends. Moreover, other chemical incompatibilities, including products of aborted ligation, are sufficient to disrupt end pairing. Based on these observations, we propose a mechanism for iterative repair of DSBs by NHEJ. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Helix-length compensation studies reveal the adaptability of the VS ribozyme architecture.

PubMed

Lacroix-Labonté, Julie; Girard, Nicolas; Lemieux, Sébastien; Legault, Pascale

2012-03-01

Compensatory mutations in RNA are generally regarded as those that maintain base pairing, and their identification forms the basis of phylogenetic predictions of RNA secondary structure. However, other types of compensatory mutations can provide higher-order structural and evolutionary information. Here, we present a helix-length compensation study for investigating structure-function relationships in RNA. The approach is demonstrated for stem-loop I and stem-loop V of the Neurospora VS ribozyme, which form a kissing-loop interaction important for substrate recognition. To rapidly characterize the substrate specificity (k(cat)/K(M)) of several substrate/ribozyme pairs, a procedure was established for simultaneous kinetic characterization of multiple substrates. Several active substrate/ribozyme pairs were identified, indicating the presence of limited substrate promiscuity for stem Ib variants and helix-length compensation between stems Ib and V. 3D models of the I/V interaction were generated that are compatible with the kinetic data. These models further illustrate the adaptability of the VS ribozyme architecture for substrate cleavage and provide global structural information on the I/V kissing-loop interaction. By exploring higher-order compensatory mutations in RNA our approach brings a deeper understanding of the adaptability of RNA structure, while opening new avenues for RNA research.

Age-Related Differences in Recognition Memory for Items and Associations: Contribution of Individual Differences in Working Memory and Metamemory

PubMed Central

Bender, Andrew R.; Raz, Naftali

2012-01-01

Ability to form new associations between unrelated items is particularly sensitive to aging, but the reasons for such differential vulnerability are unclear. In this study, we examined the role of objective and subjective factors (working memory and beliefs about memory strategies) on differential relations of age with recognition of items and associations. Healthy adults (N = 100, age 21 to 79) studied word pairs, completed item and association recognition tests, and rated the effectiveness of shallow (e.g., repetition) and deep (e.g., imagery or sentence generation) encoding strategies. Advanced age was associated with reduced working memory (WM) capacity and poorer associative recognition. In addition, reduced WM capacity, beliefs in the utility of ineffective encoding strategies, and lack of endorsement of effective ones were independently associated with impaired associative memory. Thus, maladaptive beliefs about memory in conjunction with reduced cognitive resources account in part for differences in associative memory commonly attributed to aging. PMID:22251381

Robust Point Set Matching for Partial Face Recognition.

PubMed

Weng, Renliang; Lu, Jiwen; Tan, Yap-Peng

2016-03-01

Over the past three decades, a number of face recognition methods have been proposed in computer vision, and most of them use holistic face images for person identification. In many real-world scenarios especially some unconstrained environments, human faces might be occluded by other objects, and it is difficult to obtain fully holistic face images for recognition. To address this, we propose a new partial face recognition approach to recognize persons of interest from their partial faces. Given a pair of gallery image and probe face patch, we first detect keypoints and extract their local textural features. Then, we propose a robust point set matching method to discriminatively match these two extracted local feature sets, where both the textural information and geometrical information of local features are explicitly used for matching simultaneously. Finally, the similarity of two faces is converted as the distance between these two aligned feature sets. Experimental results on four public face data sets show the effectiveness of the proposed approach.

Molecular recognition on a cavitand-functionalized silicon surface.

PubMed

Biavardi, Elisa; Favazza, Maria; Motta, Alessandro; Fragalà, Ignazio L; Massera, Chiara; Prodi, Luca; Montalti, Marco; Melegari, Monica; Condorelli, Guglielmo G; Dalcanale, Enrico

2009-06-03

A Si(100) surface featuring molecular recognition properties was obtained by covalent functionalization with a tetraphosphonate cavitand (Tiiii), able to complex positively charged species. Tiiii cavitand was grafted onto the Si by photochemical hydrosilylation together with 1-octene as a spatial spectator. The recognition properties of the Si-Tiiii surface were demonstrated through two independent analytical techniques, namely XPS and fluorescence spectroscopy, during the course of reversible complexation-guest exchange-decomplexation cycles with specifically designed ammonium and pyridinium salts. Control experiments employing a Si(100) surface functionalized with a structurally similar, but complexation inactive, tetrathiophosphonate cavitand (TSiiii) demonstrated no recognition events. This provides evidence for the complexation properties of the Si-Tiiii surface, ruling out the possibility of nonspecific interactions between the substrate and the guests. The residual Si-O(-) terminations on the surface replace the guests' original counterions, thus stabilizing the complex ion pairs. These results represent a further step toward the control of self-assembly of complex supramolecular architectures on surfaces.

Free recall test experience potentiates strategy-driven effects of value on memory.

PubMed

Cohen, Michael S; Rissman, Jesse; Hovhannisyan, Mariam; Castel, Alan D; Knowlton, Barbara J

2017-10-01

People tend to show better memory for information that is deemed valuable or important. By one mechanism, individuals selectively engage deeper, semantic encoding strategies for high value items (Cohen, Rissman, Suthana, Castel, & Knowlton, 2014). By another mechanism, information paired with value or reward is automatically strengthened in memory via dopaminergic projections from midbrain to hippocampus (Shohamy & Adcock, 2010). We hypothesized that the latter mechanism would primarily enhance recollection-based memory, while the former mechanism would strengthen both recollection and familiarity. We also hypothesized that providing interspersed tests during study is a key to encouraging selective engagement of strategies. To test these hypotheses, we presented participants with sets of words, and each word was associated with a high or low point value. In some experiments, free recall tests were given after each list. In all experiments, a recognition test was administered 5 minutes after the final word list. Process dissociation was accomplished via remember/know judgments at recognition, a recall test probing both item memory and memory for a contextual detail (word plurality), and a task dissociation combining a recognition test for plurality (intended to probe recollection) with a speeded item recognition test (to probe familiarity). When recall tests were administered after study lists, high value strengthened both recollection and familiarity. When memory was not tested after each study list, but rather only at the end, value increased recollection but not familiarity. These dual process dissociations suggest that interspersed recall tests guide learners' use of metacognitive control to selectively apply effective encoding strategies. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Quantification of the transferability of a designed protein specificity switch reveals extensive epistasis in molecular recognition

DOE PAGES

Melero, Cristina; Ollikainen, Noah; Harwood, Ian; ...

2014-10-13

Re-engineering protein–protein recognition is an important route to dissecting and controlling complex interaction networks. Experimental approaches have used the strategy of “second-site suppressors,” where a functional interaction is inferred between two proteins if a mutation in one protein can be compensated by a mutation in the second. Mimicking this strategy, computational design has been applied successfully to change protein recognition specificity by predicting such sets of compensatory mutations in protein–protein interfaces. To extend this approach, it would be advantageous to be able to “transplant” existing engineered and experimentally validated specificity changes to other homologous protein–protein complexes. Here, we test thismore » strategy by designing a pair of mutations that modulates peptide recognition specificity in the Syntrophin PDZ domain, confirming the designed interaction biochemically and structurally, and then transplanting the mutations into the context of five related PDZ domain–peptide complexes. We find a wide range of energetic effects of identical mutations in structurally similar positions, revealing a dramatic context dependence (epistasis) of designed mutations in homologous protein–protein interactions. To better understand the structural basis of this context dependence, we apply a structure-based computational model that recapitulates these energetic effects and we use this model to make and validate forward predictions. The context dependence of these mutations is captured by computational predictions, our results both highlight the considerable difficulties in designing protein–protein interactions and provide challenging benchmark cases for the development of improved protein modeling and design methods that accurately account for the context.« less

Quantification of the transferability of a designed protein specificity switch reveals extensive epistasis in molecular recognition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Melero, Cristina; Ollikainen, Noah; Harwood, Ian

Re-engineering protein–protein recognition is an important route to dissecting and controlling complex interaction networks. Experimental approaches have used the strategy of “second-site suppressors,” where a functional interaction is inferred between two proteins if a mutation in one protein can be compensated by a mutation in the second. Mimicking this strategy, computational design has been applied successfully to change protein recognition specificity by predicting such sets of compensatory mutations in protein–protein interfaces. To extend this approach, it would be advantageous to be able to “transplant” existing engineered and experimentally validated specificity changes to other homologous protein–protein complexes. Here, we test thismore » strategy by designing a pair of mutations that modulates peptide recognition specificity in the Syntrophin PDZ domain, confirming the designed interaction biochemically and structurally, and then transplanting the mutations into the context of five related PDZ domain–peptide complexes. We find a wide range of energetic effects of identical mutations in structurally similar positions, revealing a dramatic context dependence (epistasis) of designed mutations in homologous protein–protein interactions. To better understand the structural basis of this context dependence, we apply a structure-based computational model that recapitulates these energetic effects and we use this model to make and validate forward predictions. The context dependence of these mutations is captured by computational predictions, our results both highlight the considerable difficulties in designing protein–protein interactions and provide challenging benchmark cases for the development of improved protein modeling and design methods that accurately account for the context.« less

An isoleucine to leucine mutation that switches the cofactor requirement of the EcoRV restriction endonuclease from magnesium to manganese.

PubMed

Vipond, I B; Moon, B J; Halford, S E

1996-02-13

The EcoRV restriction endonuclease cleaves DNA at its recognition sequence more readily with Mg2+ as the cofactor than with Mn2+ but, at noncognate sequences that differ from the EcoRV site by one base pair, Mn2+ gives higher rates than Mg2+. A mutant of EcoRV, in which an isoleucine near the active site was replaced by leucine, showed the opposite behavior. It had low activity with Mg2+, but, in the presence of Mn2+ ions, it cleaved the recognition site faster than wild-type EcoRV with either Mn2+ or Mg2+. The mutant was also more specific for the recognition sequence than the native enzyme: the noncognate DNA cleavages by wild-type EcoRV and Mn2+ were not detected with the mutant. Further mutagenesis showed that the protein required the same acidic residues at its active site as wild-type EcoRV. The Ile-->Leu mutation seems to perturb the configuration of the metal-binding ligands at the active site so that the protein has virtually no affinity for Mg2+ yet it can still bind Mn2+ ions, though the latter only occurs when the protein is at the recognition site. This contrasts to wild-type EcoRV, where Mn2+ ions bind readily to complexes with either cognate and noncognate DNA and only Mg2+ shows the discrimination between the complexes. The structural perturbation is a specific consequence of leucine in place of isoleucine, since mutants with valine or alanine were similar to wild-type EcoRV.

DNA interrogation by the CRISPR RNA-guided endonuclease Cas9.

PubMed

Sternberg, Samuel H; Redding, Sy; Jinek, Martin; Greene, Eric C; Doudna, Jennifer A

2014-03-06

The clustered regularly interspaced short palindromic repeats (CRISPR)-associated enzyme Cas9 is an RNA-guided endonuclease that uses RNA-DNA base-pairing to target foreign DNA in bacteria. Cas9-guide RNA complexes are also effective genome engineering agents in animals and plants. Here we use single-molecule and bulk biochemical experiments to determine how Cas9-RNA interrogates DNA to find specific cleavage sites. We show that both binding and cleavage of DNA by Cas9-RNA require recognition of a short trinucleotide protospacer adjacent motif (PAM). Non-target DNA binding affinity scales with PAM density, and sequences fully complementary to the guide RNA but lacking a nearby PAM are ignored by Cas9-RNA. Competition assays provide evidence that DNA strand separation and RNA-DNA heteroduplex formation initiate at the PAM and proceed directionally towards the distal end of the target sequence. Furthermore, PAM interactions trigger Cas9 catalytic activity. These results reveal how Cas9 uses PAM recognition to quickly identify potential target sites while scanning large DNA molecules, and to regulate scission of double-stranded DNA.

Shy children are less sensitive to some cues to facial recognition.

PubMed

Brunet, Paul M; Mondloch, Catherine J; Schmidt, Louis A

2010-02-01

Temperamental shyness in children is characterized by avoidance of faces and eye contact, beginning in infancy. We conducted two studies to determine whether temperamental shyness was associated with deficits in sensitivity to some cues to facial identity. In Study 1, 40 typically developing 10-year-old children made same/different judgments about pairs of faces that differed in the appearance of individual features, the shape of the external contour, or the spacing among features; their parent completed the Colorado childhood temperament inventory (CCTI). Children who scored higher on CCTI shyness made more errors than their non-shy counterparts only when discriminating faces based on the spacing of features. Differences in accuracy were not related to other scales of the CCTI. In Study 2, we showed that these differences were face-specific and cannot be attributed to differences in task difficulty. Findings suggest that shy children are less sensitive to some cues to facial recognition possibly underlying their inability to distinguish certain facial emotions in others, leading to a cascade of secondary negative effects in social behaviour.

Crystal structures of the SAM-III/SMK riboswitch reveal the SAM-dependent translation inhibition mechanism

PubMed Central

Lu, Changrui; Smith, Angela M; Fuchs, Ryan T; Ding, Fang; Rajashankar, Kanagalaghatta; Henkin, Tina M; Ke, Ailong

2011-01-01

Three distinct classes of S-adenosyl-l-methionine (SAM)-responsive riboswitches have been identified that regulate bacterial gene expression at the levels of transcription attenuation or translation inhibition. The SMK box (SAM-III) translational riboswitch has been identified in the SAM synthetase gene in members of the Lactobacillales. Here we report the 2.2-Å crystal structure of the Enterococcus faecalis SMK box riboswitch. The Y-shaped riboswitch organizes its conserved nucleotides around a three-way junction for SAM recognition. The Shine-Dalgarno sequence, which is sequestered by base-pairing with the anti–Shine-Dalgarno sequence in response to SAM binding, also directly participates in SAM recognition. The riboswitch makes extensive interactions with the adenosine and sulfonium moieties of SAM but does not appear to recognize the tail of the methionine moiety. We captured a structural snapshot of the SMK box riboswitch sampling the near-cognate ligand S-adenosyl-l-homocysteine (SAH) in which SAH was found to adopt an alternative conformation and fails to make several key interactions. PMID:18806797

Single-stranded DNA cleavage by divergent CRISPR-Cas9 enzymes

PubMed Central

Ma, Enbo; Harrington, Lucas B.; O’Connell, Mitchell R.; Zhou, Kaihong; Doudna, Jennifer A.

2015-01-01

Summary Double-stranded DNA (dsDNA) cleavage by Cas9 is a hallmark of type II CRISPR-Cas immune systems. Cas9–guide RNA complexes recognize 20-base-pair sequences in DNA and generate a site-specific double-strand break, a robust activity harnessed for genome editing. DNA recognition by all studied Cas9 enzymes requires a protospacer adjacent motif (PAM) next to the target site. We show that Cas9 enzymes from evolutionarily divergent bacteria can recognize and cleave single-stranded DNA (ssDNA) by an RNA-guided, PAM-independent recognition mechanism. Comparative analysis shows that in contrast to the type II-A S. pyogenes Cas9 that is widely used for genome engineering, the smaller type II-C Cas9 proteins have limited dsDNA binding and unwinding activity and promiscuous guide-RNA specificity. These results indicate that inefficiency of type II-C Cas9 enzymes for genome editing results from a limited ability to cleave dsDNA, and suggest that ssDNA cleavage was an ancestral function of the Cas9 enzyme family. PMID:26545076

Crystal structures of the SAM-III/S[subscript MK] riboswitch reveal the SAM-dependent translation inhibition mechanism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lu, C.; Smith, A.M.; Fuchs, R.T.

2010-01-07

Three distinct classes of S-adenosyl-L-methionine (SAM)-responsive riboswitches have been identified that regulate bacterial gene expression at the levels of transcription attenuation or translation inhibition. The SMK box (SAM-III) translational riboswitch has been identified in the SAM synthetase gene in members of the Lactobacillales. Here we report the 2.2-{angstrom} crystal structure of the Enterococcus faecalis SMK box riboswitch. The Y-shaped riboswitch organizes its conserved nucleotides around a three-way junction for SAM recognition. The Shine-Dalgarno sequence, which is sequestered by base-pairing with the anti-Shine-Dalgarno sequence in response to SAM binding, also directly participates in SAM recognition. The riboswitch makes extensive interactions withmore » the adenosine and sulfonium moieties of SAM but does not appear to recognize the tail of the methionine moiety. We captured a structural snapshot of the SMK box riboswitch sampling the near-cognate ligand S-adenosyl-L-homocysteine (SAH) in which SAH was found to adopt an alternative conformation and fails to make several key interactions.« less

DNA interrogation by the CRISPR RNA-guided endonuclease Cas9

NASA Astrophysics Data System (ADS)

Sternberg, Samuel H.; Redding, Sy; Jinek, Martin; Greene, Eric C.; Doudna, Jennifer A.

2014-03-01

The clustered regularly interspaced short palindromic repeats (CRISPR)-associated enzyme Cas9 is an RNA-guided endonuclease that uses RNA-DNA base-pairing to target foreign DNA in bacteria. Cas9-guide RNA complexes are also effective genome engineering agents in animals and plants. Here we use single-molecule and bulk biochemical experiments to determine how Cas9-RNA interrogates DNA to find specific cleavage sites. We show that both binding and cleavage of DNA by Cas9-RNA require recognition of a short trinucleotide protospacer adjacent motif (PAM). Non-target DNA binding affinity scales with PAM density, and sequences fully complementary to the guide RNA but lacking a nearby PAM are ignored by Cas9-RNA. Competition assays provide evidence that DNA strand separation and RNA-DNA heteroduplex formation initiate at the PAM and proceed directionally towards the distal end of the target sequence. Furthermore, PAM interactions trigger Cas9 catalytic activity. These results reveal how Cas9 uses PAM recognition to quickly identify potential target sites while scanning large DNA molecules, and to regulate scission of double-stranded DNA.

Real-time observation of DNA recognition and rejection by the RNA-guided endonuclease Cas9.

PubMed

Singh, Digvijay; Sternberg, Samuel H; Fei, Jingyi; Doudna, Jennifer A; Ha, Taekjip

2016-09-14

Binding specificity of Cas9-guide RNA complexes to DNA is important for genome-engineering applications; however, how mismatches influence target recognition/rejection kinetics is not well understood. Here we used single-molecule FRET to probe real-time interactions between Cas9-RNA and DNA targets. The bimolecular association rate is only weakly dependent on sequence; however, the dissociation rate greatly increases from <0.006 s(-1) to >2 s(-1) upon introduction of mismatches proximal to protospacer-adjacent motif (PAM), demonstrating that mismatches encountered early during heteroduplex formation induce rapid rejection of off-target DNA. In contrast, PAM-distal mismatches up to 11 base pairs in length, which prevent DNA cleavage, still allow formation of a stable complex (dissociation rate <0.006 s(-1)), suggesting that extremely slow rejection could sequester Cas9-RNA, increasing the Cas9 expression level necessary for genome-editing, thereby aggravating off-target effects. We also observed at least two different bound FRET states that may represent distinct steps in target search and proofreading.

The effects of environmental context on recognition memory and claims of remembering.

PubMed

Hockley, William E

2008-11-01

Recognition memory for words was tested in same or different contexts using the remember/know response procedure. Context was manipulated by presenting words in different screen colors and locations and by presenting words against real-world photographs. Overall hit and false-alarm rates were higher for tests presented in an old context compared to a new context. This concordant effect was seen in both remember responses and estimates of familiarity. Similar results were found for rearranged pairings of old study contexts and targets, for study contexts that were unique or were repeated with different words, and for new picture contexts that were physically similar to old contexts. Similar results were also found when subjects focused attention on the study words, but a different pattern of results was obtained when subjects explicitly associated the study words with their picture context. The results show that subjective feelings of recollection play a role in the effects of environmental context but are likely based more on a sense of familiarity that is evoked by the context than on explicit associations between targets and their study context.

[Design and synthesis of imine compound for metal cation logical gates recognition and setup of double-control fluorescent molecule switch].

PubMed

Huang, Tao; Zhu, Yu-lian; Dai, Xue-qin; Zhang, Qi; Huang, Yan

2011-07-01

The Schiff base's reduced product N,N-bis(4-methoxybenzyl) ethane-1,2-diamine, which was used as a receptor L, was designed and synthesized for the first time in the present article. It was found that Cu2+ and Fe3+ could quench L in fluorescence observably and Zn2+ and Cd2+ could enhance L remarkably. So the two pair metal cation could set up "OR" logical gate relation with the receptor molecule L, then a logical recognition system be formed. The data of resolved ZnL's single crystal indicated that ZnL belonged to monoclinic (CCDC No. 747994). Integrated spectrum instrument was used to characterize the structure of its alike series of complex compound. According to ZnL's excellent fluorescence character and the ability to exchange with contiguous metal cation, ZnZ+/ZnL/Co2+, Zn2+/ZnL/Nit+ fluorescent molecule switch was designed. It is hoped that the work above could be positive for the development of molecule computer, bio-intellectualized inspection technology (therapy) and instrument.

Chemistry, mechanism and clinical status of antisense oligonucleotides and duplex RNAs

PubMed Central

Shen, Xiulong; Corey, David R

2018-01-01

Abstract RNA plays a central role in the expression of all genes. Because any sequence within RNA can be recognized by complementary base pairing, synthetic oligonucleotides and oligonucleotide mimics offer a general strategy for controlling processes that affect disease. The two primary antisense approaches for regulating expression through recognition of cellular RNAs are single-stranded antisense oligonucleotides and duplex RNAs. This review will discuss the chemical modifications and molecular mechanisms that make synthetic nucleic acid drugs possible. Lessons learned from recent clinical trials will be summarized. Ongoing clinical trials are likely to decisively test the adequacy of our current generation of antisense nucleic acid technologies and highlight areas where more basic research is needed. PMID:29240946

Unnatural substrates reveal the importance of 8-oxoguanine for in vivo mismatch repair by MutY

PubMed Central

Livingston, Alison L.; O’Shea, Valerie L.; Kim, Taewoo; Kool, Eric T.; David, Sheila S.

2009-01-01

Escherchia coli MutY plays an important role in preventing mutations associated with the oxidative lesion 7,8-dihydro-8-oxo-2′-deoxyguanosine (OG) in DNA by excising adenines from OG:A mismatches as the first step of base excision repair. To determine the importance of specific steps in the base pair recognition and base removal process of MutY, we have evaluated the effects of modifications of the OG:A substrate on the kinetics of base removal, mismatch affinity and repair to G:C in an Escherchia coli-based assay. Surprisingly, adenine modification was tolerated in the cellular assay, while modification of OG results in minimal cellular repair. High affinity for the mismatch and efficient base removal require the presence of OG. Taken together, these results suggest that the presence of OG is a critical feature for MutY to locate OG:A mismatches and select the appropriate adenines for excision to initiate repair in vivo prior to replication. PMID:18026095

Binary zone-plate array for a parallel joint transform correlator applied to face recognition.

PubMed

Kodate, K; Hashimoto, A; Thapliya, R

1999-05-10

Taking advantage of small aberrations, high efficiency, and compactness, we developed a new, to our knowledge, design procedure for a binary zone-plate array (BZPA) and applied it to a parallel joint transform correlator for the recognition of the human face. Pairs of reference and unknown images of faces are displayed on a liquid-crystal spatial light modulator (SLM), Fourier transformed by the BZPA, intensity recorded on an optically addressable SLM, and inversely Fourier transformed to obtain correlation signals. Consideration of the bandwidth allows the relations among the channel number, the numerical aperture of the zone plates, and the pattern size to be determined. Experimentally a five-channel parallel correlator was implemented and tested successfully with a 100-person database. The design and the fabrication of a 20-channel BZPA for phonetic character recognition are also included.

Mismatched expressions decrease face recognition and corresponding ERP old/new effects in schizophrenia.

PubMed

Guillaume, Fabrice; Guillem, François; Tiberghien, Guy; Stip, Emmanuel

2012-09-01

The objective was to investigate the electrophysiological (ERP) correlates of mismatched expression on face recognition in schizophrenia. Expression-change effects and associated ERPs were explored in patients with schizophrenia (n = 20) and paired comparison participants (n = 20) on a long-term face-recognition task. A facial-expression change decreased discriminability for patients with schizophrenia than for healthy participants. The patients' recognition deficit was accompanied by the absence of the midfrontal FN400 and late parietal ERP old/new effects in the mismatched-expression condition. By contrast, preserved midfrontal FN400 and late parietal ERP old/new effects were found in both groups in the unchanged-expression condition. Thus, the preserved parietal old/new effect previously observed in schizophrenia was no longer found here in the situation in which expression changes took place between the study and recognition phases. These findings suggest that, when they are not supposed to take the change of expression into account, the recognition deficit observed here in patients with schizophrenia resulted from an impairment in the mechanisms underlying the emergence, assessment, or utilization of familiarity--as indexed by the ERP old/new effects. In these natural conditions, the impact of the expression change on the implementation of retrieval processes offers new insight into schizophrenia-linked deficits in face recognition, with substantial phenomenological differences with respect to the emergence of familiarity.

Capturing specific abilities as a window into human individuality: The example of face recognition

PubMed Central

Wilmer, Jeremy B.; Germine, Laura; Chabris, Christopher F.; Chatterjee, Garga; Gerbasi, Margaret; Nakayama, Ken

2013-01-01

Proper characterization of each individual's unique pattern of strengths and weaknesses requires good measures of diverse abilities. Here, we advocate combining our growing understanding of neural and cognitive mechanisms with modern psychometric methods in a renewed effort to capture human individuality through a consideration of specific abilities. We articulate five criteria for the isolation and measurement of specific abilities, then apply these criteria to face recognition. We cleanly dissociate face recognition from more general visual and verbal recognition. This dissociation stretches across ability as well as disability, suggesting that specific developmental face recognition deficits are a special case of a broader specificity that spans the entire spectrum of human face recognition performance. Item-by-item results from 1,471 web-tested participants, included as supplementary information, fuel item analyses, validation, norming, and item response theory (IRT) analyses of our three tests: (a) the widely used Cambridge Face Memory Test (CFMT); (b) an Abstract Art Memory Test (AAMT), and (c) a Verbal Paired-Associates Memory Test (VPMT). The availability of this data set provides a solid foundation for interpreting future scores on these tests. We argue that the allied fields of experimental psychology, cognitive neuroscience, and vision science could fuel the discovery of additional specific abilities to add to face recognition, thereby providing new perspectives on human individuality. PMID:23428079

Effects of ecstasy/polydrug use on memory for associative information.

PubMed

Gallagher, Denis T; Fisk, John E; Montgomery, Catharine; Judge, Jeannie; Robinson, Sarita J; Taylor, Paul J

2012-08-01

Associative learning underpins behaviours that are fundamental to the everyday functioning of the individual. Evidence pointing to learning deficits in recreational drug users merits further examination. A word pair learning task was administered to examine associative learning processes in ecstasy/polydrug users. After assignment to either single or divided attention conditions, 44 ecstasy/polydrug users and 48 non-users were presented with 80 word pairs at encoding. Following this, four types of stimuli were presented at the recognition phase: the words as originally paired (old pairs), previously presented words in different pairings (conjunction pairs), old words paired with new words, and pairs of new words (not presented previously). The task was to identify which of the stimuli were intact old pairs. Ecstasy/ploydrug users produced significantly more false-positive responses overall compared to non-users. Increased long-term frequency of ecstasy use was positively associated with the propensity to produce false-positive responses. It was also associated with a more liberal signal detection theory decision criterion value. Measures of long term and recent cannabis use were also associated with these same word pair learning outcome measures. Conjunction word pairs, irrespective of drug use, generated the highest level of false-positive responses and significantly more false-positive responses were made in the divided attention condition compared to the single attention condition. Overall, the results suggest that long-term ecstasy exposure may induce a deficit in associative learning and this may be in part a consequence of users adopting a more liberal decision criterion value.

Definition of a high-affinity Gag recognition structure mediating packaging of a retroviral RNA genome

PubMed Central

Gherghe, Cristina; Lombo, Tania; Leonard, Christopher W.; Datta, Siddhartha A. K.; Bess, Julian W.; Gorelick, Robert J.; Rein, Alan; Weeks, Kevin M.

2010-01-01

All retroviral genomic RNAs contain a cis-acting packaging signal by which dimeric genomes are selectively packaged into nascent virions. However, it is not understood how Gag (the viral structural protein) interacts with these signals to package the genome with high selectivity. We probed the structure of murine leukemia virus RNA inside virus particles using SHAPE, a high-throughput RNA structure analysis technology. These experiments showed that NC (the nucleic acid binding domain derived from Gag) binds within the virus to the sequence UCUG-UR-UCUG. Recombinant Gag and NC proteins bound to this same RNA sequence in dimeric RNA in vitro; in all cases, interactions were strongest with the first U and final G in each UCUG element. The RNA structural context is critical: High-affinity binding requires base-paired regions flanking this motif, and two UCUG-UR-UCUG motifs are specifically exposed in the viral RNA dimer. Mutating the guanosine residues in these two motifs—only four nucleotides per genomic RNA—reduced packaging 100-fold, comparable to the level of nonspecific packaging. These results thus explain the selective packaging of dimeric RNA. This paradigm has implications for RNA recognition in general, illustrating how local context and RNA structure can create information-rich recognition signals from simple single-stranded sequence elements in large RNAs. PMID:20974908

[The study of the recognition gap on the quality of life in people with epilepsy between the affected pediatric and adolescent patient's families and the attending physicians].

PubMed

Awaya, Yutaka; Kubota, Hidemoto

2011-01-01

The aims of this study were to investigate the recognition gap on the quality of life (QOL) in people with epilepsy (PWE) between the affected pediatric and adolescent patient's families and the attending physicians, and to devise future management strategies for epilepsy based on the results. We conducted a large-scale questionnaire survey on the QOL in 5,122 PWE/their families who were members of the Japanese Epilepsy Association in 2006 and 1,701 PWE/their families and 502 attending physicians responded. Out of the responders, 107 matched pairs of PWE aged under 16 years (with an adult family member actually responding by proxy) and their physicians responding to the questionnaire were examined. The results demonstrated that the physicians were not sufficiently aware of 1) concern about drug therapy for epilepsy from the perspective of their patients/families, 2) ictal and post-ictal symptoms recognized by the patients/their families, and 3) the worry about the disease of the patients/their families. Thus, efforts are needed to minimize the recognition gap within the limited consultation hour in routine clinical practice between children and adolescents having epilepsy/their families and physicians : physicians should efficiently acquire necessary information from PWE/their families, and should negotiate with PWE/their families about the goal of therapy and future management strategies for epilepsy.

Interplay of oxytocin, vasopressin, and sex hormones in the regulation of social recognition.

PubMed

Gabor, Christopher S; Phan, Anna; Clipperton-Allen, Amy E; Kavaliers, Martin; Choleris, Elena

2012-02-01

Social Recognition is a fundamental skill that forms the basis of behaviors essential to the proper functioning of pair or group living in most social species. We review here various neurobiological and genetic studies that point to an interplay of oxytocin (OT), arginine-vasopressin (AVP), and the gonadal hormones, estrogens and testosterone, in the mediation of social recognition. Results of a number of studies have shown that OT and its actions at the medial amygdala seem to be essential for social recognition in both sexes. Estrogens facilitate social recognition, possibly by regulating OT production in the hypothalamus and the OT receptors at the medial amygdala. Estrogens also affect social recognition on a rapid time scale, likely through nongenomic actions. The mechanisms of these rapid effects are currently unknown but available evidence points at the hippocampus as the possible site of action. Male rodents seem to be more dependent on AVP acting at the level of the lateral septum for social recognition than female rodents. Results of various studies suggest that testosterone and its metabolites (including estradiol) influence social recognition in males primarily through the AVP V1a receptor. Overall, it appears that gonadal hormone modulation of OT and AVP regulates and fine tunes social recognition and those behaviors that depend upon it (e.g., social bonds, social hierarchies) in a sex specific manner. This points at an important role for these neuroendocrine systems in the regulation of the sex differences that are evident in social behavior and of sociality as a whole.

A fast and low-cost genotyping method for hepatitis B virus based on pattern recognition in point-of-care settings

PubMed Central

Qiu, Xianbo; Song, Liuwei; Yang, Shuo; Guo, Meng; Yuan, Quan; Ge, Shengxiang; Min, Xiaoping; Xia, Ningshao

2016-01-01

A fast and low-cost method for HBV genotyping especially for genotypes A, B, C and D was developed and tested. A classifier was used to detect and analyze a one-step immunoassay lateral flow strip functionalized with genotype-specific monoclonal antibodies (mAbs) on multiple capture lines in the form of pattern recognition for point-of-care (POC) diagnostics. The fluorescent signals from the capture lines and the background of the strip were collected via multiple optical channels in parallel. A digital HBV genotyping model, whose inputs are the fluorescent signals and outputs are a group of genotype-specific digital binary codes (0/1), was developed based on the HBV genotyping strategy. Meanwhile, a companion decoding table was established to cover all possible pairing cases between the states of a group of genotype-specific digital binary codes and the HBV genotyping results. A logical analyzing module was constructed to process the detected signals in parallel without program control, and its outputs were used to drive a set of LED indicators, which determine the HBV genotype. Comparing to the nucleic acid analysis to HBV viruses, much faster HBV genotyping with significantly lower cost can be obtained with the developed method. PMID:27306485

Real-time road detection in infrared imagery

NASA Astrophysics Data System (ADS)

Andre, Haritini E.; McCoy, Keith

1990-09-01

Automatic road detection is an important part in many scene recognition applications. The extraction of roads provides a means of navigation and position update for remotely piloted vehicles or autonomous vehicles. Roads supply strong contextual information which can be used to improve the performance of automatic target recognition (ATh) systems by directing the search for targets and adjusting target classification confidences. This paper will describe algorithmic techniques for labeling roads in high-resolution infrared imagery. In addition, realtime implementation of this structural approach using a processor array based on the Martin Marietta Geometric Arithmetic Parallel Processor (GAPPTh) chip will be addressed. The algorithm described is based on the hypothesis that a road consists of pairs of line segments separated by a distance "d" with opposite gradient directions (antiparallel). The general nature of the algorithm, in addition to its parallel implementation in a single instruction, multiple data (SIMD) machine, are improvements to existing work. The algorithm seeks to identify line segments meeting the road hypothesis in a manner that performs well, even when the side of the road is fragmented due to occlusion or intersections. The use of geometrical relationships between line segments is a powerful yet flexible method of road classification which is independent of orientation. In addition, this approach can be used to nominate other types of objects with minor parametric changes.

Repeating Patterns in Kindergarten: Findings from Children's Enactments of Two Activities

ERIC Educational Resources Information Center

Tsamir, Pessia; Tirosh, Dina; Levenson, Esther S.; Barkai, Ruthi; Tabach, Michal

2017-01-01

This paper describes kindergarten children's engagement with two patterning activities. The first activity includes two tasks in which children are asked to choose possible ways for extending two different repeating patterns and the second activity calls for comparing different pairs of repeating patterns. Children's recognition of the unit of…

Perceptual Effects of Social Salience: Evidence from Self-Prioritization Effects on Perceptual Matching

ERIC Educational Resources Information Center

Sui, Jie; He, Xun; Humphreys, Glyn W.

2012-01-01

We present novel evidence showing that new self-relevant visual associations can affect performance in simple shape recognition tasks. Participants associated labels for themselves, other people, or neutral terms with geometric shapes and then immediately judged whether subsequent label-shape pairings were matched. Across 4 experiments there was a…

The Role of Somatosensory Information in Speech Perception: Imitation Improves Recognition of Disordered Speech

ERIC Educational Resources Information Center

Borrie, Stephanie A.; Schäfer, Martina C. M.

2015-01-01

Purpose: Perceptual learning paradigms involving written feedback appear to be a viable clinical tool to reduce the intelligibility burden of dysarthria. The underlying theoretical assumption is that pairing the degraded acoustics with the intended lexical targets facilitates a remapping of existing mental representations in the lexicon. This…

State Department Program Pairs Foreign Students with Community Colleges

ERIC Educational Resources Information Center

Fischer, Karin

2009-01-01

Educational exchanges and fellowships are not new; the best known, the Fulbright Program, is more than 60 years old. But the Community College Summit Initiative Program, as this fledgling effort is known, reflects a growing recognition among American government officials that the United States must do a better job in its public-diplomacy outreach…

Down Syndrome and Automatic Processing of Familiar and Unfamiliar Emotional Faces

ERIC Educational Resources Information Center

Morales, Guadalupe E.; Lopez, Ernesto O.

2010-01-01

Participants with Down syndrome (DS) were required to participate in a face recognition experiment to recognize familiar (DS faces) and unfamiliar emotional faces (non DS faces), by using an affective priming paradigm. Pairs of emotional facial stimuli were presented (one face after another) with a short Stimulus Onset Asynchrony of 300…

Tactile memory of deaf-blind adults on four tasks.

PubMed

Arnold, Paul; Heiron, Karen

2002-02-01

The performance of ten deaf-blind and ten sighted-hearing participants on four tactile memory tasks was investigated. Recognition and recall memory tasks and a matching pairs game were used. It was hypothesized that deaf-blind participants would be superior on each task. Performance was measured in terms of the time taken, and the number of items correctly recalled. In Experiments 1 and 2, which measured recognition memory in terms of the time taken to remember target items, the hypothesis was supported, but not by the length of time taken to recognize the target items, or for the number of target items correctly identified. The hypothesis was supported by Experiment 3, which measured recall memory, with regard to time taken to complete some of the tasks but not for the number of correctly recalled positions. Experiment 4, which used the matching pairs game, supported the hypothesis in terms of both time taken and the number of moves required. It is concluded that the deaf-blind people's tactile encoding is more efficient than that of sighted-hearing people, and that it is probable that their storage and retrieval are normal.

Fraudulent ID using face morphs: Experiments on human and automatic recognition

PubMed Central

Robertson, David J.; Kramer, Robin S. S.

2017-01-01

Matching unfamiliar faces is known to be difficult, and this can give an opportunity to those engaged in identity fraud. Here we examine a relatively new form of fraud, the use of photo-ID containing a graphical morph between two faces. Such a document may look sufficiently like two people to serve as ID for both. We present two experiments with human viewers, and a third with a smartphone face recognition system. In Experiment 1, viewers were asked to match pairs of faces, without being warned that one of the pair could be a morph. They very commonly accepted a morphed face as a match. However, in Experiment 2, following very short training on morph detection, their acceptance rate fell considerably. Nevertheless, there remained large individual differences in people’s ability to detect a morph. In Experiment 3 we show that a smartphone makes errors at a similar rate to ‘trained’ human viewers—i.e. accepting a small number of morphs as genuine ID. We discuss these results in reference to the use of face photos for security. PMID:28328928

Fraudulent ID using face morphs: Experiments on human and automatic recognition.

PubMed

Robertson, David J; Kramer, Robin S S; Burton, A Mike

2017-01-01

Matching unfamiliar faces is known to be difficult, and this can give an opportunity to those engaged in identity fraud. Here we examine a relatively new form of fraud, the use of photo-ID containing a graphical morph between two faces. Such a document may look sufficiently like two people to serve as ID for both. We present two experiments with human viewers, and a third with a smartphone face recognition system. In Experiment 1, viewers were asked to match pairs of faces, without being warned that one of the pair could be a morph. They very commonly accepted a morphed face as a match. However, in Experiment 2, following very short training on morph detection, their acceptance rate fell considerably. Nevertheless, there remained large individual differences in people's ability to detect a morph. In Experiment 3 we show that a smartphone makes errors at a similar rate to 'trained' human viewers-i.e. accepting a small number of morphs as genuine ID. We discuss these results in reference to the use of face photos for security.

In situ synthesis of twelve dialkyltartrate-boric acid complexes and two polyols-boric acid complexes and their applications as chiral ion-pair selectors in nonaqueous capillary electrophoresis.

PubMed

Wang, Li-Juan; Yang, Juan; Yang, Geng-Liang; Chen, Xing-Guo

2012-07-27

In this paper, twelve dialkyltartrate-boric acid complexes and two polyols-boric acid complexes were in situ synthesized by the reaction of different dialkyltartrates or polyols with boric acid in methanol containing triethylamine. All of the twelve dialkyltartrate-boric acid complexes were found to have relatively good chiral separation performance in nonaqueous capillary electrophoresis (NACE). Their chiral recognition effects in terms of both enantioselectivity (α) and resolution (R(s)) were similar when the number of carbon atoms was below six in the alkyl group of alcohol moiety. The dialkyltartrates containing alkyl groups of different structures but the same number of carbon atoms, i.e. one of straight chain and one of branched chain, also provided similar chiral recognition effects. Furthermore, it was demonstrated for the first time that two methanol insoluble polyols, D-mannitol and D-sorbitol, could react with boric acid to prepare chiral ion-pair selectors using methanol as the solvent medium. Copyright © 2012 Elsevier B.V. All rights reserved.

Mechanism for verification of mismatched and homoduplex DNAs by nucleotides-bound MutS analyzed by molecular dynamics simulations.

PubMed

Ishida, Hisashi; Matsumoto, Atsushi

2016-09-01

In order to understand how MutS recognizes mismatched DNA and induces the reaction of DNA repair using ATP, the dynamics of the complexes of MutS (bound to the ADP and ATP nucleotides, or not) and DNA (with mismatched and matched base-pairs) were investigated using molecular dynamics simulations. As for DNA, the structure of the base-pairs of the homoduplex DNA which interacted with the DNA recognition site of MutS was intermittently disturbed, indicating that the homoduplex DNA was unstable. As for MutS, the disordered loops in the ATPase domains, which are considered to be necessary for the induction of DNA repair, were close to (away from) the nucleotide-binding sites in the ATPase domains when the nucleotides were (not) bound to MutS. This indicates that the ATPase domains changed their structural stability upon ATP binding using the disordered loop. Conformational analysis by principal component analysis showed that the nucleotide binding changed modes which have structurally solid ATPase domains and the large bending motion of the DNA from higher to lower frequencies. In the MutS-mismatched DNA complex bound to two nucleotides, the bending motion of the DNA at low frequency modes may play a role in triggering the formation of the sliding clamp for the following DNA-repair reaction step. Moreover, MM-PBSA/GBSA showed that the MutS-homoduplex DNA complex bound to two nucleotides was unstable because of the unfavorable interactions between MutS and DNA. This would trigger the ATP hydrolysis or separation of MutS and DNA to continue searching for mismatch base-pairs. Proteins 2016; 84:1287-1303. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Contribution of familiarity and recollection to associative recognition memory: insights from event-related potentials.

PubMed

Opitz, Bertram; Cornell, Sonia

2006-09-01

Within the dual-process perspective of recognition memory, it has been claimed that familiarity is sufficient to support recognition of single items, but recollection is necessary for associative recognition of item pairs. However, there are some reports suggesting that familiarity might support associative recognition judgments when the items form an easy to access bound representation. In contrast, recollection seems to be required for the recognition of bindings that might be flexibly rearranged in novel situations. We investigated whether both forms of binding are mediated by different mechanisms as reflected by a qualitatively different spatiotemporal eventrelated potential (ERP) pattern. In a recognition memory experiment, subjects gave old/new judgments to words learned by focusing either on interitem associations or on size relation of word triplets. Results revealed higher hit rates in the relational condition as compared to the associative condition. In addition, the proportion of triplets from which all three items were remembered was significantly larger in the relational condition suggesting that memory retrieval in this condition relies primarily on bound representations of word triplets. The ERP revealed a late parietal old/new effect for both conditions, with relational processing resulting in a greater effect. In contrast, an early frontal old/new effect was solely present in the associative condition. Taken together, these data provide evidence that familiarity might support associative recognition if the associated components are coherently encoded into a bound representation. Recollection might foster the recognition of relational bindings among items. This indicates that the contribution of familiarity and recollection to associative recognition depends on the kind of binding operations performed on the items rather than on the single versus multiple item distinction.

Caffeine cravings impair memory and metacognition.

PubMed

Palmer, Matthew A; Sauer, James D; Ling, Angus; Riza, Joshua

2017-10-01

Cravings for food and other substances can impair cognition. We extended previous research by testing the effects of caffeine cravings on cued-recall and recognition memory tasks, and on the accuracy of judgements of learning (JOLs; predicted future recall) and feeling-of-knowing (FOK; predicted future recognition for items that cannot be recalled). Participants (N = 55) studied word pairs (POND-BOOK) and completed a cued-recall test and a recognition test. Participants made JOLs prior to the cued-recall test and FOK judgements prior to the recognition test. Participants were randomly allocated to a craving or control condition; we manipulated caffeine cravings via a combination of abstinence, cue exposure, and imagery. Cravings impaired memory performance on the cued-recall and recognition tasks. Cravings also impaired resolution (the ability to distinguish items that would be remembered from those that would not) for FOK judgements but not JOLs, and reduced calibration (correspondence between predicted and actual accuracy) for JOLs but not FOK judgements. Additional analysis of the cued-recall data suggested that cravings also reduced participants' ability to monitor the likely accuracy of answers during the cued-recall test. These findings add to prior research demonstrating that memory strength manipulations have systematically different effects on different types of metacognitive judgements.

Getting the Gist of Events: Recognition of Two-Participant Actions from Brief Displays

PubMed Central

Hafri, Alon; Papafragou, Anna; Trueswell, John C.

2013-01-01

Unlike rapid scene and object recognition from brief displays, little is known about recognition of event categories and event roles from minimal visual information. In three experiments, we displayed naturalistic photographs of a wide range of two-participant event scenes for 37 ms and 73 ms followed by a mask, and found that event categories (the event gist, e.g., ‘kicking’, ‘pushing’, etc.) and event roles (i.e., Agent and Patient) can be recognized rapidly, even with various actor pairs and backgrounds. Norming ratings from a subsequent experiment revealed that certain physical features (e.g., outstretched extremities) that correlate with Agent-hood could have contributed to rapid role recognition. In a final experiment, using identical twin actors, we then varied these features in two sets of stimuli, in which Patients had Agent-like features or not. Subjects recognized the roles of event participants less accurately when Patients possessed Agent-like features, with this difference being eliminated with two-second durations. Thus, given minimal visual input, typical Agent-like physical features are used in role recognition but, with sufficient input from multiple fixations, people categorically determine the relationship between event participants. PMID:22984951

Phylogeny of the beaked whale genus Mesoplodon (Ziphiidae: Cetacea) revealed by nuclear introns: implications for the evolution of male tusks.

PubMed

Dalebout, Merel L; Steel, Debbie; Baker, C Scott

2008-12-01

With 14 species currently recognized, the beaked whale genus Mesoplodon (family Ziphiidae) is the most speciose in the order Cetacea. Beaked whales are widely distributed but are rarely seen at sea due to their oceanic distribution, deep-diving capacity, and apparent low abundance. Morphological differentiation among Mesoplodon species is relatively limited, with the exception of tooth form in adult males. Based on scarring patterns, males appear to use their tusk-like teeth as weapons in aggressive encounters with other males. Females are effectively toothless. We used sequences from seven nuclear introns (3348 base pairs) to construct a robust and highly resolved phylogeny, which was then used as a framework to test predictions from four hypotheses seeking to explain patterns of Mesoplodon tusk morphology and/or the processes that have driven the diversification of this genus: (1) linear progression of tusk form; (2) allopatric speciation through isolation in adjacent deep-sea canyons; (3) sympatric speciation through sexual selection on tusks; and (4) selection for species-recognition cues. Maximum-likelihood and Bayesian reconstructions confirmed the monophyly of the genus and revealed that what were considered ancestral and derived tusk forms have in fact arisen independently on several occasions, contrary to predictions from the linear-progression hypothesis. Further, none of the three well-supported species clades was confined to a single ocean basin, as might have been expected from the deep-sea canyon-isolation or sexual-selection hypotheses, and some species with similar tusks have overlapping distributions, contrary to predictions from the species-recognition hypothesis. However, the divergent tusk forms and sympatric distributions of three of the four sister-species pairs identified suggest that sexual selection on male tusks has likely played an important role in this unique radiation, although other forces are clearly also involved. To our knowledge, this is the first time that sexual selection has been explicitly implicated in the radiation of a mammalian group outside terrestrial ungulates.

Electrophysiological evidence for phonological priming in Spanish Sign Language lexical access.

PubMed

Gutiérrez, Eva; Müller, Oliver; Baus, Cristina; Carreiras, Manuel

2012-06-01

Interactive activation models of lexical access assume that the presentation of a given word activates not only its lexical representation but also those corresponding to words similar in form. Current theories are based on data from oral and written languages, and therefore signed languages represent a special challenge for existing theories of word recognition and lexical access since they allow us to question what the genuine fundamentals of human language are and what might be modality-specific adaptation. The aim of the present study is to determine the electrophysiological correlates and time course of phonological processing of Spanish Sign Language (LSE). Ten deaf native LSE signers and ten deaf non-native but highly proficient LSE signers participated in the experiment. We used the ERP methodology and form-based priming in the context of a delayed lexical decision task, manipulating phonological overlap (i.e. related prime-target pairs shared either handshape or location parameters). Results showed that both parameters under study modulated brain responses to the stimuli in different time windows. Phonological priming of location resulted in a higher amplitude of the N400 component (300-500 ms window) for signs but not for non-signs. This effect may be explained in terms of initial competition among candidates. Moreover, the fact that a higher amplitude N400 for related pairs was found for signs but not for non-signs points to an effect at the lexical level. Handshape overlap produced a later effect (600-800 ms window). In this window, a more negative-going wave for the related condition than for the unrelated condition was found for non-signs in the native signers group. The findings are discussed in relation to current models of lexical access and word recognition. Finally, differences between native and non-native signers point to a less efficient use of phonological information among the non-native signers. Copyright © 2012 Elsevier Ltd. All rights reserved.

Simultaneous fluorescence light-up and selective multicolor nucleobase recognition based on sequence-dependent strong binding of berberine to DNA abasic site.

PubMed

Wu, Fei; Shao, Yong; Ma, Kun; Cui, Qinghua; Liu, Guiying; Xu, Shujuan

2012-04-28

Label-free DNA nucleobase recognition by fluorescent small molecules has received much attention due to its simplicity in mutation identification and drug screening. However, sequence-dependent fluorescence light-up nucleobase recognition and multicolor emission with individual emission energy for individual nucleobases have been seldom realized. Herein, an abasic site (AP site) in a DNA duplex was employed as a binding field for berberine, one of isoquinoline alkaloids. Unlike weak binding of berberine to the fully matched DNAs without the AP site, strong binding of berberine to the AP site occurs and the berberine's fluorescence light-up behaviors are highly dependent on the target nucleobases opposite the AP site in which the targets thymine and cytosine produce dual emission bands, while the targets guanine and adenine only give a single emission band. Furthermore, more intense emissions are observed for the target pyrimidines than purines. The flanking bases of the AP site also produce some modifications of the berberine's emission behavior. The binding selectivity of berberine at the AP site is also confirmed by measurements of fluorescence resonance energy transfer, excited-state lifetime, DNA melting and fluorescence quenching by ferrocyanide and sodium chloride. It is expected that the target pyrimidines cause berberine to be stacked well within DNA base pairs near the AP site, which results in a strong resonance coupling of the electronic transitions to the particular vibration mode to produce the dual emissions. The fluorescent signal-on and emission energy-modulated sensing for nucleobases based on this fluorophore is substantially advantageous over the previously used fluorophores. We expect that this approach will be developed as a practical device for differentiating pyrimidines from purines by positioning an AP site toward a target that is available for readout by this alkaloid probe. This journal is © The Royal Society of Chemistry 2012

The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mullins, Elwood A.; Shi, Rongxin; Parsons, Zachary D.

Threats to genomic integrity arising from DNA damage are mitigated by DNA glycosylases, which initiate the base excision repair pathway by locating and excising aberrant nucleobases. How these enzymes find small modifications within the genome is a current area of intensive research. A hallmark of these and other DNA repair enzymes is their use of base flipping to sequester modified nucleotides from the DNA helix and into an active site pocket. Consequently, base flipping is generally regarded as an essential aspect of lesion recognition and a necessary precursor to base excision. In this paper, we present the first, to ourmore » knowledge, DNA glycosylase mechanism that does not require base flipping for either binding or catalysis. Using the DNA glycosylase AlkD from Bacillus cereus, we crystallographically monitored excision of an alkylpurine substrate as a function of time, and reconstructed the steps along the reaction coordinate through structures representing substrate, intermediate and product complexes. Instead of directly interacting with the damaged nucleobase, AlkD recognizes aberrant base pairs through interactions with the phosphoribose backbone, while the lesion remains stacked in the DNA duplex. Quantum mechanical calculations revealed that these contacts include catalytic charge–dipole and CH–π interactions that preferentially stabilize the transition state. We show in vitro and in vivo how this unique means of recognition and catalysis enables AlkD to repair large adducts formed by yatakemycin, a member of the duocarmycin family of antimicrobial natural products exploited in bacterial warfare and chemotherapeutic trials. Bulky adducts of this or any type are not excised by DNA glycosylases that use a traditional base-flipping mechanism. Finally and hence, these findings represent a new model for DNA repair and provide insights into catalysis of base excision.« less

The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions

DOE PAGES

Mullins, Elwood A.; Shi, Rongxin; Parsons, Zachary D.; ...

2015-10-28

Threats to genomic integrity arising from DNA damage are mitigated by DNA glycosylases, which initiate the base excision repair pathway by locating and excising aberrant nucleobases. How these enzymes find small modifications within the genome is a current area of intensive research. A hallmark of these and other DNA repair enzymes is their use of base flipping to sequester modified nucleotides from the DNA helix and into an active site pocket. Consequently, base flipping is generally regarded as an essential aspect of lesion recognition and a necessary precursor to base excision. In this paper, we present the first, to ourmore » knowledge, DNA glycosylase mechanism that does not require base flipping for either binding or catalysis. Using the DNA glycosylase AlkD from Bacillus cereus, we crystallographically monitored excision of an alkylpurine substrate as a function of time, and reconstructed the steps along the reaction coordinate through structures representing substrate, intermediate and product complexes. Instead of directly interacting with the damaged nucleobase, AlkD recognizes aberrant base pairs through interactions with the phosphoribose backbone, while the lesion remains stacked in the DNA duplex. Quantum mechanical calculations revealed that these contacts include catalytic charge–dipole and CH–π interactions that preferentially stabilize the transition state. We show in vitro and in vivo how this unique means of recognition and catalysis enables AlkD to repair large adducts formed by yatakemycin, a member of the duocarmycin family of antimicrobial natural products exploited in bacterial warfare and chemotherapeutic trials. Bulky adducts of this or any type are not excised by DNA glycosylases that use a traditional base-flipping mechanism. Finally and hence, these findings represent a new model for DNA repair and provide insights into catalysis of base excision.« less

Electronic single-molecule identification of carbohydrate isomers by recognition tunnelling

NASA Astrophysics Data System (ADS)

Im, Jongone; Biswas, Sovan; Liu, Hao; Zhao, Yanan; Sen, Suman; Biswas, Sudipta; Ashcroft, Brian; Borges, Chad; Wang, Xu; Lindsay, Stuart; Zhang, Peiming

2016-12-01

Carbohydrates are one of the four main building blocks of life, and are categorized as monosaccharides (sugars), oligosaccharides and polysaccharides. Each sugar can exist in two alternative anomers (in which a hydroxy group at C-1 takes different orientations) and each pair of sugars can form different epimers (isomers around the stereocentres connecting the sugars). This leads to a vast combinatorial complexity, intractable to mass spectrometry and requiring large amounts of sample for NMR characterization. Combining measurements of collision cross section with mass spectrometry (IM-MS) helps, but many isomers are still difficult to separate. Here, we show that recognition tunnelling (RT) can classify many anomers and epimers via the current fluctuations they produce when captured in a tunnel junction functionalized with recognition molecules. Most importantly, RT is a nanoscale technique utilizing sub-picomole quantities of analyte. If integrated into a nanopore, RT would provide a unique approach to sequencing linear polysaccharides.

Visual attention: low-level and high-level viewpoints

NASA Astrophysics Data System (ADS)

Stentiford, Fred W. M.

2012-06-01

This paper provides a brief outline of the approaches to modeling human visual attention. Bottom-up and top-down mechanisms are described together with some of the problems that they face. It has been suggested in brain science that memory functions by trading measurement precision for associative power; sensory inputs from the environment are never identical on separate occasions, but the associations with memory compensate for the differences. A graphical representation for image similarity is described that relies on the size of maximally associative structures (cliques) that are found to reflect between pairs of images. This is applied to the recognition of movie posters, the location and recognition of characters, and the recognition of faces. The similarity mechanism is shown to model popout effects when constraints are placed on the physical separation of pixels that correspond to nodes in the maximal cliques. The effect extends to modeling human visual behaviour on the Poggendorff illusion.

The Effect of Signal-to-Noise Ratio on Linguistic Processing in a Semantic Judgment Task: An Aging Study.

PubMed

Stanley, Nicholas; Davis, Tara; Estis, Julie

2017-03-01

Aging effects on speech understanding in noise have primarily been assessed through speech recognition tasks. Recognition tasks, which focus on bottom-up, perceptual aspects of speech understanding, intentionally limit linguistic and cognitive factors by asking participants to only repeat what they have heard. On the other hand, linguistic processing tasks require bottom-up and top-down (linguistic, cognitive) processing skills and are, therefore, more reflective of speech understanding abilities used in everyday communication. The effect of signal-to-noise ratio (SNR) on linguistic processing ability is relatively unknown for either young (YAs) or older adults (OAs). To determine if reduced SNRs would be more deleterious to the linguistic processing of OAs than YAs, as measured by accuracy and reaction time in a semantic judgment task in competing speech. In the semantic judgment task, participants indicated via button press whether word pairs were a semantic Match or No Match. This task was performed in quiet, as well as, +3, 0, -3, and -6 dB SNR with two-talker speech competition. Seventeen YAs (20-30 yr) with normal hearing sensitivity and 17 OAs (60-68 yr) with normal hearing sensitivity or mild-to-moderate sensorineural hearing loss within age-appropriate norms. Accuracy, reaction time, and false alarm rate were measured and analyzed using a mixed design analysis of variance. A decrease in SNR level significantly reduced accuracy and increased reaction time in both YAs and OAs. However, poor SNRs affected accuracy and reaction time of Match and No Match word pairs differently. Accuracy for Match pairs declined at a steeper rate than No Match pairs in both groups as SNR decreased. In addition, reaction time for No Match pairs increased at a greater rate than Match pairs in more difficult SNRs, particularly at -3 and -6 dB SNR. False-alarm rates indicated that participants had a response bias to No Match pairs as the SNR decreased. Age-related differences were limited to No Match pair accuracies at -6 dB SNR. The ability to correctly identify semantically matched word pairs was more susceptible to disruption by a poor SNR than semantically unrelated words in both YAs and OAs. The effect of SNR on this semantic judgment task implies that speech competition differentially affected the facilitation of semantically related words and the inhibition of semantically incompatible words, although processing speed, as measured by reaction time, remained faster for semantically matched pairs. Overall, the semantic judgment task in competing speech elucidated the effect of a poor listening environment on the higher order processing of words. American Academy of Audiology

Hapten mediated display and pairing of recombinant antibodies accelerates assay assembly for biothreat countermeasures.

PubMed

Sherwood, Laura J; Hayhurst, Andrew

2012-01-01

A bottle-neck in recombinant antibody sandwich immunoassay development is pairing, demanding protein purification and modification to distinguish captor from tracer. We developed a simple pairing scheme using microliter amounts of E. coli osmotic shockates bearing site-specific biotinylated antibodies and demonstrated proof of principle with a single domain antibody (sdAb) that is both captor and tracer for polyvalent Marburgvirus nucleoprotein. The system could also host pairs of different sdAb specific for the 7 botulinum neurotoxin (BoNT) serotypes, enabling recognition of the cognate serotype. Inducible supE co-expression enabled sdAb populations to be propagated as either phage for more panning from repertoires or expressed as soluble sdAb for screening within a single host strain. When combined with streptavidin-g3p fusions, a novel transdisplay system was formulated to retrofit a semi-synthetic sdAb library which was mined for an anti-Ebolavirus sdAb which was immediately immunoassay ready, thereby speeding up the recombinant antibody discovery and utilization processes.

Hapten Mediated Display and Pairing of Recombinant Antibodies Accelerates Assay Assembly for Biothreat Countermeasures

PubMed Central

Sherwood, Laura J.; Hayhurst, Andrew

2012-01-01

A bottle-neck in recombinant antibody sandwich immunoassay development is pairing, demanding protein purification and modification to distinguish captor from tracer. We developed a simple pairing scheme using microliter amounts of E. coli osmotic shockates bearing site-specific biotinylated antibodies and demonstrated proof of principle with a single domain antibody (sdAb) that is both captor and tracer for polyvalent Marburgvirus nucleoprotein. The system could also host pairs of different sdAb specific for the 7 botulinum neurotoxin (BoNT) serotypes, enabling recognition of the cognate serotype. Inducible supE co-expression enabled sdAb populations to be propagated as either phage for more panning from repertoires or expressed as soluble sdAb for screening within a single host strain. When combined with streptavidin-g3p fusions, a novel transdisplay system was formulated to retrofit a semi-synthetic sdAb library which was mined for an anti-Ebolavirus sdAb which was immediately immunoassay ready, thereby speeding up the recombinant antibody discovery and utilization processes. PMID:23150778

Recombination Proteins Mediate Meiotic Spatial Chromosome Organization and Pairing

PubMed Central

Storlazzi, Aurora; Gargano, Silvana; Ruprich-Robert, Gwenael; Falque, Matthieu; David, Michelle; Kleckner, Nancy; Zickler, Denise

2010-01-01

SUMMARY Meiotic chromosome pairing involves not only recognition of homology but also juxtaposition of entire chromosomes in a topologically regular way. Analysis of filamentous fungus Sordaria macrospora reveals that recombination proteins Mer3, Msh4 and Mlh1 play direct roles in all of these aspects, in advance of their known roles in recombination. Absence of Mer3 helicase results in interwoven chromosomes, thereby revealing the existence of features that specifically ensure “entanglement avoidance”. Entanglements that remain at zygotene, i.e. “interlockings”, require Mlh1 for resolution, likely to eliminate constraining recombinational connections. Patterns of Mer3 and Msh4 foci along aligned chromosomes show that the double-strand breaks mediating homologous alignment have spatially separated ends, one localized to each partner axis, and that pairing involves interference among developing interhomolog interactions. We propose that Mer3, Msh4 and Mlh1 execute all of these roles during pairing by modulating the state of nascent double-strand break/partner DNA contacts within axis-associated recombination complexes. PMID:20371348

In vitro excision of adeno-associated virus DNA from recombinant plasmids: Isolation of an enzyme fraction from HeLa cells that cleaves DNA at poly(G) sequences

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gottlieb, J.; Muzyczka, N.

1988-06-01

When circular recombinant plasmids containing adeno-associated virus (AAV) DNA sequences are transfected into human cells, the AAV provirus is rescued. Using these circular AAV plasmids as substrates, the authors isolated an enzyme fraction from HeLa cell nuclear extracts that excises intact AAV DNA in vitro from vector DNA and produces linear DNA products. The recognition signal for the enzyme is a polypurine-polypyrimidine sequence which is at least 9 residues long and rich in G . C base pairs. Such sequences are present in AAV recombinant plasmids as part of the first 15 base pairs of the AAV terminal repeat andmore » in some cases as the result of cloning the AAV genome by G . C tailing. The isolated enzyme fraction does not have significant endonucleolytic activity on single-stranded or double-stranded DNA. Plasmid DNA that is transfected into tissue culture cells is cleaved in vivo to produce a pattern of DNA fragments similar to that seen with purified enzyme in vitro. The activity has been called endo R for rescue, and its behavior suggests that it may have a role in recombination of cellular chromosomes.« less

Noncanonical self-assembly of multifunctional DNA nanoflowers for biomedical applications.

PubMed

Zhu, Guizhi; Hu, Rong; Zhao, Zilong; Chen, Zhuo; Zhang, Xiaobing; Tan, Weihong

2013-11-06

DNA nanotechnology has been extensively explored to assemble various functional nanostructures for versatile applications. Mediated by Watson-Crick base-pairing, these DNA nanostructures have been conventionally assembled through hybridization of many short DNA building blocks. Here we report the noncanonical self-assembly of multifunctional DNA nanostructures, termed as nanoflowers (NFs), and the versatile biomedical applications. These NFs were assembled from long DNA building blocks generated via rolling circle replication (RCR) of a designer template. NF assembly was driven by liquid crystallization and dense packaging of building blocks, without relying on Watson-Crick base-pairing between DNA strands, thereby avoiding the otherwise conventional complicated DNA sequence design. NF sizes were readily tunable in a wide range, by simply adjusting such parameters as assembly time and template sequences. NFs were exceptionally resistant to nuclease degradation, denaturation, or dissociation at extremely low concentration, presumably resulting from the dense DNA packaging in NFs. The exceptional biostability is critical for biomedical applications. By rational design, NFs can be readily incorporated with myriad functional moieties. All these properties make NFs promising for versatile applications. As a proof-of-principle demonstration, in this study, NFs were integrated with aptamers, bioimaging agents, and drug loading sites, and the resultant multifunctional NFs were demonstrated for selective cancer cell recognition, bioimaging, and targeted anticancer drug delivery.

Noncanonical self-assembly of multifunctional DNA nanoflowers for biomedical applications

PubMed Central

Zhu, Guizhi; Hu, Rong; Zhao, Zilong; Chen, Zhuo; Zhang, Xiaobing; Tan, Weihong

2013-01-01

DNA nanotechnology has been extensively explored to assemble various functional nanostructures for versatile applications. Mediated by Watson-Crick base-pairing, these DNA nanostructures have been conventionally assembled through hybridization of many short DNA building blocks. Here we report the noncanonical self-assembly of multifunctional DNA nanostructures, termed as nanoflowers (NFs), and the versatile biomedical applications. These NFs were assembled from long DNA building blocks generated via Rolling Circle Replication (RCR) of a designer template. NF assembly was driven by liquid crystallization and dense packaging of building blocks, without relying on Watson-Crick base-pairing between DNA strands, thereby avoiding the otherwise conventional complicated DNA sequence design. NF sizes were readily tunable in a wide range, by simply adjusting such parameters as assembly time and template sequences. NFs were exceptionally resistant to nuclease degradation, denaturation, or dissociation at extremely low concentration, presumably resulting from the dense DNA packaging in NFs. The exceptional biostability is critical for biomedical applications. By rational design, NFs can be readily incorporated with myriad functional moieties. All these properties make NFs promising for versatile applications. As a proof-of-principle demonstration, in this study, NFs were integrated with aptamers, bioimaging agents, and drug loading sites, and the resultant multifunctional NFs were demonstrated for selective cancer cell recognition, bioimaging, and targeted anticancer drug delivery. PMID:24164620

Design method of ARM based embedded iris recognition system

NASA Astrophysics Data System (ADS)

Wang, Yuanbo; He, Yuqing; Hou, Yushi; Liu, Ting

2008-03-01

With the advantages of non-invasiveness, uniqueness, stability and low false recognition rate, iris recognition has been successfully applied in many fields. Up to now, most of the iris recognition systems are based on PC. However, a PC is not portable and it needs more power. In this paper, we proposed an embedded iris recognition system based on ARM. Considering the requirements of iris image acquisition and recognition algorithm, we analyzed the design method of the iris image acquisition module, designed the ARM processing module and its peripherals, studied the Linux platform and the recognition algorithm based on this platform, finally actualized the design method of ARM-based iris imaging and recognition system. Experimental results show that the ARM platform we used is fast enough to run the iris recognition algorithm, and the data stream can flow smoothly between the camera and the ARM chip based on the embedded Linux system. It's an effective method of using ARM to actualize portable embedded iris recognition system.

Getting into Teams in Physical Education and Exclusion Processes among Students

ERIC Educational Resources Information Center

Grimminger, Elke

2014-01-01

Although splitting up a class into teams is a consistent didactical element in physical education (PE), it is under-investigated in terms of how students handle the social dynamics in these situations. Therefore, the present study examines the strategies of exclusion as markers for non-recognition when students are split up into teams/pairs. The…

Word Associations and the Recognition of Flashed Words. Final Report.

ERIC Educational Resources Information Center

Samuels, S. Jay

Two separate studies were designed to investigate the effect of reading the first word of a pair on the speed of recognizing the second. One study drew its subjects from the college level; the other from the fourth grade. A Scientific Prototype Three-Channel Tachistoscope was used, and an erasing image was flashed immediately following the…

Differential Memory of Picture and Word Stimuli in a Paired-Associate Learning Task.

ERIC Educational Resources Information Center

Bartels, Laura Grand; Feinbloom, Jessica

Ten concrete nouns represented in either a pictorial or a linguistic mode and accompanied by ten nonsense syllables were shown to 77 college students in a study of how pictorial stimuli varied in recall and recognition tasks. The group receiving pictorial stimuli recalled and recognized significantly more nonsense syllables than did the group…

Reliability and Magnitude of Laterality Effects in Dichotic Listening with Exogenous Cueing

ERIC Educational Resources Information Center

Voyer, Daniel

2004-01-01

The purpose of the present study was to replicate and extend to word recognition previous findings of reduced magnitude and reliability of laterality effects when exogenous cueing was used in a dichotic listening task with syllable pairs. Twenty right-handed undergraduate students with normal hearing (10 females, 10 males) completed a dichotic…

Transcriptional Analysis of In vivo Plasmodium yoelii Liver Stage Gene Expression

DTIC Science & Technology

2005-04-26

reaction was added to a PCR master mix with one of several oligonucleotide primer pairs (Table S6). The primers were designed and the specific conditions ...Koonin EV. Using the COG database to improve gene recognition in complete genomes. Genetica 2000;108:9–17. 26] Florens L, Washburn MP, Raine JD, et al

Function Follows Form: Activation of Shape and Function Features during Object Identification

ERIC Educational Resources Information Center

Yee, Eiling; Huffstetler, Stacy; Thompson-Schill, Sharon L.

2011-01-01

Most theories of semantic memory characterize knowledge of a given object as comprising a set of semantic features. But how does conceptual activation of these features proceed during object identification? We present the results of a pair of experiments that demonstrate that object recognition is a dynamically unfolding process in which function…

Language Nonselective Lexical Access in Bilingual Toddlers

ERIC Educational Resources Information Center

Von Holzen, Katie; Mani, Nivedita

2012-01-01

We examined how words from bilingual toddlers' second language (L2) primed recognition of related target words in their first language (L1). On critical trials, prime-target word pairs were either (a) phonologically related, with L2 primes overlapped phonologically with L1 target words [e.g., "slide" (L2 prime)-"Kleid" (L1 target, "dress")], or…

The Use of Error Data to Study the Development of Verbal Encoding of Pictorial Stimuli.

ERIC Educational Resources Information Center

Cramer, Phebe

If older children automatically label pictorial stimuli, then their performance should be impaired on tasks in which such labeling would increase the error rate. Children were asked to learn pairs of verbal or pictorial stimuli which, when combined, formed a different compound word (BUTTER-FLY). Subsequently, a false recognition test that included…

Promoter scanning of the Human COX-2 gene with 8-ring polyamides: unexpected weakening of polyamide-DNA binding and selectivity by replacing an internal N-Me-pyrrole with β-alanine

PubMed Central

Aston, Karl; Ramos, Joseph P.; Koeller, Kevin J.; Nanjunda, Rupesh; He, Gaofei

2012-01-01

Rules for polyamide DNA recognition have proved invaluable for the design of sequence-selective DNA-binding agents in cell-free systems. However, these rules are not fully transferrable to predicting activity in cells, tissues or animals, and additional refinements to our understanding of DNA recognition would help biomedical studies. Similar complexities are encountered when using internal β-alanines as polyamide building blocks in place of N-methyl pyrrole; β-alanines were introduced in polyamide designs to maintain good hydrogen bonding registry with the target DNA, especially for long polyamides or those with several GC bp (P.B. Dervan, A.R. Urbach, Essays Contemp. Chem. (2001) 327–339). Thus, to clarify important subtleties of molecular recognition, we studied the effects of replacing a single pyrrole with β-alanine in 8-ring polyamides designed against the Ets-1 transcription factor. Replacement of a single internal N-methylpyrrole with β-alanine to generate a β/Im pairing in two 8-ring polyamides causes a decrease in DNA binding affinity by two orders of magnitude and decreases DNA binding selectivity, contrary to expectations based on the literature. Measurements were made by fluorescence spectroscopy, quantitative DNA footprinting and surface plasmon resonance, with these vastly different techniques showing excellent agreement. Furthermore, results were validated for a range of DNA substrates from small hairpins to long dsDNA sequences. Docking studies helped show that β-alanine does not make efficient hydrophobic contacts with the rest of the polyamide or nearby DNA, in contrast to pyrrole. These results help refine design principles and expectations for polyamide-DNA recognition. PMID:23023196

Selective attention and recognition: effects of congruency on episodic learning.

PubMed

Rosner, Tamara M; D'Angelo, Maria C; MacLellan, Ellen; Milliken, Bruce

2015-05-01

Recent research on cognitive control has focused on the learning consequences of high selective attention demands in selective attention tasks (e.g., Botvinick, Cognit Affect Behav Neurosci 7(4):356-366, 2007; Verguts and Notebaert, Psychol Rev 115(2):518-525, 2008). The current study extends these ideas by examining the influence of selective attention demands on remembering. In Experiment 1, participants read aloud the red word in a pair of red and green spatially interleaved words. Half of the items were congruent (the interleaved words had the same identity), and the other half were incongruent (the interleaved words had different identities). Following the naming phase, participants completed a surprise recognition memory test. In this test phase, recognition memory was better for incongruent than for congruent items. In Experiment 2, context was only partially reinstated at test, and again recognition memory was better for incongruent than for congruent items. In Experiment 3, all of the items contained two different words, but in one condition the words were presented close together and interleaved, while in the other condition the two words were spatially separated. Recognition memory was better for the interleaved than for the separated items. This result rules out an interpretation of the congruency effects on recognition in Experiments 1 and 2 that hinges on stronger relational encoding for items that have two different words. Together, the results support the view that selective attention demands for incongruent items lead to encoding that improves recognition.

Recognition memory for social and non-social odors: differential effects of neurotoxic lesions to the hippocampus and perirhinal cortex.

PubMed

Feinberg, Leila M; Allen, Timothy A; Ly, Denise; Fortin, Norbert J

2012-01-01

The contributions of the hippocampus (HC) and perirhinal cortex (PER) to recognition memory are currently topics of debate in neuroscience. Here we used a rapidly-learned (seconds) spontaneous novel odor recognition paradigm to assess the effects of pre-training N-methyl-D-aspartate lesions to the HC or PER on odor recognition memory. We tested memory for both social and non-social odor stimuli. Social odors were acquired from conspecifics, while non-social odors were household spices. Conspecific odor stimuli are ethologically-relevant and have a high degree of overlapping features compared to non-social household spices. Various retention intervals (5 min, 20 min, 1h, 24h, or 48 h) were used between study and test phases, each with a unique odor pair, to assess changes in novelty preference over time. Consistent with findings in other paradigms, modalities, and species, we found that HC lesions yielded no significant recognition memory deficits. In contrast, PER lesions caused significant deficits for social odor recognition memory at long retention intervals, demonstrating a critical role for PER in long-term memory for social odors. PER lesions had no effect on memory for non-social odors. The results are consistent with a general role for PER in long-term recognition memory for stimuli that have a high degree of overlapping features, which must be distinguished by conjunctive representations. Copyright © 2011 Elsevier Inc. All rights reserved.

[Hemispheric differences in letter matching of hiragana and katakana].

PubMed

Iizuka, K; Sato, H

1992-07-01

The purpose of the present study was to examine the hemispheric differences in letter matching of hiragana and katakana. The stimuli with a pair of each one letter of hiragana and katakana were presented unilaterally to the right or left visual hemifield with a tachistoscope. The subjects were 40 male right handers. They were required to judge whether a pair of letters had the same name or different one. A significant right visual hemifield superiority was observed for both the accuracy of recognition and reaction time. The results suggest that the callosal relay model of Zaidel may be applied to the name matching task.

cis-Acting elements important for retroviral RNA packaging specificity.

PubMed

Beasley, Benjamin E; Hu, Wei-Shau

2002-05-01

Spleen necrosis virus (SNV) proteins can package RNA from distantly related murine leukemia virus (MLV), whereas MLV proteins cannot package SNV RNA efficiently. We used this nonreciprocal recognition to investigate regions of packaging signals that influence viral RNA encapsidation specificity. Although the MLV and SNV packaging signals (Psi and E, respectively) do not contain significant sequence homology, they both contain a pair of hairpins. This hairpin pair was previously proposed to be the core element in MLV Psi. In the present study, MLV-based vectors were generated to contain chimeric SNV/MLV packaging signals in which the hairpins were replaced with the heterologous counterpart. The interactions between these chimeras and MLV or SNV proteins were examined by virus replication and RNA analyses. SNV proteins recognized all of the chimeras, indicating that these chimeras were functional. We found that replacing the hairpin pair did not drastically alter the ability of MLV proteins to package these chimeras. These results indicate that, despite the important role of the hairpin pair in RNA packaging, it is not the major motif responsible for the ability of MLV proteins to discriminate between the MLV and SNV packaging signals. To determine the role of sequences flanking the hairpins in RNA packaging specificity, vectors with swapped flanking regions were generated and evaluated. SNV proteins packaged all of these chimeras efficiently. In contrast, MLV proteins strongly favored chimeras with the MLV 5'-flanking regions. These data indicated that MLV Gag recognizes multiple elements in the viral packaging signal, including the hairpin structure and flanking regions.

The bacterial type III-secreted protein AvrRps4 is a bipartite effector

PubMed Central

Spears, Benjamin J.; Garner, Christopher M.; Rogan, Conner J.; Su, Jianbin; Bhattacharjee, Saikat

2018-01-01

Bacterial effector proteins secreted into host plant cells manipulate those cells to the benefit of the pathogen, but effector-triggered immunity (ETI) occurs when effectors are recognized by host resistance proteins. The RPS4/RRS1 pair recognizes the Pseudomonas syringae pv. pisi effector AvrRps4. AvrRps4 is processed in planta into AvrRps4N (133 amino acids), homologous to the N-termini of other effectors including the native P. syringae pv. tomato strain DC3000 effector HopK1, and AvrRps4C (88 amino acids). Previous data suggested that AvrRps4C alone is necessary and sufficient for resistance when overexpressed in heterologous systems. We show that delivering AvrRps4C from DC3000, but not from a DC3000 hopK1- strain, triggers resistance in the Arabidopsis accession Col-0. Delivering AvrRps4C in tandem with AvrRps4N, or as a chimera with HopK1N, fully complements AvrRps4-triggered immunity. AvrRps4N in the absence of AvrRps4C enhances virulence in Col-0. In addition, AvrRps4N triggers a hypersensitive response in lettuce that is attenuated by coexpression of AvrRps4C, further supporting the role of AvrRps4N as a bona fide effector domain. Based on these results we propose that evolutionarily, fusion of AvrRps4C to AvrRps4N may have counteracted recognition of AvrRps4N, and that the plant RPS4/RRS1 resistance gene pair was selected as a countermeasure. We conclude that AvrRps4 represents an unusual chimeric effector, with recognition in Arabidopsis by RPS4/RRS1 requiring the presence of both processed effector moieties. PMID:29601603

The bacterial type III-secreted protein AvrRps4 is a bipartite effector.

PubMed

Halane, Morgan K; Kim, Sang Hee; Spears, Benjamin J; Garner, Christopher M; Rogan, Conner J; Okafor, Elizabeth C; Su, Jianbin; Bhattacharjee, Saikat; Gassmann, Walter

2018-03-01

Bacterial effector proteins secreted into host plant cells manipulate those cells to the benefit of the pathogen, but effector-triggered immunity (ETI) occurs when effectors are recognized by host resistance proteins. The RPS4/RRS1 pair recognizes the Pseudomonas syringae pv. pisi effector AvrRps4. AvrRps4 is processed in planta into AvrRps4N (133 amino acids), homologous to the N-termini of other effectors including the native P. syringae pv. tomato strain DC3000 effector HopK1, and AvrRps4C (88 amino acids). Previous data suggested that AvrRps4C alone is necessary and sufficient for resistance when overexpressed in heterologous systems. We show that delivering AvrRps4C from DC3000, but not from a DC3000 hopK1- strain, triggers resistance in the Arabidopsis accession Col-0. Delivering AvrRps4C in tandem with AvrRps4N, or as a chimera with HopK1N, fully complements AvrRps4-triggered immunity. AvrRps4N in the absence of AvrRps4C enhances virulence in Col-0. In addition, AvrRps4N triggers a hypersensitive response in lettuce that is attenuated by coexpression of AvrRps4C, further supporting the role of AvrRps4N as a bona fide effector domain. Based on these results we propose that evolutionarily, fusion of AvrRps4C to AvrRps4N may have counteracted recognition of AvrRps4N, and that the plant RPS4/RRS1 resistance gene pair was selected as a countermeasure. We conclude that AvrRps4 represents an unusual chimeric effector, with recognition in Arabidopsis by RPS4/RRS1 requiring the presence of both processed effector moieties.

Riboswitch-based sensor in low optical background

NASA Astrophysics Data System (ADS)

Harbaugh, Svetlana V.; Davidson, Molly E.; Chushak, Yaroslav G.; Kelley-Loughnane, Nancy; Stone, Morley O.

2008-08-01

Riboswitches are a type of natural genetic control element that use untranslated sequence in the RNA to recognize and bind to small molecules that regulate expression of that gene. Creation of synthetic riboswitches to novel ligands depends on the ability to screen for analyte binding sensitivity and specificity. In our work, we have coupled a synthetic riboswitch to an optical reporter assay based on fluorescence resonance energy transfer (FRET) between two genetically-coded fluorescent proteins. Specifically, a theophylline-sensitive riboswitch was placed upstream of the Tobacco Etch Virus (TEV) protease coding sequence, and a FRET-based construct, BFP-eGFP or eGFP-REACh, was linked by a peptide encoding the recognition sequence for TEV protease. Cells expressing the riboswitch showed a marked optical difference in fluorescence emission in the presence of theophylline. However, the BFP-eGFP FRET pair posses significant optical background that reduces the sensitivity of a FRET-based assay. To improve the optical assay, we designed a nonfluorescent yellow fluorescent protein (YFP) mutant called REACh (for Resonance Energy-Accepting Chromoprotein) as the FRET acceptor for eGFP. The advantage of using an eGFP-REACh pair is the elimination of acceptor fluorescence which leads to an improved detection of FRET via better signal-to-noise ratio. The EGFP-REACh fusion protein was constructed with the TEV protease cleavage site; thus upon TEV translation, cleavage occurs diminishing REACh quenching and increasing eGFP emission resulting in a 4.5-fold improvement in assay sensitivity.

Lune/eye gone, a Pax-like protein, uses a partial paired domain and a homeodomain for DNA recognition.

PubMed

Jun, S; Wallen, R V; Goriely, A; Kalionis, B; Desplan, C

1998-11-10

Pax proteins, characterized by the presence of a paired domain, play key regulatory roles during development. The paired domain is a bipartite DNA-binding domain that contains two helix-turn-helix domains joined by a linker region. Each of the subdomains, the PAI and RED domains, has been shown to be a distinct DNA-binding domain. The PAI domain is the most critical, but in specific circumstances, the RED domain is involved in DNA recognition. We describe a Pax protein, originally called Lune, that is the product of the Drosophila eye gone gene (eyg). It is unique among Pax proteins, because it contains only the RED domain. eyg seems to play a role both in the organogenesis of the salivary gland during embryogenesis and in the development of the eye. A high-affinity binding site for the Eyg RED domain was identified by using systematic evolution of ligands by exponential enrichment techniques. This binding site is related to a binding site previously identified for the RED domain of the Pax-6 5a isoform. Eyg also contains another DNA-binding domain, a Prd-class homeodomain (HD), whose palindromic binding site is similar to other Prd-class HDs. The ability of Pax proteins to use the PAI, RED, and HD, or combinations thereof, may be one mechanism that allows them to be used at different stages of development to regulate various developmental processes through the activation of specific target genes.

Lune/eye gone, a Pax-like protein, uses a partial paired domain and a homeodomain for DNA recognition

PubMed Central

Jun, Susie; Wallen, Robert V.; Goriely, Anne; Kalionis, Bill; Desplan, Claude

1998-01-01

Pax proteins, characterized by the presence of a paired domain, play key regulatory roles during development. The paired domain is a bipartite DNA-binding domain that contains two helix–turn–helix domains joined by a linker region. Each of the subdomains, the PAI and RED domains, has been shown to be a distinct DNA-binding domain. The PAI domain is the most critical, but in specific circumstances, the RED domain is involved in DNA recognition. We describe a Pax protein, originally called Lune, that is the product of the Drosophila eye gone gene (eyg). It is unique among Pax proteins, because it contains only the RED domain. eyg seems to play a role both in the organogenesis of the salivary gland during embryogenesis and in the development of the eye. A high-affinity binding site for the Eyg RED domain was identified by using systematic evolution of ligands by exponential enrichment techniques. This binding site is related to a binding site previously identified for the RED domain of the Pax-6 5a isoform. Eyg also contains another DNA-binding domain, a Prd-class homeodomain (HD), whose palindromic binding site is similar to other Prd-class HDs. The ability of Pax proteins to use the PAI, RED, and HD, or combinations thereof, may be one mechanism that allows them to be used at different stages of development to regulate various developmental processes through the activation of specific target genes. PMID:9811867

Facial recognition in children after perinatal stroke.

PubMed

Ballantyne, A O; Trauner, D A

1999-04-01

To examine the effects of prenatal or perinatal stroke on the facial recognition skills of children and young adults. It was hypothesized that the nature and extent of facial recognition deficits seen in patients with early-onset lesions would be different from that seen in adults with later-onset neurologic impairment. Numerous studies with normal and neurologically impaired adults have found a right-hemisphere superiority for facial recognition. In contrast, little is known about facial recognition in children after early focal brain damage. Forty subjects had single, unilateral brain lesions from pre- or perinatal strokes (20 had left-hemisphere damage, and 20 had right-hemisphere damage), and 40 subjects were controls who were individually matched to the lesion subjects on the basis of age, sex, and socioeconomic status. Each subject was given the Short-Form of Benton's Test of Facial Recognition. Data were analyzed using the Wilcoxon matched-pairs signed-rank test and multiple regression. The lesion subjects performed significantly more poorly than did matched controls. There was no clear-cut lateralization effect, with the left-hemisphere group performing significantly more poorly than matched controls and the right-hemisphere group showing a trend toward poorer performance. Parietal lobe involvement, regardless of lesion side, adversely affected facial recognition performance in the lesion group. Results could not be accounted for by IQ differences between lesion and control groups, nor was lesion severity systematically related to facial recognition performance. Pre- or perinatal unilateral brain damage results in a subtle disturbance in facial recognition ability, independent of the side of the lesion. Parietal lobe involvement, in particular, has an adverse effect on facial recognition skills. These findings suggest that the parietal lobes may be involved in the acquisition of facial recognition ability from a very early point in brain development, but that there is sufficient potential to reorganize or compensate such that the residual deficits, though significant, are subtle.

Enhancing the response rate of strand displacement-based electrochemical aptamer sensors using bivalent binding aptamer-cDNA probes.

PubMed

Zhang, Ziping; Tao, Cancan; Yin, Jungang; Wang, Yunhui; Li, Yanshen

2018-04-30

Electrochemical aptamer (EA) sensors based on aptamer-cDNA duplex probes (cDNA: complementary DNA) and target induced strand displacement (TISD) recognition are sensitive, selective and capable of detecting a wide variety of target analytes. While substantial research efforts have focused on engineering of new signaling mechanisms for the improvement of sensor sensitivity, little attention was paid to the enhancement of sensor response rate. Typically, the previous TISD based EA sensors exhibited relatively long response times larger than 30min, which mainly resulted from the suboptimal aptamer-cDNA probe structure in which most of aptamer bases were paired to the cDNA bases. In an effort to improve the response rate of this type of sensors, we report here the rational engineering of a quickly responsive and sensitive aptamer-cDNA probe by employing the conception of bivalent interaction in supramolecular chemistry. We design a bivalent cDNA strand through linking two short monovalent cDNA sequences, and it is simultaneously hybridized to two electrode-immobilized aptamer probes to form a bivalent binding (BB) aptamer-cDNA probe. This class of BB probe possesses the advantages of less aptamer bases paired to the cDNA bases for quick response rate and good structural stability for high sensor sensitivity. By use of the rationally designed BB aptamer-cDNA probe, a TISD based EA sensor against ATP with significantly enhanced response rate (with a displacement equilibrium time of 4min) and high sensitivity was successfully constructed. We believe that our BB probe conception will help guide future designs and applications of TISD based EA sensors. Copyright © 2017 Elsevier B.V. All rights reserved.

NMR solution structure of an N2-guanine DNA adduct derived from the potent tumorigen dibenzo[a,l]pyrene: Intercalation from the minor groove with ruptured Watson-Crick base pairing

PubMed Central

Tang, Yijin; Liu, Zhi; Ding, Shuang; Lin, Chin H.; Cai, Yuqin; Rodriguez, Fabian A.; Sayer, Jane M.; Jerina, Donald M.; Amin, Shantu; Broyde, Suse; Geacintov, Nicholas E.

2012-01-01

The most potent tumorigen identified among the polycyclic aromatic hydrocarbons (PAH) is the non-planar fjord region dibenzo[a,l]pyrene (DB[a,l]P). It is metabolically activated in vivo through the widely-studied diol epoxide (DE) pathway to form covalent adducts with DNA bases, predominantly guanine and adenine. The (+)-11S,12R,13R,14S DE enantiomer forms adducts via its C14-position with the exocyclic amino group of guanine. Here, we present the first NMR solution structure of a DB[a,l]P-derived adduct, the 14R (+)-trans-anti-DB[a,l]P–N2-dG (DB[a,l]P-dG) lesion in double-stranded DNA. In contrast to the stereochemically identical benzo[a]pyrene-derived N2-dG adduct (B[a]P-dG) in which the B[a]P rings reside in the B-DNA minor groove on the 3’-side of the modifed deoxyguanosine, in the DB[a,l]P-derived adduct the DB[a,l]P rings intercalate into the duplex on the 3’-side of the modified base from the sterically crowded minor groove. Watson-Crick base pairing of the modified guanine with the partner cytosine is broken, but these bases retain some stacking with the bulky DB[a,l]P ring system. This new theme in PAH DE - DNA adduct conformation differs from: (1) the classical intercalation motif where Watson-Crick base-pairing is intact at the lesion site, and (2) the base-displaced intercalation motif in which the damaged base and its partner are extruded from the helix . The structural considerations that lead to the intercalated conformation of the DB[a,l]P-dG lesion in contrast to the minor groove alignment of the B[a]P-dG adduct, and the implications of the DB[a,l]P-dG conformational motif for the recognition of such DNA lesions by the human nucleotide excision repair apparatus, are discussed. PMID:23121427

Nuclear magnetic resonance solution structure of an N(2)-guanine DNA adduct derived from the potent tumorigen dibenzo[a,l]pyrene: intercalation from the minor groove with ruptured Watson-Crick base pairing.

PubMed

Tang, Yijin; Liu, Zhi; Ding, Shuang; Lin, Chin H; Cai, Yuqin; Rodriguez, Fabian A; Sayer, Jane M; Jerina, Donald M; Amin, Shantu; Broyde, Suse; Geacintov, Nicholas E

2012-12-04

The most potent tumorigen identified among the polycyclic aromatic hydrocarbons (PAH) is the nonplanar fjord region dibenzo[a,l]pyrene (DB[a,l]P). It is metabolically activated in vivo through the widely studied diol epoxide (DE) pathway to form covalent adducts with DNA bases, predominantly guanine and adenine. The (+)-11S,12R,13R,14S DE enantiomer forms adducts via its C14 position with the exocyclic amino group of guanine. Here, we present the first nuclear magnetic resonance solution structure of a DB[a,l]P-derived adduct, the 14R-(+)-trans-anti-DB[a,l]P-N(2)-dG (DB[a,l]P-dG) lesion in double-stranded DNA. In contrast to the stereochemically identical benzo[a]pyrene-derived N(2)-dG adduct (B[a]P-dG) in which the B[a]P rings reside in the B-DNA minor groove on the 3'-side of the modifed deoxyguanosine, in the DB[a,l]P-derived adduct the DB[a,l]P rings intercalate into the duplex on the 3'-side of the modified base from the sterically crowded minor groove. Watson-Crick base pairing of the modified guanine with the partner cytosine is broken, but these bases retain some stacking with the bulky DB[a,l]P ring system. This new theme in PAH DE-DNA adduct conformation differs from (1) the classical intercalation motif in which Watson-Crick base pairing is intact at the lesion site and (2) the base-displaced intercalation motif in which the damaged base and its partner are extruded from the helix. The structural considerations that lead to the intercalated conformation of the DB[a,l]P-dG lesion in contrast to the minor groove alignment of the B[a]P-dG adduct, and the implications of the DB[a,l]P-dG conformational motif for the recognition of such DNA lesions by the human nucleotide excision repair apparatus, are discussed.

Tactile recognition and localization using object models: the case of polyhedra on a plane.

PubMed

Gaston, P C; Lozano-Perez, T

1984-03-01

This paper discusses how data from multiple tactile sensors may be used to identify and locate one object, from among a set of known objects. We use only local information from sensors: 1) the position of contact points and 2) ranges of surface normals at the contact points. The recognition and localization process is structured as the development and pruning of a tree of consistent hypotheses about pairings between contact points and object surfaces. In this paper, we deal with polyhedral objects constrained to lie on a known plane, i.e., having three degrees of positioning freedom relative to the sensors. We illustrate the performance of the algorithm by simulation.

Base pair mismatch recognition using plasmon resonant particle labels.

PubMed

Oldenburg, Steven J; Genick, Christine C; Clark, Keith A; Schultz, David A

2002-10-01

We demonstrate the use of silver plasmon resonant particles (PRPs), as reporter labels, in a microarray-based DNA hybridization assay in which we screen for a known polymorphic site in the breast cancer gene BRCA1. PRPs (40-100 nm in diameter) image as diffraction-limited points of colored light in a standard microscope equipped with dark-field illumination, and can be individually identified and discriminated against background scatter. Rather than overall intensity, the number of PRPs counted in a CCD image by a software algorithm serves as the signal in these assays. In a typical PRP hybridization assay, we achieve a detection sensitivity that is approximately 60 x greater than that achieved by using fluorescent labels. We conclude that single particle counting is robust, generally applicable to a wide variety of assay platforms, and can be integrated into low-cost and quantitative detection systems for single nucleotide polymorphism analysis.

A multiplexable TALE-based binary expression system for in vivo cellular interaction studies.

PubMed

Toegel, Markus; Azzam, Ghows; Lee, Eunice Y; Knapp, David J H F; Tan, Ying; Fa, Ming; Fulga, Tudor A

2017-11-21

Binary expression systems have revolutionised genetic research by enabling delivery of loss-of-function and gain-of-function transgenes with precise spatial-temporal resolution in vivo. However, at present, each existing platform relies on a defined exogenous transcription activator capable of binding a unique recognition sequence. Consequently, none of these technologies alone can be used to simultaneously target different tissues or cell types in the same organism. Here, we report a modular system based on programmable transcription activator-like effector (TALE) proteins, which enables parallel expression of multiple transgenes in spatially distinct tissues in vivo. Using endogenous enhancers coupled to TALE drivers, we demonstrate multiplexed orthogonal activation of several transgenes carrying cognate variable activating sequences (VAS) in distinct neighbouring cell types of the Drosophila central nervous system. Since the number of combinatorial TALE-VAS pairs is virtually unlimited, this platform provides an experimental framework for highly complex genetic manipulation studies in vivo.

The Inversion Effect for Chinese Characters is Modulated by Radical Organization.

PubMed

Luo, Canhuang; Chen, Wei; Zhang, Ye

2017-06-01

In studies of visual object recognition, strong inversion effects accompany the acquisition of expertise and imply the involvement of configural processing. Chinese literacy results in sensitivity to the orthography of Chinese characters. While there is some evidence that this orthographic sensitivity results in an inversion effect, and thus involves configural processing, that processing might depend on exact orthographic properties. Chinese character recognition is believed to involve a hierarchical process, involving at least two lower levels of representation: strokes and radicals. Radicals are grouped into characters according to certain types of structure, i.e. left-right structure, top-bottom structure, or simple characters with only one radical by itself. These types of radical structures vary in both familiarity, and in hierarchical level (compound versus simple characters). In this study, we investigate whether the hierarchical-level or familiarity of radical-structure has an impact on the magnitude of the inversion effect. Participants were asked to do a matching task on pairs of either upright or inverted characters with all the types of structure. Inversion effects were measured based on both reaction time and response sensitivity. While an inversion effect was observed in all 3 conditions, the magnitude of the inversion effect varied with radical structure, being significantly larger for the most familiar type of structure: characters consisting of 2 radicals organized from left to right. These findings indicate that character recognition involves extraction of configural structure as well as radical processing which play different roles in the processing of compound characters and simple characters.

Self-supervised online metric learning with low rank constraint for scene categorization.

PubMed

Cong, Yang; Liu, Ji; Yuan, Junsong; Luo, Jiebo

2013-08-01

Conventional visual recognition systems usually train an image classifier in a bath mode with all training data provided in advance. However, in many practical applications, only a small amount of training samples are available in the beginning and many more would come sequentially during online recognition. Because the image data characteristics could change over time, it is important for the classifier to adapt to the new data incrementally. In this paper, we present an online metric learning method to address the online scene recognition problem via adaptive similarity measurement. Given a number of labeled data followed by a sequential input of unseen testing samples, the similarity metric is learned to maximize the margin of the distance among different classes of samples. By considering the low rank constraint, our online metric learning model not only can provide competitive performance compared with the state-of-the-art methods, but also guarantees convergence. A bi-linear graph is also defined to model the pair-wise similarity, and an unseen sample is labeled depending on the graph-based label propagation, while the model can also self-update using the more confident new samples. With the ability of online learning, our methodology can well handle the large-scale streaming video data with the ability of incremental self-updating. We evaluate our model to online scene categorization and experiments on various benchmark datasets and comparisons with state-of-the-art methods demonstrate the effectiveness and efficiency of our algorithm.

Effects of intelligibility on working memory demand for speech perception.

PubMed

Francis, Alexander L; Nusbaum, Howard C

2009-08-01

Understanding low-intelligibility speech is effortful. In three experiments, we examined the effects of intelligibility on working memory (WM) demands imposed by perception of synthetic speech. In all three experiments, a primary speeded word recognition task was paired with a secondary WM-load task designed to vary the availability of WM capacity during speech perception. Speech intelligibility was varied either by training listeners to use available acoustic cues in a more diagnostic manner (as in Experiment 1) or by providing listeners with more informative acoustic cues (i.e., better speech quality, as in Experiments 2 and 3). In the first experiment, training significantly improved intelligibility and recognition speed; increasing WM load significantly slowed recognition. A significant interaction between training and load indicated that the benefit of training on recognition speed was observed only under low memory load. In subsequent experiments, listeners received no training; intelligibility was manipulated by changing synthesizers. Improving intelligibility without training improved recognition accuracy, and increasing memory load still decreased it, but more intelligible speech did not produce more efficient use of available WM capacity. This suggests that perceptual learning modifies the way available capacity is used, perhaps by increasing the use of more phonetically informative features and/or by decreasing use of less informative ones.

Arginine Vasopressin selectively enhances recognition of sexual cues in male humans.

PubMed

Guastella, Adam J; Kenyon, Amanda R; Unkelbach, Christian; Alvares, Gail A; Hickie, Ian B

2011-02-01

Arginine Vasopressin modulates complex social and sexual behavior by enhancing social recognition, pair bonding, and aggression in non-human mammals. The influence of Arginine Vasopressin in human social and sexual behavior is, however, yet to be fully understood. We evaluated whether Arginine Vasopressin nasal spray facilitated recognition of positive and negative social and sexual stimuli over non-social stimuli. We used a recognition task that has already been shown to be sensitive to the influence of Oxytocin nasal spray (Unkelbach et al., 2008). In a double-blind, randomized, placebo-controlled, between-subjects design, 41 healthy male volunteers were administered Arginine Vasopressin (20 IU) or a placebo nasal spray after a 45 min wait period and then completed the recognition task. Results showed that the participants administered Arginine Vasopressin nasal spray were faster to detect sexual words over other types of words. This effect appeared for both positively and negatively valenced words. Results demonstrate for the first time that Arginine Vasopressin selectively enhances human cognition for sexual stimuli, regardless of valence. They further extend animal and human genetic studies linking Arginine Vasopressin to sexual behavior in males. Findings suggest an important cognitive mechanism that could enhance sexual behaviors in humans. Crown Copyright © 2010. Published by Elsevier Ltd. All rights reserved.

A genomically modified Escherichia coli strain carrying an orthogonal E. coli histidyl-tRNA synthetase•tRNAHis pair.

PubMed

Englert, Markus; Vargas-Rodriguez, Oscar; Reynolds, Noah M; Wang, Yane-Shih; Söll, Dieter; Umehara, Takuya

2017-11-01

Development of new aminoacyl-tRNA synthetase (aaRS)•tRNA pairs is central for incorporation of novel non-canonical amino acids (ncAAs) into proteins via genetic code expansion (GCE). The Escherichia coli and Caulobacter crescentus histidyl-tRNA synthetases (HisRS) evolved divergent mechanisms of tRNA His recognition that prevent their cross-reactivity. Although the E. coli HisRS•tRNA His pair is a good candidate for GCE, its use in C. crescentus is limited by the lack of established genetic selection methods and by the low transformation efficiency of C. crescentus. E. coli was genetically engineered to use a C. crescentus HisRS•tRNA His pair. Super-folder green fluorescent protein (sfGFP) and chloramphenicol acetyltransferase (CAT) were used as reporters for read-through assays. A library of 313 ncAAs coupled with the sfGFP reporter system was employed to investigate the specificity of E. coli HisRS in vivo. A genomically modified E. coli strain (named MEOV1) was created. MEVO1 requires an active C. crescentus HisRS•tRNA His pair for growth, and displays a similar doubling time as the parental E. coli strain. sfGFP- and CAT-based assays showed that the E. coli HisRS•tRNA His pair is orthogonal in MEOV1 cells. A mutation in the anticodon loop of E. coli tRNA His CUA elevated its suppression efficiency by 2-fold. The C. crescentus HisRS•tRNA His pair functionally complements an E. coli ΔhisS strain. The E. coli HisRS•tRNA His is orthogonal in MEOV1 cells. E. coli tRNA His CUA is an efficient amber suppressor in MEOV1. We developed a platform that allows protein engineering of E. coli HisRS that should facilitate GCE in E. coli. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue. Copyright © 2017 Elsevier B.V. All rights reserved.

The importance of unitization for familiarity-based learning.

PubMed

Parks, Colleen M; Yonelinas, Andrew P

2015-05-01

It is often assumed that recollection is necessary to support memory for novel associations, whereas familiarity supports memory for single items. However, the levels of unitization framework assumes that familiarity can support associative memory under conditions in which the components of an association are unitized (i.e., treated as a single coherent item). In the current study we tested two critical assumptions of this framework. First, does unitization reflect a specialized form of learning or is it simply a form of semantic or elaborative encoding, and, second, can the beneficial effects of unitization on familiarity be observed for across-domain associations or are they limited to creating new associations between items that are from the same stimulus domains? Unitization was found to increase associative recognition but not item recognition. It affected familiarity more than recollection, increased associative but not item priming, and was dissociable from levels of processing effects. Moreover, unitization effects were found to be particularly effective in supporting face-word and fractal-sound pairs. The current results indicate that unitization reflects a specialized form of learning that supports associative familiarity of within- and across-domain associations. (c) 2015 APA, all rights reserved).

The importance of unitization for familiarity-based learning

PubMed Central

Parks, Colleen M.; Yonelinas, Andrew P.

2014-01-01

It is often assumed that recollection is necessary to support memory for novel associations, whereas familiarity supports memory for single items. However, the levels of unitization (LOU) framework assumes that familiarity can support associative memory under conditions in which the components of an association are unitized (i.e., treated as a single coherent item). In the current study we test two critical assumptions of this framework. First, does unitization reflect a specialized form of learning or is it simply a form of semantic or elaborative encoding, and, second, can the beneficial effects of unitization on familiarity be observed for across-domain associations or are they limited to creating new associations between items that are from the same stimulus domains? Unitization was found to increase associative recognition but not item recognition, it affected familiarity more so than recollection, it increased associative but not item priming, and it was dissociable from levels of processing effects. Moreover, unitization effects were found to be particularly effective in supporting face-word and fractal-sound pairs. The current results indicate that unitization reflects a specialized form of learning that supports associative familiarity of within- and across-domain associations. PMID:25329077

Formation of linear dominance relationship in captive jungle crows (Corvus macrorhynchos): implications for individual recognition.

PubMed

Izawa, Ei-Ichi; Watanabe, Shigeru

2008-05-01

Jungle crows (Corvus macrorhynchos) flexibly change their social forms depending on their age, time of the day, and the season. In the daytime, paired adults behave territorially and unpaired subadults form small flocks of ten birds, whereas at night hundreds of birds roost together. In the breeding season, pairings remain in their nest all day. This fission-fusion raises questions about the underlying social structure and the cognitive capability of jungle crows. In this study, dyadic encounters were used to investigate dominance relationships (linear or non-linear) and the underlying mechanisms in captive jungle crows. Fourteen crows were tested in 455 encounters (i.e., 5 encounters per dyad), and a stable linear dominance relationship emerged. Sex and aggressiveness were determinants as individual characteristics for dominance formation. Males dominated females, and more aggressive individuals dominated less aggressive ones. Aggressive interactions in dyads occurred primarily during the first encounter and drastically declined during subsequent encounters without any signs of a confidence effect. These results suggest that, in captive jungle crow, a linear form of dominance is intrinsically determined by sex and aggressiveness and maintained extrinsically by memories of past outcomes associated with specific individuals, implying individual recognition.

Unequal crossing-over associated with asymmetrical synapsis between nomadic elements in the Drosophila melanogaster genome

PubMed Central

Goldberg, Michael L.; Sheen, Jenq-Yunn; Gehring, Walter J.; Green, M. M.

1983-01-01

The molecular structure of reciprocal duplications and deficiencies produced by unequal crossing-over at the white (w) locus of Drosophila melanogaster females heterozygous for the alleles wa and wa4 has been examined. A transposable, copia-like element is found at the rearrangement breakpoints. Further characterization indicates that asymmetrical pairing between two copies of this element, which are at least 60 kilobases apart in the parental chromosomes, followed by a crossover within the paired elements, is responsible for the duplication and deficiencies observed. The frequency of these events is high compared with normal homologous exchange, implying that synaptic pairing during meiosis must be sufficiently flexible as to allow efficient recognition of sequences located in nonidentical positions on homologous chromosomes. These results suggest a possible mechanism for the generation of tandem duplications in eukaryotic organisms. Images PMID:16593354

Adaptive and Qualitative Changes in Encoding Strategy With Experience: Evidence From the Test-Expectancy Paradigm

PubMed Central

Finley, Jason R.; Benjamin, Aaron S.

2012-01-01

Three experiments demonstrated learners’ abilities to adaptively and qualitatively accommodate their encoding strategies to the demands of an upcoming test. Stimuli were word pairs. In Experiment 1, test expectancy was induced for either cued recall (of targets given cues) or free recall (of targets only) across 4 study–test cycles of the same test format, followed by a final critical cycle featuring either the expected or the unexpected test format. For final tests of both cued and free recall, participants who had expected that test format outperformed those who had not. This disordinal interaction, supported by recognition and self-report data, demonstrated not mere differences in effort based on anticipated test difficulty, but rather qualitative and appropriate differences in encoding strategies based on expected task demands. Participants also came to appropriately modulate metacognitive monitoring (Experiment 2) and study-time allocation (Experiment 3) across study–test cycles. Item and associative recognition performance, as well as self-report data, revealed shifts in encoding strategies across trials; these results were used to characterize and evaluate the different strategies that participants employed for cued versus free recall and to assess the optimality of participants’ metacognitive control of encoding strategies. Taken together, these data illustrate a sophisticated form of metacognitive control, in which learners qualitatively shift encoding strategies to match the demands of anticipated tests. PMID:22103783

dsRNA-protein interactions studied by molecular dynamics techniques. Unravelling dsRNA recognition by DCL1.

PubMed

Drusin, Salvador I; Suarez, Irina P; Gauto, Diego F; Rasia, Rodolfo M; Moreno, Diego M

2016-04-15

Double stranded RNA (dsRNA) participates in several biological processes, where RNA molecules acquire secondary structure inside the cell through base complementarity. The double stranded RNA binding domain (dsRBD) is one of the main protein folds that is able to recognize and bind to dsRNA regions. The N-terminal dsRBD of DCL1 in Arabidopsis thaliana (DCL1-1), in contrast to other studied dsRBDs, lacks a stable structure, behaving as an intrinsically disordered protein. DCL1-1 does however recognize dsRNA by acquiring a canonical fold in the presence of its substrate. Here we present a detailed modeling and molecular dynamics study of dsRNA recognition by DCL1-1. We found that DCL1-1 forms stable complexes with different RNAs and we characterized the residues involved in binding. Although the domain shows a binding loop substantially shorter than other homologs, it can still interact with the dsRNA and results in bending of the dsRNA A-type helix. Furthermore, we found that R8, a non-conserved residue located in the first dsRNA binding region, recognizes preferentially mismatched base pairs. We discuss our findings in the context of the function of DCL1-1 within the microRNA processing complex. Copyright © 2016 Elsevier Inc. All rights reserved.

Understanding the mechanisms of protein-DNA interactions

NASA Astrophysics Data System (ADS)

Lavery, Richard

2004-03-01

Structural, biochemical and thermodynamic data on protein-DNA interactions show that specific recognition cannot be reduced to a simple set of binary interactions between the partners (such as hydrogen bonds, ion pairs or steric contacts). The mechanical properties of the partners also play a role and, in the case of DNA, variations in both conformation and flexibility as a function of base sequence can be a significant factor in guiding a protein to the correct binding site. All-atom molecular modeling offers a means of analyzing the role of different binding mechanisms within protein-DNA complexes of known structure. This however requires estimating the binding strengths for the full range of sequences with which a given protein can interact. Since this number grows exponentially with the length of the binding site it is necessary to find a method to accelerate the calculations. We have achieved this by using a multi-copy approach (ADAPT) which allows us to build a DNA fragment with a variable base sequence. The results obtained with this method correlate well with experimental consensus binding sequences. They enable us to show that indirect recognition mechanisms involving the sequence dependent properties of DNA play a significant role in many complexes. This approach also offers a means of predicting protein binding sites on the basis of binding energies, which is complementary to conventional lexical techniques.

Thermodynamic basis for engineering high-affinity, high-specificity binding-induced DNA clamp nanoswitches.

PubMed

Idili, Andrea; Plaxco, Kevin W; Vallée-Bélisle, Alexis; Ricci, Francesco

2013-12-23

Naturally occurring chemoreceptors almost invariably employ structure-switching mechanisms, an observation that has inspired the use of biomolecular switches in a wide range of artificial technologies in the areas of diagnostics, imaging, and synthetic biology. In one mechanism for generating such behavior, clamp-based switching, binding occurs via the clamplike embrace of two recognition elements onto a single target molecule. In addition to coupling recognition with a large conformational change, this mechanism offers a second advantage: it improves both affinity and specificity simultaneously. To explore the physics of such switches we have dissected here the thermodynamics of a clamp-switch that recognizes a target DNA sequence through both Watson-Crick base pairing and triplex-forming Hoogsteen interactions. When compared to the equivalent linear DNA probe (which relies solely on Watson-Crick interactions), the extra Hoogsteen interactions in the DNA clamp-switch increase the probe's affinity for its target by ∼0.29 ± 0.02 kcal/mol/base. The Hoogsteen interactions of the clamp-switch likewise provide an additional specificity check that increases the discrimination efficiency toward a single-base mismatch by 1.2 ± 0.2 kcal/mol. This, in turn, leads to a 10-fold improvement in the width of the "specificity window" of this probe relative to that of the equivalent linear probe. Given these attributes, clamp-switches should be of utility not only for sensing applications but also, in the specific field of DNA nanotechnology, for applications calling for a better control over the building of nanostructures and nanomachines.

Food marketing towards children: brand logo recognition, food-related behavior and BMI among 3-13-year-olds in a south Indian town.

PubMed

Ueda, Peter; Tong, Leilei; Viedma, Cristobal; Chandy, Sujith J; Marrone, Gaetano; Simon, Anna; Stålsby Lundborg, Cecilia

2012-01-01

To assess exposure to marketing of unhealthy food products and its relation to food related behavior and BMI in children aged 3-13, from different socioeconomic backgrounds in a south Indian town. Child-parent pairs (n=306) were recruited at pediatric clinics. Exposure to food marketing was assessed by a digital logo recognition test. Children matched 18 logos of unhealthy food (high in fat/sugar/salt) featured in promotion material from the food industry to pictures of corresponding products. Children's nutritional knowledge, food preferences, purchase requests, eating behavior and socioeconomic characteristics were assessed by a digital game and parental questionnaires. Anthropometric measurements were recorded. Recognition rates for the brand logos ranged from 30% to 80%. Logo recognition ability increased with age (p<0.001) and socioeconomic level (p<0.001 comparing children in the highest and lowest of three socioeconomic groups). Adjusted for gender, age and socioeconomic group, logo recognition was associated with higher BMI (p=0.022) and nutritional knowledge (p<0.001) but not to unhealthy food preferences or purchase requests. Children from higher socioeconomic groups in the region had higher brand logo recognition ability and are possibly exposed to more food marketing. The study did not lend support to a link between exposure to marketing and poor eating behavior, distorted nutritional knowledge or increased purchase requests. The correlation between logo recognition and BMI warrants further investigation on food marketing towards children and its potential role in the increasing burden of non-communicable diseases in this part of India.

Implicit phonological priming during visual word recognition.

PubMed

Wilson, Lisa B; Tregellas, Jason R; Slason, Erin; Pasko, Bryce E; Rojas, Donald C

2011-03-15

Phonology is a lower-level structural aspect of language involving the sounds of a language and their organization in that language. Numerous behavioral studies utilizing priming, which refers to an increased sensitivity to a stimulus following prior experience with that or a related stimulus, have provided evidence for the role of phonology in visual word recognition. However, most language studies utilizing priming in conjunction with functional magnetic resonance imaging (fMRI) have focused on lexical-semantic aspects of language processing. The aim of the present study was to investigate the neurobiological substrates of the automatic, implicit stages of phonological processing. While undergoing fMRI, eighteen individuals performed a lexical decision task (LDT) on prime-target pairs including word-word homophone and pseudoword-word pseudohomophone pairs with a prime presentation below perceptual threshold. Whole-brain analyses revealed several cortical regions exhibiting hemodynamic response suppression due to phonological priming including bilateral superior temporal gyri (STG), middle temporal gyri (MTG), and angular gyri (AG) with additional region of interest (ROI) analyses revealing response suppression in the left lateralized supramarginal gyrus (SMG). Homophone and pseudohomophone priming also resulted in different patterns of hemodynamic responses relative to one another. These results suggest that phonological processing plays a key role in visual word recognition. Furthermore, enhanced hemodynamic responses for unrelated stimuli relative to primed stimuli were observed in midline cortical regions corresponding to the default-mode network (DMN) suggesting that DMN activity can be modulated by task requirements within the context of an implicit task. Copyright © 2010 Elsevier Inc. All rights reserved.

An Intact Social Cognitive Process in Schizophrenia: Situational Context Effects on Perception of Facial Affect

PubMed Central

Lee, Junghee; Kern, Robert S.; Harvey, Philippe-Olivier; Horan, William P.; Kee, Kimmy S.; Ochsner, Kevin; Penn, David L.; Green, Michael F.

2013-01-01

Background Impaired facial affect recognition is the most consistent social cognitive finding in schizophrenia. Although social situations provide powerful constraints on our perception, little is known about how situational context modulates facial affect recognition in schizophrenia. Methods Study 1 was a single-site study with 34 schizophrenia patients and 22 healthy controls. Study 2 was a 2-site study with 68 schizophrenia patients and 28 controls. Both studies administered a Situational Context Facial Affect Recognition Task with 2 conditions: a situational context condition and a no-context condition. For the situational context condition, a briefly shown face was preceded by a sentence describing either a fear- or surprise-inducing event. In the no-context condition, a face was presented without a sentence. For both conditions, subjects rated how fearful or surprised the face appeared on a 9-point Likert scale. Results For the situational context condition of study 1, both patients and controls rated faces as more afraid when they were paired with fear-inducing sentences and as more surprised when they were paired with surprise-inducing sentences. The degree of modulation was comparable across groups. For the no-context condition, patients rated faces comparably to controls. The findings of study 2 replicated those from study 1. Conclusions Despite previous abnormalities in other types of context paradigms, this study found intact situational context processing in schizophrenia, suggesting that patients benefit from situational context when interpreting ambiguous facial expression. This area of relative social cognitive strength in schizophrenia has implications for social cognitive training programs. PMID:22532704

Age differences in false memory: The importance of retrieval monitoring processes and their modulation by memory quality.

PubMed

Fandakova, Yana; Sander, Myriam C; Grandy, Thomas H; Cabeza, Roberto; Werkle-Bergner, Markus; Shing, Yee Lee

2018-02-01

Older adults are more likely than younger adults to falsely recall past episodes that occurred differently or not at all. We examined whether older adults' propensity for false associative memory is related to declines in postretrieval monitoring processes and their modulation with varying memory representations. Younger (N = 20) and older adults (N = 32) studied and relearned unrelated scene-word pairs, followed by a final cued recall that was used to distribute the pairs for an associative recognition test 24 hours later. This procedure allowed individualized formation of rearranged pairs that were made up of elements of pairs that were correctly recalled in the final cued recall ("high-quality" pairs), and of pairs that were not correctly recalled ("low-quality" pairs). Both age groups falsely recognized more low-quality than high-quality rearranged pairs, with a less pronounced reduction in false alarms to high-quality pairs in older adults. In younger adults, cingulo-opercular activity was enhanced for false alarms and for low-quality correct rejections, consistent with its role in postretrieval monitoring. Older adults did not show such modulated recruitment, suggesting deficits in their selective engagement of monitoring processes given variability in the fidelity of memory representations. There were no age differences in hippocampal activity, which was higher for high-quality than low-quality correct rejections in both age groups. These results demonstrate that the engagement of cingulo-opercular monitoring mechanisms varies with memory representation quality and contributes to age-related deficits in false associative memory. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Underlying mathematics in diversification of human olfactory receptors in different loci.

PubMed

Hassan, Sk Sarif; Choudhury, Pabitra Pal; Goswami, Arunava

2013-12-01

As per conservative estimate, approximately 51-105 Olfactory Receptors (ORs) loci are present in human genome occurring in clusters. These clusters are apparently unevenly spread as mosaics over 21 pairs of human chromosomes. Olfactory Receptor (OR) gene families which are thought to have expanded for the need to provide recognition capability for a huge number of pure and complex odorants, form the largest known multigene family in the human genome. Recent studies have shown that 388 full length and 414 OR pseudo-genes are present in these OR genomic clusters. In this paper, the authors report a classification method for all human ORs based on their sequential quantitative information like presence of poly strings of nucleotides bases, long range correlation and so on. An L-System generated sequence has been taken as an input into a star-model of specific subfamily members and resultant sequence has been mapped to a specific OR based on the classification scheme using fractal parameters like Hurst exponent and fractal dimensions.

Neural Correlates of Encoding Within- and Across-Domain Inter-Item Associations

PubMed Central

Park, Heekyeong; Rugg, Michael D.

2012-01-01

The neural correlates of the encoding of associations between pairs of words, pairs of pictures, and word-picture pairs were compared. The aims were to determine first, whether the neural correlates of associative encoding vary according to study material and second, whether encoding of across- versus within-material item pairs is associated with dissociable patterns of hippocampal and perirhinal activity, as predicted by the ‘domain dichotomy’ hypothesis of medial temporal lobe (MTL) function. While undergoing fMRI scanning, subjects (n = 24) were presented with the three classes of study pairs, judging which of the denoted objects fit into the other. Outside of the scanner, subjects then undertook an associative recognition task, discriminating between intact study pairs, rearranged pairs comprising items that had been presented on different study trials, and unstudied item pairs. The neural correlates of successful associative encoding – subsequent associative memory effects – were operationalized as the difference in activity between study pairs correctly judged intact versus pairs incorrectly judged rearranged on the subsequent memory test. Pair type-independent subsequent memory effects were evident in the left inferior frontal gyrus (IFG) and the hippocampus. Picture-picture pairs elicited material-selective effects in regions of fusiform cortex that were also activated to a greater extent on picture trials than word trials, while word-word pairs elicited material-selective subsequent memory effects in left lateral temporal cortex. Contrary to the domain-dichotomy hypothesis, neither hippocampal nor perirhinal subsequent memory effects differed depending on whether they were elicited by within- versus across-material study pairs. It is proposed that the left IFG plays a domain-general role in associative encoding, that associative encoding can also be facilitated by enhanced processing in material-selective cortical regions, and that the hippocampus and perirhinal cortex contribute equally to the formation of inter-item associations regardless of whether the items belong to the same or to different processing domains. PMID:21254802

Recognition-Based Pedagogy: Teacher Candidates' Experience of Deficit

ERIC Educational Resources Information Center

Parkison, Paul T.; DaoJensen, Thuy

2014-01-01

This study seeks to introduce what we call "recognition-based pedagogy" as a conceptual frame through which teachers and instructors can collaboratively develop educative experiences with students. Recognition-based pedagogy connects the theories of critical pedagogy, identity politics, and the politics of recognition with the educative…

Differential Effects of the Factor Structure of the Wechsler Memory Scale-Revised on the Cortical Thickness and Complexity of Patients Aged Over 75 Years in a Memory Clinic Setting.

PubMed

Kinno, Ryuta; Shiromaru, Azusa; Mori, Yukiko; Futamura, Akinori; Kuroda, Takeshi; Yano, Satoshi; Murakami, Hidetomo; Ono, Kenjiro

2017-01-01

The Wechsler Memory Scale-Revised (WMS-R) is one of the internationally well-known batteries for memory assessment in a general memory clinic setting. Several factor structures of the WMS-R for patients aged under 74 have been proposed. However, little is known about the factor structure of the WMS-R for patients aged over 75 years and its neurological significance. Thus, we conducted exploratory factor analysis to determine the factor structure of the WMS-R for patients aged over 75 years in a memory clinic setting. Regional cerebral blood flow (rCBF) was calculated from single-photon emission computed tomography data. Cortical thickness and cortical fractal dimension, as the marker of cortical complexity, were calculated from high resolution magnetic resonance imaging data. We found that the four factors appeared to be the most appropriate solution to the model, including recognition memory, paired associate memory, visual-and-working memory, and attention as factors. Patients with mild cognitive impairments showed significantly higher factor scores for paired associate memory, visual-and-working memory, and attention than patients with Alzheimer's disease. Regarding the neuroimaging data, the factor scores for paired associate memory positively correlated with rCBF in the left pericallosal and hippocampal regions. Moreover, the factor score for paired associate memory showed most robust correlations with the cortical thickness in the limbic system, whereas the factor score for attention correlated with the cortical thickness in the bilateral precuneus. Furthermore, each factor score correlated with the cortical fractal dimension in the bilateral frontotemporal regions. Interestingly, the factor scores for the visual-and-working memory and attention selectively correlated with the cortical fractal dimension in the right posterior cingulate cortex and right precuneus cortex, respectively. These findings demonstrate that recognition memory, paired associate memory, visual-and-working memory, and attention can be crucial factors for interpreting the WMS-R results of elderly patients aged over 75 years in a memory clinic setting. Considering these findings, the results of WMS-R in elderly patients aged over 75 years in a memory clinic setting should be cautiously interpreted.

The Rice Resistance Protein Pair RGA4/RGA5 Recognizes the Magnaporthe oryzae Effectors AVR-Pia and AVR1-CO39 by Direct Binding[W][OA

PubMed Central

Cesari, Stella; Thilliez, Gaëtan; Ribot, Cécile; Chalvon, Véronique; Michel, Corinne; Jauneau, Alain; Rivas, Susana; Alaux, Ludovic; Kanzaki, Hiroyuki; Okuyama, Yudai; Morel, Jean-Benoit; Fournier, Elisabeth; Tharreau, Didier; Terauchi, Ryohei; Kroj, Thomas

2013-01-01

Resistance (R) proteins recognize pathogen avirulence (Avr) proteins by direct or indirect binding and are multidomain proteins generally carrying a nucleotide binding (NB) and a leucine-rich repeat (LRR) domain. Two NB-LRR protein-coding genes from rice (Oryza sativa), RGA4 and RGA5, were found to be required for the recognition of the Magnaporthe oryzae effector AVR1-CO39. RGA4 and RGA5 also mediate recognition of the unrelated M. oryzae effector AVR-Pia, indicating that the corresponding R proteins possess dual recognition specificity. For RGA5, two alternative transcripts, RGA5-A and RGA5-B, were identified. Genetic analysis showed that only RGA5-A confers resistance, while RGA5-B is inactive. Yeast two-hybrid, coimmunoprecipitation, and fluorescence resonance energy transfer–fluorescence lifetime imaging experiments revealed direct binding of AVR-Pia and AVR1-CO39 to RGA5-A, providing evidence for the recognition of multiple Avr proteins by direct binding to a single R protein. Direct binding seems to be required for resistance as an inactive AVR-Pia allele did not bind RGA5-A. A small Avr interaction domain with homology to the Avr recognition domain in the rice R protein Pik-1 was identified in the C terminus of RGA5-A. This reveals a mode of Avr protein recognition through direct binding to a novel, non-LRR interaction domain. PMID:23548743

Examination of soldier target recognition with direct view optics

NASA Astrophysics Data System (ADS)

Long, Frederick H.; Larkin, Gabriella; Bisordi, Danielle; Dorsey, Shauna; Marianucci, Damien; Goss, Lashawnta; Bastawros, Michael; Misiuda, Paul; Rodgers, Glenn; Mazz, John P.

2017-10-01

Target recognition and identification is a problem of great military and scientific importance. To examine the correlation between target recognition and optical magnification, ten U.S. Army soldiers were tasked with identifying letters on targets at 800 and 1300 meters away. Letters were used since they are a standard method for measuring visual acuity. The letters were approximately 90 cm high, which is the size of a well-known rifle. Four direct view optics with angular magnifications of 1.5x, 4x, 6x, and 9x were used. The goal of this approach was to measure actual probabilities for correct target identification. Previous scientific literature suggests that target recognition can be modeled as a linear response problem in angular frequency space using the established values for the contrast sensitivity function for a healthy human eye and the experimentally measured modulation transfer function of the optic. At the 9x magnification, the soldiers could identify the letters with almost no errors (i.e., 97% probability of correct identification). At lower magnification, errors in letter identification were more frequent. The identification errors were not random but occurred most frequently with a few pairs of letters (e.g., O and Q), which is consistent with the literature for letter recognition. In addition, in the small subject sample of ten soldiers, there was considerable variation in the observer recognition capability at 1.5x and a range of 800 meters. This can be directly attributed to the variation in the observer visual acuity.

To pair or not to pair: Sources of social variability with white-faced saki monkeys (Pithecia pithecia) as a case study.

PubMed

Thompson, Cynthia L

2016-05-01

Intraspecific variability in social systems is gaining increased recognition in primatology. Many primate species display variability in pair-living social organizations through incorporating extra adults into the group. While numerous models exist to explain primate pair-living, our tools to assess how and why variation in this trait occurs are currently limited. Here I outline an approach which: (i) utilizes conceptual models to identify the selective forces driving pair-living; (ii) outlines novel possible causes for variability in social organization; and (iii) conducts a holistic species-level analysis of social behavior to determine the factors contributing to variation in pair-living. A case study on white-faced sakis (Pithecia pithecia) is used to exemplify this approach. This species lives in either male-female pairs or groups incorporating "extra" adult males and/or females. Various conceptual models of pair-living suggest that high same-sex aggression toward extra-group individuals is a key component of the white-faced saki social system. Variable pair-living in white-faced sakis likely represents alternative strategies to achieve competency in this competition, in which animals experience conflicting selection pressures between achieving successful group defense and maintaining sole reproductive access to mates. Additionally, independent decisions by individuals may generate social variation by preventing other animals from adopting a social organization that maximizes fitness. White-faced saki inter-individual relationships and demographic patterns also lend conciliatory support to this conclusion. By utilizing both model-level and species-level approaches, with a consideration for potential sources of variation, researchers can gain insight into the factors generating variation in pair-living social organizations. © 2014 The Authors. American Journal of Primatology published by Wiley Periodicals, Inc.

Structural studies on Pax-8 Prd domain/DNA complex.

PubMed

Campagnolo, M; Pesaresi, A; Zelezetsky, I; Geremia, S; Randaccio, L; Bisca, A; Tell, G

2007-04-01

Pax-8 is a member of the Pax family of transcription factors and is essential in the development of thyroid follicular cells. Pax-8 has two DNA-binding domains: the paired domain and the homeo domain. In this study, a preliminary X-ray diffraction analysis of the mammalian Pax-8 paired domain in complex with the C-site of the thyroglobulin promoter was achieved. The Pax-8 paired domain was crystallized by the hanging-drop vapor-diffusion method in complex with both a blunt-ended 26 bp DNA fragment and with a sticky-ended 24 bp DNA fragment with two additional overhanging bases. Crystallization experiments make clear that the growth of transparent crystals with large dimensions and regular shape is particularly influenced by ionic strength. The crystals of Pax-8 complex with blunt-ended and sticky-ended DNA, diffracted synchrotron radiation to 6.0 and 8.0 A resolution and belongs both to the C centered monoclinic system with cell dimensions: a = 89.88 A, b = 80.05 A, c = 67.73 A, and beta = 124.3 degrees and a = 256.56, b = 69.07, c = 99.32 A, and beta = 98.1 degrees , respectively. Fluorescence experiments suggest that the crystalline disorder, deduced by the poor diffraction, can be attributed to the low homogeneity of the protein-DNA sample. The theoretical comparative model of the Pax-8 paired domain complexed with the C-site of the thyroglobulin promoter shows the probable presence of some specific protein-DNA interactions already observed in other Pax proteins and the important role of the cysteine residues of PAI subdomain in the redox control of the DNA recognition.

pH-responsive self-assembly by molecular recognition on a macroscopic scale.

PubMed

Zheng, Yongtai; Hashidzume, Akihito; Harada, Akira

2013-07-12

Macroscopic pH-responsive self-assembly is successfully constructed by polyacrylamide(pAAm)-based gels carrying dansyl (Dns) and β-cyclodextrin (βCD) residues, which are represented as Dns-gel and βCD-gel, respectively. Dns-gel and βCD-gel assemble together at pH ≥ 4.0, but disassemble at pH ≤ 3.0. The adhesion strengths for pairs of Dns-gel/βCD-gel increase with increasing pH. The fluorescence study on the model system of pAAm modified with 1 mol% Dns moieties (pAAm/Dns) reveals that Dns residues are protonated at a lower pH, which results in the reduction in binding constant (K) for Dns residues and βCD. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Lateralization of kin recognition signals in the human face

PubMed Central

Dal Martello, Maria F.; Maloney, Laurence T.

2010-01-01

When human subjects view photographs of faces, their judgments of identity, gender, emotion, age, and attractiveness depend more on one side of the face than the other. We report an experiment testing whether allocentric kin recognition (the ability to judge the degree of kinship between individuals other than the observer) is also lateralized. One hundred and twenty-four observers judged whether or not pairs of children were biological siblings by looking at photographs of their faces. In three separate conditions, (1) the right hemi-face was masked, (2) the left hemi-face was masked, or (3) the face was fully visible. The d′ measures for the masked left hemi-face and masked right hemi-face were 1.024 and 1.004, respectively (no significant difference), and the d′ measure for the unmasked face was 1.079, not significantly greater than that for either of the masked conditions. We conclude, first, that there is no superiority of one or the other side of the observed face in kin recognition, second, that the information present in the left and right hemi-faces relevant to recognizing kin is completely redundant, and last that symmetry cues are not used for kin recognition. PMID:20884584

A training program to enhance recognition of depression in nursing homes, assisted living, and other long-term care settings: Description and evaluation.

PubMed

Abrams, Robert C; Nathanson, Mark; Silver, Stephanie; Ramirez, Mildred; Toner, John A; Teresi, Jeanne A

2017-01-01

Low levels of symptom recognition by staff have been "gateway" barriers to the management of depression in long-term care. The study aims were to refine a depression training program for front-line staff in long-term care and provide evaluative knowledge outcome data. Three primary training modules provide an overview of depression symptoms; a review of causes and situational and environmental contributing factors; and communication strategies, medications, and clinical treatment strategies. McNemar's chi-square tests and paired t-tests were used to examine change in knowledge. Data were analyzed for up to 143 staff members, the majority from nursing. Significant changes (p < .001) in knowledge were observed for all modules, with an average change of between 2 and 3 points. Evidence was provided that participants acquired desired information in the recognition, detection, and differential diagnosis and treatment strategies for those persons at significant risk for a depressive disorder.

Super Normal Vector for Human Activity Recognition with Depth Cameras.

PubMed

Yang, Xiaodong; Tian, YingLi

2017-05-01

The advent of cost-effectiveness and easy-operation depth cameras has facilitated a variety of visual recognition tasks including human activity recognition. This paper presents a novel framework for recognizing human activities from video sequences captured by depth cameras. We extend the surface normal to polynormal by assembling local neighboring hypersurface normals from a depth sequence to jointly characterize local motion and shape information. We then propose a general scheme of super normal vector (SNV) to aggregate the low-level polynormals into a discriminative representation, which can be viewed as a simplified version of the Fisher kernel representation. In order to globally capture the spatial layout and temporal order, an adaptive spatio-temporal pyramid is introduced to subdivide a depth video into a set of space-time cells. In the extensive experiments, the proposed approach achieves superior performance to the state-of-the-art methods on the four public benchmark datasets, i.e., MSRAction3D, MSRDailyActivity3D, MSRGesture3D, and MSRActionPairs3D.

The Calcineurin Signaling Network Evolves Via Conserved Kinase–Phosphatase Modules That Transcend Substrate Identity

PubMed Central

Bodenmiller, Bernd; Wanka, Stefanie; Landry, Christian R.; Aebersold, Ruedi; Cyert, Martha S.

2014-01-01

Summary To define the first functional network for calcineurin, the conserved Ca2+/calmodulin-regulated phosphatase, we systematically identified its substrates in S. cerevisiae using phosphoproteomics and bioinformatics, followed by co-purification and dephosphorylation assays. This study establishes new calcineurin functions and reveals mechanisms that shape calcineurin network evolution. Analyses of closely related yeasts show that many proteins were recently recruited to the network by acquiring a calcineurin-recognition motif. Calcineurin substrates in yeast and mammals are distinct due to network rewiring but surprisingly are phosphorylated by similar kinases. We postulate that co-recognition of conserved substrate features, including phosphorylation and docking motifs, preserves calcineurin-kinase opposition during evolution. One example we document is a composite docking site that confers substrate recognition by both calcineurin and MAPK. We propose that conserved kinase-phosphatase pairs define the architecture of signaling networks and allow other connections between kinases and phosphatases to develop and establish common regulatory motifs in signaling networks. PMID:24930733

Recognition of familiar food activates feeding via an endocrine serotonin signal in Caenorhabditis elegans

PubMed Central

Song, Bo-mi; Faumont, Serge; Lockery, Shawn; Avery, Leon

2013-01-01

Familiarity discrimination has a significant impact on the pattern of food intake across species. However, the mechanism by which the recognition memory controls feeding is unclear. Here, we show that the nematode Caenorhabditis elegans forms a memory of particular foods after experience and displays behavioral plasticity, increasing the feeding response when they subsequently recognize the familiar food. We found that recognition of familiar food activates the pair of ADF chemosensory neurons, which subsequently increase serotonin release. The released serotonin activates the feeding response mainly by acting humorally and directly activates SER-7, a type 7 serotonin receptor, in MC motor neurons in the feeding organ. Our data suggest that worms sense the taste and/or smell of novel bacteria, which overrides the stimulatory effect of familiar bacteria on feeding by suppressing the activity of ADF or its upstream neurons. Our study provides insight into the mechanism by which familiarity discrimination alters behavior. DOI: http://dx.doi.org/10.7554/eLife.00329.001 PMID:23390589

Recognition of familiar food activates feeding via an endocrine serotonin signal in Caenorhabditis elegans.

PubMed

Song, Bo-Mi; Faumont, Serge; Lockery, Shawn; Avery, Leon

2013-02-05

Familiarity discrimination has a significant impact on the pattern of food intake across species. However, the mechanism by which the recognition memory controls feeding is unclear. Here, we show that the nematode Caenorhabditis elegans forms a memory of particular foods after experience and displays behavioral plasticity, increasing the feeding response when they subsequently recognize the familiar food. We found that recognition of familiar food activates the pair of ADF chemosensory neurons, which subsequently increase serotonin release. The released serotonin activates the feeding response mainly by acting humorally and directly activates SER-7, a type 7 serotonin receptor, in MC motor neurons in the feeding organ. Our data suggest that worms sense the taste and/or smell of novel bacteria, which overrides the stimulatory effect of familiar bacteria on feeding by suppressing the activity of ADF or its upstream neurons. Our study provides insight into the mechanism by which familiarity discrimination alters behavior.DOI:http://dx.doi.org/10.7554/eLife.00329.001.

Testing the encoding elaboration hypothesis: The effects of exemplar ranking on recognition and recall.

PubMed

Schnur, P

1977-11-01

Two experiments investigated the effects of exemplar ranking on retention. High-ranking exemplars are words judged to be prototypical of a given category; low-ranking exemplars are words judged to be atypical of a given category. In Experiment 1, an incidental learning paradigm was used to measure reaction time to answer an encoding question as well as subsequent recognition. It was found that low-ranking exemplars were classified more slowly but recognized better than high-ranking exemplars. Other comparisons of the effects of category encoding, rhyme encoding, and typescript encoding on response latency and recognition replicated the results of Craik and Tulving (1975). In Experiment 2, unanticipated free recall of live previously learned paired associate lists revealed that a list composed of low-ranking exemplars was better recalled than a comparable list composed of high-ranking exemplars. Moreover, this was true only when the lists were studied in the context of appropriate category cues. These findings are discussed in terms of the encoding elaboration hypothesis.

3D visual mechinism by neural networkings

NASA Astrophysics Data System (ADS)

Sugiyama, Shigeki

2007-04-01

There are some computer vision systems that are available on a market but those are quite far from a real usage of our daily life in a sense of security guard or in a sense of a usage of recognition of a target object behaviour. Because those surroundings' sensing might need to recognize a detail description of an object, like "the distance to an object" and "an object detail figure" and "its figure of edging", which are not possible to have a clear picture of the mechanisms of them with the present recognition system. So for doing this, here studies on mechanisms of how a pair of human eyes can recognize a distance apart, an object edging, and an object in order to get basic essences of vision mechanisms. And those basic mechanisms of object recognition are simplified and are extended logically for applying to a computer vision system. Some of the results of these studies are introduced on this paper.

Emotion recognition in body dysmorphic disorder: application of the Reading the Mind in the Eyes Task.

PubMed

Buhlmann, Ulrike; Winter, Anna; Kathmann, Norbert

2013-03-01

Body dysmorphic disorder (BDD) is characterized by perceived appearance-related defects, often tied to aspects of the face or head (e.g., acne). Deficits in decoding emotional expressions have been examined in several psychological disorders including BDD. Previous research indicates that BDD is associated with impaired facial emotion recognition, particularly in situations that involve the BDD sufferer him/herself. The purpose of this study was to further evaluate the ability to read other people's emotions among 31 individuals with BDD, and 31 mentally healthy controls. We applied the Reading the Mind in the Eyes task, in which participants are presented with a series of pairs of eyes, one at a time, and are asked to identify the emotion that describes the stimulus best. The groups did not differ with respect to decoding other people's emotions by looking into their eyes. Findings are discussed in light of previous research examining emotion recognition in BDD. Copyright © 2013. Published by Elsevier Ltd.

Visual associations to retrieve episodic memory across healthy elderly, mild cognitive impairment, and patients with Alzheimer's disease.

PubMed

Meyer, Sascha R A; De Jonghe, Jos F M; Schmand, Ben; Ponds, Rudolf W H M

2018-05-16

Episodic memory tests need to determine the degree to which patients with moderate to severe memory deficits can still benefit from retrieval support. Especially in the case of Alzheimer's disease (AD), this may support health care to be more closely aligned with patients' memory capacities. We investigated whether the different measures of episodic memory of the Visual Association Test-Extended (VAT-E) can provide a more detailed and informative assessment on memory disturbances across a broad range of cognitive decline, from normal to severe impairment as seen in AD, by examining differences in floor effects. The VAT-E consists of 24 pairs of black-and-white line drawings. In a within-group design, we compared score distributions of VAT-E subtests in healthy elderly controls, mild cognitive impairment (MCI), and AD (n = 144), as well as in relation to global cognitive impairment. Paired associate recall showed a floor effect in 41% of MCI patients and 62% of AD patients. Free recall showed a floor effect in 73% of MCI patients and 84% of AD patients. Multiple-choice cued recognition did not show a floor effect in either of the patient groups. We conclude that the VAT-E covers a broad range of episodic memory decline in patients. As expected, paired associate recall was of intermediate difficulty, free recall was most difficult, and multiple-choice cued recognition was least difficult for patients. These varying levels of difficulty enable a more accurate determination of the level of retrieval support that can still benefit patients across a broad range of cognitive decline.

Profile of Executive and Memory Function Associated with Amphetamine and Opiate Dependence

PubMed Central

Ersche, Karen D; Clark, Luke; London, Mervyn; Robbins, Trevor W; Sahakian, Barbara J

2007-01-01

Cognitive function was assessed in chronic drug users on neurocognitive measures of executive and memory function. Current amphetamine users were contrasted with current opiate users, and these two groups were compared with former users of these substances (abstinent for at least one year). Four groups of participants were recruited: amphetamine-dependent individuals, opiate-dependent individuals, former users of amphetamines, and/or opiates and healthy non-drug taking controls. Participants were administered the Tower of London (TOL) planning task and the 3D-IDED attentional set-shifting task to assess executive function, and Paired Associates Learning and Delayed Pattern Recognition Memory tasks to assess visual memory function. The three groups of substance users showed significant impairments on TOL planning, Pattern Recognition Memory and Paired Associates Learning. Current amphetamine users displayed a greater degree of impairment than current opiate users. Consistent with previous research showing that healthy men are performing better on visuo-spatial tests than women, our male controls remembered significantly more paired associates than their female counterparts. This relationship was reversed in drug users. While performance of female drug users was normal, male drug users showed significant impairment compared to both their female counterparts and male controls. There was no difference in performance between current and former drug users. Neither years of drug abuse nor years of drug abstinence were associated with performance. Chronic drug users display pronounced neuropsychological impairment in the domains of executive and memory function. Impairment persists after several years of drug abstinence and may reflect neuropathology in frontal and temporal cortices. PMID:16160707

Perceptual asymmetry during free viewing of words and faces: The effect of context on recognition.

PubMed

Vakil, Eli; Liberman, Hadas

2016-11-01

There is ample evidence supporting the dissociation between the role of the left and right cerebral hemispheres in processing words and faces, respectively. Nevertheless, research has not yet studied the effect of perceptual asymmetry in memory context effect tasks using words and faces. Thus, the present study researches the advantages of presenting information in the right versus left hemispace and the effect of context on recognition when using faces compared to words presented in the right versus left hemispace. Participants (n=60) were assigned either to the group presented with pairs of words, or with pairs of faces. One stimulus in each pair was designated as the target (i.e., to be remembered) and the other served as context (i.e., to be ignored). Half of the targets were presented in the right hemispace, and half were presented in the left hemispace. As predicted, words were better recognized when presented in the right hemispace, while faces were better remembered when presented in the left hemispace. The most interesting finding is the influence of context on lateralized processing of words and pictures. That is, only when words or faces were presented in the left hemispace did contextual information affect target memory (though it yielded a different pattern of effect). Hence, the findings of the present study may be interpreted either as reflecting attentional bias to the left hemispace or structural differences between the hemispheres. Thus, cognitive processes and the content of the stimuli determine which hemisphere will be involved in processing contextual information. Copyright © 2016 Elsevier Inc. All rights reserved.

Decomposing global self-esteem.

PubMed

Tafarodi, Romin W; Milne, Alan B

2002-08-01

We argue in this paper for distinguishing two dimensions of global self-esteem, self-competence and self-liking. Studies 1 and 2 identify a corresponding pair of factors in Rosenberg's (1965) Self-Esteem Scale. Studies 3 and 4 examine the predictive value of the two-dimensional approach to self-esteem as reflected in the unique associations of self-competence and self-liking with negative life events and word recognition.

Design and isolation of ribozyme-substrate pairs using RNase P-based ribozymes containing altered substrate binding sites.

PubMed Central

Mobley, E M; Pan, T

1999-01-01

Substrate recognition and cleavage by the bacterial RNase P RNA requires two domains, a specificity domain, or S-domain, and a catalytic domain, or C-domain. The S-domain binds the T stem-loop region in a pre-tRNA substrate to confer specificity for tRNA substrates. In this work, the entire S-domain of the Bacillus subtilis RNase P RNA is replaced with an artificial substrate binding module. New RNA substrates are isolated by in vitro selection using two libraries containing random regions of 60 nt. At the end of the selection, the cleavage rates of the substrate library are approximately 0.7 min(-1)in 10 mM MgCl(2)at 37 degrees C, approximately 4-fold better than the cleavage of a pre-tRNA substrate by the wild-type RNase P RNA under the same conditions. The contribution of the S-domain replacement to the catalytic efficiency is from 6- to 22 000-fold. Chemical and nuclease mapping of two ribozyme-product complexes shows that this contribution correlates with direct interactions between the S-domain replacement and the selected substrate. These results demonstrate the feasibility of design and isolation of RNase P-based, matching ribozyme-substrate pairs without prior knowledge of the sequence or structure of the interactive modules in the ribozyme or substrate. PMID:10518624

Bioactivity evaluation-based ultra high-performance liquid chromatography coupled with electrospray ionization tandem quadrupole-time-of-flight mass spectrometry and novel distinction of multi-subchemome compatibility recognition strategy with Astragali Radix-Fructus Corni herb-pair as a case study.

PubMed

Duan, Yu; Pei, Ke; Cai, Hao; Tu, Sicong; Zhang, Zhengwei; Cheng, Xinwei; Qiao, Fengxian; Fan, Kailei; Qin, Kunming; Liu, Xiao; Cai, Baochang

2016-09-10

The approach to investigate traditional Chinese medicine (TCM) is still in its infancy and has been facing enormous challenge. In this paper, a generally applicable strategy was developed for investigation on TCM systematically with an introduced interesting idea about a novel research system which called subchemome. A representative herb-pair, Astragali Radix-Fructus Corni, was successfully employed to expound this novel strategy. Firstly, subchemomes were prepared individually by applying the suitable column chromatography, each of them was detected by UV spectrophotometer or HPLC-DAD detector. The components in each part were then identified based on the mass spectrometric fragmentation patterns and tandem mass spectrometric data by using UHPLC-Q-TOF-MS. Using renal mesangial cell (RMC) viability assay as the evaluation of the pharmacological activity of each group, we developed the new mini herbal formulae aimed at diabetic nephropathy and identified fifteen marker components between the group of new mini herbal formulae and other groups from the angle of the constituent, and then explored the effects of new mini herbal formulae from another angle of the molecular mechanism. Overall, the presently developed strategy should be beneficial and widely used in the investigation on TCM from a new perspective. Copyright © 2016 Elsevier B.V. All rights reserved.

Insights into an original pocket-ligand pair classification: a promising tool for ligand profile prediction.

PubMed

Pérot, Stéphanie; Regad, Leslie; Reynès, Christelle; Spérandio, Olivier; Miteva, Maria A; Villoutreix, Bruno O; Camproux, Anne-Claude

2013-01-01

Pockets are today at the cornerstones of modern drug discovery projects and at the crossroad of several research fields, from structural biology to mathematical modeling. Being able to predict if a small molecule could bind to one or more protein targets or if a protein could bind to some given ligands is very useful for drug discovery endeavors, anticipation of binding to off- and anti-targets. To date, several studies explore such questions from chemogenomic approach to reverse docking methods. Most of these studies have been performed either from the viewpoint of ligands or targets. However it seems valuable to use information from both ligands and target binding pockets. Hence, we present a multivariate approach relating ligand properties with protein pocket properties from the analysis of known ligand-protein interactions. We explored and optimized the pocket-ligand pair space by combining pocket and ligand descriptors using Principal Component Analysis and developed a classification engine on this paired space, revealing five main clusters of pocket-ligand pairs sharing specific and similar structural or physico-chemical properties. These pocket-ligand pair clusters highlight correspondences between pocket and ligand topological and physico-chemical properties and capture relevant information with respect to protein-ligand interactions. Based on these pocket-ligand correspondences, a protocol of prediction of clusters sharing similarity in terms of recognition characteristics is developed for a given pocket-ligand complex and gives high performances. It is then extended to cluster prediction for a given pocket in order to acquire knowledge about its expected ligand profile or to cluster prediction for a given ligand in order to acquire knowledge about its expected pocket profile. This prediction approach shows promising results and could contribute to predict some ligand properties critical for binding to a given pocket, and conversely, some key pocket properties for ligand binding.

Insights into an Original Pocket-Ligand Pair Classification: A Promising Tool for Ligand Profile Prediction

PubMed Central

Reynès, Christelle; Spérandio, Olivier; Miteva, Maria A.; Villoutreix, Bruno O.; Camproux, Anne-Claude

2013-01-01

Pockets are today at the cornerstones of modern drug discovery projects and at the crossroad of several research fields, from structural biology to mathematical modeling. Being able to predict if a small molecule could bind to one or more protein targets or if a protein could bind to some given ligands is very useful for drug discovery endeavors, anticipation of binding to off- and anti-targets. To date, several studies explore such questions from chemogenomic approach to reverse docking methods. Most of these studies have been performed either from the viewpoint of ligands or targets. However it seems valuable to use information from both ligands and target binding pockets. Hence, we present a multivariate approach relating ligand properties with protein pocket properties from the analysis of known ligand-protein interactions. We explored and optimized the pocket-ligand pair space by combining pocket and ligand descriptors using Principal Component Analysis and developed a classification engine on this paired space, revealing five main clusters of pocket-ligand pairs sharing specific and similar structural or physico-chemical properties. These pocket-ligand pair clusters highlight correspondences between pocket and ligand topological and physico-chemical properties and capture relevant information with respect to protein-ligand interactions. Based on these pocket-ligand correspondences, a protocol of prediction of clusters sharing similarity in terms of recognition characteristics is developed for a given pocket-ligand complex and gives high performances. It is then extended to cluster prediction for a given pocket in order to acquire knowledge about its expected ligand profile or to cluster prediction for a given ligand in order to acquire knowledge about its expected pocket profile. This prediction approach shows promising results and could contribute to predict some ligand properties critical for binding to a given pocket, and conversely, some key pocket properties for ligand binding. PMID:23840299

Novel Blind Recognition Algorithm of Frame Synchronization Words Based on Soft-Decision in Digital Communication Systems.

PubMed

Qin, Jiangyi; Huang, Zhiping; Liu, Chunwu; Su, Shaojing; Zhou, Jing

2015-01-01

A novel blind recognition algorithm of frame synchronization words is proposed to recognize the frame synchronization words parameters in digital communication systems. In this paper, a blind recognition method of frame synchronization words based on the hard-decision is deduced in detail. And the standards of parameter recognition are given. Comparing with the blind recognition based on the hard-decision, utilizing the soft-decision can improve the accuracy of blind recognition. Therefore, combining with the characteristics of Quadrature Phase Shift Keying (QPSK) signal, an improved blind recognition algorithm based on the soft-decision is proposed. Meanwhile, the improved algorithm can be extended to other signal modulation forms. Then, the complete blind recognition steps of the hard-decision algorithm and the soft-decision algorithm are given in detail. Finally, the simulation results show that both the hard-decision algorithm and the soft-decision algorithm can recognize the parameters of frame synchronization words blindly. What's more, the improved algorithm can enhance the accuracy of blind recognition obviously.

Support vector machine-based facial-expression recognition method combining shape and appearance

NASA Astrophysics Data System (ADS)

Han, Eun Jung; Kang, Byung Jun; Park, Kang Ryoung; Lee, Sangyoun

2010-11-01

Facial expression recognition can be widely used for various applications, such as emotion-based human-machine interaction, intelligent robot interfaces, face recognition robust to expression variation, etc. Previous studies have been classified as either shape- or appearance-based recognition. The shape-based method has the disadvantage that the individual variance of facial feature points exists irrespective of similar expressions, which can cause a reduction of the recognition accuracy. The appearance-based method has a limitation in that the textural information of the face is very sensitive to variations in illumination. To overcome these problems, a new facial-expression recognition method is proposed, which combines both shape and appearance information, based on the support vector machine (SVM). This research is novel in the following three ways as compared to previous works. First, the facial feature points are automatically detected by using an active appearance model. From these, the shape-based recognition is performed by using the ratios between the facial feature points based on the facial-action coding system. Second, the SVM, which is trained to recognize the same and different expression classes, is proposed to combine two matching scores obtained from the shape- and appearance-based recognitions. Finally, a single SVM is trained to discriminate four different expressions, such as neutral, a smile, anger, and a scream. By determining the expression of the input facial image whose SVM output is at a minimum, the accuracy of the expression recognition is much enhanced. The experimental results showed that the recognition accuracy of the proposed method was better than previous researches and other fusion methods.

Submolecular Structure and Orientation of Oligonucleotide Duplexes Tethered to Gold Electrodes Probed by Infrared Reflection Absorption Spectroscopy: Effect of the Electrode Potentials.

PubMed

Kékedy-Nagy, László; Ferapontova, Elena E; Brand, Izabella

2017-02-23

Unique electronic and ligand recognition properties of the DNA double helix provide basis for DNA applications in biomolecular electronic and biosensor devices. However, the relation between the structure of DNA at electrified interfaces and its electronic properties is still not well understood. Here, potential-driven changes in the submolecular structure of DNA double helices composed of either adenine-thymine (dAdT) 25 or cytosine-guanine (dGdC) 20 base pairs tethered to the gold electrodes are for the first time analyzed by in situ polarization modulation infrared reflection absorption spectroscopy (PM IRRAS) performed under the electrochemical control. It is shown that the conformation of the DNA duplexes tethered to gold electrodes via the C 6 alkanethiol linker strongly depends on the nucleic acid sequence composition. The tilt of purine and pyrimidine rings of the complementary base pairs (dAdT and dGdC) depends on the potential applied to the electrode. By contrast, neither the conformation nor orientation of the ionic in character phosphate-sugar backbone is affected by the electrode potentials. At potentials more positive than the potential of zero charge (pzc), a gradual tilting of the double helix is observed. In this tilted orientation, the planes of the complementary purine and pyrimidine rings lie ideally parallel to each other. These potentials do not affect the integral stability of the DNA double helix at the charged interface. At potentials more negative than the pzc, DNA helices adopt a vertical to the gold surface orientation. Tilt of the purine and pyrimidine rings depends on the composition of the double helix. In monolayers composed of (dAdT) 25 molecules the rings of the complementary base pairs lie parallel to each other. By contrast, the tilt of purine and pyrimidine rings in (dGdC) 20 helices depends on the potential applied to the electrode. Such potential-induced mobility of the complementary base pairs can destabilize the helix structure at a submolecular level. These pioneer results on the potential-driven changes in the submolecular structure of double stranded DNA adsorbed on conductive supports contribute to further understanding of the potential-driven sequence-specific electronic properties of surface-tethered oligonucleotides.

Target-context unitization effect on the familiarity-related FN400: a face recognition exclusion task.

PubMed

Guillaume, Fabrice; Etienne, Yann

2015-03-01

Using two exclusion tasks, the present study examined how the ERP correlates of face recognition are affected by the nature of the information to be retrieved. Intrinsic (facial expression) and extrinsic (background scene) visual information were paired with face identity and constituted the exclusion criterion at test time. Although perceptual information had to be taken into account in both situations, the FN400 old-new effect was observed only for old target faces on the expression-exclusion task, whereas it was found for both old target and old non-target faces in the background-exclusion situation. These results reveal that the FN400, which is generally interpreted as a correlate of familiarity, was modulated by the retrieval of intra-item and intrinsic face information, but not by the retrieval of extrinsic information. The observed effects on the FN400 depended on the nature of the information to be retrieved and its relationship (unitization) to the recognition target. On the other hand, the parietal old-new effect (generally described as an ERP correlate of recollection) reflected the retrieval of both types of contextual features equivalently. The current findings are discussed in relation to recent controversies about the nature of the recognition processes reflected by the ERP correlates of face recognition. Copyright © 2015 Elsevier B.V. All rights reserved.

The effects of sleep deprivation on item and associative recognition memory.

PubMed

Ratcliff, Roger; Van Dongen, Hans P A

2018-02-01

Sleep deprivation adversely affects the ability to perform cognitive tasks, but theories range from predicting an overall decline in cognitive functioning because of reduced stability in attentional networks to specific deficits in various cognitive domains or processes. We measured the effects of sleep deprivation on two memory tasks, item recognition ("was this word in the list studied") and associative recognition ("were these two words studied in the same pair"). These tasks test memory for information encoded a few minutes earlier and so do not address effects of sleep deprivation on working memory or consolidation after sleep. A diffusion model was used to decompose accuracy and response time distributions to produce parameter estimates of components of cognitive processing. The model assumes that over time, noisy evidence from the task stimulus is accumulated to one of two decision criteria, and parameters governing this process are extracted and interpreted in terms of distinct cognitive processes. Results showed that sleep deprivation reduces drift rate (evidence used in the decision process), with little effect on the other components of the decision process. These results contrast with the effects of aging, which show little decline in item recognition but large declines in associative recognition. The results suggest that sleep deprivation degrades the quality of information stored in memory and that this may occur through degraded attentional processes. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

On a problematic procedure to manipulate response biases in recognition experiments: the case of "implied" base rates.

PubMed

Bröder, Arndt; Malejka, Simone

2017-07-01

The experimental manipulation of response biases in recognition-memory tests is an important means for testing recognition models and for estimating their parameters. The textbook manipulations for binary-response formats either vary the payoff scheme or the base rate of targets in the recognition test, with the latter being the more frequently applied procedure. However, some published studies reverted to implying different base rates by instruction rather than actually changing them. Aside from unnecessarily deceiving participants, this procedure may lead to cognitive conflicts that prompt response strategies unknown to the experimenter. To test our objection, implied base rates were compared to actual base rates in a recognition experiment followed by a post-experimental interview to assess participants' response strategies. The behavioural data show that recognition-memory performance was estimated to be lower in the implied base-rate condition. The interview data demonstrate that participants used various second-order response strategies that jeopardise the interpretability of the recognition data. We thus advice researchers against substituting actual base rates with implied base rates.