The unique role of the visual word form area in reading.

PubMed

Dehaene, Stanislas; Cohen, Laurent

2011-06-01

Reading systematically activates the left lateral occipitotemporal sulcus, at a site known as the visual word form area (VWFA). This site is reproducible across individuals/scripts, attuned to reading-specific processes, and partially selective for written strings relative to other categories such as line drawings. Lesions affecting the VWFA cause pure alexia, a selective deficit in word recognition. These findings must be reconciled with the fact that human genome evolution cannot have been influenced by such a recent and culturally variable activity as reading. Capitalizing on recent functional magnetic resonance imaging experiments, we provide strong corroborating evidence for the hypothesis that reading acquisition partially recycles a cortical territory evolved for object and face recognition, the prior properties of which influenced the form of writing systems. Copyright © 2011 Elsevier Ltd. All rights reserved.

Relationships between alexithymia, affect recognition, and empathy after traumatic brain injury.

PubMed

Neumann, Dawn; Zupan, Barbra; Malec, James F; Hammond, Flora

2014-01-01

To determine (1) alexithymia, affect recognition, and empathy differences in participants with and without traumatic brain injury (TBI); (2) the amount of affect recognition variance explained by alexithymia; and (3) the amount of empathy variance explained by alexithymia and affect recognition. Sixty adults with moderate-to-severe TBI; 60 age and gender-matched controls. Participants were evaluated for alexithymia (difficulty identifying feelings, difficulty describing feelings, and externally-oriented thinking); facial and vocal affect recognition; and affective and cognitive empathy (empathic concern and perspective-taking, respectively). Participants with TBI had significantly higher alexithymia; poorer facial and vocal affect recognition; and lower empathy scores. For TBI participants, facial and vocal affect recognition variances were significantly explained by alexithymia (12% and 8%, respectively); however, the majority of the variances were accounted for by externally-oriented thinking alone. Affect recognition and alexithymia significantly accounted for 16.5% of cognitive empathy. Again, the majority of the variance was primarily explained by externally-oriented thinking. Affect recognition and alexithymia did not explain affective empathy. Results suggest that people who have a tendency to avoid thinking about emotions (externally-oriented thinking) are more likely to have problems recognizing others' emotions and assuming others' points of view. Clinical implications are discussed.

Vocal Affect Recognition and Psychopathy: Converging Findings Across Traditional and Cluster Analytic Approaches to Assessing the Construct

PubMed Central

Bagley, Amy D.; Abramowitz, Carolyn S.; Kosson, David S.

2010-01-01

Deficits in emotion processing have been widely reported to be central to psychopathy. However, few prior studies have examined vocal affect recognition in psychopaths, and these studies suffer from significant methodological limitations. Moreover, prior studies have yielded conflicting findings regarding the specificity of psychopaths’ affect recognition deficits. This study examined vocal affect recognition in 107 male inmates under conditions requiring isolated prosodic vs. semantic analysis of affective cues and compared subgroups of offenders identified via cluster analysis on vocal affect recognition. Psychopaths demonstrated deficits in vocal affect recognition under conditions requiring use of semantic cues and conditions requiring use of prosodic cues. Moreover, both primary and secondary psychopaths exhibited relatively similar emotional deficits in the semantic analysis condition compared to nonpsychopathic control participants. This study demonstrates that psychopaths’ vocal affect recognition deficits are not due to methodological limitations of previous studies and provides preliminary evidence that primary and secondary psychopaths exhibit generally similar deficits in vocal affect recognition. PMID:19413412

Applying Affect Recognition in Serious Games: The PlayMancer Project

NASA Astrophysics Data System (ADS)

Ben Moussa, Maher; Magnenat-Thalmann, Nadia

This paper presents an overview and the state-of-art in the applications of 'affect' recognition in serious games for the support of patients in behavioral and mental disorder treatments and chronic pain rehabilitation, within the framework of the European project PlayMancer. Three key technologies are discussed relating to facial affect recognition, fusion of different affect recognition methods, and the application of affect recognition in serious games.

Participation of the Classical Speech Areas in Auditory Long-Term Memory

PubMed Central

Karabanov, Anke Ninija; Paine, Rainer; Chao, Chi Chao; Schulze, Katrin; Scott, Brian; Hallett, Mark; Mishkin, Mortimer

2015-01-01

Accumulating evidence suggests that storing speech sounds requires transposing rapidly fluctuating sound waves into more easily encoded oromotor sequences. If so, then the classical speech areas in the caudalmost portion of the temporal gyrus (pSTG) and in the inferior frontal gyrus (IFG) may be critical for performing this acoustic-oromotor transposition. We tested this proposal by applying repetitive transcranial magnetic stimulation (rTMS) to each of these left-hemisphere loci, as well as to a nonspeech locus, while participants listened to pseudowords. After 5 minutes these stimuli were re-presented together with new ones in a recognition test. Compared to control-site stimulation, pSTG stimulation produced a highly significant increase in recognition error rate, without affecting reaction time. By contrast, IFG stimulation led only to a weak, non-significant, trend toward recognition memory impairment. Importantly, the impairment after pSTG stimulation was not due to interference with perception, since the same stimulation failed to affect pseudoword discrimination examined with short interstimulus intervals. Our findings suggest that pSTG is essential for transforming speech sounds into stored motor plans for reproducing the sound. Whether or not the IFG also plays a role in speech-sound recognition could not be determined from the present results. PMID:25815813

Participation of the classical speech areas in auditory long-term memory.

PubMed

Karabanov, Anke Ninija; Paine, Rainer; Chao, Chi Chao; Schulze, Katrin; Scott, Brian; Hallett, Mark; Mishkin, Mortimer

2015-01-01

Accumulating evidence suggests that storing speech sounds requires transposing rapidly fluctuating sound waves into more easily encoded oromotor sequences. If so, then the classical speech areas in the caudalmost portion of the temporal gyrus (pSTG) and in the inferior frontal gyrus (IFG) may be critical for performing this acoustic-oromotor transposition. We tested this proposal by applying repetitive transcranial magnetic stimulation (rTMS) to each of these left-hemisphere loci, as well as to a nonspeech locus, while participants listened to pseudowords. After 5 minutes these stimuli were re-presented together with new ones in a recognition test. Compared to control-site stimulation, pSTG stimulation produced a highly significant increase in recognition error rate, without affecting reaction time. By contrast, IFG stimulation led only to a weak, non-significant, trend toward recognition memory impairment. Importantly, the impairment after pSTG stimulation was not due to interference with perception, since the same stimulation failed to affect pseudoword discrimination examined with short interstimulus intervals. Our findings suggest that pSTG is essential for transforming speech sounds into stored motor plans for reproducing the sound. Whether or not the IFG also plays a role in speech-sound recognition could not be determined from the present results.

Early prediction of student goals and affect in narrative-centered learning environments

NASA Astrophysics Data System (ADS)

Lee, Sunyoung

Recent years have seen a growing recognition of the role of goal and affect recognition in intelligent tutoring systems. Goal recognition is the task of inferring users' goals from a sequence of observations of their actions. Because of the uncertainty inherent in every facet of human computer interaction, goal recognition is challenging, particularly in contexts in which users can perform many actions in any order, as is the case with intelligent tutoring systems. Affect recognition is the task of identifying the emotional state of a user from a variety of physical cues, which are produced in response to affective changes in the individual. Accurately recognizing student goals and affect states could contribute to more effective and motivating interactions in intelligent tutoring systems. By exploiting knowledge of student goals and affect states, intelligent tutoring systems can dynamically modify their behavior to better support individual students. To create effective interactions in intelligent tutoring systems, goal and affect recognition models should satisfy two key requirements. First, because incorrectly predicted goals and affect states could significantly diminish the effectiveness of interactive systems, goal and affect recognition models should provide accurate predictions of user goals and affect states. When observations of users' activities become available, recognizers should make accurate early" predictions. Second, goal and affect recognition models should be highly efficient so they can operate in real time. To address key issues, we present an inductive approach to recognizing student goals and affect states in intelligent tutoring systems by learning goals and affect recognition models. Our work focuses on goal and affect recognition in an important new class of intelligent tutoring systems, narrative-centered learning environments. We report the results of empirical studies of induced recognition models from observations of students' interactions in narrative-centered learning environments. Experimental results suggest that induced models can make accurate early predictions of student goals and affect states, and they are sufficiently efficient to meet the real-time performance requirements of interactive learning environments.

Event-Related Potential Responses to Beloved and Familiar Faces in Different Marriage Styles: Evidence from Mosuo Subjects.

PubMed

Wu, Haiyan; Luo, Li; Dai, Junqiang; Yang, Suyong; Wang, Naiyi; Luo, Yue-Jia

2016-01-01

Research on familiar face recognition has largely focused on the neural correlates of recognizing a beloved partner or family member. However, no research has explored the effect of marriage style on the recognition of a beloved partner's face, especially in matriarchal societies. Here, we examined the time course of event-related potentials (ERP) in response to the face of a beloved partner, sibling, or unknown person in a sample of individuals from the matriarchal Mosuo tribe. Two groups were assessed: intermarriage and walking marriage groups (i.e., couples in a committed relationship who do not cohabitate during the daytime). In agreement with previous reports, ERP results revealed more positive VPP, N250, and P300 waveforms for beloved faces than sibling faces in both groups. Moreover, P300 was more positive for beloved partner versus sibling faces; however, this difference emerged at fronto-central sites for the walking marriage group and at posterior sites for the intermarriage group. Overall, we observed that marriage style affects the later stage processing of a beloved partner's face, and this may be associated with greater affective arousal and familiarity.

Event-Related Potential Responses to Beloved and Familiar Faces in Different Marriage Styles: Evidence from Mosuo Subjects

PubMed Central

Wu, Haiyan; Luo, Li; Dai, Junqiang; Yang, Suyong; Wang, Naiyi; Luo, Yue-jia

2016-01-01

Research on familiar face recognition has largely focused on the neural correlates of recognizing a beloved partner or family member. However, no research has explored the effect of marriage style on the recognition of a beloved partner’s face, especially in matriarchal societies. Here, we examined the time course of event-related potentials (ERP) in response to the face of a beloved partner, sibling, or unknown person in a sample of individuals from the matriarchal Mosuo tribe. Two groups were assessed: intermarriage and walking marriage groups (i.e., couples in a committed relationship who do not cohabitate during the daytime). In agreement with previous reports, ERP results revealed more positive VPP, N250, and P300 waveforms for beloved faces than sibling faces in both groups. Moreover, P300 was more positive for beloved partner versus sibling faces; however, this difference emerged at fronto-central sites for the walking marriage group and at posterior sites for the intermarriage group. Overall, we observed that marriage style affects the later stage processing of a beloved partner’s face, and this may be associated with greater affective arousal and familiarity. PMID:26925002

Neurobiological mechanisms associated with facial affect recognition deficits after traumatic brain injury.

PubMed

Neumann, Dawn; McDonald, Brenna C; West, John; Keiski, Michelle A; Wang, Yang

2016-06-01

The neurobiological mechanisms that underlie facial affect recognition deficits after traumatic brain injury (TBI) have not yet been identified. Using functional magnetic resonance imaging (fMRI), study aims were to 1) determine if there are differences in brain activation during facial affect processing in people with TBI who have facial affect recognition impairments (TBI-I) relative to people with TBI and healthy controls who do not have facial affect recognition impairments (TBI-N and HC, respectively); and 2) identify relationships between neural activity and facial affect recognition performance. A facial affect recognition screening task performed outside the scanner was used to determine group classification; TBI patients who performed greater than one standard deviation below normal performance scores were classified as TBI-I, while TBI patients with normal scores were classified as TBI-N. An fMRI facial recognition paradigm was then performed within the 3T environment. Results from 35 participants are reported (TBI-I = 11, TBI-N = 12, and HC = 12). For the fMRI task, TBI-I and TBI-N groups scored significantly lower than the HC group. Blood oxygenation level-dependent (BOLD) signals for facial affect recognition compared to a baseline condition of viewing a scrambled face, revealed lower neural activation in the right fusiform gyrus (FG) in the TBI-I group than the HC group. Right fusiform gyrus activity correlated with accuracy on the facial affect recognition tasks (both within and outside the scanner). Decreased FG activity suggests facial affect recognition deficits after TBI may be the result of impaired holistic face processing. Future directions and clinical implications are discussed.

Affect Recognition in Adults with Attention-Deficit/Hyperactivity Disorder

PubMed Central

Miller, Meghan; Hanford, Russell B.; Fassbender, Catherine; Duke, Marshall; Schweitzer, Julie B.

2014-01-01

Objective This study compared affect recognition abilities between adults with and without Attention-Deficit/Hyperactivity Disorder (ADHD). Method The sample included 51 participants (34 men, 17 women) divided into 3 groups: ADHD-Combined Type (ADHD-C; n = 17), ADHD-Predominantly Inattentive Type (ADHD-I; n = 16), and controls (n = 18). The mean age was 34 years. Affect recognition abilities were assessed by the Diagnostic Analysis of Nonverbal Accuracy (DANVA). Results Analyses of Variance showed that the ADHD-I group made more fearful emotion errors relative to the control group. Inattentive symptoms were positively correlated while hyperactive-impulsive symptoms were negatively correlated with affect recognition errors. Conclusion These results suggest that affect recognition abilities may be impaired in adults with ADHD and that affect recognition abilities are more adversely affected by inattentive than hyperactive-impulsive symptoms. PMID:20555036

Relation between facial affect recognition and configural face processing in antipsychotic-free schizophrenia.

PubMed

Fakra, Eric; Jouve, Elisabeth; Guillaume, Fabrice; Azorin, Jean-Michel; Blin, Olivier

2015-03-01

Deficit in facial affect recognition is a well-documented impairment in schizophrenia, closely connected to social outcome. This deficit could be related to psychopathology, but also to a broader dysfunction in processing facial information. In addition, patients with schizophrenia inadequately use configural information-a type of processing that relies on spatial relationships between facial features. To date, no study has specifically examined the link between symptoms and misuse of configural information in the deficit in facial affect recognition. Unmedicated schizophrenia patients (n = 30) and matched healthy controls (n = 30) performed a facial affect recognition task and a face inversion task, which tests aptitude to rely on configural information. In patients, regressions were carried out between facial affect recognition, symptom dimensions and inversion effect. Patients, compared with controls, showed a deficit in facial affect recognition and a lower inversion effect. Negative symptoms and lower inversion effect could account for 41.2% of the variance in facial affect recognition. This study confirms the presence of a deficit in facial affect recognition, and also of dysfunctional manipulation in configural information in antipsychotic-free patients. Negative symptoms and poor processing of configural information explained a substantial part of the deficient recognition of facial affect. We speculate that this deficit may be caused by several factors, among which independently stand psychopathology and failure in correctly manipulating configural information. PsycINFO Database Record (c) 2015 APA, all rights reserved.

Polyhydroxylated [60]fullerene binds specifically to functional recognition sites on a monomeric and a dimeric ubiquitin

NASA Astrophysics Data System (ADS)

Zanzoni, Serena; Ceccon, Alberto; Assfalg, Michael; Singh, Rajesh K.; Fushman, David; D'Onofrio, Mariapina

2015-04-01

The use of nanoparticles (NPs) in biomedical applications requires an in-depth understanding of the mechanisms by which NPs interact with biomolecules. NPs associating with proteins may interfere with protein-protein interactions and affect cellular communication pathways, however the impact of NPs on biomolecular recognition remains poorly characterized. In this respect, particularly relevant is the study of NP-induced functional perturbations of proteins implicated in the regulation of key biochemical pathways. Ubiquitin (Ub) is a prototypical protein post-translational modifier playing a central role in numerous essential biological processes. To contribute to the understanding of the interactions between this universally distributed biomacromolecule and NPs, we investigated the adsorption of polyhydroxylated [60]fullerene on monomeric Ub and on a minimal polyubiquitin chain in vitro at atomic resolution. Site-resolved chemical shift and intensity perturbations of Ub's NMR signals, together with 15N spin relaxation rate changes, exchange saturation transfer effects, and fluorescence quenching data were consistent with the reversible formation of soluble aggregates incorporating fullerenol clusters. The specific interaction epitopes were identified, coincident with functional recognition sites in a monomeric and lysine48-linked dimeric Ub. Fullerenol appeared to target the open state of the dynamic structure of a dimeric Ub according to a conformational selection mechanism. Importantly, the protein-NP association prevented the enzyme-catalyzed synthesis of polyubiquitin chains. Our findings provide an experiment-based insight into protein/fullerenol recognition, with implications in functional biomolecular communication, including regulatory protein turnover, and for the opportunity of therapeutic intervention in Ub-dependent cellular pathways.The use of nanoparticles (NPs) in biomedical applications requires an in-depth understanding of the mechanisms by which NPs interact with biomolecules. NPs associating with proteins may interfere with protein-protein interactions and affect cellular communication pathways, however the impact of NPs on biomolecular recognition remains poorly characterized. In this respect, particularly relevant is the study of NP-induced functional perturbations of proteins implicated in the regulation of key biochemical pathways. Ubiquitin (Ub) is a prototypical protein post-translational modifier playing a central role in numerous essential biological processes. To contribute to the understanding of the interactions between this universally distributed biomacromolecule and NPs, we investigated the adsorption of polyhydroxylated [60]fullerene on monomeric Ub and on a minimal polyubiquitin chain in vitro at atomic resolution. Site-resolved chemical shift and intensity perturbations of Ub's NMR signals, together with 15N spin relaxation rate changes, exchange saturation transfer effects, and fluorescence quenching data were consistent with the reversible formation of soluble aggregates incorporating fullerenol clusters. The specific interaction epitopes were identified, coincident with functional recognition sites in a monomeric and lysine48-linked dimeric Ub. Fullerenol appeared to target the open state of the dynamic structure of a dimeric Ub according to a conformational selection mechanism. Importantly, the protein-NP association prevented the enzyme-catalyzed synthesis of polyubiquitin chains. Our findings provide an experiment-based insight into protein/fullerenol recognition, with implications in functional biomolecular communication, including regulatory protein turnover, and for the opportunity of therapeutic intervention in Ub-dependent cellular pathways. Electronic supplementary information (ESI) available: Experimental details. Fig. S1. Characterization of fullerenol by dynamic light scattering. Fig. S2. Size-exclusion chromatography. Fig. S3. 15N R1 spin relaxation rates of Ub and Ub2 upon subsequent additions of fullerenol. See DOI: 10.1039/c5nr00539f

Affect recognition across manic and euthymic phases of bipolar disorder in Han-Chinese patients.

PubMed

Pan, Yi-Ju; Tseng, Huai-Hsuan; Liu, Shi-Kai

2013-11-01

Patients with bipolar disorder (BD) have affect recognition deficits. Whether affect recognition deficits constitute a state or trait marker of BD has great etiopathological significance. The current study aims to explore the interrelationships between affect recognition and basic neurocognitive functions for patients with BD across different mood states, using the Diagnostic Analysis of Non-Verbal Accuracy-2, Taiwanese version (DANVA-2-TW) as the index measure for affect recognition. To our knowledge, this is the first study examining affect recognition deficits of BPD across mood states in the Han Chinese population. Twenty-nine manic patients, 16 remitted patients with BD, and 40 control subjects are included in the study. Distinct association patterns between affect recognition and neurocognitive functions are demonstrated for patients with BD and control subjects, implicating alternations in emotion associated neurocognitive processing. Compared to control subjects, manic patients but not remitted subjects perform significantly worse in the recognition of negative emotions as a whole and specifically anger, after adjusting for differences in general intellectual ability and basic neurocognitive functions. Affect recognition deficit may be a relatively independent impairment in BD rather than consequences arising from deficits in other basic neurocognition. The impairments of manic patients in the recognition of negative emotions, specifically anger, may further our understanding of core clinical psychopathology of BD and have implications in treating bipolar patients across distinct mood phases. © 2013 Elsevier B.V. All rights reserved.

Thermodynamic Modeling of Donor Splice Site Recognition in pre-mRNA

NASA Astrophysics Data System (ADS)

Aalberts, Daniel P.; Garland, Jeffrey A.

2004-03-01

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

Thermodynamic modeling of donor splice site recognition in pre-mRNA

NASA Astrophysics Data System (ADS)

Garland, Jeffrey A.; Aalberts, Daniel P.

2004-04-01

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

Word position affects stimulus recognition: evidence for early ERP short-term plastic modulation.

PubMed

Spironelli, Chiara; Galfano, Giovanni; Umiltà, Carlo; Angrilli, Alessandro

2011-12-01

The present study was aimed at investigating the short-term plastic changes that follow word learning at a neurophysiological level. The main hypothesis was that word position (left or right visual field, LVF/RH or RVF/LH) in the initial learning phase would leave a trace that affected, in the subsequent recognition phase, the Recognition Potential (i.e., the first negative component distinguishing words from other stimuli) elicited 220-240 ms after centrally presented stimuli. Forty-eight students were administered, in the learning phase, 125 words for 4s, randomly presented half in the left and half in the right visual field. In the recognition phase, participants were split into two equal groups, one was assigned to the Word task, the other to the Picture task (in which half of the 125 pictures were new, and half matched prior studied words). During the Word task, old RVF/LH words elicited significantly greater negativity in left posterior sites with respect to old LVF/RH words, which in turn showed the same pattern of activation evoked by new words. Therefore, correspondence between stimulus spatial position and hemisphere specialized in automatic word recognition created a robust prime for subsequent recognition. During the Picture task, pictures matching old RVF/LH words showed no differences compared with new pictures, but evoked significantly greater negativity than pictures matching old LVF/RH words. Thus, the priming effect vanished when the task required a switch from visual analysis to stored linguistic information, whereas the lack of correspondence between stimulus position and network specialized in automatic word recognition (i.e., when words were presented to the LVF/RH) revealed the implicit costs for recognition. Results support the view that short-term plastic changes occurring in a linguistic learning task interact with both stimulus position and modality (written word vs. picture representation). Copyright © 2011 Elsevier B.V. All rights reserved.

Iconic gestures prime related concepts: an ERP study.

PubMed

Wu, Ying Croon; Coulson, Seana

2007-02-01

To assess priming by iconic gestures, we recorded EEG (at 29 scalp sites) in two experiments while adults watched short, soundless videos of spontaneously produced, cospeech iconic gestures followed by related or unrelated probe words. In Experiment 1, participants classified the relatedness between gestures and words. In Experiment 2, they attended to stimuli, and performed an incidental recognition memory test on words presented during the EEG recording session. Event-related potentials (ERPs) time-locked to the onset of probe words were measured, along with response latencies and word recognition rates. Although word relatedness did not affect reaction times or recognition rates, contextually related probe words elicited less-negative ERPs than did unrelated ones between 300 and 500 msec after stimulus onset (N400) in both experiments. These findings demonstrate sensitivity to semantic relations between iconic gestures and words in brain activity engendered during word comprehension.

On Assisting a Visual-Facial Affect Recognition System with Keyboard-Stroke Pattern Information

NASA Astrophysics Data System (ADS)

Stathopoulou, I.-O.; Alepis, E.; Tsihrintzis, G. A.; Virvou, M.

Towards realizing a multimodal affect recognition system, we are considering the advantages of assisting a visual-facial expression recognition system with keyboard-stroke pattern information. Our work is based on the assumption that the visual-facial and keyboard modalities are complementary to each other and that their combination can significantly improve the accuracy in affective user models. Specifically, we present and discuss the development and evaluation process of two corresponding affect recognition subsystems, with emphasis on the recognition of 6 basic emotional states, namely happiness, sadness, surprise, anger and disgust as well as the emotion-less state which we refer to as neutral. We find that emotion recognition by the visual-facial modality can be aided greatly by keyboard-stroke pattern information and the combination of the two modalities can lead to better results towards building a multimodal affect recognition system.

TU-FG-209-12: Treatment Site and View Recognition in X-Ray Images with Hierarchical Multiclass Recognition Models

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

Chang, X; Mazur, T; Yang, D

Purpose: To investigate an approach of automatically recognizing anatomical sites and imaging views (the orientation of the image acquisition) in 2D X-ray images. Methods: A hierarchical (binary tree) multiclass recognition model was developed to recognize the treatment sites and views in x-ray images. From top to bottom of the tree, the treatment sites are grouped hierarchically from more general to more specific. Each node in the hierarchical model was designed to assign images to one of two categories of anatomical sites. The binary image classification function of each node in the hierarchical model is implemented by using a PCA transformationmore » and a support vector machine (SVM) model. The optimal PCA transformation matrices and SVM models are obtained by learning from a set of sample images. Alternatives of the hierarchical model were developed to support three scenarios of site recognition that may happen in radiotherapy clinics, including two or one X-ray images with or without view information. The performance of the approach was tested with images of 120 patients from six treatment sites – brain, head-neck, breast, lung, abdomen and pelvis – with 20 patients per site and two views (AP and RT) per patient. Results: Given two images in known orthogonal views (AP and RT), the hierarchical model achieved a 99% average F1 score to recognize the six sites. Site specific view recognition models have 100 percent accuracy. The computation time to process a new patient case (preprocessing, site and view recognition) is 0.02 seconds. Conclusion: The proposed hierarchical model of site and view recognition is effective and computationally efficient. It could be useful to automatically and independently confirm the treatment sites and views in daily setup x-ray 2D images. It could also be applied to guide subsequent image processing tasks, e.g. site and view dependent contrast enhancement and image registration. The senior author received research grants from ViewRay Inc. and Varian Medical System.« less

Role of adolescent and maternal depressive symptoms on transactional emotion recognition: context and state affect matter.

PubMed

Luebbe, Aaron M; Fussner, Lauren M; Kiel, Elizabeth J; Early, Martha C; Bell, Debora J

2013-12-01

Depressive symptomatology is associated with impaired recognition of emotion. Previous investigations have predominantly focused on emotion recognition of static facial expressions neglecting the influence of social interaction and critical contextual factors. In the current study, we investigated how youth and maternal symptoms of depression may be associated with emotion recognition biases during familial interactions across distinct contextual settings. Further, we explored if an individual's current emotional state may account for youth and maternal emotion recognition biases. Mother-adolescent dyads (N = 128) completed measures of depressive symptomatology and participated in three family interactions, each designed to elicit distinct emotions. Mothers and youth completed state affect ratings pertaining to self and other at the conclusion of each interaction task. Using multiple regression, depressive symptoms in both mothers and adolescents were associated with biased recognition of both positive affect (i.e., happy, excited) and negative affect (i.e., sadness, anger, frustration); however, this bias emerged primarily in contexts with a less strong emotional signal. Using actor-partner interdependence models, results suggested that youth's own state affect accounted for depression-related biases in their recognition of maternal affect. State affect did not function similarly in explaining depression-related biases for maternal recognition of adolescent emotion. Together these findings suggest a similar negative bias in emotion recognition associated with depressive symptoms in both adolescents and mothers in real-life situations, albeit potentially driven by different mechanisms.

Functional and Neuroanatomical Specificity of Episodic Memory Dysfunction in Schizophrenia: An fMRI study of the Relational and Item-Specific Encoding Task

PubMed Central

Ragland, J. Daniel; Ranganath, Charan; Harms, Michael P.; Barch, Deanna M.; Gold, James M.; Layher, Evan; Lesh, Tyler A.; MacDonald, Angus W.; Niendam, Tara A.; Phillips, Joshua; Silverstein, Steven M.; Yonelinas, Andrew P.; Carter, Cameron S.

2015-01-01

Importance Individuals with schizophrenia (SZ) can encode item-specific information to support familiarity-based recognition, but are disproportionately impaired encoding inter-item relationships (relational encoding) and recollecting information. The Relational and Item-Specific Encoding (RiSE) paradigm has been used to disentangle these encoding and retrieval processes, which may be dependent on specific medial temporal lobe (MTL) and prefrontal cortex (PFC) subregions. Functional imaging during RiSE task performance could help to specify dysfunctional neural circuits in SZ that can be targeted for interventions to improve memory and functioning in the illness. Objectives To use functional magnetic resonance imaging (fMRI) to test the hypothesis that SZ disproportionately affects MTL and PFC subregions during relational encoding and retrieval, relative to item-specific memory processes. Imaging results from healthy comparison subjects (HC) will also be used to establish neural construct validity for RiSE. Design, Setting, and Participants This multi-site, case-control, cross-sectional fMRI study was conducted at five CNTRACS sites. The final sample included 52 clinically stable outpatients with SZ, and 57 demographically matched HC. Main Outcomes and Measures Behavioral performance speed and accuracy (d’) on item recognition and associative recognition tasks. Voxelwise statistical parametric maps for a priori MTL and PFC regions of interest (ROI), testing activation differences between relational and item-specific memory during encoding and retrieval. Results Item recognition was disproportionately impaired in SZ patients relative to controls following relational encoding. The differential deficit was accompanied by reduced dorsolateral prefrontal cortex (DLPFC) activation during relational encoding in SZ, relative to HC. Retrieval success (hits > misses) was associated with hippocampal (HI) activation in HC during relational item recognition and associative recognition conditions, and HI activation was specifically reduced in SZ for recognition of relational but not item-specific information. Conclusions In this unique, multi-site fMRI study, HC results supported RiSE construct validity by revealing expected memory effects in PFC and MTL subregions during encoding and retrieval. Comparison of SZ and HC revealed disproportionate memory deficits in SZ for relational versus item-specific information, accompanied by regionally and functionally specific deficits in DLPFC and HI activation. PMID:26200928

Using Temporal Modulation Sensitivity to Select Stimulation Sites for Processor MAPs in Cochlear Implant Listeners

PubMed Central

Garadat, Soha N.; Zwolan, Teresa A.; Pfingst, Bryan E.

2013-01-01

Previous studies in our laboratory showed that temporal acuity as assessed by modulation detection thresholds (MDTs) varied across activation sites and that this site-to-site variability was subject specific. Using two 10-channel MAPs, the previous experiments showed that processor MAPs that had better across-site mean (ASM) MDTs yielded better speech recognition than MAPs with poorer ASM MDTs tested in the same subject. The current study extends our earlier work on developing more optimal fitting strategies to test the feasibility of using a site-selection approach in the clinical domain. This study examined the hypothesis that revising the clinical speech processor MAP for cochlear implant (CI) recipients by turning off selected sites that have poorer temporal acuity and reallocating frequencies to the remaining electrodes would lead to improved speech recognition. Twelve CI recipients participated in the experiments. We found that site selection procedure based on MDTs in the presence of a masker resulted in improved performance on consonant recognition and recognition of sentences in noise. In contrast, vowel recognition was poorer with the experimental MAP than with the clinical MAP, possibly due to reduced spectral resolution when sites were removed from the experimental MAP. Overall, these results suggest a promising path for improving recipient outcomes using personalized processor-fitting strategies based on a psychophysical measure of temporal acuity. PMID:23881208

Structural study of the Fox-1 RRM protein hydration reveals a role for key water molecules in RRM-RNA recognition

PubMed Central

Blatter, Markus; Cléry, Antoine; Damberger, Fred F.

2017-01-01

Abstract The Fox-1 RNA recognition motif (RRM) domain is an important member of the RRM protein family. We report a 1.8 Å X-ray structure of the free Fox-1 containing six distinct monomers. We use this and the nuclear magnetic resonance (NMR) structure of the Fox-1 protein/RNA complex for molecular dynamics (MD) analyses of the structured hydration. The individual monomers of the X-ray structure show diverse hydration patterns, however, MD excellently reproduces the most occupied hydration sites. Simulations of the protein/RNA complex show hydration consistent with the isolated protein complemented by hydration sites specific to the protein/RNA interface. MD predicts intricate hydration sites with water-binding times extending up to hundreds of nanoseconds. We characterize two of them using NMR spectroscopy, RNA binding with switchSENSE and free-energy calculations of mutant proteins. Both hydration sites are experimentally confirmed and their abolishment reduces the binding free-energy. A quantitative agreement between theory and experiment is achieved for the S155A substitution but not for the S122A mutant. The S155 hydration site is evolutionarily conserved within the RRM domains. In conclusion, MD is an effective tool for predicting and interpreting the hydration patterns of protein/RNA complexes. Hydration is not easily detectable in NMR experiments but can affect stability of protein/RNA complexes. PMID:28505313

Perceptual fluency and affect without recognition.

PubMed

Anand, P; Sternthal, B

1991-05-01

A dichotic listening task was used to investigate the affect-without-recognition phenomenon. Subjects performed a distractor task by responding to the information presented in one ear while ignoring the target information presented in the other ear. The subjects' recognition of and affect toward the target information as well as toward foils was measured. The results offer evidence for the affect-without-recognition phenomenon. Furthermore, the data suggest that the subjects' affect toward the stimuli depended primarily on the extent to which the stimuli were perceived as familiar (i.e., subjective familiarity), and this perception was influenced by the ear in which the distractor or the target information was presented. These data are interpreted in terms of current models of recognition memory and hemispheric lateralization.

The involvement of emotion recognition in affective theory of mind.

PubMed

Mier, Daniela; Lis, Stefanie; Neuthe, Kerstin; Sauer, Carina; Esslinger, Christine; Gallhofer, Bernd; Kirsch, Peter

2010-11-01

This study was conducted to explore the relationship between emotion recognition and affective Theory of Mind (ToM). Forty subjects performed a facial emotion recognition and an emotional intention recognition task (affective ToM) in an event-related fMRI study. Conjunction analysis revealed overlapping activation during both tasks. Activation in some of these conjunctly activated regions was even stronger during affective ToM than during emotion recognition, namely in the inferior frontal gyrus, the superior temporal sulcus, the temporal pole, and the amygdala. In contrast to previous studies investigating ToM, we found no activation in the anterior cingulate, commonly assumed as the key region for ToM. The results point to a close relationship of emotion recognition and affective ToM and can be interpreted as evidence for the assumption that at least basal forms of ToM occur by an embodied, non-cognitive process. Copyright © 2010 Society for Psychophysiological Research.

Bovine serum albumin surface imprinted polymer fabricated by surface grafting copolymerization on zinc oxide rods and its application for protein recognition.

PubMed

Li, Xiangjie; Zhou, Jingjing; Tian, Lei; Li, Wei; Zhang, Baoliang; Zhang, Hepeng; Zhang, Qiuyu

2015-10-01

A novel bovine serum albumin (BSA) surface imprinted polymer based on ZnO rods was synthesized by surface grafting copolymerization. It exhibited an excellent recognition performance to bovine serum albumin. The adsorption capacity and imprinting factor of bovine serum albumin could reach 89.27 mg/g and 2.35, respectively. Furthermore, the fluorescence property of ZnO was used for tracing the process of protein imprinting and it implied the excellent optical sensing property of this material. More importantly, the hypothesis that the surface charge of carrier could affect the imprinting process was confirmed. That is, ZnO with positive surface charge could not only improve the recognition specificity of binding sites to template proteins (pI < 7), but also deteriorate the bindings between sites and non-template proteins (pI > 7). It was also important that the reusability of ZnO@BSA molecularly imprinted polymers was satisfactory. This implied that the poor mechanical/chemical stability of traditional zinc oxide sensors could be solved by the introduction of surface grafting copolymerization. These results revealed that the ZnO@BSA molecularly imprinted polymers are a promising optical/electrochemical sensor element. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

H-Bond Self-Assembly: Folding versus Duplex Formation.

PubMed

Núñez-Villanueva, Diego; Iadevaia, Giulia; Stross, Alexander E; Jinks, Michael A; Swain, Jonathan A; Hunter, Christopher A

2017-05-17

Linear oligomers equipped with complementary H-bond donor (D) and acceptor (A) sites can interact via intermolecular H-bonds to form duplexes or fold via intramolecular H-bonds. These competing equilibria have been quantified using NMR titration and dilution experiments for seven systems featuring different recognition sites and backbones. For all seven architectures, duplex formation is observed for homo-sequence 2-mers (AA·DD) where there are no competing folding equilibria. The corresponding hetero-sequence AD 2-mers also form duplexes, but the observed self-association constants are strongly affected by folding equilibria in the monomeric states. When the backbone is flexible (five or more rotatable bonds separating the recognition sites), intramolecular H-bonding is favored, and the folded state is highly populated. For these systems, the stability of the AD·AD duplex is 1-2 orders of magnitude lower than that of the corresponding AA·DD duplex. However, for three architectures which have more rigid backbones (fewer than five rotatable bonds), intramolecular interactions are not observed, and folding does not compete with duplex formation. These systems are promising candidates for the development of longer, mixed-sequence synthetic information molecules that show sequence-selective duplex formation.

Influence of continuous magnetic field on the separation of ephedrine enantiomers by molecularly imprinted polymers.

PubMed

Guerreiro, António R; Korkhov, Vadim; Mijangos, Irene; Piletska, Elena V; Rodins, Juris; Turner, Anthony P F; Piletsky, Sergey A

2008-02-28

A set of polymers was imprinted with (-)-ephedrine using UV initiation, under the influence of a constant external magnetic field with intensities ranging from 0 to 1.55 T. Synthesised materials were characterised by X-ray crystallography, infrared spectroscopy, swelling and surface area. Recognition properties were assessed by the ability to discriminate between (+) and (-)-ephedrine and by Scatchard analyses on chromatographic mode. It was shown that polymer morphology and recognition properties are affected by the magnetic field. This resulted in considerable improvements in the chromatographic resolution of ephedrine enantiomers by materials synthesised under the influence of magnetic field. Apparently the magnetic field improved the ordering of the polymer structure and facilitated the formation of more uniform imprinting sites.

Matrine- and oxymatrine-imprinted monodisperse polymers prepared by precipitation polymerization and their applications for the selective extraction of matrine-type alkaloids from Sophora flavescens Aiton.

PubMed

Funaya, Noriko; Haginaka, Jun

2012-07-27

Matrine (MT)- and oxymatrine (OMT)-imprinted monodisperse polymers have been prepared by precipitation polymerization. The prepared molecularly imprinted polymers (MIPs) for MT and OMT, MIP(MT) and MIP(OMT), were monodispersed microspheres of 3.3 and 3.9 μm in diameter, respectively. Binding experiments and Scatchard analyses revealed that two classes of binding sites were formed on MIP(MT) and MIP(OMT). In addition to shape recognition, ionic and hydrophobic interactions seemed to affect the retention and recognition of MT and OMT on MIP(MT) and MIP(OMT), respectively, in low acetonitrile content, and ionic and hydrophilic interactions affected these properties in high acetonitrile content. MIP(MT) was used to selectively extract MT and sophocarpine (13,14-dehydromatrine) from Sophora flavescens root, while MIP(OMT) was used to extract OMT and oxysophocarpine (13,14-dehydrooxymatrine). Copyright © 2012 Elsevier B.V. All rights reserved.

Facial Affect Recognition and Social Anxiety in Preschool Children

ERIC Educational Resources Information Center

Ale, Chelsea M.; Chorney, Daniel B.; Brice, Chad S.; Morris, Tracy L.

2010-01-01

Research relating anxiety and facial affect recognition has focused mostly on school-aged children and adults and has yielded mixed results. The current study sought to demonstrate an association among behavioural inhibition and parent-reported social anxiety, shyness, social withdrawal and facial affect recognition performance in 30 children,…

Assessing collective affect recognition via the Emotional Aperture Measure.

PubMed

Sanchez-Burks, Jeffrey; Bartel, Caroline A; Rees, Laura; Huy, Quy

2016-01-01

Curiosity about collective affect is undergoing a revival in many fields. This literature, tracing back to Le Bon's seminal work on crowd psychology, has established the veracity of collective affect and demonstrated its influence on a wide range of group dynamics. More recently, an interest in the perception of collective affect has emerged, revealing a need for a methodological approach for assessing collective emotion recognition to complement measures of individual emotion recognition. This article addresses this need by introducing the Emotional Aperture Measure (EAM). Three studies provide evidence that collective affect recognition requires a processing style distinct from individual emotion recognition and establishes the validity and reliability of the EAM. A sample of working managers further shows how the EAM provides unique insights into how individuals interact with collectives. We discuss how the EAM can advance several lines of research on collective affect.

Across-site patterns of modulation detection: Relation to speech recognitiona)

PubMed Central

Garadat, Soha N.; Zwolan, Teresa A.; Pfingst, Bryan E.

2012-01-01

The aim of this study was to identify across-site patterns of modulation detection thresholds (MDTs) in subjects with cochlear implants and to determine if removal of sites with the poorest MDTs from speech processor programs would result in improved speech recognition. Five hundred millisecond trains of symmetric-biphasic pulses were modulated sinusoidally at 10 Hz and presented at a rate of 900 pps using monopolar stimulation. Subjects were asked to discriminate a modulated pulse train from an unmodulated pulse train for all electrodes in quiet and in the presence of an interleaved unmodulated masker presented on the adjacent site. Across-site patterns of masked MDTs were then used to construct two 10-channel MAPs such that one MAP consisted of sites with the best masked MDTs and the other MAP consisted of sites with the worst masked MDTs. Subjects’ speech recognition skills were compared when they used these two different MAPs. Results showed that MDTs were variable across sites and were elevated in the presence of a masker by various amounts across sites. Better speech recognition was observed when the processor MAP consisted of sites with best masked MDTs, suggesting that temporal modulation sensitivity has important contributions to speech recognition with a cochlear implant. PMID:22559376

Conformational changes in the P site and mRNA entry channel evoked by AUG recognition in yeast translation preinitiation complexes

PubMed Central

Zhang, Fan; Saini, Adesh K.; Shin, Byung-Sik; Nanda, Jagpreet; Hinnebusch, Alan G.

2015-01-01

The translation preinitiation complex (PIC) is thought to assume an open conformation when scanning the mRNA leader, with AUG recognition evoking a closed conformation and more stable P site interaction of Met-tRNAi; however, physical evidence is lacking that AUG recognition constrains interaction of mRNA with the 40S binding cleft. We compared patterns of hydroxyl radical cleavage of rRNA by Fe(II)-BABE tethered to unique sites in eIF1A in yeast PICs reconstituted with mRNA harboring an AUG or near-cognate (AUC) start codon. rRNA residues in the P site display reduced cleavage in AUG versus AUC PICs; and enhanced cleavage in the AUC complexes was diminished by mutations of scanning enhancer elements of eIF1A that increase near-cognate recognition in vivo. This suggests that accessibility of these rRNA residues is reduced by accommodation of Met-tRNAi in the P site (PIN state) and by their interactions with the anticodon stem of Met-tRNAi. Our cleavage data also provide evidence that AUG recognition evokes dissociation of eIF1 from its 40S binding site, ejection of the eIF1A-CTT from the P-site and rearrangement to a closed conformation of the entry channel with reduced mobility of mRNA. PMID:25670678

Mapping correspondence between facial mimicry and emotion recognition in healthy subjects.

PubMed

Ponari, Marta; Conson, Massimiliano; D'Amico, Nunzia Pina; Grossi, Dario; Trojano, Luigi

2012-12-01

We aimed at verifying the hypothesis that facial mimicry is causally and selectively involved in emotion recognition. For this purpose, in Experiment 1, we explored the effect of tonic contraction of muscles in upper or lower half of participants' face on their ability to recognize emotional facial expressions. We found that the "lower" manipulation specifically impaired recognition of happiness and disgust, the "upper" manipulation impaired recognition of anger, while both manipulations affected recognition of fear; recognition of surprise and sadness were not affected by either blocking manipulations. In Experiment 2, we verified whether emotion recognition is hampered by stimuli in which an upper or lower half-face showing an emotional expression is combined with a neutral half-face. We found that the neutral lower half-face interfered with recognition of happiness and disgust, whereas the neutral upper half impaired recognition of anger; recognition of fear and sadness was impaired by both manipulations, whereas recognition of surprise was not affected by either manipulation. Taken together, the present findings support simulation models of emotion recognition and provide insight into the role of mimicry in comprehension of others' emotional facial expressions. PsycINFO Database Record (c) 2012 APA, all rights reserved.

[Measuring impairment of facial affects recognition in schizophrenia. Preliminary study of the facial emotions recognition task (TREF)].

PubMed

Gaudelus, B; Virgile, J; Peyroux, E; Leleu, A; Baudouin, J-Y; Franck, N

2015-06-01

The impairment of social cognition, including facial affects recognition, is a well-established trait in schizophrenia, and specific cognitive remediation programs focusing on facial affects recognition have been developed by different teams worldwide. However, even though social cognitive impairments have been confirmed, previous studies have also shown heterogeneity of the results between different subjects. Therefore, assessment of personal abilities should be measured individually before proposing such programs. Most research teams apply tasks based on facial affects recognition by Ekman et al. or Gur et al. However, these tasks are not easily applicable in a clinical exercise. Here, we present the Facial Emotions Recognition Test (TREF), which is designed to identify facial affects recognition impairments in a clinical practice. The test is composed of 54 photos and evaluates abilities in the recognition of six universal emotions (joy, anger, sadness, fear, disgust and contempt). Each of these emotions is represented with colored photos of 4 different models (two men and two women) at nine intensity levels from 20 to 100%. Each photo is presented during 10 seconds; no time limit for responding is applied. The present study compared the scores of the TREF test in a sample of healthy controls (64 subjects) and people with stabilized schizophrenia (45 subjects) according to the DSM IV-TR criteria. We analysed global scores for all emotions, as well as sub scores for each emotion between these two groups, taking into account gender differences. Our results were coherent with previous findings. Applying TREF, we confirmed an impairment in facial affects recognition in schizophrenia by showing significant differences between the two groups in their global results (76.45% for healthy controls versus 61.28% for people with schizophrenia), as well as in sub scores for each emotion except for joy. Scores for women were significantly higher than for men in the population without psychiatric diagnosis. The study also allowed the identification of cut-off scores; results below 2 standard deviations of the healthy control average (61.57%) pointed to a facial affect recognition deficit. The TREF appears to be a useful tool to identify facial affects recognition impairment in schizophrenia. Neuropsychologists, who have tried this task, have positive feedback. The TREF is easy to use (duration of about 15 minutes), easy to apply in subjects with attentional difficulties, and tests facial affects recognition at ecological intensity levels. These results have to be confirmed in the future with larger sample sizes, and in comparison with other tasks, evaluating the facial affects recognition processes. Copyright © 2014 L’Encéphale, Paris. Published by Elsevier Masson SAS. All rights reserved.

Stereotypes and prejudice affect the recognition of emotional body postures.

PubMed

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

2018-03-26

Most research on emotion recognition focuses on facial expressions. However, people communicate emotional information through bodily cues as well. Prior research on facial expressions has demonstrated that emotion recognition is modulated by top-down processes. Here, we tested whether this top-down modulation generalizes to the recognition of emotions from body postures. We report three studies demonstrating that stereotypes and prejudice about men and women may affect how fast people classify various emotional body postures. Our results suggest that gender cues activate gender associations, which affect the recognition of emotions from body postures in a top-down fashion. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Perceptual and affective mechanisms in facial expression recognition: An integrative review.

PubMed

Calvo, Manuel G; Nummenmaa, Lauri

2016-09-01

Facial expressions of emotion involve a physical component of morphological changes in a face and an affective component conveying information about the expresser's internal feelings. It remains unresolved how much recognition and discrimination of expressions rely on the perception of morphological patterns or the processing of affective content. This review of research on the role of visual and emotional factors in expression recognition reached three major conclusions. First, behavioral, neurophysiological, and computational measures indicate that basic expressions are reliably recognized and discriminated from one another, albeit the effect may be inflated by the use of prototypical expression stimuli and forced-choice responses. Second, affective content along the dimensions of valence and arousal is extracted early from facial expressions, although this coarse affective representation contributes minimally to categorical recognition of specific expressions. Third, the physical configuration and visual saliency of facial features contribute significantly to expression recognition, with "emotionless" computational models being able to reproduce some of the basic phenomena demonstrated in human observers. We conclude that facial expression recognition, as it has been investigated in conventional laboratory tasks, depends to a greater extent on perceptual than affective information and mechanisms.

Two-step interrogation then recognition of DNA binding site by Integration Host Factor: an architectural DNA-bending protein.

PubMed

Velmurugu, Yogambigai; Vivas, Paula; Connolly, Mitchell; Kuznetsov, Serguei V; Rice, Phoebe A; Ansari, Anjum

2018-02-28

The dynamics and mechanism of how site-specific DNA-bending proteins initially interrogate potential binding sites prior to recognition have remained elusive for most systems. Here we present these dynamics for Integration Host factor (IHF), a nucleoid-associated architectural protein, using a μs-resolved T-jump approach. Our studies show two distinct DNA-bending steps during site recognition by IHF. While the faster (∼100 μs) step is unaffected by changes in DNA or protein sequence that alter affinity by >100-fold, the slower (1-10 ms) step is accelerated ∼5-fold when mismatches are introduced at DNA sites that are sharply kinked in the specific complex. The amplitudes of the fast phase increase when the specific complex is destabilized and decrease with increasing [salt], which increases specificity. Taken together, these results indicate that the fast phase is non-specific DNA bending while the slow phase, which responds only to changes in DNA flexibility at the kink sites, is specific DNA kinking during site recognition. Notably, the timescales for the fast phase overlap with one-dimensional diffusion times measured for several proteins on DNA, suggesting that these dynamics reflect partial DNA bending during interrogation of potential binding sites by IHF as it scans DNA.

Probing binding hot spots at protein-RNA recognition sites.

PubMed

Barik, Amita; Nithin, Chandran; Karampudi, Naga Bhushana Rao; Mukherjee, Sunandan; Bahadur, Ranjit Prasad

2016-01-29

We use evolutionary conservation derived from structure alignment of polypeptide sequences along with structural and physicochemical attributes of protein-RNA interfaces to probe the binding hot spots at protein-RNA recognition sites. We find that the degree of conservation varies across the RNA binding proteins; some evolve rapidly compared to others. Additionally, irrespective of the structural class of the complexes, residues at the RNA binding sites are evolutionary better conserved than those at the solvent exposed surfaces. For recognitions involving duplex RNA, residues interacting with the major groove are better conserved than those interacting with the minor groove. We identify multi-interface residues participating simultaneously in protein-protein and protein-RNA interfaces in complexes where more than one polypeptide is involved in RNA recognition, and show that they are better conserved compared to any other RNA binding residues. We find that the residues at water preservation site are better conserved than those at hydrated or at dehydrated sites. Finally, we develop a Random Forests model using structural and physicochemical attributes for predicting binding hot spots. The model accurately predicts 80% of the instances of experimental ΔΔG values in a particular class, and provides a stepping-stone towards the engineering of protein-RNA recognition sites with desired affinity. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Ligation site in proteins recognized in silico

PubMed Central

Brylinski, Michal; Konieczny, Leszek; Roterman, Irena

2006-01-01

Recognition of a ligation site in a protein molecule is important for identifying its biological activity. The model for in silico recognition of ligation sites in proteins is presented. The idealized hydrophobic core stabilizing protein structure is represented by a three-dimensional Gaussian function. The experimentally observed distribution of hydrophobicity compared with the theoretical distribution reveals differences. The area of high differences indicates the ligation site. Availability http://bioinformatics.cm-uj.krakow.pl/activesite PMID:17597871

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

How the extra methylene group affects the ligation properties of Glu vs. Asp and Gln vs. Asn amino acids: a DFT/PCM study.

PubMed

Dudev, Todor; Doudeva, Lyudmila

2017-02-01

The effect of the extra methylene group on the ligation properties of glutamic (Glu) vs. aspartic (Asp) acid, and glutamine (Gln) vs. asparagine (Asn) amino acids-two pairs of protein building blocks differing by the length of their side chains-has been studied by employing DFT calculations combined with polarizable continuum model (PCM) computations. Complexes of the nominal species with partner ligands of various structures, charge states, and degree of solvent exposure have been examined. The results obtained reveal that the difference in the alkyl chain length of these amino acid residues does not affect the mode of their binding. This, however, influences the thermodynamics of the ligand-ligand and ligand-metal recognition thus bestowing unique ligation characteristics on the competing entities. The calculations reveal that the competition between the longer-chain and shorter-chain analogs is entropy driven and that the differential electronic effects are of minor importance for the process. Thus, the outcome of the rivalry between Asp and Glu, and Asn and Gln is almost unaffected by the nature of the partner ligand, its charge state and, in most cases, the dielectric properties of the binding site. The longer-chain Glu, as opposed to its shorter-chain Asp counterpart, is the preferred partner ligand in various protein binding sites. Contrariwise, the shorter-chain Asn binds more favorably to the respective binding sites than its longer-chain Gln analog. The results obtained shed additional light on the intimate mechanism of the ligand-ligand and ligand-metal recognition in proteins and could be employed as guidelines in protein engineering and design.

Biomimetic/Optical Sensors for Detecting Bacterial Species

NASA Technical Reports Server (NTRS)

Homer, Margie; Ksendzov, Alexander; Yen, Shiao-Pin; Ryan, Margaret; Lazazzera, Beth

2006-01-01

Biomimetic/optical sensors have been proposed as means of real-time detection of bacteria in liquid samples through real-time detection of compounds secreted by the bacteria. Bacterial species of interest would be identified through detection of signaling compounds unique to those species. The best-characterized examples of quorum-signaling compounds are acyl-homoserine lactones and peptides. Each compound, secreted by each bacterium of an affected species, serves as a signal to other bacteria of the same species to engage in a collective behavior when the population density of that species reaches a threshold level analogous to a quorum. A sensor according to the proposal would include a specially formulated biomimetic film, made of a molecularly imprinted polymer (MIP), that would respond optically to the signaling compound of interest. The MIP film would be integrated directly onto an opticalwaveguide- based ring resonator for optical readout. Optically, the sensor would resemble the one described in Chemical Sensors Based on Optical Ring Resonators (NPO-40601), NASA Tech Briefs, Vol. 29, No. 10 (October 2005), page 32. MIPs have been used before as molecular- recognition compounds, though not in the manner of the present proposal. Molecular imprinting is an approach to making molecularly selective cavities in a polymer matrix. These cavities function much as enzyme receptor sites: the chemical functionality and shape of a cavity in the polymer matrix cause the cavity to bind to specific molecules. An MIP matrix is made by polymerizing monomers in the presence of the compound of interest (template molecule). The polymer forms around the template. After the polymer solidifies, the template molecules are removed from the polymer matrix by decomplexing them from their binding sites and then dissolving them, leaving cavities that are matched to the template molecules in size, shape, and chemical functionality. The cavities thus become molecular-recognition sites that bind only to molecules matched to the sites; other molecules are excluded. In a sensor according to the proposal, the MIP would feature molecular recognition sites that would bind the specific signaling molecules selectively according to their size, shape, and chemical functionality (see figure). As the film took up the signaling molecules in the molecular recognition sites, the index of refraction and thickness of the film would change, causing a wavelength shift of the peak of the resonance spectrum. It has been estimated that by measuring this wavelength shift, it should be possible to detect as little as 10 picomoles of a peptide signaling compound.

Psychometric properties of the NEPSY-II affect recognition subtest in a preschool sample: a Rasch modeling approach.

PubMed

Yao, Shih-Ying; Bull, Rebecca; Khng, Kiat Hui; Rahim, Anisa

2018-01-01

Understanding a child's ability to decode emotion expressions is important to allow early interventions for potential difficulties in social and emotional functioning. This study applied the Rasch model to investigate the psychometric properties of the NEPSY-II Affect Recognition subtest, a U.S. normed measure for 3-16 year olds which assesses the ability to recognize facial expressions of emotion. Data were collected from 1222 children attending preschools in Singapore. We first performed the Rasch analysis with the raw item data, and examined the technical qualities and difficulty pattern of the studied items. We subsequently investigated the relation of the estimated affect recognition ability from the Rasch analysis to a teacher-reported measure of a child's behaviors, emotions, and relationships. Potential gender differences were also examined. The Rasch model fits our data well. Also, the NEPSY-II Affect Recognition subtest was found to have reasonable technical qualities, expected item difficulty pattern, and desired association with the external measure of children's behaviors, emotions, and relationships for both boys and girls. Overall, findings from this study suggest that the NEPSY-II Affect Recognition subtest is a promising measure of young children's affect recognition ability. Suggestions for future test improvement and research were discussed.

TALE-PvuII fusion proteins--novel tools for gene targeting.

PubMed

Yanik, Mert; Alzubi, Jamal; Lahaye, Thomas; Cathomen, Toni; Pingoud, Alfred; Wende, Wolfgang

2013-01-01

Zinc finger nucleases (ZFNs) consist of zinc fingers as DNA-binding module and the non-specific DNA-cleavage domain of the restriction endonuclease FokI as DNA-cleavage module. This architecture is also used by TALE nucleases (TALENs), in which the DNA-binding modules of the ZFNs have been replaced by DNA-binding domains based on transcription activator like effector (TALE) proteins. Both TALENs and ZFNs are programmable nucleases which rely on the dimerization of FokI to induce double-strand DNA cleavage at the target site after recognition of the target DNA by the respective DNA-binding module. TALENs seem to have an advantage over ZFNs, as the assembly of TALE proteins is easier than that of ZFNs. Here, we present evidence that variant TALENs can be produced by replacing the catalytic domain of FokI with the restriction endonuclease PvuII. These fusion proteins recognize only the composite recognition site consisting of the target site of the TALE protein and the PvuII recognition sequence (addressed site), but not isolated TALE or PvuII recognition sites (unaddressed sites), even at high excess of protein over DNA and long incubation times. In vitro, their preference for an addressed over an unaddressed site is > 34,000-fold. Moreover, TALE-PvuII fusion proteins are active in cellula with minimal cytotoxicity.

Towards Real-Time Speech Emotion Recognition for Affective E-Learning

ERIC Educational Resources Information Center

Bahreini, Kiavash; Nadolski, Rob; Westera, Wim

2016-01-01

This paper presents the voice emotion recognition part of the FILTWAM framework for real-time emotion recognition in affective e-learning settings. FILTWAM (Framework for Improving Learning Through Webcams And Microphones) intends to offer timely and appropriate online feedback based upon learner's vocal intonations and facial expressions in order…

Construction of proteins with molecular recognition capabilities using α3β3 de novo protein scaffolds.

PubMed

Okura, Hiromichi; Mihara, Hisakazu; Takahashi, Tsuyoshi

2013-10-01

The molecular recognition ability of proteins is essential in biological systems, and therefore a considerable amount of effort has been devoted to constructing desired target-binding proteins using a variety of naturally occurring proteins as scaffolds. However, since generating a binding site in a native protein can often affect its structural properties, highly stable de novo protein scaffolds may be more amenable than the native proteins. We previously reported the generation of de novo proteins comprising three α-helices and three β-strands (α3β3) from a genetic library coding simplified amino acid sets. Two α3β3 de novo proteins, vTAJ13 and vTAJ36, fold into a native-like stable and molten globule-like structures, respectively, even though the proteins have similar amino acid compositions. Here, we attempted to create binding sites for the vTAJ13 and vTAJ36 proteins to prove the utility of de novo designed artificial proteins as a molecular recognition tool. Randomization of six amino acids at two linker sites of vTAJ13 and vTAJ36 followed by biopanning generated binding proteins that recognize the target molecules, fluorescein and green fluorescent protein, with affinities of 10(-7)-10(-8) M. Of note, the selected proteins from the vTAJ13-based library tended to recognize the target molecules with high specificity, probably due to the native-like stable structure of vTAJ13. Our studies provide an example of the potential of de novo protein scaffolds, which are composed of a simplified amino acid set, to recognize a variety of target compounds.

Ring-through-ring molecular shuttling in a saturated [3]rotaxane

NASA Astrophysics Data System (ADS)

Zhu, Kelong; Baggi, Giorgio; Loeb, Stephen J.

2018-06-01

Mechanically interlocked molecules such as rotaxanes and catenanes comprise two or more components whose motion relative to each other can be controlled. A [2]rotaxane molecular shuttle, for example, consists of an axle bearing two recognition sites and a single macrocyclic wheel that can undergo a to-and-fro motion along the axle—shuttling between the recognition sites. The ability of mechanically interlocked molecules to undergo this type of large-amplitude change is the core mechanism behind almost every interlocked molecular switch or machine, including sophisticated mechanical systems such as a molecular elevator and a peptide synthesizer. Here, as a way to expand the scope of dynamics possible at the molecular level, we have developed a molecular shuttling mechanism involving the exchange of rings between two recognition sites in a saturated [3]rotaxane (one with no empty recognition sites). This was accomplished by passing a smaller ring through a larger one, thus achieving ring-through-ring molecular shuttling.

Functional cooperation between exonucleases and endonucleases—basis for the evolution of restriction enzymes

PubMed Central

Raghavendra, Nidhanapathi K.; Rao, Desirazu N.

2003-01-01

Many types of restriction enzymes cleave DNA away from their recognition site. Using the type III restriction enzyme, EcoP15I, which cleaves DNA 25–27 bp away from its recognition site, we provide evidence to show that an intact recognition site on the cleaved DNA sequesters the restriction enzyme and decreases the effective concentration of the enzyme. EcoP15I restriction enzyme is shown here to perform only a single round of DNA cleavage. Significantly, we show that an exonuclease activity is essential for EcoP15I restriction enzyme to perform multiple rounds of DNA cleavage. This observation may hold true for all restriction enzymes cleaving DNA sufficiently far away from their recognition site. Our results highlight the importance of functional cooperation in the modulation of enzyme activity. Based on results presented here and other data on well-characterised restriction enzymes, a functional evolutionary hierarchy of restriction enzymes is discussed. PMID:12655005

Deciphering common recognition principles of nucleoside mono/di and tri-phosphates binding in diverse proteins via structural matching of their binding sites.

PubMed

Bhagavat, Raghu; Srinivasan, Narayanaswamy; Chandra, Nagasuma

2017-09-01

Nucleoside triphosphate (NTP) ligands are of high biological importance and are essential for all life forms. A pre-requisite for them to participate in diverse biochemical processes is their recognition by diverse proteins. It is thus of great interest to understand the basis for such recognition in different proteins. Towards this, we have used a structural bioinformatics approach and analyze structures of 4677 NTP complexes available in Protein Data Bank (PDB). Binding sites were extracted and compared exhaustively using PocketMatch, a sensitive in-house site comparison algorithm, which resulted in grouping the entire dataset into 27 site-types. Each of these site-types represent a structural motif comprised of two or more residue conservations, derived using another in-house tool for superposing binding sites, PocketAlign. The 27 site-types could be grouped further into 9 super-types by considering partial similarities in the sites, which indicated that the individual site-types comprise different combinations of one or more site features. A scan across PDB using the 27 structural motifs determined the motifs to be specific to NTP binding sites, and a computational alanine mutagenesis indicated that residues identified to be highly conserved in the motifs are also most contributing to binding. Alternate orientations of the ligand in several site-types were observed and rationalized, indicating the possibility of some residues serving as anchors for NTP recognition. The presence of multiple site-types and the grouping of multiple folds into each site-type is strongly suggestive of convergent evolution. Knowledge of determinants obtained from this study will be useful for detecting function in unknown proteins. Proteins 2017; 85:1699-1712. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Face memory and face recognition in children and adolescents with attention deficit hyperactivity disorder: A systematic review.

PubMed

Romani, Maria; Vigliante, Miriam; Faedda, Noemi; Rossetti, Serena; Pezzuti, Lina; Guidetti, Vincenzo; Cardona, Francesco

2018-06-01

This review focuses on facial recognition abilities in children and adolescents with attention deficit hyperactivity disorder (ADHD). A systematic review, using PRISMA guidelines, was conducted to identify original articles published prior to May 2017 pertaining to memory, face recognition, affect recognition, facial expression recognition and recall of faces in children and adolescents with ADHD. The qualitative synthesis based on different studies shows a particular focus of the research on facial affect recognition without paying similar attention to the structural encoding of facial recognition. In this review, we further investigate facial recognition abilities in children and adolescents with ADHD, providing synthesis of the results observed in the literature, while detecting face recognition tasks used on face processing abilities in ADHD and identifying aspects not yet explored. Copyright © 2018 Elsevier Ltd. All rights reserved.

Speaker information affects false recognition of unstudied lexical-semantic associates.

PubMed

Luthra, Sahil; Fox, Neal P; Blumstein, Sheila E

2018-05-01

Recognition of and memory for a spoken word can be facilitated by a prior presentation of that word spoken by the same talker. However, it is less clear whether this speaker congruency advantage generalizes to facilitate recognition of unheard related words. The present investigation employed a false memory paradigm to examine whether information about a speaker's identity in items heard by listeners could influence the recognition of novel items (critical intruders) phonologically or semantically related to the studied items. In Experiment 1, false recognition of semantically associated critical intruders was sensitive to speaker information, though only when subjects attended to talker identity during encoding. Results from Experiment 2 also provide some evidence that talker information affects the false recognition of critical intruders. Taken together, the present findings indicate that indexical information is able to contact the lexical-semantic network to affect the processing of unheard words.

Warmth of familiarity and chill of error: affective consequences of recognition decisions.

PubMed

Chetverikov, Andrey

2014-04-01

The present research aimed to assess the effect of recognition decision on subsequent affective evaluations of recognised and non-recognised objects. Consistent with the proposed account of post-decisional preferences, results showed that the effect of recognition on preferences depends upon objective familiarity. If stimuli are recognised, liking ratings are positively associated with exposure frequency; if stimuli are not recognised, this link is either absent (Experiment 1) or negative (Experiments 2 and 3). This interaction between familiarity and recognition exists even when recognition accuracy is at chance level and the "mere exposure" effect is absent. Finally, data obtained from repeated measurements of preferences and using manipulations of task order confirm that recognition decisions have a causal influence on preferences. The findings suggest that affective evaluation can provide fine-grained access to the efficacy of cognitive processing even in simple cognitive tasks.

Structural analysis of substrate recognition by glucose isomerase in Mn2+ binding mode at M2 site in S. rubiginosus.

PubMed

Bae, Ji-Eun; Hwang, Kwang Yeon; Nam, Ki Hyun

2018-06-16

Glucose isomerase (GI) catalyzes the reversible enzymatic isomerization of d-glucose and d-xylose to d-fructose and d-xylulose, respectively. This is one of the most important enzymes in the production of high-fructose corn syrup (HFCS) and biofuel. We recently determined the crystal structure of GI from S. rubiginosus (SruGI) complexed with a xylitol inhibitor in one metal binding mode. Although we assessed inhibitor binding at the M1 site, the metal binding at the M2 site and the substrate recognition mechanism for SruGI remains the unclear. Here, we report the crystal structure of the two metal binding modes of SruGI and its complex with glucose. This study provides a snapshot of metal binding at the SruGI M2 site in the presence of Mn 2+ , but not in the presence of Mg 2+ . Metal binding at the M2 site elicits a configuration change at the M1 site. Glucose molecule can only bind to the M1 site in presence of Mn 2+ at the M2 site. Glucose and Mn 2+ at the M2 site were bridged by water molecules using a hydrogen bonding network. The metal binding geometry of the M2 site indicates a distorted octahedral coordination with an angle of 55-110°, whereas the M1 site has a relatively stable octahedral coordination with an angle of 85-95°. We suggest a two-step sequential process for SruGI substrate recognition, in Mn 2+ binding mode, at the M2 site. Our results provide a better understanding of the molecular role of the M2 site in GI substrate recognition. Copyright © 2018. Published by Elsevier Inc.

Emotion recognition and social skills in child and adolescent offspring of parents with schizophrenia.

PubMed

Horton, Leslie E; Bridgwater, Miranda A; Haas, Gretchen L

2017-05-01

Emotion recognition, a social cognition domain, is impaired in people with schizophrenia and contributes to social dysfunction. Whether impaired emotion recognition emerges as a manifestation of illness or predates symptoms is unclear. Findings from studies of emotion recognition impairments in first-degree relatives of people with schizophrenia are mixed and, to our knowledge, no studies have investigated the link between emotion recognition and social functioning in that population. This study examined facial affect recognition and social skills in 16 offspring of parents with schizophrenia (familial high-risk/FHR) compared to 34 age- and sex-matched healthy controls (HC), ages 7-19. As hypothesised, FHR children exhibited impaired overall accuracy, accuracy in identifying fearful faces, and overall recognition speed relative to controls. Age-adjusted facial affect recognition accuracy scores predicted parent's overall rating of their child's social skills for both groups. This study supports the presence of facial affect recognition deficits in FHR children. Importantly, as the first known study to suggest the presence of these deficits in young, asymptomatic FHR children, it extends findings to a developmental stage predating symptoms. Further, findings point to a relationship between early emotion recognition and social skills. Improved characterisation of deficits in FHR children could inform early intervention.

Molecular recognition in protein modification with rhodium metallopeptides

PubMed Central

Ball, Zachary T.

2015-01-01

Chemical manipulation of natural, unengineered proteins is a daunting challenge which tests the limits of reaction design. By combining transition-metal or other catalysts with molecular recognition ideas, it is possible to achieve site-selective protein reactivity without the need for engineered recognition sequences or reactive sites. Some recent examples in this area have used ruthenium photocatalysis, pyridine organocatalysis, and rhodium(II) metallocarbene catalysis, indicating that the fundamental ideas provide opportunities for using diverse reactivity on complex protein substrates and in complex cell-like environments. PMID:25588960

Facial affect recognition deficit as a marker of genetic vulnerability to schizophrenia.

PubMed

Alfimova, Margarita V; Abramova, Lilia I; Barhatova, Aleksandra I; Yumatova, Polina E; Lyachenko, Galina L; Golimbet, Vera E

2009-05-01

The aim of this study was to investigate the possibility that affect recognition impairments are associated with genetic liability to schizophrenia. In a group of 55 unaffected relatives of schizophrenia patients (parents and siblings) we examined the capacity to detect facially expressed emotions and its relationship to schizotypal personality, neurocognitive functioning, and the subject's actual emotional state. The relatives were compared with 103 schizophrenia patients and 99 healthy subjects without any family history of psychoses. Emotional stimuli were nine black-and-white photos of actors, who portrayed six basic emotions as well as interest, contempt, and shame. The results evidenced the affect recognition deficit in relatives, though milder than that in patients themselves. No correlation between the deficit and schizotypal personality measured with SPQ was detected in the group of relatives. Neither cognitive functioning, including attention, verbal memory and linguistic ability, nor actual emotional states accounted for their affect recognition impairments. The results suggest that the facial affect recognition deficit in schizophrenia may be related to genetic predisposition to the disorder and may serve as an endophenotype in molecular-genetic studies.

Detection of possible restriction sites for type II restriction enzymes in DNA sequences.

PubMed

Gagniuc, P; Cimponeriu, D; Ionescu-Tîrgovişte, C; Mihai, Andrada; Stavarachi, Monica; Mihai, T; Gavrilă, L

2011-01-01

In order to make a step forward in the knowledge of the mechanism operating in complex polygenic disorders such as diabetes and obesity, this paper proposes a new algorithm (PRSD -possible restriction site detection) and its implementation in Applied Genetics software. This software can be used for in silico detection of potential (hidden) recognition sites for endonucleases and for nucleotide repeats identification. The recognition sites for endonucleases may result from hidden sequences through deletion or insertion of a specific number of nucleotides. Tests were conducted on DNA sequences downloaded from NCBI servers using specific recognition sites for common type II restriction enzymes introduced in the software database (n = 126). Each possible recognition site indicated by the PRSD algorithm implemented in Applied Genetics was checked and confirmed by NEBcutter V2.0 and Webcutter 2.0 software. In the sequence NG_008724.1 (which includes 63632 nucleotides) we found a high number of potential restriction sites for ECO R1 that may be produced by deletion (n = 43 sites) or insertion (n = 591 sites) of one nucleotide. The second module of Applied Genetics has been designed to find simple repeats sizes with a real future in understanding the role of SNPs (Single Nucleotide Polymorphisms) in the pathogenesis of the complex metabolic disorders. We have tested the presence of simple repetitive sequences in five DNA sequence. The software indicated exact position of each repeats detected in the tested sequences. Future development of Applied Genetics can provide an alternative for powerful tools used to search for restriction sites or repetitive sequences or to improve genotyping methods.

TALE-PvuII Fusion Proteins – Novel Tools for Gene Targeting

PubMed Central

Yanik, Mert; Alzubi, Jamal; Lahaye, Thomas; Cathomen, Toni; Pingoud, Alfred; Wende, Wolfgang

2013-01-01

Zinc finger nucleases (ZFNs) consist of zinc fingers as DNA-binding module and the non-specific DNA-cleavage domain of the restriction endonuclease FokI as DNA-cleavage module. This architecture is also used by TALE nucleases (TALENs), in which the DNA-binding modules of the ZFNs have been replaced by DNA-binding domains based on transcription activator like effector (TALE) proteins. Both TALENs and ZFNs are programmable nucleases which rely on the dimerization of FokI to induce double-strand DNA cleavage at the target site after recognition of the target DNA by the respective DNA-binding module. TALENs seem to have an advantage over ZFNs, as the assembly of TALE proteins is easier than that of ZFNs. Here, we present evidence that variant TALENs can be produced by replacing the catalytic domain of FokI with the restriction endonuclease PvuII. These fusion proteins recognize only the composite recognition site consisting of the target site of the TALE protein and the PvuII recognition sequence (addressed site), but not isolated TALE or PvuII recognition sites (unaddressed sites), even at high excess of protein over DNA and long incubation times. In vitro, their preference for an addressed over an unaddressed site is > 34,000-fold. Moreover, TALE-PvuII fusion proteins are active in cellula with minimal cytotoxicity. PMID:24349308

Theory of Mind, Emotion Recognition and Social Perception in Individuals at Clinical High Risk for Psychosis: findings from the NAPLS-2 cohort.

PubMed

Barbato, Mariapaola; Liu, Lu; Cadenhead, Kristin S; Cannon, Tyrone D; Cornblatt, Barbara A; McGlashan, Thomas H; Perkins, Diana O; Seidman, Larry J; Tsuang, Ming T; Walker, Elaine F; Woods, Scott W; Bearden, Carrie E; Mathalon, Daniel H; Heinssen, Robert; Addington, Jean

2015-09-01

Social cognition, the mental operations that underlie social interactions, is a major construct to investigate in schizophrenia. Impairments in social cognition are present before the onset of psychosis, and even in unaffected first-degree relatives, suggesting that social cognition may be a trait marker of the illness. In a large cohort of individuals at clinical high risk for psychosis (CHR) and healthy controls, three domains of social cognition (theory of mind, facial emotion recognition and social perception) were assessed to clarify which domains are impaired in this population. Six-hundred and seventy-five CHR individuals and 264 controls, who were part of the multi-site North American Prodromal Longitudinal Study, completed The Awareness of Social Inference Test , the Penn Emotion Recognition task , the Penn Emotion Differentiation task , and the Relationship Across Domains , measures of theory of mind, facial emotion recognition, and social perception, respectively. Social cognition was not related to positive and negative symptom severity, but was associated with age and IQ. CHR individuals demonstrated poorer performance on all measures of social cognition. However, after controlling for age and IQ, the group differences remained significant for measures of theory of mind and social perception, but not for facial emotion recognition. Theory of mind and social perception are impaired in individuals at CHR for psychosis. Age and IQ seem to play an important role in the arising of deficits in facial affect recognition. Future studies should examine the stability of social cognition deficits over time and their role, if any, in the development of psychosis.

Protein Surface Structural Recognition in Inactive Areas: A New Immobilization Strategy for Acetylcholinesterase.

PubMed

Diao, Jianxiong; Yu, Xiaolu; Ma, Lin; Li, Yuanqing; Sun, Ying

2018-05-16

This work reported a new method of design for the immobilization of acetylcholinesterase (AChE) based on its molecular structure to improve its sensitivity and stability. The immobilization binding site on the surface of AChE was determined using MOLCAD's multi-channel functionality. Then, 11 molecules ((+)-catechin, (-)-epicatechin, (-)-gallocatechin, hesperetin, naringenin, quercetin, taxifolin, (-)-epicatechin gallate, flupirtine, atropine, and hyoscyamine) were selected from the ZINC database (about 50 000 molecules) as candidate affinity ligands for AChE. The fluorescence results showed that the binding constant K b between AChE and the ligands ranged from 0.01344 × 10 4 to 4.689 × 10 4 M -1 and there was one independent class of binding site for the ligands on AChE. The AChE-ligand binding free energy ranged from -12.14 to -26.65 kJ mol -1 . Naringenin, hesperetin, and quercetin were the three most potent immobilized affinity ligands. In addition, it was confirmed that the binding between the immobilized ligands only occurred at a single site, located in an inactive area on the surface of AChE, and did not affect the enzymatic activity as shown through a competition experiment and enzyme assay. This method based on protein surface structural recognition with high sensitivity and stability can be used as a generic approach for design of the enzyme immobilization and biosensor development.

Antibody Light-Chain-Restricted Recognition of the Site of Immune Pressure in the RV144 HIV-1 Vaccine Trial Is Phylogenetically Conserved

DOE PAGES

Wiehe, Kevin; Easterhoff, David; Luo, Kan; ...

2014-11-29

In HIV-1, the ability to mount antibody responses to conserved, neutralizing epitopes is critical for protection. Here we have studied the light chain usage of human and rhesus macaque antibodies targeted to a dominant region of the HIV-1 envelope second variable (V2) region involving lysine (K) 169, the site of immune pressure in the RV144 vaccine efficacy trial. We found that humans and rhesus macaques used orthologous lambda variable gene segments encoding a glutamic acid-aspartic acid (ED) motif for K169 recognition. Structure determination of an unmutated ancestor antibody demonstrated that the V2 binding site was preconfigured for ED motif-mediated recognitionmore » prior to maturation. Thus, light chain usage for recognition of the site of immune pressure in the RV144 trial is highly conserved across species. In conclusion, these data indicate that the HIV-1 K169-recognizing ED motif has persisted over the diversification between rhesus macaques and humans, suggesting an evolutionary advantage of this antibody recognition mode.« less

Antibody Light-Chain-Restricted Recognition of the Site of Immune Pressure in the RV144 HIV-1 Vaccine Trial Is Phylogenetically Conserved

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

Wiehe, Kevin; Easterhoff, David; Luo, Kan

In HIV-1, the ability to mount antibody responses to conserved, neutralizing epitopes is critical for protection. Here we have studied the light chain usage of human and rhesus macaque antibodies targeted to a dominant region of the HIV-1 envelope second variable (V2) region involving lysine (K) 169, the site of immune pressure in the RV144 vaccine efficacy trial. We found that humans and rhesus macaques used orthologous lambda variable gene segments encoding a glutamic acid-aspartic acid (ED) motif for K169 recognition. Structure determination of an unmutated ancestor antibody demonstrated that the V2 binding site was preconfigured for ED motif-mediated recognitionmore » prior to maturation. Thus, light chain usage for recognition of the site of immune pressure in the RV144 trial is highly conserved across species. In conclusion, these data indicate that the HIV-1 K169-recognizing ED motif has persisted over the diversification between rhesus macaques and humans, suggesting an evolutionary advantage of this antibody recognition mode.« less

Long range dynamic effects of point-mutations trap a response regulator in an active conformation

PubMed Central

Bobay, Benjamin G.; Thompson, Richele J.; Hoch, James A.; Cavanagh, John

2010-01-01

When a point-mutation in a protein elicits a functional change, it is most common to assign this change to local structural perturbations. Here we show that point-mutations, distant from an essential highly dynamic kinase recognition loop in the response regulator Spo0F, lock this loop in an active conformation. This ‘conformational trapping’ results in functionally hyperactive Spo0F. Consequently, point-mutations are seen to affect functionally critical motions both close to and far from the mutational site. PMID:20828564

In-vitro and in-vivo phenotype of type Asia 1 foot-and-mouth disease viruses utilizing two non-RGD receptor recognition sites

PubMed Central

2011-01-01

Background Foot-and-mouth disease virus (FMDV) uses a highly conserved Arg-Gly-Asp (RGD) triplet for attachment to host cells and this motif is believed to be essential for virus viability. Previous sequence analyses of the 1D-encoding region of an FMDV field isolate (Asia1/JS/CHA/05) and its two derivatives indicated that two viruses, which contained an Arg-Asp-Asp (RDD) or an Arg-Ser-Asp (RSD) triplet instead of the RGD integrin recognition motif, were generated serendipitously upon short-term evolution of field isolate in different biological environments. To examine the influence of single amino acid substitutions in the receptor binding site of the RDD-containing FMD viral genome on virus viability and the ability of non-RGD FMDVs to cause disease in susceptible animals, we constructed an RDD-containing FMDV full-length cDNA clone and derived mutant molecules with RGD or RSD receptor recognition motifs. Following transfection of BSR cells with the full-length genome plasmids, the genetically engineered viruses were examined for their infectious potential in cell culture and susceptible animals. Results Amino acid sequence analysis of the 1D-coding region of different derivatives derived from the Asia1/JS/CHA/05 field isolate revealed that the RDD mutants became dominant or achieved population equilibrium with coexistence of the RGD and RSD subpopulations at an early phase of type Asia1 FMDV quasispecies evolution. Furthermore, the RDD and RSD sequences remained genetically stable for at least 20 passages. Using reverse genetics, the RDD-, RSD-, and RGD-containing FMD viruses were rescued from full-length cDNA clones, and single amino acid substitution in RDD-containing FMD viral genome did not affect virus viability. The genetically engineered viruses replicated stably in BHK-21 cells and had similar growth properties to the parental virus. The RDD parental virus and two non-RGD recombinant viruses were virulent to pigs and bovines that developed typical clinical disease and viremia. Conclusions FMDV quasispecies evolving in a different biological environment gained the capability of selecting different receptor recognition site. The RDD-containing FMD viral genome can accommodate substitutions in the receptor binding site without additional changes in the capsid. The viruses expressing non-RGD receptor binding sites can replicate stably in vitro and produce typical FMD clinical disease in susceptible animals. PMID:21711567

A Method to Recognize Anatomical Site and Image Acquisition View in X-ray Images.

PubMed

Chang, Xiao; Mazur, Thomas; Li, H Harold; Yang, Deshan

2017-12-01

A method was developed to recognize anatomical site and image acquisition view automatically in 2D X-ray images that are used in image-guided radiation therapy. The purpose is to enable site and view dependent automation and optimization in the image processing tasks including 2D-2D image registration, 2D image contrast enhancement, and independent treatment site confirmation. The X-ray images for 180 patients of six disease sites (the brain, head-neck, breast, lung, abdomen, and pelvis) were included in this study with 30 patients each site and two images of orthogonal views each patient. A hierarchical multiclass recognition model was developed to recognize general site first and then specific site. Each node of the hierarchical model recognized the images using a feature extraction step based on principal component analysis followed by a binary classification step based on support vector machine. Given two images in known orthogonal views, the site recognition model achieved a 99% average F1 score across the six sites. If the views were unknown in the images, the average F1 score was 97%. If only one image was taken either with or without view information, the average F1 score was 94%. The accuracy of the site-specific view recognition models was 100%.

Affect recognition and the quality of mother-infant interaction: understanding parenting difficulties in mothers with schizophrenia.

PubMed

Healy, Sarah J; Lewin, Jona; Butler, Stephen; Vaillancourt, Kyla; Seth-Smith, Fiona

2016-02-01

This study investigated the quality of mother-infant interaction and maternal ability to recognise adult affect in three study groups consisting of mothers with a diagnosis of schizophrenia, mothers with depression and healthy controls. Sixty-four mothers were recruited from a Mother and Baby Unit and local children's centres. A 5-min mother-infant interaction was coded on a number of caregiving variables. Affect recognition and discrimination abilities were tested via a series of computerised tasks. Group differences were found both in measures of affect recognition and in the mother-infant interaction. Mothers with schizophrenia showed consistent impairments across most of the parenting measures and all measures of affect recognition and discrimination. Mothers with depression fell between the mothers with schizophrenia and healthy controls on most measures. However, depressed women's parenting was not significantly poorer than controls on any of the measures, and only showed trends for differences with mothers with schizophrenia on a few measures. Regression analyses found impairments in affect recognition and a diagnosis of schizophrenia to predict the occurrence of odd or unusual speech in the mother-infant interaction. Results add to the growing body of knowledge on the mother-infant interaction in mothers with schizophrenia and mothers with depression compared to healthy controls, suggesting a need for parenting interventions aimed at mothers with these conditions. While affect recognition impairments were not found to fully explain differences in parenting among women with schizophrenia, further research is needed to understand the psychopathology of parenting disturbances within this clinical group.

Glycosylation at Asn91 of H1N1 haemagglutinin affects binding to glycan receptors

PubMed Central

Jayaraman, Akila; Koh, Xiaoying; Li, Jing; Raman, Rahul; Viswanathan, Karthik; Shriver, Zachary; Sasisekharan, Ram

2012-01-01

The glycoprotein HA (haemagglutinin) on the surface of influenza A virus plays a central role in recognition and binding to specific host cell-surface glycan receptors and in fusion of viral membrane to the host nuclear membrane during viral replication. Given the abundance of HA on the viral surface, this protein is also the primary target for host innate and adaptive immune responses. Although addition of glycosylation sites on HA are a part of viral evolution to evade the host immune responses, there are specific glycosylation sites that are conserved during most of the evolution of the virus. In the present study, it was demonstrated that one such conserved glycosylation site at Asn91 in H1N1 HA critically governs the glycan receptor-binding specificity and hence would potentially impinge on the host adaptation of the virus. PMID:22642577

Glycosylation at Asn91 of H1N1 haemagglutinin affects binding to glycan receptors.

PubMed

Jayaraman, Akila; Koh, Xiaoying; Li, Jing; Raman, Rahul; Viswanathan, Karthik; Shriver, Zachary; Sasisekharan, Ram

2012-06-15

The glycoprotein HA (haemagglutinin) on the surface of influenza A virus plays a central role in recognition and binding to specific host cell-surface glycan receptors and in fusion of viral membrane to the host nuclear membrane during viral replication. Given the abundance of HA on the viral surface, this protein is also the primary target for host innate and adaptive immune responses. Although addition of glycosylation sites on HA are a part of viral evolution to evade the host immune responses, there are specific glycosylation sites that are conserved during most of the evolution of the virus. In the present study, it was demonstrated that one such conserved glycosylation site at Asn(91) in H1N1 HA critically governs the glycan receptor-binding specificity and hence would potentially impinge on the host adaptation of the virus.

ACCA phosphopeptide recognition by the BRCT repeats of BRCA1.

PubMed

Ray, Hind; Moreau, Karen; Dizin, Eva; Callebaut, Isabelle; Venezia, Nicole Dalla

2006-06-16

The tumour suppressor gene BRCA1 encodes a 220 kDa protein that participates in multiple cellular processes. The BRCA1 protein contains a tandem of two BRCT repeats at its carboxy-terminal region. The majority of disease-associated BRCA1 mutations affect this region and provide to the BRCT repeats a central role in the BRCA1 tumour suppressor function. The BRCT repeats have been shown to mediate phospho-dependant protein-protein interactions. They recognize phosphorylated peptides using a recognition groove that spans both BRCT repeats. We previously identified an interaction between the tandem of BRCA1 BRCT repeats and ACCA, which was disrupted by germ line BRCA1 mutations that affect the BRCT repeats. We recently showed that BRCA1 modulates ACCA activity through its phospho-dependent binding to ACCA. To delineate the region of ACCA that is crucial for the regulation of its activity by BRCA1, we searched for potential phosphorylation sites in the ACCA sequence that might be recognized by the BRCA1 BRCT repeats. Using sequence analysis and structure modelling, we proposed the Ser1263 residue as the most favourable candidate among six residues, for recognition by the BRCA1 BRCT repeats. Using experimental approaches, such as GST pull-down assay with Bosc cells, we clearly showed that phosphorylation of only Ser1263 was essential for the interaction of ACCA with the BRCT repeats. We finally demonstrated by immunoprecipitation of ACCA in cells, that the whole BRCA1 protein interacts with ACCA when phosphorylated on Ser1263.

Acute effects of delta-9-tetrahydrocannabinol, cannabidiol and their combination on facial emotion recognition: a randomised, double-blind, placebo-controlled study in cannabis users.

PubMed

Hindocha, Chandni; Freeman, Tom P; Schafer, Grainne; Gardener, Chelsea; Das, Ravi K; Morgan, Celia J A; Curran, H Valerie

2015-03-01

Acute administration of the primary psychoactive constituent of cannabis, Δ-9-tetrahydrocannabinol (THC), impairs human facial affect recognition, implicating the endocannabinoid system in emotional processing. Another main constituent of cannabis, cannabidiol (CBD), has seemingly opposite functional effects on the brain. This study aimed to determine the effects of THC and CBD, both alone and in combination on emotional facial affect recognition. 48 volunteers, selected for high and low frequency of cannabis use and schizotypy, were administered, THC (8mg), CBD (16mg), THC+CBD (8mg+16mg) and placebo, by inhalation, in a 4-way, double-blind, placebo-controlled crossover design. They completed an emotional facial affect recognition task including fearful, angry, happy, sad, surprise and disgust faces varying in intensity from 20% to 100%. A visual analogue scale (VAS) of feeling 'stoned' was also completed. In comparison to placebo, CBD improved emotional facial affect recognition at 60% emotional intensity; THC was detrimental to the recognition of ambiguous faces of 40% intensity. The combination of THC+CBD produced no impairment. Relative to placebo, both THC alone and combined THC+CBD equally increased feelings of being 'stoned'. CBD did not influence feelings of 'stoned'. No effects of frequency of use or schizotypy were found. In conclusion, CBD improves recognition of emotional facial affect and attenuates the impairment induced by THC. This is the first human study examining the effects of different cannabinoids on emotional processing. It provides preliminary evidence that different pharmacological agents acting upon the endocannabinoid system can both improve and impair recognition of emotional faces. Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.

Acute effects of delta-9-tetrahydrocannabinol, cannabidiol and their combination on facial emotion recognition: A randomised, double-blind, placebo-controlled study in cannabis users

PubMed Central

Hindocha, Chandni; Freeman, Tom P.; Schafer, Grainne; Gardener, Chelsea; Das, Ravi K.; Morgan, Celia J.A.; Curran, H. Valerie

2015-01-01

Acute administration of the primary psychoactive constituent of cannabis, Δ-9-tetrahydrocannabinol (THC), impairs human facial affect recognition, implicating the endocannabinoid system in emotional processing. Another main constituent of cannabis, cannabidiol (CBD), has seemingly opposite functional effects on the brain. This study aimed to determine the effects of THC and CBD, both alone and in combination on emotional facial affect recognition. 48 volunteers, selected for high and low frequency of cannabis use and schizotypy, were administered, THC (8 mg), CBD (16 mg), THC+CBD (8 mg+16 mg) and placebo, by inhalation, in a 4-way, double-blind, placebo-controlled crossover design. They completed an emotional facial affect recognition task including fearful, angry, happy, sad, surprise and disgust faces varying in intensity from 20% to 100%. A visual analogue scale (VAS) of feeling ‘stoned’ was also completed. In comparison to placebo, CBD improved emotional facial affect recognition at 60% emotional intensity; THC was detrimental to the recognition of ambiguous faces of 40% intensity. The combination of THC+CBD produced no impairment. Relative to placebo, both THC alone and combined THC+CBD equally increased feelings of being ‘stoned’. CBD did not influence feelings of ‘stoned’. No effects of frequency of use or schizotypy were found. In conclusion, CBD improves recognition of emotional facial affect and attenuates the impairment induced by THC. This is the first human study examining the effects of different cannabinoids on emotional processing. It provides preliminary evidence that different pharmacological agents acting upon the endocannabinoid system can both improve and impair recognition of emotional faces. PMID:25534187

Oral lichen planus.

PubMed

Olson, Meredith A; Rogers, Roy S; Bruce, Alison J

2016-01-01

Lichen planus is an inflammatory mucocutaneous disease that can affect the skin, hair, nails, and mucosal surfaces. Mucosal sites of involvement include oral, genital, ocular, otic, esophageal, and, less commonly, bladder, nasal, laryngeal, and anal surfaces. Oral lichen planus is a mucosal variant of lichen planus, which tends to affect women more often than men, with a typically more chronic course and potential for significant morbidity. Treatment can be challenging, and there is potentially a low risk of malignant transformation; however, therapeutic benefits can be obtained with various topical and systemic medications. Clinical monitoring is recommended to ensure symptomatic control. Increasing awareness and recognition of this entity have continued to fuel advances in therapy and in our understanding of the disease. Copyright © 2016 Elsevier Inc. 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).

Insights into structural features of HDAC1 and its selectivity inhibition elucidated by Molecular dynamic simulation and Molecular Docking.

PubMed

Sixto-López, Yudibeth; Bello, Martiniano; Correa-Basurto, José

2018-03-06

Histone deacetylases (HDACs) are a family of proteins whose main function is the removal of acetyl groups from lysine residues located on histone and non-histone substrates, which regulates gene transcription and other activities in cells. HDAC1 dysfunction has been implicated in cancer development and progression; thus, its inhibition has emerged as a new therapeutic strategy. Two additional metal binding sites (Site 1 and Site 2) in HDACs have been described that are primarily occupied by potassium ions, suggesting a possible structural role that affects HDAC activity. In this work, we explored the structural role of potassium ions in Site 1 and Site 2 and how they affect the interactions of compounds with high affinities for HDAC1 (AC1OCG0B, Chlamydocin, Dacinostat and Quisinostat) and SAHA (a pan-inhibitor) using molecular docking and molecular dynamics (MD) simulations in concert with a Molecular-Mechanics-Generalized-Born-Surface-Area (MMGBSA) approach. Four models were generated: one with a potassium ion (K + ) in both sites (HDAC1 k ), a second with K + only at site 1 (HDAC1 ks1 ), a third with K + only at site 2 (HDAC1 ks2 ) and a fourth with no K + (HDAC1 wk ). We found that the presence or absence of K + not only impacted the structural flexibility of HDAC1, but also its molecular recognition, consistent with experimental findings. These results could therefore be useful for further structure-based drug design studies addressing new HDAC1 inhibitors.

Relationship between individual differences in functional connectivity and facial-emotion recognition abilities in adults with traumatic brain injury.

PubMed

Rigon, A; Voss, M W; Turkstra, L S; Mutlu, B; Duff, M C

2017-01-01

Although several studies have demonstrated that facial-affect recognition impairment is common following moderate-severe traumatic brain injury (TBI), and that there are diffuse alterations in large-scale functional brain networks in TBI populations, little is known about the relationship between the two. Here, in a sample of 26 participants with TBI and 20 healthy comparison participants (HC) we measured facial-affect recognition abilities and resting-state functional connectivity (rs-FC) using fMRI. We then used network-based statistics to examine (A) the presence of rs-FC differences between individuals with TBI and HC within the facial-affect processing network, and (B) the association between inter-individual differences in emotion recognition skills and rs-FC within the facial-affect processing network. We found that participants with TBI showed significantly lower rs-FC in a component comprising homotopic and within-hemisphere, anterior-posterior connections within the facial-affect processing network. In addition, within the TBI group, participants with higher emotion-labeling skills showed stronger rs-FC within a network comprised of intra- and inter-hemispheric bilateral connections. Findings indicate that the ability to successfully recognize facial-affect after TBI is related to rs-FC within components of facial-affective networks, and provide new evidence that further our understanding of the mechanisms underlying emotion recognition impairment in TBI.

Facial affect recognition in symptomatically remitted patients with schizophrenia and bipolar disorder.

PubMed

Yalcin-Siedentopf, Nursen; Hoertnagl, Christine M; Biedermann, Falko; Baumgartner, Susanne; Deisenhammer, Eberhard A; Hausmann, Armand; Kaufmann, Alexandra; Kemmler, Georg; Mühlbacher, Moritz; Rauch, Anna-Sophia; Fleischhacker, W Wolfgang; Hofer, Alex

2014-02-01

Both schizophrenia and bipolar disorder (BD) have consistently been associated with deficits in facial affect recognition (FAR). These impairments have been related to various aspects of social competence and functioning and are relatively stable over time. However, individuals in remission may outperform patients experiencing an acute phase of the disorders. The present study directly contrasted FAR in symptomatically remitted patients with schizophrenia or BD and healthy volunteers and investigated its relationship with patients' outcomes. Compared to healthy control subjects, schizophrenia patients were impaired in the recognition of angry, disgusted, sad and happy facial expressions, while BD patients showed deficits only in the recognition of disgusted and happy facial expressions. When directly comparing the two patient groups individuals suffering from BD outperformed those with schizophrenia in the recognition of expressions depicting anger. There was no significant association between affect recognition abilities and symptomatic or psychosocial outcomes in schizophrenia patients. Among BD patients, relatively higher depression scores were associated with impairments in both the identification of happy faces and psychosocial functioning. Overall, our findings indicate that during periods of symptomatic remission the recognition of facial affect may be less impaired in patients with BD than in those suffering from schizophrenia. However, in the psychosocial context BD patients seem to be more sensitive to residual symptomatology. Copyright © 2013 Elsevier B.V. All rights reserved.

Audio-visual affective expression recognition

NASA Astrophysics Data System (ADS)

Huang, Thomas S.; Zeng, Zhihong

2007-11-01

Automatic affective expression recognition has attracted more and more attention of researchers from different disciplines, which will significantly contribute to a new paradigm for human computer interaction (affect-sensitive interfaces, socially intelligent environments) and advance the research in the affect-related fields including psychology, psychiatry, and education. Multimodal information integration is a process that enables human to assess affective states robustly and flexibly. In order to understand the richness and subtleness of human emotion behavior, the computer should be able to integrate information from multiple sensors. We introduce in this paper our efforts toward machine understanding of audio-visual affective behavior, based on both deliberate and spontaneous displays. Some promising methods are presented to integrate information from both audio and visual modalities. Our experiments show the advantage of audio-visual fusion in affective expression recognition over audio-only or visual-only approaches.

Association of enhanced limbic response to threat with decreased cortical facial recognition memory response in schizophrenia

PubMed Central

Satterthwaite, Theodore D.; Wolf, Daniel H.; Loughead, James; Ruparel, Kosha; Valdez, Jeffrey N.; Siegel, Steven J.; Kohler, Christian G.; Gur, Raquel E.; Gur, Ruben C.

2014-01-01

Objective Recognition memory of faces is impaired in patients with schizophrenia, as is the neural processing of threat-related signals, but how these deficits interact to produce symptoms is unclear. Here we used an affective face recognition paradigm to examine possible interactions between cognitive and affective neural systems in schizophrenia. Methods fMRI (3T) BOLD response was examined in 21 controls and 16 patients during a two-choice recognition task using images of human faces. Each target face had previously been displayed with a threatening or non-threatening affect, but here were displayed with neutral affect. Responses to successful recognition and for the effect of previously threatening vs. non-threatening affect were evaluated, and correlations with total BPRS examined. Functional connectivity analyses examined the relationship between activation in the amygdala and cortical regions involved in recognition memory. Results Patients performed the task more slowly than controls. Controls recruited the expected cortical regions to a greater degree than patients, and patients with more severe symptoms demonstrated proportionally less recruitment. Increased symptoms were also correlated with augmented amygdala and orbitofrontal cortex response to threatening faces. Controls exhibited a negative correlation between activity in the amygdala and cortical regions involved in cognition, while patients showed a weakening of that relationship. Conclusions Increased symptoms were related to an enhanced threat response in limbic regions and a diminished recognition memory response in cortical regions, supporting a link between two brain systems often examined in isolation. This finding suggests that abnormal processing of threat-related signals in the environment may exacerbate cognitive impairment in schizophrenia. PMID:20194482

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.

Changes in exon–intron structure during vertebrate evolution affect the splicing pattern of exons

PubMed Central

Gelfman, Sahar; Burstein, David; Penn, Osnat; Savchenko, Anna; Amit, Maayan; Schwartz, Schraga; Pupko, Tal; Ast, Gil

2012-01-01

Exon–intron architecture is one of the major features directing the splicing machinery to the short exons that are located within long flanking introns. However, the evolutionary dynamics of exon–intron architecture and its impact on splicing is largely unknown. Using a comparative genomic approach, we analyzed 17 vertebrate genomes and reconstructed the ancestral motifs of both 3′ and 5′ splice sites, as also the ancestral length of exons and introns. Our analyses suggest that vertebrate introns increased in length from the shortest ancestral introns to the longest primate introns. An evolutionary analysis of splice sites revealed that weak splice sites act as a restrictive force keeping introns short. In contrast, strong splice sites allow recognition of exons flanked by long introns. Reconstruction of the ancestral state suggests these phenomena were not prevalent in the vertebrate ancestor, but appeared during vertebrate evolution. By calculating evolutionary rate shifts in exons, we identified cis-acting regulatory sequences that became fixed during the transition from early vertebrates to mammals. Experimental validations performed on a selection of these hexamers confirmed their regulatory function. We additionally revealed many features of exons that can discriminate alternative from constitutive exons. These features were integrated into a machine-learning approach to predict whether an exon is alternative. Our algorithm obtains very high predictive power (AUC of 0.91), and using these predictions we have identified and successfully validated novel alternatively spliced exons. Overall, we provide novel insights regarding the evolutionary constraints acting upon exons and their recognition by the splicing machinery. PMID:21974994

Affect Recognition in Adults with ADHD

ERIC Educational Resources Information Center

Miller, Meghan; Hanford, Russell B.; Fassbender, Catherine; Duke, Marshall; Schweitzer, Julie B.

2011-01-01

Objective: This study compared affect recognition abilities between adults with and without ADHD. Method: The sample consisted of 51 participants (34 men, 17 women) divided into 3 groups: ADHD-combined type (ADHD-C; n = 17), ADHD-predominantly inattentive type (ADHD-I; n = 16), and controls (n = 18). The mean age was 34 years. Affect recognition…

Predicting the Accuracy of Facial Affect Recognition: The Interaction of Child Maltreatment and Intellectual Functioning

ERIC Educational Resources Information Center

Shenk, Chad E.; Putnam, Frank W.; Noll, Jennie G.

2013-01-01

Previous research demonstrates that both child maltreatment and intellectual performance contribute uniquely to the accurate identification of facial affect by children and adolescents. The purpose of this study was to extend this research by examining whether child maltreatment affects the accuracy of facial recognition differently at varying…

Whole-transcriptome RNA-seq, gene set enrichment pathway analysis, and exon coverage analysis of two plastid RNA editing mutants.

PubMed

Hackett, Justin B; Lu, Yan

2017-05-04

In land plants, plastid and mitochondrial RNAs are subject to post-transcriptional C-to-U RNA editing. T-DNA insertions in the ORGANELLE RNA RECOGNITION MOTIF PROTEIN6 gene resulted in reduced photosystem II (PSII) activity and smaller plant and leaf sizes. Exon coverage analysis of the ORRM6 gene showed that orrm6-1 and orrm6-2 are loss-of-function mutants. Compared to other ORRM proteins, ORRM6 affects a relative small number of RNA editing sites. Sanger sequencing of reverse transcription-PCR products of plastid transcripts revealed 2 plastid RNA editing sites that are substantially affected in the orrm6 mutants: psbF-C77 and accD-C794. The psbF gene encodes the β subunit of cytochrome b 559 , an essential component of PSII. The accD gene encodes the β subunit of acetyl-CoA carboxylase, a protein required in plastid fatty acid biosynthesis. Whole-transcriptome RNA-seq demonstrated that editing at psbF-C77 is nearly absent and the editing extent at accD-C794 was significantly reduced. Gene set enrichment pathway analysis showed that expression of multiple gene sets involved in photosynthesis, especially photosynthetic electron transport, is significantly upregulated in both orrm6 mutants. The upregulation could be a mechanism to compensate for the reduced PSII electron transport rate in the orrm6 mutants. These results further demonstrated that Organelle RNA Recognition Motif protein ORRM6 is required in editing of specific RNAs in the Arabidopsis (Arabidopsis thaliana) plastid.

One recognition sequence, seven restriction enzymes, five reaction mechanisms

PubMed Central

Gowers, Darren M.; Bellamy, Stuart R.W.; Halford, Stephen E.

2004-01-01

The diversity of reaction mechanisms employed by Type II restriction enzymes was investigated by analysing the reactions of seven endonucleases at the same DNA sequence. NarI, KasI, Mly113I, SfoI, EgeI, EheI and BbeI cleave DNA at several different positions in the sequence 5′-GGCGCC-3′. Their reactions on plasmids with one or two copies of this sequence revealed five distinct mechanisms. These differ in terms of the number of sites the enzyme binds, and the number of phosphodiester bonds cleaved per turnover. NarI binds two sites, but cleaves only one bond per DNA-binding event. KasI also cuts only one bond per turnover but acts at individual sites, preferring intact to nicked sites. Mly113I cuts both strands of its recognition sites, but shows full activity only when bound to two sites, which are then cleaved concertedly. SfoI, EgeI and EheI cut both strands at individual sites, in the manner historically considered as normal for Type II enzymes. Finally, BbeI displays an absolute requirement for two sites in close physical proximity, which are cleaved concertedly. The range of reaction mechanisms for restriction enzymes is thus larger than commonly imagined, as is the number of enzymes needing two recognition sites. PMID:15226412

DEVELOPMENT OF A SAFETY COMMUNICATION AND RECOGNITION PROGRAM FOR CONSTRUCTION

PubMed Central

SPARER, EMILY H.; HERRICK, ROBERT F.; DENNERLEIN, JACK T.

2017-01-01

Leading-indicator–based (e.g., hazard recognition) incentive programs provide an alternative to controversial lagging-indicator–based (e.g., injury rates) programs. We designed a leading-indicator–based safety communication and recognition program that incentivized safe working conditions. The program was piloted for two months on a commercial construction worksite, and then redesigned using qualitative interview and focus group data from management and workers. We then ran the redesigned program for six months on the same worksite. Foremen received detailed weekly feedback from safety inspections, and posters displayed worksite and subcontractor safety scores. In the final program design, the whole site, not individual subcontractors, was the unit of analysis and recognition. This received high levels of acceptance from workers, who noted increased levels of site unity and team-building. This pilot program showed that construction workers value solidarity with others on site, demonstrating the importance of health and safety programs that engage all workers through a reliable and consistent communication infrastructure. PMID:25815741

Social-cognitive remediation in schizophrenia: generalization of effects of the Training of Affect Recognition (TAR).

PubMed

Wölwer, Wolfgang; Frommann, Nicole

2011-09-01

In the last decade, several social cognitive remediation programs have been developed for use in schizophrenia. Though existing evidence indicates that such programs can improve social cognition, which is essential for successful social functioning, it remains unclear whether the improvements generalize to social cognitive domains not primarily addressed by the intervention and whether the improved test performance transfers into everyday social functioning. The present study investigated whether, beyond its known effects on facial affect recognition, the Training of Affect Recognition (TAR) has effects on prosodic affect recognition, theory of mind (ToM) performance, social competence in a role-play task, and more general social and occupational functioning. Thirty-eight inpatients with a diagnosis of schizophrenia or schizoaffective disorder were randomly assigned to 6 weeks of treatment with the TAR--primarily targeted at facial affect recognition-or Cognitive Remediation Training (CRT)--primarily targeted at neurocognition. Intention-to-treat analyses found significantly larger pre-post improvements with TAR than with CRT in prosodic affect recognition, ToM, and social competence and a trend effect in global social functioning. However, the effects on ToM and social competence were no longer significant in the smaller group of patients who completed treatment according to protocol. Results suggest that TAR effects generalize to other social cognitive domains not primarily addressed. TAR may also enhance social skills and social functioning, although this has to be confirmed. Results are discussed with regard to the need to improve functional outcome in schizophrenia against the background of current evidence from other social cognitive remediation approaches.

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.

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

Transfer-Appropriate Processing in Recognition Memory: Perceptual and Conceptual Effects on Recognition Memory Depend on Task Demands

ERIC Educational Resources Information Center

Parks, Colleen M.

2013-01-01

Research examining the importance of surface-level information to familiarity in recognition memory tasks is mixed: Sometimes it affects recognition and sometimes it does not. One potential explanation of the inconsistent findings comes from the ideas of dual process theory of recognition and the transfer-appropriate processing framework, which…

A nonlinear heartbeat dynamics model approach for personalized emotion recognition.

PubMed

Valenza, Gaetano; Citi, Luca; Lanatà, Antonio; Scilingo, Enzo Pasquale; Barbieri, Riccardo

2013-01-01

Emotion recognition based on autonomic nervous system signs is one of the ambitious goals of affective computing. It is well-accepted that standard signal processing techniques require relative long-time series of multivariate records to ensure reliability and robustness of recognition and classification algorithms. In this work, we present a novel methodology able to assess cardiovascular dynamics during short-time (i.e. < 10 seconds) affective stimuli, thus overcoming some of the limitations of current emotion recognition approaches. We developed a personalized, fully parametric probabilistic framework based on point-process theory where heartbeat events are modelled using a 2(nd)-order nonlinear autoregressive integrative structure in order to achieve effective performances in short-time affective assessment. Experimental results show a comprehensive emotional characterization of 4 subjects undergoing a passive affective elicitation using a sequence of standardized images gathered from the international affective picture system. Each picture was identified by the IAPS arousal and valence scores as well as by a self-reported emotional label associating a subjective positive or negative emotion. Results show a clear classification of two defined levels of arousal, valence and self-emotional state using features coming from the instantaneous spectrum and bispectrum of the considered RR intervals, reaching up to 90% recognition accuracy.

Association of enhanced limbic response to threat with decreased cortical facial recognition memory response in schizophrenia.

PubMed

Satterthwaite, Theodore D; Wolf, Daniel H; Loughead, James; Ruparel, Kosha; Valdez, Jeffrey N; Siegel, Steven J; Kohler, Christian G; Gur, Raquel E; Gur, Ruben C

2010-04-01

Recognition memory of faces is impaired in patients with schizophrenia, as is the neural processing of threat-related signals, but how these deficits interact to produce symptoms is unclear. The authors used an affective face recognition paradigm to examine possible interactions between cognitive and affective neural systems in schizophrenia. Blood-oxygen-level-dependent response was examined by means of functional magnetic resonance imaging (3 Tesla) in healthy comparison subjects (N=21) and in patients with schizophrenia (N=12) or schizoaffective disorder, depressed type (N=4), during a two-choice recognition task that used images of human faces. Each target face, previously displayed with a threatening or nonthreatening affect, was displayed with neutral affect. Responses to successful recognition and responses to the effect of previously threatening versus nonthreatening affect were evaluated, and correlations with symptom severity (total Brief Psychiatric Rating Scale score) were examined. Functional connectivity analyses examined the relationship between activation in the amygdala and cortical regions involved in recognition memory. Patients performed the task more slowly than healthy comparison subjects. Comparison subjects recruited the expected cortical regions to a greater degree than patients, and patients with more severe symptoms demonstrated proportionally less recruitment. Increased symptoms were also correlated with augmented amygdala and orbitofrontal cortex response to threatening faces. Comparison subjects exhibited a negative correlation between activity in the amygdala and cortical regions involved in cognition, while patients showed weakening of this relationship. Increased symptoms were related to an enhanced threat response in limbic regions and a diminished recognition memory response in cortical regions, supporting a link between these two brain systems that are often examined in isolation. This finding suggests that abnormal processing of threat-related signals in the environment may exacerbate cognitive impairment in schizophrenia.

Identification of novel antibody-reactive detection sites for comprehensive gluten monitoring.

PubMed

Röckendorf, Niels; Meckelein, Barbara; Scherf, Katharina A; Schalk, Kathrin; Koehler, Peter; Frey, Andreas

2017-01-01

Certain cereals like wheat, rye or barley contain gluten, a protein mixture that can trigger celiac disease (CD). To make gluten-free diets available for affected individuals the gluten content of foodstuff must be monitored. For this purpose, antibody-based assays exist which rely on the recognition of certain linear gluten sequence motifs. Yet, not all CD-active gluten constituents and fragments formed during food processing/fermentation may be covered by those tests. In this study, we therefore assayed the coverage of reportedly CD-active gluten components by currently available detection antibodies and determined the antibody-inducing capacity of wheat gluten constituents in order to provide novel diagnostic targets for comprehensive gluten quantitation. Immunizations of outbred mice with purified gliadins and glutenins were conducted and the linear target recognition profile of the sera was recorded using synthetic peptide arrays that covered the sequence space of gluten constituents present in those preparations. The resulting murine immunorecognition profile of gluten demonstrated that further linear binding sites beyond those recognized by the monoclonal antibodies α20, R5 and G12 exist and may be exploitable as diagnostic targets. We conclude that the safety of foodstuffs for CD patients can be further improved by complementing current tests with antibodies directed against additional CD-active gluten components. Currently unrepresented linear gluten detection sites in glutenins and α-gliadins suggest sequences QQQYPS, PQQSFP, QPGQGQQG and QQPPFS as novel targets for antibody generation.

Access channels to the buried active site control substrate specificity in CYP1A P450 enzymes.

PubMed

Urban, Philippe; Truan, Gilles; Pompon, Denis

2015-04-01

A cytochrome P450 active site is buried within the protein molecule and several channels connect the catalytic cavity to the protein surface. Their role in P450 catalysis is still matter of debate. The aim of this study was to understand the possible relations existing between channels and substrate specificity. Time course studies were carried out with a collection of polycyclic substrates of increasing sizes assayed with a library of wild-type and chimeric CYP1A enzymes. This resulted in a matrix of activities sufficiently large to allow statistical analysis. Multivariate statistical tools were used to decipher the correlation between observed activity shifts and sequence segment swaps. The global kinetic behavior of CYP1A enzymes toward polycyclic substrates is significantly different depending on the size of the substrate. Mutations which are close or lining the P450 channels significantly affect this discrimination, whereas mutations distant from the P450 channels do not. Size discrimination is taking place for polycyclic substrates at the entrance of the different P450 access channels. It is thus hypothesized that channels differentiate small from large substrates in CYP1A enzymes, implying that residues located at the surface of the protein may be implied in this differential recognition. Catalysis thus occurs after a two-step recognition process, one at the surface of the protein and the second within the catalytic cavity in enzymes with a buried active site. Copyright © 2014 Elsevier B.V. All rights reserved.

Identification of novel antibody-reactive detection sites for comprehensive gluten monitoring

PubMed Central

Röckendorf, Niels; Meckelein, Barbara; Scherf, Katharina A.; Schalk, Kathrin; Koehler, Peter

2017-01-01

Certain cereals like wheat, rye or barley contain gluten, a protein mixture that can trigger celiac disease (CD). To make gluten-free diets available for affected individuals the gluten content of foodstuff must be monitored. For this purpose, antibody-based assays exist which rely on the recognition of certain linear gluten sequence motifs. Yet, not all CD-active gluten constituents and fragments formed during food processing/fermentation may be covered by those tests. In this study, we therefore assayed the coverage of reportedly CD-active gluten components by currently available detection antibodies and determined the antibody-inducing capacity of wheat gluten constituents in order to provide novel diagnostic targets for comprehensive gluten quantitation. Immunizations of outbred mice with purified gliadins and glutenins were conducted and the linear target recognition profile of the sera was recorded using synthetic peptide arrays that covered the sequence space of gluten constituents present in those preparations. The resulting murine immunorecognition profile of gluten demonstrated that further linear binding sites beyond those recognized by the monoclonal antibodies α20, R5 and G12 exist and may be exploitable as diagnostic targets. We conclude that the safety of foodstuffs for CD patients can be further improved by complementing current tests with antibodies directed against additional CD-active gluten components. Currently unrepresented linear gluten detection sites in glutenins and α-gliadins suggest sequences QQQYPS, PQQSFP, QPGQGQQG and QQPPFS as novel targets for antibody generation. PMID:28759621

Structural analysis of DNA binding by C.Csp231I, a member of a novel class of R-M controller proteins regulating gene expression

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

Shevtsov, M. B.; Streeter, S. D.; Thresh, S.-J.

2015-02-01

The structure of the new class of controller proteins (exemplified by C.Csp231I) in complex with its 21 bp DNA-recognition sequence is presented, and the molecular basis of sequence recognition in this class of proteins is discussed. An unusual extended spacer between the dimer binding sites suggests a novel interaction between the two C-protein dimers. In a wide variety of bacterial restriction–modification systems, a regulatory ‘controller’ protein (or C-protein) is required for effective transcription of its own gene and for transcription of the endonuclease gene found on the same operon. We have recently turned our attention to a new class ofmore » controller proteins (exemplified by C.Csp231I) that have quite novel features, including a much larger DNA-binding site with an 18 bp (∼60 Å) spacer between the two palindromic DNA-binding sequences and a very different recognition sequence from the canonical GACT/AGTC. Using X-ray crystallography, the structure of the protein in complex with its 21 bp DNA-recognition sequence was solved to 1.8 Å resolution, and the molecular basis of sequence recognition in this class of proteins was elucidated. An unusual aspect of the promoter sequence is the extended spacer between the dimer binding sites, suggesting a novel interaction between the two C-protein dimers when bound to both recognition sites correctly spaced on the DNA. A U-bend model is proposed for this tetrameric complex, based on the results of gel-mobility assays, hydrodynamic analysis and the observation of key contacts at the interface between dimers in the crystal.« less

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.

High Fractional Occupancy of a Tandem Maf Recognition Element and Its Role in Long-Range β-Globin Gene Regulation

PubMed Central

Stees, Jared R.; Hossain, Mir A.; Sunose, Tomoki; Kudo, Yasushi; Pardo, Carolina E.; Nabilsi, Nancy H.; Darst, Russell P.; Poudyal, Rosha; Igarashi, Kazuhiko; Kladde, Michael P.

2015-01-01

Enhancers and promoters assemble protein complexes that ultimately regulate the recruitment and activity of RNA polymerases. Previous work has shown that at least some enhancers form stable protein complexes, leading to the formation of enhanceosomes. We analyzed protein-DNA interactions in the murine β-globin gene locus using the methyltransferase accessibility protocol for individual templates (MAPit). The data show that a tandem Maf recognition element (MARE) in locus control region (LCR) hypersensitive site 2 (HS2) reveals a remarkably high degree of occupancy during differentiation of mouse erythroleukemia cells. Most of the other transcription factor binding sites in LCR HS2 or in the adult β-globin gene promoter regions exhibit low fractional occupancy, suggesting highly dynamic protein-DNA interactions. Targeting of an artificial zinc finger DNA-binding domain (ZF-DBD) to the HS2 tandem MARE caused a reduction in the association of MARE-binding proteins and transcription complexes at LCR HS2 and the adult βmajor-globin gene promoter but did not affect expression of the βminor-globin gene. The data demonstrate that a stable MARE-associated footprint in LCR HS2 is important for the recruitment of transcription complexes to the adult βmajor-globin gene promoter during erythroid cell differentiation. PMID:26503787

Emotional dampening in persons with elevated blood pressure: affect dysregulation and risk for hypertension.

PubMed

McCubbin, James A; Loveless, James P; Graham, Jack G; Hall, Gabrielle A; Bart, Ryan M; Moore, DeWayne D; Merritt, Marcellus M; Lane, Richard D; Thayer, Julian F

2014-02-01

Persons with higher blood pressure have emotional dampening in some contexts. This may reflect interactive changes in central nervous system control of affect and autonomic function in the early stages of hypertension development. The purpose of this study is to determine the independence of cardiovascular emotional dampening from alexithymia to better understand the role of affect dysregulation in blood pressure elevations. Ninety-six normotensives were assessed for resting systolic and diastolic (DBP) blood pressure, recognition of emotions in faces and sentences using the Perception of Affect Task (PAT), alexithymia, anxiety, and defensiveness. Resting DBP significantly predicted PAT emotion recognition accuracy in men after adjustment for age, self-reported affect, and alexithymia. Cardiovascular emotional dampening is independent of alexithymia and affect in men. Dampened emotion recognition could potentially influence interpersonal communication and psychosocial distress, thereby further contributing to BP dysregulation and increased cardiovascular risk.

Functional Characterization of the Role of the N-terminal Domain of the c/Nip1 Subunit of Eukaryotic Initiation Factor 3 (eIF3) in AUG Recognition*

PubMed Central

Karásková, Martina; Gunišová, Stanislava; Herrmannová, Anna; Wagner, Susan; Munzarová, Vanda; Valášek, Leoš Shivaya

2012-01-01

In eukaryotes, for a protein to be synthesized, the 40 S subunit has to first scan the 5′-UTR of the mRNA until it has encountered the AUG start codon. Several initiation factors that ensure high fidelity of AUG recognition were identified previously, including eIF1A, eIF1, eIF2, and eIF5. In addition, eIF3 was proposed to coordinate their functions in this process as well as to promote their initial binding to 40 S subunits. Here we subjected several previously identified segments of the N-terminal domain (NTD) of the eIF3c/Nip1 subunit, which mediates eIF3 binding to eIF1 and eIF5, to semirandom mutagenesis to investigate the molecular mechanism of eIF3 involvement in these reactions. Three major classes of mutant substitutions or internal deletions were isolated that affect either the assembly of preinitiation complexes (PICs), scanning for AUG, or both. We show that eIF5 binds to the extreme c/Nip1-NTD (residues 1–45) and that impairing this interaction predominantly affects the PIC formation. eIF1 interacts with the region (60–137) that immediately follows, and altering this contact deregulates AUG recognition. Together, our data indicate that binding of eIF1 to the c/Nip1-NTD is equally important for its initial recruitment to PICs and for its proper functioning in selecting the translational start site. PMID:22718758

Variola virus topoisomerase: DNA cleavage specificity and distribution of sites in Poxvirus genomes.

PubMed

Minkah, Nana; Hwang, Young; Perry, Kay; Van Duyne, Gregory D; Hendrickson, Robert; Lefkowitz, Elliot J; Hannenhalli, Sridhar; Bushman, Frederic D

2007-08-15

Topoisomerase enzymes regulate superhelical tension in DNA resulting from transcription, replication, repair, and other molecular transactions. Poxviruses encode an unusual type IB topoisomerase that acts only at conserved DNA sequences containing the core pentanucleotide 5'-(T/C)CCTT-3'. In X-ray structures of the variola virus topoisomerase bound to DNA, protein-DNA contacts were found to extend beyond the core pentanucleotide, indicating that the full recognition site has not yet been fully defined in functional studies. Here we report quantitation of DNA cleavage rates for an optimized 13 bp site and for all possible single base substitutions (40 total sites), with the goals of understanding the molecular mechanism of recognition and mapping topoisomerase sites in poxvirus genome sequences. The data allow a precise definition of enzyme-DNA interactions and the energetic contributions of each. We then used the resulting "action matrix" to show that favorable topoisomerase sites are distributed all along the length of poxvirus DNA sequences, consistent with a requirement for local release of superhelical tension in constrained topological domains. In orthopox genomes, an additional central cluster of sites was also evident. A negative correlation of predicted topoisomerase sites was seen relative to early terminators, but no correlation was seen with early or late promoters. These data define the full variola virus topoisomerase recognition site and provide a new window on topoisomerase function in vivo.

Re-evaluating the kinetics of ATP hydrolysis during initiation of DNA sliding by Type III restriction enzymes

PubMed Central

Tóth, Júlia; Bollins, Jack; Szczelkun, Mark D.

2015-01-01

DNA cleavage by the Type III restriction enzymes requires long-range protein communication between recognition sites facilitated by thermally-driven 1D diffusion. This ‘DNA sliding’ is initiated by hydrolysis of multiple ATPs catalysed by a helicase-like domain. Two distinct ATPase phases were observed using short oligoduplex substrates; the rapid consumption of ∼10 ATPs coupled to a protein conformation switch followed by a slower phase, the duration of which was dictated by the rate of dissociation from the recognition site. Here, we show that the second ATPase phase is both variable and only observable when DNA ends are proximal to the recognition site. On DNA with sites more distant from the ends, a single ATPase phase coupled to the conformation switch was observed and subsequent site dissociation required little or no further ATP hydrolysis. The overall DNA dissociation kinetics (encompassing site release, DNA sliding and escape via a DNA end) were not influenced by the second phase. Although the data simplifies the ATP hydrolysis scheme for Type III restriction enzymes, questions remain as to why multiple ATPs are hydrolysed to prepare for DNA sliding. PMID:26538601

Understanding the molecular differential recognition of muramyl peptide ligands by LRR domains of human NOD receptors.

PubMed

Vijayrajratnam, Sukhithasri; Pushkaran, Anju Choorakottayil; Balakrishnan, Aathira; Vasudevan, Anil Kumar; Biswas, Raja; Mohan, Chethampadi Gopi

2017-07-27

Human nucleotide-binding oligomerization domain proteins, hNOD1 and hNOD2, are host intracellular receptors with C-terminal leucine-rich repeat (LRR) domains, which recognize specific bacterial peptidoglycan (PG) fragments as their ligands. The specificity of this recognition is dependent on the third amino acid of the stem peptide of the PG ligand, which is usually meso -diaminopimelic acid ( meso DAP) or l-lysine (l-Lys). Since the LRR domains of hNOD receptors had been experimentally shown to confer the PG ligand-sensing specificity, we developed three-dimensional structures of hNOD1-LRR and the hNOD2-LRR to understand the mechanism of differential recognition of muramyl peptide ligands by hNOD receptors. The hNOD1-LRR and hNOD2-LRR receptor models exhibited right-handed curved solenoid shape. The hot-spot residues experimentally proved to be critical for ligand recognition were located in the concavity of the NOD-LRR and formed the recognition site. Our molecular docking analyses and molecular electrostatic potential mapping studies explain the activation of hNOD-LRRs, in response to effective molecular interactions of PG ligands at the recognition site; and conversely, the inability of certain PG ligands to activate hNOD-LRRs, by deviations from the recognition site. Based on molecular docking studies using PG ligands, we propose few residues - G825, D826 and N850 in hNOD1-LRR and L904, G905, W931, L932 and S933 in hNOD2-LRR, evolutionarily conserved across different host species, which may play a major role in ligand recognition. Thus, our integrated experimental and computational approach elucidates the molecular basis underlying the differential recognition of PG ligands by hNOD receptors. © 2017 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society.

The chemical structure of DNA sequence signals for RNA transcription

NASA Technical Reports Server (NTRS)

George, D. G.; Dayhoff, M. O.

1982-01-01

The proposed recognition sites for RNA transcription for E. coli NRA polymerase, bacteriophage T7 RNA polymerase, and eukaryotic RNA polymerase Pol II are evaluated in the light of the requirements for efficient recognition. It is shown that although there is good experimental evidence that specific nucleic acid sequence patterns are involved in transcriptional regulation in bacteria and bacterial viruses, among the sequences now available, only in the case of the promoters recognized by bacteriophage T7 polymerase does it seem likely that the pattern is sufficient. It is concluded that the eukaryotic pattern that is investigated is not restrictive enough to serve as a recognition site.

Cost-sensitive learning for emotion robust speaker recognition.

PubMed

Li, Dongdong; Yang, Yingchun; Dai, Weihui

2014-01-01

In the field of information security, voice is one of the most important parts in biometrics. Especially, with the development of voice communication through the Internet or telephone system, huge voice data resources are accessed. In speaker recognition, voiceprint can be applied as the unique password for the user to prove his/her identity. However, speech with various emotions can cause an unacceptably high error rate and aggravate the performance of speaker recognition system. This paper deals with this problem by introducing a cost-sensitive learning technology to reweight the probability of test affective utterances in the pitch envelop level, which can enhance the robustness in emotion-dependent speaker recognition effectively. Based on that technology, a new architecture of recognition system as well as its components is proposed in this paper. The experiment conducted on the Mandarin Affective Speech Corpus shows that an improvement of 8% identification rate over the traditional speaker recognition is achieved.

A preliminary analysis of human factors affecting the recognition accuracy of a discrete word recognizer for C3 systems

NASA Astrophysics Data System (ADS)

Yellen, H. W.

1983-03-01

Literature pertaining to Voice Recognition abounds with information relevant to the assessment of transitory speech recognition devices. In the past, engineering requirements have dictated the path this technology followed. But, other factors do exist that influence recognition accuracy. This thesis explores the impact of Human Factors on the successful recognition of speech, principally addressing the differences or variability among users. A Threshold Technology T-600 was used for a 100 utterance vocubalary to test 44 subjects. A statistical analysis was conducted on 5 generic categories of Human Factors: Occupational, Operational, Psychological, Physiological and Personal. How the equipment is trained and the experience level of the speaker were found to be key characteristics influencing recognition accuracy. To a lesser extent computer experience, time or week, accent, vital capacity and rate of air flow, speaker cooperativeness and anxiety were found to affect overall error rates.

Cost-Sensitive Learning for Emotion Robust Speaker Recognition

PubMed Central

Li, Dongdong; Yang, Yingchun

2014-01-01

In the field of information security, voice is one of the most important parts in biometrics. Especially, with the development of voice communication through the Internet or telephone system, huge voice data resources are accessed. In speaker recognition, voiceprint can be applied as the unique password for the user to prove his/her identity. However, speech with various emotions can cause an unacceptably high error rate and aggravate the performance of speaker recognition system. This paper deals with this problem by introducing a cost-sensitive learning technology to reweight the probability of test affective utterances in the pitch envelop level, which can enhance the robustness in emotion-dependent speaker recognition effectively. Based on that technology, a new architecture of recognition system as well as its components is proposed in this paper. The experiment conducted on the Mandarin Affective Speech Corpus shows that an improvement of 8% identification rate over the traditional speaker recognition is achieved. PMID:24999492

Transgenerational effects of maternal depression on affect recognition in children.

PubMed

Kluczniok, Dorothea; Hindi Attar, Catherine; Fydrich, Thomas; Fuehrer, Daniel; Jaite, Charlotte; Domes, Gregor; Winter, Sibylle; Herpertz, Sabine C; Brunner, Romuald; Boedeker, Katja; Bermpohl, Felix

2016-01-01

The association between maternal depression and adverse emotional and behavioral outcomes in children is well established. One associated factor might be altered affect recognition which may be transmitted transgenerationally. Individuals with history of depression show biased recognition of sadness. Our aim was to investigate parallels in maternal and children's affect recognition with remitted depressed mothers. 60 Mother-child dyads completed an affect recognition morphing task. We examined two groups of remitted depressed mothers, with and without history of physical or sexual abuse, and a group of healthy mothers without history of physical or sexual abuse. Children were between 5 and 12 years old. Across groups, mothers identified happy faces fastest. Mothers with remitted depression showed a higher accuracy and response bias for sadness. We found corresponding results in their children. Maternal and children's bias and accuracy for sadness were positively correlated. Effects of remitted depression were found independent of maternal history of physical or sexual abuse. Our sample size was relatively small and further longitudinal research is needed to investigate how maternal and children's affect recognition are associated with behavioral and emotional outcomes in the long term. Our data suggest a negative processing bias in mothers with remitted depression which might represent both the perpetuation of and vulnerability to depression. Children of remitted depressed mothers appear to be exposed to this processing bias outside acute depressive episodes. This may promote the development of a corresponding processing bias in the children and could make children of depressed mothers more vulnerable to depressive disorders themselves. Copyright © 2015 Elsevier B.V. All rights reserved.

Development of a safety communication and recognition program for construction.

PubMed

Sparer, Emily H; Herrick, Robert F; Dennerlein, Jack T

2015-05-01

Leading-indicator-based (e.g., hazard recognition) incentive programs provide an alternative to controversial lagging-indicator-based (e.g., injury rates) programs. We designed a leading-indicator-based safety communication and recognition program that incentivized safe working conditions. The program was piloted for two months on a commercial construction worksite and then redesigned using qualitative interview and focus group data from management and workers. We then ran the redesigned program for six months on the same worksite. Foremen received detailed weekly feedback from safety inspections, and posters displayed worksite and subcontractor safety scores. In the final program design, the whole site, not individual subcontractors, was the unit of analysis and recognition. This received high levels of acceptance from workers, who noted increased levels of site unity and team-building. This pilot program showed that construction workers value solidarity with others on site, demonstrating the importance of health and safety programs that engage all workers through a reliable and consistent communication infrastructure. © The Author(s) 2015 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

Molecular recognition principles and stationary-phase characteristics of topoisomer-selective chemoaffinity materials for chromatographic separation of circular plasmid DNA topoisomers.

PubMed

Mahut, Marek; Lindner, Wolfgang; Lämmerhofer, Michael

2012-01-18

We recently discovered the molecular recognition capability of a quinine carbamate ligand attached to silica as a powerful chemoaffinity material for the chromatographic separation of circular plasmid topoisomers of different linking numbers. In this paper we develop structure-selectivity relationship studies to figure out the essential structural features for topoisomer recognition. By varying different moieties of the original cinchonan-derived selector, it was shown that intercalation by the quinoline moiety of the ligand as assumed initially as the working hypothesis is not an essential feature for topoisomer recognition during chromatography. We found that the key elements for topoisomer selectivity are the presence of a rigid weak anion-exchange site and a H-donor site separated from each other in a defined distance by a 4-atom spacer. Additionally, incorporation of the weak anion-exchange site into a cyclic ring structure provides greater rigidity of the ligand molecule and turned out to be advantageous, if not mandatory, for (close to) baseline separation. © 2011 American Chemical Society

Does humor in radio advertising affect recognition of novel product brand names?

PubMed

Berg, E M; Lippman, L G

2001-04-01

The authors proposed that item selection during shopping is based on brand name recognition rather than recall. College students rated advertisements and news stories of a simulated radio program for level of amusement (orienting activity) before participating in a surprise recognition test. Humor level of the advertisements was varied systematically, and content was controlled. According to signal detection analysis, humor did not affect the strength of recognition memory for brand names (nonsense units). However, brand names and product types were significantly more likely to be associated when appearing in humorous advertisements than in nonhumorous advertisements. The results are compared with prior findings concerning humor and recall.

Magical ideation associated social cognition in adolescents: signs of a negative facial affect recognition deficit.

PubMed

Canli, Derya; Ozdemir, Hatice; Kocak, Orhan Murat

2015-08-01

Studies provide evidence for impaired social cognition in schizotypy and its association with negative symptoms. Cognitive features related to magical ideation - a component of the positive dimension of schizotypy - have been less investigated. We aimed to assess social cognitive functioning among adolescents with high magical ideation scores, mainly focusing on face and emotion recognition. 22 subjects with magical ideation scale scores above the cut off level and 22 controls with lowest scores from among 250 students screened with this scale were included in the study. A face and emotion recognition n-back test, the empathy quotient, theory of mind tests and the Physical Anhedonia Scale were applied to both magical ideation and control groups. The magical ideation group performed significantly worse than controls on both face and emotion recognition tests. Emotion recognition performance was found to be affected by memory load, with sadness, among emotions, revealing a difference between the two groups. Empathy and theory of mind tests did not distinguish the magical ideation group from controls. Our findings provide evidence for a deficit in negative emotion recognition affected by memory load associated with magical ideation in adolescents. Copyright © 2015 Elsevier Inc. All rights reserved.

Association of impaired facial affect recognition with basic facial and visual processing deficits in schizophrenia.

PubMed

Norton, Daniel; McBain, Ryan; Holt, Daphne J; Ongur, Dost; Chen, Yue

2009-06-15

Impaired emotion recognition has been reported in schizophrenia, yet the nature of this impairment is not completely understood. Recognition of facial emotion depends on processing affective and nonaffective facial signals, as well as basic visual attributes. We examined whether and how poor facial emotion recognition in schizophrenia is related to basic visual processing and nonaffective face recognition. Schizophrenia patients (n = 32) and healthy control subjects (n = 29) performed emotion discrimination, identity discrimination, and visual contrast detection tasks, where the emotionality, distinctiveness of identity, or visual contrast was systematically manipulated. Subjects determined which of two presentations in a trial contained the target: the emotional face for emotion discrimination, a specific individual for identity discrimination, and a sinusoidal grating for contrast detection. Patients had significantly higher thresholds (worse performance) than control subjects for discriminating both fearful and happy faces. Furthermore, patients' poor performance in fear discrimination was predicted by performance in visual detection and face identity discrimination. Schizophrenia patients require greater emotional signal strength to discriminate fearful or happy face images from neutral ones. Deficient emotion recognition in schizophrenia does not appear to be determined solely by affective processing but is also linked to the processing of basic visual and facial information.

Arousal Rather than Basic Emotions Influence Long-Term Recognition Memory in Humans

PubMed Central

Marchewka, Artur; Wypych, Marek; Moslehi, Abnoos; Riegel, Monika; Michałowski, Jarosław M.; Jednoróg, Katarzyna

2016-01-01

Emotion can influence various cognitive processes, however its impact on memory has been traditionally studied over relatively short retention periods and in line with dimensional models of affect. The present study aimed to investigate emotional effects on long-term recognition memory according to a combined framework of affective dimensions and basic emotions. Images selected from the Nencki Affective Picture System were rated on the scale of affective dimensions and basic emotions. After 6 months, subjects took part in a surprise recognition test during an fMRI session. The more negative the pictures the better they were remembered, but also the more false recognitions they provoked. Similar effects were found for the arousal dimension. Recognition success was greater for pictures with lower intensity of happiness and with higher intensity of surprise, sadness, fear, and disgust. Consecutive fMRI analyses showed a significant activation for remembered (recognized) vs. forgotten (not recognized) images in anterior cingulate and bilateral anterior insula as well as in bilateral caudate nuclei and right thalamus. Further, arousal was found to be the only subjective rating significantly modulating brain activation. Higher subjective arousal evoked higher activation associated with memory recognition in the right caudate and the left cingulate gyrus. Notably, no significant modulation was observed for other subjective ratings, including basic emotion intensities. These results emphasize the crucial role of arousal for long-term recognition memory and support the hypothesis that the memorized material, over time, becomes stored in a distributed cortical network including the core salience network and basal ganglia. PMID:27818626

Arousal Rather than Basic Emotions Influence Long-Term Recognition Memory in Humans.

PubMed

Marchewka, Artur; Wypych, Marek; Moslehi, Abnoos; Riegel, Monika; Michałowski, Jarosław M; Jednoróg, Katarzyna

2016-01-01

Emotion can influence various cognitive processes, however its impact on memory has been traditionally studied over relatively short retention periods and in line with dimensional models of affect. The present study aimed to investigate emotional effects on long-term recognition memory according to a combined framework of affective dimensions and basic emotions. Images selected from the Nencki Affective Picture System were rated on the scale of affective dimensions and basic emotions. After 6 months, subjects took part in a surprise recognition test during an fMRI session. The more negative the pictures the better they were remembered, but also the more false recognitions they provoked. Similar effects were found for the arousal dimension. Recognition success was greater for pictures with lower intensity of happiness and with higher intensity of surprise, sadness, fear, and disgust. Consecutive fMRI analyses showed a significant activation for remembered (recognized) vs. forgotten (not recognized) images in anterior cingulate and bilateral anterior insula as well as in bilateral caudate nuclei and right thalamus. Further, arousal was found to be the only subjective rating significantly modulating brain activation. Higher subjective arousal evoked higher activation associated with memory recognition in the right caudate and the left cingulate gyrus. Notably, no significant modulation was observed for other subjective ratings, including basic emotion intensities. These results emphasize the crucial role of arousal for long-term recognition memory and support the hypothesis that the memorized material, over time, becomes stored in a distributed cortical network including the core salience network and basal ganglia.

Affective and contextual values modulate spatial frequency use in object recognition

PubMed Central

Caplette, Laurent; West, Gregory; Gomot, Marie; Gosselin, Frédéric; Wicker, Bruno

2014-01-01

Visual object recognition is of fundamental importance in our everyday interaction with the environment. Recent models of visual perception emphasize the role of top-down predictions facilitating object recognition via initial guesses that limit the number of object representations that need to be considered. Several results suggest that this rapid and efficient object processing relies on the early extraction and processing of low spatial frequencies (LSF). The present study aimed to investigate the SF content of visual object representations and its modulation by contextual and affective values of the perceived object during a picture-name verification task. Stimuli consisted of pictures of objects equalized in SF content and categorized as having low or high affective and contextual values. To access the SF content of stored visual representations of objects, SFs of each image were then randomly sampled on a trial-by-trial basis. Results reveal that intermediate SFs between 14 and 24 cycles per object (2.3–4 cycles per degree) are correlated with fast and accurate identification for all categories of objects. Moreover, there was a significant interaction between affective and contextual values over the SFs correlating with fast recognition. These results suggest that affective and contextual values of a visual object modulate the SF content of its internal representation, thus highlighting the flexibility of the visual recognition system. PMID:24904514

Action Recognition in a Crowded Environment

PubMed Central

Nieuwenhuis, Judith; Bülthoff, Isabelle; Barraclough, Nick; de la Rosa, Stephan

2017-01-01

So far, action recognition has been mainly examined with small point-light human stimuli presented alone within a narrow central area of the observer’s visual field. Yet, we need to recognize the actions of life-size humans viewed alone or surrounded by bystanders, whether they are seen in central or peripheral vision. Here, we examined the mechanisms in central vision and far periphery (40° eccentricity) involved in the recognition of the actions of a life-size actor (target) and their sensitivity to the presence of a crowd surrounding the target. In Experiment 1, we used an action adaptation paradigm to probe whether static or idly moving crowds might interfere with the recognition of a target’s action (hug or clap). We found that this type of crowds whose movements were dissimilar to the target action hardly affected action recognition in central and peripheral vision. In Experiment 2, we examined whether crowd actions that were more similar to the target actions affected action recognition. Indeed, the presence of that crowd diminished adaptation aftereffects in central vision as wells as in the periphery. We replicated Experiment 2 using a recognition task instead of an adaptation paradigm. With this task, we found evidence of decreased action recognition accuracy, but this was significant in peripheral vision only. Our results suggest that the presence of a crowd carrying out actions similar to that of the target affects its recognition. We outline how these results can be understood in terms of high-level crowding effects that operate on action-sensitive perceptual channels. PMID:29308177

Individual differences in language and working memory affect children's speech recognition in noise.

PubMed

McCreery, Ryan W; Spratford, Meredith; Kirby, Benjamin; Brennan, Marc

2017-05-01

We examined how cognitive and linguistic skills affect speech recognition in noise for children with normal hearing. Children with better working memory and language abilities were expected to have better speech recognition in noise than peers with poorer skills in these domains. As part of a prospective, cross-sectional study, children with normal hearing completed speech recognition in noise for three types of stimuli: (1) monosyllabic words, (2) syntactically correct but semantically anomalous sentences and (3) semantically and syntactically anomalous word sequences. Measures of vocabulary, syntax and working memory were used to predict individual differences in speech recognition in noise. Ninety-six children with normal hearing, who were between 5 and 12 years of age. Higher working memory was associated with better speech recognition in noise for all three stimulus types. Higher vocabulary abilities were associated with better recognition in noise for sentences and word sequences, but not for words. Working memory and language both influence children's speech recognition in noise, but the relationships vary across types of stimuli. These findings suggest that clinical assessment of speech recognition is likely to reflect underlying cognitive and linguistic abilities, in addition to a child's auditory skills, consistent with the Ease of Language Understanding model.

PEG-stabilized core-shell surface-imprinted nanoparticles.

PubMed

Moczko, Ewa; Guerreiro, Antonio; Piletska, Elena; Piletsky, Sergey

2013-08-06

Here we present a simple technique to produce target-specific molecularly imprinted polymeric nanoparticles (MIP NPs) and their surface modification in order to prevent the aggregation process that is ever-present in most nanomaterial suspensions/dispersions. Specifically, we studied the influence of surface modification of MIP NPs with polymerizable poly(ethylene glycol) on their degree of stability in water, in phosphate buffer, and in the presence of serum proteins. Grafting a polymer shell on the surface of nanoparticles decreases the surface energy, enhances the polarity, and as a result improves the dispersibility, storage, and colloidal stability as compared to those of core (unmodified) particles. Because of the unique solid-phase approach used for synthesis, the binding sites of MIP NPs are protected during grafting, and the recognition properties of nanoparticles are not affected. These results are significant for developing nanomaterials with selective molecular recognition, increased biocompatibility, and stability in solution. Materials synthesized this way have the potential to be used in a variety of technological fields, including in vivo applications such as drug delivery and imaging.

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.

How Does Adult Attachment Affect Human Recognition of Love-related and Sex-related Stimuli: An ERP Study

PubMed Central

Hou, Juan; Chen, Xin; Liu, Jinqun; Yao, Fangshu; Huang, Jiani; Ndasauka, Yamikani; Ma, Ru; Zhang, Yuting; Lan, Jing; Liu, Lu; Fang, Xiaoyi

2016-01-01

In the present study, we investigated the relationship among three emotion-motivation systems (adult attachment, romantic love, and sex). We recorded event-related potentials in 37 healthy volunteers who had experienced romantic love while they viewed SEX, LOVE, FRIEND, SPORT, and NEUTRAL images. We also measured adult attachment styles, level of passionate love and sexual attitudes. As expected, results showed that, firstly, response to love-related image-stimuli and sex-related image-stimuli on the electrophysiological data significantly different on N1, N2, and positive slow wave (PSW) components. Secondly, the different adult attachment styles affected individuals’ recognition processing in response to love-related and sex-related images, especially, to sex-related images. Further analysis showed that voltages elicited by fearful attachment style individuals were significantly lower than voltages elicited by secure and dismissing attachment style individuals on sex-related images at frontal sites, on N1 and N2 components. Thirdly, from behavior data, we found that adult attachment styles were not significantly related to any dimension of sexual attitudes but were significantly related to passionate love scale (PLS) total points. Thus, the behavior results were not in line with the electrophysiological results. The present study proved that adult attachment styles might mediate individuals’ lust and attraction systems. PMID:27199830

How Does Adult Attachment Affect Human Recognition of Love-related and Sex-related Stimuli: An ERP Study.

PubMed

Hou, Juan; Chen, Xin; Liu, Jinqun; Yao, Fangshu; Huang, Jiani; Ndasauka, Yamikani; Ma, Ru; Zhang, Yuting; Lan, Jing; Liu, Lu; Fang, Xiaoyi

2016-01-01

In the present study, we investigated the relationship among three emotion-motivation systems (adult attachment, romantic love, and sex). We recorded event-related potentials in 37 healthy volunteers who had experienced romantic love while they viewed SEX, LOVE, FRIEND, SPORT, and NEUTRAL images. We also measured adult attachment styles, level of passionate love and sexual attitudes. As expected, results showed that, firstly, response to love-related image-stimuli and sex-related image-stimuli on the electrophysiological data significantly different on N1, N2, and positive slow wave (PSW) components. Secondly, the different adult attachment styles affected individuals' recognition processing in response to love-related and sex-related images, especially, to sex-related images. Further analysis showed that voltages elicited by fearful attachment style individuals were significantly lower than voltages elicited by secure and dismissing attachment style individuals on sex-related images at frontal sites, on N1 and N2 components. Thirdly, from behavior data, we found that adult attachment styles were not significantly related to any dimension of sexual attitudes but were significantly related to passionate love scale (PLS) total points. Thus, the behavior results were not in line with the electrophysiological results. The present study proved that adult attachment styles might mediate individuals' lust and attraction systems.

Structural basis for norovirus neutralization by an HBGA blocking human IgA antibody.

PubMed

Shanker, Sreejesh; Czakó, Rita; Sapparapu, Gopal; Alvarado, Gabriela; Viskovska, Maria; Sankaran, Banumathi; Atmar, Robert L; Crowe, James E; Estes, Mary K; Prasad, B V Venkataram

2016-10-04

Human noroviruses (HuNoVs) cause sporadic and epidemic gastroenteritis worldwide. They are classified into two major genogroups (GI and GII), with each genogroup further divided into multiple genotypes. Susceptibility to these viruses is influenced by genetically determined histo-blood group antigen (HBGA) expression. HBGAs function as cell attachment factors by binding to a surface-exposed region in the protruding (P) domain of the capsid protein. Sequence variations in this region that result in differential HBGA binding patterns and antigenicity are suggested to form a basis for strain diversification. Recent studies show that serum antibodies that block HBGA binding correlate with protection against illness. Although genogroup-dependent variation in HBGA binding specificity is structurally well characterized, an understanding of how antibodies block HBGA binding and how genotypic variations affect such blockade is lacking. Our crystallographic studies of the GI.1 P domain in complex with the Fab fragment of a human IgA monoclonal antibody (IgA 5I2) with HBGA blocking activity show that the antibody recognizes a conformational epitope formed by two surface-exposed loop clusters in the P domain. The antibody engulfs the HBGA binding site but does not affect its structural integrity. An unusual feature of the antigen recognition by IgA 5I2 is the predominant involvement of the CDR light chain 1 in contrast to the commonly observed CDR heavy chain 3, providing a unique perspective into antibody diversity in antigen recognition. Identification of the antigenic site in the P domain shows how genotypic variations might allow escape from antibody neutralization and exemplifies the interplay between antigenicity and HBGA specificity in HuNoV evolution.

Redundancy of primary RNA-binding functions of the bacterial transcription terminator Rho

PubMed Central

Shashni, Rajesh; Qayyum, M. Zuhaib; Vishalini, V.; Dey, Debashish; Sen, Ranjan

2014-01-01

The bacterial transcription terminator, Rho, terminates transcription at half of the operons. According to the classical model derived from in vitro assays on a few terminators, Rho is recruited to the transcription elongation complex (EC) by recognizing specific sites (rut) on the nascent RNA. Here, we explored the mode of in vivo recruitment process of Rho. We show that sequence specific recognition of the rut site, in majority of the Rho-dependent terminators, can be compromised to a great extent without seriously affecting the genome-wide termination function as well as the viability of Escherichia coli. These terminators function optimally only through a NusG-assisted recruitment and activation of Rho. Our data also indicate that at these terminators, Rho-EC-bound NusG interaction facilitates the isomerization of Rho into a translocase-competent form by stabilizing the interactions of mRNA with the secondary RNA binding site, thereby overcoming the defects of the primary RNA binding functions. PMID:25081210

Orthographic Consistency Affects Spoken Word Recognition at Different Grain-Sizes

ERIC Educational Resources Information Center

Dich, Nadya

2014-01-01

A number of previous studies found that the consistency of sound-to-spelling mappings (feedback consistency) affects spoken word recognition. In auditory lexical decision experiments, words that can only be spelled one way are recognized faster than words with multiple potential spellings. Previous studies demonstrated this by manipulating…

How Cross-Language Similarity and Task Demands Affect Cognate Recognition

ERIC Educational Resources Information Center

Dijkstra, Ton; Miwa, Koji; Brummelhuis, Bianca; Sappelli, Maya; Baayen, Harald

2010-01-01

This study examines how the cross-linguistic similarity of translation equivalents affects bilingual word recognition. Performing one of three tasks, Dutch-English bilinguals processed cognates with varying degrees of form overlap between their English and Dutch counterparts (e.g., "lamp-lamp" vs. "flood-vloed" vs. "song-lied"). In lexical…

Rpn1 provides adjacent receptor sites for substrate binding and deubiquitination by the proteasome

PubMed Central

Shi, Yuan; Chen, Xiang; Elsasser, Suzanne; Stocks, Bradley B.; Tian, Geng; Lee, Byung-Hoon; Shi, Yanhong; Zhang, Naixia; de Poot, Stefanie A. H.; Tuebing, Fabian; Sun, Shuangwu; Vannoy, Jacob; Tarasov, Sergey G.; Engen, John R.; Finley, Daniel; Walters, Kylie J.

2016-01-01

Structured Abstract INTRODUCTION The ubiquitin-proteasome system comprises hundreds of distinct pathways of degradation, which converge at the step of ubiquitin recognition by the proteasome. Five proteasomal ubiquitin receptors have been identified, two that are intrinsic to the proteasome (Rpn10 and Rpn13) and three reversibly associated proteasomal ubiquitin receptors (Rad23, Dsk2, and Ddi1). RATIONALE We found that the five known proteasomal ubiquitin receptors of yeast are collectively nonessential for ubiquitin recognition by the proteasome. We therefore screened for additional ubiquitin receptors in the proteasome and identified subunit Rpn1 as a candidate. We used nuclear magnetic resonance (NMR) spectroscopy to characterize the structure of the binding site within Rpn1, which we term the T1 site. Mutational analysis of this site showed its functional importance within the context of intact proteasomes. T1 binds both ubiquitin and ubiquitin-like (UBL) proteins, in particular the substrate-delivering shuttle factor Rad23. A second site within the Rpn1 toroid, T2, recognizes the UBL domain of deubiquitinating enzyme Ubp6, as determined by hydrogen-deuterium exchange mass spectrometry analysis and validated by amino acid substitution and functional assays. The Rpn1 toroid thus serves a critical scaffolding role within the proteasome, helping to assemble multiple proteasome cofactors as well as substrates. RESULTS Our results indicate that proteasome subunit Rpn1 can recognize both ubiquitin and UBL domains of substrate shuttling factors that themselves bind ubiquitin and function as reversibly-associated proteasomal ubiquitin receptors. Recognition is mediated by the T1 site within the Rpn1 toroid, which supports proteasome function in vivo. We found that the capacity of T1 to recognize both ubiquitin and UBL proteins was shared with Rpn10 and Rpn13. The surprising multiplicity of ubiquitin-recognition domains within the proteasome may promote enhanced, multipoint binding of ubiquitin chains. The structures of the T1 site in its free state and complexed with monoubiquitin or K48-linked diubiquitin were solved, revealing that three neighboring outer helices from the T1 toroid engage two ubiquitins. This binding mode leads to a preference for certain ubiquitin chain types, especially K6- and K48-linked chains, in a distinct configuration that can position substrates close to the entry port of the proteasome. The fate of proteasome-docked ubiquitin conjugates is determined by a competition between deubiquitination and substrate degradation. We find that proximal to the T1 site within the Rpn1 toroid is a second UBL-binding site, T2, that does not assist in ubiquitin chain recognition, but rather in chain disassembly, by binding to the UBL domain of deubiquitinating enzyme Ubp6. Importantly, the UBL interactors at T1 and T2 are distinct, assigning substrate localization to T1 and substrate deubiquitination to T2. CONCLUSION A ligand-binding hotspot was identified in the Rpn1 toroid, consisting of two adjacent receptor sites, T1 and T2. The Rpn1 toroid represents a novel class of binding domains for ubiquitin and UBL proteins. This study thus defines a novel two-site recognition domain intrinsic to the proteasome that uses homologous ubiquitin/UBL-class ligands to assemble substrates, substrate shuttling factors, and a deubiquitinating enzyme in close proximity. A ligand-binding hotspot in the proteasome for assembling substrates and cofactors Schematic (top) and model structure (bottom, left) mapping the UBL-binding Rpn1 T1 (indigo) and T2 (orange) sites. (Bottom, right) Enlarged region of the proteasome to illustrate the Rpn1 T1 and T2 sites bound to a ubiquitin chain (yellow) and deubiquitinating enzyme Ubp6 (green), respectively. PDB 4CR2 and 2B9R were used for this figure. Hundreds of pathways for degradation converge at ubiquitin recognition by proteasome. Here we found that the five known proteasomal ubiquitin receptors are collectively nonessential for ubiquitin recognition, and identified a sixth receptor, Rpn1. A site (T1) in the Rpn1 toroid recognized ubiquitin and ubiquitin-like (UBL) domains of substrate shuttling factors. T1 structures with monoubiquitin or K48 diubiquitin show three neighboring outer helices engaging two ubiquitins. T1 contributes a distinct substrate-binding pathway with preference for K48-linked chains. Proximal to T1 within the Rpn1 toroid is a second UBL-binding site (T2) that assists in ubiquitin chain disassembly, by binding the UBL of deubiquitinating enzyme Ubp6. Thus a two-site recognition domain intrinsic to the proteasome uses homologous ubiquitin/UBL-class ligands to assemble substrates, shuttling factors, and a deubiquitinating enzyme. PMID:26912900

Role of IUCN WCPA Geoheritage Specialist Group for geoheritage conservation and recognition of World Heritage Sites, Global Geoparks and other protected areas

NASA Astrophysics Data System (ADS)

Woo, Kyung Sik

2017-04-01

Geoheritage comprises those elements of the Earth's geodiversity that are considered to have significant scientific, educational, cultural/aesthetic, ecological or ecosystem service values. IUCN Resolutions at Barcelona (2008), at Jeju (2012) and at Hawaii (2016) clearly recognised that geodiversity is part of nature and geoheritage is part of natural heritage. Formal recognition of the geodiversity component of protected areas was made in 2008 in the revised 'IUCN Guidelines for Applying Protected Area Management Categories'. All 6 of the IUCN Protected Area Management Categories are applicable to the protection of geosites and the wider landscape values of geodiversity. Recognising the wider values of geodiversity therefore provides opportunities to integrate geoheritage much more closely in protected area networks, as the approach advocated by the Geoheritage Specialist Group (GSG) of the IUCN World Commission on Protected Areas. Although geoparks are not a protected area category as such and only includes some parts of protected areas as geosites, the UNESCO Global Geoparks Network also provides an international framework to conserve and enhance geoheritage values as UNESCO World Heritage sites has provided. GSG will pursue significant roles for geoheritage recognition and conservation as follows: 1) Establish the Best Practice Guideline of geoheritage sites for protected areas in the world, 2) Revise the Thematic Study on volcanic sites of Outstanding Universal Values and International Significance, 3) Revise Criterion (viii) for WH recognition, and 4) Initiate 'Key Geoheritage Site' concept in the future.

Age-Related Differences in Face Recognition: Neural Correlates of Repetition and Semantic Priming in Young and Older Adults

ERIC Educational Resources Information Center

Wiese, Holger; Komes, Jessica; Tüttenberg, Simone; Leidinger, Jana; Schweinberger, Stefan R.

2017-01-01

Difficulties in person recognition are among the common complaints associated with cognitive ageing. The present series of experiments therefore investigated face and person recognition in young and older adults. The authors examined how within-domain and cross-domain repetition as well as semantic priming affect familiar face recognition and…

Combining functional neuroimaging with off-line brain stimulation: modulation of task-related activity in language areas.

PubMed

Andoh, Jamila; Paus, Tomás

2011-02-01

Repetitive TMS (rTMS) provides a noninvasive tool for modulating neural activity in the human brain. In healthy participants, rTMS applied over the language-related areas in the left hemisphere, including the left posterior temporal area of Wernicke (LTMP) and inferior frontal area of Broca, have been shown to affect performance on word recognition tasks. To investigate the neural substrate of these behavioral effects, off-line rTMS was combined with fMRI acquired during the performance of a word recognition task. Twenty right-handed healthy men underwent fMRI scans before and after a session of 10-Hz rTMS applied outside the magnetic resonance scanner. Functional magnetic resonance images were acquired during the performance of a word recognition task that used English or foreign-language words. rTMS was applied over the LTMP in one group of 10 participants (LTMP group), whereas the homologue region in the right hemisphere was stimulated in another group of 10 participants (RTMP group). Changes in task-related fMRI response (English minus foreign languages) and task performances (response time and accuracy) were measured in both groups and compared between pre-rTMS and post-rTMS. Our results showed that rTMS increased task-related fMRI response in the homologue areas contralateral to the stimulated sites. We also found an effect of rTMS on response time for the LTMP group only. These findings provide insights into changes in neural activity in cortical regions connected to the stimulated site and are consistent with a hypothesis raised in a previous review about the role of the homologue areas in the contralateral hemisphere for preserving behavior after neural interference.

Callous-unemotional traits and empathy deficits: Mediating effects of affective perspective-taking and facial emotion recognition.

PubMed

Lui, Joyce H L; Barry, Christopher T; Sacco, Donald F

2016-09-01

Although empathy deficits are thought to be associated with callous-unemotional (CU) traits, findings remain equivocal and little is known about what specific abilities may underlie these purported deficits. Affective perspective-taking (APT) and facial emotion recognition may be implicated, given their independent associations with both empathy and CU traits. The current study examined how CU traits relate to cognitive and affective empathy and whether APT and facial emotion recognition mediate these relations. Participants were 103 adolescents (70 males) aged 16-18 attending a residential programme. CU traits were negatively associated with cognitive and affective empathy to a similar degree. The association between CU traits and affective empathy was partially mediated by APT. Results suggest that assessing mechanisms that may underlie empathic deficits, such as perspective-taking, may be important for youth with CU traits and may inform targets of intervention.

Post-analysis report on Chesapeake Bay data processing. [spectral analysis and recognition computer signature extension

NASA Technical Reports Server (NTRS)

Thomson, F.

1972-01-01

The additional processing performed on data collected over the Rhode River Test Site and Forestry Site in November 1970 is reported. The techniques and procedures used to obtain the processed results are described. Thermal data collected over three approximately parallel lines of the site were contoured, and the results color coded, for the purpose of delineating important scene constituents and to identify trees attacked by pine bark beetles. Contouring work and histogram preparation are reviewed and the important conclusions from the spectral analysis and recognition computer (SPARC) signature extension work are summarized. The SPARC setup and processing records are presented and recommendations are made for future data collection over the site.

Homing endonucleases: from basics to therapeutic applications.

PubMed

Marcaida, Maria J; Muñoz, Inés G; Blanco, Francisco J; Prieto, Jesús; Montoya, Guillermo

2010-03-01

Homing endonucleases (HE) are double-stranded DNAses that target large recognition sites (12-40 bp). HE-encoding sequences are usually embedded in either introns or inteins. Their recognition sites are extremely rare, with none or only a few of these sites present in a mammalian-sized genome. However, these enzymes, unlike standard restriction endonucleases, tolerate some sequence degeneracy within their recognition sequence. Several members of this enzyme family have been used as templates to engineer tools to cleave DNA sequences that differ from their original wild-type targets. These custom HEs can be used to stimulate double-strand break homologous recombination in cells, to induce the repair of defective genes with very low toxicity levels. The use of tailored HEs opens up new possibilities for gene therapy in patients with monogenic diseases that can be treated ex vivo. This review provides an overview of recent advances in this field.

Structure of the mouse galectin-4 N-terminal carbohydrate-recognition domain reveals the mechanism of oligosaccharide recognition

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

Krejciríková, Veronika; Pachl, Petr; Fábry, Milan

2011-11-18

Galectin-4, a member of the tandem-repeat subfamily of galectins, participates in cell-membrane interactions and plays an important role in cell adhesion and modulation of immunity and malignity. The oligosaccharide specificity of the mouse galectin-4 carbohydrate-recognition domains (CRDs) has been reported previously. In this work, the structure and binding properties of the N-terminal domain CRD1 were further investigated and the crystal structure of CRD1 in complex with lactose was determined at 2.1 {angstrom} resolution. The lactose-binding affinity was characterized by fluorescence measurements and two lactose-binding sites were identified: a high-affinity site with a K{sub d} value in the micromolar range (K{submore » d1} = 600 {+-} 70 {mu}M) and a low-affinity site with K{sub d2} = 28 {+-} 10 mM.« less

Prosody recognition and audiovisual emotion matching in schizophrenia: the contribution of cognition and psychopathology.

PubMed

Castagna, Filomena; Montemagni, Cristiana; Maria Milani, Anna; Rocca, Giuseppe; Rocca, Paola; Casacchia, Massimo; Bogetto, Filippo

2013-02-28

This study aimed to evaluate the ability to decode emotion in the auditory and audiovisual modality in a group of patients with schizophrenia, and to explore the role of cognition and psychopathology in affecting these emotion recognition abilities. Ninety-four outpatients in a stable phase and 51 healthy subjects were recruited. Patients were assessed through a psychiatric evaluation and a wide neuropsychological battery. All subjects completed the comprehensive affect testing system (CATS), a group of computerized tests designed to evaluate emotion perception abilities. With respect to the controls, patients were not impaired in the CATS tasks involving discrimination of nonemotional prosody, naming of emotional stimuli expressed by voice and judging the emotional content of a sentence, whereas they showed a specific impairment in decoding emotion in a conflicting auditory condition and in the multichannel modality. Prosody impairment was affected by executive functions, attention and negative symptoms, while deficit in multisensory emotion recognition was affected by executive functions and negative symptoms. These emotion recognition deficits, rather than being associated purely with emotion perception disturbances in schizophrenia, are affected by core symptoms of the illness. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

CACNA1C risk variant affects facial emotion recognition in healthy individuals.

PubMed

Nieratschker, Vanessa; Brückmann, Christof; Plewnia, Christian

2015-11-27

Recognition and correct interpretation of facial emotion is essential for social interaction and communication. Previous studies have shown that impairments in this cognitive domain are common features of several psychiatric disorders. Recent association studies identified CACNA1C as one of the most promising genetic risk factors for psychiatric disorders and previous evidence suggests that the most replicated risk variant in CACNA1C (rs1006737) is affecting emotion recognition and processing. However, studies investigating the influence of rs1006737 on this intermediate phenotype in healthy subjects at the behavioral level are largely missing to date. Here, we applied the "Reading the Mind in the Eyes" test, a facial emotion recognition paradigm in a cohort of 92 healthy individuals to address this question. Whereas accuracy was not affected by genotype, CACNA1C rs1006737 risk-allele carries (AA/AG) showed significantly slower mean response times compared to individuals homozygous for the G-allele, indicating that healthy risk-allele carriers require more information to correctly identify a facial emotion. Our study is the first to provide evidence for an impairing behavioral effect of the CACNA1C risk variant rs1006737 on facial emotion recognition in healthy individuals and adds to the growing number of studies pointing towards CACNA1C as affecting intermediate phenotypes of psychiatric disorders.

Novel DNA packaging recognition in the unusual bacteriophage N15

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

Feiss, Michael; Geyer, Henriette, E-mail: henriettegeyer@gmail.com; Division of Viral Infections, Robert Koch Institute, Berlin

Phage lambda's cosB packaging recognition site is tripartite, consisting of 3 TerS binding sites, called R sequences. TerS binding to the critical R3 site positions the TerL endonuclease for nicking cosN to generate cohesive ends. The N15 cos (cos{sup N15}) is closely related to cos{sup λ}, but whereas the cosB{sup N15} subsite has R3, it lacks the R2 and R1 sites and the IHF binding site of cosB{sup λ}. A bioinformatic study of N15-like phages indicates that cosB{sup N15} also has an accessory, remote rR2 site, which is proposed to increase packaging efficiency, like R2 and R1 of lambda. N15more » plus five prophages all have the rR2 sequence, which is located in the TerS-encoding 1 gene, approximately 200 bp distal to R3. An additional set of four highly related prophages, exemplified by Monarch, has R3 sequence, but also has R2 and R1 sequences characteristic of cosB–λ. The DNA binding domain of TerS-N15 is a dimer. - Highlights: • There are two classes of DNA packaging signals in N15-related phages. • Phage N15's TerS binding site: a critical site and a possible remote accessory site. • Viral DNA recognition signals by the λ-like bacteriophages: the odd case of N15.« less

Recognition memory probes affect what is remembered in schizophrenia.

PubMed

Schwartz, Barbara L; Parker, Elizabeth S; Rosse, Richard B; Deutsch, Stephen I

2009-05-15

Cognitive psychology offers tools to localize the memory processes most vulnerable to disruption in schizophrenia and to identify how patients with schizophrenia best remember. In this research, we used the University of Southern California Repeatable Episodic Memory Test (USC-REMT; Parker, E.S., Landau, S.M., Whipple, S.C., Schwartz, B.L., 2004. Aging, recall, and recognition: A study on the sensitivity of the University of Southern California Repeatable Episodic Memory Test (USC-REMT). Journal of Clinical and Experimental Neuropsychology 26(3), 428-440.) to examine how two different recognition memory probes affect memory performance in patients with schizophrenia and matched controls. Patients with schizophrenia studied equivalent word lists and were tested by yes-no recognition and forced-choice recognition following identical encoding and storage conditions. Compared with controls, patients with schizophrenia were particularly impaired when tested by yes-no recognition relative to forced-choice recognition. Patients had greatest deficits on hits in yes-no recognition but did not exhibit elevated false alarms. The data point to the importance of retrieval processes in schizophrenia, and highlight the need for further research on ways to help patients with schizophrenia access what they have learned.

Mechanism of substrate recognition by the novel Botulinum Neurotoxin subtype F5.

PubMed

Guo, Jiubiao; Chan, Edward Wai Chi; Chen, Sheng

2016-01-22

Botulinum Neurotoxins (BoNTs) are the causative agents of botulism, which act by potently inhibiting the neurotransmitter release in motor neurons. Seven serotypes of BoNTs designated as BoNT/A-G have been identified. Recently, two novel types of Botulinum neurotoxins, which cleave a novel scissile bond, L(54)-E(55), of VAMP-2 have been reported including BoNT/F subtype F5 and serotype H. However, little has been known on how these BoNTs recognize their substrates. The present study addressed for the first time the unique substrate recognition mechanism of LC/F5. Our data indicated that the optimal peptide required for efficient LC/F5 substrate cleavage is VAMP-2 (20-65). Interestingly, the overall mode of substrate recognition adopted by LC/F5 was similar to LC/F1, except that its recognition sites were shifted one helix toward the N-terminus of VAMP-2 when compared to that of LC/F1. The composition of LC/F5 pockets were found to have changed accordingly to facilitate specific recognition of these new sites of VAMP-2, including the P2', P1', P2, P3, B3, B2 and B1 sites. The study provides direct evidence of the evolutionary adaption of BoNT to recognize its substrate which is useful for effective antitoxin and inhibitor development.

Dissecting partner recognition by an intrinsically disordered protein using descriptive random mutagenesis.

PubMed

Gruet, Antoine; Dosnon, Marion; Vassena, Andrea; Lombard, Vincent; Gerlier, Denis; Bignon, Christophe; Longhi, Sonia

2013-09-23

In view of getting insights into the molecular determinants of the binding efficiency of intrinsically disordered proteins (IDPs), we used random mutagenesis. As a proof of concept, we chose the interaction between the intrinsically disordered C-terminal domain of the measles virus nucleoprotein (NTAIL) and the X domain (XD) of the viral phosphoprotein and assessed how amino acid substitutions introduced at random within NTAIL affect partner recognition. In contrast with directed evolution approaches, we did not apply any selection and used the gene library approach not for production purposes but for achieving a better understanding of the NTAIL/XD interaction. For that reason, and to differentiate our approach from similar approaches that make use of systematic (i.e., targeted) mutagenesis, we propose to call it "descriptive random mutagenesis" (DRM). NTAIL variants generated by error-prone PCR were picked at random in the absence of selection pressure and were characterized in terms of sequence and binding abilities toward XD. DRM not only identified determinants of NTAIL/XD interaction that were in good agreement with previous work but also provided new insights. In particular, we discovered that the primary interaction site is poorly evolvable in terms of binding abilities toward XD. We also identified a critical NTAIL residue whose role in stabilizing the NTAIL/XD complex had previously escaped detection, and we identified NTAIL regulatory sites that dampen the interaction while being located outside the primary interaction site. Results show that DRM is a valuable approach to study binding abilities of IDPs. © 2013 Elsevier Ltd. All rights reserved.

RNA splicing factors as oncoproteins and tumor suppressors

PubMed Central

Dvinge, Heidi; Kim, Eunhee; Abdel-Wahab, Omar; Bradley, Robert K.

2016-01-01

Preface The recent genomic characterization of cancers has revealed recurrent somatic point mutations and copy number changes affecting genes encoding RNA splicing factors. Initial studies of these ‘spliceosomal mutations’ suggest that the proteins bearing these mutations exhibit altered splice site and/or exon recognition preferences relative to their wild-type counterparts, resulting in cancer-specific mis-splicing. Such changes in the splicing machinery may create novel vulnerabilities in cancer cells that can be therapeutically exploited using compounds that can influence the splicing process. Further studies to dissect the biochemical, genomic, and biological effects of spliceosomal mutations are critical for the development of cancer therapies targeted to these mutations. PMID:27282250

Are there differential deficits in facial emotion recognition between paranoid and non-paranoid schizophrenia? A signal detection analysis.

PubMed

Huang, Charles Lung-Cheng; Hsiao, Sigmund; Hwu, Hai-Gwo; Howng, Shen-Long

2013-10-30

This study assessed facial emotion recognition abilities in subjects with paranoid and non-paranoid schizophrenia (NPS) using signal detection theory. We explore the differential deficits in facial emotion recognition in 44 paranoid patients with schizophrenia (PS) and 30 non-paranoid patients with schizophrenia (NPS), compared to 80 healthy controls. We used morphed faces with different intensities of emotion and computed the sensitivity index (d') of each emotion. The results showed that performance differed between the schizophrenia and healthy controls groups in the recognition of both negative and positive affects. The PS group performed worse than the healthy controls group but better than the NPS group in overall performance. Performance differed between the NPS and healthy controls groups in the recognition of all basic emotions and neutral faces; between the PS and healthy controls groups in the recognition of angry faces; and between the PS and NPS groups in the recognition of happiness, anger, sadness, disgust, and neutral affects. The facial emotion recognition impairment in schizophrenia may reflect a generalized deficit rather than a negative-emotion specific deficit. The PS group performed worse than the control group, but better than the NPS group in facial expression recognition, with differential deficits between PS and NPS patients. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Emotion recognition deficits associated with ventromedial prefrontal cortex lesions are improved by gaze manipulation.

PubMed

Wolf, Richard C; Pujara, Maia; Baskaya, Mustafa K; Koenigs, Michael

2016-09-01

Facial emotion recognition is a critical aspect of human communication. Since abnormalities in facial emotion recognition are associated with social and affective impairment in a variety of psychiatric and neurological conditions, identifying the neural substrates and psychological processes underlying facial emotion recognition will help advance basic and translational research on social-affective function. Ventromedial prefrontal cortex (vmPFC) has recently been implicated in deploying visual attention to the eyes of emotional faces, although there is mixed evidence regarding the importance of this brain region for recognition accuracy. In the present study of neurological patients with vmPFC damage, we used an emotion recognition task with morphed facial expressions of varying intensities to determine (1) whether vmPFC is essential for emotion recognition accuracy, and (2) whether instructed attention to the eyes of faces would be sufficient to improve any accuracy deficits. We found that vmPFC lesion patients are impaired, relative to neurologically healthy adults, at recognizing moderate intensity expressions of anger and that recognition accuracy can be improved by providing instructions of where to fixate. These results suggest that vmPFC may be important for the recognition of facial emotion through a role in guiding visual attention to emotionally salient regions of faces. Copyright © 2016 Elsevier Ltd. All rights reserved.

Inferential false memories of events: negative consequences protect from distortions when the events are free from further elaboration.

PubMed

Mirandola, Chiara; Toffalini, Enrico; Grassano, Massimo; Cornoldi, Cesare; Melinder, Annika

2014-01-01

The present experiment was conducted to investigate whether negative emotionally charged and arousing content of to-be-remembered scripted material would affect propensity towards memory distortions. We further investigated whether elaboration of the studied material through free recall would affect the magnitude of memory errors. In this study participants saw eight scripts. Each of the scripts included an effect of an action, the cause of which was not presented. Effects were either negatively emotional or neutral. Participants were assigned to either a yes/no recognition test group (recognition), or to a recall and yes/no recognition test group (elaboration + recognition). Results showed that participants in the recognition group produced fewer memory errors in the emotional condition. Conversely, elaboration + recognition participants had lower accuracy and produced more emotional memory errors than the other group, suggesting a mediating role of semantic elaboration on the generation of false memories. The role of emotions and semantic elaboration on the generation of false memories is discussed.

Type III restriction-modification enzymes: a historical perspective.

PubMed

Rao, Desirazu N; Dryden, David T F; Bheemanaik, Shivakumara

2014-01-01

Restriction endonucleases interact with DNA at specific sites leading to cleavage of DNA. Bacterial DNA is protected from restriction endonuclease cleavage by modifying the DNA using a DNA methyltransferase. Based on their molecular structure, sequence recognition, cleavage position and cofactor requirements, restriction-modification (R-M) systems are classified into four groups. Type III R-M enzymes need to interact with two separate unmethylated DNA sequences in inversely repeated head-to-head orientations for efficient cleavage to occur at a defined location (25-27 bp downstream of one of the recognition sites). Like the Type I R-M enzymes, Type III R-M enzymes possess a sequence-specific ATPase activity for DNA cleavage. ATP hydrolysis is required for the long-distance communication between the sites before cleavage. Different models, based on 1D diffusion and/or 3D-DNA looping, exist to explain how the long-distance interaction between the two recognition sites takes place. Type III R-M systems are found in most sequenced bacteria. Genome sequencing of many pathogenic bacteria also shows the presence of a number of phase-variable Type III R-M systems, which play a role in virulence. A growing number of these enzymes are being subjected to biochemical and genetic studies, which, when combined with ongoing structural analyses, promise to provide details for mechanisms of DNA recognition and catalysis.

Computational Modeling Approach in Probing the Effects of Cytosine Methylation on the Transcription Factor Binding to DNA.

PubMed

Tenayuca, John; Cousins, Kimberley; Yang, Shumei; Zhang, Lubo

2017-01-01

Cytosine methylation at CpG dinucleotides is a chief mechanism in epigenetic modification of gene expression patterns. Previous studies demonstrated that increased CpG methylation of Sp1 sites at -268 and -346 of protein kinase C ε promoter repressed the gene expression. The present study investigated the impact of CpG methylation on the Sp1 binding via molecular modeling and electrophoretic mobility shift assay. Each of the Sp1 sites contain two CpGs. Methylation of either CpG lowered the binding affinity of Sp1, whereas methylation of both CpGs produced a greater decrease in the binding affinity. Computation of van der Waals (VDW) energy of Sp1 in complex with the Sp1 sites demonstrated increased VDW values from one to two sites of CpG methylation. Molecular modeling indicated that single CpG methylation caused underwinding of the DNA fragment, with the phosphate groups at C1, C4 and C5 reoriented from their original positions. Methylation of both CpGs pinched the minor groove and increased the helical twist concomitant with a shallow, hydrophobic major groove. Additionally, double methylation eliminated hydrogen bonds on recognition helix residues located at positions -1 and 1, which were essential for interaction with O6/N7 of G-bases. Bonding from linker residues Arg565, Lys595 and Lys596 were also reduced. Methylation of single or both CpGs significantly affected hydrogen bonding from all three Sp1 DNA binding domains, demonstrating that the consequences of cytosine modification extend beyond the neighboring nucleotides. The results indicate that cytosine methylation causes subtle structural alterations in Sp1 binding sites consequently resulting in inhibition of side chain interactions critical for specific base recognition and reduction of the binding affinity of Sp1. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Recognition of functional sites in protein structures.

PubMed

Shulman-Peleg, Alexandra; Nussinov, Ruth; Wolfson, Haim J

2004-06-04

Recognition of regions on the surface of one protein, that are similar to a binding site of another is crucial for the prediction of molecular interactions and for functional classifications. We first describe a novel method, SiteEngine, that assumes no sequence or fold similarities and is able to recognize proteins that have similar binding sites and may perform similar functions. We achieve high efficiency and speed by introducing a low-resolution surface representation via chemically important surface points, by hashing triangles of physico-chemical properties and by application of hierarchical scoring schemes for a thorough exploration of global and local similarities. We proceed to rigorously apply this method to functional site recognition in three possible ways: first, we search a given functional site on a large set of complete protein structures. Second, a potential functional site on a protein of interest is compared with known binding sites, to recognize similar features. Third, a complete protein structure is searched for the presence of an a priori unknown functional site, similar to known sites. Our method is robust and efficient enough to allow computationally demanding applications such as the first and the third. From the biological standpoint, the first application may identify secondary binding sites of drugs that may lead to side-effects. The third application finds new potential sites on the protein that may provide targets for drug design. Each of the three applications may aid in assigning a function and in classification of binding patterns. We highlight the advantages and disadvantages of each type of search, provide examples of large-scale searches of the entire Protein Data Base and make functional predictions.

Perspective: Watching low-frequency vibrations of water in biomolecular recognition by THz spectroscopy.

PubMed

Xu, Yao; Havenith, Martina

2015-11-07

Terahertz (THz) spectroscopy has turned out to be a powerful tool which is able to shed new light on the role of water in biomolecular processes. The low frequency spectrum of the solvated biomolecule in combination with MD simulations provides deep insights into the collective hydrogen bond dynamics on the sub-ps time scale. The absorption spectrum between 1 THz and 10 THz of solvated biomolecules is sensitive to changes in the fast fluctuations of the water network. Systematic studies on mutants of antifreeze proteins indicate a direct correlation between biological activity and a retardation of the (sub)-ps hydration dynamics at the protein binding site, i.e., a "hydration funnel." Kinetic THz absorption studies probe the temporal changes of THz absorption during a biological process, and give access to the kinetics of the coupled protein-hydration dynamics. When combined with simulations, the observed results can be explained in terms of a two-tier model involving a local binding and a long range influence on the hydration bond dynamics of the water around the binding site that highlights the significance of the changes in the hydration dynamics at recognition site for biomolecular recognition. Water is shown to assist molecular recognition processes.

Perspective: Watching low-frequency vibrations of water in biomolecular recognition by THz spectroscopy

NASA Astrophysics Data System (ADS)

Xu, Yao; Havenith, Martina

2015-11-01

Terahertz (THz) spectroscopy has turned out to be a powerful tool which is able to shed new light on the role of water in biomolecular processes. The low frequency spectrum of the solvated biomolecule in combination with MD simulations provides deep insights into the collective hydrogen bond dynamics on the sub-ps time scale. The absorption spectrum between 1 THz and 10 THz of solvated biomolecules is sensitive to changes in the fast fluctuations of the water network. Systematic studies on mutants of antifreeze proteins indicate a direct correlation between biological activity and a retardation of the (sub)-ps hydration dynamics at the protein binding site, i.e., a "hydration funnel." Kinetic THz absorption studies probe the temporal changes of THz absorption during a biological process, and give access to the kinetics of the coupled protein-hydration dynamics. When combined with simulations, the observed results can be explained in terms of a two-tier model involving a local binding and a long range influence on the hydration bond dynamics of the water around the binding site that highlights the significance of the changes in the hydration dynamics at recognition site for biomolecular recognition. Water is shown to assist molecular recognition processes.

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.

Fold independent structural comparisons of protein-ligand binding sites for exploring functional relationships.

PubMed

Gold, Nicola D; Jackson, Richard M

2006-02-03

The rapid growth in protein structural data and the emergence of structural genomics projects have increased the need for automatic structure analysis and tools for function prediction. Small molecule recognition is critical to the function of many proteins; therefore, determination of ligand binding site similarity is important for understanding ligand interactions and may allow their functional classification. Here, we present a binding sites database (SitesBase) that given a known protein-ligand binding site allows rapid retrieval of other binding sites with similar structure independent of overall sequence or fold similarity. However, each match is also annotated with sequence similarity and fold information to aid interpretation of structure and functional similarity. Similarity in ligand binding sites can indicate common binding modes and recognition of similar molecules, allowing potential inference of function for an uncharacterised protein or providing additional evidence of common function where sequence or fold similarity is already known. Alternatively, the resource can provide valuable information for detailed studies of molecular recognition including structure-based ligand design and in understanding ligand cross-reactivity. Here, we show examples of atomic similarity between superfamily or more distant fold relatives as well as between seemingly unrelated proteins. Assignment of unclassified proteins to structural superfamiles is also undertaken and in most cases substantiates assignments made using sequence similarity. Correct assignment is also possible where sequence similarity fails to find significant matches, illustrating the potential use of binding site comparisons for newly determined proteins.

Infant Visual Recognition Memory

ERIC Educational Resources Information Center

Rose, Susan A.; Feldman, Judith F.; Jankowski, Jeffery J.

2004-01-01

Visual recognition memory is a robust form of memory that is evident from early infancy, shows pronounced developmental change, and is influenced by many of the same factors that affect adult memory; it is surprisingly resistant to decay and interference. Infant visual recognition memory shows (a) modest reliability, (b) good discriminant…

Orthographic Facilitation in Chinese Spoken Word Recognition: An ERP Study

ERIC Educational Resources Information Center

Zou, Lijuan; Desroches, Amy S.; Liu, Youyi; Xia, Zhichao; Shu, Hua

2012-01-01

Orthographic influences in spoken word recognition have been previously examined in alphabetic languages. However, it is unknown whether orthographic information affects spoken word recognition in Chinese, which has a clean dissociation between orthography (O) and phonology (P). The present study investigated orthographic effects using event…

Changing concepts of geologic structure and the problem of siting nuclear reactors: Examples from Washington State

NASA Astrophysics Data System (ADS)

Tabor, R. W.

1986-09-01

The conflict between regulation and healthy evolution of geological science has contributed to the difficulties of siting nuclear reactors. On the Columbia Plateau in Washington, but for conservative design of the Hanford reactor facility, the recognition of the little-understood Olympic-Wallowa lineament as a major, possibly still active structural alinement might have jeopardized the acceptability of the site for nuclear reactors. On the Olympic Peninsula, evolving concepts of compressive structures and their possible recent activity and the current recognition of a subducting Juan de Fuca plate and its potential for generating great earthquakes—both concepts little-considered during initial site selection—may delay final acceptance of the Satsop site. Conflicts of this sort are inevitable but can be accommodated if they are anticipated in the reactor-licensing process. More important, society should be increasing its store of geologic knowledge now, during the current recess in nuclear reactor siting.

Engineering analysis of LANDSAT 1 data for Southeast Asian agriculture

NASA Technical Reports Server (NTRS)

Mcnair, A. J.; Heydt, H. L.; Liang, T.; Levine, G. (Principal Investigator)

1976-01-01

The author has identified the following significant results. LANDSAT spatial resolution was estimated to be adequate, but barely so, for the purpose of detailed assessment of rice or site status. This was due to the spatially fine grain, heterogenous nature of most rice areas. Use of two spectral bands of digital data (MSS 5 and MSS 6 or 7) appeared to be adequate for site recognition and gross site status assessment. Spectral/temporal signatures were found to be more powerful than spectra signatures alone and virtually essential for most analyses of rice growth and rice sites in the Philippine environment. Two band, two date signatures were estimated to be adequate for most purposes, although good results were achieved using one band two- or four-date signatures. A radiometric resolution of 64 levels in each band was found adequate for the analyses of LANDSAT digital data for site recognition and gross site or rice growth assessment.

Identification of a novel K311 ubiquitination site critical for androgen receptor transcriptional activity

PubMed Central

Cork, David M.W.; Darby, Steven; Ryan-Munden, Claudia A.; Nakjang, Sirintra; Mendes Côrtes, Leticia; Treumann, Achim; Gaughan, Luke

2017-01-01

Abstract The androgen receptor (AR) is the main driver of prostate cancer (PC) development and progression, and the primary therapeutic target in PC. To date, two functional ubiquitination sites have been identified on AR, both located in its C-terminal ligand binding domain (LBD). Recent reports highlight the emergence of AR splice variants lacking the LBD that can arise during disease progression and contribute to castrate resistance. Here, we report a novel N-terminal ubiquitination site at lysine 311. Ubiquitination of this site plays a role in AR stability and is critical for its transcriptional activity. Inactivation of this site causes AR to accumulate on chromatin and inactivates its transcriptional function as a consequence of inability to bind to p300. Additionally, mutation at lysine 311 affects cellular transcriptome altering the expression of genes involved in chromatin organization, signaling, adhesion, motility, development and metabolism. Even though this site is present in clinically relevant AR-variants it can only be ubiquitinated in cells when AR retains LBD suggesting a role for AR C-terminus in E2/E3 substrate recognition. We report that as a consequence AR variants lacking the LBD cannot be ubiquitinated in the cellular environment and their protein turnover must be regulated via an alternate pathway. PMID:27903893

Recognition of facial emotion and affective prosody in children with ASD (+ADHD) and their unaffected siblings.

PubMed

Oerlemans, Anoek M; van der Meer, Jolanda M J; van Steijn, Daphne J; de Ruiter, Saskia W; de Bruijn, Yvette G E; de Sonneville, Leo M J; Buitelaar, Jan K; Rommelse, Nanda N J

2014-05-01

Autism is a highly heritable and clinically heterogeneous neuropsychiatric disorder that frequently co-occurs with other psychopathologies, such as attention-deficit/hyperactivity disorder (ADHD). An approach to parse heterogeneity is by forming more homogeneous subgroups of autism spectrum disorder (ASD) patients based on their underlying, heritable cognitive vulnerabilities (endophenotypes). Emotion recognition is a likely endophenotypic candidate for ASD and possibly for ADHD. Therefore, this study aimed to examine whether emotion recognition is a viable endophenotypic candidate for ASD and to assess the impact of comorbid ADHD in this context. A total of 90 children with ASD (43 with and 47 without ADHD), 79 ASD unaffected siblings, and 139 controls aged 6-13 years, were included to test recognition of facial emotion and affective prosody. Our results revealed that the recognition of both facial emotion and affective prosody was impaired in children with ASD and aggravated by the presence of ADHD. The latter could only be partly explained by typical ADHD cognitive deficits, such as inhibitory and attentional problems. The performance of unaffected siblings could overall be considered at an intermediate level, performing somewhat worse than the controls and better than the ASD probands. Our findings suggest that emotion recognition might be a viable endophenotype in ASD and a fruitful target in future family studies of the genetic contribution to ASD and comorbid ADHD. Furthermore, our results suggest that children with comorbid ASD and ADHD are at highest risk for emotion recognition problems.

Graphene/graphite paste electrode incorporated with molecularly imprinted polymer nanoparticles as a novel sensor for differential pulse voltammetry determination of fluoxetine.

PubMed

Alizadeh, Taher; Azizi, Sorour

2016-07-15

Molecularly imprinted polymer (MIP) nanoparticles including highly selective recognition sites for fluoxetine were synthesized, utilizing precipitation polymerization. Methacrylic acid and vinyl benzene were used as functional monomers. Ethylene glycol dimethacrylate was used as cross-linker agent. The obtained polymeric nanoparticles were incorporated with carbon paste electrode (CPE) in order to construct a fluoxetine selective sensor. The response of the MIP-CP electrode to fluoxetine was remarkably higher than the electrode, modified with the non-imprinted polymer, indicating the excellent efficiency of the MIP sites for target molecule recognition. It was found that the addition of a little amount of graphene, synthesized via modified hummer's method, to the MIP-CP resulted in considerable enhancement in the sensitivity of the electrode to fluoxetine. Also, the style of electrode components mixing, before carbon paste preparation, was demonstrated to be influential factor in the electrode response. Some parameters, affecting sensor response, were optimized and then a calibration curve was plotted. A dynamic linear range of 6×10(-9)-1.0×10(-7)molL(-1) was obtained. The detection limit of the sensor was calculated equal to 2.8×10(-9)molL(-1) (3Sb/m). This sensor was used successfully for fluoxetine determination in the spiked plasma samples as well as fluoxetine capsules. Copyright © 2016 Elsevier B.V. All rights reserved.

Impact of vitamin D receptor gene polymorphisms in pathogenesis of Type-1 diabetes mellitus

PubMed Central

Kamel, Mahmoud M; Fouad, Shawky A; Salaheldin, Omina; El-Razek, Abd El-Rahman A Abd; El-Fatah, Abeer I Abd

2014-01-01

Background: Type 1 diabetes mellitus (TIDM) results from an immune-mediated destruction of insulin-producing-cells in the pancreatic islets of Langerhans. There are clear differences in immunogenetic predisposition to type1 diabetes among countries. Studies have indicated that vitamin D supplementation in early childhood decreases the risk of TIDM. Vitamin D exerts its action via the nuclear vitamin D receptor (VDR), which shows an extensive polymorphism. VDR gene polymorphisms have been associated with altered gene expression or gene function. Four single nucleotide polymorphisms (SNPs) in the VDR gene produce variation in four recognition sites. These recognition sites variants include Fok I, Bsm I, Apa I and Taq I. Aim of the study: TO investigate the relationship between VDR gene polymorphisms (at positions Taq I and Apa I) and the incidence of TIDM in Egyptian peoples. Subjects and methods: This study included 74 patients with type 1 DM in addition to 28 healthy age and sex matched control subjects. All of them were subjected to full history taking and clinical examination. Three ml of venous blood were withdrawn from each patient at fasting and postprandial times and used for genomic DNA extraction, estimation of Hb A1C, as well as, fasting and postprandial C-peptide and blood glucose levels. Results: Apa I recognition site was found in low frequency in diabetic patients (14/74) 18.9% while, its frequency was high (16/28) 57.1% among normal subjects. Taq I has two recognition sites. The first was found at nucleotide number 293 that was found in a frequency of (2/28) 7.1% in normal non-diabetic individuals while it was detected in (14/74) 18.9% in diabetic patients. The second Taq I recognition site was found at nucleotide number 494 without any differences between diabetic and normal individuals. Conclusion: This study indicates that there is an association between VDR genetic polymorphism and incidence of TIDM in Egyptian patients. PMID:25664062

Computer-Assisted Face Processing Instruction Improves Emotion Recognition, Mentalizing, and Social Skills in Students with ASD.

PubMed

Rice, Linda Marie; Wall, Carla Anne; Fogel, Adam; Shic, Frederick

2015-07-01

This study examined the extent to which a computer-based social skills intervention called FaceSay was associated with improvements in affect recognition, mentalizing, and social skills of school-aged children with Autism Spectrum Disorder (ASD). FaceSay offers students simulated practice with eye gaze, joint attention, and facial recognition skills. This randomized control trial included school-aged children meeting educational criteria for autism (N = 31). Results demonstrated that participants who received the intervention improved their affect recognition and mentalizing skills, as well as their social skills. These findings suggest that, by targeting face-processing skills, computer-based interventions may produce changes in broader cognitive and social-skills domains in a cost- and time-efficient manner.

The Relation of Facial Affect Recognition and Empathy to Delinquency in Youth Offenders

ERIC Educational Resources Information Center

Carr, Mary B.; Lutjemeier, John A.

2005-01-01

Associations among facial affect recognition, empathy, and self-reported delinquency were studied in a sample of 29 male youth offenders at a probation placement facility. Youth offenders were asked to recognize facial expressions of emotions from adult faces, child faces, and cartoon faces. Youth offenders also responded to a series of statements…

Assessing the Utility of a Virtual Environment for Enhancing Facial Affect Recognition in Adolescents with Autism

ERIC Educational Resources Information Center

Bekele, Esubalew; Crittendon, Julie; Zheng, Zhi; Swanson, Amy; Weitlauf, Amy; Warren, Zachary; Sarkar, Nilanjan

2014-01-01

Teenagers with autism spectrum disorder (ASD) and age-matched controls participated in a dynamic facial affect recognition task within a virtual reality (VR) environment. Participants identified the emotion of a facial expression displayed at varied levels of intensity by a computer generated avatar. The system assessed performance (i.e.,…

Interdependence of Inhibitor Recognition in HIV-1 Protease

PubMed Central

2017-01-01

Molecular recognition is a highly interdependent process. Subsite couplings within the active site of proteases are most often revealed through conditional amino acid preferences in substrate recognition. However, the potential effect of these couplings on inhibition and thus inhibitor design is largely unexplored. The present study examines the interdependency of subsites in HIV-1 protease using a focused library of protease inhibitors, to aid in future inhibitor design. Previously a series of darunavir (DRV) analogs was designed to systematically probe the S1′ and S2′ subsites. Co-crystal structures of these analogs with HIV-1 protease provide the ideal opportunity to probe subsite interdependency. All-atom molecular dynamics simulations starting from these structures were performed and systematically analyzed in terms of atomic fluctuations, intermolecular interactions, and water structure. These analyses reveal that the S1′ subsite highly influences other subsites: the extension of the hydrophobic P1′ moiety results in 1) reduced van der Waals contacts in the P2′ subsite, 2) more variability in the hydrogen bond frequencies with catalytic residues and the flap water, and 3) changes in the occupancy of conserved water sites both proximal and distal to the active site. In addition, one of the monomers in this homodimeric enzyme has atomic fluctuations more highly correlated with DRV than the other monomer. These relationships intricately link the HIV-1 protease subsites and are critical to understanding molecular recognition and inhibitor binding. More broadly, the interdependency of subsite recognition within an active site requires consideration in the selection of chemical moieties in drug design; this strategy is in contrast to what is traditionally done with independent optimization of chemical moieties of an inhibitor. PMID:28358514

Interdependence of Inhibitor Recognition in HIV-1 Protease.

PubMed

Paulsen, Janet L; Leidner, Florian; Ragland, Debra A; Kurt Yilmaz, Nese; Schiffer, Celia A

2017-05-09

Molecular recognition is a highly interdependent process. Subsite couplings within the active site of proteases are most often revealed through conditional amino acid preferences in substrate recognition. However, the potential effect of these couplings on inhibition and thus inhibitor design is largely unexplored. The present study examines the interdependency of subsites in HIV-1 protease using a focused library of protease inhibitors, to aid in future inhibitor design. Previously a series of darunavir (DRV) analogs was designed to systematically probe the S1' and S2' subsites. Co-crystal structures of these analogs with HIV-1 protease provide the ideal opportunity to probe subsite interdependency. All-atom molecular dynamics simulations starting from these structures were performed and systematically analyzed in terms of atomic fluctuations, intermolecular interactions, and water structure. These analyses reveal that the S1' subsite highly influences other subsites: the extension of the hydrophobic P1' moiety results in 1) reduced van der Waals contacts in the P2' subsite, 2) more variability in the hydrogen bond frequencies with catalytic residues and the flap water, and 3) changes in the occupancy of conserved water sites both proximal and distal to the active site. In addition, one of the monomers in this homodimeric enzyme has atomic fluctuations more highly correlated with DRV than the other monomer. These relationships intricately link the HIV-1 protease subsites and are critical to understanding molecular recognition and inhibitor binding. More broadly, the interdependency of subsite recognition within an active site requires consideration in the selection of chemical moieties in drug design; this strategy is in contrast to what is traditionally done with independent optimization of chemical moieties of an inhibitor.

Event-related theta synchronization predicts deficit in facial affect recognition in schizophrenia.

PubMed

Csukly, Gábor; Stefanics, Gábor; Komlósi, Sarolta; Czigler, István; Czobor, Pál

2014-02-01

Growing evidence suggests that abnormalities in the synchronized oscillatory activity of neurons in schizophrenia may lead to impaired neural activation and temporal coding and thus lead to neurocognitive dysfunctions, such as deficits in facial affect recognition. To gain an insight into the neurobiological processes linked to facial affect recognition, we investigated both induced and evoked oscillatory activity by calculating the Event Related Spectral Perturbation (ERSP) and the Inter Trial Coherence (ITC) during facial affect recognition. Fearful and neutral faces as well as nonface patches were presented to 24 patients with schizophrenia and 24 matched healthy controls while EEG was recorded. The participants' task was to recognize facial expressions. Because previous findings with healthy controls showed that facial feature decoding was associated primarily with oscillatory activity in the theta band, we analyzed ERSP and ITC in this frequency band in the time interval of 140-200 ms, which corresponds to the N170 component. Event-related theta activity and phase-locking to facial expressions, but not to nonface patches, predicted emotion recognition performance in both controls and patients. Event-related changes in theta amplitude and phase-locking were found to be significantly weaker in patients compared with healthy controls, which is in line with previous investigations showing decreased neural synchronization in the low frequency bands in patients with schizophrenia. Neural synchrony is thought to underlie distributed information processing. Our results indicate a less effective functioning in the recognition process of facial features, which may contribute to a less effective social cognition in schizophrenia. PsycINFO Database Record (c) 2014 APA, all rights reserved.

Corona Phase Molecular Recognition (CoPhMoRe) to Enable New Nanosensor Interfaces

NASA Astrophysics Data System (ADS)

Strano, Michael

2015-03-01

Our lab at MIT has been interested in how the 1D and 2D electronic structures of carbon nanotubes and graphene respectively can be utilized to advance new concepts in molecular detection. We introduce CoPhMoRe or corona phase molecular recognition as a method of discovering synthetic antibodies, or nanotube-templated recognition sites from a heteropolymer library. We show that certain synthetic heteropolymers, once constrained onto a single-walled carbon nanotube by chemical adsorption, also form a new corona phase that exhibits highly selective recognition for specific molecules. To prove the generality of this phenomenon, we report three examples of heteropolymers-nanotube recognition complexes for riboflavin, L-thyroxine and estradiol. The platform opens new opportunities to create synthetic recognition sites for molecular detection. We have also extended this molecular recognition technique to neurotransmitters, producing the first fluorescent sensor for dopamine. Another area of advancement in biosensor development is the use of near infrared fluorescent carbon nanotube sensors for in-vivo detection. Here, we show that PEG-ligated d(AAAT)7 DNA wrapped SWNT are selective for nitric oxide, a vasodilator of blood vessels, and can be tail vein injected into mice and localized within the viable mouse liver. We use an SJL mouse model to study liver inflammation in vivo using the spatially and spectrally resolved nIR signature of the localized SWNT sensors.

Empathic Accuracy in Male Adolescents with Conduct Disorder and Higher versus Lower Levels of Callous-Unemotional Traits.

PubMed

Martin-Key, N; Brown, T; Fairchild, G

2017-10-01

Adolescents with disruptive behavior disorders are reported to show deficits in empathy and emotion recognition. However, prior studies have mainly used questionnaires to measure empathy or experimental paradigms that are lacking in ecological validity. We used an empathic accuracy (EA) task to study EA, emotion recognition, and affective empathy in 77 male adolescents aged 13-18 years: 37 with Conduct Disorder (CD) and 40 typically-developing controls. The CD sample was divided into higher callous-emotional traits (CD/CU+) and lower callous-unemotional traits (CD/CU-) subgroups using a median split. Participants watched films of actors recalling happy, sad, surprised, angry, disgusted or fearful autobiographical experiences and provided continuous ratings of emotional intensity (assessing EA), as well as naming the emotion (recognition) and reporting the emotion they experienced themselves (affective empathy). The CD and typically-developing groups did not significantly differ in EA and there were also no differences between the CD/CU+ and CD/CU- subgroups. Participants with CD were significantly less accurate than controls in recognizing sadness, fear, and disgust, all ps < 0.050, rs ≥ 0.30, whilst the CD/CU- and CD/CU+ subgroups did not differ in emotion recognition. Participants with CD also showed affective empathy deficits for sadness, fear, and disgust relative to controls, all ps < 0.010, rs ≥ 0.33, whereas the CD/CU+ and CD/CU- subgroups did not differ in affective empathy. These results extend prior research by demonstrating affective empathy and emotion recognition deficits in adolescents with CD using a more ecologically-valid task, and challenge the view that affective empathy deficits are specific to CD/CU+.

Developments in Molecular Recognition and Sensing at Interfaces

PubMed Central

Ariga, Katsuhiko; Hill, Jonathan P.; Endo, Hiroshi

2007-01-01

In biological systems, molecular recognition events occur mostly within interfacial environments such as at membrane surfaces, enzyme reaction sites, or at the interior of the DNA double helix. Investigation of molecular recognition at model interfaces provides great insights into biological phenomena. Molecular recognition at interfaces not only has relevance to biological systems but is also important for modern applications such as high sensitivity sensors. Selective binding of guest molecules in solution to host molecules located at solid surfaces is crucial for electronic or photonic detection of analyte substances. In response to these demands, molecular recognition at interfaces has been investigated extensively during the past two decades using Langmuir monolayers, self-assembled monolayers, and lipid assemblies as recognition media. In this review, advances of molecular recognition at interfaces are briefly summarized.

Facial Emotion Recognition in Child Psychiatry: A Systematic Review

ERIC Educational Resources Information Center

Collin, Lisa; Bindra, Jasmeet; Raju, Monika; Gillberg, Christopher; Minnis, Helen

2013-01-01

This review focuses on facial affect (emotion) recognition in children and adolescents with psychiatric disorders other than autism. A systematic search, using PRISMA guidelines, was conducted to identify original articles published prior to October 2011 pertaining to face recognition tasks in case-control studies. Used in the qualitative…

The association between PTSD and facial affect recognition.

PubMed

Williams, Christian L; Milanak, Melissa E; Judah, Matt R; Berenbaum, Howard

2018-05-05

The major aims of this study were to examine how, if at all, having higher levels of PTSD would be associated with performance on a facial affect recognition task in which facial expressions of emotion are superimposed on emotionally valenced, non-face images. College students with trauma histories (N = 90) completed a facial affect recognition task as well as measures of exposure to traumatic events, and PTSD symptoms. When the face and context matched, participants with higher levels of PTSD were significantly more accurate. When the face and context were mismatched, participants with lower levels of PTSD were more accurate than were those with higher levels of PTSD. These findings suggest that PTSD is associated with how people process affective information. Furthermore, these results suggest that the enhanced attention of people with higher levels of PTSD to affective information can be either beneficial or detrimental to their ability to accurately identify facial expressions of emotion. Limitations, future directions and clinical implications are discussed. Copyright © 2018 Elsevier B.V. All rights reserved.

Effect of Dopamine Therapy on Nonverbal Affect Burst Recognition in Parkinson's Disease

PubMed Central

Péron, Julie; Grandjean, Didier; Drapier, Sophie; Vérin, Marc

2014-01-01

Background Parkinson's disease (PD) provides a model for investigating the involvement of the basal ganglia and mesolimbic dopaminergic system in the recognition of emotions from voices (i.e., emotional prosody). Although previous studies of emotional prosody recognition in PD have reported evidence of impairment, none of them compared PD patients at different stages of the disease, or ON and OFF dopamine replacement therapy, making it difficult to determine whether their impairment was due to general cognitive deterioration or to a more specific dopaminergic deficit. Methods We explored the involvement of the dopaminergic pathways in the recognition of nonverbal affect bursts (onomatopoeias) in 15 newly diagnosed PD patients in the early stages of the disease, 15 PD patients in the advanced stages of the disease and 15 healthy controls. The early PD group was studied in two conditions: ON and OFF dopaminergic therapy. Results Results showed that the early PD patients performed more poorly in the ON condition than in the OFF one, for overall emotion recognition, as well as for the recognition of anger, disgust and fear. Additionally, for anger, the early PD ON patients performed more poorly than controls. For overall emotion recognition, both advanced PD patients and early PD ON patients performed more poorly than controls. Analysis of continuous ratings on target and nontarget visual analog scales confirmed these patterns of results, showing a systematic emotional bias in both the advanced PD and early PD ON (but not OFF) patients compared with controls. Conclusions These results i) confirm the involvement of the dopaminergic pathways and basal ganglia in emotional prosody recognition, and ii) suggest a possibly deleterious effect of dopatherapy on affective abilities in the early stages of PD. PMID:24651759

A global optimization algorithm for protein surface alignment

PubMed Central

2010-01-01

Background A relevant problem in drug design is the comparison and recognition of protein binding sites. Binding sites recognition is generally based on geometry often combined with physico-chemical properties of the site since the conformation, size and chemical composition of the protein surface are all relevant for the interaction with a specific ligand. Several matching strategies have been designed for the recognition of protein-ligand binding sites and of protein-protein interfaces but the problem cannot be considered solved. Results In this paper we propose a new method for local structural alignment of protein surfaces based on continuous global optimization techniques. Given the three-dimensional structures of two proteins, the method finds the isometric transformation (rotation plus translation) that best superimposes active regions of two structures. We draw our inspiration from the well-known Iterative Closest Point (ICP) method for three-dimensional (3D) shapes registration. Our main contribution is in the adoption of a controlled random search as a more efficient global optimization approach along with a new dissimilarity measure. The reported computational experience and comparison show viability of the proposed approach. Conclusions Our method performs well to detect similarity in binding sites when this in fact exists. In the future we plan to do a more comprehensive evaluation of the method by considering large datasets of non-redundant proteins and applying a clustering technique to the results of all comparisons to classify binding sites. PMID:20920230

Reaction Time of Facial Affect Recognition in Asperger's Disorder for Cartoon and Real, Static and Moving Faces

ERIC Educational Resources Information Center

Miyahara, Motohide; Bray, Anne; Tsujii, Masatsugu; Fujita, Chikako; Sugiyama, Toshiro

2007-01-01

This study used a choice reaction-time paradigm to test the perceived impairment of facial affect recognition in Asperger's disorder. Twenty teenagers with Asperger's disorder and 20 controls were compared with respect to the latency and accuracy of response to happy or disgusted facial expressions, presented in cartoon or real images and in…

Distinct roles of beta1 metal ion-dependent adhesion site (MIDAS), adjacent to MIDAS (ADMIDAS), and ligand-associated metal-binding site (LIMBS) cation-binding sites in ligand recognition by integrin alpha2beta1.

PubMed

Valdramidou, Dimitra; Humphries, Martin J; Mould, A Paul

2008-11-21

Integrin-ligand interactions are regulated in a complex manner by divalent cations, and previous studies have identified ligand-competent, stimulatory, and inhibitory cation-binding sites. In collagen-binding integrins, such as alpha2beta1, ligand recognition takes place exclusively at the alpha subunit I domain. However, activation of the alphaI domain depends on its interaction with a structurally similar domain in the beta subunit known as the I-like or betaI domain. The top face of the betaI domain contains three cation-binding sites: the metal-ion dependent adhesion site (MIDAS), the ADMIDAS (adjacent to MIDAS), and LIMBS (ligand-associated metal-binding site). The role of these sites in controlling ligand binding to the alphaI domain has yet to be elucidated. Mutation of the MIDAS or LIMBS completely blocked collagen binding to alpha2beta1; in contrast mutation of the ADMIDAS reduced ligand recognition but this effect could be overcome by the activating monoclonal antibody TS2/16. Hence, the MIDAS and LIMBS appear to be essential for the interaction between alphaI and betaI, whereas occupancy of the ADMIDAS has an allosteric effect on the conformation of betaI. An activating mutation in the alpha2 I domain partially restored ligand binding to the MIDAS and LIMBS mutants. Analysis of the effects of Ca(2+), Mg(2+), and Mn(2+) on ligand binding to these mutants showed that the MIDAS is a ligand-competent site through which Mn(2+) stimulates ligand binding, whereas the LIMBS is a stimulatory Ca(2+)-binding site, occupancy of which increases the affinity of Mg(2+) for the MIDAS.

The time course of ventrolateral prefrontal cortex involvement in memory formation.

PubMed

Machizawa, Maro G; Kalla, Roger; Walsh, Vincent; Otten, Leun J

2010-03-01

Human neuroimaging studies have implicated a number of brain regions in long-term memory formation. Foremost among these is ventrolateral prefrontal cortex. Here, we used double-pulse transcranial magnetic stimulation (TMS) to assess whether the contribution of this part of cortex is crucial for laying down new memories and, if so, to examine the time course of this process. Healthy adult volunteers performed an incidental encoding task (living/nonliving judgments) on sequences of words. In separate series, the task was performed either on its own or while TMS was applied to one of two sites of experimental interest (left/right anterior inferior frontal gyrus) or a control site (vertex). TMS pulses were delivered at 350, 750, or 1,150 ms following word onset. After a delay of 15 min, memory for the items was probed with a recognition memory test including confidence judgments. TMS to all three sites nonspecifically affected the speed and accuracy with which judgments were made during the encoding task. However, only TMS to prefrontal cortex affected later memory performance. Stimulation of left or right inferior frontal gyrus at all three time points reduced the likelihood that a word would later be recognized by a small, but significant, amount (approximately 4%). These findings indicate that bilateral ventrolateral prefrontal cortex plays an essential role in memory formation, exerting its influence between > or = 350 and 1,150 ms after an event is encountered.

Molecular mechanisms of substrate recognition and specificity of botulinum neurotoxin serotype F.

PubMed

Chen, Sheng; Wan, Hoi Ying

2011-01-15

BoNTs (botulinum neurotoxins) are both deadly neurotoxins and natural toxins that are widely used in protein therapies to treat numerous neurological disorders of dystonia and spinal spasticity. Understanding the mechanism of action and substrate specificity of BoNTs is a prerequisite to develop antitoxin and novel BoNT-derived protein therapy. To date, there is a lack of detailed information with regard to how BoNTs recognize and hydrolyse the substrate VAMP-2 (vesicle-associated membrane protein 2), even though it is known to be cleaved by four of the seven BoNT serotypes, B, D, F, G and TeNT (tetanus neurotoxin). In the present study we dissected the molecular mechanisms of VAMP-2 recognition by BoNT serotype F for the first time. The initial substrate recognition was mediated through sequential binding of VAMP-2 to the B1, B2 and B3 pockets in LC/F (light chain of BoNT serotype F), which directed VAMP-2 to the active site of LC/F and stabilized the active site substrate recognition, where the P2, P1' and P2' sites of VAMP-2 were specifically recognized by the S2, S1' and S2' pockets of LC/F to promote substrate hydrolysis. The understanding of the molecular mechanisms of LC/F substrate recognition provides insights into the development of antitoxins and engineering novel BoNTs to optimize current therapy and extend therapeutic interventions.

Chain Assembly and Disassembly Processes Differently Affect the Conformational Space of Ubiquitin Chains.

PubMed

Kniss, Andreas; Schuetz, Denise; Kazemi, Sina; Pluska, Lukas; Spindler, Philipp E; Rogov, Vladimir V; Husnjak, Koraljka; Dikic, Ivan; Güntert, Peter; Sommer, Thomas; Prisner, Thomas F; Dötsch, Volker

2018-02-06

Ubiquitination is the most versatile posttranslational modification. The information is encoded by linkage type as well as chain length, which are translated by ubiquitin binding domains into specific signaling events. Chain topology determines the conformational space of a ubiquitin chain and adds an additional regulatory layer to this ubiquitin code. In particular, processes that modify chain length will be affected by chain conformations as they require access to the elongation or cleavage sites. We investigated conformational distributions in the context of chain elongation and disassembly using pulsed electron-electron double resonance spectroscopy in combination with molecular modeling. Analysis of the conformational space of diubiquitin revealed conformational selection or remodeling as mechanisms for chain recognition during elongation or hydrolysis, respectively. Chain elongation to tetraubiquitin increases the sampled conformational space, suggesting that a high intrinsic flexibility of K48-linked chains may contribute to efficient proteasomal degradation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Exploration of G-quadruplex function in c-Myb gene and its transcriptional regulation by topotecan.

PubMed

Li, Fangyuan; Zhou, Jiang; Xu, Ming; Yuan, Gu

2018-02-01

Our bioinformatics research shows that there are four G-rich sequences (S1-S4) in the upstream region of the transcription start site of c-Myb gene, and we have proved that these sequences have the ability to form G-quadruplex structures. This work mainly focuses on G-quadruplex function, recognition and transcription regulation in c-Myb gene, revealing a novel regulatory element in c-Myb proximal promoter region, and its transcription regulation by G-quadruplex binder. The research has identified that the enhancer effect in c-Myb transcription was primarily affected by the G-quadruplex formed by S1 sequence, and the up-regulation effect may due to the removal of repressive progress of MZF-1 by stabilizing G-quadruplex. Attentions were being paid to the development of G-quadruplex binders for selective recognition, and topotecan was found to have high binding affinity in vitro and could effectively affect the c-Myb transcription activities in cells. The regulation of G-quadruplex with binders in transcriptional, translational levels by Q-RT-PCR and western blot was in expectation of providing a strategy for gene expression modulation. In conclusion, our study revealed a G-quadruplex structure in c-Myb proximal promoter region, which was of great importance in the regulation of c-Myb function. Copyright © 2017 Elsevier B.V. All rights reserved.

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.

Deficits in facial affect recognition among antisocial populations: a meta-analysis.

PubMed

Marsh, Abigail A; Blair, R J R

2008-01-01

Individuals with disorders marked by antisocial behavior frequently show deficits in recognizing displays of facial affect. Antisociality may be associated with specific deficits in identifying fearful expressions, which would implicate dysfunction in neural structures that subserve fearful expression processing. A meta-analysis of 20 studies was conducted to assess: (a) if antisocial populations show any consistent deficits in recognizing six emotional expressions; (b) beyond any generalized impairment, whether specific fear recognition deficits are apparent; and (c) if deficits in fear recognition are a function of task difficulty. Results show a robust link between antisocial behavior and specific deficits in recognizing fearful expressions. This impairment cannot be attributed solely to task difficulty. These results suggest dysfunction among antisocial individuals in specified neural substrates, namely the amygdala, involved in processing fearful facial affect.

DNA looping by FokI: the impact of synapse geometry on loop topology at varied site orientations

PubMed Central

Rusling, David A.; Laurens, Niels; Pernstich, Christian; Wuite, Gijs J. L.; Halford, Stephen E.

2012-01-01

Most restriction endonucleases, including FokI, interact with two copies of their recognition sequence before cutting DNA. On DNA with two sites they act in cis looping out the intervening DNA. While many restriction enzymes operate symmetrically at palindromic sites, FokI acts asymmetrically at a non-palindromic site. The directionality of its sequence means that two FokI sites can be bridged in either parallel or anti-parallel alignments. Here we show by biochemical and single-molecule biophysical methods that FokI aligns two recognition sites on separate DNA molecules in parallel and that the parallel arrangement holds for sites in the same DNA regardless of whether they are in inverted or repeated orientations. The parallel arrangement dictates the topology of the loop trapped between sites in cis: the loop from inverted sites has a simple 180° bend, while that with repeated sites has a convoluted 360° turn. The ability of FokI to act at asymmetric sites thus enabled us to identify the synapse geometry for sites in trans and in cis, which in turn revealed the relationship between synapse geometry and loop topology. PMID:22362745

Recognition in Programmes for Children with Special Needs

ERIC Educational Resources Information Center

Šmid, Marjeta

2016-01-01

The purpose of this article is to examine the factors that affect the inclusion of pupils in programmes for children with special needs from the perspective of the theory of recognition. The concept of recognition, which includes three aspects of social justice (economic, cultural and political), argues that the institutional arrangements that…

Late-onset spastic paraplegia: Aberrant SPG11 transcripts generated by a novel splice site donor mutation.

PubMed

Kawarai, Toshitaka; Miyamoto, Ryosuke; Mori, Atsuko; Oki, Ryosuke; Tsukamoto-Miyashiro, Ai; Matsui, Naoko; Miyazaki, Yoshimichi; Orlacchio, Antonio; Izumi, Yuishin; Nishida, Yoshihiko; Kaji, Ryuji

2015-12-15

We identified a novel homozygous mutation in the splice site donor (SSD) of intron 30 (c.5866+1G>A) in consanguineous Japanese SPG11 siblings showing late-onset spastic paraplegia using the whole-exome sequencing. Phenotypic variability was observed, including age-at-onset, dysarthria and pes cavus. Coding DNA sequencing revealed that the mutation affected the recognition of the constitutive SSD of intron 30, splicing upstream onto a nearby cryptic SSD in exon 30. The use of constitutive splice sites of intron 29 was confirmed by sequencing. The mutant transcripts are mostly subject to degradation by the nonsense-mediated mRNA decay system. SPG11 transcripts, escaping from the nonsense-mediated mRNA decay pathway, would generate a truncated protein (p.Tyr1900Phefs5X) containing the first 1899 amino acids and followed by 4 aberrant amino acids. This study showed a successful clinical application of whole-exome sequencing in spastic paraplegia and demonstrated a further evidence of allelic heterogeneity in SPG11. The confirmation of aberrant transcript by splice site mutation is a prerequisite for a more precise molecular diagnosis. Copyright © 2015 Elsevier B.V. All rights reserved.

Facial affect recognition in early and late-stage schizophrenia patients.

PubMed

Romero-Ferreiro, María Verónica; Aguado, Luis; Rodriguez-Torresano, Javier; Palomo, Tomás; Rodriguez-Jimenez, Roberto; Pedreira-Massa, José Luis

2016-04-01

Prior studies have shown deficits in social cognition and emotion perception in first-episode psychosis (FEP) and multi-episode schizophrenia (MES) patients. These studies compared patients at different stages of the illness with only a single control group which differed in age from at least one clinical group. The present study provides new evidence of a differential pattern of deficit in facial affect recognition in FEP and MES patients using a double age-matched control design. Compared to their controls, FEP patients only showed impaired recognition of fearful faces (p=.007). In contrast to this, the MES patients showed a more generalized deficit compared to their age-matched controls, with impaired recognition of angry, sad and fearful faces (ps<.01) and an increased misattribution of emotional meaning to neutral faces. PANSS scores of FEP patients on Depressed factor correlated positively with the accuracy to recognize fearful expressions (r=.473). For the MES group fear recognition correlated positively with negative PANSS factor (r=.498) and recognition of sad and neutral expressions was inversely correlated with disorganized PANSS factor (r=-.461 and r=-.541, respectively). These results provide evidence that a generalized impairment of affect recognition is observed in advanced-stage patients and is not characteristic of the early stages of schizophrenia. Moreover, the finding that anomalous attribution of emotional meaning to neutral faces is observed only in MES patients suggests that an increased attribution of salience to social stimuli is a characteristic of social cognition in advanced stages of the disorder. Copyright © 2016 Elsevier B.V. All rights reserved.

Recognition intent and visual word recognition.

PubMed

Wang, Man-Ying; Ching, Chi-Le

2009-03-01

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

Statistical Profiling of One Promiscuous Protein Binding Site: Illustrated by Urokinase Catalytic Domain.

PubMed

Cerisier, Natacha; Regad, Leslie; Triki, Dhoha; Petitjean, Michel; Flatters, Delphine; Camproux, Anne-Claude

2017-10-01

While recent literature focuses on drug promiscuity, the characterization of promiscuous binding sites (ability to bind several ligands) remains to be explored. Here, we present a proteochemometric modeling approach to analyze diverse ligands and corresponding multiple binding sub-pockets associated with one promiscuous binding site to characterize protein-ligand recognition. We analyze both geometrical and physicochemical profile correspondences. This approach was applied to examine the well-studied druggable urokinase catalytic domain inhibitor binding site, which results in a large number of complex structures bound to various ligands. This approach emphasizes the importance of jointly characterizing pocket and ligand spaces to explore the impact of ligand diversity on sub-pocket properties and to establish their main profile correspondences. This work supports an interest in mining available 3D holo structures associated with a promiscuous binding site to explore its main protein-ligand recognition tendency. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Enhancement of GABAergic transmission by zolpidem, an imidazopyridine with preferential affinity for type I benzodiazepine receptors.

PubMed

Biggio, G; Concas, A; Corda, M G; Serra, M

1989-02-28

The effect of zolpidem, an imidazopyridine derivative with high affinity at the type I benzodiazepine recognition site, on the function of the GABAA/ionophore receptor complex was studied in vitro. Zolpidem, mimicking the action of diazepam, increased [3H]GABA binding, enhanced muscimol-stimulated 36Cl- uptake and reduced [35S]TBPS binding in rat cortical membrane preparations. Zolpidem was less effective than diazepam on the above parameters. Zolpidem induced a lower increase of [3H]GABA binding (23 vs. 35%) and muscimol-stimulated 36Cl- uptake (22 vs. 40%) and a smaller decrease of [35S]TBPS binding (47 vs. 77%) than diazepam. The finding that zolpidem enhanced the function of GABAergic synapses with an efficacy qualitatively and quantitatively different from that of diazepam suggests that this compound is a partial agonist at the benzodiazepine recognition site. Thus, our results are consistent with the view that the biochemical and pharmacological profile of a benzodiazepine recognition site ligand reflects its efficacy to enhance GABAergic transmission. Whether the preferential affinity of zolpidem at the type I site is involved in its atypical biochemical and pharmacological profile remains to be clarified.

Recognition of DNA abasic site nanocavity by fluorophore-switched probe: Suitable for all sequence environments

NASA Astrophysics Data System (ADS)

Wang, Ying; Hu, Yuehua; Wu, Tao; Zhang, Lihua; Liu, Hua; Zhou, Xiaoshun; Shao, Yong

2016-01-01

Removal of a damaged base in DNA produces an abasic site (AP site) nanocavity. If left un-repaired in vivo by the specific enzyme, this nanocavity will result in nucleotide mutation in the following DNA replication. Therefore, selective recognition of AP site nanocavity by small molecules is important for identification of such DNA damage and development of genetic drugs. In this work, we investigate the fluorescence behavior of isoquinoline alkaloids including palmatine (PAL), berberine (BER), epiberberine (EPI), jatrorrhizine (JAT), coptisine (COP), coralyne (COR), worenine (WOR), berberrubine (BEU), sanguinarine (SAN), chelerythrine (CHE), and nitidine (NIT) upon binding with the AP nanocavity. PAL is screened out as the most efficient fluorophore-switched probe to recognize the AP nanocavity over the fully matched DNA. Its fluorescence enhancement occurs for all of the AP nanocavity sequence environments, which has not been achieved by the previously used probes. The bridged π conjugation effect should partially contribute to the AP nanocavity-specific fluorescence, as opposed to the solvent effect. Due to the strong binding with the AP nanocavity, PAL will find wide applications in the DNA damage recognition and sensor development.

Identification of amino acids in the N-terminal SH2 domain of phospholipase C gamma 1 important in the interaction with epidermal growth factor receptor.

PubMed

Gergel, J R; McNamara, D J; Dobrusin, E M; Zhu, G; Saltiel, A R; Miller, W T

1994-12-13

Photoaffinity labeling and site-directed mutagenesis have been used to identify amino acid residues of the phospholipase C gamma 1 (PLC gamma 1) N-terminal SH2 domain involved in recognition of the activated epidermal growth factor receptor (EGFR). The photoactive amino acid p-benzoylphenylalanine (Bpa) was incorporated into phosphotyrosine-containing peptides derived from EGFR autophosphorylation sites Tyr992 and Tyr1068. Irradiation of these labels in the presence of SH2 domains showed cross-linking which was time-dependent and specific; labeling was inhibited with non-Bpa-containing peptides from EGFR in molar excess. The phosphotyrosine residue on the peptides was important for SH2 recognition, as dephosphorylated peptides did not cross-link. Radiolabeled peptides were used to identify sites of cross-linking to the N-terminal SH2 of PLC gamma 1. Bpa peptide-SH2 complexes were digested with trypsin, and radioactive fragments were purified by HPLC and analyzed by Edman sequencing. These experiments showed Arg562 and an additional site in the alpha A-beta B region of the SH2 domain, most likely Glu587, to be labeled by the Tyr992-derived peptide. Similar analysis of the reaction with the Tyr1068-derived photoaffinity label identified Leu653 as the cross-linked site. Mutation of the neighboring residues of Glu587 decreased photo-cross-linking, emphasizing the importance of this region of the molecule for recognition. These results are consistent with evidence from the v-Src crystal structure and implicate the loop spanning residues Gln640-Ser654 of PLC gamma 1 in specific recognition of phosphopeptides.

Conserved sequence-specific lincRNA-steroid receptor interactions drive transcriptional repression and direct cell fate

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

Hudson, William H.; Pickard, Mark R.; de Vera, Ian Mitchelle S.

2014-12-23

The majority of the eukaryotic genome is transcribed, generating a significant number of long intergenic noncoding RNAs (lincRNAs). Although lincRNAs represent the most poorly understood product of transcription, recent work has shown lincRNAs fulfill important cellular functions. In addition to low sequence conservation, poor understanding of structural mechanisms driving lincRNA biology hinders systematic prediction of their function. Here we report the molecular requirements for the recognition of steroid receptors (SRs) by the lincRNA growth arrest-specific 5 (Gas5), which regulates steroid-mediated transcriptional regulation, growth arrest and apoptosis. We identify the functional Gas5-SR interface and generate point mutations that ablate the SR-Gas5more » lincRNA interaction, altering Gas5-driven apoptosis in cancer cell lines. Further, we find that the Gas5 SR-recognition sequence is conserved among haplorhines, with its evolutionary origin as a splice acceptor site. This study demonstrates that lincRNAs can recognize protein targets in a conserved, sequence-specific manner in order to affect critical cell functions.« less

Time course of brain activation elicited by basic emotions.

PubMed

Hot, Pascal; Sequeira, Henrique

2013-11-13

Whereas facial emotion recognition protocols have shown that each discrete emotion has a specific time course of brain activation, there is no electrophysiological evidence to support these findings for emotional induction by complex pictures. Our objective was to specify the differences between the time courses of brain activation elicited by feelings of happiness and, with unpleasant pictures, by feelings of disgust and sadness. We compared event-related potentials (ERPs) elicited by the watching of high-arousing pictures from the International Affective Picture System, selected to induce specific emotions. In addition to a classical arousal effect on late positive components, we found specific ERP patterns for each emotion in early temporal windows (<200 ms). Disgust was the first emotion to be associated with different brain processing after 140 ms, whereas happiness and sadness differed in ERPs elicited at the frontal and central sites after 160 ms. Our findings highlight the limits of the classical averaging of ERPs elicited by different emotions inside the same valence and suggest that each emotion could elicit a specific temporal pattern of brain activation, similar to those observed with emotional face recognition.

PEG-Stabilized Core–Shell Surface-Imprinted Nanoparticles

PubMed Central

Moczko, Ewa; Guerreiro, Antonio; Piletska, Elena; Piletsky, Sergey

2016-01-01

Here we present a simple technique to produce target-specific molecularly imprinted polymeric nanoparticles (MIP NPs) and their surface modification in order to prevent the aggregation process that is ever-present in most nanomaterial suspensions/dispersions. Specifically, we studied the influence of surface modification of MIP NPs with polymerizable poly(ethylene glycol) on their degree of stability in water, in phosphate buffer, and in the presence of serum proteins. Grafting a polymer shell on the surface of nanoparticles decreases the surface energy, enhances the polarity, and as a result improves the dispersibility, storage, and colloidal stability as compared to those of core (unmodified) particles. Because of the unique solid-phase approach used for synthesis, the binding sites of MIP NPs are protected during grafting, and the recognition properties of nanoparticles are not affected. These results are significant for developing nanomaterials with selective molecular recognition, increased biocompatibility, and stability in solution. Materials synthesized this way have the potential to be used in a variety of technological fields, including in vivo applications such as drug delivery and imaging. PMID:23855734

Redundancy of primary RNA-binding functions of the bacterial transcription terminator Rho.

PubMed

Shashni, Rajesh; Qayyum, M Zuhaib; Vishalini, V; Dey, Debashish; Sen, Ranjan

2014-09-01

The bacterial transcription terminator, Rho, terminates transcription at half of the operons. According to the classical model derived from in vitro assays on a few terminators, Rho is recruited to the transcription elongation complex (EC) by recognizing specific sites (rut) on the nascent RNA. Here, we explored the mode of in vivo recruitment process of Rho. We show that sequence specific recognition of the rut site, in majority of the Rho-dependent terminators, can be compromised to a great extent without seriously affecting the genome-wide termination function as well as the viability of Escherichia coli. These terminators function optimally only through a NusG-assisted recruitment and activation of Rho. Our data also indicate that at these terminators, Rho-EC-bound NusG interaction facilitates the isomerization of Rho into a translocase-competent form by stabilizing the interactions of mRNA with the secondary RNA binding site, thereby overcoming the defects of the primary RNA binding functions. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Discovering amino acid patterns on binding sites in protein complexes

PubMed Central

Kuo, Huang-Cheng; Ong, Ping-Lin; Lin, Jung-Chang; Huang, Jen-Peng

2011-01-01

Discovering amino acid (AA) patterns on protein binding sites has recently become popular. We propose a method to discover the association relationship among AAs on binding sites. Such knowledge of binding sites is very helpful in predicting protein-protein interactions. In this paper, we focus on protein complexes which have protein-protein recognition. The association rule mining technique is used to discover geographically adjacent amino acids on a binding site of a protein complex. When mining, instead of treating all AAs of binding sites as a transaction, we geographically partition AAs of binding sites in a protein complex. AAs in a partition are treated as a transaction. For the partition process, AAs on a binding site are projected from three-dimensional to two-dimensional. And then, assisted with a circular grid, AAs on the binding site are placed into grid cells. A circular grid has ten rings: a central ring, the second ring with 6 sectors, the third ring with 12 sectors, and later rings are added to four sectors in order. As for the radius of each ring, we examined the complexes and found that 10Å is a suitable range, which can be set by the user. After placing these recognition complexes on the circular grid, we obtain mining records (i.e. transactions) from each sector. A sector is regarded as a record. Finally, we use the association rule to mine these records for frequent AA patterns. If the support of an AA pattern is larger than the predetermined minimum support (i.e. threshold), it is called a frequent pattern. With these discovered patterns, we offer the biologists a novel point of view, which will improve the prediction accuracy of protein-protein recognition. In our experiments, we produced the AA patterns by data mining. As a result, we found that arginine (arg) most frequently appears on the binding sites of two proteins in the recognition protein complexes, while cysteine (cys) appears the fewest. In addition, if we discriminate the shape of binding sites between concave and convex further, we discover that patterns {arg, glu, asp} and {arg, ser, asp} on the concave shape of binding sites in a protein more frequently (i.e. higher probability) make contact with {lys} or {arg} on the convex shape of binding sites in another protein. Thus, we can confidently achieve a rate of at least 78%. On the other hand {val, gly, lys} on the convex surface of binding sites in proteins is more frequently in contact with {asp} on the concave site of another protein, and the confidence achieved is over 81%. Applying data mining in biology can reveal more facts that may otherwise be ignored or not easily discovered by the naked eye. Furthermore, we can discover more relationships among AAs on binding sites by appropriately rotating these residues on binding sites from a three-dimension to two-dimension perspective. We designed a circular grid to deposit the data, which total to 463 records consisting of AAs. Then we used the association rules to mine these records for discovering relationships. The proposed method in this paper provides an insight into the characteristics of binding sites for recognition complexes. PMID:21464838

Development of the Ability to Use Facial, Situational, and Vocal Cues to Infer Others' Affective States.

ERIC Educational Resources Information Center

Farber, Ellen A.; Moely, Barbara E.

Results of two studies investigating children's abilities to use different kinds of cues to infer another's affective state are reported in this paper. In the first study, 48 children (3, 4, and 6 to 7 years of age) were given three different kinds of tasks (interpersonal task, facial recognition task, and vocal recognition task). A cross-age…

Metacognitive deficits predict future levels of negative symptoms in schizophrenia controlling for neurocognition, affect recognition, and self-expectation of goal attainment.

PubMed

Lysaker, Paul H; Kukla, Marina; Dubreucq, Julien; Gumley, Andrew; McLeod, Hamish; Vohs, Jenifer L; Buck, Kelly D; Minor, Kyle S; Luther, Lauren; Leonhardt, Bethany L; Belanger, Elizabeth A; Popolo, Raffaele; Dimaggio, Giancarlo

2015-10-01

The recalcitrance of negative symptoms in the face of pharmacologic treatment has spurred interest in understanding the psychological factors that contribute to their formation and persistence. Accordingly, this study investigated whether deficits in metacognition, or the ability to form integrated ideas about oneself, others, and the world, prospectively predicted levels of negative symptoms independent of deficits in neurocognition, affect recognition and defeatist beliefs. Participants were 53 adults with a schizophrenia spectrum disorder. Prior to entry into a rehabilitation program, all participants completed concurrent assessments of metacognition with the Metacognitive Assessment Scale-Abbreviated, negative symptoms with the Positive and Negative Syndrome Scale, neurocognition with the MATRICS battery, affect recognition with the Bell Lysaker Emotion Recognition Task, and one form of defeatist beliefs with the Recovery Assessment Scale. Negative symptoms were then reassessed one week, 9weeks, and 17weeks after entry into the program. A mixed effects regression model revealed that after controlling for baseline negative symptoms, a general index of neurocognition, defeatist beliefs and capacity for affect recognition, lower levels of metacognition predicted higher levels of negative symptoms across all subsequent time points. Poorer metacognition was able to predict later levels of elevated negative symptoms even after controlling for initial levels of negative symptoms. Results may suggest that metacognitive deficits are a risk factor for elevated levels of negative symptoms in the future. Clinical implications are also discussed. Published by Elsevier B.V.

psRNATarget: a plant small RNA target analysis server

PubMed Central

Dai, Xinbin; Zhao, Patrick Xuechun

2011-01-01

Plant endogenous non-coding short small RNAs (20–24 nt), including microRNAs (miRNAs) and a subset of small interfering RNAs (ta-siRNAs), play important role in gene expression regulatory networks (GRNs). For example, many transcription factors and development-related genes have been reported as targets of these regulatory small RNAs. Although a number of miRNA target prediction algorithms and programs have been developed, most of them were designed for animal miRNAs which are significantly different from plant miRNAs in the target recognition process. These differences demand the development of separate plant miRNA (and ta-siRNA) target analysis tool(s). We present psRNATarget, a plant small RNA target analysis server, which features two important analysis functions: (i) reverse complementary matching between small RNA and target transcript using a proven scoring schema, and (ii) target-site accessibility evaluation by calculating unpaired energy (UPE) required to ‘open’ secondary structure around small RNA’s target site on mRNA. The psRNATarget incorporates recent discoveries in plant miRNA target recognition, e.g. it distinguishes translational and post-transcriptional inhibition, and it reports the number of small RNA/target site pairs that may affect small RNA binding activity to target transcript. The psRNATarget server is designed for high-throughput analysis of next-generation data with an efficient distributed computing back-end pipeline that runs on a Linux cluster. The server front-end integrates three simplified user-friendly interfaces to accept user-submitted or preloaded small RNAs and transcript sequences; and outputs a comprehensive list of small RNA/target pairs along with the online tools for batch downloading, key word searching and results sorting. The psRNATarget server is freely available at http://plantgrn.noble.org/psRNATarget/. PMID:21622958

The effect of fenoterol stereochemistry on the β2 adrenergic receptor system: ligand directed chiral recognition

PubMed Central

Jozwiak, Krzysztof; Plazinska, Anita; Toll, Lawrence; Jimenez, Lucita; Woo, Anthony Yiu-Ho; Xiao, Rui-Ping; Wainer, Irving W.

2011-01-01

The β2 adrenergic receptor (β2-AR) is a model system for studying the ligand recognition process in G-protein coupled receptors. Fenoterol (FEN) is a β2-AR selective agonist that has two centers of chirality and exists as four stereoisomers. Radioligand binding studies determined that stereochemistry greatly influences the binding affinity. Subsequent Van’t Hoff analysis shows very different thermodynamics of binding depending on the stereoconfiguration of the molecule. The binding of (S,x’)-isomers is almost entirely enthalpy controlled whereas binding of (R,x’)-isomers is purely entropy driven. Stereochemistry of FEN molecule also affects the coupling of the receptor to different G proteins. In a rat cardiomyocyte contractility model, (R,R’)-FEN was shown to selectively activate Gs protein signaling while the (S,R’)- isomer activated both Gi and Gs protein. The overall data demonstrate that the chirality at the two chiral centers of the FEN molecule influences the magnitude of binding affinity, thermodynamics of local interactions within the binding site and the global mechanism of β2-AR activation. Differences in thermodynamic parameters and non-uniform G-protein coupling suggest a mechanism of chiral recognition in which observed enantioselectivities arise from the interaction of the (R,x’)-FEN stereoisomers with a different receptor conformation than the one with which the (S,x’)-isomer interacts. PMID:21618615

Effect of fenoterol stereochemistry on the β2 adrenergic receptor system: ligand-directed chiral recognition.

PubMed

Jozwiak, Krzysztof; Plazinska, Anita; Toll, Lawrence; Jimenez, Lucita; Woo, Anthony Yiu-Ho; Xiao, Rui-Ping; Wainer, Irving W

2011-01-01

The β(2) adrenergic receptor (β(2)-AR) is a model system for studying the ligand recognition process in G protein-coupled receptors. Fenoterol (FEN) is a β(2)-AR selective agonist that has two centers of chirality and exists as four stereoisomers. Radioligand binding studies determined that stereochemistry greatly influences the binding affinity. Subsequent Van't Hoff analysis shows very different thermodynamics of binding depending on the stereoconfiguration of the molecule. The binding of (S,x')-isomers is almost entirely enthalpy controlled whereas binding of (R,x')-isomers is purely entropy driven. Stereochemistry of FEN molecule also affects the coupling of the receptor to different G proteins. In a rat cardiomyocyte contractility model, (R,R')-FEN was shown to selectively activate G(s) protein signaling while the (S,R')-isomer activated both G(i) and G(s) protein. The overall data demonstrate that the chirality at the two chiral centers of the FEN molecule influences the magnitude of binding affinity, thermodynamics of local interactions within the binding site, and the global mechanism of β(2)-AR activation. Differences in thermodynamic parameters and nonuniform G-protein coupling suggest a mechanism of chiral recognition in which observed enantioselectivities arise from the interaction of the (R,x')-FEN stereoisomers with a different receptor conformation than the one with which the (S,x')-isomer interacts. Copyright © 2011 Wiley-Liss, Inc.

Facial-affect recognition deficit as a predictor of different aspects of social-communication impairment in traumatic brain injury.

PubMed

Rigon, Arianna; Turkstra, Lyn S; Mutlu, Bilge; Duff, Melissa C

2018-05-01

To examine the relationship between facial-affect recognition and different aspects of self- and proxy-reported social-communication impairment following moderate-severe traumatic brain injury (TBI). Forty-six adults with chronic TBI (>6 months postinjury) and 42 healthy comparison (HC) adults were administered the La Trobe Communication Questionnaire (LCQ) Self and Other forms to assess different aspects of communication competence and the Emotion Recognition Test (ERT) to measure their ability to recognize facial affects. Individuals with TBI underperformed HC adults in the ERT and self-reported, as well as were reported by close others, as having more communication problems than did HC adults. TBI group ERT scores were significantly and negatively correlated with LCQ-Other (but not LCQ-Self) scores (i.e., participants with lower emotion-recognition scores were rated by close others as having more communication problems). Multivariate regression analysis revealed that adults with higher ERT scores self-reported more problems with disinhibition-impulsivity and partner sensitivity and had fewer other-reported problems with disinhibition-impulsivity and conversational effectiveness. Our findings support growing evidence that emotion-recognition deficits play a role in specific aspects of social-communication outcomes after TBI and should be considered in treatment planning. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

The Low-Frequency Encoding Disadvantage: Word Frequency Affects Processing Demands

ERIC Educational Resources Information Center

Diana, Rachel A.; Reder, Lynne M.

2006-01-01

Low-frequency words produce more hits and fewer false alarms than high-frequency words in a recognition task. The low-frequency hit rate advantage has sometimes been attributed to processes that operate during the recognition test (e.g., L. M. Reder et al., 2000). When tasks other than recognition, such as recall, cued recall, or associative…

Emotion Recognition in Children and Adolescents with Autism Spectrum Disorders

ERIC Educational Resources Information Center

Kuusikko, Sanna; Haapsamo, Helena; Jansson-Verkasalo, Eira; Hurtig, Tuula; Mattila, Marja-Leena; Ebeling, Hanna; Jussila, Katja; Bolte, Sven; Moilanen, Irma

2009-01-01

We examined upper facial basic emotion recognition in 57 subjects with autism spectrum disorders (ASD) (M = 13.5 years) and 33 typically developing controls (M = 14.3 years) by using a standardized computer-aided measure (The Frankfurt Test and Training of Facial Affect Recognition, FEFA). The ASD group scored lower than controls on the total…

Thermodynamics of DNA target site recognition by homing endonucleases

PubMed Central

Eastberg, Jennifer H.; Smith, Audrey McConnell; Zhao, Lei; Ashworth, Justin; Shen, Betty W.; Stoddard, Barry L.

2007-01-01

The thermodynamic profiles of target site recognition have been surveyed for homing endonucleases from various structural families. Similar to DNA-binding proteins that recognize shorter target sites, homing endonucleases display a narrow range of binding free energies and affinities, mediated by structural interactions that balance the magnitude of enthalpic and entropic forces. While the balance of ΔH and TΔS are not strongly correlated with the overall extent of DNA bending, unfavorable ΔHbinding is associated with unstacking of individual base steps in the target site. The effects of deleterious basepair substitutions in the optimal target sites of two LAGLIDADG homing endonucleases, and the subsequent effect of redesigning one of those endonucleases to accommodate that DNA sequence change, were also measured. The substitution of base-specific hydrogen bonds in a wild-type endonuclease/DNA complex with hydrophobic van der Waals contacts in a redesigned complex reduced the ability to discriminate between sites, due to nonspecific ΔSbinding. PMID:17947319

Face recognition performance of individuals with Asperger syndrome on the Cambridge Face Memory Test.

PubMed

Hedley, Darren; Brewer, Neil; Young, Robyn

2011-12-01

Although face recognition deficits in individuals with Autism Spectrum Disorder (ASD), including Asperger syndrome (AS), are widely acknowledged, the empirical evidence is mixed. This in part reflects the failure to use standardized and psychometrically sound tests. We contrasted standardized face recognition scores on the Cambridge Face Memory Test (CFMT) for 34 individuals with AS with those for 42, IQ-matched non-ASD individuals, and age-standardized scores from a large Australian cohort. We also examined the influence of IQ, autistic traits, and negative affect on face recognition performance. Overall, participants with AS performed significantly worse on the CFMT than the non-ASD participants and when evaluated against standardized test norms. However, while 24% of participants with AS presented with severe face recognition impairment (>2 SDs below the mean), many individuals performed at or above the typical level for their age: 53% scored within +/- 1 SD of the mean and 9% demonstrated superior performance (>1 SD above the mean). Regression analysis provided no evidence that IQ, autistic traits, or negative affect significantly influenced face recognition: diagnostic group membership was the only significant predictor of face recognition performance. In sum, face recognition performance in ASD is on a continuum, but with average levels significantly below non-ASD levels of performance. Copyright © 2011, International Society for Autism Research, Wiley-Liss, Inc.

Social cues at encoding affect memory in 4-month-old infants.

PubMed

Kopp, Franziska; Lindenberger, Ulman

2012-01-01

Available evidence suggests that infants use adults' social cues for learning by the second half of the first year of life. However, little is known about the short-term or long-term effects of joint attention interactions on learning and memory in younger infants. In the present study, 4-month-old infants were familiarized with visually presented objects in either of two conditions that differed in the degree of joint attention (high vs. low). Brain activity in response to familiar and novel objects was assessed immediately after the familiarization phase (immediate recognition), and following a 1-week delay (delayed recognition). The latency of the Nc component differentiated between recognition of old versus new objects. Pb amplitude and latency were affected by joint attention in delayed recognition. Moreover, the frequency of infant gaze to the experimenter during familiarization differed between the two experimental groups and modulated the Pb response. Results show that joint attention affects the mechanisms of long-term retention in 4-month-old infants. We conclude that joint attention helps children at this young age to recognize the relevance of learned items.

Between Efficiency, Capability and Recognition: Competing Epistemes in Global Governance Reforms

ERIC Educational Resources Information Center

Chan, Jennifer

2007-01-01

This article examines global governance reforms as a site of contestation between three different "truths"/epistemes (the market, human rights principles, and cultural identity) in terms of the competing principles of efficiency, capability, and recognition. Nancy Fraser's conceptions of participation parity and a dialogical approach of…

Identifying differences in biased affective information processing in major depression.

PubMed

Gollan, Jackie K; Pane, Heather T; McCloskey, Michael S; Coccaro, Emil F

2008-05-30

This study investigates the extent to which participants with major depression differ from healthy comparison participants in the irregularities in affective information processing, characterized by deficits in facial expression recognition, intensity categorization, and reaction time to identifying emotionally salient and neutral information. Data on diagnoses, symptom severity, and affective information processing using a facial recognition task were collected from 66 participants, male and female between ages 18 and 54 years, grouped by major depressive disorder (N=37) or healthy non-psychiatric (N=29) status. Findings from MANCOVAs revealed that major depression was associated with a significantly longer reaction time to sad facial expressions compared with healthy status. Also, depressed participants demonstrated a negative bias towards interpreting neutral facial expressions as sad significantly more often than healthy participants. In turn, healthy participants interpreted neutral faces as happy significantly more often than depressed participants. No group differences were observed for facial expression recognition and intensity categorization. The observed effects suggest that depression has significant effects on the perception of the intensity of negative affective stimuli, delayed speed of processing sad affective information, and biases towards interpreting neutral faces as sad.

Age-related differences in brain electrical activity during extended continuous face recognition in younger children, older children and adults.

PubMed

Van Strien, Jan W; Glimmerveen, Johanna C; Franken, Ingmar H A; Martens, Vanessa E G; de Bruin, Eveline A

2011-09-01

To examine the development of recognition memory in primary-school children, 36 healthy younger children (8-9 years old) and 36 healthy older children (11-12 years old) participated in an ERP study with an extended continuous face recognition task (Study 1). Each face of a series of 30 faces was shown randomly six times interspersed with distracter faces. The children were required to make old vs. new decisions. Older children responded faster than younger children, but younger children exhibited a steeper decrease in latencies across the five repetitions. Older children exhibited better accuracy for new faces, but there were no age differences in recognition accuracy for repeated faces. For the N2, N400 and late positive complex (LPC), we analyzed the old/new effects (repetition 1 vs. new presentation) and the extended repetition effects (repetitions 1 through 5). Compared to older children, younger children exhibited larger frontocentral N2 and N400 old/new effects. For extended face repetitions, negativity of the N2 and N400 decreased in a linear fashion in both age groups. For the LPC, an ERP component thought to reflect recollection, no significant old/new or extended repetition effects were found. Employing the same face recognition paradigm in 20 adults (Study 2), we found a significant N400 old/new effect at lateral frontal sites and a significant LPC repetition effect at parietal sites, with LPC amplitudes increasing linearly with the number of repetitions. This study clearly demonstrates differential developmental courses for the N400 and LPC pertaining to recognition memory for faces. It is concluded that face recognition in children is mediated by early and probably more automatic than conscious recognition processes. In adults, the LPC extended repetition effect indicates that adult face recognition memory is related to a conscious and graded recollection process rather than to an automatic recognition process. © 2011 Blackwell Publishing Ltd.

A unique dual recognition hairpin probe mediated fluorescence amplification method for sensitive detection of uracil-DNA glycosylase and endonuclease IV activities.

PubMed

Wu, Yushu; Yan, Ping; Xu, Xiaowen; Jiang, Wei

2016-03-07

Uracil-DNA glycosylase (UDG) and endonuclease IV (Endo IV) play cooperative roles in uracil base-excision repair (UBER) and inactivity of either will interrupt the UBER to cause disease. Detection of UDG and Endo IV activities is crucial to evaluate the UBER process in fundamental research and diagnostic application. Here, a unique dual recognition hairpin probe mediated fluorescence amplification method was developed for sensitively and selectively detecting UDG and Endo IV activities. For detecting UDG activity, the uracil base in the probe was excised by the target enzyme to generate an apurinic/apyrimidinic (AP) site, achieving the UDG recognition. Then, the AP site was cleaved by a tool enzyme Endo IV, releasing a primer to trigger rolling circle amplification (RCA) reaction. Finally, the RCA reaction produced numerous repeated G-quadruplex sequences, which interacted with N-methyl-mesoporphyrin IX to generate an enhanced fluorescence signal. Alternatively, for detecting Endo IV activity, the uracil base in the probe was first converted into an AP site by a tool enzyme UDG. Next, the AP site was cleaved by the target enzyme, achieving the Endo IV recognition. The signal was then generated and amplified in the same way as those in the UDG activity assay. The detection limits were as low as 0.00017 U mL(-1) for UDG and 0.11 U mL(-1) for Endo IV, respectively. Moreover, UDG and Endo IV can be well distinguished from their analogs. This method is beneficial for properly evaluating the UBER process in function studies and disease prognoses.

DISTINCT ROLES OF β1 MIDAS, ADMIDAS AND LIMBS CATION-BINDING SITES IN LIGAND RECOGNITION BY INTEGRIN α2β1*

PubMed Central

Valdramidou, Dimitra; Humphries, Martin J.; Mould, A. Paul

2012-01-01

Integrin-ligand interactions are regulated in a complex manner by divalent cations, and previous studies have identified ligand-competent, stimulatory, and inhibitory cation-binding sites. In collagen-binding integrins, such as α2β1, ligand recognition takes place exclusively at the α subunit I domain. However, activation of the αI domain depends on its interaction with a structurally similar domain in the β subunit known as the I-like or βI domain. The top face of the βI domain contains three cation-binding sites: the metal-ion dependent adhesion site (MIDAS), the ADMIDAS (adjacent to MIDAS) and LIMBS (ligand-associated metal binding site). The role of these sites in controlling ligand binding to the αI domain has yet to be elucidated. Mutation of the MIDAS or LIMBS completely blocked collagen binding to α2β1; in contrast mutation of the ADMIDAS reduced ligand recognition but this effect could be overcome by the activating mAb TS2/16. Hence, the MIDAS and LIMBS appear to be essential for the interaction between αI and βI whereas occupancy of the ADMIDAS has an allosteric effect on the conformation of βI. An activating mutation in the α2 I domain partially restored ligand binding to the MIDAS and LIMBS mutants. Analysis of the effects of Ca2+, Mg2+ and Mn2+ on ligand binding to these mutants showed that the MIDAS is a ligand-competent site through which Mn2+ stimulates ligand binding, whereas the LIMBS is a stimulatory Ca2+-binding site, occupancy of which increases the affinity of Mg2+ for the MIDAS. PMID:18820259

Electrostatically Accelerated Coupled Binding and Folding of Intrinsically Disordered Proteins

PubMed Central

Ganguly, Debabani; Otieno, Steve; Waddell, Brett; Iconaru, Luigi; Kriwacki, Richard W.; Chen, Jianhan

2012-01-01

Intrinsically disordered proteins (IDPs) are now recognized to be prevalent in biology, and many potential functional benefits have been discussed. However, the frequent requirement of peptide folding in specific interactions of IDPs could impose a kinetic bottleneck, which could be overcome only by efficient folding upon encounter. Intriguingly, existing kinetic data suggest that specific binding of IDPs is generally no slower than that of globular proteins. Here, we exploited the cell cycle regulator p27Kip1 (p27) as a model system to understand how IDPs might achieve efficient folding upon encounter for facile recognition. Combining experiments and coarse-grained modeling, we demonstrate that long-range electrostatic interactions between enriched charges on p27 and near its binding site on cyclin A not only enhance the encounter rate (i.e., electrostatic steering), but also promote folding-competent topologies in the encounter complexes, allowing rapid subsequent formation of short-range native interactions en route to the specific complex. In contrast, nonspecific hydrophobic interactions, while hardly affecting the encounter rate, can significantly reduce the efficiency of folding upon encounter and lead to slower binding kinetics. Further analysis of charge distributions in a set of known IDP complexes reveals that, although IDP binding sites tend to be more hydrophobic compared to the rest of the target surface, their vicinities are frequently enriched with charges to complement those on IDPs. This observation suggests that electrostatically accelerated encounter and induced folding might represent a prevalent mechanism for promoting facile IDP recognition. PMID:22721951

Kinetic Dissection of the Pre-existing Conformational Equilibrium in the Trypsin Fold*

PubMed Central

Vogt, Austin D.; Chakraborty, Pradipta; Di Cera, Enrico

2015-01-01

Structural biology has recently documented the conformational plasticity of the trypsin fold for both the protease and zymogen in terms of a pre-existing equilibrium between closed (E*) and open (E) forms of the active site region. How such plasticity is manifested in solution and affects ligand recognition by the protease and zymogen is poorly understood in quantitative terms. Here we dissect the E*-E equilibrium with stopped-flow kinetics in the presence of excess ligand or macromolecule. Using the clotting protease thrombin and its zymogen precursor prethrombin-2 as relevant models we resolve the relative distribution of the E* and E forms and the underlying kinetic rates for their interconversion. In the case of thrombin, the E* and E forms are distributed in a 1:4 ratio and interconvert on a time scale of 45 ms. In the case of prethrombin-2, the equilibrium is shifted strongly (10:1 ratio) in favor of the closed E* form and unfolds over a faster time scale of 4.5 ms. The distribution of E* and E forms observed for thrombin and prethrombin-2 indicates that zymogen activation is linked to a significant shift in the pre-existing equilibrium between closed and open conformations that facilitates ligand binding to the active site. These findings broaden our mechanistic understanding of how conformational transitions control ligand recognition by thrombin and its zymogen precursor prethrombin-2 and have direct relevance to other members of the trypsin fold. PMID:26216877

78 FR 48909 - SGS North America, Inc. (formerly SGS U.S. Testing Company, Inc.)

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-12

... of one test site. OSHA also recognizes the removal of one test site and 13 test standards from SGS's... expand its recognition to include one additional test site located at 620 Old Peachtree Road, Suwanee, GA... this move, SGS requests the removal of one test site, located at 291 Fairfield Avenue, Fairfield, NJ...

Recognition of the 3′ splice site RNA by the U2AF heterodimer involves a dynamic population shift

PubMed Central

Voith von Voithenberg, Lena; Sánchez-Rico, Carolina; Kang, Hyun-Seo; Madl, Tobias; Zanier, Katia; Barth, Anders; Warner, Lisa R.; Sattler, Michael; Lamb, Don C.

2016-01-01

An essential early step in the assembly of human spliceosomes onto pre-mRNA involves the recognition of regulatory RNA cis elements in the 3′ splice site by the U2 auxiliary factor (U2AF). The large (U2AF65) and small (U2AF35) subunits of the U2AF heterodimer contact the polypyrimidine tract (Py-tract) and the AG-dinucleotide, respectively. The tandem RNA recognition motif domains (RRM1,2) of U2AF65 adopt closed/inactive and open/active conformations in the free form and when bound to bona fide Py-tract RNA ligands. To investigate the molecular mechanism and dynamics of 3′ splice site recognition by U2AF65 and the role of U2AF35 in the U2AF heterodimer, we have combined single-pair FRET and NMR experiments. In the absence of RNA, the RRM1,2 domain arrangement is highly dynamic on a submillisecond time scale, switching between closed and open conformations. The addition of Py-tract RNA ligands with increasing binding affinity (strength) gradually shifts the equilibrium toward an open conformation. Notably, the protein–RNA complex is rigid in the presence of a strong Py-tract but exhibits internal motion with weak Py-tracts. Surprisingly, the presence of U2AF35, whose UHM domain interacts with U2AF65 RRM1, increases the population of the open arrangement of U2AF65 RRM1,2 in the absence and presence of a weak Py-tract. These data indicate that the U2AF heterodimer promotes spliceosome assembly by a dynamic population shift toward the open conformation of U2AF65 to facilitate the recognition of weak Py-tracts at the 3′ splice site. The structure and RNA binding of the heterodimer was unaffected by cancer-linked myelodysplastic syndrome mutants. PMID:27799531

The Memory State Heuristic: A Formal Model Based on Repeated Recognition Judgments

ERIC Educational Resources Information Center

Castela, Marta; Erdfelder, Edgar

2017-01-01

The recognition heuristic (RH) theory predicts that, in comparative judgment tasks, if one object is recognized and the other is not, the recognized one is chosen. The memory-state heuristic (MSH) extends the RH by assuming that choices are not affected by recognition judgments per se, but by the memory states underlying these judgments (i.e.,…

Face Recognition Is Affected by Similarity in Spatial Frequency Range to a Greater Degree Than Within-Category Object Recognition

ERIC Educational Resources Information Center

Collin, Charles A.; Liu, Chang Hong; Troje, Nikolaus F.; McMullen, Patricia A.; Chaudhuri, Avi

2004-01-01

Previous studies have suggested that face identification is more sensitive to variations in spatial frequency content than object recognition, but none have compared how sensitive the 2 processes are to variations in spatial frequency overlap (SFO). The authors tested face and object matching accuracy under varying SFO conditions. Their results…

Kanji Recognition by Second Language Learners: Exploring Effects of First Language Writing Systems and Second Language Exposure

ERIC Educational Resources Information Center

Matsumoto, Kazumi

2013-01-01

This study investigated whether learners of Japanese with different first language (L1) writing systems use different recognition strategies and whether second language (L2) exposure affects L2 kanji recognition. The study used a computerized lexical judgment task with 3 types of kanji characters to investigate these questions: (a)…

Substrate recognition by ribonucleoprotein ribonuclease MRP

PubMed Central

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

2011-01-01

The ribonucleoprotein complex ribonuclease (RNase) MRP is a site-specific endoribonuclease essential for the survival of the eukaryotic cell. RNase MRP closely resembles RNase P (a universal endoribonuclease responsible for the maturation of the 5′ ends of tRNA) but recognizes distinct substrates including pre-rRNA and mRNA. Here we report the results of an in vitro selection of Saccharomyces cerevisiae RNase MRP substrates starting from a pool of random sequences. The results indicate that RNase MRP cleaves single-stranded RNA and is sensitive to sequences in the immediate vicinity of the cleavage site requiring a cytosine at the position +4 relative to the cleavage site. Structural implications of the differences in substrate recognition by RNases P and MRP are discussed. PMID:21173200

Substrate recognition by ribonucleoprotein ribonuclease MRP.

PubMed

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

2011-02-01

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

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

Enemy at the gates: traffic at the plant cell pathogen interface.

PubMed

Hoefle, Caroline; Hückelhoven, Ralph

2008-12-01

The plant apoplast constitutes a space for early recognition of potentially harmful non-self. Basal pathogen recognition operates via dynamic sensing of conserved microbial patterns by pattern recognition receptors or of elicitor-active molecules released from plant cell walls during infection. Recognition elicits defence reactions depending on cellular export via SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) complex-mediated vesicle fusion or plasma membrane transporter activity. Lipid rafts appear also involved in focusing immunity-associated proteins to the site of pathogen contact. Simultaneously, pathogen effectors target recognition, apoplastic host proteins and transport for cell wall-associated defence. This microreview highlights most recent reports on the arms race for plant disease and immunity at the cell surface.

Dynamic nanoplatforms in biosensor and membrane constitutional systems.

PubMed

Mahon, Eugene; Aastrup, Teodor; Barboiu, Mihail

2012-01-01

Molecular recognition in biological systems occurs mainly at interfacial environments such as membrane surfaces, enzyme active sites, or the interior of the DNA double helix. At the cell membrane surface, carbohydrate-protein recognition principles apply to a range of specific non-covalent interactions including immune response, cell proliferation, adhesion and death, cell-cell interaction and communication. Protein-protein recognition meanwhile accounts for signalling processes and ion channel structure. In this chapter we aim to describe such constitutional dynamic interfaces for biosensing and membrane transport applications. Constitutionally adaptive interfaces may mimic the recognition capabilities intrinsic to natural recognition processes. We present some recent examples of 2D and 3D constructed sensors and membranes of this type and describe their sensing and transport capabilities.

Relationships between egg-recognition and egg-ejection in a grasp-ejector species.

PubMed

Soler, Manuel; Ruiz-Raya, Francisco; Roncalli, Gianluca; Ibáñez-Álamo, Juan Diego

2017-01-01

Brood parasitism frequently leads to a total loss of host fitness, which selects for the evolution of defensive traits in host species. Experimental studies have demonstrated that recognition and rejection of the parasite egg is the most common and efficient defence used by host species. Egg-recognition experiments have advanced our knowledge of the evolutionary and coevolutionary implications of egg recognition and rejection. However, our understanding of the proximate mechanisms underlying both processes remains poor. Egg rejection is a complex behavioural process consisting of three stages: egg recognition, the decision whether or not to reject the putative parasitic egg and the act of ejection itself. We have used the blackbird (Turdus merula) as a model species to explore the relationship between egg recognition and the act of egg ejection. We have manipulated the two main characteristics of parasitic eggs affecting egg ejection in this grasp-ejector species: the degree of colour mimicry (mimetic and non-mimetic, which mainly affects the egg-recognition stage of the egg-rejection process) and egg size (small, medium and large, which affects the decision to eject), while maintaining a control group of non-parasitized nests. The behaviour of the female when confronted with an experimental egg was filmed using a video camera. Our results show that egg touching is an indication of egg recognition and demonstrate that blackbirds recognized (i.e., touched) non-mimetic experimental eggs significantly more than mimetic eggs. However, twenty per cent of the experimental eggs were touched but not subsequently ejected, which confirms that egg recognition does not necessarily mean egg ejection and that accepting parasitic eggs, at least sometimes, is the consequence of acceptance decisions. Regarding proximate mechanisms, our results show that the delay in egg ejection is not only due to recognition problems as usually suggested, given that experimental eggs are not touched significantly more often. Thus, the delay in egg ejection is mainly the consequence of a delay in the decision to eject, probably triggered by mechanical constraints imposed by eggs that are harder to eject (i.e. larger). Our results offer important information on the relationships between recognition and ejection and contribute to a better understanding of host defences against brood parasites.

Relationships between egg-recognition and egg-ejection in a grasp-ejector species

PubMed Central

Soler, Manuel; Ruiz-Raya, Francisco; Roncalli, Gianluca; Ibáñez-Álamo, Juan Diego

2017-01-01

Brood parasitism frequently leads to a total loss of host fitness, which selects for the evolution of defensive traits in host species. Experimental studies have demonstrated that recognition and rejection of the parasite egg is the most common and efficient defence used by host species. Egg-recognition experiments have advanced our knowledge of the evolutionary and coevolutionary implications of egg recognition and rejection. However, our understanding of the proximate mechanisms underlying both processes remains poor. Egg rejection is a complex behavioural process consisting of three stages: egg recognition, the decision whether or not to reject the putative parasitic egg and the act of ejection itself. We have used the blackbird (Turdus merula) as a model species to explore the relationship between egg recognition and the act of egg ejection. We have manipulated the two main characteristics of parasitic eggs affecting egg ejection in this grasp-ejector species: the degree of colour mimicry (mimetic and non-mimetic, which mainly affects the egg-recognition stage of the egg-rejection process) and egg size (small, medium and large, which affects the decision to eject), while maintaining a control group of non-parasitized nests. The behaviour of the female when confronted with an experimental egg was filmed using a video camera. Our results show that egg touching is an indication of egg recognition and demonstrate that blackbirds recognized (i.e., touched) non-mimetic experimental eggs significantly more than mimetic eggs. However, twenty per cent of the experimental eggs were touched but not subsequently ejected, which confirms that egg recognition does not necessarily mean egg ejection and that accepting parasitic eggs, at least sometimes, is the consequence of acceptance decisions. Regarding proximate mechanisms, our results show that the delay in egg ejection is not only due to recognition problems as usually suggested, given that experimental eggs are not touched significantly more often. Thus, the delay in egg ejection is mainly the consequence of a delay in the decision to eject, probably triggered by mechanical constraints imposed by eggs that are harder to eject (i.e. larger). Our results offer important information on the relationships between recognition and ejection and contribute to a better understanding of host defences against brood parasites. PMID:28170402

Economics/Environment/Educational Outcomes of Site Planning.

ERIC Educational Resources Information Center

Grube, Karl W.; Bewley, Mary

Few school leaders and school architects have recognized or comprehended the potential symbiosis between school site resources and the enrichment of the instructional program, the urgency of repairing and improving the biosphere, the broadening of community life onto school sites, and the recognition of the responsibility role of stewardship of…

Mutations in the BAF-Complex Subunit DPF2 Are Associated with Coffin-Siris Syndrome.

PubMed

Vasileiou, Georgia; Vergarajauregui, Silvia; Endele, Sabine; Popp, Bernt; Büttner, Christian; Ekici, Arif B; Gerard, Marion; Bramswig, Nuria C; Albrecht, Beate; Clayton-Smith, Jill; Morton, Jenny; Tomkins, Susan; Low, Karen; Weber, Astrid; Wenzel, Maren; Altmüller, Janine; Li, Yun; Wollnik, Bernd; Hoganson, George; Plona, Maria-Renée; Cho, Megan T; Thiel, Christian T; Lüdecke, Hermann-Josef; Strom, Tim M; Calpena, Eduardo; Wilkie, Andrew O M; Wieczorek, Dagmar; Engel, Felix B; Reis, André

2018-03-01

Variants affecting the function of different subunits of the BAF chromatin-remodelling complex lead to various neurodevelopmental syndromes, including Coffin-Siris syndrome. Furthermore, variants in proteins containing PHD fingers, motifs recognizing specific histone tail modifications, have been associated with several neurological and developmental-delay disorders. Here, we report eight heterozygous de novo variants (one frameshift, two splice site, and five missense) in the gene encoding the BAF complex subunit double plant homeodomain finger 2 (DPF2). Affected individuals share common clinical features described in individuals with Coffin-Siris syndrome, including coarse facial features, global developmental delay, intellectual disability, speech impairment, and hypoplasia of fingernails and toenails. All variants occur within the highly conserved PHD1 and PHD2 motifs. Moreover, missense variants are situated close to zinc binding sites and are predicted to disrupt these sites. Pull-down assays of recombinant proteins and histone peptides revealed that a subset of the identified missense variants abolish or impaire DPF2 binding to unmodified and modified H3 histone tails. These results suggest an impairment of PHD finger structural integrity and cohesion and most likely an aberrant recognition of histone modifications. Furthermore, the overexpression of these variants in HEK293 and COS7 cell lines was associated with the formation of nuclear aggregates and the recruitment of both wild-type DPF2 and BRG1 to these aggregates. Expression analysis of truncating variants found in the affected individuals indicated that the aberrant transcripts escape nonsense-mediated decay. Altogether, we provide compelling evidence that de novo variants in DPF2 cause Coffin-Siris syndrome and propose a dominant-negative mechanism of pathogenicity. Copyright © 2018 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Nature and extent of person recognition impairments associated with Capgras syndrome in Lewy body dementia

PubMed Central

Fiacconi, Chris M.; Barkley, Victoria; Finger, Elizabeth C.; Carson, Nicole; Duke, Devin; Rosenbaum, R. Shayna; Gilboa, Asaf; Köhler, Stefan

2014-01-01

Patients with Capgras syndrome (CS) adopt the delusional belief that persons well-known to them have been replaced by an imposter. Several current theoretical models of CS attribute such misidentification problems to deficits in covert recognition processes related to the generation of appropriate affective autonomic signals. These models assume intact overt recognition processes for the imposter and, more broadly, for other individuals. As such, it has been suggested that CS could reflect the “mirror-image” of prosopagnosia. The purpose of the current study was to determine whether overt person recognition abilities are indeed always spared in CS. Furthermore, we examined whether CS might be associated with any impairments in overt affective judgments of facial expressions. We pursued these goals by studying a patient with Dementia with Lewy bodies (DLB) who showed clear signs of CS, and by comparing him to another patient with DLB who did not experience CS, as well as to a group of healthy control participants. Clinical magnetic resonance imaging scans revealed medial prefrontal cortex (mPFC) atrophy that appeared to be uniquely associated with the presence CS. We assessed overt person recognition with three fame recognition tasks, using faces, voices, and names as cues. We also included measures of confidence and probed pertinent semantic knowledge. In addition, participants rated the intensity of fearful facial expressions. We found that CS was associated with overt person recognition deficits when probed with faces and voices, but not with names. Critically, these deficits were not present in the DLB patient without CS. In addition, CS was associated with impairments in overt judgments of affect intensity. Taken together, our findings cast doubt on the traditional view that CS is the mirror-image of prosopagnosia and that it spares overt recognition abilities. These findings can still be accommodated by models of CS that emphasize deficits in autonomic responding, to the extent that the potential role of interoceptive awareness in overt judgments is taken into account. PMID:25309399

Analysis of hard protein corona composition on selective iron oxide nanoparticles by MALDI-TOF mass spectrometry: identification and amplification of a hidden mastitis biomarker in milk proteome.

PubMed

Magro, Massimiliano; Zaccarin, Mattia; Miotto, Giovanni; Da Dalt, Laura; Baratella, Davide; Fariselli, Piero; Gabai, Gianfranco; Vianello, Fabio

2018-05-01

Surface active maghemite nanoparticles (SAMNs) are able to recognize and bind selected proteins in complex biological systems, forming a hard protein corona. Upon a 5-min incubation in bovine whey from mastitis-affected cows, a significant enrichment of a single peptide characterized by a molecular weight at 4338 Da originated from the proteolysis of a S1 -casein was observed. Notably, among the large number of macromolecules in bovine milk, the detection of this specific peptide can hardly be accomplished by conventional analytical techniques. The selective formation of a stable binding between the peptide and SAMNs is due to the stability gained by adsorption-induced surface restructuration of the nanomaterial. We attributed the surface recognition properties of SAMNs to the chelation of iron(III) sites on their surface by sterically compatible carboxylic groups of the peptide. The specific peptide recognition by SAMNs allows its easy determination by MALDI-TOF mass spectrometry, and a threshold value of its normalized peak intensity was identified by a logistic regression approach and suggested for the rapid diagnosis of the pathology. Thus, the present report proposes the analysis of hard protein corona on nanomaterials as a perspective for developing fast analytical procedures for the diagnosis of mastitis in cows. Moreover, the huge simplification of proteome complexity by exploiting the selectivity derived by the peculiar SAMN surface topography, due to the iron(III) distribution pattern, could be of general interest, leading to competitive applications in food science and in biomedicine, allowing the rapid determination of hidden biomarkers by a cutting edge diagnostic strategy. Graphical abstract The topography of iron(III) sites on surface active maghemite nanoparticles (SAMNs) allows the recognition of sterically compatible carboxylic groups on proteins and peptides in complex biological matrixes. The analysis of hard protein corona on SAMNs led to the determination of a biomarker for cow mastitis in milk by MALDI-TOF mass spectrometry.

Sleep deprivation impairs the accurate recognition of human emotions.

PubMed

van der Helm, Els; Gujar, Ninad; Walker, Matthew P

2010-03-01

Investigate the impact of sleep deprivation on the ability to recognize the intensity of human facial emotions. Randomized total sleep-deprivation or sleep-rested conditions, involving between-group and within-group repeated measures analysis. Experimental laboratory study. Thirty-seven healthy participants, (21 females) aged 18-25 y, were randomly assigned to the sleep control (SC: n = 17) or total sleep deprivation group (TSD: n = 20). Participants performed an emotional face recognition task, in which they evaluated 3 different affective face categories: Sad, Happy, and Angry, each ranging in a gradient from neutral to increasingly emotional. In the TSD group, the task was performed once under conditions of sleep deprivation, and twice under sleep-rested conditions following different durations of sleep recovery. In the SC group, the task was performed twice under sleep-rested conditions, controlling for repeatability. In the TSD group, when sleep-deprived, there was a marked and significant blunting in the recognition of Angry and Happy affective expressions in the moderate (but not extreme) emotional intensity range; differences that were most reliable and significant in female participants. No change in the recognition of Sad expressions was observed. These recognition deficits were, however, ameliorated following one night of recovery sleep. No changes in task performance were observed in the SC group. Sleep deprivation selectively impairs the accurate judgment of human facial emotions, especially threat relevant (Anger) and reward relevant (Happy) categories, an effect observed most significantly in females. Such findings suggest that sleep loss impairs discrete affective neural systems, disrupting the identification of salient affective social cues.

Eyes on crowding: crowding is preserved when responding by eye and similarly affects identity and position accuracy.

PubMed

Yildirim, Funda; Meyer, Vincent; Cornelissen, Frans W

2015-02-16

Peripheral vision guides recognition and selection of targets for eye movements. Crowding—a decline in recognition performance that occurs when a potential target is surrounded by other, similar, objects—influences peripheral object recognition. A recent model study suggests that crowding may be due to increased uncertainty about both the identity and the location of peripheral target objects, but very few studies have assessed these properties in tandem. Eye tracking can integrally provide information on both the perceived identity and the position of a target and therefore could become an important approach in crowding studies. However, recent reports suggest that around the moment of saccade preparation crowding may be significantly modified. If these effects were to generalize to regular crowding tasks, it would complicate the interpretation of results obtained with eye tracking and the comparison to results obtained using manual responses. For this reason, we first assessed whether the manner by which participants responded—manually or by eye—affected their performance. We found that neither recognition performance nor response time was affected by the response type. Hence, we conclude that crowding magnitude was preserved when observers responded by eye. In our main experiment, observers made eye movements to the location of a tilted Gabor target while we varied flanker tilt to manipulate target-flanker similarity. The results indicate that this similarly affected the accuracy of peripheral recognition and saccadic target localization. Our results inform about the importance of both location and identity uncertainty in crowding. © 2015 ARVO.

Good initialization model with constrained body structure for scene text recognition

NASA Astrophysics Data System (ADS)

Zhu, Anna; Wang, Guoyou; Dong, Yangbo

2016-09-01

Scene text recognition has gained significant attention in the computer vision community. Character detection and recognition are the promise of text recognition and affect the overall performance to a large extent. We proposed a good initialization model for scene character recognition from cropped text regions. We use constrained character's body structures with deformable part-based models to detect and recognize characters in various backgrounds. The character's body structures are achieved by an unsupervised discriminative clustering approach followed by a statistical model and a self-build minimum spanning tree model. Our method utilizes part appearance and location information, and combines character detection and recognition in cropped text region together. The evaluation results on the benchmark datasets demonstrate that our proposed scheme outperforms the state-of-the-art methods both on scene character recognition and word recognition aspects.

Homology modeling, molecular dynamics, and docking studies of pattern-recognition transmembrane protein-lipopolysaccharide and β-1,3 glucan-binding protein from Fenneropenaeus indicus.

PubMed

Sivakamavalli, Jeyachandran; Tripathi, Sunil Kumar; Singh, Sanjeev Kumar; Vaseeharan, Baskaralingam

2015-01-01

Lipopolysaccharide and β-1,3 glucan-binding protein (LGBP) is a family of pattern-recognition transmembrane proteins (PRPs) which plays a vital role in the immune mechanism of crustaceans in adverse conditions. Fenneropenaeus indicus LGBP-deduced amino acid has conserved potential recognition motif for β-1,3 linkages of polysaccharides and putative RGD (Arg-Gly-Asp) cell adhesion sites for the activation of innate defense mechanism. In order to understand the stimulating activity of β-1,3 glucan (β-glucan) and its interaction with LGBP, a 3D model of LGBP is generated. Molecular docking is performed with this model, and the results indicate Arg71 with strong hydrogen bond from RGD domain of LGBP. Moreover, from the docking studies, we also suggest that Arg34, Lys68, Val135, and Ala146 in LGBP are important amino acid residues in binding as they have strong bonding interaction in the active site of LGBP. In our in vitro studies, yeast agglutination results suggest that shrimp F. indicus LGBP possesses sugar binding and recognition sites in its structure, which is responsible for agglutination reaction. Our results were synchronized with the already reported evidence both in vivo and in vitro experiments. This investigation may be valuable for further experimental investigation in the synthesis of novel immunomodulator.

Emotion Analysis of Telephone Complaints from Customer Based on Affective Computing.

PubMed

Gong, Shuangping; Dai, Yonghui; Ji, Jun; Wang, Jinzhao; Sun, Hai

2015-01-01

Customer complaint has been the important feedback for modern enterprises to improve their product and service quality as well as the customer's loyalty. As one of the commonly used manners in customer complaint, telephone communication carries rich emotional information of speeches, which provides valuable resources for perceiving the customer's satisfaction and studying the complaint handling skills. This paper studies the characteristics of telephone complaint speeches and proposes an analysis method based on affective computing technology, which can recognize the dynamic changes of customer emotions from the conversations between the service staff and the customer. The recognition process includes speaker recognition, emotional feature parameter extraction, and dynamic emotion recognition. Experimental results show that this method is effective and can reach high recognition rates of happy and angry states. It has been successfully applied to the operation quality and service administration in telecom and Internet service company.

Emotion Analysis of Telephone Complaints from Customer Based on Affective Computing

PubMed Central

Gong, Shuangping; Ji, Jun; Wang, Jinzhao; Sun, Hai

2015-01-01

Customer complaint has been the important feedback for modern enterprises to improve their product and service quality as well as the customer's loyalty. As one of the commonly used manners in customer complaint, telephone communication carries rich emotional information of speeches, which provides valuable resources for perceiving the customer's satisfaction and studying the complaint handling skills. This paper studies the characteristics of telephone complaint speeches and proposes an analysis method based on affective computing technology, which can recognize the dynamic changes of customer emotions from the conversations between the service staff and the customer. The recognition process includes speaker recognition, emotional feature parameter extraction, and dynamic emotion recognition. Experimental results show that this method is effective and can reach high recognition rates of happy and angry states. It has been successfully applied to the operation quality and service administration in telecom and Internet service company. PMID:26633967

Gender affects body language reading.

PubMed

Sokolov, Arseny A; Krüger, Samuel; Enck, Paul; Krägeloh-Mann, Ingeborg; Pavlova, Marina A

2011-01-01

Body motion is a rich source of information for social cognition. However, gender effects in body language reading are largely unknown. Here we investigated whether, and, if so, how recognition of emotional expressions revealed by body motion is gender dependent. To this end, females and males were presented with point-light displays portraying knocking at a door performed with different emotional expressions. The findings show that gender affects accuracy rather than speed of body language reading. This effect, however, is modulated by emotional content of actions: males surpass in recognition accuracy of happy actions, whereas females tend to excel in recognition of hostile angry knocking. Advantage of women in recognition accuracy of neutral actions suggests that females are better tuned to the lack of emotional content in body actions. The study provides novel insights into understanding of gender effects in body language reading, and helps to shed light on gender vulnerability to neuropsychiatric and neurodevelopmental impairments in visual social cognition.

Domain repertoires as a tool to derive protein recognition rules.

PubMed

Zucconi, A; Panni, S; Paoluzi, S; Castagnoli, L; Dente, L; Cesareni, G

2000-08-25

Several approaches, some of which are described in this issue, have been proposed to assemble a complete protein interaction map. These are often based on high throughput methods that explore the ability of each gene product to bind any other element of the proteome of the organism. Here we propose that a large number of interactions can be inferred by revealing the rules underlying recognition specificity of a small number (a few hundreds) of families of protein recognition modules. This can be achieved through the construction and characterization of domain repertoires. A domain repertoire is assembled in a combinatorial fashion by allowing each amino acid position in the binding site of a given protein recognition domain to vary to include all the residues allowed at that position in the domain family. The repertoire is then searched by phage display techniques with any target of interest and from the primary structure of the binding site of the selected domains one derives rules that are used to infer the formation of complexes between natural proteins in the cell.

Not all sounds sound the same: Parkinson's disease affects differently emotion processing in music and in speech prosody.

PubMed

Lima, César F; Garrett, Carolina; Castro, São Luís

2013-01-01

Does emotion processing in music and speech prosody recruit common neurocognitive mechanisms? To examine this question, we implemented a cross-domain comparative design in Parkinson's disease (PD). Twenty-four patients and 25 controls performed emotion recognition tasks for music and spoken sentences. In music, patients had impaired recognition of happiness and peacefulness, and intact recognition of sadness and fear; this pattern was independent of general cognitive and perceptual abilities. In speech, patients had a small global impairment, which was significantly mediated by executive dysfunction. Hence, PD affected differently musical and prosodic emotions. This dissociation indicates that the mechanisms underlying the two domains are partly independent.

Interplay between affect and arousal in recognition memory.

PubMed

Greene, Ciara M; Bahri, Pooja; Soto, David

2010-07-23

Emotional states linked to arousal and mood are known to affect the efficiency of cognitive performance. However, the extent to which memory processes may be affected by arousal, mood or their interaction is poorly understood. Following a study phase of abstract shapes, we altered the emotional state of participants by means of exposure to music that varied in both mood and arousal dimensions, leading to four different emotional states: (i) positive mood-high arousal; (ii) positive mood-low arousal; (iii) negative mood-high arousal; (iv) negative mood-low arousal. Following the emotional induction, participants performed a memory recognition test. Critically, there was an interaction between mood and arousal on recognition performance. Memory was enhanced in the positive mood-high arousal and in the negative mood-low arousal states, relative to the other emotional conditions. Neither mood nor arousal alone but their interaction appears most critical to understanding the emotional enhancement of memory.

How Psychological Stress Affects Emotional Prosody.

PubMed

Paulmann, Silke; Furnes, Desire; Bøkenes, Anne Ming; Cozzolino, Philip J

2016-01-01

We explored how experimentally induced psychological stress affects the production and recognition of vocal emotions. In Study 1a, we demonstrate that sentences spoken by stressed speakers are judged by naïve listeners as sounding more stressed than sentences uttered by non-stressed speakers. In Study 1b, negative emotions produced by stressed speakers are generally less well recognized than the same emotions produced by non-stressed speakers. Multiple mediation analyses suggest this poorer recognition of negative stimuli was due to a mismatch between the variation of volume voiced by speakers and the range of volume expected by listeners. Together, this suggests that the stress level of the speaker affects judgments made by the receiver. In Study 2, we demonstrate that participants who were induced with a feeling of stress before carrying out an emotional prosody recognition task performed worse than non-stressed participants. Overall, findings suggest detrimental effects of induced stress on interpersonal sensitivity.

How Psychological Stress Affects Emotional Prosody

PubMed Central

Paulmann, Silke; Furnes, Desire; Bøkenes, Anne Ming; Cozzolino, Philip J.

2016-01-01

We explored how experimentally induced psychological stress affects the production and recognition of vocal emotions. In Study 1a, we demonstrate that sentences spoken by stressed speakers are judged by naïve listeners as sounding more stressed than sentences uttered by non-stressed speakers. In Study 1b, negative emotions produced by stressed speakers are generally less well recognized than the same emotions produced by non-stressed speakers. Multiple mediation analyses suggest this poorer recognition of negative stimuli was due to a mismatch between the variation of volume voiced by speakers and the range of volume expected by listeners. Together, this suggests that the stress level of the speaker affects judgments made by the receiver. In Study 2, we demonstrate that participants who were induced with a feeling of stress before carrying out an emotional prosody recognition task performed worse than non-stressed participants. Overall, findings suggest detrimental effects of induced stress on interpersonal sensitivity. PMID:27802287

Modulation of α power and functional connectivity during facial affect recognition.

PubMed

Popov, Tzvetan; Miller, Gregory A; Rockstroh, Brigitte; Weisz, Nathan

2013-04-03

Research has linked oscillatory activity in the α frequency range, particularly in sensorimotor cortex, to processing of social actions. Results further suggest involvement of sensorimotor α in the processing of facial expressions, including affect. The sensorimotor face area may be critical for perception of emotional face expression, but the role it plays is unclear. The present study sought to clarify how oscillatory brain activity contributes to or reflects processing of facial affect during changes in facial expression. Neuromagnetic oscillatory brain activity was monitored while 30 volunteers viewed videos of human faces that changed their expression from neutral to fearful, neutral, or happy expressions. Induced changes in α power during the different morphs, source analysis, and graph-theoretic metrics served to identify the role of α power modulation and cross-regional coupling by means of phase synchrony during facial affect recognition. Changes from neutral to emotional faces were associated with a 10-15 Hz power increase localized in bilateral sensorimotor areas, together with occipital power decrease, preceding reported emotional expression recognition. Graph-theoretic analysis revealed that, in the course of a trial, the balance between sensorimotor power increase and decrease was associated with decreased and increased transregional connectedness as measured by node degree. Results suggest that modulations in α power facilitate early registration, with sensorimotor cortex including the sensorimotor face area largely functionally decoupled and thereby protected from additional, disruptive input and that subsequent α power decrease together with increased connectedness of sensorimotor areas facilitates successful facial affect recognition.

The Effect of Lexical Content on Dichotic Speech Recognition in Older Adults.

PubMed

Findlen, Ursula M; Roup, Christina M

2016-01-01

Age-related auditory processing deficits have been shown to negatively affect speech recognition for older adult listeners. In contrast, older adults gain benefit from their ability to make use of semantic and lexical content of the speech signal (i.e., top-down processing), particularly in complex listening situations. Assessment of auditory processing abilities among aging adults should take into consideration semantic and lexical content of the speech signal. The purpose of this study was to examine the effects of lexical and attentional factors on dichotic speech recognition performance characteristics for older adult listeners. A repeated measures design was used to examine differences in dichotic word recognition as a function of lexical and attentional factors. Thirty-five older adults (61-85 yr) with sensorineural hearing loss participated in this study. Dichotic speech recognition was evaluated using consonant-vowel-consonant (CVC) word and nonsense CVC syllable stimuli administered in the free recall, directed recall right, and directed recall left response conditions. Dichotic speech recognition performance for nonsense CVC syllables was significantly poorer than performance for CVC words. Dichotic recognition performance varied across response condition for both stimulus types, which is consistent with previous studies on dichotic speech recognition. Inspection of individual results revealed that five listeners demonstrated an auditory-based left ear deficit for one or both stimulus types. Lexical content of stimulus materials affects performance characteristics for dichotic speech recognition tasks in the older adult population. The use of nonsense CVC syllable material may provide a way to assess dichotic speech recognition performance while potentially lessening the effects of lexical content on performance (i.e., measuring bottom-up auditory function both with and without top-down processing). American Academy of Audiology.

Face and Word Recognition Can Be Selectively Affected by Brain Injury or Developmental Disorders.

PubMed

Robotham, Ro J; Starrfelt, Randi

2017-01-01

Face and word recognition have traditionally been thought to rely on highly specialised and relatively independent cognitive processes. Some of the strongest evidence for this has come from patients with seemingly category-specific visual perceptual deficits such as pure prosopagnosia, a selective face recognition deficit, and pure alexia, a selective word recognition deficit. Together, the patterns of impaired reading with preserved face recognition and impaired face recognition with preserved reading constitute a double dissociation. The existence of these selective deficits has been questioned over the past decade. It has been suggested that studies describing patients with these pure deficits have failed to measure the supposedly preserved functions using sensitive enough measures, and that if tested using sensitive measurements, all patients with deficits in one visual category would also have deficits in the other. The implications of this would be immense, with most textbooks in cognitive neuropsychology requiring drastic revisions. In order to evaluate the evidence for dissociations, we review studies that specifically investigate whether face or word recognition can be selectively affected by acquired brain injury or developmental disorders. We only include studies published since 2004, as comprehensive reviews of earlier studies are available. Most of the studies assess the supposedly preserved functions using sensitive measurements. We found convincing evidence that reading can be preserved in acquired and developmental prosopagnosia and also evidence (though weaker) that face recognition can be preserved in acquired or developmental dyslexia, suggesting that face and word recognition are at least in part supported by independent processes.

Effect of camera resolution and bandwidth on facial affect recognition.

PubMed

Cruz, Mario; Cruz, Robyn Flaum; Krupinski, Elizabeth A; Lopez, Ana Maria; McNeeley, Richard M; Weinstein, Ronald S

2004-01-01

This preliminary study explored the effect of camera resolution and bandwidth on facial affect recognition, an important process and clinical variable in mental health service delivery. Sixty medical students and mental health-care professionals were recruited and randomized to four different combinations of commonly used teleconferencing camera resolutions and bandwidths: (1) one chip charged coupling device (CCD) camera, commonly used for VHSgrade taping and in teleconferencing systems costing less than $4,000 with a resolution of 280 lines, and 128 kilobytes per second bandwidth (kbps); (2) VHS and 768 kbps; (3) three-chip CCD camera, commonly used for Betacam (Beta) grade taping and in teleconferencing systems costing more than $4,000 with a resolution of 480 lines, and 128 kbps; and (4) Betacam and 768 kbps. The subjects were asked to identify four facial affects dynamically presented on videotape by an actor and actress presented via a video monitor at 30 frames per second. Two-way analysis of variance (ANOVA) revealed a significant interaction effect for camera resolution and bandwidth (p = 0.02) and a significant main effect for camera resolution (p = 0.006), but no main effect for bandwidth was detected. Post hoc testing of interaction means, using the Tukey Honestly Significant Difference (HSD) test and the critical difference (CD) at the 0.05 alpha level = 1.71, revealed subjects in the VHS/768 kbps (M = 7.133) and VHS/128 kbps (M = 6.533) were significantly better at recognizing the displayed facial affects than those in the Betacam/768 kbps (M = 4.733) or Betacam/128 kbps (M = 6.333) conditions. Camera resolution and bandwidth combinations differ in their capacity to influence facial affect recognition. For service providers, this study's results support the use of VHS cameras with either 768 kbps or 128 kbps bandwidths for facial affect recognition compared to Betacam cameras. The authors argue that the results of this study are a consequence of the VHS camera resolution/bandwidth combinations' ability to improve signal detection (i.e., facial affect recognition) by subjects in comparison to Betacam camera resolution/bandwidth combinations.

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

Structural basis for the recognition and cleavage of abasic DNA in Neisseria meningitidis

PubMed Central

Lu, Duo; Silhan, Jan; MacDonald, James T.; Carpenter, Elisabeth P.; Jensen, Kirsten; Tang, Christoph M.; Baldwin, Geoff S.; Freemont, Paul S.

2012-01-01

Base excision repair (BER) is a highly conserved DNA repair pathway throughout all kingdoms from bacteria to humans. Whereas several enzymes are required to complete the multistep repair process of damaged bases, apurinic-apyrimidic (AP) endonucleases play an essential role in enabling the repair process by recognizing intermediary abasic sites cleaving the phosphodiester backbone 5′ to the abasic site. Despite extensive study, there is no structure of a bacterial AP endonuclease bound to substrate DNA. Furthermore, the structural mechanism for AP-site cleavage is incomplete. Here we report a detailed structural and biochemical study of the AP endonuclease from Neisseria meningitidis that has allowed us to capture structural intermediates providing more complete snapshots of the catalytic mechanism. Our data reveal subtle differences in AP-site recognition and kinetics between the human and bacterial enzymes that may reflect different evolutionary pressures. PMID:23035246

The Impact of Sex Differences on Odor Identification and Facial Affect Recognition in Patients with Schizophrenia Spectrum Disorders.

PubMed

Mossaheb, Nilufar; Kaufmann, Rainer M; Schlögelhofer, Monika; Aninilkumparambil, Thushara; Himmelbauer, Claudia; Gold, Anna; Zehetmayer, Sonja; Hoffmann, Holger; Traue, Harald C; Aschauer, Harald

2018-01-01

Social interactive functions such as facial emotion recognition and smell identification have been shown to differ between women and men. However, little is known about how these differences are mirrored in patients with schizophrenia and how these abilities interact with each other and with other clinical variables in patients vs. healthy controls. Standardized instruments were used to assess facial emotion recognition [Facially Expressed Emotion Labelling (FEEL)] and smell identification [University of Pennsylvania Smell Identification Test (UPSIT)] in 51 patients with schizophrenia spectrum disorders and 79 healthy controls; furthermore, working memory functions and clinical variables were assessed. In both the univariate and the multivariate results, illness showed a significant influence on UPSIT and FEEL. The inclusion of age and working memory in the MANOVA resulted in a differential effect with sex and working memory as remaining significant factors. Duration of illness was correlated with both emotion recognition and smell identification in men only, whereas immediate general psychopathology and negative symptoms were associated with emotion recognition only in women. Being affected by schizophrenia spectrum disorder impacts one's ability to correctly recognize facial affects and identify odors. Converging evidence suggests a link between the investigated basic and social cognitive abilities in patients with schizophrenia spectrum disorders with a strong contribution of working memory and differential effects of modulators in women vs. men.

Recognition of Mannosylated Ligands and Influenza A Virus by Human Surfactant Protein D: Contributions of an Extended Site and Residue 343

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

Crouch, E.; Hartshorn, K; Horlacher, T

2009-01-01

Surfactant protein D (SP-D) plays important roles in antiviral host defense. Although SP-D shows a preference for glucose/maltose, the protein also recognizes d-mannose and a variety of mannose-rich microbial ligands. This latter preference prompted an examination of the mechanisms of mannose recognition, particularly as they relate to high-mannose viral glycans. Trimeric neck plus carbohydrate recognition domains from human SP-D (hNCRD) preferred ?1-2-linked dimannose (DM) over the branched trimannose (TM) core, ?1-3 or ?1-6 DM, or d-mannose. Previous studies have shown residues flanking the carbohydrate binding site can fine-tune ligand recognition. A mutant with valine at 343 (R343V) showed enhanced bindingmore » to mannan relative to wild type and R343A. No alteration in affinity was observed for d-mannose or for ?1-3- or ?1-6-linked DM; however, substantially increased affinity was observed for ?1-2 DM. Both proteins showed efficient recognition of linear and branched subdomains of high-mannose glycans on carbohydrate microarrays, and R343V showed increased binding to a subset of the oligosaccharides. Crystallographic analysis of an R343V complex with 1,2-DM showed a novel mode of binding. The disaccharide is bound to calcium by the reducing sugar ring, and a stabilizing H-bond is formed between the 2-OH of the nonreducing sugar ring and Arg349. Although hNCRDs show negligible binding to influenza A virus (IAV), R343V showed markedly enhanced viral neutralizing activity. Hydrophobic substitutions for Arg343 selectively blocked binding of a monoclonal antibody (Hyb 246-05) that inhibits IAV binding activity. Our findings demonstrate an extended ligand binding site for mannosylated ligands and the significant contribution of the 343 side chain to specific recognition of multivalent microbial ligands, including high-mannose viral glycans.« less

Genetic mapping uncovers cis-regulatory landscape of RNA editing.

PubMed

Ramaswami, Gokul; Deng, Patricia; Zhang, Rui; Anna Carbone, Mary; Mackay, Trudy F C; Li, Jin Billy

2015-09-16

Adenosine-to-inosine (A-to-I) RNA editing, catalysed by ADAR enzymes conserved in metazoans, plays an important role in neurological functions. Although the fine-tuning mechanism provided by A-to-I RNA editing is important, the underlying rules governing ADAR substrate recognition are not well understood. We apply a quantitative trait loci (QTL) mapping approach to identify genetic variants associated with variability in RNA editing. With very accurate measurement of RNA editing levels at 789 sites in 131 Drosophila melanogaster strains, here we identify 545 editing QTLs (edQTLs) associated with differences in RNA editing. We demonstrate that many edQTLs can act through changes in the local secondary structure for edited dsRNAs. Furthermore, we find that edQTLs located outside of the edited dsRNA duplex are enriched in secondary structure, suggesting that distal dsRNA structure beyond the editing site duplex affects RNA editing efficiency. Our work will facilitate the understanding of the cis-regulatory code of RNA editing.

78 FR 38388 - SGS North America, Inc. (Formerly SGS U.S. Testing Company, Inc.)

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-26

... of one test site and the removal of one test site. This notice presents the Agency's preliminary...'s expansion request covers the addition of one additional test site. SGS's also requests the removal of one test site from its NRTL scope of recognition. SGS informed OSHA of a change in name from SGS U...

Activity-based probes for the ubiquitin conjugation-deconjugation machinery: new chemistries, new tools, and new insights.

PubMed

Hewings, David S; Flygare, John A; Bogyo, Matthew; Wertz, Ingrid E

2017-05-01

The reversible post-translational modification of proteins by ubiquitin and ubiquitin-like proteins regulates almost all cellular processes, by affecting protein degradation, localization, and complex formation. Deubiquitinases (DUBs) are proteases that remove ubiquitin modifications or cleave ubiquitin chains. Most DUBs are cysteine proteases, which makes them well suited for study by activity-based probes. These DUB probes report on deubiquitinase activity by reacting covalently with the active site in an enzyme-catalyzed manner. They have proven to be important tools to study DUB selectivity and proteolytic activity in different settings, to identify novel DUBs, and to characterize deubiquitinase inhibitors. Inspired by the efficacy of activity-based probes for DUBs, several groups have recently reported probes for the ubiquitin conjugation machinery (E1, E2, and E3 enzymes). Many of these enzymes, while not proteases, also posses active site cysteine residues and can be targeted by covalent probes. In this review, we will discuss how features of the probe (cysteine-reactive group, recognition element, and reporter tag) affect reactivity and suitability for certain experimental applications. We will also review the diverse applications of the current probes, and discuss the need for new probe types to study emerging aspects of ubiquitin biology. © 2017 Federation of European Biochemical Societies.

Functional specificity of a Hox protein mediated by the recognition of minor groove structure.

PubMed

Joshi, Rohit; Passner, Jonathan M; Rohs, Remo; Jain, Rinku; Sosinsky, Alona; Crickmore, Michael A; Jacob, Vinitha; Aggarwal, Aneel K; Honig, Barry; Mann, Richard S

2007-11-02

The recognition of specific DNA-binding sites by transcription factors is a critical yet poorly understood step in the control of gene expression. Members of the Hox family of transcription factors bind DNA by making nearly identical major groove contacts via the recognition helices of their homeodomains. In vivo specificity, however, often depends on extended and unstructured regions that link Hox homeodomains to a DNA-bound cofactor, Extradenticle (Exd). Using a combination of structure determination, computational analysis, and in vitro and in vivo assays, we show that Hox proteins recognize specific Hox-Exd binding sites via residues located in these extended regions that insert into the minor groove but only when presented with the correct DNA sequence. Our results suggest that these residues, which are conserved in a paralog-specific manner, confer specificity by recognizing a sequence-dependent DNA structure instead of directly reading a specific DNA sequence.

Specific minor groove solvation is a crucial determinant of DNA binding site recognition

PubMed Central

Harris, Lydia-Ann; Williams, Loren Dean; Koudelka, Gerald B.

2014-01-01

The DNA sequence preferences of nearly all sequence specific DNA binding proteins are influenced by the identities of bases that are not directly contacted by protein. Discrimination between non-contacted base sequences is commonly based on the differential abilities of DNA sequences to allow narrowing of the DNA minor groove. However, the factors that govern the propensity of minor groove narrowing are not completely understood. Here we show that the differential abilities of various DNA sequences to support formation of a highly ordered and stable minor groove solvation network are a key determinant of non-contacted base recognition by a sequence-specific binding protein. In addition, disrupting the solvent network in the non-contacted region of the binding site alters the protein's ability to recognize contacted base sequences at positions 5–6 bases away. This observation suggests that DNA solvent interactions link contacted and non-contacted base recognition by the protein. PMID:25429976

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

Three RNA recognition motifs participate in RNA recognition and structural organization by the pro-apoptotic factor TIA-1

PubMed Central

Bauer, William J.; Heath, Jason; Jenkins, Jermaine L.; Kielkopf, Clara L.

2012-01-01

T-cell intracellular antigen-1 (TIA-1) regulates developmental and stress-responsive pathways through distinct activities at the levels of alternative pre-mRNA splicing and mRNA translation. The TIA-1 polypeptide contains three RNA recognition motifs (RRMs). The central RRM2 and C-terminal RRM3 associate with cellular mRNAs. The N-terminal RRM1 enhances interactions of a C-terminal Q-rich domain of TIA-1 with the U1-C splicing factor, despite linear separation of the domains in the TIA-1 sequence. Given the expanded functional repertoire of the RRM family, it was unknown whether TIA-1 RRM1 contributes to RNA binding as well as documented protein interactions. To address this question, we used isothermal titration calorimetry and small-angle X-ray scattering (SAXS) to dissect the roles of the TIA-1 RRMs in RNA recognition. Notably, the fas RNA exhibited two binding sites with indistinguishable affinities for TIA-1. Analyses of TIA-1 variants established that RRM1 was dispensable for binding AU-rich fas sites, yet all three RRMs were required to bind a polyU RNA with high affinity. SAXS analyses demonstrated a `V' shape for a TIA-1 construct comprising the three RRMs, and revealed that its dimensions became more compact in the RNA-bound state. The sequence-selective involvement of TIA-1 RRM1 in RNA recognition suggests a possible role for RNA sequences in regulating the distinct functions of TIA-1. Further implications for U1-C recruitment by the adjacent TIA-1 binding sites of the fas pre-mRNA and the bent TIA-1 shape, which organizes the N- and C-termini on the same side of the protein, are discussed. PMID:22154808

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.

Multiple nucleotide preferences determine cleavage-site recognition by the HIV-1 and M-MuLV RNases H.

PubMed

Schultz, Sharon J; Zhang, Miaohua; Champoux, James J

2010-03-19

The RNase H activity of reverse transcriptase is required during retroviral replication and represents a potential target in antiviral drug therapies. Sequence features flanking a cleavage site influence the three types of retroviral RNase H activity: internal, DNA 3'-end-directed, and RNA 5'-end-directed. Using the reverse transcriptases of HIV-1 (human immunodeficiency virus type 1) and Moloney murine leukemia virus (M-MuLV), we evaluated how individual base preferences at a cleavage site direct retroviral RNase H specificity. Strong test cleavage sites (designated as between nucleotide positions -1 and +1) for the HIV-1 and M-MuLV enzymes were introduced into model hybrid substrates designed to assay internal or DNA 3'-end-directed cleavage, and base substitutions were tested at specific nucleotide positions. For internal cleavage, positions +1, -2, -4, -5, -10, and -14 for HIV-1 and positions +1, -2, -6, and -7 for M-MuLV significantly affected RNase H cleavage efficiency, while positions -7 and -12 for HIV-1 and positions -4, -9, and -11 for M-MuLV had more modest effects. DNA 3'-end-directed cleavage was influenced substantially by positions +1, -2, -4, and -5 for HIV-1 and positions +1, -2, -6, and -7 for M-MuLV. Cleavage-site distance from the recessed end did not affect sequence preferences for M-MuLV reverse transcriptase. Based on the identified sequence preferences, a cleavage site recognized by both HIV-1 and M-MuLV enzymes was introduced into a sequence that was otherwise resistant to RNase H. The isolated RNase H domain of M-MuLV reverse transcriptase retained sequence preferences at positions +1 and -2 despite prolific cleavage in the absence of the polymerase domain. The sequence preferences of retroviral RNase H likely reflect structural features in the substrate that favor cleavage and represent a novel specificity determinant to consider in drug design. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Intracellular Zn(2+) signaling in the dentate gyrus is required for object recognition memory.

PubMed

Takeda, Atsushi; Tamano, Haruna; Ogawa, Taisuke; Takada, Shunsuke; Nakamura, Masatoshi; Fujii, Hiroaki; Ando, Masaki

2014-11-01

The role of perforant pathway-dentate granule cell synapses in cognitive behavior was examined focusing on synaptic Zn(2+) signaling in the dentate gyrus. Object recognition memory was transiently impaired when extracellular Zn(2+) levels were decreased by injection of clioquinol and N,N,N',N'-tetrakis-(2-pyridylmethyl) ethylendediamine. To pursue the effect of the loss and/or blockade of Zn(2+) signaling in dentate granule cells, ZnAF-2DA (100 pmol, 0.1 mM/1 µl), an intracellular Zn(2+) chelator, was locally injected into the dentate molecular layer of rats. ZnAF-2DA injection, which was estimated to chelate intracellular Zn(2+) signaling only in the dentate gyrus, affected object recognition memory 1 h after training without affecting intracellular Ca(2+) signaling in the dentate molecular layer. In vivo dentate gyrus long-term potentiation (LTP) was affected under the local perfusion of the recording region (the dentate granule cell layer) with 0.1 mM ZnAF-2DA, but not with 1-10 mM CaEDTA, an extracellular Zn(2+) chelator, suggesting that the blockade of intracellular Zn(2+) signaling in dentate granule cells affects dentate gyrus LTP. The present study demonstrates that intracellular Zn(2+) signaling in the dentate gyrus is required for object recognition memory, probably via dentate gyrus LTP expression. Copyright © 2014 Wiley Periodicals, Inc.

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).

The role of visual imagery in the retention of information from sentences.

PubMed

Drose, G S; Allen, G L

1994-01-01

We conducted two experiments to evaluate a multiple-code model for sentence memory that posits both propositional and visual representational systems. Both sentences involved recognition memory. The results of Experiment 1 indicated that subjects' recognition memory for concrete sentences was superior to their recognition memory for abstract sentences. Instructions to use visual imagery to enhance recognition performance yielded no effects. Experiment 2 tested the prediction that interference by a visual task would differentially affect recognition memory for concrete sentences. Results showed the interference task to have had a detrimental effect on recognition memory for both concrete and abstract sentences. Overall, the evidence provided partial support for both a multiple-code model and a semantic integration model of sentence memory.

Post-oil-spill fires at Ugbomro (Niger Delta): a new vista in soil-pollution studies.

PubMed

Osuji, Leo C; Ukale, Eseoghene E

2005-10-01

Reconnaissance of the post-oil-spill, fire-scourged site at Ugbomro, in the Niger Delta, was contingent upon the loud public outcry and galvanizing hue that ensued the widespread conflagration. Sampling was carried out by the grid technique, and fire-scourged soils and their unaffected controls were analyzed. Contrary to the 'celebrated' opinion of some that the fires improvised bush fallowing for cropping, the site had witnessed severe impoverishment as evidenced by the hitherto neglected insidious impact of such infernos on soil macronutrients. Alterations in physico-chemical properties (pH, conductivity, etc.) provided adequate bases for this conclusion, and offered broad explanations for the paucity of macronutrients in affected soils. For instance, a pH range of 3.1-3.8 hindered N2 fixation and other metabolic activities that enhance mineralization. Elaeis guineensis in a density of 3 stands/m2 at the control site was the only tree-form not charred beyond recognition.Against future fires, it is important to strengthen contingencies for more-expedient clean-up responses to oil spills to severe possibilities of in situ conflagrations. Nutrient supplementations, revegetation, and site surveillance should disengage the 'unsighted fingers' of sabotage. A careful husbandry of these measures might re-establish nutrient stability, and forestall future re-occurrence of such effacing incidents.

Synthesis of molecularly imprinted organic-inorganic hybrid azobenzene materials by sol-gel for radiation induced selective recognition of 2,4-dichlorophenoxyacetic acid

NASA Astrophysics Data System (ADS)

Shuai Jiang, Guang; An Zhong, Shi; Chen, Lan; Blakey, Idriss; Whitaker, Andrew

2011-02-01

A novel photoresponsive functional monomer bearing a siloxane polymerisable group and azobenzene moieties was synthesized. This monomer was then used to prepare photoresponsive molecularly imprinted polymers (MIP), which have specific binding sites for 2,4-dichlorophenoxyacetic acid (2,4-D) through hydrogen bonding moieties. The binding affinity of the imprinted recognition sites was switchable by alternate irradiations with ultraviolet and visible light, suggesting that azobenzene groups located inside the binding sites could be used as chemical sensors and the trans-cis isomerization could regulate the affinity for the 2,4-D. In addition, the concentration of the 2,4-D was able to be quantified by monitoring the trans-to-cis photoisomerization rate constant.

A real time mobile-based face recognition with fisherface methods

NASA Astrophysics Data System (ADS)

Arisandi, D.; Syahputra, M. F.; Putri, I. L.; Purnamawati, S.; Rahmat, R. F.; Sari, P. P.

2018-03-01

Face Recognition is a field research in Computer Vision that study about learning face and determine the identity of the face from a picture sent to the system. By utilizing this face recognition technology, learning process about people’s identity between students in a university will become simpler. With this technology, student won’t need to browse student directory in university’s server site and look for the person with certain face trait. To obtain this goal, face recognition application use image processing methods consist of two phase, pre-processing phase and recognition phase. In pre-processing phase, system will process input image into the best image for recognition phase. Purpose of this pre-processing phase is to reduce noise and increase signal in image. Next, to recognize face phase, we use Fisherface Methods. This methods is chosen because of its advantage that would help system of its limited data. Therefore from experiment the accuracy of face recognition using fisherface is 90%.

Molecular evolution of the CYP2D subfamily in primates: purifying selection on substrate recognition sites without the frequent or long-tract gene conversion.

PubMed

Yasukochi, Yoshiki; Satta, Yoko

2015-03-25

The human cytochrome P450 (CYP) 2D6 gene is a member of the CYP2D gene subfamily, along with the CYP2D7P and CYP2D8P pseudogenes. Although the CYP2D6 enzyme has been studied extensively because of its clinical importance, the evolution of the CYP2D subfamily has not yet been fully understood. Therefore, the goal of this study was to reveal the evolutionary process of the human drug metabolic system. Here, we investigate molecular evolution of the CYP2D subfamily in primates by comparing 14 CYP2D sequences from humans to New World monkey genomes. Window analysis and statistical tests revealed that entire genomic sequences of paralogous genes were extensively homogenized by gene conversion during molecular evolution of CYP2D genes in primates. A neighbor-joining tree based on genomic sequences at the nonsubstrate recognition sites showed that CYP2D6 and CYP2D8 genes were clustered together due to gene conversion. In contrast, a phylogenetic tree using amino acid sequences at substrate recognition sites did not cluster the CYP2D6 and CYP2D8 genes, suggesting that the functional constraint on substrate specificity is one of the causes for purifying selection at the substrate recognition sites. Our results suggest that the CYP2D gene subfamily in primates has evolved to maintain the regioselectivity for a substrate hydroxylation activity between individual enzymes, even though extensive gene conversion has occurred across CYP2D coding sequences. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Critical Determinants of Substrate Recognition by Cyclin-Dependent Kinase-like 5 (CDKL5).

PubMed

Katayama, Syouichi; Sueyoshi, Noriyuki; Kameshita, Isamu

2015-05-19

Cyclin-dependent kinase-like 5 (CDKL5) is a Ser/Thr protein kinase known to be associated with X-linked neurodevelopmental disorders. In a previous study, we identified amphiphysin 1 (Amph1) as a potential substrate for CDKL5 and identified a single phosphorylation site at Ser-293. In this study, we investigated the molecular mechanisms of substrate recognition by CDKL5 using Amph1 as a model substrate. Amph1 served as an efficient CDKL5 substrate, whereas Amph2, a structurally related homologue of Amph1, was not phosphorylated by CDKL5. The sequence around the Amph1 phosphorylation site is RPR(293)SPSQ, while the corresponding sequence in Amph2 is IPK(332)SPSQ. To define the amino acid sequence specificity of the substrate, various point mutants of Amph1 and Amph2 were prepared and phosphorylated by CDKL5. Both Amph2(I329R) and Amph1 served as efficient CDKL5 substrates, but Amph1(R290I) did not, indicating that the arginyl residue at the P -3 position is critical for substrate recognition. With regard to prolyl residues around the phosphorylation site of Amph1, Pro-291 at the P -2 position, but not Pro-294 at the P +1 position, is indispensable for phosphorylation by CDKL5. Phosphorylation experiments using various deletion mutants of Amph1 revealed that the proline-rich domain (PRD) (amino acids 247-315) alone was not phosphorylated by CDKL5. In contrast, Amph1(247-385), which comprised the PRD and CLAP domains, served as an efficient CDKL5 substrate. These results, taken together, suggest that both the phosphorylation site sequence (RPXSX) and the CLAP domain structure in Amph1 play crucial roles in recognition and phosphorylation by CDKL5.

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

PubMed Central

Yasukochi, Yoshiki; Satta, Yoko

2015-01-01

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

Mannose-recognition mutant of the galactose/N-acetylgalactosamine-specific C-type lectin CEL-I engineered by site-directed mutagenesis.

PubMed

Moriuchi, Hiromi; Unno, Hideaki; Goda, Shuichiro; Tateno, Hiroaki; Hirabayashi, Jun; Hatakeyama, Tomomitsu

2015-07-01

CEL-I is a galactose/N-acetylgalactosamine-specific C-type lectin isolated from the sea cucumber Cucumaria echinata. Its carbohydrate-binding site contains a QPD (Gln-Pro-Asp) motif, which is generally recognized as the galactose specificity-determining motif in the C-type lectins. In our previous study, replacement of the QPD motif by an EPN (Glu-Pro-Asn) motif led to a weak binding affinity for mannose. Therefore, we examined the effects of an additional mutation in the carbohydrate-binding site on the specificity of the lectin. Trp105 of EPN-CEL-I was replaced by a histidine residue using site-directed mutagenesis, and the binding affinity of the resulting mutant, EPNH-CEL-I, was examined by sugar-polyamidoamine dendrimer assay, isothermal titration calorimetry, and glycoconjugate microarray analysis. Tertiary structure of the EPNH-CEL-I/mannose complex was determined by X-ray crystallographic analysis. Sugar-polyamidoamine dendrimer assay and glycoconjugate microarray analysis revealed a drastic change in the specificity of EPNH-CEL-I from galactose/N-acetylgalactosamine to mannose. The association constant of EPNH-CEL-I for mannose was determined to be 3.17×10(3) M(-1) at 25°C. Mannose specificity of EPNH-CEL-I was achieved by stabilization of the binding of mannose in a correct orientation, in which the EPN motif can form proper hydrogen bonds with 3- and 4-hydroxy groups of the bound mannose. Specificity of CEL-I can be engineered by mutating a limited number of amino acid residues in addition to the QPD/EPN motifs. Versatility of the C-type carbohydrate-recognition domain structure in the recognition of various carbohydrate chains could become a promising platform to develop novel molecular recognition proteins. Copyright © 2015 Elsevier B.V. All rights reserved.

Word recognition in Alzheimer's disease: Effects of semantic degeneration.

PubMed

Cuetos, Fernando; Arce, Noemí; Martínez, Carmen; Ellis, Andrew W

2017-03-01

Impairments of word recognition in Alzheimer's disease (AD) have been less widely investigated than impairments affecting word retrieval and production. In particular, we know little about what makes individual words easier or harder for patients with AD to recognize. We used a lexical selection task in which participants were shown sets of four items, each set consisting of one word and three non-words. The task was simply to point to the word on each trial. Forty patients with mild-to-moderate AD were significantly impaired on this task relative to matched controls who made very few errors. The number of patients with AD able to recognize each word correctly was predicted by the frequency, age of acquisition, and imageability of the words, but not by their length or number of orthographic neighbours. Patient Mini-Mental State Examination and phonological fluency scores also predicted the number of words recognized. We propose that progressive degradation of central semantic representations in AD differentially affects the ability to recognize low-imageability, low-frequency, late-acquired words, with the same factors affecting word recognition as affecting word retrieval. © 2015 The British Psychological Society.

Parallel effects of processing fluency and positive affect on familiarity-based recognition decisions for faces.

PubMed

Duke, Devin; Fiacconi, Chris M; Köhler, Stefan

2014-01-01

According to attribution models of familiarity assessment, people can use a heuristic in recognition-memory decisions, in which they attribute the subjective ease of processing of a memory probe to a prior encounter with the stimulus in question. Research in social cognition suggests that experienced positive affect may be the proximal cue that signals fluency in various experimental contexts. In the present study, we compared the effects of positive affect and fluency on recognition-memory judgments for faces with neutral emotional expression. We predicted that if positive affect is indeed the critical cue that signals processing fluency at retrieval, then its manipulation should produce effects that closely mirror those produced by manipulations of processing fluency. In two experiments, we employed a masked-priming procedure in combination with a Remember-Know (RK) paradigm that aimed to separate familiarity- from recollection-based memory decisions. In addition, participants performed a prime-discrimination task that allowed us to take inter-individual differences in prime awareness into account. We found highly similar effects of our priming manipulations of processing fluency and of positive affect. In both cases, the critical effect was specific to familiarity-based recognition responses. Moreover, in both experiments it was reflected in a shift toward a more liberal response bias, rather than in changed discrimination. Finally, in both experiments, the effect was found to be related to prime awareness; it was present only in participants who reported a lack of such awareness on the prime-discrimination task. These findings add to a growing body of evidence that points not only to a role of fluency, but also of positive affect in familiarity assessment. As such they are consistent with the idea that fluency itself may be hedonically marked.

Does Employee Recognition Affect Positive Psychological Functioning and Well-Being?

PubMed

Merino, M Dolores; Privado, Jesús

2015-09-14

Employee recognition is one of the typical characteristics of healthy organizations. The majority of research on recognition has studied the consequences of this variable on workers. But few investigations have focused on understanding what mechanisms mediate between recognition and its consequences. This work aims to understand whether the relationship between employee recognition and well-being, psychological resources mediate. To answer this question a sample of 1831 workers was used. The variables measured were: employee recognition, subjective well-being and positive psychological functioning (PPF), which consists of 11 psychological resources. In the analysis of data, structural equation models were applied. The results confirmed our hypothesis and showed that PPF mediate the relationship between recognition and well-being. The effect of recognition over PPF is two times greater (.39) with peer-recognition than with supervisor-recognition (.20), and, the effect of PPF over well-being is .59. This study highlights the importance of promoting employee recognition policies in organizations for the impact it has, not only on well-being, but also on the positive psychological functioning of the workers.

Depression Literacy and Awareness of Psychopathological Symptoms During the Perinatal Period.

PubMed

Fonseca, Ana; Silva, Sheila; Canavarro, Maria Cristina

To characterize women's depression literacy during the perinatal period, including their ability to recognize clinically significant symptoms of depression. A quantitative, cross-sectional, survey design. Internet communities and Web sites focused on the topics of pregnancy and motherhood. A total of 194 women during the perinatal period (32.5% pregnant, 67.5% postnatal) completed the survey; 34.0% had clinically significant psychopathological symptoms. Most women were married/cohabiting (82.0%) and employed (71.8%). Women answered self-report questionnaires to assess depression literacy, symptoms of depression, emotional competence, and awareness/recognition of psychopathological symptoms. Women had moderate levels of depression literacy during the perinatal period, with higher literacy levels concerning depression-related characteristics than depression-related treatments. Lower education and lower income were associated with poor depression literacy, whereas prior history of psychiatric problems or treatments was associated with higher levels of depression literacy. An indirect effect through emotional competence in the relationship between depression literacy and awareness/recognition of symptoms was found: women with poor depression literacy tended to have a greater lack of emotional clarity, which negatively affected their symptom awareness and recognition. Our results support the need to improve women's mental health literacy during the perinatal period. Education on mental health topics in the context of a trusting relationship with health professionals may contribute to the promotion of women's depression literacy and emotional competence. Copyright © 2017 AWHONN, the Association of Women’s Health, Obstetric and Neonatal Nurses. Published by Elsevier Inc. All rights reserved.

Structural Basis for Carbohydrate Recognition and Anti-inflammatory Modulation by Gastrointestinal Nematode Parasite Toxascaris leonina Galectin*

PubMed Central

Hwang, Eun Young; Jeong, Mi Suk; Park, Sang Kyun; Ha, Sung Chul; Yu, Hak Sun; Jang, Se Bok

2016-01-01

Toxascaris leonina galectin (Tl-gal) is a galectin-9 homologue protein isolated from an adult worm of the canine gastrointestinal nematode parasite, and Tl-gal-vaccinated challenge can inhibit inflammation in inflammatory bowel disease-induced mice. We determined the first X-ray structures of full-length Tl-gal complexes with carbohydrates (lactose, N-acetyllactosamine, lacto-N-tetraose, sialyllactose, and glucose). Bonds were formed on concave surfaces of both carbohydrate recognition domains (CRDs) in Tl-gal. All binding sites were found in the HXXXR and WGXEER motifs. Charged Arg61/Arg196 and Glu80/Glu215 on the conserved motif of Tl-gal N-terminal CRD and C-terminal CRD are critical amino acids for recognizing carbohydrate binding, and the residues can affect protein folding and structure. The polar amino acids His, Asn, and Trp are also important residues for the interaction with carbohydrates through hydrogen bonding. Hemagglutination activities of Tl-gal were inhibited by interactions with carbohydrates and mutations. We found that the mutation of Tl-gal (E80A/E215A) at the carbohydrate binding region induced protein aggregation and could be caused in many diseases. The short linker region between the N-terminal and C-terminal CRDs of Tl-gal was very stable against proteolysis and maintained its biological activity. This structural information is expected to elucidate the carbohydrate recognition mechanism of Tl-gal and improve our understanding of anti-inflammatory mediators and modulators of immune response. PMID:27742836

Schizotypy and impaired basic face recognition? Another non-confirmatory study.

PubMed

Bell, Vaughan; Halligan, Peter

2015-12-01

Although schizotypy has been found to be reliably associated with a reduced recognition of facial affect, the few studies that have tested the association between basic face recognition abilities and schizotypy have found mixed results. This study formally tested the association in a large non-clinical sample with established neurological measures of face recognition. Two hundred and twenty-seven participants completed the Oxford-Liverpool Inventory of Feelings and Experiences schizotypy scale and completed the Famous Faces Test and the Cardiff Repeated Recognition Test for Faces. No association between any schizotypal dimension and performance on either of the facial recognition and learning tests was found. The null results can be accepted with a high degree of confidence. Further additional evidence is provided for a lack of association between schizotypy and basic face recognition deficits. © 2014 Wiley Publishing Asia Pty Ltd.

[The Relationship Between Emotion Recognition and the Symptoms of Attention Deficit and Impulsivity in Adult Patients With Attention Deficit Hyperactivity Disorder].

PubMed

Baran Tatar, Zeynep; Yargıç, İlhan; Oflaz, Serap; Büyükgök, Deniz

2015-01-01

Interpersonal relationship disorders in adults with Attention Deficit Hyperactivity Disorder (ADHD) can be associated with the impairment of non-verbal communication. The purpose of our study was to compare the emotion recognition, facial recognition and neuropsychological assessments of adult ADHD patients with those of healthy controls, and to thus determine the effect of neuropsychological data on the recognition of emotional expressions. This study, which was based on a case-control model, was conducted with patients diagnosed with ADHD according to the DSM-IV-TR, being followed and monitored at the adult ADHD clinic of the Psychiatry Department of the Istanbul University Istanbul Medical Faculty Hospital. The study group consisted of 40 adults (27.5% female) between the ages of 20-65 (mean age 25.96 ± 6.07; education level: 15.02±2.34 years) diagnosed with ADHD, and 40 controls who were matched/similar with the study group with respect to age, gender, and education level. In the ADHD group, 14 (35%) of the patients had concomitant diseases. Pictures of Facial Affect, the Benton Face Recognition Test, and the Continuous Performance Test were used to respectively evaluate emotion recognition, facial recognition, and attention deficit and impulsivity of the patients. It was determined that, in comparison to the control group, the ADHD group made more mistakes in recognizing all types of emotional expressions and neutral expressions. The ADHD group also demonstrated more cognitive mistakes. Facial recognition was similar in both groups. It was determined that impulsivity had a significant effect on facial recognition. The social relationship disorders observed in ADHD can be affected by emotion recognition processes. In future studies, it may be possible to investigate the effects that early psychopharmacological and psychotherapeutic interventions administered for the main symptoms of ADHD have on the impairment of emotion recognition.

OhioHealth web site wins awards. Draws leadership recognition for outstanding redesign.

PubMed

Rees, Tom

2004-01-01

OhioHealth, Columbus, Ohio, has redesigned its web site, making it especially useful and appealing to women. For the collaborative effort, which included the Mayo Clinic and The VIA Group, Portland Maine, it has received numerous awards.

Dynamics Govern Specificity of a Protein-Protein Interface: Substrate Recognition by Thrombin.

PubMed

Fuchs, Julian E; Huber, Roland G; Waldner, Birgit J; Kahler, Ursula; von Grafenstein, Susanne; Kramer, Christian; Liedl, Klaus R

2015-01-01

Biomolecular recognition is crucial in cellular signal transduction. Signaling is mediated through molecular interactions at protein-protein interfaces. Still, specificity and promiscuity of protein-protein interfaces cannot be explained using simplistic static binding models. Our study rationalizes specificity of the prototypic protein-protein interface between thrombin and its peptide substrates relying solely on binding site dynamics derived from molecular dynamics simulations. We find conformational selection and thus dynamic contributions to be a key player in biomolecular recognition. Arising entropic contributions complement chemical intuition primarily reflecting enthalpic interaction patterns. The paradigm "dynamics govern specificity" might provide direct guidance for the identification of specific anchor points in biomolecular recognition processes and structure-based drug design.

Pseudoknot and translational control in the expression of the S15 ribosomal protein.

PubMed

Bénard, L; Philippe, C; Ehresmann, B; Ehresmann, C; Portier, C

1996-01-01

Translational autocontrol of the expression of the ribosomal protein S15 proceeds through the transitory formation of a pseudoknot. A synopsis of the known data is used to propose a molecular model of the mechanism involved and for the role of the pseudoknot. This latter structure is able to recruit 30S ribosomal subunits to initiate translation, but also to bind S15 and to stop translation by trapping the ribosome on its loading site. Information on the S15 protein recognition of the messenger RNA site was deduced from mutational analyses and chemical probing. A comparison of this messenger site with the S15 ribosomal binding site was conducted by analysing hydroxyl radical footprintings of these two sites. The existence of two subsites in 16S RNA suggests that the ribosomal protein S15 might present either two different binding sites or at least one common subsite. Clues for the presence of a common site between the messenger and 16S RNA are given which cannot rule out that recognition specificity is linked to a few other determinants. Whether these determinants are different or not remains an open question.

Impaired Spermatogenesis, Muscle, and Erythrocyte Function in U12 Intron Splicing-Defective Zrsr1 Mutant Mice.

PubMed

Horiuchi, Keiko; Perez-Cerezales, Serafín; Papasaikas, Panagiotis; Ramos-Ibeas, Priscila; López-Cardona, Angela Patricia; Laguna-Barraza, Ricardo; Fonseca Balvís, Noelia; Pericuesta, Eva; Fernández-González, Raul; Planells, Benjamín; Viera, Alberto; Suja, Jose Angel; Ross, Pablo Juan; Alén, Francisco; Orio, Laura; Rodriguez de Fonseca, Fernando; Pintado, Belén; Valcárcel, Juan; Gutiérrez-Adán, Alfonso

2018-04-03

The U2AF35-like ZRSR1 has been implicated in the recognition of 3' splice site during spliceosome assembly, but ZRSR1 knockout mice do not show abnormal phenotypes. To analyze ZRSR1 function and its precise role in RNA splicing, we generated ZRSR1 mutant mice containing truncating mutations within its RNA-recognition motif. Homozygous mutant mice exhibited severe defects in erythrocytes, muscle stretch, and spermatogenesis, along with germ cell sloughing and apoptosis, ultimately leading to azoospermia and male sterility. Testis RNA sequencing (RNA-seq) analyses revealed increased intron retention of both U2- and U12-type introns, including U12-type intron events in genes with key functions in spermatogenesis and spermatid development. Affected U2 introns were commonly found flanking U12 introns, suggesting functional cross-talk between the two spliceosomes. The splicing and tissue defects observed in mutant mice attributed to ZRSR1 loss of function suggest a physiological role for this factor in U12 intron splicing. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

Exploring Symmetry to Assist Alzheimer's Disease Diagnosis

NASA Astrophysics Data System (ADS)

Illán, I. A.; Górriz, J. M.; Ramírez, J.; Salas-Gonzalez, D.; López, M.; Padilla, P.; Chaves, R.; Segovia, F.; Puntonet, C. G.

Alzheimer's disease (AD) is a progressive neurodegenerative disorder first affecting memory functions and then gradually affecting all cognitive functions with behavioral impairments and eventually causing death. Functional brain imaging as Single-Photon Emission Computed Tomography (SPECT) is commonly used to guide the clinician's diagnosis. The essential left-right symmetry of human brains is shown to play a key role in coding and recognition. In the present work we explore the implications of this symmetry in AD diagnosis, showing that recognition may be enhanced when considering this latent symmetry.

Arginine vasopressin 1a receptor RS3 promoter microsatellites in schizophrenia: a study of the effect of the "risk" allele on clinical symptoms and facial affect recognition.

PubMed

Golimbet, Vera; Alfimova, Margarita; Abramova, Lilia; Kaleda, Vasily; Gritsenko, Inga

2015-02-28

We studied AVPR1A RS3 polymorphism in schizophrenic patients and controls. AVPR1A RS3 was not associated with schizophrenia. The allele 327bp implicated in autism and social behavior was associated with negative symptoms and tended to be linked to patient facial affect recognition suggesting its impact on schizophrenia social phenotypes. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Oil-in-Water Emulsion Exhibits Bitterness-Suppressing Effects in a Sensory Threshold Study.

PubMed

Torrico, Damir Dennis; Sae-Eaw, Amporn; Sriwattana, Sujinda; Boeneke, Charles; Prinyawiwatkul, Witoon

2015-06-01

Little is known about how emulsion characteristics affect saltiness/bitterness perception. Sensory detection and recognition thresholds of NaCl, caffeine, and KCl in aqueous solution compared with oil-in-water emulsion systems were evaluated. For emulsions, NaCl, KCl, or caffeine were dissolved in water + emulsifier and mixed with canola oil (20% by weight). Two emulsions were prepared: emulsion 1 (viscosity = 257 cP) and emulsion 2 (viscosity = 59 cP). The forced-choice ascending concentration series method of limits (ASTM E-679-04) was used to determine detection and/or recognition thresholds at 25 °C. Group best estimate threshold (GBET) geometric means were expressed as g/100 mL. Comparing NaCl with KCl, there were no significant differences in detection GBET values for all systems (0.0197 - 0.0354). For saltiness recognition thresholds, KCl GBET values were higher compared with NaCl GBET (0.0822 - 0.1070 compared with 0.0471 - 0.0501). For NaCl and KCl, emulsion 1 and/or emulsion 2 did not significantly affect the saltiness recognition threshold compared with that of the aqueous solution. However, the bitterness recognition thresholds of caffeine and KCl in solution were significantly lower than in the emulsions (0.0242 - 0.0586 compared with 0.0754 - 0.1025). Gender generally had a marginal effect on threshold values. This study showed that, compared with the aqueous solutions, emulsions did not significantly affect the saltiness recognition threshold of NaCl and KCl, but exhibited bitterness-suppressing effects on KCl and/or caffeine. © 2015 Institute of Food Technologists®

How a Hat May Affect 3-Month-Olds' Recognition of a Face: An Eye-Tracking Study

PubMed Central

Bulf, Hermann; Valenza, Eloisa; Turati, Chiara

2013-01-01

Recent studies have shown that infants’ face recognition rests on a robust face representation that is resilient to a variety of facial transformations such as rotations in depth, motion, occlusion or deprivation of inner/outer features. Here, we investigated whether 3-month-old infants’ ability to represent the invariant aspects of a face is affected by the presence of an external add-on element, i.e. a hat. Using a visual habituation task, three experiments were carried out in which face recognition was investigated by manipulating the presence/absence of a hat during face encoding (i.e. habituation phase) and face recognition (i.e. test phase). An eye-tracker system was used to record the time infants spent looking at face-relevant information compared to the hat. The results showed that infants’ face recognition was not affected by the presence of the external element when the type of the hat did not vary between the habituation and test phases, and when both the novel and the familiar face wore the same hat during the test phase (Experiment 1). Infants’ ability to recognize the invariant aspects of a face was preserved also when the hat was absent in the habituation phase and the same hat was shown only during the test phase (Experiment 2). Conversely, when the novel face identity competed with a novel hat, the hat triggered the infants’ attention, interfering with the recognition process and preventing the infants’ preference for the novel face during the test phase (Experiment 3). Findings from the current study shed light on how faces and objects are processed when they are simultaneously presented in the same visual scene, contributing to an understanding of how infants respond to the multiple and composite information available in their surrounding environment. PMID:24349378

How a hat may affect 3-month-olds' recognition of a face: an eye-tracking study.

PubMed

Bulf, Hermann; Valenza, Eloisa; Turati, Chiara

2013-01-01

Recent studies have shown that infants' face recognition rests on a robust face representation that is resilient to a variety of facial transformations such as rotations in depth, motion, occlusion or deprivation of inner/outer features. Here, we investigated whether 3-month-old infants' ability to represent the invariant aspects of a face is affected by the presence of an external add-on element, i.e. a hat. Using a visual habituation task, three experiments were carried out in which face recognition was investigated by manipulating the presence/absence of a hat during face encoding (i.e. habituation phase) and face recognition (i.e. test phase). An eye-tracker system was used to record the time infants spent looking at face-relevant information compared to the hat. The results showed that infants' face recognition was not affected by the presence of the external element when the type of the hat did not vary between the habituation and test phases, and when both the novel and the familiar face wore the same hat during the test phase (Experiment 1). Infants' ability to recognize the invariant aspects of a face was preserved also when the hat was absent in the habituation phase and the same hat was shown only during the test phase (Experiment 2). Conversely, when the novel face identity competed with a novel hat, the hat triggered the infants' attention, interfering with the recognition process and preventing the infants' preference for the novel face during the test phase (Experiment 3). Findings from the current study shed light on how faces and objects are processed when they are simultaneously presented in the same visual scene, contributing to an understanding of how infants respond to the multiple and composite information available in their surrounding environment.

News Conference: The Big Bangor Day Meeting Lecture: Charterhouse plays host to a physics day Festival: Science on Stage festival 2013 arrives in Poland Event: Scottish Physics Teachers' Summer School Meeting: Researchers and educators meet at Lund University Conference: Exeter marks the spot Recognition: European Physical Society uncovers an historic site Education: Initial teacher education undergoes big changes Forthcoming events

NASA Astrophysics Data System (ADS)

2013-09-01

Conference: The Big Bangor Day Meeting Lecture: Charterhouse plays host to a physics day Festival: Science on Stage festival 2013 arrives in Poland Event: Scottish Physics Teachers' Summer School Meeting: Researchers and educators meet at Lund University Conference: Exeter marks the spot Recognition: European Physical Society uncovers an historic site Education: Initial teacher education undergoes big changes Forthcoming events

Antigen clasping by two antigen-binding sites of an exceptionally specific antibody for histone methylation

DOE PAGES

Hattori, Takamitsu; Lai, Darson; Dementieva, Irina S.; ...

2016-02-09

Antibodies have a well-established modular architecture wherein the antigen-binding site residing in the antigen-binding fragment (Fab or Fv) is an autonomous and complete unit for antigen recognition. Here, we describe antibodies departing from this paradigm. We developed recombinant antibodies to trimethylated lysine residues on histone H3, important epigenetic marks and challenging targets for molecular recognition. Quantitative characterization demonstrated their exquisite specificity and high affinity, and they performed well in common epigenetics applications. Surprisingly, crystal structures and biophysical analyses revealed that two antigen-binding sites of these antibodies form a head-to-head dimer and cooperatively recognize the antigen in the dimer interface. Thismore » “antigen clasping” produced an expansive interface where trimethylated Lys bound to an unusually extensive aromatic cage in one Fab and the histone N terminus to a pocket in the other, thereby rationalizing the high specificity. A long-neck antibody format with a long linker between the antigen-binding module and the Fc region facilitated antigen clasping and achieved both high specificity and high potency. Antigen clasping substantially expands the paradigm of antibody–antigen recognition and suggests a strategy for developing extremely specific antibodies.« less

Antigen clasping by two antigen-binding sites of an exceptionally specific antibody for histone methylation

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

Hattori, Takamitsu; Lai, Darson; Dementieva, Irina S.

Antibodies have a well-established modular architecture wherein the antigen-binding site residing in the antigen-binding fragment (Fab or Fv) is an autonomous and complete unit for antigen recognition. Here, we describe antibodies departing from this paradigm. We developed recombinant antibodies to trimethylated lysine residues on histone H3, important epigenetic marks and challenging targets for molecular recognition. Quantitative characterization demonstrated their exquisite specificity and high affinity, and they performed well in common epigenetics applications. Surprisingly, crystal structures and biophysical analyses revealed that two antigen-binding sites of these antibodies form a head-to-head dimer and cooperatively recognize the antigen in the dimer interface. Thismore » “antigen clasping” produced an expansive interface where trimethylated Lys bound to an unusually extensive aromatic cage in one Fab and the histone N terminus to a pocket in the other, thereby rationalizing the high specificity. A long-neck antibody format with a long linker between the antigen-binding module and the Fc region facilitated antigen clasping and achieved both high specificity and high potency. Antigen clasping substantially expands the paradigm of antibody–antigen recognition and suggests a strategy for developing extremely specific antibodies.« less

Visual encoding impairment in patients with schizophrenia: contribution of reduced working memory span, decreased processing speed, and affective symptoms.

PubMed

Brébion, Gildas; Stephan-Otto, Christian; Huerta-Ramos, Elena; Ochoa, Susana; Usall, Judith; Abellán-Vega, Helena; Roca, Mercedes; Haro, Josep Maria

2015-01-01

Previous research has revealed the contribution of decreased processing speed and reduced working memory span in verbal and visual memory impairment in patients with schizophrenia. The role of affective symptoms in verbal memory has also emerged in a few studies. The authors designed a picture recognition task to investigate the impact of these factors on visual encoding. Two types of pictures (black and white vs. colored) were presented under 2 different conditions of context encoding (either displayed at a specific location or in association with another visual stimulus). It was assumed that the process of encoding associated pictures was more effortful than that of encoding pictures that were presented alone. Working memory span and processing speed were assessed. In the patient group, working memory span was significantly associated with the recognition of the associated pictures but not significantly with that of the other pictures. Controlling for processing speed eliminated the patients' deficit in the recognition of the colored pictures and greatly reduced their deficit in the recognition of the black-and-white pictures. The recognition of the black-and-white pictures was inversely related to anxiety in men and to depression in women. Working memory span constrains the effortful visual encoding processes in patients, whereas processing speed decrement accounts for most of their visual encoding deficit. Affective symptoms also have an impact on visual encoding, albeit differently in men and women. PsycINFO Database Record (c) 2015 APA, all rights reserved.

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.

Directing an artificial zinc finger protein to new targets by fusion to a non-DNA-binding domain.

PubMed

Lim, Wooi F; Burdach, Jon; Funnell, Alister P W; Pearson, Richard C M; Quinlan, Kate G R; Crossley, Merlin

2016-04-20

Transcription factors are often regarded as having two separable components: a DNA-binding domain (DBD) and a functional domain (FD), with the DBD thought to determine target gene recognition. While this holds true for DNA bindingin vitro, it appears thatin vivoFDs can also influence genomic targeting. We fused the FD from the well-characterized transcription factor Krüppel-like Factor 3 (KLF3) to an artificial zinc finger (AZF) protein originally designed to target the Vascular Endothelial Growth Factor-A (VEGF-A) gene promoter. We compared genome-wide occupancy of the KLF3FD-AZF fusion to that observed with AZF. AZF bound to theVEGF-Apromoter as predicted, but was also found to occupy approximately 25,000 other sites, a large number of which contained the expected AZF recognition sequence, GCTGGGGGC. Interestingly, addition of the KLF3 FD re-distributes the fusion protein to new sites, with total DNA occupancy detected at around 50,000 sites. A portion of these sites correspond to known KLF3-bound regions, while others contained sequences similar but not identical to the expected AZF recognition sequence. These results show that FDs can influence and may be useful in directing AZF DNA-binding proteins to specific targets and provide insights into how natural transcription factors operate. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Restriction enzyme body doubles and PCR cloning: on the general use of type IIs restriction enzymes for cloning.

PubMed

Tóth, Eszter; Huszár, Krisztina; Bencsura, Petra; Kulcsár, Péter István; Vodicska, Barbara; Nyeste, Antal; Welker, Zsombor; Tóth, Szilvia; Welker, Ervin

2014-01-01

The procedure described here allows the cloning of PCR fragments containing a recognition site of the restriction endonuclease (Type IIP) used for cloning in the sequence of the insert. A Type IIS endonuclease--a Body Double of the Type IIP enzyme--is used to generate the same protruding palindrome. Thus, the insert can be cloned to the Type IIP site of the vector without digesting the PCR product with the same Type IIP enzyme. We achieve this by incorporating the recognition site of a Type IIS restriction enzyme that cleaves the DNA outside of its recognition site in the PCR primer in such a way that the cutting positions straddle the desired overhang sequence. Digestion of the PCR product by the Body Double generates the required overhang. Hitherto the use of Type IIS restriction enzymes in cloning reactions has only been used for special applications, the approach presented here makes Type IIS enzymes as useful as Type IIP enzymes for general cloning purposes. To assist in finding Body Double enzymes, we summarised the available Type IIS enzymes which are potentially useful for Body Double cloning and created an online program (http://group.szbk.u-szeged.hu/welkergr/body_double/index.html) for the selection of suitable Body Double enzymes and the design of the appropriate primers.

A Unitary Anesthetic Binding Site at High Resolution

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

Vedula, L. Sangeetha; Brannigan, Grace; Economou, Nicoleta J.

2009-10-21

Propofol is the most widely used injectable general anesthetic. Its targets include ligand-gated ion channels such as the GABA{sub A} receptor, but such receptor-channel complexes remain challenging to study at atomic resolution. Until structural biology methods advance to the point of being able to deal with systems such as the GABA{sub A} receptor, it will be necessary to use more tractable surrogates to probe the molecular details of anesthetic recognition. We have previously shown that recognition of inhalational general anesthetics by the model protein apoferritin closely mirrors recognition by more complex and clinically relevant protein targets; here we show thatmore » apoferritin also binds propofol and related GABAergic anesthetics, and that the same binding site mediates recognition of both inhalational and injectable anesthetics. Apoferritin binding affinities for a series of propofol analogs were found to be strongly correlated with the ability to potentiate GABA responses at GABA{sub A} receptors, validating this model system for injectable anesthetics. High resolution x-ray crystal structures reveal that, despite the presence of hydrogen bond donors and acceptors, anesthetic recognition is mediated largely by van der Waals forces and the hydrophobic effect. Molecular dynamics simulations indicate that the ligands undergo considerable fluctuations about their equilibrium positions. Finally, apoferritin displays both structural and dynamic responses to anesthetic binding, which may mimic changes elicited by anesthetics in physiologic targets like ion channels.« less

A Unitary Anesthetic Binding Site at High Resolution

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

L Vedula; G Brannigan; N Economou

2011-12-31

Propofol is the most widely used injectable general anesthetic. Its targets include ligand-gated ion channels such as the GABA{sub A} receptor, but such receptor-channel complexes remain challenging to study at atomic resolution. Until structural biology methods advance to the point of being able to deal with systems such as the GABA{sub A} receptor, it will be necessary to use more tractable surrogates to probe the molecular details of anesthetic recognition. We have previously shown that recognition of inhalational general anesthetics by the model protein apoferritin closely mirrors recognition by more complex and clinically relevant protein targets; here we show thatmore » apoferritin also binds propofol and related GABAergic anesthetics, and that the same binding site mediates recognition of both inhalational and injectable anesthetics. Apoferritin binding affinities for a series of propofol analogs were found to be strongly correlated with the ability to potentiate GABA responses at GABA{sub A} receptors, validating this model system for injectable anesthetics. High resolution x-ray crystal structures reveal that, despite the presence of hydrogen bond donors and acceptors, anesthetic recognition is mediated largely by van der Waals forces and the hydrophobic effect. Molecular dynamics simulations indicate that the ligands undergo considerable fluctuations about their equilibrium positions. Finally, apoferritin displays both structural and dynamic responses to anesthetic binding, which may mimic changes elicited by anesthetics in physiologic targets like ion channels.« less

A Unitary Anesthetic-Binding Site at High Resolution

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

Vedula, L.; Brannigan, G; Economou, N

2009-01-01

Propofol is the most widely used injectable general anesthetic. Its targets include ligand-gated ion channels such as the GABAA receptor, but such receptor-channel complexes remain challenging to study at atomic resolution. Until structural biology methods advance to the point of being able to deal with systems such as the GABA{sub A} receptor, it will be necessary to use more tractable surrogates to probe the molecular details of anesthetic recognition. We have previously shown that recognition of inhalational general anesthetics by the model protein apoferritin closely mirrors recognition by more complex and clinically relevant protein targets; here we show that apoferritinmore » also binds propofol and related GABAergic anesthetics, and that the same binding site mediates recognition of both inhalational and injectable anesthetics. Apoferritin binding affinities for a series of propofol analogs were found to be strongly correlated with the ability to potentiate GABA responses at GABA{sub A} receptors, validating this model system for injectable anesthetics. High resolution x-ray crystal structures reveal that, despite the presence of hydrogen bond donors and acceptors, anesthetic recognition is mediated largely by van der Waals forces and the hydrophobic effect. Molecular dynamics simulations indicate that the ligands undergo considerable fluctuations about their equilibrium positions. Finally, apoferritin displays both structural and dynamic responses to anesthetic binding, which may mimic changes elicited by anesthetics in physiologic targets like ion channels.« less

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

PubMed

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

2014-01-01

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

Monodisperse, molecularly imprinted polymers for creatinine by modified precipitation polymerization and their applications to creatinine assays for human serum and urine.

PubMed

Miura, Chitose; Funaya, Noriko; Matsunaga, Hisami; Haginaka, Jun

2013-11-01

Molecularly imprinted polymers (MIPs) for creatinine were prepared by modified precipitation polymerization using methacrylic acid as a functional monomer and divinylbenzene as a crosslinker. The prepared MIPs were monodispersed with a narrow particle size distribution. Binding experiments and Scatchard analyses revealed that two classes of binding sites, high- and low-affinity sites, were formed on the MIPs. The retention and molecular-recognition properties of the MIPs were evaluated by hydrophilic interaction chromatography using a mixture of ammonium acetate buffer and acetonitrile as a mobile phase. With an increase of acetonitrile content, the retention factor of creatinine was increased on the MIP. In addition to shape recognition, hydrophilic interactions seemed to enhance the recognition of creatinine on the MIP. The MIPs' molecular-recognition ability was specific for creatinine; the structurally related compounds such as hydantoin, 1-methylhydantoin, 2-pyrrolidone, N-hydroxysuccinimide and creatine were not recognized. Furthermore, the creatinine concentrations in human serum and urine were successfully determined by direct injection of the deproteinized serum and diluted urine samples onto the MIP. Copyright © 2013 Elsevier B.V. All rights reserved.

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.

Italian normative data and validation of two neuropsychological tests of face recognition: Benton Facial Recognition Test and Cambridge Face Memory Test.

PubMed

Albonico, Andrea; Malaspina, Manuela; Daini, Roberta

2017-09-01

The Benton Facial Recognition Test (BFRT) and Cambridge Face Memory Test (CFMT) are two of the most common tests used to assess face discrimination and recognition abilities and to identify individuals with prosopagnosia. However, recent studies highlighted that participant-stimulus match ethnicity, as much as gender, has to be taken into account in interpreting results from these tests. Here, in order to obtain more appropriate normative data for an Italian sample, the CFMT and BFRT were administered to a large cohort of young adults. We found that scores from the BFRT are not affected by participants' gender and are only slightly affected by participant-stimulus ethnicity match, whereas both these factors seem to influence the scores of the CFMT. Moreover, the inclusion of a sample of individuals with suspected face recognition impairment allowed us to show that the use of more appropriate normative data can increase the BFRT efficacy in identifying individuals with face discrimination impairments; by contrast, the efficacy of the CFMT in classifying individuals with a face recognition deficit was confirmed. Finally, our data show that the lack of inversion effect (the difference between the total score of the upright and inverted versions of the CFMT) could be used as further index to assess congenital prosopagnosia. Overall, our results confirm the importance of having norms derived from controls with a similar experience of faces as the "potential" prosopagnosic individuals when assessing face recognition abilities.

Structural Probing of Off-Target G Protein-Coupled Receptor Activities within a Series of Adenosine/Adenine Congeners

PubMed Central

Paoletta, Silvia; Tosh, Dilip K.; Salvemini, Daniela; Jacobson, Kenneth A.

2014-01-01

We studied patterns of off-target receptor interactions, mostly at G protein-coupled receptors (GPCRs) in the µM range, of nucleoside derivatives that are highly engineered for nM interaction with adenosine receptors (ARs). Because of the considerable interest of using AR ligands for treating diseases of the CNS, we used the Psychoactive Drug Screening Program (PDSP) for probing promiscuity of these adenosine/adenine congeners at 41 diverse receptors, channels and a transporter. The step-wise truncation of rigidified, trisubstituted (at N6, C2, and 5′ positions) nucleosides revealed unanticipated interactions mainly with biogenic amine receptors, such as adrenergic receptors and serotonergic receptors, with affinities as high as 61 nM. The unmasking of consistent sets of structure activity relationship (SAR) at novel sites suggested similarities between receptor families in molecular recognition. Extensive molecular modeling of the GPCRs affected suggested binding modes of the ligands that supported the patterns of SAR at individual receptors. In some cases, the ligand docking mode closely resembled AR binding and in other cases the ligand assumed different orientations. The recognition patterns for different GPCRs were clustered according to which substituent groups were tolerated and explained in light of the complementarity with the receptor binding site. Thus, some likely off-target interactions, a concern for secondary drug effects, can be predicted for analogues of this set of substructures, aiding the design of additional structural analogues that either eliminate or accentuate certain off-target activities. Moreover, similar analyses could be performed for unrelated structural families for other GPCRs. PMID:24859150

Structural probing of off-target G protein-coupled receptor activities within a series of adenosine/adenine congeners.

PubMed

Paoletta, Silvia; Tosh, Dilip K; Salvemini, Daniela; Jacobson, Kenneth A

2014-01-01

We studied patterns of off-target receptor interactions, mostly at G protein-coupled receptors (GPCRs) in the µM range, of nucleoside derivatives that are highly engineered for nM interaction with adenosine receptors (ARs). Because of the considerable interest of using AR ligands for treating diseases of the CNS, we used the Psychoactive Drug Screening Program (PDSP) for probing promiscuity of these adenosine/adenine congeners at 41 diverse receptors, channels and a transporter. The step-wise truncation of rigidified, trisubstituted (at N6, C2, and 5' positions) nucleosides revealed unanticipated interactions mainly with biogenic amine receptors, such as adrenergic receptors and serotonergic receptors, with affinities as high as 61 nM. The unmasking of consistent sets of structure activity relationship (SAR) at novel sites suggested similarities between receptor families in molecular recognition. Extensive molecular modeling of the GPCRs affected suggested binding modes of the ligands that supported the patterns of SAR at individual receptors. In some cases, the ligand docking mode closely resembled AR binding and in other cases the ligand assumed different orientations. The recognition patterns for different GPCRs were clustered according to which substituent groups were tolerated and explained in light of the complementarity with the receptor binding site. Thus, some likely off-target interactions, a concern for secondary drug effects, can be predicted for analogues of this set of substructures, aiding the design of additional structural analogues that either eliminate or accentuate certain off-target activities. Moreover, similar analyses could be performed for unrelated structural families for other GPCRs.

Legal Marriage, Unequal Recognition, and Mental Health among Same-Sex Couples.

PubMed

LeBlanc, Allen J; Frost, David M; Bowen, Kayla

2018-04-01

The authors examined whether the perception of unequal relationship recognition, a novel, couple-level minority stressor, has negative consequences for mental health among same-sex couples. Data came from a dyadic study of 100 ( N = 200) same-sex couples in the U.S. Being in a legal marriage was associated with lower perceived unequal recognition and better mental health; being in a registered domestic partnership or civil union - not also legally married - was associated with greater perceived unequal recognition and worse mental health. Actor Partner Interdependence Models tested associations between legal relationship status, unequal relationship recognition, and mental health (nonspecific psychological distress, depressive symptomatology, and problematic drinking), net controls (age, gender, race/ethnicity, education, and income). Unequal recognition was consistently associated with worse mental health, independent of legal relationship status. Legal changes affecting relationship recognition should not be seen as simple remedies for addressing the mental health effects of institutionalized discrimination.

Local Navon letter processing affects skilled behavior: a golf-putting experiment.

PubMed

Lewis, Michael B; Dawkins, Gemma

2015-04-01

Expert or skilled behaviors (for example, face recognition or sporting performance) are typically performed automatically and with little conscious awareness. Previous studies, in various domains of performance, have shown that activities immediately prior to a task demanding a learned skill can affect performance. In sport, describing the to-be-performed action is detrimental, whereas in face recognition, describing a face or reading local Navon letters is detrimental. Two golf-putting experiments are presented that compare the effects that these three tasks have on experienced and novice golfers. Experiment 1 found a Navon effect on golf performance for experienced players. Experiment 2 found, for experienced players only, that performance was impaired following the three tasks described above, when compared with reading or global Navon tasks. It is suggested that the three tasks affect skilled performance by provoking a shift from automatic behavior to a more analytic style. By demonstrating similarities between effects in face recognition and sporting behavior, it is hoped to better understand concepts in both fields.

Affective theory of mind inferences contextually influence the recognition of emotional facial expressions.

PubMed

Stewart, Suzanne L K; Schepman, Astrid; Haigh, Matthew; McHugh, Rhian; Stewart, Andrew J

2018-03-14

The recognition of emotional facial expressions is often subject to contextual influence, particularly when the face and the context convey similar emotions. We investigated whether spontaneous, incidental affective theory of mind inferences made while reading vignettes describing social situations would produce context effects on the identification of same-valenced emotions (Experiment 1) as well as differently-valenced emotions (Experiment 2) conveyed by subsequently presented faces. Crucially, we found an effect of context on reaction times in both experiments while, in line with previous work, we found evidence for a context effect on accuracy only in Experiment 1. This demonstrates that affective theory of mind inferences made at the pragmatic level of a text can automatically, contextually influence the perceptual processing of emotional facial expressions in a separate task even when those emotions are of a distinctive valence. Thus, our novel findings suggest that language acts as a contextual influence to the recognition of emotional facial expressions for both same and different valences.

Twenty years of audiology in a patient with Norrie disease.

PubMed

Halpin, Chris; Sims, Katherine

2008-11-01

To describe disease progression and treatment outcomes over a 20-year period (ages 5-25) in a young man with Norrie disease (occuloacousticocerebral dysplasia), ND; OMIM #310600. Affected individuals are born blind and develop progressive sensory loss with onset in adolescence. This disease is X-linked and has been associated with mutations of the NDP gene (Xp11.4). The patient was followed using repeated audiograms, as well as reports of educational progress and hearing aid use. The specific mutation was found by molecular analysis. The patient demonstrated progressive sensory loss with good preservation of word recognition. The loss was initially high frequency and asymmetric in adolescence and became more severe, more symmetric and affected practically all frequencies by the end of childhood. Educational progress was affected by the cognitive effects of the syndrome, and hearing aid use was very effective. A bilateral progressive sensory loss with good preservation of word recognition was documented in detail. The residual word recognition supported good use of hearing aids in this case.

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.

Adaptive false memory: Imagining future scenarios increases false memories in the DRM paradigm.

PubMed

Dewhurst, Stephen A; Anderson, Rachel J; Grace, Lydia; van Esch, Lotte

2016-10-01

Previous research has shown that rating words for their relevance to a future scenario enhances memory for those words. The current study investigated the effect of future thinking on false memory using the Deese/Roediger-McDermott (DRM) procedure. In Experiment 1, participants rated words from 6 DRM lists for relevance to a past or future event (with or without planning) or in terms of pleasantness. In a surprise recall test, levels of correct recall did not vary between the rating tasks, but the future rating conditions led to significantly higher levels of false recall than the past and pleasantness conditions did. Experiment 2 found that future rating led to higher levels of false recognition than did past and pleasantness ratings but did not affect correct recognition. The effect in false recognition was, however, eliminated when DRM items were presented in random order. Participants in Experiment 3 were presented with both DRM lists and lists of unrelated words. Future rating increased levels of false recognition for DRM lures but did not affect correct recognition for DRM or unrelated lists. The findings are discussed in terms of the view that false memories can be associated with adaptive memory functions.

Prediction of the thermal imaging minimum resolvable (circle) temperature difference with neural network application.

PubMed

Fang, Yi-Chin; Wu, Bo-Wen

2008-12-01

Thermal imaging is an important technology in both national defense and the private sector. An advantage of thermal imaging is its ability to be deployed while fully engaged in duties, not limited by weather or the brightness of indoor or outdoor conditions. However, in an outdoor environment, many factors, including atmospheric decay, target shape, great distance, fog, temperature out of range and diffraction limits can lead to bad image formation, which directly affects the accuracy of object recognition. The visual characteristics of the human eye mean that it has a much better capacity for picture recognition under normal conditions than artificial intelligence does. However, conditions of interference significantly reduce this capacity for picture recognition for instance, fatigue impairs human eyesight. Hence, psychological and physiological factors can affect the result when the human eye is adopted to measure MRTD (minimum resolvable temperature difference) and MRCTD (minimum resolvable circle temperature difference). This study explores thermal imaging recognition, and presents a method for effectively choosing the characteristic values and processing the images fully. Neural network technology is successfully applied to recognize thermal imaging and predict MRTD and MRCTD (Appendix A), exceeding thermal imaging recognition under fatigue and the limits of the human eye.

Recognition memory across the lifespan: the impact of word frequency and study-test interval on estimates of familiarity and recollection

PubMed Central

Meier, Beat; Rey-Mermet, Alodie; Rothen, Nicolas; Graf, Peter

2013-01-01

The goal of this study was to investigate recognition memory performance across the lifespan and to determine how estimates of recollection and familiarity contribute to performance. In each of three experiments, participants from five groups from 14 up to 85 years of age (children, young adults, middle-aged adults, young-old adults, and old-old adults) were presented with high- and low-frequency words in a study phase and were tested immediately afterwards and/or after a one day retention interval. The results showed that word frequency and retention interval affected recognition memory performance as well as estimates of recollection and familiarity. Across the lifespan, the trajectory of recognition memory followed an inverse u-shape function that was neither affected by word frequency nor by retention interval. The trajectory of estimates of recollection also followed an inverse u-shape function, and was especially pronounced for low-frequency words. In contrast, estimates of familiarity did not differ across the lifespan. The results indicate that age differences in recognition memory are mainly due to differences in processes related to recollection while the contribution of familiarity-based processes seems to be age-invariant. PMID:24198796

Negative ion treatment increases positive emotional processing in seasonal affective disorder.

PubMed

Harmer, C J; Charles, M; McTavish, S; Favaron, E; Cowen, P J

2012-08-01

Antidepressant drug treatments increase the processing of positive compared to negative affective information early in treatment. Such effects have been hypothesized to play a key role in the development of later therapeutic responses to treatment. However, it is unknown whether these effects are a common mechanism of action for different treatment modalities. High-density negative ion (HDNI) treatment is an environmental manipulation that has efficacy in randomized clinical trials in seasonal affective disorder (SAD). The current study investigated whether a single session of HDNI treatment could reverse negative affective biases seen in seasonal depression using a battery of emotional processing tasks in a double-blind, placebo-controlled randomized study. Under placebo conditions, participants with seasonal mood disturbance showed reduced recognition of happy facial expressions, increased recognition memory for negative personality characteristics and increased vigilance to masked presentation of negative words in a dot-probe task compared to matched healthy controls. Negative ion treatment increased the recognition of positive compared to negative facial expression and improved vigilance to unmasked stimuli across participants with seasonal depression and healthy controls. Negative ion treatment also improved recognition memory for positive information in the SAD group alone. These effects were seen in the absence of changes in subjective state or mood. These results are consistent with the hypothesis that early change in emotional processing may be an important mechanism for treatment action in depression and suggest that these effects are also apparent with negative ion treatment in seasonal depression.

Systematic Functional Analysis of Active-Site Residues in l-Threonine Dehydrogenase from Thermoplasma volcanium

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

Desjardins, Morgan; Mak, Wai Shun; O’Brien, Terrence E.

Enzymes have been through millions of years of evolution during which their active-site microenvironments are fine-tuned. Active-site residues are commonly conserved within protein families, indicating their importance for substrate recognition and catalysis. In this work, we systematically mutated active-site residues of l-threonine dehydrogenase from Thermoplasma volcanium and characterized the mutants against a panel of substrate analogs. Our results demonstrate that only a subset of these residues plays an essential role in substrate recognition and catalysis and that the native enzyme activity can be further enhanced roughly 4.6-fold by a single point mutation. Kinetic characterization of mutants on substrate analogs showsmore » that l-threonine dehydrogenase possesses promiscuous activities toward other chemically similar compounds not previously observed. Quantum chemical calculations on the hydride-donating ability of these substrates also reveal that this enzyme did not evolve to harness the intrinsic substrate reactivity for enzyme catalysis. Our analysis provides insights into connections between the details of enzyme active-site structure and specific function. Finally, these results are directly applicable to rational enzyme design and engineering.« less

Systematic Functional Analysis of Active-Site Residues in l-Threonine Dehydrogenase from Thermoplasma volcanium

DOE PAGES

Desjardins, Morgan; Mak, Wai Shun; O’Brien, Terrence E.; ...

2017-07-07

Enzymes have been through millions of years of evolution during which their active-site microenvironments are fine-tuned. Active-site residues are commonly conserved within protein families, indicating their importance for substrate recognition and catalysis. In this work, we systematically mutated active-site residues of l-threonine dehydrogenase from Thermoplasma volcanium and characterized the mutants against a panel of substrate analogs. Our results demonstrate that only a subset of these residues plays an essential role in substrate recognition and catalysis and that the native enzyme activity can be further enhanced roughly 4.6-fold by a single point mutation. Kinetic characterization of mutants on substrate analogs showsmore » that l-threonine dehydrogenase possesses promiscuous activities toward other chemically similar compounds not previously observed. Quantum chemical calculations on the hydride-donating ability of these substrates also reveal that this enzyme did not evolve to harness the intrinsic substrate reactivity for enzyme catalysis. Our analysis provides insights into connections between the details of enzyme active-site structure and specific function. Finally, these results are directly applicable to rational enzyme design and engineering.« less

Defining the mRNA recognition signature of a bacterial toxin protein

DOE PAGES

Schureck, Marc A.; Dunkle, Jack A.; Maehigashi, Tatsuya; ...

2015-10-27

Bacteria contain multiple type II toxins that selectively degrade mRNAs bound to the ribosome to regulate translation and growth and facilitate survival during the stringent response. Ribosome-dependent toxins recognize a variety of three-nucleotide codons within the aminoacyl (A) site, but how these endonucleases achieve substrate specificity remains poorly understood. In this paper, we identify the critical features for how the host inhibition of growth B (HigB) toxin recognizes each of the three A-site nucleotides for cleavage. X-ray crystal structures of HigB bound to two different codons on the ribosome illustrate how HigB uses a microbial RNase-like nucleotide recognition loop tomore » recognize either cytosine or adenosine at the second A-site position. Strikingly, a single HigB residue and 16S rRNA residue C1054 form an adenosine-specific pocket at the third A-site nucleotide, in contrast to how tRNAs decode mRNA. Finally, our results demonstrate that the most important determinant for mRNA cleavage by ribosome-dependent toxins is interaction with the third A-site nucleotide.« less

Defining the mRNA recognition signature of a bacterial toxin protein

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

Schureck, Marc A.; Dunkle, Jack A.; Maehigashi, Tatsuya

Bacteria contain multiple type II toxins that selectively degrade mRNAs bound to the ribosome to regulate translation and growth and facilitate survival during the stringent response. Ribosome-dependent toxins recognize a variety of three-nucleotide codons within the aminoacyl (A) site, but how these endonucleases achieve substrate specificity remains poorly understood. In this paper, we identify the critical features for how the host inhibition of growth B (HigB) toxin recognizes each of the three A-site nucleotides for cleavage. X-ray crystal structures of HigB bound to two different codons on the ribosome illustrate how HigB uses a microbial RNase-like nucleotide recognition loop tomore » recognize either cytosine or adenosine at the second A-site position. Strikingly, a single HigB residue and 16S rRNA residue C1054 form an adenosine-specific pocket at the third A-site nucleotide, in contrast to how tRNAs decode mRNA. Finally, our results demonstrate that the most important determinant for mRNA cleavage by ribosome-dependent toxins is interaction with the third A-site nucleotide.« less

How Chinese Semantics Capability Improves Interpretation in Visual Communication

ERIC Educational Resources Information Center

Cheng, Chu-Yu; Ou, Yang-Kun; Kin, Ching-Lung

2017-01-01

A visual representation involves delivering messages through visually communicated images. The study assumed that semantic recognition can affect visual interpretation ability, and the result showed that students graduating from a general high school achieve satisfactory results in semantic recognition and image interpretation tasks than students…

38 CFR 3.206 - Divorce.

Code of Federal Regulations, 2013 CFR

2013-07-01

... a divorce decree regular on its face, will be questioned by the Department of Veterans Affairs only... Department of Veterans Affairs benefits would be affected thereby. In cases where recognition of the decree... veteran following a divorce, the matter of recognition of the divorce by the Department of Veterans...

38 CFR 3.206 - Divorce.

Code of Federal Regulations, 2012 CFR

2012-07-01

... a divorce decree regular on its face, will be questioned by the Department of Veterans Affairs only... Department of Veterans Affairs benefits would be affected thereby. In cases where recognition of the decree... veteran following a divorce, the matter of recognition of the divorce by the Department of Veterans...

38 CFR 3.206 - Divorce.

Code of Federal Regulations, 2014 CFR

2014-07-01

... a divorce decree regular on its face, will be questioned by the Department of Veterans Affairs only... Department of Veterans Affairs benefits would be affected thereby. In cases where recognition of the decree... veteran following a divorce, the matter of recognition of the divorce by the Department of Veterans...

38 CFR 3.206 - Divorce.

Code of Federal Regulations, 2010 CFR

2010-07-01

... a divorce decree regular on its face, will be questioned by the Department of Veterans Affairs only... Department of Veterans Affairs benefits would be affected thereby. In cases where recognition of the decree... veteran following a divorce, the matter of recognition of the divorce by the Department of Veterans...

38 CFR 3.206 - Divorce.

Code of Federal Regulations, 2011 CFR

2011-07-01

... a divorce decree regular on its face, will be questioned by the Department of Veterans Affairs only... Department of Veterans Affairs benefits would be affected thereby. In cases where recognition of the decree... veteran following a divorce, the matter of recognition of the divorce by the Department of Veterans...

Transfer-appropriate processing in recognition memory: perceptual and conceptual effects on recognition memory depend on task demands.

PubMed

Parks, Colleen M

2013-07-01

Research examining the importance of surface-level information to familiarity in recognition memory tasks is mixed: Sometimes it affects recognition and sometimes it does not. One potential explanation of the inconsistent findings comes from the ideas of dual process theory of recognition and the transfer-appropriate processing framework, which suggest that the extent to which perceptual fluency matters on a recognition test depends in large part on the task demands. A test that recruits perceptual processing for discrimination should show greater perceptual effects and smaller conceptual effects than standard recognition, similar to the pattern of effects found in perceptual implicit memory tasks. This idea was tested in the current experiment by crossing a levels of processing manipulation with a modality manipulation on a series of recognition tests that ranged from conceptual (standard recognition) to very perceptually demanding (a speeded recognition test with degraded stimuli). Results showed that the levels of processing effect decreased and the effect of modality increased when tests were made perceptually demanding. These results support the idea that surface-level features influence performance on recognition tests when they are made salient by the task demands. PsycINFO Database Record (c) 2013 APA, all rights reserved.

Early Sign Language Experience Goes Along with an Increased Cross-modal Gain for Affective Prosodic Recognition in Congenitally Deaf CI Users.

PubMed

Fengler, Ineke; Delfau, Pia-Céline; Röder, Brigitte

2018-04-01

It is yet unclear whether congenitally deaf cochlear implant (CD CI) users' visual and multisensory emotion perception is influenced by their history in sign language acquisition. We hypothesized that early-signing CD CI users, relative to late-signing CD CI users and hearing, non-signing controls, show better facial expression recognition and rely more on the facial cues of audio-visual emotional stimuli. Two groups of young adult CD CI users-early signers (ES CI users; n = 11) and late signers (LS CI users; n = 10)-and a group of hearing, non-signing, age-matched controls (n = 12) performed an emotion recognition task with auditory, visual, and cross-modal emotionally congruent and incongruent speech stimuli. On different trials, participants categorized either the facial or the vocal expressions. The ES CI users more accurately recognized affective prosody than the LS CI users in the presence of congruent facial information. Furthermore, the ES CI users, but not the LS CI users, gained more than the controls from congruent visual stimuli when recognizing affective prosody. Both CI groups performed overall worse than the controls in recognizing affective prosody. These results suggest that early sign language experience affects multisensory emotion perception in CD CI users.

Single-Stranded γPNAs for In Vivo Site-Specific Genome Editing via Watson-Crick Recognition

PubMed Central

Bahal, Raman; Quijano, Elias; McNeer, Nicole Ali; Liu, Yanfeng; Bhunia, Dinesh C.; López-Giráldez, Francesco; Fields, Rachel J.; Saltzman, W. Mark; Ly, Danith H.; Glazer, Peter M.

2014-01-01

Triplex-forming peptide nucleic acids (PNAs) facilitate gene editing by stimulating recombination of donor DNAs within genomic DNA via site-specific formation of altered helical structures that further stimulate DNA repair. However, PNAs designed for triplex formation are sequence restricted to homopurine sites. Herein we describe a novel strategy where next generation single-stranded gamma PNAs (γPNAs) containing miniPEG substitutions at the gamma position can target genomic DNA in mouse bone marrow at mixed-sequence sites to induce targeted gene editing. In addition to enhanced binding, γPNAs confer increased solubility and improved formulation into poly(lactic-co-glycolic acid) (PLGA) nanoparticles for efficient intracellular delivery. Single-stranded γPNAs induce targeted gene editing at frequencies of 0.8% in mouse bone marrow cells treated ex vivo and 0.1% in vivo via IV injection, without detectable toxicity. These results suggest that γPNAs may provide a new tool for induced gene editing based on Watson-Crick recognition without sequence restriction. PMID:25174576

Single-stranded γPNAs for in vivo site-specific genome editing via Watson-Crick recognition.

PubMed

Bahal, Raman; Quijano, Elias; McNeer, Nicole A; Liu, Yanfeng; Bhunia, Dinesh C; Lopez-Giraldez, Francesco; Fields, Rachel J; Saltzman, William M; Ly, Danith H; Glazer, Peter M

2014-01-01

Triplex-forming peptide nucleic acids (PNAs) facilitate gene editing by stimulating recombination of donor DNAs within genomic DNA via site-specific formation of altered helical structures that further stimulate DNA repair. However, PNAs designed for triplex formation are sequence restricted to homopurine sites. Herein we describe a novel strategy where next generation single-stranded gamma PNAs (γPNAs) containing miniPEG substitutions at the gamma position can target genomic DNA in mouse bone marrow at mixed-sequence sites to induce targeted gene editing. In addition to enhanced binding, γPNAs confer increased solubility and improved formulation into poly(lactic-co-glycolic acid) (PLGA) nanoparticles for efficient intracellular delivery. Single-stranded γPNAs induce targeted gene editing at frequencies of 0.8% in mouse bone marrow cells treated ex vivo and 0.1% in vivo via IV injection, without detectable toxicity. These results suggest that γPNAs may provide a new tool for induced gene editing based on Watson-Crick recognition without sequence restriction.

Structural Basis of Immune Evasion at the Site of CD4 Attachment on HIV-1 gp120

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

Chen, Lei; Kwon, Young Do; Zhou, Tongqing

2010-01-13

The site on HIV-1 gp120 that binds to the CD4 receptor is vulnerable to antibodies. However, most antibodies that interact with this site cannot neutralize HIV-1. To understand the basis of this resistance, we determined co-crystal structures for two poorly neutralizing, CD4-binding site (CD4BS) antibodies, F105 and b13, in complexes with gp120. Both antibodies exhibited approach angles to gp120 similar to those of CD4 and a rare, broadly neutralizing CD4BS antibody, b12. Slight differences in recognition, however, resulted in substantial differences in F105- and b13-bound conformations relative to b12-bound gp120. Modeling and binding experiments revealed these conformations to be poorlymore » compatible with the viral spike. This incompatibility, the consequence of slight differences in CD4BS recognition, renders HIV-1 resistant to all but the most accurately targeted antibodies.« less

Dynamics Govern Specificity of a Protein-Protein Interface: Substrate Recognition by Thrombin

PubMed Central

Fuchs, Julian E.; Huber, Roland G.; Waldner, Birgit J.; Kahler, Ursula; von Grafenstein, Susanne; Kramer, Christian; Liedl, Klaus R.

2015-01-01

Biomolecular recognition is crucial in cellular signal transduction. Signaling is mediated through molecular interactions at protein-protein interfaces. Still, specificity and promiscuity of protein-protein interfaces cannot be explained using simplistic static binding models. Our study rationalizes specificity of the prototypic protein-protein interface between thrombin and its peptide substrates relying solely on binding site dynamics derived from molecular dynamics simulations. We find conformational selection and thus dynamic contributions to be a key player in biomolecular recognition. Arising entropic contributions complement chemical intuition primarily reflecting enthalpic interaction patterns. The paradigm “dynamics govern specificity” might provide direct guidance for the identification of specific anchor points in biomolecular recognition processes and structure-based drug design. PMID:26496636

Diversity in recognition of glycans by F-type lectins and galectins: molecular, structural, and biophysical aspects

PubMed Central

Vasta, Gerardo R.; Ahmed, Hafiz; Bianchet, Mario A.; Fernández-Robledo, José A.; Amzel, L. Mario

2013-01-01

Although lectins are “hard-wired” in the germline, the presence of tandemly arrayed carbohydrate recognition domains (CRDs), of chimeric structures displaying distinct CRDs, of polymorphic genes resulting in multiple isoforms, and in some cases, of a considerable recognition plasticity of their carbohydrate binding sites, significantly expand the lectin ligand-recognition spectrum and lectin functional diversification. Analysis of structural/functional aspects of galectins and F-lectins—the most recently identified lectin family characterized by a unique CRD sequence motif (a distinctive structural fold) and nominal specificity for l-Fuc—has led to a greater understanding of self/nonself recognition by proteins with tandemly arrayed CRDs. For lectins with a single CRD, however, recognition of self and nonself glycans can only be rationalized in terms of protein oligomerization and ligand clustering and presentation. Spatial and temporal changes in lectin expression, secretion, and local concentrations in extracellular microenvironments, as well as structural diversity and spatial display of their carbohydrate ligands on the host or microbial cell surface, are suggestive of a dynamic interplay of their recognition and effector functions in development and immunity. PMID:22973821

Role of fusiform and anterior temporal cortical areas in facial recognition.

PubMed

Nasr, Shahin; Tootell, Roger B H

2012-11-15

Recent fMRI studies suggest that cortical face processing extends well beyond the fusiform face area (FFA), including unspecified portions of the anterior temporal lobe. However, the exact location of such anterior temporal region(s), and their role during active face recognition, remain unclear. Here we demonstrate that (in addition to FFA) a small bilateral site in the anterior tip of the collateral sulcus ('AT'; the anterior temporal face patch) is selectively activated during recognition of faces but not houses (a non-face object). In contrast to the psychophysical prediction that inverted and contrast reversed faces are processed like other non-face objects, both FFA and AT (but not other visual areas) were also activated during recognition of inverted and contrast reversed faces. However, response accuracy was better correlated to recognition-driven activity in AT, compared to FFA. These data support a segregated, hierarchical model of face recognition processing, extending to the anterior temporal cortex. Copyright © 2012 Elsevier Inc. All rights reserved.

Role of Fusiform and Anterior Temporal Cortical Areas in Facial Recognition

PubMed Central

Nasr, Shahin; Tootell, Roger BH

2012-01-01

Recent FMRI studies suggest that cortical face processing extends well beyond the fusiform face area (FFA), including unspecified portions of the anterior temporal lobe. However, the exact location of such anterior temporal region(s), and their role during active face recognition, remain unclear. Here we demonstrate that (in addition to FFA) a small bilateral site in the anterior tip of the collateral sulcus (‘AT’; the anterior temporal face patch) is selectively activated during recognition of faces but not houses (a non-face object). In contrast to the psychophysical prediction that inverted and contrast reversed faces are processed like other non-face objects, both FFA and AT (but not other visual areas) were also activated during recognition of inverted and contrast reversed faces. However, response accuracy was better correlated to recognition-driven activity in AT, compared to FFA. These data support a segregated, hierarchical model of face recognition processing, extending to the anterior temporal cortex. PMID:23034518

Protein diffusion along DNA: on the effect of roadblocks and crowders

NASA Astrophysics Data System (ADS)

Krepel, Dana; Levy, Yaakov

2016-12-01

Rapid recognition by a protein of its DNA target site is achieved through a combination of one- and three-dimensional (1D and 3D) diffusion, which allows efficient scanning of the many alternative sites. This facilitated diffusion mechanism is expected to be affected by cellular conditions, particularly crowding, given that up to 40% of the total cellular volume may by occupied by macromolecules. Both experimental and theoretical studies showed that crowding particles can enhance facilitated diffusion and accelerate search kinetics. This effect may originate from crowding forcing a trade-off between 3D and 1D diffusion. In this study, using coarse-grained molecular dynamic simulations, we investigate how the molecular properties of the crowders may modulate the effect exerted by crowding on a searcher protein. We show that crowders with an affinity to the DNA are less effective search facilitators than particles whose contribution is solely entropic. Crowders that have affinity to DNA may occupy DNA sites and thereby function as obstacles or roadblocks that slow down the searcher protein, and they may also produce a smaller excluded volume effect and so reduce usage of the hopping searching mode in favor of less-effective 3D diffusion in the bulk. We discuss how strong repulsive interactions between the crowding particles themselves may affect the overall dynamics of the crowders and their excluded volume effect. Our study shows that search kinetics and its mechanism are modulated not only by salt concentration and crowding occupancy, but also by the properties of the crowding particles.

Crystal structure and novel recognition motif of rho ADP-ribosylating C3 exoenzyme from Clostridium botulinum: structural insights for recognition specificity and catalysis.

PubMed

Han, S; Arvai, A S; Clancy, S B; Tainer, J A

2001-01-05

Clostridium botulinum C3 exoenzyme inactivates the small GTP-binding protein family Rho by ADP-ribosylating asparagine 41, which depolymerizes the actin cytoskeleton. C3 thus represents a major family of the bacterial toxins that transfer the ADP-ribose moiety of NAD to specific amino acids in acceptor proteins to modify key biological activities in eukaryotic cells, including protein synthesis, differentiation, transformation, and intracellular signaling. The 1.7 A resolution C3 exoenzyme structure establishes the conserved features of the core NAD-binding beta-sandwich fold with other ADP-ribosylating toxins despite little sequence conservation. Importantly, the central core of the C3 exoenzyme structure is distinguished by the absence of an active site loop observed in many other ADP-ribosylating toxins. Unlike the ADP-ribosylating toxins that possess the active site loop near the central core, the C3 exoenzyme replaces the active site loop with an alpha-helix, alpha3. Moreover, structural and sequence similarities with the catalytic domain of vegetative insecticidal protein 2 (VIP2), an actin ADP-ribosyltransferase, unexpectedly implicates two adjacent, protruding turns, which join beta5 and beta6 of the toxin core fold, as a novel recognition specificity motif for this newly defined toxin family. Turn 1 evidently positions the solvent-exposed, aromatic side-chain of Phe209 to interact with the hydrophobic region of Rho adjacent to its GTP-binding site. Turn 2 evidently both places the Gln212 side-chain for hydrogen bonding to recognize Rho Asn41 for nucleophilic attack on the anomeric carbon of NAD ribose and holds the key Glu214 catalytic side-chain in the adjacent catalytic pocket. This proposed bipartite ADP-ribosylating toxin turn-turn (ARTT) motif places the VIP2 and C3 toxin classes into a single ARTT family characterized by analogous target protein recognition via turn 1 aromatic and turn 2 hydrogen-bonding side-chain moieties. Turn 2 centrally anchors the catalytic Glu214 within the ARTT motif, and furthermore distinguishes the C3 toxin class by a conserved turn 2 Gln and the VIP2 binary toxin class by a conserved turn 2 Glu for appropriate target side-chain hydrogen-bonding recognition. Taken together, these structural results provide a molecular basis for understanding the coupled activity and recognition specificity for C3 and for the newly defined ARTT toxin family, which acts in the depolymerization of the actin cytoskeleton. This beta5 to beta6 region of the toxin fold represents an experimentally testable and potentially general recognition motif region for other ADP-ribosylating toxins that have a similar beta-structure framework. Copyright 2001 Academic Press.

The influence of writing practice on letter recognition in preschool children: a comparison between handwriting and typing.

PubMed

Longcamp, Marieke; Zerbato-Poudou, Marie-Thérèse; Velay, Jean-Luc

2005-05-01

A large body of data supports the view that movement plays a crucial role in letter representation and suggests that handwriting contributes to the visual recognition of letters. If so, changing the motor conditions while children are learning to write by using a method based on typing instead of handwriting should affect their subsequent letter recognition performances. In order to test this hypothesis, we trained two groups of 38 children (aged 3-5 years) to copy letters of the alphabet either by hand or by typing them. After three weeks of learning, we ran two recognition tests, one week apart, to compare the letter recognition performances of the two groups. The results showed that in the older children, the handwriting training gave rise to a better letter recognition than the typing training.

Optical character recognition of camera-captured images based on phase features

NASA Astrophysics Data System (ADS)

Diaz-Escobar, Julia; Kober, Vitaly

2015-09-01

Nowadays most of digital information is obtained using mobile devices specially smartphones. In particular, it brings the opportunity for optical character recognition in camera-captured images. For this reason many recognition applications have been recently developed such as recognition of license plates, business cards, receipts and street signal; document classification, augmented reality, language translator and so on. Camera-captured images are usually affected by geometric distortions, nonuniform illumination, shadow, noise, which make difficult the recognition task with existing systems. It is well known that the Fourier phase contains a lot of important information regardless of the Fourier magnitude. So, in this work we propose a phase-based recognition system exploiting phase-congruency features for illumination/scale invariance. The performance of the proposed system is tested in terms of miss classifications and false alarms with the help of computer simulation.

The level of cognitive function and recognition of emotions in older adults

PubMed Central

Singh-Manoux, Archana; Batty, G. David; Ebmeier, Klaus P.; Jokela, Markus; Harmer, Catherine J.; Kivimäki, Mika

2017-01-01

Background The association between cognitive decline and the ability to recognise emotions in interpersonal communication is not well understood. We aimed to investigate the association between cognitive function and the ability to recognise emotions in other people’s facial expressions across the full continuum of cognitive capacity. Methods Cross-sectional analysis of 4039 participants (3016 men, 1023 women aged 59 to 82 years) in the Whitehall II study. Cognitive function was assessed using a 30-item Mini-Mental State Examination (MMSE), further classified into 8 groups: 30, 29, 28, 27, 26, 25, 24, and <24 (possible dementia) MMSE points. The Facial Expression Recognition Task (FERT) was used to examine recognition of anger, fear, disgust, sadness, and happiness. Results The multivariable adjusted difference in the percentage of accurate recognition between the highest and lowest MMSE group was 14.9 (95%CI, 11.1–18.7) for anger, 15.5 (11.9–19.2) for fear, 18.5 (15.2–21.8) for disgust, 11.6 (7.3–16.0) for sadness, and 6.3 (3.1–9.4) for happiness. However, recognition of several emotions was reduced already after 1 to 2-point reduction in MMSE and with further points down in MMSE, the recognition worsened at an accelerated rate. Conclusions The ability to recognize emotion in facial expressions is affected at an early stage of cognitive impairment and might decline at an accelerated rate with the deterioration of cognitive function. Accurate recognition of happiness seems to be less affected by a severe decline in cognitive performance than recognition of negatively valued emotions. PMID:28977015

Prediction of consonant recognition in quiet for listeners with normal and impaired hearing using an auditory model.

PubMed

Jürgens, Tim; Ewert, Stephan D; Kollmeier, Birger; Brand, Thomas

2014-03-01

Consonant recognition was assessed in normal-hearing (NH) and hearing-impaired (HI) listeners in quiet as a function of speech level using a nonsense logatome test. Average recognition scores were analyzed and compared to recognition scores of a speech recognition model. In contrast to commonly used spectral speech recognition models operating on long-term spectra, a "microscopic" model operating in the time domain was used. Variations of the model (accounting for hearing impairment) and different model parameters (reflecting cochlear compression) were tested. Using these model variations this study examined whether speech recognition performance in quiet is affected by changes in cochlear compression, namely, a linearization, which is often observed in HI listeners. Consonant recognition scores for HI listeners were poorer than for NH listeners. The model accurately predicted the speech reception thresholds of the NH and most HI listeners. A partial linearization of the cochlear compression in the auditory model, while keeping audibility constant, produced higher recognition scores and improved the prediction accuracy. However, including listener-specific information about the exact form of the cochlear compression did not improve the prediction further.

Using eye movements as an index of implicit face recognition in autism spectrum disorder.

PubMed

Hedley, Darren; Young, Robyn; Brewer, Neil

2012-10-01

Individuals with an autism spectrum disorder (ASD) typically show impairment on face recognition tasks. Performance has usually been assessed using overt, explicit recognition tasks. Here, a complementary method involving eye tracking was used to examine implicit face recognition in participants with ASD and in an intelligence quotient-matched non-ASD control group. Differences in eye movement indices between target and foil faces were used as an indicator of implicit face recognition. Explicit face recognition was assessed using old-new discrimination and reaction time measures. Stimuli were faces of studied (target) or unfamiliar (foil) persons. Target images at test were either identical to the images presented at study or altered by changing the lighting, pose, or by masking with visual noise. Participants with ASD performed worse than controls on the explicit recognition task. Eye movement-based measures, however, indicated that implicit recognition may not be affected to the same degree as explicit recognition. Autism Res 2012, 5: 363-379. © 2012 International Society for Autism Research, Wiley Periodicals, Inc. © 2012 International Society for Autism Research, Wiley Periodicals, Inc.

Processing of facial affect in social drinkers: a dose-response study of alcohol using dynamic emotion expressions.

PubMed

Kamboj, Sunjeev K; Joye, Alyssa; Bisby, James A; Das, Ravi K; Platt, Bradley; Curran, H Valerie

2013-05-01

Studies of affect recognition can inform our understanding of the interpersonal effects of alcohol and help develop a more complete neuropsychological profile of this drug. The objective of the study was to examine affect recognition in social drinkers using a novel dynamic affect-recognition task, sampling performance across a range of evolutionarily significant target emotions and neutral expressions. Participants received 0, 0.4 or 0.8 g/kg alcohol in a double-blind, independent groups design. Relatively naturalistic changes in facial expression-from neutral (mouth open) to increasing intensities of target emotions, as well as neutral (mouth closed)-were simulated using computer-generated dynamic morphs. Accuracy and reaction time were measured and a two-high-threshold model applied to hits and false-alarm data to determine sensitivity and response bias. While there was no effect on the principal emotion expressions (happiness, sadness, fear, anger and disgust), compared to those receiving 0.8 g/kg of alcohol and placebo, participants administered with 0.4 g/kg alcohol tended to show an enhanced response bias to neutral expressions. Exploration of this effect suggested an accompanying tendency to misattribute neutrality to sad expressions following the 0.4-g/kg dose. The 0.4-g/kg alcohol-but not 0.8 g/kg-produced a limited and specific modification in affect recognition evidenced by a neutral response bias and possibly an accompanying tendency to misclassify sad expressions as neutral. In light of previous findings on involuntary negative memory following the 0.4-g/kg dose, we suggest that moderate-but not high-doses of alcohol have a special relevance to emotional processing in social drinkers.

Impact of brain tumour location on emotion and personality: a voxel-based lesion-symptom mapping study on mentalization processes.

PubMed

Campanella, Fabio; Shallice, Tim; Ius, Tamara; Fabbro, Franco; Skrap, Miran

2014-09-01

Patients affected by brain tumours may show behavioural and emotional regulation deficits, sometimes showing flattened affect and sometimes experiencing a true 'change' in personality. However, little evidence is available to the surgeon as to what changes are likely to occur with damage at specific sites, as previous studies have either relied on single cases or provided only limited anatomical specificity, mostly reporting associations rather than dissociations of symptoms. We investigated these aspects in patients undergoing surgery for the removal of cerebral tumours. We argued that many of the problems described can be ascribed to the onset of difficulties in one or more of the different levels of the process of mentalizing (i.e. abstracting and reflecting upon) emotion and intentions, which impacts on everyday behaviour. These were investigated in terms of (i) emotion recognition; (ii) Theory of Mind; (iii) alexithymia; and (iv) self-maturity (personality disorder). We hypothesized that temporo/limbic areas would be critical for processing emotion and intentions at a more perceptual level, while frontal lobe structures would be more critical when higher levels of mentalization/abstraction are required. We administered four different tasks, Task 1: emotion recognition of Ekman faces; Task 2: the Eyes Test (Theory of Mind); Task 3: Toronto Alexithymia Scale; and Task 4: Temperament and Character Inventory (a personality inventory), both immediately before and few days after the operation for the removal of brain tumours in a series of 71 patients (age range: 18-75 years; 33 female) with lesions located in the left or right frontal, temporal and parietal lobes. Lobe-based and voxel-based analysis confirmed that tasks requiring interpretation of emotions and intentions at more basic (less mentalized) levels (Tasks 1 and 2) were more affected by temporo/insular lesions, with emotion recognition (Task 1) being maximally impaired by anterior temporal and amygdala lesions and Task 2 (found to be a 'basic' Theory of Mind task involving only limited mentalization) being mostly impaired by posterior temporoparietal lesions. Tasks relying on higher-level mentalization (Tasks 3 and 4) were maximally affected by prefrontal lesions, with the alexithymia scale (Task 3) being mostly associated with anterior/medial lesions and the self-maturity measure (Task 4) with lateral prefrontal ones. © The Author (2014). Published by Oxford University Press on behalf of the Guarantors of Brain. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Prenatal flavor exposure affects flavor recognition and stress-related behavior of piglets.

PubMed

Oostindjer, Marije; Bolhuis, J Elizabeth; van den Brand, Henry; Kemp, Bas

2009-11-01

Exposure to flavors in the amniotic fluid and mother's milk derived from the maternal diet has been shown to modulate food preferences and neophobia of young animals of several species. Aim of the experiment was to study the effects of pre- and postnatal flavor exposure on behavior of piglets during (re)exposure to this flavor. Furthermore, we investigated whether varying stress levels, caused by different test settings, affected behavior of animals during (re)exposure. Piglets were exposed to anisic flavor through the maternal diet during late gestation and/or during lactation or never. Piglets that were prenatally exposed to the flavor through the maternal diet behaved differently compared with unexposed pigs during reexposure to the flavor in several tests, suggesting recognition of the flavor. The differences between groups were more pronounced in tests with relatively high stress levels. This suggests that stress levels, caused by the design of the test, can affect the behavior shown in the presence of the flavor. We conclude that prenatal flavor exposure affects behaviors of piglets that are indicative of recognition and that these behaviors are influenced by stress levels during (re)exposure.

The application of automatic recognition techniques in the Apollo 9 SO-65 experiment

NASA Technical Reports Server (NTRS)

Macdonald, R. B.

1970-01-01

A synoptic feature analysis is reported on Apollo 9 remote earth surface photographs that uses the methods of statistical pattern recognition to classify density points and clusterings in digital conversion of optical data. A computer derived geological map of a geological test site indicates that geological features of the range are separable, but that specific rock types are not identifiable.

Pragmatic Competency and Obsessive-Compulsive Disorder: A Comparative Assessment with Normal Controls

ERIC Educational Resources Information Center

Ghahari, Shima; Hassani, Hamidreza; Purmofrad, Maryam

2017-01-01

Unlike such cognitive impairments as autism and schizophrenia, the speech pattern in obsessive-compulsive disorder (OCD) has largely remained underrepresented. We examined the pragmatic competence of OCD-affected individuals under two variant modes: pragmatic recognition and pragmatic production. In the recognition phase, the informants completed…

The heparin-binding site in tetranectin is located in the N-terminal region and binding does not involve the carbohydrate recognition domain.

PubMed Central

Lorentsen, R H; Graversen, J H; Caterer, N R; Thogersen, H C; Etzerodt, M

2000-01-01

Tetranectin is a homotrimeric plasma and extracellular-matrix protein that binds plasminogen and complex sulphated polysaccharides including heparin. In terms of primary and tertiary structure, tetranectin is related to the collectin family of Ca(2+)-binding C-type lectins. Tetranectin is encoded in three exons. Exon 3 encodes the carbohydrate recognition domain, which binds to kringle 4 in plasminogen at low levels of Ca(2+). Exon 2 encodes an alpha-helix, which is necessary and sufficient to govern the trimerization of tetranectin by assembling into a triple-helical coiled-coil structural element. Here we show that the heparin-binding site in tetranectin resides not in the carbohydrate recognition domain but within the N-terminal region, comprising the 16 amino acid residues encoded by exon 1. In particular, the lysine residues in the decapeptide segment KPKKIVNAKK (tetranectin residues 6-15) are shown to be of primary importance in heparin binding. PMID:10727405

The heparin-binding site in tetranectin is located in the N-terminal region and binding does not involve the carbohydrate recognition domain.

PubMed

Lorentsen, R H; Graversen, J H; Caterer, N R; Thogersen, H C; Etzerodt, M

2000-04-01

Tetranectin is a homotrimeric plasma and extracellular-matrix protein that binds plasminogen and complex sulphated polysaccharides including heparin. In terms of primary and tertiary structure, tetranectin is related to the collectin family of Ca(2+)-binding C-type lectins. Tetranectin is encoded in three exons. Exon 3 encodes the carbohydrate recognition domain, which binds to kringle 4 in plasminogen at low levels of Ca(2+). Exon 2 encodes an alpha-helix, which is necessary and sufficient to govern the trimerization of tetranectin by assembling into a triple-helical coiled-coil structural element. Here we show that the heparin-binding site in tetranectin resides not in the carbohydrate recognition domain but within the N-terminal region, comprising the 16 amino acid residues encoded by exon 1. In particular, the lysine residues in the decapeptide segment KPKKIVNAKK (tetranectin residues 6-15) are shown to be of primary importance in heparin binding.

Emotion recognition and social adjustment in school-aged girls and boys.

PubMed

Leppänen, J M; Hietanen, J K

2001-12-01

The present study investigated emotion recognition accuracy and its relation to social adjustment in 7-10 year-old children. The ability to recognize basic emotions from facial and vocal expressions was measured and compared to peer popularity and to teacher-rated social competence. The results showed that emotion recognition was related to these measures of social adjustment, but the gender of a child and emotion category affected this relationship. Emotion recognition accuracy was significantly related to social adjustment for the girls, but not for the boys. For the girls, especially the recognition of surprise was related to social adjustment. Together, these results suggest that the ability to recognize others' emotional states from nonverbal cues is an important socio-cognitive ability for school-aged girls.

The spine in Paget’s disease

PubMed Central

Dell’Atti, C.; Lalam, R. K.; Tins, B. J.; Tyrrell, P. N. M.

2007-01-01

Paget’s disease (PD) is a chronic metabolically active bone disease, characterized by a disturbance in bone modelling and remodelling due to an increase in osteoblastic and osteoclastic activity. The vertebra is the second most commonly affected site. This article reviews the various spinal pathomechanisms and osseous dynamics involved in producing the varied imaging appearances and their clinical relevance. Advanced imaging of osseous, articular and bone marrow manifestations of PD in all the vertebral components are presented. Pagetic changes often result in clinical symptoms including back pain, spinal stenosis and neural dysfunction. Various pathological complications due to PD involvement result in these clinical symptoms. Recognition of the imaging manifestations of spinal PD and the potential complications that cause the clinical symptoms enables accurate assessment of patients prior to appropriate management. PMID:17410356

Canine olfactory receptor gene polymorphism and its relation to odor detection performance by sniffer dogs.

PubMed

Lesniak, Anna; Walczak, Marta; Jezierski, Tadeusz; Sacharczuk, Mariusz; Gawkowski, Maciej; Jaszczak, Kazimierz

2008-01-01

The outstanding sensitivity of the canine olfactory system has been acknowledged by using sniffer dogs in military and civilian service for detection of a variety of odors. It is hypothesized that the canine olfactory ability is determined by polymorphisms in olfactory receptor (OR) genes. We investigated 5 OR genes for polymorphic sites which might affect the olfactory ability of service dogs in different fields of specific substance detection. All investigated OR DNA sequences proved to have allelic variants, the majority of which lead to protein sequence alteration. Homozygous individuals at 2 gene loci significantly differed in their detection skills from other genotypes. This suggests a role of specific alleles in odor detection and a linkage between single-nucleotide polymorphism and odor recognition efficiency.

Behavioural interactions between West African dwarf nanny goats and their twin-born kids during the first 48 h post-partum.

PubMed

Awotwi; Oppong-Anane; Addae; Oddoye

2000-07-01

West African dwarf nanny goats and their twin-born kids were tested to determine their behavioural response to separation and their mutual recognition during the first 48 h post-partum. Does and their kids were given scores ranging from 1 to 5, depending on how they performed in the tests. Animals that showed maximum response and recognition ability were given a score of 5, while those with minimum response and recognition ability scored 1. The kids were prevented from sucking 2 h prior to the tests, which were carried out at 18, 24, 36 and 48 h post-partum. Chi-square procedure was used to determine whether age, sex and birthweight of kids as well as hours post-partum and parity of dams had any effect on these post-partum behaviours. Out of 48 twin-born kids tested, 32 (67%) responded actively to separation from dams (i.e. had scores of 3 or more). The age, sex and birthweight of kids did not significantly affect (P>0.05) their response to separation from their dams. The hours post-partum and the parity of does also did not affect their response to separation from their kids. The dam recognition ability of twin-born kids was very poor. Out of a total of 48 kids tested, only 17 (35%) were able to recognize their dams (i.e. had scores of 3 or more). Even at 36 h, only four out of 14 (26%) could recognize their dams. It was only at 48 h that the majority of kids tested (i.e. 75%) successfully identified their dams. At 48 h, the dam recognition ability of kids was significantly better (P<0.05) than that of 18-h-old kids. Sex and birthweight of 24-48-h-old twin-born kids did not significantly affect (P>0.05) their ability to recognize their dams. The majority of does tested (i.e. 20 out of 24) were able to recognize their twin-born kids. The hour post-partum and parity of does did not significantly affect (P>0.05) their kid recognition ability.

Crystal structure of the DNA-binding domain of the LysR-type transcriptional regulator CbnR in complex with a DNA fragment of the recognition-binding site in the promoter region.

PubMed

Koentjoro, Maharani Pertiwi; Adachi, Naruhiko; Senda, Miki; Ogawa, Naoto; Senda, Toshiya

2018-03-01

LysR-type transcriptional regulators (LTTRs) are among the most abundant transcriptional regulators in bacteria. CbnR is an LTTR derived from Cupriavidus necator (formerly Alcaligenes eutrophus or Ralstonia eutropha) NH9 and is involved in transcriptional activation of the cbnABCD genes encoding chlorocatechol degradative enzymes. CbnR interacts with a cbnA promoter region of approximately 60 bp in length that contains the recognition-binding site (RBS) and activation-binding site (ABS). Upon inducer binding, CbnR seems to undergo conformational changes, leading to the activation of the transcription. Since the interaction of an LTTR with RBS is considered to be the first step of the transcriptional activation, the CbnR-RBS interaction is responsible for the selectivity of the promoter to be activated. To understand the sequence selectivity of CbnR, we determined the crystal structure of the DNA-binding domain of CbnR in complex with RBS of the cbnA promoter at 2.55 Å resolution. The crystal structure revealed details of the interactions between the DNA-binding domain and the promoter DNA. A comparison with the previously reported crystal structure of the DNA-binding domain of BenM in complex with its cognate RBS showed several differences in the DNA interactions, despite the structural similarity between CbnR and BenM. These differences explain the observed promoter sequence selectivity between CbnR and BenM. Particularly, the difference between Thr33 in CbnR and Ser33 in BenM appears to affect the conformations of neighboring residues, leading to the selective interactions with DNA. Atomic coordinates and structure factors for the DNA-binding domain of Cupriavidus necatorNH9 CbnR in complex with RBS are available in the Protein Data Bank under the accession code 5XXP. © 2018 Federation of European Biochemical Societies.

Basal forebrain amnesia: does the nucleus accumbens contribute to human memory?

PubMed Central

Goldenberg, G.; Schuri, U.; Gromminger, O.; Arnold, U.

1999-01-01

OBJECTIVE—To analyse amnesia caused by basal forebrain lesions.
METHODS—A single case study of a patient with amnesia after bleeding into the anterior portion of the left basal ganglia. Neuropsychological examination included tests of attention, executive function, working memory, recall, and recognition of verbal and non-verbal material, and recall from remote semantic and autobiographical memory. The patient's MRI and those of other published cases of basal forebrain amnesia were reviewed to specify which structures within the basal forebrain are crucial for amnesia.
RESULTS—Attention and executive function were largely intact. There was anterograde amnesia for verbal material which affected free recall and recognition. With both modes of testing the patient produced many false positive responses and intrusions when lists of unrelated words had been memorised. However, he confabulated neither on story recall nor in day to day memory, nor in recall from remote memory. The lesion affected mainly the nucleus accumbens, but encroached on the inferior limb of the capsula interna and the most ventral portion of the nucleus caudatus and globus pallidus, and there was evidence of some atrophy of the head of the caudate nucleus. The lesion spared the nucleus basalis Meynert, the diagnonal band, and the septum, which are the sites of cholinergic cell concentrations.
CONCLUSIONS—It seems unlikely that false positive responses were caused by insufficient strategic control of memory retrieval. This speaks against a major role of the capsular lesion which might disconnect the prefrontal cortex from the thalamus. It is proposed that the lesion of the nucleus accumbens caused amnesia.

 PMID:10406982

Docking glycosaminoglycans to proteins: analysis of solvent inclusion

NASA Astrophysics Data System (ADS)

Samsonov, Sergey A.; Teyra, Joan; Pisabarro, M. Teresa

2011-05-01

Glycosaminoglycans (GAGs) are anionic polysaccharides, which participate in key processes in the extracellular matrix by interactions with protein targets. Due to their charged nature, accurate consideration of electrostatic and water-mediated interactions is indispensable for understanding GAGs binding properties. However, solvent is often overlooked in molecular recognition studies. Here we analyze the abundance of solvent in GAG-protein interfaces and investigate the challenges of adding explicit solvent in GAG-protein docking experiments. We observe PDB GAG-protein interfaces being significantly more hydrated than protein-protein interfaces. Furthermore, by applying molecular dynamics approaches we estimate that about half of GAG-protein interactions are water-mediated. With a dataset of eleven GAG-protein complexes we analyze how solvent inclusion affects Autodock 3, eHiTs, MOE and FlexX docking. We develop an approach to de novo place explicit solvent into the binding site prior to docking, which uses the GRID program to predict positions of waters and to locate possible areas of solvent displacement upon ligand binding. To investigate how solvent placement affects docking performance, we compare these results with those obtained by taking into account information about the solvent position in the crystal structure. In general, we observe that inclusion of solvent improves the results obtained with these methods. Our data show that Autodock 3 performs best, though it experiences difficulties to quantitatively reproduce experimental data on specificity of heparin/heparan sulfate disaccharides binding to IL-8. Our work highlights the current challenges of introducing solvent in protein-GAGs recognition studies, which is crucial for exploiting the full potential of these molecules for rational engineering.

The Molecular Origin of the MMR-dependent Apoptosis Pathway from Dynamics Analysis of MutSα-DNA Complexes

PubMed Central

Negureanu, Lacramioara; Salsbury, Freddie R.

2012-01-01

The cellular response to DNA damage signaling by MMR proteins is incompletely understood. It is generally accepted that MMR-dependent apoptosis pathway in response to DNA damage detection is independent of MMR's DNA repair function. In this study we investigate correlated motions in response to the binding of mismatched and PCL DNA fragments by MutSα, as derived from 50 ns molecular dynamics simulations. The protein dynamics in response to the mismatched and damaged DNA recognition suggests that MutSα signals their recognition through independent pathways providing evidence for the molecular origin of the MMR-dependent apoptosis. MSH2 subunit is indicated to play a key role in signaling both mismatched and damaged DNA recognition; localized and collective motions within the protein allow identifying sites on the MSH2 surface possible involved in recruiting proteins responsible for downstream events. Unlike in the mismatch complex, predicted key communication sites specific for the damage recognition are on the list of known cancer causing mutations or deletions. This confirms MSH2's role in signaling DNA-damage induced apoptosis and suggests that defects in MMR alone is sufficient to trigger tumorigenesis, supporting the experimental evidence that MMR-damage response function could protect from the early occurrence of tumors. Identifying these particular communication sites may have implications for the treatment of cancers that are not defective for MMR, but are unable to function optimally for MMR-dependent responses following DNA damage such as the case of resistance to cisplatin. PMID:22712459

Conduct symptoms and emotion recognition in adolescent boys with externalization problems.

PubMed

Aspan, Nikoletta; Vida, Peter; Gadoros, Julia; Halasz, Jozsef

2013-01-01

In adults with antisocial personality disorder, marked alterations in the recognition of facial affect were described. Less consistent data are available on the emotion recognition in adolescents with externalization problems. The aim of the present study was to assess the relation between the recognition of emotions and conduct symptoms in adolescent boys with externalization problems. Adolescent boys with externalization problems referred to Vadaskert Child Psychiatry Hospital participated in the study after informed consent (N = 114, 11-17 years, mean = 13.4). The conduct problems scale of the strengths and difficulties questionnaire (parent and self-report) was used. The performance in a facial emotion recognition test was assessed. Conduct problems score (parent and self-report) was inversely correlated with the overall emotion recognition. In the self-report, conduct problems score was inversely correlated with the recognition of anger, fear, and sadness. Adolescents with high conduct problems scores were significantly worse in the recognition of fear, sadness, and overall recognition than adolescents with low conduct scores, irrespective of age and IQ. Our results suggest that impaired emotion recognition is dimensionally related to conduct problems and might have importance in the development of antisocial behavior.

Facial emotion recognition deficits following moderate-severe Traumatic Brain Injury (TBI): re-examining the valence effect and the role of emotion intensity.

PubMed

Rosenberg, Hannah; McDonald, Skye; Dethier, Marie; Kessels, Roy P C; Westbrook, R Frederick

2014-11-01

Many individuals who sustain moderate-severe traumatic brain injuries (TBI) are poor at recognizing emotional expressions, with a greater impairment in recognizing negative (e.g., fear, disgust, sadness, and anger) than positive emotions (e.g., happiness and surprise). It has been questioned whether this "valence effect" might be an artifact of the wide use of static facial emotion stimuli (usually full-blown expressions) which differ in difficulty rather than a real consequence of brain impairment. This study aimed to investigate the valence effect in TBI, while examining emotion recognition across different intensities (low, medium, and high). Twenty-seven individuals with TBI and 28 matched control participants were tested on the Emotion Recognition Task (ERT). The TBI group was more impaired in overall emotion recognition, and less accurate recognizing negative emotions. However, examining the performance across the different intensities indicated that this difference was driven by some emotions (e.g., happiness) being much easier to recognize than others (e.g., fear and surprise). Our findings indicate that individuals with TBI have an overall deficit in facial emotion recognition, and that both people with TBI and control participants found some emotions more difficult than others. These results suggest that conventional measures of facial affect recognition that do not examine variance in the difficulty of emotions may produce erroneous conclusions about differential impairment. They also cast doubt on the notion that dissociable neural pathways underlie the recognition of positive and negative emotions, which are differentially affected by TBI and potentially other neurological or psychiatric disorders.

Dissociation between recognition and detection advantage for facial expressions: a meta-analysis.

PubMed

Nummenmaa, Lauri; Calvo, Manuel G

2015-04-01

Happy facial expressions are recognized faster and more accurately than other expressions in categorization tasks, whereas detection in visual search tasks is widely believed to be faster for angry than happy faces. We used meta-analytic techniques for resolving this categorization versus detection advantage discrepancy for positive versus negative facial expressions. Effect sizes were computed on the basis of the r statistic for a total of 34 recognition studies with 3,561 participants and 37 visual search studies with 2,455 participants, yielding a total of 41 effect sizes for recognition accuracy, 25 for recognition speed, and 125 for visual search speed. Random effects meta-analysis was conducted to estimate effect sizes at population level. For recognition tasks, an advantage in recognition accuracy and speed for happy expressions was found for all stimulus types. In contrast, for visual search tasks, moderator analysis revealed that a happy face detection advantage was restricted to photographic faces, whereas a clear angry face advantage was found for schematic and "smiley" faces. Robust detection advantage for nonhappy faces was observed even when stimulus emotionality was distorted by inversion or rearrangement of the facial features, suggesting that visual features primarily drive the search. We conclude that the recognition advantage for happy faces is a genuine phenomenon related to processing of facial expression category and affective valence. In contrast, detection advantages toward either happy (photographic stimuli) or nonhappy (schematic) faces is contingent on visual stimulus features rather than facial expression, and may not involve categorical or affective processing. (c) 2015 APA, all rights reserved).

Designing of MIP based QCM sensor having thymine recognition sites based on biomimicking DNA approach.

PubMed

Diltemiz, S Emir; Hür, D; Ersöz, A; Denizli, A; Say, R

2009-11-15

Quartz crystal microbalance (QCM) sensors coated with molecular imprinted polymers (MIP) have been developed for the determination of thymine. In this method, methacryloylamidoadenine (MA-Ade) have used as a new monomer and thymine template for inspiration of DNA nucleobases interaction. The thymine can be simultaneously hydrogen binding to MA-Ade and fit into the shape-selective cavities. Thus, the interaction between nucleobases has an effect on the binding ability of the QCM sensors. The binding affinity of the thymine imprinted sensors has investigated by using the Langmuir isotherm. The thymine imprinted QCM electrodes have shown homogeneous binding sites for thymine (K(a): 1.0 x 10(5)M(-1)) while heterogeneous binding sites for uracil. On the other hand, recognition selectivity of the QCM sensor based on thymine imprinted polymer toward to uracil, ssDNA and ssRNA has been reported in this work.

Spatial, Hysteretic, and Adaptive Host-Guest Chemistry in a Metal-Organic Framework with Open Watson-Crick Sites.

PubMed

Cai, Hong; Li, Mian; Lin, Xiao-Rong; Chen, Wei; Chen, Guang-Hui; Huang, Xiao-Chun; Li, Dan

2015-09-01

Biological and artificial molecules and assemblies capable of supramolecular recognition, especially those with nucleobase pairing, usually rely on autonomous or collective binding to function. Advanced site-specific recognition takes advantage of cooperative spatial effects, as in local folding in protein-DNA binding. Herein, we report a new nucleobase-tagged metal-organic framework (MOF), namely ZnBTCA (BTC=benzene-1,3,5-tricarboxyl, A=adenine), in which the exposed Watson-Crick faces of adenine residues are immobilized periodically on the interior crystalline surface. Systematic control experiments demonstrated the cooperation of the open Watson-Crick sites and spatial effects within the nanopores, and thermodynamic and kinetic studies revealed a hysteretic host-guest interaction attributed to mild chemisorption. We further exploited this behavior for adenine-thymine binding within the constrained pores, and a globally adaptive response of the MOF host was observed. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The consequences of sequence erosion in the evolution of recombination hotspots.

PubMed

Tiemann-Boege, Irene; Schwarz, Theresa; Striedner, Yasmin; Heissl, Angelika

2017-12-19

Meiosis is initiated by a double-strand break (DSB) introduced in the DNA by a highly controlled process that is repaired by recombination. In many organisms, recombination occurs at specific and narrow regions of the genome, known as recombination hotspots, which overlap with regions enriched for DSBs. In recent years, it has been demonstrated that conversions and mutations resulting from the repair of DSBs lead to a rapid sequence evolution at recombination hotspots eroding target sites for DSBs. We still do not fully understand the effect of this erosion in the recombination activity, but evidence has shown that the binding of trans -acting factors like PRDM9 is affected. PRDM9 is a meiosis-specific, multi-domain protein that recognizes DNA target motifs by its zinc finger domain and directs DSBs to these target sites. Here we discuss the changes in affinity of PRDM9 to eroded recognition sequences, and explain how these changes in affinity of PRDM9 can affect recombination, leading sometimes to sterility in the context of hybrid crosses. We also present experimental data showing that DNA methylation reduces PRDM9 binding in vitro Finally, we discuss PRDM9-independent hotspots, posing the question how these hotspots evolve and change with sequence erosion.This article is part of the themed issue 'Evolutionary causes and consequences of recombination rate variation in sexual organisms'. © 2017 The Authors.

The consequences of sequence erosion in the evolution of recombination hotspots

PubMed Central

Schwarz, Theresa; Heissl, Angelika

2017-01-01

Meiosis is initiated by a double-strand break (DSB) introduced in the DNA by a highly controlled process that is repaired by recombination. In many organisms, recombination occurs at specific and narrow regions of the genome, known as recombination hotspots, which overlap with regions enriched for DSBs. In recent years, it has been demonstrated that conversions and mutations resulting from the repair of DSBs lead to a rapid sequence evolution at recombination hotspots eroding target sites for DSBs. We still do not fully understand the effect of this erosion in the recombination activity, but evidence has shown that the binding of trans-acting factors like PRDM9 is affected. PRDM9 is a meiosis-specific, multi-domain protein that recognizes DNA target motifs by its zinc finger domain and directs DSBs to these target sites. Here we discuss the changes in affinity of PRDM9 to eroded recognition sequences, and explain how these changes in affinity of PRDM9 can affect recombination, leading sometimes to sterility in the context of hybrid crosses. We also present experimental data showing that DNA methylation reduces PRDM9 binding in vitro. Finally, we discuss PRDM9-independent hotspots, posing the question how these hotspots evolve and change with sequence erosion. This article is part of the themed issue ‘Evolutionary causes and consequences of recombination rate variation in sexual organisms’. PMID:29109225

Structural polymorphism at LCR and its role in beta-globin gene regulation.

PubMed

Kukreti, Shrikant; Kaur, Harpreet; Kaushik, Mahima; Bansal, Aparna; Saxena, Sarika; Kaushik, Shikha; Kukreti, Ritushree

2010-09-01

Information on the secondary structures and conformational manifestations of eukaryotic DNA and their biological significance with reference to gene regulation and expression is limited. The human beta-globin gene Locus Control Region (LCR), a dominant regulator of globin gene expression, is a contiguous piece of DNA with five tissue-specific DNase I-hypersensitive sites (HSs). Since these HSs have a high density of transcription factor binding sites, structural interdependencies between HSs and different promoters may directly or indirectly regulate LCR functions. Mutations and SNPs may stabilize or destabilize the local secondary structures, affecting the gene expression by changes in the protein-DNA recognition patterns. Various palindromic or quasi-palindromic segments within LCR, could cause structural polymorphism and geometrical switching of DNA. This emphasizes the importance of understanding of the sequence-dependent variations of the DNA structure. Such structural motifs might act as regulatory elements. The local conformational variability of a DNA segment or action of a DNA specific protein is key to create and maintain active chromatin domains and affect transcription of various tissue specific beta-globin genes. We, summarize here the current status of beta-globin LCR structure and function. Further structural studies at molecular level and functional genomics might solve the regulatory puzzles that control the beta-globin gene locus. Copyright (c) 2010 Elsevier Masson SAS. All rights reserved.

MO-F-CAMPUS-J-02: Automatic Recognition of Patient Treatment Site in Portal Images Using Machine Learning

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

Chang, X; Yang, D

Purpose: To investigate the method to automatically recognize the treatment site in the X-Ray portal images. It could be useful to detect potential treatment errors, and to provide guidance to sequential tasks, e.g. automatically verify the patient daily setup. Methods: The portal images were exported from MOSAIQ as DICOM files, and were 1) processed with a threshold based intensity transformation algorithm to enhance contrast, and 2) where then down-sampled (from 1024×768 to 128×96) by using bi-cubic interpolation algorithm. An appearance-based vector space model (VSM) was used to rearrange the images into vectors. A principal component analysis (PCA) method was usedmore » to reduce the vector dimensions. A multi-class support vector machine (SVM), with radial basis function kernel, was used to build the treatment site recognition models. These models were then used to recognize the treatment sites in the portal image. Portal images of 120 patients were included in the study. The images were selected to cover six treatment sites: brain, head and neck, breast, lung, abdomen and pelvis. Each site had images of the twenty patients. Cross-validation experiments were performed to evaluate the performance. Results: MATLAB image processing Toolbox and scikit-learn (a machine learning library in python) were used to implement the proposed method. The average accuracies using the AP and RT images separately were 95% and 94% respectively. The average accuracy using AP and RT images together was 98%. Computation time was ∼0.16 seconds per patient with AP or RT image, ∼0.33 seconds per patient with both of AP and RT images. Conclusion: The proposed method of treatment site recognition is efficient and accurate. It is not sensitive to the differences of image intensity, size and positions of patients in the portal images. It could be useful for the patient safety assurance. The work was partially supported by a research grant from Varian Medical System.« less

Towards a smart glove: arousal recognition based on textile Electrodermal Response.

PubMed

Valenza, Gaetano; Lanata, Antonio; Scilingo, Enzo Pasquale; De Rossi, Danilo

2010-01-01

This paper investigates the possibility of using Electrodermal Response, acquired by a sensing fabric glove with embedded textile electrodes, as reliable means for emotion recognition. Here, all the essential steps for an automatic recognition system are described, from the recording of physiological data set to a feature-based multiclass classification. Data were collected from 35 healthy volunteers during arousal elicitation by means of International Affective Picture System (IAPS) pictures. Experimental results show high discrimination after twenty steps of cross validation.

The effects of list-method directed forgetting on recognition memory.

PubMed

Benjamin, Aaron S

2006-10-01

It is an almost universally accepted claim that the list-method procedure of inducing directed forgetting does not affect recognition. However, previous studies have omitted a critical comparison in reaching this conclusion. This article reports evidence that recognition of material learned after cue presentation is superior for conditions in which the material that preceded cue presentation was designated as to-be-forgotten. Because the absence of an effect of directed-forgetting instructions on recognition is the linchpin of the theoretical claim that retrieval inhibition and not selective rehearsal underlies that effect, the present results call into question the need to postulate a role for inhibition in directed forgetting.

A system for activity recognition using multi-sensor fusion.

PubMed

Gao, Lei; Bourke, Alan K; Nelson, John

2011-01-01

This paper proposes a system for activity recognition using multi-sensor fusion. In this system, four sensors are attached to the waist, chest, thigh, and side of the body. In the study we present two solutions for factors that affect the activity recognition accuracy: the calibration drift and the sensor orientation changing. The datasets used to evaluate this system were collected from 8 subjects who were asked to perform 8 scripted normal activities of daily living (ADL), three times each. The Naïve Bayes classifier using multi-sensor fusion is adopted and achieves 70.88%-97.66% recognition accuracies for 1-4 sensors.

Carbohydrate recognition by the antiviral lectin cyanovirin-N

PubMed Central

Fujimoto, Yukiji K.; Green, David F.

2012-01-01

Cyanovirin-N is a cyanobacterial lectin with potent antiviral activity, and has been the focus of extensive pre-clinical investigation as a potential prophylactic for the prevention of the sexual transmission of the human immunodeficiency virus (HIV). Here we present a detailed analysis of carbohydrate recognition by this important protein, using a combination of computational methods, including extensive molecular dynamics simulations and Molecular-Mechanics/ Poisson–Boltzmann/Surface-Area (MM/PBSA) energetic analysis. The simulation results strongly suggest that the observed tendency of wildtype CVN to form domain-swapped dimers is the result of a previously unidentified cis-peptide bond present in the monomeric state. The energetic analysis additionally indicates that the highest-affinity ligand for CVN characterized to date (α-Man-(1,2)-α-Man-(1,2)-α-Man) is recognized asymmetrically by the two binding sites. Finally, we are able to provide a detailed map of the role of all binding site functional groups (both backbone and side chain) to various aspects of molecular recognition: general affinity for cognate ligands, specificity for distinct oligosaccharide targets and the asymmetric recognition of α-Man-(1,2)-α-Man-(1,2)-α-Man. Taken as a whole, these results complement past experimental characterization (both structural and thermodynamic) to provide the most complete understanding of carbohydrate recognition by CVN to date. The results also provide strong support for the application of similar approaches to the understanding of other protein–carbohydrate complexes. PMID:23057413

Improved localization of cellular membrane receptors using combined fluorescence microscopy and simultaneous topography and recognition imaging

NASA Astrophysics Data System (ADS)

Duman, M.; Pfleger, M.; Zhu, R.; Rankl, C.; Chtcheglova, L. A.; Neundlinger, I.; Bozna, B. L.; Mayer, B.; Salio, M.; Shepherd, D.; Polzella, P.; Moertelmaier, M.; Kada, G.; Ebner, A.; Dieudonne, M.; Schütz, G. J.; Cerundolo, V.; Kienberger, F.; Hinterdorfer, P.

2010-03-01

The combination of fluorescence microscopy and atomic force microscopy has a great potential in single-molecule-detection applications, overcoming many of the limitations coming from each individual technique. Here we present a new platform of combined fluorescence and simultaneous topography and recognition imaging (TREC) for improved localization of cellular receptors. Green fluorescent protein (GFP) labeled human sodium-glucose cotransporter (hSGLT1) expressed Chinese Hamster Ovary (CHO) cells and endothelial cells (MyEnd) from mouse myocardium stained with phalloidin-rhodamine were used as cell systems to study AFM topography and fluorescence microscopy on the same surface area. Topographical AFM images revealed membrane features such as lamellipodia, cytoskeleton fibers, F-actin filaments and small globular structures with heights ranging from 20 to 30 nm. Combined fluorescence and TREC imaging was applied to detect density, distribution and localization of YFP-labeled CD1d molecules on α-galactosylceramide (αGalCer)-loaded THP1 cells. While the expression level, distribution and localization of CD1d molecules on THP1 cells were detected with fluorescence microscopy, the nanoscale distribution of binding sites was investigated with molecular recognition imaging by using a chemically modified AFM tip. Using TREC on the inverted light microscope, the recognition sites of cell receptors were detected in recognition images with domain sizes ranging from ~ 25 to ~ 160 nm, with the smaller domains corresponding to a single CD1d molecule.

Improved localization of cellular membrane receptors using combined fluorescence microscopy and simultaneous topography and recognition imaging.

PubMed

Duman, M; Pfleger, M; Zhu, R; Rankl, C; Chtcheglova, L A; Neundlinger, I; Bozna, B L; Mayer, B; Salio, M; Shepherd, D; Polzella, P; Moertelmaier, M; Kada, G; Ebner, A; Dieudonne, M; Schütz, G J; Cerundolo, V; Kienberger, F; Hinterdorfer, P

2010-03-19

The combination of fluorescence microscopy and atomic force microscopy has a great potential in single-molecule-detection applications, overcoming many of the limitations coming from each individual technique. Here we present a new platform of combined fluorescence and simultaneous topography and recognition imaging (TREC) for improved localization of cellular receptors. Green fluorescent protein (GFP) labeled human sodium-glucose cotransporter (hSGLT1) expressed Chinese Hamster Ovary (CHO) cells and endothelial cells (MyEnd) from mouse myocardium stained with phalloidin-rhodamine were used as cell systems to study AFM topography and fluorescence microscopy on the same surface area. Topographical AFM images revealed membrane features such as lamellipodia, cytoskeleton fibers, F-actin filaments and small globular structures with heights ranging from 20 to 30 nm. Combined fluorescence and TREC imaging was applied to detect density, distribution and localization of YFP-labeled CD1d molecules on alpha-galactosylceramide (alphaGalCer)-loaded THP1 cells. While the expression level, distribution and localization of CD1d molecules on THP1 cells were detected with fluorescence microscopy, the nanoscale distribution of binding sites was investigated with molecular recognition imaging by using a chemically modified AFM tip. Using TREC on the inverted light microscope, the recognition sites of cell receptors were detected in recognition images with domain sizes ranging from approximately 25 to approximately 160 nm, with the smaller domains corresponding to a single CD1d molecule.

Quantification of mRNA expression by competitive PCR using non-homologous competitors containing a shifted restriction site

PubMed Central

Watzinger, Franz; Hörth, Elfriede; Lion, Thomas

2001-01-01

Despite the recent introduction of real-time PCR methods, competitive PCR techniques continue to play an important role in nucleic acid quantification because of the significantly lower cost of equipment and consumables. Here we describe a shifted restriction-site competitive PCR (SRS-cPCR) assay based on a modified type of competitor. The competitor fragments are designed to contain a recognition site for a restriction endonuclease that is also present in the target sequence to be quantified, but in a different position. Upon completion of the PCR, the amplicons are digested in the same tube with a single restriction enzyme, without the need to purify PCR products. The generated competitor- and target-specific restriction fragments display different sizes, and can be readily separated by electrophoresis and quantified by image analysis. Suboptimal digestion affects competitor- and target-derived amplicons to the same extent, thus eliminating the problem of incorrect quantification as a result of incomplete digestion of PCR products. We have established optimized conditions for a panel of 20 common restriction endonucleases permitting efficient digestion in PCR buffer. It is possible, therefore, to find a suitable restriction site for competitive PCR in virtually any sequence of interest. The assay presented is inexpensive, widely applicable, and permits reliable and accurate quantification of nucleic acid targets. PMID:11376164

Criteria for recognition and taphonomy of coprolites from the Serra da Galga Member, Marília Formation (Upper Cretaceous), Minas Gerais, Brazil

NASA Astrophysics Data System (ADS)

de Oliveira, Fábio Antônio; Santucci, Rodrigo Miloni

2017-10-01

The Cretaceous sedimentary rocks from Uberaba, Minas Gerais, have provided a rich vertebrate fauna unearthed from rocks of the Serra da Galga Member, Marília Formation, Bauru Group, of Maastrichtian age. Together with these fossils, a large number of coprolites have also been found from two main localities, here called the Peirópolis and Serra da Galga sites. During field trips carried out in the last few years, 340 samples have been collected, prepared, and analyzed in laboratory. By using parameters such as weight, density, mineralogical composition, and content, we identified 199 coprolites and 141 inorganic nodules (pseudocoprolites). The coprolites have been divided into four morphotypes, which suggest their producers varied in feeding strategies and size. The taphonomic study, based on morphological characters such as wear, presence of pebbles or pebble marks, and desiccation cracks, suggests they underwent temporal and spatial-mixing, and that the material from the Peirópolis Site were transported essentially by alluvial processes (alluvial fans), whereas the material from the Serra da Galga Site were reworked mainly by fluvial streams. The same taphonomic processes may well have affected other fossils from these sites, which are highly abundant in the rocks of this area. Because of that, this taphonomic aspect becomes an important parameter to be taken into account in future studies on the biota of the region.

Age, cognitive style, and traffic signs.

PubMed

Lambert, L D; Fleury, M

1994-04-01

This study assessed the efficiency with which young and older adults of varying field dependence extract information from traffic signs. It also identified some visual attributes of signs which affect recognition time. Two experiments were conducted. In Exp. 1, digitized signs, embedded in rural and urban backgrounds, were presented on a computer monitor. Subjects indicated on which side a target sign had appeared. Analysis showed that recognition times were dependent on age and field-dependence scores. Also, visual backgrounds and spatial frequency of pictographs affected RTs. In Exp. 2, recognition RT to 2 signs with redesigned pictographs was measured as well as time taken to detect signs. The signs showing reduced spatial frequency were the fastest to recognize, although no effect was noticed during detection. The subjects who showed the worst performance when facing the original signs benefitted the most from the modifications.

Slow potentials in a melody recognition task.

PubMed

Verleger, R; Schellberg, D

1990-01-01

In a previous study, slow negative shifts were found in the EEG of subjects listening to well-known melodies. The two experiments reported here were designed to investigate the variables to which these slow potentials are related. In the first experiment, two opposite hypotheses were tested: The slow shifts might express subjects' acquaintance with the melodies or, on the contrary, the effort invested to identify them. To this end, some of the melodies were presented in the rhythms of other melodies to make recognition more difficult. Further, melodies rated as very well-known and as very unknown were analysed separately. However, the slow shifts were not affected by these experimental variations. Therefore in the second experiment, on the one hand the purely physical parameters intensity and duration were varied, but this variation had no impact on the slow shifts either. On the other hand, recognition was made more difficult by monotonously repeating the pitch of the 4th tone for the rest of some melodies. The slow negative shifts were enhanced with these monotonous melodies. This enhancement supports the "effort" hypothesis. Accordingly, the ofter shifts obtained in both experiments might likewise reflect effort. But since the task was not demanding, it is suggested that these constant shifts reflect the effort invested for coping with the entire underarousing situation rather than with the task. Frequently, slow eye movements occurred in the same time range as the slow potentials, resulting in EOG potentials spreading to the EEG recording sites. Yet results did not change substantially when the EEG recordings were corrected for the influence of EOG potentials.

Structural Basis for Carbohydrate Recognition and Anti-inflammatory Modulation by Gastrointestinal Nematode Parasite Toxascaris leonina Galectin.

PubMed

Hwang, Eun Young; Jeong, Mi Suk; Park, Sang Kyun; Ha, Sung Chul; Yu, Hak Sun; Jang, Se Bok

2016-12-02

Toxascaris leonina galectin (Tl-gal) is a galectin-9 homologue protein isolated from an adult worm of the canine gastrointestinal nematode parasite, and Tl-gal-vaccinated challenge can inhibit inflammation in inflammatory bowel disease-induced mice. We determined the first X-ray structures of full-length Tl-gal complexes with carbohydrates (lactose, N-acetyllactosamine, lacto-N-tetraose, sialyllactose, and glucose). Bonds were formed on concave surfaces of both carbohydrate recognition domains (CRDs) in Tl-gal. All binding sites were found in the HXXXR and WGXEER motifs. Charged Arg 61 /Arg 196 and Glu 80 /Glu 215 on the conserved motif of Tl-gal N-terminal CRD and C-terminal CRD are critical amino acids for recognizing carbohydrate binding, and the residues can affect protein folding and structure. The polar amino acids His, Asn, and Trp are also important residues for the interaction with carbohydrates through hydrogen bonding. Hemagglutination activities of Tl-gal were inhibited by interactions with carbohydrates and mutations. We found that the mutation of Tl-gal (E80A/E215A) at the carbohydrate binding region induced protein aggregation and could be caused in many diseases. The short linker region between the N-terminal and C-terminal CRDs of Tl-gal was very stable against proteolysis and maintained its biological activity. This structural information is expected to elucidate the carbohydrate recognition mechanism of Tl-gal and improve our understanding of anti-inflammatory mediators and modulators of immune response. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

75 FR 65521 - FM Approvals; Expansion of Recognition

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-25

... Laboratory (NRTL). FM's expansion covers the use of additional test standards. OSHA's current scope of... the NRTL may test, with each type specified by its applicable test standard; (2) the recognized site(s) that has/have the technical capability to perform the testing and certification activities for test...

Ab initio DNA synthesis by Bst polymerase in the presence of nicking endonucleases Nt.AlwI, Nb.BbvCI, and Nb.BsmI.

PubMed

Antipova, Valeriya N; Zheleznaya, Lyudmila A; Zyrina, Nadezhda V

2014-08-01

In the absence of added DNA, thermophilic DNA polymerases synthesize double-stranded DNA from free dNTPs, which consist of numerous repetitive units (ab initio DNA synthesis). The addition of thermophilic restriction endonuclease (REase), or nicking endonuclease (NEase), effectively stimulates ab initio DNA synthesis and determines the nucleotide sequence of reaction products. We have found that NEases Nt.AlwI, Nb.BbvCI, and Nb.BsmI with non-palindromic recognition sites stimulate the synthesis of sequences organized mainly as palindromes. Moreover, the nucleotide sequence of the palindromes appeared to be dependent on NEase recognition/cleavage modes. Thus, the heterodimeric Nb.BbvCI stimulated the synthesis of palindromes composed of two recognition sites of this NEase, which were separated by AT-reach sequences or (A)n (T)m spacers. Palindromic DNA sequences obtained in the ab initio DNA synthesis with the monomeric NEases Nb.BsmI and Nt.AlwI contained, along with the sites of these NEases, randomly synthesized sequences consisted of blocks of short repeats. These findings could help investigation of the potential abilities of highly productive ab initio DNA synthesis for the creation of DNA molecules with desirable sequence. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

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.

Computer-aided active-site-directed modeling of the Herpes Simplex Virus 1 and human thymidine kinase

NASA Astrophysics Data System (ADS)

Folkers, Gerd; Trumpp-Kallmeyer, Susanne; Gutbrod, Oliver; Krickl, Sabine; Fetzer, Jürgen; Keil, Günther M.

1991-10-01

Thymidine kinase (TK), which is induced by Herpes Simplex Virus 1 (HSV1), plays a key role in the antiviral activity of guanine derivatives such as aciclovir (ACV). In contrast, ACV shows only low affinity to the corresponding host cell enzyme. In order to define the differences in substrate binding of the two enzymes on molecular level, models for the three-dimensional (3-D) structures of the active sites of HSV1-TK and human TK were developed. The reconstruction of the active sites started from primary and secondary structure analysis of various kinases. The results were validated to homologous enzymes with known 3-D structures. The models predict that both enzymes consist of a central core β-sheet structure, connected by loops and α-helices very similar to the overall structure of other nucleotide binding enzymes. The phosphate binding is made up of a highly conserved glycine-rich loop at the N-terminus of the proteins and a conserved region at the C-terminus. The thymidine recognition site was found about 100 amino acids downstream from the phosphate binding loop. The differing substrate specificity of human and HSV1-TK can be explained by amino-acid substitutions in the homologous regions. To achieve a better understanding of the structure of the active site and how the thymidine kinase proteins interact with their substrates, the corresponding complexes of thymidine and dihydroxypropoxyguanine (DHPG) with HSV1 and human TK were built. For the docking of the guanine derivative, the X-ray structure of Elongation Factor Tu (EF-Tu), co-crystallized with guanosine diphosphate, was taken as reference. Fitting of thymidine into the active sites was done with respect to similar interactions found in thymidylate kinase. To complement the analysis of the 3-D structures of the two kinases and the substrate enzyme interactions, site-directed mutagenesis of the thymidine recognition site of HSV1-TK has been undertaken, changing Asp162 in the thymidine recognition site into Asn. First investigations reveal that the enzymatic activity of the mutant protein is destroyed.

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

Facial Emotion Recognition in Bipolar Disorder and Healthy Aging.

PubMed

Altamura, Mario; Padalino, Flavia A; Stella, Eleonora; Balzotti, Angela; Bellomo, Antonello; Palumbo, Rocco; Di Domenico, Alberto; Mammarella, Nicola; Fairfield, Beth

2016-03-01

Emotional face recognition is impaired in bipolar disorder, but it is not clear whether this is specific for the illness. Here, we investigated how aging and bipolar disorder influence dynamic emotional face recognition. Twenty older adults, 16 bipolar patients, and 20 control subjects performed a dynamic affective facial recognition task and a subsequent rating task. Participants pressed a key as soon as they were able to discriminate whether the neutral face was assuming a happy or angry facial expression and then rated the intensity of each facial expression. Results showed that older adults recognized happy expressions faster, whereas bipolar patients recognized angry expressions faster. Furthermore, both groups rated emotional faces more intensely than did the control subjects. This study is one of the first to compare how aging and clinical conditions influence emotional facial recognition and underlines the need to consider the role of specific and common factors in emotional face recognition.

Challenging ocular image recognition

NASA Astrophysics Data System (ADS)

Pauca, V. Paúl; Forkin, Michael; Xu, Xiao; Plemmons, Robert; Ross, Arun A.

2011-06-01

Ocular recognition is a new area of biometric investigation targeted at overcoming the limitations of iris recognition performance in the presence of non-ideal data. There are several advantages for increasing the area beyond the iris, yet there are also key issues that must be addressed such as size of the ocular region, factors affecting performance, and appropriate corpora to study these factors in isolation. In this paper, we explore and identify some of these issues with the goal of better defining parameters for ocular recognition. An empirical study is performed where iris recognition methods are contrasted with texture and point operators on existing iris and face datasets. The experimental results show a dramatic recognition performance gain when additional features are considered in the presence of poor quality iris data, offering strong evidence for extending interest beyond the iris. The experiments also highlight the need for the direct collection of additional ocular imagery.

Monopolar Detection Thresholds Predict Spatial Selectivity of Neural Excitation in Cochlear Implants: Implications for Speech Recognition

PubMed Central

2016-01-01

The objectives of the study were to (1) investigate the potential of using monopolar psychophysical detection thresholds for estimating spatial selectivity of neural excitation with cochlear implants and to (2) examine the effect of site removal on speech recognition based on the threshold measure. Detection thresholds were measured in Cochlear Nucleus® device users using monopolar stimulation for pulse trains that were of (a) low rate and long duration, (b) high rate and short duration, and (c) high rate and long duration. Spatial selectivity of neural excitation was estimated by a forward-masking paradigm, where the probe threshold elevation in the presence of a forward masker was measured as a function of masker-probe separation. The strength of the correlation between the monopolar thresholds and the slopes of the masking patterns systematically reduced as neural response of the threshold stimulus involved interpulse interactions (refractoriness and sub-threshold adaptation), and spike-rate adaptation. Detection threshold for the low-rate stimulus most strongly correlated with the spread of forward masking patterns and the correlation reduced for long and high rate pulse trains. The low-rate thresholds were then measured for all electrodes across the array for each subject. Subsequently, speech recognition was tested with experimental maps that deactivated five stimulation sites with the highest thresholds and five randomly chosen ones. Performance with deactivating the high-threshold sites was better than performance with the subjects’ clinical map used every day with all electrodes active, in both quiet and background noise. Performance with random deactivation was on average poorer than that with the clinical map but the difference was not significant. These results suggested that the monopolar low-rate thresholds are related to the spatial neural excitation patterns in cochlear implant users and can be used to select sites for more optimal speech recognition performance. PMID:27798658

Two-color SERS microscopy for protein co-localization in prostate tissue with primary antibody-protein A/G-gold nanocluster conjugates

NASA Astrophysics Data System (ADS)

Salehi, Mohammad; Schneider, Lilli; Ströbel, Philipp; Marx, Alexander; Packeisen, Jens; Schlücker, Sebastian

2014-01-01

SERS microscopy is a novel staining technique in immunohistochemistry, which is based on antibodies labeled with functionalized noble metal colloids called SERS labels or nanotags for optical detection. Conventional covalent bioconjugation of these SERS labels cannot prevent blocking of the antigen recognition sites of the antibody. We present a rational chemical design for SERS label-antibody conjugates which addresses this issue. Highly sensitive, silica-coated gold nanoparticle clusters as SERS labels are non-covalently conjugated to primary antibodies by using the chimeric protein A/G, which selectively recognizes the Fc part of antibodies and therefore prevents blocking of the antigen recognition sites. In proof-of-concept two-color imaging experiments for the co-localization of p63 and PSA on non-neoplastic prostate tissue FFPE specimens, we demonstrate the specificity and signal brightness of these rationally designed primary antibody-protein A/G-gold nanocluster conjugates.SERS microscopy is a novel staining technique in immunohistochemistry, which is based on antibodies labeled with functionalized noble metal colloids called SERS labels or nanotags for optical detection. Conventional covalent bioconjugation of these SERS labels cannot prevent blocking of the antigen recognition sites of the antibody. We present a rational chemical design for SERS label-antibody conjugates which addresses this issue. Highly sensitive, silica-coated gold nanoparticle clusters as SERS labels are non-covalently conjugated to primary antibodies by using the chimeric protein A/G, which selectively recognizes the Fc part of antibodies and therefore prevents blocking of the antigen recognition sites. In proof-of-concept two-color imaging experiments for the co-localization of p63 and PSA on non-neoplastic prostate tissue FFPE specimens, we demonstrate the specificity and signal brightness of these rationally designed primary antibody-protein A/G-gold nanocluster conjugates. Electronic supplementary information (ESI) available. See DOI: 10.1039/c3nr05890e

Risk or resilience? Empathic abilities in patients with bipolar disorders and their first-degree relatives.

PubMed

Seidel, Eva-Maria; Habel, Ute; Finkelmeyer, Andreas; Hasmann, Alexander; Dobmeier, Matthias; Derntl, Birgit

2012-03-01

Endophenotypes are intermediate phenotypes which are considered a more promising marker of genetic risk than illness itself. While previous research mostly used cognitive deficits, emotional functions are of greater relevance for bipolar disorder regarding the characteristic emotional hyper-reactability and deficient social-emotional competence. Hence, the aim of the present study was to clarify whether empathic abilities can serve as a possible endophenotype of bipolar disorder by applying a newly developed task in bipolar patients and their first-degree relatives. Three components of empathy (emotion recognition, perspective taking and affective responsiveness) have been assessed in a sample of 21 bipolar patients, 21 first-degree relatives and 21 healthy controls. Data analysis indicated significant differences between controls and patients for emotion recognition and affective responsiveness but not for perspective taking. This shows that in addition to difficulties in recognizing facial emotional expressions, bipolar patients have difficulties in identifying emotions they would experience in a given situation. However, the ability to take the perspective of another person in an emotional situation was intact but decreased with increasing severity of residual hypomanic and depressive symptoms. Relatives performed comparably bad on emotion recognition but did not differ from controls or patients in affective responsiveness. This study is the first to show that deficient emotion recognition is the only component of empathy which forms a possible endophenotype of bipolar disorder. This has important implications for prevention strategies. Furthermore, changes in affective responsiveness in first-degree relatives show a potential resilience marker. Copyright © 2011 Elsevier Ltd. All rights reserved.

[Impact of facial emotional recognition alterations in Dementia of the Alzheimer type].

PubMed

Rubinstein, Wanda; Cossini, Florencia; Politis, Daniel

2016-07-01

Face recognition of basic emotions is independent of other deficits in dementia of the Alzheimer type. Among these deficits, there is disagreement about what emotions are more difficult to recognize. Our aim was to study the presence of alterations in the process of facial recognition of basic emotions, and to investigate if there were differences in the recognition of each type of emotion in Alzheimer's disease. With three tests of recognition of basic facial emotions we evaluated 29 patients who had been diagnosed with dementia of the Alzheimer type and 18 control subjects. Significant differences were obtained in tests of recognition of basic facial emotions and between each. Since the amygdala, one of the brain structures responsible for emotional reaction, is affected in the early stages of this disease, our findings become relevant to understand how this alteration of the process of emotional recognition impacts the difficulties these patients have in both interpersonal relations and behavioral disorders.

On the Application of Image Processing Methods for Bubble Recognition to the Study of Subcooled Flow Boiling of Water in Rectangular Channels

PubMed Central

Paz, Concepción; Conde, Marcos; Porteiro, Jacobo; Concheiro, Miguel

2017-01-01

This work introduces the use of machine vision in the massive bubble recognition process, which supports the validation of boiling models involving bubble dynamics, as well as nucleation frequency, active site density and size of the bubbles. The two algorithms presented are meant to be run employing quite standard images of the bubbling process, recorded in general-purpose boiling facilities. The recognition routines are easily adaptable to other facilities if a minimum number of precautions are taken in the setup and in the treatment of the information. Both the side and front projections of subcooled flow-boiling phenomenon over a plain plate are covered. Once all of the intended bubbles have been located in space and time, the proper post-process of the recorded data become capable of tracking each of the recognized bubbles, sketching their trajectories and size evolution, locating the nucleation sites, computing their diameters, and so on. After validating the algorithm’s output against the human eye and data from other researchers, machine vision systems have been demonstrated to be a very valuable option to successfully perform the recognition process, even though the optical analysis of bubbles has not been set as the main goal of the experimental facility. PMID:28632158

Efficient synthesis of molecularly imprinted polymers with bio-recognition sites for the selective separation of bovine hemoglobin.

PubMed

Zhang, Zulei; Li, Lei

2018-06-01

We developed a facile approach to the construction of bio-recognition sites in silica nanoparticles for efficient separation of bovine hemoglobin based on amino-functionalized silica nanoparticles grafting by 3-aminopropyltriethoxylsilane providing hydrogen bonds with bovine hemoglobin through surface molecularly imprinting technology. The resulting amino-functionalized silica surface molecularly imprinted polymers were characterized using scanning electron microscope, transmission electronic microscopy, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, and thermogravimetric analysis. Results showed that the as-synthesized imprinted polymers exhibited spherical morphology and favorable thermal stability. The binding adsorption experiments showed that the imprinted polymers can reach equilibrium within 1 h. The Langmuir isotherm and pseudo-second-order kinetic model fitted the adsorption data well. Meanwhile, the imprinted polymers possessed a maximum binding capacity up to 90.3 mg/g and highly selectivity for the recognition of bovine hemoglobin. Moreover, such high binding capacity and selectivity retained after eight cycles, indicating the good stability and reusability of the imprinted polymers. Finally, successful application in the selective recognition of bovine hemoglobin from a real bovine blood sample indicated that the imprinted polymers displayed great potentials in efficient purification and separation of target proteins. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

CD56 Is a Pathogen Recognition Receptor on Human Natural Killer Cells.

PubMed

Ziegler, Sabrina; Weiss, Esther; Schmitt, Anna-Lena; Schlegel, Jan; Burgert, Anne; Terpitz, Ulrich; Sauer, Markus; Moretta, Lorenzo; Sivori, Simona; Leonhardt, Ines; Kurzai, Oliver; Einsele, Hermann; Loeffler, Juergen

2017-07-21

Aspergillus (A.) fumigatus is an opportunistic fungal mold inducing invasive aspergillosis (IA) in immunocompromised patients. Although antifungal activity of human natural killer (NK) cells was shown in previous studies, the underlying cellular mechanisms and pathogen recognition receptors (PRRs) are still unknown. Using flow cytometry we were able to show that the fluorescence positivity of the surface receptor CD56 significantly decreased upon fungal contact. To visualize the interaction site of NK cells and A. fumigatus we used SEM, CLSM and dSTORM techniques, which clearly demonstrated that NK cells directly interact with A. fumigatus via CD56 and that CD56 is re-organized and accumulated at this interaction site time-dependently. The inhibition of the cytoskeleton showed that the receptor re-organization was an active process dependent on actin re-arrangements. Furthermore, we could show that CD56 plays a role in the fungus mediated NK cell activation, since blocking of CD56 surface receptor reduced fungal mediated NK cell activation and reduced cytokine secretion. These results confirmed the direct interaction of NK cells and A. fumigatus, leading to the conclusion that CD56 is a pathogen recognition receptor. These findings give new insights into the functional role of CD56 in the pathogen recognition during the innate immune response.

Nonintrusive Finger-Vein Recognition System Using NIR Image Sensor and Accuracy Analyses According to Various Factors

PubMed Central

Pham, Tuyen Danh; Park, Young Ho; Nguyen, Dat Tien; Kwon, Seung Yong; Park, Kang Ryoung

2015-01-01

Biometrics is a technology that enables an individual person to be identified based on human physiological and behavioral characteristics. Among biometrics technologies, face recognition has been widely used because of its advantages in terms of convenience and non-contact operation. However, its performance is affected by factors such as variation in the illumination, facial expression, and head pose. Therefore, fingerprint and iris recognitions are preferred alternatives. However, the performance of the former can be adversely affected by the skin condition, including scarring and dryness. In addition, the latter has the disadvantages of high cost, large system size, and inconvenience to the user, who has to align their eyes with the iris camera. In an attempt to overcome these problems, finger-vein recognition has been vigorously researched, but an analysis of its accuracies according to various factors has not received much attention. Therefore, we propose a nonintrusive finger-vein recognition system using a near infrared (NIR) image sensor and analyze its accuracies considering various factors. The experimental results obtained with three databases showed that our system can be operated in real applications with high accuracy; and the dissimilarity of the finger-veins of different people is larger than that of the finger types and hands. PMID:26184214

Nonintrusive Finger-Vein Recognition System Using NIR Image Sensor and Accuracy Analyses According to Various Factors.

PubMed

Pham, Tuyen Danh; Park, Young Ho; Nguyen, Dat Tien; Kwon, Seung Yong; Park, Kang Ryoung

2015-07-13

Biometrics is a technology that enables an individual person to be identified based on human physiological and behavioral characteristics. Among biometrics technologies, face recognition has been widely used because of its advantages in terms of convenience and non-contact operation. However, its performance is affected by factors such as variation in the illumination, facial expression, and head pose. Therefore, fingerprint and iris recognitions are preferred alternatives. However, the performance of the former can be adversely affected by the skin condition, including scarring and dryness. In addition, the latter has the disadvantages of high cost, large system size, and inconvenience to the user, who has to align their eyes with the iris camera. In an attempt to overcome these problems, finger-vein recognition has been vigorously researched, but an analysis of its accuracies according to various factors has not received much attention. Therefore, we propose a nonintrusive finger-vein recognition system using a near infrared (NIR) image sensor and analyze its accuracies considering various factors. The experimental results obtained with three databases showed that our system can be operated in real applications with high accuracy; and the dissimilarity of the finger-veins of different people is larger than that of the finger types and hands.

Effects of oxytocin on behavioral and ERP measures of recognition memory for own-race and other-race faces in women and men

PubMed Central

Herzmann, Grit; Bird, Christopher W.; Freeman, Megan; Curran, Tim

2013-01-01

Oxytocin has been shown to affect human social information processing including recognition memory for faces. Here we investigated the neural processes underlying the effect of oxytocin on memorizing own-race and other-race faces in men and women. In a placebo-controlled, doubleblind, between-subject study, participants received either oxytocin or placebo before studying own-race and other-race faces. We recorded event-related potentials (ERPs) during both the study and recognition phase to investigate neural correlates of oxytocin’s effect on memory encoding, memory retrieval, and perception. Oxytocin increased the accuracy of familiarity judgments in the recognition test. Neural correlates for this effect were found in ERPs related to memory encoding and retrieval but not perception. In contrast to its facilitating effects on familiarity, oxytocin impaired recollection judgments, but in men only. Oxytocin did not differentially affect own-race and other-race faces. This study shows that oxytocin influences memory, but not perceptual processes, in a face recognition task and is the first to reveal sex differences in the effect of oxytocin on face memory. Contrary to recent findings in oxytocin and moral decision making, oxytocin did not preferentially improve memory for own-race faces. PMID:23648370

Effects of oxytocin on behavioral and ERP measures of recognition memory for own-race and other-race faces in women and men.

PubMed

Herzmann, Grit; Bird, Christopher W; Freeman, Megan; Curran, Tim

2013-10-01

Oxytocin has been shown to affect human social information processing including recognition memory for faces. Here we investigated the neural processes underlying the effect of oxytocin on memorizing own-race and other-race faces in men and women. In a placebo-controlled, double-blind, between-subject study, participants received either oxytocin or placebo before studying own-race and other-race faces. We recorded event-related potentials (ERPs) during both the study and recognition phase to investigate neural correlates of oxytocin's effect on memory encoding, memory retrieval, and perception. Oxytocin increased the accuracy of familiarity judgments in the recognition test. Neural correlates for this effect were found in ERPs related to memory encoding and retrieval but not perception. In contrast to its facilitating effects on familiarity, oxytocin impaired recollection judgments, but in men only. Oxytocin did not differentially affect own-race and other-race faces. This study shows that oxytocin influences memory, but not perceptual processes, in a face recognition task and is the first to reveal sex differences in the effect of oxytocin on face memory. Contrary to recent findings in oxytocin and moral decision making, oxytocin did not preferentially improve memory for own-race faces. Copyright © 2013 Elsevier Ltd. All rights reserved.

Delayed Video Self-Recognition in Children with High Vo Functioning Autism and Asperger's Disorder

ERIC Educational Resources Information Center

Dissanayake, Cheryl; Shembrey, Joh; Suddendorf, Thomas

2010-01-01

Two studies are reported which investigate delayed video self-recognition (DSR) in children with autistic disorder and Asperger's disorder relative to one another and to their typically developing peers. A secondary aim was to establish whether DSR ability is dependent on metarepresentational ability. Children's verbal and affective responses to…

Effect of Interest on Attentional Shift, Recognition, and Recall in Young Children.

ERIC Educational Resources Information Center

Renninger, K. Ann; Wozniak, Robert H.

1985-01-01

Interests of preschool children were naturalistically identified through patterns of attention in the classroom and were related to assessing (1) direction of attentional shift, (2) level of recognition, and (3) likelihood of recall. Findings are interpreted in terms of cognitive/affective conceptualization of interest as central figure of…

Cortical Reorganization in Dyslexic Children after Phonological Training: Evidence from Early Evoked Potentials

ERIC Educational Resources Information Center

Spironelli, Chiara; Penolazzi, Barbara; Vio, Claudio; Angrilli, Alessandro

2010-01-01

Brain plasticity was investigated in 14 Italian children affected by developmental dyslexia after 6 months of phonological training. The means used to measure language reorganization was the recognition potential, an early wave, also called N150, elicited by automatic word recognition. This component peaks over the left temporo-occipital cortex…

Researching the Use of Voice Recognition Writing Software.

ERIC Educational Resources Information Center

Honeycutt, Lee

2003-01-01

Notes that voice recognition technology (VRT) has become accurate and fast enough to be useful in a variety of writing scenarios. Contends that little is known about how this technology might affect writing process or perceptions of silent writing. Explores future use of VRT by examining past research in the technology of dictation. (PM)

Representation of 3-Dimenstional Objects by the Rat Perirhinal Cortex

PubMed Central

Burke, S.N.; Maurer, A.P.; Hartzell, A.L.; Nematollahi, S.; Uprety, A.; Wallace, J.L.; Barnes, C.A.

2012-01-01

The perirhinal cortex (PRC) is known to play an important role in object recognition. Little is known, however, regarding the activity of PRC neurons during the presentation of stimuli that are commonly used for recognition memory tasks in rodents, that is, 3-dimensional objects. Rats in the present study were exposed to 3-dimensional objects while they traversed a circular track for food reward. Under some behavioral conditions the track contained novel objects, familiar objects, or no objects. Approximately 38% of PRC neurons demonstrated ‘object fields’ (a selective increase in firing at the location of one or more objects). Although the rats spent more time exploring the objects when they were novel compared to familiar, indicating successful recognition memory, the proportion of object fields and the firing rates of PRC neurons were not affected by the rats’ previous experience with the objects. Together these data indicate that the activity of PRC cells is powerfully affected by the presence of objects while animals navigate through an environment, but under these conditions, the firing patterns are not altered by the relative novelty of objects during successful object recognition. PMID:22987680

Not all repetition is alike: Different benefits of repetition in amnesia and normal memory

PubMed Central

Verfaellie, Mieke; Rajaram, Suparna; Fossum, Karen; Williams, Lisa

2008-01-01

While it is well known that repetition can enhance memory in amnesia, little is known about which forms of repetition are most beneficial. This study compared the effect on recognition memory of repetition of words in the same semantic context and in varied semantic contexts. To gain insight into the mechanisms by which these forms of repetition affect performance, participants were asked to make Remember/Know judgments during recognition. These judgments were used to make inferences about the contribution of recollection and familiarity to performance. For individuals with intact memory, the two forms of repetition were equally beneficial to overall recognition, and were associated with both enhanced Remember and Know responses. However, varied repetition was associated with a higher likelihood of Remember responses than was fixed repetition. The two forms of repetition also conferred equivalent benefits on overall recognition in amnesia, but in both cases, this enhancement was manifest exclusively in enhanced Know responses. We conclude that the repetition of information, and especially repetition in varied contexts, enhances recollection in individuals with intact memory, but exclusively affects familiarity in patients with severe amnesia. PMID:18419835

[Several mechanisms of visual gnosis disorders in local brain lesions].

PubMed

Meerson, Ia A

1981-01-01

The object of the studies were peculiarities of recognizing visual images by patients with local cerebral lesions under conditions of incomplete sets of the image features, disjunction of the latter, distortion of their spatial arrangement, and unusual spatial orientation of the image as a whole. It was found that elimination of even one essential feature sharply hampered the recognition of the image both by healthy individuals (control), and patients with extraoccipital lesions, whereas elimination of several nonessential features only slowed down the process. In distinction from this the difficulties of the recognition of incomplete images by patients with occipital lesions were directly proportional to the number of the eliminated features irrespective of the latters' significance, i.e. these patients were unable to evaluate the hierarchy of the features. The recognition process in these patients were followed the way of scanning individual features. The reaccumulation and summation. The recognition of the fragmental, spatially distorted and unusually oriented images was found to be affected selectively in patients with parietal lobe affections. The patients with occipital lesions recognized such images practically as good as the ordinary ones.

Word attributes and lateralization revisited: implications for dual coding and discrete versus continuous processing.

PubMed

Boles, D B

1989-01-01

Three attributes of words are their imageability, concreteness, and familiarity. From a literature review and several experiments, I previously concluded (Boles, 1983a) that only familiarity affects the overall near-threshold recognition of words, and that none of the attributes affects right-visual-field superiority for word recognition. Here these conclusions are modified by two experiments demonstrating a critical mediating influence of intentional versus incidental memory instructions. In Experiment 1, subjects were instructed to remember the words they were shown, for subsequent recall. The results showed effects of both imageability and familiarity on overall recognition, as well as an effect of imageability on lateralization. In Experiment 2, word-memory instructions were deleted and the results essentially reinstated the findings of Boles (1983a). It is concluded that right-hemisphere imagery processes can participate in word recognition under intentional memory instructions. Within the dual coding theory (Paivio, 1971), the results argue that both discrete and continuous processing modes are available, that the modes can be used strategically, and that continuous processing can occur prior to response stages.

The effects of exposure to dynamic expressions of affect on 5-month-olds' memory.

PubMed

Flom, Ross; Janis, Rebecca B; Garcia, Darren J; Kirwan, C Brock

2014-11-01

The purpose of this study was to examine the behavioral effects of adults' communicated affect on 5-month-olds' visual recognition memory. Five-month-olds were exposed to a dynamic and bimodal happy, angry, or neutral affective (face-voice) expression while familiarized to a novel geometric image. After familiarization to the geometric image and exposure to the affective expression, 5-month-olds received either a 5-min or 1-day retention interval. Following the 5-min retention interval, infants exposed to the happy affective expressions showed a reliable preference for a novel geometric image compared to the recently familiarized image. Infants exposed to the neutral or angry affective expression failed to show a reliable preference following a 5-min delay. Following the 1-day retention interval, however, infants exposed to the neutral expression showed a reliable preference for the novel geometric image. These results are the first to demonstrate that 5-month-olds' visual recognition memory is affected by the presentation of affective information at the time of encoding. Copyright © 2014 Elsevier Inc. All rights reserved.

Acute stress negatively affects object recognition early memory consolidation and memory retrieval unrelated to state-dependency.

PubMed

Nelissen, Ellis; Prickaerts, Jos; Blokland, Arjan

2018-06-01

It is well known that stress affects memory performance. However, there still appears to be inconstancy in literature about how acute stress affects the different stages of memory: acquisition, consolidation and retrieval. In this study, we exposed rats to acute stress and measured the effect on memory performance in the object recognition task as a measure for episodic memory. Stress was induced 30 min prior to the learning phase to affect acquisition, directly after the learning phase to affect consolidation, or 30 min before the retrieval phase to affect retrieval. Additionally, we induced stress both 30 min prior to the learning phase and 30 min prior to the retrieval phase to test whether the effects were related to state-dependency. As expected, we found that acute stress did not affect acquisition but had a negative impact on retrieval. To our knowledge, we are the first to show that early consolidation was negatively affected by acute stress. We also show that stress does not have a state-dependent effect on memory. Copyright © 2018 Elsevier B.V. All rights reserved.

Speech recognition technology: an outlook for human-to-machine interaction.

PubMed

Erdel, T; Crooks, S

2000-01-01

Speech recognition, as an enabling technology in healthcare-systems computing, is a topic that has been discussed for quite some time, but is just now coming to fruition. Traditionally, speech-recognition software has been constrained by hardware, but improved processors and increased memory capacities are starting to remove some of these limitations. With these barriers removed, companies that create software for the healthcare setting have the opportunity to write more successful applications. Among the criticisms of speech-recognition applications are the high rates of error and steep training curves. However, even in the face of such negative perceptions, there remains significant opportunities for speech recognition to allow healthcare providers and, more specifically, physicians, to work more efficiently and ultimately spend more time with their patients and less time completing necessary documentation. This article will identify opportunities for inclusion of speech-recognition technology in the healthcare setting and examine major categories of speech-recognition software--continuous speech recognition, command and control, and text-to-speech. We will discuss the advantages and disadvantages of each area, the limitations of the software today, and how future trends might affect them.

Affective responsiveness is influenced by intake of oral contraceptives.

PubMed

Radke, Sina; Derntl, Birgit

2016-06-01

Despite the widespread use of oral contraceptive pills (OCs), little is known about their impact on psychological processes and emotional competencies. Recent data indicate impaired emotion recognition in OC users compared to naturally cycling females. Building upon these findings, the current study investigated the influence of OC use on three components of empathy, i.e., emotion recognition, perspective-taking, and affective responsiveness. We compared naturally cycling women to two groups of OC users, one being tested in their pill-free week and one in the phase of active intake. Whereas groups did not differ in emotion recognition and perspective-taking, an effect of pill phase was evident for affective responsiveness: Females currently taking the pill showed better performance than those in their pill-free week. These processing advantages complement previous findings on menstrual cycle effects and thereby suggest an association with changes in endogenous and exogenous reproductive hormones. The current study highlights the need for future research to shed more light on the neuroendocrine alterations accompanying OC intake. Copyright © 2016 Elsevier B.V. and ECNP. All rights reserved.

Age Deficits in Facial Affect Recognition: The Influence of Dynamic Cues.

PubMed

Grainger, Sarah A; Henry, Julie D; Phillips, Louise H; Vanman, Eric J; Allen, Roy

2017-07-01

Older adults have difficulties in identifying most facial expressions of emotion. However, most aging studies have presented static photographs of intense expressions, whereas in everyday experience people see emotions that develop and change. The present study was designed to assess whether age-related difficulties with emotion recognition are reduced when more ecologically valid (i.e., dynamic) stimuli are used. We examined the effect of stimuli format (i.e., static vs. dynamic) on facial affect recognition in two separate studies that included independent samples and distinct stimuli sets. In addition to younger and older participants, a middle-aged group was included in Study 1 and eye gaze patterns were assessed in Study 2. Across both studies, older adults performed worse than younger adults on measures of facial affect recognition. In Study 1, older and-middle aged adults benefited from dynamic stimuli, but only when the emotional displays were subtle. Younger adults gazed more at the eye region of the face relative to older adults (Study 2), but dynamic presentation increased attention towards the eye region for younger adults only. Together, these studies provide important and novel insights into the specific circumstances in which older adults may be expected to experience difficulties in perceiving facial emotions. © The Author 2015. Published by Oxford University Press on behalf of The Gerontological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Learned Non-Rigid Object Motion is a View-Invariant Cue to Recognizing Novel Objects

PubMed Central

Chuang, Lewis L.; Vuong, Quoc C.; Bülthoff, Heinrich H.

2012-01-01

There is evidence that observers use learned object motion to recognize objects. For instance, studies have shown that reversing the learned direction in which a rigid object rotated in depth impaired recognition accuracy. This motion reversal can be achieved by playing animation sequences of moving objects in reverse frame order. In the current study, we used this sequence-reversal manipulation to investigate whether observers encode the motion of dynamic objects in visual memory, and whether such dynamic representations are encoded in a way that is dependent on the viewing conditions. Participants first learned dynamic novel objects, presented as animation sequences. Following learning, they were then tested on their ability to recognize these learned objects when their animation sequence was shown in the same sequence order as during learning or in the reverse sequence order. In Experiment 1, we found that non-rigid motion contributed to recognition performance; that is, sequence-reversal decreased sensitivity across different tasks. In subsequent experiments, we tested the recognition of non-rigidly deforming (Experiment 2) and rigidly rotating (Experiment 3) objects across novel viewpoints. Recognition performance was affected by viewpoint changes for both experiments. Learned non-rigid motion continued to contribute to recognition performance and this benefit was the same across all viewpoint changes. By comparison, learned rigid motion did not contribute to recognition performance. These results suggest that non-rigid motion provides a source of information for recognizing dynamic objects, which is not affected by changes to viewpoint. PMID:22661939

Emotion and language: Valence and arousal affect word recognition

PubMed Central

Brysbaert, Marc; Warriner, Amy Beth

2014-01-01

Emotion influences most aspects of cognition and behavior, but emotional factors are conspicuously absent from current models of word recognition. The influence of emotion on word recognition has mostly been reported in prior studies on the automatic vigilance for negative stimuli, but the precise nature of this relationship is unclear. Various models of automatic vigilance have claimed that the effect of valence on response times is categorical, an inverted-U, or interactive with arousal. The present study used a sample of 12,658 words, and included many lexical and semantic control factors, to determine the precise nature of the effects of arousal and valence on word recognition. Converging empirical patterns observed in word-level and trial-level data from lexical decision and naming indicate that valence and arousal exert independent monotonic effects: Negative words are recognized more slowly than positive words, and arousing words are recognized more slowly than calming words. Valence explained about 2% of the variance in word recognition latencies, whereas the effect of arousal was smaller. Valence and arousal do not interact, but both interact with word frequency, such that valence and arousal exert larger effects among low-frequency words than among high-frequency words. These results necessitate a new model of affective word processing whereby the degree of negativity monotonically and independently predicts the speed of responding. This research also demonstrates that incorporating emotional factors, especially valence, improves the performance of models of word recognition. PMID:24490848

Gender-specific automatic valence recognition of affective olfactory stimulation through the analysis of the electrodermal activity.

PubMed

Greco, Alberto; Lanata, Antonio; Valenza, Gaetano; Di Francesco, Fabio; Scilingo, Enzo Pasquale

2016-08-01

This study reports on the development of a gender-specific classification system able to discern between two valence levels of smell, through information gathered from electrodermal activity (EDA) dynamics. Specifically, two odorants were administered to 32 healthy volunteers (16 males) while monitoring EDA. CvxEDA model was used to process the EDA signal and extract features from both tonic and phasic components. The feature set was used as input to a K-NN classifier implementing a leave-one-subject-out procedure. Results show strong differences in the accuracy of valence recognition between men (62.5%) and women (78%). We can conclude that affective olfactory stimulation significantly affect EDA dynamics with a highly specific gender dependency.

Results from the Crop Identification Technology Assessment for Remote Sensing (CITARS) project

NASA Technical Reports Server (NTRS)

Bauer, M. E. (Principal Investigator); Davis, B. J.; Bizzell, R. M.; Hall, F. G.; Feiveson, A. H.; Malila, W. A.; Rice, D. P.

1976-01-01

The author has identified the following significant results. It was found that several factors had a significant effect on crop identification performance: (1) crop maturity and site characteristics, (2) which of several different single date automatic data processing procedures was used for local recognition, (3) nonlocal recognition, both with and without preprocessing for the extension of recognition signatures, and (4) use of multidate data. It also was found that classification accuracy for field center pixels was not a reliable indicator of proportion estimation performance for whole areas, that bias was present in proportion estimates, and that training data and procedures strongly influenced crop identification performance.

RNA editing site recognition in heterologous plant mitochondria.

PubMed

Choury, David; Araya, Alejandro

2006-12-01

RNA editing is a process that modifies the information content of mitochondrial messenger RNAs in flowering plants changing specific cytosine residues into uridine. To gain insight into editing site recognition, we used electroporation to introduce engineered wheat (Triticum aestivum) or potato (Solanum tuberosum) mitochondrial cox2 genes, and an atp9-containing chimeric gene, into non-cognate mitochondria, and observed the efficiency of editing in these contexts. Both wheat and potato mitochondria were able to express "foreign" constructs, and their products were properly spliced. Seventeen and twelve editing sites are present in the coding regions of wheat and potato cox2 transcripts, respectively. Eight are common to both plants, whereas nine are specific to wheat, and four to potato. An analogous situation is found for the atp9 mRNA coding regions from these species. We found that both mitochondria were able to recognize sites that are already present as T at the genomic level, making RNA editing unnecessary for that specific residue in the cognate organelle. Our results demonstrate that non-cognate mitochondria are able to edit residues that are not edited in their own transcripts, and support the hypothesis that the same trans-acting factor may recognize several editing sites.

Probing Conformational Changes and Interfacial Recognition Site of Lipases With Surfactants and Inhibitors.

PubMed

Mateos-Diaz, E; Amara, S; Roussel, A; Longhi, S; Cambillau, C; Carrière, F

2017-01-01

Structural studies on lipases by X-ray crystallography have revealed conformational changes occurring in the presence of surfactants/inhibitors and the pivotal role played by a molecular "lid" of variable size and structure depending on the enzyme. Besides controlling the access to the enzyme active site, the lid is involved in lipase activation, formation of the interfacial recognition site (IRS), and substrate docking within the active site. The combined use of surfactants and inhibitors has been critical for a better understanding of lipase structure-function relationships. An overview of crystal structures of lipases in complex with surfactants and inhibitors reveals common structural features and shows how surfactants monomers interact with the lid in its open conformation. The location of surfactants, inhibitors, and hydrophobic residues exposed upon lid opening provides insights into the IRS of lipases. The mechanism by which surfactants promote the lid opening can be further investigated in solution by site-directed spin labeling of lipase coupled to electron paramagnetic resonance spectroscopy. These experimental approaches are illustrated here by results obtained with mammalian digestive lipases, fungal lipases, and cutinases. © 2017 Elsevier Inc. All rights reserved.

Dopamine D1 receptor stimulation modulates the formation and retrieval of novel object recognition memory: Role of the prelimbic cortex

PubMed Central

Pezze, Marie A.; Marshall, Hayley J.; Fone, Kevin C.F.; Cassaday, Helen J.

2015-01-01

Previous studies have shown that dopamine D1 receptor antagonists impair novel object recognition memory but the effects of dopamine D1 receptor stimulation remain to be determined. This study investigated the effects of the selective dopamine D1 receptor agonist SKF81297 on acquisition and retrieval in the novel object recognition task in male Wistar rats. SKF81297 (0.4 and 0.8 mg/kg s.c.) given 15 min before the sampling phase impaired novel object recognition evaluated 10 min or 24 h later. The same treatments also reduced novel object recognition memory tested 24 h after the sampling phase and when given 15 min before the choice session. These data indicate that D1 receptor stimulation modulates both the encoding and retrieval of object recognition memory. Microinfusion of SKF81297 (0.025 or 0.05 μg/side) into the prelimbic sub-region of the medial prefrontal cortex (mPFC) in this case 10 min before the sampling phase also impaired novel object recognition memory, suggesting that the mPFC is one important site mediating the effects of D1 receptor stimulation on visual recognition memory. PMID:26277743

The Formation and Stability of DC-SIGN Microdomains Require its Extracellular Moiety

PubMed Central

Liu, Ping; Wang, Xiang; Itano, Michelle S.; Neumann, Aaron K.; Jacobson, Ken; Thompson, Nancy L.

2012-01-01

DC-SIGN (Dendritic cell-specific ICAM-3-grabbing non-integrin) is a Ca2+-dependent transmembrane lectin that binds a large variety of pathogens and facilitates their uptake for subsequent antigen presentation. This receptor is present in cell surface microdomains, but factors involved in microdomain formation and their exceptional stability are not clear. To determine which domain/motif of DC-SIGN facilitates its presence in microdomains, we studied mutations at key locations including truncation of the cytoplasmic tail, and ectodomain mutations that resulted in removal of the N-linked glycosylation site, the tandem repeats and the carbohydrate recognition domain (CRD) as well as modification of the calcium sites in the CRD required for carbohydrate binding. Confocal imaging and FRAP measurements showed that the cytoplasmic domain and N-linked glycosylation site do not affect the ability of DC-SIGN to form stable microdomains. However, truncation of the CRD results in complete loss of visible microdomains and subsequent lateral diffusion of the mutants. Apart from cell adhesions, membrane domains are thought to be localized primarily via the cytoskeleton. By contrast, we propose that interactions between the CRD of DC-SIGN and the extracellular matrix and/or cis interactions with transmembrane scaffolding protein(s) play an essential role in organizing these microdomains. PMID:22292921

Inhibition of HMGA2 binding to DNA by netropsin

PubMed Central

Miao, Yi; Cui, Tengjiao; Leng, Fenfei; Wilson, W. David

2008-01-01

The design of small synthetic molecules that can be used to affect gene expression is an area of active interest for development of agents in therapeutic and biotechnology applications. Many compounds that target the minor groove in AT sequences in DNA are well characterized and are promising reagents for use as modulators of protein-DNA complexes. The mammalian high mobility group transcriptional factor, HMGA2, also targets the DNA minor groove and plays critical roles in disease processes from cancer to obesity. Biosensor-surface plasmon resonance methods were used to monitor HMGA2 binding to target sites on immobilized DNA and a competition assay for inhibition of the HMGA2-DNA complex was designed. HMGA2 binds strongly to the DNA through AT hook domains with KD values of 20 - 30 nM depending on the DNA sequence. The well-characterized minor groove binder, netropsin, was used to develop and test the assay. The compound has two binding sites in the protein-DNA interaction sequence and this provides an advantage for inhibition. An equation for analysis of results when the inhibitor has two binding sites in the biopolymer recognition surface is presented with the results. The assay provides a platform for discovery of HMGA2 inhibitors. PMID:18023407

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.

Structural and functional consequences of antigenic modulation of red blood cells with methoxypoly(ethylene glycol).

PubMed

Murad, K L; Mahany, K L; Brugnara, C; Kuypers, F A; Eaton, J W; Scott, M D

1999-03-15

We previously showed that the covalent modification of the red blood cell (RBC) surface with methoxypoly(ethylene glycol) [mPEG; MW approximately 5 kD] could significantly attenuate the immunologic recognition of surface antigens. However, to make these antigenically silent RBC a clinically viable option, the mPEG-modified RBC must maintain normal cellular structure and functions. To this end, mPEG-derivatization was found to have no significant detrimental effects on RBC structure or function at concentrations that effectively blocked antigenic recognition of a variety of RBC antigens. Importantly, RBC lysis, morphology, and hemoglobin oxidation state were unaffected by mPEG-modification. Furthermore, as shown by functional studies of Band 3, a major site of modification, PEG-binding does not affect protein function, as evidenced by normal SO4- flux. Similarly, Na+ and K+ homeostasis were unaffected. The functional aspects of the mPEG-modified RBC were also maintained, as evidenced by normal oxygen binding and cellular deformability. Perhaps most importantly, mPEG-derivatized mouse RBC showed normal in vivo survival ( approximately 50 days) with no sensitization after repeated transfusions. These data further support the hypothesis that the covalent attachment of nonimmunogenic materials (eg, mPEG) to intact RBC may have significant application in transfusion medicine, especially for the chronically transfused and/or allosensitized patient.

"Multiple partial recognitions in dynamic equilibrium" in the binding sites of proteins form the molecular basis of promiscuous recognition of structurally diverse ligands.

PubMed

Kohda, Daisuke

2018-04-01

Promiscuous recognition of ligands by proteins is as important as strict recognition in numerous biological processes. In living cells, many short, linear amino acid motifs function as targeting signals in proteins to specify the final destination of the protein transport. In general, the target signal is defined by a consensus sequence containing wild-characters, and hence represented by diverse amino acid sequences. The classical lock-and-key or induced-fit/conformational selection mechanism may not cover all aspects of the promiscuous recognition. On the basis of our crystallographic and NMR studies on the mitochondrial Tom20 protein-presequence interaction, we proposed a new hypothetical mechanism based on "a rapid equilibrium of multiple states with partial recognitions". This dynamic, multiple recognition mode enables the Tom20 receptor to recognize diverse mitochondrial presequences with nearly equal affinities. The plant Tom20 is evolutionally unrelated to the animal Tom20 in our study, but is a functional homolog of the animal/fungal Tom20. NMR studies by another research group revealed that the presequence binding by the plant Tom20 was not fully explained by simple interaction modes, suggesting the presence of a similar dynamic, multiple recognition mode. Circumstantial evidence also suggested that similar dynamic mechanisms may be applicable to other promiscuous recognitions of signal peptides by the SRP54/Ffh and SecA proteins.

Introduction to pseudobulbar affect: setting the stage for recognition and familiarity with this challenging disorder.

PubMed

Demler, Tammie Lee

2017-12-01

Pseudobulbar affect (PBA), despite its prevalence and distinctive symptoms, is widely underrecognized and undertreated. It is characterized by uncontrollable laughing or crying that can occur in an exaggerated manner or inappropriately to a given situation or stimuli. PBA is thought to center around preexisting neurological conditions, which include Parkinson disease, multiple sclerosis, amyotrophic lateral sclerosis, Alzheimer disease, traumatic brain injury, and stroke. The PBA Registry Series trial was created to measure the prevalence of PBA among patients with these underlying neurological conditions. Through greater awareness, recognition, and diagnosis, treatment for patients with PBA can be improved.

Surface imprinted beads for the recognition of human serum albumin.

PubMed

Bonini, Francesca; Piletsky, Sergey; Turner, Anthony P F; Speghini, Adolfo; Bossi, Alessandra

2007-04-15

The synthesis of poly-aminophenylboronic acid (ABPA) imprinted beads for the recognition of the protein human serum albumin (HSA) is reported. In order to create homogeneous recognition sites, covalent immobilisation of the template HSA was exploited. The resulting imprinted beads were selective for HSA. The indirect imprinting factor (IF) calculated from supernatant was 1.6 and the direct IF, evaluated from the protein recovered from the beads, was 1.9. The binding capacity was 1.4 mg/g, which is comparable to commercially available affinity materials. The specificity of the HSA recognition was evaluated with competitive experiments, indicating a molar ratio 4.5/1 of competitor was necessary to displace half of the bound HSA. The recognition and binding of the imprinted beads was also tested with a complex sample, human serum and targeted removal of HSA without a loss of the other protein components was demonstrated. The easy preparation protocol of derivatised beads and a good protein recognition properties make the approach an attractive solution to analytical and bio-analytical problems in the field of biotechnology.

Small Molecule Interactome Mapping by Photoaffinity Labeling Reveals Binding Site Hotspots for the NSAIDs.

PubMed

Gao, Jinxu; Mfuh, Adelphe; Amako, Yuka; Woo, Christina M

2018-03-28

Many therapeutics elicit cell-type specific polypharmacology that is executed by a network of molecular recognition events between a small molecule and the whole proteome. However, measurement of the structures that underpin the molecular associations between the proteome and even common therapeutics, such as the nonsteroidal anti-inflammatory drugs (NSAIDs), is limited by the inability to map the small molecule interactome. To address this gap, we developed a platform termed small molecule interactome mapping by photoaffinity labeling (SIM-PAL) and applied it to the in cellulo direct characterization of specific NSAID binding sites. SIM-PAL uses (1) photochemical conjugation of NSAID derivatives in the whole proteome and (2) enrichment and isotope-recoding of the conjugated peptides for (3) targeted mass spectrometry-based assignment. Using SIM-PAL, we identified the NSAID interactome consisting of over 1000 significantly enriched proteins and directly characterized nearly 200 conjugated peptides representing direct binding sites of the photo-NSAIDs with proteins from Jurkat and K562 cells. The enriched proteins were often identified as parts of complexes, including known targets of NSAID activity (e.g., NF-κB) and novel interactions (e.g., AP-2, proteasome). The conjugated peptides revealed direct NSAID binding sites from the cell surface to the nucleus and a specific binding site hotspot for the three photo-NSAIDs on histones H2A and H2B. NSAID binding stabilized COX-2 and histone H2A by cellular thermal shift assay. Since small molecule stabilization of protein complexes is a gain of function regulatory mechanism, it is conceivable that NSAIDs affect biological processes through these broader proteomic interactions. SIM-PAL enabled characterization of NSAID binding site hotspots and is amenable to map global binding sites for virtually any molecule of interest.

Tree Hazards Recognition and Reduction in Recreation Sites

Treesearch

David W. Johnson

1981-01-01

Defective trees are potential hazards to people and property in recreation areas. Most reported tree failures within recreation sites in the Rocky Mountain Region occur in lodgepole pine. Defective root systems account for the greatest percentage of failures. External indicators of defects are used to identify trees that may fail. Some tree species, particularly aspen...

Height Growth of Mahogany Seedlings

Treesearch

C. B. Briscoe; R. W. Nobles

1962-01-01

Since the recognition of natural hybridization of small-leaf (West Indies) mahogany (Swietenia mahagoni Jacq.) with bigleaf (Honduras) mahogany (S. macrophylla King) there has been conjecture about their relative growth rates. One would expect small-leaf to be the fastest growing on dry sites, the hybrids to be fastest on intermediate sites, and bigleaf to excel on wet...

The Readability of Information Literacy Content on Academic Library Web Sites

ERIC Educational Resources Information Center

Lim, Adriene

2010-01-01

This article reports on a study addressing the readability of content on academic libraries' Web sites, specifically content intended to improve users' information literacy skills. Results call for recognition of readability as an evaluative component of text in order to better meet the needs of diverse user populations. (Contains 8 tables.)

Recognition of AT-Rich DNA Binding Sites by the MogR Repressor

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

Shen, Aimee; Higgins, Darren E.; Panne, Daniel

2009-07-22

The MogR transcriptional repressor of the intracellular pathogen Listeria monocytogenes recognizes AT-rich binding sites in promoters of flagellar genes to downregulate flagellar gene expression during infection. We describe here the 1.8 A resolution crystal structure of MogR bound to the recognition sequence 5' ATTTTTTAAAAAAAT 3' present within the flaA promoter region. Our structure shows that MogR binds as a dimer. Each half-site is recognized in the major groove by a helix-turn-helix motif and in the minor groove by a loop from the symmetry-related molecule, resulting in a 'crossover' binding mode. This oversampling through minor groove interactions is important for specificity.more » The MogR binding site has structural features of A-tract DNA and is bent by approximately 52 degrees away from the dimer. The structure explains how MogR achieves binding specificity in the AT-rich genome of L. monocytogenes and explains the evolutionary conservation of A-tract sequence elements within promoter regions of MogR-regulated flagellar genes.« less

Radioligand Recognition of Insecticide Targets.

PubMed

Casida, John E

2018-04-04

Insecticide radioligands allow the direct recognition and analysis of the targets and mechanisms of toxic action critical to effective and safe pest control. These radioligands are either the insecticides themselves or analogs that bind at the same or coupled sites. Preferred radioligands and their targets, often in both insects and mammals, are trioxabicyclooctanes for the γ-aminobutyric acid (GABA) receptor, avermectin for the glutamate receptor, imidacloprid for the nicotinic receptor, ryanodine and chlorantraniliprole for the ryanodine receptor, and rotenone or pyridaben for NADH + ubiquinone oxidoreductase. Pyrethroids and other Na + channel modulator insecticides are generally poor radioligands due to lipophilicity and high nonspecific binding. For target site validation, the structure-activity relationships competing with the radioligand in the binding assays should be the same as that for insecticidal activity or toxicity except for rapidly detoxified or proinsecticide analogs. Once the radioligand assay is validated for relevance, it will often help define target site modifications on selection of resistant pest strains, selectivity between insects and mammals, and interaction with antidotes and other chemicals at modulator sites. Binding assays also serve for receptor isolation and photoaffinity labeling to characterize the interactions involved.

Alteration of gene expression by restriction enzymes electroporated into plant cells.

PubMed

Ashraf, M; Altschuler, M; Galasinski, S; Griffiths, T D

1993-06-01

The alteration in the expression of a beta-glucuronidase (GUS) reporter gene was used to monitor the effect of restriction endonucleases electroporated into the tobacco (Nicotiana tabacum L.) protoplasts. Restriction enzyme (RE) Hind III which does not have a recognition site within the gene cassette, had little effect on enzyme activity. In contrast restriction endonucleases Hae III and Sau3A1 which possess 8 and 16 recognition sites in the GUS cassette, were found to reduce the enzyme activity by 89% and 94% respectively when compared to control electroporations. Restriction-site mutation analysis (RSM) and Southern blot analysis indicated the enzymatic degradation of GUS coding sequence by the REs Hae III and Sau3A1. Results of this study suggest that on electroporation, REs can enter into plant cells and alter the expression of the GUS gene. The alteration of gene expression is thus correlated with the digestion of GUS template DNA. Future applications of this technique could include addressing fundamental questions with regard to DNA repair, site-specific recombination, identifying mutations, insertional mutagenesis, enhancement of stable transformation and gene tagging in plants.

Crystal structures of botulinum neurotoxin DC in complex with its protein receptors synaptotagmin I and II.

PubMed

Berntsson, Ronnie Per-Arne; Peng, Lisheng; Svensson, Linda Marie; Dong, Min; Stenmark, Pål

2013-09-03

Botulinum neurotoxins (BoNTs) can cause paralysis at exceptionally low concentrations and include seven serotypes (BoNT/A-G). The chimeric BoNT/DC toxin has a receptor binding domain similar to the same region in BoNT/C. However, BoNT/DC does not share protein receptor with BoNT/C. Instead, it shares synaptotagmin (Syt) I and II as receptors with BoNT/B, despite their low sequence similarity. Here, we present the crystal structures of the binding domain of BoNT/DC in complex with the recognition domains of its protein receptors, Syt-I and Syt-II. The structures reveal that BoNT/DC possesses a Syt binding site, distinct from the established Syt-II binding site in BoNT/B. Structure-based mutagenesis further shows that hydrophobic interactions play a key role in Syt binding. The structures suggest that the BoNT/DC ganglioside binding sites are independent of the protein receptor binding site. Our results reveal the remarkable versatility in the receptor recognition of the BoNTs. Copyright © 2013 Elsevier Ltd. All rights reserved.

Can color changes alter the neural correlates of recognition memory? Manipulation of processing affects an electrophysiological indicator of conceptual implicit memory.

PubMed

Cui, Xiaoyu; Gao, Chuanji; Zhou, Jianshe; Guo, Chunyan

2016-09-28

It has been widely shown that recognition memory includes two distinct retrieval processes: familiarity and recollection. Many studies have shown that recognition memory can be facilitated when there is a perceptual match between the studied and the tested items. Most event-related potential studies have explored the perceptual match effect on familiarity on the basis of the hypothesis that the specific event-related potential component associated with familiarity is the FN400 (300-500 ms mid-frontal effect). However, it is currently unclear whether the FN400 indexes familiarity or conceptual implicit memory. In addition, on the basis of the findings of a previous study, the so-called perceptual manipulations in previous studies may also involve some conceptual alterations. Therefore, we sought to determine the influence of perceptual manipulation by color changes on recognition memory when the perceptual or the conceptual processes were emphasized. Specifically, different instructions (perceptually or conceptually oriented) were provided to the participants. The results showed that color changes may significantly affect overall recognition memory behaviorally and that congruent items were recognized with a higher accuracy rate than incongruent items in both tasks, but no corresponding neural changes were found. Despite the evident familiarity shown in the two tasks (the behavioral performance of recognition memory was much higher than at the chance level), the FN400 effect was found in conceptually oriented tasks, but not perceptually oriented tasks. It is thus highly interesting that the FN400 effect was not induced, although color manipulation of recognition memory was behaviorally shown, as seen in previous studies. Our findings of the FN400 effect for the conceptual but not perceptual condition support the explanation that the FN400 effect indexes conceptual implicit memory.

Emotional face recognition deficits and medication effects in pre-manifest through stage-II Huntington's disease.

PubMed

Labuschagne, Izelle; Jones, Rebecca; Callaghan, Jenny; Whitehead, Daisy; Dumas, Eve M; Say, Miranda J; Hart, Ellen P; Justo, Damian; Coleman, Allison; Dar Santos, Rachelle C; Frost, Chris; Craufurd, David; Tabrizi, Sarah J; Stout, Julie C

2013-05-15

Facial emotion recognition impairments have been reported in Huntington's disease (HD). However, the nature of the impairments across the spectrum of HD remains unclear. We report on emotion recognition data from 344 participants comprising premanifest HD (PreHD) and early HD patients, and controls. In a test of recognition of facial emotions, we examined responses to six basic emotional expressions and neutral expressions. In addition, and within the early HD sample, we tested for differences on emotion recognition performance between those 'on' vs. 'off' neuroleptic or selective serotonin reuptake inhibitor (SSRI) medications. The PreHD groups showed significant (p<0.05) impaired recognition, compared to controls, on fearful, angry and surprised faces; whereas the early HD groups were significantly impaired across all emotions including neutral expressions. In early HD, neuroleptic use was associated with worse facial emotion recognition, whereas SSRI use was associated with better facial emotion recognition. The findings suggest that emotion recognition impairments exist across the HD spectrum, but are relatively more widespread in manifest HD than in the premanifest period. Commonly prescribed medications to treat HD-related symptoms also appear to affect emotion recognition. These findings have important implications for interpersonal communication and medication usage in HD. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Speech-perception training for older adults with hearing loss impacts word recognition and effort.

PubMed

Kuchinsky, Stefanie E; Ahlstrom, Jayne B; Cute, Stephanie L; Humes, Larry E; Dubno, Judy R; Eckert, Mark A

2014-10-01

The current pupillometry study examined the impact of speech-perception training on word recognition and cognitive effort in older adults with hearing loss. Trainees identified more words at the follow-up than at the baseline session. Training also resulted in an overall larger and faster peaking pupillary response, even when controlling for performance and reaction time. Perceptual and cognitive capacities affected the peak amplitude of the pupil response across participants but did not diminish the impact of training on the other pupil metrics. Thus, we demonstrated that pupillometry can be used to characterize training-related and individual differences in effort during a challenging listening task. Importantly, the results indicate that speech-perception training not only affects overall word recognition, but also a physiological metric of cognitive effort, which has the potential to be a biomarker of hearing loss intervention outcome. Copyright © 2014 Society for Psychophysiological Research.

Fine epitope signature of antibody neutralization breadth at the HIV-1 envelope CD4-binding site.

PubMed

Cheng, Hao D; Grimm, Sebastian K; Gilman, Morgan Sa; Gwom, Luc Christian; Sok, Devin; Sundling, Christopher; Donofrio, Gina; Hedestam, Gunilla B Karlsson; Bonsignori, Mattia; Haynes, Barton F; Lahey, Timothy P; Maro, Isaac; von Reyn, C Fordham; Gorny, Miroslaw K; Zolla-Pazner, Susan; Walker, Bruce D; Alter, Galit; Burton, Dennis R; Robb, Merlin L; Krebs, Shelly J; Seaman, Michael S; Bailey-Kellogg, Chris; Ackerman, Margaret E

2018-03-08

Major advances in donor identification, antigen probe design, and experimental methods to clone pathogen-specific antibodies have led to an exponential growth in the number of newly characterized broadly neutralizing antibodies (bnAbs) that recognize the HIV-1 envelope glycoprotein. Characterization of these bnAbs has defined new epitopes and novel modes of recognition that can result in potent neutralization of HIV-1. However, the translation of envelope recognition profiles in biophysical assays into an understanding of in vivo activity has lagged behind, and identification of subjects and mAbs with potent antiviral activity has remained reliant on empirical evaluation of neutralization potency and breadth. To begin to address this discrepancy between recombinant protein recognition and virus neutralization, we studied the fine epitope specificity of a panel of CD4-binding site (CD4bs) antibodies to define the molecular recognition features of functionally potent humoral responses targeting the HIV-1 envelope site bound by CD4. Whereas previous studies have used neutralization data and machine-learning methods to provide epitope maps, here, this approach was reversed, demonstrating that simple binding assays of fine epitope specificity can prospectively identify broadly neutralizing CD4bs-specific mAbs. Building on this result, we show that epitope mapping and prediction of neutralization breadth can also be accomplished in the assessment of polyclonal serum responses. Thus, this study identifies a set of CD4bs bnAb signature amino acid residues and demonstrates that sensitivity to mutations at signature positions is sufficient to predict neutralization breadth of polyclonal sera with a high degree of accuracy across cohorts and across clades.

Heterospecific eavesdropping in ant-following birds of the Neotropics is a learned behaviour.

PubMed

Pollock, Henry S; Martínez, Ari E; Kelley, J Patrick; Touchton, Janeene M; Tarwater, Corey E

2017-10-25

Animals eavesdrop on other species to obtain information about their environments. Heterospecific eavesdropping can yield tangible fitness benefits by providing valuable information about food resources and predator presence. The ability to eavesdrop may therefore be under strong selection, although extensive research on alarm-calling in avian mixed-species flocks has found only limited evidence that close association with another species could select for innate signal recognition. Nevertheless, very little is known about the evolution of eavesdropping behaviour and the mechanism of heterospecific signal recognition, particularly in other ecological contexts, such as foraging. To understand whether heterospecific eavesdropping was an innate or learned behaviour in a foraging context, we studied heterospecific signal recognition in ant-following birds of the Neotropics, which eavesdrop on vocalizations of obligate ant-following species to locate and recruit to swarms of the army ant Eciton burchellii , a profitable food resource. We used a playback experiment to compare recruitment of ant-following birds to vocalizations of two obligate species at a mainland site (where both species are present) and a nearby island site (where one species remains whereas the other went extinct approx. 40 years ago). We found that ant-following birds recruited strongly to playbacks of the obligate species present at both island and mainland sites, but the island birds did not recruit to playbacks of the absent obligate species. Our results strongly suggest that (i) ant-following birds learn to recognize heterospecific vocalizations from ecological experience and (ii) island birds no longer recognize the locally extinct obligate species after eight generations of absence from the island. Although learning appears to be the mechanism of heterospecific signal recognition in ant-following birds, more experimental tests are needed to fully understand the evolution of eavesdropping behaviour. © 2017 The Author(s).

Proactive Interference Slows Recognition by Eliminating Fast Assessments of Familiarity

ERIC Educational Resources Information Center

Oztekin, Ilke; McElree, Brian

2007-01-01

The response-signal speed-accuracy tradeoff (SAT) procedure was used to investigate how proactive interference (PI) affects retrieval from working memory. Participants were presented with 6-item study lists, followed immediately by a recognition probe. A variant of a release from PI design was used: All items in a list were from the same semantic…

Within-Category VOT Affects Recovery from "Lexical" Garden-Paths: Evidence against Phoneme-Level Inhibition

ERIC Educational Resources Information Center

McMurray, Bob; Tanenhaus, Michael K.; Aslin, Richard N.

2009-01-01

Spoken word recognition shows gradient sensitivity to within-category voice onset time (VOT), as predicted by several current models of spoken word recognition, including TRACE (McClelland, J., & Elman, J. (1986). The TRACE model of speech perception. "Cognitive Psychology," 18, 1-86). It remains unclear, however, whether this sensitivity is…

How Do Professional Mutual Recognition Agreements Affect Higher Education? Examining Regional Policy in North America

ERIC Educational Resources Information Center

Sa, Creso; Gaviria, Patricia

2011-01-01

Professional mutual recognition agreements (MRAs) are one of the policy instruments employed in global and regional trade agreements to facilitate the mobility of skilled labour. While such agreements have been noted in the literature examining cross-border academic mobility, little is known about how they impact higher education. This paper…

Criterion Noise in Ratings-Based Recognition: Evidence from the Effects of Response Scale Length on Recognition Accuracy

ERIC Educational Resources Information Center

Benjamin, Aaron S.; Tullis, Jonathan G.; Lee, Ji Hae

2013-01-01

Rating scales are a standard measurement tool in psychological research. However, research has suggested that the cognitive burden involved in maintaining the criteria used to parcel subjective evidence into ratings introduces "decision noise" and affects estimates of performance in the underlying task. There has been debate over whether…

Testing the Recognition and Perception of Errors in Context

ERIC Educational Resources Information Center

Brandenburg, Laura C.

2015-01-01

This study tests the recognition of errors in context and whether the presence of errors affects the reader's perception of the writer's ethos. In an experimental, posttest only design, participants were randomly assigned a memo to read in an online survey: one version with errors and one version without. Of the six intentional errors in version…

Computer-Assisted Face Processing Instruction Improves Emotion Recognition, Mentalizing, and Social Skills in Students with ASD

ERIC Educational Resources Information Center

Rice, Linda Marie; Wall, Carla Anne; Fogel, Adam; Shic, Frederick

2015-01-01

This study examined the extent to which a computer-based social skills intervention called "FaceSay"™ was associated with improvements in affect recognition, mentalizing, and social skills of school-aged children with Autism Spectrum Disorder (ASD). "FaceSay"™ offers students simulated practice with eye gaze, joint attention,…

Facial Emotion Recognition in Children with High Functioning Autism and Children with Social Phobia

ERIC Educational Resources Information Center

Wong, Nina; Beidel, Deborah C.; Sarver, Dustin E.; Sims, Valerie

2012-01-01

Recognizing facial affect is essential for effective social functioning. This study examines emotion recognition abilities in children aged 7-13 years with High Functioning Autism (HFA = 19), Social Phobia (SP = 17), or typical development (TD = 21). Findings indicate that all children identified certain emotions more quickly (e.g., happy [less…

A Case Study of the Recognition of the Foundation Degree Qualification for Pharmacy Technicians

ERIC Educational Resources Information Center

Herrera, Helena; Brown, David; Portlock, Jane

2013-01-01

The Foundation Degree (FD) is a work-related, intermediate-level higher education qualification. Issues around its recognition can affect success in attracting students where the literature suggests that uptake should be adequate. This research represented a case study which explored for the first time, whether the above applied to the FD for…

Word Recognition is Affected by the Meaning of Orthographic Neighbours: Evidence from Semantic Decision Tasks

ERIC Educational Resources Information Center

Boot, Inge; Pecher, Diane

2008-01-01

Many models of word recognition predict that neighbours of target words will be activated during word processing. Cascaded models can make the additional prediction that semantic features of those neighbours get activated before the target has been uniquely identified. In two semantic decision tasks neighbours that were congruent (i.e., from the…

The Effects of Textual Enhancement Type on L2 Form Recognition and Reading Comprehension in Spanish

ERIC Educational Resources Information Center

LaBrozzi, Ryan M.

2016-01-01

Previous research investigating the effectiveness of textual enhancement as a tool to draw adult second language (L2) learners' attention to the targeted linguistic form has consistently produced mixed results. This article examines how L2 form recognition and reading comprehension are affected by different types of textual enhancement.…

Does Perceived Race Affect Discrimination and Recognition of Ambiguous-Race Faces? A Test of the Sociocognitive Hypothesis

ERIC Educational Resources Information Center

Rhodes, Gillian; Lie, Hanne C.; Ewing, Louise; Evangelista, Emma; Tanaka, James W.

2010-01-01

Discrimination and recognition are often poorer for other-race than own-race faces. These other-race effects (OREs) have traditionally been attributed to reduced perceptual expertise, resulting from more limited experience, with other-race faces. However, recent findings suggest that sociocognitive factors, such as reduced motivation to…

Orientation and Affective Expression Effects on Face Recognition in Williams Syndrome and Autism

ERIC Educational Resources Information Center

Rose, Fredric E.; Lincoln, Alan J.; Lai, Zona; Ene, Michaela; Searcy, Yvonne M.; Bellugi, Ursula

2007-01-01

We sought to clarify the nature of the face processing strength commonly observed in individuals with Williams syndrome (WS) by comparing the face recognition ability of persons with WS to that of persons with autism and to healthy controls under three conditions: Upright faces with neutral expressions, upright faces with varying affective…

RNA editing of microRNA prevents RNA-induced silencing complex recognition of target mRNA

PubMed Central

Cui, Yalei; Huang, Tianzhi; Zhang, Xiaobo

2015-01-01

MicroRNAs (miRNAs) integrate with Argonaut (Ago) to create the RNA-induced silencing complex, and regulate gene expression by silencing target mRNAs. RNA editing of miRNA may affect miRNA processing, assembly of the Ago complex and target mRNA binding. However, the function of edited miRNA, assembled within the Ago complex, has not been extensively investigated. In this study, sequence analysis of the Ago complex of Marsupenaeus japonicus shrimp infected with white spot syndrome virus (WSSV) revealed that host ADAR (adenosine deaminase acting on RNA) catalysed A-to-I RNA editing of a viral miRNA (WSSV-miR-N12) at the +16 site. This editing of the non-seed sequence did not affect association of the edited miRNA with the Ago protein, but inhibited interaction between the miRNA and its target gene (wsv399). The WSSV early gene wsv399 inhibited WSSV infection. As a result, the RNA editing of miRNA caused virus latency. Our results highlight a novel example of miRNA editing in the miRNA-induced silencing complex. PMID:26674414

Affect-Based Adaptation of an Applied Video Game for Educational Purposes

ERIC Educational Resources Information Center

Bontchev, Boyan; Vassileva, Dessislava

2017-01-01

Purpose: This paper aims to clarify how affect-based adaptation can improve implicit recognition of playing style of individuals during game sessions. This study presents the "Rush for Gold" game using dynamic difficulty adjustment of tasks based on both player performance and affectation inferred through electrodermal activity and…

[Post-academic dental specialties 18. The graduate programme in periodontology].

PubMed

van der Velden, U

2008-07-01

In 1987, the Dutch Society of Periodontology (NVvP) made it possible for dentists to be recognized as specialists in periodontology. This recognition lasts for 5 years after which, on the basis of an evaluation of the Consilium Parodontologicum of the NVvP, continuation of the recognition for another period of 5 years is possible. The Academic Centre for Dentistry at the University of Amsterdam and the University Medical Centre St Radboud at Nijmegen University provide a 3 year full time specialisation programme in periodontology. These programmes are approved by the European Federation of Periodontology. After successful completion of one of these programmes, recognition as periodontist by the Dutch Society of Periodontology can be requested. Possible recognition is based on an extensive evaluation during a one day site visit in the practice by the Consilium Parodontologicum.

Molecularly imprinted polymers for the recognition of proteins: the state of the art.

PubMed

Bossi, A; Bonini, F; Turner, A P F; Piletsky, S A

2007-01-15

Molecular imprinting has proved to be an effective technique for the creation of recognition sites on a polymer scaffold. Protein imprinting has been a focus for many chemists working in the area of molecular recognition, since the creation of synthetic polymers that can specifically recognise proteins is a very challenging but potentially extremely rewarding objective. It is expected that molecularly imprinted polymers (MIPs) with specificity for proteins will find application in medicine, diagnostics, proteomics, environmental analysis, sensors and drug delivery. In this review, the authors provide an overview of the progress achieved in the decade between 1994 and 2005, with respect to the challenging area of MIPs for protein recognition. The discussion furnishes a comparative analysis of different approaches developed, underlining their relative advantages and disadvantages and highlighting trends and possible future directions.

High-resolution topography and geomorphology of select archeological sites in Glen Canyon National Recreation Area, Arizona

USGS Publications Warehouse

Collins, Brian D.; Corbett, Skye C.; Sankey, Joel B.; Fairley, Helen C.

2014-01-01

Along the Colorado River corridor between Glen Canyon Dam and Lees Ferry, Arizona, located some 25 km downstream from the dam, archaeological sites dating from 8,000 years before present through the modern era are located within and on top of fluvial and alluvial terraces of the prehistorically undammed river. These terraces are known to have undergone significant erosion and retreat since emplacement of Glen Canyon Dam in 1963. Land managers and policy makers associated with managing the flow of the Colorado River are interested in understanding how the operations of Glen Canyon Dam have affected the archeological sites associated with these terraces and how dam-controlled flows currently interact with other landscape-shaping processes. In 2012, the U.S. Geological Survey initiated a research project in Glen Canyon to study the types and causes of erosion of the terraces. This report provides the first step towards this understanding by presenting comparative analyses on several types of high-resolution topographic data (airborne lidar, terrestrial lidar, and airborne photogrammetry) that can be used in the future to document and analyze changes to terrace-based archaeological sites. Herein, we present topographic and geomorphologic data of four archaeological sites within a 14 km segment of Glen Canyon using each of the three data sources. In addition to comparing each method’s suitability for adequately representing the topography of the sites, we also analyze the data within each site’s context and describe the geomorphological processes responsible for erosion. Our results show that each method has its own strengths and weaknesses, and that terrestrial and airborne lidar are essentially interchangeable for many important topographic characterization and monitoring purposes. However, whereas terrestrial lidar provides enhanced capacity for feature recognition and gully morphology delineation, airborne methods (whether by way of laser or optical sensors) are better suited for reach- and regional-scale mapping. Our site-specific geomorphic analyses of the four archeological sites indicate that their current topographical conditions are a result of different and sometimes competing erosional agents, including bedrock- and terrace-based overland flow, fluvial-induced terrace bank collapse, and alluvial-fan-generated debris flows. Although the influences of anthropogenic-induced erosion from dam operations are not specifically analyzed in this report, we do identify geomorphic settings where dam operations are either more or less likely to affect archeological site stability. This information can be used to assist with future monitoring efforts of these sites and identification of similar conditions for other archeological sites along the Colorado River corridor in Glen Canyon.

Aging and solid shape recognition: Vision and haptics.

PubMed

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

2015-10-01

The ability of 114 younger and older adults to recognize naturally-shaped objects was evaluated in three experiments. The participants viewed or haptically explored six randomly-chosen bell peppers (Capsicum annuum) in a study session and were later required to judge whether each of twelve bell peppers was "old" (previously presented during the study session) or "new" (not presented during the study session). When recognition memory was tested immediately after study, the younger adults' (Experiment 1) performance for vision and haptics was identical when the individual study objects were presented once. Vision became superior to haptics, however, when the individual study objects were presented multiple times. When 10- and 20-min delays (Experiment 2) were inserted in between study and test sessions, no significant differences occurred between vision and haptics: recognition performance in both modalities was comparable. When the recognition performance of older adults was evaluated (Experiment 3), a negative effect of age was found for visual shape recognition (younger adults' overall recognition performance was 60% higher). There was no age effect, however, for haptic shape recognition. The results of the present experiments indicate that the visual recognition of natural object shape is different from haptic recognition in multiple ways: visual shape recognition can be superior to that of haptics and is affected by aging, while haptic shape recognition is less accurate and unaffected by aging. Copyright © 2015 Elsevier Ltd. All rights reserved.

Cotinine improves visual recognition memory and decreases cortical Tau phosphorylation in the Tg6799 mice.

PubMed

Grizzell, J Alex; Patel, Sagar; Barreto, George E; Echeverria, Valentina

2017-08-01

Alzheimer's disease (AD) is associated with the progressive aggregation of hyperphosphorylated forms of the microtubule associated protein Tau in the central nervous system. Cotinine, the main metabolite of nicotine, reduced working memory deficits, synaptic loss, and amyloid β peptide aggregation into oligomers and plaques as well as inhibited the cerebral Tau kinase, glycogen synthase 3β (GSK3β) in the transgenic (Tg)6799 (5XFAD) mice. In this study, the effect of cotinine on visual recognition memory and cortical Tau phosphorylation at the GSK3β sites Serine (Ser)-396/Ser-404 and phospho-CREB were investigated in the Tg6799 and non-transgenic (NT) littermate mice. Tg mice showed short-term visual recognition memory impairment in the novel object recognition test, and higher levels of Tau phosphorylation when compared to NT mice. Cotinine significantly improved visual recognition memory performance increased CREB phosphorylation and reduced cortical Tau phosphorylation. Potential mechanisms underlying theses beneficial effects are discussed. Copyright © 2017. Published by Elsevier Inc.

Distinct parietal sites mediate the influences of mood, arousal, and their interaction on human recognition memory.

PubMed

Greene, Ciara M; Flannery, Oliver; Soto, David

2014-12-01

The two dimensions of emotion, mood valence and arousal, have independent effects on recognition memory. At present, however, it is not clear how those effects are reflected in the human brain. Previous research in this area has generally dealt with memory for emotionally valenced or arousing stimuli, but the manner in which interacting mood and arousal states modulate responses in memory substrates remains poorly understood. We investigated memory for emotionally neutral items while independently manipulating mood valence and arousal state by means of music exposure. Four emotional conditions were created: positive mood/high arousal, positive mood/low arousal, negative mood/high arousal, and negative mood/low arousal. We observed distinct effects of mood valence and arousal in parietal substrates of recognition memory. Positive mood increased activity in ventral posterior parietal cortex (PPC) and orbitofrontal cortex, whereas arousal condition modulated activity in dorsal PPC and the posterior cingulate. An interaction between valence and arousal was observed in left ventral PPC, notably in a parietal area distinct from the those identified for the main effects, with a stronger effect of mood on recognition memory responses here under conditions of relative high versus low arousal. We interpreted the PPC activations in terms of the attention-to-memory hypothesis: Increased arousal may lead to increased top-down control of memory, and hence dorsal PPC activation, whereas positive mood valence may result in increased activity in ventral PPC regions associated with bottom-up attention to memory. These findings indicate that distinct parietal sites mediate the influences of mood, arousal, and their interplay during recognition memory.

Structural basis of glycan specificity in neonate-specific bovine-human reassortant rotavirus

DOE PAGES

Hu, Liya; Ramani, Sasirekha; Czako, Rita; ...

2015-09-30

We report that strain-dependent variation of glycan recognition during initial cell attachment of viruses is a critical determinant of host specificity, tissue-tropism and zoonosis. Rotaviruses (RVs), which cause life-threatening gastroenteritis in infants and children, display significant genotype-dependent variations in glycan recognition resulting from sequence alterations in the VP8* domain of the spike protein VP4. The structural basis of this genotype-dependent glycan specificity, particularly in human RVs, remains poorly understood. Here, from crystallographic studies, we show how genotypic variations configure a novel binding site in the VP8* of a neonate-specific bovine-human reassortant to uniquely recognize either type I or type IImore » precursor glycans, and to restrict type II glycan binding in the bovine counterpart. In conclusion, such a distinct glycan-binding site that allows differential recognition of the precursor glycans, which are developmentally regulated in the neonate gut and abundant in bovine and human milk provides a basis for age-restricted tropism and zoonotic transmission of G10P[11] rotaviruses.« less

Structural basis of glycan specificity in neonate-specific bovine-human reassortant rotavirus

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

Hu, Liya; Ramani, Sasirekha; Czako, Rita

We report that strain-dependent variation of glycan recognition during initial cell attachment of viruses is a critical determinant of host specificity, tissue-tropism and zoonosis. Rotaviruses (RVs), which cause life-threatening gastroenteritis in infants and children, display significant genotype-dependent variations in glycan recognition resulting from sequence alterations in the VP8* domain of the spike protein VP4. The structural basis of this genotype-dependent glycan specificity, particularly in human RVs, remains poorly understood. Here, from crystallographic studies, we show how genotypic variations configure a novel binding site in the VP8* of a neonate-specific bovine-human reassortant to uniquely recognize either type I or type IImore » precursor glycans, and to restrict type II glycan binding in the bovine counterpart. In conclusion, such a distinct glycan-binding site that allows differential recognition of the precursor glycans, which are developmentally regulated in the neonate gut and abundant in bovine and human milk provides a basis for age-restricted tropism and zoonotic transmission of G10P[11] rotaviruses.« less

Multipoint molecular recognition within a calix[6]arene funnel complex

PubMed Central

Coquière, David; de la Lande, Aurélien; Martí, Sergio; Parisel, Olivier; Prangé, Thierry; Reinaud, Olivia

2009-01-01

A multipoint recognition system based on a calix[6]arene is described. The calixarene core is decorated on alternating aromatic subunits by 3 imidazole arms at the small rim and 3 aniline groups at the large rim. This substitution pattern projects the aniline nitrogens toward each other when Zn(II) binds at the Tris-imidazole site or when a proton binds at an aniline. The XRD structure of the monoprotonated complex having an acetonitrile molecule bound to Zn(II) in the cavity revealed a constrained geometry at the metal center reminiscent of an entatic state. Computer modeling suggests that the aniline groups behave as a tritopic monobasic site in which only 1 aniline unit is protonated and interacts with the other 2 through strong hydrogen bonding. The metal complex selectively binds a monoprotonated diamine vs. a monoamine through multipoint recognition: coordination to the metal ion at the small rim, hydrogen bonding to the calix-oxygen core, CH/π interaction within the cavity's aromatic walls, and H-bonding to the anilines at the large rim. PMID:19237564

Investigating the variability of memory distortion for an analogue trauma.

PubMed

Strange, Deryn; Takarangi, Melanie K T

2015-01-01

In this paper, we examine whether source monitoring (SM) errors might be one mechanism that accounts for traumatic memory distortion. Participants watched a traumatic film with some critical (crux) and non-critical (non-crux) scenes removed. Twenty-four hours later, they completed a memory test. To increase the likelihood participants would notice the film's gaps, we inserted visual static for the length of each missing scene. We then added manipulations designed to affect people's SM behaviour. To encourage systematic SM, before watching the film, we warned half the participants that we had removed some scenes. To encourage heuristic SM some participants also saw labels describing the missing scenes. Adding static highlighting, the missing scenes did not affect false recognition of those missing scenes. However, a warning decreased, while labels increased, participants' false recognition rates. We conclude that manipulations designed to affect SM behaviour also affect the degree of memory distortion in our paradigm.

Effects of Plinian Eruptions of Somma-vesuvius On People, Animals, Structures and Objects: Inferences From Avellino (3760 Yr B.p.) and Pompei (79 A.d.) Events.

NASA Astrophysics Data System (ADS)

Mastrolorenzo, G.; Petrone, P. P.; Geraci, G.; Guarino, F.; Incoronato, A.

An interdisciplinary approach to the archaeological sites affected by Avellino (3750 yr. B.P.) and Pompei (79 A.D.) plinian eruptions of Somma-Vesuvius provides new data relative to the depositional mechanisms. Large scale stratigraphy and local evi- dences provide new informations about the physical conditions at the emplacement of PDCs and their effects on structures, people and environment. Field evidences indicate that fine grained pyroclastic deposits related to the column collapses propagate up to a distance of about 15 km from the crater and emplaced with conspicuous thickness. In both Avellino and Pompei eruptions, direct evidences from archaeological sites in- dicate that the emplacement in intermediate and distal areas was relatively quite (low mechanical energy). The recognition of thin, continuous, fine grained surge deposits up to a distance of ca. 15 km from the crater suggests that turbulence was important and the PDCs advanced as a relatively thick dilute current, very poorly controlled by the topography. Furthermore, due to the very small sizes, the particles were always transported in suspension, even at very low current velocity, thus avoiding vertical grading to occur. However, due to the very high depositional mass rate, the emplace- ment was very rapid causing buildings and hut, objects, animals and people to be engulfed within the ash deposits thus preserving their original position, as seen at Herculaneum, Oplontis, Pompeii (79 AD) and Nola (3760 bp). The skeletons of hu- man as well animal victims show high temperature effects. In particular, microscopic bones texture of the victims in the sites affected by the 79 A.D are consistent with very high temperatures, which are anomalous in pyroclastic surge clouds.

A direct comparison of two nonviral gene therapy vectors for somatic integration: in vivo evaluation of the bacteriophage integrase phiC31 and the Sleeping Beauty transposase.

PubMed

Ehrhardt, Anja; Xu, Hui; Huang, Zan; Engler, Jeffrey A; Kay, Mark A

2005-05-01

In this study we performed a head-to-head comparison of the integrase phiC31 derived from a Streptomyces phage and the Sleeping Beauty (SB) transposase, a member of the TC1/mariner superfamily of transposable elements. Mouse liver was cotransfused with a vector containing our most robust human coagulation factor IX expression cassette and the appropriate recombinase recognition site and either a phiC31- or a SB transposase-expressing vector. To analyze transgene persistence and to prove somatic integration in vivo we induced cell cycling of mouse hepatocytes and found that the transgene expression levels dropped by only 16 to 21% and 56 to 66% in mice that received phiC31 and SB, respectively. Notably, no difference in the toxicity profile was detected in mice treated with either recombinase. Moreover we observed that with the integrase-mediated gene transfer, transgene expression levels were dependent on the remaining noncoding vector sequences, which also integrate into the host genome. Further analyses of a hot spot of integration after phiC31-mediated integration revealed small chromosomal deletions at the target site and that the recombination process was not dependent on the orientation in which the phiC31 recognition site attached to the pseudo-recognition sites in the host genome. Coupled together with ongoing improvements in both systems this study suggests that both nonviral vector systems will have important roles in achieving stable gene transfer in vivo.

Effects of emotion recognition training on mood among individuals with high levels of depressive symptoms: study protocol for a randomised controlled trial

PubMed Central

2013-01-01

Background We have developed a new paradigm that targets the recognition of facial expression of emotions. Here we report the protocol of a randomised controlled trial of the effects of emotion recognition training on mood in a sample of individuals with depressive symptoms over a 6-week follow-up period. Methods/Design We will recruit 190 adults from the general population who report high levels of depressive symptoms (defined as a score ≥ 14 on the Beck Depression Inventory-II). Participants will attend a screening session and will be randomised to intervention or control procedures, repeated five times over consecutive days (Monday to Friday). A follow-up session will take place at end-of -treatment, 2-weeks and 6-weeks after training. Our primary study outcome will be depressive symptoms, Beck Depression Inventory- II (rated over the past two weeks). Our secondary outcomes are: depressive symptoms, Hamilton Rating Scale for Depression; anxiety symptoms, Beck Anxiety Inventory (rated over the past month); positive affect, Positive and Negative Affect Schedule (rated as ‘how you feel right now’); negative affect, Positive and Negative Affect Schedule (rated as ‘how you feel right now’); emotion sensitivity, Emotion Recognition Task (test phase); approach motivation and persistence, the Fishing Game; and depressive interpretation bias, Scrambled Sentences Test. Discussion This study is of a novel cognitive bias modification technique that targets biases in emotional processing characteristic of depression, and can be delivered automatically via computer, Internet or Smartphone. It therefore has potential to be a valuable cost-effective adjunctive treatment for depression which may be used together with more traditional psychotherapy, cognitive-behavioural therapy and pharmacotherapy. Trial registration Current Controlled Trials: ISRCTN17767674 PMID:23725208

Effects of emotion recognition training on mood among individuals with high levels of depressive symptoms: study protocol for a randomised controlled trial.

PubMed

Adams, Sally; Penton-Voak, Ian S; Harmer, Catherine J; Holmes, Emily A; Munafò, Marcus R

2013-06-01

We have developed a new paradigm that targets the recognition of facial expression of emotions. Here we report the protocol of a randomised controlled trial of the effects of emotion recognition training on mood in a sample of individuals with depressive symptoms over a 6-week follow-up period. We will recruit 190 adults from the general population who report high levels of depressive symptoms (defined as a score ≥ 14 on the Beck Depression Inventory-II). Participants will attend a screening session and will be randomised to intervention or control procedures, repeated five times over consecutive days (Monday to Friday). A follow-up session will take place at end-of -treatment, 2-weeks and 6-weeks after training. Our primary study outcome will be depressive symptoms, Beck Depression Inventory- II (rated over the past two weeks). Our secondary outcomes are: depressive symptoms, Hamilton Rating Scale for Depression; anxiety symptoms, Beck Anxiety Inventory (rated over the past month); positive affect, Positive and Negative Affect Schedule (rated as 'how you feel right now'); negative affect, Positive and Negative Affect Schedule (rated as 'how you feel right now'); emotion sensitivity, Emotion Recognition Task (test phase); approach motivation and persistence, the Fishing Game; and depressive interpretation bias, Scrambled Sentences Test. This study is of a novel cognitive bias modification technique that targets biases in emotional processing characteristic of depression, and can be delivered automatically via computer, Internet or Smartphone. It therefore has potential to be a valuable cost-effective adjunctive treatment for depression which may be used together with more traditional psychotherapy, cognitive-behavioural therapy and pharmacotherapy. Current Controlled Trials: ISRCTN17767674.

Perception, memory and aesthetics of indeterminate art.

PubMed

Ishai, Alumit; Fairhall, Scott L; Pepperell, Robert

2007-07-12

Indeterminate art, in which familiar objects are only suggestive, invokes a perceptual conundrum as apparently detailed and vivid images resist identification. We hypothesized that compared with paintings that depict meaningful content, object recognition in indeterminate images would be delayed, and tested whether aesthetic affect depends on meaningful content. Subjects performed object recognition and judgment of aesthetic affect tasks. Response latencies were significantly longer for indeterminate images and subjects perceived recognizable objects in 24% of these paintings. Although the aesthetic affect rating of all paintings was similar, judgement latencies for the indeterminate paintings were significantly longer. A surprise memory test revealed that more representational than indeterminate paintings were remembered and that affective strength increased the probability of subsequent recall. Our results suggest that perception and memory of art depend on semantic aspects, whereas, aesthetic affect depends on formal visual features. The longer latencies associated with indeterminate paintings reflect the underlying cognitive processes that mediate object resolution. Indeterminate art works therefore comprise a rich set of stimuli with which the neural correlates of visual perception can be investigated.

Identification of the antigenic determinants of factors 8, 9, and 34 of genus Candida.

PubMed

Kobayashi, H; Oyamada, H; Suzuki, A; Shibata, N; Suzuki, S; Okawa, Y

1996-10-21

We investigated the antigenic determinants of factors 8, 9, and 34 of the genus Candida among pathogenic yeasts by enzyme-linked immunosorbent assay (ELISA) using mannans of Saccharomyces cerevisiae wild type and mutant types, mnn 1-mnn 4 and mnn 2. Results of ELISA including antisera against the antigenic factors of genus Candida (Candida Check, latron; FAbs) indicated that these three types of mannan distinctly react with FAbs 34, 8 and 9, respectively. To identify the recognition sites of these FAbs, we compared the ability of various oligosaccharides to inhibit the binding of the mannans to FAbs. The results indicated that FAb 34 preferentially recognizes linear side chains containing a non-reducing terminal alpha-1,3-linked mannose residue, Man(alpha)1 --> 3Man(alpha)1 --> (2Man(alpha)1 --> )n(2Man) (n > or = 0), and that one of the recognition sites of FAb 9 is linear alpha-1,6-linked oligomannosyl series, Man(alpha)1 --> (6Man(alpha)1 --> )n(6Man) (n > or = 2). On the other hand, the recognition site of FAb 8 apparently consisted of two alpha-1,2-linked oligomannosyl side chains and an alpha-1,6-linked mannose residue that originated from the mannan backbone, Man(alpha)1 --> 2Man(alpha)1 --> 2(Man(alpha)1 -->2Man(alpha)1 --> 6)Man.

Prediction of TF target sites based on atomistic models of protein-DNA complexes

PubMed Central

Angarica, Vladimir Espinosa; Pérez, Abel González; Vasconcelos, Ana T; Collado-Vides, Julio; Contreras-Moreira, Bruno

2008-01-01

Background The specific recognition of genomic cis-regulatory elements by transcription factors (TFs) plays an essential role in the regulation of coordinated gene expression. Studying the mechanisms determining binding specificity in protein-DNA interactions is thus an important goal. Most current approaches for modeling TF specific recognition rely on the knowledge of large sets of cognate target sites and consider only the information contained in their primary sequence. Results Here we describe a structure-based methodology for predicting sequence motifs starting from the coordinates of a TF-DNA complex. Our algorithm combines information regarding the direct and indirect readout of DNA into an atomistic statistical model, which is used to estimate the interaction potential. We first measure the ability of our method to correctly estimate the binding specificities of eight prokaryotic and eukaryotic TFs that belong to different structural superfamilies. Secondly, the method is applied to two homology models, finding that sampling of interface side-chain rotamers remarkably improves the results. Thirdly, the algorithm is compared with a reference structural method based on contact counts, obtaining comparable predictions for the experimental complexes and more accurate sequence motifs for the homology models. Conclusion Our results demonstrate that atomic-detail structural information can be feasibly used to predict TF binding sites. The computational method presented here is universal and might be applied to other systems involving protein-DNA recognition. PMID:18922190

Food restriction affects Y-maze spatial recognition memory in developing mice.

PubMed

Fu, Yu; Chen, Yanmei; Li, Liane; Wang, Yumei; Kong, Xiangyang; Wang, Jianhong

2017-08-01

The ambiguous effects of food restriction (FR) on cognition in rodents have been mostly explored in the aged brain by a variety of paradigms, in which either rewards or punishments are involved. This study aims to examine the effects of chronic and acute FR with varying intensities on spatial recognition memory in developing mice. We have used a Y-maze task that is based on the innate tendency of rodents to explore novel environments. In chronic FR, mice had 70-30% chow of control for seven weeks. In acute FR, mice were food restricted for 12-48h before the tests. We found that chronic FR had no effect on the preference of mice for novelty in the Y-maze, but severe FR (50-30% of control) caused impairment on spatial recognition memory. The impairment significantly correlated with the slow weight growth induced by FR. Acute FR also did not affect the novelty preference of mice, but either improved or impaired the memory retention. These data suggest chronic FR impairs Y-maze spatial recognition memory in developing mice depending on FR intensity and individual tolerability of the FR. Moreover, acute FR exerts diverse effects on the memory, either positive or negative. Our findings have revealed new insights on the effects of FR on spatial recognition memory in developing animals. Copyright © 2017 ISDN. Published by Elsevier Ltd. All rights reserved.

Dissociable roles of internal feelings and face recognition ability in facial expression decoding.

PubMed

Zhang, Lin; Song, Yiying; Liu, Ling; Liu, Jia

2016-05-15

The problem of emotion recognition has been tackled by researchers in both affective computing and cognitive neuroscience. While affective computing relies on analyzing visual features from facial expressions, it has been proposed that humans recognize emotions by internally simulating the emotional states conveyed by others' expressions, in addition to perceptual analysis of facial features. Here we investigated whether and how our internal feelings contributed to the ability to decode facial expressions. In two independent large samples of participants, we observed that individuals who generally experienced richer internal feelings exhibited a higher ability to decode facial expressions, and the contribution of internal feelings was independent of face recognition ability. Further, using voxel-based morphometry, we found that the gray matter volume (GMV) of bilateral superior temporal sulcus (STS) and the right inferior parietal lobule was associated with facial expression decoding through the mediating effect of internal feelings, while the GMV of bilateral STS, precuneus, and the right central opercular cortex contributed to facial expression decoding through the mediating effect of face recognition ability. In addition, the clusters in bilateral STS involved in the two components were neighboring yet separate. Our results may provide clues about the mechanism by which internal feelings, in addition to face recognition ability, serve as an important instrument for humans in facial expression decoding. Copyright © 2016 Elsevier Inc. All rights reserved.

Deep and shallow encoding effects on face recognition: an ERP study.

PubMed

Marzi, Tessa; Viggiano, Maria Pia

2010-12-01

Event related potentials (ERPs) were employed to investigate whether and when brain activity related to face recognition varies according to the processing level undertaken at encoding. Recognition was assessed when preceded by a "shallow" (orientation judgement) or by a "deep" study task (occupation judgement). Moreover, we included a further manipulation by presenting at encoding faces either in the upright or inverted orientation. As expected, deeply encoded faces were recognized more accurately and more quickly with respect to shallowly encoded faces. The ERP showed three main findings: i) as witnessed by more positive-going potentials for deeply encoded faces, at early and later processing stage, face recognition was influenced by the processing strategy adopted during encoding; ii) structural encoding, indexed by the N170, turned out to be "cognitively penetrable" showing repetition priming effects for deeply encoded faces; iii) face inversion, by disrupting configural processing during encoding, influenced memory related processes for deeply encoded faces and impaired the recognition of faces shallowly processed. The present study adds weight to the concept that the depth of processing during memory encoding affects retrieval. We found that successful retrieval following deep encoding involved both familiarity- and recollection-related processes showing from 500 ms a fronto-parietal distribution, whereas shallow encoding affected only earlier processing stages reflecting perceptual priming. Copyright © 2010 Elsevier B.V. All rights reserved.

Is Listening in Noise Worth It? The Neurobiology of Speech Recognition in Challenging Listening Conditions.

PubMed

Eckert, Mark A; Teubner-Rhodes, Susan; Vaden, Kenneth I

2016-01-01

This review examines findings from functional neuroimaging studies of speech recognition in noise to provide a neural systems level explanation for the effort and fatigue that can be experienced during speech recognition in challenging listening conditions. Neuroimaging studies of speech recognition consistently demonstrate that challenging listening conditions engage neural systems that are used to monitor and optimize performance across a wide range of tasks. These systems appear to improve speech recognition in younger and older adults, but sustained engagement of these systems also appears to produce an experience of effort and fatigue that may affect the value of communication. When considered in the broader context of the neuroimaging and decision making literature, the speech recognition findings from functional imaging studies indicate that the expected value, or expected level of speech recognition given the difficulty of listening conditions, should be considered when measuring effort and fatigue. The authors propose that the behavioral economics or neuroeconomics of listening can provide a conceptual and experimental framework for understanding effort and fatigue that may have clinical significance.

Is Listening in Noise Worth It? The Neurobiology of Speech Recognition in Challenging Listening Conditions

PubMed Central

Eckert, Mark A.; Teubner-Rhodes, Susan; Vaden, Kenneth I.

2016-01-01

This review examines findings from functional neuroimaging studies of speech recognition in noise to provide a neural systems level explanation for the effort and fatigue that can be experienced during speech recognition in challenging listening conditions. Neuroimaging studies of speech recognition consistently demonstrate that challenging listening conditions engage neural systems that are used to monitor and optimize performance across a wide range of tasks. These systems appear to improve speech recognition in younger and older adults, but sustained engagement of these systems also appears to produce an experience of effort and fatigue that may affect the value of communication. When considered in the broader context of the neuroimaging and decision making literature, the speech recognition findings from functional imaging studies indicate that the expected value, or expected level of speech recognition given the difficulty of listening conditions, should be considered when measuring effort and fatigue. We propose that the behavioral economics and/or neuroeconomics of listening can provide a conceptual and experimental framework for understanding effort and fatigue that may have clinical significance. PMID:27355759

Job stress, recognition, job performance and intention to stay at work among Jordanian hospital nurses.

PubMed

AbuAlRub, Raeda Fawzi; Al-Zaru, Ibtisam Moawiah

2008-04-01

To investigate: (1) relationships between job stress, recognition of nurses' performance, job performance and intention to stay among hospital nurses; and (2) the buffering effect of recognition of staff performance on the 'stress-intention to stay at work' relationship. Workplace stress tremendously affects today's workforce. Recognition of nurses' performance needs further investigation to determine if it enhances the level of intention to stay at work and if it can buffer the negative effects of stress on nurses' intention to stay at work. The sample of the present study was a convenience one. It consisted of 206 Jordanian staff nurses who completed a structured questionnaire. The findings of the study indicated a direct and a buffering effect of recognition of nurses' performance on job stress and the level of intention to stay at work. The results of the study indicated the importance of recognition for outstanding performance as well as achievements. Implications for nursing management The results of this study support the need to focus on the implementation of recognition strategies in the workplace to reduce job stress and enhance retention.

Textual emotion recognition for enhancing enterprise computing

NASA Astrophysics Data System (ADS)

Quan, Changqin; Ren, Fuji

2016-05-01

The growing interest in affective computing (AC) brings a lot of valuable research topics that can meet different application demands in enterprise systems. The present study explores a sub area of AC techniques - textual emotion recognition for enhancing enterprise computing. Multi-label emotion recognition in text is able to provide a more comprehensive understanding of emotions than single label emotion recognition. A representation of 'emotion state in text' is proposed to encompass the multidimensional emotions in text. It ensures the description in a formal way of the configurations of basic emotions as well as of the relations between them. Our method allows recognition of the emotions for the words bear indirect emotions, emotion ambiguity and multiple emotions. We further investigate the effect of word order for emotional expression by comparing the performances of bag-of-words model and sequence model for multi-label sentence emotion recognition. The experiments show that the classification results under sequence model are better than under bag-of-words model. And homogeneous Markov model showed promising results of multi-label sentence emotion recognition. This emotion recognition system is able to provide a convenient way to acquire valuable emotion information and to improve enterprise competitive ability in many aspects.

Affective State Level Recognition in Naturalistic Facial and Vocal Expressions.

PubMed

Meng, Hongying; Bianchi-Berthouze, Nadia

2014-03-01

Naturalistic affective expressions change at a rate much slower than the typical rate at which video or audio is recorded. This increases the probability that consecutive recorded instants of expressions represent the same affective content. In this paper, we exploit such a relationship to improve the recognition performance of continuous naturalistic affective expressions. Using datasets of naturalistic affective expressions (AVEC 2011 audio and video dataset, PAINFUL video dataset) continuously labeled over time and over different dimensions, we analyze the transitions between levels of those dimensions (e.g., transitions in pain intensity level). We use an information theory approach to show that the transitions occur very slowly and hence suggest modeling them as first-order Markov models. The dimension levels are considered to be the hidden states in the Hidden Markov Model (HMM) framework. Their discrete transition and emission matrices are trained by using the labels provided with the training set. The recognition problem is converted into a best path-finding problem to obtain the best hidden states sequence in HMMs. This is a key difference from previous use of HMMs as classifiers. Modeling of the transitions between dimension levels is integrated in a multistage approach, where the first level performs a mapping between the affective expression features and a soft decision value (e.g., an affective dimension level), and further classification stages are modeled as HMMs that refine that mapping by taking into account the temporal relationships between the output decision labels. The experimental results for each of the unimodal datasets show overall performance to be significantly above that of a standard classification system that does not take into account temporal relationships. In particular, the results on the AVEC 2011 audio dataset outperform all other systems presented at the international competition.

Body schema and corporeal self-recognition in the alien hand syndrome.

PubMed

Olgiati, Elena; Maravita, Angelo; Spandri, Viviana; Casati, Roberta; Ferraro, Francesco; Tedesco, Lucia; Agostoni, Elio Clemente; Bolognini, Nadia

2017-07-01

The alien hand syndrome (AHS) is a rare neuropsychological disorder characterized by involuntary, yet purposeful, hand movements. Patients with the AHS typically complain about a loss of agency associated with a feeling of estrangement for actions performed by the affected limb. The present study explores the integrity of the body representation in AHS, focusing on 2 main processes: multisensory integration and visual self-recognition of body parts. Three patients affected by AHS following a right-hemisphere stroke, with clinical symptoms akin to the posterior variant of AHS, were tested and their performance was compared with that of 18 age-matched healthy controls. AHS patients and controls underwent 2 experimental tasks: a same-different visual matching task for body postures, which assessed the ability of using your own body schema for encoding others' body postural changes (Experiment 1), and an explicit self-hand recognition task, which assessed the ability to visually recognize your own hands (Experiment 2). As compared to controls, all AHS patients were unable to access a reliable multisensory representation of their alien hand and use it for decoding others' postural changes; however, they could rely on an efficient multisensory representation of their intact (ipsilesional) hand. Two AHS patients also presented with a specific impairment in the visual self-recognition of their alien hand, but normal recognition of their intact hand. This evidence suggests that the AHS following a right-hemisphere stroke may involve a disruption of the multisensory representation of the alien limb; instead, self-hand recognition mechanisms may be spared. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

The ties that bind what is known to the recognition of what is new.

PubMed

Nelson, D L; Zhang, N; McKinney, V M

2001-09-01

Recognition success varies with how information is encoded (e.g., level of processing) and with what is already known as a result of past learning (e.g., word frequency). This article presents the results of experiments showing that preexisting connections involving the associates of studied words facilitate their recognition regardless of whether the words are intentionally encoded or are incidentally encoded under semantic or nonsemantic conditions. Words are more likely to be recognized when they have either more resonant connections coming back to them from their associates or more connections among their associates. Such results occur even though attention is never drawn to these associates. Regression analyses showed that these connections affect recognition independently of frequency, so the present results add to the literature showing that prior lexical knowledge contributes to episodic recognition. In addition, equations that use free-association data to derive composite strength indices of resonance and connectivity were evaluated. Implications for theories of recognition are discussed.

Inhibition of GABA-gated chloride channels by 12,14-dichlorodehydroabietic acid in mammalian brain

PubMed Central

Nicholson, Russell A; Lees, George; Zheng, Jian; Verdon, Bernard

1999-01-01

12,14-dichlorodehydroabietic acid (12,14-Cl2DHA) reduced GABA-stimulated uptake of 36Cl− into mouse brain synaptoneurosomes suggesting inhibition of mammalian GABAA receptor function. 12,14-Cl2DHA did not affect the binding of [3H]-muscimol to brain membranes but displaced specifically bound [3H]-EBOB. The inhibitory effect on [3H]-EBOB binding was not reversible. 12,14-Cl2DHA reduced the availability of [3H]-EBOB binding sites (Bmax) without changing the KD of the radioligand for remaining sites. 12,14-Cl2DHA did not affect the rate of association of [3H]-EBOB with its chloride channel receptor, but increased the initial rate of [3H]-EBOB dissociation. 12,14-Cl2DHA enhanced the incidence of EPSCs when rapidly applied to cultured rat cortical neurones. Longer exposures produced block of IPSCs with marked increases in the frequency of EPSCs and min EPSCs. 12,14-Cl2DHA also irreversibly suppressed chloride currents evoked by pulses of exogenous GABA in these cells. Ultimately, 12,14-Cl2DHA inhibited all synaptic traffic and action currents in current clamped cells indicating that, in contrast to picrotoxinin (which causes paroxysmal bursting), it is not fully selective for the GABAA receptor-chloride channel complex. The depolarizing block seen with 12,14-Cl2DHA in amphotericin-perforated preparations implicates loss of Ca2+ buffering in the polarity change and this may account for inhibition of spontaneous action potentials. Our investigation demonstrates that 12,14-Cl2DHA blocks GABA-dependent chloride entry in mammalian brain and operates as a non-competitive insurmountable GABAA antagonist. The mechanism likely involves either irreversible binding of 12,14-Cl2DHA to the trioxabicyclooctane recognition site or a site that is allosterically coupled to it. We cannot exclude, however, the possibility that 12,14-Cl2DHA causes localized proteolysis or more extensive conformational change within a critical subunit of the chloride channel. PMID:10204999

Limited Bandwidth Recognition of Collective Behaviors in Bio-Inspired Swarms

DTIC Science & Technology

2014-05-01

Nevai, K. M. Passino, and P. Srinivasan. Stability of choice in the honey bee nest-site selection processs. Journal of Theoretical Biology , 263(1):93...and N. Franks. Collective memory and spatial sorting in animal groups. Journal of Theoretical Biology , 218(1):1–11, 2002. [4] D. Cvetkovic, P...motion from local attraction. Journal of Theoretical Biology , 283(1):145–151, 2011. [18] G. Sukthankar and K. Sycara. Robust recognition of physical team

The recognition and modification sites for the bacterial type I restriction systems KpnAI, StySEAI, StySENI and StySGI

PubMed Central

Kasarjian, Julie K. A.; Hidaka, Masumi; Horiuchi, Takashi; Iida, Masatake; Ryu, Junichi

2004-01-01

Using an in vivo plasmid transformation method, we have determined the DNA sequences recognized by the KpnAI, StySEAI, StySENI and StySGI R-M systems from Klebsiella oxytoca strain M5a1, Salmonella eastbourne, Salmonella enteritidis and Salmonella gelsenkirchen, respectively. These type I restriction-modification systems were originally identified using traditional phage assay, and described here is the plasmid transformation test and computer program used to determine their DNA recognition sequences. For this test, we constructed two sets of plasmids, pL and pE, that contain phage lambda and Escherichia coli K-12 chromosomal DNA fragments, respectively. Further, using the methylation sensitivities of various known type II restriction enzymes, we identified the target adenines for methylation (listed in bold italics below as A or T in case of the complementary strand). The recognition sequence and methylation sites are GAA(6N)TGCC (KpnAI), ACA(6N)TYCA (StySEAI), CGA(6N)TACC (StySENI) and TAAC(7N)RTCG (StySGI). These DNA recognition sequences all have a typical type I bipartite pattern and represent three novel specificities and one isoschizomer (StySENI). For confirmation, oligonucleotides containing each of the predicted sequences were synthesized, cloned into plasmid pMECA and transformed into each strain, resulting in a large reduction in efficiency of transformation (EOT). PMID:15199175

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

Barnes, N.M.; Costall, B.; Egli, P.

The angiotensin converting enzyme (ACE) inhibitor ({sup 3}H)SQ29,852 identified a single high affinity recognition site (defined by 10.0 microM captopril) in the human temporal cortex (pKD 8.62 +/- 0.03; Bmax 248 +/- 24 fmol mg-1 protein, mean +/- S.E.M., n = 4). ACE inhibitors and thiorphan competed to a similar level for the ({sup 3}H)SQ29,852 binding site in the human temporal cortex with a rank order of affinity (pKi values mean +/- S.E.M., n = 3), lisinopril (9.49 +/- 0.02), captopril (9.16 +/- 0.08), SQ29,852 (8.58 +/- 0.04), epicaptopril (7.09 +/- 0.08), fosinopril (7.08 +/- 0.05) and thiorphan (6.40 +/-more » 0.04). Since this rank order of affinity is similar to the affinity of these compounds to inhibit brain ACE activity it is concluded that ({sup 3}H)SQ29,852 selectively labels the inhibitor recognition site of ACE in the human temporal cortex.« less

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

Structural modeling of glucanase-substrate complexes suggests a conserved tyrosine is involved in carbohydrate recognition in plant 1,3-1,4-β- d-glucanases

NASA Astrophysics Data System (ADS)

Tsai, Li-Chu; Chen, Yi-Ning; Shyur, Lie-Fen

2008-12-01

Glycosyl hydrolase family 16 (GHF16) truncated Fibrobacter succinogenes (TFs) and GHF17 barley 1,3-1,4-β- d-glucanases (β-glucanases) possess different structural folds, β-jellyroll and (β/α)8, although they both catalyze the specific hydrolysis of β-1,4 glycosidic bonds adjacent to β-1,3 linkages in mixed β-1,3 and β-1,4 β- d-glucans or lichenan. Differences in the active site region residues of TFs β-glucanase and barley β-glucanase create binding site topographies that require different substrate conformations. In contrast to barley β-glucanase, TFs β-glucanase possesses a unique and compact active site. The structural analysis results suggest that the tyrosine residue, which is conserved in all known 1,3-1,4-β- d-glucanases, is involved in the recognition of mixed β-1,3 and β-1,4 linked polysaccharide.

On random field Completely Automated Public Turing Test to Tell Computers and Humans Apart generation.

PubMed

Kouritzin, Michael A; Newton, Fraser; Wu, Biao

2013-04-01

Herein, we propose generating CAPTCHAs through random field simulation and give a novel, effective and efficient algorithm to do so. Indeed, we demonstrate that sufficient information about word tests for easy human recognition is contained in the site marginal probabilities and the site-to-nearby-site covariances and that these quantities can be embedded directly into certain conditional probabilities, designed for effective simulation. The CAPTCHAs are then partial random realizations of the random CAPTCHA word. We start with an initial random field (e.g., randomly scattered letter pieces) and use Gibbs resampling to re-simulate portions of the field repeatedly using these conditional probabilities until the word becomes human-readable. The residual randomness from the initial random field together with the random implementation of the CAPTCHA word provide significant resistance to attack. This results in a CAPTCHA, which is unrecognizable to modern optical character recognition but is recognized about 95% of the time in a human readability study.

The Relationship between Language Anxiety, Interpretation of Anxiety, Intrinsic Motivation and the Use of Learning Strategies

ERIC Educational Resources Information Center

Nishitani, Mari; Matsuda, Toshiki

2011-01-01

Researches in language anxiety have focused on the level of language anxiety so far. This study instead, hypothesizes that the interpretation of anxiety and the recognition of failure have an impact on learning and investigates how language anxiety and intrinsic motivation affect the use of learning strategies through the recognition of failure.…

Evidence for Impaired Verbal Identification but Intact Nonverbal Recognition of Fearful Body Postures in Asperger's Syndrome

ERIC Educational Resources Information Center

Doody, John P.; Bull, Peter

2013-01-01

While most studies of emotion recognition in Asperger's Syndrome (AS) have focused solely on the verbal decoding of affective states, the current research employed the novel technique of using both nonverbal matching and verbal labeling tasks to examine the decoding of emotional body postures and facial expressions. AS participants performed…

A STUDY OF THE RELATIONSHIP BETWEEN THE PERCEPTION OF MUSICAL PROCESSES AND THE ENJOYMENT OF MUSIC.

ERIC Educational Resources Information Center

DUERKSEN, GEORGE L.

STUDENT RECOGNITION OF THEMES IN MUSIC THAT WERE REPEATED OR ALTERED THROUGHOUT 14 MUSICAL ITEMS WAS MEASURED BY USE OF AN AUDIOVISUAL TESTING DEVICE. AFFECTIVE RESPONSE TO THE THEMES WAS INDICATED, USING A SEVEN-POINT SCALE OF LIKE-DISLIKE. ASSOCIATIONS BETWEEN THE MEASURED RECOGNITION AND SUCH ITEMS AS MUSICAL EXPERIENCE, ACADEMIC APTITUDE, AND…